WorldWideScience

Sample records for opacity protein loops

  1. Functional characterization of antibodies against Neisseria gonorrhoeae opacity protein loops.

    Directory of Open Access Journals (Sweden)

    Jessica G Cole

    Full Text Available BACKGROUND: The development of a gonorrhea vaccine is challenged by the lack of correlates of protection. The antigenically variable neisserial opacity (Opa proteins are expressed during infection and have a semivariable (SV and highly conserved (4L loop that could be targeted in a vaccine. Here we compared antibodies to linear (Ab(linear and cyclic (Ab(cyclic peptides that correspond to the SV and 4L loops and selected hypervariable (HV(2 loops for surface-binding and protective activity in vitro and in vivo. METHODS/FINDINGS: Ab(SV cyclic bound a greater number of different Opa variants than Ab(SV linear, including variants that differed by seven amino acids. Antibodies to the 4L peptide did not bind Opa-expressing bacteria. Ab(SV (cyclic and Ab(HV2 (cyclic, but not Ab(SV (linear or Ab(HV2 linear agglutinated homologous Opa variants, and Ab(HV2BD (cyclic but not Ab(HV2BD (linear blocked the association of OpaB variants with human endocervical cells. Only Ab(HV2BD (linear were bactericidal against the serum resistant parent strain. Consistent with host restrictions in the complement cascade, the bactericidal activity of Ab(HV2BD (linear was increased 8-fold when rabbit complement was used. None of the antibodies was protective when administered vaginally to mice. Antibody duration in the vagina was short-lived, however, with <50% of the antibodies recovered 3 hrs post-administration. CONCLUSIONS: We conclude that an SV loop-specific cyclic peptide can be used to induce antibodies that recognize a broad spectrum of antigenically distinct Opa variants and have agglutination abilities. HV(2 loop-specific cyclic peptides elicited antibodies with agglutination and adherence blocking abilities. The use of human complement when testing the bactericidal activity of vaccine-induced antibodies against serum resistant gonococci is also important.

  2. Opacity

    CERN Document Server

    Huebner, Walter F

    2014-01-01

    The interaction of radiation with matter is a fundamental process in the universe; in particular, the absorption and scattering of radiation by matter (the opacity) govern the formation, evolution, and structure of stars and planets.  But opacity is also important in many terrestrial applications in which radiation is the dominant means of energy transfer, such as controlled nuclear-fusion, laser ablation, atmospheric entry and reentry, and the "greenhouse" effect.  This book covers all aspects of opacity and equations of state for plasmas, gases, vapors, and dust and emphasizes the continuous transformation of phases and molecular compositions with changing density and temperature under conditions of local thermodynamic equilibrium (LTE) while preserving the basic abundances of the chemical elements in a mixture.

  3. Purification and partial characterization of the opacity-associated proteins of Neisseria gonorrhoeae

    OpenAIRE

    1984-01-01

    Gonococci, grown on agar, frequently give rise to opaque colonies. This opacity phenotype is associated with the presence of one or more outer membrane proteins of approximately 28,000 mol weight. These proteins are included within a class of proteins named proteins II. A method is described to isolate and purify the opacity-associated proteins from Neisseria gonorrhoeae. This method uses high concentrations of calcium and a zwitterionic detergent at pH 4.0. Under these conditions proteins II...

  4. Crystal packing effects on protein loops.

    Science.gov (United States)

    Rapp, Chaya S; Pollack, Rena M

    2005-07-01

    The effects of crystal packing on protein loop structures are examined by (1) a comparison of loops in proteins that have been crystallized in alternate packing arrangements, and (2) theoretical prediction of loops both with and without the inclusion of the crystal environment. Results show that in a minority of cases, loop geometries are dependent on crystal packing effects. Explicit representation of the crystal environment in a loop prediction algorithm can be used to model these effects and to reconstruct the structures, and relative energies, of a loop in alternative packing environments. By comparing prediction results with and without the inclusion of the crystal environment, the loop prediction algorithm can further be used to identify cases in which a crystal structure does not represent the most stable state of a loop in solution. We anticipate that this capability has implications for structural biology.

  5. LoopIng: a template-based tool for predicting the structure of protein loops.

    KAUST Repository

    Messih, Mario Abdel

    2015-08-06

    Predicting the structure of protein loops is very challenging, mainly because they are not necessarily subject to strong evolutionary pressure. This implies that, unlike the rest of the protein, standard homology modeling techniques are not very effective in modeling their structure. However, loops are often involved in protein function, hence inferring their structure is important for predicting protein structure as well as function.We describe a method, LoopIng, based on the Random Forest automated learning technique, which, given a target loop, selects a structural template for it from a database of loop candidates. Compared to the most recently available methods, LoopIng is able to achieve similar accuracy for short loops (4-10 residues) and significant enhancements for long loops (11-20 residues). The quality of the predictions is robust to errors that unavoidably affect the stem regions when these are modeled. The method returns a confidence score for the predicted template loops and has the advantage of being very fast (on average: 1 min/loop).www.biocomputing.it/loopinganna.tramontano@uniroma1.itSupplementary data are available at Bioinformatics online.

  6. Stellar Opacity

    Energy Technology Data Exchange (ETDEWEB)

    Rogers, F J; Iglesias, C A

    1999-11-07

    The monochromatic opacity, {kappa}{sub v}, quantifies the property of a material to remove energy of frequency v from a radiation field. A harmonic average of {kappa}{sub v}, known as the Rosseland mean, {kappa}{sub R}, is frequently used to simplify the calculation of energy transport in stars. The term ''opacity'' is commonly understood to refer to {kappa}{sub R}. Opacity plays an important role in stellar modeling because for most stars radiation is the primary mechanism for transporting energy from the nuclear burning region in the core to the surface. Depending on the mass, convection and electron thermal conduction can also be important modes of stellar energy transport. The efficiency of energy transport is related to the temperature gradient, which is directly proportional to the mean radiative opacity in radiation dominated regions. When the radiative opacity is large, convection can become the more efficient energy transport mechanism. Electron conductive opacity, the resistance of matter to thermal conduction, is inversely proportional to electron thermal conductivity. Thermal conduction becomes the dominant mode of energy transport at high density and low temperature.

  7. Adaptive Simulated Annealing Based Protein Loop Modeling of Neurotoxins

    Institute of Scientific and Technical Information of China (English)

    陈杰; 黄丽娜; 彭志红

    2003-01-01

    A loop modeling method, adaptive simulated annealing, for ab initio prediction of protein loop structures, as an optimization problem of searching the global minimum of a given energy function, is proposed. An interface-friendly toolbox-LoopModeller in Windows and Linux systems, VC++ and OpenGL environments is developed for analysis and visualization. Simulation results of three short-chain neurotoxins modeled by LoopModeller show that the method proposed is fast and efficient.

  8. Loops In Proteins (LIP)--a comprehensive loop database for homology modelling.

    Science.gov (United States)

    Michalsky, E; Goede, A; Preissner, R

    2003-12-01

    One of the most important and challenging tasks in protein modelling is the prediction of loops, as can be seen in the large variety of existing approaches. Loops In Proteins (LIP) is a database that includes all protein segments of a length up to 15 residues contained in the Protein Data Bank (PDB). In this study, the applicability of LIP to loop prediction in the framework of homology modelling is investigated. Searching the database for loop candidates takes less than 1 s on a desktop PC, and ranking them takes a few minutes. This is an order of magnitude faster than most existing procedures. The measure of accuracy is the root mean square deviation (RMSD) with respect to the main-chain atoms after local superposition of target loop and predicted loop. Loops of up to nine residues length were modelled with a local RMSD <1 A and those of length up to 14 residues with an accuracy better than 2 A. The results were compared in detail with a thoroughly evaluated and tested ab initio method published recently and additionally with two further methods for a small loop test set. The LIP method produced very good predictions. In particular for longer loops it outperformed other methods.

  9. Mining protein loops using a structural alphabet and statistical exceptionality

    Directory of Open Access Journals (Sweden)

    Martin Juliette

    2010-02-01

    Full Text Available Abstract Background Protein loops encompass 50% of protein residues in available three-dimensional structures. These regions are often involved in protein functions, e.g. binding site, catalytic pocket... However, the description of protein loops with conventional tools is an uneasy task. Regular secondary structures, helices and strands, have been widely studied whereas loops, because they are highly variable in terms of sequence and structure, are difficult to analyze. Due to data sparsity, long loops have rarely been systematically studied. Results We developed a simple and accurate method that allows the description and analysis of the structures of short and long loops using structural motifs without restriction on loop length. This method is based on the structural alphabet HMM-SA. HMM-SA allows the simplification of a three-dimensional protein structure into a one-dimensional string of states, where each state is a four-residue prototype fragment, called structural letter. The difficult task of the structural grouping of huge data sets is thus easily accomplished by handling structural letter strings as in conventional protein sequence analysis. We systematically extracted all seven-residue fragments in a bank of 93000 protein loops and grouped them according to the structural-letter sequence, named structural word. This approach permits a systematic analysis of loops of all sizes since we consider the structural motifs of seven residues rather than complete loops. We focused the analysis on highly recurrent words of loops (observed more than 30 times. Our study reveals that 73% of loop-lengths are covered by only 3310 highly recurrent structural words out of 28274 observed words. These structural words have low structural variability (mean RMSd of 0.85 Å. As expected, half of these motifs display a flanking-region preference but interestingly, two thirds are shared by short (less than 12 residues and long loops. Moreover, half of

  10. Protein digestion and absorption in the blind loop syndrome.

    Science.gov (United States)

    Curtis, K J; Prizont, R; Kim, Y S

    1979-12-01

    Protein digestion and absorption was studied in rats with 6-week-old surgically constructed self-filling intestinal blind loops and steatorrhea, ie, blind-loop animals and controls were fed a 14C-labeled protein meal containing a nonabsorbable marker, 51CrCl3, and sacrificed 1 or 2 hr later. Intestinal contents were analyzed for 14C, 51Cr, protein, trypsin, and the products of digestion. At 1 hr, 14C absorption was greater in controls, but at 2 hr there was no difference in absorption between the two groups. Marker studies showed that blind-loop filling resulted in a delay of the progression of intestinal contents distally. Intraluminal trypsin and porteolysis were similar in the two groups. Endogenous protein was greater in the blind-loop animals. The early stages of the blind-loop syndrome may be characterized by delayed protein absorption secondary to blind-loop filling, which is compensated for by the distal gut resulting in an absence of overall protein malabsorption.

  11. ArchDB 2014: structural classification of loops in proteins

    Science.gov (United States)

    Bonet, Jaume; Planas-Iglesias, Joan; Garcia-Garcia, Javier; Marín-López, Manuel A.; Fernandez-Fuentes, Narcis; Oliva, Baldo

    2014-01-01

    The function of a protein is determined by its three-dimensional structure, which is formed by regular (i.e. β-strands and α-helices) and non-periodic structural units such as loops. Compared to regular structural elements, non-periodic, non-repetitive conformational units enclose a much higher degree of variability—raising difficulties in the identification of regularities, and yet represent an important part of the structure of a protein. Indeed, loops often play a pivotal role in the function of a protein and different aspects of protein folding and dynamics. Therefore, the structural classification of protein loops is an important subject with clear applications in homology modelling, protein structure prediction, protein design (e.g. enzyme design and catalytic loops) and function prediction. ArchDB, the database presented here (freely available at http://sbi.imim.es/archdb), represents such a resource and has been an important asset for the scientific community throughout the years. In this article, we present a completely reworked and updated version of ArchDB. The new version of ArchDB features a novel, fast and user-friendly web-based interface, and a novel graph-based, computationally efficient, clustering algorithm. The current version of ArchDB classifies 149,134 loops in 5739 classes and 9608 subclasses. PMID:24265221

  12. Efficient algorithms to explore conformation spaces of flexible protein loops.

    Science.gov (United States)

    Yao, Peggy; Dhanik, Ankur; Marz, Nathan; Propper, Ryan; Kou, Charles; Liu, Guanfeng; van den Bedem, Henry; Latombe, Jean-Claude; Halperin-Landsberg, Inbal; Altman, Russ Biagio

    2008-01-01

    Several applications in biology - e.g., incorporation of protein flexibility in ligand docking algorithms, interpretation of fuzzy X-ray crystallographic data, and homology modeling - require computing the internal parameters of a flexible fragment (usually, a loop) of a protein in order to connect its termini to the rest of the protein without causing any steric clash. One must often sample many such conformations in order to explore and adequately represent the conformational range of the studied loop. While sampling must be fast, it is made difficult by the fact that two conflicting constraints - kinematic closure and clash avoidance - must be satisfied concurrently. This paper describes two efficient and complementary sampling algorithms to explore the space of closed clash-free conformations of a flexible protein loop. The "seed sampling" algorithm samples broadly from this space, while the "deformation sampling" algorithm uses seed conformations as starting points to explore the conformation space around them at a finer grain. Computational results are presented for various loops ranging from 5 to 25 residues. More specific results also show that the combination of the sampling algorithms with a functional site prediction software (FEATURE) makes it possible to compute and recognize calcium-binding loop conformations. The sampling algorithms are implemented in a toolkit (LoopTK), which is available at https://simtk.org/home/looptk.

  13. Examination of Neisseria Gonorrhoeae Opacity Protein Expression During Experimental Murine Genital Tract Infection

    Science.gov (United States)

    2005-01-01

    E., M. Virji, K. Zak and J. N. Fletcher (1987). "Immunobiology of gonococcal outer membrane protein I." Antonie Van Leeuwenhoek 53(6): 461-4. 88...pathogenic Neisseriae." Antonie Van Leeuwenhoek 53(6): 435-40. 146. Murphy, G. L., T. D. Connell, D. S. Barritt, M. Koomey and J. G. Cannon (1989

  14. Cyclic coordinate descent: A robotics algorithm for protein loop closure.

    Science.gov (United States)

    Canutescu, Adrian A; Dunbrack, Roland L

    2003-05-01

    In protein structure prediction, it is often the case that a protein segment must be adjusted to connect two fixed segments. This occurs during loop structure prediction in homology modeling as well as in ab initio structure prediction. Several algorithms for this purpose are based on the inverse Jacobian of the distance constraints with respect to dihedral angle degrees of freedom. These algorithms are sometimes unstable and fail to converge. We present an algorithm developed originally for inverse kinematics applications in robotics. In robotics, an end effector in the form of a robot hand must reach for an object in space by altering adjustable joint angles and arm lengths. In loop prediction, dihedral angles must be adjusted to move the C-terminal residue of a segment to superimpose on a fixed anchor residue in the protein structure. The algorithm, referred to as cyclic coordinate descent or CCD, involves adjusting one dihedral angle at a time to minimize the sum of the squared distances between three backbone atoms of the moving C-terminal anchor and the corresponding atoms in the fixed C-terminal anchor. The result is an equation in one variable for the proposed change in each dihedral. The algorithm proceeds iteratively through all of the adjustable dihedral angles from the N-terminal to the C-terminal end of the loop. CCD is suitable as a component of loop prediction methods that generate large numbers of trial structures. It succeeds in closing loops in a large test set 99.79% of the time, and fails occasionally only for short, highly extended loops. It is very fast, closing loops of length 8 in 0.037 sec on average.

  15. A self-organizing algorithm for modeling protein loops.

    Directory of Open Access Journals (Sweden)

    Pu Liu

    2009-08-01

    Full Text Available Protein loops, the flexible short segments connecting two stable secondary structural units in proteins, play a critical role in protein structure and function. Constructing chemically sensible conformations of protein loops that seamlessly bridge the gap between the anchor points without introducing any steric collisions remains an open challenge. A variety of algorithms have been developed to tackle the loop closure problem, ranging from inverse kinematics to knowledge-based approaches that utilize pre-existing fragments extracted from known protein structures. However, many of these approaches focus on the generation of conformations that mainly satisfy the fixed end point condition, leaving the steric constraints to be resolved in subsequent post-processing steps. In the present work, we describe a simple solution that simultaneously satisfies not only the end point and steric conditions, but also chirality and planarity constraints. Starting from random initial atomic coordinates, each individual conformation is generated independently by using a simple alternating scheme of pairwise distance adjustments of randomly chosen atoms, followed by fast geometric matching of the conformationally rigid components of the constituent amino acids. The method is conceptually simple, numerically stable and computationally efficient. Very importantly, additional constraints, such as those derived from NMR experiments, hydrogen bonds or salt bridges, can be incorporated into the algorithm in a straightforward and inexpensive way, making the method ideal for solving more complex multi-loop problems. The remarkable performance and robustness of the algorithm are demonstrated on a set of protein loops of length 4, 8, and 12 that have been used in previous studies.

  16. Knotted vs. unknotted proteins: evidence of knot-promoting loops.

    Directory of Open Access Journals (Sweden)

    Raffaello Potestio

    Full Text Available Knotted proteins, because of their ability to fold reversibly in the same topologically entangled conformation, are the object of an increasing number of experimental and theoretical studies. The aim of the present investigation is to assess, on the basis of presently available structural data, the extent to which knotted proteins are isolated instances in sequence or structure space, and to use comparative schemes to understand whether specific protein segments can be associated to the occurrence of a knot in the native state. A significant sequence homology is found among a sizeable group of knotted and unknotted proteins. In this family, knotted members occupy a primary sub-branch of the phylogenetic tree and differ from unknotted ones only by additional loop segments. These "knot-promoting" loops, whose virtual bridging eliminates the knot, are found in various types of knotted proteins. Valuable insight into how knots form, or are encoded, in proteins could be obtained by targeting these regions in future computational studies or excision experiments.

  17. Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions

    KAUST Repository

    Najibi, Seyed Morteza

    2017-02-08

    Recently, the study of protein structures using angular representations has attracted much attention among structural biologists. The main challenge is how to efficiently model the continuous conformational space of the protein structures based on the differences and similarities between different Ramachandran plots. Despite the presence of statistical methods for modeling angular data of proteins, there is still a substantial need for more sophisticated and faster statistical tools to model the large-scale circular datasets. To address this need, we have developed a nonparametric method for collective estimation of multiple bivariate density functions for a collection of populations of protein backbone angles. The proposed method takes into account the circular nature of the angular data using trigonometric spline which is more efficient compared to existing methods. This collective density estimation approach is widely applicable when there is a need to estimate multiple density functions from different populations with common features. Moreover, the coefficients of adaptive basis expansion for the fitted densities provide a low-dimensional representation that is useful for visualization, clustering, and classification of the densities. The proposed method provides a novel and unique perspective to two important and challenging problems in protein structure research: structure-based protein classification and angular-sampling-based protein loop structure prediction.

  18. Universe opacity and EBL

    CERN Document Server

    Vavrycuk, Vaclav

    2016-01-01

    The observed extragalactic background light (EBL) is affected by light attenuation due to absorption of light by galactic and intergalactic dust in the Universe. Even galactic opacity of 10-20 percent and minute universe intergalactic opacity of $0.01\\,\\mathrm{mag}\\,h\\,\\mathrm{Gpc}^{-1}$ at the local Universe have a significant impact on the EBL because obscuration of galaxies and density of intergalactic dust increase with redshift as $\\left(1+z\\right)^3$. Consequently, intergalactic opacity increases and the Universe becomes considerably opaque at $z > 3$. Adopting realistic values for galactic and intergalactic opacity, the estimates of the EBL for the expanding dusty universe are close to observations. The luminosity density evolution fits well measurements. The model reproduces a steep increase of the luminosity density at $z3.5$.

  19. DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics

    Science.gov (United States)

    Laurens, Niels; Rusling, David A.; Pernstich, Christian; Brouwer, Ineke; Halford, Stephen E.; Wuite, Gijs J. L.

    2012-01-01

    Protein-induced DNA looping is crucial for many genetic processes such as transcription, gene regulation and DNA replication. Here, we use tethered-particle motion to examine the impact of DNA bending and twisting rigidity on loop capture and release, using the restriction endonuclease FokI as a test system. To cleave DNA efficiently, FokI bridges two copies of an asymmetric sequence, invariably aligning the sites in parallel. On account of the fixed alignment, the topology of the DNA loop is set by the orientation of the sites along the DNA. We show that both the separation of the FokI sites and their orientation, altering, respectively, the twisting and the bending of the DNA needed to juxtapose the sites, have profound effects on the dynamics of the looping interaction. Surprisingly, the presence of a nick within the loop does not affect the observed rigidity of the DNA. In contrast, the introduction of a 4-nt gap fully relaxes all of the torque present in the system but does not necessarily enhance loop stability. FokI therefore employs torque to stabilise its DNA-looping interaction by acting as a ‘torsional’ catch bond. PMID:22373924

  20. SuperLooper--a prediction server for the modeling of loops in globular and membrane proteins.

    Science.gov (United States)

    Hildebrand, Peter W; Goede, Andrean; Bauer, Raphael A; Gruening, Bjoern; Ismer, Jochen; Michalsky, Elke; Preissner, Robert

    2009-07-01

    SuperLooper provides the first online interface for the automatic, quick and interactive search and placement of loops in proteins (LIP). A database containing half a billion segments of water-soluble proteins with lengths up to 35 residues can be screened for candidate loops. A specified database containing 180,000 membrane loops in proteins (LIMP) can be searched, alternatively. Loop candidates are scored based on sequence criteria and the root mean square deviation (RMSD) of the stem atoms. Searching LIP, the average global RMSD of the respective top-ranked loops to the original loops is benchmarked to be <2 A, for loops up to six residues or <3 A for loops shorter than 10 residues. Other suitable conformations may be selected and directly visualized on the web server from a top-50 list. For user guidance, the sequence homology between the template and the original sequence, proline or glycine exchanges or close contacts between a loop candidate and the remainder of the protein are denoted. For membrane proteins, the expansions of the lipid bilayer are automatically modeled using the TMDET algorithm. This allows the user to select the optimal membrane protein loop concerning its relative orientation to the lipid bilayer. The server is online since October 2007 and can be freely accessed at URL: http://bioinformatics.charite.de/superlooper/.

  1. SuperLooper—a prediction server for the modeling of loops in globular and membrane proteins

    Science.gov (United States)

    Hildebrand, Peter W.; Goede, Andrean; Bauer, Raphael A.; Gruening, Bjoern; Ismer, Jochen; Michalsky, Elke; Preissner, Robert

    2009-01-01

    SuperLooper provides the first online interface for the automatic, quick and interactive search and placement of loops in proteins (LIP). A database containing half a billion segments of water-soluble proteins with lengths up to 35 residues can be screened for candidate loops. A specified database containing 180 000 membrane loops in proteins (LIMP) can be searched, alternatively. Loop candidates are scored based on sequence criteria and the root mean square deviation (RMSD) of the stem atoms. Searching LIP, the average global RMSD of the respective top-ranked loops to the original loops is benchmarked to be <2 Å, for loops up to six residues or <3 Å for loops shorter than 10 residues. Other suitable conformations may be selected and directly visualized on the web server from a top-50 list. For user guidance, the sequence homology between the template and the original sequence, proline or glycine exchanges or close contacts between a loop candidate and the remainder of the protein are denoted. For membrane proteins, the expansions of the lipid bilayer are automatically modeled using the TMDET algorithm. This allows the user to select the optimal membrane protein loop concerning its relative orientation to the lipid bilayer. The server is online since October 2007 and can be freely accessed at URL: http://bioinformatics.charite.de/superlooper/ PMID:19429894

  2. Universe opacity and EBL

    Science.gov (United States)

    Vavryčuk, Václav

    2017-02-01

    The observed extragalactic background light (EBL) is affected by light attenuation due to absorption of light by galactic and intergalactic dust in the Universe. Even galactic opacity of 10-20 per cent and minute universe intergalactic opacity of 0.01 mag h Gpc-1 at the local Universe have a significant impact on the EBL because obscuration of galaxies and density of intergalactic dust increase with redshift as (1 + z)3. Consequently, intergalactic opacity increases and the Universe becomes considerably opaque at z > 3. Adopting realistic values for galactic and intergalactic opacity, the estimates of the EBL for the expanding dusty universe are close to observations. The luminosity density evolution fits well measurements. The model reproduces a steep increase of the luminosity density at z EBL ranges from 100 to 200 nW m-2 sr-1 and is within the limits of 40 and 200 nW m-2 sr-1 of current EBL observations. The model predicts 98 per cent of the EBL coming from radiation of galaxies at z 3.5.

  3. Including Functional Annotations and Extending the Collection of Structural Classifications of Protein Loops (ArchDB

    Directory of Open Access Journals (Sweden)

    Antoni Hermoso

    2007-01-01

    Full Text Available Loops represent an important part of protein structures. The study of loop is critical for two main reasons: First, loops are often involved in protein function, stability and folding. Second, despite improvements in experimental and computational structure prediction methods, modeling the conformation of loops remains problematic. Here, we present a structural classification of loops, ArchDB, a mine of information with application in both mentioned fields: loop structure prediction and function prediction. ArchDB (http://sbi.imim.es/archdb is a database of classified protein loop motifs. The current database provides four different classification sets tailored for different purposes. ArchDB-40, a loop classification derived from SCOP40, well suited for modeling common loop motifs. Since features relevant to loop structure or function can be more easily determined on well-populated clusters, we have developed ArchDB-95, a loop classification derived from SCOP95. This new classification set shows a ∼40% increase in the number of subclasses, and a large 7-fold increase in the number of putative structure/function-related subclasses. We also present ArchDB-EC, a classification of loop motifs from enzymes, and ArchDB-KI, a manually annotated classification of loop motifs from kinases. Information about ligand contacts and PDB sites has been included in all classification sets. Improvements in our classification scheme are described, as well as several new database features, such as the ability to query by conserved annotations, sequence similarity, or uploading 3D coordinates of a protein. The lengths of classified loops range between 0 and 36 residues long. ArchDB offers an exhaustive sampling of loop structures. Functional information about loops and links with related biological databases are also provided. All this information and the possibility to browse/query the database through a web-server outline an useful tool with application in the

  4. Domain Hierarchy of Protein Loop-Lock Structure (DHoPLLS): a server for decomposition of a protein structure on set of closed loops

    CERN Document Server

    Kogan, Simon

    2011-01-01

    DHoPLLS (http://leah.haifa.ac.il/~skogan/Apache/mydata1/main.html) is a web server that identifies closed loops, which constitute a structural basis for the protein domain hierarchy. The server was created in 2005 year on basis Prof. Trifonov's lab in Genome Diversity Center, Institute of Evolution at University of Haifa. It is based on theory of loop-lock structure developed by Prof. Trifonov's group in Weizmann Institute of Science. This theory declares that all globular protein can be decomposed on set of almost closed loop with mean length about 30 aminoacids. The lock is a place, where a loop meets itself. Investigations of Trifonov's group demonstrates that some aminoacid's sequences (about 30 aminoacids) are usually exists in proteins in form of closed loops. On basis computer programs, developed for the server, we checked the simplest assumption that most of closed loop or locks in proteins have some alphabet of consensus sequences. Unfortunately our results demonstrate that such alphabet doesn't exis...

  5. Overapplication opacity in phonological acquisition

    Directory of Open Access Journals (Sweden)

    Olga Urek

    2013-02-01

    Full Text Available Normal 0 false false false EN-US JA X-NONE Phonological opacity is a challenge for parallel OT, which does not allow for intermediate levels of representation. Several modifications of the theory have been proposed over the years to incorporate opacity, all of them falling short of accounting for spontaneous opacity effects in developing grammars. In this paper I demonstrate that if certain independently motivated adjustments are made to the recent OT-based theory of opacity called Optimality Theory with Candidate Chains (OT-CC, see McCarthy 2007, it can successfully deal with spontaneous opacity effects.

  6. Molecular opacities for exoplanets.

    Science.gov (United States)

    Bernath, Peter F

    2014-04-28

    Spectroscopic observations of exoplanets are now possible by transit methods and direct emission. Spectroscopic requirements for exoplanets are reviewed based on existing measurements and model predictions for hot Jupiters and super-Earths. Molecular opacities needed to simulate astronomical observations can be obtained from laboratory measurements, ab initio calculations or a combination of the two approaches. This discussion article focuses mainly on laboratory measurements of hot molecules as needed for exoplanet spectroscopy.

  7. Structural families in loops of homologous proteins: automatic classification, modelling and application to antibodies.

    Science.gov (United States)

    Martin, A C; Thornton, J M

    1996-11-15

    Loop regions of polypeptide in homologous proteins may be classified into structural families. A method is described by which this classification may be performed automatically and "key residue" templates, which may be responsible for the loop adopting a given conformation, are defined. The technique has been applied to the hypervariable loops of antibodies and the results are compared with the previous definition of canonical classes. We have extended these definitions and provide complete sets of structurally determining residues (SDRs) for the observed clusters including the first set of key residues for seven-residue CDR-H3 loops.

  8. Kinks, loops, and protein folding, with protein A as an example

    Energy Technology Data Exchange (ETDEWEB)

    Krokhotin, Andrey, E-mail: Andrei.Krokhotine@cern.ch [Department of Physics and Astronomy and Science for Life Laboratory, Uppsala University, P.O. Box 803, S-75108 Uppsala (Sweden); Liwo, Adam, E-mail: adam@chem.univ.gda.pl [Faculty of Chemistry, University of Gdansk, ul. Sobieskiego 18, 80-952 Gdansk (Poland); Maisuradze, Gia G., E-mail: gm56@cornell.edu; Scheraga, Harold A., E-mail: has5@cornell.edu [Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301 (United States); Niemi, Antti J., E-mail: Antti.Niemi@physics.uu.se [Department of Physics and Astronomy and Science for Life Laboratory, Uppsala University, P.O. Box 803, S-75108 Uppsala (Sweden); Laboratoire de Mathematiques et Physique Theorique CNRS UMR 6083, Fédération Denis Poisson, Université de Tours, Parc de Grandmont, F37200 Tours, France and Department of Physics, Beijing Institute of Technology, Haidian District, Beijing 100081 (China)

    2014-01-14

    The dynamics and energetics of formation of loops in the 46-residue N-terminal fragment of the B-domain of staphylococcal protein A has been studied. Numerical simulations have been performed using coarse-grained molecular dynamics with the united-residue (UNRES) force field. The results have been analyzed in terms of a kink (heteroclinic standing wave solution) of a generalized discrete nonlinear Schrödinger (DNLS) equation. In the case of proteins, the DNLS equation arises from a C{sup α}-trace-based energy function. Three individual kink profiles were identified in the experimental three-α-helix structure of protein A, in the range of the Glu16-Asn29, Leu20-Asn29, and Gln33-Asn44 residues, respectively; these correspond to two loops in the native structure. UNRES simulations were started from the full right-handed α-helix to obtain a clear picture of kink formation, which would otherwise be blurred by helix formation. All three kinks emerged during coarse-grained simulations. It was found that the formation of each is accompanied by a local free energy increase; this is expressed as the change of UNRES energy which has the physical sense of the potential of mean force of a polypeptide chain. The increase is about 7 kcal/mol. This value can thus be considered as the free energy barrier to kink formation in full α-helical segments of polypeptide chains. During the simulations, the kinks emerge, disappear, propagate, and annihilate each other many times. It was found that the formation of a kink is initiated by an abrupt change in the orientation of a pair of consecutive side chains in the loop region. This resembles the formation of a Bloch wall along a spin chain, where the C{sup α} backbone corresponds to the chain, and the amino acid side chains are interpreted as the spin variables. This observation suggests that nearest-neighbor side chain–side chain interactions are responsible for initiation of loop formation. It was also found that the individual

  9. Looping in on Ndc80 - how does a protein loop at the kinetochore control chromosome segregation?

    DEFF Research Database (Denmark)

    Nilsson, Jakob

    2012-01-01

    Segregation of chromosomes during mitosis requires the interaction of dynamic microtubules with the kinetochore, a large protein structure established on the centromere region of sister chromatids. The core microtubule-binding activity of the kinetochore resides in the KMN network, an outer...

  10. Evaluation of Neisseria Gonorrhoeae Opacity (Opa) Protein Loops as Targets for Passive Vaccination and Investigation of the Role of Opa Proteins During Infection of a Female Host

    Science.gov (United States)

    2009-08-24

    lymphocyte activation (23, 135), and hindered by degradation of IgA1 by a secreted IgA protease (138, 139), generation of blocking antibodies against the... fluoroquinolones from recommended treatments (1), and underscores the importance of identifying new preventive measures against gonorrhea. The...References 1. 2007. Update to CDC’s sexually transmitted diseases treatment guidelines, 2006: fluoroquinolones no longer recommended for treatment of

  11. Multilevel deconstruction of the In vivo behavior of looped DNA-protein complexes.

    Directory of Open Access Journals (Sweden)

    Leonor Saiz

    Full Text Available Protein-DNA complexes with loops play a fundamental role in a wide variety of cellular processes, ranging from the regulation of DNA transcription to telomere maintenance. As ubiquitous as they are, their precise in vivo properties and their integration into the cellular function still remain largely unexplored. Here, we present a multilevel approach that efficiently connects in both directions molecular properties with cell physiology and use it to characterize the molecular properties of the looped DNA-lac repressor complex while functioning in vivo. The properties we uncover include the presence of two representative conformations of the complex, the stabilization of one conformation by DNA architectural proteins, and precise values of the underlying twisting elastic constants and bending free energies. Incorporation of all this molecular information into gene-regulation models reveals an unprecedented versatility of looped DNA-protein complexes at shaping the properties of gene expression.

  12. Improving predicted protein loop structure ranking using a Pareto-optimality consensus method

    Directory of Open Access Journals (Sweden)

    Jakobsson Eric

    2010-07-01

    Full Text Available Abstract Background Accurate protein loop structure models are important to understand functions of many proteins. Identifying the native or near-native models by distinguishing them from the misfolded ones is a critical step in protein loop structure prediction. Results We have developed a Pareto Optimal Consensus (POC method, which is a consensus model ranking approach to integrate multiple knowledge- or physics-based scoring functions. The procedure of identifying the models of best quality in a model set includes: 1 identifying the models at the Pareto optimal front with respect to a set of scoring functions, and 2 ranking them based on the fuzzy dominance relationship to the rest of the models. We apply the POC method to a large number of decoy sets for loops of 4- to 12-residue in length using a functional space composed of several carefully-selected scoring functions: Rosetta, DOPE, DDFIRE, OPLS-AA, and a triplet backbone dihedral potential developed in our lab. Our computational results show that the sets of Pareto-optimal decoys, which are typically composed of ~20% or less of the overall decoys in a set, have a good coverage of the best or near-best decoys in more than 99% of the loop targets. Compared to the individual scoring function yielding best selection accuracy in the decoy sets, the POC method yields 23%, 37%, and 64% less false positives in distinguishing the native conformation, indentifying a near-native model (RMSD Conclusions By integrating multiple knowledge- and physics-based scoring functions based on Pareto optimality and fuzzy dominance, the POC method is effective in distinguishing the best loop models from the other ones within a loop model set.

  13. Atomic-accuracy prediction of protein loop structures through an RNA-inspired Ansatz.

    Directory of Open Access Journals (Sweden)

    Rhiju Das

    Full Text Available Consistently predicting biopolymer structure at atomic resolution from sequence alone remains a difficult problem, even for small sub-segments of large proteins. Such loop prediction challenges, which arise frequently in comparative modeling and protein design, can become intractable as loop lengths exceed 10 residues and if surrounding side-chain conformations are erased. Current approaches, such as the protein local optimization protocol or kinematic inversion closure (KIC Monte Carlo, involve stages that coarse-grain proteins, simplifying modeling but precluding a systematic search of all-atom configurations. This article introduces an alternative modeling strategy based on a 'stepwise ansatz', recently developed for RNA modeling, which posits that any realistic all-atom molecular conformation can be built up by residue-by-residue stepwise enumeration. When harnessed to a dynamic-programming-like recursion in the Rosetta framework, the resulting stepwise assembly (SWA protocol enables enumerative sampling of a 12 residue loop at a significant but achievable cost of thousands of CPU-hours. In a previously established benchmark, SWA recovers crystallographic conformations with sub-Angstrom accuracy for 19 of 20 loops, compared to 14 of 20 by KIC modeling with a comparable expenditure of computational power. Furthermore, SWA gives high accuracy results on an additional set of 15 loops highlighted in the biological literature for their irregularity or unusual length. Successes include cis-Pro touch turns, loops that pass through tunnels of other side-chains, and loops of lengths up to 24 residues. Remaining problem cases are traced to inaccuracies in the Rosetta all-atom energy function. In five additional blind tests, SWA achieves sub-Angstrom accuracy models, including the first such success in a protein/RNA binding interface, the YbxF/kink-turn interaction in the fourth 'RNA-puzzle' competition. These results establish all-atom enumeration as

  14. A modular perspective of protein structures; application to fragment based loop modeling

    Science.gov (United States)

    Fernandez-Fuentes, Narcis; Fiser, Andras

    2013-01-01

    Summary Proteins can be decomposed into supersecondary structure modules. We used a generic definition of supersecondary structure elements, so-called Smotifs, which are composed of two flanking regular secondary structures connected by a loop, to explore the evolution and current variety of structure building blocks. Here, we discuss recent observations about the saturation of Smotif geometries in protein structures and how it opens new avenues in protein structure modeling and design. As a first application of these observations we describe our loop conformation modeling algorithm, ArchPred that takes advantage of Smotifs classification. In this application, instead of focusing on specific loop properties the method narrows down possible template conformations in other, often not homologous structures, by identifying the most likely supersecondary structure environment that cradles the loop. Beyond identifying the correct starting supersecondary structure geometry, it takes into account information of fit of anchor residues, sterical clashes, match of predicted and observed dihedral angle preferences, and local sequence signal. PMID:22987351

  15. The dynamic mechanism of presenilin-function: Sensitive gate dynamics and loop unplugging control protein access

    DEFF Research Database (Denmark)

    Somavarapu, Arun Kumar; Kepp, Kasper Planeta

    2016-01-01

    molecular dynamics in an explicit membrane with particular account of the as yet unexplored loop dynamics. We find that mature PSEN1 contains multiple distinct conformational states whereas non-mature PSEN1 is a typical one-state protein. We confirm a previously suggested gating mechanism, and find......There is no molecular explanation for the many presenilin 1 (PSEN1) mutations causing Alzheimer's disease, but both gain of function relating to amyloid production and loss of isolated PSEN1 function have been implied. We report here the first detailed dynamic all-atom model of mature PSEN1 from...... that the 106-131 loop acts as a "hinge" for the TM2 and TM6 "doors". More importantly, we identify an unplugging mechanism of the Exon 9 loop associated only with mature PSEN1. Proper opening of both the "gate" and "plug" in the membrane produces channel-like morphologies and access to the catalytic aspartates...

  16. Enhancing OPAC Records for Discovery

    Directory of Open Access Journals (Sweden)

    Patrick Griffis

    2009-09-01

    Full Text Available This article proposes adding keywords and descriptors to the catalog records of electronic databases and media items to enhance their discovery. The authors contend that subject liaisons can add value to OPAC records and enhance discovery of electronic databases and media items by providing searchable keywords and resource descriptions. The authors provide an examination of OPAC records at their own library, which illustrates the disparity of useful keywords and descriptions within the notes field for media item records versus electronic database records. The authors outline methods for identifying useful keywords for indexing OPAC records of electronic databases. Also included is an analysis of the advantages of using Encore’s Community Tag and Community Review features to allow subject liaisons to work directly in the catalog instead of collaborating with cataloging staff

  17. Protein loop modeling using a new hybrid energy function and its application to modeling in inaccurate structural environments.

    Directory of Open Access Journals (Sweden)

    Hahnbeom Park

    Full Text Available Protein loop modeling is a tool for predicting protein local structures of particular interest, providing opportunities for applications involving protein structure prediction and de novo protein design. Until recently, the majority of loop modeling methods have been developed and tested by reconstructing loops in frameworks of experimentally resolved structures. In many practical applications, however, the protein loops to be modeled are located in inaccurate structural environments. These include loops in model structures, low-resolution experimental structures, or experimental structures of different functional forms. Accordingly, discrepancies in the accuracy of the structural environment assumed in development of the method and that in practical applications present additional challenges to modern loop modeling methods. This study demonstrates a new strategy for employing a hybrid energy function combining physics-based and knowledge-based components to help tackle this challenge. The hybrid energy function is designed to combine the strengths of each energy component, simultaneously maintaining accurate loop structure prediction in a high-resolution framework structure and tolerating minor environmental errors in low-resolution structures. A loop modeling method based on global optimization of this new energy function is tested on loop targets situated in different levels of environmental errors, ranging from experimental structures to structures perturbed in backbone as well as side chains and template-based model structures. The new method performs comparably to force field-based approaches in loop reconstruction in crystal structures and better in loop prediction in inaccurate framework structures. This result suggests that higher-accuracy predictions would be possible for a broader range of applications. The web server for this method is available at http://galaxy.seoklab.org/loop with the PS2 option for the scoring function.

  18. Quantitative assessment of the p53-Mdm2 feedback loop using protein lysate microarrays.

    Science.gov (United States)

    Ramalingam, Sundhar; Honkanen, Peter; Young, Lynn; Shimura, Tsutomu; Austin, John; Steeg, Patricia S; Nishizuka, Satoshi

    2007-07-01

    Mathematical simulations of the p53-Mdm2 feedback loop suggest that both proteins will exhibit impulsive expression characteristics in response to high cellular stress levels. However, little quantitative experimental evaluation has been done, particularly of the phosphorylated forms. To evaluate the mathematical models experimentally, we used lysate microarrays from an isogenic pair of gamma-ray-irradiated cell lysates from HCT116 (p53(+/+) and p53(-/-)). Both p53 and Mdm2 proteins showed expected pulses in the wild type, whereas no pulses were seen in the knockout. Based on experimental observations, we determined model parameters and generated an in silico "knockout," reflecting the experimental data, including phosphorylated proteins.

  19. The mechanics of DNA loops bridged by proteins unveiled by single-molecule experiments.

    Science.gov (United States)

    Tardin, Catherine

    2017-08-10

    Protein-induced DNA bridging and looping is a common mechanism for various and essential processes in bacterial chromosomes. This mechanism is preserved despite the very different bacterial conditions and their expected influence on the thermodynamic and kinetic characteristics of the bridge formation and stability. Over the last two decades, single-molecule techniques carried out on in vitro DNA systems have yielded valuable results which, in combination with theoretical works, have clarified the effects of different parameters of nucleoprotein complexes on the protein-induced DNA bridging and looping process. In this review, I will outline the features that can be measured for such processes with various single-molecule techniques in use in the field. I will then describe both the experimental results and the theoretical models that illuminate the contribution of the DNA molecule itself as well as that of the bridging proteins in the DNA looping mechanism at play in the nucleoid of E. coli. Copyright © 2017. Published by Elsevier B.V.

  20. Role of loops connecting secondary structure elements in the stabilization of proteins isolated from thermophilic organisms.

    Science.gov (United States)

    Balasco, Nicole; Esposito, Luciana; De Simone, Alfonso; Vitagliano, Luigi

    2013-07-01

    It has been recently discovered that the connection of secondary structure elements (ββ-unit, βα- and αβ-units) in proteins follows quite stringent principles regarding the chirality and the orientation of the structural units (Koga et al., Nature 2012;491:222-227). By exploiting these rules, a number of protein scaffolds endowed with a remarkable thermal stability have been designed (Koga et al., Nature 2012;491:222-227). By using structural databases of proteins isolated from either mesophilic or thermophilic organisms, we here investigate the influence of supersecondary associations on the thermal stability of natural proteins. Our results suggest that β-hairpins of proteins from thermophilic organisms are very frequently characterized by shortenings of the loops. Interestingly, this shortening leads to states that display a very strong preference for the most common connectivity of the strands observed in native protein hairpins. The abundance of selective states in these proteins suggests that they may achieve a high stability by adopting a strategy aimed to reduce the possible conformations of the unfolded ensemble. In this scenario, our data indicate that the shortening is effective if it increases the adherence to these rules. We also show that this mechanism may operate in the stabilization of well-known protein folds (thioredoxin and RNase A). These findings suggest that future investigations aimed at defining mechanism of protein stabilization should also consider these effects.

  1. Structural delineation of stem-loop RNA binding by human TAF15 protein.

    Science.gov (United States)

    Kashyap, Maruthi; Ganguly, Akshay Kumar; Bhavesh, Neel Sarovar

    2015-11-27

    Human TATA binding protein associated factor 2 N (TAF15) and Fused in sarcoma (FUS) are nucleic acid binding proteins belonging to the conserved FET family of proteins. They are involved in diverse processes such as pre-mRNA splicing, mRNA transport, and DNA binding. The absence of information regarding the structural mechanism employed by the FET family in recognizing and discriminating their cognate and non-cognate RNA targets has hampered the attainment of consensus on modes of protein-RNA binding for this family. Our study provides a molecular basis of this RNA recognition using a combination of solution-state NMR spectroscopy, calorimetry, docking and molecular dynamics simulation. Analysis of TAF15-RRM solution structure and its binding with stem-loop RNA has yielded conclusive evidence of a non-canonical mode of RNA recognition. Rather than classical stacking interactions that occur across nitrogen bases and aromatic amino acids on ribonucleoprotein sites, moderate-affinity hydrogen bonding network between the nitrogen bases in the stem-loop RNA and a concave face on the RRM surface primarily mediate TAF15-RRM RNA interaction. We have compared the binding affinities across a set of single-stranded RNA oligonucleotides to conclusively establish that RNA binding is dependent upon structural elements in the RNA rather than sequence.

  2. Iron opacity experiments for the solar interior

    Science.gov (United States)

    Nagayama, T.; Bailey, J. E.; Loisel, G.; Rochau, G. A.; Hansen, S. B.; Blancard, C.; Cosse, Ph.; Faussurier, G.; Gilleron, F.; Pain, J.-C.; Pradhan, A. K.; Orban, C.; Pinsonneault, M.; Nahar, S. N.; Iglesias, C. A.; Wilson, B.; Colgan, J.; Fontes, C.; Kilcrease, D.; Sherrill, M.; Macfarlane, J. J.; Golovkin, I.; Mancini, R. C.

    2014-10-01

    Iron opacity experiments near solar interior conditions are performed at SNL Z-machine to better constrain solar models. The SNL opacity science platform satisfies the many challenging requirements for opacity measurements and successfully determines iron opacities at multiple conditions. We found that the agreement between the modeled opacity and the measured opacity deteriorates as Te and ne are raised to approach solar interior conditions. While the inaccuracy of the modeled opacity partially resolves the solar abundance problem, the announcement of such discrepancies has a high impact on the astrophysics, atomic physics, and high energy density physics, and thus more scrutiny on the potential experimental flaws is critical. We report the synthetic investigation for potential sources of systematic uncertainties in the experiments. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy under Contract DE-AC04-94AL85000.

  3. High affinity binding of proteins HMG1 and HMG2 to semicatenated DNA loops

    Directory of Open Access Journals (Sweden)

    Strauss François

    2000-10-01

    Full Text Available Abstract Background Proteins HMG1 and HMG2 are two of the most abundant non histone proteins in the nucleus of mammalian cells, and contain a domain of homology with many proteins implicated in the control of development, such as the sex-determination factor Sry and the Sox family of proteins. In vitro studies of interactions of HMG1/2 with DNA have shown that these proteins can bind to many unusual DNA structures, in particular to four-way junctions, with binding affinities of 107 to 109 M-1. Results Here we show that HMG1 and HMG2 bind with a much higher affinity, at least 4 orders of magnitude higher, to a new structure, Form X, which consists of a DNA loop closed at its base by a semicatenated DNA junction, forming a DNA hemicatenane. The binding constant of HMG1 to Form X is higher than 5 × 1012 M-1, and the half-life of the complex is longer than one hour in vitro. Conclusions Of all DNA structures described so far with which HMG1 and HMG2 interact, we have found that Form X, a DNA loop with a semicatenated DNA junction at its base, is the structure with the highest affinity by more than 4 orders of magnitude. This suggests that, if similar structures exist in the cell nucleus, one of the functions of these proteins might be linked to the remarkable property of DNA hemicatenanes to associate two distant regions of the genome in a stable but reversible manner.

  4. An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network

    Directory of Open Access Journals (Sweden)

    Amoutzias Grigoris D

    2007-08-01

    Full Text Available Abstract Background Alternative representations of biochemical networks emphasise different aspects of the data and contribute to the understanding of complex biological systems. In this study we present a variety of automated methods for visualisation of a protein-protein interaction network, using the basic helix-loop-helix (bHLH family of transcription factors as an example. Results Network representations that arrange nodes (proteins according to either continuous or discrete information are investigated, revealing the existence of protein sub-families and the retention of interactions following gene duplication events. Methods of network visualisation in conjunction with a phylogenetic tree are presented, highlighting the evolutionary relationships between proteins, and clarifying the context of network hubs and interaction clusters. Finally, an optimisation technique is used to create a three-dimensional layout of the phylogenetic tree upon which the protein-protein interactions may be projected. Conclusion We show that by incorporating secondary genomic, functional or phylogenetic information into network visualisation, it is possible to move beyond simple layout algorithms based on network topology towards more biologically meaningful representations. These new visualisations can give structure to complex networks and will greatly help in interpreting their evolutionary origins and functional implications. Three open source software packages (InterView, TVi and OptiMage implementing our methods are available.

  5. Line Broadening and the Solar Opacity Problem

    Science.gov (United States)

    Krief, M.; Feigel, A.; Gazit, D.

    2016-06-01

    The calculation of line widths constitutes theoretical and computational challenges in the calculation of opacities of hot, dense plasmas. Opacity models use line broadening approximations that are untested at stellar interior conditions. Moreover, calculations of atomic spectra of the Sun indicate a large discrepancy in the K-shell line widths between several atomic codes and the Opacity-Project (OP). In this work, the atomic code STAR is used to study the sensitivity of solar opacities to line broadening. Variations in the solar opacity profile due to an increase of the Stark widths resulting from discrepancies with OP, are compared, in light of the solar opacity problem, with the required opacity variations of the present day Sun, as imposed by helioseismic and neutrino observations. The resulting variation profile is much larger than the discrepancy between different atomic codes, agrees qualitatively with the missing opacity profile, recovers about half of the missing opacity nearby the convection boundary, and has a little effect in the internal regions. Since it is hard to estimate quantitatively the uncertainty in the Stark widths, we show that an increase of all line widths by a factor of about ˜100 recovers quantitatively the missing opacity. These results emphasize the possibility that photoexcitation processes are not modeled properly, and more specifically, highlight the need for a better theoretical characterization of the line broadening phenomena at stellar interior conditions, and of the uncertainty due to the way it is implemented by atomic codes.

  6. Depletion of the chromatin looping proteins CTCF and cohesin causes chromatin compaction: insight into chromatin folding by polymer modelling.

    Directory of Open Access Journals (Sweden)

    Mariliis Tark-Dame

    2014-10-01

    Full Text Available Folding of the chromosomal fibre in interphase nuclei is an important element in the regulation of gene expression. For instance, physical contacts between promoters and enhancers are a key element in cell-type-specific transcription. We know remarkably little about the principles that control chromosome folding. Here we explore the view that intrachromosomal interactions, forming a complex pattern of loops, are a key element in chromosome folding. CTCF and cohesin are two abundant looping proteins of interphase chromosomes of higher eukaryotes. To investigate the role of looping in large-scale (supra Mb folding of human chromosomes, we knocked down the gene that codes for CTCF and the one coding for Rad21, an essential subunit of cohesin. We measured the effect on chromosome folding using systematic 3D fluorescent in situ hybridization (FISH. Results show that chromatin becomes more compact after reducing the concentration of these two looping proteins. The molecular basis for this counter-intuitive behaviour is explored by polymer modelling usingy the Dynamic Loop model (Bohn M, Heermann DW (2010 Diffusion-driven looping provides a consistent framework for chromatin organization. PLoS ONE 5: e12218.. We show that compaction can be explained by selectively decreasing the number of short-range loops, leaving long-range looping unchanged. In support of this model prediction it has recently been shown by others that CTCF and cohesin indeed are responsible primarily for short-range looping. Our results suggest that the local and the overall changes in of chromosome structure are controlled by a delicate balance between short-range and long-range loops, allowing easy switching between, for instance, open and more compact chromatin states.

  7. Importance of the extracellular loops in G protein-coupled receptors for ligand recognition and receptor activation.

    Science.gov (United States)

    Peeters, M C; van Westen, G J P; Li, Q; IJzerman, A P

    2011-01-01

    G protein-coupled receptors (GPCRs) are the major drug target of medicines on the market today. Therefore, much research is and has been devoted to the elucidation of the function and three-dimensional structure of this large family of membrane proteins, which includes multiple conserved transmembrane domains connected by intra- and extracellular loops. In the last few years, the less conserved extracellular loops have garnered increasing interest, particularly after the publication of several GPCR crystal structures that clearly show the extracellular loops to be involved in ligand binding. This review will summarize the recent progress made in the clarification of the ligand binding and activation mechanism of class-A GPCRs and the role of extracellular loops in this process.

  8. Functions of Replication Protein A as a Sensor of R Loops and a Regulator of RNaseH1.

    Science.gov (United States)

    Nguyen, Hai Dang; Yadav, Tribhuwan; Giri, Sumanprava; Saez, Borja; Graubert, Timothy A; Zou, Lee

    2017-03-02

    R loop, a transcription intermediate containing RNA:DNA hybrids and displaced single-stranded DNA (ssDNA), has emerged as a major source of genomic instability. RNaseH1, which cleaves the RNA in RNA:DNA hybrids, plays an important role in R loop suppression. Here we show that replication protein A (RPA), an ssDNA-binding protein, interacts with RNaseH1 and colocalizes with both RNaseH1 and R loops in cells. In vitro, purified RPA directly enhances the association of RNaseH1 with RNA:DNA hybrids and stimulates the activity of RNaseH1 on R loops. An RPA binding-defective RNaseH1 mutant is not efficiently stimulated by RPA in vitro, fails to accumulate at R loops in cells, and loses the ability to suppress R loops and associated genomic instability. Thus, in addition to sensing DNA damage and replication stress, RPA is a sensor of R loops and a regulator of RNaseH1, extending the versatile role of RPA in suppression of genomic instability. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. Analytical opacity formulas for low Z plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Rubiano, J; Rodriguez, R; Gil, J M; Florido, R; Martel, P; Mendoza, M A; Suarez, D [Departamento de FIasica, Universidad de Las Palmas de GC, 35017 Las Palmas de GC (Spain); Minguez, E [Instituto de Fusion Nuclear DENIM. Universidad Politecnica de Madrid, 28019 Madrid (Spain)], E-mail: jgarcia@dfis.ulpgc.es

    2008-05-01

    The accurate computation of radiative opacities is basic in the ICF target physics analysis, in which the radiation is an important feature to determine in detail. For this reason, accurate analytical formulas for giving mean opacities versus temperature and density of the plasma seem to be a useful tool. In this work we analyse some analytical expressions found in the literature for the opacity low Z plasmas in a wide range of temperature and densities. The validity of these formulas for computing the opacity under NLTE conditions is investigated using the new code ABAKO.

  10. External loops at the ferredoxin-NADP(+) reductase protein-partner binding cavity contribute to substrates allocation.

    Science.gov (United States)

    Sánchez-Azqueta, Ana; Martínez-Júlvez, Marta; Hervás, Manuel; Navarro, José A; Medina, Milagros

    2014-02-01

    Ferredoxin-NADP(+) reductase (FNR) is the structural prototype of a family of FAD-containing reductases that catalyze electron transfer between low potential proteins and NAD(P)(+)/H, and that display a two-domain arrangement with an open cavity at their interface. The inner part of this cavity accommodates the reacting atoms during catalysis. Loops at its edge are highly conserved among plastidic FNRs, suggesting that they might contribute to both flavin stabilization and competent disposition of substrates. Here we pay attention to two of these loops in Anabaena FNR. The first is a sheet-loop-sheet motif, loop102-114, that allocates the FAD adenosine. It was thought to determine the extended FAD conformation, and, indirectly, to modulate isoalloxazine electronic properties, partners binding, catalytic efficiency and even coenzyme specificity. The second, loop261-269, contains key residues for the allocation of partners and coenzyme, including two glutamates, Glu267 and Glu268, proposed as candidates to facilitate the key displacement of the C-terminal tyrosine (Tyr303) from its stacking against the isoalloxazine ring during the catalytic cycle. Our data indicate that the main function of loop102-114 is to provide the inter-domain cavity with flexibility to accommodate protein partners and to guide the coenzyme to the catalytic site, while the extended conformation of FAD must be induced by other protein determinants. Glu267 and Glu268 appear to assist the conformational changes that occur in the loop261-269 during productive coenzyme binding, but their contribution to Tyr303 displacement is minor than expected. Additionally, loop261-269 appears a determinant to ensure reversibility in photosynthetic FNRs. Copyright © 2013 Elsevier B.V. All rights reserved.

  11. Encoded loop-lanthanide-binding tags for long-range distance measurements in proteins by NMR and EPR spectroscopy.

    Science.gov (United States)

    Barthelmes, Dominic; Gränz, Markus; Barthelmes, Katja; Allen, Karen N; Imperiali, Barbara; Prisner, Thomas; Schwalbe, Harald

    2015-11-01

    We recently engineered encodable lanthanide binding tags (LBTs) into proteins and demonstrated their applicability in Nuclear Magnetic Resonance (NMR) spectroscopy, X-ray crystallography and luminescence studies. Here, we engineered two-loop-LBTs into the model protein interleukin-1β (IL1β) and measured (1)H, (15)N-pseudocontact shifts (PCSs) by NMR spectroscopy. We determined the Δχ-tensors associated with each Tm(3+)-loaded loop-LBT and show that the experimental PCSs yield structural information at the interface between the two metal ion centers at atomic resolution. Such information is very valuable for the determination of the sites of interfaces in protein-protein-complexes. Combining the experimental PCSs of the two-loop-LBT construct IL1β-S2R2 and the respective single-loop-LBT constructs IL1β-S2, IL1β-R2 we additionally determined the distance between the metal ion centers. Further, we explore the use of two-loop LBTs loaded with Gd(3+) as a novel tool for distance determination by Electron Paramagnetic Resonance spectroscopy and show the NMR-derived distances to be remarkably consistent with distances derived from Pulsed Electron-Electron Dipolar Resonance.

  12. DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation

    Science.gov (United States)

    Boedicker, James Q.; Garcia, Hernan G.; Johnson, Stephanie; Phillips, Rob

    2013-12-01

    As the chief informational molecule of life, DNA is subject to extensive physical manipulations. The energy required to deform double-helical DNA depends on sequence, and this mechanical code of DNA influences gene regulation, such as through nucleosome positioning. Here we examine the sequence-dependent flexibility of DNA in bacterial transcription factor-mediated looping, a context for which the role of sequence remains poorly understood. Using a suite of synthetic constructs repressed by the Lac repressor and two well-known sequences that show large flexibility differences in vitro, we make precise statistical mechanical predictions as to how DNA sequence influences loop formation and test these predictions using in vivo transcription and in vitro single-molecule assays. Surprisingly, sequence-dependent flexibility does not affect in vivo gene regulation. By theoretically and experimentally quantifying the relative contributions of sequence and the DNA-bending protein HU to DNA mechanical properties, we reveal that bending by HU dominates DNA mechanics and masks intrinsic sequence-dependent flexibility. Such a quantitative understanding of how mechanical regulatory information is encoded in the genome will be a key step towards a predictive understanding of gene regulation at single-base pair resolution.

  13. DNA replication catalyzed by herpes simplex virus type 1 proteins reveals trombone loops at the fork.

    Science.gov (United States)

    Bermek, Oya; Willcox, Smaranda; Griffith, Jack D

    2015-01-30

    Using purified replication factors encoded by herpes simplex virus type 1 and a 70-base minicircle template, we obtained robust DNA synthesis with leading strand products of >20,000 nucleotides and lagging strand fragments from 600 to 9,000 nucleotides as seen by alkaline gel electrophoresis. ICP8 was crucial for the synthesis on both strands. Visualization of the deproteinized products using electron microscopy revealed long, linear dsDNAs, and in 87%, one end, presumably the end with the 70-base circle, was single-stranded. The remaining 13% had multiple single-stranded segments separated by dsDNA segments 500 to 1,000 nucleotides in length located at one end. These features are diagnostic of the trombone mechanism of replication. Indeed, when the products were examined with the replication proteins bound, a dsDNA loop was frequently associated with the replication complex located at one end of the replicated DNA. Furthermore, the frequency of loops correlated with the fraction of DNA undergoing Okazaki fragment synthesis.

  14. Introducing a rigid loop structure from deer into mouse prion protein increases its propensity for misfolding in vitro.

    Directory of Open Access Journals (Sweden)

    Leah M Kyle

    Full Text Available Prion diseases are fatal neurodegenerative disorders characterized by misfolding of the cellular prion protein (PrP(c into the disease-associated isoform (PrP(Sc that has increased β-sheet content and partial resistance to proteolytic digestion. Prion diseases from different mammalian species have varying propensities for transmission upon exposure of an uninfected host to the infectious agent. Chronic Wasting Disease (CWD is a highly transmissible prion disease that affects free ranging and farmed populations of cervids including deer, elk and moose, as well as other mammals in experimental settings. The molecular mechanisms allowing CWD to maintain comparatively high transmission rates have not been determined. Previous work has identified a unique structural feature in cervid PrP, a rigid loop between β-sheet 2 and α-helix 2 on the surface of the protein. This study was designed to test the hypothesis that the rigid loop has a direct influence on the misfolding process. The rigid loop was introduced into murine PrP as the result of two amino acid substitutions: S170N and N174T. Wild-type and rigid loop murine PrP were expressed in E. coli and purified. Misfolding propensity was compared for the two proteins using biochemical techniques and cell free misfolding and conversion systems. Murine PrP with a rigid loop misfolded in cell free systems with greater propensity than wild type murine PrP. In a lipid-based conversion assay, rigid loop PrP converted to a PK resistant, aggregated isoform at lower concentrations than wild-type PrP. Using both proteins as substrates in real time quaking-induced conversion, rigid loop PrP adopted a misfolded isoform more readily than wild type PrP. Taken together, these findings may help explain the high transmission rates observed for CWD within cervids.

  15. The GUI OPAC: Approach with Caution.

    Science.gov (United States)

    Hildreth, Charles R.

    1995-01-01

    Discusses the graphical user interface (GUI) online public access catalog (OPAC), a user interface that uses images to represent options. Topics include user interface design for information retrieval; designing effective bibliographic displays, including subject headings; two design principles; and what GUIs can bring to OPACs. (LRW)

  16. Stem-loop binding protein is a multifaceted cellular regulator of HIV-1 replication

    Science.gov (United States)

    Tucker, Lynne D.; Asara, John M.; Cheruiyot, Collins K.; Lu, Huafei; Wu, Zhijin J.; Newstein, Michael C.; Dooner, Mark S.; Friedman, Jennifer; Lally, Michelle A.; Ramratnam, Bharat

    2016-01-01

    A rare subset of HIV-1–infected individuals is able to maintain plasma viral load (VL) at low levels without antiretroviral treatment. Identifying the mechanisms underlying this atypical response to infection may lead to therapeutic advances for treating HIV-1. Here, we developed a proteomic analysis to compare peripheral blood cell proteomes in 20 HIV-1–infected individuals who maintained either high or low VL with the aim of identifying host factors that impact HIV-1 replication. We determined that the levels of multiple histone proteins were markedly decreased in cohorts of individuals with high VL. This reduction was correlated with lower levels of stem-loop binding protein (SLBP), which is known to control histone metabolism. Depletion of cellular SLBP increased promoter engagement with the chromatin structures of the host gene high mobility group protein A1 (HMGA1) and viral long terminal repeat (LTR), which led to higher levels of HIV-1 genomic integration and proviral transcription. Further, we determined that TNF-α regulates expression of SLBP and observed that plasma TNF-α levels in HIV-1–infected individuals correlated directly with VL levels and inversely with cellular SLBP levels. Our findings identify SLBP as a potentially important cellular regulator of HIV-1, thereby establishing a link between histone metabolism, inflammation, and HIV-1 infection. PMID:27454292

  17. SA-Mot: a web server for the identification of motifs of interest extracted from protein loops.

    Science.gov (United States)

    Regad, Leslie; Saladin, Adrien; Maupetit, Julien; Geneix, Colette; Camproux, Anne-Claude

    2011-07-01

    The detection of functional motifs is an important step for the determination of protein functions. We present here a new web server SA-Mot (Structural Alphabet Motif) for the extraction and location of structural motifs of interest from protein loops. Contrary to other methods, SA-Mot does not focus only on functional motifs, but it extracts recurrent and conserved structural motifs involved in structural redundancy of loops. SA-Mot uses the structural word notion to extract all structural motifs from uni-dimensional sequences corresponding to loop structures. Then, SA-Mot provides a description of these structural motifs using statistics computed in the loop data set and in SCOP superfamily, sequence and structural parameters. SA-Mot results correspond to an interactive table listing all structural motifs extracted from a target structure and their associated descriptors. Using this information, the users can easily locate loop regions that are important for the protein folding and function. The SA-Mot web server is available at http://sa-mot.mti.univ-paris-diderot.fr.

  18. The protein C omega-loop substitution Asn2Ile is associated with reduced protein C anticoagulant activity.

    LENUS (Irish Health Repository)

    Preston, Roger J S

    2012-02-01

    We report a kindred with heritable protein C (PC) deficiency in which two siblings with severe thrombosis showed a composite type I and IIb PC deficiency phenotype, identified using commercial PC assays (proband: PC antigen 42 u\\/dl, amidolytic activity 40 u\\/dl, anticoagulant activity 9 u\\/dl). The independent PROC nucleotide variations c.669C>A (predictive of Ser181Arg) and c.131C>T (predictive of Asn2Ile) segregated with the type I and type IIb PC deficiency phenotypes respectively, but co-segregated in the siblings with severe thrombosis. Soluble thrombomodulin (sTM)-mediated inhibition of plasma thrombin generation from an individual with PC-Asn2Ile was lower (endogenous thrombin potential (ETP) 56 +\\/- 1% that of ETP determined without sTM) than control plasma (ETP 15 +\\/- 2%) indicating reduced PC anticoagulant activity. Recombinant APC-Asn2Ile exhibited normal amidolytic activity but impaired anticoagulant activity. Protein S (PS)-dependent anticoagulant activity of recombinant APC-Asn2Ile and binding of recombinant APC-Asn2Ile to endothelial protein C receptor (EPCR) were reduced compared to recombinant wild-type APC. Asn2 lies within the omega-loop of the PC\\/APC Gla domain and this region is critical for calcium-induced folding and subsequent interactions with anionic phospholipids, EPCR and PS. The disruption of these interactions in this naturally-occurring PC variant highlights their collective importance in mediating APC anticoagulant activity in vivo.

  19. Role of the EHD2 unstructured loop in dimerization, protein binding and subcellular localization.

    Directory of Open Access Journals (Sweden)

    Kriti Bahl

    Full Text Available The C-terminal Eps 15 Homology Domain proteins (EHD1-4 play important roles in regulating endocytic trafficking. EHD2 is the only family member whose crystal structure has been solved, and it contains an unstructured loop consisting of two proline-phenylalanine (PF motifs: KPFRKLNPF. In contrast, despite EHD2 having nearly 70% amino acid identity with its paralogs, EHD1, EHD3 and EHD4, the latter proteins contain a single KPF or RPF motif, but no NPF motif. In this study, we sought to define the precise role of each PF motif in EHD2's homo-dimerization, binding with the protein partners, and subcellular localization. To test the role of the NPF motif, we generated an EHD2 NPF-to-NAF mutant to mimic the homologous sequences of EHD1 and EHD3. We demonstrated that this mutant lost both its ability to dimerize and bind to Syndapin2. However, it continued to localize primarily to the cytosolic face of the plasma membrane. On the other hand, EHD2 NPF-to-APA mutants displayed normal dimerization and Syndapin2 binding, but exhibited markedly increased nuclear localization and reduced association with the plasma membrane. We then hypothesized that the single PF motif of EHD1 (that aligns with the KPF of EHD2 might be responsible for both binding and localization functions of EHD1. Indeed, the EHD1 RPF motif was required for dimerization, interaction with MICAL-L1 and Syndapin2, as well as localization to tubular recycling endosomes. Moreover, recycling assays demonstrated that EHD1 RPF-to-APA was incapable of supporting normal receptor recycling. Overall, our data suggest that the EHD2 NPF phenylalanine residue is crucial for EHD2 localization to the plasma membrane, whereas the proline residue is essential for EHD2 dimerization and binding. These studies support the recently proposed model in which the EHD2 N-terminal region may regulate the availability of the unstructured loop for interactions with neighboring EHD2 dimers, thus promoting

  20. Molecular recognition in helix-loop-helix and helix-loop-helix-leucine zipper domains. Design of repertoires and selection of high affinity ligands for natural proteins.

    Science.gov (United States)

    Ciarapica, Roberta; Rosati, Jessica; Cesareni, Gianni; Nasi, Sergio

    2003-04-04

    Helix-loop-helix (HLH) and helix-loop-helix-leucine zipper (HLHZip) are dimerization domains that mediate selective pairing among members of a large transcription factor family involved in cell fate determination. To investigate the molecular rules underlying recognition specificity and to isolate molecules interfering with cell proliferation and differentiation control, we assembled two molecular repertoires obtained by directed randomization of the binding surface in these two domains. For this strategy we selected the Heb HLH and Max Zip regions as molecular scaffolds for the randomization process and displayed the two resulting molecular repertoires on lambda phage capsids. By affinity selection, many domains were isolated that bound to the proteins Mad, Rox, MyoD, and Id2 with different levels of affinity. Although several residues along an extended surface within each domain appeared to contribute to dimerization, some key residues critically involved in molecular recognition could be identified. Furthermore, a number of charged residues appeared to act as switch points facilitating partner exchange. By successfully selecting ligands for four of four HLH or HLHZip proteins, we have shown that the repertoires assembled are rather general and possibly contain elements that bind with sufficient affinity to any natural HLH or HLHZip molecule. Thus they represent a valuable source of ligands that could be used as reagents for molecular dissection of functional regulatory pathways.

  1. Line broadening and the solar opacity problem

    CERN Document Server

    Krief, M; Gazit, D

    2016-01-01

    The calculation of line widths constitutes a theoretical as well as a computational challenge in the calculation of opacities of hot dense plasmas. Opacity models use line broadening approximations that are untested at stellar interior conditions. Moreover, calculations of atomic spectra nearby the convection zone boundary (CZB) of the sun, indicate a large discrepancy in the K-shell line widths between several atomic codes and the Opacity-Project. In this work, the atomic code STAR is used to study the sensitivity of solar opacities to line-broadening. Atomic spectra of several elements are analyzed and compared within the solar interior. Variations in the solar opacity profile due to changes in the Stark widths are shown to be significant and to result mainly due to K-shell lines. In light of the solar opacity problem, the results are compared with the required opacity variations of the present day sun, as imposed by helioseismic and neutrino observations. It is shown that an increase of the line widths res...

  2. Restricted fish feeding reduces cod otolith opacity

    DEFF Research Database (Denmark)

    Høie, H.; Folkvord, A.; Mosegaard, Henrik

    2008-01-01

    The purpose of this work was to examine the effect of reduced feeding and constant temperature on cod otolith opacity. Three groups of juvenile cod were given restricted food rations at different times for 4 months, resulting in depressed somatic growth. Otolith opacity was measured on pictures...... in otolith opacity were found between individual fish both within groups and between groups. In two of the three groups significantly more translucent otolith material was deposited in response to reduced feeding. Our results show that variations in feeding and hence fish growth resulted in variation...

  3. Summary of Fe opacity measurement platform

    Energy Technology Data Exchange (ETDEWEB)

    Nagayama, Taisuke

    2016-05-01

    This powerpoint presentation goes over the Fe opacity measurement platform, including how the experiment works, what can be gathered from the measurements, what can be gathered from the simulations, and the limitations of the experiment.

  4. The neutrino opacity of neutron rich matter

    Energy Technology Data Exchange (ETDEWEB)

    Alcain, P.N., E-mail: pabloalcain@gmail.com [Departamento de Física, FCEyN, UBA and IFIBA, Conicet, Pabellón 1, Ciudad Universitaria, 1428 Buenos Aires (Argentina); IFIBA-CONICET (Argentina); Dorso, C.O. [Departamento de Física, FCEyN, UBA and IFIBA, Conicet, Pabellón 1, Ciudad Universitaria, 1428 Buenos Aires (Argentina); IFIBA-CONICET (Argentina)

    2017-05-15

    The study of neutron rich matter, present in neutron star, proto-neutron stars and core-collapse supernovae, can lead to further understanding of the behavior of nuclear matter in highly asymmetric nuclei. Heterogeneous structures are expected to exist in these systems, often referred to as nuclear pasta. We have carried out a systematic study of neutrino opacity for different thermodynamic conditions in order to assess the impact that the structure has on it. We studied the dynamics of the neutrino opacity of the heterogeneous matter at different thermodynamic conditions with semiclassical molecular dynamics model already used to study nuclear multifragmentation. For different densities, proton fractions and temperature, we calculate the very long range opacity and the cluster distribution. The neutrino opacity is of crucial importance for the evolution of the core-collapse supernovae and the neutrino scattering.

