Astrophysical opacity library

International Nuclear Information System (INIS)

Huebner, W.F.; Merts, A.L.; Magee, N.H. Jr.; Argo, M.F.

1977-08-01

The astrophysical elements opacity library includes equation of state data, various mean opacities, and 2000 values of the frequency-dependent extinction coefficients in equally spaced intervals u identical with hν/kT from 0 to 20 for 41 degeneracy parameters eta from -28 (nondegenerate) to 500 and 46 temperatures kT from 1 eV to 100 keV. Among available auxiliary quantities are the free electron density, mass density, and plasma cutoff frequency. A library-associated program can produce opacities for mixtures with up to 20 astrophysically abundant constituent elements at 4 levels of utility for the user

Some investigations about the Carson opacities

International Nuclear Information System (INIS)

Cox, A.N.; Kidman, R.B.

1983-01-01

Accurate opacities for stellar composition mixtures are needed for all studies of stellar structure, evolution, stability, and pulsation. Three problem areas where increased opacities would be welcome are: the observed broadening of the upper main sequence that can be produced with larger opacities that tend to expand the stars; the existence of the double-mode Cepheids and their anomalously low period ratios which can be predicted to be lower, as observed, if opacities are larger; and the small sensitivity of the low mass population II horizontal branch luminosity to the metal content of their compositions that would be more effective if their opacity were increased. Several other problems that could be solved by larger opacities have been widely discussed, but we feel that they are not justifiably an opacity problem. The conclusion of our considerations are that the Thomas-Fermi method for getting opacities used by Carson and his collaborators does not produce values appreciably different from those obtained without this method at Los Alamos, and that these persistent astrophysical problems must be solved in other ways. We here propose a possible error in the Carson opacities, and, further, we mention another that seems to be the correct reconciliation between these two opacity sets

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.

Asset Opacity and Liquidity

OpenAIRE

Stenzel, A.; Wagner, W.B.

2013-01-01

Abstract: We consider a model of private information acquisition in which the cost of information depends on an asset's opacity. The model generates a hump-shaped relationship between opacity and the equilibrium amount of private information. In particular, the incentives to acquire information are largest for assets of intermediate opacity; such assets hence display low liquidity in the secondary market due to adverse selection. We also show that costly information acquisition generates ince...

Thus Spake the OPAC User.

Science.gov (United States)

Markey, Karen

1983-01-01

Findings of focused-group interviews conducted for OCLC study of library users and online public access catalogs (OPACs) indicate users like OPACs, have problems finding right subject heading, envision features to improve subject access, want access to more than books, and want OPACs to provide new services. Eight references are listed. (EJS)

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

International Nuclear Information System (INIS)

Krokhotin, Andrey; Liwo, Adam; Maisuradze, Gia G.; Scheraga, Harold A.; Niemi, Antti J.

2014-01-01

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 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 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 kinks are

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

Helioseismic Tests of Radiative Opacities.

Energy Technology Data Exchange (ETDEWEB)

Guzik, J. A. (Joyce Ann); Neuforge, C. M. (Corinne M.); Keady, J. J.; Magee, N. H. (Norman H.); Bradley, P. A. (Paul A.)

2002-01-01

During the past fifteen years, thousands of solar acoustic oscillation modes have been measured to remarkable precision, in many cases to within 0.01%. These frequencies have been used to infer the interior structure of the sun and test the physical input to solar models. Here we summarize the procedures, input physics and assumptions for calculating a standard solar evolution model. We compare the observed and calculated sound speed profile and oscillation frequencies of solar models calibrated using the new Los Alamos LEDCOP and Livermore OPAL Rosseland mean opacities for the same element mixture. We show that solar oscillations are extremely sensitive to opacities, with opacity differences of only a few percent producing an easily detectable effect on the sound speed and predicted frequencies. The oscillation data indicate that agreement would be improved by an opacity increase of several percent below the convection zone for both the LEDCOP and OPAL opacities.

Asset Opacity and Liquidity

NARCIS (Netherlands)

Stenzel, A.; Wagner, W.B.

2013-01-01

Abstract: We consider a model of private information acquisition in which the cost of information depends on an asset's opacity. The model generates a hump-shaped relationship between opacity and the equilibrium amount of private information. In particular, the incentives to acquire information are

Recent progress on astrophysical opacity

International Nuclear Information System (INIS)

Rogers, F.J.; Iglesias, C.A.

1992-08-01

Improvements in the calculation of the opacity of astrophysical plasmas has helped to resolve several long-standing puzzles in the modeling of variable stars. The most significant opacity enhancements over the Los Alamos Astrophysical Library (LAOL) are due to improvements in the equation of state and atomic physics. Comparison with experiment has corroborated the predicted large opacity increases due to transitions in M-shell iron. We give a summary of recent developments

LINE BROADENING AND THE SOLAR OPACITY PROBLEM

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)

2016-06-20

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.

Detailed Opacity Calculations for Astrophysical Applications

Directory of Open Access Journals (Sweden)

Jean-Christophe Pain

2017-05-01

Full Text Available Nowadays, several opacity codes are able to provide data for stellar structure models, but the computed opacities may show significant differences. In this work, we present state-of-the-art 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 involving hot dense plasmas produced by ultra-high-intensity laser irradiation. The measured spectra are systematically compared with the fine-structure opacity code SCO-RCG. The focus is on iron, due to its crucial role in understanding asteroseismic observations of β Cephei-type and Slowly Pulsating B stars, as well as of the Sun. For instance, in β Cephei-type stars, the iron-group opacity peak excites acoustic modes through the “kappa-mechanism”. Particular attention is paid to the higher-than-predicted iron opacity measured at the Sandia Z-machine at solar interior conditions. We discuss some theoretical aspects such as density effects, photo-ionization, autoionization or the “filling-the-gap” effect of highly excited states.

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

Full cyclic coordinate descent: solving the protein loop closure problem in Cα space

Directory of Open Access Journals (Sweden)

Hamelryck Thomas

2005-06-01

Full Text Available Abstract Background Various forms of the so-called loop closure problem are crucial to protein structure prediction methods. Given an N- and a C-terminal end, the problem consists of finding a suitable segment of a certain length that bridges the ends seamlessly. In homology modelling, the problem arises in predicting loop regions. In de novo protein structure prediction, the problem is encountered when implementing local moves for Markov Chain Monte Carlo simulations. Most loop closure algorithms keep the bond angles fixed or semi-fixed, and only vary the dihedral angles. This is appropriate for a full-atom protein backbone, since the bond angles can be considered as fixed, while the (φ, ψ dihedral angles are variable. However, many de novo structure prediction methods use protein models that only consist of Cα atoms, or otherwise do not make use of all backbone atoms. These methods require a method that alters both bond and dihedral angles, since the pseudo bond angle between three consecutive Cα atoms also varies considerably. Results Here we present a method that solves the loop closure problem for Cα only protein models. We developed a variant of Cyclic Coordinate Descent (CCD, an inverse kinematics method from the field of robotics, which was recently applied to the loop closure problem. Since the method alters both bond and dihedral angles, which is equivalent to applying a full rotation matrix, we call our method Full CCD (FCDD. FCCD replaces CCD's vector-based optimization of a rotation around an axis with a singular value decomposition-based optimization of a general rotation matrix. The method is easy to implement and numerically stable. Conclusion We tested the method's performance on sets of random protein Cα segments between 5 and 30 amino acids long, and a number of loops of length 4, 8 and 12. FCCD is fast, has a high success rate and readily generates conformations close to those of real loops. The presence of constraints

Deep neural network convolution (NNC) for three-class classification of diffuse lung disease opacities in high-resolution CT (HRCT): consolidation, ground-glass opacity (GGO), and normal opacity

Science.gov (United States)

Hashimoto, Noriaki; Suzuki, Kenji; Liu, Junchi; Hirano, Yasushi; MacMahon, Heber; Kido, Shoji

2018-02-01

Consolidation and ground-glass opacity (GGO) are two major types of opacities associated with diffuse lung diseases. Accurate detection and classification of such opacities are crucially important in the diagnosis of lung diseases, but the process is subjective, and suffers from interobserver variability. Our study purpose was to develop a deep neural network convolution (NNC) system for distinguishing among consolidation, GGO, and normal lung tissue in high-resolution CT (HRCT). We developed ensemble of two deep NNC models, each of which was composed of neural network regression (NNR) with an input layer, a convolution layer, a fully-connected hidden layer, and a fully-connected output layer followed by a thresholding layer. The output layer of each NNC provided a map for the likelihood of being each corresponding lung opacity of interest. The two NNC models in the ensemble were connected in a class-selection layer. We trained our NNC ensemble with pairs of input 2D axial slices and "teaching" probability maps for the corresponding lung opacity, which were obtained by combining three radiologists' annotations. We randomly selected 10 and 40 slices from HRCT scans of 172 patients for each class as a training and test set, respectively. Our NNC ensemble achieved an area under the receiver-operating-characteristic (ROC) curve (AUC) of 0.981 and 0.958 in distinction of consolidation and GGO, respectively, from normal opacity, yielding a classification accuracy of 93.3% among 3 classes. Thus, our deep-NNC-based system for classifying diffuse lung diseases achieved high accuracies for classification of consolidation, GGO, and normal opacity.

Looping and clustering model for the organization of protein-DNA complexes on the bacterial genome

Science.gov (United States)

Walter, Jean-Charles; Walliser, Nils-Ole; David, Gabriel; Dorignac, Jérôme; Geniet, Frédéric; Palmeri, John; Parmeggiani, Andrea; Wingreen, Ned S.; Broedersz, Chase P.

2018-03-01

The bacterial genome is organized by a variety of associated proteins inside a structure called the nucleoid. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIP-Seq experiments show that ParB proteins localize around centromere-like parS sites on the DNA to which ParB binds specifically, and spreads from there over large sections of the chromosome. Recent theoretical and experimental studies suggest that DNA-bound ParB proteins can interact with each other to condense into a coherent 3D complex on the DNA. However, the structural organization of this protein-DNA complex remains unclear, and a predictive quantitative theory for the distribution of ParB proteins on DNA is lacking. Here, we propose the looping and clustering model, which employs a statistical physics approach to describe protein-DNA complexes. The looping and clustering model accounts for the extrusion of DNA loops from a cluster of interacting DNA-bound proteins that is organized around a single high-affinity binding site. Conceptually, the structure of the protein-DNA complex is determined by a competition between attractive protein interactions and loop closure entropy of this protein-DNA cluster on the one hand, and the positional entropy for placing loops within the cluster on the other. Indeed, we show that the protein interaction strength determines the ‘tightness’ of the loopy protein-DNA complex. Thus, our model provides a theoretical framework for quantitatively computing the binding profiles of ParB-like proteins around a cognate (parS) binding site.

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

Science.gov (United States)

Li, Yaohang; Rata, Ionel; Chiu, See-wing; Jakobsson, Eric

2010-07-20

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. 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 approximately 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 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.

Protein intercalation in DNA as one of main modes of fixation of the most stable chromatin loop domains

Directory of Open Access Journals (Sweden)

М. I. Chopei

2014-08-01

Full Text Available The main mechanism of DNA track formation during comet assay of nucleoids, obtained after removal of cell membranes and most of proteins, is the extension to anode of negatively supercoiled DNA loops attached to proteins, remaining in nucleoid after lysis treatment. The composition of these residual protein structures and the nature of their strong interaction with the loop ends remain poorly studied. In this work we investigated the influence of chloroquine intercalation and denaturation of nucleoid proteins on the efficiency of electrophoretic track formation during comet assay. The results obtained suggest that even gentle protein denaturation is sufficient to reduce considerably the effectiveness of the DNA loop migration due to an increase in the loops size. The same effect was observed under local DNA unwinding upon chloroquine intercalation around the sites of the attachment of DNA to proteins. The topological interaction (protein intercalation into the double helix between DNA loop ends and nucleoid proteins is discussed.

Function of the activated protein C (APC) autolysis loop in activated FVIII inactivation.

Science.gov (United States)

Cramer, Thomas J; Gale, Andrew J

2011-06-01

Activated protein C (APC) binds to its substrates activated factor V (FVa) and activated factor VIII (FVIIIa) with a basic exosite that consists of loops 37, 60, 70 and the autolysis loop. These loops have a high density of basic residues, resulting in a positive charge on the surface of APC. Many of these residues are important in the interaction of APC with FVa and FVIIIa. The current study focused on the function of the autolysis loop in the interaction with FVIIIa. This loop was previously shown to interact with FVa, and it inhibits APC inactivation by plasma serpins. Charged residues of the autolysis loop were individually mutated to alanine and the activity of these mutants was assessed in functional FVIIIa inactivation assays. The autolysis loop was functionally important for FVIIIa inactivation. Mutation of R306, K311 and R314 each resulted in significantly reduced FVIIIa inactivation. The inactivating cleavages of FVIIIa at R336 and R562 were affected equally by the mutations. Protein S and FV stimulated cleavage at R562 more than cleavage at R336, independent of mutations in the autolysis loop. Together, these results confirmed that the autolysis loop plays a significant role as part of the basic exosite on APC in the interaction with FVIIIa. © 2011 Blackwell Publishing Ltd.

HELIOSEISMIC TESTS OF THE NEW LOS ALAMOS OPACITIES

Energy Technology Data Exchange (ETDEWEB)

J. GUZIK; ET AL

2001-01-01

We compare the helioseismic properties of two solar models, one calibrated with the OPAL opacities and the other with the recent Los Alamos LEDCOP opacities. We show that, in the radiative interior of the Sun, the small differences between the two sets of opacities (up to 6% near the base of the convection zone) lead to noticeable differences in the solar structure (up to 0.4% in sound speed), with the OPAL model being the closest to the helioseismic data. More than half of the difference between the two opacity sets results from the interpolation scheme and from the relatively widely spaced temperature grids used in the tables. The remaining 3% intrinsic difference between the OPAL and the LEDCOP opacities in the radiative interior of the Sun is well within the error bars on the opacity calculations resulting from the uncertainties on the physics. We conclude that the OPAL and LEDCOP opacity sets do about as well in the radiative interior of the Sun.

Web OPAC Interfaces: An Overview.

Science.gov (United States)

Babu, B. Ramesh; O'Brien, Ann

2000-01-01

Discussion of Web-based online public access catalogs (OPACs) focuses on a review of six Web OPAC interfaces in use in academic libraries in the United Kingdom. Presents a checklist and guidelines of important features and functions that are currently available, including search strategies, access points, display, links, and layout. (Author/LRW)

SOLAR OPACITY CALCULATIONS USING THE SUPER-TRANSITION-ARRAY METHOD

International Nuclear Information System (INIS)

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

2016-01-01

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

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.

Update on the opal opacity code

International Nuclear Information System (INIS)

Rogers, F.J.; Iglesias, C.A.; Wilson, B.G.

1990-01-01

Persisting discrepancies between theory and observation in a number of astrophysical properties has led to the conjecture that opacity databases may be inaccurate. The OPAL opacity code has been developed to address this question. The physical basis of OPAL removes several of the approximations present in past calculations. For example, it utilizes a much larger and more detailed set of atomic data than was used to construct the los Alamos Astrophysical Library. This data is generated online, in LS or intermediate coupling, from prefitted analytic effective potentials and is of similar quality as single configuration, relativistic, self-consistent-field calculations. The OPAL code has been used to calculate opacities for the solar core and for Cepheid variable stars. In both cases, significant increases in the opacity compared to the Los Alamos Astrophysical Library were found

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...... in otolith opacity, but the effect was minor compared to that of variations in ambient temperature. The combined influence of these effects, which both act on fish metabolism, are most likely controlling the seasonal opacity changes observed in wild fish. Our results help explain the variations seen in fish...

Contrasting HIV phylogenetic relationships and V3 loop protein similarities

Energy Technology Data Exchange (ETDEWEB)

Korber, B. (Los Alamos National Lab., NM (United States) Santa Fe Inst., NM (United States)); Myers, G. (Los Alamos National Lab., NM (United States))

1992-01-01

At least five distinct sequence subtypes of HIV-I can be identified from the major centers of the AMS pandemic. While it is too early to tell whether these subtypes are serologically or phenotypically similar or distinct in terms of properties such as pathogenicity and transmissibility, we can begin to investigate their potential for phenotypic divergence at the protein sequence level. Phylogenetic analysis of HIV DNA sequences is being widely used to examine lineages of different viral strains as they evolve and spread throughout the globe. We have identified five distinct HIV-1 subtypes (designated A-E), or clades, based on phylogenetic clustering patterns generated from genetic information from both the gag and envelope (env) genes from a spectrum of international isolates. Our initial observations concerning both HIV-1 and HIV-2 sequences indicate that conserved patterns in protein chemistry may indeed exist across distant lineages. Such patterns in V3 loop amino acid chemistry may be indicative of stable lineages or convergence within this highly variable, though functionally and immunologically critical, region. We think that there may be parallels between the apparently stable HIV-2 V3 lineage and the previously mentioned HIV-1 V3 loops which are very similar at the protein level despite being distant by cladistic analysis, and which do not possess the distinctive positively charged residues. Highly conserved V3 loop protein sequences are also encountered in SIVAGMs and CIVs (chimpanzee viral strains), which do not appear to be pathogenic in their wild-caught natural hosts.

Contrasting HIV phylogenetic relationships and V3 loop protein similarities

Energy Technology Data Exchange (ETDEWEB)

Korber, B. [Los Alamos National Lab., NM (United States)]|[Santa Fe Inst., NM (United States); Myers, G. [Los Alamos National Lab., NM (United States)

1992-12-31

At least five distinct sequence subtypes of HIV-I can be identified from the major centers of the AMS pandemic. While it is too early to tell whether these subtypes are serologically or phenotypically similar or distinct in terms of properties such as pathogenicity and transmissibility, we can begin to investigate their potential for phenotypic divergence at the protein sequence level. Phylogenetic analysis of HIV DNA sequences is being widely used to examine lineages of different viral strains as they evolve and spread throughout the globe. We have identified five distinct HIV-1 subtypes (designated A-E), or clades, based on phylogenetic clustering patterns generated from genetic information from both the gag and envelope (env) genes from a spectrum of international isolates. Our initial observations concerning both HIV-1 and HIV-2 sequences indicate that conserved patterns in protein chemistry may indeed exist across distant lineages. Such patterns in V3 loop amino acid chemistry may be indicative of stable lineages or convergence within this highly variable, though functionally and immunologically critical, region. We think that there may be parallels between the apparently stable HIV-2 V3 lineage and the previously mentioned HIV-1 V3 loops which are very similar at the protein level despite being distant by cladistic analysis, and which do not possess the distinctive positively charged residues. Highly conserved V3 loop protein sequences are also encountered in SIVAGMs and CIVs (chimpanzee viral strains), which do not appear to be pathogenic in their wild-caught natural hosts.

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.

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.

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.

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.

Origin and Diversification of Basic-Helix-Loop-Helix Proteins in Plants

OpenAIRE

Pires, Nuno; Dolan, Liam

2009-01-01

Basic helix-loop-helix (bHLH) proteins are a class of transcription factors found throughout eukaryotic organisms. Classification of the complete sets of bHLH proteins in the sequenced genomes of Arabidopsis thaliana and Oryza sativa (rice) has defined the diversity of these proteins among flowering plants. However, the evolutionary relationships of different plant bHLH groups and the diversity of bHLH proteins in more ancestral groups of plants are currently unknown. In this study, we use wh...

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.

Performance audit procedures for opacity monitors

International Nuclear Information System (INIS)

Plaisance, S.J.; Peeler, J.W.

1987-04-01

This manual contains monitor-specific performance audit procedures and data forms for use in conducting audits of installed opacity continuous emission monitoring systems (CEMS). General auditing procedures and acceptance limits for various audit criteria are discussed. Practical considerations and common problems encountered in conducting audits are delineated, and recommendations are included to optimize the successful completion of performance audits. Performance audit procedures and field-data forms were developed for six common opacity CEMS: (1) Lear Siegler, Inc. Model RM-41; (2) Lear Siegler, Inc. Model RM-4; (3) Dynatron Model 1100; (4) Thermo Electron, Inc. Model 400; (5) Thermo Electron, Inc. Model 1000A; and (6) Enviroplan Model D-R280 AV. Generic audit procedures are included for use in evaluating opacity CEMS with multiple transmissometers and combiner devices. In addition, several approaches for evaluating the zero-alignment or clear-path zero response are described. The zero-alignment procedures are included since the factor is fundamental to the accuracy of opacity monitoring data, even though the zero-alignment checks cannot usually be conducted during a performance audit

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.