  5. New Generation of Los Alamos Opacity Tables

    Science.gov (United States)

    Colgan, James; Kilcrease, D. P.; Magee, N. H.; Sherrill, M. E.; Abdallah, J.; Hakel, P.; Fontes, C. J.; Guzik, J. A.; Mussack, K. A.

    2016-05-01

    We present a new generation of Los Alamos OPLIB opacity tables that have been computed using the ATOMIC code. Our tables have been calculated for all 30 elements from hydrogen through zinc and are publicly available through our website. In this poster we discuss the details of the calculations that underpin the new opacity tables. We also show several recent applications of the use of our opacity tables to solar modeling and other astrophysical applications. In particular, we demonstrate that use of the new opacities improves the agreement between solar models and helioseismology, but does not fully resolve the long-standing `solar abundance' problem. The Los Alamos National Laboratory is operated by Los Alamos National Security, LLC for the National Nuclear Security Administration of the U.S. Department of Energy under Contract No. DE-AC5206NA25396.

  6. Opacity Issues in Games with Imperfect Information

    Directory of Open Access Journals (Sweden)

    Bastien Maubert

    2011-06-01

    Full Text Available We study in depth the class of games with opacity condition, which are two-player games with imperfect information in which one of the players only has imperfect information, and where the winning condition relies on the information he has along the play. Those games are relevant for security aspects of computing systems: a play is opaque whenever the player who has imperfect information never "knows" for sure that the current position is one of the distinguished "secret" positions. We study the problems of deciding the existence of a winning strategy for each player, and we call them the opacity-violate problem and the opacity-guarantee problem. Focusing on the player with perfect information is new in the field of games with imperfect-information because when considering classical winning conditions it amounts to solving the underlying perfect-information game. We establish the EXPTIME-completeness of both above-mentioned problems, showing that our winning condition brings a gap of complexity for the player with perfect information, and we exhibit the relevant opacity-verify problem, which noticeably generalizes approaches considered in the literature for opacity analysis in discrete-event systems. In the case of blindfold games, this problem relates to the two initial ones, yielding the determinacy of blindfold games with opacity condition and the PSPACE-completeness of the three problems.

  7. Observational Constraints on Submillimeter Dust Opacity

    CERN Document Server

    Shirley, Yancy L; Pontoppidan, Klaus M; Wilner, David J; Stutz, Amelia M; Bieging, John H; Evans, Neal J

    2010-01-01

    Infrared extinction maps and submillimeter dust continuum maps are powerful probes of the density structure in the envelope of star-forming cores. We make a direct comparison between infrared and submillimeter dust continuum observations of the low-mass Class 0 core, B335, to constrain the ratio of submillimeter to infrared opacity (\\kaprat) and the submillimeter opacity power-law index ($\\kappa \\propto \\lambda^{-\\beta}$). Using the average value of theoretical dust opacity models at 2.2 \\micron, we constrain the dust opacity at 850 and 450 \\micron . Using new dust continuum models based upon the broken power-law density structure derived from interferometric observations of B335 and the infall model derived from molecular line observations of B335, we find that the opacity ratios are $\\frac{\\kappa_{850}}{\\kappa_{2.2}} = (3.21 - 4.80)^{+0.44}_{-0.30} \\times 10^{-4}$ and $\\frac{\\kappa_{450}}{\\kappa_{2.2}} = (12.8 - 24.8)^{+2.4}_{-1.3} \\times 10^{-4}$ with a submillimeter opacity power-law index of $\\beta_{smm}...

  8. Radiation Transport for Explosive Outflows: Opacity Regrouping

    CERN Document Server

    Wollaeger, Ryan T

    2014-01-01

    Implicit Monte Carlo (IMC) and Discrete Diffusion Monte Carlo (DDMC) are methods used to stochastically solve the radiative transport and diffusion equations, respectively. These methods combine into a hybrid transport-diffusion method we refer to as IMC-DDMC. We explore a multigroup IMC-DDMC scheme that, in DDMC, combines frequency groups with sufficient optical thickness. We term this procedure "opacity regrouping". Opacity regrouping has previously been applied to IMC-DDMC calculations for problems in which the dependence of the opacity on frequency is monotonic. We generalize opacity regrouping to non-contiguous groups and implement this in \\supernu, a code designed to do radiation transport in high-velocity outflows with non-monotonic opacities. We find that regrouping of non-contiguous opacity groups generally improves the speed of IMC-DDMC radiation transport. We present an asymptotic analysis that informs the nature of the Doppler shift in DDMC groups and summarize the derivation of the Gentile-Fleck ...

  9. Analytical opacity formulas for ICF elements

    Energy Technology Data Exchange (ETDEWEB)

    Minguez, E. E-mail: minguez@denim.upm.es; Martel, P.; Gil, J.M.; Rubiano, J.G.; Rodriguez, R

    2002-01-01

    Local Thermodynamic Equilibrium (LTE) opacity codes have been developed by the Instituto de Fusion Nuclear (DENIM) during the last years. JIMENA code (Laser and Particle Beams 6 (1998) 265; Laser and Particle Beams 10 (1992) 651) is an opacity code that solves self-consistently, for each temperature and density, the radial Dirac equation with a local spherically symmetrical potential. Very recently we have developed a new opacity code, called ANALOP, that uses an analytical potential (JQSRT 54 (1995) 621), which can include density and temperature effects for atomic data calculations. Opacities are determined with these two codes for selected elements at different plasma conditions. This work is focused on the determination of Rosseland and Planck mean analytical formulas for several single elements used in ICF targets. A scaling law of these mean opacities is given as a function of the plasma parameters: electron temperature and plasma density. These opacities have been tested with numerical results from other codes and with available experimental results.

  10. Structural ordering of disordered ligand-binding loops of biotin protein ligase into active conformations as a consequence of dehydration.

    Directory of Open Access Journals (Sweden)

    Vibha Gupta

    Full Text Available Mycobacterium tuberculosis (Mtb, a dreaded pathogen, has a unique cell envelope composed of high fatty acid content that plays a crucial role in its pathogenesis. Acetyl Coenzyme A Carboxylase (ACC, an important enzyme that catalyzes the first reaction of fatty acid biosynthesis, is biotinylated by biotin acetyl-CoA carboxylase ligase (BirA. The ligand-binding loops in all known apo BirAs to date are disordered and attain an ordered structure only after undergoing a conformational change upon ligand-binding. Here, we report that dehydration of Mtb-BirA crystals traps both the apo and active conformations in its asymmetric unit, and for the first time provides structural evidence of such transformation. Recombinant Mtb-BirA was crystallized at room temperature, and diffraction data was collected at 295 K as well as at 120 K. Transfer of crystals to paraffin and paratone-N oil (cryoprotectants prior to flash-freezing induced lattice shrinkage and enhancement in the resolution of the X-ray diffraction data. Intriguingly, the crystal lattice rearrangement due to shrinkage in the dehydrated Mtb-BirA crystals ensued structural order of otherwise flexible ligand-binding loops L4 and L8 in apo BirA. In addition, crystal dehydration resulted in a shift of approximately 3.5 A in the flexible loop L6, a proline-rich loop unique to Mtb complex as well as around the L11 region. The shift in loop L11 in the C-terminal domain on dehydration emulates the action responsible for the complex formation with its protein ligand biotin carboxyl carrier protein (BCCP domain of ACCA3. This is contrary to the involvement of loop L14 observed in Pyrococcus horikoshii BirA-BCCP complex. Another interesting feature that emerges from this dehydrated structure is that the two subunits A and B, though related by a noncrystallographic twofold symmetry, assemble into an asymmetric dimer representing the ligand-bound and ligand-free states of the protein, respectively. In

  11. Functional importance of GGXG sequence motifs in putative reentrant loops of 2HCT and ESS transport proteins.

    Science.gov (United States)

    Dobrowolski, Adam; Lolkema, Juke S

    2009-08-11

    The 2HCT and ESS families are two families of secondary transporters. Members of the two families are unrelated in amino acid sequence but share similar hydropathy profiles, which suggest a similar folding of the proteins in membranes. Structural models show two homologous domains containing five transmembrane segments (TMSs) each, with a reentrant or pore loop between the fourth and fifth TMSs in each domain. Here we show that GGXG sequence motifs present in the putative reentrant loops are important for the activity of the transporters. Mutation of the conserved Gly residues to Cys in the motifs of the Na(+)-citrate transporter CitS in the 2HCT family and the Na(+)-glutamate transporter GltS in the ESS family resulted in strongly reduced transport activity. Similarly, mutation of the variable residue "X" to Cys in the N-terminal half of GltS essentially inactivated the transporter. The corresponding mutations in the N- and C-terminal halves of CitS reduced transport activity to 60 and 25% of that of the wild type, respectively. Residual activity of any of the mutants could be further reduced by treatment with the membrane permeable thiol reagent N-ethylmaleimide (NEM). The X to Cys mutation (S405C) in the cytoplasmic loop in the C-terminal half of CitS rendered the protein sensitive to the bulky, membrane impermeable thiol reagent 4-acetamido-4'-maleimidylstilbene-2,2'-disulfonic acid (AmdiS) added at the periplasmic side of the membrane, providing further evidence that this part of the loop is positioned between the transmembrane segments. The putative reentrant loop in the C-terminal half of the ESS family does not contain the GGXG motif, but a conserved stretch rich in Gly residues. Cysteine-scanning mutagenesis of a stretch of 18 residues in the GltS protein revealed two residues important for function. Mutant N356C was completely inactivated by treatment with NEM, and mutant P351C appeared to be the counterpart of mutant S405C of CitS; the mutant was

  12. RADIATION TRANSPORT FOR EXPLOSIVE OUTFLOWS: OPACITY REGROUPING

    Energy Technology Data Exchange (ETDEWEB)

    Wollaeger, Ryan T. [Department of Nuclear Engineering and Engineering Physics, University of Wisconsin, Madison 1500 Engineering Drive, 410 ERB, Madison, WI 53706 (United States); Van Rossum, Daniel R., E-mail: wollaeger@wisc.edu, E-mail: daan@flash.uchicago.edu [Flash Center for Computational Science, Department of Astronomy and Astrophysics, University of Chicago, Chicago, IL 60637 (United States)

    2014-10-01

    Implicit Monte Carlo (IMC) and Discrete Diffusion Monte Carlo (DDMC) are methods used to stochastically solve the radiative transport and diffusion equations, respectively. These methods combine into a hybrid transport-diffusion method we refer to as IMC-DDMC. We explore a multigroup IMC-DDMC scheme that in DDMC, combines frequency groups with sufficient optical thickness. We term this procedure ''opacity regrouping''. Opacity regrouping has previously been applied to IMC-DDMC calculations for problems in which the dependence of the opacity on frequency is monotonic. We generalize opacity regrouping to non-contiguous groups and implement this in SuperNu, a code designed to do radiation transport in high-velocity outflows with non-monotonic opacities. We find that regrouping of non-contiguous opacity groups generally improves the speed of IMC-DDMC radiation transport. We present an asymptotic analysis that informs the nature of the Doppler shift in DDMC groups and summarize the derivation of the Gentile-Fleck factor for modified IMC-DDMC. We test SuperNu using numerical experiments including a quasi-manufactured analytic solution, a simple 10 group problem, and the W7 problem for Type Ia supernovae. We find that opacity regrouping is necessary to make our IMC-DDMC implementation feasible for the W7 problem and possibly Type Ia supernova simulations in general. We compare the bolometric light curves and spectra produced by the SuperNu and PHOENIX radiation transport codes for the W7 problem. The overall shape of the bolometric light curves are in good agreement, as are the spectra and their evolution with time. However, for the numerical specifications we considered, we find that the peak luminosity of the light curve calculated using SuperNu is ∼10% less than that calculated using PHOENIX.

  13. Trans-activation of the DNA-damage signalling protein kinase Chk2 by T-loop exchange.

    Science.gov (United States)

    Oliver, Antony W; Paul, Angela; Boxall, Katherine J; Barrie, S Elaine; Aherne, G Wynne; Garrett, Michelle D; Mittnacht, Sibylle; Pearl, Laurence H

    2006-07-12

    The protein kinase Chk2 (checkpoint kinase 2) is a major effector of the replication checkpoint. Chk2 activation is initiated by phosphorylation of Thr68, in the serine-glutamine/threonine-glutamine cluster domain (SCD), by ATM. The phosphorylated SCD-segment binds to the FHA domain of a second Chk2 molecule, promoting dimerisation of the protein and triggering phosphorylation of the activation segment/T-loop in the kinase domain. We have now determined the structure of the kinase domain of human Chk2 in complexes with ADP and a small-molecule inhibitor debromohymenialdisine. The structure reveals a remarkable dimeric arrangement in which T-loops are exchanged between protomers, to form an active kinase conformation in trans. Biochemical data suggest that this dimer is the biologically active state promoted by ATM-phosphorylation, and also suggests a mechanism for dimerisation-driven activation of Chk2 by trans-phosphorylation.

  14. Displacement of the occluding loop by the parasite protein, chagasin, results in efficient inhibition of human cathepsin B.

    Science.gov (United States)

    Redzynia, Izabela; Ljunggren, Anna; Abrahamson, Magnus; Mort, John S; Krupa, Joanne C; Jaskolski, Mariusz; Bujacz, Grzegorz

    2008-08-15

    Cathepsin B is a papain-like cysteine protease showing both endo- and exopeptidase activity, the latter due to a unique occluding loop that restricts access to the active site cleft. To clarify the mode by which natural protein inhibitors manage to overcome this obstacle, we have analyzed the structure and function of cathepsin B in complexes with the Trypanosoma cruzi inhibitor, chagasin. Kinetic analysis revealed that substitution of His-110e, which anchors the loop in occluding position, results in 3-fold increased chagasin affinity (Ki for H110A cathepsin B, 0.35 nm) due to an improved association rate (kon, 5 x 10(5) m(-1)s(-1)). The structure of chagasin in complex with cathepsin B was solved in two crystal forms (1.8 and 2.67 angstroms resolution), demonstrating that the occluding loop is displaced to allow chagasin binding with its three loops, L4, L2, and L6, spanning the entire active site cleft. The occluding loop is differently displaced in the two structures, indicating a large range of movement and adoption of conformations forced by the inhibitor. The area of contact is slightly larger than in chagasin complexes with the endopeptidase, cathepsin L. However, residues important for high affinity to both enzymes are mainly found in the outer loops L4 and L6 of chagasin. The chagasin-cathepsin B complex provides a structural framework for modeling and design of inhibitors for cruzipain, the parasite cysteine protease and a virulence factor in Chagas disease.

  15. The opacity of spiral galaxy disks V. Dust opacity, HI distributions and sub-mm emission

    NARCIS (Netherlands)

    Holwerda, BW; Gonzalez, RA; Allen, RJ; van der Kruit, PC

    2005-01-01

    The opacity of spiral galaxy disks, from counts of distant galaxies, is compared to HI column densities. The opacity measurements are calibrated using the "Synthetic Field Method" from Gonzalez et al. (1998, ApJ, 506, 152), Holwerda et al. (2005a, AJ, 129, 1381). When compared for individual disks,

  16. OPserver: opacities and radiative accelerations on demand

    Science.gov (United States)

    Mendoza, C.; González, J.; Seaton, M. J.; Buerger, P.; Bellorín, A.; Meléndez, M.; Rodríguez, L. S.; Delahaye, F.; Zeippen, C. J.; Palacios, E.; Pradhan, A. K.

    2009-05-01

    We report on developments carried out within the Opacity Project (OP) to upgrade atomic database services to comply with e-infrastructure requirements. We give a detailed description of an interactive, online server for astrophysical opacities, referred to as OPserver, to be used in sophisticated stellar modelling where Rosseland mean opacities and radiative accelerations are computed at every depth point and each evolution cycle. This is crucial, for instance, in chemically peculiar stars and in the exploitation of the new asteroseismological data. OPserver, downloadable with the new OPCD_3.0 release from the Centre de Données Astronomiques de Strasbourg, France, computes mean opacities and radiative data for arbitrary chemical mixtures from the OP monochromatic opacities. It is essentially a client-server network restructuring and optimization of the suite of codes included in the earlier OPCD_2.0 release. The server can be installed locally or, alternatively, accessed remotely from the Ohio Supercomputer Center, Columbus, Ohio, USA. The client is an interactive web page or a subroutine library that can be linked to the user code. The suitability of this scheme in grid computing environments is emphasized, and its extension to other atomic database services for astrophysical purposes is discussed.

  17. Npas4, a novel helix-loop-helix PAS domain protein, is regulated in response to cerebral ischemia

    DEFF Research Database (Denmark)

    Shamloo, Mehrdad; Soriano, Liza; von Schack, David

    2006-01-01

    Basic helix-loop-helix PAS domain proteins form a growing family of transcription factors. These proteins are involved in the process of adaptation to cellular stresses and environmental factors such as a change in oxygen concentration. We describe the identification and characterization of a rec......Basic helix-loop-helix PAS domain proteins form a growing family of transcription factors. These proteins are involved in the process of adaptation to cellular stresses and environmental factors such as a change in oxygen concentration. We describe the identification and characterization...... of a recently cloned PAS domain protein termed Npas4 in ischemic rat brain. Using gene expression profiling following middle cerebral artery occlusion, we showed that the Npas4 mRNA is differentially expressed in ischemic tissue. The full-length gene was cloned from rat brain and its spatial and temporal...... expression characterized with in situ hybridization and Northern blotting. The Npas4 mRNA is specifically expressed in the brain and is highly up-regulated in ischemic tissues following both focal and global cerebral ischemic insults. Immunohistochemistry revealed a strong expression in the limbic system...

  18. Iron and molecular opacities and the evolution of Population I stars

    Science.gov (United States)

    Stothers, Richard B.; Chin, Chao-Wen

    1993-01-01

    Effects of recent opacity revisions on the evolution of Population I stars are explored over the range 1.5-60 solar masses. Opacity parameters considered include the angular momentum coupling scheme for iron, the relative iron abundance, the total metal abundance, and diatomic and triatomic molecular sources. Only the total metal abundance exerts an important control over the evolutionary tracks. Blue loops on the H-R diagram during core helium burning can be very sensitive to opacity, but only insofar as the simple formation or suppression of a blue loop is concerned. The blue loops are most robust for stellar masses around 10 solar masses. We confirm, from a comparison of stellar models with observational data, that the total metal abundance is close to solar and that convective core overshooting is likely to be very slight. The new models predict the existence of an iron convection zone in the envelope and a great widening of the main-sequence band in the H-R diagram at luminosities brighter than 100,000 solar luminosities.

  19. Features of a spatially constrained cystine loop in the p10 FAST protein ectodomain define a new class of viral fusion peptides.

    Science.gov (United States)

    Barry, Christopher; Key, Tim; Haddad, Rami; Duncan, Roy

    2010-05-28

    The reovirus fusion-associated small transmembrane (FAST) proteins are the smallest known viral membrane fusion proteins. With ectodomains of only approximately 20-40 residues, it is unclear how such diminutive fusion proteins can mediate cell-cell fusion and syncytium formation. Contained within the 40-residue ectodomain of the p10 FAST protein resides an 11-residue sequence of moderately apolar residues, termed the hydrophobic patch (HP). Previous studies indicate the p10 HP shares operational features with the fusion peptide motifs found within the enveloped virus membrane fusion proteins. Using biotinylation assays, we now report that two highly conserved cysteine residues flanking the p10 HP form an essential intramolecular disulfide bond to create a cystine loop. Mutagenic analyses revealed that both formation of the cystine loop and p10 membrane fusion activity are highly sensitive to changes in the size and spatial arrangement of amino acids within the loop. The p10 cystine loop may therefore function as a cystine noose, where fusion peptide activity is dependent on structural constraints within the noose that force solvent exposure of key hydrophobic residues. Moreover, inhibitors of cell surface thioreductase activity indicate that disruption of the disulfide bridge is important for p10-mediated membrane fusion. This is the first example of a viral fusion peptide composed of a small, spatially constrained cystine loop whose function is dependent on altered loop formation, and it suggests the p10 cystine loop represents a new class of viral fusion peptides.

  20. Design of the opacity spectrometer for opacity measurements at the National Ignition Facility

    Science.gov (United States)

    Ross, P. W.; Heeter, R. F.; Ahmed, M. F.; Dodd, E.; Huffman, E. J.; Liedahl, D. A.; King, J. A.; Opachich, Y. P.; Schneider, M. B.; Perry, T. S.

    2016-11-01

    Recent experiments at the Sandia National Laboratory Z facility have called into question models used in calculating opacity, of importance for modeling stellar interiors. An effort is being made to reproduce these results at the National Ignition Facility (NIF). These experiments require a new X-ray opacity spectrometer (OpSpec) spanning 540 eV-2100 eV with a resolving power E/ΔE > 700. The design of the OpSpec is presented. Photometric calculations based on expected opacity data are also presented. First use on NIF is expected in September 2016.

  1. Collective estimation of multiple bivariate density functions with application to angular-sampling-based protein loop modeling

    KAUST Repository

    Maadooliat, Mehdi

    2015-10-21

    This paper develops a method for simultaneous estimation of density functions for a collection of populations of protein backbone angle pairs using a data-driven, shared basis that is constructed by bivariate spline functions defined on a triangulation of the bivariate domain. The circular nature of angular data is taken into account by imposing appropriate smoothness constraints across boundaries of the triangles. Maximum penalized likelihood is used to fit the model and an alternating blockwise Newton-type algorithm is developed for computation. A simulation study shows that the collective estimation approach is statistically more efficient than estimating the densities individually. The proposed method was used to estimate neighbor-dependent distributions of protein backbone dihedral angles (i.e., Ramachandran distributions). The estimated distributions were applied to protein loop modeling, one of the most challenging open problems in protein structure prediction, by feeding them into an angular-sampling-based loop structure prediction framework. Our estimated distributions compared favorably to the Ramachandran distributions estimated by fitting a hierarchical Dirichlet process model; and in particular, our distributions showed significant improvements on the hard cases where existing methods do not work well.

  2. Detailed opacity calculations for stellar models

    Science.gov (United States)

    Pain, Jean-Christophe; Gilleron, Franck

    2016-10-01

    We present a state of the art of precise spectral opacity calculations illustrated by stellar applications. The essential role of laboratory experiments to check the quality of the computed data is underlined. We review some X-ray and XUV laser and Z-pinch photo-absorption measurements as well as X-ray emission spectroscopy experiments of hot dense plasmas produced by ultra-high-intensity laser interaction. The measured spectra are systematically compared with the fine-structure opacity code SCO-RCG. Focus is put on iron, due to its crucial role in the understanding of asteroseismic observations of Beta Cephei-type and Slowly Pulsating B stars, as well as in the Sun. For instance, in Beta Cephei-type stars (which should not be confused with Cepheid variables), the iron-group opacity peak excites acoustic modes through the kappa-mechanism. A particular attention is paid to the higher-than-predicted iron opacity measured on Sandia's Z facility at solar interior conditions (boundary of the convective zone). We discuss some theoretical aspects such as orbital relaxation, electron collisional broadening, ionic Stark effect, oscillator-strength sum rules, photo-ionization, or the ``filling-the-gap'' effect of highly excited states.

  3. Solar opacity calculations using the super-transition-array method

    CERN Document Server

    Krief, M; Gazit, D

    2016-01-01

    An opacity model based on the Super-Transition-Array (STA) method for the calculation of monochromatic opacities of local thermodynamic equilibrium plasmas was developed. The model is described and used to calculate spectral opacities for a solar model implementing the recent AGSS09 composition. Calculations are carried throughout the solar radiative zone. The relative contributions of different chemical elements and photon-matter processes to the total Rosseland mean opacity are analyzed in detail. Monochromatic opacities and charge state distributions were compared with the widely used Opacity-Project (OP) code, for several elements near the radiation-convection interface. STA Rosseland opacities for the solar mixture show a very good agreement with OP and the OPAL opacity code, throughout the radiation zone. Finally, an explicit STA calculation of the full AGSS09 photospheric mixture, including all heavy metals was performed. It was shown that due to their extremely low abundance, and despite being very go...

  4. Phylogeny, Functional Annotation, and Protein Interaction Network Analyses of the Xenopus tropicalis Basic Helix-Loop-Helix Transcription Factors

    Directory of Open Access Journals (Sweden)

    Wuyi Liu

    2013-01-01

    Full Text Available The previous survey identified 70 basic helix-loop-helix (bHLH proteins, but it was proved to be incomplete, and the functional information and regulatory networks of frog bHLH transcription factors were not fully known. Therefore, we conducted an updated genome-wide survey in the Xenopus tropicalis genome project databases and identified 105 bHLH sequences. Among the retrieved 105 sequences, phylogenetic analyses revealed that 103 bHLH proteins belonged to 43 families or subfamilies with 46, 26, 11, 3, 15, and 4 members in the corresponding supergroups. Next, gene ontology (GO enrichment analyses showed 65 significant GO annotations of biological processes and molecular functions and KEGG pathways counted in frequency. To explore the functional pathways, regulatory gene networks, and/or related gene groups coding for Xenopus tropicalis bHLH proteins, the identified bHLH genes were put into the databases KOBAS and STRING to get the signaling information of pathways and protein interaction networks according to available public databases and known protein interactions. From the genome annotation and pathway analysis using KOBAS, we identified 16 pathways in the Xenopus tropicalis genome. From the STRING interaction analysis, 68 hub proteins were identified, and many hub proteins created a tight network or a functional module within the protein families.

  5. Interaction of sweet proteins with their receptor. A conformational study of peptides corresponding to loops of brazzein, monellin and thaumatin.

    Science.gov (United States)

    Tancredi, Teodorico; Pastore, Annalisa; Salvadori, Severo; Esposito, Veronica; Temussi, Piero A

    2004-06-01

    The mechanism of interaction of sweet proteins with the T1R2-T1R3 sweet taste receptor has not yet been elucidated. Low molecular mass sweeteners and sweet proteins interact with the same receptor, the human T1R2-T1R3 receptor. The presence on the surface of the proteins of "sweet fingers", i.e. protruding features with chemical groups similar to those of low molecular mass sweeteners that can probe the active site of the receptor, would be consistent with a single mechanism for the two classes of compounds. We have synthesized three cyclic peptides corresponding to the best potential "sweet fingers" of brazzein, monellin and thaumatin, the sweet proteins whose structures are well characterized. NMR data show that all three peptides have a clear tendency, in aqueous solution, to assume hairpin conformations consistent with the conformation of the same sequences in the parent proteins. The peptide corresponding to the only possible loop of brazzein, c[CFYDEKRNLQC(37-47)], exists in solution in a well ordered hairpin conformation very similar to that of the same sequence in the parent protein. However, none of the peptides has a sweet taste. This finding strongly suggests that sweet proteins recognize a binding site different from the one that binds small molecular mass sweeteners. The data of the present work support an alternative mechanism of interaction, the "wedge model", recently proposed for sweet proteins [Temussi, P. A. (2002) FEBS Lett.526, 1-3.].

  6. The ZEB1/miR-200c feedback loop regulates invasion via actin interacting proteins MYLK and TKS5.

    Science.gov (United States)

    Sundararajan, Vignesh; Gengenbacher, Nicolas; Stemmler, Marc P; Kleemann, Julia A; Brabletz, Thomas; Brabletz, Simone

    2015-09-29

    Epithelial to mesenchymal transition (EMT) is a developmental process which is aberrantly activated during cancer invasion and metastasis. Elevated expression of EMT-inducers like ZEB1 enables tumor cells to detach from the primary tumor and invade into the surrounding tissue. The main antagonist of ZEB1 in controlling EMT is the microRNA-200 family that is reciprocally linked to ZEB1 in a double negative feedback loop. Here, we further elucidate how the ZEB1/miR-200 feedback loop controls invasion of tumor cells. The process of EMT is attended by major changes in the actin cytoskeleton. Via in silico screening of genes encoding for actin interacting proteins, we identified two novel targets of miR-200c - TKS5 and MYLK (MLCK). Co-expression of both genes with ZEB1 was observed in several cancer cell lines as well as in breast cancer patients and correlated with low miR-200c levels. Depletion of TKS5 or MYLK in breast cancer cells reduced their invasive potential and their ability to form invadopodia. Whereas TKS5 is known to be a major component, we could identify MYLK as a novel player in invadopodia formation. In summary, TKS5 and MYLK represent two mediators of invasive behavior of cancer cells that are regulated by the ZEB1/miR-200 feedback loop.

  7. Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins

    DEFF Research Database (Denmark)

    Maragakis, Paul; Lindorff-Larsen, Kresten; Eastwood, Michael P

    2008-01-01

    methods. However, apparent systematic discrepancies between order parameters extracted from simulations and experiments are common, particularly for elements of noncanonical secondary structure. In this paper, results from a 1.2 micros explicit solvent MD simulation of the protein ubiquitin are compared...... with previously determined backbone order parameters derived from NMR relaxation experiments [Tjandra, N.; Feller, S. E.; Pastor, R. W.; Bax, A. J. Am. Chem. Soc. 1995, 117, 12562-12566]. The simulation reveals fluctuations in three loop regions that occur on time scales comparable to or longer than...

  8. Inhibition of a type III secretion system by the deletion of a short loop in one of its membrane proteins

    Energy Technology Data Exchange (ETDEWEB)

    Meshcheryakov, Vladimir A. [Okinawa Instiute of Science and Technology, Okinawa 904-0495 (Japan); Kitao, Akio [University of Tokyo, Tokyo 113-0032 (Japan); Core Research for Evolutionary Science and Technology, Tokyo 113-0032 (Japan); Matsunami, Hideyuki; Samatey, Fadel A., E-mail: f.a.samatey@oist.jp [Okinawa Instiute of Science and Technology, Okinawa 904-0495 (Japan)

    2013-05-01

    Crystal structures of the cytoplasmic domain of FlhB from S. typhimurium and A. aeolicus were solved at 2.45 and 2.55 Å resolution, respectively. The deletion of a short loop in the cytoplasmic domain of Salmonella FlhB completely abolishes secretion by the type III secretion system. A molecular-dynamics simulation shows that the deletion of the loop affects the flexibility of a linker between the transmembrane and cytoplasmic domains of FlhB. The membrane protein FlhB is a highly conserved component of the flagellar secretion system. It is composed of an N-terminal transmembrane domain and a C-terminal cytoplasmic domain (FlhB{sub C}). Here, the crystal structures of FlhB{sub C} from Salmonella typhimurium and Aquifex aeolicus are described at 2.45 and 2.55 Å resolution, respectively. These flagellar FlhB{sub C} structures are similar to those of paralogues from the needle type III secretion system, with the major difference being in a linker that connects the transmembrane and cytoplasmic domains of FlhB. It was found that deletion of a short flexible loop in a globular part of Salmonella FlhB{sub C} leads to complete inhibition of secretion by the flagellar secretion system. Molecular-dynamics calculations demonstrate that the linker region is the most flexible part of FlhB{sub C} and that the deletion of the loop reduces this flexibility. These results are in good agreement with previous studies showing the importance of the linker in the function of FlhB and provide new insight into the relationship between the different parts of the FlhB{sub C} molecule.

  9. Stem-loop binding protein is required for retinal cell proliferation, neurogenesis, and intraretinal axon pathfinding in zebrafish.

    Science.gov (United States)

    Imai, Fumiyasu; Yoshizawa, Asuka; Matsuzaki, Ayako; Oguri, Eri; Araragi, Masato; Nishiwaki, Yuko; Masai, Ichiro

    2014-10-01

    In the developing retina, neurogenesis and cell differentiation are coupled with cell proliferation. However, molecular mechanisms that coordinate cell proliferation and differentiation are not fully understood. In this study, we found that retinal neurogenesis is severely delayed in the zebrafish stem-loop binding protein (slbp) mutant. SLBP binds to a stem-loop structure at the 3'-end of histone mRNAs, and regulates a replication-dependent synthesis and degradation of histone proteins. Retinal cell proliferation becomes slower in the slbp1 mutant, resulting in cessation of retinal stem cell proliferation. Although retinal stem cells cease proliferation by 2 days postfertilization (dpf) in the slbp mutant, retinal progenitor cells in the central retina continue to proliferate and generate neurons until at least 5dpf. We found that this progenitor proliferation depends on Notch signaling, suggesting that Notch signaling maintains retinal progenitor proliferation when faced with reduced SLBP activity. Thus, SLBP is required for retinal stem cell maintenance. SLBP and Notch signaling are required for retinal progenitor cell proliferation and subsequent neurogenesis. We also show that SLBP1 is required for intraretinal axon pathfinding, probably through morphogenesis of the optic stalk, which expresses attractant cues. Taken together, these data indicate important roles of SLBP in retinal development.

  10. Radio-opacity of commonly consumed bony fish in kelantan, malaysia.

    Science.gov (United States)

    Irfan, M; Ahmad Helmy, A K; Wan Shah Jihan, W D

    2012-10-01

    Fish is one of the major sources of protein among Malaysians. This has made incidents of fish bones lodged in the throat fairly common clinical problems. Plain radiograph, which is the first line of imaging in such cases, has been reported to have low sensitivity. Besides the location, the degree of radio-opacity of the bone is another important factor and is species dependent. This study was undertaken to determine the radio-opacity of bones from commonly consumed fish in Malaysia. A total of 15 types of fish were identified, six of them were opaque even when embedded and three were visualized in the simulated airway. In terms of radio-opacity, the commonly consumed fish in Malaysia possessed opaque bones and this fact can help doctors identify the location of the foreign body in the throat.

  11. Opacity of Shock-Generated Argon Plasmas

    Institute of Scientific and Technical Information of China (English)

    王藩侯; 陈敬平; 周显明; 李西军; 经福谦; 孟续军; 孙永盛

    2001-01-01

    Argon plasmas with uniform density and temperature are generated by a planar shock wave through argon gas. The opacities of argon plasma, covering the thermodynamic states at temperatures of 1.4-2.2eV and in densities of 0.0083- 0.015 g/cm3, are investigated by measuring the emitted radiance versus time at several visible wavelengths. Comparison of the measured opacities with those calculated demonstrates that the average atom model can be used well to describe the essential transport behaviour of photons in argon plasma under the abovementioned thermodynamic condition. A simplified and self-consistent method to deduce the reflectivity R(λ) at the baseplate surface is applied. It demonstrates that the values of R(λ) are all around 0.4 in the experiments, which are basically in agreement with those given by Erskine previously (1994 J. Quant. Spectrosc. Radiat.Transfer 51 97).

  12. Revitalizing the Library OPAC: Interface, Searching, and Display Challenges

    Directory of Open Access Journals (Sweden)

    Jia Mi

    2008-03-01

    Full Text Available The behavior of academic library users has drastically changed in recent years. Internet search engines have become the preferred tool over the library online public access catalog (OPAC for finding information. Libraries are losing ground to online search engines. In this paper, two aspects of OPAC use are studied: (1 the current OPAC interface and searching capabilities, and (2 the OPAC bibliographic display. The purpose of the study is to find answers to the following questions: Why is the current OPAC ineffective? What can libraries and librarians do to deliver an OPAC that is as good as search engines to better serve our users? Revitalizing the library OPAC is one of the pressing issues that has to be accomplished.

  13. Extended Opacity Tables with Higher Temperature-Density-Frequency Resolution

    Science.gov (United States)

    Schillaci, Mark; Orban, Chris; Delahaye, Franck; Pinsonneault, Marc; Nahar, Sultana; Pradhan, Anil

    2015-05-01

    Theoretical models for plasma opacities underpin our understanding of radiation transport in many different astrophysical objects. These opacity models are also relevant to HEDP experiments such as ignition scale experiments on NIF. We present a significantly expanded set of opacity data from the widely utilized Opacity Project, and make these higher resolution data publicly available through OSU's portal with dropbox.com. This expanded data set is used to assess how accurate the interpolation of opacity data in temperature-density-frequency dimensions must be in order to adequately model the properties of most stellar types. These efforts are the beginning of a larger project to improve the theoretical opacity models in light of experimental results at the Sandia Z-pinch showing that the measured opacity of Iron disagrees strongly with all current models.

  14. Hohlraum calculations for the NIF opacity platform

    Science.gov (United States)

    Dodd, E. S.; Perry, T. S.; Tregillis, I. L.; Kline, J. L.; Heeter, R. F.; Liedahl, D. A.; Opachich, Y. P.

    2015-11-01

    A summary of initial hohlraum calculations for planned opacity experiments at the National Ignition Facility (NIF) will be given. The purpose of these experiments is to make LTE opacity measurements of iron at the same conditions as previous experiments on Sandia's Z facility: 156 eV and 190 eV. Ongoing discrepancies between opacity data and theory make corroborating data highly important. The target considered in these calculations is a standard cylindrical hohlraum, with diameter 5.75 mm, but baffles have been placed between the laser hot spot and the sample to maintain the iron in LTE. The hohlraum is driven with a 3 ns flat top laser pulse, but limited to 500 kJ and only the outer beams. The inner beams will be used to drive a capsule implosion, which backlights the iron for the absorption measurements. The iron itself is a thin disk, mixed with magnesium as a spectroscopic tracer, and tamped with beryllium to minimize expansion. A description of the experimental set-up will be given. Supported under the US DOE by the Los Alamos National Security, LLC under contract DE-AC52-06NA25396.

  15. The sea urchin stem–loop-binding protein: a maternally expressed protein that probably functions in expression of multiple classes of histone mRNA

    Science.gov (United States)

    Robertson, Anthony J.; Howard, Jason T.; Dominski, Zbigniew; Schnackenberg, Bradley J.; Sumerel, Jan L.; McCarthy, John J.; Coffman, James A.; Marzluff, William F.

    2004-01-01

    Following the completion of oogenesis and oocyte maturation, histone mRNAs are synthesized and stored in the sea urchin egg pronucleus. Histone mRNAs are the only mRNAs that are not polyadenylated but instead end in a stem–loop which has been conserved in evolution. The 3′ end binds the stem–loop-binding protein (SLBP), and SLBP is required for histone pre-mRNA processing as well as translation of the histone mRNAs. A cDNA encoding a 59 kDa sea urchin SLBP (suSLBP) has been cloned from an oocyte cDNA library. The suSLBP contains an RNA-binding domain that is similar to the RNA-binding domain found in SLBPs from other species, although there is no similarity between the rest of the suSLBP and other SLBPs. The suSLBP is present at constant levels in eggs and for the first 12 h of development. The levels of suSLBP then decline and remain at a low level for the rest of embryogenesis. The suSLBP is concentrated in the egg pronucleus and is released from the nucleus only when cells enter the first mitosis. SuSLBP expressed by in vitro translation does not bind the stem–loop RNA, suggesting that suSLBP is modified to activate RNA binding in sea urchin embryos. PMID:14762208

  16. Evidence supporting the existence of a NUPR1-like family of helix-loop-helix chromatin proteins related to, yet distinct from, AT hook-containing HMG proteins.

    Science.gov (United States)

    Urrutia, Raul; Velez, Gabriel; Lin, Marisa; Lomberk, Gwen; Neira, Jose Luis; Iovanna, Juan

    2014-08-01

    NUPR1, a small chromatin protein, plays a critical role in cancer development, progression, and resistance to therapy. Here, using a combination of structural bioinformatics and molecular modeling methods, we report several novel findings that enhance our understanding of the biochemical function of this protein. We find that NUPR1 has been conserved throughout evolution, and over time it has undergone duplications and transpositions to form other transcriptional regulators. Using threading, homology-based molecular modeling, molecular mechanics calculations, and molecular dynamics simulations, we generated structural models for four of these proteins: NUPR1a, NUPR1b, NUPR2, and the NUPR-like domain of GTF2-I. Comparative analyses of these models combined with extensive linear motif identification reveal that these four proteins, though similar in their propensities for folding, differ in size, surface changes, and sites amenable for posttranslational modification. Lastly, taking NUPR1a as the paradigm for this family, we built models of a NUPR-DNA complex. Additional structural comparisons revealed that NUPR1 defines a new family of small-groove-binding proteins that share structural features with, yet are distinct from, helix-loop-helix AT-hook-containing HMG proteins. These models and inferences should lead to a better understanding of the function of this group of chromatin proteins, which play a critical role in the development of human malignant diseases.

  17. Galactic cold cores. V. Dust opacity

    Science.gov (United States)

    Juvela, M.; Ristorcelli, I.; Marshall, D. J.; Montillaud, J.; Pelkonen, V.-M.; Ysard, N.; McGehee, P.; Paladini, R.; Pagani, L.; Malinen, J.; Rivera-Ingraham, A.; Lefèvre, C.; Tóth, L. V.; Montier, L. A.; Bernard, J.-P.; Martin, P.

    2015-12-01

    Context. The project Galactic Cold Cores has carried out Herschel photometric observations of interstellar clouds where the Planck satellite survey has located cold and compact clumps. The sources represent different stages of cloud evolution from starless clumps to protostellar cores and are located in different Galactic environments. Aims: We examine this sample of 116 Herschel fields to estimate the submillimetre dust opacity and to search for variations that might be attributed to the evolutionary stage of the sources or to environmental factors, including the location within the Galaxy. Methods: The submillimetre dust opacity was derived from Herschel data, and near-infrared observations of the reddening of background stars are converted into near-infrared optical depth. We investigated the systematic errors affecting these parameters and used modelling to correct for the expected biases. The ratio of 250 μm and J band opacities is correlated with the Galactic location and the star formation activity. We searched for local variations in the ratio τ(250 μm)/τ(J) using the correlation plots and opacity ratio maps. Results: We find a median ratio of τ(250 μm) /τ(J) = (1.6 ± 0.2) × 10-3, which is more than three times the mean value reported for the diffuse medium. Assuming an opacity spectral index β = 1.8 instead of β = 2.0, the value would be lower by ~ 30%. No significant systematic variation is detected with Galactocentric distance or with Galactic height. Examination of the τ(250 μm) /τ(J) maps reveals six fields with clear indications of a local increase of submillimetre opacity of up to τ(250 μm) /τ(J) ~ 4 × 10-3 towards the densest clumps. These are all nearby fields with spatially resolved clumps of high column density. Conclusions: We interpret the increase in the far-infrared opacity as a sign of grain growth in the densest and coldest regions of interstellar clouds. Planck (http://www.esa.int/Planck) is a project of the European

  18. The Fusion Loops of the Initial Prefusion Conformation of Herpes Simplex Virus 1 Fusion Protein Point Toward the Membrane

    Directory of Open Access Journals (Sweden)

    Juan Fontana

    2017-08-01

    Full Text Available All enveloped viruses, including herpesviruses, must fuse their envelope with the host membrane to deliver their genomes into target cells, making this essential step subject to interference by antibodies and drugs. Viral fusion is mediated by a viral surface protein that transits from an initial prefusion conformation to a final postfusion conformation. Strikingly, the prefusion conformation of the herpesvirus fusion protein, gB, is poorly understood. Herpes simplex virus (HSV, a model system for herpesviruses, causes diseases ranging from mild skin lesions to serious encephalitis and neonatal infections. Using cryo-electron tomography and subtomogram averaging, we have characterized the structure of the prefusion conformation and fusion intermediates of HSV-1 gB. To this end, we have set up a system that generates microvesicles displaying full-length gB on their envelope. We confirmed proper folding of gB by nondenaturing electrophoresis-Western blotting with a panel of monoclonal antibodies (MAbs covering all gB domains. To elucidate the arrangement of gB domains, we labeled them by using (i mutagenesis to insert fluorescent proteins at specific positions, (ii coexpression of gB with Fabs for a neutralizing MAb with known binding sites, and (iii incubation of gB with an antibody directed against the fusion loops. Our results show that gB starts in a compact prefusion conformation with the fusion loops pointing toward the viral membrane and suggest, for the first time, a model for gB’s conformational rearrangements during fusion. These experiments further illustrate how neutralizing antibodies can interfere with the essential gB structural transitions that mediate viral entry and therefore infectivity.

  19. Complex folding and misfolding effects of deer-specific amino acid substitutions in the β2-α2 loop of murine prion protein

    Science.gov (United States)

    Agarwal, Sonya; Döring, Kristina; Gierusz, Leszek A.; Iyer, Pooja; Lane, Fiona M.; Graham, James F.; Goldmann, Wilfred; Pinheiro, Teresa J. T.; Gill, Andrew C.

    2015-10-01

    The β2-α2 loop of PrPC is a key modulator of disease-associated prion protein misfolding. Amino acids that differentiate mouse (Ser169, Asn173) and deer (Asn169, Thr173) PrPC appear to confer dramatically different structural properties in this region and it has been suggested that amino acid sequences associated with structural rigidity of the loop also confer susceptibility to prion disease. Using mouse recombinant PrP, we show that mutating residue 173 from Asn to Thr alters protein stability and misfolding only subtly, whilst changing Ser to Asn at codon 169 causes instability in the protein, promotes oligomer formation and dramatically potentiates fibril formation. The doubly mutated protein exhibits more complex folding and misfolding behaviour than either single mutant, suggestive of differential effects of the β2-α2 loop sequence on both protein stability and on specific misfolding pathways. Molecular dynamics simulation of protein structure suggests a key role for the solvent accessibility of Tyr168 in promoting molecular interactions that may lead to prion protein misfolding. Thus, we conclude that ‘rigidity’ in the β2-α2 loop region of the normal conformer of PrP has less effect on misfolding than other sequence-related effects in this region.

  20. Simulation, Control and Optimization of Single Cell Protein Production in a U-Loop Reactor

    DEFF Research Database (Denmark)

    2012-01-01

    In 2011, the world population passed 7 billions inhabitants. While this number witnesses the success of humankind on earth, it also rises among other things questions about food supply. Declining live stock in the wild, rising price of energy combined with climatic change give a new economic...... report simulation results. In addition we design and compare dierent regulatory control systems for regulation of SCP production in the U-Loop reactor. The purpose of the regulatory control systems is to keep the process at a steady state and to reject disturbances. We design and implement such control...... systems based upon PID and MPC technology. In particular, we design these control systems such that they can be used as the regulatory layer in a process control hierarchy and enable resilient transition from one operating point to another. The optimal operating points are determined by the real...

  1. Modelling and simulation of a U-loop Reactor for Single Cell Protein Production

    DEFF Research Database (Denmark)

    Wu, Mengzhe; Huusom, Jakob Kjøbsted; Gernaey, Krist

    2016-01-01

    In this work, two approaches of modelling a one phase U-loop reactor are presented. A simple CSTR model consisting of first-principles dynamic process equations was implemented in Matlab. The results give a good indication of the basic understanding of the effect of changing operation conditions...... on process performance. For a given product yield, the work investigates how process parameters such as dilution rate (D) or the methanol concentration should be selected to optimize the production. Nevertheless, this simple model exhibits some limitations hindering the development of the optimal operation......-dimensional one-phase model using Computational Fluid Dynamics (CFD) methods is proposed. By introducing the momentum balances in the simulation, the results can capture the flow velocity fields in three dimensions. It is thereby possible to indicate the influence of the geometric design on the production yield...

  2. A Dual Mechanism Controls Nuclear Localization in the Atypical Basic-Helix-Loop-Helix Protein PAR1 of Arabidopsis thaliana

    Institute of Scientific and Technical Information of China (English)

    Anahit Galstyan; Jordi Bou-Torrent; Irma Roig-Villanova; Jaime F. Martínez-García

    2012-01-01

    PAR1 is an atypical basic-helix-loop-helix (bHLH) protein that negatively regulates the shade avoidance syndrome in Arabidopsis thaliana acting as a transcriptional cofactor.Consistently with this function,PAR1 has to be in the nucleus to display biological activity.Previous structure-function analyses revealed that the N-terminal region of PAR1 drives the protein to the nucleus.However,truncated forms of PAR1 lacking this region still display biological activity,implying that PAR1 has additional mechanisms to localize into the nucleus.In this work,we compared the primary structure of PAR1 and various related and unrelated plant bHLH proteins,which led us to suggest that PAR1 contains a non-canonical nuclear localization signal (NLS) in the N-terminal region.By overexpressing truncated and mutated derivatives of PAR1,we have also investigated the importance of other regions of PAR1,such as the acidic and the extended HLH dimerization domains,for its nuclear localization.We found that,in the absence of the N-terminal region,a functional HLH domain is required for nuclear localization.Our results suggest the existence of a dual mechanism for PAR1 nuclear localization:(1) one mediated by the N-terminal non-consensus NLS and (2) a second one that involves interaction with other proteins via the dimerization domain.

  3. Porphyrin Binding to Gun4 Protein, Facilitated by a Flexible Loop, Controls Metabolite Flow through the Chlorophyll Biosynthetic Pathway.

    Science.gov (United States)

    Kopečná, Jana; Cabeza de Vaca, Israel; Adams, Nathan B P; Davison, Paul A; Brindley, Amanda A; Hunter, C Neil; Guallar, Victor; Sobotka, Roman

    2015-11-20

    In oxygenic phototrophs, chlorophylls, hemes, and bilins are synthesized by a common branched pathway. Given the phototoxic nature of tetrapyrroles, this pathway must be tightly regulated, and an important regulatory role is attributed to magnesium chelatase enzyme at the branching between the heme and chlorophyll pathway. Gun4 is a porphyrin-binding protein known to stimulate in vitro the magnesium chelatase activity, but how the Gun4-porphyrin complex acts in the cell was unknown. To address this issue, we first performed simulations to determine the porphyrin-docking mechanism to the cyanobacterial Gun4 structure. After correcting crystallographic loop contacts, we determined the binding site for magnesium protoporphyrin IX. Molecular modeling revealed that the orientation of α6/α7 loop is critical for the binding, and the magnesium ion held within the porphyrin is coordinated by Asn-211 residue. We also identified the basis for stronger binding in the Gun4-1 variant and for weaker binding in the W192A mutant. The W192A-Gun4 was further characterized in magnesium chelatase assay showing that tight porphyrin binding in Gun4 facilitates its interaction with the magnesium chelatase ChlH subunit. Finally, we introduced the W192A mutation into cells and show that the Gun4-porphyrin complex is important for the accumulation of ChlH and for channeling metabolites into the chlorophyll biosynthetic pathway.

  4. Mean gas opacity for circumstellar environments and equilibrium temperature degeneracy

    CERN Document Server

    Malygin, M G; Klahr, H; Dullemond, C P; Henning, Th

    2014-01-01

    In a molecular cloud dust opacity typically dominates over gas opacity, yet in the vicinities of forming stars dust is depleted, and gas is the sole provider of opacity. In the optically thin circumstellar environments the radiation temperature cannot be assumed to be equal to the gas temperature, hence the two-temperature Planck means are necessary to calculate the radiative equilibrium. By using the two-temperature mean opacity one does obtain the proper equilibrium gas temperature in a circumstellar environment, which is in a chemical equilibrium. A careful consideration of a radiative transfer problem reveals that the equilibrium temperature solution can be degenerate in an optically thin gaseous environment. We compute mean gas opacities based on the publicly available code DFSYNTHE by Kurucz and Castelli. We performed the calculations assuming local thermodynamic equilibrium and an ideal gas equation of state. The values were derived by direct integration of the high-resolution opacity spectrum. We prod...

  5. IPOPv2 online service for the generation of opacity tables

    Science.gov (United States)

    Delahaye, Franck; Zwölf, Carlo Maria; Zeippen, Claude J.; Mendoza, Claudio

    2016-03-01

    In the framework of the present phase - IPOPv2 - of the international Opacity Project (OP), a new web service has been implemented based on the latest release of the OP opacities. The user may construct online opacity tables to be conveniently included in stellar evolution codes in the format most commonly adopted by stellar physicists, namely the OPAL format. This facility encourages the use and comparison of both the OPAL and OP data sets in applications. The present service allows for the calculation of multi-element mixtures containing the 17 species (H, He, C, N, O, Ne, Na, Mg, Al, Si, S, Ar, Ca, Cr, Mn, Fe and Ni) considered by the OP, and underpins the latest release of OP opacities. This new service provides tables of Rosseland mean opacites using OP atomic data. We provide an alternative to the OPAL opacity services allowing direct comparison as well as study of the effect of uncertainties in stellar modeling due to mean opacities.

  6. IPOPv2 online service for the generation of opacity tables

    CERN Document Server

    Delahaye, F; Zeippen, C; Mendoza, C

    2015-01-01

    In the framework of the present phase -- IPOPv2 -- of the international Opacity Project (OP), a new web service has been implemented based on the latest release of the OP opacities. The user may construct online opacity tables to be conveniently included in stellar evolution codes in the format most commonly adopted by stellar physicists, namely the OPAL format. This facility encourages the use and comparison of both the OPAL and OP data sets in applications. The present service allows for the calculation of multi-element mixtures containing the 17 species (H, He, C, N, O, Ne, Na, Mg, Al, Si, S, Ar, Ca, Cr, Mn, Fe and Ni) considered by the OP, and underpins the latest release of OP opacities. This new service provides tables of Rosseland mean opacites using OP atomic data. We provide an alternative to the OPAL opacity services allowing direct comparison as well as study of the effect of uncertainties in stellar modeling due to mean opacities.

  7. QM/MD studies of the dynamics of the MTSL spin label in Aurora-A kinase protein activation loop

    CERN Document Server

    Concilio, Maria Grazia; Bayliss, Richard; Burgess, Selena

    2015-01-01

    Molecular dynamics(MD)simulations using a graphics processing unit (GPU) has been employed in order to determine the conformational space of the methane-thiosulfonate spin label (MTSL) attached to the activation loop of the Aurora-A kinase protein and compared with quantum mechanical (QM) methods rooted on density functional theory (DFT). MD provided a wealth of information about interactions between the MTSL and the residues of the protein and on the different motional contributions to the overall dynamics of the MTSL. Data obtained from MD were seen to be in good agreement with those obtained from QM but the dynamics of the system revealed more interactions than those observed from QM methods. A strong correlation between the tumbling of the protein and the transitions of the X4 and X5 dihedral angles of the MTSL, was observed with a consequent effect also the distribution of the nitroxide(NO)group in the space. Theoretical EPR spectra calculated from opportunely selected MD frames showing interactions betw...

  8. Solar Opacity Calculations Using the Super-transition-array Method

    Science.gov (United States)

    Krief, M.; Feigel, A.; Gazit, D.

    2016-04-01

    A new opacity model has been developed based on the Super-Transition-Array (STA) method for the calculation of monochromatic opacities of plasmas in local thermodynamic equilibrium. The atomic code, named STAR (STA-Revised), is described and used to calculate spectral opacities for a solar model implementing the recent AGSS09 composition. Calculations are carried out throughout the solar radiative zone. The relative contributions of different chemical elements and atomic processes to the total Rosseland mean opacity are analyzed in detail. Monochromatic opacities and charge-state distributions are compared with the widely used Opacity Project (OP) code, for several elements near the radiation-convection interface. STAR Rosseland opacities for the solar mixture show a very good agreement with OP and the OPAL opacity code throughout the radiation zone. Finally, an explicit STA calculation was performed of the full AGSS09 photospheric mixture, including all heavy metals. It was shown that, due to their extremely low abundance, and despite being very good photon absorbers, the heavy elements do not affect the Rosseland opacity.

  9. SOLAR OPACITY CALCULATIONS USING THE SUPER-TRANSITION-ARRAY METHOD

    Energy Technology Data Exchange (ETDEWEB)

    Krief, M.; Feigel, A.; Gazit, D., E-mail: menahem.krief@mail.huji.ac.il [The Racah Institute of Physics, The Hebrew University, 91904 Jerusalem (Israel)

    2016-04-10

    A new opacity model has been developed based on the Super-Transition-Array (STA) method for the calculation of monochromatic opacities of plasmas in local thermodynamic equilibrium. The atomic code, named STAR (STA-Revised), is described and used to calculate spectral opacities for a solar model implementing the recent AGSS09 composition. Calculations are carried out throughout the solar radiative zone. The relative contributions of different chemical elements and atomic processes to the total Rosseland mean opacity are analyzed in detail. Monochromatic opacities and charge-state distributions are compared with the widely used Opacity Project (OP) code, for several elements near the radiation–convection interface. STAR Rosseland opacities for the solar mixture show a very good agreement with OP and the OPAL opacity code throughout the radiation zone. Finally, an explicit STA calculation was performed of the full AGSS09 photospheric mixture, including all heavy metals. It was shown that, due to their extremely low abundance, and despite being very good photon absorbers, the heavy elements do not affect the Rosseland opacity.

  10. First solar models with OPAS opacity tables

    CERN Document Server

    Pennec, Maëlle Le; Salmon, Sébastien; Blancard, Christophe; Cossé, Philippe; Faussurier, Gérald; Mondet, Guillaume

    2015-01-01

    Stellar seismology appears more and more as a powerful tool for a better determination of the fundamental properties of solar-type stars. However the particular case of Sun is still challenging. The helioseismic sound speed determination continues to disagree with the Standard Solar Model (SSM) prediction for about a decade, questioning the reliability of this model. One of the sources of uncertainty could be in the treatment of the transport of radiation from the solar core to the surface. In this letter, we use the new OPAS opacity tables, recently available for solar modelling, to address this issue. We discuss first the peculiarities of these tables, then we quantify their impact on the solar sound speed and density profiles using the reduced OPAS tables taken on the grids of the OPAL ones. We use the two evolution codes MESA and CLES that led to similar conclusions in the solar radiative zone. In comparison to commonly used OPAL opacity tables, the new solar models computed, for the most recent photosphe...

  11. Nicotinic acetylcholine receptor α7 subunits with a C2 cytoplasmic loop yellow fluorescent protein insertion form functional receptors

    Institute of Scientific and Technical Information of China (English)

    Teresa A MURRAY; Qiang LIU; Paul WHITEAKER; Jie WU; Ronald J LUKAS

    2009-01-01

    Aim: Several nicotinic acetylcholine receptor (nAChR) subunits have been engineered as fluorescent protein (FP) fusions and exploited to illuminate features of nAChRs. The aim of this work was to create a FP fusion in the nAChR a.7 subunit without compromising formation of functional receptors.Methods: A gene construct was generated to introduce yellow fluorescent protein (YFP), in frame, into the otherwise unaltered, large, second cytoplamsic loop between the third and fourth transmembrane domains of the mouse nAChR al sub-unit (a7Y). SH-EP1 cells were transfected with mouse nAChR wild type a.7 subunits (a.7) or with a7Y subunits, alone or with the chaperone protein, hRJC-3. Receptor function was assessed using whole-cell current recording. Receptor expression was measured with 125I-labeled a-bungarotoxin (I-Bgt) binding, laser scanning confocal microscopy, and total internal reflectance fluorescence (TIRF) microscopy.Results: Whole-cell currents revealed that a7Y nAChRs and al nAChRs were functional with comparable EC50 values for the a7 nAChR-selective agonist, choline, and IC50 values for the a.7 nAChR-selective antagonist, methyllycaconitine. I-Bgt binding was detected only after co-expression with hRIC-3. Confocal microscopy revealed that a7Y had primarily intracel-lular rather than surface expression. TIRF microscopy confirmed that little a7Y localized to the plasma membrane, typical of a7 nAChRs.Conclusion: nAChRs composed as homooligomers of a7Y subunits containing cytoplasmic loop YFP have functional, ligand binding, and trafficking characteristics similar to those of a.7 nAChRs. a7Y nAChRs may be used to elucidate properties of a.7 nAChRs and to identify and develop novel probes for these receptors, perhaps in high-throughput fashion.

  12. Caught red-handed: Rc encodes a basic helix-loop-helix protein conditioning red pericarp in rice.

    Science.gov (United States)

    Sweeney, Megan T; Thomson, Michael J; Pfeil, Bernard E; McCouch, Susan

    2006-02-01

    Rc is a domestication-related gene required for red pericarp in rice (Oryza sativa). The red grain color is ubiquitous among the wild ancestors of O. sativa, in which it is closely associated with seed shattering and dormancy. Rc encodes a basic helix-loop-helix (bHLH) protein that was fine-mapped to an 18.5-kb region on rice chromosome 7 using a cross between Oryza rufipogon (red pericarp) and O. sativa cv Jefferson (white pericarp). Sequencing of the alleles from both mapping parents as well as from two independent genetic stocks of Rc revealed that the dominant red allele differed from the recessive white allele by a 14-bp deletion within exon 6 that knocked out the bHLH domain of the protein. A premature stop codon was identified in the second mutant stock that had a light red pericarp. RT-PCR experiments confirmed that the Rc gene was expressed in both red- and white-grained rice but that a shortened transcript was present in white varieties. Phylogenetic analysis, supported by comparative mapping in rice and maize (Zea mays), showed that Rc, a positive regulator of proanthocyanidin, is orthologous with INTENSIFIER1, a negative regulator of anthocyanin production in maize, and is not in the same clade as rice bHLH anthocyanin regulators.

  13. Recombinant Envelope-Proteins with Mutations in the Conserved Fusion Loop Allow Specific Serological Diagnosis of Dengue-Infections.

    Directory of Open Access Journals (Sweden)

    Alexandra Rockstroh

    2015-11-01

    Full Text Available Dengue virus (DENV is a mosquito-borne flavivirus and a major international public health concern in many tropical and sub-tropical areas worldwide. DENV is divided into four major serotypes, and infection with one serotype leads to immunity against the same, but not the other serotypes. The specific diagnosis of DENV-infections via antibody-detection is problematic due to the high degree of cross-reactivity displayed by antibodies against related flaviviruses, such as West Nile virus (WNV, Yellow Fever virus (YFV or Tick-borne encephalitis virus (TBEV. Especially in areas where several flaviviruses co-circulate or in the context of vaccination e.g. against YFV or TBEV, this severely complicates diagnosis and surveillance. Most flavivirus cross-reactive antibodies are produced against the highly conserved fusion loop (FL domain in the viral envelope (E protein. We generated insect-cell derived recombinant E-proteins of the four DENV-serotypes which contain point mutations in the FL domain. By using specific mixtures of these mutant antigens, cross-reactivity against heterologous flaviviruses was strongly reduced, enabling sensitive and specific diagnosis of the DENV-infected serum samples in IgG and IgM-measurements. These results have indications for the development of serological DENV-tests with improved specificity.

  14. 蛋白质中strand-loop-strand模体的分类%THE CLASSIFICATION OF STRAND-LOOP-STRAND MOTIFS IN PROTEINS

    Institute of Scientific and Technical Information of China (English)

    高苏娟; 胡秀珍

    2009-01-01

    从蛋白质一级序列出发,以氨基酸紧邻关联为参数,用离散量的方法,采用5交叉检验,对蛋白质中的strand-loop-strand模体进行了分类.文中使用了两个数据库,采用了不同的截取方式和序列模式长,均得到了较好的预测效果.

  15. What Controls DNA Looping?

    Directory of Open Access Journals (Sweden)

    Pamela J. Perez

    2014-08-01

    Full Text Available The looping of DNA provides a means of communication between sequentially distant genomic sites that operate in tandem to express, copy, and repair the information encoded in the DNA base sequence. The short loops implicated in the expression of bacterial genes suggest that molecular factors other than the naturally stiff double helix are involved in bringing the interacting sites into close spatial proximity. New computational techniques that take direct account of the three-dimensional structures and fluctuations of protein and DNA allow us to examine the likely means of enhancing such communication. Here, we describe the application of these approaches to the looping of a 92 base-pair DNA segment between the headpieces of the tetrameric Escherichia coli Lac repressor protein. The distortions of the double helix induced by a second protein—the nonspecific nucleoid protein HU—increase the computed likelihood of looping by several orders of magnitude over that of DNA alone. Large-scale deformations of the repressor, sequence-dependent features in the DNA loop, and deformability of the DNA operators also enhance looping, although to lesser degrees. The correspondence between the predicted looping propensities and the ease of looping derived from gene-expression and single-molecule measurements lends credence to the derived structural picture.

  16. Isolation of the new antigen receptor from wobbegong sharks, and use as a scaffold for the display of protein loop libraries.

    Science.gov (United States)

    Nuttall, S D; Krishnan, U V; Hattarki, M; De Gori, R; Irving, R A; Hudson, P J

    2001-08-01

    The new antigen receptor (NAR) from nurse sharks consists of an immunoglobulin variable domain attached to five constant domains, and is hypothesised to function as an antigen-binding antibody-like molecule. To determine whether the NAR is present in other species we have isolated a number of new antigen receptor variable domains from the spotted wobbegong shark (Orectolobus maculatus) and compared their structure to that of the nurse shark protein. To determine whether these wNARs can function as antigen-binding proteins, we have used them as scaffolds for the construction of protein libraries in which the CDR3 loop was randomised, and displayed the resulting recombinant domains on the surface of fd bacteriophages. On selection against several protein antigens, the highest affinity wNAR proteins were generated against the Gingipain K protease from Porphyromonas gingivalis. One wNAR protein bound Gingipain K specifically by ELISA and BIAcore analysis and, when expressed in E. coli and purified by affinity chromatography, eluted from an FPLC column as a single peak consistent with folding into a monomeric protein. Naturally occurring nurse shark and wobbegong NAR variable domains exhibit conserved cysteine residues within the CDR1 and CDR3 loops which potentially form disulphide linkages and enhance protein stability; proteins isolated from the in vitro NAR wobbegong library showed similar selection for such paired cysteine residues. Thus, the New Antigen Receptor represents a protein scaffold with possible stability advantages over conventional antibodies when used in in vitro molecular libraries.

  17. Calculation of Free-Free Opacities

    Science.gov (United States)

    Bhatia, A. K.; Maiden, D.; Ritchie, A. B., Jr.

    2003-01-01

    Free-free absorption is an important contribution to the opacity for radiation transport through hot materials Temperatures can be as high as several keV, such that it becomes a computational challenge to solve the Schrodinger equation efficiently for rapidly oscillating continuum functions for high angular momenta. Several groups\\footnots, including ours, have studied the phase amplitude solution (PAS) of the Schrodinger equation, in which one solves equations for the wave function amplitude and phase, which are: smooth functions of the electron energy. It is also important to have an accurate Schroudinger benchmark for the development of the PAS method. We present results for dipole matrix elements, Gaunt factors, and cross sections for the absorption of radiation at various energies for Cs XIX at temperature=100 eV and density=0.187 g/cc for our newly developed PAS and Schrodinger benchmark.

  18. Surgery for Pulmonary Multiple Ground Glass Opacities

    Directory of Open Access Journals (Sweden)

    Qun WANG

    2016-06-01

    Full Text Available The incidence of pulmonary ground glass opacity (GGO has been increasing in recent years, with a great number of patients having multiple GGOs. Unfortunately, the management of multiple GGOs is still controversial. Pulmonary GGO is a radiological term, consisting of different pathological types. Some of the GGOs are early-staged lung cancer. GGO is an indolent nodule, only a small proportion of GGOs change during observation, which does not influence the efficacy of surgery. . The timing of surgery for multiple GGOs mainly depends on the predominant nodule and surgery is recommended if the solid component of the predominant nodule >5 mm. Either lobectomy or sub-lobectomy is feasible. GGOs other than the predominant nodule can be left unresected. Multiple GGOs with high risk factors need mediastinal lymph node dissection or sampling.

  19. An opacity-sampled treatment of water vapor

    Science.gov (United States)

    Alexander, David R.; Augason, Gordon C.; Johnson, Hollis R.

    1989-01-01

    Although the bands of H2O are strong in the spectra of cool stars and calculations have repeatedly demonstrated their significance as opacity sources, only approximate opacities are currently available, due both to the difficulty of accounting for the millions of lines involved and to the inadequacy of laboratory and theoretical data. To overcome these obstacles, a new treatment is presented, based upon a statistical representation of the water vapor spectrum derived from available laboratory data. This statistical spectrum of water vapor employs an exponential distribution of line strengths and random positions of lines whose overall properties are forced to reproduce the mean opacities observed in the laboratory. The resultant data set is then treated by the opacity-sampling method exactly as are all other lines, both molecular and atomic. Significant differences are found between the results of this improved treatment and the results obtained with previous treatments of water-vapor opacity.

  20. A New Generation of Los Alamos Opacity Tables

    CERN Document Server

    Colgan, J; Magee, N H; Sherrill, M E; Abdallah,, J; Hakel, P; Fontes, C J; Guzik, J A; Mussack, K A

    2016-01-01

    We present a new, publicly available, set of Los Alamos OPLIB opacity tables for the elements hydrogen through zinc. Our tables are computed using the Los Alamos ATOMIC opacity and plasma modeling code, and make use of atomic structure calculations that use fine-structure detail for all the elements considered. Our equation-of-state (EOS) model, known as ChemEOS, is based on the minimization of free energy in a chemical picture and appears to be a reasonable and robust approach to determining atomic state populations over a wide range of temperatures and densities. In this paper we discuss in detail the calculations that we have performed for the 30 elements considered, and present some comparisons of our monochromatic opacities with measurements and other opacity codes. We also use our new opacity tables in solar modeling calculations and compare and contrast such modeling with previous work.

  1. The V4 and V5 Variable Loops of HIV-1 Envelope Glycoprotein Are Tolerant to Insertion of Green Fluorescent Protein and Are Useful Targets for Labeling.

    Science.gov (United States)

    Nakane, Shuhei; Iwamoto, Aikichi; Matsuda, Zene

    2015-06-12

    The mature human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) comprises the non-covalently associated gp120 and gp41 subunits generated from the gp160 precursor. Recent structural analyses have provided quaternary structural models for gp120/gp41 trimers, including the variable loops (V1-V5) of gp120. In these models, the V3 loop is located under V1/V2 at the apical center of the Env trimer, and the V4 and V5 loops project outward from the trimeric protomers. In addition, the V4 and V5 loops are predicted to have less movement upon receptor binding during membrane fusion events. We performed insertional mutagenesis using a GFP variant, GFPOPT, placed into the variable loops of HXB2 gp120. This allowed us to evaluate the current structural models and to simultaneously generate a GFP-tagged HIV-1 Env, which was useful for image analyses. All GFP-inserted mutants showed similar levels of whole-cell expression, although certain mutants, particularly V3 mutants, showed lower levels of cell surface expression. Functional evaluation of their fusogenicities in cell-cell and virus-like particle-cell fusion assays revealed that V3 was the most sensitive to the insertion and that the V1/V2 loops were less sensitive than V3. The V4 and V5 loops were the most tolerant to insertion, and certain tag proteins other than GFPOPT could also be inserted without functional consequences. Our results support the current structural models and provide a GFPOPT-tagged Env construct for imaging studies.

  2. Protein loops, solitons and side-chain visualization with applications to the left-handed helix region

    CERN Document Server

    Lundgren, Martin; Sha, Fan

    2012-01-01

    Folded proteins have a modular assembly. They are constructed from regular secondary structures like alpha-helices and beta-strands that are joined together by loops. Here we develop a visualization technique that is adapted to describe this modular structure. In complement to the widely employed Ramachandran plot that is based on toroidal geometry, our approach utilizes the geometry of a two-sphere. Unlike the more conventional approaches that only describea given peptide unit, ours is capable of describing the entire backbone environment including the neighboring peptide units. It maps the positions of each atom to the surface of the two-sphere exactly how these atoms are seen by an observer who is located at the position of the central C-alpha atom. At each level of side-chain atoms we observe a strong correlation between the positioning of the atom and the underlying local secondary structure with very little if any variation between the different amino acids. As a concrete example we analyze the left-han...

  3. Molecular mechanisms for the regulation of histone mRNA stem-loop-binding protein by phosphorylation

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Jun; Tan, Dazhi; DeRose, Eugene F.; Perera, Lalith; Dominski, Zbigniew; Marzluff, William F.; Tong, Liang; Tanaka Hall, Traci M. [NIH; (UNC); (Columbia)

    2014-08-06

    Replication-dependent histone mRNAs end with a conserved stem loop that is recognized by stem-loop–binding protein (SLBP). The minimal RNA-processing domain of SLBP is phosphorylated at an internal threonine, and Drosophila SLBP (dSLBP) also is phosphorylated at four serines in its 18-aa C-terminal tail. We show that phosphorylation of dSLBP increases RNA-binding affinity dramatically, and we use structural and biophysical analyses of dSLBP and a crystal structure of human SLBP phosphorylated on the internal threonine to understand the striking improvement in RNA binding. Together these results suggest that, although the C-terminal tail of dSLBP does not contact the RNA, phosphorylation of the tail promotes SLBP conformations competent for RNA binding and thereby appears to reduce the entropic penalty for the association. Increased negative charge in this C-terminal tail balances positively charged residues, allowing a more compact ensemble of structures in the absence of RNA.