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.

Dynameomics: data-driven methods and models for utilizing large-scale protein structure repositories for improving fragment-based loop prediction.

Science.gov (United States)

Rysavy, Steven J; Beck, David A C; Daggett, Valerie

2014-11-01

Protein function is intimately linked to protein structure and dynamics yet experimentally determined structures frequently omit regions within a protein due to indeterminate data, which is often due protein dynamics. We propose that atomistic molecular dynamics simulations provide a diverse sampling of biologically relevant structures for these missing segments (and beyond) to improve structural modeling and structure prediction. Here we make use of the Dynameomics data warehouse, which contains simulations of representatives of essentially all known protein folds. We developed novel computational methods to efficiently identify, rank and retrieve small peptide structures, or fragments, from this database. We also created a novel data model to analyze and compare large repositories of structural data, such as contained within the Protein Data Bank and the Dynameomics data warehouse. Our evaluation compares these structural repositories for improving loop predictions and analyzes the utility of our methods and models. Using a standard set of loop structures, containing 510 loops, 30 for each loop length from 4 to 20 residues, we find that the inclusion of Dynameomics structures in fragment-based methods improves the quality of the loop predictions without being dependent on sequence homology. Depending on loop length, ∼ 25-75% of the best predictions came from the Dynameomics set, resulting in lower main chain root-mean-square deviations for all fragment lengths using the combined fragment library. We also provide specific cases where Dynameomics fragments provide better predictions for NMR loop structures than fragments from crystal structures. Online access to these fragment libraries is available at http://www.dynameomics.org/fragments. © 2014 The Protein Society.

INTERPLAY OF NEUTRINO OPACITIES IN CORE-COLLAPSE SUPERNOVA SIMULATIONS

Energy Technology Data Exchange (ETDEWEB)

Lentz, Eric J. [Department of Physics and Astronomy, University of Tennessee, Knoxville, TN 37996-1200 (United States); Mezzacappa, Anthony; Hix, W. Raphael [Physics Division, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831-6354 (United States); Messer, O. E. Bronson [National Center for Computational Sciences, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN 37831-6164 (United States); Bruenn, Stephen W., E-mail: elentz@utk.edu [Department of Physics, Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33431-0991 (United States)

2012-11-20

We have conducted a series of numerical experiments using spherically symmetric, general relativistic, neutrino radiation hydrodynamics with the code Agile-BOLTZTRAN to examine the effects of modern neutrino opacities on the development of supernova simulations. We test the effects of opacities by removing opacities or by undoing opacity improvements for individual opacities and groups of opacities. We find that improvements to electron capture (EC) on nuclei, namely EC on an ensemble of nuclei using modern nuclear structure models rather than the simpler independent-particle approximation (IPA) for EC on a mean nucleus, plays the most important role during core collapse of all tested neutrino opacities. Low-energy neutrinos emitted by modern nuclear EC preferentially escape during collapse without the energy downscattering on electrons required to enhance neutrino escape and deleptonization for the models with IPA nuclear EC. During shock breakout the primary influence on the emergent neutrinos arises from non-isoenergetic scattering (NIS) on electrons. For the accretion phase, NIS on free nucleons and pair emission by e {sup +} e {sup -} annihilation have the largest impact on the neutrino emission and shock evolution. Other opacities evaluated, including nucleon-nucleon bremsstrahlung and especially neutrino-positron scattering, have little measurable impact on neutrino emission or shock dynamics. Modern treatments of nuclear EC, e {sup +} e {sup -}-annihilation pair emission, and NIS on electrons and free nucleons are critical elements of core-collapse simulations of all dimensionality.

Effective Opacity for Gold-Doped Foam Plasmas

International Nuclear Information System (INIS)

Huang Cheng-Wu; Song Tian-Ming; Zhao Yang; Zhu Tuo; Shang Wan-Li; Xiong Gang; Zhang Ji-Yan; Yang Jia-Min; Jiang Shao-En

2012-01-01

Radiation flow through gold-doped hydrocarbon foam is investigated and a model is presented to calculate effective opacity for an inhomogeneous, pressure-equilibrated gold/foam mixture based on the Levermore—Pomraning method for binary stochastic media. The effective opacity dependance on the size of the gold particles and the foam temperature are studied. The results suggest that when the mixture temperature is lower than 250 eV, the opacity difference between the 5 μm particle mix case and the atomic mix case is large enough to induce a significant discrepancy in radiation transport, which is confirmed by the hydrodynamic simulation

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.

Near-native protein loop sampling using nonparametric density estimation accommodating sparcity.

Science.gov (United States)

Joo, Hyun; Chavan, Archana G; Day, Ryan; Lennox, Kristin P; Sukhanov, Paul; Dahl, David B; Vannucci, Marina; Tsai, Jerry

2011-10-01

Unlike the core structural elements of a protein like regular secondary structure, template based modeling (TBM) has difficulty with loop regions due to their variability in sequence and structure as well as the sparse sampling from a limited number of homologous templates. We present a novel, knowledge-based method for loop sampling that leverages homologous torsion angle information to estimate a continuous joint backbone dihedral angle density at each loop position. The φ,ψ distributions are estimated via a Dirichlet process mixture of hidden Markov models (DPM-HMM). Models are quickly generated based on samples from these distributions and were enriched using an end-to-end distance filter. The performance of the DPM-HMM method was evaluated against a diverse test set in a leave-one-out approach. Candidates as low as 0.45 Å RMSD and with a worst case of 3.66 Å were produced. For the canonical loops like the immunoglobulin complementarity-determining regions (mean RMSD 7.0 Å), this sampling method produces a population of loop structures to around 3.66 Å for loops up to 17 residues. In a direct test of sampling to the Loopy algorithm, our method demonstrates the ability to sample nearer native structures for both the canonical CDRH1 and non-canonical CDRH3 loops. Lastly, in the realistic test conditions of the CASP9 experiment, successful application of DPM-HMM for 90 loops from 45 TBM targets shows the general applicability of our sampling method in loop modeling problem. These results demonstrate that our DPM-HMM produces an advantage by consistently sampling near native loop structure. The software used in this analysis is available for download at http://www.stat.tamu.edu/~dahl/software/cortorgles/.

Near-native protein loop sampling using nonparametric density estimation accommodating sparcity.

Directory of Open Access Journals (Sweden)

Hyun Joo

2011-10-01

Full Text Available Unlike the core structural elements of a protein like regular secondary structure, template based modeling (TBM has difficulty with loop regions due to their variability in sequence and structure as well as the sparse sampling from a limited number of homologous templates. We present a novel, knowledge-based method for loop sampling that leverages homologous torsion angle information to estimate a continuous joint backbone dihedral angle density at each loop position. The φ,ψ distributions are estimated via a Dirichlet process mixture of hidden Markov models (DPM-HMM. Models are quickly generated based on samples from these distributions and were enriched using an end-to-end distance filter. The performance of the DPM-HMM method was evaluated against a diverse test set in a leave-one-out approach. Candidates as low as 0.45 Å RMSD and with a worst case of 3.66 Å were produced. For the canonical loops like the immunoglobulin complementarity-determining regions (mean RMSD 7.0 Å, this sampling method produces a population of loop structures to around 3.66 Å for loops up to 17 residues. In a direct test of sampling to the Loopy algorithm, our method demonstrates the ability to sample nearer native structures for both the canonical CDRH1 and non-canonical CDRH3 loops. Lastly, in the realistic test conditions of the CASP9 experiment, successful application of DPM-HMM for 90 loops from 45 TBM targets shows the general applicability of our sampling method in loop modeling problem. These results demonstrate that our DPM-HMM produces an advantage by consistently sampling near native loop structure. The software used in this analysis is available for download at http://www.stat.tamu.edu/~dahl/software/cortorgles/.

Near-Native Protein Loop Sampling Using Nonparametric Density Estimation Accommodating Sparcity

Science.gov (United States)

Day, Ryan; Lennox, Kristin P.; Sukhanov, Paul; Dahl, David B.; Vannucci, Marina; Tsai, Jerry

2011-01-01

Unlike the core structural elements of a protein like regular secondary structure, template based modeling (TBM) has difficulty with loop regions due to their variability in sequence and structure as well as the sparse sampling from a limited number of homologous templates. We present a novel, knowledge-based method for loop sampling that leverages homologous torsion angle information to estimate a continuous joint backbone dihedral angle density at each loop position. The φ,ψ distributions are estimated via a Dirichlet process mixture of hidden Markov models (DPM-HMM). Models are quickly generated based on samples from these distributions and were enriched using an end-to-end distance filter. The performance of the DPM-HMM method was evaluated against a diverse test set in a leave-one-out approach. Candidates as low as 0.45 Å RMSD and with a worst case of 3.66 Å were produced. For the canonical loops like the immunoglobulin complementarity-determining regions (mean RMSD 7.0 Å), this sampling method produces a population of loop structures to around 3.66 Å for loops up to 17 residues. In a direct test of sampling to the Loopy algorithm, our method demonstrates the ability to sample nearer native structures for both the canonical CDRH1 and non-canonical CDRH3 loops. Lastly, in the realistic test conditions of the CASP9 experiment, successful application of DPM-HMM for 90 loops from 45 TBM targets shows the general applicability of our sampling method in loop modeling problem. These results demonstrate that our DPM-HMM produces an advantage by consistently sampling near native loop structure. The software used in this analysis is available for download at http://www.stat.tamu.edu/~dahl/software/cortorgles/. PMID:22028638

Serendipity and Holism: The Beauty of OPACs.

Science.gov (United States)

Rice, James

1988-01-01

Identifies factors which may account for user dissatisfaction with online public access catalogs (OPACs) and discusses some advantages of OPACs over card catalogs: (1) design for subject searching; (2) flexibility; (3) browsing capability; (4) precision; (5) availability of status information; and (6) development of microcomputer software to…

Dynameomics: Data-driven methods and models for utilizing large-scale protein structure repositories for improving fragment-based loop prediction

Science.gov (United States)

Rysavy, Steven J; Beck, David AC; Daggett, Valerie

2014-01-01

Protein function is intimately linked to protein structure and dynamics yet experimentally determined structures frequently omit regions within a protein due to indeterminate data, which is often due protein dynamics. We propose that atomistic molecular dynamics simulations provide a diverse sampling of biologically relevant structures for these missing segments (and beyond) to improve structural modeling and structure prediction. Here we make use of the Dynameomics data warehouse, which contains simulations of representatives of essentially all known protein folds. We developed novel computational methods to efficiently identify, rank and retrieve small peptide structures, or fragments, from this database. We also created a novel data model to analyze and compare large repositories of structural data, such as contained within the Protein Data Bank and the Dynameomics data warehouse. Our evaluation compares these structural repositories for improving loop predictions and analyzes the utility of our methods and models. Using a standard set of loop structures, containing 510 loops, 30 for each loop length from 4 to 20 residues, we find that the inclusion of Dynameomics structures in fragment-based methods improves the quality of the loop predictions without being dependent on sequence homology. Depending on loop length, ∼25–75% of the best predictions came from the Dynameomics set, resulting in lower main chain root-mean-square deviations for all fragment lengths using the combined fragment library. We also provide specific cases where Dynameomics fragments provide better predictions for NMR loop structures than fragments from crystal structures. Online access to these fragment libraries is available at http://www.dynameomics.org/fragments. PMID:25142412

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

KAUST Repository

Messih, Mario Abdel; Lepore, Rosalba; Tramontano, Anna

2015-01-01

) 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

IPOPv2 online service for the generation of opacity tables

International Nuclear Information System (INIS)

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

2016-01-01

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. - Highlights: • A new opacity table service is presented. • This is an alternative to the OPAL service, using The Opacity Project (OP) data. • These tables can directly replace the OPAL data in stellar code without any change in the code.

Using Web Services for a Mobile OPAC

Directory of Open Access Journals (Sweden)

Denis Galvin

2011-04-01

Full Text Available The purpose of this paper is to discuss the creation and intended evolution of the Rice University mobile online public access catalog (OPAC. The focus of the article is on how SirsiDynix’s Symphony Web Services can be used to create a mobile OPAC.

SOLAR MIXTURE OPACITY CALCULATIONS USING DETAILED CONFIGURATION AND LEVEL ACCOUNTING TREATMENTS

International Nuclear Information System (INIS)

Blancard, Christophe; Cossé, Philippe; Faussurier, Gérald

2012-01-01

An opacity model (OPAS) combining detailed configuration and level accounting treatments has been developed to calculate radiative opacity of plasmas in local thermodynamic equilibrium. The model is presented and used to compute spectral opacities of a solar mixture. Various density-temperature couples have been considered from the solar center up to the vicinity of the radiative/convective zone interface. For a given solar thermodynamic path, OPAS calculations are compared to Opacity Project (OP) and OPAL data. Rosseland mean opacity values are in very good agreement over all the considered solar thermodynamic path, while OPAS and OP spectral opacities of each element may vary considerably. Main sources of discrepancy are discussed.

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. Copyright © 2010 Elsevier Ltd. All rights reserved.

Impact of Neutrino Opacities on Core-collapse Supernova Simulations

Science.gov (United States)

Kotake, Kei; Takiwaki, Tomoya; Fischer, Tobias; Nakamura, Ko; Martínez-Pinedo, Gabriel

2018-02-01

The accurate description of neutrino opacities is central to both the core-collapse supernova (CCSN) phenomenon and the validity of the explosion mechanism itself. In this work, we study in a systematic fashion the role of a variety of well-selected neutrino opacities in CCSN simulations where the multi-energy, three-flavor neutrino transport is solved using the isotropic diffusion source approximation (IDSA) scheme. To verify our code, we first present results from one-dimensional (1D) simulations following the core collapse, bounce, and ∼250 ms postbounce of a 15 {M}ȯ star using a standard set of neutrino opacities by Bruenn. A detailed comparison with published results supports the reliability of our three-flavor IDSA scheme using the standard opacity set. We then investigate in 1D simulations how individual opacity updates lead to differences with the baseline run with the standard opacity set. Through detailed comparisons with previous work, we check the validity of our implementation of each update in a step-by-step manner. Individual neutrino opacities with the largest impact on the overall evolution in 1D simulations are selected for systematic comparisons in our two-dimensional (2D) simulations. Special attention is given to the criterion of explodability in the 2D models. We discuss the implications of these results as well as its limitations and the requirements for future, more elaborate CCSN modeling.

Investigating the Effect of Cosmic Opacity on Standard Candles

International Nuclear Information System (INIS)

Hu, J.; Yu, H.; Wang, F. Y.

2017-01-01

Standard candles can probe the evolution of dark energy over a large redshift range. But the cosmic opacity can degrade the quality of standard candles. In this paper, we use the latest observations, including Type Ia supernovae (SNe Ia) from the “joint light-curve analysis” sample and Hubble parameters, to probe the opacity of the universe. A joint fitting of the SNe Ia light-curve parameters, cosmological parameters, and opacity is used in order to avoid the cosmological dependence of SNe Ia luminosity distances. The latest gamma-ray bursts are used in order to explore the cosmic opacity at high redshifts. The cosmic reionization process is considered at high redshifts. We find that the sample supports an almost transparent universe for flat ΛCDM and XCDM models. Meanwhile, free electrons deplete photons from standard candles through (inverse) Compton scattering, which is known as an important component of opacity. This Compton dimming may play an important role in future supernova surveys. From analysis, we find that about a few per cent of the cosmic opacity is caused by Compton dimming in the two models, which can be corrected.

Opacity

International Nuclear Information System (INIS)

Reina N, Ramon

2003-01-01

Their objective is to specify and to clarify many of the terms that are frequently employees and routinely in the description of the discoveries that appear in the x-rays of the thorax and in its complementary studies as it is the case of the computerized tomography; for the previous reason, it is considered important to include the term of opacity this it should be the first term to use when it is an abnormal discovery in the x-ray that causes an increase in the lung density of any etiology

Model-independent Constraints on Cosmic Curvature and Opacity

Energy Technology Data Exchange (ETDEWEB)

Wang, Guo-Jian; Li, Zheng-Xiang; Xia, Jun-Qing; Zhu, Zong-Hong [Department of Astronomy, Beijing Normal University, Beijing 100875 (China); Wei, Jun-Jie, E-mail: gjwang@mail.bnu.edu.cn, E-mail: zxli918@bnu.edu.cn, E-mail: xiajq@bnu.edu.cn, E-mail: zhuzh@bnu.edu.cn, E-mail: jjwei@pmo.ac.cn [Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210008 (China)

2017-09-20

In this paper, we propose to estimate the spatial curvature of the universe and the cosmic opacity in a model-independent way with expansion rate measurements, H ( z ), and type Ia supernova (SNe Ia). On the one hand, using a nonparametric smoothing method Gaussian process, we reconstruct a function H ( z ) from opacity-free expansion rate measurements. Then, we integrate the H ( z ) to obtain distance modulus μ {sub H}, which is dependent on the cosmic curvature. On the other hand, distances of SNe Ia can be determined by their photometric observations and thus are opacity-dependent. In our analysis, by confronting distance moduli μ {sub H} with those obtained from SNe Ia, we achieve estimations for both the spatial curvature and the cosmic opacity without any assumptions for the cosmological model. Here, it should be noted that light curve fitting parameters, accounting for the distance estimation of SNe Ia, are determined in a global fit together with the cosmic opacity and spatial curvature to get rid of the dependence of these parameters on cosmology. In addition, we also investigate whether the inclusion of different priors for the present expansion rate ( H {sub 0}: global estimation, 67.74 ± 0.46 km s{sup −1} Mpc{sup −1}, and local measurement, 73.24 ± 1.74 km s{sup −1} Mpc{sup −1}) exert influence on the reconstructed H ( z ) and the following estimations of the spatial curvature and cosmic opacity. Results show that, in general, a spatially flat and transparent universe is preferred by the observations. Moreover, it is suggested that priors for H {sub 0} matter a lot. Finally, we find that there is a strong degeneracy between the curvature and the opacity.

Economic Optimizing Control for Single-Cell Protein Production in a U-Loop Reactor

DEFF Research Database (Denmark)

Drejer, André; Ritschel, Tobias Kasper Skovborg; Jørgensen, Sten Bay

2017-01-01

The production of single-cell protein (SCP) in a U-loop reactor by a methanotroph is a cost efficient sustainable alternative to protein from fish meal obtained by over-fishing the oceans. SCP serves as animal feed. In this paper, we present a mathematical model that describes the dynamics of SCP...

Solar opacities constrained by solar neutrinos and solar oscillations

International Nuclear Information System (INIS)

Cox, A.N.

1989-01-01

This review discusses the current situation for opacities at the solar center, the solar surface, and for the few million kelvin temperatures that occur below the convection zone. The solar center conditions are important because they are crucial for the neutrino production, which continues to be predicted about 4 times that observed. The main extinction effects there are free-free photon absorption in the electric fields of the hydrogen, helium and the CNO atoms, free electron scattering of photons, and the bound-free and bound-bound absorption of photons by iron atoms with two electrons in the 1s bound level. An assumption that the iron is condensed-out below the convection zone, and the opacity in the central regions is thereby reduced, results in about a 25 percent reduction in the central opacity but only a 5 percent reduction at the base of the convection zone. Furthermore, the p-mode solar oscillations are changed with this assumption, and do not fit the observed ones as well as for standard models. A discussion of the large effective opacity reduction by weakly interacting massive particles also results in poor agreement with observed p-mode oscillation frequencies. The much larger opacities for the solar surface layers from the Los Alamos Astrophysical Opacity Library instead of the widely used Cox and Tabor values show small improvements in oscillation frequency predictions, but the largest effect is in the discussion of p-mode stability. Solar oscillation frequencies can serve as an opacity experiment for the temperatures and densities, respectively, of a few million kelvin and between 0.1 and 10 g/cm 3 . Current oscillation frequency calculations indicate that possibly the Opacity Library values need an increase of typically 15 percent just at the bottom of the convection zone at 3 x 10 6 K. 41 refs., 15 figs., 1 tab

The Rosseland mean opacity of interstellar grain

International Nuclear Information System (INIS)

Ali, A.; El Shalaby, M.A.; El-Nawawy, M.S.