  4. Bridging of anions by hydrogen bonds in nest motifs and its significance for Schellman loops and other larger motifs within proteins.

    Science.gov (United States)

    Afzal, Avid M; Al-Shubailly, Fawzia; Leader, David P; Milner-White, E James

    2014-11-01

    The nest is a protein motif of three consecutive amino acid residues with dihedral angles 1,2-αR αL (RL nests) or 1,2-αL αR (LR nests). Many nests form a depression in which an anion or δ-negative acceptor atom is bound by hydrogen bonds from the main chain NH groups. We have determined the extent and nature of this bridging in a database of protein structures using a computer program written for the purpose. Acceptor anions are bound by a pair of bridging hydrogen bonds in 40% of RL nests and 20% of LR nests. Two thirds of the bridges are between the NH groups at Positions 1 and 3 of the motif (N1N3-bridging)-which confers a concavity to the nest; one third are of the N2N3 type-which does not. In bridged LR nests N2N3-bridging predominates (14% N1N3: 75% N2N3), whereas in bridged RL nests the reverse is true (69% N1N3: 25% N2N3). Most bridged nests occur within larger motifs: 45% in (hexapeptide) Schellman loops with an additional 4 → 0 hydrogen bond (N1N3), 11% in Schellman loops with an additional 5 → 1 hydrogen bond (N2N3), 12% in a composite structure including a type 1β-bulge loop and an asx- or ST- motif (N1N3)-remarkably homologous to the N1N3-bridged Schellman loop-and 3% in a composite structure including a type 2β-bulge loop and an asx-motif (N2N3). A third hydrogen bond is a previously unrecognized feature of Schellman loops as those lacking bridged nests have an additional 4 → 0 hydrogen bond.

  5. The lumenal loop M672-P707 of the Menkes protein (ATP7A) transfers copper to peptidylglycine monooxygenase

    Energy Technology Data Exchange (ETDEWEB)

    Otoikhian, Adenike [Oregon Health & Sciences University; Barry, Amanda N. [Los Alamos National Laboratory; Mayfield, Mary [Oregon Health & Science University; Nilges, Mark [Illinois EPR Center; Huang, Yiping [Johns Hopkins University; Lutsenko, Svetlana [Johns Hopkins University; Blackburn, Ninian [Oregon Health & Science University

    2012-05-14

    Copper transfer to cuproproteins located in vesicular compartments of the secretory pathway depends on activity of the copper translocating ATPase (ATP7A or ATP7B) but the mechanism of transfer is largely unexplored. Copper-ATPase ATP7A is unique in having a sequence rich in histidine and methionine residues located on the lumenal side of the membrane. The corresponding fragment binds Cu(I) when expressed as a chimera with a scaffold protein, and mutations or deletions of His and/or Met residues in its sequence inhibit dephosphorylation of the ATPase, a catalytic step associated with copper release. Here we present evidence for a potential role of this lumenal region of ATP7A in copper transfer to cuproenzymes. Both Cu(II) and Cu(I) forms were investigated since the form in which copper is transferred to acceptor proteins is currently unknown. Analysis of Cu(II) using EPR demonstrated that at Cu:P ratios below 1:1, 15N-substituted protein had Cu(II) bound by 4 His residues, but this coordination changed as the Cu(II) to protein ratio increased towards 2:1. XAS confirmed this coordination via analysis of the intensity of outer-shell scattering from imidazole residues. The Cu(II) complexes could be reduced to their Cu(I) counterparts by ascorbate, but here again, as shown by EXAFS and XANES spectroscopy, the coordination was dependent on copper loading. At low copper Cu(I) was bound by a mixed ligand set of His + Met while at higher ratios His coordination predominated. The copper-loaded loop was able to transfer either Cu(II) or Cu(I) to peptidylglycine monooxygenase in the presence of chelating resin, generating catalytically active enzyme in a process that appeared to involve direct interaction between the two partners. The variation of coordination with copper loading suggests copper-dependent conformational change which in turn could act as a signal for regulating copper release by the ATPase pump.

  6. Rosseland and Flux Mean Opacities for Compton Scattering

    Science.gov (United States)

    Poutanen, Juri

    2017-02-01

    Rosseland mean opacity plays an important role in theories of stellar evolution and X-ray burst models. In the high-temperature regime, when most of the gas is completely ionized, the opacity is dominated by Compton scattering. Our aim here is to critically evaluate previous works on this subject and to compute the exact Rosseland mean opacity for Compton scattering over a broad range of temperature and electron degeneracy parameter. We use relativistic kinetic equations for Compton scattering and compute the photon mean free path as a function of photon energy by solving the corresponding integral equation in the diffusion limit. As a byproduct we also demonstrate the way to compute photon redistribution functions in the case of degenerate electrons. We then compute the Rosseland mean opacity as a function of temperature and electron degeneracy and present useful approximate expressions. We compare our results to previous calculations and find a significant difference in the low-temperature regime and strong degeneracy. We then proceed to compute the flux mean opacity in both free-streaming and diffusion approximations, and show that the latter is nearly identical to the Rosseland mean opacity. We also provide a simple way to account for the true absorption in evaluating the Rosseland and flux mean opacities.

  7. Replicating the Z iron opacity experiments on the NIF

    Science.gov (United States)

    Perry, T. S.; Heeter, R. F.; Opachich, Y. P.; Ross, P. W.; Kline, J. L.; Flippo, K. A.; Sherrill, M. E.; Dodd, E. S.; DeVolder, B. G.; Cardenas, T.; Archuleta, T. N.; Craxton, R. S.; Zhang, R.; McKenty, P. W.; Garcia, E. M.; Huffman, E. J.; King, J. A.; Ahmed, M. F.; Emig, J. A.; Ayers, S. L.; Barrios, M. A.; May, M. J.; Schneider, M. B.; Liedahl, D. A.; Wilson, B. G.; Urbatsch, T. J.; Iglesias, C. A.; Bailey, J. E.; Rochau, G. A.

    2017-06-01

    X-ray opacity is a crucial factor of all radiation-hydrodynamics calculations, yet it is one of the least validated of the material properties in the simulation codes. Recent opacity experiments at the Sandia Z-machine have shown up to factors of two discrepancies between theory and experiment, casting doubt on the validity of the opacity models. Therefore, a new experimental opacity platform is being developed on the National Ignition Facility (NIF) not only to verify the Z-machine experimental results but also to extend the experiments to other temperatures and densities. The first experiments will be directed towards measuring the opacity of iron at a temperature of ∼160 eV and an electron density of ∼7 × 1021 cm-3. Preliminary experiments on NIF have demonstrated the ability to create a sufficiently bright point backlighter using an imploding plastic capsule and also a hohlraum that can heat the opacity sample to the desired conditions. The first of these iron opacity experiments is expected to be performed in 2017.

  8. Linear opacities on HRCT in bronchiolitis obliterans organising pneumonia

    Energy Technology Data Exchange (ETDEWEB)

    Murphy, J.M.; Flower, C.D.R. [Dept. of Radiology, Addenbrookes Hospital, Univ. of Cambridge (United Kingdom); Schnyder, P.; Leuenberger, P. [Depts. of Radiology and Medicine, University Hospital, CHUV, Lausanne (Switzerland); Verschakelen, J. [Dept. of Radiology, University Hospital, Leuven (Belgium)

    1999-07-01

    The aim of this study was to report the high-resolution computed tomography (HRCT) appearances of linear opacities that may occur in isolation or in combination with other changes in bronchiolitis obliterans organising pneumonia (BOOP). Eleven patients with BOOP and linear opacities on HRCT were identified at three independent teaching hospitals. The HRCT images and clinical course of each patient were reviewed. Two distinct types of linear opacity were identified. The type-1 opacity extended in a radial manner along the line of the bronchi towards the pleura and was usually intimately related to bronchi. The type-2 opacity occurred in a sub-pleural location and bore no relationship to the bronchi. Both types occurred most commonly in the lower lobes, frequently were associated with multi-focal areas of consolidation and usually completely resolved with treatment. There was no associated bronchiectasis, irreversible volume loss or a reticular or honeycomb pattern. In 2 patients linear opacities were the sole abnormality on HRCT. Bronchiolitis obliterans organising pneumonia may occur in a pure ''linear form'' or HRCT may demonstrate linear opacities in addition to multi-focal consolidation. (orig.)

  9. The haloarchaeal MCM proteins: bioinformatic analysis and targeted mutagenesis of the β7-β8 and β9-β10 hairpin loops and conserved zinc binding domain cysteines

    Directory of Open Access Journals (Sweden)

    Tatjana P Kristensen

    2014-03-01

    Full Text Available The hexameric MCM complex is the catalytic core of the replicative helicase in eukaryotic and archaeal cells. Here we describe the first in vivo analysis of archaeal MCM protein structure and function relationships using the genetically tractable haloarchaeon Haloferax volcanii as a model system. Hfx. volcanii encodes a single MCM protein that is part of the previously identified core group of haloarchaeal MCM proteins. Three structural features of the N-terminal domain of the Hfx. volcanii MCM protein were targeted for mutagenesis: the β7-β8 and β9-β10 β-hairpin loops and putative zinc binding domain. Five strains carrying single point mutations in the β7-β8 β-hairpin loop were constructed, none of which displayed impaired cell growth under normal conditions or when treated with the DNA damaging agent mitomycin C. However, short sequence deletions within the β7-β8 β-hairpin were not tolerated and neither was replacement of the highly conserved residue glutamate 187 with alanine. Six strains carrying paired alanine substitutions within the β9-β10 β-hairpin loop were constructed, leading to the conclusion that no individual amino acid within that hairpin loop is absolutely required for MCM function, although one of the mutant strains displays greatly enhanced sensitivity to mitomycin C. Deletions of two or four amino acids from the β9-β10 β-hairpin were tolerated but mutants carrying larger deletions were inviable. Similarly, it was not possible to construct mutants in which any of the conserved zinc binding cysteines was replaced with alanine, underlining the likely importance of zinc binding for MCM function. The results of these studies demonstrate the feasibility of using Hfx. volcanii as a model system for reverse genetic analysis of archaeal MCM protein function and provide important confirmation of the in vivo importance of conserved structural features identified by previous bioinformatic, biochemical and structural

  10. The Basic/Helix-Loop-Helix Protein Family in Gossypium: Reference Genes and Their Evolution during Tetraploidization.

    Directory of Open Access Journals (Sweden)

    Qian Yan

    Full Text Available Basic/helix-loop-helix (bHLH proteins comprise one of the largest transcription factor families and play important roles in diverse cellular and molecular processes. Comprehensive analyses of the composition and evolution of the bHLH family in cotton are essential to elucidate their functions and the molecular basis of cotton development. By searching bHLH homologous genes in sequenced diploid cotton genomes (Gossypium raimondii and G. arboreum, a set of cotton bHLH reference genes containing 289 paralogs were identified and named as GobHLH001-289. Based on their phylogenetic relationships, these cotton bHLH proteins were clustered into 27 subfamilies. Compared to those in Arabidopsis and cacao, cotton bHLH proteins generally increased in number, but unevenly in different subfamilies. To further uncover evolutionary changes of bHLH genes during tetraploidization of cotton, all genes of S5a and S5b subfamilies in upland cotton and its diploid progenitors were cloned and compared, and their transcript profiles were determined in upland cotton. A total of 10 genes of S5a and S5b subfamilies (doubled from A- and D-genome progenitors maintained in tetraploid cottons. The major sequence changes in upland cotton included a 15-bp in-frame deletion in GhbHLH130D and a long terminal repeat retrotransposon inserted in GhbHLH062A, which eliminated GhbHLH062A expression in various tissues. The S5a and S5b bHLH genes of A and D genomes (except GobHLH062 showed similar transcription patterns in various tissues including roots, stems, leaves, petals, ovules, and fibers, while the A- and D-genome genes of GobHLH110 and GobHLH130 displayed clearly different transcript profiles during fiber development. In total, this study represented a genome-wide analysis of cotton bHLH family, and revealed significant changes in sequence and expression of these genes in tetraploid cottons, which paved the way for further functional analyses of bHLH genes in the cotton genus.

  11. Computing NLTE Opacities -- Node Level Parallel Calculation

    Energy Technology Data Exchange (ETDEWEB)

    Holladay, Daniel [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-09-11

    Presentation. The goal: to produce a robust library capable of computing reasonably accurate opacities inline with the assumption of LTE relaxed (non-LTE). Near term: demonstrate acceleration of non-LTE opacity computation. Far term (if funded): connect to application codes with in-line capability and compute opacities. Study science problems. Use efficient algorithms that expose many levels of parallelism and utilize good memory access patterns for use on advanced architectures. Portability to multiple types of hardware including multicore processors, manycore processors such as KNL, GPUs, etc. Easily coupled to radiation hydrodynamics and thermal radiative transfer codes.

  12. Calculation and Analysis of Mean Opacity of Gold Mixtures

    Institute of Scientific and Technical Information of China (English)

    YAN An-ying; JIANG Ming; CHENG Xin-lu; YANG Xiang-dong

    2007-01-01

    A screened hydrogenic model for l splitting (SHML) is used to calculate the Rosseland mean opacities of high-Z Au, Ta, Yb, Ho, Gd, Sm, Nd, Sn, Ag plasmas and mixtures of gold and these elements at high temperature (T=200-400eV) and dense (ρ=1g/cm3).From the calculated Rosseland mean opacities of the mixtures, Au-Nd seems to be a better choice than other mixtures.Simultaneously, the reason that the mean opacities of mixture of Au-Sn decrease slightly when T=400eV is analyzed.

  13. Opacity Calculations for Non-Local Thermodynamic Equilibrium Mixtures

    Institute of Scientific and Technical Information of China (English)

    吴泽清; 韩国兴; 逄锦桥

    2002-01-01

    Based on the average atom model, a non-local thermodynamic equilibrium (non-LTE) model is developed to calculate opacity for mixtures. This model could be applied to high-Z problems. The mean ionization degrees of SiO2 of the present calculation are slightly higher compared with another model for mixtures. As an example, the opacity of Au and Nd mixture is calculated. The results show concrete non-LTE effects and the increase in opacity of the mixture is shown clearly.

  14. Protein loops, solitons, and side-chain visualization with applications to the left-handed helix region.

    Science.gov (United States)

    Lundgren, Martin; Niemi, Antti J; Sha, Fan

    2012-06-01

    Folded proteins have a modular assembly. They are constructed from regular secondary structures like α helices and β strands that are joined together by loops. Here we develop a visualization technique that is adapted to describe this modular structure. In complement to the widely employed Ramachandran plot that is based on toroidal geometry, our approach utilizes the geometry of a two sphere. Unlike the more conventional approaches that describe only a given peptide unit, ours is capable of describing the entire backbone environment including the neighboring peptide units. It maps the positions of each atom to the surface of the two-sphere exactly how these atoms are seen by an observer who is located at the position of the central C_{α} atom. At each level of side-chain atoms we observe a strong correlation between the positioning of the atom and the underlying local secondary structure with very little if any variation between the different amino acids. As a concrete example we analyze the left-handed helix region of nonglycyl amino acids. This region corresponds to an isolated and highly localized residue independent sector in the direction of the C_{β} carbons on the two-sphere. We show that the residue independent localization extends to C_{γ} and C_{δ} carbons and to side-chain oxygen and nitrogen atoms in the case of asparagine and aspartic acid. When we extend the analysis to the side-chain atoms of the neighboring residues, we observe that left-handed β turns display a regular and largely amino acid independent structure that can extend to seven consecutive residues. This collective pattern is due to the presence of a backbone soliton. We show how one can use our visualization techniques to analyze and classify the different solitons in terms of selection rules that we describe in detail.

  15. The Role of the β5-α11 Loop in the Active-Site Dynamics of Acylated Penicillin-Binding Protein A from Mycobacterium tuberculosis

    Energy Technology Data Exchange (ETDEWEB)

    Fedarovich, Alena; Nicholas, Robert A.; Davies, Christopher [MUSC; (UNC)

    2013-04-22

    Penicillin-binding protein A (PBPA) is a class B penicillin-binding protein that is important for cell division in Mycobacterium tuberculosis. We have determined a second crystal structure of PBPA in apo form and compared it with an earlier structure of apoenzyme. Significant structural differences in the active site region are apparent, including increased ordering of a β-hairpin loop and a shift of the SxN active site motif such that it now occupies a position that appears catalytically competent. Using two assays, including one that uses the intrinsic fluorescence of a tryptophan residue, we have also measured the second-order acylation rate constants for the antibiotics imipenem, penicillin G, and ceftriaxone. Of these, imipenem, which has demonstrable anti-tubercular activity, shows the highest acylation efficiency. Crystal structures of PBPA in complex with the same antibiotics were also determined, and all show conformational differences in the β5–α11 loop near the active site, but these differ for each β-lactam and also for each of the two molecules in the crystallographic asymmetric unit. Overall, these data reveal the β5–α11 loop of PBPA as a flexible region that appears important for acylation and provide further evidence that penicillin-binding proteins in apo form can occupy different conformational states.

  16. The second intracellular loop of the human cannabinoid CB2 receptor governs G protein coupling in coordination with the carboxyl terminal domain.

    Directory of Open Access Journals (Sweden)

    Congxia Zheng

    Full Text Available The major effects of cannabinoids and endocannabinoids are mediated via two G protein-coupled receptors, CB1 and CB2, elucidation of the mechanism and structural determinants of the CB2 receptor coupling with G proteins will have a significant impact on drug discovery. In the present study, we systematically investigated the role of the intracellular loops in the interaction of the CB2 receptor with G proteins using chimeric receptors alongside the characterization of cAMP accumulation and ERK1/2 phosphorylation. We provided evidence that ICL2 was significantly involved in G protein coupling in coordination with the C-terminal end. Moreover, a single alanine substitution of the Pro-139 in the CB2 receptor that corresponds to Leu-222 in the CB1 receptor resulted in a moderate impairment in the inhibition of cAMP accumulation, whereas mutants P139F, P139M and P139L were able to couple to the Gs protein in a CRE-driven luciferase assay. With the ERK activation experiments, we further found that P139L has the ability to activate ERK through both Gi- and Gs-mediated pathways. Our findings defined an essential role of the second intracellular loop of the CB2 receptor in coordination with the C-terminal tail in G protein coupling and receptor activation.

  17. Rosseland and flux mean opacities for Compton scattering

    CERN Document Server

    Poutanen, Juri

    2016-01-01

    Rosseland mean opacity plays an important role in theories of stellar evolution and X-ray burst models. In the high-temperature regime, when most of the gas is completely ionized, the opacity is dominated by Compton scattering. Our aim here is to critically evaluate previous works on this subject and to compute exact Rosseland mean opacity for Compton scattering in a broad range of temperatures and electron degeneracy parameter. We use relativistic kinetic equations for Compton scattering and compute the photon mean free path as a function of photon energy by solving the corresponding integral equation in the diffusion limit. As a byproduct we also demonstrate the way to compute photon redistribution functions in case of degenerate electrons. We then compute the Rosseland mean opacity as a function of temperature and electron degeneracy. We compare our results to the previous calculations and find a significant difference in the low-temperature regime and strong degeneracy. We find useful analytical expressio...

  18. Is Seeing Believing? Consumer Responses to Opacity of Product Packaging

    National Research Council Canada - National Science Library

    Sucharita Chandran; Rishtee Kumar Batra; Benjamin Lawrence

    2009-01-01

      Prior studies have shown that product and packaging design influences consumer reactions and purchase behaviors, however, research has neglected to examine a package's opacity or lack of transparency...

  19. Opacity Experiments At The National Ignition Facility (NIF)

    Science.gov (United States)

    Perry, T. S.; Kline, J. L.; Flippo, K. A.; Sherrill, M. E.; Dodd, E. S.; Devolder, B. G.; Urbatsch, T. J.; Heeter, R. F.; Schneider, M. B.; Liedahl, D. A.; Wilson, B. G.; Iglesias, C. A.; Opachich, Y. P.; Ross, P. W.; Bailey, J. E.; Rochau, G. A.

    2016-10-01

    X-ray opacities are essential to the radiation-hydrodynamic simulations used to model astrophysical systems or inertial confinement fusion experiments. Recent opacity experiments have shown up to a factor of two discrepancy between theory and experiment. To address this issue a new experimental opacity platform is being developed on the NIF to crosscheck the recent results. The first experiments, starting in 2017, will begin by measuring the opacity of iron at a temperature of 160 eV and an electron density of 7x1021 cm-3. This and several following presentations will describe this effort. This work was performed under the auspices of the U.S. Department of Energy by Los Alamos National Lab under Contract DE-AC52-06NA25396.

  20. The roles of the conserved tyrosine in the β2-α2 loop of the prion protein.

    Science.gov (United States)

    Huang, Danzhi; Caflisch, Amedeo

    2015-01-01

    Prions cause neurodegenerative diseases for which no cure exists. Despite decades of research activities the function of the prion protein (PrP) in mammalians is not known. Moreover, little is known on the molecular mechanisms of the self-assembly of the PrP from its monomeric state (cellular PrP, PrP(C)) to the multimeric state. The latter state includes the toxic species (scrapie PrP, PrP(Sc)) knowledge of which would facilitate the development of drugs against prion diseases. Here we analyze the role of a tyrosine residue (Y169) which is strictly conserved in mammalian PrPs. Nuclear magnetic resonance (NMR) spectroscopy studies of many mammalian PrP(C) proteins have provided evidence of a conformational equilibrium between a 3(10)-helical turn and a type I β turn conformation in the β2-α2 loop (residues 165-175). In vitro cell-free experiments of the seeded conversion of PrP(C) indicate that non-aromatic residues at position 169 reduce the formation of proteinase K-resistant PrP. Recent molecular dynamics (MD) simulations of monomeric PrP and several single-point mutants show that Y169 stabilizes the 3(10)-helical turn conformation more than single-point mutants at position 169 or residues in contact with it. In the 3(10)-helical turn conformation the hydrophobic and aggregation-prone segment 169-YSNQNNF-175 is buried and thus not-available for self-assembly. From the combined analysis of simulation and experimental results it emerges that Y169 is an aggregation gatekeeper with a twofold role. Mutations related to 3 human prion diseases are interpreted on the basis of the gatekeeper role in the monomeric state. Another potential role of the Y169 side chain is the stabilization of the ordered aggregates, i.e., reduction of frangibility of filamentous protofibrils and fibrils, which is likely to reduce the generation of toxic species.

  1. Experiment to measure oxygen opacity at high density and temperature

    Science.gov (United States)

    Keiter, Paul; Mussack, Katie; Orban, Chris; Colgan, James; Ducret, Jean-Eric; Fontes, Christopher J.; Guzik, Joyce Ann; Heeter, Robert F.; Kilcrease, Dave; Le Pennec, Maelle; Mancini, Roberto; Perry, Ted; Turck-Chièze, Sylvaine; Trantham, Matt

    2017-06-01

    In recent years, there has been a debate over the abundances of heavy elements (Z >2) in the solar interior. Recent solar atmosphere models [Asplund 2009] find a significantly lower abundance for C, N, and O compared to models used roughly a decade ago. This discrepancy has led to an investigation of opacities through laboratory experiments and improved opacity models for many of the larger contributors to the sun’s opacity, including iron and oxygen. Recent opacity measurements of iron disagree with opacity model predictions [Bailey et al, 2015]. Although these results are still controversial, repeated scrutiny of the experiment and data has not produced a conclusive reason for the discrepancy. New models have been implemented in the ATOMIC opacity code for C, O and Fe to address the solar abundance issue [Colgan, 2013]. Armstrong et al [2014] have also implemented changes in the ATOMIC code for low-Z elements. However, no data currently exists to test the low-Z material models in the regime relevant to the solar convection zone. We present an experimental design using the opacity platform developed at the National Ignition Facility to study the oxygen opacity at densities and temperatures near the solar convection zone conditions.This work is funded by the U.S. DOE, through the NNSA-DS and SC-OFES Joint Program in HEDPLP, grant No. DE-NA0001840, and the NLUF Program, grant No. DE-NA0000850, and through LLE, University of Rochester by the NNSA/OICF under Agreement No. DE-FC52-08NA28302.

  2. Analytical expressions for radiative opacities of low Z plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Rubiano, J G; Martel, P; Gil, J M; Rodriguez, R; Florido, R; Mendoza, M A [Departamento de Fisica, Universidad de Las Palmas de GC, Las Palmas de GC (Spain); Minguez, E, E-mail: jgarcia@dfis.ulpgc.e [Instituto de Fusion Nuclear (DENIM), Universidad Politecnica de Madrid, Madrid (Spain)

    2010-08-01

    In this work we obtain analytical expressions for the radiative opacity of several low Z plasmas (He, Li, Be, and B) in a wide range of temperatures and densities. These formulas are obtained by fitting the proposed expression to mean opacities data calculated by using the code ABAKO/ RAPCAL. This code computes the radiative properties of plasmas, both in LTE and NLTE conditions, under the detailed-level-accounting approach. It has been successfully validated in the range of interest in previous works.

  3. Opacity spectra of silicon and carbon in ICF plasmas

    Science.gov (United States)

    Benredjem, D.; Calisti, A.; Ferri, S.; Gilleron, F.; Mondet, G.; Pain, J.-C.

    2017-03-01

    The knowledge of opacity is very important when one investigates the radiative properties of ICF and astrophysical plasmas. Germanium and silicon are good candidates as dopants in the ablator of some ICF schemes (LMJ in France, NIF at Livermore). In this work we calculate the opacity spectra of silicon and carbon mixtures. Two competitive methods were used. The first one is based on a detailed line calculation in which the atomic database is provided by the MCDF code. A lineshape code based on a fast algorithm was then adapted to the calculation of opacity profiles. All major line broadening mechanisms, including Zeeman splitting and Stark effect, are taken into account. This approach provides accurate opacity spectra but becomes rapidly prohibitive when the number of lines is large. To account for systems involving many ionic stages and thousands of lines, a second approach combines detailed line calculations and statistical calculations. This approach necessitates much smaller calculation times than the first one and is then more appropriate for extensive calculations. The monochromatic opacity and the Rosseland and Planck mean opacities are calculated for relevant densities and temperatures.

  4. Computational design of short pulse laser driven iron opacity experiments

    Science.gov (United States)

    Martin, M. E.; London, R. A.; Goluoglu, S.; Whitley, H. D.

    2017-02-01

    The resolution of current disagreements between solar parameters calculated from models and observations would benefit from the experimental validation of theoretical opacity models. Iron's complex ionic structure and large contribution to the opacity in the radiative zone of the sun make iron a good candidate for validation. Short pulse lasers can be used to heat buried layer targets to plasma conditions comparable to the radiative zone of the sun, and the frequency dependent opacity can be inferred from the target's measured x-ray emission. Target and laser parameters must be optimized to reach specific plasma conditions and meet x-ray emission requirements. The HYDRA radiation hydrodynamics code is used to investigate the effects of modifying laser irradiance and target dimensions on the plasma conditions, x-ray emission, and inferred opacity of iron and iron-magnesium buried layer targets. It was determined that plasma conditions are dominantly controlled by the laser energy and the tamper thickness. The accuracy of the inferred opacity is sensitive to tamper emission and optical depth effects. Experiments at conditions relevant to the radiative zone of the sun would investigate the validity of opacity theories important to resolving disagreements between solar parameters calculated from models and observations.

  5. Recursive method for opacity expansion at finite temperature%Recursive method for opacity expansion at finite temperature

    Institute of Scientific and Technical Information of China (English)

    刘嘉; 康忠波; 王恩科

    2011-01-01

    Using a reaction operator approach, we derive the multiple-scattering induced gluon number distribution function to all orders in powers of opacity at finite temperature. The detailed balance effect is analyzed by taking into account both gluon emission a

  6. Mass Spectrometry-based Footprinting Reveals Structural Dynamics of Loop E of the Chlorophyll-binding Protein CP43 during Photosystem II Assembly in the Cyanobacterium Synechocystis 6803*

    Science.gov (United States)

    Liu, Haijun; Chen, Jiawei; Huang, Richard Y.-C.; Weisz, Daniel; Gross, Michael L.; Pakrasi, Himadri B.

    2013-01-01

    The PSII repair cycle is required for sustainable photosynthesis in oxygenic photosynthetic organisms. In cyanobacteria and higher plants, proteolysis of the precursor D1 protein (pD1) to expose a C-terminal carboxylate group is an essential step leading to coordination of the Mn4CaO5 cluster, the site of water oxidation. Psb27 appears to associate with both pD1- and D1-containing PSII assembly intermediates by closely interacting with CP43. Here, we report that reduced binding affinity between CP43 and Psb27 is triggered by the removal of the C-terminal extension of the pD1 protein. A mass spectrometry-based footprinting strategy was adopted to probe solvent-exposed aspartic and glutamic acid residues on the CP43 protein. By comparing the extent of footprinting between HT3ΔctpAΔ27PSII and HT3ΔctpAPSII, two genetically modified PSII assembly complexes, we found that Psb27 binds to CP43 on the side of Loop E distal to the pseudo-symmetrical D1-D2 axis. By comparing a second pair of PSII assembly complexes, we discovered that Loop E of CP43 undergoes a significant conformational rearrangement due to the removal of the pD1 C-terminal extension, altering the Psb27-CP43 binding interface. The significance of this conformational rearrangement is discussed in the context of recruitment of the PSII lumenal extrinsic proteins and Mn4CaO5 cluster assembly. In addition to CP43's previously known function as one of the core PSII antenna proteins, this work demonstrates that Loop E of CP43 plays an important role in the functional assembly of the Water Oxidizing Center (WOC) during PSII biogenesis. PMID:23546881

  7. Utilization of paramagnetic relaxation enhancements for high-resolution NMR structure determination of a soluble loop-rich protein with sparse NOE distance restraints

    Energy Technology Data Exchange (ETDEWEB)

    Furuita, Kyoko; Kataoka, Saori; Sugiki, Toshihiko; Hattori, Yoshikazu; Kobayashi, Naohiro; Ikegami, Takahisa [Osaka University, Institute for Protein Research (Japan); Shiozaki, Kazuhiro [Nara Institute of Science and Technology, Graduate School of Biological Sciences (Japan); Fujiwara, Toshimichi; Kojima, Chojiro, E-mail: kojima@protein.osaka-u.ac.jp [Osaka University, Institute for Protein Research (Japan)

    2015-01-15

    NMR structure determination of soluble proteins depends in large part on distance restraints derived from NOE. In this study, we examined the impact of paramagnetic relaxation enhancement (PRE)-derived distance restraints on protein structure determination. A high-resolution structure of the loop-rich soluble protein Sin1 could not be determined by conventional NOE-based procedures due to an insufficient number of NOE restraints. By using the 867 PRE-derived distance restraints obtained from the NOE-based structure determination procedure, a high-resolution structure of Sin1 could be successfully determined. The convergence and accuracy of the determined structure were improved by increasing the number of PRE-derived distance restraints. This study demonstrates that PRE-derived distance restraints are useful in the determination of a high-resolution structure of a soluble protein when the number of NOE constraints is insufficient.

  8. Fluorescence Resonance Energy Transfer (FRET as a method to calculate the dimerization strength of basic Helix-Loop-Helix (bHLH proteins

    Directory of Open Access Journals (Sweden)

    Centonze Victoria E.

    2004-01-01

    Full Text Available Post-translational modifications such as phosphorylation play a vital role in the regulation of protein function. In our study of the basic Helix-loop-Helix (bHLH transcription factor HAND1, we show that HAND1 is phosphorylated during the trophoblast giant cell differentiation on residues residing in Helix I of the bHLH domain. Our hypothesis is that these modifications result in changes in HAND1 dimerization affinities with other bHLH factors. To test this idea, we employed FRET to measure the protein-protein interactions of HAND1 and HAND1 point mutants in HEK293 cells using YFP and CFP fusion proteins and laser scanning confocal microscopy.

  9. Conformational dynamics and the energetics of protein--ligand interactions: role of interdomain loop in human cytochrome P450 reductase.

    Science.gov (United States)

    Grunau, Alex; Geraki, Kalotina; Grossmann, J Günter; Gutierrez, Aldo

    2007-07-17

    A combination of mutagenesis, calorimetry, kinetics, and small-angle X-ray scattering (SAXS) has been used to study the mechanism of ligand binding energy propagation through human cytochrome P450 reductase (CPR). Remarkably, the energetics of 2',5'-ADP binding to R597 at the FAD-binding domain are affected by mutations taking place at an interdomain loop located 60 A away. Either deletion of a 7 amino acid long segment (T236-G237-E238-E239-S240-S241-I242) or its replacement by poly-proline repeats (5 and 10 residues) results in a significant increase in 2',5'-ADP enthalpy of binding (DeltaHB). This is accompanied by a decrease in the number of thermodynamic microstates available for the ligand-CPR complex. Moreover, the estimated heat capacity change (DeltaCp) for this interaction changes from -220 cal mol-1 K-1 in the wild-type enzyme to -580 cal mol-1 K-1 in the deletion mutant. Pre-steady-state kinetics measurements reveal a 50-fold decrease in the microscopic rate for interdomain (FAD --> FMN) electron transfer in the deletion mutant (kobs = 0.4 s-1). Multiple turnover cytochome c reduction assays indicate that these mutations impair the ability of the FMN-binding domain to shuttle electrons from the FAD-binding domain to the cytochrome partner. Binding of 2',5'-ADP to wild-type CPR triggers a large-scale structural rearrangement resulting in the complex having a more compact domain organization, and the maximum molecular dimension (Dmax) decreases from 110 A in ligand-free enzyme to 100 A in the ligand-bound CPR. The SAXS experiments also demonstrate that what is affected by the mutations is indeed the relative diffusional motion of the domains. Furthemore, ab initio shape reconstruction and homology modeling would suggest that-in the deletion mutant-hindering of domain motion occurs concomitantly with dimerization. The results presented here show that the energetics of this highly localized interaction (2',5'-ADP binding) have a global character, and are

  10. Protein distributions from a stochastic model of the lac operon of E. coli with DNA looping: analytical solution and comparison with experiments.

    Directory of Open Access Journals (Sweden)

    Krishna Choudhary

    Full Text Available Although noisy gene expression is widely accepted, its mechanisms are subjects of debate, stimulated largely by single-molecule experiments. This work is concerned with one such study, in which Choi et al., 2008, obtained real-time data and distributions of Lac permease in E. coli. They observed small and large protein bursts in strains with and without auxiliary operators. They also estimated the size and frequency of these bursts, but these were based on a stochastic model of a constitutive promoter. Here, we formulate and solve a stochastic model accounting for the existence of auxiliary operators and DNA loops. We find that DNA loop formation is so fast that small bursts are averaged out, making it impossible to extract their size and frequency from the data. In contrast, we can extract not only the size and frequency of the large bursts, but also the fraction of proteins derived from them. Finally, the proteins follow not the negative binomial distribution, but a mixture of two distributions, which reflect the existence of proteins derived from small and large bursts.

  11. Natively unstructured loops differ from other loops.

    Directory of Open Access Journals (Sweden)

    Avner Schlessinger

    2007-07-01

    Full Text Available Natively unstructured or disordered protein regions may increase the functional complexity of an organism; they are particularly abundant in eukaryotes and often evade structure determination. Many computational methods predict unstructured regions by training on outliers in otherwise well-ordered structures. Here, we introduce an approach that uses a neural network in a very different and novel way. We hypothesize that very long contiguous segments with nonregular secondary structure (NORS regions differ significantly from regular, well-structured loops, and that a method detecting such features could predict natively unstructured regions. Training our new method, NORSnet, on predicted information rather than on experimental data yielded three major advantages: it removed the overlap between testing and training, it systematically covered entire proteomes, and it explicitly focused on one particular aspect of unstructured regions with a simple structural interpretation, namely that they are loops. Our hypothesis was correct: well-structured and unstructured loops differ so substantially that NORSnet succeeded in their distinction. Benchmarks on previously used and new experimental data of unstructured regions revealed that NORSnet performed very well. Although it was not the best single prediction method, NORSnet was sufficiently accurate to flag unstructured regions in proteins that were previously not annotated. In one application, NORSnet revealed previously undetected unstructured regions in putative targets for structural genomics and may thereby contribute to increasing structural coverage of large eukaryotic families. NORSnet found unstructured regions more often in domain boundaries than expected at random. In another application, we estimated that 50%-70% of all worm proteins observed to have more than seven protein-protein interaction partners have unstructured regions. The comparative analysis between NORSnet and DISOPRED2 suggested

  12. Natively unstructured loops differ from other loops.

    Science.gov (United States)

    Schlessinger, Avner; Liu, Jinfeng; Rost, Burkhard

    2007-07-01

    Natively unstructured or disordered protein regions may increase the functional complexity of an organism; they are particularly abundant in eukaryotes and often evade structure determination. Many computational methods predict unstructured regions by training on outliers in otherwise well-ordered structures. Here, we introduce an approach that uses a neural network in a very different and novel way. We hypothesize that very long contiguous segments with nonregular secondary structure (NORS regions) differ significantly from regular, well-structured loops, and that a method detecting such features could predict natively unstructured regions. Training our new method, NORSnet, on predicted information rather than on experimental data yielded three major advantages: it removed the overlap between testing and training, it systematically covered entire proteomes, and it explicitly focused on one particular aspect of unstructured regions with a simple structural interpretation, namely that they are loops. Our hypothesis was correct: well-structured and unstructured loops differ so substantially that NORSnet succeeded in their distinction. Benchmarks on previously used and new experimental data of unstructured regions revealed that NORSnet performed very well. Although it was not the best single prediction method, NORSnet was sufficiently accurate to flag unstructured regions in proteins that were previously not annotated. In one application, NORSnet revealed previously undetected unstructured regions in putative targets for structural genomics and may thereby contribute to increasing structural coverage of large eukaryotic families. NORSnet found unstructured regions more often in domain boundaries than expected at random. In another application, we estimated that 50%-70% of all worm proteins observed to have more than seven protein-protein interaction partners have unstructured regions. The comparative analysis between NORSnet and DISOPRED2 suggested that long

  13. OsbHLH148, a basic helix-loop-helix protein, interacts with OsJAZ proteins in a jasmonate signaling pathway leading to drought tolerance in rice.

    Science.gov (United States)

    Seo, Ju-Seok; Joo, Joungsu; Kim, Min-Jeong; Kim, Yeon-Ki; Nahm, Baek Hie; Song, Sang Ik; Cheong, Jong-Joo; Lee, Jong Seob; Kim, Ju-Kon; Choi, Yang Do

    2011-03-01

    Jasmonates play important roles in development, stress responses and defense in plants. Here, we report the results of a study using a functional genomics approach that identified a rice basic helix-loop-helix domain gene, OsbHLH148, that conferred drought tolerance as a component of the jasmonate signaling module in rice. OsbHLH148 transcript levels were rapidly increased by treatment with methyl jasmonate (MeJA) or abscisic acid, and abiotic stresses including dehydration, high salinity, low temperature and wounding. Transgenic over-expression of OsbHLH148 in rice confers plant tolerance to drought stress. Expression profiling followed by DNA microarray and RNA gel-blot analyses of transgenic versus wild-type rice identified genes that are up-regulated by OsbHLH148 over-expression. These include OsDREB and OsJAZ genes that are involved in stress responses and the jasmonate signaling pathway, respectively. OsJAZ1, a rice ZIM domain protein, interacted with OsbHLH148 in yeast two-hybrid and pull-down assays, but it interacted with the putative OsCOI1 only in the presence of coronatine. Furthermore, the OsJAZ1 protein was degraded by rice and Arabidopsis extracts in the presence of coronatine, and its degradation was inhibited by MG132, a 26S proteasome inhibitor, suggesting 26S proteasome-mediated degradation of OsJAZ1 via the SCF(OsCOI1) complex. The transcription level of OsJAZ1 increased upon exposure of rice to MeJA. These results show that OsJAZ1 could act as a transcriptional regulator of the OsbHLH148-related jasmonate signaling pathway leading to drought tolerance. Thus, our study suggests that OsbHLH148 acts on an initial response of jasmonate-regulated gene expression toward drought tolerance, constituting the OsbHLH148-OsJAZ-OsCOI1 signaling module in rice.

  14. SIRT1 Promotes N-Myc Oncogenesis through a Positive Feedback Loop Involving the Effects of MKP3 and ERK on N-Myc Protein Stability

    Science.gov (United States)

    Gherardi, Samuele; Scarlett, Christopher J.; Bedalov, Antonio; Xu, Ning; Iraci, Nuncio; Valli, Emanuele; Ling, Dora; Thomas, Wayne; van Bekkum, Margo; Sekyere, Eric; Jankowski, Kacper; Trahair, Toby; MacKenzie, Karen L.; Haber, Michelle; Norris, Murray D.; Biankin, Andrew V.; Perini, Giovanni; Liu, Tao

    2011-01-01

    The N-Myc oncoprotein is a critical factor in neuroblastoma tumorigenesis which requires additional mechanisms converting a low-level to a high-level N-Myc expression. N-Myc protein is stabilized when phosphorylated at Serine 62 by phosphorylated ERK protein. Here we describe a novel positive feedback loop whereby N-Myc directly induced the transcription of the class III histone deacetylase SIRT1, which in turn increased N-Myc protein stability. SIRT1 binds to Myc Box I domain of N-Myc protein to form a novel transcriptional repressor complex at gene promoter of mitogen-activated protein kinase phosphatase 3 (MKP3), leading to transcriptional repression of MKP3, ERK protein phosphorylation, N-Myc protein phosphorylation at Serine 62, and N-Myc protein stabilization. Importantly, SIRT1 was up-regulated, MKP3 down-regulated, in pre-cancerous cells, and preventative treatment with the SIRT1 inhibitor Cambinol reduced tumorigenesis in TH-MYCN transgenic mice. Our data demonstrate the important roles of SIRT1 in N-Myc oncogenesis and SIRT1 inhibitors in the prevention and therapy of N-Myc–induced neuroblastoma. PMID:21698133

  15. Pentacam-based phototherapeutic keratectomy outcome in superficial corneal opacities

    Directory of Open Access Journals (Sweden)

    Rashad MA

    2012-06-01

    Full Text Available Mohammad A RashadOphthalmology Department, Faculty of Medicine, Ain Shams University, Cairo, EgyptPurpose: This study aimed to evaluate the effectiveness of phototherapeutic keratectomy (PTK as an alternative treatment to keratoplasty using the Pentacam to assess depth of dense opacities.Methodology: PTK was performed in eleven eyes of ten patients with superficial corneal opacities after assessment by Scheimpflug images of the Pentacam for central corneal thickness (CCT and opacity level and depth.Results: The best-corrected spectacle visual acuity (BCSVA significantly improved. The preoperative mean logMAR was 0.85 (0.14 decimal equivalent, 6/42 Snellen's equivalent, and the final postoperative mean logMAR was 0.58 (0.26 decimal equivalent, 6/23 Snellen's equivalent. The mean preoperative CCT was 465.64 ± 71.94 µm. The mean programmed ablation depth was 142.09 ± 47.58 µm. The programmed ablation depth was correlated to mean logMAR early (1 month and not correlated later (6 months. None of the eyes lost lines of BCSVA or developed serious complications, such as keratectasia, delayed epithelialization, or corneal melting.Conclusion: Corneal scars extending beyond the anterior one-fifth of the cornea can be treated safely and effectively by PTK due to the smoothing effect, with reduction of the cylinder rather than complete opacity removal. This can decrease the need for keratoplasty.Keywords: phototherapeutic keratectomy, PTK, corneal opacities, Pentacam

  16. General anesthetic action at an internal protein site involving the S4-S5 cytoplasmic loop of a neuronal K(+) channel.

    Science.gov (United States)

    Harris, T; Shahidullah, M; Ellingson, J S; Covarrubias, M

    2000-02-18

    The structural bases of general anesthetic action on a neuronal K(+) channel were investigated using the series of homologous 1-alkanols, electrophysiology, and mutational analysis. Domain swapping between dShaw2 (alkanol-sensitive) and hKv3.4 (alkanol-resistant) and site-directed mutagenesis demonstrated that a 13-amino acid cytoplasmic loop (S4-S5) determines the selective inhibition of native dShaw2 channels by 1-alkanols. The S4-S5 loop may contribute to a receptor for both 1-alkanols and the inactivation particle, because the enhanced 1-alkanol sensitivity of hKv3.4 channels hosting S4-S5 mutations correlates directly with disrupted channel inactivation. Evidence of a discrete protein site was also obtained from the analysis of the relationship between potency and alkyl chain length, which begins to level off after 1-hexanol. Rapid application to the cytoplasmic side of inside-out membrane patches shows that the interaction between dShaw2 channels and 1-alkanols equilibrates in 1000-fold slower when the drug is applied externally to outside-out membrane patches. The data strongly favor a mechanism of inhibition involving a discrete internal site for 1-alkanols in dShaw2 K(+) channels. A new working hypothesis proposes that 1-alkanols lock dShaw2 channels in their closed conformation by a direct interaction at a crevice formed by the S4-S5 loop.

  17. Loss of the histone pre-mRNA processing factor stem-loop binding protein in Drosophila causes genomic instability and impaired cellular proliferation.

    Directory of Open Access Journals (Sweden)

    Harmony R Salzler

    Full Text Available BACKGROUND: Metazoan replication-dependent histone mRNAs terminate in a conserved stem-loop structure rather than a polyA tail. Formation of this unique mRNA 3' end requires Stem-loop Binding Protein (SLBP, which directly binds histone pre-mRNA and stimulates 3' end processing. The 3' end stem-loop is necessary for all aspects of histone mRNA metabolism, including replication coupling, but its importance to organism fitness and genome maintenance in vivo have not been characterized. METHODOLOGY/PRINCIPAL FINDINGS: In Drosophila, disruption of the Slbp gene prevents normal histone pre-mRNA processing and causes histone pre-mRNAs to utilize the canonical 3' end processing pathway, resulting in polyadenylated histone mRNAs that are no longer properly regulated. Here we show that Slbp mutants display genomic instability, including loss of heterozygosity (LOH, increased presence of chromosome breaks, tetraploidy, and changes in position effect variegation (PEV. During imaginal disc growth, Slbp mutant cells show defects in S phase and proliferate more slowly than control cells. CONCLUSIONS/SIGNIFICANCE: These data are consistent with a model in which changing the 3' end of histone mRNA disrupts normal replication-coupled histone mRNA biosynthesis and alters chromatin assembly, resulting in genomic instability, inhibition of cell proliferation, and impaired development.

  18. 225 GHz Atmospheric Opacity Measurements from Two Arctic Sites

    CERN Document Server

    Matsushita, S; Martin-Cocher, P; Asada, K; Chen, C -P; Inoue, M; Paine, S; Turner, D; Steinbring, E

    2012-01-01

    We report the latest results of 225 GHz atmospheric opacity measurements from two arctic sites; one on high coastal terrain near the Eureka weather station, on Ellesmere Island, Canada, and the other at the Summit Station near the peak of the Greenland icecap. This is a campaign to search for a site to deploy a new telescope for submillimeter Very Long Baseline Interferometry and THz astronomy in the northern hemisphere. Since 2011, we have obtained 3 months of winter data near Eureka, and about one year of data at the Summit Station. The results indicate that these sites offer a highly transparent atmosphere for observations in submillimeter wavelengths. The Summit Station is particularly excellent, and its zenith opacity at 225 GHz is statistically similar to the Atacama Large Milllimeter/submillimeter Array in Chile. In winter, the opacity at the Summit Station is even comparable to that observed at the South Pole.

  19. Age of old objects constraints on cosmic opacity

    CERN Document Server

    Holanda, R F L; Dantas, M A

    2016-01-01

    In this paper, it is proposed a cosmological model independent method to constrain the cosmic opacity. As an approach never seen before in literature, we use the ages of 32 old passive galaxies distributed over the redshift interval $0.11 < z < 1.84$ and of 9 extremely old globular clusters in M31 galaxy to obtain opacity free luminosity distance. By comparing them to the 580 distance moduli of supernovae from the so-called Union 2.1 compilation we put limits on the cosmic opacity parametrized by $\\tau(z) = \\epsilon z/(1+z)$ (for $\\epsilon =0$ the transparent universe is recovered). Considering the cosmic background radiation constraints on the spatial curvature of the Universe no significant deviation from transparency is verified.

  20. Design And First Use of the NIF Opacity Spectrometer

    Science.gov (United States)

    King, J. A.; Ross, P. W.; Huffman, E. J.; Opachich, Y. P.; Heeter, R. F.; Ahmed, M.; Liedahl, D. A.; Schneider, M. B.; Dodd, E.; Flippo, K. A.; Kline, J. L.; Lopez, F. E.; Archuleta, T. N.; Perry, T. S.

    2016-10-01

    Recent experiments at the Sandia Z facility have raised questions about models used in calculating L-shell opacities of mid-Z elements. A platform is being developed to check these results at the National Ignition Facility (NIF). The NIF experiments require a new X-ray opacity spectrometer (OpSpec) for the iron L-shell X-ray band, spanning photon energies from 540 eV - 2100 eV with a resolving power E/ ΔE >700. The design of the OpSpec and photometric calculations based on expected opacity data are also presented. First use on NIF is expected in September 2016. This work was performed by National Security Technologies, LLC, under Contract No. DE-AC52-06NA25946 with the U.S. Department of Energy. DOE/NV/25946-2891.

  1. Infrared Opacities in Dense Atmospheres of Cool White Dwarf Stars

    CERN Document Server

    Kowalski, Piotr M; Dufour, Patrick

    2016-01-01

    Dense, He-rich atmospheres of cool white dwarfs represent a challenge to the modeling. This is because these atmospheres are constituted of a dense fluid in which strong multi-atomic interactions determine their physics and chemistry. Therefore, the ideal-gas-based description of absorption is no longer adequate, which makes the opacities of these atmospheres difficult to model. This is illustrated with severe problems in fitting the spectra of cool, He-rich stars. Good description of the infrared (IR) opacity is essential for proper assignment of the atmospheric parameters of these stars. Using methods of computational quantum chemistry we simulate the IR absorption of dense He/H media. We found a significant IR absorption from He atoms (He-He-He CIA opacity) and a strong pressure distortion of the H$_2$-He collision-induced absorption (CIA). We discuss the implication of these results for interpretation of the spectra of cool stars.

  2. Fractal Particles: Titan's Thermal Structure and IR Opacity

    Science.gov (United States)

    McKay, C. P.; Rannou, P.; Guez, L.; Young, E. F.; DeVincenzi, Donald (Technical Monitor)

    1998-01-01

    Titan's haze particles are the principle opacity at solar wavelengths. Most past work in modeling these particles has assumed spherical particles. However, observational evidence strongly favors fractal shapes for the haze particles. We consider the implications of fractal particles for the thermal structure and near infrared opacity of Titan's atmosphere. We find that assuming fractal particles with the optical properties based on laboratory tholin material and with a production rate that allows for a match to the geometric albedo results in warmer troposphere and surface temperatures compared to spherical particles. In the near infrared (1-3 microns) the predicted opacity of the fractal particles is up to a factor of two less than for spherical particles. This has implications for the ability of Cassini to image Titan's surface at 1 micron.

  3. Infrared Opacities in Dense Atmospheres of Cool White Dwarf Stars

    Science.gov (United States)

    Kowalski, P. M.; Blouin, S.; Dufour, P.

    2017-03-01

    Dense, He-rich atmospheres of cool white dwarfs represent a challenge to the modeling. This is because these atmospheres are constituted of a dense fluid in which strong multi-atomic interactions determine their physics and chemistry. Therefore, the ideal-gas-based description of absorption is no longer adequate, which makes the opacities of these atmospheres difficult to model. This is illustrated with severe problems in fitting the spectra of cool, He-rich stars. Good description of the infrared (IR) opacity is essential for proper assignment of the atmospheric parameters of these stars. Using methods of computational quantum chemistry we simulate the IR absorption of dense He/H media. We found a significant IR absorption from He atoms (He-He-He CIA opacity) and a strong pressure distortion of the H2-He collision-induced absorption (CIA). We discuss the implication of these results for the interpretation of the spectra of cool stars.

  4. Verification of Opacity and Diagnosability for Pushdown Systems

    Directory of Open Access Journals (Sweden)

    Koichi Kobayashi

    2013-01-01

    Full Text Available In control theory of discrete event systems (DESs, one of the challenging topics is the extension of theory of finite-state DESs to that of infinite-state DESs. In this paper, we discuss verification of opacity and diagnosability for infinite-state DESs modeled by pushdown automata (called here pushdown systems. First, we discuss opacity of pushdown systems and prove that opacity of pushdown systems is in general undecidable. In addition, a decidable class is clarified. Next, in diagnosability, we prove that under a certain assumption, which is different from the assumption in the existing result, diagnosability of pushdown systems is decidable. Furthermore, a necessary condition and a sufficient condition using finite-state approximations are derived. Finally, as one of the applications, we consider data integration using XML (Extensible Markup Language. The obtained result is useful for developing control theory of infinite-state DESs.

  5. Measuring the opacity of stellar interior matter in terrestrial laboratories

    Science.gov (United States)

    Bailey, James

    2015-11-01

    How does energy propagate from the core to the surface of the Sun, where it emerges to warm the Earth? Nearly a century ago Eddington recognized that the attenuation of radiation by stellar matter controls the internal structure of stars like the sun. Opacities for high energy density (HED) matter are challenging to calculate because accurate and complete descriptions of the energy levels, populations, and plasma effects such as continuum lowering and line broadening are needed for partially ionized atoms. This requires approximations, in part because billions of bound-bound and bound-free electronic transitions can contribute to the opacity. Opacity calculations, however, have never been benchmarked against laboratory measurements at stellar interior conditions. Laboratory opacity measurements were limited in the past by the challenges of creating and diagnosing sufficiently large and uniform samples at the extreme conditions found inside stars. In research conducted over more than 10 years, we developed an experimental platform on the Z facility and measured wavelength-resolved iron opacity at electron temperatures Te = 156-195 eV and densities ne = 0.7-4.0 x 1022 cm-3 - conditions very similar to the radiation/convection boundary zone within the Sun. The wavelength-dependent opacity in the 975-1775 eV photon energy range is 30-400% higher than models predict. This raises questions about how well we understand the behavior of atoms in HED plasma. These measurements may also help resolve decade-old discrepancies between solar model predictions and helioseismic observations. This talk will provide an overview of the measurements, investigations of possible errors, and ongoing experiments aimed at testing hypotheses to resolve the model-data discrepancy. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy under contract DE-AC04-94AL85000.

  6. FTS Measurements of Submillimeter-Wave Atmospheric Opacity at Pampa la Bola: III. Water Vapor, Liquid Water, and 183GHz Water Vapor Line Opacities

    Science.gov (United States)

    Matsushita, Satoki; Matsuo, Hiroshi

    2003-02-01

    Further analysis has been made on the millimeter- and submillimeter-wave (100-1600GHz or 3mm-188 μm) atmospheric opacity data taken with the Fourier Transform Spectrometer (FTS) at Pampa la Bola, 4800 m above the sea level in northern Chile, which is the site of the Atacama Large Millimeter/submillimeter Array (ALMA). Time-sequence plots of millimeter- and submillimeter-wave opacities show similar variations to each other, except for during the periods with liquid water (fog or clouds) in the atmosphere. Using millimeter- and submillimeter-wave opacity correlations under two conditions, which are affected and not affected by liquid water, we succeeded to separate the measured opacity into water vapor and liquid water opacity components. The water vapor opacity shows a good correlation with the 183GHz water vapor line opacity, which is also covered in the measured spectra. On the other hand, the liquid water opacity and the 183GHz line opacity show no correlation. S ince only the water vapor component is expected to affect the phase of interferometers significantly, and the submillimeter-wave opacity is less affected by the liquid water component, it may be possible to use the submillimeter-wave opacity for a phase correction of submillimeter interferometers.

  7. The Non-local Thermodynamical Equilibrium Effects on Opacity

    Institute of Scientific and Technical Information of China (English)

    WU Ze-Qing; ZHANG Ben-Ai; QIU Yu-Bo

    2001-01-01

    Based on the detailed configuration accounting (DCA) model, a method is developed to include the resonant photoionization and the excitation-autoionization in the non-local thermodynamical equilibrium (NLTE) average atom(AA) model. Using this new model, the mean charge states and the opacity are calculated for NLTE high-Z plasmas and compared with other results. The agreement w ith AA model is poor at low electron density. The present results agree well with those of DCA model within 10%. The calculations show that the NLTE effects on opacity are strong.

  8. Model-independent constraints on the cosmic opacity

    CERN Document Server

    Holanda, R F L; Alcaniz, J S

    2012-01-01

    We use current measurements of the expansion rate $H(z)$ and cosmic background radiation bounds on the spatial curvature of the Universe to impose cosmological model-independent constraints on cosmic opacity. To perform our analyses, we compare opacity-free distance modulus from $H(z)$ data with those from two supernovae Ia compilations, namely, the Union2 and Sloan Digital Sky Survey samples. The influence of different SNe Ia light-curve fitters (SALT2 and MLCS2K2) on the results is also discussed. We find that these fitters present a significant conflict, with the MLCS2K2 method being incompatible with a flat and transparent universe.

  9. Ultra-dense Hot Low Z Line Transition Opacity Simulations

    Science.gov (United States)

    Sauvan, P.; Mínguez, E.; Gil, J. M.; Rodríguez, R.; Rubiano, J. G.; Martel, P.; Angelo, P.; Schott, R.; Philippe, F.; Leboucher-Dalimier, E.; Mancini, R.; Calisti, A.

    2002-12-01

    In this work two atomic physics models (the IDEFIX code using the dicenter model and the code based on parametric potentials ANALOP) have been used to calculate the opacities for bound-bound transitions in hot ultra-dense, low Z plasmas. These simulations are in connection with experiments carried out at LULI during the last two years, focused on bound-bound radiation. In this paper H-like opacities for aluminum and fluorine plasmas have been simulated, using both theoretical models, in a wide range of densities and temperatures higher than 200 eV.

  10. Streptomycin affinity depends on 13 amino acids forming a loop in homology modelled ribosomal S12 protein (rpsL gene) of Lysinibacillus sphaericus DSLS5 associated with marine sponge (Tedania anhelans).

    Science.gov (United States)

    Suriyanarayanan, Balasubramanian; Lakshmi, Praveena Pothuraju; Santhosh, Ramachandran Sarojini; Dhevendaran, Kandasamy; Priya, Balakrishnan; Krishna, Shivaani

    2016-06-01

    Streptomycin, an antibiotic used against microbial infections, inhibits the protein synthesis by binding to ribosomal protein S12, encoded by rpsL12 gene, and associated mutations cause streptomycin resistance. A streptomycin resistant, Lysinibacillus sphaericus DSLS5 (MIC >300 µg/mL for streptomycin), was isolated from a marine sponge (Tedania anhelans). The characterisation of rpsL12 gene showed a region having similarity to long terminal repeat sequences of murine lukemia virus which added 13 amino acids for loop formation in RpsL12; in addition, a K56R mutation which corresponds to K43R mutation present in streptomycin-resistant Escherichia coli is also present. The RpsL12 protein was modelled and compared with that of Lysinibacillus boronitolerans, Escherichia coli and Mycobacterium tuberculosis. The modelled proteins docked with streptomycin indicate compound had less affinity. The effect of loop on streptomycin resistance was analysed by constructing three different models of RpsL12 by, (i) removing both loop and mutation, (ii) removing the loop alone while retaining the mutation and (iii) without mutation having loop. The results showed that the presence of loop causes streptomycin resistance (decreases the affinity), and it further enhanced in the presence of mutation at 56th codon. Further study will help in understanding the evolution of streptomycin resistance in organisms.

  11. 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.

    Science.gov (United States)

    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.

  12. Stepwise assembly of multiple Lin28 proteins on the terminal loop of let-7 miRNA precursors.

    Science.gov (United States)

    Desjardins, Alexandre; Bouvette, Jonathan; Legault, Pascale

    2014-04-01

    Lin28 inhibits the biogenesis of let-7 miRNAs through direct interactions with let-7 precursors. Previous studies have described seemingly inconsistent Lin28 binding sites on pre-let-7 RNAs. Here, we reconcile these data by examining the binding mechanism of Lin28 to the terminal loop of pre-let-7g (TL-let-7g) using biochemical and biophysical methods. First, we investigate Lin28 binding to TL-let-7g variants and short RNA fragments and identify three independent binding sites for Lin28 on TL-let-7g. We then determine that Lin28 assembles in a stepwise manner on TL-let-7g to form a stable 1:3 complex. We show that the cold-shock domain (CSD) of Lin28 is responsible for remodelling the terminal loop of TL-let-7g, whereas the NCp7-like domain facilitates the initial binding of Lin28 to TL-let-7g. This stable binding of multiple Lin28 molecules to the terminal loop of pre-let-7g extends to other precursors of the let-7 family, but not to other pre-miRNAs tested. We propose a model for stepwise assembly of the 1:1, 1:2 and 1:3 pre-let-7g/Lin28 complexes. Stepwise multimerization of Lin28 on pre-let-7 is required for maximum inhibition of Dicer cleavage for a least one member of the let-7 family and may be important for orchestrating the activity of the several factors that regulate let-7 biogenesis.

  13. FIRST NEW SOLAR MODELS WITH OPAS OPACITY TABLES

    Energy Technology Data Exchange (ETDEWEB)

    Le Pennec, M.; Turck-Chièze, S.; Salmon, S. [CEA/IRFU/Service d’Astrophysique, CE Saclay, F-91191 Gif sur Yvette (France); Blancard, C.; Cossé, P.; Faussurier, G.; Mondet, G. [CEA, DAM, DIF, F-91297 Arpajon (France)

    2015-11-10

    Stellar seismology appears more and more as a powerful tool for a better determination of the fundamental properties of solar-type stars. However, the particular case of the Sun is still challenging. For about a decade now, the helioseismic sound-speed determination has continued to disagree with the standard solar model (SSM) prediction, questioning the reliability of this model. One of the sources of uncertainty could be in the treatment of the transport of radiation from the solar core to the surface. In this Letter, we use the new OPAS opacity tables, recently available for solar modeling, to address this issue. We discuss first the peculiarities of these tables, then we quantify their impact on the solar sound-speed and density profiles using the reduced OPAS tables taken on the grids of the OPAL ones. We use the two evolution codes, Modules for Experiments in Stellar Astrophysics and Code Liégeois d’Evolution Stellaire, that led to similar conclusions in the solar radiative zone. In comparison to commonly used OPAL opacity tables, the new solar models are computed for the most recent photospheric composition with OPAS tables and present improvements to the location of the base of the convective zone and to the description of the solar radiative zone in comparison to the helioseismic observations, even if the differences in the Rosseland mean opacity do not exceed 6%. We finally carry out a comparison to a solar model computed with the OP opacity tables.

  14. Design Parameter Studies of Emission-Based Iron Opacity Measurements

    Science.gov (United States)

    Martin, Madison E.; London, Richard A.; Goluoglu, Sedat; Whitley, Heather D.

    2016-10-01

    Opacity is a critical parameter in the transport of radiation in systems such as inertial confinement fusion capsules and stars. The resolution of current disagreements between solar models and helioseismological observations would benefit from experimental validation of theoretical opacity models. Short pulse lasers can be used to heat targets to higher temperatures and densities than long pulse lasers and pulsed power machines, thus potentially enabling access to x-ray emission spectra at conditions relevant to solar models. The radiation-hydrodynamic code HYDRA is used to investigate the effects of modifying laser energy, laser pulse length, and target dimensions on the plasma conditions, x-ray emission, and inferred opacity of a buried layer iron target. The accuracy of the opacity inference is sensitive to tamper emission and optical depth effects. An example design that reaches temperatures and densities relevant to the radiative zone of the sun while reducing optical depth and tamper emission effects will be discussed. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. Lawrence Livermore National Security, LLC.

  15. 40 CFR 75.14 - Specific provisions for monitoring opacity.

    Science.gov (United States)

    2010-07-01

    ... calendar year. (d) Diesel-fired units and dual-fuel reciprocating engine units. The owner or operator of an affected diesel-fired unit or a dual-fuel reciprocating engine unit is exempt from the opacity monitoring... unit by changing its fuel mix, the owner or operator shall install, operate, and certify a continuous...

  16. The fog of change : opacity and asperity in organizations.

    OpenAIRE

    Hannan, M.T.; Pólos, L.; Carroll, G.R.

    2003-01-01

    Initial architectural change in organizations often induces other subsequent changes, generating lengthy cascades of changes in subordinate units. This article extends a formal model of cascading organizational change by examining the implications for organizational change of the limited foresight of those who initiate such change about unit interconnections (structural opacity) and the normative restrictiveness imposed on architectural features by organizational culture (cultural asperity). ...

  17. FTS measurements of submillimeter-wave opacity at Pampa la Bola

    Science.gov (United States)

    Matsuo, Hiroshi; Sakamoto, Akihiro; Matsushita, Satoki

    1998-07-01

    The first measurement of submillimeter-wave atmospheric opacity spectra at the Pampa la Bola site (Northern Chile, Atacama 4800 m altitude) has been performed during the winter season using a Fourier transform spectrometer (FTS). Atmospheric emission spectra, as a function of airmass, were measured under various weather conditions. Atmospheric opacity was evaluated from sky temperature at zenith as well as from tipping measurements, which are independent measure but give consistent results. The FTS opacity measurements also show good match with 220 GHz radiometer measurements. Correlations between millimeter-wave and submillimeter-wave opacities get worse when 220 GHz opacity is larger than 0.1. Deviations from the opacity correlation at each frequency show good correlations themselves but have different relative variations at each frequency. This indicates that atmospheric transparency cannot be characterized only by millimeter-wave opacity buy requires simultaneous opacity measurements at millimeter and submillimeter-wavelengths.

  18. Loop-to-loop coupling.

    Energy Technology Data Exchange (ETDEWEB)

    Warne, Larry Kevin; Lucero, Larry Martin; Langston, William L.; Salazar, Robert Austin; Coleman, Phillip Dale; Basilio, Lorena I.; Bacon, Larry Donald

    2012-05-01

    This report estimates inductively-coupled energy to a low-impedance load in a loop-to-loop arrangement. Both analytical models and full-wave numerical simulations are used and the resulting fields, coupled powers and energies are compared. The energies are simply estimated from the coupled powers through approximations to the energy theorem. The transmitter loop is taken to be either a circular geometry or a rectangular-loop (stripline-type) geometry that was used in an experimental setup. Simple magnetic field models are constructed and used to estimate the mutual inductance to the receiving loop, which is taken to be circular with one or several turns. Circuit elements are estimated and used to determine the coupled current and power (an equivalent antenna picture is also given). These results are compared to an electromagnetic simulation of the transmitter geometry. Simple approximate relations are also given to estimate coupled energy from the power. The effect of additional loads in the form of attached leads, forming transmission lines, are considered. The results are summarized in a set of susceptibility-type curves. Finally, we also consider drives to the cables themselves and the resulting common-to-differential mode currents in the load.

  19. On the Blue Loops of Intermediate-Mass Stars

    CERN Document Server

    Walmswell, J J; Eldridge, J J

    2015-01-01

    We consider the blue loops in the Hertzsprung-Russell diagram that occur when intermediate-mass stars begin core helium burning. It has long been known that the excess of helium above the burning shell, the result of the contraction of the convective core during core hydrogen burning, has the effect of making such stars redder and larger than they would be otherwise. The outward motion of the burning shell in mass removes this excess and triggers the loop. Hitherto nobody has attempted to demonstrate why the excess helium has this effect. We consider the effect of the local opacity, which is reduced by excess helium, the shell fuel supply, which is also reduced, and the local mean molecular weight, which is increased. We demonstrate that the mean molecular weight is the decisive reddening factor. The opacity has a much smaller effect and a reduced fuel supply actually favours blueward motion.

  20. Roles of the protruding loop of factor B essential for the localization of lipoproteins (LolB) in the anchoring of bacterial triacylated proteins to the outer membrane.

    Science.gov (United States)

    Hayashi, Yumi; Tsurumizu, Ryoji; Tsukahara, Jun; Takeda, Kazuki; Narita, Shin-ichiro; Mori, Makiko; Miki, Kunio; Tokuda, Hajime

    2014-04-11

    The Lol system comprising five Lol proteins, LolA through LolE, sorts Escherichia coli lipoproteins to outer membranes. The LolCDE complex, an ATP binding cassette transporter in inner membranes, releases outer membrane-specific lipoproteins in an ATP-dependent manner, causing formation of the LolA-lipoprotein complex in the periplasm. LolA transports lipoproteins through the periplasm to LolB on outer membranes. LolB is itself a lipoprotein anchored to outer membranes, although the membrane anchor is functionally dispensable. LolB then localizes lipoproteins to outer membranes through largely unknown mechanisms. The crystal structure of LolB is similar to that of LolA, and it possesses a hydrophobic cavity that accommodates acyl chains of lipoproteins. To elucidate the molecular function of LolB, a periplasmic version of LolB, mLolB, was mutagenized at various conserved residues. Despite the lack of acyl chains, most defective mutants were insoluble. However, a derivative with glutamate in place of leucine 68 was soluble and unable to localize lipoproteins to outer membranes. This leucine is present in a loop protruding from mLolB into an aqueous environment, and no analogous loop is present in LolA. Thus, leucine 68 was replaced with other residues. Replacement by acidic, but not hydrophobic, residues generated for the first time mLolB derivatives that can accept but cannot localize lipoproteins to outer membranes. Moreover, deletion of the leucine with neighboring residues impaired the lipoprotein receptor activity. Based on these observations, the roles of the protruding loop of LolB in the last step of lipoprotein sorting are discussed.

  1. 77 FR 13997 - Quality Assurance Requirements for Continuous Opacity Monitoring Systems at Stationary Sources

    Science.gov (United States)

    2012-03-08

    ... AGENCY 40 CFR Part 60 RIN 2060-AH23 Quality Assurance Requirements for Continuous Opacity Monitoring... rule titled, ``Quality Assurance Requirements for Continuous Opacity Monitoring Systems at Stationary....regulations.gov or in hard copy at the Procedure 3--Quality Assurance Requirements for Continuous Opacity...

  2. Elevated endogenous expression of the dominant negative basic helix-loop-helix protein ID1 correlates with significant centrosome abnormalities in human tumor cells

    Directory of Open Access Journals (Sweden)

    Gutmann Anja

    2010-01-01

    Full Text Available Abstract Background ID proteins are dominant negative inhibitors of basic helix-loop-helix transcription factors that have multiple functions during development and cellular differentiation. Ectopic (over-expression of ID1 extends the lifespan of primary human epithelial cells. High expression levels of ID1 have been detected in multiple human malignancies, and in some have been correlated with unfavorable clinical prognosis. ID1 protein is localized at the centrosomes and forced (over-expression of ID1 results in errors during centrosome duplication. Results Here we analyzed the steady state expression levels of the four ID-proteins in 18 tumor cell lines and assessed the number of centrosome abnormalities. While expression of ID1, ID2, and ID3 was detected, we failed to detect protein expression of ID4. Expression of ID1 correlated with increased supernumerary centrosomes in most cell lines analyzed. Conclusions This is the first report that shows that not only ectopic expression in tissue culture but endogenous levels of ID1 modulate centrosome numbers. Thus, our findings support the hypothesis that ID1 interferes with centrosome homeostasis, most likely contributing to genomic instability and associated tumor aggressiveness.

  3. EVIDENCE FOR ENVIRONMENTAL CHANGES IN THE SUBMILLIMETER DUST OPACITY

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Peter G.; Roy, Arabindo; Miville-Deschenes, Marc-Antoine [Canadian Institute for Theoretical Astrophysics, University of Toronto, 60 St. George Street, Toronto, ON M5S 3H8 (Canada); Bontemps, Sylvain [Observatoire de Bordeaux, BP 89, F-33270 Floirac (France); Ade, Peter A. R.; Griffin, Matthew; Hargrave, Peter C.; Mauskopf, Philip [Department of Physics and Astronomy, Cardiff University, 5 The Parade, Cardiff, CF24 3AA (United Kingdom); Bock, James J. [Jet Propulsion Laboratory, Pasadena, CA 91109-8099 (United States); Chapin, Edward L.; Halpern, Mark; Marsden, Gaelen [Department of Physics and Astronomy, University of British Columbia, 6224 Agricultural Road, Vancouver, BC V6T 1Z1 (Canada); Devlin, Mark J.; Dicker, Simon R.; Klein, Jeff [Department of Physics and Astronomy, University of Pennsylvania, 209 South 33rd Street, Philadelphia, PA 19104 (United States); Gundersen, Joshua O. [Department of Physics, University of Miami, 1320 Campo Sano Drive, Carol Gables, FL 33146 (United States); Hughes, David H. [Instituto Nacional de Astrofisica Optica y Electronica (INAOE), Aptdo. Postal 51 y 72000 Puebla (Mexico); Netterfield, Calvin B. [Department of Astronomy and Astrophysics, University of Toronto, 50 St. George Street, Toronto, ON M5S 3H4 (Canada); Olmi, Luca [INAF, Osservatorio Astrofisico di Arcetri, Largo E. Fermi 5, I-50125 (Italy); Patanchon, Guillaume [Laboratoire APC, 10, rue Alice Domon et Leonie Duquet F-75205 Paris (France); and others

    2012-05-20

    The submillimeter opacity of dust in the diffuse interstellar medium (ISM) in the Galactic plane has been quantified using a pixel-by-pixel correlation of images of continuum emission with a proxy for column density. We used multi-wavelength continuum data: three Balloon-borne Large Aperture Submillimeter Telescope bands at 250, 350, and 500 {mu}m and one IRAS band at 100 {mu}m. The proxy is the near-infrared color excess, E(J - K{sub s}), obtained from the Two Micron All Sky Survey. Based on observations of stars, we show how well this color excess is correlated with the total hydrogen column density for regions of moderate extinction. The ratio of emission to column density, the emissivity, is then known from the correlations, as a function of frequency. The spectral distribution of this emissivity can be fit by a modified blackbody, whence the characteristic dust temperature T and the desired opacity {sigma}{sub e}(1200) at 1200 GHz or 250 {mu}m can be obtained. We have analyzed 14 regions near the Galactic plane toward the Vela molecular cloud, mostly selected to avoid regions of high column density (N{sub H} > 10{sup 22} cm{sup -2}) and small enough to ensure a uniform dust temperature. We find {sigma}{sub e}(1200) is typically (2-4) Multiplication-Sign 10{sup -25} cm{sup 2} H{sup -1} and thus about 2-4 times larger than the average value in the local high Galactic latitude diffuse atomic ISM. This is strong evidence for grain evolution. There is a range in total power per H nucleon absorbed (and re-radiated) by the dust, reflecting changes in the strength of the interstellar radiation field and/or the dust absorption opacity. These changes in emission opacity and power affect the equilibrium T, which is typically 15 K, colder than at high latitudes. Our analysis extends, to higher opacity and lower temperature, the trend of increasing {sigma}{sub e}(1200) with decreasing T that was found at high latitudes. The recognition of changes in the emission opacity

  4. Crystallographic and molecular dynamics analysis of loop motions unmasking the peptidoglycan-binding site in stator protein MotB of flagellar motor.

    Directory of Open Access Journals (Sweden)

    Cyril F Reboul

    Full Text Available BACKGROUND: The C-terminal domain of MotB (MotB-C shows high sequence similarity to outer membrane protein A and related peptidoglycan (PG-binding proteins. It is believed to anchor the power-generating MotA/MotB stator unit of the bacterial flagellar motor to the peptidoglycan layer of the cell wall. We previously reported the first crystal structure of this domain and made a puzzling observation that all conserved residues that are thought to be essential for PG recognition are buried and inaccessible in the crystal structure. In this study, we tested a hypothesis that peptidoglycan binding is preceded by, or accompanied by, some structural reorganization that exposes the key conserved residues. METHODOLOGY/PRINCIPAL FINDINGS: We determined the structure of a new crystalline form (Form B of Helicobacter pylori MotB-C. Comparisons with the existing Form A revealed conformational variations in the petal-like loops around the carbohydrate binding site near one end of the β-sheet. These variations are thought to reflect natural flexibility at this site required for insertion into the peptidoglycan mesh. In order to understand the nature of this flexibility we have performed molecular dynamics simulations of the MotB-C dimer. The results are consistent with the crystallographic data and provide evidence that the three loops move in a concerted fashion, exposing conserved MotB residues that have previously been implicated in binding of the peptide moiety of peptidoglycan. CONCLUSION/SIGNIFICANCE: Our structural analysis provides a new insight into the mechanism by which MotB inserts into the peptidoglycan mesh, thus anchoring the power-generating complex to the cell wall.

  5. Nuclear reaction rates and opacity in massive star evolution calculations

    Energy Technology Data Exchange (ETDEWEB)

    Bahena, D [Astronomical Institute of the Academy of Sciences, BocnI II 1401, 14131 Praha 4 (Czech Republic); Klapp, J [Instituto Nacional de Investigaciones Nucleares, Km. 36.5 Carr. Mexico-Toluca, 52750 Edo. de Mexico (Mexico); Dehnen, H, E-mail: jaime.klapp@inin.gob.m [Universitaet Konstanz, Fachbereich Physik, Fach M568, D-78457 Konstanz (Germany)

    2010-07-01

    Nuclear reaction rates and opacity are important parameters in stellar evolution. The input physics in a stellar evolution code determines the main theoretical characteristics of the stellar structure, evolution and nucleosynthesis of a star. For different input physics, in this work we calculate stellar evolution models of very massive first stars during the hydrogen and helium burning phases. We have considered 100 and 200M{sub s}un galactic and pregalactic stars with metallicity Z = 10{sup -6} and 10{sup 9}, respectively. The results show important differences from old to new formulations for the opacity and nuclear reaction rates, in particular the evolutionary tracks are significantly affected, that indicates the importance of using up to date and reliable input physics. The triple alpha reaction activates sooner for pregalactic than for galactic stars.

  6. Towards a new model of OPAC. From information to knowledge.

    Directory of Open Access Journals (Sweden)

    Antonella Iacono

    2013-07-01

    Full Text Available Il contributo analizza l’evoluzione dei cataloghi elettronici delle biblioteche alla luce delle nuove tecnologie del Web semantico e dei linked data. La trattazione è suddivisa in due parti distinte. In questa prima parte muovendo da un’analisi critica del modello funzionale degli ‘OPAC di nuova generazione’ e discovery tools si propone la necessità di una revisione del paradigma corrente di sviluppo che accogliendo le teorie dell’information behavior possa fondarsi sull'utente, sui suoi bisogni informativi, i suoi comportamenti e sull'analisi delle componenti che entrano in gioco nel processo di ricerca dell'informazione.Nella seconda parte, di prossima pubblicazione si è esplorerà la possibilità che i linked data possano essere la tecnologia più appropriata per la costruzione di nuovi OPAC basati sulla produzione di conoscenza all’interno del processo informativo. 

  7. Model-independent constraints on the cosmic opacity

    Energy Technology Data Exchange (ETDEWEB)

    Holanda, R.F.L. [Departamento de Física, Universidade Estadual da Paraíba, 58429-500, Campina Grande - PB (Brazil); Carvalho, J.C.; Alcaniz, J.S., E-mail: holanda@uepb.edu.br, E-mail: carvalho@dfte.ufrn.br, E-mail: alcaniz@on.br [Departamento de Astronomia, Observatório Nacional, 20921-400, Rio de Janeiro - RJ (Brazil)

    2013-04-01

    We use current measurements of the expansion rate H(z) and cosmic background radiation bounds on the spatial curvature of the Universe to impose cosmological model-independent constraints on cosmic opacity. To perform our analyses, we compare opacity-free distance modulus from H(z) data with those from two type Ia supernovae compilations, namely, the Union2.1 plus the most distant spectroscopically confirmed SNe Ia (SCP-0401 at z = 1.713) and two Sloan Digital Sky Survey (SDSS) subsamples. We find that a completely transparent universe is in full agreement with the Union 2.1 + SNe Ia SCP-0401 sample. For the SDSS compilations, such universe is compatible with observations at < 1.5σ level regardless the SNe Ia light-curve fitting used.

  8. Design of Initial Opacity Platform at the National Ignition Facility

    Science.gov (United States)

    Heeter, R. F.; Ahmed, M. F.; Ayers, S. L.; Emig, J. A.; Iglesias, C. A.; Liedahl, D. A.; Schneider, M. B.; Wilson, B. G.; Huffman, E. J.; King, J. A.; Opachich, Y. P.; Ross, P. W.; Bailey, J. E.; Rochau, G. A.; Craxton, R. S.; Garcia, E. M.; McKenty, P. W.; Zhang, R.; Cardenas, T.; Devolder, B. G.; Dodd, E. S.; Kline, J. L.; Sherrill, M. E.; Perry, T. S.

    2016-10-01

    The absorption and re-emission of x-rays by partly stripped ions plays a critical role in stars and in many laboratory plasmas. A NIF Opacity Platform has been designed to resolve a persistent disagreement between theory and experiments on the Sandia Z facility, studying iron in conditions closely related to the solar radiation-convection transition boundary. A laser heated hohlraum ``oven'' will produce iron plasmas at temperatures >150 eV and electron densities >=7x1021/cm3, and be probed with continuum X-rays from a capsule implosion backlighter source. The resulting X-ray transmission spectra will be recorded on a specially designed Opacity Spectrometer. This work was performed under the auspices of the U.S. Department of Energy by LLNL under Contract DE-AC52-07NA27344.

  9. Equation of state and opacities for warm dense matter

    Directory of Open Access Journals (Sweden)

    Cotelo Manuel

    2013-11-01

    Full Text Available This work presents recent developments in the calculation of opacity and equation of state tables suitable for including in the radiation hydrodynamic code ARWEN [1] to study processes like ICF or X-ray secondary sources. For these calculations we use the code bigbart to compute opacities in LTE conditions, with self-consistent data generated with the Flexible Atomic Code (FAC [2]. Non-LTE effects are approximately taken into account by means of the new RADIOM model developed in [3], which makes use of existing LTE data tables. We use the screened-hydrogenic model [4] to derive the Equation of State (EOS using the population and energy of each level.

  10. Skewed gas flow technology offers antidote to opacity derates

    Energy Technology Data Exchange (ETDEWEB)

    Boyd, M. [ATCO Power AB (Canada). Battle River Generating Station

    2001-06-01

    Deratings due to opacity problems at the Battle River Generating Station in Alberta, Canada led ATCO Power to evaluate and install skewed gas flow technology (SGFT) in one-half of the Unit 5 twin-casing electrostatic precipitator during the August 2000 outage. Preliminary operating results show that the modified casing produces opacity readings at the outlet 40% lower than those seen at the outlet of the unmodified casing. The dust loading tests indicate a 27.5% improvement in collector efficiency. This article includes a technical review and evaluation of Battle River's SGFT installation, as well as the rationale used to provide the initial economic justification. 3 figs., 1 tab., 1 photo.

  11. Opacity calculations for Non-Local-Thermodynamic-Equilibrium plasmas

    Institute of Scientific and Technical Information of China (English)

    PANG Jin-qiao; WU Ze-qing; YAN Jun; HAN Guo-xing

    2004-01-01

    In this paper, we presented a method to calculate the spectral-resolved opacity for Non-Local-Thermodynamic-Equilibrium (non-LTE) plasmas. By solving the rate equations, we get the population. In the rate equations, configuration-averaged rate coefficients are used and the cross sections are calculated based on the first-perturbation theory. Using the detailed configuration accounting with the term structures treated by the unresolved transition array model, we calculated the spectral-resolved opacity of Al plasmas. The results are compared with those of other theoretical models. From the comparison, we can see that the present results fit well with other models for low-Z plasmas. For high-Z plasmas, we will give detailed discussion in the future.

  12. [Glycosaminoglycans in subepithelial opacity after excimer laser keratectomy].

    Science.gov (United States)

    Nakayasu, K; Gotoh, T; Ishikawa, T; Kanai, A

    1996-05-01

    We evaluated histochemically the characteristics of glycosaminoglycans and proteoglycans in the corneal subepithelial opacity after excimer laser keratectomy on rabbit corneas. We also performed the same evaluations on the cornea after mechanical keratectomy. Twenty days after the operations, the area immediately subjacent to the epithelium showed strong staining with toluidine blue, alcian blue, and colloidal iron. However, after treatment with chondroitinase ABC or chondroitinase AC, alcian blue staining in this area decreased dramatically. Antilarge proteoglycan antibody also reacted strongly in this area. Histochemical and immunohistochemical examination of the cornea where mechanical keratectomy was done showed basically similar findings with the cornea of excimer laser keratectomy. These results suggest that large-molecula proteoglycans with chondroitine sulfate side chains become localized in the subepithelial area after two different kinds of keratectomies. We presume from histochemical and immunohistochemical observations that the subepithelial opacity observed after excimer laser keratectomy is not a special reaction to excimer laser but simply a corneal scar formed after stromal resection.

  13. A broadly flavivirus cross-neutralizing monoclonal antibody that recognizes a novel epitope within the fusion loop of E protein.

    Directory of Open Access Journals (Sweden)

    Yong-Qiang Deng

    Full Text Available Flaviviruses are a group of human pathogenic, enveloped RNA viruses that includes dengue (DENV, yellow fever (YFV, West Nile (WNV, and Japanese encephalitis (JEV viruses. Cross-reactive antibodies against Flavivirus have been described, but most of them are generally weakly neutralizing. In this study, a novel monoclonal antibody, designated mAb 2A10G6, was determined to have broad cross-reactivity with DENV 1-4, YFV, WNV, JEV, and TBEV. Phage-display biopanning and structure modeling mapped 2A10G6 to a new epitope within the highly conserved flavivirus fusion loop peptide, the (98DRXW(101 motif. Moreover, in vitro and in vivo experiments demonstrated that 2A10G6 potently neutralizes DENV 1-4, YFV, and WNV and confers protection from lethal challenge with DENV 1-4 and WNV in murine model. Furthermore, functional studies revealed that 2A10G6 blocks infection at a step after viral attachment. These results define a novel broadly flavivirus cross-reactive mAb with highly neutralizing activity that can be further developed as a therapeutic agent against severe flavivirus infections in humans.

  14. An IL-12/Shh-C domain fusion protein-based IL-12 autocrine loop for sustained natural killer cell activation.

    Science.gov (United States)

    Zhu, Lining; Zhao, Zhihui; Wei, Yanzhang; Marcotte, William; Wagner, Thomas E; Yu, Xianzhong

    2012-08-01

    The dependency of activated natural killer (NK) cells on the continuous support of exogenous interleukin (IL)-2 for their in vivo survival, tumor localization and consequently, their antitumor effect, is a major obstacle for NK cell-mediated tumor therapy. In the present study, a fusion gene between IL-12 and mouse sonic hedgehog C-terminal domain (Shh-C) was constructed. The fusion protein was autocatalytically processed to form cholesterol-modified IL-12 molecules and an autocrine loop of IL-12 was established for the sustained activation of NK cells. The transduced NK cells matured more rapidly in vitro with the enhanced expression of granule-related proteins. NKIL-12/Shh-C cells reached the same proliferation rate as NK cells transduced with enhanced green fluorescent protein (EGFP)/Shh-C (NKEGFP/Shh-C) with Shh-C cells 5 and 7 days after transduction was significantly higher than that in the supernatants of NKIL-12 cells. Immunofluorescent staining of lung tissues from B16-bearing mice which had received an intravenous injection of lentivirus-transduced NK cells without exogenous IL-2 confirmed that donor NK cells successfully infiltrated into the lung tissues. The survival time of the mice which had received NKIL-12/Shh-C cells was significantly prolonged compared to the mice which had received NKEGFP/Shh-C cells.

  15. FTS Measurements of Submillimeter-Wave Atmospheric Opacity at Pampa la Bola

    Science.gov (United States)

    Matsuo, Hiroshi; Sakamoto, Akihiro; Matsushita, Satoki

    1998-06-01

    The first measurements of submillimeter-wave atmospheric opacity spectra at the Pampa la Bola site (Northern Chile, Atacama, 4800 m altitude) have been performed during the winter season using a Fourier transform spectrometer (FTS). Atmospheric emission spectra, as a function of airmass, were measured under various weather conditions. Atmospheric opacity was evaluated from sky temperature at the zenith as well as from tipping measurements, which are independent measures but give consistent results. Correlation diagrams between 220 GHz and 345 GHz, 410 GHz, 492 GHz, 675 GHz, 691 GHz, 809 GHz, 875 GHz are shown. Correlations between millimeter-wave and submillimeter-wave opacities get worse when 220 GHz opacity is larger than 0.1. Deviations from the opacity correlation at each frequency show good correlations themselves, but have different relative variations at each frequency. This indicates that atmospheric transparency cannot be characterized only by millimeter-wave opacity, but requires simultaneous opacity measurements at millimeter and submillimeter-wavelengths.

  16. Controlled opacity in a class of nonlinear dielectric media

    Science.gov (United States)

    Bittencourt, E.; Camargo, G. H. S.; De Lorenci, V. A.; Klippert, R.

    2017-03-01

    Motivated by new technologies for designing and tailoring metamaterials, we seek properties for certain classes of nonlinear optical materials that allow room for a reversibly controlled opacity-to-transparency phase transition through the application of external electromagnetic fields. We examine some mathematically simple models for the dielectric parameters of the medium and compute the relevant geometric quantities that describe the speed and polarization of light rays.

  17. The EOSTA model for opacities and EOS calculations

    Science.gov (United States)

    Barshalom, Avraham; Oreg, Joseph

    2007-11-01

    The EOSTA model developed recently combines the STA and INFERNO models to calculate opacities and EOS on the same footing. The quantum treatment of the plasma continuum and the inclusion of the resulted shape resonances yield a smooth behavior of the EOS and opacity global quantities vs density and temperature. We will describe the combined model and focus on its latest improvements. In particular we have extended the use of the special representation of the relativistic virial theorem to obtain an exact differential equation for the free energy. This equation, combined with a boundary condition at the zero pressure point, serves to advance the LDA EOS results significantly. The method focuses on applicability to high temperature and high density plasmas, warm dens matter etc. but applies at low temperatures as well treating fluids and even solids. Excellent agreement is obtained with experiments covering a wide range of density and temperature. The code is now used to create EOS and opacity databases for the use of hydro-dynamical simulations.

  18. Formation of Jupiter using opacities based on detailed grain physics

    CERN Document Server

    Movshovitz, Naor; Podolak, Morris; Lissauer, Jack J

    2010-01-01

    Numerical simulations, based on the core-nucleated accretion model, are presented for the formation of Jupiter at 5.2 AU in 3 primordial disks with three different assumed values of the surface density of solid particles. The grain opacities in the envelope of the protoplanet are computed using a detailed model that includes settling and coagulation of grains and that incorporates a recalculation of the grain size distribution at each point in time and space. We generally find lower opacities than the 2% of interstellar values used in previous calculations [Hubickyj, O., Bodenheimer, P., Lissauer, J. J., 2005. Icarus 179, 415--431; Lissauer, J. J., Hubickyj, O., D'Angelo, G., Bodenheimer, P., 2009. Icarus 199, 338-350]. These lower opacities result in more rapid heat loss from and more rapid contraction of the protoplanetary envelope. For a given surface density of solids, the new calculations result in a substantial speedup in formation time as compared with those previous calculations. Formation times are c...

  19. Lens opacities after repeated exposure to ultraviolet radiation.

    Science.gov (United States)

    Michael, R; Löfgren, S; Söderberg, P G

    1999-12-01

    To investigate the effect of the interval between two, near-threshold exposures to ultraviolet radiation (UVR) on cataract development. One eye of Sprague-Dawley rats was exposed twice to 4 kJ/m2 narrow band UVR (lambdaMAX=300 nm) for 15 min each. The interval between exposures was 0, 6, 24 or 48 h. One week after the first exposure both lenses were removed for photography and measurement of the intensity of forward light scattering to quantify lens opacities. All exposed lenses developed cataract. Forward light scattering was the same after double exposure with no interval or a 6 h interval. Forward light scattering after a 24 or 48 h interval was nearly twofold greater than that following no interval or a 6 h interval. The exposed lenses in all groups had mild anterior surface opacities and intense equatorial opacities as judged with a stereomicroscope. Two, near-threshold UVR exposures at 0 or a 6 h interval produce the same degree of lens opacification. When the second exposure follows 24 or 48 h after the first, lenticular damage increases. Repair processes between 24 and 48 h after exposure appear to be sensitive to UVR, and an additional exposure during this time may aggravate cataract development.

  20. Enforcement of opacity security properties for ship information system

    Directory of Open Access Journals (Sweden)

    Bowen Xing

    2016-09-01

    Full Text Available In this paper, we consider the cybersecurity issue of ship information system (SIS from a new perspective which is called opacity. For a SIS, its confidential information (named as “secret” may be leaked through the working behaviors of each Distributed Control Unit (DCU from an outside observer called an “intruder” which is able to determine ship's mission state by detecting the source of each data flow from the corresponding DCUs in SIS. Therefore we proposed a dual layer mechanism to enforce opacity by activating non-essential DCU during secret mission. This mechanism is calculated by two types of insertion functions: Safety-assured insertion function (fIS and Admissibility-assured insertion function (fIA. Due to different objectives, fIS is designed to confuse intruder by constructing a non-secret behaviors from a unsafe one, and the division of fIA is to polish the modified output behaviors back to normal. We define the property of “I2–Enforceability” that dual layer insertion functions has the ability to enforce opacity. By a given mission map of SIS and the marked secret missions, we propose an algorithm to select fIS and compute its matchable fIA and then the DCUs which should be activated to release non-essential data flow in each step is calculable.

  1. An improved and robust DNA immunization method to develop antibodies against extracellular loops of multi-transmembrane proteins.

    Science.gov (United States)

    Hazen, Meredith; Bhakta, Sunil; Vij, Rajesh; Randle, Steven; Kallop, Dara; Chiang, Vicki; Hötzel, Isidro; Jaiswal, Bijay S; Ervin, Karen E; Li, Bing; Weimer, Robby M; Polakis, Paul; Scheller, Richard H; Junutula, Jagath R; Hongo, Jo-Anne S

    2014-01-01

    Multi-transmembrane proteins are especially difficult targets for antibody generation largely due to the challenge of producing a protein that maintains its native conformation in the absence of a stabilizing membrane. Here, we describe an immunization strategy that successfully resulted in the identification of monoclonal antibodies that bind specifically to extracellular epitopes of a 12 transmembrane protein, multi-drug resistant protein 4 (MRP4). These monoclonal antibodies were developed following hydrodynamic tail vein immunization with a cytomegalovirus (CMV) promoter-based plasmid expressing MRP4 cDNA and were characterized by flow cytometry. As expected, the use of the immune modulators fetal liver tyrosine kinase 3 ligand (Flt3L) and granulocyte-macrophage colony-stimulating factor positively enhanced the immune response against MRP4. Imaging studies using CMV-based plasmids expressing luciferase showed that the in vivo half-life of the target antigen was less than 48 h using CMV-based plasmids, thus necessitating frequent boosting with DNA to achieve an adequate immune response. We also describe a comparison of plasmids, which contained MRP4 cDNA with either the CMV or CAG promoters, used for immunizations. The observed luciferase activity in this comparison demonstrated that the CAG promoter-containing plasmid pCAGGS induced prolonged constitutive expression of MRP4 and an increased anti-MRP4 specific immune response even when the plasmid was injected less frequently. The method described here is one that can be broadly applicable as a general immunization strategy to develop antibodies against multi-transmembrane proteins, as well as target antigens that are difficult to express or purify in native and functionally active conformation.

  2. Effective Tree Scattering and Opacity at L-Band

    Science.gov (United States)

    Kurum, Mehmet; O'Neill, Peggy E.; Lang, Roger H.; Joseph, Alicia T.; Cosh, Michael H.; Jackson, Thomas J.

    2011-01-01

    This paper investigates vegetation effects at L-band by using a first-order radiative transfer (RT) model and truck-based microwave measurements over natural conifer stands to assess the applicability of the tau-omega) model over trees. The tau-omega model is a zero-order RT solution that accounts for vegetation effects with effective vegetation parameters (vegetation opacity and single-scattering albedo), which represent the canopy as a whole. This approach inherently ignores multiple-scattering effects and, therefore, has a limited validity depending on the level of scattering within the canopy. The fact that the scattering from large forest components such as branches and trunks is significant at L-band requires that zero-order vegetation parameters be evaluated (compared) along with their theoretical definitions to provide a better understanding of these parameters in the retrieval algorithms as applied to trees. This paper compares the effective vegetation opacities, computed from multi-angular pine tree brightness temperature data, against the results of two independent approaches that provide theoretical and measured optical depths. These two techniques are based on forward scattering theory and radar corner reflector measurements, respectively. The results indicate that the effective vegetation opacity values are smaller than but of similar magnitude to both radar and theoretical estimates. The effective opacity of the zero-order model is thus set equal to the theoretical opacity and an explicit expression for the effective albedo is then obtained from the zero- and first- order RT model comparison. The resultant albedo is found to have a similar magnitude as the effective albedo value obtained from brightness temperature measurements. However, it is less than half of that estimated using the theoretical calculations (0.5 - 0.6 for tree canopies at L-band). This lower observed albedo balances the scattering darkening effect of the large theoretical albedo

  3. RCD+: Fast loop modeling server.

    Science.gov (United States)

    López-Blanco, José Ramón; Canosa-Valls, Alejandro Jesús; Li, Yaohang; Chacón, Pablo

    2016-07-08

    Modeling loops is a critical and challenging step in protein modeling and prediction. We have developed a quick online service (http://rcd.chaconlab.org) for ab initio loop modeling combining a coarse-grained conformational search with a full-atom refinement. Our original Random Coordinate Descent (RCD) loop closure algorithm has been greatly improved to enrich the sampling distribution towards near-native conformations. These improvements include a new workflow optimization, MPI-parallelization and fast backbone angle sampling based on neighbor-dependent Ramachandran probability distributions. The server starts by efficiently searching the vast conformational space from only the loop sequence information and the environment atomic coordinates. The generated closed loop models are subsequently ranked using a fast distance-orientation dependent energy filter. Top ranked loops are refined with the Rosetta energy function to obtain accurate all-atom predictions that can be interactively inspected in an user-friendly web interface. Using standard benchmarks, the average root mean squared deviation (RMSD) is 0.8 and 1.4 Å for 8 and 12 residues loops, respectively, in the challenging modeling scenario in where the side chains of the loop environment are fully remodeled. These results are not only very competitive compared to those obtained with public state of the art methods, but also they are obtained ∼10-fold faster. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. The cold-induced basic helix-loop-helix transcription factor gene MdCIbHLH1 encodes an ICE-like protein in apple

    Science.gov (United States)

    2012-01-01

    Background Plant growth is greatly affected by low temperatures, and the expression of a number of genes is induced by cold stress. Although many genes in the cold signaling pathway have been identified in Arabidopsis, little is known about the transcription factors involved in the cold stress response in apple. Results Here, we show that the apple bHLH (basic helix-loop-helix) gene MdCIbHLH1 (Cold-Induced bHLH1), which encodes an ICE-like protein, was noticeably induced in response to cold stress. The MdCIbHLH1 protein specifically bound to the MYC recognition sequences in the AtCBF3 promoter, and MdCIbHLH1 overexpression enhanced cold tolerance in transgenic Arabidopsis. In addition, the MdCIbHLH1 protein bound to the promoters of MdCBF2 and favorably contributed to cold tolerance in transgenic apple plants by upregulating the expression of MdCBF2 through the CBF (C-repeat-binding factor) pathway. Our findings indicate that MdCIbHLH1 functions in stress tolerance in different species. For example, ectopic MdCIbHLH1 expression conferred enhanced chilling tolerance in transgenic tobacco. Finally, we observed that cold induces the degradation of the MdCIbHLH1 protein in apple and that this degradation was potentially mediated by ubiquitination and sumoylation. Conclusions Based on these findings, MdCIbHLH1 encodes a transcription factor that is important for the cold tolerance response in apple. PMID:22336381

  5. Internalization and down-regulation of human muscarinic acetylcholine receptor m2 subtypes. Role of third intracellular m2 loop and G protein-coupled receptor kinase 2.

    Science.gov (United States)

    Tsuga, H; Kameyama, K; Haga, T; Honma, T; Lameh, J; Sadée, W

    1998-02-27

    Internalization and down-regulation of human muscarinic acetylcholine m2 receptors (hm2 receptors) and a hm2 receptor mutant lacking a central part of the third intracellular loop (I3-del m2 receptor) were examined in Chinese hamster ovary (CHO-K1) cells stably expressing these receptors and G protein-coupled receptor kinase 2 (GRK2). Agonist-induced internalization of up to 80-90% of hm2 receptors was demonstrated by measuring loss of [3H]N-methylscopolamine binding sites from the cell surface, and transfer of [3H]quinuclidinyl benzilate binding sites from the plasma membrane into the light-vesicle fractions separated by sucrose density gradient centrifugation. Additionally, translocation of hm2 receptors with endocytic vesicles were visualized by immunofluorescence confocal microscopy. Agonist-induced down-regulation of up to 60-70% of hm2 receptors was demonstrated by determining the loss of [3H]quinuclidinyl benzilate binding sites in the cells. The half-time (t1/2) of internalization and down-regulation in the presence of 10(-4) M carbamylcholine was estimated to be 9.5 min and 2.3 h, respectively. The rates of both internalization and down-regulation of hm2 receptors in the presence of 10(-6) M or lower concentrations of carbamylcholine were markedly increased by coexpression of GRK2. Agonist-induced internalization of I3-del m2 receptors was barely detectable upon incubation of cells for 1 h, but agonist-induced down-regulation of up to 40-50% of I3-del m2 receptors occurred upon incubation with 10(-4) M carbamylcholine for 16 h. However, the rate of down-regulation was lower compared with wild type receptors (t1/2 = 9.9 versus 2.3 h). These results indicate that rapid internalization of hm2 receptors is facilitated by their phosphorylation with GRK2 and does not occur in the absence of the third intracellular loop, but down-regulation of hm2 receptors may occur through both GRK2-facilitating pathway and third intracellular loop-independent pathways.

  6. Pleckstrin homology domain-containing protein PHLDB3 supports cancer growth via a negative feedback loop involving p53

    Science.gov (United States)

    Chao, Tengfei; Zhou, Xiang; Cao, Bo; Liao, Peng; Liu, Hongbing; Chen, Yun; Park, Hee-Won; Zeng, Shelya X.; Lu, Hua

    2016-01-01

    The tumour suppressor p53 transactivates the expression of its target genes to exert its functions. Here, we identify a pleckstrin homology domain-containing protein (PHLDB3)-encoding gene as a p53 target. PHLDB3 overexpression increases proliferation and restrains apoptosis of wild-type p53-harboring cancer cells by reducing p53 protein levels. PHLDB3 binds to MDM2 (mouse double minute 2 homolog) and facilitates MDM2-mediated ubiquitination and degradation of p53. Knockdown of PHLDB3 more efficiently inhibits the growth of mouse xenograft tumours derived from human colon cancer HCT116 cells that contain wild type p53 compared with p53-deficient HCT116 cells, and also sensitizes tumour cells to doxorubicin and 5-Fluorouracil. Analysis of cancer genomic databases reveals that PHLDB3 is amplified and/or highly expressed in numerous human cancers. Altogether, these results demonstrate that PHLDB3 promotes tumour growth by inactivating p53 in a negative feedback fashion and suggest PHLDB3 as a potential therapeutic target in various human cancers. PMID:28008906

  7. Radiation attenuation and opacity in smoke and water sprays

    Science.gov (United States)

    Parent, Gilles; Boulet, Pascal; Morlon, Romain; Blanchard, Elizabeth

    2017-08-01

    Radiation attenuation through sprays, smoke and mixings of both media was studied in the infrared and in the visible range, by conducting real scale experiments in a corridor. The effect of water injection by a water mist nozzle and a sprinkler device was investigated. Radiation attenuation in the infrared range and opacity in the visible range were measured, by using a FTIR spectrometer and a dedicated opacimetry device especially designed for the present application. Experiments were done using either a blackbody source for attenuation characterization, or a heptane pool fire aimed at producing smoke for opacity measurements. For tests with smoke, the difficulties raised by the harsh environment involving a hot mixing of gas plus soot and vapor carrying water droplets were circumvented with an original device involving an optical fiber network. Mean infrared transmission was found equal to 12% for the water mist (with a 25 L/min water flowrate) and 37% for the sprinkler (with a 91 L/min water flowrate). Fitting the infrared transmission spectra with results obtained using a Monte Carlo simulation provided an estimation of the water volumetric fraction in the spray. It was shown that the better attenuation capability of the water mist is due to two factors: (1) a higher extinction coefficient of the water mist for a given water volumetric fraction due to the small size of the injected droplets and (2) a higher water volumetric fraction. Opacity measurements in the visible range yielded a measured extinction coefficient in good agreement with an estimation obtained with the Mie theory and the identified water volumetric fraction. Moreover, the water sprays (sprinkler or water mist) was seen to lead to a quick de-stratification of the smoke layer. When the spraying operation was stopped, the visibility re-increased in two main steps: a first step of fast increase and a second step of slow increase needing a few tens of seconds to get again a fully stratified smoke

  8. Sound speed and oscillation frequencies for solar models evolved with Los Alamos ATOMIC opacities

    CERN Document Server

    Guzik, Joyce A; Walczak, P; Wood, S R; Mussack, K; Farag, E

    2016-01-01

    Los Alamos National Laboratory has calculated a new generation of radiative opacities (OPLIB data using the ATOMIC code) for elements with atomic number Z=1-30 with improved physics input, updated atomic data, and finer temperature grid to replace the Los Alamos LEDCOP opacities released in the year 2000. We calculate the evolution of standard solar models including these new opacities, and compare with models evolved using the Lawrence Livermore National Laboratory OPAL (Iglesias and Rogers 1996) opacities. We use the solar abundance mixture of Asplund et al. (2009). The new Los Alamos ATOMIC opacities have steeper opacity derivatives than those of OPAL for temperatures and densities of the solar interior radiative zone. We compare the calculated nonadiabatic solar oscillation frequencies and solar interior sound speed to observed frequencies and helioseismic inferences. The calculated sound-speed profiles are similar for models evolved using either the updated Iben evolution code (see \\cite{Guzik2010}), or ...

  9. Prevalence of Lens Opacities in Adult Chinese Americans: The Chinese American Eye Study (CHES)

    OpenAIRE

    Varma, Rohit; Sun, Jie; Torres, Mina; Wu, Shuang; Hsu, Chunyi; Azen, Stanley Paul; McKean-Cowdin, Roberta; ,

    2016-01-01

    Purpose We determined the age- and sex-specific prevalence of posterior subcapsular (PSC), nuclear, cortical, and mixed lens opacities in a population-based sample of Chinese-American adults. Methods A population-based sample of Chinese-Americans 50 years and older, from 10 census tracts in Monterey Park, CA, USA, underwent a detailed interview and a comprehensive clinical examination that included assessment of different types of lens opacities by the slit-lamp–based Lens Opacities Classific...

  10. FTS measurements of submillimeter opacity and other site testing at Pampa la Bola

    Science.gov (United States)

    Matsushita, Satoki; Matsuo, Hiroshi; Sakamoto, Akihiro; Pardo, Juan R.

    2000-07-01

    We have carried out Fourier Transform Spectrometer (FTS) measurements of the millimeter and submillimeter-wave (150 - 1500 GHz or 2 mm - 200 micrometer) atmospheric opacity at Pampa la Bola, 4800 m above sea level in northern Chile on September 1997 and June 1998. One of the best transmission spectra show up to approximately 67% transmission at well- known submillimeter-wave windows. Supra-terahertz windows (located around 1035 GHz, 1350 GHz, and 1500 GHz) were identified in the same spectrum. The observed spectra can be well modeled by newly developed radiative-transfer calculations. Correlations between 220 GHz opacities and those of the center of submillimeter-wave windows or even those of the supra-terahertz windows are obtained using the entire data set. Good correlations were obtained except for the periods affected by the liquid water opacity component. We succeeded to separate the total opacity in two parts: the water vapor opacity and the liquid water opacity, using two frequencies, one in the millimeter domain and another one in the submillimeter. The separated water vapor opacity component shows good correlation with the 183 GHz pure water vapor line opacity which is also covered in the measured spectra, but the liquid water opacity component shows no correlation. The liquid water opacity component also shows no correlation with the phase fluctuation measured with the 11 GHz radio seeing monitor. Modeling of this component is currently under way. Combined with a statistical study of the 225 GHz opacity data of the Chajnantor site (approximately 7 km apart from Pampa la Bola), it is estimated that submillimeter-wave observations can be done with zenith opacity less than 1.0 (at the most transparent frequency in those windows) for about 50% of the winter season, assuming no presence of liquid water absorption.

  11. Detailed Opacity Comparison for an Improved Stellar Modeling of the Envelopes of Massive Stars

    Science.gov (United States)

    Turck-Chièze, S.; Le Pennec, M.; Ducret, J. E.; Colgan, J.; Kilcrease, D. P.; Fontes, C. J.; Magee, N.; Gilleron, F.; Pain, J. C.

    2016-06-01

    Seismic observations have led to doubts or ambiguities concerning the opacity calculations used in stellar physics. Here, we concentrate on the iron-group opacity peak, due to iron, nickel, and chromium, located around T = 200,000 K for densities from {10}-8 {to} {10}-4 {{g}} {{cm}}-3, which creates some convective layers in stellar radiative envelopes for masses between 3 and 18 {M}⊙ . These conditions were extensively studied in the 1980s. More recently, inconsistencies between OP and OPAL opacity calculations have complicated the interpretation of seismic observations as the iron-group opacity peak excites acoustic and gravity modes in SPB, β Cephei, and sdB stars. We investigate the reliability of the theoretical opacity calculations using the modern opacity codes ATOMIC and SCO-RCG. We show their temperature and density dependence for conditions that are achievable in the laboratory and equivalent to astrophysical conditions. We also compare new theoretical opacity spectra with OP spectra and quantify how different approximations impact the Rosseland mean calculations.This detailed study estimates new ATOMIC and SCO-RCG Rosseland mean values for astrophysical conditions which we compare to OP values. Some puzzling questions are still under investigation for iron, but we find a strong increase in the Rosseland mean nickel opacity of a factor between 2 and 6 compared to OP. This appears to be due to the use of extrapolated atomic data for the Ni opacity within the OP calculations. A study on chromium is also shown.

  12. Rapid and sensitive detection of Dasheen mosaic virus infecting elephant foot yam by reverse transcription loop mediated isothermal amplification of coat protein gene.

    Science.gov (United States)

    Kamala, S; Makeshkumar, T

    2015-09-15

    Dasheen mosaic virus (DsMV), the pathogen causing mosaic disease of elephant foot yam (Amorphophallus paeoniifoilius) is disseminated mainly through vegetative propagation of the tubers. For the rapid and sensitive detection of the virus, a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay based on the coat protein gene has been developed. A final concentration of 5.4 mM magnesium sulphate and 0.7 M betaine in the reaction mixture was found to be optimum for getting characteristic ladder like bands of the amplified product after gel electrophoresis. The reaction was set at 65°C for 50 min followed by reaction termination at 86°C for 5 min in a water bath. The sensitivity of the assay was found to be 100 times higher than that of RT-PCR. The virus was indexed successfully from tubers of elephant foot yam. In tube detection of the DsMV was carried out using fluorescence detection reagents. The assay was validated with field samples from various regions of Kerala state, India. Copyright © 2015 Elsevier B.V. All rights reserved.

  13. A Feedback Regulatory Loop between G3P and Lipid Transfer Proteins DIR1 and AZI1 Mediates Azelaic-Acid-Induced Systemic Immunity

    Directory of Open Access Journals (Sweden)

    Keshun Yu

    2013-04-01

    Full Text Available Systemic acquired resistance (SAR, a highly desirable form of plant defense, provides broad-spectrum immunity against diverse pathogens. The recent identification of seemingly unrelated chemical inducers of SAR warrants an investigation of their mutual interrelationships. We show that SAR induced by the dicarboxylic acid azelaic acid (AA requires the phosphorylated sugar derivative glycerol-3-phosphate (G3P. Pathogen inoculation induced the release of free unsaturated fatty acids (FAs and thereby triggered AA accumulation, because these FAs serve as precursors for AA. AA accumulation in turn increased the levels of G3P, which is required for AA-conferred SAR. The lipid transfer proteins DIR1 and AZI1, both of which are required for G3P- and AA-induced SAR, were essential for G3P accumulation. Conversely, reduced G3P resulted in decreased AZI1 and DIR1 transcription. Our results demonstrate that an intricate feedback regulatory loop among G3P, DIR1, and AZI1 regulates SAR and that AA functions upstream of G3P in this pathway.

  14. Investigation by two-photon fluorescence correlation spectroscopy of the interaction of the nucleocapsid protein of HIV-1 with hairpin loop DNA sequences

    Science.gov (United States)

    Mely, Yves; Azoulay, Joel; Beltz, Herve; Clamme, Jean-Pierre; Bernacchi, Serena; Ficheux, Damien; Roques, Bernard P.; Darlix, Jean-Luc

    2004-09-01

    The nucleocapsid protein NCp7 of HIV-1 possesses nucleic acid chaperone properties that are critical for the two strand transfer reactions required during reverse transcription. The first DNA strand transfer relies on the destabilization by NCp7 of double-stranded segments of the transactivation response element, TAR sequence, at the 3' end of the genomic RNA and the complementary sequence cTAR at the 3" terminus of the early product of reverse transcription. To characterize NCp7-mediated nucleic acid destabilization, we investigated by steady-state and time-resolved fluorescence spectroscopy and two photon fluorescence correlation spectroscopy, the interaction of a doubly-labelled cTAR sequence with NCp7. The conformational fluctuations observed in the absence of NCp7 were associated with the rapid opening and closing (fraying) of the double stranded terminal segment of cTAR. NCp7 destabilizes cTAR mainly through a large increase of the opening rate constant. Additionally, the various destabilizing structures (bulges, internal loop, mismatches) spread all over cTAR secondary structure were found to be critical for NCp7 chaperone activity. Taken together, our data enabled us to propose a molecular mechanism for the destabilizing activity of NCp7 on cTAR which is crucial for the formation of the cTAR-TAR complex during the first strand transfer reaction.

  15. Evidence for Environmental Changes in the Submillimeter Dust Opacity

    CERN Document Server

    Martin, Peter G; Bontemps, Sylvain; Miville-Deschênes, Marc-Antoine; Ade, Peter A R; Bock, James J; Chapin, Edward L; Devlin, Mark J; Dicker, Simon R; Griffin, Matthew; Gundersen, Joshua O; Halpern, Mark; Hargrave, Peter C; Hughes, David H; Klein, Jeff; Marsden, Gaelen; Mauskopf, Philip; Netterfield, Calvin B; Olmi, Luca; Patanchon, Guillaume; Rex, Marie; Scott, Douglas; Semisch, Christopher; Truch, Matthew D P; Tucker, Carole; Tucker, Gregory S; Viero, Marco P; Wiebe, Donald V

    2011-01-01

    The submillimeter opacity of dust in the diffuse Galactic interstellar medium (ISM) has been quantified using a pixel-by-pixel correlation of images of continuum emission with a proxy for column density. We used three BLAST bands at 250, 350, and 500 \\mu m and one IRAS at 100 \\mu m. The proxy is the near-infrared color excess, E(J-Ks), obtained from 2MASS. Based on observations of stars, we show how well this color excess is correlated with the total hydrogen column density for regions of moderate extinction. The ratio of emission to column density, the emissivity, is then known from the correlations, as a function of frequency. The spectral distribution of this emissivity can be fit by a modified blackbody, whence the characteristic dust temperature T and the desired opacity \\sigma_e(1200) at 1200 GHz can be obtained. We have analyzed 14 regions near the Galactic plane toward the Vela molecular cloud, mostly selected to avoid regions of high column density (N_H > 10^{22} cm^-2) and small enough to ensure a u...

  16. Iron Opacity Platform Performance Characterization at the National Ignition Facility

    Science.gov (United States)

    Opachich, Y. P.; Ross, P. W.; Heeter, R. F.; Barrios, M. A.; Liedahl, D. A.; May, M. J.; Schneider, M. B.; Craxton, R. S.; Garcia, E. M.; McKenty, P. W.; Zhang, R.; Weaver, J. L.; Flippo, K. A.; Kline, J. L.; Perry, T. S.; Los Alamos National Laboratory Collaboration; Naval Research Laboratory Collaboration; University of Rochester LaboratoryLaser Energetics Collaboration; Lawrence Livermore National Lab Collaboration; National Security Technologies, LLC Collaboration

    2016-10-01

    A high temperature opacity platform has been fielded at the National Ignition Facility (NIF). The platform will be used to study opacity in iron at a temperature of 160 eV. The platform uses a 6 mm diameter hohlraum driven by 128 laser beams with 530 kJ of energy in a 3 ns pulse to heat an iron sample. Absorption spectra of the heated sample are generated with a broadband pulsed X-ray backlighter produced by imploding a vacuum-filled CH shell. The shell is 2 mm in diameter and 20 microns thick, driven by 64 beams with 250 kJ in a 2.5 ns pulse. The hohlraum and backlighter performance have both been investigated recently and will be discussed in this presentation. This work was performed by National Security Technologies, LLC, under Contract No. DE-AC52-06NA25946 with the U.S. Department of Energy. DOE/NV/25946-2892.

  17. Iron Opacity and the Pulsar of SN 1987A

    CERN Document Server

    Fryer, C L; Pinto, P A

    1999-01-01

    Neutron stars formed in Type II supernovae are likely to be initially obscured by late-time fallback. Although much of the late-time fallback is quickly accreted via neutrino cooling, some material remains on the neutron star, forming an atmosphere which slowly accretes through photon emission. In this paper, we derive structure equations of the fallback atmosphere and present results of one-dimensional simulations of that fallback. The atmosphere remaining after neutrino cooling becomes unimportant (less than the Compton Eddington limit) is only a fraction of the total mass accreted (10^-8 of the accreted mass or 10^-9 solar masses.) Recombined iron dominates the opacity in the outer regions leading to an opacity 1000-10,000 times higher than that of electron scattering alone. The resultant photon emission of the remnant atmosphere is limited to 1/1000th the Compton Eddington Luminosity. The late-time evolution of this system leads to the formation of a photon-driven wind from the accretion of the inner port...

  18. New dust opacity mapping from Viking Infrared Thermal Mapper data

    Science.gov (United States)

    Martin, Terry Z.; Richardson, Mark I.

    1993-01-01

    Global dust opacity mapping for Mars has been carried forward using the approach described by Martin (1986) for Viking IR Thermal Mapper data. New maps are presented for the period from the beginning of Viking observations, until Ls 210 deg in 1979 (1.36 Mars years). This range includes the second and more extensive planet-encircling dust storm observed by Viking, known as storm 1977b. Improvements in approach result in greater time resolution and smaller noise than in the earlier work. A strong local storm event filled the Hellas basin at Ls 170 deg, prior to the 1977a storm. Dust is retained in equatorial regions following the 1977b storm far longer than in mid-latitudes. Minor dust events appear to raise the opacity in northern high latitudes during northern spring. Additional mapping with high time resolution has been done for the periods of time near the major storm origins in order to search for clues to the mechanism of storm initiation. The first evidence of the start of the 1977b storm is pushed back to Ls 274.2 deg, preceding signs of the storm in images by about 15 hours.

  19. Galactic cold cores VI. Dust opacity spectral index

    CERN Document Server

    Juvela, M; Doi, Y; Hughes, A; Lefevre, C; Marshall, D J; Meny, C; Montillaud, J; Pagani, L; Paradis, D; Ristorcelli, I; Malinen, J; Montier, L A; Paladini, R; Pelkonen, V -M; Rivera-Ingraham, A

    2015-01-01

    The Galactic Cold Cores project has made Herschel observations of 116 fields where the Planck survey has found signs of cold dust emission. The fields contain sources in different environments and different phases of star formation. The dust opacity spectral index beta and the dust colour temperature T are derived using Herschel and Planck data. The relation between beta and T is examined for the whole sample and inside individual fields. Based on IRAS and Planck data, the fields are characterised by a median colour temperature of 16.1 K and a median opacity spectral index of beta=1.84. We observe a clear T-beta anti-correlation. In Herschel observations, constrained at lower resolution by Planck data, the variations follow the column density structure and beta(FIR) can rise to ~2.2 in individual clumps. The Planck 217 GHz band shows a systematic excess that is consistent with a general flattening of the dust emission spectrum at millimetre wavelengths. When fitted separately below and above 700 um, the media...

  20. A Mutant of Hepatitis B Virus X Protein (HBxΔ127 Promotes Cell Growth through A Positive Feedback Loop Involving 5-Lipoxygenase and Fatty Acid Synthase

    Directory of Open Access Journals (Sweden)

    Qi Wang

    2010-02-01

    Full Text Available Hepatocellular carcinoma (HCC is one of the most common malignant tumors worldwide. Hepatitis B virus X protein (HBx contributes to the development of HCC, whereas HBx with COOH-terminal deletion is a frequent event in the HCC tissues. Previously, we identified a natural mutant of HBx-truncated 27 amino acids at the COOH-terminal (termed HBxΔ127, which strongly enhanced cell growth. In the present study, we focused on investigating the mechanism. Accordingly, fatty acid synthase (FAS plays a crucial role in cancer cell survival and proliferation; thus, we examined the signaling pathways involving FAS. Our data showed that HBxΔ127 strongly increased the transcriptional activities of FAS in human hepatoma HepG2 and H7402 cells. Moreover, we found that 5-lipoxygenase (5-LOX was responsible for the up-regulation of FAS by using MK886 (an inhibitor of 5-LOX and 5-LOX small interfering RNA. We observed that HBxΔ127 could upregulate 5-LOX through phosphorylated extracellular signal-regulated protein kinases 1/2 and thus resulted in the increase of released leukotriene B4 (LTB4, a metabolite of 5-LOX by ELISA. The additional LTB4 could upregulate the expression of FAS in the cells as well. Interestingly, we found that FAS was able to upregulate the expression of 5-LOX in a feedback manner by using cerulenin (an inhibitor of FAS. Collectively, HBxΔ127 promotes cell growth through a positive feedback loop involving 5-LOX and FAS, in which released LTB4 is involved in the up-regulation of FAS. Thus, our finding provides a new insight into the mechanism involving the promotion of cell growth mediated by HBxΔ127.

  1. DDB1 and CUL4 associated factor 11 (DCAF11) mediates degradation of Stem-loop binding protein at the end of S phase.

    Science.gov (United States)

    Djakbarova, Umidahan; Marzluff, William F; Köseoğlu, M Murat

    2016-08-02

    In eukaryotes, bulk histone expression occurs in the S phase of the cell cycle. This highly conserved system is crucial for genomic stability and proper gene expression. In metazoans, Stem-loop binding protein (SLBP), which binds to 3' ends of canonical histone mRNAs, is a key factor in histone biosynthesis. SLBP is mainly expressed in S phase and this is a major mechanism to limit bulk histone production to the S phase. At the end of S phase, SLBP is rapidly degraded by proteasome, depending on two phosphorylations on Thr 60 and Thr 61. Previously, we showed that SLBP fragment (aa 51-108) fused to GST, is sufficient to mimic the late S phase (S/G2) degradation of SLBP. Here, using this fusion protein as bait, we performed pull-down experiments and found that DCAF11, which is a substrate receptor of CRL4 complexes, binds to the phosphorylated SLBP fragment. We further confirmed the interaction of full-length SLBP with DCAF11 and Cul4A by co-immunoprecipitation experiments. We also showed that DCAF11 cannot bind to the Thr61/Ala mutant SLBP, which is not degraded at the end of S phase. Using ectopic expression and siRNA experiments, we demonstrated that SLBP expression is inversely correlated with DCAF11 levels, consistent with the model that DCAF11 mediates SLBP degradation. Finally, we found that ectopic expression of the S/G2 stable mutant SLBP (Thr61/Ala) is significantly more toxic to the cells, in comparison to wild type SLBP. Overall, we concluded that CRL4-DCAF11 mediates the degradation of SLBP at the end of S phase and this degradation is essential for the viability of cells.

  2. A P-loop Mutation in G[alpha] Subunits Prevents Transition to the Active State: Implications for G-protein Signaling in Fungal Pathogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Bosch, Dustin E.; Willard, Francis S.; Ramanujam, Ravikrishna; Kimple, Adam J.; Willard, Melinda D.; Naqvi, Naweed I.; Siderovski, David P. (UNC); (Singapore)

    2012-10-23

    Heterotrimeric G-proteins are molecular switches integral to a panoply of different physiological responses that many organisms make to environmental cues. The switch from inactive to active G{alpha}{beta}{gamma} heterotrimer relies on nucleotide cycling by the G{alpha} subunit: exchange of GTP for GDP activates G{alpha}, whereas its intrinsic enzymatic activity catalyzes GTP hydrolysis to GDP and inorganic phosphate, thereby reverting G{alpha} to its inactive state. In several genetic studies of filamentous fungi, such as the rice blast fungus Magnaporthe oryzae, a G42R mutation in the phosphate-binding loop of G{alpha} subunits is assumed to be GTPase-deficient and thus constitutively active. Here, we demonstrate that G{alpha}(G42R) mutants are not GTPase deficient, but rather incapable of achieving the activated conformation. Two crystal structure models suggest that Arg-42 prevents a typical switch region conformational change upon G{alpha}{sub i1}(G42R) binding to GDP {center_dot} AlF{sub 4}{sup -} or GTP, but rotameric flexibility at this locus allows for unperturbed GTP hydrolysis. G{alpha}(G42R) mutants do not engage the active state-selective peptide KB-1753 nor RGS domains with high affinity, but instead favor interaction with G{beta}{gamma} and GoLoco motifs in any nucleotide state. The corresponding G{alpha}{sub q}(G48R) mutant is not constitutively active in cells and responds poorly to aluminum tetrafluoride activation. Comparative analyses of M. oryzae strains harboring either G42R or GTPase-deficient Q/L mutations in the G{alpha} subunits MagA or MagB illustrate functional differences in environmental cue processing and intracellular signaling outcomes between these two G{alpha} mutants, thus demonstrating the in vivo functional divergence of G42R and activating G-protein mutants.

  3. A single amino acid of human immunodeficiency virus type 2 capsid protein affects conformation of two external loops and viral sensitivity to TRIM5α.

    Directory of Open Access Journals (Sweden)

    Tadashi Miyamoto

    Full Text Available We previously reported that human immunodeficiency virus type 2 (HIV-2 carrying alanine or glutamine but not proline at position 120 of the capsid protein (CA could grow in the presence of anti-viral factor TRIM5α of cynomolgus monkey (CM. To elucidate details of the interaction between the CA and TRIM5α, we generated mutant HIV-2 viruses, each carrying one of the remaining 17 possible amino acid residues, and examined their sensitivity to CM TRIM5α-mediated restriction. Results showed that hydrophobic residues or those with ring structures were associated with sensitivity, while those with small side chains or amide groups conferred resistance. Molecular dynamics simulation study revealed a structural basis for the differential TRIM5α sensitivities. The mutations at position 120 in the loop between helices 6 and 7 (L6/7 affected conformation of the neighboring loop between helices 4 and 5 (L4/5, and sensitive viruses had a common L4/5 conformation. In addition, the common L4/5 structures of the sensitive viruses were associated with a decreased probability of hydrogen bond formation between the 97th aspartic acid in L4/5 and the 119th arginine in L6/7. When we introduced aspartic acid-to-alanine substitution at position 97 (D97A of the resistant virus carrying glutamine at position 120 to disrupt hydrogen bond formation, the resultant virus became moderately sensitive. Interestingly, the virus carrying glutamic acid at position 120 showed resistance, while its predicted L4/5 conformation was similar to those of sensitive viruses. The D97A substitution failed to alter the resistance of this particular virus, indicating that the 120th amino acid residue itself is also involved in sensitivity regardless of the L4/5 conformation. These results suggested that a hydrogen bond between the L4/5 and L6/7 modulates the overall structure of the exposed surface of the CA, but the amino acid residue at position 120 is also directly involved in CM TRIM5

  4. Alternative loop rings

    CERN Document Server

    Goodaire, EG; Polcino Milies, C

    1996-01-01

    For the past ten years, alternative loop rings have intrigued mathematicians from a wide cross-section of modern algebra. As a consequence, the theory of alternative loop rings has grown tremendously. One of the main developments is the complete characterization of loops which have an alternative but not associative, loop ring. Furthermore, there is a very close relationship between the algebraic structures of loop rings and of group rings over 2-groups. Another major topic of research is the study of the unit loop of the integral loop ring. Here the interaction between loop rings and group ri

  5. Grain opacity and the bulk composition of extrasolar planets. II. An analytical model for the grain opacity in protoplanetary atmospheres

    CERN Document Server

    Mordasini, C

    2014-01-01

    Context. We investigate the grain opacity k_gr in the atmosphere of protoplanets. This is important for the planetary mass-radius relation since k_gr affects the H/He envelope mass of low-mass planets and the critical core mass of giant planets. Aims. The goal of this study is to derive an analytical model for k_gr. Methods. Our model is based on the comparison of the timescales of microphysical processes like grain settling in the Stokes and Epstein regime, growth by Brownian motion coagulation and differential settling, grain evaporation, and grain advection due to envelope contraction. With these timescales we derive the grain size, abundance, and opacity. Results. We find that the main growth process is differential settling. In this regime, k_gr has a simple functional form and is given as 27 Q/8 H rho in the Epstein regime and as 2 Q/H rho for Stokes drag. Grain dynamics lead to a typical radial structure of k_gr with high ISM-like values in the top layers but a strong decrease in the deeper parts where...

  6. 77 FR 13977 - Quality Assurance Requirements for Continuous Opacity Monitoring Systems at Stationary Sources

    Science.gov (United States)

    2012-03-08

    ... AGENCY 40 CFR Part 60 RIN 2060-AH23 Quality Assurance Requirements for Continuous Opacity Monitoring... final rule titled, ``Quality Assurance Requirements for Continuous Opacity Monitoring Systems at... electronically in www.regulations.gov or in hard copy at the Procedure 3--Quality Assurance Requirements for...

  7. 77 FR 8160 - Quality Assurance Requirements for Continuous Opacity Monitoring Systems at Stationary Sources

    Science.gov (United States)

    2012-02-14

    ... AGENCY 40 CFR Part 60 RIN 2060-AH23 Quality Assurance Requirements for Continuous Opacity Monitoring...--Quality Assurance Requirements for Continuous Opacity Monitoring Systems at Stationary Sources Docket, EPA.... Rules establishing quality assurance requirements impose no costs independent from national emission...

  8. 77 FR 18709 - Quality Assurance Requirements for Continuous Opacity Monitoring Systems at Stationary Sources

    Science.gov (United States)

    2012-03-28

    ... AGENCY 40 CFR Part 60 RIN 2060-AH23 Quality Assurance Requirements for Continuous Opacity Monitoring... final rule. SUMMARY: The EPA published a direct final rule titled ``Quality Assurance Requirements for....regulations.gov or in hard copy at the Procedure 3--Quality Assurance Requirements for Continuous Opacity...

  9. 40 CFR Figure 1 to Subpart Qqq of... - Data Summary Sheet for Determination of Average Opacity

    Science.gov (United States)

    2010-07-01

    ... 40 Protection of Environment 12 2010-07-01 2010-07-01 true Data Summary Sheet for Determination of.... 63, Subpt. QQQ, Fig. 1 Figure 1 to Subpart QQQ of Part 63—Data Summary Sheet for Determination of Average Opacity Clock time Number of converters blowing Converter aisle activity Average opacity for...

  10. Cfs1p, a Novel Membrane Protein in the PQ-Loop Family, Is Involved in Phospholipid Flippase Functions in Yeast

    Directory of Open Access Journals (Sweden)

    Takaharu Yamamoto

    2017-01-01

    Full Text Available Type 4 P-type ATPases (P4-ATPases function as phospholipid flippases, which translocate phospholipids from the exoplasmic leaflet to the cytoplasmic leaflet of the lipid bilayer, to generate and maintain asymmetric distribution of phospholipids at the plasma membrane and endosomal/Golgi membranes. The budding yeast Saccharomyces cerevisiae has four heteromeric flippases (Drs2p, Dnf1p, Dnf2p, and Dnf3p, associated with the Cdc50p family noncatalytic subunit, and one monomeric flippase, Neo1p. They have been suggested to function in vesicle formation in membrane trafficking pathways, but details of their mechanisms remain to be clarified. Here, to search for novel factors that functionally interact with flippases, we screened transposon insertional mutants for strains that suppressed the cold-sensitive growth defect in the cdc50Δ mutant. We identified a mutation of YMR010W encoding a novel conserved membrane protein that belongs to the PQ-loop family including the cystine transporter cystinosin and the SWEET sugar transporters. We named this gene CFS1 (cdc fifty suppressor 1. GFP-tagged Cfs1p was partially colocalized with Drs2p and Neo1p to endosomal/late Golgi membranes. Interestingly, the cfs1Δ mutation suppressed growth defects in all flippase mutants. Accordingly, defects in membrane trafficking in the flippase mutants were also suppressed. These results suggest that Cfs1p and flippases function antagonistically in membrane trafficking pathways. A growth assay to assess sensitivity to duramycin, a phosphatidylethanolamine (PE-binding peptide, suggested that the cfs1Δ mutation changed PE asymmetry in the plasma membrane. Cfs1p may thus be a novel regulator of phospholipid asymmetry.

  11. Structural Characterization of the Loop at the Alpha-Subunit C-Terminus of the Mixed Lineage Leukemia Protein Activating Protease Taspase1.

    Directory of Open Access Journals (Sweden)

    Johannes van den Boom

    Full Text Available Type 2 asparaginases, a subfamily of N-terminal nucleophile (Ntn hydrolases, are activated by limited proteolysis. This activation yields a heterodimer and a loop region at the C-terminus of the α-subunit is released. Since this region is unresolved in all type 2 asparaginase crystal structures but is close to the active site residues, we explored this loop region in six members of the type 2 asparaginase family using homology modeling. As the loop model for the childhood cancer-relevant protease Taspase1 differed from the other members, Taspase1 activation as well as the conformation and dynamics of the 56 amino acids loop were investigated by CD and NMR spectroscopy. We propose a helix-turn-helix motif, which can be exploited as novel anticancer target to inhibit Taspase1 proteolytic activity.

  12. Modulation of DNA loop lifetimes by the free energy of loop formation

    CERN Document Server

    Chen, Yi-Ju; Mulligan, Peter; Spakowitz, Andrew J; Phillips, Rob

    2015-01-01

    Storage and retrieval of the genetic information in cells is a dynamic process that requires the DNA to undergo dramatic structural rearrangements. DNA looping is a prominent example of such a structural rearrangement that is essential for transcriptional regulation in both prokaryotes and eukaryotes, and the speed of such regulations affects the fitness of individuals. Here, we examine the in vitro looping dynamics of the classic Lac repressor gene-regulatory motif. We show that both loop association and loop dissociation at the DNA-repressor junctions depend on the elastic deformation of the DNA and protein, and that both looping and unlooping rates approximately scale with the looping J factor, which reflects the system's deformation free energy. We explain this observation by transition state theory and model the DNA-protein complex as an effective worm-like chain with twist. We introduce a finite protein-DNA binding interaction length, in competition with the characteristic DNA deformation length scale, ...

  13. Fine-Tuning Two-Particle Interferometry; 2, Opacity Effects

    CERN Document Server

    Tomasik, Boris; Tomasik, Boris; Heinz, Ulrich

    1998-01-01

    We present a model study of single-particle spectra and two-particle Bose-Einstein correlations for opaque sources. We study the transverse mass dependence of the correlation radii R_\\perp, R_\\parallel and R_0 in the YKP parametrization and find a strong sensitivity of the temporal radius parameter R_0^2 to the source opacity. A simple comparison with the published data from 158 A GeV/c Pb+Pb collisions at CERN indicates that the pion source created in these collisions emits particles from the whole reaction volume and is not opaque. For opaque sources we find certain regions of inapplicability of the YKP parametrization which can be avoided by a slightly different parametrization for the correlator. The physical meaning of the modified parameters is briefly discussed.

  14. Galactic cold cores. VI. Dust opacity spectral index

    Science.gov (United States)

    Juvela, M.; Demyk, K.; Doi, Y.; Hughes, A.; Lefèvre, C.; Marshall, D. J.; Meny, C.; Montillaud, J.; Pagani, L.; Paradis, D.; Ristorcelli, I.; Malinen, J.; Montier, L. A.; Paladini, R.; Pelkonen, V.-M.; Rivera-Ingraham, A.

    2015-12-01

    Context. The Galactic Cold Cores project has carried out Herschel photometric observations of 116 fields where the Planck survey has found signs of cold dust emission. The fields contain sources in different environments and different phases of star formation. Previous studies have revealed variations in their dust submillimetre opacity. Aims: The aim is to measure the value of dust opacity spectral index and to understand its variations spatially and with respect to other parameters, such as temperature, column density, and Galactic location. Methods: The dust opacity spectral index β and the dust colour temperature T are derived using Herschel and Planck data. The relation between β and T is examined for the whole sample and inside individual fields. Results: Based on IRAS and Planck data, the fields are characterised by a median colour temperature of 16.1 K and a median opacity spectral index of β = 1.84. The values are not correlated with Galactic longitude. We observe a clear T-β anti-correlation. In Herschel observations, constrained at lower resolution by Planck data, the variations follow the column density structure and βFIR can rise to ~2.2 in individual clumps. The highest values are found in starless clumps. The Planck 217 GHz band shows a systematic excess that is not restricted to cold clumps and is thus consistent with a general flattening of the dust emission spectrum at millimetre wavelengths. When fitted separately below and above 700 μm, the median spectral index values are βFIR ~ 1.91 and β(mm) ~ 1.66. Conclusions: The spectral index changes as a function of column density and wavelength. The comparison of different data sets and the examination of possible error sources show that our results are robust. However, β variations are partly masked by temperature gradients and the changes in the intrinsic grain properties may be even greater. Planck http://www.esa.int/Planck is a project of the European Space Agency - ESA - with instruments

  15. Opacity measurements in shock-generated argon plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Erskine, D.

    1993-07-01

    Dense plasmas having uniform and constant density and temperature are generated by passage of a planar shock wave through gas. The opacity of the plasma is accurately measured versus wavelength by recording the risetime of emitted light. This technique is applicable to a wide variety of species and plasma conditions. Initial experiments in argon have produced plasmas with 2 eV temperatures, 0.004--0.04 g/cm{sup 3} densities, and coupling parameters {Gamma} {approximately}0.3--0.7. Measurements in visible light are compared with calculations using the HOPE code. An interesting peak in the capacity at 400 nm is observed for the first time and is identified with the 4s-5p transition in excited neutral argon atoms.

  16. The hybrid opacity code SCO-RCG: recent developments

    CERN Document Server

    Pain, Jean-Christophe; Porcherot, Quentin; Blenski, Thomas

    2013-01-01

    Absorption and emission spectra of multicharged-ion plasmas contain a huge number of electron configurations and electric-dipolar lines, which can be handled by global methods. However, some transition arrays consist only of a small bunch of lines. For that reason, we developed the hybrid opacity code SCO-RCG combining the (statistical) super-transition-array method and the (detailed) fine-structure calculation (requiring the diagonalization of the Hamiltonian matrix) of atomic structure. In order to decide whether a detailed treatment of lines is necessary and to determine the validity of statistical methods, the code involves criteria taking into account coalescence of lines and porosity (localized absence of lines) in transition arrays. Data required for the calculation of detailed transition arrays (Slater, spin-orbit and dipolar integrals) are provided by the super-configuration code SCO, which takes into account plasma screening effects on wavefunctions. Then, level energies and lines are calculated by ...

  17. Rosseland Mean Opacity of a High-Z Mixture Plasma

    Institute of Scientific and Technical Information of China (English)

    杨家敏; 许琰; 丁耀南; 丁永坤; 江少恩; 郑志坚; 缪文勇

    2003-01-01

    An eight-beam 0.351-μm laser with pulse duration of about 1.0ns and energy of 260 J per beam was injected into a cylindrical cavity to generate intense x-ray radiation on the Shengguang Ⅱ high power laser facility. A mixture foil of gold and gadolinium and a gold foil were attached on portion of a diagnostic hole in the mid-plane of the cavity and ablated by the intense x-ray radiation. The propagating time of the radiation heat wave in the mixture and the pure gold foil were measured with soft-x-ray spectrometer and by adopting space- and timeresolved measurement technology, respectively. The results show that the mixture of gold and gadolinium has higher Rosseland mean opacity than the gold sample in our experiment.

  18. Iron Opacity Bump Changes the Stability and Structure of Accretion Disks in Active Galactic Nuclei

    CERN Document Server

    Jiang, Yan-Fei; Stone, James

    2016-01-01

    Accretion disks around supermassive black holes have regions where the Rosseland mean opacity can be much larger than the electron scattering opacity primarily due to the large number of bound-bound transitions in iron. We study the effects of this iron opacity "bump" on the thermal stability and vertical structure of radiation pressure dominated accretion disks, utilizing three dimensional radiation magneto-hydrodynamic simulations in the local shearing box approximation. The simulations self-consistently calculate the heating due to MHD turbulence caused by magneto-rotational instability and radiative cooling by using the radiative transfer module based on a variable Eddington tensor in Athena. For a $5\\times 10^8$ solar mass black hole with $\\sim 3\\%$ of the Eddington luminosity, a model including the iron opacity bump maintains its structure for more than $10$ thermal times without showing significant signs of thermal runaway. In contrast, if only electron scattering and free-free opacity are included as ...

  19. The statistical properties of stars and their dependence on metallicity: the effects of opacity

    CERN Document Server

    Bate, Matthew R

    2014-01-01

    We report the statistical properties of stars and brown dwarfs obtained from four radiation hydrodynamical simulations of star cluster formation that resolve masses down to the opacity limit for fragmentation. The calculations are identical except for their dust and gas opacities. Assuming dust opacity is proportional to metallicity, the calculations span a range of metallicities from 1/100 to 3 times solar, although we emphasise that changing the metallicity has other thermodynamic effects that the calculations do not capture (e.g. on the thermal coupling between gas and dust). All four calculations produce stellar populations whose statistical properties are difficult to distinguish from observed stellar systems, and we find no significant dependence of stellar properties on opacity. The mass functions and properties of multiple stellar systems are consistent with each other. However, we find protostellar mergers are more common with lower opacities. Combining the results from the three calculations with th...

  20. OPACITY MEASUREMENT AND THEORETICAL INVESTIGATION OF HOT SILICON PLASMA

    Energy Technology Data Exchange (ETDEWEB)

    Xiong, Gang; Yang, Jiamin; Zhang, Jiyan; Hu, Zhimin; Zhao, Yang; Qing, Bo; Yang, Guohong; Wei, Minxi; Yi, Rongqing; Song, Tianming; Li, Hang; Yuan, Zheng; Lv, Min [Research Center of Laser Fusion, China Academy of Engineering Physics, Mianyang 621900 (China); Meng, Xujun; Xu, Yan; Wu, Zeqing; Yan, Jun, E-mail: zhangjiyanzjy@sina.com, E-mail: zhimin.hu@yahoo.com [Institute of Applied Physics and Computational Mathematics, Beijing 100088 (China)

    2016-01-01

    We report on opacity measurements of a silicon (Si) plasma at a temperature of (72 ± 5) eV and a density of (6.0 ± 1.2) mg cm{sup −3} in the photon energy range of 1790–1880 eV. A 23 μg cm{sup −2} Si foil tamped by 50 μg cm{sup −2} CH layers on each side was heated to a hot-dense plasma state by X-ray radiation emitted from a D-shaped gold cavity that was irradiated by intense lasers. Absorption lines of 1s − 2p transitions of Si xiii to Si ix ions have been measured using point-projection spectroscopy. The transmission spectrum of the silicon plasma was determined by comparing the light passing through the plasma to the light from the same shot passing by the plasma. The density of the Si plasma was determined experimentally by side-on radiography and the temperature was estimated from the radiation flux data. Radiative hydrodynamic simulations were performed to obtain the temporal evolutions of the density and temperature of the Si plasma. The experimentally obtained transmission spectra of the Si sample plasma have been reproduced using a detailed term account model with the local thermodynamic equilibrium approximation. The energy levels, oscillator strengths and photoionization cross-sections used in the calculation were generated by the flexible atomic code. The experimental transmission spectrum was compared with the theoretical calculation and good agreement was found. The present experimental spectrum and theoretical calculation were also compared with the new opacities available in the Los Alamos OPLIB database.