1990-10-01

We have calculated the opacity of interstellar grains in the temperature range 10 deg. K - 1500 deg. K. Two composite grain models have been considered. One of them consists of silicate coated with ice mantle and the second has a graphite core coated also with ice mantle. These models are compared with isolated grain models. An exact analytical and computational development of Guettler's formulae for composite grain models has been used to calculate the extinction coefficient. It has been found that the thickness of the mantle affects the opacity of the interstellar grains. The opacity of composite models differs from that of the isolated models. The effect of the different species (ice, silicate and graphite) is also clear. (author). 22 refs, 4 figs, 1 tab

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.

Comparative pulsation calculations with OP and OPAL opacities

Science.gov (United States)

Kanbur, Shashi M.; Simon, Norman R.

1994-01-01

Comparative linear nonadiabatic pulsation calculations are presented using the OPAL and Opacity Project opacities. The two sets of opacities include effects due to intermediate coupling and fine structure as well as new abundances. We used two mass luminosity (M-L) relations, one standard (BIT), and one employing substantial convective core overshoot (COV). The two sets of opacities cannot be differentiated on the basis of the stellar pulsation calculations presented here. The BIT relation can model the beat and bump Cepheids with masses between 4 and 7 solar mass, while if the overshoot relation is used, masses between 2 and 6 solar mass are required. In the RR Lyrae regime, we find the inferred masses of globular cluster RRd stars to be little influenced by the choice of OPAL or OP. Finally, the limited modeling we have done is not able to constrain the Cepheid M-L relation based upon period ratios observed in the beat and bump stars.

Los Alamos Opacities: Transition from LEDCOP to ATOMIC

International Nuclear Information System (INIS)

Magee, N.H.; Abdallah, J.; Colgan, J.; Hakel, P.; Kilcrease, D.P.; Mazevet, S.; Sherrill, M.; Fontes, C.J.; Zhang, H.L.

2004-01-01

This paper discusses the development of the ATOMIC code, a new low to mid Z opacity code, which will replace the current Los Alamos low Z opacity code LEDCOP. The ATOMIC code is based on the FINE code, long used by the Los Alamos group for spectral comparisons in local thermodynamic equilibrium (LTE) and for non-LTE calculations, utilizing the extensive databases from the atomic physics suite of codes based on the work of R. D. Cowan. Many of the plasma physics packages in LEDCOP, such as line broadening and free-free absorption, are being transferred to the new ATOMIC code. A new equation of state (EOS) model is being developed to allow higher density calculations than were possible with either the FINE or LEDCOP codes. Extensive modernization for both ATOMIC and the atomic physics code suites, including conversion to Fortran 90 and parallelization, are under way to speed up the calculations and to allow the use of expanded databases for both the LTE opacity tables and the non-LTE calculations. Future plans will be outlined, including considerations for new generation opacity tables

Terrien's marginal degeneration accompanied by latticed stromal opacities.

Science.gov (United States)

Zhang, Yibing; Jia, Hui

2014-05-01

We report a case of Terrien's marginal degeneration (TMD) with a unilaterally typical narrow band of peripheral corneal stroma thinning, accompanied by the presence of an unusual network of opacities diffusing throughout the anterior stroma layers. A 43-year-old woman presented with superior nasal peripheral corneal thinning and an unusual network of polygonal stromal opacities in the anterior corneal stroma of the right eye. Latticed corneal changes were unusually extensive and distributed diffusely in the stroma. No abnormalities were found in the corneal epithelium and in the basal epithelial cells. No noticeable changes were found in the left eye. Because of a progressively worse ocular irritation of the right eye, a diagnosis of TMD was made for this patient. This case of TMD accompanied by keratopathy was unusual. The branching stromal lattice pattern of the corneal opacities was difficult to distinguish from lattice corneal dystrophy. In this case, the polygonal stromal opacities were located in the anterior corneal stroma and therefore were distinguished from a similar manifestation in posterior crocodile shagreen.

Universe opacity and CMB

Science.gov (United States)

Vavryčuk, Václav

2018-04-01

A cosmological model, in which the cosmic microwave background (CMB) is a thermal radiation of intergalactic dust instead of a relic radiation of the Big Bang, is revived and revisited. The model suggests that a virtually transparent local Universe becomes considerably opaque at redshifts z > 2 - 3. Such opacity is hardly to be detected in the Type Ia supernova data, but confirmed using quasar data. The opacity steeply increases with redshift because of a high proper density of intergalactic dust in the previous epochs. The temperature of intergalactic dust increases as (1 + z) and exactly compensates the change of wavelengths due to redshift, so that the dust radiation looks apparently like the radiation of the blackbody with a single temperature. The predicted dust temperature is TD = 2.776 K, which differs from the CMB temperature by 1.9% only, and the predicted ratio between the total CMB and EBL intensities is 13.4 which is close to 12.5 obtained from observations. The CMB temperature fluctuations are caused by EBL fluctuations produced by galaxy clusters and voids in the Universe. The polarization anomalies of the CMB correlated with temperature anisotropies are caused by the polarized thermal emission of needle-shaped conducting dust grains aligned by large-scale magnetic fields around clusters and voids. A strong decline of the luminosity density for z > 4 is interpreted as the result of high opacity of the Universe rather than of a decline of the global stellar mass density at high redshifts.

Method-Unifying View of Loop-Formation Kinetics in Peptide and Protein Folding.

Science.gov (United States)

Jacob, Maik H; D'Souza, Roy N; Schwarzlose, Thomas; Wang, Xiaojuan; Huang, Fang; Haas, Elisha; Nau, Werner M

2018-04-26

Protein folding can be described as a probabilistic succession of events in which the peptide chain forms loops closed by specific amino acid residue contacts, herein referred to as loop nodes. To measure loop rates, several photophysical methods have been introduced where a pair of optically active probes is incorporated at selected chain positions and the excited probe undergoes contact quenching (CQ) upon collision with the second probe. The quenching mechanisms involved triplet-triplet energy transfer, photoinduced electron transfer, and collision-induced fluorescence quenching, where the fluorescence of Dbo, an asparagine residue conjugated to 2,3-diazabicyclo[2.2.2]octane, is quenched by tryptophan. The discrepancy between the loop rates afforded from these three CQ techniques has, however, remained unresolved. In analyzing this discrepancy, we now report two short-distance FRET methods where Dbo acts as an energy acceptor in combination with tryptophan and naphtylalanine, two donors with largely different fluorescence lifetimes of 1.3 and 33 ns, respectively. Despite the different quenching mechanisms, the rates from FRET and CQ methods were, surprisingly, of comparable magnitude. This combination of FRET and CQ data led to a unifying physical model and to the conclusion that the rate of loop formation in folding reactions varies not only with the kind and number of residues that constitute the chain but also in particular with the size and properties of the residues that constitute the loop node.

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

Prion protein β2-α2 loop conformational landscape.

Science.gov (United States)

Caldarulo, Enrico; Barducci, Alessandro; Wüthrich, Kurt; Parrinello, Michele

2017-09-05

In transmissible spongiform encephalopathies (TSEs), which are lethal neurodegenerative diseases that affect humans and a wide range of other mammalian species, the normal "cellular" prion protein ([Formula: see text]) is transformed into amyloid aggregates representing the "scrapie form" of the protein ([Formula: see text]). Continued research on this system is of keen interest, since new information on the physiological function of [Formula: see text] in healthy organisms is emerging, as well as new data on the mechanism of the transformation of [Formula: see text] to [Formula: see text] In this paper we used two different approaches: a combination of the well-tempered ensemble (WTE) and parallel tempering (PT) schemes and metadynamics (MetaD) to characterize the conformational free-energy surface of [Formula: see text] The focus of the data analysis was on an 11-residue polypeptide segment in mouse [Formula: see text](121-231) that includes the [Formula: see text]2-[Formula: see text]2 loop of residues 167-170, for which a correlation between structure and susceptibility to prion disease has previously been described. This study includes wild-type mouse [Formula: see text] and a variant with the single-residue replacement Y169A. The resulting detailed conformational landscapes complement in an integrative manner the available experimental data on [Formula: see text], providing quantitative insights into the nature of the structural transition-related function of the [Formula: see text]2-[Formula: see text]2 loop.

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.

Opacity of expanding media: The effect of spectral lines

International Nuclear Information System (INIS)

Karp, A.H.; Lasher, G.; Chan, K.L.; Salpeter, E.E.

1977-01-01

Spectral lines are more effective in slowing the transport of radiation in expanding (or contracting) objects than in static ones. The velocity gradient associated with the expansion causes the frequency of the photons to be continuously redshifted relative to the rest frame of the gas through which they travel. Those photons which are redshifted to the frequency of a sufficiently strong line will be absorbed by the corresponding bound-bound transition, and the net effect will be to increase the effective opacity of the gas. In certain cases the effect can be taken into account by using an effective opacity, the expansion opacity, which is a function not only of the temperature and density but also of the velocity gradient.Practical formulae for computing the expansion opacity and its Rosseland mean in terms of sums over spectral lines are derived. It is shown that the cumulative effect of many weak lines can be important, implying that a large list of spectral lines is required to obtain results of even modest accuracy. Numerical computations using the 260,000-entry line list of Kurucz and Peytremann have been completed and some samples of the result are given. The general effect may be important in many astronomical objects, but only in some of these will be detailed approach of this paper be appropriate. In optically thick supernova shells, the effect is important both in maintaining the radiation in thermal equilibrium as it diffuses out of the shell and in increasing the value of the total opacity. The enhancement of the opacity ranges from less than 1% to more than an order of magnitude, depending on the temperature, density, and velocity gradient

An Evaluation of Online Help for the NOTIS OPAC.

Science.gov (United States)

White, Frank

1994-01-01

Discussion of online help systems in online public access catalogs (OPACs) focuses on a study that evaluated the online help system for the NOTIS (Northwestern Online Total Integrated System) OPAC. Features of the system reviewed include online functions; training features; general interface features; access points; and message content and display…

The cellular RNA-binding protein EAP recognizes a conserved stem-loop in the Epstein-Barr virus small RNA EBER 1.

Science.gov (United States)

Toczyski, D P; Steitz, J A

1993-01-01

EAP (EBER-associated protein) is an abundant, 15-kDa cellular RNA-binding protein which associates with certain herpesvirus small RNAs. We have raised polyclonal anti-EAP antibodies against a glutathione S-transferase-EAP fusion protein. Analysis of the RNA precipitated by these antibodies from Epstein-Barr virus (EBV)- or herpesvirus papio (HVP)-infected cells shows that > 95% of EBER 1 (EBV-encoded RNA 1) and the majority of HVP 1 (an HVP small RNA homologous to EBER 1) are associated with EAP. RNase protection experiments performed on native EBER 1 particles with affinity-purified anti-EAP antibodies demonstrate that EAP binds a stem-loop structure (stem-loop 3) of EBER 1. Since bacterially expressed glutathione S-transferase-EAP fusion protein binds EBER 1, we conclude that EAP binding is independent of any other cellular or viral protein. Detailed mutational analyses of stem-loop 3 suggest that EAP recognizes the majority of the nucleotides in this hairpin, interacting with both single-stranded and double-stranded regions in a sequence-specific manner. Binding studies utilizing EBER 1 deletion mutants suggest that there may also be a second, weaker EAP-binding site on stem-loop 4 of EBER 1. These data and the fact that stem-loop 3 represents the most highly conserved region between EBER 1 and HVP 1 suggest that EAP binding is a critical aspect of EBER 1 and HVP 1 function. Images PMID:8380232

Experiment to measure oxygen opacity at high density and temperature

Science.gov (United States)

Keiter, Paul; Butler, Hannah; Trantham, Matt; Mussack, Katie; Colgan, James; Fontes, Chris; Guzik, Joyce; Kilcrease, David; Perry, Ted; Orban, Chris; Ducret, Jean-Eric; La Pennec, Maelle; Turck-Chieze, Sylvaine; Mancini, Roberto; Heeter, Robert

2017-10-01

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. Recent opacity measurements of iron disagree with opacity model predictions [Bailey et al., 2015]. 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 low-Z elements [Colgan, 2013, Armstrong 2014], 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 HEDLP, Grant Number DE-NA0002956, and the NLUF Program, Grant Number DE-NA0002719, and through the LLE, University of Rochester by the NNSA/OICF under No. DE-NA0001944.

Protein Structure Classification and Loop Modeling Using Multiple Ramachandran Distributions

KAUST Repository

Najibi, Seyed Morteza; Maadooliat, Mehdi; Zhou, Lan; Huang, Jianhua Z.; Gao, Xin

2017-01-01

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.

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.

Prion protein β2–α2 loop conformational landscape

Science.gov (United States)

Caldarulo, Enrico; Wüthrich, Kurt; Parrinello, Michele

2017-01-01

In transmissible spongiform encephalopathies (TSEs), which are lethal neurodegenerative diseases that affect humans and a wide range of other mammalian species, the normal “cellular” prion protein (PrPC) is transformed into amyloid aggregates representing the “scrapie form” of the protein (PrPSc). Continued research on this system is of keen interest, since new information on the physiological function of PrPC in healthy organisms is emerging, as well as new data on the mechanism of the transformation of PrPC to PrPSc. In this paper we used two different approaches: a combination of the well-tempered ensemble (WTE) and parallel tempering (PT) schemes and metadynamics (MetaD) to characterize the conformational free-energy surface of PrPC. The focus of the data analysis was on an 11-residue polypeptide segment in mouse PrPC(121–231) that includes the β2–α2 loop of residues 167–170, for which a correlation between structure and susceptibility to prion disease has previously been described. This study includes wild-type mouse PrPC and a variant with the single-residue replacement Y169A. The resulting detailed conformational landscapes complement in an integrative manner the available experimental data on PrPC, providing quantitative insights into the nature of the structural transition-related function of the β2–α2 loop. PMID:28827331

Terrien’s Marginal Degeneration Accompanied by Latticed Stromal Opacities

Science.gov (United States)

Zhang, Yibing; Jia, Hui

2014-01-01

ABSTRACT Purpose We report a case of Terrien’s marginal degeneration (TMD) with a unilaterally typical narrow band of peripheral corneal stroma thinning, accompanied by the presence of an unusual network of opacities diffusing throughout the anterior stroma layers. Case Report A 43-year-old woman presented with superior nasal peripheral corneal thinning and an unusual network of polygonal stromal opacities in the anterior corneal stroma of the right eye. Latticed corneal changes were unusually extensive and distributed diffusely in the stroma. No abnormalities were found in the corneal epithelium and in the basal epithelial cells. No noticeable changes were found in the left eye. Because of a progressively worse ocular irritation of the right eye, a diagnosis of TMD was made for this patient. Conclusions This case of TMD accompanied by keratopathy was unusual. The branching stromal lattice pattern of the corneal opacities was difficult to distinguish from lattice corneal dystrophy. In this case, the polygonal stromal opacities were located in the anterior corneal stroma and therefore were distinguished from a similar manifestation in posterior crocodile shagreen. PMID:24681833

Opacity calculations for extreme physical systems: code RACHEL

Science.gov (United States)

Drska, Ladislav; Sinor, Milan

1996-08-01

Computer simulations of physical systems under extreme conditions (high density, temperature, etc.) require the availability of extensive sets of atomic data. This paper presents basic information on a self-consistent approach to calculations of radiative opacity, one of the key characteristics of such systems. After a short explanation of general concepts of the atomic physics of extreme systems, the structure of the opacity code RACHEL is discussed and some of its applications are presented.

Effect of T- and C-loop mutations on the Herbaspirillum seropedicae GlnB protein in nitrogen signalling.

Science.gov (United States)

Bonatto, Ana C; Souza, Emanuel M; Pedrosa, Fábio O; Yates, M Geoffrey; Benelli, Elaine M

2005-01-01

Proteins of the PII family are found in species of all kingdoms. Although these proteins usually share high identity, their functions are specific to the different organisms. Comparison of structural data from Escherichia coli GlnB and GlnK and Herbaspirillum seropedicae GlnB showed that the T-loop and C-terminus were variable regions. To evaluate the role of these regions in signal transduction by the H. seropedicae GlnB protein, four mutants were constructed: Y51F, G108A/P109a, G108W and Q3R/T5A. The activities of the native and mutated proteins were assayed in an E. coli background constitutively expressing the Klebsiella pneumoniae nifLA operon. The results suggested that the T-loop and C-terminus regions of H. seropedicae GlnB are involved in nitrogen signal transduction.

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.

Independence of protein kinase C-delta activity from activation loop phosphorylation: structural basis and altered functions in cells.

Science.gov (United States)

Liu, Yin; Belkina, Natalya V; Graham, Caroline; Shaw, Stephen

2006-04-28

Activation loop phosphorylation plays critical regulatory roles for many kinases. Unlike other protein kinase Cs (PKC), PKC-delta does not require phosphorylation of its activation loop (Thr-507) for in vitro activity. We investigated the structural basis for this unusual capacity and its relevance to PKC-delta function in intact cells. Mutational analysis demonstrated that activity without Thr-507 phosphorylation depends on 20 residues N-terminal to the kinase domain and a pair of phenylalanines (Phe-500/Phe-527) unique to PKC-delta in/near the activation loop. Molecular modeling demonstrated that these elements stabilize the activation loop by forming a hydrophobic chain of interactions from the C-lobe to activation loop to N-terminal (helical) extension. In cells PKC-delta mediates both apoptosis and transcription regulation. We found that the T507A mutant of the PKC-delta kinase domain resembled the corresponding wild type in mediating apoptosis in transfected HEK293T cells. But the T507A mutant was completely defective in AP-1 and NF-kappaB reporter assays. A novel assay in which the kinase domain of PKC-delta and its substrate (a fusion protein of PKC substrate peptide with green fluorescent protein) were co-targeted to lipid rafts revealed a major substrate-selective defect of the T507A mutant in phosphorylating the substrate in cells. In vitro analysis showed strong product inhibition on the T507A mutant with particular substrates whose characteristics suggest it contributes to the substrate selective defect of the PKC-delta T507A mutant in cells. Thus, activation loop phosphorylation of PKC-delta may regulate its function in cells in a novel way.

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.

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

colistin, nystatin, trimethoprim , and streptomycin sulfate) was as described (91). Generation of antibodies Affinity-purified rabbit polyclonal... determined empirically: AbHV2 linear (0.87-1.2 µg/mL), AbSV linear (2.2 µg/mL), Ab4L linear (2.4 µg/ml), and AbHV2 cyclic (1:100) and AbSV cyclic (1...killing of the target strains in the absence of added antibody as determined by Garvin 44 et al. (59). For testing Opa loop-specific antibodies

Perilaku Pemustaka Dalam Temu Kembali Koleksi Dengan Menggunakan OPAC Berbasis SLIMS

Directory of Open Access Journals (Sweden)

Mujiati Mujiati

2014-07-01

Full Text Available Abstract: An  increase of  library collection and  information explosion causes  problems  on    information  retrieval  for  library  users.  Those explosion will be helpful for users using Online Public Access Catalog (OPAC. This article tries to explore the use of OPAC based SLIMs on STAIN Ponorogo  library. OPAC proves  to help users  on  retrieval  be easier and faster, beside its obstacles

Sphinx: merging knowledge-based and ab initio approaches to improve protein loop prediction.