  1. Measurements of the 492 GHz Atmospheric Opacity at Pampa la Bola and Rio Frio in Northern Chile

    Science.gov (United States)

    Hirota, Tomoya; Yamamoto, Satoshi; Sekimoto, Yutaro; Kohno, Kotaro; Nakai, Naomasa; Kawabe, Ryohei

    1998-02-01

    We have developed a transportable 492 GHz tipping radiometer to measure the atmospheric opacity at potential sites for future ground-based astronomical observations in the submillimeter-wave band. With this radiometer, we measured the atmospheric opacity at two sites in northern Chile, Pampa la Bola (elevation 4800 m) and Rio Frio (elevation 4100 m), each for a few days. The 492 GHz opacity mostly ranged from 0.5 to 1.5 during the measurements. The 220 GHz opacity was also measured at the same time. The 492 GHz opacity correlates well with the 220 GHz opacity, the ratio between the 492 and 220 GHz opacities being 21.2 +/- 0.4. This result supports the standard atmospheric model, and can be used to evaluate the observable fraction of time for submillimeter-wave observations on the basis of the long-term 220 GHz opacity data. } %

  2. 3.5 Year Monitoring of 225 GHz Opacity at the Summit of Greenland

    Science.gov (United States)

    Matsushita, Satoki; Asada, Keiichi; Martin-Cocher, Pierre L.; Chen, Ming-Tang; Ho, Paul T. P.; Inoue, Makoto; Koch, Patrick M.; Paine, Scott N.; Turner, David D.

    2017-02-01

    We present the 3.5 years monitoring results of 225 GHz opacity at the summit of the Greenland ice sheet (Greenland Summit Camp) at an altitude of 3200 m using a tipping radiometer. We chose this site as our submillimeter telescope (Greenland Telescope) site, because conditions are expected to have low submillimeter opacity and because its location offers favorable baselines to existing submillimeter telescopes for global-scale Very Long Baseline Interferometry. The site shows a clear seasonal variation with the average opacity lower by a factor of two during winter. The 25%, 50%, and 75% quartiles of the 225 GHz opacity during the winter months of November through April are 0.046, 0.060, and 0.080, respectively. For the winter quartiles of 25% and 50%, the Greenland site is about 10%-30% worse than the Atacama Large Millimeter/submillimeter Array (ALMA) or the South Pole sites. Estimated atmospheric transmission spectra in winter season are similar to the ALMA site at lower frequencies (\\lt 450 GHz), which are transparent enough to perform astronomical observations almost all of the winter time with opacities \\lt 0.5, but 10%-25% higher opacities at higher frequencies (\\gt 450 GHz) than those at the ALMA site. This is due to the lower altitude of the Greenland site and the resulting higher line wing opacity from pressure-broadened saturated water lines in addition to higher dry air continuum absorption at higher frequencies. Nevertheless, half of the winter time at the Greenland Summit Camp can be used for astronomical observations at frequencies between 450 GHz and 1000 GHz with opacities \\lt 1.2, and 10% of the time show \\gt 10 % transmittance in the THz (1035 GHz, 1350 GHz, and 1500 GHz) windows. Summer season is good for observations at frequencies lower than 380 GHz. One major advantage of the Greenland Summit Camp site in winter is that there is no diurnal variation due to the polar night condition, and therefore the durations of low-opacity conditions

  3. A positive feedback loop between HEAT SHOCK PROTEIN101 and HEAT STRESS-ASSOCIATED 32-KD PROTEIN modulates long-term acquired thermotolerance illustrating diverse heat stress responses in rice varieties.

    Science.gov (United States)

    Lin, Meng-yi; Chai, Kuo-hsing; Ko, Swee-suak; Kuang, Lin-yun; Lur, Huu-sheng; Charng, Yee-yung

    2014-04-01

    Heat stress is an important factor that has a negative impact on rice (Oryza sativa) production. To alleviate this problem, it is necessary to extensively understand the genetic basis of heat tolerance and adaptability to heat stress in rice. Here, we report the molecular mechanism underlying heat acclimation memory that confers long-term acquired thermotolerance (LAT) in this monocot plant. Our results showed that a positive feedback loop formed by two heat-inducible genes, HEAT SHOCK PROTEIN101 (HSP101) and HEAT STRESS-ASSOCIATED 32-KD PROTEIN (HSA32), at the posttranscriptional level prolongs the effect of heat acclimation in rice seedlings. The interplay between HSP101 and HSA32 also affects basal thermotolerance of rice seeds. These findings are similar to those reported for the dicot plant Arabidopsis (Arabidopsis thaliana), suggesting a conserved function in plant heat stress response. Comparison between two rice cultivars, japonica Nipponbare and indica N22 showed opposite performance in basal thermotolerance and LAT assays. 'N22' seedlings have a higher basal thermotolerance level than cv Nipponbare and vice versa at the LAT level, indicating that these two types of thermotolerance can be decoupled. The HSP101 and HSA32 protein levels were substantially higher in cv Nipponbare than in cv N22 after a long recovery following heat acclimation treatment, at least partly explaining the difference in the LAT phenotype. Our results point out the complexity of thermotolerance diversity in rice cultivars, which may need to be taken into consideration when breeding for heat tolerance for different climate scenarios.

  4. The impact of enhanced iron opacity on massive star pulsations: updated instability strips

    Science.gov (United States)

    Moravveji, Ehsan

    2016-01-01

    Recently, Bailey et al. made a direct measurement of the iron opacity at the physical conditions of the solar tachocline. They found that the wavelength-integrated iron opacity is roughly 75 per cent higher than what the Opacity Project (OP) and OPAL models predict. Here, we compute new opacity tables with enhanced iron and nickel contributions to the Rosseland mean opacity by 75 per cent each, and compute three dense MESA grids of evolutionary models for Galactic O- and B-type stars covering from 2.5 to 25 M⊙ from zero-age main sequence (ZAMS) until Teff = 10 000 K after the core hydrogen exhaustion. We carry out non-adiabatic mode stability analysis with GYRE, and update the extension of the instability strips of heat-driven p- and g-mode pulsators, and the hybrid slowly pulsating B (SPB) - β Cep stars. We compare the position of two confirmed late O-type β Cep and eight confirmed hybrid B-type pulsators with the new instability domains, and justify that ˜75 per cent enhancement, only in iron opacity, is sufficient to consistently reproduce the observed position of these stars on the log Teff versus log g plane. We propose that this improvement in opacities be incorporated in the input physics of new stellar models.

  5. Detailed investigations on radiative opacity and emissivity of tin plasmas in the extreme-ultraviolet region.

    Science.gov (United States)

    Zeng, Jiaolong; Gao, Cheng; Yuan, Jianmin

    2010-08-01

    Radiative opacity and emissivity of tin plasmas at average ionization degree of about 10 was investigated in detail by using a fully relativistic detailed level accounting approach, in which main physical effects on the opacity were carefully taken into account. Among these physical effects, configuration interaction, in particular core-valence electron correlations, plays an important role on the determination of accurate atomic data required in the calculation of opacity. It results in a strong narrowing of lines from all transition arrays and strong absorption is located in a narrow wavelength region of 12.5-14 nm for Sn plasmas. Using a complete accurate atomic data, we investigated the opacity of Sn plasmas at a variety of physical condition. Among the respective ions of Xe6+-Xe15+ , Xe10+ has the largest absorption cross section at 13.5 nm, while the favorable physical condition for maximal absorption at 13.5 nm do not mean that Xe10+ has the largest fraction. Comparison with other theoretical results showed that a complete set of consistent accurate atomic data, which lacks very much, is essential to predict accurate opacity. Our atomic model is useful and can be applied to interpret opacity experiments. Further benchmark experiments are urgently needed to clarify the physical effects on the opacity of Sn plasmas.

  6. Using xRage to Model Heat Flow for Experiments to Measure Opacities in HED Plasmas

    Science.gov (United States)

    Elgin, L.; Vandervort, R.; Keiter, P.; Drake, R. P.; Mussack, K.; Orban, C.

    2015-11-01

    We are developing a NIF proposal to measure opacities of C, N and O at temperatures and densities relevant to the base of the solar convection zone. Our proposed experiments would provide the first opacity measurements for these elements within this HED regime. A critical feature of our experimental platform is a super-sonic radiation front propagating within the targets. Under these conditions, density remains constant across the radiation front for a couple nanoseconds, enabling a window during which the opacities of the hot and cold target may be measured simultaneously. Afterwards, hydrodynamic effects create temperature and density gradients, which would obfuscate analysis of opacity data. We are using xRage to simulate heat flow within our targets in order to estimate the time scale over which temperature and density gradients evolve. These simulations will better inform our target design and diagnostic requirements. If successful, our experiments could yield the data necessary to validate existing opacity models or provide physical insights to inform the development of new opacity models. Accurate opacity models are essential to the understanding of radiation transport within HED systems, with applications ranging from astrophysics to ICF. U.S. Department of Energy, through the NNSA-DS and SC-OFES Joint Program in High-Energy-Density Laboratory Plasmas, grant #DE-NA0001840. Los Alamos National Laboratory, LA-UR-15-25490.

  7. Cloning of full-length cDNA of Microsporum canis membrane protein PQ-loop repeat protein gene%犬小孢子菌膜蛋白PQ-LRP基因全长cDNA的克隆

    Institute of Scientific and Technical Information of China (English)

    庞娟; 祝逸平; 杨国玲

    2012-01-01

    Objective To clone the full-length cDNA of Microsporum canis membrane protein PQ-loop repeat protein (PQ-LRP) gene,so as to investigate the roles of PQ-LRP in the pathogenesis of tinea capitis.Methods A Microsporum canis strain (A518) from a patient with tinea capitis served as the experimental strain.Rapid cDNA end amplification (RACE) was performed to clone the full length cDNA sequence of PQLRP gene.Bioinformatics methods were used to make a preliminary functional analysis of the gene.Results The cDNA of PQ-LRP gene was obtained with a full length of 1522 bp,including the 5' untranslated region (49 bp),coding region (1080 bp) and 3' untranslated region (393 bp).The coding region encoded a protein precursor including 359 amino acid residues.The cloned cDNA of PQ-LRP gene shared an 81% nucleotide identity with that of Trichophyton tonsurans and a 79% nucleotide identity with that of Trichophyton rubrum.Conclusions The full-length cDNA of Microsporum canis membrane protein PQ-LRP gene has been successfully cloned,which will provide an important basis for further researches into the roles of PQ-LRP in Microsporum canis-associated diseases.%目的 克隆犬小孢子菌膜蛋白PQ-LRP(PQ-loop repeat protein)基因全长cDNA,探讨在头癣发病机制中的作用.方法 选用犬小孢子菌头癣株(A518)为实验株,采用cDNA快速末端扩增法(RACE),克隆PQ-LRP基因的全长序列.结合生物信息学方法对获得的序列进行初步功能分析.结果 获得犬小孢子菌PQ-LRP全长序列为1522 bp,拥有一个1080 bp的开放阅读框,编码359个氨基酸,5 '非编码区为49 bp,3 '非编码区为393 bp;同源性比对与断发毛癣菌的PQ-LRP同源性达到81%,与红色毛癣菌PQ-LRP同源性达到79%.结论 克隆出犬小孢子菌膜蛋白PQ-LRP cDNA全长序列,为研究膜蛋白PQ-LRP基因在犬小孢子菌病中的功能奠定基础.

  8. The finite Bruck Loops

    CERN Document Server

    Baumeister, Barbara

    2009-01-01

    We continue the work by Aschbacher, Kinyon and Phillips [AKP] as well as of Glauberman [Glaub1,2] by describing the structure of the finite Bruck loops. We show essentially that a finite Bruck loop $X$ is the direct product of a Bruck loop of odd order with either a soluble Bruck loop of 2-power order or a product of loops related to the groups $PSL_2(q)$, $q= 9$ or $q \\geq 5$ a Fermat prime. The latter possibillity does occur as is shown in [Nag1, BS]. As corollaries we obtain versions of Sylow's, Lagrange's and Hall's Theorems for loops.

  9. Systematic measurements of opacity dependence on temperature, density, and atomic number at stellar interior conditions

    Science.gov (United States)

    Bailey, James; Nagayama, T.; Loisel, G. P.; Rochau, G. A.; Blancard, C.; Colgan, J.; Cosse, Ph.; Faussurier, G.; Fontes, C. J.; Golovkin, I.; Hansen, S. B.; Iglesias, C. A.; Kilcrease, D. P.; Macfarlane, J. J.; Mancini, R. C.; Nahar, S. N.; Orban, C.; Pradhan, A. K.; Sherrill, M.; Wilson, B. G.; Pain, J. C.; Gilleron, F.

    2016-10-01

    Model predictions for iron opacity are notably different from measurements performed at conditions similar to the boundary between the solar radiation and convection zone. New measurements at the Sandia Z facility with chromium, iron, and nickel are providing a systematic study of how opacity changes with temperature, density, and atomic number. These measurements help further evaluate possibilities for experiment errors and help constrain hypotheses for opacity model refinements. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy under contract DE-AC04-94AL85000.

  10. Theoretical Study of the Opacity for Mixture Materials at High Temperatures

    Institute of Scientific and Technical Information of China (English)

    颜君; 吴泽清; 逄锦桥; 邱玉波

    2002-01-01

    Using a detailed configuration accounting model with term structures treated by the unresolved transition array model, we have extensively investigated the opacities of mixt ure materials. For plasmas at the temperat ure of 250eV and density of 1 g/cm3, our calculated Rosseland mean opacities are in good agreement with other theoretical results. A high increase in the Rosseland mean opacity to 2944 cm2/g is achieved for a multi-element mixture compared to the value of 1729 cm2/g for pure gold. Various mixtures at other plasma conditions are also studied.

  11. Transcriptome Analysis of the Central and Peripheral Nervous Systems of the Spider Cupiennius salei Reveals Multiple Putative Cys-Loop Ligand Gated Ion Channel Subunits and an Acetylcholine Binding Protein.

    Directory of Open Access Journals (Sweden)

    Päivi H Torkkeli

    Full Text Available Invertebrates possess a diverse collection of pentameric Cys-loop ligand gated ion channel (LGIC receptors whose molecular structures, evolution and relationships to mammalian counterparts have been intensely investigated in several clinically and agriculturally important species. These receptors are targets for a variety of control agents that may also harm beneficial species. However, little is known about Cys-loop receptors in spiders, which are important natural predators of insects. We assembled de novo transcriptomes from the central and peripheral nervous systems of the Central American wandering spider Cupiennius salei, a model species for neurophysiological, behavioral and developmental studies. We found 15 Cys-loop receptor subunits that are expected to form anion or cation permeable channels, plus a putative acetylcholine binding protein (AChBP that has only previously been reported in molluscs and one annelid. We used phylogenetic and sequence analysis to compare the spider subunits to homologous receptors in other species and predicted the 3D structures of each protein using the I-Tasser server. The quality of homology models improved with increasing sequence identity to the available high-resolution templates. We found that C. salei has orthologous γ-aminobutyric acid (GABA, GluCl, pHCl, HisCl and nAChα LGIC subunits to other arthropods, but some subgroups are specific to arachnids, or only to spiders. C. salei sequences were phylogenetically closest to gene fragments from the social spider, Stegodyphus mimosarum, indicating high conservation within the Araneomorphae suborder of spiders. C. salei sequences had similar ligand binding and transmembrane regions to other invertebrate and vertebrate LGICs. They also had motifs associated with high sensitivity to insecticides and antiparasitic agents such as fipronil, dieldrin and ivermectin. Development of truly selective control agents for pest species will require information about

  12. Mixed quotation: The grammar of apparently transparent opacity

    Directory of Open Access Journals (Sweden)

    Emar Maier

    2014-05-01

    Full Text Available The phenomenon of mixed quotation exhibits clear signs of both the apparent transparency of compositional language use and the opacity of pure quotation. I argue that the interpretation of a mixed quotation in- volves the resolution of a metalinguistic presupposition. The leading idea behind my proposal is that a mixed-quoted expression, say, “has an anomalous feature”, means what x referred to with the words ‘has an anomalous feature’. To understand how this solves the paradox, I set up a precise grammatical framework, explicitly connecting various levels of linguistic analysis: phonological forms, categorial syntax, and a dynamic picture of the semantics–pragmatics interface. In this framework I formalize and evaluate a presuppositional account of mixed quotation. Finally, I address the phenomenon of unquotation and argue that it is an essential ingredient for an elegant and empirically adequate analysis of mixed quotation in natural language. http://dx.doi.org/10.3765/sp.7.7 BibTeX info

  13. Formation of Chromosomal Domains by Loop Extrusion

    Directory of Open Access Journals (Sweden)

    Geoffrey Fudenberg

    2016-05-01

    Full Text Available Topologically associating domains (TADs are fundamental structural and functional building blocks of human interphase chromosomes, yet the mechanisms of TAD formation remain unclear. Here, we propose that loop extrusion underlies TAD formation. In this process, cis-acting loop-extruding factors, likely cohesins, form progressively larger loops but stall at TAD boundaries due to interactions with boundary proteins, including CTCF. Using polymer simulations, we show that this model produces TADs and finer-scale features of Hi-C data. Each TAD emerges from multiple loops dynamically formed through extrusion, contrary to typical illustrations of single static loops. Loop extrusion both explains diverse experimental observations—including the preferential orientation of CTCF motifs, enrichments of architectural proteins at TAD boundaries, and boundary deletion experiments—and makes specific predictions for the depletion of CTCF versus cohesin. Finally, loop extrusion has potentially far-ranging consequences for processes such as enhancer-promoter interactions, orientation-specific chromosomal looping, and compaction of mitotic chromosomes.

  14. Modeling loop entropy.

    Science.gov (United States)

    Chirikjian, Gregory S

    2011-01-01

    Proteins fold from a highly disordered state into a highly ordered one. Traditionally, the folding problem has been stated as one of predicting "the" tertiary structure from sequential information. However, new evidence suggests that the ensemble of unfolded forms may not be as disordered as once believed, and that the native form of many proteins may not be described by a single conformation, but rather an ensemble of its own. Quantifying the relative disorder in the folded and unfolded ensembles as an entropy difference may therefore shed light on the folding process. One issue that clouds discussions of "entropy" is that many different kinds of entropy can be defined: entropy associated with overall translational and rotational Brownian motion, configurational entropy, vibrational entropy, conformational entropy computed in internal or Cartesian coordinates (which can even be different from each other), conformational entropy computed on a lattice, each of the above with different solvation and solvent models, thermodynamic entropy measured experimentally, etc. The focus of this work is the conformational entropy of coil/loop regions in proteins. New mathematical modeling tools for the approximation of changes in conformational entropy during transition from unfolded to folded ensembles are introduced. In particular, models for computing lower and upper bounds on entropy for polymer models of polypeptide coils both with and without end constraints are presented. The methods reviewed here include kinematics (the mathematics of rigid-body motions), classical statistical mechanics, and information theory.

  15. Pseudonoise code tracking loop

    Science.gov (United States)

    Laflame, D. T. (Inventor)

    1980-01-01

    A delay-locked loop is presented for tracking a pseudonoise (PN) reference code in an incoming communication signal. The loop is less sensitive to gain imbalances, which can otherwise introduce timing errors in the PN reference code formed by the loop.

  16. Large enhancement in high-energy photoionization of Fe XVII and missing continuum plasma opacity

    CERN Document Server

    Nahar, Sultana N

    2016-01-01

    Aimed at solving the outstanding problem of solar opacity, and radiation transport plasma models in general, we report substantial photoabsorption in the high-energy regime due to atomic core photo-excitations not heretofore considered. In extensive R-Matrix calculations of unprecedented complexity for an important iron ion Fe xvii (Fe$^{16+}$), with a wave function expansion of 99 Fe xviii (Fe$^{17+}$) LS core states from $n \\leq 4$ complexes (equivalent to 218 fine structure levels), we find: i) up to orders of magnitude enhancement in background photoionization cross sections, in addition to strongly peaked photo-excitation-of-core resonances not considered in current opacity models, and ii) demonstrate convergence with respect to successive core excitations. The resulting increase in the monochromatic continuum, and 35% in the Rosseland Mean Opacity, are compared with the "higher-than-predicted" iron opacity measured at the Sandia Z-pinch fusion device at solar interior conditions.

  17. Radiative opacity of plasmas studied by detailed term (level) accounting approaches

    Institute of Scientific and Technical Information of China (English)

    ZENG Jiao-long; JIN Feng-tao; YUAN Jian-min

    2006-01-01

    Detailed term and level accounting (DTA and DLA) schemes have been developed to calculate the spectrally resolved and Rosseland and Planck mean opacities of plasmas in local thermodynamic equilibrium.Various physical effects,such as configuration interaction effect (including core-valence electron correlations effect and relativistic effect),detailed line width effect (including the line saturation effect),etc.,on the opacity of plasmas have been investigated in detail.Some of these physical effects are less capable or even impossible to be taken into account by statistical models such as unresolved transition arrays,super-transitionarray or average atom models.Our detailed model can obtain accurate opacity of plasmas.Using this model,we have systematically investigated the radiative opacities of low,medium and high-Z plasmas under different conditions of temperature and density.For example,for aluminum plasma,in the X-ray region,we demonstrated the effects of autoionization resonance broadening on the opacity for the first time.Furthermore,the relativistic effects play an important role on the opacity as well.Our results are in good agreement with other theoretical ones although better agreement can be obtained after the effects of autoionization resonance broadening and relativity have been considered.Our results also show that the modelling of the opacity is very complicated,since too many physical effects influence the accuracy of opacity.``For medium and high-Z plasmas,however,there are systematic discrepancies unexplained so far between the theoretical and experimental opacities.Here,the theoretical opacities are mainly obtained by statistical models.To clarify the discrepaneies,efforts from both sides are needed.From the viewpoint of theory,however,a DLA method,in which various physical effects can be taken into account,should be useful in resolving the difference.Taking gold plasma as an example,we studied in detail the effects of core-valence electron

  18. Computational Design of Short Pulse Laser Driven Iron Opacity Measurements at Stellar-Relevant Conditions

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Madison E. [Univ. of Florida, Gainesville, FL (United States)

    2017-05-20

    Opacity is a critical parameter in the simulation of radiation transport in systems such as inertial con nement fusion capsules and stars. The resolution of current disagreements between solar models and helioseismological observations would bene t from experimental validation of theoretical opacity models. Overall, short pulse laser heated iron experiments reaching stellar-relevant conditions have been designed with consideration of minimizing tamper emission and optical depth effects while meeting plasma condition and x-ray emission goals.

  19. OPAC AS DOCUMENT RETRIEVAL TOOL: A CASE STUDY OF THE UNIVERSITY OF KASHMIR

    Directory of Open Access Journals (Sweden)

    Uzma Qadri, Research Scholar,

    2012-01-01

    Full Text Available The application of the information and communication technology has changed the entireenvironment of the library including cataloguing. Today, a number of libraries are providingOnline Public Access Cataloguing service to their users to find out their documents and theAllama Iqbal Library, University of Kashmir isn’t an exception. The main purpose of the study isto measure the faculty wise use of OPAC by the P G students of University of Kashmir. Toaccomplish the purpose of the study, survey method was adopted and questionnaire was used asdata collection tool. The questionnaire was distributed among 260 students selecting 10 students from each department in the month of May 2012. However, only 241 students returned the filled questionnaire with response rate of 92.69 %. The results revealed that 60% of the respondents use OPAC to search the library collection whereas 40% don’t use it at all. The students who use OPAC cite many features like time saving; fast response; remote access etc. and the students don’t use OPAC mostly due to awareness problem. This study found that most of the student learn to operate OPAC from themselves followed by friends/colleagues and library staff. The students search the library material mostly through subject, author and title approach. At the end, the fruitful suggestions are provided for greater use of OPAC.

  20. How the machine ‘thinks’: Understanding opacity in machine learning algorithms

    Directory of Open Access Journals (Sweden)

    Jenna Burrell

    2016-01-01

    Full Text Available This article considers the issue of opacity as a problem for socially consequential mechanisms of classification and ranking, such as spam filters, credit card fraud detection, search engines, news trends, market segmentation and advertising, insurance or loan qualification, and credit scoring. These mechanisms of classification all frequently rely on computational algorithms, and in many cases on machine learning algorithms to do this work. In this article, I draw a distinction between three forms of opacity: (1 opacity as intentional corporate or state secrecy, (2 opacity as technical illiteracy, and (3 an opacity that arises from the characteristics of machine learning algorithms and the scale required to apply them usefully. The analysis in this article gets inside the algorithms themselves. I cite existing literatures in computer science, known industry practices (as they are publicly presented, and do some testing and manipulation of code as a form of lightweight code audit. I argue that recognizing the distinct forms of opacity that may be coming into play in a given application is a key to determining which of a variety of technical and non-technical solutions could help to prevent harm.

  1. Coagulation and Fragmentation in molecular clouds. II. The opacity of the dust aggregate size distribution

    CERN Document Server

    Ormel, C W; Tielens, A G G M; Dominik, C; Paszun, D

    2011-01-01

    The dust size distribution in molecular clouds can be strongly affected by ice-mantle formation and (subsequent) grain coagulation. Following previous work where the dust size distribution has been calculated from a state-of-the art collision model for dust aggregates that involves both coagulation and fragmentation (Paper I), the corresponding opacities are presented in this study. The opacities are calculated by applying the effective medium theory assuming that the dust aggregates are a mix of 0.1{\\mu}m silicate and graphite grains and vacuum. In particular, we explore how the coagulation affects the near-IR opacities and the opacity in the 9.7{\\mu}m silicate feature. We find that as dust aggregates grow to {\\mu}m-sizes both the near-IR color excess and the opacity in the 9.7 {\\mu}m feature increases. Despite their coagulation, porous aggregates help to prolong the presence of the 9.7{\\mu}m feature. We find that the ratio between the opacity in the silicate feature and the near-IR color excess becomes lowe...

  2. How the machine ‘thinks’: Understanding opacity in machine learning algorithms

    Directory of Open Access Journals (Sweden)

    Jenna Burrell

    2016-01-01

    Full Text Available This article considers the issue of opacity as a problem for socially consequential mechanisms of classification and ranking, such as spam filters, credit card fraud detection, search engines, news trends, market segmentation and advertising, insurance or loan qualification, and credit scoring. These mechanisms of classification all frequently rely on computational algorithms, and in many cases on machine learning algorithms to do this work. In this article, I draw a distinction between three forms of opacity: (1 opacity as intentional corporate or state secrecy, (2 opacity as technical illiteracy, and (3 an opacity that arises from the characteristics of machine learning algorithms and the scale required to apply them usefully. The analysis in this article gets inside the algorithms themselves. I cite existing literatures in computer science, known industry practices (as they are publicly presented, and do some testing and manipulation of code as a form of lightweight code audit. I argue that recognizing the distinct forms of opacity that may be coming into play in a given application is a key to determining which of a variety of technical and non-technical solutions could help to prevent harm.

  3. Supersymmetric Wilson loops at two loops

    CERN Document Server

    Bassetto, Antonio; Pucci, Fabrizio; Seminara, Domenico

    2008-01-01

    We study the quantum properties of certain BPS Wilson loops in ${\\cal N}=4$ supersymmetric Yang-Mills theory. They belong to a general family, introduced recently, in which the addition of particular scalar couplings endows generic loops on $S^3$ with a fraction of supersymmetry. When restricted to $S^2$, their quantum average has been further conjectured to be exactly computed by the matrix model governing the zero-instanton sector of YM$_2$ on the sphere. We perform a complete two-loop analysis on a class of cusped Wilson loops lying on a two-dimensional sphere, finding perfect agreement with the conjecture. The perturbative computation reproduces the matrix-model expectation through a highly non-trivial interplay between ladder diagrams and self-energies/vertex contributions, suggesting the existence of a localization procedure.

  4. R-loopDB: a database for R-loop forming sequences (RLFS) and R-loops

    Science.gov (United States)

    Jenjaroenpun, Piroon; Wongsurawat, Thidathip; Sutheeworapong, Sawannee; Kuznetsov, Vladimir A.

    2017-01-01

    R-loopDB (http://rloop.bii.a-star.edu.sg) was originally constructed as a collection of computationally predicted R-loop forming sequences (RLFSs) in the human genic regions. The renewed R-loopDB provides updates, improvements and new options, including access to recent experimental data. It includes genome-scale prediction of RLFSs for humans, six other animals and yeast. Using the extended quantitative model of RLFSs (QmRLFS), we significantly increased the number of RLFSs predicted in the human genes and identified RLFSs in other organism genomes. R-loopDB allows searching of RLFSs in the genes and in the 2 kb upstream and downstream flanking sequences of any gene. R-loopDB exploits the Ensembl gene annotation system, providing users with chromosome coordinates, sequences, gene and genomic data of the 1 565 795 RLFSs distributed in 121 056 genic or proximal gene regions of the covered organisms. It provides a comprehensive annotation of Ensembl RLFS-positive genes including 93 454 protein coding genes, 12 480 long non-coding RNA and 7 568 small non-coding RNA genes and 7 554 pseudogenes. Using new interface and genome viewers of R-loopDB, users can search the gene(s) in multiple species with keywords in a single query. R-loopDB provides tools to carry out comparative evolution and genome-scale analyses in R-loop biology. PMID:27899586

  5. Iron Opacity Bump Changes the Stability and Structure of Accretion Disks in Active Galactic Nuclei

    Science.gov (United States)

    Jiang, Yan-Fei; Davis, Shane W.; Stone, James M.

    2016-08-01

    Accretion disks around supermassive black holes have regions where the Rosseland mean opacity can be larger than the electron scattering opacity due to the large number of bound-bound transitions in iron. We study the effects of this iron opacity “bump” on the thermal stability and vertical structure of radiation-pressure-dominated accretion disks, utilizing three-dimensional radiation magnetohydrodynamic (MHD) simulations in the local shearing box approximation. The simulations self-consistently calculate the heating due to MHD turbulence caused by magneto-rotational instability and radiative cooling by using the radiative transfer module based on a variable Eddington tensor in Athena. For a 5 × 108 solar mass black hole with ˜3% of the Eddington luminosity, a model including the iron opacity bump maintains its structure for more than 10 thermal times without showing significant signs of thermal runaway. In contrast, if only electron scattering and free-free opacity are included as in the standard thin disk model, the disk collapses on the thermal timescale. The difference is caused by a combination of (1) an anti-correlation between the total optical depth and the midplane pressure, and (2) enhanced vertical advective energy transport. These results suggest that the iron opacity bump may have a strong impact on the stability and structure of active galactic nucleus (AGN) accretion disks, and may contribute to a dependence of AGN properties on metallicity. Since this opacity is relevant primarily in UV emitting regions of the flow, it may help to explain discrepancies between observation and theory that are unique to AGNs.

  6. Experimental Validation of Modeled Fe Opacities at Conditions Approaching the Base of the Solar Convection Zone

    Science.gov (United States)

    Nagayama, Taisuke

    2013-10-01

    Knowledge of the Sun is a foundation for other stars. However, after the solar abundance revision in 2005, standard solar models disagree with helioseismic measurements particularly at the solar convection zone base (CZB, r ~ 0 . 7 ×RSun) [Basu, et al., Physics Reports 457, 217 (2008)]. One possible explanation is an underestimate in the Fe opacity at the CZB [Bailey et al., Phys. Plasmas 16, 058101 (2009)]. Modeled opacities are important physics inputs for plasma simulations (e.g. standard solar models). However, modeled opacities are not experimentally validated at high temperatures because of three challenging criteria required for reliable opacity measurements: 1) smooth and strong backlighter, 2) plasma condition uniformity, and 3) simultaneous measurements of plasma condition and transmission. Fe opacity experiments are performed at the Sandia National Laboratories (SNL) Z-machine aiming at conditions close to those at the CZB (i.e. Te = 190 eV, ne = 1 ×1023 cm-3). To verify the quality of the experiments, it is critical to investigate how well the three requirements are satisfied. The smooth and strong backlighter is provided by the SNL Z-pinch dynamic hohlraum. Fe plasma condition is measured by mixing Mg into the Fe sample and employing Mg K-shell line transmission spectroscopy. Also, an experiment is designed and performed to measure the level of non-uniformity in the Fe plasma by mixing Al and Mg dopants on the opposite side of the Fe sample and analyzing their spectra. We will present quantitative results on these investigations as well as the comparison of the measured opacity to modeled opacities. Sandia is a multi-program laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy under contract DE-AC04-94AL85000.

  7. The influence of urban area opacity on biologically active UV-B irradiance

    Science.gov (United States)

    Chubarova, Nataly; Rozental', Victor

    2013-04-01

    The study of UV irradiance changes in urban area is an essential problem due to the significant effect of UV irradiance on human health which can be positive (vitamin D synthesis) and negative (erythema, skin cancer, eye damage). According to the results of several experiments within the Moscow megacity we studied the effects of urban area opacity on the different types of biologically active UV-B irradiance on the base of a specially developed mobile photometric complex snd additional measurements of the urban opacity by Nikon Fisheye Converter FC-E8. We analyzed both the level of erythemally-active irradiance and the UV eye damaging radiation using the broadband UVB-1 YES pyranometer calibrated against ultraviolet spectroradiometer Bentham DTM-300 of the Medical University of Innsbruck (courtesy of Dr. M.Blumthaler). In order to estimate the effects of the urban opacity the measurements were normalized on similar measurements at the Meteorological Observatory of Moscow State University with zero opacity. This ratio is defined as an urban radiative transmittance (URT). Different atmospheric conditions were considered. In cloudy conditions the effect of opacity on URT is much less than that in conditions when the sun disk is open from clouds. We revealed some spectral features in transmittance of biologically active UV-B irradiance which is characterized by higher URT variations in overcast cloudy conditions due to more intensive scattering and smaller direct solar radiation component. In the absence of cloudiness the effect of opacity was studied for open and screening solar disk conditions. We obtained much higher URT in UVB spectral region compared with that for total solar irradiance for screening solar disk conditions with a significant URT dependence on the opacity only in UVB spectral region. No URT dependence was obtained for total solar irradiance in these conditions. Some model calculations were fulfilled to match the experimental results.

  8. Loop residues and catalysis in OMP synthase

    DEFF Research Database (Denmark)

    Wang, Gary P.; Hansen, Michael Riis; Grubmeyer, Charles

    2012-01-01

    (preceding paper in this issue, DOI 10.1021/bi300083p)]. The full expression of KIEs by H105A and E107A may result from a less secure closure of the catalytic loop. The lower level of expression of the KIE by K103A suggests that in these mutant proteins the major barrier to catalysis is successful closure...... of the catalytic loop, which when closed, produces rapid and reversible catalysis....

  9. Cosmic string loop shapes

    CERN Document Server

    Blanco-Pillado, Jose J; Shlaer, Benjamin

    2015-01-01

    We analyze the shapes of cosmic string loops found in large-scale simulations of an expanding-universe string network. The simulation does not include gravitational back reaction, but we model that process by smoothing the loop using Lorentzian convolution. We find that loops at formation consist of generally straight segments separated by kinks. We do not see cusps or any cusp-like structure at the scale of the entire loop, although we do see very small regions of string that move with large Lorentz boosts. However, smoothing of the string almost always introduces two cusps on each loop. The smoothing process does not lead to any significant fragmentation of loops that were in non-self-intersecting trajectories before smoothing.

  10. Coxeter-Chein Loops

    CERN Document Server

    Blok, Rieuwert J

    2011-01-01

    In 1974 Orin Chein discovered a new family of Moufang loops which are now called Chein loops. Such a loop can be created from any group $W$ together with $\\mathbb{Z}_2$ by a variation on a semi-direct product. We study these loops in the case where $W$ is a Coxeter group and show that it has what we call a Chein-Coxeter system, a small set of generators of order 2, together with a set of relations closely related to the Coxeter relations and Chein relations. As a result we are able to give amalgam presentations for Coxeter-Chein loops. This is to our knowledge the first such presentation for a Moufang loop.

  11. Features of a Spatially Constrained Cystine Loop in the p10 FAST Protein Ectodomain Define a New Class of Viral Fusion Peptides*

    OpenAIRE

    Barry, Christopher; Key, Tim; Haddad, Rami; Duncan, Roy

    2010-01-01

    The reovirus fusion-associated small transmembrane (FAST) proteins are the smallest known viral membrane fusion proteins. With ectodomains of only ∼20–40 residues, it is unclear how such diminutive fusion proteins can mediate cell-cell fusion and syncytium formation. Contained within the 40-residue ectodomain of the p10 FAST protein resides an 11-residue sequence of moderately apolar residues, termed the hydrophobic patch (HP). Previous studies indicate the p10 HP shares operational features ...

  12. Coxeter-Chein Loops

    OpenAIRE

    Blok, Rieuwert J.; Gagola III, Stephen

    2011-01-01

    In 1974 Orin Chein discovered a new family of Moufang loops which are now called Chein loops. Such a loop can be created from any group $W$ together with $\\mathbb{Z}_2$ by a variation on a semi-direct product. We study these loops in the case where $W$ is a Coxeter group and show that it has what we call a Chein-Coxeter system, a small set of generators of order 2, together with a set of relations closely related to the Coxeter relations and Chein relations. As a result we are able to give am...

  13. Observational Evidence for Loop-Loop Interaction

    Science.gov (United States)

    Guiping, W.; Guangli, H.; Yuhua, T.; Aoao, X.

    2004-01-01

    Through analysis of the data including the hard x-ray(BASTE) microwave(NoRP) and magnetogram(MDI from SOHO) as well as the images of soft x-ray(YHKOH) and EIT(SOHO) on Apr. 151998 solar flare in the active region 8203(N30W12) we found: (1) there are similar quasi period oscillation in the profile of hard x-ray flux (25-5050-100keV) and microwave flux(1GHz) with duration of 85+/-25s every peak includes two sub-peak structures; (2) in the preheat phase of the flare active magnetic field changes apparently and a s-pole spot emerges ; (3) several EIT and soft x-ray loops exist and turn into bright . All of these may suggest that loop-loop interaction indeed exist. Through reconnection the electrons may be accelerated and the hard x-ray and microwave emission take place.

  14. Modification of a loop sequence between α-helices 6 and 7 of virus capsid (CA protein in a human immunodeficiency virus type 1 (HIV-1 derivative that has simian immunodeficiency virus (SIVmac239 vif and CA α-helices 4 and 5 loop improves replication in cynomolgus monkey cells

    Directory of Open Access Journals (Sweden)

    Adachi Akio

    2009-08-01

    Full Text Available Abstract Background Human immunodeficiency virus type 1 (HIV-1 productively infects only humans and chimpanzees but not cynomolgus or rhesus monkeys while simian immunodeficiency virus isolated from macaque (SIVmac readily establishes infection in those monkeys. Several HIV-1 and SIVmac chimeric viruses have been constructed in order to develop an animal model for HIV-1 infection. Construction of an HIV-1 derivative which contains sequences of a SIVmac239 loop between α-helices 4 and 5 (L4/5 of capsid protein (CA and the entire SIVmac239 vif gene was previously reported. Although this chimeric virus could grow in cynomolgus monkey cells, it did so much more slowly than did SIVmac. It was also reported that intrinsic TRIM5α restricts the post-entry step of HIV-1 replication in rhesus and cynomolgus monkey cells, and we previously demonstrated that a single amino acid in a loop between α-helices 6 and 7 (L6/7 of HIV type 2 (HIV-2 CA determines the susceptibility of HIV-2 to cynomolgus monkey TRIM5α. Results In the study presented here, we replaced L6/7 of HIV-1 CA in addition to L4/5 and vif with the corresponding segments of SIVmac. The resultant HIV-1 derivatives showed enhanced replication capability in established T cell lines as well as in CD8+ cell-depleted primary peripheral blood mononuclear cells from cynomolgus monkey. Compared with the wild type HIV-1 particles, the viral particles produced from a chimeric HIV-1 genome with those two SIVmac loops were less able to saturate the intrinsic restriction in rhesus monkey cells. Conclusion We have succeeded in making the replication of simian-tropic HIV-1 in cynomolgus monkey cells more efficient by introducing into HIV-1 the L6/7 CA loop from SIVmac. It would be of interest to determine whether HIV-1 derivatives with SIVmac CA L4/5 and L6/7 can establish infection of cynomolgus monkeys in vivo.

  15. Abundances of Cloud-Related Gases in the Venus Atmosphere as Inferred from Observed Radio Opacity.

    Science.gov (United States)

    Steffes, Paul Gregory

    1982-03-01

    Various radio-analytical techniques have detected microwave opacity in the middle atmosphere of Venus, well above the main carbon dioxide opacity of the lower atmosphere. Consideration of the amount, distribution, and effects of the constituents which produce the main cloud layer at about 50 km altitude, indicate that such cloud-related gases, especially sulfuric acid vapor, are the predominant source of the observed opacity of the middle atmosphere. Theoretical and laboratory studies were made of the microwave absorption from three cloud-related gases: sulfur dioxide, sulfur trioxide, and gaseous sulfuric acid. While the measured absorption from sulfur dioxide under conditions for the middle atmosphere of Venus was found to be 50% larger than suggested by theory, the amount of sulfur dioxide required to explain the opacity as measured by radio occultation exceeded the abundance measured in situ by atmospheric probes, suggesting that there must be another important source of opacity. Sulfur trioxide was tested and found to be relatively transparent, but laboratory measurements of the microwave opacity of gaseous sulfuric acid under Venus atmospheric conditions indicate that it is an exceptionally strong absorber with absorptivity that has a surprisingly weak dependence on radio frequency. Initial theoretical studies also indicate a large absorptivity and weak frequency dependence, although the measured opacity is larger than the computed value, presumably due to deviations from Van Vleck-Weisskopf theory. The absorbing characteristics of sulfuric acid vapor appear to reconcile past inconsistencies among measurements and deductions concerning the constituents of the atmosphere of Venus, and radio occultation, radar reflection, and radio emission measurements of its opacity. The results of the current studies are used with previous data for the absorptivity of water vapor and carbon dioxide to model relative contributions to opacity as a function of height, in a way

  16. Crystal structure of an antigenic outer-membrane protein from Salmonella Typhi suggests a potential antigenic loop and an efflux mechanism.

    Science.gov (United States)

    Guan, Hong-Hsiang; Yoshimura, Masato; Chuankhayan, Phimonphan; Lin, Chien-Chih; Chen, Nai-Chi; Yang, Ming-Chi; Ismail, Asma; Fun, Hoong-Kun; Chen, Chun-Jung

    2015-11-13

    ST50, an outer-membrane component of the multi-drug efflux system from Salmonella enterica serovar Typhi, is an obligatory diagnostic antigen for typhoid fever. ST50 is an excellent and unique diagnostic antigen with 95% specificity and 90% sensitivity and is used in the commercial diagnosis test kit (TYPHIDOT(TM)). The crystal structure of ST50 at a resolution of 2.98 Å reveals a trimer that forms an α-helical tunnel and a β-barrel transmembrane channel traversing the periplasmic space and outer membrane. Structural investigations suggest significant conformational variations in the extracellular loop regions, especially extracellular loop 2. This is the location of the most plausible antibody-binding domain that could be used to target the design of new antigenic epitopes for the development of better diagnostics or drugs for the treatment of typhoid fever. A molecule of the detergent n-octyl-β-D-glucoside is observed in the D-cage, which comprises three sets of Asp361 and Asp371 residues at the periplasmic entrance. These structural insights suggest a possible substrate transport mechanism in which the substrate first binds at the periplasmic entrance of ST50 and subsequently, via iris-like structural movements to open the periplasmic end, penetrates the periplasmic domain for efflux pumping of molecules, including poisonous metabolites or xenobiotics, for excretion outside the pathogen.

  17. The Impact of Enhanced Iron Opacity on Massive Star Pulsations: Updated Instability Strips

    CERN Document Server

    Moravveji, Ehsan

    2015-01-01

    Recently, Bailey et al. (2015) made a direct measurement of the Iron opacity at the physical conditions of the solar tachocline. They found that the wavelength-integrated Iron opacity is roughly 75% higher that what the OP and OPAL models predict. Here, we compute new opacity tables with enhanced Iron and Nickel contributions to the Rosseland mean opacity by 75% each, and compute three dense MESA grids of evolutionary models for Galactic O- and B-type stars covering from 2.5 to 25 M$_\\odot$ from ZAMS until $T_{\\rm eff}=10\\,000$ K after the core hydrogen exhaustion. We carry out non-adiabatic mode stability analysis with GYRE, and update the extension of the instability strips of heat-driven p- and g-mode pulsators, and the hybrid pulsating SPB - $\\beta$ Cep stars. We compare the position of two confirmed late O-type $\\beta$ Cep and eight confirmed hybrid B-type pulsators with the new instability domains, and justify that $\\sim$75% enhancement, only in Iron opacity, is sufficient to consistently reproduce the ...

  18. Tamper asymmetry and its effect on transmission for x-ray driven opacity simulations

    Science.gov (United States)

    Morris, H. E.; Tregillis, I. L.; Hoffman, N. M.; Sherrill, M. E.; Fontes, C. J.; Marshall, A. J.; Urbatsch, T. J.; Bradley, P. A.

    2017-09-01

    This paper reports on synthetic transmission results from Lasnex [Zimmerman and Kruer, Comments Plasma Phys. 2, 51 (1975)] radiation-hydrodynamics simulations of opacity experiments carried out at Sandia National Laboratories' recently upgraded ZR facility. The focus is on experiments utilizing disk targets composed of a half-moon Fe/Mg mixture tamped on either end with 10-μm CH and an additional 35-μm beryllium tamper accessory on the end facing the spectrometer. Five x-ray sources with peak power ranging from 10 to 24 TW were used in the simulations to heat and backlight the opacity target. The dominant effect is that the beryllium behind the Fe/Mg mixture is denser and more opaque than the beryllium unshielded by metal during the times of greatest importance for the transmission measurement for all drives. This causes the simulated transmission to be lower than expected, and this is most pronounced for the case using the lowest drive power. While beryllium has a low opacity, its areal density is sufficiently high such that the expected reduction of the measured transmission is significant. This situation leads to an overestimate of iron opacity by 10%-215% for a photon energy range of 975-1775 eV for the 10-TW case. It is shown that if the tamper conditions are known, the transmission through each component of the target can be calculated and the resulting opacity can be corrected.

  19. Iron and Nickel spectral opacity calculations in conditions relevant for pulsating stellar envelopes and experiments

    Directory of Open Access Journals (Sweden)

    Gilles D.

    2013-11-01

    Full Text Available Seismology of stars is strongly developing. To address this question we have formed an international collaboration, OPAC, to perform specific experimental measurements, compare opacity calculations, and improve the opacity calculations in stellar codes [1]. We consider the following opacity codes: SCO, CASSANDRA, STA, OPAS, LEDCOP, OP, SCO-RCG. Their comparison has shown large differences for Fe and Ni in equivalent conditions of envelopes of type II supernova precursors, temperatures between 15 and 40 eV and densities of a few mg/cm3 [2–4]. LEDCOP, OPAS, SCO-RCG structure codes and STA give similar results and differ from OP ones for the lower temperatures and for spectral interval values [3]. In this work we discuss the role of Configuration Interaction (CI and the influence of the number of used configurations. We present and include in the opacity code comparisons new HULLAC-v9 calculations [5, 6] that include full CI. To illustrate the importance of this effect we compare different CI approximations (modes available in HULLAC-v9 [7]. These results are compared to previous predictions and to experimental data. Differences with OP results are discussed.

  20. Low-temperature gas opacity - AESOPUS: a versatile and quick computational tool

    CERN Document Server

    Marigo, Paola

    2009-01-01

    We introduce a new tool - AESOPUS: Accurate Equation of State and OPacity Utility Software - for computing the equation of state and the Rosseland mean (RM) opacities of matter in the ideal gas phase. Results are given as a function of one pair of state variables, (i.e. temperature T in the range 3.2 <= log(T) <= 4.5, and parameter R= rho/(T/10^6 K)^3 in the range -8 <= log(R) <= 1), and arbitrary chemical mixture. The chemistry is presently solved for about 800 species, consisting of almost 300 atomic and 500 molecular species. The gas opacities account for many continuum and discrete sources, including atomic opacities, molecular absorption bands, and collision-induced absorption. Several tests made on AESOPUS have proved that the new opacity tool is accurate in the results,flexible in the management of the input prescriptions, and agile in terms of computational time requirement. We set up a web-interface (http://stev.oapd.inaf.it/aesopus) which enables the user to compute and shortly retrieve ...

  1. Simultaneous unfolding of compression and opacity from time-resolved radiography

    Science.gov (United States)

    Swift, D.; Hawreliak, J.; Rothman, S.; Kritcher, A.; Doeppner, T.; Collins, G.; Gaffney, J.; Rose, S.

    2013-06-01

    Radiographs of symmetric objects can be analyzed to give the spatial variation of attenuation, as in the Abel inversion of an axisymmetric object. If the opacity is known, the mass density can be derived from the attenuation. The space- and time-variation of density is needed to make equation of state (EOS) measurements by radiography, e.g. by measuring the speed and compression of a shock. However, in our experiments using hohlraum drive at the National Ignition Facility (NIF) to perform EOS measurements at gigabar pressures with spherically-converging shocks, the opacity may vary by an order of magnitude because of ionization. We have developed a new algorithm to simultaneously deduce the compression and opacity of the sample given time-resolved radiographs with a Lagrangian location behind the shock, such as the edge of the sample. This approach relies on spatial integration to deduce the opacity in the region just behind the shock from the difference between the known and apparent mass. We assume that the change in opacity is dominated by shock-heating, so that subsequent variations, as shocked material is either released or compressed further, are negligible or can be accounted for by a model. We used this algorithm to analyze our NIF data on the Hugoniot of CH at 10-40 TPa. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

  2. The significance of recurrent lung opacities in neonates on surfactant treatment for respiratory distress syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Odita, J.C. [Dept. of Radiology, Louisiana State Univ. Health Sciences Center, Shreveport (United States)

    2001-02-01

    Purpose. To determine the significance of recurrent opacities in chest radiographs of neonates on surfactant therapy for respiratory distress syndrome (RDS) after an initial period of improvement. Materials and methods. Serial pre- and post-surfactant chest radiographs on 94 preterm infants with RDS were analyzed and the pattern of chest radiographic response was classified as (a) clear, (b) recurrent opacities, and (c) no response. Their clinical characteristics were also recorded. Results. In 34 infants the RDS changes cleared within 3 days. 31 infants developed lung opacities within 10 days after an initial period of improvement. Twenty-nine infants failed to respond to the surfactant. The corresponding mean birth weights for the three groups were 1.74, 1.19, and 0.76 kg and the mean gestation ages 32.6, 27.7, and 25.4 weeks. The incidence of bronchopulmonary dysplasia (BPD) was highest among the slumping infants (72. % vs 50 % in no responders, P < 0.001) Conclusions. The pattern of chest radiographic response is primarily affected by gestation age and birth weight. Recurrent lung opacity after an initial positive response to surfactant therapy may be caused by such factors as edema from barotrauma and patent ductus arteriosus. Infants with intraventricular hemorrhage may demonstrate neurogenic edema. Other contributory factors include pneumonia and abnormal consumption of surfactant. Recurrent lung opacities after surfactant may be a predictor of chronic lung disease in the preterm infant. (orig.)

  3. Iron and Nickel spectral opacity calculations in conditions relevant for pulsating stellar envelopes and experiments

    CERN Document Server

    Gilles, D; Busquet, M; Thais, F; Loisel, G; Piau, L; Ducret, J E; Blenski, T; Blancard, C; Cossé, P; Faussurier, G; Gilleron, F; Pain, J C; Porcherot, Q; Guzik, J A; Kilcrease, D P; Magee, N H; Harris, J; Bastiani-Ceccotti, S; Delahaye, F; Zeippen, C J

    2012-01-01

    Seismology of stars is strongly developing. To address this question we have formed an international collaboration OPAC to perform specific experimental measurements, compare opacity calculations and improve the opacity calculations in the stellar codes [1]. We consider the following opacity codes: SCO, CASSANDRA, STA, OPAS, LEDCOP, OP, SCO-RCG. Their comparison has shown large differences for Fe and Ni in equivalent conditions of envelopes of type II supernova precursors, temperatures between 15 and 40 eV and densities of a few mg/cm3 [2, 3, 4]. LEDCOP, OPAS, SCO-RCG structure codes and STA give similar results and differ from OP ones for the lower temperatures and for spectral interval values [3]. In this work we discuss the role of Configuration Interaction (CI) and the influence of the number of used configurations. We present and include in the opacity code comparisons new HULLAC-v9 calculations [5, 6] that include full CI. To illustrate the importance of this effect we compare different CI approximation...

  4. Atomic structure considerations for the low-temperature opacity of Sn

    Science.gov (United States)

    Colgan, J.; Kilcrease, D. P.; Abdallah, J.; Sherrill, M. E.; Fontes, C. J.; Hakel, P.; Armstrong, G. S. J.

    2017-06-01

    We have begun a preliminary investigation into the opacity of Sn at low temperatures (emissivity and opacity of Sn is a crucial factor in determining the utility of Sn in EUV lithography, with numerous industrial implications. To this end, we have been exploring the accuracy of some approximations used in opacity models for the relevant ion stages of Sn (neutral through ∼ 18 times ionized). We find that the use of intermediate-coupling, as compared to full configuration-interaction, is not adequate to obtain accurate line positions of the important bound-bound transitions in Sn. One requires full configuration-interaction to properly describe the strong mixing between the various n = 4 sub-shells that give rise to the Δ n = 0 transitions that dominate the opacity spectrum at low temperatures. Since calculations that include full configuration-interaction for large numbers of configurations quickly become computationally prohibitive, we have explored hybrid calculations, in which full configuration-interaction is retained for the most important transitions, while intermediate-coupling is employed for all other transitions. After extensive exploration of the atomic structure properties, local-thermodynamic-equilibrium (LTE) opacities are generated using the ATOMIC code at selected temperatures and densities and compared to experiment.

  5. The second extracellular loop of pore-forming subunits of ATP-binding cassette transporters for basic amino acids plays a crucial role in interaction with the cognate solute binding protein(s).

    Science.gov (United States)

    Eckey, Viola; Weidlich, Daniela; Landmesser, Heidi; Bergmann, Ulf; Schneider, Erwin

    2010-04-01

    In the thermophile Geobacillus stearothermophilus, the uptake of basic amino acids is mediated by an ABC transporter composed of the substrate binding protein (receptor) ArtJ and a homodimer each of the pore-forming subunit, ArtM, and the nucleotide-binding subunit, ArtP. We recently identified two putative binding sites in ArtJ that might interact with the Art(MP)(2) complex, thereby initiating the transport cycle (A. Vahedi-Faridi et al., J. Mol. Biol. 375:448-459, 2008). Here we investigated the contribution of charged amino acid residues in the second extracellular loop of ArtM to contact with ArtJ. Our results demonstrate a crucial role for residues K177, R185, and E188, since mutations to oppositely charged amino acids or glutamine led to a complete loss of ArtJ-stimulated ATPase activity of the complex variants in proteoliposomes. The defects could not be suppressed by ArtJ variants carrying mutations in site I (K39E and K152E) or II (E163K and D170K), suggesting a more complex interplay than that by a single salt bridge. These findings were supported by cross-linking assays demonstrating physical proximity between ArtJ(N166C) and ArtM(E182C). The importance of positively charged residues for receptor-transporter interaction was underscored by mutational analysis of the closely related transporter HisJ/LAO-HisQMP(2) of Salmonella enterica serovar Typhimurium. While transporter variants with mutated positively charged residues in HisQ displayed residual ATPase activities, corresponding mutants of HisM could no longer be stimulated by HisJ/LAO. Interestingly, the ATPase activity of the HisQM(K187E)P(2) variant was inhibited by l- and d-histidine in detergent, suggesting a role of the residue in preventing free histidine from gaining access to the substrate binding site within HisQM.

  6. Capsule implosions for continuum x-ray backlighting of opacity samples at the National Ignition Facility

    Science.gov (United States)

    Opachich, Y. P.; Heeter, R. F.; Barrios, M. A.; Garcia, E. M.; Craxton, R. S.; King, J. A.; Liedahl, D. A.; McKenty, P. W.; Schneider, M. B.; May, M. J.; Zhang, R.; Ross, P. W.; Kline, J. L.; Moore, A. S.; Weaver, J. L.; Flippo, K. A.; Perry, T. S.

    2017-06-01

    Direct drive implosions of plastic capsules have been performed at the National Ignition Facility to provide a broad-spectrum (500-2000 eV) X-ray continuum source for X-ray transmission spectroscopy. The source was developed for the high-temperature plasma opacity experimental platform. Initial experiments using 2.0 mm diameter polyalpha-methyl styrene capsules with ˜20 μm thickness have been performed. X-ray yields of up to ˜1 kJ/sr have been measured using the Dante multichannel diode array. The backlighter source size was measured to be ˜100 μm FWHM, with ˜350 ps pulse duration during the peak emission stage. Results are used to simulate transmission spectra for a hypothetical iron opacity sample at 150 eV, enabling the derivation of photometrics requirements for future opacity experiments.

  7. A consistent approach for mixed detailed and statistical calculation of opacities in hot plasmas

    CERN Document Server

    Porcherot, Quentin; Gilleron, Franck; Blenski, Thomas

    2011-01-01

    Absorption and emission spectra of plasmas with multicharged-ions contain transition arrays with a huge number of coalescent electric-dipole (E1) lines, which are well suited for treatment by the unresolved transition array and derivative methods. But, some transition arrays show detailed features whose description requires diagonalization of the Hamiltonian matrix. We developed a hybrid opacity code, called SCORCG, which combines statistical approaches with fine-structure calculations consistently. Data required for the computation of detailed transition arrays (atomic configurations and atomic radial integrals) are calculated by the super-configuration code SCO (Super-Configuration Opacity), which provides an accurate description of the plasma screening effects on the wave-functions. Level energies as well as position and strength of spectral lines are computed by an adapted RCG routine of R. D. Cowan. The resulting code provides opacities for hot plasmas and can handle mid-Z elements. The code is also a po...

  8. Atomic and Molecular Opacities for Brown Dwarf and Giant Planet Atmospheres

    CERN Document Server

    Sharp, C M; Sharp, Christopher M.; Burrows, Adam

    2006-01-01

    We present a comprehensive description of the theory and practice of opacity calculations from the infrared to the ultraviolet needed to generate models of the atmospheres of brown dwarfs and extrasolar giant planets. Methods for using existing line lists and spectroscopic databases in disparate formats are presented and plots of the resulting absorptive opacities versus wavelength for the most important molecules and atoms at representative temperature/pressure points are provided. Electronic, ro-vibrational, bound-free, bound-bound, free-free, and collision-induced transitions and monochromatic opacities are derived, discussed, and analyzed. The species addressed include the alkali metals, iron, heavy metal oxides, metal hydrides, $H_2$, $H_2O$, $CH_4$, $CO$, $NH_3$, $H_2S$, $PH_3$, and representative grains. [Abridged

  9. Smoke opacity in agricultural tractor in function of interior and metropolitano diesel mixture in mamona biodiesel

    Energy Technology Data Exchange (ETDEWEB)

    Tabile, Rubens Andre [Universidade de Sao Paulo (EESC/USP), Sao Carlos, SP (Brazil). Escola de Engenharia; Lopes, Afonso; Camara, Felipe Thomas da; Grotta, Danilo Cesar Checchio; Furlani, Carlos Eduardo Angeli [Universidade Estadual Paulista (DER/UNESP), Jaboticabal, SP (Brazil). Dept. de Engenharia Rural

    2008-07-01

    The great demand for energy sources by production systems allied to scarcity of fossil fuels has motivated the development and production of biodiesel, which is a fuel produced from renewable sources. Given that, the aim of this study was to compare smoke opacity of an agricultural tractor engine, working with metropolitano and interior diesel mixed to mamona biodiesel, in seven proportions. The tests were conducted in the Departamento de Engenharia Rural of UNESP/Jaboticabal - SP. The results showed that the diesel type did influence opacity of smoke, and metropolitano diesel showed best quality. It was also observed that, as biodiesel proportion increased, smoke opacity decreased until B75, turning to increase to B100. (author)

  10. The Hybrid Detailed / Statistical Opacity Code SCO-RCG: New Developments and Applications

    CERN Document Server

    Pain, Jean-Christophe; Porcherot, Quentin; Blenski, Thomas

    2013-01-01

    We present the hybrid opacity code SCO-RCG which combines statistical approaches with fine-structure calculations. Radial integrals needed for the computation of detailed transition arrays are calculated by the code SCO (Super-configuration Code for Opacity), which calculates atomic structure at finite temperature and density, taking into account plasma effects on the wave-functions. Levels and spectral lines are then computed by an adapted RCG routine of R. D. Cowan. SCO-RCG now includes the Partially Resolved Transition Array model, which allows one to replace a complex transition array by a small-scale detailed calculation preserving energy and variance of the genuine transition array and yielding improved high-order moments. An approximate method for studying the impact of strong magnetic field on opacity and emissivity was also recently implemented.

  11. Testing loop quantum cosmology

    Science.gov (United States)

    Wilson-Ewing, Edward

    2017-03-01

    Loop quantum cosmology predicts that quantum gravity effects resolve the big-bang singularity and replace it by a cosmic bounce. Furthermore, loop quantum cosmology can also modify the form of primordial cosmological perturbations, for example by reducing power at large scales in inflationary models or by suppressing the tensor-to-scalar ratio in the matter bounce scenario; these two effects are potential observational tests for loop quantum cosmology. In this article, I review these predictions and others, and also briefly discuss three open problems in loop quantum cosmology: its relation to loop quantum gravity, the trans-Planckian problem, and a possible transition from a Lorentzian to a Euclidean space-time around the bounce point.

  12. Mitotic chromosome compaction via active loop extrusion

    Science.gov (United States)

    Goloborodko, Anton; Imakaev, Maxim; Marko, John; Mirny, Leonid; MIT-Northwestern Team

    During cell division, two copies of each chromosome are segregated from each other and compacted more than hundred-fold into the canonical X-shaped structures. According to earlier microscopic observations and the recent Hi-C study, chromosomes are compacted into arrays of consecutive loops of ~100 kilobases. Mechanisms that lead to formation of such loop arrays are largely unknown. Here we propose that, during cell division, chromosomes can be compacted by enzymes that extrude loops on chromatin fibers. First, we use computer simulations and analytical modeling to show that a system of loop-extruding enzymes on a chromatin fiber self-organizes into an array of consecutive dynamic loops. Second, we model the process of loop extrusion in 3D and show that, coupled with the topo II strand-passing activity, it leads to robust compaction and segregation of sister chromatids. This mechanism of chromosomal condensation and segregation does not require additional proteins or specific DNA markup and is robust against variations in the number and properties of such loop extruding enzymes. Work at NU was supported by the NSF through Grants DMR-1206868 and MCB-1022117, and by the NIH through Grants GM105847 and CA193419. Work at MIT was supported by the NIH through Grants GM114190 R01HG003143.

  13. Clinical, pathological, and radiological characteristics of solitary ground-glass opacity lung nodules on high-resolution computed tomography

    Directory of Open Access Journals (Sweden)

    Qiu ZX

    2016-09-01

    Full Text Available Zhi-Xin Qiu,1 Yue Cheng,1 Dan Liu,1 Wei-Ya Wang,2 Xia Wu,2 Wei-Lu Wu,2 Wei-Min Li1,2 1Department of Respiratory Medicine, 2Department of Pathology, West China Hospital, Sichuan University, Chengdu, People’s Republic of China Background: Lung nodules are being detected at an increasing rate year by year with high-resolution computed tomography (HRCT being widely used. Ground-glass opacity nodule is one of the special types of pulmonary nodules that is confirmed to be closely associated with early stage of lung cancer. Very little is known about solitary ground-glass opacity nodules (SGGNs. In this study, we analyzed the clinical, pathological, and radiological characteristics of SGGNs on HRCT.Methods: A total of 95 resected SGGNs were evaluated with HRCT scan. The clinical, pathological, and radiological characteristics of these cases were analyzed.Results: Eighty-one adenocarcinoma and 14 benign nodules were observed. The nodules included 12 (15% adenocarcinoma in situ (AIS, 14 (17% minimally invasive adenocarcinoma (MIA, and 55 (68% invasive adenocarcinoma (IA. No patients with recurrence till date have been identified. The positive expression rates of anaplastic lymphoma kinase and ROS-1 (proto-oncogene tyrosine-protein kinase ROS were only 2.5% and 8.6%, respectively. The specificity and accuracy of HRCT of invasive lung adenocarcinoma were 85.2% and 87.4%. The standard uptake values of only two patients determined by 18F-FDG positron emission tomography/computed tomography (PET/CT were above 2.5. The size, density, shape, and pleural tag of nodules were significant factors that differentiated IA from AIS and MIA. Moreover, the size, shape, margin, pleural tag, vascular cluster, bubble-like sign, and air bronchogram of nodules were significant determinants for mixed ground-glass opacity nodules (all P<0.05.Conclusion: We analyzed the clinical, pathological, and radiological characteristics of SGGNs on HRCT and found that the size, density

  14. Sound speed and oscillation frequencies for a solar model evolved with Los Alamos ATOMIC opacities

    Science.gov (United States)

    Guzik, Joyce Ann; Fontes, Christopher; Walczak, Przemyslaw; Wood, Suzannah R.; Mussack, Katie

    2015-08-01

    Los Alamos has calculated a new generation of radiative opacities for elements with atomic number Z=1-30 with improved physics input, updated atomic data, and finer temperature grid to replace the Los Alamos LEDCOP opacities released in the year 2000. We calculate the evolution of a standard solar model including these new opacities, and compare with a model evolved using the Lawrence Livermore National Laboratory OPAL opacities released about 1996. We use the solar abundance mixture of Asplund, Grevesse, Sauval, and Scott (2009), including 2015 updates. The Los Alamos ATOMIC opacities (Colgan et al. 2013a,b) are somewhat higher than those of OPAL for temperatures and densities near the base of the solar convection zone. We compare the calculated nonadiabatic solar oscillation frequencies and solar interior sound speed to observed frequencies and helioseismic inferences. We discuss the potential for increased opacities to partially mitigate the ‘solar abundance problem’.References:J. Colgan, D.P. Kilcrease, N.H. Magee, Jr., G.S.J. Armstrong, J. Abdallah, Jr., M.E. Sherrill, C.J. Fontes, H.L. Zhang and P. Hakel, Eighth International Conference on Atomic and Molecular Data and their Applications: ICAMDATA, Gaithersburg, MD 2012, AIP Conf. Proc. No. 1545, (AIP, New York, 2013a), pp. 17-26.J. Colgan, D.P. Kilcrease, N.H. Magee, Jr, G.S.J. Armstrong, J. Abdallah, Jr., M.E. Sherrill, C.J. Fontes, H.L. Zhang and P. Hakel, High Energy Density Physics 9, 369 (2013b).

  15. Streptococcal Serum Opacity Factor Increases Hepatocyte Uptake of Human Plasma High Density Lipoprotein-Cholesterol1

    Science.gov (United States)

    Gillard, Baiba K.; Rosales, Corina; Pillai, Biju K.; Lin, Hu Yu; Courtney, Harry S.; Pownall, Henry J.

    2010-01-01

    Serum opacity factor (SOF), a virulence determinant of Streptococcus pyogenes, converts plasma high density lipoproteins (HDL) to three distinct species: lipid-free apolipoprotein (apo) A-I, neo HDL, a small discoidal HDL-like particle, and a large cholesteryl ester-rich microemulsion (CERM), that contains the cholesterol esters (CE) of up to ~400,000 HDL particles and apo E as its major protein. Similar SOF reaction products are obtained with HDL, total plasma lipoproteins and whole plasma. We hypothesized that hepatic uptake of CERM-CE via multiple apo E dependent receptors would be faster than that of HDL-CE. We tested our hypothesis using human hepatoma cells and lipoprotein receptor-specific Chinese hamster ovary (CHO) cells. [3H]CE uptake by HepG2 and Huh7 cells from HDL after SOF treatment, which transfers >90% of HDL-CE to CERM, was respectively 2.4 and 4.5 times faster than from control HDL. CERM-[3H]CE uptake was inhibited by LDL and HDL, suggestive of uptake by both the LDL receptor (LDL-R) and scavenger receptor class B type I (SR-BI). Studies in CHO cells specifically expressing LDL-R and SR-BI confirmed CERM-[3H]CE uptake by both receptors. RAP and heparin inhibit CERM-[3H]CE but not HDL-[3H]CE uptake thereby implicating LRP-1 and cell surface proteoglycans in this process. These data demonstrate that SOF treatment of HDL increases CE uptake via multiple hepatic apo E receptors. In so doing, SOF might increase hepatic disposal of plasma cholesterol in a way that is therapeutically useful. PMID:20879789

  16. Determining Visible Opacity of Emissions Using the Digital Opacity Compliance System II: Look Out EPA Method 9, Here Comes the Digital Equivalent (Finally)

    Science.gov (United States)

    2010-06-16

    Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 2 TECHNICAL APROACH • DoD Recognition of the Costs and Subjectivity of Method 9 Monitoring...Image Capture Induction Analysis Report Interface XML Service Form Print TECHNICAL APROACH •Automate Method 9 Opacity Readings •Provide Compliance...Background = JPG EXIF Example Images From a Safe Distance Capture The Plume and Background TECHNICAL APROACH 6 Induction • Registration Method • Minimization

  17. Metal Hydride and Alkali Halide Opacities in Extrasolar Giant Planets and Cool Stellar Atmospheres

    Science.gov (United States)

    Weck, Philippe F.; Stancil, Phillip C.; Kirby, Kate; Schweitzer, Andreas; Hauschildt, Peter H.

    2006-01-01

    The lack of accurate and complete molecular line and continuum opacity data has been a serious limitation to developing atmospheric models of cool stars and Extrasolar Giant Planets (EGPs). We report our recent calculations of molecular opacities resulting from the presence of metal hydrides and alkali halides. The resulting data have been included in the PHOENIX stellar atmosphere code (Hauschildt & Baron 1999). The new models, calculated using spherical geometry for all gravities considered, also incorporate our latest database of nearly 670 million molecular lines, and updated equations of state.

  18. Image Analysis on Corneal Opacity:A Novel Method to Estimate Postmortem Interval in Rabbits

    Institute of Scientific and Technical Information of China (English)

    周兰; 刘艳; 刘良; 卓荦; 梁曼; 杨帆; 任亮; 朱少华

    2010-01-01

    Corneal opacity is one of the most commonly used parameters for estimating postmortem interval(PMI).This paper proposes a new method to study the relationship between changes of corneal opacity and PMI by processing and analyzing cornea images.Corneal regions were extracted from images of rabbits' eyes and described by color-based and texture-based features,which could represent the changes of cornea at different PMI.A KNN classifier was used to reveal the association of image features and PMI.The result of...

  19. Complex asteroseismology of the hybrid B-type pulsator $\\gamma$ Pegasi: a test of stellar opacities

    CERN Document Server

    Walczak, Przemysław

    2010-01-01

    Using the updated oscillation spectrum of $\\gamma$ Pegasi, we construct a set of seismic models which reproduce two pulsational frequencies corresponding to the $\\ell=0$, p$_1$ and $\\ell=1$, g$_1$ modes. Then, we single out models which reproduce other well identified modes. Finally, we extend our seismic modelling by a requirement of fitting also values of the complex, nonadiabatic parameter $f$ associated to each mode frequency. Such complex asteroseismology of the B-type pulsators provides a unique test of stellar metallicity and opacities. In contrast to our previous studies, results for $\\gamma$ Peg indicate that both opacity tables, OPAL and OP, are equally preferred.

  20. QIKMIX: a quick-turnaround computer program for computing opacities of mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Abdallah, J. Jr.; Huebner, W.F.

    1979-05-01

    QIKMIX is a quick-turnaround computer code developed to compute the radiative Rosseland mean opacity of specified mixtures at specified temperature and density points. The QIKLIB data base, which QIKMIX uses, has been derived from the OPLIB library. For most mixtures, QIKMIX can compute opacities over a temperature range of 50 to 25,000 eV in less than 1 min of CDC 7600 computer time. The purpose of this report is to discuss the QIKLIB data base and the operation of the QIKMIX code.