Science.gov (United States)

Marks, Claire; Nowak, Jaroslaw; Klostermann, Stefan; Georges, Guy; Dunbar, James; Shi, Jiye; Kelm, Sebastian; Deane, Charlotte M

2017-05-01

Loops are often vital for protein function, however, their irregular structures make them difficult to model accurately. Current loop modelling algorithms can mostly be divided into two categories: knowledge-based, where databases of fragments are searched to find suitable conformations and ab initio, where conformations are generated computationally. Existing knowledge-based methods only use fragments that are the same length as the target, even though loops of slightly different lengths may adopt similar conformations. Here, we present a novel method, Sphinx, which combines ab initio techniques with the potential extra structural information contained within loops of a different length to improve structure prediction. We show that Sphinx is able to generate high-accuracy predictions and decoy sets enriched with near-native loop conformations, performing better than the ab initio algorithm on which it is based. In addition, it is able to provide predictions for every target, unlike some knowledge-based methods. Sphinx can be used successfully for the difficult problem of antibody H3 prediction, outperforming RosettaAntibody, one of the leading H3-specific ab initio methods, both in accuracy and speed. Sphinx is available at http://opig.stats.ox.ac.uk/webapps/sphinx. deane@stats.ox.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press.

Activation loop targeting strategy for design of receptor-interacting protein kinase 2 (RIPK2) inhibitors.

Science.gov (United States)

Suebsuwong, Chalada; Pinkas, Daniel M; Ray, Soumya S; Bufton, Joshua C; Dai, Bing; Bullock, Alex N; Degterev, Alexei; Cuny, Gregory D

2018-02-15

Development of selective kinase inhibitors remains a challenge due to considerable amino acid sequence similarity among family members particularly in the ATP binding site. Targeting the activation loop might offer improved inhibitor selectivity since this region of kinases is less conserved. However, the strategy presents difficulties due to activation loop flexibility. Herein, we report the design of receptor-interacting protein kinase 2 (RIPK2) inhibitors based on pan-kinase inhibitor regorafenib that aim to engage basic activation loop residues Lys169 or Arg171. We report development of CSR35 that displayed >10-fold selective inhibition of RIPK2 versus VEGFR2, the target of regorafenib. A co-crystal structure of CSR35 with RIPK2 revealed a resolved activation loop with an ionic interaction between the carboxylic acid installed in the inhibitor and the side-chain of Lys169. Our data provides principle feasibility of developing activation loop targeting type II inhibitors as a complementary strategy for achieving improved selectivity. Copyright © 2018 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Assessment of subpleural opacities on high-resolution CT

International Nuclear Information System (INIS)

Choi, Hee Seok; Kim, Jeung Sook; Kang, Eun Young; Kim, Hak Hee

2007-01-01

The purpose of this study was to assess the value of HRCT for determining the cause of subpleural opacities. We evaluated 49 cases of subpleural opacities on HRCT scan, among with the patients with subpleural opacities seen on the conventional chest radiographs. Two 'blinded' reviewers retrospectively analyzed the CT scans by working in consensus. The patients consisted of COP (n = 14), NSIP (n = 13), UIP (n = 10), fibrosis associated with connective tissue disease or drug toxicity (n = 4), CEP (n = 4), Churg-Strauss syndrome (n = 2), DIP (n = 1) and AIP (n = 1). The predominant findings were consolidation (57%) with a peribronchovascular distribution (57%) in the COP patients, GGO (69%) and the associated focal reticular densities (61%) in the NSIP patients, and reticular or reticulonodular densities with a paucity of GGO in the UIP patients (100%). For the diagnosis of COP, NSIP and UIP, the use of HRCT demonstrated a high sensitivity (86%, 85% and 90%, respectively), specificity (97%, 86% and 95%) and accuracy (94%, 86% and 94%). Although an overlap of CT findings is seen for diseases showing subpleural opacities, consolidation with a subpleural and peribronchovascular distribution is highly suggestive for COP, subpleural GGO is highly suggestive of NSIP, subpleural reticular or reticulonodular densities with a paucity of GGO is highly suggestive of UIP and subpleural consolidation accompanied by reticular densities is suggestive of fibrosis

Assessment of subpleural opacities on high-resolution CT

Energy Technology Data Exchange (ETDEWEB)

Choi, Hee Seok; Kim, Jeung Sook [Dngguk University International Hospital, Goyang (Korea, Republic of); Kang, Eun Young [Korea University Guro Hospital, Seoul (Korea, Republic of); Kim, Hak Hee [Asan Medical Center, University of Ulsan College of Medicine, Seoul (Korea, Republic of)

2007-11-15

The purpose of this study was to assess the value of HRCT for determining the cause of subpleural opacities. We evaluated 49 cases of subpleural opacities on HRCT scan, among with the patients with subpleural opacities seen on the conventional chest radiographs. Two 'blinded' reviewers retrospectively analyzed the CT scans by working in consensus. The patients consisted of COP (n = 14), NSIP (n = 13), UIP (n = 10), fibrosis associated with connective tissue disease or drug toxicity (n = 4), CEP (n = 4), Churg-Strauss syndrome (n = 2), DIP (n = 1) and AIP (n = 1). The predominant findings were consolidation (57%) with a peribronchovascular distribution (57%) in the COP patients, GGO (69%) and the associated focal reticular densities (61%) in the NSIP patients, and reticular or reticulonodular densities with a paucity of GGO in the UIP patients (100%). For the diagnosis of COP, NSIP and UIP, the use of HRCT demonstrated a high sensitivity (86%, 85% and 90%, respectively), specificity (97%, 86% and 95%) and accuracy (94%, 86% and 94%). Although an overlap of CT findings is seen for diseases showing subpleural opacities, consolidation with a subpleural and peribronchovascular distribution is highly suggestive for COP, subpleural GGO is highly suggestive of NSIP, subpleural reticular or reticulonodular densities with a paucity of GGO is highly suggestive of UIP and subpleural consolidation accompanied by reticular densities is suggestive of fibrosis.

A Rare Form of Corneal Opacity Associated with Spondyloepiphyseal Dysplasia Congenita

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Yuichiro Ishida

2018-02-01

Full Text Available A 13-year-old Japanese female diagnosed with spondyloepiphyseal dysplasia congenita (SEDC was referred for ophthalmologic evaluation. Examination with slit-lamp and optical coherence tomography revealed bilateral thin cornea with diffuse corneal opacity which was localised at the posterior stromal depth in the central cornea. Unlike the two previously reported cases of diffuse and nodular patterns of corneal opacity in SEDC, the current case exhibited a rare form of corneal opacity. SEDC is one of the type II collagenopathies, characterised by dwarfism because the mutations in COL2A1 prevent bone growth. Although the existence of type II collagen has not been reported in the human corneal stroma, the aetiology of the opacity in the corneal stroma in SEDC type II collagenopathy is of interest.

OPACs in the Clouds

Science.gov (United States)

Webb, Paula L.; Nero, Muriel D.

2009-01-01

In today's world of instant everything, everyone has been exposed to some form of Web 2.0 technology, and higher education is not exempt from its long reach. Libraries of all types are incorporating Web 2.0 features to attract users as well as to showcase library services. The Online Public Access Catalog (OPAC) has become more user-friendly with…

Anchoring protein crystals to mounting loops with hydrogel using inkjet technology.

Science.gov (United States)

Shinoda, Akira; Tanaka, Yoshikazu; Yao, Min; Tanaka, Isao

2014-11-01

X-ray crystallography is an important technique for structure-based drug discovery, mainly because it is the only technique that can reveal whether a ligand binds to the target protein as well as where and how it binds. However, ligand screening by X-ray crystallography involves a crystal-soaking experiment, which is usually performed manually. Thus, the throughput is not satisfactory for screening large numbers of candidate ligands. In this study, a technique to anchor protein crystals to mounting loops by using gel and inkjet technology has been developed; the method allows soaking of the mounted crystals in ligand-containing solution. This new technique may assist in the design of a fully automated drug-screening pipeline.

OPACs en Web: entre la tradición y la innovación = OPACs on the Web: Between tradition and innovation

Directory of Open Access Journals (Sweden)

Purificación Moscoso

2002-06-01

Full Text Available El desarrollo de Internet ha impulsado la implementación de OPACs en este entorno. Se analizan los cambios que estos nuevos OPACs suponen en cuanto a: estructura, gestión y mantenimiento del catálogo; sistemas de recuperación e interfaz del usuario. La pervivencia de prácticas tradicionales en la estructura y organización de la información impide que se les considere una herramienta innovadora. Se estudia la estructura de la base de datos, así como los principios tradicionales que rigen su elaboración. Se analizan las repercusiones que lleva consigo seguir utilizando reglas y formatos diseñados para un entorno manual que nada tiene que ver con el nuevo entorno tecnológico en el que hoy en día nos movemos = Internet development has driven the implementation of OPACs in that environment. Changes of these new OPACs as referred to catalog structure, management, and maintenance, retrieval systems and user interface are analyzed. The survival of traditional practices in the information structure and organization avoids them to be considered an innovative tool. The database structure is studied as well as the traditional principles that govern their elaboration. Effects of keeping using rules and formats designed for a manual environment, which is absolutely different from the present day technological environment are analyzed.

OPACs en Web: entre la tradición y la innovación OPACs on the Web: Between tradition and innovation

Directory of Open Access Journals (Sweden)

Purificación Moscoso

2002-06-01

Full Text Available El desarrollo de Internet ha impulsado la implementación de OPACs en este entorno. Se analizan los cambios que estos nuevos OPACs suponen en cuanto a: estructura, gestión y mantenimiento del catálogo; sistemas de recuperación e interfaz del usuario. La pervivencia de prácticas tradicionales en la estructura y organización de la información impide que se les considere una herramienta innovadora. Se estudia la estructura de la base de datos, así como los principios tradicionales que rigen su elaboración. Se analizan las repercusiones que lleva consigo seguir utilizando reglas y formatos diseñados para un entorno manual que nada tiene que ver con el nuevo entorno tecnológico en el que hoy en día nos movemos.Internet development has driven the implementation of OPACs in that environment. Changes of these new OPACs as referred to catalog structure, management, and maintenance, retrieval systems and user interface are analyzed. The survival of traditional practices in the information structure and organization avoids them to be considered an innovative tool. The database structure is studied as well as the traditional principles that govern their elaboration. Effects of keeping using rules and formats designed for a manual environment, which is absolutely different from the present day technological environment are analyzed.

Dialogue with an OPAC: How Visionary Was Swanson in 1964?

Science.gov (United States)

Su, Shiao-Feng

1994-01-01

Traces the development of online public access catalogs (OPACs) and compares what has occurred with a 1964 article that outlined recommendations for a future card catalog. Subject access is emphasized, including Library of Congress Subject Headings, expansion of OPACs, user-friendly interfaces, new technologies, and current visions of the future…

A Molecular Staple: D-Loops in the I Domain of Bacteriophage P22 Coat Protein Make Important Intercapsomer Contacts Required for Procapsid Assembly

Science.gov (United States)

D'Lima, Nadia G.

2015-01-01

ABSTRACT Bacteriophage P22, a double-stranded DNA (dsDNA) virus, has a nonconserved 124-amino-acid accessory domain inserted into its coat protein, which has the canonical HK97 protein fold. This I domain is involved in virus capsid size determination and stability, as well as protein folding. The nuclear magnetic resonance (NMR) solution structure of the I domain revealed the presence of a D-loop, which was hypothesized to make important intersubunit contacts between coat proteins in adjacent capsomers. Here we show that amino acid substitutions of residues near the tip of the D-loop result in aberrant assembly products, including tubes and broken particles, highlighting the significance of the D-loops in proper procapsid assembly. Using disulfide cross-linking, we showed that the tips of the D-loops are positioned directly across from each other both in the procapsid and the mature virion, suggesting their importance in both states. Our results indicate that D-loop interactions act as “molecular staples” at the icosahedral 2-fold symmetry axis and significantly contribute to stabilizing the P22 capsid for DNA packaging. IMPORTANCE Many dsDNA viruses have morphogenic pathways utilizing an intermediate capsid, known as a procapsid. These procapsids are assembled from a coat protein having the HK97 fold in a reaction driven by scaffolding proteins or delta domains. Maturation of the capsid occurs during DNA packaging. Bacteriophage HK97 uniquely stabilizes its capsid during maturation by intercapsomer cross-linking, but most virus capsids are stabilized by alternate means. Here we show that the I domain that is inserted into the coat protein of bacteriophage P22 is important in the process of proper procapsid assembly. Specifically, the I domain allows for stabilizing interactions across the capsid 2-fold axis of symmetry via a D-loop. When amino acid residues at the tip of the D-loop are mutated, aberrant assembly products, including tubes, are formed instead

First cytoplasmic loop of glucagon-like peptide-1 receptor can function at the third cytoplasmic loop position of rhodopsin.

Science.gov (United States)

Yamashita, Takahiro; Tose, Koji; Shichida, Yoshinori

2008-01-01

G protein-coupled receptors (GPCRs) are classified into several families based on their amino acid sequences. In family 1, GPCRs such as rhodopsin and adrenergic receptor, the structure-function relationship has been extensively investigated to demonstrate that exposure of the third cytoplasmic loop is essential for selective G protein activation. In contrast, much less is known about other families. Here we prepared chimeric mutants between Gt-coupled rhodopsin and Gi/Go- and Gs-coupled glucagon-like peptide-1 (GLP-1) receptor of family 2 and tried to identify the loop region that functions at the third cytoplasmic loop position of rhodopsin. We succeeded in expressing a mutant having the first cytoplasmic loop of GLP-1 receptor and found that this mutant activated Gi and Go efficiently but did not activate Gt. Moreover, the rhodopsin mutant having the first loop of Gs-coupled secretin receptor of family 2 decreased the Gi and Go activation efficiencies. Therefore, the first loop of GLP-1 receptor would share a similar role to the third loop of rhodopsin in G protein activation. This result strongly suggested that different families of GPCRs have maintained molecular architectures of their ancestral types to generate a common mechanism, namely exposure of the cytoplasmic loop, to activate peripheral G protein.

Use of Fourier-Domain Optical Coherence Tomography to Evaluate Anterior Stromal Opacities in Donor Corneas

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Matthew R. Bald

2013-01-01

Full Text Available Purpose. To evaluate Fourier-domain optical coherence tomography (FD-OCT as an adjunct to traditional slit lamp examination of donor corneas with suspected Anterior Stromal Opacities. Methods. Seven corneas suspected of having anterior stromal opacities by slit lamp examination were evaluated with FD-OCT. Each cornea was evaluated to confirm the presence of opacity and, if present, the depth of opacity was measured. Results. The opacity depth ranged from 82 μm to 624 μm. The initial slit lamp impressions of five of the seven corneas were confirmed by OCT. In two corneas, the OCT findings were different from the initial slit lamp impressions. Slit lamp examination of the first cornea gave the impression of anterior stromal scarring, but OCT showed that the opacity was limited to the epithelium. Slit lamp examination of the second cornea suggested opacity limited to the epithelium, but OCT identified significant sub-Bowman's scarring. In all cases, the Eye Bank Technicians reported that the location and depth of corneal opacity were more sharply defined by OCT than by slit lamp. Conclusion. The high resolution of OCT makes it easier to determine the location of corneal opacities compared to slit lamp examinations. This enhanced visualization can improve decisions regarding transplant suitability of donor corneas.

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.

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.

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.

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

Science.gov (United States)

Nagayama, Taisuke

2017-10-01

Model predictions for iron opacity are notably different from measurements performed at matter conditions similar to the boundary between the solar radiation and convection zones. The calculated iron opacities have narrower spectral lines, weaker quasi-continuum at short wavelength, and deeper opacity windows than the measurements. If correct, these measurements help resolve a decade old problem in solar physics. A key question is therefore: What is responsible for the model-data discrepancy? The answer is complex because the experiments are challenging and opacity theories depend on multiple entangled physical processes such as the influence of completeness and accuracy of atomic states, line broadening, contributions from myriad transitions from excited states, and multi-photon absorption processes. To help determine the cause of this discrepancy, a systematic study of opacity variation with temperature, density, and atomic number is underway. Measurements of chromium, iron, and nickel opacities have been performed at two different temperatures and densities. The collection of measured opacities provides constraints on hypotheses to explain the discrepancy. We will discuss implications of measured opacities, experimental errors, and possible opacity model refinements. Sandia National Laboratories is a multi-mission laboratory managed and operated by National Technology and Engineering Solutions of Sandia, LLC., a wholly owned subsidiary of Honeywell International, Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525.

Neutrino opacities and the pasta phase structure

International Nuclear Information System (INIS)

Menezes, D.P.; Alloy, M.D.

2011-01-01

The diffusion coefficients that are related to the neutrino opacities are calculated in such a way that the formation of nuclear pasta and homogeneous matter at low densities are taken into account. Two methods are developed to build the pasta phase and their differences are outlined. One of them is chosen as part of a complete equation of state used in the calculation of the diffusion coefficients. Our results show that the mean free paths are significantly altered by the presence of nuclear pasta in stellar matter when compared with the results obtained with pure homogeneous matter. These differences in neutrino opacities will have consequences in the calculation of the Kelvin-Helmholtz phase of protoneutron stars. (author)

Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs.

Science.gov (United States)

Regad, Leslie; Martin, Juliette; Camproux, Anne-Claude

2011-06-20

One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet), which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i) ubiquitous motifs, shared by several superfamilies and (ii) superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P) and SAH/SAM. Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.

Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs

Directory of Open Access Journals (Sweden)

Martin Juliette

2011-06-01

Full Text Available Abstract Background One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Results Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet, which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i ubiquitous motifs, shared by several superfamilies and (ii superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P and SAH/SAM. Conclusions Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.

Nuclear 'pasta phase' and its consequences on neutrino opacities

International Nuclear Information System (INIS)

Alloy, M. D.; Menezes, D. P.

2011-01-01

In this paper, we calculate the diffusion coefficients that are related to the neutrino opacities considering the formation of nuclear pasta and homogeneous matter at low densities. Our results show that the mean-free paths are significantly altered by the presence of nuclear pasta in stellar matter when compared with the results obtained with homogeneous matter. These differences in neutrino opacities certainly influence the Kelvin-Helmholtz phase of protoneutron stars and consequently the results of supernova explosion simulations.

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.

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

KAUST Repository

Maadooliat, Mehdi; Zhou, Lan; Najibi, Seyed Morteza; Gao, Xin; Huang, Jianhua Z.

2015-01-01

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.

Presenting a model for display and user interface specifications of web based OPACs on the basis of available universal standards and experts views in order to compare the Iranian library and information centers OPACs

OpenAIRE

Zavaraqi, Rasoul

2005-01-01

The aim of this study is to present a model for display and user interface specifications of web-based OPACs on the basis of available universal standards and experts’ views in order to compare the present Iranian library and information centers OPACs. Three method were used for data collection in this research: literature review, survey of opinions by means of a checklist, and evaluation of the available web-based OPACs. The community of Iranian experts in OPAC issues and all of 6 available ...

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.

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

A fully blanketed early B star LTE model atmosphere using an opacity sampling technique

International Nuclear Information System (INIS)

Phillips, A.P.; Wright, S.L.

1980-01-01

A fully blanketed LTE model of a stellar atmosphere with Tsub(e) = 21914 K (thetasub(e) = 0.23), log g = 4 is presented. The model includes an explicit representation of the opacity due to the strongest lines, and uses a statistical opacity sampling technique to represent the weaker line opacity. The sampling technique is subjected to several tests and the model is compared with an atmosphere calculated using the line-distribution function method. The limitations of the distribution function method and the particular opacity sampling method used here are discussed in the light of the results obtained. (author)

A complex approach to the blue-loop problem

Science.gov (United States)

Ostrowski, Jakub; Daszynska-Daszkiewicz, Jadwiga

2015-08-01

The problem of the blue loops during the core helium burning, outstanding for almost fifty years, is one of the most difficult and poorly understood problems in stellar astrophysics. Most of the work focused on the blue loops done so far has been performed with old stellar evolution codes and with limited computational resources. In the end the obtained conclusions were based on a small sample of models and could not have taken into account more advanced effects and interactions between them.The emergence of the blue loops depends on many details of the evolution calculations, in particular on chemical composition, opacity, mixing processes etc. The non-linear interactions between these factors contribute to the statement that in most cases it is hard to predict without a precise stellar modeling whether a loop will emerge or not. The high sensitivity of the blue loops to even small changes of the internal structure of a star yields one more issue: a sensitivity to numerical problems, which are common in calculations of stellar models on advanced stages of the evolution.To tackle this problem we used a modern stellar evolution code MESA. We calculated a large grid of evolutionary tracks (about 8000 models) with masses in the range of 3.0 - 25.0 solar masses from the zero age main sequence to the depletion of helium in the core. In order to make a comparative analysis, we varied metallicity, helium abundance and different mixing parameters resulting from convective overshooting, rotation etc.The better understanding of the properties of the blue loops is crucial for our knowledge of the population of blue supergiants or pulsating variables such as Cepheids, α-Cygni or Slowly Pulsating B-type supergiants. In case of more massive models it is also of great importance for studies of the progenitors of supernovae.

Experimental investigation of opacity models for stellar interior, inertial fusion, and high energy density plasmas

International Nuclear Information System (INIS)

Bailey, J. E.; Rochau, G. A.; Mancini, R. C.; Iglesias, C. A.; MacFarlane, J. J.; Golovkin, I. E.; Blancard, C.; Cosse, Ph.; Faussurier, G.

2009-01-01

Theoretical opacities are required for calculating energy transport in plasmas. In particular, understanding stellar interiors, inertial fusion, and Z pinches depends on the opacities of mid-atomic-number elements over a wide range of temperatures. The 150-300 eV temperature range is particularly interesting. The opacity models are complex and experimental validation is crucial. For example, solar models presently disagree with helioseismology and one possible explanation is inadequate theoretical opacities. Testing these opacities requires well-characterized plasmas at temperatures high enough to produce the ion charge states that exist in the sun. Typical opacity experiments heat a sample using x rays and measure the spectrally resolved transmission with a backlight. The difficulty grows as the temperature increases because the heating x-ray source must supply more energy and the backlight must be bright enough to overwhelm the plasma self-emission. These problems can be overcome with the new generation of high energy density (HED) facilities. For example, recent experiments at Sandia's Z facility [M. K. Matzen et al., Phys. Plasmas 12, 055503 (2005)] measured the transmission of a mixed Mg and Fe plasma heated to 156±6 eV. This capability will also advance opacity science for other HED plasmas. This tutorial reviews experimental methods for testing opacity models, including experiment design, transmission measurement methods, accuracy evaluation, and plasma diagnostics. The solar interior serves as a focal problem and Z facility experiments illustrate the techniques.

Ultra-dense hot low Z line transition opacity simulations

International Nuclear Information System (INIS)

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

2002-01-01

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

CD-loop Extension in Zika Virus Envelope Protein Key for Stability and Pathogenesis.

Science.gov (United States)

Gallichotte, Emily N; Dinnon, Kenneth H; Lim, Xin-Ni; Ng, Thiam-Seng; Lim, Elisa X Y; Menachery, Vineet D; Lok, Shee-Mei; Baric, Ralph S

2017-12-05

With severe disease manifestations including microcephaly, congenital malformation, and Guillain-Barré syndrome, Zika virus (ZIKV) remains a persistent global public health threat. Despite antigenic similarities with dengue viruses, structural studies have suggested the extended CD-loop and hydrogen-bonding interaction network within the ZIKV envelope protein contribute to stability differences between the viral families. This enhanced stability may lead to the augmented infection, disease manifestation, and persistence in body fluids seen following ZIKV infection. To examine the role of these motifs in infection, we generated a series of ZIKV recombinant viruses that disrupted the hydrogen-bonding network (350A, 351A, and 350A/351A) or the CD-loop extension (Δ346). Our results demonstrate a key role for the ZIKV extended CD-loop in cell-type-dependent replication, virion stability, and in vivo pathogenesis. Importantly, the Δ346 mutant maintains similar antigenicity to wild-type virus, opening the possibility for its use as a live-attenuated vaccine platform for ZIKV and other clinically relevant flaviviruses. © The Author(s) 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

Dimerization of the docking/adaptor protein HEF1 via a carboxy-terminal helix-loop-helix domain.

Science.gov (United States)

Law, S F; Zhang, Y Z; Fashena, S J; Toby, G; Estojak, J; Golemis, E A

1999-10-10

HEF1, p130(Cas), and Efs define a family of multidomain docking proteins which plays a central coordinating role for tyrosine-kinase-based signaling related to cell adhesion. HEF1 function has been specifically implicated in signaling pathways important for cell adhesion and differentiation in lymphoid and epithelial cells. While the SH3 domains and SH2-binding site domains (substrate domains) of HEF1 family proteins are well characterized and binding partners known, to date the highly conserved carboxy-terminal domains of the three proteins have lacked functional definition. In this study, we have determined that the carboxy-terminal domain of HEF1 contains a divergent helix-loop-helix (HLH) motif. This motif mediates HEF1 homodimerization and HEF1 heterodimerization with a recognition specificity similar to that of the transcriptional regulatory HLH proteins Id2, E12, and E47. We had previously demonstrated that the HEF1 carboxy-terminus expressed as a separate domain in yeast reprograms cell division patterns, inducing constitutive pseudohyphal growth. Here we show that pseudohyphal induction by HEF1 requires an intact HLH, further supporting the idea that this motif has an effector activity for HEF1, and implying that HEF1 pseudohyphal activity derives in part from interactions with yeast helix-loop-helix proteins. These combined results provide initial insight into the mode of function of the HEF1 carboxy-terminal domain and suggest that the HEF1 protein may interact with cellular proteins which control differentiation. Copyright 1999 Academic Press.

Ground-glass opacity in lung metastasis from adenocarcinoma of the stomach: a case report

International Nuclear Information System (INIS)

Jung, Mi Ran; Kim, Jeong Kon; Lee, Jin Seong; Song, Koun Sik; Lim, Tae Hwan

2000-01-01

Ground-glass opacity is a frequent but nonspecific finding seen on high-resolution CT scans of lung parenchyma. Histologically, this appearance is observed when thickening of the alveolar wall and septal interstitium is minimal or the alveolar lumen is partially filled with fluid, macrophage, neutrophils, or amorphous material. It has been shown that ground-glass opacity may be caused not only by an active inflammatory process but also by fibrotic processes. When a focal area of ground-glass opacity persists or increases in size, the possibility of neoplasm-bronchioloalveolar carcinoma or adenoma, or lymphoma, for example, should be considered. Diffuse nonsegmental ground-glass opacity in both lung fields was incidentally found on follow up abdominal CT in a stomach cancer patient and signet-ring cell-type metastatic lung cancer was confirmed by transbronchial lung biopsy. We report a case of diffuse ground-glass opacity seen in metastatic lung cancer from adenocarcinoma of the stomach. (author)

Target simulations with SCROLL non-LTE opacity/emissivity databases.

Science.gov (United States)

Klapisch, M.; Colombant, D.; Bar-Shalom, A.

2001-10-01

SCROLL[1], a collisional radiative model and code based on superconfigurations, is able to compute high Z non-LTE opacities and emissivities accurately and efficiently. It was used to create opacity/emissivity databases for Pd, Lu, Au on a 50 temperatures/80 densities grid. Incident radiation field was shown to have no effect on opacities in the case of interest, and was not taken into account. These databases were introduced in the hydrocode FAST1D[2]. SCROLL also gives an ionization temperature Tz which is used in FAST1D to obtain non-LTE corrections to the equation of state. Results will be compared to those of a previous version using Busquet’s algorithm[3]. Work supported by USDOE under a contract with NRL. [1] A. Bar-Shalom, J. Oreg and M. Klapisch, J. Quant. Spectrosc. Radiat. Transfer, 65, 43(2000). [2] J. H. Gardner, A. J. Schmitt, J. P. Dahlburg, C. J. Pawley, S. E. Bodner, S. P. Obenschain, V. Serlin and Y. Aglitskiy, Phys. Plasmas, 5, 1935 (1998). [3] M. Busquet, Phys. Fluids B, 5, 4191 (1993).

Time Patterns in Remote OPAC Use.

Science.gov (United States)

Lucas, Thomas A.

1993-01-01

Describes a transaction log analysis of the New York Public Library research libraries' OPAC (online public access catalog). Much of the remote searching occurred when the libraries were closed and was more evenly distributed than internal searching, demonstrating that remote searching could expand access and reduce peak system loads. (Contains…

The effect of Livermore OPAL opacities on the evolutionary masses of RR Lyrae stars

Science.gov (United States)

Yi, Sukyoung; Lee, Young-Wook; Demarque, Pierre

1993-01-01

We have investigated the effect of the new Livermore OPAL opacities on the evolution of horizontal-branch (HB) stars. This work was motivated by the recent stellar pulsation calculations using the new Livermore opacities, which suggest that the masses of double-mode RR Lyrae stars are 0.1-0.2 solar mass larger than those based on earlier opacities. Unlike the pulsation calculations, we find that the effect of opacity change on the evolution of HB stars is not significant. In particular, the effect of the mean masses of RR Lyrae stars is very small, showing a decrease of only 0.01-0.02 solar mass compared to the models based on old Cox-Stewart opacities. Consequently, with the new Livermore OPAL opacities, both the stellar pulsation and evolution models now predict approximately the same masses for the RR Lyrae stars. Our evolutionary models suggest that the mean masses of the RR Lyrae stars are about 0.76 and about 0.71 solar mass for M15 (Oosterhoff group II) and M3 (group I), respectively. If (alpha/Fe) = 0.4, these values are decreased by about 0.03 solar mass. Variations of the mean masses of RR Lyrae stars with HB morphology and metallicity are also presented.

Development on the National Ignition Facility of a High Energy Density Opacity Platform

Energy Technology Data Exchange (ETDEWEB)

Perry, Theodore Sonne [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Dodd, Evan S. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); DeVolder, Barbara Gloria [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Johns, Heather Marie [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Cardenas, Tana [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Archuleta, Thomas Nick [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Kline, John L. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Flippo, Kirk Adler [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Vinyard, Natalia Sergeevna [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Sherrill, Manolo Edgar [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Wilde, Bernhard Heinz [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Tregillis, Ian Lee [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Urbatsch, Todd James [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Douglas, Melissa Rae [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Heeter, R. F. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Liedahl, D. A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Wilson, B. G. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Iglesias, C. A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Schneider, M. B. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Martin, M. E. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); London, R. A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Ahmed, M. F. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Thompson, N. B. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Emig, J. A. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Zika, M. R. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Opachich, Y. P. [Nevada National Security Site (NNSS), NV (United States); King, J. A. [Nevada National Security Site (NNSS), NV (United States); Ross, P. W. [Nevada National Security Site (NNSS), NV (United States); Huffman, E. J. [Nevada National Security Site (NNSS), NV (United States); Knight, R. A. [Nevada National Security Site (NNSS), NV (United States); Koch, J. A. [Nevada National Security Site (NNSS), NV (United States); Pond, T. D. [Nevada National Security Site (NNSS), NV (United States); Craxton, R. S. [Univ. of Rochester, NY (United States). Lab. for Laser Energetics; Zhang, R. [Univ. of Rochester, NY (United States). Lab. for Laser Energetics; McKenty, P. W. [Univ. of Rochester, NY (United States). Lab. for Laser Energetics; Garcia, E. M. [Univ. of Rochester, NY (United States). Lab. for Laser Energetics; Bailey, J. E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Rochau, G. A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Hansen, S. B. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

2017-10-02

X-ray opacity is a crucial factor in all radiation-hydrodynamics calculations, yet it is one of the least validated of the material properties in simulation codes for high-energy-density plasmas. Recent opacity experiments at the Sandia Z-machine have shown up to factors of two discrepancies between theory and experiment for various mid-Z elements (Fe, Cr, Ni). These discrepancies raise doubts regarding the accuracy of the opacity models which are used in ICF and stewardship as well as in astrophysics. Therefore, a new experimental opacity platform has been 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. Within the context of the national opacity strategy, the first NIF experiments were directed towards measuring the opacity of iron at a temperature of ~160 eV and an electron density of ~7xl021 cm-3(Anchor 1). The Z data agree with theory at these conditions, providing a reference point for validation of the NIF platform. Development shots on NIF have demonstrated the ability to create a sufficiently bright point backlighter using an imploding plastic capsule, and also a combined hohlraum, sample and laser drive able to produce iron plasmas at the desired conditions. Spectrometer qualification has been completed, albeit with additional improvements planned, and the first iron absorption spectra have now been obtained.

Detailed-term-accounting approximation calculations of the radiative opacity of aluminum plasmas: A systematic study

International Nuclear Information System (INIS)

Zeng Jiaolong; Yuan Jianmin

2002-01-01

The spectrally resolved radiative opacity and the Rosseland and Planck mean opacities are calculated by using the detailed-term-accounting approximation for aluminum plasmas with varieties of density and temperature. The results are presented along a 40 eV isothermal sequence, a 0.01 g/cm 3 isodense sequence, and a sequence with average ionization degree Z*∼7.13. Particular attention is given to the influence of the detailed treatment of spectral lines on the Rosseland mean opacity under different thermodynamical conditions. The results show that at densities of 0.004 g/cm 3 and higher, the opacities are not very sensitive to the spectral linewidth within a reasonable range. As examples, the Rosseland mean opacity, which is most sensitive to the detailed linewidth, at 40 eV and 0.004 g/cm 3 changes no more than 15%, when we change the electron impact spectral linewidth artificially by reducing it by 50% or increasing it twice, and at 40 eV and 0.1 g/cm 3 it changes less than 5%. For comparison, we also carried out calculations by using an average atom model. For the Rosseland mean opacities, the two models show quite large differences, in particular at low densities, while for the Planck mean opacities the results of the two models are much closer

Diagnostic performance of qualitative shear-wave elastography according to different color map opacities for breast masses.

Science.gov (United States)

Kim, Hana; Youk, Ji Hyun; Gweon, Hye Mi; Kim, Jeong-Ah; Son, Eun Ju

2013-08-01

To compare the diagnostic performance of qualitative shear-wave elastography (SWE) according to three different color map opacities for breast masses 101 patients aged 21-77 years with 113 breast masses underwent B-mode US and SWE under three different color map opacities (50%, 19% and 100%) before biopsy or surgery. Following SWE features were reviewed: visual pattern classification (pattern 1-4), color homogeneity (Ehomo) and six-point color score of maximum elasticity (Ecol). Combined with B-mode US and SWE, the likelihood of malignancy (LOM) was also scored. The area under the curve (AUC) was obtained by ROC curve analysis to assess the diagnostic performance under each color opacity. A visual color pattern, Ehomo, Ecol and LOM scoring were significantly different between benign and malignant lesions under all color opacities (Pbreast lesion under all color opacities. The difference in color map opacity did not significantly influence diagnostic performance of SWE. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Diagnostic performance of qualitative shear-wave elastography according to different color map opacities for breast masses

Energy Technology Data Exchange (ETDEWEB)

Kim, Hana; Youk, Ji Hyun, E-mail: jhyouk@yuhs.ac; Gweon, Hye Mi; Kim, Jeong-Ah; Son, Eun Ju

2013-08-15

Purpose: To compare the diagnostic performance of qualitative shear-wave elastography (SWE) according to three different color map opacities for breast masses Materials and methods: 101 patients aged 21–77 years with 113 breast masses underwent B-mode US and SWE under three different color map opacities (50%, 19% and 100%) before biopsy or surgery. Following SWE features were reviewed: visual pattern classification (pattern 1–4), color homogeneity (E{sub homo}) and six-point color score of maximum elasticity (E{sub col}). Combined with B-mode US and SWE, the likelihood of malignancy (LOM) was also scored. The area under the curve (AUC) was obtained by ROC curve analysis to assess the diagnostic performance under each color opacity. Results: A visual color pattern, E{sub homo}, E{sub col} and LOM scoring were significantly different between benign and malignant lesions under all color opacities (P < 0.001). For 50% opacity, AUCs of visual color pattern, E{sub col}, E{sub homo} and LOM scoring were 0.902, 0.951, 0.835 and 0.975. But, for each SWE feature, there was no significant difference in the AUC among three different color opacities. For all color opacities, visual color pattern and E{sub col} showed significantly higher AUC than E{sub homo}. In addition, a combined set of B-mode US and SWE showed significantly higher AUC than SWE alone for color patterns, E{sub homo}, but no significant difference was found in E{sub col}. Conclusion: Qualitative SWE was useful to differentiate benign from malignant breast lesion under all color opacities. The difference in color map opacity did not significantly influence diagnostic performance of SWE.

Diagnostic performance of qualitative shear-wave elastography according to different color map opacities for breast masses

International Nuclear Information System (INIS)

Kim, Hana; Youk, Ji Hyun; Gweon, Hye Mi; Kim, Jeong-Ah; Son, Eun Ju

2013-01-01

Purpose: To compare the diagnostic performance of qualitative shear-wave elastography (SWE) according to three different color map opacities for breast masses Materials and methods: 101 patients aged 21–77 years with 113 breast masses underwent B-mode US and SWE under three different color map opacities (50%, 19% and 100%) before biopsy or surgery. Following SWE features were reviewed: visual pattern classification (pattern 1–4), color homogeneity (E homo ) and six-point color score of maximum elasticity (E col ). Combined with B-mode US and SWE, the likelihood of malignancy (LOM) was also scored. The area under the curve (AUC) was obtained by ROC curve analysis to assess the diagnostic performance under each color opacity. Results: A visual color pattern, E homo , E col and LOM scoring were significantly different between benign and malignant lesions under all color opacities (P < 0.001). For 50% opacity, AUCs of visual color pattern, E col , E homo and LOM scoring were 0.902, 0.951, 0.835 and 0.975. But, for each SWE feature, there was no significant difference in the AUC among three different color opacities. For all color opacities, visual color pattern and E col showed significantly higher AUC than E homo . In addition, a combined set of B-mode US and SWE showed significantly higher AUC than SWE alone for color patterns, E homo , but no significant difference was found in E col . Conclusion: Qualitative SWE was useful to differentiate benign from malignant breast lesion under all color opacities. The difference in color map opacity did not significantly influence diagnostic performance of SWE

The relationship between elastomer opacity, colorimeter beam size, and measured colorimetric response.

Science.gov (United States)

Rugh, E H; Johnston, W M; Hesse, N S

1991-01-01

The effect of opacity on the colorimetric responses of large-area and small-area colorimeters was determined using an elastomer intended for maxillofacial prosthetics use and containing various pigments at different concentrations. Opacity was determined by calculating the contrast ratio of 2-mm-thick specimens against black and white backings, using Kubelka-Munk analyses to correct for thickness and backing color variations. The measure of comparison of the two colorimeters was the relative difference in tristimulus reflectance, with the tristimulus reflectance of the large-area colorimeter as the basis of the relative difference. A significant quadratic relationship was found between contrast ratio and the relative difference in tristimulus reflectance. This relationship may be used to describe opacity without the need to make optical observations or measurements of a thin layer of material on contrasting backings. The small-area colorimeter produced color parameters that are a measure of the combined effects of both color and opacity. The importance of beam size considerations of optical measuring devices for translucent natural and prosthetic materials was emphasized.

Web-based OPACs: Between Tradition and Innovation.