  1. Photoperiodic regime influences onset of lens opacities in a non-human primate

    Directory of Open Access Journals (Sweden)

    Marko Dubicanac

    2017-05-01

    Full Text Available Background Opacities of the lens are typical age-related phenomena which have a high influence on photoreception and consequently circadian rhythm. In mouse lemurs, a small bodied non-human primate, a high incidence (more than 50% when >seven years of cataracts has been previously described during aging. Previous studies showed that photoperiodically induced accelerated annual rhythms alter some of mouse lemurs’ life history traits. Whether a modification of photoperiod also affects the onset of age dependent lens opacities has not been investigated so far. The aim of this study was therefore to characterise the type of opacity and the mouse lemurs’ age at its onset in two colonies with different photoperiodic regimen. Methods Two of the largest mouse lemur colonies in Europe were investigated: Colony 1 having a natural annual photoperiodic regime and Colony 2 with an induced accelerated annual cycle. A slit-lamp was used to determine opacities in the lens. Furthermore, a subset of all animals which showed no opacities in the lens nucleus in the first examination but developed first changes in the following examination were further examined to estimate the age at onset of opacities. In total, 387 animals were examined and 57 represented the subset for age at onset estimation. Results The first and most commonly observable opacity in the lens was nuclear sclerosis. Mouse lemurs from Colony 1 showed a delayed onset of nuclear sclerosis compared to mouse lemurs from Colony 2 (4.35 ± 1.50 years vs. 2.75 ± 0.99 years. For colony 1, the chronological age was equivalent to the number of seasonal cycles experienced by the mouse lemurs. For colony 2, in which seasonal cycles were accelerated by a factor of 1.5, mouse lemurs had experienced 4.13 ± 1.50 seasonal cycles in 2.75 ± 0.99 chronological years. Discussion Our study showed clear differences in age at the onset of nuclear sclerosis formation between lemurs kept under different

  2. Force distribution in a semiflexible loop

    CERN Document Server

    Waters, James T

    2016-01-01

    Loops undergoing thermal fluctuations are prevalent in nature. Ring-like or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category. Stability of these molecules are generally described in terms of free energy, an average quantity, but it may also be impacted by local fluctuating forces acting within these systems. The full distribution of these forces can thus give us insights into mechanochemistry beyond the predictive capability of thermodynamics. In this paper, we study the force exerted by an inextensible semiflexible polymer constrained in a looped state. By using a novel simulation method termed "phase-space sampling", we generate the equilibrium distribution of chain conformations in both position and momentum space. We compute the constraint forces between the two ends of the loop in this chain ensemble using Lagrangian mechanics, and show that the mean of these forces is equal to the thermodynamic force. By analyzing kinetic and potential contribution...

  3. New insights on the role of the gamma-herpesvirus uracil-DNA glycosylase leucine loop revealed by the structure of the Epstein-Barr virus enzyme in complex with an inhibitor protein.

    Science.gov (United States)

    Géoui, Thibault; Buisson, Marlyse; Tarbouriech, Nicolas; Burmeister, Wim Pascal

    2007-02-09

    Epstein-Barr virus (EBV) is a human gamma-herpesvirus. Within its 86 open reading frame containing genome, two enzymes avoiding uracil incorporation into DNA can be found: uracil triphosphate hydrolase and uracil-DNA glycosylase (UNG). The latter one excises uracil bases that are due to cytosine deamination or uracil misincorporation from double-stranded DNA substrates. The EBV enzyme belongs to family 1 UNGs. We solved the three-dimensional structure of EBV UNG in complex with the uracil-DNA glycosylase inhibitor protein (Ugi) from bacteriophage PBS-2 at a resolution of 2.3 A by X-ray crystallography. The structure of EBV UNG encoded by the BKRF3 reading frame shows the excellent global structural conservation within the solved examples of family 1 enzymes. Four out of the five catalytic motifs are completely conserved, whereas the fifth one, the leucine loop, carries a seven residue insertion. Despite this insertion, catalytic constants of EBV UNG are similar to those of other UNGs. Modelling of the EBV UNG-DNA complex shows that the longer leucine loop still contacts DNA and is likely to fulfil its role of DNA binding and deformation differently than the enzymes with previously solved structures. We could show that despite the evolutionary distance of EBV UNG from the natural host protein, bacteriophage Ugi binds with an inhibitory constant of 8 nM to UNG. This is due to an excellent specificity of Ugi for conserved elements of UNG, four of them corresponding to catalytic motifs and a fifth one corresponding to an important beta-turn structuring the catalytic site.

  4. Open-Source Tools for Enhancing Full-Text Searching of OPACs: Use of Koha, Greenstone and Fedora

    Science.gov (United States)

    Anuradha, K. T.; Sivakaminathan, R.; Kumar, P. Arun

    2011-01-01

    Purpose: There are many library automation packages available as open-source software, comprising two modules: staff-client module and online public access catalogue (OPAC). Although the OPAC of these library automation packages provides advanced features of searching and retrieval of bibliographic records, none of them facilitate full-text…

  5. 40 CFR 62.15380 - How must I monitor opacity for air curtain incinerators that burn 100 percent yard waste?

    Science.gov (United States)

    2010-07-01

    ... waste? (a) Use EPA Reference Method 9 in Appendix A of 40 CFR part 60 to determine compliance with the opacity limit. (b) Conduct an initial test for opacity as specified in § 60.8 of subpart A of 40 CFR part... curtain incinerators that burn 100 percent yard waste? 62.15380 Section 62.15380 Protection of...

  6. 40 CFR 75.18 - Specific provisions for monitoring emissions from common and by-pass stacks for opacity.

    Science.gov (United States)

    2010-07-01

    ... emissions from common and by-pass stacks for opacity. 75.18 Section 75.18 Protection of Environment... Provisions § 75.18 Specific provisions for monitoring emissions from common and by-pass stacks for opacity. (a) Unit using common stack.When an affected unit utilizes a common stack with other affected...

  7. Introduction to Loop Heat Pipes

    Science.gov (United States)

    Ku, Jentung

    2015-01-01

    This is the presentation file for the short course Introduction to Loop Heat Pipes, to be conducted at the 2015 Thermal Fluids and Analysis Workshop, August 3-7, 2015, Silver Spring, Maryland. This course will discuss operating principles and performance characteristics of a loop heat pipe. Topics include: 1) pressure profiles in the loop; 2) loop operating temperature; 3) operating temperature control; 4) loop startup; 4) loop shutdown; 5) loop transient behaviors; 6) sizing of loop components and determination of fluid inventory; 7) analytical modeling; 8) examples of flight applications; and 9) recent LHP developments.

  8. Sequence similarity between the erythrocyte binding domain 1 of the Plasmodium vivax Duffy binding protein and the V3 loop of HIV-1 strain MN reveals binding residues for the Duffy Antigen Receptor for Chemokines

    Directory of Open Access Journals (Sweden)

    Garry Robert F

    2011-01-01

    Full Text Available Abstract Background The surface glycoprotein (SU, gp120 of the human immunodeficiency virus (HIV must bind to a chemokine receptor, CCR5 or CXCR4, to invade CD4+ cells. Plasmodium vivax uses the Duffy Binding Protein (DBP to bind the Duffy Antigen Receptor for Chemokines (DARC and invade reticulocytes. Results Variable loop 3 (V3 of HIV-1 SU and domain 1 of the Plasmodium vivax DBP share a sequence similarity. The site of amino acid sequence similarity was necessary, but not sufficient, for DARC binding and contained a consensus heparin binding site essential for DARC binding. Both HIV-1 and P. vivax can be blocked from binding to their chemokine receptors by the chemokine, RANTES and its analog AOP-RANTES. Site directed mutagenesis of the heparin binding motif in members of the DBP family, the P. knowlesi alpha, beta and gamma proteins abrogated their binding to erythrocytes. Positively charged residues within domain 1 are required for binding of P. vivax and P. knowlesi erythrocyte binding proteins. Conclusion A heparin binding site motif in members of the DBP family may form part of a conserved erythrocyte receptor binding pocket.

  9. Gaseous Mean Opacities for Giant Planet and Ultracool Dwarf Atmospheres over a Range of Metallicities and Temperatures

    CERN Document Server

    Freedman, Richard S; Fortney, Jonathan J; Lupu, Roxana E; Marley, Mark S; Lodders, Katharina

    2014-01-01

    We present new calculations of Rosseland and Planck gaseous mean opacities relevant to the atmospheres of giant planets and ultracool dwarfs. Such calculations are used in modeling the atmospheres, interiors, formation, and evolution of these objects. Our calculations are an expansion of those presented in Freedman et al. (2008) to include lower pressures, finer temperature resolution, and also the higher metallicities most relevant for giant planet atmospheres. Calculations span 1 microbar to 300 bar, and 75 K to 4000 K, in a nearly square grid. Opacities at metallicities from solar to 50 times solar abundances are calculated. We also provide an analytic fit to the Rosseland mean opacities over the grid in pressure, temperature, and metallicity. In addition to computing mean opacities at these local temperatures, we also calculate them with weighting functions up to 7000 K, to simulate the mean opacities for incident stellar intensities, rather than locally thermally emitted intensities. The chemical equilib...

  10. Comment on "Large enhancement in high-energy photoionization of Fe XVII and missing continuum plasma opacity"

    CERN Document Server

    Blancard, C; Cossé, Ph; Faussurier, G; Fontes, C J; Gilleron, F; Golovkin, I; Hansen, S B; Iglesias, C A; Kilcrease, D P; MacFarlane, J J; More, R M; Pain, J -C; Sherrill, M; Wilson, B G

    2016-01-01

    Recent R-matrix calculations claim to produce a significant enhancement in the opacity of Fe XVII due to atomic core excitations [S. N. Nahar & A.K. Pradhan, Phys. Rev. Letters 116, 235003 (2016), arXiv:1606.02731] and assert that this enhancement is consistent with recent measurements of higher-than-predicted iron opacities [J. E. Bailey et al., Nature 517, 56 (2015)]. This comment shows that the standard opacity models which have already been directly compared with experimental data produce photon absorption cross-sections for Fe XVII that are effectively equivalent to (and in fact larger than) the new R-matrix opacities. Thus, the new R-matrix results cannot be expected to significantly impact the existing discrepancies between theory and experiment because they produce neither a "large enhancement" nor account for "missing continuum plasma opacity" relative to standard models.

  11. A loop quantum multiverse?

    CERN Document Server

    Bojowald, Martin

    2013-01-01

    Inhomogeneous space-times in loop quantum cosmology have come under better control with recent advances in effective methods. Even highly inhomogeneous situations, for which multiverse scenarios provide extreme examples, can now be considered at least qualitatively.

  12. Blind loop syndrome

    Science.gov (United States)

    ... part of the stomach) and operations for extreme obesity As a complication of inflammatory bowel disease Diseases such as diabetes or scleroderma may slow down movement in a segment of the intestine, leading to blind loop syndrome.

  13. Diffusion of Wilson Loops

    CERN Document Server

    Brzoska, A M; Negele, J W; Thies, M

    2004-01-01

    A phenomenological analysis of the distribution of Wilson loops in SU(2) Yang-Mills theory is presented in which Wilson loop distributions are described as the result of a diffusion process on the group manifold. It is shown that, in the absence of forces, diffusion implies Casimir scaling and, conversely, exact Casimir scaling implies free diffusion. Screening processes occur if diffusion takes place in a potential. The crucial distinction between screening of fundamental and adjoint loops is formulated as a symmetry property related to the center symmetry of the underlying gauge theory. The results are expressed in terms of an effective Wilson loop action and compared with various limits of SU(2) Yang-Mills theory.

  14. 77 FR 8209 - Quality Assurance Requirements for Continuous Opacity Monitoring Systems at Stationary Sources

    Science.gov (United States)

    2012-02-14

    ... AGENCY 40 CFR Part 60 RIN 2060-AH23 Quality Assurance Requirements for Continuous Opacity Monitoring... standards as specified in federally enforceable regulations. The quality assurance requirements will be... standards to the quality assurance requirements in Appendix F of 40 CFR Part 60 in the ``Rules and...

  15. Impact of Internet Search Engines on OPAC Users: A Study of Punjabi University, Patiala (India)

    Science.gov (United States)

    Kumar, Shiv

    2012-01-01

    Purpose: The aim of this paper is to study the impact of internet search engine usage with special reference to OPAC searches in the Punjabi University Library, Patiala, Punjab (India). Design/methodology/approach: The primary data were collected from 352 users comprising faculty, research scholars and postgraduate students of the university. A…

  16. Effect of Media Opacity on Retinal Nerve Fiber Layer Thickness Measurements by Optical Coherence Tomography

    Directory of Open Access Journals (Sweden)

    Dae Woong Lee

    2010-01-01

    Full Text Available Purpose: To assess the effect of ocular media opacity on retinal nerve fiber layer (RNFL thickness measurements by optical coherence tomography (OCT. Methods: In this prospective, non-randomized clinical study, ocular examinations and OCT measurements were performed on 77 cataract patients, 80 laser refractive surgery patients and 90 patients whose signal strength on OCT was different on two consecutive measurements. None of the eyes had preexisting retinal or optic nerve pathology, including glaucoma. Cataracts were classified according to the Lens Opacity Classification System III (LOCS III. All eyes were scanned with the Stratus OCT using the Fast RNFL program before and three months after surgery. Internal fixation was used during scanning and all eyes underwent circular scans around the optic disc with a diameter of 3.4 mm. Results: Average RNFL thickness, quadrant thickness and signal strength significantly increased after cataract surgery (P<0.05. Cortical and posterior subcapsular cataracts, but not nuclear cataracts, had a significant influence on RNFL thickness measurements (P<0.05. There was no significant difference between OCT parameters before and after laser refractive surgery. In eyes for which different signal strengths were observed, significantly larger RNFL thickness values were obtained on scans with higher signal strengths. Conclusion: OCT parameters are affected by ocular media opacity because of changes in signal strength; cortical cataracts have the most significant effect followed by posterior subcapsular opacities. Laser refractive procedures do not seem to affect OCT parameters significantly.

  17. Gluon Radiation off Hard Quarks in a Nuclear Environment Opacity Expansion

    CERN Document Server

    Wiedemann, Urs Achim

    2000-01-01

    We study the relation between the Baier-Dokshitzer-Mueller-Peigne-Schiff (BDMPS) and Zakharov formalisms for medium-induced gluon radiation off hard quarks, and the radiation off very few scattering centers. Based on the non-abelian Furry approximation for the motion of hard partons in a spatially extended colour field, we derive a compact diagrammatic and explicitly colour trivial expression for the N-th order term of the kt-differential gluon radiation cross section in an expansion in the opacity of the medium. Resumming this quantity to all orders in opacity, we obtain Zakharov's path-integral expression (supplemented with a regularization prescription). This provides a new proof of the equivalence of the BDMPS and Zakharov formalisms which extends previous arguments to the kt-differential cross section. We give explicit analytical results up to third order in opacity for both the gluon radiation cross section of free incoming and of in-medium produced quarks. The N-th order term in the opacity expansion o...

  18. Important consequences of atomic diffusion inside main-sequence stars: opacities, extra-mixing, oscillations

    Directory of Open Access Journals (Sweden)

    Deal M.

    2017-01-01

    Full Text Available Atomic diffusion, including the effects of radiative accelerations on individual elements, leads to important variations of the chemical composition inside stars. The accumulation of important elements in specific layers leads to a local increase of the average opacity and to hydrodynamic instabilities that modify the internal stellar structure. This can also have important consequences for asteroseismology.

  19. Opportunities for Laboratory Opacity Chemistry Studies to Facilitate Characterization of Young Giant Planets and Brown Dwarfs

    Science.gov (United States)

    Marley, Mark; Freedman, Richard S.

    2015-01-01

    The thermal emission spectra of young giant planets is shaped by the opacity of atoms and molecules residing in their atmospheres. While great strides have been made in improving the opacities of important molecules, particularly NH3 and CH4, at high temperatures, much more work is needed to understand the opacity and chemistry of atomic Na and K. The highly pressure broadened fundamental band of Na and K in the optical stretches into the near-infrared, strongly influencing the shape of the Y and K spectral bands. Since young giant planets are bright in these bands it is important to understand the influences on the spectral shape. Discerning gravity and atmospheric composition is difficult, if not impossible, without both good atomic opacities as well as an excellent understanding of the relevant atmospheric chemistry. Since Na and K condense at temperatures near 500 to 600 K, the chemistry of the condensation process must be well understood as well, particularly any disequilibrium chemical pathways. Comparisons of the current generation of sophisticated atmospheric models and available data, however, reveal important shortcomings in the models. We will review the current state of observations and theory of young giant planets and will discuss these and other specific examples where improved laboratory measurements for alkali compounds have the potential of substantially improving our understanding of these atmospheres.

  20. Influence of the atmospheric opacity cycle on the near surface environment of Gale Crater on Mars

    Science.gov (United States)

    de la Torre Juarez, Manuel; Gomez-Elvira, Javier; Guzewich, Scott David; Lemmon, Mark T.; Martinez, German; Mason, Emily; Navarro, Sara; Newman, Claire E.; Smith, Michael D.; Retortillo, Alvaro de Vicente

    2016-10-01

    The Mars atmospheric dust changes the capacity of the atmosphere to absorb solar radiation or release outgoing thermal infrared radiation. This alters the atmospheric heat exchange fluxes and can interfere with the global circulation. The response of near surface pressure, temperature and winds has been characterized at the higher northern latitudes of 45 degree N at the Viking landing sites. The Rover Environmental Monitoring Station (REMS) on Curiosity allows a similar characterization at near-equatorial latitudes of 4.5 degree S. Using MCAM-880 nm opacities as a measure of local atmospheric dust load, we analyze the response of changes in surface variables measured by REMS and compare to those observed by Viking. As on Viking, diurnal and semidiurnal pressure tide amplitudes track very closely the atmospheric opacity and the mean daily pressure shows the increased wave activity. Temperature tides show a more complex response that combines its sensitivity to changes in dust and cloud opacities. Differences in UV opacities for the REMS set of finite spectral windows are explored during the dust and clear seasons.

  1. Asymptotic Giant Branch stars at low metallicity: the challenging interplay between mass loss and molecular opacities

    CERN Document Server

    Ventura, Paolo

    2010-01-01

    We investigate the main physical properties of low-metallicity Asymptotic Giant Branch stars, with the aim of quantifying the uncertainties that presently affect the predicted chemical yields of these stars, associated to mass loss and description of molecular opacities. We find that above a threshold mass, M ~ 3.5Msun for Z=0.001, the results are little dependent on the opacity treatment, as long as hot-bottom burning prevents the surface C/O ratio from exceeding unity; the yields of these massive AGB stars are expected to be mostly determined by the efficiency of convection, with a relatively mild dependence on the mass-loss description. A much higher degree of uncertainty is associated to the yields of less massive models, which critically depend on the adopted molecular opacities. An interval of masses exists, say 2.0-3.0Msun, (the exact range depends on mass loss), in which HBB may be even extinguished following the cooling produced by the opacity of C-bearing molecules. The yields of these stars are the...

  2. From Loops to Surfaces

    CERN Document Server

    Neuberger, H

    2010-01-01

    The generating function for all antisymmetric characters of a Wilson loop matrix in SU(N) Yang Mills theory is the partition function of a fermion living on the curve describing the loop. This generalizes to fermion subsystems living on higher dimensional submanifolds, for example, surfaces. This write-up also contains some extra background, in response to some questions raised during the oral presentation.

  3. Ser⁄ Thr residues at α3⁄β5 loop of Gαs are important in morphine-induced adenylyl cyclase sensitization but not mitogen-activated protein kinase phosphorylation

    Science.gov (United States)

    Seyedabadi, Mohammad; Ostad, Seyed Nasser; Albert, Paul R.; Dehpour, Ahmad R.; Rahimian, Reza; Ghazi-Khansari, Mahmoud; Ghahremani, Mohammad H.

    2015-01-01

    The signaling switch of β2-adrenergic and μ1-opioid receptors from stimulatory G-protein (Gαs) to inhibitory G-protein (Gαi) (and vice versa) influences adenylyl cyclase (AC) and extracellular-regulated kinase (ERK)1 ⁄ 2 activation. Post-translational modifications, including dephosphorylation of Gαs, enhance opioid receptor coupling to Gαs. In the present study, we substituted the Ser ⁄ Thr residues of Gαs at the α3 ⁄ β5 and α4 ⁄ β6 loops aiming to study the role of Gαs lacking Ser ⁄ Thr phosphorylation with respect to AC sensitization and mitogen-activated protein kinase activation. Isoproterenol increased the cAMP concentration (EC50 = 22.8 ± 3.4 μM) in Gαs-transfected S49 cyc– cells but not in nontransfected cells. However, there was no significant difference between the Gαs-wild-type (wt) and mutants. Morphine (10 μM) inhibited AC activity more efficiently in cyc– compared to Gαs-wt introduced cells (P < 0.05); however, we did not find a notable difference between Gαs-wt and mutants. Interestingly, Gαs-wt transfected cells showed more sensitization with respect to AC after chronic morphine compared to nontransfected cells (101 ± 12% versus 34 ± 6%; P < 0.001); μ1-opioid receptor interacted with Gαs, and both co-immunoprecipitated after chronic morphine exposure. Furthermore, mutation of T270A and S272A (P < 0.01), as well as T270A, S272A and S261A (P < 0.05), in α3 ⁄ β5, resulted in a higher level of AC supersensitization. ERK1⁄ 2 phosphorylation was rapidly induced by isoproterenol (by 9.5 ± 2.4-fold) and morphine (22 ± 2.2-fold) in Gαs-transfected cells; mutations of α3 ⁄ β5 and α4 ⁄ β6 did not affect the pattern or extent of mitogen-activated protein kinase activation. The findings of the present study show that Gαs interacts with the μ1-opioid receptor, and the Ser ⁄ Thr mutation to Ala at the α3 ⁄ β5 loop of Gαs enhances morphine-induced AC sensitization. In addition, Gαs was required for

  4. A Novel Technique to Calculate UV Opacity at Gale Crater from MSL/REMS Measurements

    Science.gov (United States)

    Vicente-Retortillo, Álvaro; Martínez, Germán M.; Renno, Nilton O.; Lemmon, Mark T.; Mason, Emily L.; de la Torre-Juárez, Manuel

    2016-04-01

    The Rover Environmental Monitoring Station (REMS) on board the Mars Science Laboratory (MSL) mission carries a UV sensor that for the first time is measuring the solar radiation at the surface of Mars in six bands between 200 and 380 nm [1]. Here we present a novel methodology to calculate the atmospheric opacity by using the UV photodiode output currents measured by this sensor (TELRDR products) and ancillary (ADR) data. We estimate the diffuse and total radiation signals by analyzing the events in which the direct solar beam was temporarily blocked by the masthead or by the mast of the rover. Then we use a radiative transfer model with updated radiative properties of the Martian aerosols ([2], [3]) based on the Monte-Carlo method to retrieve the UV opacity from those measurements. Therefore, this methodology is not sensitive to the degradation of the sensor due to the deposition of dust on it. In addition, by using TELRDR and ADR data, inconsistencies in the processed reduced data (ENVRDR and MODRDR products, in units of W/m2) found when the solar zenith angle relative to REMS rover frame is above 30° are avoided. In order to validate our technique, we compare the UV opacities with those derived from Mastcam observations at 880 nm. We find that both opacities show a good agreement and follow a similar seasonal trend, with the UV opacity showing values generally lower than at 880 nm. The difference between both opacities varies over the year, with the minimum difference occurring during the first half of the winter, when both opacities show their annual lowest values. The temporal variation of this difference may be used to analyze changes in the dust size distribution. [1] Gómez-Elvira, J., Armiens, C., Castañer, L., Domínguez, M., Genzer, M. et al. REMS: the environmental sensor suite for the Mars Science Laboratory rover. Space Sci. Rev., 170 (1-4), 583-640, 2012. [2] Vicente-Retortillo, A., Valero, F., Vázquez, L. and Martínez, G. M. A model to calculate

  5. Research Advances: Less Expensive and More Convenient Gaucher's Disease Treatment; Structural Loop Regions: Key to Multidrug-Resistance Transporters?; New Method Identifies Proteins in Old Artwork

    Science.gov (United States)

    King, Angela G.

    2006-01-01

    The X-ray structure of EmrD, a multidrug transporter protein from Escherichia coli, common bacteria known to cause several food-borne illnesses was determined by scientists at The Scripps Research Institute. The hydrophobic residues in the EmrD internal cavity are likely to contribute to the general mechanism transporting various compounds through…

  6. Autofluorescence imaging of macular pigment: influence and correction of ocular media opacities

    Science.gov (United States)

    Sharifzadeh, Mohsen; Obana, Akira; Gohto, Yuko; Seto, Takahiko; Gellermann, Werner

    2014-09-01

    The healthy adult human retina contains in its macular region a high concentration of blue-light absorbing carotenoid compounds, known as macular pigment (MP). Consisting of the carotenoids lutein, zeaxanthin, and meso-zeaxanthin, the MP is thought to shield the vulnerable tissue layers in the retina from light-induced damage through its function as an optical attenuator and to protect the tissue cells within its immediate vicinity through its function as a potent antioxidant. Autofluorescence imaging (AFI) is emerging as a viable optical method for MP screening of large subject populations, for tracking of MP changes over time, and for monitoring MP uptake in response to dietary supplementation. To investigate the influence of ocular media opacities on AFI-based MP measurements, in particular, the influence of lens cataracts, we conducted a clinical trial with a large subject population (93 subjects) measured before and after cataract surgery. General AFI image contrast, retinal blood vessel contrast, and presurgery lens opacity scores [Lens Opacities Classification System III (LOCS III)] were investigated as potential predictors for image degradation. These clinical results show that lens cataracts can severely degrade the achievable pixel contrasts in the AFI images, which results in nominal MP optical density levels that are artifactually reduced. While LOCS III scores and blood vessel contrast are found to be only a weak predictor for this effect, a strong correlation exists between the reduction factor and the image contrast, which can be quantified via pixel intensity histogram parameters. Choosing the base width of the histogram, the presence or absence of ocular media opacities can be determined and, if needed, the nominal MP levels can be corrected with factors depending on the strength of the opacity.

  7. ATP binding by the P-loop NTPase OsYchF1 (an unconventional G protein) contributes to biotic but not abiotic stress responses.

    Science.gov (United States)

    Cheung, Ming-Yan; Li, Xiaorong; Miao, Rui; Fong, Yu-Hang; Li, Kwan-Pok; Yung, Yuk-Lin; Yu, Mei-Hui; Wong, Kam-Bo; Chen, Zhongzhou; Lam, Hon-Ming

    2016-03-01

    G proteins are involved in almost all aspects of the cellular regulatory pathways through their ability to bind and hydrolyze GTP. The YchF subfamily, interestingly, possesses the unique ability to bind both ATP and GTP, and is possibly an ancestral form of G proteins based on phylogenetic studies and is present in all kingdoms of life. However, the biological significance of such a relaxed ligand specificity has long eluded researchers. Here, we have elucidated the different conformational changes caused by the binding of a YchF homolog in rice (OsYchF1) to ATP versus GTP by X-ray crystallography. Furthermore, by comparing the 3D relationships of the ligand position and the various amino acid residues at the binding sites in the crystal structures of the apo-bound and ligand-bound versions, a mechanism for the protein's ability to bind both ligands is revealed. Mutation of the noncanonical G4 motif of the OsYchF1 to the canonical sequence for GTP specificity precludes the binding/hydrolysis of ATP and prevents OsYchF1 from functioning as a negative regulator of plant-defense responses, while retaining its ability to bind/hydrolyze GTP and its function as a negative regulator of abiotic stress responses, demonstrating the specific role of ATP-binding/hydrolysis in disease resistance. This discovery will have a significant impact on our understanding of the structure-function relationships of the YchF subfamily of G proteins in all kingdoms of life.

  8. Genetic Programming with Simple Loops

    Institute of Scientific and Technical Information of China (English)

    QI Yuesheng; WANG Baozhong; KANG Lishan

    1999-01-01

    A kind of loop function LoopN inGenetic Programming (GP) is proposed.Different from other forms of loopfunction, such as While-Do and Repeat-Until, LoopNtakes only oneargument as its loop body and makes its loop body simply run N times,soinfinite loops will never happen. The problem of how to avoid too manylayers ofloops in Genetic Programming is also solved. The advantage ofLoopN in GP is shown bythe computational results in solving the mowerproblem.

  9. A stretch of 11 amino acids in the betaB-betaC loop of the coat protein of grapevine fanleaf virus is essential for transmission by the nematode Xiphinema index.

    Science.gov (United States)

    Schellenberger, Pascale; Andret-Link, Peggy; Schmitt-Keichinger, Corinne; Bergdoll, Marc; Marmonier, Aurélie; Vigne, Emmanuelle; Lemaire, Olivier; Fuchs, Marc; Demangeat, Gérard; Ritzenthaler, Christophe

    2010-08-01

    Grapevine fanleaf virus (GFLV) and Arabis mosaic virus (ArMV) from the genus Nepovirus, family Secoviridae, cause a severe degeneration of grapevines. GFLV and ArMV have a bipartite RNA genome and are transmitted specifically by the ectoparasitic nematodes Xiphinema index and Xiphinema diversicaudatum, respectively. The transmission specificity of both viruses maps to their respective RNA2-encoded coat protein (CP). To further delineate the GFLV CP determinants of transmission specificity, three-dimensional (3D) homology structure models of virions and CP subunits were constructed based on the crystal structure of Tobacco ringspot virus, the type member of the genus Nepovirus. The 3D models were examined to predict amino acids that are exposed at the external virion surface, highly conserved among GFLV isolates but divergent between GFLV and ArMV. Five short amino acid stretches that matched these topographical and sequence conservation criteria were selected and substituted in single and multiple combinations by their ArMV counterparts in a GFLV RNA2 cDNA clone. Among the 21 chimeric RNA2 molecules engineered, transcripts of only three of them induced systemic plant infection in the presence of GFLV RNA1. Nematode transmission assays of the three viable recombinant viruses showed that swapping a stretch of (i) 11 residues in the betaB-betaC loop near the icosahedral 3-fold axis abolished transmission by X. index but was insufficient to restore transmission by X. diversicaudatum and (ii) 7 residues in the betaE-alphaB loop did not interfere with transmission by the two Xiphinema species. This study provides new insights into GFLV CP determinants of nematode transmission.

  10. Investigation of the value of a photographic tool to measure self-perception of enamel opacities

    Directory of Open Access Journals (Sweden)

    Davies Gill M

    2012-10-01

    Full Text Available Abstract Background The standard measurement of oral conditions that are mainly of cosmetic concern can be carried out by a trained clinical professional, or they can be assessed and reported by the individuals who may have the condition or be aware of others who have it. Enamel opacities of anterior teeth are examples of such a condition. At a public health level the interest is only about opacities that are of aesthetic concern, so the need for an index that records opacities that the public perceive to be a problem is clear. Measurement methods carried out by highly trained professionals, using unnatural conditions are not indicated at this level. This study reports on the testing of a novel epidemiological tool that aims to report on the prevalence and impact of self-perceived enamel opacities in a population of young adolescents. Methods A dental health survey was carried out using a random sample of 12-year-old school pupils during 2008/09 by Primary Care Organisations (PCOs in England. This included the use of a novel self-perception tool which aimed to measure individual’s self-perception of the presence and impact of enamel opacities to produce population measures. This tool comprised questions asking about the presence of white marks on their teeth and whether these marks bothered the volunteers and a sheet of grouped photographs of anterior teeth showing opacities ranging from TF 0, TF 1–2 to TF 2–3. Volunteers were asked which of the groups of photographs looked more like their own teeth. Examining teams from a convenience sample of 3 PCOs from this survey agreed to undertake additional measurements to assess the value of the self-perception tool. Volunteer pupils were asked the questions on a second occasion, some time after the first and clinical examiners recorded their assessments of the most closely matching set of photographs of the volunteers on two occasions. Results The tool was feasible to use, with 74% of pupils

  11. Loop electrosurgical excisional procedure.

    Science.gov (United States)

    Mayeaux, E J; Harper, M B

    1993-02-01

    Loop electrosurgical excisional procedure, or LEEP, also known as loop diathermy treatment, loop excision of the transformation zone (LETZ), and large loop excision of the transformation zone (LLETZ), is a new technique for outpatient diagnosis and treatment of dysplastic cervical lesions. This procedure produces good specimens for cytologic evaluation, carries a low risk of affecting childbearing ability, and is likely to replace cryotherapy or laser treatment for cervical neoplasias. LEEP uses low-current, high-frequency electrical generators and thin stainless steel or tungsten loops to excise either lesions or the entire transformation zone. Complication rates are comparable to cryotherapy or laser treatment methods and include bleeding, incomplete removal of the lesion, and cervical stenosis. Compared with other methods, the advantages of LEEP include: removal of abnormal tissue in a manner permitting cytologic study, low cost, ease of acquiring necessary skills, and the ability to treat lesions with fewer visits. Patient acceptance of the procedure is high. Widespread use of LEEP by family physicians can be expected.

  12. 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

    OpenAIRE

    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 c...

  13. An ab initio HCN/HNC rotational-vibrational line list and opacity function for astronomy

    Science.gov (United States)

    Harris, Gregory John

    HCN/HNC is an important molecule which is found throughout the universe. For example HCN/HNC is known to exist in comets, planetary atmospheres and the interstellar medium. HCN is also an important opacity source in carbon rich stars (C-stars). HCN masers have been observed in the circumstellar material around these C-stars and also in galaxies. Jorgensen and co-workers investigated model carbon star atmospheres in which they included HCN as an opacity source. They found that including a HCN opacity function had a remarkable effect: the atmosphere expanded by five times and the pressure of the atmosphere in the surface layers dropped by one or two orders of magnitude. This suggests that a full and detailed treatment of the rotational-vibrational spectrum of HCN/HNC could have a profound effect on the models of carbon stars, this provides the main motivation in this work. The temperatures of the stars in which HCN is an important opacity source Teff = 2000 - 3000 K. If HCN and HNC are in thermodynamic equilibrium it would be expected that HNC as well as HCN are found in significant populations. The transition dipoles of the fundamental bands of HNC are more than twice as strong as their HCN counter parts. These factors mean that both HCN and HNC will be considered, which makes a semiglobal treatment of the [H,C,N] system necessary. In this thesis an ab initio HCN/HNC linelist, from which accurate spectra and opacity functions can be calculated, is computed. Within this thesis I present least squares fits for ab initio semiglobal potential energy, dipole moment, relativistic correction and adiabatic correction surfaces. The potential energy surface (PES) is morphed for HNC geometries of the potential to improve the HNC representation of the surface. The PES and dipole moment surface (DMS) are used to perform quantum mechanical nuclear motion (rotational-vibrational) calculations with the DVR3D suite of codes. Preliminary calculations are made to optimise a ro

  14. Loops in Twistor Space

    CERN Document Server

    Bena, I; Kosower, D A; Roiban, R; Bena, Iosif; Bern, Zvi; Kosower, David A.; Roiban, Radu

    2004-01-01

    We elucidate the one-loop twistor-space structure corresponding to momentum-space MHV diagrams. We also discuss the infrared divergences, and argue that only a limited set of MHV diagrams contain them. We show how to introduce a twistor-space regulator corresponding to dimensional regularization for the infrared-divergent diagrams. We also evaluate explicitly the `holomorphic anomaly' pointed out by Cachazo, Svrcek, and Witten, and use the result to define modified differential operators which can be used to probe the twistor-space structure of one-loop amplitudes.

  15. Closed Loop Subspace Identification

    Directory of Open Access Journals (Sweden)

    Geir W. Nilsen

    2005-07-01

    Full Text Available A new three step closed loop subspace identifications algorithm based on an already existing algorithm and the Kalman filter properties is presented. The Kalman filter contains noise free states which implies that the states and innovation are uneorre lated. The idea is that a Kalman filter found by a good subspace identification algorithm will give an output which is sufficiently uncorrelated with the noise on the output of the actual process. Using feedback from the output of the estimated Kalman filter in the closed loop system a subspace identification algorithm can be used to estimate an unbiased model.

  16. Loop Quantum Gravity

    CERN Document Server

    Chiou, Dah-Wei

    2014-01-01

    This article presents an "in-a-nutshell" yet self-contained introductory review on loop quantum gravity (LQG) -- a background-independent, nonperturbative approach to a consistent quantum theory of gravity. Instead of rigorous and systematic derivations, it aims to provide a general picture of LQG, placing emphasis on the fundamental ideas and their significance. The canonical formulation of LQG, as the central topic of the article, is presented in a logically orderly fashion with moderate details, while the spin foam theory, black hole thermodynamics, and loop quantum cosmology are covered briefly. Current directions and open issues are also summarized.

  17. Disruption of mutually negative regulatory feedback loop between interferon-inducible p202 protein and the E2F family of transcription factors in lupus-prone mice

    Science.gov (United States)

    Panchanathan, Ravichandran; Xin, Hong; Choubey, Divaker

    2010-01-01

    Summary Studies have identified interferon-inducible Ifi202 gene as a lupus susceptibility gene (encoding p202 protein) in mouse models of lupus disease. However, signaling pathways that regulate the Ifi202 expression in cells remain to be elucidated. We found that steady-state levels of Ifi202 mRNA and protein were high in mouse embryonic fibroblasts (MEFs) from E2F1-knockout (E2F1-/-) and E2F1 and E2F2 double knockout (E2F1-/- E2F2-/-) mice than isogenic wild type MEFs. Moreover, overexpression of E2F1 in mouse fibroblasts decreased expression of p202. Furthermore, expression of E2F1, but not E2F4, transcription factor in mouse fibroblasts repressed the activity of 202-luc-reporter in promoter-reporter assays. Interestingly, the E2F1-mediated transcriptional repression of the 202-luc-reporter was independent of p53 and pRb expression. However, the repression was dependent on the ability of E2F1 to bind DNA. We have identified a potential E2F DNA-binding site in the 5′-regulatory region of the Ifi202 gene and mutations in this E2F DNA-binding site reduced the E2F1-mediated transcriptional repression of 202-luc-reporter. Because p202 inhibits the E2F1-mediated transcriptional activation of genes, we compared the expression of E2F1 and its target genes in splenic cells from lupus-prone B6.Nba2 congenic mice, which express increased levels of p202, with age-matched C57BL/6 mice. We found that increased expression of Ifi202 in the congenic mice was associated with inhibition of E2F1-mediated transcription and decreased expression of E2F1 and its target genes that encode pro-apoptotic proteins. Our observations support for the idea that increased Ifi202 expression in certain strain of mice contributes to lupus susceptibility in part by inhibiting E2F1-mediated functions. PMID:18424712

  18. An integrated mechanical-enzymatic reverse osmosis treatment of dairy industry wastewater and milk protein recovery as a fat replacer: a closed loop approach

    Directory of Open Access Journals (Sweden)

    F. Sarghini

    2013-09-01

    Full Text Available The dairy industry can be classified among the most polluting of the food industries in volume in regard to its large water consumption, generating from 0.2 to 10 L of effluent per liter of processed milk. Dairy industry effluents usually include highly dissolved organic matter with varying characteristics, and a correct waste management project is required to handle. In a framework of natural water resource availability and cost increase, wastewater treatment for water reuse can lower the overall water consumption and the global effluent volume of industrial plants. Moreover, correct dismissal of dairy industry wastewater is sometimes neglected by the operators , increasing the environmental impact due to the chemical and biological characteristics of such effluents. On the other hand, in the case of whey effluents, several by-products are still present inside, such as lactose and milk proteins. Membrane technology has some advantages including a high degree of reliability in removing dissolved, colloidal and particulate matter, like the selectivity in size of pollutants to be removed and the possibility of very compact treatment plants. For example, Reverse Osmosis (RO technology has been successfully applied for the treatment of dairy wastes (1, and as a technology for concentration and fractionation of whey. In this work a membrane treatment approach using reverse osmosis technology is investigated and implemented: the permeate obtained can be reused as clean warm water for cleaning and sanitation of production plants, while concentrated milk proteins are modified by using transglutaminase enzyme obtaining a high temperature resistant fat replacer to be used in different low-fat products like for example mozzarella cheese.

  19. The blind loop syndrome in children.

    Science.gov (United States)

    Stewart, B A; Karrer, F M; Hall, R J; Lilly, J R

    1990-08-01

    Anatomical abnormalities of the small bowel that cause intestinal stagnation result in bacterial overgrowth and a blind loop syndrome (BLS). Bacterial breakdown of bile salts and deamination of protein lead to malabsorption, steatorrhea, and fat-soluble vitamin deficiencies. Four children developed BLS as a complication of necrotizing enterocolitis, jejunal atresia, gastroschisis, and biliary atresia. BLS was suggested by abdominal pain, feculent vomiting, steatorrhea, and hypoalbuminemia. Dilated, stagnant bowel loops were demonstrated in each instance by upper gastrointestinal contrast study. Positive intestinal bacterial aspirates were confirmatory. Antibiotic treatment in two patients improved symptomatology but all children ultimately required surgery. Surgical procedures consisted of blind loop resection, intestinal plication, and catheterization of the bilioenteric conduit. All patients are now asymptomatic but one child suffers from parenteral nutrition-related cirrhosis and another requires chronic antibiotic therapy.

  20. Rovibrationally-resolved photodissociation of NH and application to the solar UV opacity

    Science.gov (United States)

    Shen, G.; Kuri, A.; Fontenla, J. M.; Stancil, P. C.; Wang, J. G.

    2014-05-01

    Rovibrationally-resolved photodissociation cross sections of NH have been evaluated using a combination of ab initio and experimentally derived potential curves and dipole transition moments. Here we present results for the three electronic transitions: 23Σ- interstellar gas, cross sections for X3Σ- (v = 0 , J = 0) to 23Σ- and 23 Π dominate, but for the high density and temperature conditions in stellar atmospheres, the LTE cross section to the A3 Π becomes competitive. Explicit application of the cross sections to the solar UV opacity will be presented. In particular, the NH photodissociation opacity is found to affect the non-LTE behavior of some species such as Cr I and V I. The work at UGA was partially supported by NASA grant HST-AR-11776.01-A. The work of JMF was supported by NASA LWS grant NNX09AJ22G. GS acknowledges travel support by the International Cooperation and Exchange Foundation of CAEP.

  1. Radiative ablation with two ionizing-fronts when opacity displays a sharp absorption edge

    CERN Document Server

    Poujade, Olivier; Vandenboomgaerde, Marc

    2014-01-01

    The interaction of a strong flux of photons with matter through an ionizing-front (I-front) is an ubiquitous phenomenon in the context of astrophysics and inertial confinement fusion (ICF) where intense sources of radiation put matter into motion. When the opacity of the irradiated material varies continuously in the radiation spectral domain, only one single I-front is formed. In contrast, as numerical simulations tend to show, when the opacity of the irradiated material presents a sharp edge in the radiation spectral domain, a second I-front (an edge-front) can form. A full description of the mechanism behind the formation of this edge-front is presented in this article. It allows to understand supernumerary shocks (edge-shocks), displayed by ICF simulations, that might affect the robustness of the design of fusion capsules in actual experiments. Moreover, it may have consequences in various domains of astrophysics where ablative flows occur.

  2. Time-Dependent Photoionization in a Dusty Medium II Evolution of Dust Distributions and Optical Opacities

    CERN Document Server

    Perna, R; Fiore, F; Perna, Rosalba; Lazzati, Davide; Fiore, Fabrizio

    2003-01-01

    The interaction of a radiation field with a dusty medium is a relevant issue in several astrophysical contexts. We use the time-dependent photoionization code in a dusty medium developed by Perna & Lazzati (2002), to study the modifications in the dust distribution and the relative optical opacities when a strong X-ray UV radiation flux propagates into a medium. We find that silicates are preferentially destroyed with respect to graphite, and the extinction curve becomes significantly flatter (hence implying less reddening), with the characteristic bump at lambda 2175 A highly suppressed, due to the destruction of the small graphite grains. This could explain the observational lack of such a feature in GRB afterglow and AGN spectra. For a very intense and highly variable source irradiating a compact and dense region, time variability in the optical opacity resulting from dust destruction can be observed on a relatively short timescale. We show that, under these circumstances, monitoring the time variabili...

  3. Femtosecond laser-assisted keratoplasty in a child with corneal opacity:case report

    Directory of Open Access Journals (Sweden)

    E. Yu. Markova

    2014-01-01

    Full Text Available Corneal opacities are the fourth cause of blindness world-wide. Over the past two centuries, various corneal transplantation (i.e., keratoplasty methods have been developed and improved. Nowadays, femtolaserssisted keratoplasty is one of most promising techniques. Femtosecond laser have several advantages that provide additional surgical benefits. Among them, no thermal injury, the ability to cut deeply on a single plane and to perform various corneal profiles should be mentioned. In children, corneal disorders are of special importance while femtosecondassisted keraatoplasty case reports are rare. Here, we describe femtosecond laserssisted penetrating keratoplasty in a girl with a rough central corneal opacity.

  4. Utilitarian Opacity Model for Aggregate Particles in Protoplanetary Nebulae and Exoplanet Atmospheres

    CERN Document Server

    Cuzzi, Jeffrey N; Davis, Sanford S

    2013-01-01

    As small solid grains grow into larger ones in protoplanetary nebulae, or in the cloudy atmospheres of exoplanets, they generally form porous aggregates rather than solid spheres. A number of previous studies have used highly sophisticated schemes to calculate opacity models for irregular, porous particles with size much smaller than a wavelength. However, mere growth itself can affect the opacity of the medium in far more significant ways than the detailed compositional and/or structural differences between grain constituents once aggregate particle sizes exceed the relevant wavelengths. This physics is not new; our goal here is to provide a model that provides physical insight and is simple to use in the increasing number of protoplanetary nebula evolution, and exoplanet atmosphere, models appearing in recent years, yet quantitatively captures the main radiative properties of mixtures of particles of arbitrary size, porosity, and composition. The model is a simple combination of effective medium theory with...

  5. Opacity of Hot and Dense Plasmas of a Mixture using an Average-Atom Approach

    Institute of Scientific and Technical Information of China (English)

    袁建民

    2002-01-01

    An average-atom model is proposed to calculate the opacities of hot and dense plasmas of a mixture. A self-consistent scheme is used to reach the requirements of the same temperature and chemical potential for all kinds ofatoms in the mixtures, the same electron density at the boundaries between the atoms, and the electrical neutralitywithin each atomic sphere. The orbital energies and wavefunctions for the bound electrons are calculated withthe Dirac-Slater equations. The occupation numbers at each orbital of each kind of atom are determined by theFermi-Dirac distribution with the same chemical potential for all kinds of atoms. As an example, the opacity ofthe mixture of Au and Cd is calculated at a few temperatures and densities.

  6. Submillimeter fourier-transform spectrometer measurements of atmospheric opacity above mauna kea.

    Science.gov (United States)

    Serabyn, E; Weisstein, E W; Lis, D C; Pardo, J R

    1998-04-20

    We present accurately calibrated submillimeter atmospheric transmission spectra obtained with a Fourier-transform spectrometer at the Caltech Submillimeter Observatory on Mauna Kea, Hawaii. These measurements cover the 0.9-0.3-mm wavelength range and are the first in a series aimed at defining the terrestrial long-wave atmospheric transmission curve. The 4.1-km altitude of the Mauna Kea site provides access to extremely low zenith water-vapor columns, permitting atmospheric observations at frequencies well above those possible from sea level. We describe the calibration procedures, present our first well-calibrated transmission spectra, and compare our results with those of a single-layer atmospheric transmission model, AT. With an empirical best-fit continuum opacity term included, this simple single-layer model provides a remarkably good fit to the opacity data for H(2)O line profiles described by either van Vleck-Weisskopf or kinetic shapes.

  7. Opacities and Spectra of the r-process Ejecta from Neutron Star Mergers

    CERN Document Server

    Kasen, Daniel; Barnes, Jennifer

    2013-01-01

    Material ejected during (or immediately following) the merger of two neutron stars may assemble into heavy elements by the r-process. The subsequent radioactive decay of the nuclei can power electromagnetic emission similar to, but significantly dimmer than, an ordinary supernova. Identifying such events is an important goal of future transient surveys, offering new perspectives on the origin of r-process nuclei and the astrophysical sources of gravitational waves. Predictions of the transient light curves and spectra, however, have suffered from the uncertain optical properties of heavy ions. Here we consider the opacity of expanding r-process material and argue that it is dominated by line transitions from those ions with the most complex valence electron structure, namely the lanthanides. For a few representative ions, we run atomic structure models to calculate radiative data for tens of millions of lines. We find that the resulting r-process opacities are orders of magnitude larger than that of ordinary ...

  8. Evolution and chemical yields of AGB stars: effects of low-temperature opacities

    CERN Document Server

    Ventura, Paolo

    2009-01-01

    The studies focused on the Thermally-Pulsing Asymptotic Giant Branch phase experienced by low- and intermediate-mass stars are extremely important in many astrophysical contexts. In particular, a detailed computation of their chemical yields is essential for several issues, ranging from the chemical evolution of galaxies, to the mechanisms behind the formation of globular clusters. Among all the uncertainties affecting the theoretical modelling of this phase, and described in the literature, it remains to be fully clarified which results are severely affected by the use of inadequate low-temperature opacities, that are in most cases calculated on the basis of the original chemical composition of the stars, and do not consider the changes in the surface chemistry due to the occurrence of the third dredge-up and hot-bottom burning. Our investigation is aimed at investigating this point. By means of full evolutionary models including new set of molecular opacities computed specifically with the AESOPUS tool, we ...

  9. Loop Quantum Gravity

    Directory of Open Access Journals (Sweden)

    Rovelli Carlo

    1998-01-01

    Full Text Available The problem of finding the quantum theory of the gravitational field, and thus understanding what is quantum spacetime, is still open. One of the most active of the current approaches is loop quantum gravity. Loop quantum gravity is a mathematically well-defined, non-perturbative and background independent quantization of general relativity, with its conventional matter couplings. Research in loop quantum gravity today forms a vast area, ranging from mathematical foundations to physical applications. Among the most significant results obtained are: (i The computation of the physical spectra of geometrical quantities such as area and volume, which yields quantitative predictions on Planck-scale physics. (ii A derivation of the Bekenstein-Hawking black hole entropy formula. (iii An intriguing physical picture of the microstructure of quantum physical space, characterized by a polymer-like Planck scale discreteness. This discreteness emerges naturally from the quantum theory and provides a mathematically well-defined realization of Wheeler's intuition of a spacetime ``foam''. Long standing open problems within the approach (lack of a scalar product, over-completeness of the loop basis, implementation of reality conditions have been fully solved. The weak part of the approach is the treatment of the dynamics: at present there exist several proposals, which are intensely debated. Here, I provide a general overview of ideas, techniques, results and open problems of this candidate theory of quantum gravity, and a guide to the relevant literature.

  10. Reversible hysteresis loop tuning

    Science.gov (United States)

    Berger, A.; Binek, Ch.; Margulies, D. T.; Moser, A.; Fullerton, E. E.

    2006-02-01

    We utilize antiferromagnetically coupled bilayer structures to magnetically tune hysteresis loop properties. Key element of this approach is the non-overlapping switching field distribution of the two magnetic layers that make up the system: a hard magnetic CoPtCrB layer (HL) and a soft magnetic CoCr layer (SL). Both layers are coupled antiferromagnetically through an only 0.6-nm-thick Ru interlayer. The non-overlapping switching field distribution allows the measurement of magnetization reversal in the SL at low fields while keeping the magnetization state of the HL unperturbed. Applying an appropriate high field or high field sequence changes the magnetic state of the HL, which then influences the SL magnetization reversal due to the interlayer coupling. In this way, the position and shape of the SL hysteresis loop can be changed or tuned in a fully reversible and highly effective manner. Here, we study specifically how the SL hysteresis loop characteristics change as we move the HL through an entire high field hysteresis loop sequence.

  11. CT opacity in the lungs was preceded by increased MDP activity on bone scintigraphy.

    Science.gov (United States)

    Song, Le; Zhang, Weifang; Zhang, Yanyan

    2014-11-01

    Elevated 99mTc-methylene diphosphonate (MDP) uptake in the left lung was demonstrated in a 41-year-old man with chronic lymphocytic leukemia. Lung infection was considered because the patient also had fever and pancytopenia. However, the thoracic CT performed the next day did not reveal abnormality which could explain the cause of left lung MDP activity. The repeated thoracic CTs weeks later demonstrated multiple ground-glass opacity in the left lung.

  12. Conceptual design of initial opacity experiments on the national ignition facility

    Science.gov (United States)

    Heeter, R. F.; Bailey, J. E.; Craxton, R. S.; Devolder, B. G.; Dodd, E. S.; Garcia, E. M.; Huffman, E. J.; Iglesias, C. A.; King, J. A.; Kline, J. L.; Liedahl, D. A.; McKenty, P. W.; Opachich, Y. P.; Rochau, G. A.; Ross, P. W.; Schneider, M. B.; Sherrill, M. E.; Wilson, B. G.; Zhang, R.; Perry, T. S.

    2017-02-01

    Accurate models of X-ray absorption and re-emission in partly stripped ions are necessary to calculate the structure of stars, the performance of hohlraums for inertial confinement fusion and many other systems in high-energy-density plasma physics. Despite theoretical progress, a persistent discrepancy exists with recent experiments at the Sandia Z facility studying iron in conditions characteristic of the solar radiative-convective transition region. The increased iron opacity measured at Z could help resolve a longstanding issue with the standard solar model, but requires a radical departure for opacity theory. To replicate the Z measurements, an opacity experiment has been designed for the National Facility (NIF). The design uses established techniques scaled to NIF. A laser-heated hohlraum will produce X-ray-heated uniform iron plasmas in local thermodynamic equilibrium (LTE) at temperatures eV and electron densities 21~\\text{cm}-3$ . The iron will be probed using continuum X-rays emitted in a ps, diameter source from a 2 mm diameter polystyrene (CH) capsule implosion. In this design, of the NIF beams deliver 500 kJ to the mm diameter hohlraum, and the remaining directly drive the CH capsule with 200 kJ. Calculations indicate this capsule backlighter should outshine the iron sample, delivering a point-projection transmission opacity measurement to a time-integrated X-ray spectrometer viewing down the hohlraum axis. Preliminary experiments to develop the backlighter and hohlraum are underway, informing simulated measurements to guide the final design.

  13. Limb-darkening opacity experiment using a laser-heated plasma

    Energy Technology Data Exchange (ETDEWEB)

    Hoffman, N.M.; Miller, L.W.; Mack, J.M.

    1978-10-01

    The limb-darkening technique, a method for measuring monochromatic opacity information, which has had successful astrophysical applications, is reviewed. The application of the technique to laser-produced plasmas in materials and regimes of temperature and density of interest to weapons designers is discussed, and the magnitude of the limb-darkening effect in such situations is estimated. Finally, an experimental study, now in progress, to evaluate the feasibility of this approach is described. 10 figures.

  14. Opacity measurement of a gold plasma at T{sub e} = 85 eV

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Jiyan; Yang Jiamin; Yang Guohong; Li Hang; Yuan Zheng; Zhao Yang; Xiong Gang; Bao Lihua; Huang Chenwu; Ding Yongkun; Zhang Baohan; Zheng Zhijian [Research Center of Laser Fusion, P. O. Box 919-986, Mianyang 621900 (China); Xu Yan; Wu Zheqing; Yan Jun [Institute of Applied Physics and Computational Mathematics, Beijing 100088 (China)

    2011-11-15

    The opacity of a gold plasma at the temperature of 85 eV and density of 0.02 g/cm{sup 3} was measured over the energy range from 150 eV to 1200 eV. The gold sample was heated by thermal x-ray radiation generated with a foam-baffled gold cavity. The sample transmission was obtained from the backlight, absorption and self-emission spectra measured by a time-gated, spatially resolved grating spectrometer, with the backlight and absorption spectra being measured simultaneously in a single shot and the self-emission in another shot. The temperature and density of the gold absorber were determined by the hydrodynamic simulation with Multi-1D code, which was partially tested by the reemission radiative flux measurements of the heated sample. This work permits the first test of opacity models over the photon energy range that dominates the Rosseland mean opacity at the temperature of interest for the inertial confinement fusion.

  15. Probing cosmic opacity at high redshifts with gamma-ray bursts

    CERN Document Server

    Holanda, R F L

    2014-01-01

    Probing the evolution of the universe at high redshifts with standard candles is a powerful way to discriminate dark energy models, where an open question nowadays is whether this component is constant or evolves with time. One possible source of ambiguity in this kind of analyses comes from cosmic opacity, which can mimick a dark enery behaviour. However, most tests of cosmic opacity have been restricted to the redshift range $z2$) for a flat $\\Lambda$CDM model. A possible degenerescence of the results with the adopted cosmological model is also investigated by considering a flat XCDM model. The limits on cosmic opacity in the redshift range $0

  16. Technical Note: Optical properties of desert dust with non-spherical particles: data incorporated to OPAC

    Directory of Open Access Journals (Sweden)

    P. Koepke

    2015-02-01

    Full Text Available Mineral desert dust particles in general are no spheres and assuming spherical particles, instead of more realistic shapes, has significant effects on modeled optical dust properties and so on the belonging remote sensing procedures for desert dust and the derived radiative forcing. Thus in a new version of the data base OPAC (Optical Properties of Aerosols and Clouds; Hess et al., 1998, the optical properties of the mineral particles are modeled describing the particles as spheroids with size dependent aspect ratio distributions, but with the size distributions and the spectral refractive indices not changed against the previous version of OPAC. The spheroid assumption strongly improves the scattering functions, but pays regard to the limited knowledge on particle shapes in an actual case. The relative deviations of the phase functions of non-spherical mineral particles from those of spherical particles are up to +60% at scattering angles of about 130° and up to −60% in the backscatter region, but the deviations are generally small for optical properties that are independent of the scattering angle. The improved version of OPAC (4.0 is freely available under http://www.rascin.net/

  17. Changes Of Dust Opacity With Density in the Orion A Molecular Cloud

    CERN Document Server

    Roy, Arabindo; Polychroni, Danae; Bontemps, Sylvain; Abergel, Alain; Andre, Philippe; Arzoumanian, Doris; Di Francesco, James; Hill, Tracey; Konyves, Vera; Nguyen-Luong, Quang; Pezzuto, Stefano; Schneider, Nicola; Testi, Leonardo; White, Glenn

    2012-01-01

    We have studied the opacity of dust grains at submillimeter wavelengths by estimating the optical depth from imaging at 160, 250, 350, and 500 um from the Herschel Gould Belt Survey and comparing this to a column density obtained from the 2MASS-derived color excess E(J-Ks). Our main goal was to investigate the spatial variations of the opacity due to "big" grains over a variety of environmental conditions and thereby quantify how emission properties of the dust change with column (and volume) density. The central and southern areas of the Orion A molecular cloud examined here, with NH ranging from 1.5X10^21 cm^-2 to 50X10^21 cm^-2, are well suited to this approach. We fit the multi-frequency Herschel spectral energy distributions (SEDs) of each pixel with a modified blackbody to obtain the temperature, T, and optical depth, \\tau(1200), at a fiducial frequency of 1200 GHz (250 um). Using a calibration of NH/E(J-Ks)for the interstellar medium (ISM) we obtained the opacity (dust emission cross-section per H nucl...

  18. The effect of preheating and opacity on the sorption and solubility of a composite resin.

    Science.gov (United States)

    Castro, Fabrício Luscino Alves de; Pazinatto, Flávia Bittencourt; de Lima, Érick; Cesar, Paulo Francisco; Reges, Rogério Vieira

    2016-01-01

    This study evaluated the influence of material opacity and preheating on the sorption and solubility of a composite resin material. A commercially available composite resin and an 8 × 2-mm circular metallic matrix were used to fabricate a total of 60 specimens in 6 shades, of which 3 had conventional opacity (CA2, CA3, and CA3.5) and 3 were opaque (OA2, OA3, and OA3.5). Specimens were prepared at a room temperature of 25°C or preheated to 60°C (n = 5 per shade at each temperature). The specimens were weighed 3 times: M1, dried for 24 hours at 37°C; M2, stored for 7 days in 75% ethanol at 37°C; and M3, dried for an additional 24 hours at 37°C. The weights were used to calculate the sorption and solubility of the composite resin and were analyzed using 2-way analysis of variance and Tukey tests (α = 5%). Composite resin specimens heated at 60°C yielded lower values of sorption and solubility than did specimens prepared at 25°C (P composite shades were found to be similar (P > 0.05), except for shade CA2, which presented a greater mean solubility value than OA2 (P = 0.004). Therefore, preheating was beneficial, as it lowered both the sorption and solubility of the evaluated composite resin, but opacity had little effect on these properties.

  19. The assessment of lens opacity postmortem and its implication in forensics.

    Science.gov (United States)

    Stemberga, Valter; Petaros, Anja; Kovacevic, Damir; Coklo, Miran; Simicevic, Neven; Bosnar, Alan

    2013-11-01

    Visual impairment, mostly due to cataracts, has been demonstrated to be an important factor associated with traffic accidents. Although vision screening is standard procedure during licensing in order to prevent motor vehicle accidents, an eye exam is not typically administered after an accident has already occurred. Postmortem assessment of lens opacity in victims of car accidents would provide helpful information for attesting to the liability of the parties in specific accidents, determining the circumstances of the accident, and developing preventive measures for both drivers and pedestrians alike. In this paper, we explore the use of different methods and their limitations for assessing lens opacity postmortem. We discuss the possible use and benefits of a simple, but as-yet untested method: retrobulbar translucency. The method would be based on the recording of shadows formed by opaque regions of the lens while the eye is illuminated from the back with a rigid source of light. The efficacy and objectivity of the method, its reproducibility, and the inter- and intra-observer error should be tested before implementing such a technique to be regularly used to determine lens opacity in cadavers.

  20. 3.5-Year Monitoring of 225 GHz Opacity at the Summit of Greenland

    CERN Document Server

    Matsushita, Satoki; Martin-Cocher, Pierre L; Chen, Ming-Tang; Ho, Paul T P; Inoue, Makoto; Koch, Patrick M; Paine, Scott N; Turner, David D

    2016-01-01

    We present the 3.5-yr monitoring results of 225 GHz opacity at the summit of the Greenland ice sheet (Greenland Summit Camp) at an altitude of 3200 m using a tipping radiometer. We chose this site as our submillimeter telescope (Greenland Telescope; GLT) site, because its location offers favorable baselines to existing submillimeter telescopes for global-scale VLBI. The site shows a clear seasonal variation with the average opacity lower by a factor of two during winter. For the winter quartiles of 25% and 50%, the Greenland site is about 10%-30% worse than the ALMA or the South Pole sites. Estimated atmospheric transmission spectra in winter season are similar to the ALMA site at lower frequencies (450 GHz) than those at the ALMA site. This is due to the lower altitude of the Greenland site. Nevertheless, half of the winter time at the Greenland site can be used for astronomical observations at frequencies between 450 GHz and 1000 GHz with opacities 10% transmittance in the THz (1035 GHz, 1350 GHz, and 1500 ...

  1. Opacity and Color Changes of Light-Cured Ideal Makoo (IDM

    Directory of Open Access Journals (Sweden)

    M.Ghavam

    2004-03-01

    Full Text Available Statement of Problem: Esthetic materials undergo some physical and mechanical changes,during their service in oral cavity.Purpose: The aim of this study was the evaluation of the color and opacity stability of Ideal Makoo (IDM composites and compare it with Tetric ceram.Material and methods: Fifteen disk shaped samples of each material was divided into three groups of five. Different aging treatments were applied to each group. The contrast ratio of 1mm thickness and rE of the samples were evaluated at base line and after aging,using CIE system and Data Flash spectrophotometer. All the samples were kept at 37°C.Results: Baseline opacity of IDM was relatively high (77.60%±8.6. Both materials showed increased opacity after aging. The highest rE belonged to IDM samples of B group, which was significantly more than Tetric Ceram (P<0.05. Tetric Ceram, also showed some degree of color change (rE=4.60 and 5.79, on black and white background,respectively, which is noticeable clinically.Conclusion: The research showed that IDM can not be a reliable esthetic material, unless some improvements in the chemical composition will be achieved.

  2. Knoop microhardness and FT-Raman evaluation of composite resins: influence of opacity and photoactivation source

    Directory of Open Access Journals (Sweden)

    Luis Gustavo Barrotte Albino

    2011-06-01

    Full Text Available The aim of this study was to evaluate the degree of conversion by Knoop microhardness (KHN and FT-Raman spectroscopy (FTIR of one nanofilled (Filtek Supreme-3M-ESPE [FS] and one microhybrid composite (Charisma-Heraeus-Kulzer [CH], each with different opacities, namely enamel, dentin, and translucent, which were photo-activated by a quartz-tungsten-halogen lamp (QTH and a light-emitting diode (LED. Resin was bulk inserted into a disc-shaped mold that was 2.0 mm thick and 4 mm in diameter, obtaining 10 samples per group. KHN and FTIR values were analyzed by two-way ANOVA and Tukey's tests (α = 0.05. Nanofilled resin activated by a LED presented higher microhardness values than samples activated by a QTH for dentin opacity (p < 0.05. The microhybrid resin showed no differences in KHN or FTIR values with different activation sources or opacity. The nanofilled dentin and enamel resins showed lower FTIR values than the translucent resin. The KHN values of the translucent resins were not influenced by the light source.

  3. An Analysis of Source Tilting and Sub-cell Opacity Sampling for IMC

    Energy Technology Data Exchange (ETDEWEB)

    Wollaeger, Ryan T. [Los Alamos National Laboratory; Urbatsch, Todd J. [Los Alamos National Laboratory; Wollaber, Allan B. [Los Alamos National Laboratory; Densmore, Jeffery D. [Los Alamos National Laboratory

    2012-08-02

    Implicit Monte Carlo (IMC) is a stochastic method for solving the radiative transfer equations for multiphysics application with the material in local thermodynamic equilibrium. The IMC method employs a fictitious scattering term that is computed from an implicit discretization of the material temperature equation. Unfortunately, the original histogram representation of the temperature and opacity with respect to the spatial domain leads to nonphysically fast propagation of radiation waves through optically thick material. In the past, heuristic source tilting schemes have been used to mitigate the numerical teleportation error of the radiation particles in IMC that cause this overly rapid radiation wave propagation. While improving the material temperature profile throughout the time duration, these tilting schemes alone do not generally alleviate the teleportation error to suitable levels. Another means of potentially reducing teleportation error in IMC is implementing continuous sub-cell opacities based on sub-cell temperature profiles. We present here an analysis of source tilting and continuous sub-cell opacity sampling applied to various discretizations of the temperature equation. Through this analysis, we demonstrate that applying both heuristics does not necessarily yield more accurate results if the discretization of the material equation is inconsistent with the Monte Carlo sub-cell transport.

  4. Literature Review of OPAC2.0 During 2005 - 2009 in China%2005—2010年OPAC2.0国内文献研究综述

    Institute of Scientific and Technical Information of China (English)

    顾磊

    2011-01-01

    This paper gives a comprehensive literature review of OPAC2.0 during 2005 -2010 in China, which summarizes the philosophy, the overall functions and contents, the core functions, the applied techniques and the construction approach of OPAC2.0. According to the research results, the basic theory research on the OPAC2.0 in China is rich, but the practice research is relatively poor.%对2005—2010年“国内OPAC2.0”的相关研究文献进行搜集与分析,总结OPAC2.0的理念、整体功能和内容、核心功能、采用的技术及实现途径等国内发展现状。从以上研究的成果来看,我国OPAC2.0的研究在基本理论方面的探讨趋近成熟,内容丰富,但是关于实际应用方面的研究还较欠缺。

  5. Solar neutrinos and the influences of opacity, thermal instability, additional neutrino sources, and a central black hole on solar models

    Science.gov (United States)

    Stothers, R. B.; Ezer, D.

    1972-01-01

    Significant quantities that affect the internal structure of the sun are examined for factors that reduce the temperature near the sun's center. The four factors discussed are: opacity, central black hole, thermal instability, and additional neutrino sources.

  6. Parathyroid hormone-related protein drives a CD11b+Gr1+ cell-mediated positive feedback loop to support prostate cancer growth.

    Science.gov (United States)

    Park, Serk In; Lee, Changki; Sadler, W David; Koh, Amy J; Jones, Jacqueline; Seo, Jung Won; Soki, Fabiana N; Cho, Sun Wook; Daignault, Stephanie D; McCauley, Laurie K

    2013-11-15

    In the tumor microenvironment, CD11b(+)Gr1(+) bone marrow-derived cells are a predominant source of protumorigenic factors such as matrix metalloproteinases (MMP), but how distal tumors regulate these cells in the bone marrow is unclear. Here we addressed the hypothesis that the parathyroid hormone-related protein (PTHrP) potentiates CD11b(+)Gr1(+) cells in the bone marrow of prostate tumor hosts. In two xenograft models of prostate cancer, levels of tumor-derived PTHrP correlated with CD11b(+)Gr1(+) cell recruitment and microvessel density in the tumor tissue, with evidence for mediation of CD11b(+)Gr1(+) cell-derived MMP-9 but not tumor-derived VEGF-A. CD11b(+)Gr1(+) cells isolated from mice with PTHrP-overexpressing tumors exhibited relatively increased proangiogenic potential, suggesting that prostate tumor-derived PTHrP potentiates this activity of CD11b(+)Gr1(+) cells. Administration of neutralizing PTHrP monoclonal antibody reduced CD11b(+)Gr1(+) cells and MMP-9 in the tumors. Mechanistic investigations in vivo revealed that PTHrP elevated Y418 phosphorylation levels in Src family kinases in CD11b(+)Gr1(+) cells via osteoblast-derived interleukin-6 and VEGF-A, thereby upregulating MMP-9. Taken together, our results showed that prostate cancer-derived PTHrP acts in the bone marrow to potentiate CD11b(+)Gr1(+) cells, which are recruited to tumor tissue where they contribute to tumor angiogenesis and growth. ©2013 AACR

  7. Two-loop and n-loop eikonal vertex corrections

    OpenAIRE

    Kidonakis, Nikolaos

    2003-01-01

    I present calculations of two-loop vertex corrections with massive and massless partons in the eikonal approximation. I show that the $n$-loop result for the UV poles can be given in terms of the one-loop calculation.

  8. Configuration interaction effect on open M shell Fe and Ni LTE spectral opacities, Rosseland and Planck means

    Science.gov (United States)

    Gilles, D.; Busquet, M.; Gilleron, F.; Klapisch, M.; Pain, J.-C.

    2016-05-01

    We have recently shown that iron and nickel open M-shell opacity spectra, up to Δn = 2 are very sensitive to Configuration Interaction (CI) treatments at temperature around 15 eV and for various densities. To do so we had compared extensive CI calculations obtained with two opacity codes HULLAC-v9 and SCO-RCG. In this work we extend these comparisons to a first evaluation of CI effects on Rosseland and Planck means.

  9. Dynamics of DNA Looping in Nanochannels

    Science.gov (United States)

    Heidarpourroushan, Maedeh

    This thesis is devoted to the study of protein-DNA interactions and especially how proteins can mediate DNA loop formation in nanochannels. In the last decade, a large number of studies have been performed, wherein DNA molecules were confined to the channels with cross-section around the persistence length of DNA molecule. Such nanochannels provide a good model system for studying of the physics of confined DNA. The results of this thesis increase our understanding of how different DNA-binding proteins can change the DNA configuration. (Abstract shortened by ProQuest.).

  10. Consistent dust and gas models for protoplanetary disks. I. Disk shape, dust settling, opacities, and PAHs

    Science.gov (United States)

    Woitke, P.; Min, M.; Pinte, C.; Thi, W.-F.; Kamp, I.; Rab, C.; Anthonioz, F.; Antonellini, S.; Baldovin-Saavedra, C.; Carmona, A.; Dominik, C.; Dionatos, O.; Greaves, J.; Güdel, M.; Ilee, J. D.; Liebhart, A.; Ménard, F.; Rigon, L.; Waters, L. B. F. M.; Aresu, G.; Meijerink, R.; Spaans, M.

    2016-02-01

    We propose a set of standard assumptions for the modelling of Class II and III protoplanetary disks, which includes detailed continuum radiative transfer, thermo-chemical modelling of gas and ice, and line radiative transfer from optical to cm wavelengths. The first paper of this series focuses on the assumptions about the shape of the disk, the dust opacities, dust settling, and polycyclic aromatic hydrocarbons (PAHs). In particular, we propose new standard dust opacities for disk models, we present a simplified treatment of PAHs in radiative equilibrium which is sufficient to reproduce the PAH emission features, and we suggest using a simple yet physically justified treatment of dust settling. We roughly adjust parameters to obtain a model that predicts continuum and line observations that resemble typical multi-wavelength continuum and line observations of Class II T Tauri stars. We systematically study the impact of each model parameter (disk mass, disk extension and shape, dust settling, dust size and opacity, gas/dust ratio, etc.) on all mainstream continuum and line observables, in particular on the SED, mm-slope, continuum visibilities, and emission lines including [OI] 63 μm, high-J CO lines, (sub-)mm CO isotopologue lines, and CO fundamental ro-vibrational lines. We find that evolved dust properties, i.e. large grains, often needed to fit the SED, have important consequences for disk chemistry and heating/cooling balance, leading to stronger near- to far-IR emission lines in general. Strong dust settling and missing disk flaring have similar effects on continuum observations, but opposite effects on far-IR gas emission lines. PAH molecules can efficiently shield the gas from stellar UV radiation because of their strong absorption and negligible scattering opacities in comparison to evolved dust. The observable millimetre-slope of the SED can become significantly more gentle in the case of cold disk midplanes, which we find regularly in our T Tauri models

  11. Local loop near-rings

    OpenAIRE

    Franetič, Damir

    2015-01-01

    We study loop near-rings, a generalization of near-rings, where the additive structure is not necessarily associative. We introduce local loop near-rings and prove a useful detection principle for localness.