Science.gov (United States)

Moscoso, Purificacion; Ortiz-Repiso, Virginia

1999-01-01

Analyzes the change that Internet-based OPACs (Online Public Access Catalogs) have represented to the structure, administration, and maintenance of the catalogs, retrieval systems, and user interfaces. Examines the structure of databases and traditional principles that have governed systems development. Discusses repercussions of the application…

Comparison of Fe and Ni opacity calculations for a better understanding of pulsating stellar envelopes

International Nuclear Information System (INIS)

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

2011-01-01

Opacity is an important ingredient of the evolution of stars. The calculation of opacity coefficients is complicated by the fact that the plasma contains partially ionized heavy ions that contribute to opacity dominated by H and He. Up to now, the astrophysical community has greatly benefited from the work of the contributions of Los Alamos, Livermore and the Opacity Project (OP). However unexplained differences of up to 50% in the radiative forces and Rosseland mean values for Fe have been noticed for conditions corresponding to stellar envelopes. Such uncertainty has a real impact on the understanding of pulsating stellar envelopes, on the excitation of modes, and on the identification of the mode frequencies. Temperature and density conditions equivalent to those found in stars can now be produced in laboratory experiments for various atomic species. Recently the photo-absorption spectra of nickel and iron plasmas have been measured during the LULI 2010 campaign, for temperatures between 15 and 40 eV and densities of similar to 3 mg/cm 3 . A large theoretical collaboration, the 'OPAC', has been formed to prepare these experiments. We present here the set of opacity calculations performed by eight different groups for conditions relevant to the LULI 2010 experiment and to astrophysical stellar envelope conditions. (authors)

Recent status and supplementary review of lenticular opacities in proximally exposed A-bomb survivors

Energy Technology Data Exchange (ETDEWEB)

Sugimoto, S [Sugimoto Ophthalmic Hospital, Hiroshima (Japan)

1978-04-01

A review was made on the progress of lenticular opacities in proximally exposed A-bomb survivors on the basis of three experimental cases. A-bomb cataract is the first late effect of A-bomb radiation which appeared in A-bomb survivors and is the only disorder which can still be visualized at the present time. We have therefore continued to use this as one major evidence that A-bomb injuries have not been cured in spite of our for a complete ban of nuclear weapons. According to the findings of lenticular opacities of typical A-bomb cataract observed in experimental cases, there was in some cases after a latent period progression of opacities from several years to more than 10 years followed by a gradual decrease in opacities, whereas in some cases there was after a latent period a remarkable progress in opacities for several years followed by a marked decrease in the lesions. At the present time there is no evidence of progression and it appears that the progression has ceased. Incipient senile cataract which developed concurrently has completely no transitional relationship to A-bomb cataract and appears to progress slowly but steadily.

Recent status and supplementary review of lenticular opacities in proximally exposed A-bomb survivors

International Nuclear Information System (INIS)

Sugimoto, Shigenori

1978-01-01

A review was made on the progress of lenticular opacities in proximally exposed A-bomb survivors on the basis of three experimental cases. A-bomb cataract is the first late effect of A-bomb radiation which appeared in A-bomb survivors and is the only disorder which can still be visualized at the present time. We have therefore continued to use this as one major evidence that A-bomb injuries have not been cured in spite of our for a complete ban of nuclear weapons. According to the findings of lenticular opacities of typical A-bomb cataract observed in experimental cases, there was in some cases after a latent period progression of opacities from several years to more than 10 years followed by a gradual decrease in opacities, whereas in some cases there was after a latent period a remarkable progress in opacities for several years followed by a marked decrease in the lesions. At the present time there is no evidence of progression and it appears that the progression has ceased. Incipient senile cataract which developed concurrently has completely no transitional relationship to A-bomb cataract and appears to progress slowly but steadily. (auth.)

IRON OPACITY BUMP CHANGES THE STABILITY AND STRUCTURE OF ACCRETION DISKS IN ACTIVE GALACTIC NUCLEI

Energy Technology Data Exchange (ETDEWEB)

Jiang, Yan-Fei [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Davis, Shane W. [Department of Astronomy, University of Virginia, P.O. Box 400325, Charlottesville, VA 22904-4325 (United States); Stone, James M. [Department of Astrophysical Sciences, Princeton University, Princeton, NJ 08544 (United States)

2016-08-10

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 × 10{sup 8} 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.

Models for the computation of opacity of mixtures

International Nuclear Information System (INIS)

Klapisch, Marcel; Busquet, Michel

2013-01-01

We compare four models for the partial densities of the components of mixtures. These models yield different opacities as shown on polystyrene, acrylic and polyimide in local thermodynamical equilibrium (LTE). Two of these models, the ‘whole volume partial pressure’ model (M1) and its modification (M2) are not thermodynamically consistent (TC). The other two models are TC and minimize free energy. M3, the ‘partial volume equal pressure’ model, uses equality of chemical potential. M4 uses commonality of free electron density. The latter two give essentially identical results in LTE, but M4’s convergence is slower. M4 is easily generalized to non-LTE conditions. Non-LTE effects are shown by the variation of the Planck mean opacity of the mixtures with temperature and density. (paper)

Free-free opacity in dense plasmas with an average atom model

International Nuclear Information System (INIS)

Shaffer, Nathaniel R.; Ferris, Natalie G.; Colgan, James Patrick; Kilcrease, David Parker; Starrett, Charles Edward

2017-01-01

A model for the free-free opacity of dense plasmas is presented. The model uses a previously developed average atom model, together with the Kubo-Greenwood model for optical conductivity. This, in turn, is used to calculate the opacity with the Kramers-Kronig dispersion relations. Furthermore, comparisons to other methods for dense deuterium results in excellent agreement with DFT-MD simulations, and reasonable agreement with a simple Yukawa screening model corrected to satisfy the conductivity sum rule.

OPAC systému ALEPH

OpenAIRE

Pačísková, Jana

2010-01-01

This bachelor thesis presents analysis and evaluation of online catalog of integrated library system ALEPH, which was made after studying Web OPAC manual of this system and gathering information from practical testing of catalogs of National Library of Czech Republic and Regional Library of Karlovy Vary. In the first chapter, there is introduced and defined Online Public Access Catalog and its main principles and also its history is presented. In next chapters, there are described features an...

An Alternative to EPA Method 9 -- Field Validation of the Digital Opacity Compliance System (DOCS)

National Research Council Canada - National Science Library

Rasmussen, Steve L; Stone, Daniel A

2005-01-01

The Digital Opacity Compliance System (DOCS) software translates images from a commercial digital camera into visual plume opacity measurements, and is proposed as an alternate reporting method to EPA Method 9...

Opacity of financial information, adoption of international standards and legal origins

Directory of Open Access Journals (Sweden)

Renata Turola Takamatsu

2017-10-01

Full Text Available Purpose – The goal of this study was to investigate the relationship between the level of Earnings Opacity and a company’s informational environment, specifically considering accounting standards and the legal origins of the system. Design/methodology/approach – The sample consisted of publicly traded companies from 20 countries classified as emerging, based on agency Standard & Poor’s index. The sample included data from 2004 to 2013. In order to compare the indicators among the group of countries, taking into account their institutional characteristics, the Mann-Whitney test and the Kruskal-Wallis test were performed. Findings – The assessment of the informational environment measures’ behavior in emerging countries revealed that these measures were correlated, suggesting that, despite different behaviors, opacity proxies share information. The fact that earnings opacity was lower in countries that had already adopted international standards during the analyzed period was also observed. In the same sense, a higher level of income smoothing was detected in countries of French code law origins. Originality/value – This article contributes to the understanding of the relationship between the characteristics of an accounting informational environment and the levels of opacity of the information emitted by accounting. Thus, this article has helped managers, investors and regulators to understand users’ needs and how country-specific characteristics change their perspectives.

Lens opacities in children of Belarus affected by the Chernobyl accident

Energy Technology Data Exchange (ETDEWEB)

Arinchin, A.N.; Ospennikova, L.A. [Research Clinical Institute of Radiation Medicine and Endocrinology, Ministry of Health, Republic of Belarus, Aksakovschina, Minsk (Belarus)

1998-03-01

Reports about the increase in cataracts among the Ukrainian population living in the region of the Chernobyl Atomic Power Plant have been met with certain skepticism. At the same time, American specialists do not exclude the possibility of radiation genesis of lensopathias revealed among the citizens of Ukraine at the result of complex joint clinic-epidemiological study conducted by American and Ukrainian specialists in 1991. The aim of the investigation was to study the frequency and character of lens opacities in children permanently residing in the contaminated territories of the Republic of Belarus with anomalous high coefficients of {sup 137}Cs radionuclides through the food chain. It is well known that radiation cataract is one of the direct effects of ionizing radiation. Organ of sight is highly radiosensitive. The most radio-vulnerable part of eye is lens in which cataract is developing in response to both external and internal exposure. In children, focal lens opacities are localized in embryonic nucleus, but in elderly people, alongside with embryonic nucleus, they are also localized in adult nucleus and cortical layers. Lens opacity is the result of biochemical changes occurring in it, and it is caused by lens fibers damage. Frequency of occurrence of lensopathias in children from the main group made 82.1% which is by 12.5% more than in the control, mostly due to opacities in both lenses. (J.P.N.)

Lens opacities in children of Belarus affected by the Chernobyl accident

International Nuclear Information System (INIS)

Arinchin, A.N.; Ospennikova, L.A.

1998-01-01

Reports about the increase in cataracts among the Ukrainian population living in the region of the Chernobyl Atomic Power Plant have been met with certain skepticism. At the same time, American specialists do not exclude the possibility of radiation genesis of lensopathias revealed among the citizens of Ukraine at the result of complex joint clinic-epidemiological study conducted by American and Ukrainian specialists in 1991. The aim of the investigation was to study the frequency and character of lens opacities in children permanently residing in the contaminated territories of the Republic of Belarus with anomalous high coefficients of 137 Cs radionuclides through the food chain. It is well known that radiation cataract is one of the direct effects of ionizing radiation. Organ of sight is highly radiosensitive. The most radio-vulnerable part of eye is lens in which cataract is developing in response to both external and internal exposure. In children, focal lens opacities are localized in embryonic nucleus, but in elderly people, alongside with embryonic nucleus, they are also localized in adult nucleus and cortical layers. Lens opacity is the result of biochemical changes occurring in it, and it is caused by lens fibers damage. Frequency of occurrence of lensopathias in children from the main group made 82.1% which is by 12.5% more than in the control, mostly due to opacities in both lenses. (J.P.N.)

Large Enhancement in High-Energy Photoionization of Fe XVII and Missing Continuum Plasma Opacity

Science.gov (United States)

Nahar, Sultana N.; Pradhan, Anil K.

2016-06-01

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 photoexcitations not heretofore considered. In extensive R -matrix calculations of unprecedented complexity for an important iron ion Fe xvii (Fe16 + ), with a wave function expansion of 99 Fe xviii (Fe17 + ) LS core states from n ≤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.

Effects of adhesive used as modeling liquid on the stability of the color and opacity of composites.

Science.gov (United States)

Araujo, Fernanda Santos; Barros, Mellany Cristie Ramos; Santana, Márcia Luciana Carregosa; de Jesus Oliveira, Ludmila Smith; Silva, Paula Fernanda Damasceno; Lima, Giana da Silveira; Faria-E-Silva, André Luis

2018-04-01

This study evaluated the effects of adhesive type used as modeling liquid on the stability of the color and opacity of composites submitted to thermal cycling in staining solutions followed by a bleaching procedure. Thirty cylinder-shaped composite specimens (10 mm diameter × 1.5 mm thickness) were built using or not using (control) an adhesive (Adper Universal or Scotchbond Multipurpose) as the modeling liquid. After polishing procedures, the color and opacity were measured, and the specimens were submitted to 200 thermal cycles with 10 s of dwell time in baths of grape juice at 5°C, water at 37°C, and coffee at 55°C. Changes in opacity and color caused by the staining solutions were measured. Then, the specimens were bleached with 35% hydrogen peroxide for 45 minutes followed by color/opacity measurements. Data were analyzed by ANOVA and Tukey's test (α = 0.05). The use of modeling liquids did not affect the initial color and opacity of composite. Reduced changes to color (E 00  = 3.44) and opacity (+2.67%) were observed for specimens modeled using Adper Universal. Bleaching procedures reduced the color (E 00  = 1.9-3.8) and opacity (-2.3 to 3.1%) alterations caused by staining solutions but were unable to restore the values observed at baseline. The use of universal adhesive as modeling liquid significantly reduced the color and opacity changes caused by staining solutions, and the bleaching procedure partially re-established the opacity and color of the composites. This study evaluates whether using adhesive systems for modeling a composite affects the color and opacity changes caused by staining solutions followed by a bleaching procedure. The findings suggest that the use of a universal adhesive as modeling liquid can reduce the alterations in optical properties caused by staining solutions, and the application of high-concentrated hydrogen peroxide over the composite reduce the color changes without fully recover the initial color. © 2018

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

Multimedia Visualizer: An Animated, Object-Based OPAC.

Science.gov (United States)

Lee, Newton S.

1991-01-01

Describes the Multimedia Visualizer, an online public access catalog (OPAC) that uses animated visualizations to make it more user friendly. Pictures of the system are shown that illustrate the interactive objects that patrons can access, including card catalog drawers, librarian desks, and bookshelves; and access to multimedia items is described.…

Amino-acid composition after loop deletion drives domain swapping.

Science.gov (United States)

Nandwani, Neha; Surana, Parag; Udgaonkar, Jayant B; Das, Ranabir; Gosavi, Shachi

2017-10-01

Rational engineering of a protein to enable domain swapping requires an understanding of the sequence, structural and energetic factors that favor the domain-swapped oligomer over the monomer. While it is known that the deletion of loops between β-strands can promote domain swapping, the spliced sequence at the position of the loop deletion is thought to have a minimal role to play in such domain swapping. Here, two loop-deletion mutants of the non-domain-swapping protein monellin, frame-shifted by a single residue, were designed. Although the spliced sequence in the two mutants differed by only one residue at the site of the deletion, only one of them (YEIKG) promoted domain swapping. The mutant containing the spliced sequence YENKG was entirely monomeric. This new understanding that the domain swapping propensity after loop deletion may depend critically on the chemical composition of the shortened loop will facilitate the rational design of domain swapping. © 2017 The Protein Society.

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.

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

International Nuclear Information System (INIS)

Gilles, D.; Turck-Chieze, S.; Busquet, M.; Thais, F.; Loisel, G.; Piau, L.; Ducret, J. E.; Blenski, T.; Blancard, C.; Cosse, 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.

2013-01-01

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 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/cm 3 [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. (authors)

A mutation in the envelope protein fusion loop attenuates mouse neuroinvasiveness of the NY99 strain of West Nile virus

International Nuclear Information System (INIS)

Zhang Shuliu; Li Li; Woodson, Sara E.; Huang, Claire Y.-H.; Kinney, Richard M.; Barrett, Alan D.T.; Beasley, David W.C.

2006-01-01

Substitutions were engineered individually and in combinations at the fusion loop, receptor-binding domain and a stem-helix structure of the envelope protein of a West Nile virus strain, NY99, and their effects on mouse virulence and presentation of epitopes recognized by monoclonal antibodies (MAbs) were assessed. A single substitution within the fusion loop (L107F) attenuated mouse neuroinvasiveness of NY99. No substitutions attenuated NY99 neurovirulence. The L107F mutation also abolished binding of a non-neutralizing MAb, 3D9, whose epitope had not been previously identified. MAb 3D9 was subsequently shown to be broadly cross-reactive with other flaviviruses, consistent with binding near the highly conserved fusion loop

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.

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.

UTILITARIAN OPACITY MODEL FOR AGGREGATE PARTICLES IN PROTOPLANETARY NEBULAE AND EXOPLANET ATMOSPHERES

International Nuclear Information System (INIS)

Cuzzi, Jeffrey N.; Davis, Sanford S.; Estrada, Paul R.

2014-01-01

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 sizes 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 small-particle closed-form expressions, combined with suitably chosen transitions to geometric optics behavior. Calculations of wavelength-dependent emission and Rosseland mean opacity are shown and compared with Mie theory. The model's fidelity is very good in all comparisons we have made except in cases involving pure metal particles or monochromatic opacities for solid particles with sizes comparable to the wavelength

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.

The solar elemental abundances problem: Large enhancements in photoionization and bound-free opacity

Science.gov (United States)

Pradhan, A.; Nahar, S.

2016-05-01

Aimed at solving the outstanding problem of solar opacity and radiation transport, we report substantial photoabsorption in the high-energy regime due to atomic core photo-excitations not heretofore considered. In an extensive R-Matrix calculations of unprecedented complexity for an important iron ion Fe XVII, with a wave function expansion of 99 Fe XVIII core states from n current opacity models, and ii) demonstrate convergence with respect to successive core excitations. These findings may explain the ``higher-than-predicted'' monochromatic iron opacity measured recently at the Sandia Z-pinch fusion device at solar interior conditions. The findings will also impact the total atomic photoabsorption and radiation transport in laboratory and astrophysical plasmas, such as UV emission from host stars of extra-solar planets. Support: NSF, DOE, Ohio Supercomputer Center, Columbus, OH.

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.

Light element opacities of astrophysical interest from ATOMIC

Energy Technology Data Exchange (ETDEWEB)

Colgan, J.; Kilcrease, D. P.; Magee, N. H. Jr.; Armstrong, G. S. J.; Abdallah, J. Jr.; Sherrill, M. E. [Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Fontes, C. J.; Zhang, H. L.; Hakel, P. [Computational Physics Division, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)

2013-07-11

We present new calculations of local-thermodynamic-equilibrium (LTE) light element opacities from the Los Alamos ATOMIC code for systems of astrophysical interest. ATOMIC is a multi-purpose code that can generate LTE or non-LTE quantities of interest at various levels of approximation. Our calculations, which include fine-structure detail, represent a systematic improvement over previous Los Alamos opacity calculations using the LEDCOP legacy code. The ATOMIC code uses ab-initio atomic structure data computed from the CATS code, which is based on Cowan's atomic structure codes, and photoionization cross section data computed from the Los Alamos ionization code GIPPER. ATOMIC also incorporates a new equation-of-state (EOS) model based on the chemical picture. ATOMIC incorporates some physics packages from LEDCOP and also includes additional physical processes, such as improved free-free cross sections and additional scattering mechanisms. Our new calculations are made for elements of astrophysical interest and for a wide range of temperatures and densities.

[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.

Opacity and atomic analysis of double pulse laser ablated Li plasma

Science.gov (United States)

Sivakumaran, V.; Joshi, H. C.; Kumar, Ajai

2014-09-01

Opacity effects for neutral and ionic emission lines of lithium have been investigated by Atomic Data Analysis Structure (ADAS). Line ratios and opacity corrected photon emissivity coefficients are calculated over a wide range of electron temperatures and densities. The experimentally measured temporal evolution of the line profiles of the over dense Li plasma formed in the double pulse laser ablation experiment have been explained using the ADAS analysis and the plasma parameters of the plasma plume under consideration have been estimated. These results could be projected as a diagnostic tool to estimate plasma parameters of an over dense lithium plasma.

A Comparison of Keyword Subject Searching on Six British University OPACs Online Public Access Catalogs.

Science.gov (United States)

Aanonson, John

1987-01-01

Compares features of online public access catalogs (OPACs) at six British universities: (1) Cambridge; (2) Hull; (3) Newcastle; (4) Surrey; (5) Sussex; and (6) York. Results of keyword subject searches on two topics performed on each of the OPACs are reported and compared. Six references are listed. (MES)

The Searching Behavior of Remote Users: A Study of One Online Public Access Catalog (OPAC).

Science.gov (United States)

Kalin, Sally W.

1991-01-01

Describes a study that was conducted to determine whether the searching behavior of remote users of LIAS (Library Information Access System), Pennsylvania State University's online public access catalog (OPAC), differed from those using the OPAC within the library. Differences in search strategies and in user satisfaction are discussed. (eight…

Opacity measurements of tamped NaBr samples heated by z-pinch X-rays

International Nuclear Information System (INIS)

Bailey, J.E.; Arnault, P.; Blenski, T.; Dejonghe, G.; Peyrusse, O.; MacFarlane, J.J.; Mancini, R.C.; Cuneo, M.E.; Nielsen, D.S.; Rochau, G.A.

2003-01-01

Laboratory measurements provide benchmark data for wavelength-dependent plasma opacities to assist inertial confinement fusion, astrophysics, and atomic physics research. There are several potential benefits to using z-pinch radiation for opacity measurements, including relatively large cm-scale lateral sample sizes and relatively-long 3-5 ns experiment durations. These features enhance sample uniformity. The spectrally resolved transmission through a CH-tamped NaBr foil was measured. The z-pinch produced the X-rays for both the heating source and backlight source. The (50±4) eV foil electron temperature and (3±1)x10 21 cm -3 foil electron density were determined by analysis of the Na absorption features. LTE and NLTE opacity model calculations of the n=2 to 3, 4 transitions in bromine ionized into the M-shell are in reasonably good agreement with the data

Chimeric Proton-Pumping Rhodopsins Containing the Cytoplasmic Loop of Bovine Rhodopsin

Science.gov (United States)

Sasaki, Kengo; Yamashita, Takahiro; Yoshida, Kazuho; Inoue, Keiichi; Shichida, Yoshinori; Kandori, Hideki

2014-01-01

G-protein-coupled receptors (GPCRs) transmit stimuli to intracellular signaling systems. Rhodopsin (Rh), which is a prototypical GPCR, possesses an 11-cis retinal. Photoisomerization of 11-cis to all-trans leads to structural changes in the protein of cytoplasmic loops, activating G-protein. Microbial rhodopsins are similar heptahelical membrane proteins that function as bacterial sensors, light-driven ion-pumps, or light-gated channels. They possess an all-trans retinal, and photoisomerization to 13-cis triggers structural changes in protein. Despite these similarities, there is no sequence homology between visual and microbial rhodopsins, and microbial rhodopsins do not activate G-proteins. In this study, new chimeric proton-pumping rhodopsins, proteorhodopsin (PR) and Gloeobacter rhodopsin (GR) were designed by replacing cytoplasmic loops with bovine Rh loops. Although G-protein was not activated by the PR chimeras, all 12 GR chimeras activated G-protein. The GR chimera containing the second cytoplasmic loop of bovine Rh did not activate G-protein. However, the chimera with a second and third double-loop further enhanced G-protein activation. Introduction of an E132Q mutation slowed the photocycle 30-fold and enhanced activation. The highest catalytic activity of the GR chimera was still 3,200 times lower than bovine Rh but only 64 times lower than amphioxus Go-rhodopsin. This GR chimera showed a strong absorption change of the amide-I band on a light-minus-dark difference FTIR spectrum which could represent a larger helical opening, important for G-protein activation. The light-dependent catalytic activity of this GR chimera makes it a potential optogenetic tool for enzymatic activation by light. PMID:24621599

Opacity Limit for Supermassive Protostars

Science.gov (United States)

Becerra, Fernando; Marinacci, Federico; Inayoshi, Kohei; Bromm, Volker; Hernquist, Lars E.

2018-04-01

We present a model for the evolution of supermassive protostars from their formation at {M}\\star ≃ 0.1 {M}ȯ until their growth to {M}\\star ≃ {10}5 {M}ȯ . To calculate the initial properties of the object in the optically thick regime, we follow two approaches: one based on idealized thermodynamic considerations, and another based on a more detailed one-zone model. Both methods derive a similar value of {n}{{F}}≃ 2× {10}17 {cm}}-3 for the density of the object when opacity becomes important, i.e., the opacity limit. The subsequent evolution of the growing protostar is determined by the accretion of gas onto the object and can be described by a mass–radius relation of the form {R}\\star \\propto {M}\\star 1/3 during the early stages, and of the form {R}\\star \\propto {M}\\star 1/2 when internal luminosity becomes important. For the case of a supermassive protostar, this implies that the radius of the star grows from {R}\\star ≃ 0.65 {au} to {R}\\star ≃ 250 {au} during its evolution. Finally, we use this model to construct a subgrid recipe for accreting sink particles in numerical simulations. A prime ingredient thereof is a physically motivated prescription for the accretion radius and the effective temperature of the growing protostar embedded inside it. From the latter, we can conclude that photoionization feedback can be neglected until very late in the assembly process of the supermassive object.

A Looping-Based Model for Quenching Repression.

Directory of Open Access Journals (Sweden)

Yaroslav Pollak

2017-01-01

Full Text Available We model the regulatory role of proteins bound to looped DNA using a simulation in which dsDNA is represented as a self-avoiding chain, and proteins as spherical protrusions. We simulate long self-avoiding chains using a sequential importance sampling Monte-Carlo algorithm, and compute the probabilities for chain looping with and without a protrusion. We find that a protrusion near one of the chain's termini reduces the probability of looping, even for chains much longer than the protrusion-chain-terminus distance. This effect increases with protrusion size, and decreases with protrusion-terminus distance. The reduced probability of looping can be explained via an eclipse-like model, which provides a novel inhibitory mechanism. We test the eclipse model on two possible transcription-factor occupancy states of the D. melanogaster eve 3/7 enhancer, and show that it provides a possible explanation for the experimentally-observed eve stripe 3 and 7 expression patterns.

Bibliographic Displays in OPACs and Web Catalogs: How Well Do They Comply with Display Guidelines?

Science.gov (United States)

Cherry, Joan M.

1998-01-01

Evaluation of data from assessments of full bibliographic displays in academic library OPACs (online public access catalogs) and World Wide Web catalogs against a checklist of desirable features found that OPAC displays scored 58% and Web displays scored 60%. Discusses weaknesses, focusing on those found in the majority of the displays…

Ground-glass opacity at high resolution CT: an approach for differential diagnosis

International Nuclear Information System (INIS)

Spina, Juan C.; Rogondino, Jose; Vidales, Valeria; Rolnik, Maria C.; Montanari, Mariano; Salazar, Santiago N.

2004-01-01

Purpose: To evaluate the Ground-Glass Opacity in high resolution computed tomography (HRCT) with its underlying abnormality and anatomic distribution and its correlation with different etiologies. Methods: A 38 patients series, (32 men, 16 women, mean age 54,6 years, range 20-28) was retrospectively analyzed. They were evaluated with high resolution computed tomography, 2 mm thick sections and 10 mm of interval. Contrast intravenous iodinated contrast (no-ionic) was injected in 11 patients. The final diagnosis was made with sputum analysis, bronchioalveolar lavage, trans bronchial biopsy and open lung biopsy. Results: The differential diagnosis of ground glass opacity is based on analyzing their anatomic resolution and the underlying pathology in the lung parenchyma. Centrilobular distribution indicated early air-spaces pathology produced in our series by 21 infections, 4 pulmonary hemorrhages, 1 hypersensitivity pneumonitis and 1 descamative interstitial pneumonitis. Panlobular distribution, alveolar proteinosis (1 case) sarcoidosis (1 case) drug toxicity 1 case and one case of pneumocystis carinii. Peripherical distribution typical of early idiopathic fibrosis (1). Bronchiolitis obliterans with organizing pneumonia (1). Structural alterations of the lung parenchyma with bronchiectasias was seen in 16 cases, cystic lesions in 3 cases, sub pleural linear opacities 4 cases, peribronchovascular interstitial thickening or nodularity and emphysema in 10 cases. Conclusion: HRCT is useful to evaluate ground glass opacities pattern with the anatomic distribution and the underlying structural pathology. These findings under some clinical circumstances can suggest a specific diagnosis in most cases, indicating a potentially treatable disease. (author)

Opacity annotation of diffuse lung diseases using deep convolutional neural network with multi-channel information

Science.gov (United States)

Mabu, Shingo; Kido, Shoji; Hashimoto, Noriaki; Hirano, Yasushi; Kuremoto, Takashi

2018-02-01

This research proposes a multi-channel deep convolutional neural network (DCNN) for computer-aided diagnosis (CAD) that classifies normal and abnormal opacities of diffuse lung diseases in Computed Tomography (CT) images. Because CT images are gray scale, DCNN usually uses one channel for inputting image data. On the other hand, this research uses multi-channel DCNN where each channel corresponds to the original raw image or the images transformed by some preprocessing techniques. In fact, the information obtained only from raw images is limited and some conventional research suggested that preprocessing of images contributes to improving the classification accuracy. Thus, the combination of the original and preprocessed images is expected to show higher accuracy. The proposed method realizes region of interest (ROI)-based opacity annotation. We used lung CT images taken in Yamaguchi University Hospital, Japan, and they are divided into 32 × 32 ROI images. The ROIs contain six kinds of opacities: consolidation, ground-glass opacity (GGO), emphysema, honeycombing, nodular, and normal. The aim of the proposed method is to classify each ROI into one of the six opacities (classes). The DCNN structure is based on VGG network that secured the first and second places in ImageNet ILSVRC-2014. From the experimental results, the classification accuracy of the proposed method was better than the conventional method with single channel, and there was a significant difference between them.

Library OPACs on the Web: Finding and Describing Directories.

Science.gov (United States)

Henry, Marcia

1997-01-01

Provides current descriptions of some of the major directories that link to library catalogs on the World Wide Web. Highlights include LibWeb; Hytelnet; WebCats; WWW Library Directory; and techniques for finding new library OPAC (online public access catalog) directories. (LRW)

Ground-glass opacity: High-resolution computed tomography and 64-multi-slice computed tomography findings comparison

International Nuclear Information System (INIS)

Sergiacomi, Gianluigi; Ciccio, Carmelo; Boi, Luca; Velari, Luca; Crusco, Sonia; Orlacchio, Antonio; Simonetti, Giovanni

2010-01-01

Objective: Comparative evaluation of ground-glass opacity using conventional high-resolution computed tomography technique and volumetric computed tomography by 64-row multi-slice scanner, verifying advantage of volumetric acquisition and post-processing technique allowed by 64-row CT scanner. Methods: Thirty-four patients, in which was assessed ground-glass opacity pattern by previous high-resolution computed tomography during a clinical-radiological follow-up for their lung disease, were studied by means of 64-row multi-slice computed tomography. Comparative evaluation of image quality was done by both CT modalities. Results: It was reported good inter-observer agreement (k value 0.78-0.90) in detection of ground-glass opacity with high-resolution computed tomography technique and volumetric Computed Tomography acquisition with moderate increasing of intra-observer agreement (k value 0.46) using volumetric computed tomography than high-resolution computed tomography. Conclusions: In our experience, volumetric computed tomography with 64-row scanner shows good accuracy in detection of ground-glass opacity, providing a better spatial and temporal resolution and advanced post-processing technique than high-resolution computed tomography.

Constraints on cosmic opacity and beyond the standard model physics from cosmological distance measurements

International Nuclear Information System (INIS)

Avgoustidis, Anastasios; Redondo, Javier; Verde, Licia; Jimenez, Raul

2010-04-01

We update constraints on cosmic opacity by combining recent SN Type Ia data compilation with the latest measurements of the Hubble expansion at redshifts between 0 and 2. The new constraint on the parameter ε parametrising deviations from the luminosity-angular diameter distance relation (d L =d A (1+z) 2+ε ), is ε=-0.04 -0.07 +0.08 (2-σ). For the redshift range between 0.2 and 0.35 this corresponds to an opacity Δτ<0.012 (95% C.L.), a factor of 2 stronger than the previous constraint. Various models of beyond the standard model physics that predict violation of photon number conservation contribute to the opacity and can be equally constrained. In this paper we put new limits on axion-like particles, including chameleons, and minicharged particles. (orig.)

Calculation of radiative opacity of plasma mixtures using a relativistic screened hydrogenic model

International Nuclear Information System (INIS)

Mendoza, M.A.; Rubiano, J.G.; Gil, J.M.; Rodríguez, R.; Florido, R.; Espinosa, G.; Martel, P.; Mínguez, E.

2014-01-01

We present the code ATMED based on an average atom model and conceived for fast computing the population distribution and radiative properties of hot and dense single and multicomponent plasmas under LTE conditions. A relativistic screened hydrogenic model (RSHM), built on a new set of universal constants considering j-splitting, is used to calculate the required atomic data. The opacity model includes radiative bound–bound, bound–free, free–free, and scattering processes. Bound–bound line-shape function has contributions from natural, Doppler and electron-impact broadenings. An additional dielectronic broadening to account for fluctuations in the average level populations has been included, which improves substantially the Rosseland mean opacity results. To illustrate the main features of the code and its capabilities, calculations of several fundamental quantities of one-component plasmas and mixtures are presented, and a comparison with previously published data is performed. Results are satisfactorily compared with those predicted by more elaborate codes. - Highlights: • A new opacity code, ATMED, based on the average atom approximation is presented. • Atomic data are computed by means of a relativistic screened hydrogenic model. • An effective bound level degeneracy is included for accounting pressure ionization. • A new dielectronic line broadening is included to improve the mean opacities. • ATMED has the possibility to handle with single element and multicomponent plasmas

Opacplot2: Enabling tabulated EoS and opacity compatibility for HEDLP simulations with the FLASH code

Science.gov (United States)

Laune, Jordan; Tzeferacos, Petros; Feister, Scott; Fatenejad, Milad; Yurchak, Roman; Flocke, Norbert; Weide, Klaus; Lamb, Donald

2017-10-01

Thermodynamic and opacity properties of materials are necessary to accurately simulate laser-driven laboratory experiments. Such data are compiled in tabular format since the thermodynamic range that needs to be covered cannot be described with one single theoretical model. Moreover, tabulated data can be made available prior to runtime, reducing both compute cost and code complexity. This approach is employed by the FLASH code. Equation of state (EoS) and opacity data comes in various formats, matrix-layouts, and file-structures. We discuss recent developments on opacplot2, an open-source Python module that manipulates tabulated EoS and opacity data. We present software that builds upon opacplot2 and enables easy-to-use conversion of different table formats into the IONMIX format, the native tabular input used by FLASH. Our work enables FLASH users to take advantage of a wider range of accurate EoS and opacity tables in simulating HELP experiments at the National Laser User Facilities.

Night and Day: The Opacity of Clouds Measured by the Mars Orbiter Laser Altimeter (MOLA)

Science.gov (United States)

Neumann, G. A.; Wilson, R. J.

2006-01-01

The Mars Orbiter Laser Altimeter (MOLA) [l] on the Mars Global Surveyor spacecraft ranged to clouds over the course of nearly two Mars years [2] using an active laser ranging system. While ranging to the surface, the instrument was also able to measure the product of the surface reflectivity with the two-way atmospheric transmission at 1064 nm. Furthermore, the reflectivity has now been mapped over seasonal cycles using the passive radiometric capability built into MOLA [3]. Combining these measurements, the column opacity may be inferred. MOLA uniquely provides these measurements both night and day. This study examines the pronounced nighttime opacity of the aphelion season tropical water ice clouds, and the indiscernibly low opacity of the southern polar winter clouds. The water ice clouds (Figure 1) do not themselves trigger the altimeter but have measured opacities tau > 1.5 and are temporally and spatially correlated with temperature anomalies predicted by a Mars Global Circulation Model (MGCM) that incorporates cloud radiative effects [4]. The south polar CO2 ice clouds trigger the altimeter with a very high backscatter cross-section over a thickness of 3-9 m and are vertically dispersed over several km, but their total column opacities lie well below the MOLA measurement limit of tau = 0.7. These clouds correspond to regions of supercooled atmosphere that may form either very large specularly reflecting particles [2] or very compact, dense concentrations (>5x10(exp 6)/cu m) of 100-p particles

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…

Concentration and length dependence of DNA looping in transcriptional regulation.

Directory of Open Access Journals (Sweden)

Lin Han

2009-05-01

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.

Constraints on cosmic opacity and beyond the standard model physics from cosmological distance measurements

Energy Technology Data Exchange (ETDEWEB)

Avgoustidis, Anastasios [Centre for Theoretical Cosmology, DAMTP, CMS, Wilberforce Road, Cambridge CB3 0WA (United Kingdom); Burrage, Clare [Deutsches Elektronen Synchrotron DESY, Notkestrasse 85, D-22607 Hamburg (Germany); Redondo, Javier [Max Planck Institut für Physik, Föhringer Ring 6, D-80805, Munich (Germany); Verde, Licia; Jimenez, Raul, E-mail: a.avgoustidis@damtp.cam.ac.uk, E-mail: clare.burrage@desy.de, E-mail: redondo@mppmu.mpg.de, E-mail: liciaverde@icc.ub.edu, E-mail: raul.jimenez@icc.ub.edu [ICREA and Institute for Sciences of the Cosmos (ICC), University of Barcelona, IEEC, Barcelona 08028 (Spain)

2010-10-01

We update constraints on cosmic opacity by combining recent SN Type Ia data with the latest measurements of the Hubble expansion at redshifts between 0 and 2. The new constraint on the parameter ε parametrising deviations from the luminosity-angular diameter distance relation (d{sub L} = d{sub A}(1+z){sup 2+ε}), is ε = −0.04{sub −0.07}{sup +0.08} (2-σ). For the redshift range between 0.2 and 0.35 this corresponds to an opacity Δτ < 0.012 (95% C.L.), a factor of 2 stronger than the previous constraint. Various models of beyond the standard model physics that predict violation of photon number conservation contribute to the opacity and can be equally constrained. In this paper we put new limits on axion-like particles, including chameleons, and mini-charged particles.

Constraints on cosmic opacity and beyond the standard model physics from cosmological distance measurements

Energy Technology Data Exchange (ETDEWEB)

Avgoustidis, Anastasios [DAMTP, CMS, Cambridge (United Kingdom). Centre for Theoretical Cosmology; Burrage, Clare [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Redondo, Javier [Max-Planck-Institut fuer Physik, Munich (Germany); Verde, Licia; Jimenez, Raul [Barcelona Univ., IEEC (ES). ICREA and Inst. for Sciences of the Cosmos (ICC)

2010-04-15

We update constraints on cosmic opacity by combining recent SN Type Ia data compilation with the latest measurements of the Hubble expansion at redshifts between 0 and 2. The new constraint on the parameter {epsilon} parametrising deviations from the luminosity-angular diameter distance relation (d{sub L}=d{sub A}(1+z){sup 2+{epsilon}}), is {epsilon}=-0.04{sub -0.07}{sup +0.08} (2-{sigma}). For the redshift range between 0.2 and 0.35 this corresponds to an opacity {delta}{tau}<0.012 (95% C.L.), a factor of 2 stronger than the previous constraint. Various models of beyond the standard model physics that predict violation of photon number conservation contribute to the opacity and can be equally constrained. In this paper we put new limits on axion-like particles, including chameleons, and minicharged particles. (orig.)

Kinetics of Internal-Loop Formation in Polypeptide Chains: A Simulation Study

Science.gov (United States)

Doucet, Dana; Roitberg, Adrian; Hagen, Stephen J.

2007-01-01

The speed of simple diffusional motions, such as the formation of loops in the polypeptide chain, places one physical limit on the speed of protein folding. Many experimental studies have explored the kinetics of formation of end-to-end loops in polypeptide chains; however, protein folding more often requires the formation of contacts between interior points on the chain. One expects that, for loops of fixed contour length, interior loops will form more slowly than end-to-end loops, owing to the additional excluded volume associated with the “tails”. We estimate the magnitude of this effect by generating ensembles of randomly coiled, freely jointed chains, and then using the theory of Szabo, Schulten, and Schulten to calculate the corresponding contact formation rates for these ensembles. Adding just a few residues, to convert an end-to-end loop to an internal loop, sharply decreases the contact rate. Surprisingly, the relative change in rate increases for a longer loop; sufficiently long tails, however, actually reverse the effect and accelerate loop formation slightly. Our results show that excluded volume effects in real, full-length polypeptides may cause the rates of loop formation during folding to depart significantly from the values derived from recent loop-formation experiments on short peptides. PMID:17208979

Dependent lung opacity at thin-section CT: evaluation by spirometrically-gated CT of the influence of lung volume

International Nuclear Information System (INIS)

Lee, Ki Nam; Yoon, Seong Kuk; Sohn, Choon Hee; Choi, Pil Jo; Webb, W. Richard

2002-01-01

To evaluate the influence of lung volume on dependent lung opacity seen at thin-section CT. In thirteen healthy volunteers, thin-section CT scans were performed at three levels (upper, mid, and lower portion of the lung) and at different lung volumes (10, 30, 50, and 100% vital capacity), using spirometric gated CT. Using a three-point scale, two radiologists determined whether dependent opacity was present, and estimated its degree. Regional lung attenuation at a level 2 cm above the diaphragm was determined using semiautomatic segmentation, and the diameter of a branch of the right lower posterior basal segmental artery was measured at each different vital capacity. At all three anatomic levels, dependent opacity occurred significantly more often at lower vital capacities (10, 30%) than at 100% vital capacity (p = 0.001). Visually estimated dependent opacity was significantly related to regional lung attenuation (p < 0.0001), which in dependent areas progressively increased as vital capacity decreased (p < 0.0001). The presence of dependent opacity and regional lung attenuation of a dependent area correlated significantly with increased diameter of a segmental arterial branch (r = 0.493 and p = 0.0002; r = 0.486 and p 0.0003, respectively). Visual estimation and CT measurements of dependent opacity obtained by semiautomatic segmentation are significantly influenced by lung volume and are related to vascular diameter

Hohlraum modeling for opacity experiments on the National Ignition Facility

Science.gov (United States)

Dodd, E. S.; DeVolder, B. G.; Martin, M. E.; Krasheninnikova, N. S.; Tregillis, I. L.; Perry, T. S.; Heeter, R. F.; Opachich, Y. P.; Moore, A. S.; Kline, J. L.; Johns, H. M.; Liedahl, D. A.; Cardenas, T.; Olson, R. E.; Wilde, B. H.; Urbatsch, T. J.