  12. Effects of injection pressure and injection timing to exhaust gas opacity for a conventional indirect diesel engine

    Science.gov (United States)

    Budiman, Agus; Majid, Akmal Irfan; Pambayun, Nirmala Adhi Yoga; Yuswono, Lilik Chaerul; Sukoco

    2016-06-01

    In relation to pollution control and environmental friendliness, the quality of exhaust gas from diesel engine needs to be considered. The influences of injection pressure and timing to exhaust gas opacity were investigated. A series of experiments were conducted in a one-cylinder conventional diesel engine with a naturally aspirated system and indirect injection. The default specification of injection pressure was 120 kg/cm2. To investigate the injection pressure, the engine speed was retained on 1000 rpm with pressure variations from 80 to 215 kg/cm2. On the other hand, the various injection timing (8, 10, 12, 16 degrees before TDC point and exact 18 degrees before TDC point) were used to determine their effects to exhaust gas opacity. In this case, the engine speed was varied from 1000 to 2400 rpm. The injector tester was used to measure injection pressure whereas the exhaust gas opacity was determined by the smoke meter. Those data were also statistically analyzed by product moment correlation. As the results, the injection pressure of diesel engine had a non-significant positive correlation to the exhaust gas opacity with r = 0.113 and p > 5 %. Injection pressure should be adjusted to the specification listed on the diesel engine as if it was too high or too low will lead to the higher opacity. Moreover, there was a significant positive correlation between injection timing and the exhaust gas opacity in all engine speeds.

  13. GASEOUS MEAN OPACITIES FOR GIANT PLANET AND ULTRACOOL DWARF ATMOSPHERES OVER A RANGE OF METALLICITIES AND TEMPERATURES

    Energy Technology Data Exchange (ETDEWEB)

    Freedman, Richard S. [SETI Institute, Mountain View, CA (United States); Lustig-Yaeger, Jacob [Department of Physics, University of California, Santa Cruz, CA 95064 (United States); Fortney, Jonathan J. [Department of Astronomy and Astrophysics, University of California, Santa Cruz, CA 95064 (United States); Lupu, Roxana E.; Marley, Mark S. [Space Science and Astrobiology Division, NASA Ames Research Center, Moffett Field, CA (United States); Lodders, Katharina, E-mail: Richard.S.Freedman@nasa.gov [Planetary Chemistry Laboratory, Washington University, St. Louis, MO (United States)

    2014-10-01

    We present new calculations of Rosseland and Planck gaseous mean opacities relevant to the atmospheres of giant planets and ultracool dwarfs. Such calculations are used in modeling the atmospheres, interiors, formation, and evolution of these objects. Our calculations are an expansion of those presented in Freedman et al. to include lower pressures, finer temperature resolution, and also the higher metallicities most relevant for giant planet atmospheres. Calculations span 1 μbar to 300 bar, and 75-4000 K, in a nearly square grid. Opacities at metallicities from solar to 50 times solar abundances are calculated. We also provide an analytic fit to the Rosseland mean opacities over the grid in pressure, temperature, and metallicity. In addition to computing mean opacities at these local temperatures, we also calculate them with weighting functions up to 7000 K, to simulate the mean opacities for incident stellar intensities, rather than locally thermally emitted intensities. The chemical equilibrium calculations account for the settling of condensates in a gravitational field and are applicable to cloud-free giant planet and ultracool dwarf atmospheres, but not circumstellar disks. We provide our extensive opacity tables for public use.

  14. Concentration and length dependence of DNA looping in transcriptional regulation.

    Directory of Open Access Journals (Sweden)

    Lin Han

    Full Text Available In many cases, transcriptional regulation involves the binding of transcription factors at sites on the DNA that are not immediately adjacent to the promoter of interest. This action at a distance is often mediated by the formation of DNA loops: Binding at two or more sites on the DNA results in the formation of a loop, which can bring the transcription factor into the immediate neighborhood of the relevant promoter. These processes are important in settings ranging from the historic bacterial examples (bacterial metabolism and the lytic-lysogeny decision in bacteriophage, to the modern concept of gene regulation to regulatory processes central to pattern formation during development of multicellular organisms. Though there have been a variety of insights into the combinatorial aspects of transcriptional control, the mechanism of DNA looping as an agent of combinatorial control in both prokaryotes and eukaryotes remains unclear. We use single-molecule techniques to dissect DNA looping in the lac operon. In particular, we measure the propensity for DNA looping by the Lac repressor as a function of the concentration of repressor protein and as a function of the distance between repressor binding sites. As with earlier single-molecule studies, we find (at least two distinct looped states and demonstrate that the presence of these two states depends both upon the concentration of repressor protein and the distance between the two repressor binding sites. We find that loops form even at interoperator spacings considerably shorter than the DNA persistence length, without the intervention of any other proteins to prebend the DNA. The concentration measurements also permit us to use a simple statistical mechanical model of DNA loop formation to determine the free energy of DNA looping, or equivalently, the for looping.

  15. Protein

    Science.gov (United States)

    ... Food Service Resources Additional Resources About FAQ Contact Protein Protein is found throughout the body—in muscle, ... the heart and respiratory system, and death. All Protein Isn’t Alike Protein is built from building ...

  16. On the extended loop calculus

    CERN Document Server

    Griego, J R

    1995-01-01

    Some features of extended loops are considered. In particular, the behaviour under diffeomorphism transformations of the wavefunctions with support on the extended loop space are studied. The basis of a method to obtain analytical expressions of diffeomorphism invariants via extended loops are settled. Applications to knot theory and quantum gravity are considered.

  17. The Energy Landscape of Hyperstable LacI-DNA Loops

    Science.gov (United States)

    Kahn, Jason

    2009-03-01

    The Escherichia coli LacI protein represses transcription of the lac operon by blocking access to the promoter through binding at a promoter-proximal DNA operator. The affinity of tetrameric LacI (and therefore the repression efficiency) is enhanced by simultaneous binding to an auxiliary operator, forming a DNA loop. Hyperstable LacI-DNA loops were previously shown to be formed on DNA constructs that include a sequence-directed bend flanked by operators. Biochemical experiments showed that two such constructs (9C14 and 11C12) with different helical phasing between the operators and the DNA bend form different DNA loop shapes. The geometry and topology of the loops and the relevance of alternative conformations suggested by probable flexible linkers in LacI remain unclear. Bulk and single molecule fluorescence resonance energy transfer (SM-FRET, with D. English) experiments on a dual fluorophore-labeled 9C14-LacI loop demonstrate that it adopts a single, stable, rigid closed-form loop conformation. Here, we characterize the LacI-9C14 loop by SM-FRET as a function of inducer isopropyl-β,D-thiogalactoside (IPTG) concentration. Energy transfer measurements reveal partial but incomplete destabilization of loop formation by IPTG. Surprisingly, there is no change in the energy transfer efficiency of the remaining looped population. Models for the regulation of the lac operon often assume complete disruption of LacI-operator complexes upon inducer binding to LacI. Our work shows that even at saturating IPTG there is still a significant population of LacI-DNA complexes in a looped state, in accord with previous in vivo experiments that show incomplete induction (with J. Maher). Finally, we will report progress on characterizing the ``energy landscape'' for DNA looping upon systematic variation of the DNA linkers between the operators and the bending locus. Rod mechanics simulations (with N. Perkins) provide testable predictions on loop stability, topology, and FRET.

  18. Closing global material loops

    DEFF Research Database (Denmark)

    Prosman, Ernst-Jan; Wæhrens, Brian Vejrum; Liotta, Giacomo

    2017-01-01

    Replacing virgin materials with waste materials, a practice known as Industrial Symbiosis (IS), has been identified as a key strategy for closing material loops. This article adopts a critical view on geographic proximity and external coordinators – two key enablers of IS. By ‘uncovering’ a case...... where both enablers are absent, this study seeks to explore firm-level challenges of IS. We adopt an exploratory case study approach at a cement manufacturer who engages in cross-border IS without the support of external coordinators. Our research presents insights into two key areas of IS: 1) setting...... for geographic proximity and external coordinators. In doing so, our insights into firm-level challenges of long-distance IS exchanges contribute to closing global material loops by increasing the number of potential circular pathways....

  19. Loop Quantum Cosmology

    Directory of Open Access Journals (Sweden)

    Bojowald Martin

    2008-07-01

    Full Text Available Quantum gravity is expected to be necessary in order to understand situations in which classical general relativity breaks down. In particular in cosmology one has to deal with initial singularities, i.e., the fact that the backward evolution of a classical spacetime inevitably comes to an end after a finite amount of proper time. This presents a breakdown of the classical picture and requires an extended theory for a meaningful description. Since small length scales and high curvatures are involved, quantum effects must play a role. Not only the singularity itself but also the surrounding spacetime is then modified. One particular theory is loop quantum cosmology, an application of loop quantum gravity to homogeneous systems, which removes classical singularities. Its implications can be studied at different levels. The main effects are introduced into effective classical equations, which allow one to avoid the interpretational problems of quantum theory. They give rise to new kinds of early-universe phenomenology with applications to inflation and cyclic models. To resolve classical singularities and to understand the structure of geometry around them, the quantum description is necessary. Classical evolution is then replaced by a difference equation for a wave function, which allows an extension of quantum spacetime beyond classical singularities. One main question is how these homogeneous scenarios are related to full loop quantum gravity, which can be dealt with at the level of distributional symmetric states. Finally, the new structure of spacetime arising in loop quantum gravity and its application to cosmology sheds light on more general issues, such as the nature of time.

  20. Loop Quantum Cosmology

    Directory of Open Access Journals (Sweden)

    Bojowald Martin

    2005-12-01

    Full Text Available Quantum gravity is expected to be necessary in order to understand situations where classical general relativity breaks down. In particular in cosmology one has to deal with initial singularities, i.e., the fact that the backward evolution of a classical space-time inevitably comes to an end after a finite amount of proper time. This presents a breakdown of the classical picture and requires an extended theory for a meaningful description. Since small length scales and high curvatures are involved, quantum effects must play a role. Not only the singularity itself but also the surrounding space-time is then modified. One particular realization is loop quantum cosmology, an application of loop quantum gravity to homogeneous systems, which removes classical singularities. Its implications can be studied at different levels. Main effects are introduced into effective classical equations which allow to avoid interpretational problems of quantum theory. They give rise to new kinds of early universe phenomenology with applications to inflation and cyclic models. To resolve classical singularities and to understand the structure of geometry around them, the quantum description is necessary. Classical evolution is then replaced by a difference equation for a wave function which allows to extend space-time beyond classical singularities. One main question is how these homogeneous scenarios are related to full loop quantum gravity, which can be dealt with at the level of distributional symmetric states. Finally, the new structure of space-time arising in loop quantum gravity and its application to cosmology sheds new light on more general issues such as time.

  1. PAR Loop Schedule Review

    Energy Technology Data Exchange (ETDEWEB)

    Schaffer, Jr.; W.F.

    1958-04-30

    The schedule for the installation of the PAR slurry loop experiment in the South Facility of the ORR has been reviewed and revised. The design, fabrications and Installation is approximately two weeks behind schedule at this time due to many factors; however, indications are that this time can be made up. Design is estimated to be 75% complete, fabrication 32% complete and installation 12% complete.

  2. The Role of Entropic Effects on DNA Loop Formation

    Science.gov (United States)

    Wilson, David; Tkachenko, Alexei; Lillian, Todd; Perkins, Noel; Meiners, Jens Christian

    2009-03-01

    The formation of protein mediated DNA loops often regulates gene expression. Typically, a protein is simultaneously bound to two DNA operator sites. An example is the lactose repressor which binds to the Lac operon of E. coli. We characterize the mechanics of this system by calculating the free energy cost of loop formation. We construct a Hamiltonian that describes the change in DNA bending energy due to linear perturbations about the looped and open states, starting from a non-linear mechanical rod model that determines the shape and bending energy of the inter-operator DNA loop while capturing the intrinsic curvature and sequence-dependent elasticity of the DNA. The crystal structure of the LacI protein provides the boundary conditions for the DNA. We then calculate normal modes of the open and closed loops to account for the thermal fluctuations. The ratio of determinants of the two Hamiltonians yields the partition function, and the enthalphic and entropic cost of looping. This calculation goes beyond standard elastic energy models because it fully accounts for the substantial entropic differences between the two states. It also includes effects of sequence dependent curvature and stiffness and allows anisotropic variations in persistence length. From the free energy we then calculate the J-factor and ratio of loop lifetimes.

  3. Formation of chromosomal domains in interphase by loop extrusion

    Science.gov (United States)

    Fudenberg, Geoffrey

    While genomes are often considered as one-dimensional sequences, interphase chromosomes are organized in three dimensions with an essential role for regulating gene expression. Recent studies have shown that Topologically Associating Domains (TADs) are fundamental structural and functional building blocks of human interphase chromosomes. Despite observations that architectural proteins, including CTCF, demarcate and maintain the borders of TADs, the mechanisms underlying TAD formation remain unknown. Here we propose that loop extrusion underlies the formation TADs. In this process, cis-acting loop-extruding factors, likely cohesins, form progressively larger loops, but stall at TAD boundaries due to interactions with boundary proteins, including CTCF. This process dynamically forms loops of various sizes within but not between TADs. Using polymer simulations, we find that loop extrusion can produce TADs as determined by our analyses of the highest-resolution experimental data. Moreover, we find that loop extrusion can explain many diverse experimental observations, including: the preferential orientation of CTCF motifs and enrichments of architectural proteins at TAD boundaries; TAD boundary deletion experiments; and experiments with knockdown or depletion of CTCF, cohesin, and cohesin-loading factors. Together, the emerging picture from our work is that TADs are formed by rapidly associating, growing, and dissociating loops, presenting a clear framework for understanding interphase chromosomal organization.

  4. Verification of Loop Diagnostics

    Science.gov (United States)

    Winebarger, A.; Lionello, R.; Mok, Y.; Linker, J.; Mikic, Z.

    2014-01-01

    Many different techniques have been used to characterize the plasma in the solar corona: density-sensitive spectral line ratios are used to infer the density, the evolution of coronal structures in different passbands is used to infer the temperature evolution, and the simultaneous intensities measured in multiple passbands are used to determine the emission measure. All these analysis techniques assume that the intensity of the structures can be isolated through background subtraction. In this paper, we use simulated observations from a 3D hydrodynamic simulation of a coronal active region to verify these diagnostics. The density and temperature from the simulation are used to generate images in several passbands and spectral lines. We identify loop structures in the simulated images and calculate the loop background. We then determine the density, temperature and emission measure distribution as a function of time from the observations and compare with the true temperature and density of the loop. We find that the overall characteristics of the temperature, density, and emission measure are recovered by the analysis methods, but the details of the true temperature and density are not. For instance, the emission measure curves calculated from the simulated observations are much broader than the true emission measure distribution, though the average temperature evolution is similar. These differences are due, in part, to inadequate background subtraction, but also indicate a limitation of the analysis methods.

  5. Cosmic string loop microlensing

    Science.gov (United States)

    Bloomfield, Jolyon K.; Chernoff, David F.

    2014-06-01

    Cosmic superstring loops within the galaxy microlens background point sources lying close to the observer-string line of sight. For suitable alignments, multiple paths coexist and the (achromatic) flux enhancement is a factor of two. We explore this unique type of lensing by numerically solving for geodesics that extend from source to observer as they pass near an oscillating string. We characterize the duration of the flux doubling and the scale of the image splitting. We probe and confirm the existence of a variety of fundamental effects predicted from previous analyses of the static infinite straight string: the deficit angle, the Kaiser-Stebbins effect, and the scale of the impact parameter required to produce microlensing. Our quantitative results for dynamical loops vary by O(1) factors with respect to estimates based on infinite straight strings for a given impact parameter. A number of new features are identified in the computed microlensing solutions. Our results suggest that optical microlensing can offer a new and potentially powerful methodology for searches for superstring loop relics of the inflationary era.

  6. Stem–loop 4 of U1 snRNA is essential for splicing and interacts with the U2 snRNP-specific SF3A1 protein during spliceosome assembly

    Science.gov (United States)

    Sharma, Shalini; Wongpalee, Somsakul Pop; Vashisht, Ajay; Wohlschlegel, James A.; Black, Douglas L.

    2014-01-01

    The pairing of 5′ and 3′ splice sites across an intron is a critical step in spliceosome formation and its regulation. Interactions that bring the two splice sites together during spliceosome assembly must occur with a high degree of specificity and fidelity to allow expression of functional mRNAs and make particular alternative splicing choices. Here, we report a new interaction between stem–loop 4 (SL4) of the U1 snRNA, which recognizes the 5′ splice site, and a component of the U2 small nuclear ribonucleoprotein particle (snRNP) complex, which assembles across the intron at the 3′ splice site. Using a U1 snRNP complementation assay, we found that SL4 is essential for splicing in vivo. The addition of free U1-SL4 to a splicing reaction in vitro inhibits splicing and blocks complex assembly prior to formation of the prespliceosomal A complex, indicating a requirement for a SL4 contact in spliceosome assembly. To characterize the interactions of this RNA structure, we used a combination of stable isotope labeling by amino acids in cell culture (SILAC), biotin/Neutravidin affinity pull-down, and mass spectrometry. We show that U1-SL4 interacts with the SF3A1 protein of the U2 snRNP. We found that this interaction between the U1 snRNA and SF3A1 occurs within prespliceosomal complexes assembled on the pre-mRNA. Thus, SL4 of the U1 snRNA is important for splicing, and its interaction with SF3A1 mediates contact between the 5′ and 3′ splice site complexes within the assembling spliceosome. PMID:25403181

  7. Stem-loop 4 of U1 snRNA is essential for splicing and interacts with the U2 snRNP-specific SF3A1 protein during spliceosome assembly.

    Science.gov (United States)

    Sharma, Shalini; Wongpalee, Somsakul Pop; Vashisht, Ajay; Wohlschlegel, James A; Black, Douglas L

    2014-11-15

    The pairing of 5' and 3' splice sites across an intron is a critical step in spliceosome formation and its regulation. Interactions that bring the two splice sites together during spliceosome assembly must occur with a high degree of specificity and fidelity to allow expression of functional mRNAs and make particular alternative splicing choices. Here, we report a new interaction between stem-loop 4 (SL4) of the U1 snRNA, which recognizes the 5' splice site, and a component of the U2 small nuclear ribonucleoprotein particle (snRNP) complex, which assembles across the intron at the 3' splice site. Using a U1 snRNP complementation assay, we found that SL4 is essential for splicing in vivo. The addition of free U1-SL4 to a splicing reaction in vitro inhibits splicing and blocks complex assembly prior to formation of the prespliceosomal A complex, indicating a requirement for a SL4 contact in spliceosome assembly. To characterize the interactions of this RNA structure, we used a combination of stable isotope labeling by amino acids in cell culture (SILAC), biotin/Neutravidin affinity pull-down, and mass spectrometry. We show that U1-SL4 interacts with the SF3A1 protein of the U2 snRNP. We found that this interaction between the U1 snRNA and SF3A1 occurs within prespliceosomal complexes assembled on the pre-mRNA. Thus, SL4 of the U1 snRNA is important for splicing, and its interaction with SF3A1 mediates contact between the 5' and 3' splice site complexes within the assembling spliceosome. © 2014 Sharma et al.; Published by Cold Spring Harbor Laboratory Press.

  8. A test of lens opacity as an indicator of preclinical Alzheimer Disease.

    Science.gov (United States)

    Bei, Ling; Shui, Ying-Bo; Bai, Fang; Nelson, Suzanne K; Van Stavern, Gregory P; Beebe, David C

    2015-11-01

    Previous studies reported that characteristic lens opacities were present in Alzheimer Disease (AD) patients postmortem. We therefore determined whether cataract grade or lens opacity is related to the risk of Alzheimer dementia in participants who have biomarkers that predict a high risk of developing the disease. AD biomarker status was determined by positron emission tomography-Pittsburgh compound B (PET-PiB) imaging and cerebrospinal fluid (CSF) levels of Aβ42. Cognitively normal participants with a clinical dementia rating of zero (CDR = 0; N = 40) or with slight evidence of dementia (CDR = 0.5; N = 2) were recruited from longitudinal studies of memory and aging at the Washington University Knight Alzheimer's Disease Research Center. The age, sex, race, cataract type and cataract grade of all participants were recorded and an objective measure of lens light scattering was obtained for each eye using a Scheimpflug camera. Twenty-seven participants had no biomarkers of Alzheimer dementia and were CDR = 0. Fifteen participants had biomarkers indicating increased risk of AD, two of which were CDR = 0.5. Participants who were biomarker positive were older than those who were biomarker negative. Biomarker positive participants had more advanced cataracts and increased cortical light scattering, none of which reached statistical significance after adjustment for age. We conclude that cataract grade or lens opacity is unlikely to provide a non-invasive measure of the risk of developing Alzheimer dementia. Copyright © 2015 Elsevier Ltd. All rights reserved.

  9. Gamma-ray opacity of the anisotropic stratified broad-line regions in blazars

    Science.gov (United States)

    Abolmasov, Pavel; Poutanen, Juri

    2016-09-01

    The GeV-range spectra of blazars are shaped not only by non-thermal emission processes internal to the relativistic jet but also by external pair-production absorption on the thermal emission of the accretion disc and the broad-line region (BLR). For the first time, we compute here the pair-production opacities in the GeV range produced by a realistic BLR accounting for the radial stratification and radiation anisotropy. Using photoionization modelling with the CLOUDY code, we calculate a series of BLR models of different sizes, geometries, cloud densities, column densities and metallicities. The strongest emission features in the model BLR are Lyα and He II Lyα. Contribution of recombination continua is smaller, especially for hydrogen, because Ly continuum is efficiently trapped inside the large optical depth BLR clouds and converted to Lyman emission lines and higher-order recombination continua. The largest effects on the gamma-ray opacity are produced by the BLR geometry and localization of the gamma-ray source. We show that when the gamma-ray source moves further from the central source, all the absorption details move to higher energies and the overall level of absorption drops because of decreasing incidence angles between the gamma-rays and BLR photons. The observed positions of the spectral breaks can be used to measure the geometry and the location of the gamma-ray emitting region relative to the BLR. Strong dependence on geometry means that the soft photons dominating the pair-production opacity may be actually produced by a different population of BLR clouds than the bulk of the observed broad line emission.

  10. Gamma-ray opacity of the anisotropic stratified broad-line regions in blazars

    Science.gov (United States)

    Abolmasov, Pavel; Poutanen, Juri

    2017-01-01

    The GeV-range spectra of blazars are shaped not only by non-thermal emission processes internal to the relativistic jet but also by external pair-production absorption on the thermal emission of the accretion disc and the broad-line region (BLR). For the first time, we compute here the pair-production opacities in the GeV range produced by a realistic BLR accounting for the radial stratification and radiation anisotropy. Using photoionization modelling with the CLOUDY code, we calculate a series of BLR models of different sizes, geometries, cloud densities, column densities and metallicities. The strongest emission features in the model BLR are Ly α and He II Ly α. Contribution of recombination continua is smaller, especially for hydrogen, because Ly continuum is efficiently trapped inside the large optical depth BLR clouds and converted to Lyman emission lines and higher order recombination continua. The largest effects on the gamma-ray opacity are produced by the BLR geometry and localization of the gamma-ray source. We show that when the gamma-ray source moves further from the central source, all the absorption details move to higher energies and the overall level of absorption drops because of decreasing incidence angles between the gamma-rays and BLR photons. The observed positions of the spectral breaks can be used to measure the geometry and the location of the gamma-ray emitting region relative to the BLR. Strong dependence on geometry means that the soft photons dominating the pair-production opacity may be actually produced by a different population of BLR clouds than the bulk of the observed broad line emission.

  11. Pulmonary Opacities and Bronchiectasis Avid on 68Ga-PSMA PET

    DEFF Research Database (Denmark)

    Bouchelouche, Kirsten; Vendelbo, Mikkel Holm

    2017-01-01

    Prostate-specific membrane antigen (PSMA) is highly expressed in prostate cancer, and the expression increases with tumor aggressiveness, metastatic disease, and recurrence. Despite its name, PSMA is also expressed in neovasculature of other tumors including lung cancer. Here, we demonstrate a case...... of increased PSMA expression on Ga-PSMA PET/CT in benign lung opacities and bronchiectasis in a prostate cancer patient. Thus, increased PSMA activity in the lungs may be due to both benign and malignant diseases and warrants further evaluation....

  12. Lens opacities in Bloom syndrome: case report and review of the literature.

    Science.gov (United States)

    Cefle, Kivanc; Ozturk, Sukru; Gozum, Nilufer; Duman, Nilgun; Mantar, Ferhan; Guler, Kerim; Palanduz, Sukru

    2007-09-01

    Bloom syndrome is an autosomal recessive disorder characterized by proportionate short stature, photosensitivity, immunodeficiency, hypogonadism and a tendency to develop various malignancies. The greatly increased frequency of sister chromatid exchanges (reciprocal exchange of homologous segments between the two sister chromatids of a chromosome) is regarded as pathognomonic for BS. We describe an 18-year old girl who presented with short stature. She was diagnosed with BS based on an extremely increased frequency of sister chromatid exchanges. Ophthalmological examination revealed mild lens opacities bilaterally, which, to our knowledge, has not been previously reported to be associated with BS.

  13. Study of Opacity Effects on Emission Lines at EXTRAP T2R RFP

    Science.gov (United States)

    Stancalie, Viorica; Rachlew, Elisabeth

    We have investigated the influence of opacity on hydrogen (H-α and Ly-β) and Li-like oxygen emission lines from the EXTRAP T2R reversed field pinch. We used the Atomic Data Analysis System (AzDAS) based on the escape factor approximation for radiative transfer to calculate metastable and excited population densities via a collisional-radiative model. Population escape factor, emergent escape factor and modified line profiles are plotted vs. optical depth. The simulated emission line ratios in the density/temperature plane are in good agreement with experimental data for electron density and temperature measurements.

  14. Ion-ion correlation effects in opacities of ultra-dense and hot plasmas

    Energy Technology Data Exchange (ETDEWEB)

    Sauvan, P.; Minguez, E. [Instituto de Fusion Nuclear, E.T.S. de Ingenieros Industriales U.P.M., Jose Gutierrez Abascal, Madrid (Spain); Angelo, P.; Derfoul, H.; Ceccotti, T.; Poquerusse, A.; Gharbi, I.; Leboucher-Dalimier, E. [Ecole Polytechnique, Lab. pour l' Utilisation des Lasers Intenses, UMR 7605 CNRS, CEA, Ecole Polytechnique, Universite Paris 6, 91 - Palaiseau (France)

    2000-07-01

    The present work is devoted to the study of opacities for ultra-dense, hot, low Z (Z{<=}15) plasmas. The required photo-excitation and photo-ionisation cross sections are determined by the JIMENA code which allows the postprocessing of atomic data (dipole transition moments and line profiles) taking care of ion-ion correlations. These atomic data are computed with the radiative property code IDEFIX. The strong ion-ion correlation effects predicted by the simulations reinforce the impact of the experiment designed for this purpose. (authors)

  15. Beyond Nuclear Pasta: Phase Transitions and Neutrino Opacity of Non-Traditional Pasta

    CERN Document Server

    Alcain, Pablo N; Dorso, Claudio O

    2014-01-01

    In this work, we focus on different length scales within the dynamics of nucleons in conditions according to the neutron star crust, with a semiclassical molecular dynamics model, studying isospin symmetric matter at subsaturation densities. While varying the temperature, we find that a solid-liquid phase transition exists, that can be also characterized with a morphology transition. For higher temperatures, above this phase transition, we study the neutrino opacity, and find that in the liquid phase, the scattering of low momenta neutrinos remain high, even though the morphology of the structures differ significatively from those of the traditional nuclear pasta.

  16. Beyond nuclear "pasta" : Phase transitions and neutrino opacity of new "pasta" phases

    Science.gov (United States)

    Alcain, P. N.; Giménez Molinelli, P. A.; Dorso, C. O.

    2014-12-01

    In this work, we focus on different length scales within the dynamics of nucleons in conditions according to the neutron star crust, with a semiclassical molecular dynamics model, studying isospin symmetric matter at subsaturation densities. While varying the temperature, we find that a solid-liquid phase transition exists, which can be also characterized with a morphology transition. For higher temperatures, above this phase transition, we study the neutrino opacity, and find that in the liquid phase, the scattering of low momenta neutrinos remain high, even though the morphology of the structures differ significatively from those of the traditional nuclear pasta.

  17. A 65-year-old man with persistent cough and large nodular opacity.

    Science.gov (United States)

    Grimes, Brandon S; Albores, Jeffrey; Barjaktarevic, Igor

    2015-01-01

    A 65-year-old Asian man with a history of chronic hepatitis B infection presented to our pulmonary clinic for second opinion of his chronic, persistent, nonproductive cough. He was evaluated 10 months earlier with chest CT scan, which revealed a large lingular nodular opacity that was diagnosed as nodular cryptogenic organizing pneumonia by CT scan-guided percutaneous lung biopsy. Systemic corticosteroids were initiated and continued over the next 10 months. The dry cough persisted, and he developed intermittent left-sided pleuritic chest pain. He denied fevers, night sweats, hemoptysis, weight loss, or dyspnea. He was a lifelong nonsmoker and moved to the United States from China during childhood.

  18. Calculation of opacities and emissivities for carbon plasmas under NLTE and LTE conditions

    Energy Technology Data Exchange (ETDEWEB)

    Gil, J.M.; Rodriguez, R.; Florido, R.; Rubiano, J.G.; Martel, P. [Las Palmas de Gran Canaria Univ., Dept. de Fisica (Spain); Sauvan, P. [Universidad Nacional de Educacion a Distancia, Dept. de Ingenieria Energetica, Madrid (Spain); Minguez, E. [Madrid Univ. Politecnica, Instituto de Fusion Nuclear-DENIM (Spain)

    2006-06-15

    We calculate different optical properties for carbon plasma in a wide range of temperatures and densities by using ATOM3R-OP code which has been recently developed. In this code we have implemented the rate equations, the Saha equation (for local thermodynamic equilibrium) and the coronal equilibrium model. We have calculated average ionizations, level populations, opacities and emissivities and we focus our study on the identification with our code of coronal equilibrium, non-local thermodynamic equilibrium and local thermodynamic equilibrium regions for this kind of plasma. Moreover, we analyse the differences in the optical properties when they are calculated in non-local thermodynamic equilibrium and local thermodynamic equilibrium. (authors)

  19. A novel congenital ichthyosiform syndrome with associated panhypopituitarism, corneal opacities and mental retardation.

    Science.gov (United States)

    Pandhi, Deepika; Khanna, Deepshikha; Singal, Archana; Madhu, Sri Venkata

    2007-11-01

    A 15-year-old male presented with ichthyosis since infancy with panhypopituitarism, short stature and knock-knees, delayed puberty, high scrotal retractile testes, mental retardation and corneal opacities. He developed recurrent tinea capitis and tinea corporis. The clinical symptomatology indicates that this case cannot be considered as a subtype of inherited ichthyosis group, but suggests a new syndrome as a separate nosologic entity. Two previously reported cases with possibly the same syndrome also had ichthyosis associated with variable endocrinopathy. Thorough endocrinological evaluation and appropriate intervention in patients of ichthyosis with short stature may reduce the morbidity associated with retarded skeletal growth and gonadal maturation.

  20. Improving Loop Dependence Analysis

    DEFF Research Database (Denmark)

    Jensen, Nicklas Bo; Karlsson, Sven

    2017-01-01

    Programmers can no longer depend on new processors to have significantly improved single-thread performance. Instead, gains have to come from other sources such as the compiler and its optimization passes. Advanced passes make use of information on the dependencies related to loops. We improve...... the quality of that information by reusing the information given by the programmer for parallelization. We have implemented a prototype based on GCC into which we also add a new optimization pass. Our approach improves the amount of correctly classified dependencies resulting in 46% average improvement...

  1. Closing the loop.

    Science.gov (United States)

    Dassau, E; Atlas, E; Phillip, M

    2011-02-01

    Closed-loop algorithms can be found in every aspect of everyday modern life. Automation and control are used constantly to provide safety and to improve quality of life. Closed-loop systems and algorithms can be found in home appliances, automobiles, aviation and more. Can one imagine nowadays driving a car without ABS, cruise control or even anti-sliding control? Similar principles of automation and control can be used in the management of diabetes mellitus (DM). The idea of an algorithmic/technological way to control glycaemia is not new and has been researched for more than four decades. However, recent improvements in both glucose-sensing technology and insulin delivery together with advanced control and systems engineering made this dream of an artificial pancreas possible. The artificial pancreas may be the next big step in the treatment of DM since the use of insulin analogues. An artificial pancreas can be described as internal or external devices that use continuous glucose measurements to automatically manage exogenous insulin delivery with or without other hormones in an attempt to restore glucose regulation in individuals with DM using a control algorithm. This device as described can be internal or external; can use different types of control algorithms with bi-hormonal or uni-hormonal design; and can utilise different ways to administer them. The different designs and implementations have transitioned recently from in silico simulations to clinical evaluation stage with practical applications in mind. This may mark the beginning of a new era in diabetes management with the introduction of semi-closed-loop systems that can prevent or minimise nocturnal hypoglycaemia, to hybrid systems that will manage blood glucose (BG) levels with minimal user intervention to finally fully automated systems that will take the user out of the loop. More and more clinical trials will be needed for the artificial pancreas to become a reality but initial encouraging

  2. Protein (Viridiplantae): 297852830 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available QSAPSSYFSSFGESIEEFLDRPTSPETERILSGFLQTTDTSNNVDSFLHHTFNSDGTEKKPPEVKTEEDETEIPVTVTTME...972:1358 basic helix-loop-helix family protein Arabidopsis lyrata subsp. lyrata MESEFQQHHFLLHDHQHQRPRNSGLIRY

  3. A Generalized Theory of DNA Looping and Cyclization

    Science.gov (United States)

    Wilson, David; Lillian, Todd; Perkins, Noel; Tkachenko, Alexei; Meiners, Jens-Christian

    2010-03-01

    We have developed a semi-analytic method for calculating the Stockmayer Jacobson J-factor for protein mediated DNA loops. The formation of DNA loops on the order of a few persistence lengths is a key component in many biological regulatory functions. The binding of LacI protein within the Lac Operon of E.coli serves as the canonical example for loop regulated transcription. We use a non-linear rod model to determine the equilibrium shape of the inter-operator DNA loop under prescribed binding constraints while taking sequence-dependent curvature and elasticity into account. Then we construct a Hamiltonian that describes thermal fluctuations about the open and looped equilibrium states, yielding the entropic and enthalpic costs of loop formation. Our work demonstrates that even for short sequences of the order one persistence length, entropic terms contribute substantially to the J factor. We also show that entropic considerations are able to determine the most favorable binding topology. The J factor can be used to compare the relative loop lifetimes of various DNA sequences, making it a useful tool in sequence design. A corollary of this work is the computation of an effective torsional persistence length, which demonstrates how torsion bending coupling in a constrained geometry affects the conversion of writhe to twist.

  4. Loop-loop interactions govern multiple steps in indole-3-glycerol phosphate synthase catalysis.

    Science.gov (United States)

    Zaccardi, Margot J; O'Rourke, Kathleen F; Yezdimer, Eric M; Loggia, Laura J; Woldt, Svenja; Boehr, David D

    2014-03-01

    Substrate binding, product release, and likely chemical catalysis in the tryptophan biosynthetic enzyme indole-3-glycerol phosphate synthase (IGPS) are dependent on the structural dynamics of the β1α1 active-site loop. Statistical coupling analysis and molecular dynamic simulations had previously indicated that covarying residues in the β1α1 and β2α2 loops, corresponding to Arg54 and Asn90, respectively, in the Sulfolobus sulfataricus enzyme (ssIGPS), are likely important for coordinating functional motions of these loops. To test this hypothesis, we characterized site mutants at these positions for changes in catalytic function, protein stability and structural dynamics for the thermophilic ssIGPS enzyme. Although there were only modest changes in the overall steady-state kinetic parameters, solvent viscosity and solvent deuterium kinetic isotope effects indicated that these amino acid substitutions change the identity of the rate-determining step across multiple temperatures. Surprisingly, the N90A substitution had a dramatic effect on the general acid/base catalysis of the dehydration step, as indicated by the loss of the descending limb in the pH rate profile, which we had previously assigned to Lys53 on the β1α1 loop. These changes in enzyme function are accompanied with a quenching of ps-ns and µs-ms timescale motions in the β1α1 loop as measured by nuclear magnetic resonance studies. Altogether, our studies provide structural, dynamic and functional rationales for the coevolution of residues on the β1α1 and β2α2 loops, and highlight the multiple roles that the β1α1 loop plays in IGPS catalysis. Thus, substitution of covarying residues in the active-site β1α1 and β2α2 loops of indole-3-glycerol phosphate synthase results in functional, structural, and dynamic changes, highlighting the multiple roles that the β1α1 loop plays in enzyme catalysis and the importance of regulating the structural dynamics of this loop through noncovalent

  5. Loop expansion and the bosonic representation of loop quantum gravity

    Science.gov (United States)

    Bianchi, E.; Guglielmon, J.; Hackl, L.; Yokomizo, N.

    2016-10-01

    We introduce a new loop expansion that provides a resolution of the identity in the Hilbert space of loop quantum gravity on a fixed graph. We work in the bosonic representation obtained by the canonical quantization of the spinorial formalism. The resolution of the identity gives a tool for implementing the projection of states in the full bosonic representation onto the space of solutions to the Gauss and area matching constraints of loop quantum gravity. This procedure is particularly efficient in the semiclassical regime, leading to explicit expressions for the loop expansions of coherent, heat kernel and squeezed states.

  6. Loop expansion and the bosonic representation of loop quantum gravity

    CERN Document Server

    Bianchi, Eugenio; Hackl, Lucas; Yokomizo, Nelson

    2016-01-01

    We introduce a new loop expansion that provides a resolution of the identity in the Hilbert space of loop quantum gravity on a fixed graph. We work in the bosonic representation obtained by the canonical quantization of the spinorial formalism. The resolution of the identity gives a tool for implementing the projection of states in the full bosonic representation onto the space of solutions to the Gauss and area matching constraints of loop quantum gravity. This procedure is particularly efficient in the semiclassical regime, leading to explicit expressions for the loop expansions of coherent, heat kernel and squeezed states.

  7. FTS Measurements of Submillimeter-Wave Atmospheric Opacity at Pampa la Bola II : Supra-Terahertz Windows and Model Fitting

    Science.gov (United States)

    Matsushita, Satoki; Matsuo, Hiroshi; Pardo, Juan R.; Radford, Simon J. E.

    1999-10-01

    A second observing run aimed to measure the millimeter and submillimeter-wave (150-1500 GHz or 2 mm-200 mu m) atmospheric opacity was carried out with a Fourier Transform Spectrometer (FTS) at Pampa la Bola, 4800 m above sea level in northern Chile. We obtained high transmission spectra, showing up to ~ 67% transmission at submillimeter-wave windows. The observed spectra can be well modeled by newly developed radiative-transfer calculations. Correlations between 220 GHz and submillimeter-wave opacities were reanalized, including the new data set. The results show almost identical trends as the ones resulting from the first measurements. We also identified supra-terahertz windows (located around 1035 GHz, 1350 GHz, and 1500 GHz), which could not be seen in our first measurements. Opacity correlations between the 220 GHz and these new windows are derived for the first time. Combined with a statistical study of the 225 GHz opacity data of the Chajnantor site (7 km apart from Pampa la Bola), it is estimated that submillimeter-wave observations can be done with zenith opacity less than 1.0 (at the most transparent frequency in those windows) for about 50% of the winter season.

  8. High temperature storage loop :

    Energy Technology Data Exchange (ETDEWEB)

    Gill, David Dennis; Kolb, William J.

    2013-07-01

    A three year plan for thermal energy storage (TES) research was created at Sandia National Laboratories in the spring of 2012. This plan included a strategic goal of providing test capability for Sandia and for the nation in which to evaluate high temperature storage (>650ÀC) technology. The plan was to scope, design, and build a flow loop that would be compatible with a multitude of high temperature heat transfer/storage fluids. The High Temperature Storage Loop (HTSL) would be reconfigurable so that it was useful for not only storage testing, but also for high temperature receiver testing and high efficiency power cycle testing as well. In that way, HTSL was part of a much larger strategy for Sandia to provide a research and testing platform that would be integral for the evaluation of individual technologies funded under the SunShot program. DOEs SunShot program seeks to reduce the price of solar technologies to 6/kWhr to be cost competitive with carbon-based fuels. The HTSL project sought to provide evaluation capability for these SunShot supported technologies. This report includes the scoping, design, and budgetary costing aspects of this effort

  9. High temperature storage loop :

    Energy Technology Data Exchange (ETDEWEB)

    Gill, David Dennis; Kolb, William J.

    2013-07-01

    A three year plan for thermal energy storage (TES) research was created at Sandia National Laboratories in the spring of 2012. This plan included a strategic goal of providing test capability for Sandia and for the nation in which to evaluate high temperature storage (>650ÀC) technology. The plan was to scope, design, and build a flow loop that would be compatible with a multitude of high temperature heat transfer/storage fluids. The High Temperature Storage Loop (HTSL) would be reconfigurable so that it was useful for not only storage testing, but also for high temperature receiver testing and high efficiency power cycle testing as well. In that way, HTSL was part of a much larger strategy for Sandia to provide a research and testing platform that would be integral for the evaluation of individual technologies funded under the SunShot program. DOEs SunShot program seeks to reduce the price of solar technologies to 6/kWhr to be cost competitive with carbon-based fuels. The HTSL project sought to provide evaluation capability for these SunShot supported technologies. This report includes the scoping, design, and budgetary costing aspects of this effort

  10. Saturating representation of loop conformational fragments in structure databanks

    Directory of Open Access Journals (Sweden)

    Fiser András

    2006-07-01

    Full Text Available Abstract Background Short fragments of proteins are fundamental starting points in various structure prediction applications, such as in fragment based loop modeling methods but also in various full structure build-up procedures. The applicability and performance of these approaches depend on the availability of short fragments in structure databanks. Results We studied the representation of protein loop fragments up to 14 residues in length. All possible query fragments found in sequence databases (Sequence Space were clustered and cross referenced with available structural fragments in Protein Data Bank (Structure Space. We found that the expansion of PDB in the last few years resulted in a dense coverage of loop conformational fragments. For each loops of length 8 in the current Sequence Space there is at least one loop in Structure Space with 50% or higher sequence identity. By correlating sequence and structure clusters of loops we found that a 50% sequence identity generally guarantees structural similarity. These percentages of coverage at 50% sequence cutoff drop to 96, 94, 68, 53, 33 and 13% for loops of length 9, 10, 11, 12, 13, and 14, respectively. There is not a single loop in the current Sequence Space at any length up to 14 residues that is not matched with a conformational segment that shares at least 20% sequence identity. This minimum observed identity is 40% for loops of 12 residues or shorter and is as high as 50% for 10 residue or shorter loops. We also assessed the impact of rapidly growing sequence databanks on the estimated number of new loop conformations and found that while the number of sequentially unique sequence segments increased about six folds during the last five years there are almost no unique conformational segments among these up to 12 residues long fragments. Conclusion The results suggest that fragment based prediction approaches are not limited any more by the completeness of fragments in databanks but

  11. Condition Monitoring of Control Loops

    OpenAIRE

    Horch, Alexander

    2000-01-01

    The main concern of this work is the development of methodsfor automatic condition monitoring of control loops withapplication to the process industry. By condition monitoringboth detection and diagnosis of malfunctioning control loops isunderstood, using normal operating data and a minimum amount ofprocess knowledge. The use of indices for quantifying loop performance is dealtwith in the first part of the thesis. The starting point is anindex proposed by Harris (1989). This index has been mo...

  12. Parallax diagnostics of radiation source geometric dilution for iron opacity experiments

    CERN Document Server

    Nagayama, T; Loisel, G; Rochau, G A; Falcon, R E

    2014-01-01

    Experimental tests are in progress to evaluate the accuracy of the modeled iron opacity at solar interior conditions [J.E. Bailey et al., Phys. Plasmas 16, 058101 (2009)]. The iron sample is placed on top of the Sandia National Laboratories z-pinch dynamic hohlraum (ZPDH) radiation source. The samples are heated to 150 - 200 eV electron temperatures and 7e21 - 4e22 e/cc electron densities by the ZPDH radiation and backlit at its stagnation [T. Nagayama et al., Phys. Plasmas 21, 056502 (2014)]. The backlighter attenuated by the heated sample plasma is measured by four spectrometers along +/- 9 degree with respect to the z-pinch axis to infer the sample iron opacity. Here we describe measurements of the source-to-sample distance that exploit the parallax of spectrometers that view the half-moon-shaped sample from +/-9 degree. The measured sample temperature decreases with increased source-to-sample distance. This distance must be taken into account for understanding the sample heating.

  13. Temporal and spatial mapping of surface albedo and atmospheric dust opacity on Mars

    Science.gov (United States)

    Lee, S. W.; Clancy, R. T.; Gladstone, G. R.

    1993-01-01

    The Mariner 9 and Viking provided abundant evidence that eolian processes are active over much of the surface of Mars. Past studies have demonstrated that variations in regional albedo and wind-streak patterns are indicative of sediment transport through a region, while thermal inertia data (derived from the Viking Infrared Thermal Mapper (IRTM) dataset) are indicative of the degree of surface mantling by dust deposits. The visual and thermal data are therefore diagnostic of whether net erosion or deposition of dust-storm fallout is taking place currently and whether such processes have been active in a region over the long term. These previous investigations, however, have not attempted to correct for the effects of atmospheric dust loading on observations of the martian surface, so quantitative studies of current sediment transport rates have included large errors due to uncertainty in the magnitude of this 'atmospheric component' of the observations. We have developed a radiative transfer model that allows the atmospheric dust opacity to be determined from IRTM thermal observations. Corrections for the effects of atmospheric dust loading on observations of surface albedo can also be modeled. This approach to determining 'dust-corrected surface albedo' incorporates the atmospheric dust opacity, the single-scattering albedo and particle phase function of atmospheric dust, and the bidirectional reflectance of the surface, and it accounts for variable lighting and viewing geometry.

  14. Digitisation of films and texture analysis for digital classification of pulmonary opacities

    Energy Technology Data Exchange (ETDEWEB)

    Desaga, J.F.; Dengler, J.; Wolf, T.; Engelmann, U.; Scheppelmann, D.; Meinzer, H.P.

    1988-04-01

    The study aimed at evaluating the effect of different methods of digitisation of radiographic films on the digital classification of pulmonary opacities. Test sets from the standard of the International Labour Office (ILO) Classification of Radiographs of Pneumoconiosis were prepared by film digitsation using a scanning microdensitometer or a video digitiser based on a personal computer equipped with a real time digitiser board and a vidicon or a Charge Coupled Device (CCD) camera. Seven different algorithms were used for texture analysis resulting in 16 texture parameters for each region. All methods used for texture analysis were independent of the mean grey value level and the size of the image analysed. Classification was performed by discriminant analysis using the classes from the ILO classification. A hit ratio of at least 85% was achieved for a digitisation by scanner digitisation or the vidicon, while the corresponding results of the CCD camera were significantly less good. Classification by texture analysis of opacities of chest X-rays of pneumoconiosis digitised by a personal computer based video digitiser and a vidicon are of equal quality compared to digitisation by a scanning microdensitometer. Correct classification of 90% was achieved via the described statistical approach.

  15. Solar Activity and Cloud Opacity Variations A Modulated Cosmic-Ray Ionization Model

    CERN Document Server

    Marsden, D C; Marsden, David; Lingenfelter, Richard E.

    2002-01-01

    The observed correlation between global low cloud amount and the flux of high energy cosmic-rays supports the idea that ionization plays a crucial role in tropospheric cloud formation. We explore this idea quantitatively with a simple model of cosmic-ray ionization enhancement of the formation of cloud condensation nuclei. This model predicts that solar modulation of the cosmic-ray ionization rate should be correlated with cloud opacity where the atmospheric aerosol concentration is low. Using the International Satellite Cloud Climatology Project database (1983-1993), we find that the mean opacity of low latitude (40 degrees) clouds, on the other hand, show an anti-correlation with cosmic-ray flux, which we suggest may be a feedback effect resulting from the thicker low latitude clouds. We also show that the previously reported correlations of cloud amount with cosmic-ray flux probably result from the variations in longwave emissivity expected from our model, and not from variations in cloud amount. Further g...

  16. Biodegradable X-ray markers of controlled radio-opacity. Temporary position measurements in bone.

    Science.gov (United States)

    Stallmann, Hein P; Faber, Chris; Plokker, Herbert M; Wuisman, Paul I J M

    2005-02-01

    In order to analyze X-ray markers for potential use in biodegradable implants or radiostereogrammatic analysis (RSA), we combined iopromide contrast fluid with biodegradable calcium phosphate cement. The radio-opacity of 10 x 10 mm markers containing different iodine concentrations (0, 120, 240, 360 and 720 mg per gram cement) was compared to an aluminium wedge of increasing (1-10 mm) thickness. The addition of iopromide increased the radio-opacity in a dose-dependent manner, which was comparable to 9-mm aluminium at concentrations of 240-720 mg/g. Radiographs of markers placed in explanted rabbit and in human femora were made to investigate the clinical accuracy for position determination. Markers of 1 x 1 mm (120 mg/g) were clearly discernable in all femora, and could be used to adequately measure distances of 5-45 mm (accuracy 0.10-2.19 mm). These markers might be embedded in biodegradable implants or used as temporary markers in the bone to analyze postoperative position on radiographs.

  17. Consistent dust and gas models for protoplanetary disks. I. Disk shape, dust settling, opacities, and PAHs

    CERN Document Server

    Woitke, P; Pinte, C; Thi, W -F; Kamp, I; Rab, C; Anthonioz, F; Antonellini, S; Baldovin-Saavedra, C; Carmona, A; Dominik, C; Dionatos, O; Greaves, J; Güdel, M; Ilee, J D; Liebhart, A; Ménard, F; Rigon, L; Waters, L B F M; Aresu, G; Meijerink, R; Spaans, M

    2015-01-01

    We propose a set of standard assumptions for the modelling of Class II and III protoplanetary disks, which includes detailed continuum radiative transfer, thermo-chemical modelling of gas and ice, and line radiative transfer from optical to cm wavelengths. We propose new standard dust opacities for disk models, we present a simplified treatment of PAHs sufficient to reproduce the PAH emission features, and we suggest using a simple treatment of dust settling. We roughly adjust parameters to obtain a model that predicts typical Class II T Tauri star continuum and line observations. We systematically study the impact of each model parameter (disk mass, disk extension and shape, dust settling, dust size and opacity, gas/dust ratio, etc.) on all continuum and line observables, in particular on the SED, mm-slope, continuum visibilities, and emission lines including [OI] 63um, high-J CO lines, (sub-)mm CO isotopologue lines, and CO fundamental ro-vibrational lines. We find that evolved dust properties (large grains...

  18. Diagnostic development in precise opacity measurement of radiatively heated Al plasma on Shenguang II laser facility

    Energy Technology Data Exchange (ETDEWEB)

    Zhao Yang [Wuhan National Laboratory for Optoelectronics, Institute of Optoelectronics Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China); Research Center of Laser Fusion, China Academy of Engineering Physics, Mianyang 621900 (China); Yang Jiamin; Zhang Jiyan [Research Center of Laser Fusion, China Academy of Engineering Physics, Mianyang 621900 (China); Liu Jinsong; Yuan Xiao [Wuhan National Laboratory for Optoelectronics, Institute of Optoelectronics Science and Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China); Jin Fengtao [Research Center of Laser Fusion, China Academy of Engineering Physics, Mianyang 621900 (China); Department of Physics, National University of Defense Technology, Changsha 410073 (China)

    2009-04-15

    Simultaneous measurements of the self-emission spectrum, the backlighting source spectrum, and the transmission spectrum in one shot, which reduce the experimental uncertainties from shot-to-shot fluctuation, are essential for precise opacity experiments. In order to achieve precise absorption spectrum of Al plasmas, a special half sample sandwich target was designed and short backlighter was used to provide time- and space-resolving diagnostics on the Shenguang II high power laser facility. In the measurement, a cylindrical cavity with CH foam baffles was used to provide a clean x-ray radiation environment for sample heating. The x-ray source spectrum, the transmission spectrum, and the self-emission spectrum of the soft x-ray heated Al sample were recorded in one shot with a penta-erythritol tetrakis (hydroxymethy) methane C(CH{sub 2}OH){sub 4} (PET) crystal spectrometer by using the point-projection method. Experimental results have been compared with the calculation results of a detailed level accounting opacity code.

  19. FEEST: A method for tabulating equation of state and opacity tables

    Energy Technology Data Exchange (ETDEWEB)

    White, R.H.

    1993-03-01

    The tabulation of equations of state presently used by codes which carry temperature and density as independent variables, provides separate tables for pressure (P) and specific internal energy ({var_epsilon}) as functions of the temperature (T) and density ({rho}). Both P and {var_epsilon} are determined by bi-quadratic interpolation in tables of P and {var_epsilon} values arranged on a rectangular grid in the T-{rho} plane. The system was designed for use on the 709-7094 generation of computers and has been used, essentially unmodified, for approximately twenty years. It has long been recognized that this ``Bi-quadratic Tabulation`` system has several drawbacks. In this paper, the authors describe the Free Energy Equations of State Tabulation (FEEST) scheme which is intended to replace the presently used Bi-Quadratic Tabulation. The Bi-quadratic Tabulation, now used, treats opacities ({kappa}) in the same way as P and {var_epsilon} expect that (1/T) replaces T as one of the interpolation variables. Since {kappa} may vary inversely with a high (3 to 8) power of T and since bi-quadratic interpolation in (1/T) includes terms only up to T{sup {minus}2}, opacity tables have been large and difficult to produce.

  20. Opacity broadening and interpretation of suprathermal CO linewidths: Macroscopic Turbulence and Tangled Molecular Clouds

    CERN Document Server

    Hacar, A; Burkert, A; Goldsmith, P

    2016-01-01

    (Abridged) Many of the observed CO line profiles exhibit broad linewidths that greatly exceed the thermal broadening expected within molecular clouds. These suprathermal CO linewidths are assumed to be originated from the presence of unresolved supersonic motions inside clouds. Typically overlooked in the literature, in this paper we aim to quantify the impact of the opacity broadening effects on the current interpretation of the CO suprathermal line profiles. Without any additional contributions to the gas velocity field, a large fraction of the apparently supersonic (${\\cal M}\\sim$2-3) linewidths measured in both $^{12}$CO and $^{13}$CO (J=1-0) lines can be explained by the saturation of their corresponding sonic-like, optically-thin C$^{18}$O counterparts assuming standard isotopic fractionation. Combined with the presence of multiple components detected in our C$^{18}$O spectra, these opacity effects seem to be also responsible of the highly supersonic linewidths (${\\cal M}>$8-10) detected in the broadest...

  1. Gamma-ray opacity of the anisotropic stratified broad-line regions in blazars

    CERN Document Server

    Abolmasov, Pavel

    2016-01-01

    The GeV-range spectra of blazars are shaped not only by non-thermal emission processes internal to the relativistic jet but also by external pair-production absorption on the thermal emission of the accretion disc and the broad-line region (BLR). For the first time, we compute here the pair-production opacities in the GeV range produced by a realistic BLR accounting for the radial stratification and radiation anisotropy. Using photoionization modelling with the CLOUDY code, we calculate a series of BLR models of different sizes, geometries, cloud densities, column densities and metallicities. The strongest emission features in the model BLR are Ly$\\alpha$ and HeII Ly$\\alpha$. Contribution of recombination continua is smaller, especially for hydrogen, because Ly continuum is efficiently trapped inside the large optical depth BLR clouds and converted to Lyman emission lines and higher-order recombination continua. The largest effects on the gamma-ray opacity are produced by the BLR geometry and localization of ...

  2. Minimum Core Masses for Giant Planet Formation With Realistic Equations of State and Opacities

    CERN Document Server

    Piso, Ana-Maria A; Murray-Clay, Ruth A

    2014-01-01

    Giant planet formation by core accretion requires a core that is sufficiently massive to trigger runaway gas accretion in less that the typical lifetime of protoplanetary disks. We explore how the minimum required core mass, M_crit, depends on a non-ideal equation of state and on opacity changes due to grain growth, across a range of stellocentric distances from 5-100 AU. This minimum M_crit applies when planetesimal accretion does not substantially heat the atmosphere. Compared to an ideal gas polytrope, the inclusion of molecular hydrogen (H_2) dissociation and variable occupation of H_2 rotational states increases M_crit. Specifically, M_crit increases by a factor of ~2 if the H_2 spin isomers, ortho- and parahydrogen, are in thermal equilibrium, and by a factor of ~2-4 if the ortho-to-para ratio is fixed at 3:1. Lower opacities due to grain growth reduce M_crit. For a standard disk model around a Solar mass star, we calculate M_crit ~ 8 M_Earth at 5 AU, decreasing to ~5 M_Earth at 100 AU, for a realistic ...

  3. Effect of EGR on the exhaust gas temperature and exhaust opacity in compression ignition engines

    Indian Academy of Sciences (India)

    Avinash Kumar Agrawal; Shrawan Kumar Singh; Shailendra Sinha; Mritunjay Kumar Shukla

    2004-06-01

    In diesel engines, NOx formation is a highly temperature-dependent phenomenon and takes place when the temperature in the combustion chamber exceeds 2000 K. Therefore, in order to reduce NOx emissions in the exhaust, it is necessary to keep peak combustion temperatures under control. One simple way of reducing the NOx emission of a diesel engine is by late injection of fuel into the combustion chamber. This technique is effective but increases fuel consumption by 10–15%, which necessitates the use of more effective NOx reduction techniques like exhaust gas recirculation (EGR). Re-circulating part of the exhaust gas helps in reducing NOx, but appreciable particulate emissions are observed at high loads, hence there is a trade-off between NOx and smoke emission. To get maximum benefit from this trade-off, a particulate trap may be used to reduce the amount of unburnt particulates in EGR, which in turn reduce the particulate emission also. An experimental investigation was conducted to observe the effect of exhaust gas re-circulation on the exhaust gas temperatures and exhaust opacity. The experimental setup for the proposed experiments was developed on a two-cylinder, direct injection, air-cooled, compression ignition engine. A matrix of experiments was conducted for observing the effect of different quantities of EGR on exhaust gas temperatures and opacity.

  4. Understanding the role of thermal fluctuations in DNA looping

    Science.gov (United States)

    Wilson, David P.; Lillian, Todd; Goyal, Sachin; Tkachenko, Alexei V.; Perkins, Noel C.; Meiners, Jens-Christian

    2007-06-01

    Protein-mediated DNA loop formation is an important biological process that regulates key functions such as transcription. We present a mechanical model for these DNA-protein complexes that can take effects of the DNA sequence such induced curvature into account. This model provides the equilibrium shape and elastic energy of the DNA loop, using boundary conditions from the protein crystal structure. We then construct a Hamiltonian for small perturbations of the DNA around the equilibrium shape, which in turn allows us to calculate the eigenmodes and the entropic contributions of the thermal fluctuations to the free energy of the DNA loop. Here we present computations related to the short wild-type lactose repressor loop of Escheria coli (E. coli), and find that the entropic contributions are significant and amount to up to 3.9 k BT of the free energy. We also show that this entropic contribution from the stiffening of the DNA loop depends strongly on the phase angle between the two operator sites, which adds to the known phasing effect of the elastic energy of the loop.

  5. Loop Heat Pipe Startup Behaviors

    Science.gov (United States)

    Ku, Jentung

    2016-01-01

    A loop heat pipe must start successfully before it can commence its service. The startup transient represents one of the most complex phenomena in the loop heat pipe operation. This paper discusses various aspects of loop heat pipe startup behaviors. Topics include the four startup scenarios, the initial fluid distribution between the evaporator and reservoir that determines the startup scenario, factors that affect the fluid distribution between the evaporator and reservoir, difficulties encountered during the low power startup, and methods to enhance the startup success. Also addressed are the pressure spike and pressure surge during the startup transient, and repeated cycles of loop startup and shutdown under certain conditions.

  6. Opacity broadening and interpretation of suprathermal CO linewidths: Macroscopic turbulence and tangled molecular clouds

    Science.gov (United States)

    Hacar, A.; Alves, J.; Burkert, A.; Goldsmith, P.

    2016-06-01

    Context. Since their first detection in the interestellar medium, (sub-)millimeter line observations of different CO isotopic variants have routinely been employed to characterize the kinematic properties of the gas in molecular clouds. Many of these lines exhibit broad linewidths that greatly exceed the thermal broadening expected for the low temperatures found within these objects. These observed suprathermal CO linewidths are assumed to originate from unresolved supersonic motions inside clouds. Aims: The lowest rotational J transitions of some of the most abundant CO isotopologues, 12CO and 13CO, are found to present large optical depths. In addition to well-known line saturation effects, these large opacities present a non-negligible contribution to their observed linewidths. Typically overlooked in the literature, in this paper we aim to quantify the impact of these opacity broadening effects on the current interpretation of the CO suprathermal line profiles. Methods: Combining large-scale observations and LTE modeling of the ground J = 1-0 transitions of the main 12CO, 13CO, C18O isotopologues, we have investigated the correlation of the observed linewidths as a function of the line opacity in different regions of the Taurus molecular cloud. Results: Without any additional contributions to the gas velocity field, a large fraction of the apparently supersonic (ℳ ~ 2-3) linewidths measured in both 12CO and 13CO (J = 1-0) lines can be explained by the saturation of their corresponding sonic-like, optically thin C18O counterparts assuming standard isotopic fractionation. Combined with the presence of multiple components detected in some of our C18O spectra, these opacity effects also seem to be responsible for most of the highly supersonic linewidths (ℳ > 8-10) detected in some of the broadest 12CO and 13CO spectra in Taurus. Conclusions: Our results demonstrate that most of the suprathermal 12CO and 13CO linewidths reported in nearby clouds like Taurus

  7. Enzyme Selectivity Fine-Tuned through Dynamic Control of a Loop.

    Science.gov (United States)

    Vögeli, Beat; Bibow, Stefan; Chi, Celestine N

    2016-02-24

    Allostery has been revealed as an essential property of all proteins. For enzymes, shifting of the structural equilibrium distribution at one site can have substantial impacts on protein dynamics and selectivity. Promising sites of remotely shifting such a distribution by changing the dynamics would be at flexible loops because relatively large changes may be achieved with minimal modification of the protein. A ligand-selective change of binding affinity to the active site of cyclophilin is presented involving tuning of the dynamics of a highly flexible loop. Binding affinity is increased upon substitution of double Gly to Ala at the hinge regions of the loop. Quenching of the motional amplitudes of the loop slightly rearranges the active site. In particular, key residues for binding Phe60 and His126 adopt a more fixed orientation in the bound protein. Our system may serve as a model system for studying the effects of various time scales of loop motion on protein function tuned by mutations.

  8. Propuesta metodológica de evaluación de interfaces de OPACs. INNOPAC versus UNICORN.

    Directory of Open Access Journals (Sweden)

    Rodríguez Bravo, Blanca

    2004-03-01

    Full Text Available The aim of this paper is to present a model of academic OPACs evaluation with the objective of sharing a procedure and some parameters and indicators established. There are two fundamental parameters, the interface searching services and the characteristics of the interface: design, ergonomics and user-friendliness. The present work provides also, the main results of the evaluations of ten OPACs implemented with INNOPAC and UNICORN previously accomplished. Now we will contrast both systems. We consider that universities are institutions that demand OPACs with better services to those of other informative units. The present evaluation has considered the users needs in academic libraries.

    Los propósitos de este trabajo son presentar un modelo de evaluación de OPACs universitarios con el objetivo de compartir un procedimiento y unos parámetros e indicadores establecidos a este fin. Dos son los parámetros fundamentales, las prestaciones de búsqueda de la interfaz y las características de la propia interfaz: diseño, ergonomía y amigabilidad. El presente estudio ofrece, asimismo, los principales resultados de las evaluaciones realizadas en trabajos previos sobre diez OPACs implementados con INNOPAC y UNICORN, que nos permiten ahora contrastar ambos sistemas. Partimos de la consideración de que las universidades son instituciones que por su idiosincrasia exigen OPACs con prestaciones superiores a las de otras unidades informativas. En este sentido, la formalización de los criterios evaluativos ha considerado las necesidades de los usuarios de las bibliotecas universitarias.

  9. Temporal evolution of UV opacity and dust particle size at Gale Crater from MSL/REMS measurements

    Science.gov (United States)

    Vicente-Retortillo, Álvaro; Martinez, German; Renno, Nilton O.; Lemmon, Mark T.; Mason, Emily; De la Torre, Manuel

    2016-10-01

    A better characterization of the size, radiative properties and temporal variability of suspended dust in the Martian atmosphere is necessary to improve our understanding of the current climate of Mars. The REMS UV sensor onboard the Mars Science Laboratory (MSL) Curiosity rover has performed ground-based measurements of solar radiation in six different UV spectral bands for the first time on Mars.We developed a novel technique to retrieve dust opacity and particle size from REMS UV measurements. We use the electrical output current (TELRDR products) of the six photodiodes and the ancillary data (ADR products) to avoid inconsistencies found in the processed data (units of W/m2) when the solar zenith angle is above 30°. In addition, we use TELRDR and ADR data only in events during which the Sun is temporally blocked by the rover's masthead or mast to mitigate uncertainties associated to the degradation of the sensor due to the deposition of dust on it. Then we use a radiative transfer model with updated dust properties based on the Monte-Carlo method to retrieve the dust opacity and particle size.We find that the seasonal trend of UV opacity is consistent with opacity values at 880 nm derived from Mastcam images of the Sun, with annual maximum values in spring and in summer and minimum values in winter. The interannual variability is low, with two local maxima in mid-spring and mid-summer. Finally, dust particle size also varies throughout the year with typical values of the effective radius in the range between 0.5 and 2 μm. These variations in particle size occur in a similar way to those in dust opacity; the smallest sizes are found when the opacity values are the lowest.

  10. Dynamic PID loop control

    Energy Technology Data Exchange (ETDEWEB)

    Pei, L.; Klebaner, A.; Theilacker, J.; Soyars, W.; Martinez, A.; Bossert, R.; DeGraff, B.; Darve, C.; /Fermilab

    2011-06-01

    The Horizontal Test Stand (HTS) SRF Cavity and Cryomodule 1 (CM1) of eight 9-cell, 1.3GHz SRF cavities are operating at Fermilab. For the cryogenic control system, how to hold liquid level constant in the cryostat by regulation of its Joule-Thompson JT-valve is very important after cryostat cool down to 2.0 K. The 72-cell cryostat liquid level response generally takes a long time delay after regulating its JT-valve; therefore, typical PID control loop should result in some cryostat parameter oscillations. This paper presents a type of PID parameter self-optimal and Time-Delay control method used to reduce cryogenic system parameters oscillation.

  11. Inductance loop and partial

    CERN Document Server

    Paul, Clayton R

    2010-01-01

    "Inductance is an unprecedented text, thoroughly discussing "loop" inductance as well as the increasingly important "partial" inductance. These concepts and their proper calculation are crucial in designing modern high-speed digital systems. World-renowned leader in electromagnetics Clayton Paul provides the knowledge and tools necessary to understand and calculate inductance." "With the present and increasing emphasis on high-speed digital systems and high-frequency analog systems, it is imperative that system designers develop an intimate understanding of the concepts and methods in this book. Inductance is a much-needed textbook designed for senior and graduate-level engineering students, as well as a hands-on guide for working engineers and professionals engaged in the design of high-speed digital and high-frequency analog systems."--Jacket.

  12. Dynamic PID loop control

    CERN Document Server

    Pei, L; Theilacker, J; Soyars, W; Martinez, A; Bossert, R; DeGraff, B; Darve, C

    2012-01-01

    The Horizontal Test Stand (HTS) SRF Cavity and Cryomodule 1 (CM1) of eight 9-cell, 1.3GHz SRF cavities are operating at Fermilab. For the cryogenic control system, how to hold liquid level constant in the cryostat by regulation of its Joule-Thompson JT-valve is very important after cryostat cool down to 2.0 K. The 72-cell cryostat liquid level response generally takes a long time delay after regulating its JT-valve; therefore, typical PID control loop should result in some cryostat parameter oscillations. This paper presents a type of PID parameter self-optimal and Time-Delay control method used to reduce cryogenic system parameters' oscillation.

  13. Vortex loops and Majoranas

    Energy Technology Data Exchange (ETDEWEB)

    Chesi, Stefano [Department of Physics, McGill University, Montreal, Quebec H3A 2T8 (Canada); CEMS, RIKEN, Wako, Saitama 351-0198 (Japan); Jaffe, Arthur [Harvard University, Cambridge, Massachusetts 02138 (United States); Department of Physics, University of Basel, Basel (Switzerland); Institute for Theoretical Physics, ETH Zürich, Zürich (Switzerland); Loss, Daniel [CEMS, RIKEN, Wako, Saitama 351-0198 (Japan); Department of Physics, University of Basel, Basel (Switzerland); Pedrocchi, Fabio L. [Department of Physics, University of Basel, Basel (Switzerland)

    2013-11-15

    We investigate the role that vortex loops play in characterizing eigenstates of interacting Majoranas. We give some general results and then focus on ladder Hamiltonian examples as a test of further ideas. Two methods yield exact results: (i) A mapping of certain spin Hamiltonians to quartic interactions of Majoranas shows that the spectra of these two examples coincide. (ii) In cases with reflection-symmetric Hamiltonians, we use reflection positivity for Majoranas to characterize vortices in the ground states. Two additional methods suggest wider applicability of these results: (iii) Numerical evidence suggests similar behavior for certain systems without reflection symmetry. (iv) A perturbative analysis also suggests similar behavior without the assumption of reflection symmetry.

  14. Apolipoprotein AI deficiency inhibits serum opacity factor activity against plasma high density lipoprotein via a stabilization mechanism.

    Science.gov (United States)

    Rosales, Corina; Patel, Niket; Gillard, Baiba K; Yelamanchili, Dedipya; Yang, Yaliu; Courtney, Harry S; Santos, Raul D; Gotto, Antonio M; Pownall, Henry J

    2015-04-14

    The reaction of Streptococcal serum opacity factor (SOF) against plasma high-density lipoproteins (HDL) produces a large cholesteryl ester-rich microemulsion (CERM), a smaller neo HDL that is apolipoprotein (apo) AI-poor, and lipid-free apo AI. SOF is active versus both human and mouse plasma HDL. In vivo injection of SOF into mice reduces plasma cholesterol ∼40% in 3 h while forming the same products observed in vitro, but at different ratios. Previous studies supported the hypothesis that labile apo AI is required for the SOF reaction vs HDL. Here we further tested that hypothesis by studies of SOF against HDL from apo AI-null mice. When injected into apo AI-null mice, SOF reduced plasma cholesterol ∼35% in 3 h. The reaction of SOF vs apo AI-null HDL in vitro produced a CERM and neo HDL, but no lipid-free apo. Moreover, according to the rate of CERM formation, the extent and rate of the SOF reaction versus apo AI-null mouse HDL were less than that against wild-type (WT) mouse HDL. Chaotropic perturbation studies using guanidine hydrochloride showed that apo AI-null HDL was more stable than WT HDL. Human apo AI added to apo AI-null HDL was quantitatively incorporated, giving reconstituted HDL. Both SOF and guanidine hydrochloride displaced apo AI from the reconstituted HDL. These results support the conclusion that apo AI-null HDL is more stable than WT HDL because it lacks apo AI, a labile protein that is readily displaced by physicochemical and biochemical perturbations. Thus, apo AI-null HDL is less SOF-reactive than WT HDL. The properties of apo AI-null HDL can be partially restored to those of WT HDL by the spontaneous incorporation of human apo AI. It remains to be determined what other HDL functions are affected by apo AI deletion.

  15. Streptococcal serum opacity factor increases the rate of hepatocyte uptake of human plasma high-density lipoprotein cholesterol.

    Science.gov (United States)

    Gillard, Baiba K; Rosales, Corina; Pillai, Biju K; Lin, Hu Yu; Courtney, Harry S; Pownall, Henry J

    2010-11-16

    Serum opacity factor (SOF), a virulence determinant of Streptococcus pyogenes, converts plasma high-density lipoproteins (HDL) to three distinct species: lipid-free apolipoprotein (apo) A-I, neo HDL, a small discoidal HDL-like particle, and a large cholesteryl ester-rich microemulsion (CERM) that contains the cholesterol esters (CE) of up to ∼400000 HDL particles and apo E as its major protein. Similar SOF reaction products are obtained with HDL, total plasma lipoproteins, and whole plasma. We hypothesized that hepatic uptake of CERM-CE via multiple apo E-dependent receptors would be faster than that of HDL-CE. We tested our hypothesis using human hepatoma cells and lipoprotein receptor-specific Chinese hamster ovary (CHO) cells. The uptake of [(3)H]CE by HepG2 and Huh7 cells from HDL after SOF treatment, which transfers >90% of HDL-CE to CERM, was 2.4 and 4.5 times faster, respectively, than from control HDL. CERM-[(3)H]CE uptake was inhibited by LDL and HDL, suggestive of uptake by both the LDL receptor (LDL-R) and scavenger receptor class B type I (SR-BI). Studies in CHO cells specifically expressing LDL-R and SR-BI confirmed CERM-[(3)H]CE uptake by both receptors. RAP and heparin inhibit CERM-[(3)H]CE but not HDL-[(3)H]CE uptake, thereby implicating LRP-1 and cell surface proteoglycans in this process. These data demonstrate that SOF treatment of HDL increases the rate of CE uptake via multiple hepatic apo E receptors. In so doing, SOF might increase the level of hepatic disposal of plasma cholesterol in a way that is therapeutically useful.

  16. Loop Quantum Gravity

    Directory of Open Access Journals (Sweden)

    Rovelli Carlo

    2008-07-01

    Full Text Available The problem of describing the quantum behavior of gravity, and thus understanding quantum spacetime, is still open. Loop quantum gravity is a well-developed approach to this problem. It is a mathematically well-defined background-independent quantization of general relativity, with its conventional matter couplings. Today research in loop quantum gravity forms a vast area, ranging from mathematical foundations to physical applications. Among the most significant results obtained so far are: (i The computation of the spectra of geometrical quantities such as area and volume, which yield tentative quantitative predictions for Planck-scale physics. (ii A physical picture of the microstructure of quantum spacetime, characterized by Planck-scale discreteness. Discreteness emerges as a standard quantum effect from the discrete spectra, and provides a mathematical realization of Wheeler’s “spacetime foam” intuition. (iii Control of spacetime singularities, such as those in the interior of black holes and the cosmological one. This, in particular, has opened up the possibility of a theoretical investigation into the very early universe and the spacetime regions beyond the Big Bang. (iv A derivation of the Bekenstein–Hawking black-hole entropy. (v Low-energy calculations, yielding n-point functions well defined in a background-independent context. The theory is at the roots of, or strictly related to, a number of formalisms that have been developed for describing background-independent quantum field theory, such as spin foams, group field theory, causal spin networks, and others. I give here a general overview of ideas, techniques, results and open problems of this candidate theory of quantum gravity, and a guide to the relevant literature.

  17. Monte Carlo Simulation of Opacities of Hot and Dense Au Plasma in the Unresolved Transition Array Approximation

    Institute of Scientific and Technical Information of China (English)

    程新路; 杨莉; 张红; 杨向东

    2002-01-01

    The opacity, and its Planck and Rosseland mean values, of the hot and dense Au plasma in local thermodynamicsequilibrium are studied by the Monte Carlo method based on the unresolved transition array (UTA) approxima-tion. The average ion model and the Saha equation are used to determine the atomic level populations. Theresult gives a more detailed structure for frequency-dependent opacity than the popularly used super transitionarray or UTA in the photon energy range of 500eV to 2000eV. The Monte Carlo method can give a result betterthan that of the UTA, with almost the same computation effort.

  18. The Second Extracellular Loop of Pore-Forming Subunits of ATP-Binding Cassette Transporters for Basic Amino Acids Plays a Crucial Role in Interaction with the Cognate Solute Binding Protein(s)▿

    Science.gov (United States)

    Eckey, Viola; Weidlich, Daniela; Landmesser, Heidi; Bergmann, Ulf; Schneider, Erwin

    2010-01-01

    In the thermophile Geobacillus stearothermophilus, the uptake of basic amino acids is mediated by an ABC transporter composed of the substrate binding protein (receptor) ArtJ and a homodimer each of the pore-forming subunit, ArtM, and the nucleotide-binding subunit, ArtP. We recently identified two putative binding sites in ArtJ that might interact with the Art(MP)2 complex, thereby initiating the transport cycle (A. Vahedi-Faridi et al., J. Mol. Biol. 375:448-459, 2008). Here we investigated the contribution of charged amino acid residues in the second extracellular loop of ArtM to contact with ArtJ. Our results demonstrate a crucial role for residues K177, R185, and E188, since mutations to oppositely charged amino acids or glutamine led to a complete loss of ArtJ-stimulated ATPase activity of the complex variants in proteoliposomes. The defects could not be suppressed by ArtJ variants carrying mutations in site I (K39E and K152E) or II (E163K and D170K), suggesting a more complex interplay than that by a single salt bridge. These findings were supported by cross-linking assays demonstrating physical proximity between ArtJ(N166C) and ArtM(E182C). The importance of positively charged residues for receptor-transporter interaction was underscored by mutational analysis of the closely related transporter HisJ/LAO-HisQMP2 of Salmonella enterica serovar Typhimurium. While transporter variants with mutated positively charged residues in HisQ displayed residual ATPase activities, corresponding mutants of HisM could no longer be stimulated by HisJ/LAO. Interestingly, the ATPase activity of the HisQM(K187E)P2 variant was inhibited by l- and d-histidine in detergent, suggesting a role of the residue in preventing free histidine from gaining access to the substrate binding site within HisQM. PMID:20154136

  19. Decreased Degradation of Internalized Follicle-Stimulating Hormone Caused by Mutation of Aspartic Acid 6.30550 in a Protein Kinase-CK2 Consensus Sequence in the Third Intracellular Loop of Human Follicle-Stimulating Hormone Receptor1

    Science.gov (United States)

    Kluetzman, Kerri S.; Thomas, Richard M.; Nechamen, Cheryl A.; Dias, James A.

    2011-01-01

    A naturally occurring mutation in follicle-stimulating hormone receptor (FSHR) gene has been reported: an amino acid change to glycine occurs at a conserved aspartic acid 550 (D550, D567, D6.30567). This residue is contained in a protein kinase-CK2 consensus site present in human FSHR (hFSHR) intracellular loop 3 (iL3). Because CK2 has been reported to play a role in trafficking of some receptors, the potential roles for CK2 and D550 in FSHR function were evaluated by generating a D550A mutation in the hFSHR. The hFSHR-D550A binds hormone similarly to WT-hFSHR when expressed in HEK293T cells. Western blot analyses showed lower levels of mature hFSHR-D550A. Maximal cAMP production of both hFSHR-D550A as well as the naturally occurring mutation hFSHR-D550G was diminished, but constitutive activity was not observed. Unexpectedly, when 125I-hFSH bound to hFSHR-D550A or hFSHR-D550G, intracellular accumulation of radiolabeled FSH was observed. Both sucrose and dominant-negative dynamin blocked internalization of radiolabeled FSH and its commensurate intracellular accumulation. Accumulation of radiolabeled FSH in cells transfected with hFSHR-D550A is due to a defect in degradation of hFSH as measured in pulse chase studies, and confocal microscopy imaging revealed that FSH accumulated in large intracellular structures. CK2 kinase activity is not required for proper degradation of internalized FSH because inhibition of CK2 kinase activity in cells expressing hFSHR did not uncouple degradation of internalized radiolabeled FSH. Additionally, the CK2 consensus site in FSHR iL3 is not required for binding because CK2alpha coimmunoprecipitated with hFSHR-D550A. Thus, mutation of D550 uncouples the link between internalization and degradation of hFSH. PMID:21270425

  20. Phenomenology of loop quantum cosmology

    CERN Document Server

    Sakellariadou, Mairi

    2010-01-01

    After introducing the basic ingredients of Loop Quantum Cosmology, I will briefly discuss some of its phenomenological aspects. Those can give some useful insight about the full Loop Quantum Gravity theory and provide an answer to some long-standing questions in early universe cosmology.

  1. Improved code-tracking loop

    Science.gov (United States)

    Laflame, D. T.

    1980-01-01

    Delay-locked loop tracks pseudonoise codes without introducing dc timing errors, because it is not sensitive to gain imbalance between signal processing arms. "Early" and "late" reference codes pass in combined form through both arms, and each arm acts on both codes. Circuit accomodates 1 dB weaker input signals with tracking ability equal to that of tau-dither loops.

  2. Loop groups and noncommutative geometry

    CERN Document Server

    Carpi, Sebastiano

    2015-01-01

    We describe the representation theory of loop groups in terms of K-theory and noncommutative geometry. This is done by constructing suitable spectral triples associated with the level l projective unitary positive-energy representations of any given loop group LG. The construction is based on certain supersymmetric conformal field theory models associated with LG.

  3. Brane Couplings from Bulk Loops

    OpenAIRE

    Georgi, Howard; Grant, Aaron K.; Hailu, Girma

    2000-01-01

    We compute loop corrections to the effective action of a field theory on a five-dimensional $S_1/Z_2$ orbifold. We find that the quantum loop effects of interactions in the bulk produce infinite contributions that require renormalization by four-dimensional couplings on the orbifold fixed planes. Thus bulk couplings give rise to renormalization group running of brane couplings.

  4. CHANGES OF DUST OPACITY WITH DENSITY IN THE ORION A MOLECULAR CLOUD

    Energy Technology Data Exchange (ETDEWEB)

    Roy, Arabindo; Martin, Peter G.; Nguyen-Luong, Quang [Canadian Institute for Theoretical Astrophysics, University of Toronto, 60 St. George Street, Toronto, ON M5S 3H8 (Canada); Polychroni, Danae [INAF-IFSI, via Fosso del Cavaliere 100, I-00133 Roma (Italy); Bontemps, Sylvain; Schneider, Nicola [Universite de Bordeaux, LAB, UMR5804, F-33270 Floirac (France); Abergel, Alain; Konyves, Vera [IAS, CNRS (UMR 8617), Universite Paris-Sud 11, Batiment 121, F-91400 Orsay (France); Andre, Philippe; Arzoumanian, Doris; Hill, Tracey [Laboratoire AIM, C.E.A. Saclay, F-90091 Gif-sur-Yvette (France); Di Francesco, James [National Research Council of Canada, 5071 West Saanich Road, Victoria, BC V9E 2E7 (Canada); Pezzuto, Stefano [Istituto di Astrofisica e Planetologia Spaziali IAPS, Istituto Nazionale di Astrofisica INAF, via Fosso del Cavaliere 100, I-00133 Roma (Italy); Testi, Leonardo [European Southern Observatory, Karl Schwarzschild Strasse 2, D-85748 Garching (Germany); White, Glenn [Department of Physics and Astronomy, The Open University, Walton Hall, Milton Keynes, MK7 6AA (United Kingdom)

    2013-01-20

    We have studied the opacity of dust grains at submillimeter wavelengths by estimating the optical depth from imaging at 160, 250, 350, and 500 {mu}m from the Herschel Gould Belt Survey and comparing this to a column density obtained from the Two Micron All Sky Survey derived color excess E(J - K {sub s}). Our main goal was to investigate the spatial variations of the opacity due to 'big' grains over a variety of environmental conditions and thereby quantify how emission properties of the dust change with column (and volume) density. The central and southern areas of the Orion A molecular cloud examined here, with N {sub H} ranging from 1.5 Multiplication-Sign 10{sup 21} cm{sup -2} to 50 Multiplication-Sign 10{sup 21} cm{sup -2}, are well suited to this approach. We fit the multi-frequency Herschel spectral energy distributions (SEDs) of each pixel with a modified blackbody to obtain the temperature, T, and optical depth, {tau}{sub 1200}, at a fiducial frequency of 1200 GHz (250 {mu}m). Using a calibration of N {sub H}/E(J - K{sub s} ) for the interstellar medium (ISM) we obtained the opacity (dust emission cross-section per H nucleon), {sigma}{sub e}(1200), for every pixel. From a value {approx}1 Multiplication-Sign 10{sup -25} cm{sup 2} H{sup -1} at the lowest column densities that is typical of the high-latitude diffuse ISM, {sigma}{sub e}(1200) increases as N {sup 0.28} {sub H} over the range studied. This is suggestive of grain evolution. Integrating the SEDs over frequency, we also calculated the specific power P (emission power per H) for the big grains. In low column density regions where dust clouds are optically thin to the interstellar radiation field (ISRF), P is typically 3.7 Multiplication-Sign 10{sup -31} W H{sup -1}, again close to that in the high-latitude diffuse ISM. However, we find evidence for a decrease of P in high column density regions, which would be a natural outcome of attenuation of the ISRF that heats the grains, and for

  5. The relative frequencies of causes of widespread ground-glass opacity: A retrospective cohort

    Energy Technology Data Exchange (ETDEWEB)

    Hewitt, Michael G., E-mail: Mike_hewitt@me.com; Miller, Wallace T., E-mail: Wallace.miller@uphs.upenn.edu; Reilly, Thomas J., E-mail: thomasjreilly@comcast.net; Simpson, Scott, E-mail: Simpson80@gmail.com

    2014-10-15

    Highlights: • The most common cause of widespread ground-glass opacities is hydrostatic pulmonary edema. • Associated findings such as air-trapping and centrilobular nodules are highly specific for hypersensitivity pneumonitis. • The clinical setting (outpatient versus inpatient) will alter the order of the differential diagnosis. - Abstract: Purpose: The purpose of our study was to determine the relative frequencies of causes of widespread ground-glass opacity (GGO) in an unselected, consecutive patient population and to identify any associated imaging findings that can narrow or reorganize the differential. Materials and methods: The study was approved by the center's IRB and is HIPPA compliant. Cases with widespread GGO in the radiology report were identified by searching the Radiology Information System. Medical records and CT scan examinations were reviewed for the causes of widespread GGO. Associations between a less dominant imaging finding and a particular diagnosis were analyzed with the chi square test. Our study group consisted of 234 examinations with 124 women and 110 men and a mean age of 53.7 years. Results: A cause was established in 204 (87.2%) cases. Hydrostatic pulmonary edema was most common with 131 cases (56%). Interstitial lung diseases (ILD) were the next most common, most often hypersensitivity pneumonitis (HP) (n = 12, 5%) and connective tissue disease related ILD (n = 7, 3%). Infection accounted for 5% (12 cases). A few miscellaneous diseases accounted for 5 cases (2.1%). The combination of septal thickening and pleural effusions had a specificity of 0.91 for hydrostatic pulmonary edema (P < .001) while centrilobular nodules and air trapping had a specificity of 1.0 for HP. In 24 (10.2%) patients, increased opacification from expiration was incorrectly interpreted as representing widespread ground glass opacity. The relative frequency of disease dramatically changed according to the setting. In the inpatient setting, diffuse

  6. Higher dimensional loop quantum cosmology

    Science.gov (United States)

    Zhang, Xiangdong

    2016-07-01

    Loop quantum cosmology (LQC) is the symmetric sector of loop quantum gravity. In this paper, we generalize the structure of loop quantum cosmology to the theories with arbitrary spacetime dimensions. The isotropic and homogeneous cosmological model in n+1 dimensions is quantized by the loop quantization method. Interestingly, we find that the underlying quantum theories are divided into two qualitatively different sectors according to spacetime dimensions. The effective Hamiltonian and modified dynamical equations of n+1 dimensional LQC are obtained. Moreover, our results indicate that the classical big bang singularity is resolved in arbitrary spacetime dimensions by a quantum bounce. We also briefly discuss the similarities and differences between the n+1 dimensional model and the 3+1 dimensional one. Our model serves as a first example of higher dimensional loop quantum cosmology and offers the possibility to investigate quantum gravity effects in higher dimensional cosmology.

  7. Uranyl Nitrate Flow Loop

    Energy Technology Data Exchange (ETDEWEB)

    Ladd-Lively, Jennifer L [ORNL

    2008-10-01

    The objectives of the work discussed in this report were to: (1) develop a flow loop that would simulate the purified uranium-bearing aqueous stream exiting the solvent extraction process in a natural uranium conversion plant (NUCP); (2) develop a test plan that would simulate normal operation and disturbances that could be anticipated in an NUCP; (3) use the flow loop to test commercially available flowmeters for use as safeguards monitors; and (4) recommend a flowmeter for production-scale testing at an NUCP. There has been interest in safeguarding conversion plants because the intermediate products [uranium dioxide (UO{sub 2}), uranium tetrafluoride (UF{sub 4}), and uranium hexafluoride (UF{sub 6})] are all suitable uranium feedstocks for producing special nuclear materials. Furthermore, if safeguards are not applied virtually any nuclear weapons program can obtain these feedstocks without detection by the International Atomic Energy Agency (IAEA). Historically, IAEA had not implemented safeguards until the purified UF{sub 6} product was declared as feedstock for enrichment plants. H. A. Elayat et al. provide a basic definition of a safeguards system: 'The function of a safeguards system on a chemical conversion plant is in general terms to verify that no useful nuclear material is being diverted to use in a nuclear weapons program'. The IAEA now considers all highly purified uranium compounds as candidates for safeguarding. DOE is currently interested in 'developing instruments, tools, strategies, and methods that could be of use to the IAEA in the application of safeguards' for materials found in the front end of the nuclear fuel cycle-prior to the production of the uranium hexafluoride or oxides that have been the traditional starting point for IAEA safeguards. Several national laboratories, including Oak Ridge, Los Alamos, Lawrence Livermore, and Brookhaven, have been involved in developing tools or techniques for safeguarding conversion

  8. Tables of phase functions, opacities, albedos, equilibrium temperatures, and radiative accelerations of dust grains in exoplanets

    CERN Document Server

    Budaj, Jan; Salmeron, Raquel; Hubeny, Ivan

    2015-01-01

    There has been growing observational evidence for the presence of condensates in the atmospheres and/or comet-like tails of extrasolar planets. As a result, systematic and homogeneous tables of dust properties are useful in order to facilitate further observational and theoretical studies. In this paper we present calculations and analysis of non-isotropic phase functions, asymmetry parameter (mean cosine of the scattering angle), absorption and scattering opacities, single scattering albedos, equilibrium temperatures, and radiative accelerations of dust grains relevant for extrasolar planets. Our assumptions include spherical grain shape, Deirmendjian particle size distribution, and Mie theory. We consider several species: corundum/alumina, iron, olivines with 0% and 50% iron content, pyroxenes with 0%, 20% and 60% iron content, carbon at two different temperatures, water ice, liquid water, and ammonia. The presented tables cover the wavelength range of 0.2 to 500 micron and modal particle radii from 0.01 mi...

  9. Liquid refractive index sensing independent of opacity using an optofluidic sensor based on diffraction

    CERN Document Server

    Xu, Zhida

    2014-01-01

    We have implemented a multi-functional optofluidic sensor that can monitor changes in the refractive index and pressure of biofluid simultaneously and can detect free-solution molecular interaction in-situ. In this paper, we demonstrate two major improvements of this sensor proven by both simulation and experiments. One improvement is the broader measurement range of refractive index by making the diffraction grating with high-index polymer. The other improvement is the separation of refractive index sensing from opacity sensing by using the relative power ratio of diffraction orders. This simple, compact and low-cost multi-functional optofluidic sensor has the potential to be used for in-situ biofluid monitoring.

  10. Calibration of X-ray spectrometers for opacity experiments at the Orion laser facility (invited)

    Science.gov (United States)

    Bentley, C.; Allan, P.; Brent, K.; Bruce, N.; Hoarty, D.; Meadowcroft, A.; Percival, J.; Opie, C.

    2016-11-01

    Accurately calibrated and characterised x-ray diagnostics are a key requirement in the fielding of experiments on the Orion laser where absolute measurements of x-ray emission are used to underpin the validity of models of emissivity and opacity. Diffraction crystals are used in spectrometers on Orion to record the dispersed spectral features emitted by the laser produced plasma to obtain a measurement of the plasma conditions. The ability to undertake diffraction crystal calibrations supports the successful outcome of these Orion experiments. This paper details the design and commissioning of a system to undertake these calibrations in the energy range 2.0 keV to approximately 8.5 keV. Improvements to the design are detailed which will extend the commissioned range of energies to below 1 keV.

  11. All-sky Relative Opacity Mapping Using Night Time Panoramic Images

    CERN Document Server

    Shamir, L; Shamir, Lior; Nemiroff, Roberj J.

    2005-01-01

    An all-sky cloud monitoring system that generates relative opacity maps over many of the world's premier astronomical observatories is described. Photometric measurements of numerous background stars are combined with simultaneous sky brightness measurements to differentiate thin clouds from sky glow sources such as air glow and zodiacal light. The system takes a continuous pipeline of all-sky images, and compares them to canonical images taken on other nights at the same sidereal time. Data interpolation then yields transmission maps covering almost the entire sky. An implementation of this system is currently operating through the Night Sky Live network of CONCAM3s located at Cerro Pachon (Chile), Mauna Kea (Hawaii), Haleakala (Hawaii), SALT (South Africa) and the Canary Islands (Northwestern Africa).

  12. Ground-Glass Opacity Lung Nodules in the Era of Lung Cancer CT Screening

    DEFF Research Database (Denmark)

    Pedersen, Jesper Holst; Saghir, Zaigham; Winkler Wille, Mathilde Marie

    2016-01-01

    The advent of computed tomography screening for lung cancer will increase the incidence of ground-glass opacity (GGO) nodules detected and referred for diagnostic evaluation and management. GGO nodules remain a diagnostic challenge; therefore, a more systematic approach is necessary to ensure......, the National Comprehensive Cancer Network, and the British Thoracic Society. In addition, we discuss the management and follow-up of GGO nodules in the light of experience from screening trials. Minimally invasive tissue biopsies and the marking of GGO nodules for surgery are new and rapidly developing fields...... that will yield improvements in both diagnosis and treatment. The standard-of-care surgical treatment of early lung cancer is still minimally invasive lobectomy with systematic lymph node dissection. However, recent research has shown that some GGO lesions may be treated with sublobar resections; these findings...

  13. Intensity enhancement of O VI ultraviolet emission lines in solar spectra due to opacity

    CERN Document Server

    Keenan, F P; Madjarska, M S; Rose, S J; Bowler, L A; Britton, J; McCrink, L; Mathioudakis, M

    2014-01-01

    Opacity is a property of many plasmas, and it is normally expected that if an emission line in a plasma becomes optically thick, its intensity ratio to that of another transition that remains optically thin should decrease. However, radiative transfer calculations undertaken both by ourselves and others predict that under certain conditions the intensity ratio of an optically thick to thin line can show an increase over the optically thin value, indicating an enhancement in the former. These conditions include the geometry of the emitting plasma and its orientation to the observer. A similar effect can take place between lines of differing optical depth. Previous observational studies have focused on stellar point sources, and here we investigate the spatially-resolved solar atmosphere using measurements of the I(1032 A)/I(1038 A) intensity ratio of O VI in several regions obtained with the Solar Ultraviolet Measurements of Emitted Radiation (SUMER) instrument on board the Solar and Heliospheric Observatory (...

  14. Total power millimeter-wave spectrometer for measurements of dust opacity at cryogenic temperatures.

    Science.gov (United States)

    Potapov, Alexey; Lewen, Frank; Mutschke, Harald; Mohr, Pierre; Schlemmer, Stephan

    2014-07-01

    A highly sensitive total power millimeter-wave spectrometer has been built to investigate the opacity of important interstellar-dust analogues in the 10-300 K temperature range. The key elements of the spectrometer are a frequency agile synthesizer followed by a microwave amplifier and a subsequent frequency multiplier. In a first step, the frequency range of 72-120 GHz is covered by the spectrometer, and a room temperature Schottky detector is employed as a detector. A newly developed two channel (sample/reference) copper sample holder is cryogenically cooled for the 10-300 K range. Here we present the technical details of the spectrometer including examples of the obtained results. The analysis of these results will be published elsewhere.

  15. Lethality Index 2008-2014: Less shootings, same lethality, more opacity

    Directory of Open Access Journals (Sweden)

    Carlos Silva Forné

    2017-07-01

    Full Text Available This article evaluates the use of lethal force by Mexican federal security forces during shootings with presumed members of organized crime from 2008-2014. The authors use official data and press reports on deaths and wounded in shootings to construct indicators such as the number of dead civilians over the number of dead officials from the federal security forces and the number of dead civilians over the number of wounded civilians. In a context where certain factors that contribute to an excessive use of force become more common, the results of the study show a growing use of lethal force. This raises questions over the possible excessive use of lethal force as a normal or systematic practice. The study also shows a growing context of opacity in the infor­mation available to evaluate the use of lethal force and the general lack of a legal framework to regulate the use of lethal force in Mexico.

  16. Dynamical Opacity-Sampling Models of Mira Variables. I: Modelling Description and Analysis of Approximations

    CERN Document Server

    Ireland, M J; Wood, P R

    2008-01-01

    We describe the Cool Opacity-sampling Dynamic EXtended (CODEX) atmosphere models of Mira variable stars, and examine in detail the physical and numerical approximations that go in to the model creation. The CODEX atmospheric models are obtained by computing the temperature and the chemical and radiative states of the atmospheric layers, assuming gas pressure and velocity profiles from Mira pulsation models, which extend from near the H-burning shell to the outer layers of the atmosphere. Although the code uses the approximation of Local Thermodynamic Equilibrium (LTE) and a grey approximation in the dynamical atmosphere code, many key observable quantities, such as infrared diameters and low-resolution spectra, are predicted robustly in spite of these approximations. We show that in visible light, radiation from Mira variables is dominated by fluorescence scattering processes, and that the LTE approximation likely under-predicts visible-band fluxes by a factor of two.

  17. 1st oPAC Topical Workshop: Grand Challenges in Accelerator Optimisation

    CERN Document Server

    2013-01-01

    Accelerators are key instruments for fundamental research, health and industry applications. International collaboration is very important for their continued optimisation. To address this oPAC is organising this two-day international workshop on Grand Challenges in Accelerator Optimisation. The workshop will provide an overview of the current state of the art in beam physics, numerical simulations and beam instrumentation and highlight existing limitations. It will discuss research and development being undertaken and ambitions to further improve the performance of existing and future facilities. In addition to invited talks, there will be industry displays and a special seminar covering recent LHC discoveries. All participants will have an opportunity to contribute a poster.

  18. The Opacity of Russian-Ukrainian Energy Relations; Russie-Ukraine: opacite des reseaux energetiques

    Energy Technology Data Exchange (ETDEWEB)

    Dubien, A.

    2007-07-01

    Energy issues lie at the heart of Ukraine's economic, political and strategic challenges. A year after the 'orange revolution', the 'gas war' served to highlight the country's vulnerable position, being 80% dependent on imports of gas and having the world's most energy hungry economy. The 2005 crisis also highlighted the extreme opacity of the country's bilateral relations with Russia, which are governed as much by the interests surrounding Gazprom's relations as by those of the state. Yanukovich's return to power in the summer of 2006 coincided with a relative appeasement of relations with Moscow and a new division of spheres of influence in the Ukrainian energy sector. (author)

  19. Conceptual design of initial opacity experiments on the national ignition facility

    Energy Technology Data Exchange (ETDEWEB)

    Heeter, R.  F.; Bailey, J.  E.; Craxton, R.  S.; DeVolder, B.  G.; Dodd, E.  S.; Garcia, E.  M.; Huffman, E.  J.; Iglesias, C.  A.; King, J.  A.; Kline, J.  L.; Liedahl, D.  A.; McKenty, P.  W.; Opachich, Y.  P.; Rochau, G.  A.; Ross, P.  W.; Schneider, M.  B.; Sherrill, M.  E.; Wilson, B.  G.; Zhang, R.; Perry, T.  S.

    2017-01-09

    Accurate models of X-ray absorption and re-emission in partly stripped ions are necessary to calculate the structure of stars, the performance of hohlraums for inertial confinement fusion and many other systems in high-energy-density plasma physics. Despite theoretical progress, a persistent discrepancy exists with recent experiments at the Sandia Z facility studying iron in conditions characteristic of the solar radiative–convective transition region. The increased iron opacity measured at Z could help resolve a longstanding issue with the standard solar model, but requires a radical departure for opacity theory. To replicate the Z measurements, an opacity experiment has been designed for the National Facility (NIF). The design uses established techniques scaled to NIF. A laser-heated hohlraum will produce X-ray-heated uniform iron plasmas in local thermodynamic equilibrium (LTE) at temperatures${\\geqslant}150$ eV and electron densities${\\geqslant}7\\times 10^{21}~\\text{cm}^{-3}$. The iron will be probed using continuum X-rays emitted in a${\\sim}200$ ps,${\\sim}200~\\unicode[STIX]{x03BC}\\text{m}$diameter source from a 2 mm diameter polystyrene (CH) capsule implosion. In this design

  20. Heating of the Solar Corona by Alfven Waves: Self-Induced Opacity

    CERN Document Server

    Zahariev, N I

    2011-01-01

    There have been derived equations describing the static distributions of temperature and wind velocity at the transition region within the framework of the magnetohydrodynamics (MHD) of fully ionized hydrogen plasma . We have also calculated the width of the transition between the chromosphere and corona as a self-induced opacity of the high-frequency Alfven waves (AWs). The domain wall is a direct consequence of the self-consistent MHD treatment of AWs propagation. We predict considerable spectral density of the high-frequency AWs in the photosphere. The idea that Alfven waves might heat the solar corona belong to Alfven - we simply derived the corresponding MHD equations. The comparison of the solutions to those equations with the observational/measured data will be crucial for revealing the heating mechanism. The analysis of those solutions will explain how Alfven waves brick unto the corona and dissipate their energy there.

  1. Satellite and Opacity Effects on Resonance Line Shapes Produced from Short-Pulse Laser Heated Foils

    Energy Technology Data Exchange (ETDEWEB)

    Shepherd, R; Audebert, P; Chen, H-K; Fournier, K B; Peyreusse, O; Moon, S; Lee, R W; Price, D; Klein, L; Gauthier, J C; Springer, P

    2002-12-03

    We measure the He-like, time-resolved emission from thin foils consisting of 250 {angstrom} of carbon-250 {angstrom} of aluminum and 500 {angstrom} aluminum illuminated with a 150 fs laser pulse at an intensity of 1 x 10{sup 19} W/cm{sup 2}. Dielectronic satellite contributions to the 1s{sup 2}-1s2p({sup 1}P), 1s{sup 2}-1s3p({sup 1}P), and 1s{sup 2}1s4p({sup 1}P) line intensities are modeled using the configuration averaged code AVERROES and is found to be significant for all three resonance lines. The contribution of opacity broadening is inferred from the data and found to be significant only in the 1s{sup 2}-1s2p({sup 1}P).

  2. Mid-Infrared Mapping of Jupiter's Temperatures, Aerosol Opacity and Chemical Distributions with IRTF/TEXES

    CERN Document Server

    Fletcher, L N; Orton, G S; Sinclair, J A; Giles, R S; Irwin, P G J; Encrenaz, T

    2016-01-01

    Global maps of Jupiter's atmospheric temperatures, gaseous composition and aerosol opacity are derived from a programme of 5-20 $\\mu$m mid-infrared spectroscopic observations using the Texas Echelon Cross Echelle Spectrograph (TEXES) on NASA's Infrared Telescope Facility (IRTF). Image cubes from December 2014 in eight spectral channels, with spectral resolutions of $R\\sim2000-12000$ and spatial resolutions of $2-4^\\circ$ latitude, are inverted to generate 3D maps of tropospheric and stratospheric temperatures, 2D maps of upper tropospheric aerosols, phosphine and ammonia, and 2D maps of stratospheric ethane and acetylene. The results are compared to a re-analysis of Cassini Composite Infrared Spectrometer (CIRS) observations acquired during Cassini's closest approach to Jupiter in December 2000, demonstrating that this new archive of ground-based mapping spectroscopy can match and surpass the quality of previous investigations, and will permit future studies of Jupiter's evolving atmosphere. We identify mid-i...

  3. Ground-Glass Opacity Lung Nodules in the Era of Lung Cancer CT Screening

    DEFF Research Database (Denmark)

    Pedersen, Jesper Holst; Saghir, Zaigham; Wille, Mathilde Marie Winkler

    2016-01-01

    The advent of computed tomography screening for lung cancer will increase the incidence of ground-glass opacity (GGO) nodules detected and referred for diagnostic evaluation and management. GGO nodules remain a diagnostic challenge; therefore, a more systematic approach is necessary to ensure...... correct diagnosis and optimal management. Here we present the latest advances in the radiologic imaging and pathology of GGO nodules, demonstrating that radiologic features are increasingly predictive of the pathology of GGO nodules. We review the current guidelines from the Fleischner Society......, the National Comprehensive Cancer Network, and the British Thoracic Society. In addition, we discuss the management and follow-up of GGO nodules in the light of experience from screening trials. Minimally invasive tissue biopsies and the marking of GGO nodules for surgery are new and rapidly developing fields...

  4. The Next Generation Library Catalog: A Comparative Study of the OPACs of Koha, Evergreen, and Voyager

    Directory of Open Access Journals (Sweden)

    Sharon Q. Yang

    2010-09-01

    Full Text Available Open source has been the center of attention in the library world for the past several years. Koha and Evergreen are the two major open-source integrated library systems (ILSs, and they continue to grow in maturity and popularity. The question remains as to how much we have achieved in open-source development toward the next-generation catalog compared to commercial systems. Little has been written in the library literature to answer this question. This paper intends to answer this question by comparing  the next-generation features of the OPACs of two open-source ILSs (Koha and Evergreen and one proprietary ILS (Voyager’s WebVoyage.

  5. Lens Opacity and Hydrogen Sulfide in a New Zealand Geothermal Area.

    Science.gov (United States)

    Bates, Michael N; Bailey, Ian L; DiMartino, Robert B; Pope, Karl; Crane, Julian; Garrett, Nick

    2017-04-01

    Hydrogen sulfide (H2S) is a highly toxic gas with well-established, acute irritation effects on the eye. The population of Rotorua, New Zealand, sited on an active geothermal field, has some of the highest ambient H2S exposures in the world. Evidence from ecological studies in Rotorua has suggested that H2S is associated with cataract. The purpose of the present study was, using more detailed exposure characterization, clinical examinations, and anterior eye photography, to more directly investigate this previously reported association. Enrolled were 1637 adults, ages 18 to 65, from a comprehensive Rotorua primary care medical register. Patients underwent a comprehensive ophthalmic examination, including pupillary dilation and lens photography to capture evidence of any nuclear opacity, nuclear color, and cortical and posterior subcapsular opacity. Photographs were scored for all four outcomes on the LOCS III scale with decimalized interpolation between the exemplars. H2S exposure for up to the last 30 years was estimated based on networks of passive samplers set out across Rotorua and knowledge of residential, workplace, and school locations over the 30 years. Data analysis using linear and logistic regression examined associations between the degree of opacification and nuclear color or cataract (defined as a LOCS III score ≥2.0) in relation to H2S exposure. No associations were found between estimated H2S exposures and any of the four ophthalmic outcome measures. Overall, results were generally reassuring. They provided no evidence that H2S exposure at the levels found in Rotorua is associated with cataract. The previously found association between cataract and H2S exposure in the Rotorua population seems likely to be attributable to the limitations of the ecological study design. These results cannot rule out the possibility of an association with cataract at higher levels of H2S exposure.

  6. MINIMUM CORE MASSES FOR GIANT PLANET FORMATION WITH REALISTIC EQUATIONS OF STATE AND OPACITIES

    Energy Technology Data Exchange (ETDEWEB)

    Piso, Ana-Maria A.; Murray-Clay, Ruth A. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Youdin, Andrew N., E-mail: apiso@cfa.harvard.edu [Steward Observatory, University of Arizona, 933 North Cherry Avenue, Tucson, AZ 85721 (United States)

    2015-02-20

    Giant planet formation by core accretion requires a core that is sufficiently massive to trigger runaway gas accretion in less than the typical lifetime of protoplanetary disks. We explore how the minimum required core mass, M {sub crit}, depends on a non-ideal equation of state (EOS) and on opacity changes due to grain growth across a range of stellocentric distances from 5-100 AU. This minimum M {sub crit} applies when planetesimal accretion does not substantially heat the atmosphere. Compared to an ideal gas polytrope, the inclusion of molecular hydrogen (H{sub 2}) dissociation and variable occupation of H{sub 2} rotational states increases M {sub crit}. Specifically, M {sub crit} increases by a factor of ∼2 if the H{sub 2} spin isomers, ortho- and parahydrogen, are in thermal equilibrium, and by a factor of ∼2-4 if the ortho-to-para ratio is fixed at 3:1. Lower opacities due to grain growth reduce M {sub crit}. For a standard disk model around a Solar mass star, we calculate M {sub crit} ∼ 8 M {sub ⊕} at 5 AU, decreasing to ∼5 M {sub ⊕} at 100 AU, for a realistic EOS with an equilibrium ortho-to-para ratio and for grain growth to centimeter-sizes. If grain coagulation is taken into account, M {sub crit} may further reduce by up to one order of magnitude. These results for the minimum critical core mass are useful for the interpretation of surveys that find exoplanets at a range of orbital distances.

  7. Efficient blood flow visualization using flowline extraction and opacity modulation based on vascular structure analysis.

    Science.gov (United States)

    Kwon, Ohjae; Lee, Jeongjin; Kim, Bohyoung; Shin, Juneseuk; Shin, Yeong-Gil

    2017-03-01

    With the recent advances regarding the acquisition and simulation of blood flow data, blood flow visualization has been widely used in medical imaging for the diagnosis and treatment of pathological vessels. In this paper, we present a novel method for the visualization of the blood flow in vascular structures. The vessel inlet or outlet is first identified using the orthogonality metric between the normal vectors of the flow velocity and vessel surface. Then, seed points are generated on the identified inlet or outlet by Poisson disk sampling. Therefore, it is possible to achieve the automatic seeding that leads to a consistent and faster flow depiction by skipping the manual location of a seeding plane for the initiation of the line integration. In addition, the early terminated line integration in the thin curved vessels is resolved through the adaptive application of the tracing direction that is based on the flow direction at each seed point. Based on the observation that blood flow usually follows the vessel track, the representative flowline for each branch is defined by the vessel centerline. Then, the flowlines are rendered through an opacity assignment according to the similarity between their shape and the vessel centerline. Therefore, the flowlines that are similar to the vessel centerline are shown transparently, while the different ones are shown opaquely. Accordingly, the opacity modulation method enables the flowlines with an unusual flow pattern to appear more noticeable, while the visual clutter and line occlusion are minimized. Finally, Hue-Saturation-Value color coding is employed for the simultaneous exhibition of flow attributes such as local speed and residence time. The experiment results show that the proposed technique is suitable for the depiction of the blood flow in vascular structures. The proposed approach is applicable to many kinds of tubular structures with embedded flow information.

  8. Effect of resin shades on opacity of ceramic veneers and polymerization efficiency through ceramics.

    Science.gov (United States)

    Öztürk, Elif; Chiang, Yu-Chih; Coşgun, Erdal; Bolay, Şükran; Hickel, Reinhard; Ilie, Nicoleta

    2013-11-01

    The aim of this study was to assess the effect of different resin cement shades on the opacity and color difference of ceramics and to determine the polymerization efficiency of the resin cement at different shades after curing through ceramics. Two different ceramics (IPS e.max Press and IPS Empress(®)CAD, Ivoclar Vivadent) were used for this study. A light-cured veneer luting resin (Variolink Veneer, Ivoclar Vivadent) in four different shades of HV+1, HV+3, LV-1, and LV-3 was used for the colorimetric measurements. The color and spectral reflectance of the ceramics were measured according to the CIELab color scale relative to the standard illuminant D65 on a reflection spectrophotometer (ColorEye7000A, USA). Color differences (ΔE values) and the contrast ratios (CR) of the different groups of samples were calculated. In order to analyse the polymerization efficiency of the resin cements, the micromechanical properties of the resins were measured with an automatic microhardness indenter (Fisherscope H100C, Germany). The results were analysed using one-way ANOVA and Tukey's HSD post hoc tests (SPSS 18.0). The one-way ANOVA test showed that the values of ΔE and CR of the different specimen groups were significantly different (p<0.05). Group 1 (20.7 ± 0.5) (IPS-CAD without resin cement) exhibited the highest and group 10 (14.8 ± 0.5) (e.max:HV+3) exhibited the lowest ΔE value. Significant differences in the micromechanical properties were identified among the tested resin cements in different shades (p<0.05). Resin cement shade is an important factor for the opacity of a restoration. Furthermore, the resin shade affects the micromechanical properties of the underlying resin cement. Copyright © 2013 Elsevier Ltd. All rights reserved.

  9. The extragalactic background light revisited and the cosmic photon-photon opacity

    Science.gov (United States)

    Franceschini, Alberto; Rodighiero, Giulia

    2017-07-01

    Context. In addition to its relevant astrophysical and cosmological significance, the extragalactic background light (EBL) is a fundamental source of opacity for cosmic high energy photons, as well as a limitation for the propagation of high-energy particles in the Universe. Aims: We review our previously published determinations of the EBL photon density in the Universe and its evolution with cosmic time, in the light of recent surveys of IR sources at long wavelengths. Methods: We exploit deep survey observations by the Herschel Space Observatory and the Spitzer telescope, matched to optical and near-IR photometric and spectroscopic data, to re-estimate number counts and luminosity functions longwards of a few microns, and the contribution of resolved sources to the EBL. Results: These new data indicate slightly lower photon densities in the mid- and far-infrared and sub-millimeter compared to previous determinations. This implies slightly lower cosmic opacity for photon-photon interactions. Conclusions: The new data do not modify previously published EBL modeling in the UV-optical and near-IR up to several microns, while reducing the photon density at longer wavelengths. This improved model of the EBL alleviates some tension that had emerged in the interpretation of the highest-energy TeV observations of local blazars, reducing the case for new physics beyond the standard model (like violations of the Lorenz Invariance, LIV, at the highest particle energies), or for exotic astrophysics, that had sometimes been called for to explain it. Applications of this improved EBL model on current data are considered, as well as perspectives for future instrumentation, the Cherenkov Telescope Array (CTA) in particular.

  10. The loop gravity string

    CERN Document Server

    Freidel, Laurent; Pranzetti, Daniele

    2016-01-01

    In this work we study canonical gravity in finite regions for which we introduce a generalisation of the Gibbons-Hawking boundary term including the Immirzi parameter. We study the canonical formulation on a spacelike hypersuface with a boundary sphere and show how the presence of this term leads to an unprecedented type of degrees of freedom coming from the restoration of the gauge and diffeomorphism symmetry at the boundary. In the presence of a loop quantum gravity state, these boundary degrees of freedom localize along a set of punctures on the boundary sphere. We demonstrate that these degrees of freedom are effectively described by auxiliary strings with a 3-dimensional internal target space attached to each puncture. We show that the string currents represent the local frame field, that the string angular momenta represent the area flux and that the string stress tensor represents the two dimensional metric on the boundary of the region of interest. Finally, we show that the commutators of these broken...

  11. Effect of a High Opacity on the Light Curves of Radioactively Powered Transients from Compact Object Mergers

    CERN Document Server

    Barnes, Jennifer

    2013-01-01

    The coalescence of compact objects are a promising astrophysical sources of gravitational wave (GW) signals. The ejection of r-process material from such mergers may lead to a radioactively-powered electromagnetic counterpart which, if discovered, would enhance the science return of a GW detection. As very little is known about the optical properties of heavy r-process elements, previous light curve models have adopted opacities similar to those of iron group elements. Here we report that the presence of heavier elements, particularly the lanthanides, increase the ejecta opacity by several orders of magnitude. We include these higher opacities in time dependent, multi-wavelength radiative transport calculations to predict the broadband light curves of one-dimensional models over a range of parameters (ejecta masses from 0.001 to 0.1 solar masses and velocities from 0.1 to 0.3c). We find that the higher opacities lead to much longer duration light curves which can last a week or more. The emission is shifted t...

  12. 40 CFR 60.1450 - How must I monitor opacity for air curtain incinerators that burn 100 percent yard waste?

    Science.gov (United States)

    2010-07-01

    ... curtain incinerators that burn 100 percent yard waste? 60.1450 Section 60.1450 Protection of Environment... Air Curtain Incinerators That Burn 100 Percent Yard Waste § 60.1450 How must I monitor opacity for air curtain incinerators that burn 100 percent yard waste? (a) Use EPA Reference Method 9 in appendix A...

  13. 40 CFR 60.1925 - How must I monitor opacity for air curtain incinerators that burn 100 percent yard waste?

    Science.gov (United States)

    2010-07-01

    ... curtain incinerators that burn 100 percent yard waste? 60.1925 Section 60.1925 Protection of Environment... or Before August 30, 1999 Model Rule-Air Curtain Incinerators That Burn 100 Percent Yard Waste § 60.1925 How must I monitor opacity for air curtain incinerators that burn 100 percent yard waste? (a)...

  14. Interpretation of the BRITE oscillation data of the hybrid pulsator ν Eridani: a call for the modification of stellar opacities

    Science.gov (United States)

    Daszyńska-Daszkiewicz, J.; Pamyatnykh, A. A.; Walczak, P.; Colgan, J.; Fontes, C. J.; Kilcrease, D. P.

    2017-04-01

    The analysis of the BRIght Target Explorer (BRITE) oscillation spectrum of the main-sequence early B-type star ν Eridani is presented. Only models with the modified mean opacity profile can account for the observed frequency ranges as well as for the values of some individual frequencies. The number of the κ-modified seismic models is constrained by the non-adiabatic parameter f, which is very sensitive to the opacity changes in the subphotospheric layers, where the pulsations are driven. We present an example of the model that satisfies all the above conditions. It seems that the OPLIB opacities are preferred over those from the OPAL and OP projects. Moreover, we discuss additional consequences of the opacity modification, namely, an enhancement of the efficiency of convection in the Z bump as well as an occurrence of close radial modes which is a kind of avoided-crossing phenomenon common for non-radial modes in standard main-sequence models.

  15. The effect of including molecular opacities of variable composition on the evolution of intermediate-mass AGB stars

    CERN Document Server

    Fishlock, C K; Stancliffe, R J

    2013-01-01

    Calculations from stellar evolutionary models of low- and intermediate-mass asymptotic giant branch (AGB) stars provide predictions of elemental abundances and yields for comparison to observations. However, there are many uncertainties that reduce the accuracy of these predictions. One such uncertainty involves the treatment of low-temperature molecular opacities that account for the surface abundance variations of C, N, and O. A number of prior calculations of intermediate-mass AGB stellar models that incorporate both efficient third dredge-up and hot bottom burning include a molecular opacity treatment which does not consider the depletion of C and O due to hot bottom burning. Here we update the molecular opacity treatment and investigate the effect of this improvement on calculations of intermediate-mass AGB stellar models. We perform tests on two masses, 5 M$_{\\odot}$ and 6 M$_{\\odot}$, and two metallicities, $Z~=~0.001$ and $Z~=~0.02$, to quantify the variations between two opacity treatments. We find t...

  16. Large loop conformation sampling using the activation relaxation technique, ART-nouveau method.

    Science.gov (United States)

    St-Pierre, Jean-François; Mousseau, Normand

    2012-07-01

    We present an adaptation of the ART-nouveau energy surface sampling method to the problem of loop structure prediction. This method, previously used to study protein folding pathways and peptide aggregation, is well suited to the problem of sampling the conformation space of large loops by targeting probable folding pathways instead of sampling exhaustively that space. The number of sampled conformations needed by ART nouveau to find the global energy minimum for a loop was found to scale linearly with the sequence length of the loop for loops between 8 and about 20 amino acids. Considering the linear scaling dependence of the computation cost on the loop sequence length for sampling new conformations, we estimate the total computational cost of sampling larger loops to scale quadratically compared to the exponential scaling of exhaustive search methods.

  17. Study of the radio-opacity of base and liner dental materials using a digital radiography system.

    Science.gov (United States)

    Lachowski, K M; Botta, S B; Lascala, C A; Matos, A B; Sobral, M A P

    2013-01-01

    This study investigated the radio-opacity of commercially available glass ionomer cements (GICs), flowable resin composites (FRCs) and calcium hydroxide cements (CHCs) and compared this with the radio-opacity of enamel, dentine and aluminium stepwedge. 16 GICs, 8 FRCs and 4 CHCs were analysed. Three sets of three samples were prepared: 1 mm, 2 mm and 3 mm thickness for GIC and FRC and 1 mm thickness for CHC. Specimens of enamel and dentine with the same thicknesses were obtained. As a control, an aluminium stepwedge was used. Radiographs were taken with a digital Kodak RVG 5000 (0.32 s, 30 cm). The images were analysed using the Image Tool(®) program (v. 2.00; The University of Texas Health Science Center, San Antonio, TV) to obtain the mean grey values. Analysis of variance was used to investigate the significance of differences among the groups. For pairwise comparisons, the Tukey test was applied (p < 0.05). The GICs Ionomaster (Wilcos, Petrópolis, Brazil), Maxxion (FGM, Joinville, Brazil), Bioglass R (Biodinâmica, Ibiporã, Brazil), Bioglass F (Biodinâmica), Vidrion R (SS White, Rio de Janerio, Brazil) and Vidrion F (SS White), presented radio-opacity lower than that of dentine. All FRCs and CHCs studied showed radio-opacity higher than that of dentine. Vitro Fil (DFL, Rio de Janeiro, Brazil), Magic Glass (Vigodent, Rio de Janeiro, Brazil), Vitrebond (3M, Sumaré SP, Brazil), Riva Self Cure (SDI, Victoria, Australia), Riva Light Cure (SDI), Fill Magic (Vigodent), Opallis (FGM, Joinville, Brazil), Surefil SDR (Dentsply, Milford, DE), Tetric N (Ivoclar Vivadent, Schaan, Lichtenstein), Tetric (Ivoclar Vivadent), Hydro C (Dentsply, Petrópolis, Brazil), Hydcal (Technew, Madalena, Portugal) and Liner (Vigodent) showed radio-opacity similar to or greater than that of enamel for all thicknesses. The increased thickness of the materials studied increases their radio-opacity. Some commercially available GICs used as a base and liner for restorations

  18. Hard Loops, Soft Loops, and High Density Effective Field Theory

    CERN Document Server

    Schäfer, T

    2003-01-01

    We study several issues related to the use of effective field theories in QCD at large baryon density. We show that the power counting is complicated by the appearance of two scales inside loop integrals. Hard dense loops involve the large scale $mu^2$ and lead to phenomena such as screening and damping at the scale $gmu$. Soft loops only involve small scales and lead to superfluidity and non-Fermi liquid behavior at exponentially small scales. Four-fermion operators in the effective theory are suppressed by powers of $1/mu$, but they get enhanced by hard loops. As a consequence their contribution to the pairing gap is only suppressed by powers of the coupling constant, and not powers of $1/mu$. We determine the coefficients of four-fermion operators in the effective theory by matching quark-quark scattering amplitudes. Finally, we introduce a perturbative scheme for computing corrections to the gap parameter in the superfluid phase

  19. Serum opacity factor unmasks human plasma high-density lipoprotein instability via selective delipidation and apolipoprotein A-I desorption.

    Science.gov (United States)

    Gillard, Baiba K; Courtney, Harry S; Massey, John B; Pownall, Henry J

    2007-11-13

    Human plasma high-density lipoproteins (HDL) are important vehicles in reverse cholesterol transport, the cardioprotective mechanism by which peripheral tissue-cholesterol is transported to the liver for disposal. HDL is the target of serum opacity factor (SOF), a substance produced by Streptococcus pyogenes that turns mammalian serum cloudy. Using a recombinant (r) SOF, we studied opacification and its mechanism. rSOF catalyzes the partial disproportionation of HDL into a cholesteryl ester-rich microemulsion (CERM) and a new HDL-like particle, neo HDL, with the concomitant release of lipid-free (LF)-apo A-I. Opacification is unique; rSOF transfers apo E and nearly all neutral lipids of approximately 100,000 HDL particles into a single large CERM whose size increases with HDL-CE content (r approximately 100-250 nm) leaving a neo HDL that is enriched in PL (41%) and protein (48%), especially apo A-II. rSOF is potent; within 30 min at 37 degrees C, 10 nM rSOF opacifies 4 microM HDL. At respective low and high physiological HDL concentrations, LF-apo A-I is monomeric and tetrameric. CERM formation and apo A-I release have similar kinetics suggesting parallel or rapid sequential steps. According to the reaction products and kinetics, rSOF is a heterodivalent fusogenic protein that uses a docking site to displace apo A-I and bind to exposed CE surfaces on HDL; the resulting rSOF-HDL complex recruits additional HDL with its binding-delipidation site and through multiple fusion steps forms a CERM. rSOF may be a clinically useful and novel modality for improving reverse cholesterol transport. With apo E and a high CE content, CERM could transfer large amounts of cholesterol to the liver for disposal via the LDL receptor; neo HDL is likely a better acceptor of cellular cholesterol than HDL; LF-apo A-I could enhance efflux via the ATP-binding casette transporter ABCA1.

  20. Radial propagators and Wilson loops

    CERN Document Server

    Leupold, S; Leupold, Stefan; Weigert, Heribert

    1996-01-01

    We present a relation which connects the propagator in the radial (Fock-Schwinger) gauge with a gauge invariant Wilson loop. It is closely related to the well-known field strength formula and can be used to calculate the radial gauge propagator. The result is shown to diverge in four-dimensional space even for free fields, its singular nature is however naturally explained using the renormalization properties of Wilson loops with cusps and self-intersections. Using this observation we provide a consistent regularization scheme to facilitate loop calculations. Finally we compare our results with previous approaches to derive a propagator in Fock-Schwinger gauge.

  1. Force distribution in a semiflexible loop

    Science.gov (United States)

    Waters, James T.; Kim, Harold D.

    2017-01-01

    Loops undergoing thermal fluctuations are prevalent in nature. Ringlike or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category. Stability of these molecules are generally described in terms of free energy, an average quantity, but it may also be impacted by local fluctuating forces acting within these systems. The full distribution of these forces can thus give us insights into mechanochemistry beyond the predictive capability of thermodynamics. In this paper, we study the force exerted by an inextensible semiflexible polymer constrained in a looped state. By using a simulation method termed “phase-space sampling,” we generate the equilibrium distribution of chain conformations in both position and momentum space. We compute the constraint forces between the two ends of the loop in this chain ensemble using Lagrangian mechanics, and show that the mean of these forces is equal to the thermodynamic force. By analyzing kinetic and potential contributions to the forces, we find that the mean force acts in the direction of increasing extension not because of bending stress, but in spite of it. Furthermore, we obtain a distribution of constraint forces as a function of chain length, extension, and stiffness. Notably, increasing contour length decreases the average force, but the additional freedom allows fluctuations in the constraint force to increase. The force distribution is asymmetric and falls off less sharply than a Gaussian distribution. Our work exemplifies a system where large-amplitude fluctuations occur in a way unforeseen by a purely thermodynamic framework, and offers computational tools useful for efficient, unbiased simulation of a constrained system. PMID:27176436

  2. Flare loop radiative hydrodynamics. III - Nonlocal radiative transfer effects

    Science.gov (United States)

    Canfield, R. C.; Fisher, G. H.; Mcclymont, A. N.

    1983-01-01

    The study has three goals. The first is to demonstrate that processes exist whose intrinsic nonlocal nature cannot be represented by local approximations. The second is to elucidate the physical nature and origins of these nonlocal processes. The third is to suggest that the methods and results described here may prove useful in constructing semiempirical models of the chromosphere by means more efficient than trial and error. Matrices are computed that describe the effect of a temperature perturbation at an arbitrary point in the loop on density, hydrogen ionized fraction, total radiative loss rate, and radiative loss rate of selected hydrogen lines and continua at all other points. It is found that the dominant nonlocal radiative transfer effects can be separated into flux divergence coefficient effects and upper level population effects. The former are most important when the perturbation takes place in a region of significant opacity. Upper level population effects arise in both optically thick and thin regions in response to nonlocal density, ionization, and interlocking effects.

  3. Product Integrals and Wilson loops

    CERN Document Server

    Karp, R L

    2001-01-01

    Using product integrals we review the unambiguous mathematical representation of Wilson line and Wilson loop operators, including their behavior under gauge transformations and the non-abelian Stokes theorem. Interesting consistency conditions among Wilson lines are also presented.

  4. Thermal fluctuations in loop cosmology

    CERN Document Server

    Magueijo, J; Magueijo, Joao; Singh, Parampreet

    2007-01-01

    Quantum gravitational effects in loop quantum cosmology lead to a resolution of the initial singularity and have the potential to solve the horizon problem and generate a quasi scale-invariant spectrum of density fluctuations. We consider loop modifications to the behavior of the inverse scale factor below a critical scale in closed models and assume a purely thermal origin for the fluctuations. We show that the no-go results for scale invariance in classical thermal models can be evaded even if we just consider modifications to the background (zeroth order) gravitational dynamics. Since a complete and systematic treatment of the perturbed Einstein equations in loop cosmology is still lacking, we simply parameterize their expected modifications. These change quantitatively, but not qualitatively, our conclusions. We thus urge the community to more fully work out this complex aspect of loop cosmology, since the full picture would not only fix the free parameters of the theory, but also provide a model for a no...

  5. Loop Quantum Cosmology Gravitational Baryogenesis

    CERN Document Server

    Odintsov, S D

    2016-01-01

    Loop Quantum Cosmology is an appealing quantum completion of classical cosmology, which brings along various theoretical features which in many cases offer remedy or modify various classical cosmology aspects. In this paper we address the gravitational baryogenesis mechanism in the context of Loop Quantum Cosmology. As we demonstrate, when Loop Quantum Cosmology effects are taken into account in the resulting Friedmann equations for a flat Friedmann-Robertson-Walker Universe, then even for a radiation dominated Universe, the predicted baryon-to-entropy ratio from the gravitational baryogenesis mechanism is non-zero, in contrast to the Einstein-Hilbert case, in which case the baryon-to-entropy ratio is zero. We also discuss various other cases apart from the radiation domination case, and we discuss how the baryon-to-entropy ratio is affected from the parameters of the quantum theory. In addition, we use illustrative exact solutions of Loop Quantum Cosmology and we investigate under which circumstances the bar...

  6. Illuminating the structure and function of Cys-loop receptors

    DEFF Research Database (Denmark)

    Pless, Stephan Alexander; Lynch, Joseph W

    2008-01-01

    transitional and steady state conformations and serves as a real time correlate of the channel structure and its function. Voltage-clamp fluorometry experiments on Cys-loop receptors have yielded a large body of data concerning the mechanisms by which agonists, antagonists and modulators act on these receptors......Cys-loop receptors are an important class of ligand-gated ion channels. They mediate fast synaptic neurotransmission, are implicated in various 'channelopathies' and are important pharmacological targets. Recent progress in X-ray crystallography and electron microscopy has provided a considerable...... insight into the structure of Cys-loop receptors. However, data from these experiments only provide 'snapshots' of the proteins under investigation. They cannot provide information about the various conformations the protein adopts during transition from the closed to the open and desensitized states...

  7. Continuous smearing of Wilson Loops

    CERN Document Server

    Lohmayer, Robert

    2011-01-01

    Continuum smearing was introduced in section 4.1 of JHEP03, 064 (2006) as a meaningful continuum analogue of the well known set of lattice techniques by the same name. Here we apply continuous smearing in continuous space-time to Wilson loops in order to clarify what it does in the context of field theory and also in the context of the loop calculus of the Makeenko-Migdal equation.

  8. The Projectile inside the Loop

    OpenAIRE

    Varieschi, Gabriele U.

    2005-01-01

    In this paper we describe an alternative use of the loop-the-loop apparatus, which can be used to study an interesting case of projectile motion. We also present an effective way to perform and analyze these experiments, by using video capture software together with a digital video camera. These experiments can be integrated into classroom demonstrations for general physics courses, or become part of laboratory activities.

  9. Introduction to Loop Quantum Gravity

    OpenAIRE

    Mercuri, Simone

    2010-01-01

    The questions I have been asked during the 5th International School on Field Theory and Gravitation, have compelled me to give an account of the premises that I consider important for a beginner's approach to Loop Quantum Gravity. After a description of some general arguments and an introduction to the canonical theory of gravity, I review the background independent approach to quantum gravity, giving only a brief survey of Loop Quantum Gravity.

  10. Bifurcations of nontwisted heteroclinic loop

    Institute of Scientific and Technical Information of China (English)

    田清平; 朱德明

    2000-01-01

    Bifurcations of nontwisted and fine heteroclinic loops are studied for higher dimensional systems. The existence and its associated existing regions are given for the 1-hom orbit and the 1-per orbit, respectively, and bifurcation surfaces of the two-fold periodic orbit are also obtained. At last, these bifurcation results are applied to the fine heteroclinic loop for the planar system, which leads to some new and interesting results.

  11. Sequencing Analysis of Mutant Allele $cdc$28-$srm$ of Protein Kinase CDC28 and Molecular Dynamics Study of Glycine-Rich Loop in Wild-Type and Mutant Allele G16S of CDK2 as Model

    CERN Document Server

    Koltovaya, N A; Kholmurodov, Kh T; Kretov, D A

    2005-01-01

    The central role that cyclin-dependent kinases play in the timing of cell division and the high incidence of genetic alteration of CDKs or deregulation of CDK inhibitors in a number of cancers make CDC28 of the yeast \\textit{Saccharomyces cerevisiae }very attractive model for studies of mechanisms of CDK regulation. Earlier it was found that certain gene mutations including \\textit{cdc28-srm} affect cell cycle progression, maintenance of different genetic structures and increase cell sensitivity to ionizing radiation. A~\\textit{cdc28-srm} mutation is not temperature-sensitive mutation and differs from the known \\textit{cdc28-ts }mutations because it has the evident phenotypic manifestations at 30 $^{\\circ}$C. Sequencing analysis of \\textit{cdc28-srm} revealed a single nucleotide substitution G20S. This is a third glycine in a conserved sequence GxGxxG in the G-rich loop positioned opposite the activation T-loop. Despite its demonstrated importance, the role of the G-loop has remained unclear. The crystal stru...

  12. Flowering Buds of Globular Proteins: Transpiring Simplicity of Protein Organization

    Science.gov (United States)

    Berezovsky, Igor N.

    2002-01-01

    Structural and functional complexity of proteins is dramatically reduced to a simple linear picture when the laws of polymer physics are considered. A basic unit of the protein structure is a nearly standard closed loop of 25–35 amino acid residues, and every globular protein is built of consecutively connected closed loops. The physical necessity of the closed loops had been apparently imposed on the early stages of protein evolution. Indeed, the most frequent prototype sequence motifs in prokaryotic proteins have the same sequence size, and their high match representatives are found as closed loops in crystallized proteins. Thus, the linear organization of the closed loop elements is a quintessence of protein evolution, structure and folding. PMID:18629251

  13. Optimization of a β-sheet-cap for long loop closure.

    Science.gov (United States)

    Anderson, Jordan M; Shcherbakov, Alexander A; Kier, Brandon L; Kellock, Jackson; Shu, Irene; Byrne, Aimee L; Eidenschink, Lisa A; Andersen, Niels H

    2017-03-01

    Protein loops make up a large portion of the secondary structure in nature. But very little is known concerning loop closure dynamics and the effects of loop composition on fold stability. We have designed a small system with stable β-sheet structures, including features that allow us to probe these questions. Using paired Trp residues that form aromatic clusters on folding, we are able to stabilize two β-strands connected by varying loop lengths and composition (an example sequence: RWITVTI - loop - KKIRVWE). Using NMR and CD, both fold stability and folding dynamics can be investigated for these systems. With the 16 residue loop peptide (sequence: RWITVTI-(GGGGKK)2 GGGG-KKIRVWE) remaining folded (ΔGU  = 1.6 kJ/mol at 295K). To increase stability and extend the series to longer loops, we added an additional Trp/Trp pair in the loop flanking position. With this addition to the strands, the 16 residue loop (sequence: RWITVRIW-(GGGGKK)2 GGGG-WKTIRVWE) supports a remarkably stable β-sheet (ΔGU  = 6.3 kJ/mol at 295 K, Tm  = ∼55°C). Given the abundance of loops in binding motifs and between secondary structures, these constructs can be powerful tools for peptide chemists to study loop effects; with the Trp/Trp pair providing spectroscopic probes for assessing both stability and dynamics by NMR. © 2016 Wiley Periodicals, Inc.

  14. Disruption of human plasma high-density lipoproteins by streptococcal serum opacity factor requires labile apolipoprotein A-I.

    Science.gov (United States)

    Han, Mikyung; Gillard, Baiba K; Courtney, Harry S; Ward, Kathryn; Rosales, Corina; Khant, Htet; Ludtke, Steven J; Pownall, Henry J

    2009-02-24

    Human plasma high-density lipoproteins (HDL), the primary vehicle for reverse cholesterol transport, are the target of serum opacity factor (SOF), a virulence determinant of Streptococcus pyogenes that turns serum opaque. HDL comprise a core of neutral lipidscholesteryl esters and some triglyceridesurrounded by a surface monolayer of cholesterol, phospholipids, and specialized proteins [apolipoproteins (apos) A-I and A-II]. A HDL is an unstable particle residing in a kinetic trap from which it can escape via chaotropic, detergent, or thermal perturbation. Recombinant (r) SOF catalyzes the transfer of nearly all neutral lipids of approximately 100,000 HDL particles (D approximately 8.5 nm) into a single, large cholesteryl ester-rich microemulsion (CERM; D > 100 nm), leaving a new HDL-like particle [neo HDL (D approximately 5.8 nm)] while releasing lipid-free (LF) apo A-I. CERM formation and apo A-I release have similar kinetics, suggesting parallel or rapid consecutive steps. By using complementary physicochemical methods, we have refined the mechanistic model for HDL opacification. According to size exclusion chromatography, a HDL containing nonlabile apo A-I resists rSOF-mediated opacification. On the basis of kinetic cryo-electron microscopy, rSOF (10 nM) catalyzes the conversion of HDL (4 microM) to neo HDL via a stepwise mechanism in which intermediate-sized particles are seen. Kinetic turbidimetry revealed opacification as a rising exponential reaction with a rate constant k of (4.400 +/- 0.004) x 10(-2) min(-1). Analysis of the kinetic data using transition state theory gave an enthalpy (DeltaH()), entropy (DeltaS(++)), and free energy (DeltaG()) of activation of 73.9 kJ/mol, -66.87 J/K, and 94.6 kJ/mol, respectively. The free energy of activation for opacification is nearly identical to that for the displacement of apo A-I from HDL by guanidine hydrochloride. We conclude that apo A-I lability is required for HDL opacification, LF apo A-I desorption is the

  15. Bol loops of odd prime exponent

    CERN Document Server

    Foguel, Tuval

    2009-01-01

    Although any finite Bol loop of odd prime exponent is solvable, we show there exist such Bol loops with trivial center. We also construct finitely generated, infinite, simple Bruck loops of odd prime exponent for sufficiently large primes. This shows that the Burnside problem for Bruck loops has a negative answer.

  16. Classifying Finitely Generated Indecomposable RA Loops

    CERN Document Server

    Cornelissen, Mariana

    2012-01-01

    In 1995, E. Jespers, G. Leal and C. Polcino Milies classified all finite ring alternative loops (RA loops for short) which are not direct products of proper subloops. In this paper we extend this result to finitely generated RA loops and provide an explicit description of all such loops.

  17. Kalman Orbit Optimized Loop Tracking

    Science.gov (United States)

    Young, Lawrence E.; Meehan, Thomas K.

    2011-01-01

    Under certain conditions of low signal power and/or high noise, there is insufficient signal to noise ratio (SNR) to close tracking loops with individual signals on orbiting Global Navigation Satellite System (GNSS) receivers. In addition, the processing power available from flight computers is not great enough to implement a conventional ultra-tight coupling tracking loop. This work provides a method to track GNSS signals at very low SNR without the penalty of requiring very high processor throughput to calculate the loop parameters. The Kalman Orbit-Optimized Loop (KOOL) tracking approach constitutes a filter with a dynamic model and using the aggregate of information from all tracked GNSS signals to close the tracking loop for each signal. For applications where there is not a good dynamic model, such as very low orbits where atmospheric drag models may not be adequate to achieve the required accuracy, aiding from an IMU (inertial measurement unit) or other sensor will be added. The KOOL approach is based on research JPL has done to allow signal recovery from weak and scintillating signals observed during the use of GPS signals for limb sounding of the Earth s atmosphere. That approach uses the onboard PVT (position, velocity, time) solution to generate predictions for the range, range rate, and acceleration of the low-SNR signal. The low- SNR signal data are captured by a directed open loop. KOOL builds on the previous open loop tracking by including feedback and observable generation from the weak-signal channels so that the MSR receiver will continue to track and provide PVT, range, and Doppler data, even when all channels have low SNR.

  18. Study of the Open Loop and Closed Loop Oscillator Techniques

    Energy Technology Data Exchange (ETDEWEB)

    Imel, George R. [Idaho State Univ., Pocatello, ID (United States); Baker, Benjamin [Idaho National Lab. (INL), Idaho Falls, ID (United States); Riley, Tony [Knolls Atomic Power Lab. (KAPL), Schenectady, NY (United States); Langbehn, Adam [Puget Sound Naval Base, Bremerton, WA (United States); Aryal, Harishchandra [Idaho State Univ., Pocatello, ID (United States); Benzerga, M. Lamine [Idaho State Univ., Pocatello, ID (United States)

    2015-04-11

    This report presents the progress and completion of a five-year study undertaken at Idaho State University of the measurement of very small worth reactivity samples comparing open and closed loop oscillator techniques.The study conclusively demonstrated the equivalency of the two techniques with regard to uncertainties in reactivity values, i.e., limited by reactor noise. As those results are thoroughly documented in recent publications, in this report we will concentrate on the support work that was necessary. For example, we describe in some detail the construction and calibration of a pilot rod for the closed loop system. We discuss the campaign to measure the required reactor parameters necessary for inverse-kinetics. Finally, we briefly discuss the transfer of the open loop technique to other reactor systems.

  19. BPS Wilson Loops on S^2 at Higher Loops

    CERN Document Server

    Young, Donovan

    2008-01-01

    We consider supersymmetric Wilson loops of the variety constructed by Drukker, Giombi, Ricci, and Trancanelli, whose spatial contours lie on a two-sphere. Working to second order in the 't Hooft coupling in planar N=4 Supersymmetric Yang-Mills Theory (SYM), we compute the vacuum expectation value of a wavy-latitude and of a loop composed of two longitudes. We evaluate the resulting integrals numerically and find that the results are consistent with the zero-instanton sector calculation of Wilson loops in 2-d Yang-Mills on S^2 performed by Bassetto and Griguolo. We also consider the connected correlator of two distinct latitudes to third order in the 't Hooft coupling in planar N=4 SYM. We compare the result in the limit where the latitudes become coincident to a perturbative calculation in 2-d Yang-Mills on S^2 using a light-cone Wu-Mandelstam-Leibbrandt prescription. The two calculations produce differing results.

  20. Generalized loop space and TMDs

    Directory of Open Access Journals (Sweden)

    Mertens Tom

    2014-06-01

    Full Text Available The Standard Model describes the three (of four basic interactions known in Nature in terms of the quantum fields which are constituted by representations of special unitary gauge groups of symmetry. However, the physical observables do not always coincide with the fundamental degrees of freedom of the Standard Model. Therefore it can be useful to switch to the loop space representation of the gauge theory, where the variables are inherently gauge invariant but the degrees of freedom are absorbed in the path/loop dependence. Over-completeness of this space requires the introduction of an equivalence relation which is provided by Wilson loop functionals operating on piecewise regular paths. It is well known that certain Wilson loops show the same singularity structure as some Transverse Momentum Dependent PDFs (TMDs, which are not renormalizable by the common methods due to exactly this singularity structure. By introducing geometrical operators, like the area-derivative, we were able to derive an evolution equation for these Wilson loops and we hope to apply this method in the future to find some renormalization schemes for TMDs.