2018-06-01

This paper discusses the modeling of experiments that measure iron opacity in local thermodynamic equilibrium (LTE) using laser-driven hohlraums at the National Ignition Facility (NIF). A previous set of experiments fielded at Sandia's Z facility [Bailey et al., Nature 517, 56 (2015)] have shown up to factors of two discrepancies between the theory and experiment, casting doubt on the validity of the opacity models. The purpose of the new experiments is to make corroborating measurements at the same densities and temperatures, with the initial measurements made at a temperature of 160 eV and an electron density of 0.7 × 1022 cm-3. The X-ray hot spots of a laser-driven hohlraum are not in LTE, and the iron must be shielded from a direct line-of-sight to obtain the data [Perry et al., Phys. Rev. B 54, 5617 (1996)]. This shielding is provided either with the internal structure (e.g., baffles) or external wall shapes that divide the hohlraum into a laser-heated portion and an LTE portion. In contrast, most inertial confinement fusion hohlraums are simple cylinders lacking complex gold walls, and the design codes are not typically applied to targets like those for the opacity experiments. We will discuss the initial basis for the modeling using LASNEX, and the subsequent modeling of five different hohlraum geometries that have been fielded on the NIF to date. This includes a comparison of calculated and measured radiation temperatures.

Lightweight, high-opacity Bible paper by fiber loading

Science.gov (United States)

Klaus Doelle; Oliver Heise; John H. Klungness; Said M. AbuBakr

2000-01-01

This paper has been prepared in order to discuss Fiber Loading™ for lightweight, high-opacity bible paper. Incorporating fillers within pulp fibers has been subject to research since 1960 (Green et al. 1962, Scallan et al. 1985, Allen et al. 1992). Fiber Loading™ is a method for manufacturing precipitated calcium carbonate (PCC) directly within the pulp processing...

A systematic classification of Plasmodium falciparum P-loop NTPases: structural and functional correlation

Directory of Open Access Journals (Sweden)

Chauhan Virander S

2009-04-01

Full Text Available Abstract Background The P-loop NTPases constitute one of the largest groups of globular protein domains that play highly diverse functional roles in most of the organisms. Even with the availability of nearly 300 different Hidden Markov Models representing the P-loop NTPase superfamily, not many P-loop NTPases are known in Plasmodium falciparum. A number of characteristic attributes of the genome have resulted into the lack of knowledge about this functionally diverse, but important class of proteins. Method In the study, protein sequences with characteristic motifs of NTPase domain (Walker A and Walker B are computationally extracted from the P. falciparum database. A detailed secondary structure analysis, functional classification, phylogenetic and orthology studies of the NTPase domain of repertoire of 97 P. falciparum P-loop NTPases is carried out. Results Based upon distinct sequence features and secondary structure profile of the P-loop domain of obtained sequences, a cladistic classification is also conceded: nucleotide kinases and GTPases, ABC and SMC family, SF1/2 helicases, AAA+ and AAA protein families. Attempts are made to identify any ortholog(s for each of these proteins in other Plasmodium sp. as well as its vertebrate host, Homo sapiens. A number of P. falciparum P-loop NTPases that have no homologue in the host, as well as those annotated as hypothetical proteins and lack any characteristic functional domain are identified. Conclusion The study suggests a strong correlation between sequence and secondary structure profile of P-loop domains and functional roles of these proteins and thus provides an opportunity to speculate the role of many hypothetical proteins. The study provides a methodical framework for the characterization of biologically diverse NTPases in the P. falciparum genome. The efforts made in the analysis are first of its kind; and the results augment to explore the functional role of many of these proteins from

An investigation of the opacity of high-Z mixture and implications for inertial confinement fusion hohlraum design

International Nuclear Information System (INIS)

Wang, P.; MacFarlane, J.J.; Orzechowski, T.J.

1997-01-01

We use an unresolved transition array model to investigate the opacities of high-Z materials and their mixtures which are of interest to indirect-drive inertial confinement fusion hohlraum design. In particular, we report on calculated opacities for pure Au, Gd, and Sm, as well as Au endash Sm and Au endash Gd mixtures. Our results indicate that mixtures of Au endash Gd and Au endash Sm can produce a significant enhancement in the Rosseland mean opacity. Radiation hydrodynamics simulations of Au radiation burnthrough are also presented, and compared with NOVA experimental data. copyright 1997 American Institute of Physics

Non-LTE H2+ as the source of missing opacity in the solar atmosphere

Science.gov (United States)

Swamy, K. S. K.; Stecher, T. P.

1974-01-01

The population of the various vibrational levels of the H2+ molecule has been calculated from the consideration of formation and destruction mechanisms. The resulting population is used in calculating the total absorption due to H2+ and is compared with the other known sources of opacity at several optical depths of the solar atmosphere. It is shown that the absorption due to H2+ can probably account for the missing ultraviolet opacity in the solar atmosphere.

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.

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

Osmotic mechanism of the loop extrusion process

Science.gov (United States)

Yamamoto, Tetsuya; Schiessel, Helmut

2017-09-01

The loop extrusion theory assumes that protein factors, such as cohesin rings, act as molecular motors that extrude chromatin loops. However, recent single molecule experiments have shown that cohesin does not show motor activity. To predict the physical mechanism involved in loop extrusion, we here theoretically analyze the dynamics of cohesin rings on a loop, where a cohesin loader is in the middle and unloaders at the ends. Cohesin monomers bind to the loader rather frequently and cohesin dimers bind to this site only occasionally. Our theory predicts that a cohesin dimer extrudes loops by the osmotic pressure of cohesin monomers on the chromatin fiber between the two connected rings. With this mechanism, the frequency of the interactions between chromatin segments depends on the loading and unloading rates of dimers at the corresponding sites.

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)

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.

Measurement of nurses' attitudes and knowledge regarding acute care older patients: Psychometrics of the OPACS-US combined with the KOP-Q.

Science.gov (United States)

Dikken, Jeroen; Hoogerduijn, Jita G; Lagerwey, Mary D; Shortridge-Baggett, Lillie; Klaassen, Sharon; Schuurmans, Marieke J

In clinical practice, identifying positive and negative attitudes toward older patients is very important to improve quality of care provided to them. The Older People in Acute Care Survey - United States (OPACS-US) is an instrument measuring hospital nurses attitudes regarding older patients. However, psychometrics have never been assessed. Furthermore, knowledge being related to attitude and behavior should also be measured complementing the OPACS-US. The purpose of this study was to assess structural validity and reliability of the OPACS-US and assess whether the OPACS-US can be complemented with the Knowledge about Older Patients-Quiz (KOP-Q). A multicenter cross sectional design was conducted. Registered nurses (n = 130, mean age 39,9 years; working experience 14,6 years) working in four general hospitals were included in the study. Nurses completed the OPACS-US section A: practice experiences, B: general opinion and the KOP-Q online. Findings demonstrated that the OPACS-US is a valid and reliable survey instrument that measures practice experiences and general opinion. Furthermore, the OPACS-US can be combined with the KOP-Q adding a knowledge construct, and is ready for use within education and/or quality improvement programs in the USA. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

Molecular analysis of the interaction between the intracellular loops of the human serotonin receptor type 6 (5-HT6) and the α subunit of GS protein

International Nuclear Information System (INIS)

Kang, Hatan; Lee, Won Kyu; Choi, Yun Hui; Vukoti, Krishna Moorthy; Bang, Won Gi; Yu, Yeon Gyu

2005-01-01

The serotonin type 6 (5-HT 6 ) receptor is a G-protein coupled receptor (GPCR) coupled to a stimulatory G-protein (G S ). To identify the structural basis for the interaction of the 5-HT 6 receptor with the G S protein, we have dissected the interaction between GST-fusion proteins containing the second intracellular loop (iL2), the third intracellular loop (iL3), or the C-terminal tail of the 5-HT 6 receptor and the α subunit of G S (Gα S ). The direct interaction of iL3 and Gα S was demonstrated by co-immunoprecipitation. Furthermore, the kinetic parameters of the interaction between iL3 and Gα S were measured by surface plasmon resonance, and the apparent dissociation constant was determined to be 0.9 x 10 -6 M. In contrast, the second intracellular loop and C-terminal tail regions showed negligible affinity to Gα S . The critical residues within the iL3 region for the interaction with Gα S were identified as conserved positively charged residues near the C-terminus of iL3 by measuring the cellular levels of cAMP produced in response to 5-HT stimulation of cells transfected with 5-HT 6 receptor mutants

Radiative properties of stellar envelopes: Comparison of asteroseismic results to opacity calculations and measurements for iron and nickel

International Nuclear Information System (INIS)

Turck-Chieze, S.; Gilles, D.; Le Pennec, M.; Blenski, T.; Thais, F.; Bastiani-Ceccotti, S.; Blancard, C.; Caillaud, T.; Cosse, P.; Faussurier, G.; Gilleron, F.; Pain, J.C.; Reverdin, C.; Silvert, V.; Villette, B.; Busquet, M.; Colgan, J.; Guzik, J.; Kilcrease, D.P.; Magee, N.H.; Delahaye, F.; Zeippen, C.J.; Ducreta, J.E.; Fontes, C.J.; Harris, J.W.; Loisel, G.

2013-01-01

The international OPAC consortium consists of astrophysicists, plasma physicists and experimentalists who examine opacity calculations used in stellar physics that appear questionable and perform new calculations and laser experiments to understand the differences and improve the calculations. We report on iron and nickel opacities for envelopes of stars from 2 to 14 M and deliver our first conclusions concerning the reliability of the used calculations by illustrating the importance of the configuration interaction and of the completeness of the calculations for temperatures around 15-27 eV. (authors)

Structural consequences of cutting a binding loop: two circularly permuted variants of streptavidin

International Nuclear Information System (INIS)

Le Trong, Isolde; Chu, Vano; Xing, Yi; Lybrand, Terry P.; Stayton, Patrick S.; Stenkamp, Ronald E.

2013-01-01

The crystal structures of two circularly permuted streptavidins probe the role of a flexible loop in the tight binding of biotin. Molecular-dynamics calculations for one of the mutants suggests that increased fluctuations in a hydrogen bond between the protein and biotin are associated with cleavage of the binding loop. Circular permutation of streptavidin was carried out in order to investigate the role of a main-chain amide in stabilizing the high-affinity complex of the protein and biotin. Mutant proteins CP49/48 and CP50/49 were constructed to place new N-termini at residues 49 and 50 in a flexible loop involved in stabilizing the biotin complex. Crystal structures of the two mutants show that half of each loop closes over the binding site, as observed in wild-type streptavidin, while the other half adopts the open conformation found in the unliganded state. The structures are consistent with kinetic and thermodynamic data and indicate that the loop plays a role in enthalpic stabilization of the bound state via the Asn49 amide–biotin hydrogen bond. In wild-type streptavidin, the entropic penalties of immobilizing a flexible portion of the protein to enhance binding are kept to a manageable level by using a contiguous loop of medium length (six residues) which is already constrained by its anchorage to strands of the β-barrel protein. A molecular-dynamics simulation for CP50/49 shows that cleavage of the binding loop results in increased structural fluctuations for Ser45 and that these fluctuations destabilize the streptavidin–biotin complex

Autosomal mutations affecting Y chromosome loops in Drosophila melanogaster

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Petrucci Romano

2008-04-01

Full Text Available Abstract Background The Y chromosome of Drosophila melanogaster harbors several genes required for male fertility. The genes for these fertility factors are very large in size and contain conspicuous amounts of repetitive DNA and transposons. Three of these loci (ks-1, kl-3 and kl-5 have the ability to develop giant lampbrush-like loops in primary spermatocytes, a cytological manifestation of their active state in these cells. Y-loops bind a number of non-Y encoded proteins, but the mechanisms regulating their development and their specific functions are still to be elucidated. Results Here we report the results of a screen of 726 male sterile lines to identify novel autosomal genes controlling Y-loop function. We analyzed mutant testis preparations both in vivo and by immunofluorescence using antibodies directed against Y-loop-associated proteins. This screen enabled us to isolate 17 mutations at 15 loci whose wild-type function is required for proper Y-loop morphogenesis. Six of these loci are likely to specifically control loop development, while the others display pleiotropic effects on both loops and meiotic processes such as spermiogenesis, sperm development and maturation. We also determined the map position of the mutations affecting exclusively Y-loop morphology. Conclusion Our cytological screening permitted us to identify novel genetic functions required for male spermatogenesis, some of which show pleiotropic effects. Analysis of these mutations also shows that loop development can be uncoupled from meiosis progression. These data represent a useful framework for the characterization of Y-loop development at a molecular level and for the study of the genetic control of heterochromatin.

Color and opacity of composites protected with surface sealants and submitted to artificial accelerated aging.

Science.gov (United States)

Aguilar, Fabiano Gamero; Roberti Garcia, Lucas da Fonseca; Cruvinel, Diogo Rodrigues; Sousa, Ana Beatriz Silva; de Carvalho Panzeri Pires-de-Souza, Fernanda

2012-01-01

To evaluate the color similarity, stability and opacity of composites (TPH, Charisma, and Concept, shade A2) protected with surface sealants (Fortify Plus and Biscover) and cyanoacrylate (Super Bonder). Forty specimens of each composite were made and separated into 4 groups (n=10) according to the surface protection: GI - without sealant; GII - cyanoacrylate; GIII - Fortify Plus; GIV - Biscover. Color and opacity readings were taken before and after Artificial Acelerated Aging (AAA) and the values obtained for color stability were submitted to statistical analysis by 2-way ANOVA and Bonferroni's test (P<.05). The values acquired for color similarity were submitted to 1-way ANOVA and Tukey's test (P<.05). The specimen sufaces were compared before and after AAA using Scanning Electronic Microscopy (SEM). Studied composites did not present the same values for the coordinates L*, a* and b * before AAA, indicating that there was no color similarity among them. All composites presented color alteration after AAA with clinically unacceptable values. Protected groups presented lower opacity variation after AAA, in comparison with the control goup. SEM evaluation demonstrated that AAA increased the surface irregularities in all of the studied groups. Surface sealants were not effective in maintaining composite color, but were able to maintain opacity.

Medical management of bilateral corneal opacity in an Asian elephant (Elephas maximus: A case report

Directory of Open Access Journals (Sweden)

Pranab Paul

2018-03-01

Full Text Available Objective: This study was aimed at studying efficacy of medical management of corneal opacity in an Asian elephant (Elephas maximus. Material and methods: A 42 years old male Asian elephant was brought to the Teaching Veterinary Hospital (TVH at Chittagong Veterinary and Animal Sciences University (CVASU with a history of chronic lacrimation and impaired vision. On clinical examination, the animal was found apparently healthy. Opthalmological examination tentatively revealed the condition as corneal opacity. The left eye was much more affected as compared to the right one. Medical management was instituted with topical administration of ciprofloxacin, dexamethasone, subconjunctival prednisolone and dexamethasone along with intramuscular ketoprofen (at 1 mg/Kg bwt and vitamin A (at 5000 IU/Kg bwt. Results: The “mahout” (elepenat caretaker of the elephant was kept in close contact over cell phone to follow up the progress of the condition. Clinical examination after 19 days revealed complete recovery of the cornel opacity. There was no sign of lacrimation and the animal regained its normal vision. Conclusion: The treatment protocol successfully eliminated the discomfort along with corneal opacity and lacrimation in an Asian elephant. [J Adv Vet Anim Res 2018; 5(1.000: 98-100

OPAC Design Enhancements and Their Effects on Circulation and Resource Sharing within the Library Consortium Environment

Directory of Open Access Journals (Sweden)

Michael J. Bennett

2007-03-01

Full Text Available A longitudinal study of three discrete online public access catalog (OPAC design enhancements examined the possible effects such changes may have on circulation and resource sharing within the automated library consortium environment. Statistical comparisons were made of both circulation and interlibrary loan (ILL figures from the year before enhancement to the year after implementation. Data from sixteen libraries covering a seven-year period were studied in order to determine the degree to which patrons may or may not utilize increasingly broader OPAC ILL options over time. Results indicated that while ILL totals increased significantly after each OPAC enhancement, such gains did not result in significant corresponding changes in total circulation.

Effect of Biodiesel of Spent Cooking Oil Addition at Diesel Fuel to Opacity and Gas Emission Throw Away of CO, CO2 and HC

International Nuclear Information System (INIS)

Setyadji, Moch; Endang Susiantini

2007-01-01

Investigation of biodiesel spent cooking oil addition effect at diesel fuel to opacity and gas emission throw away on various engine rotation speed has been done. The variables observed were fuel specific used i.e. pure diesel fuel, biodiesel mix 5% (B5), mix 10% (B10), mix 15% (B15), mix 20% (B20) and engine rotation speed. Gas emission throw away observed were CO, CO 2 , HC and opacity. Opacity and gas emission throwaway were observed by Opacity Sagem apparatus and gas analyzer. Result of experiment showed that biodiesel addition at diesel fuel was very decreasing opacity and gas emission throw away. The opacity lowest on B20, gas emission throw away lowest of CO on B10, CO 2 on B10 and HC on B20. (author)

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.

Detection of artificial air space opacities with digital radiography. Ex vivo study on enhanced latitude post-processing

International Nuclear Information System (INIS)

Biederer, Juergen; Bolte, H.; Schmidt, T.; Charalambous, N.; Both, M.; Hoffmann, B.; Heller, M.; Kopp, U.; Freitag-Wolf, S.; Van Metter, R.

2010-01-01

Purpose: To evaluate in a.-p. digital chest radiograms of an ex vivo system if increased latitude and enhanced image detail contrast (EVP) improve the accuracy of detecting artificial air space opacities in parts of the lung that are superimposed by the diaphragm. Materials and Methods: 19 porcine lungs were inflated inside a chest phantom, prepared with 20-50 ml gelatin-stabilized liquid to generate alveolar air space opacities, and examined with direct radiography (3.0 x 2.5 k detector/125 kVp/4 mAs). 276 a.-p. images with and without EVP of 1.0-3.0 were presented to 6 observers. 8 regions were read for opacities, the reference was defined by CT. Statistics included sensitivity/specificity, interobserver variability, and calculation of Az (area under ROC curve). Results: Behind the diaphragm (opacities in 32/92 regions), the median sensitivity increased from 0.35 without EVP to 0.53 - 0.56 at EVP 1.5 - 3.0 (significant in 5/6 observers). The specificity decreased from 0.96 to 0.90 (significant in 6/6), and the Az value and interobserver correlation increased from 0.66 to 0.74 and 0.39 to 0.48, respectively. Above the diaphragm, the median sensitivity for artificial opacities (136/276 regions) increased from 0.71 to 0.77 - 0.82 with EVP (significant in 4/6 observers). The specificity and Az value decreased from 0.76 to 0.62 and 0.74 to 0.70, respectively, (significant in 3/6). Conclusion: In this ex vivo experiment, EVP improved the diagnostic accuracy for artificial air space opacities in the superimposed parts of the lung (area under the ROC curve). Above the diaphragm, the accuracy was not affected due to a tradeoff in sensitivity/specificity. (orig.)

Experimental study of self-backlighting method for opacity

International Nuclear Information System (INIS)

Ding Yaonan; Yang Jiamin; Li Sanwei; Cao Leifeng; Wang Yaomei; Zhang Wenhai; Chen Bo; Yu Yanning; Wang Hongbin

2001-01-01

Self-backlighting method for opacity measurement has been suggested and studied, based on the actual condition of Xingguang II laser facility. An 80 J and 350 nm laser, which has a duration of about 700 ps, irradiates on a newly designed target and creates intense X-ray radiation acting as both heating source and backlighter source. The heated sample has been spatially imaged to obtain X-ray spectra from X-ray source region, transmission region and self-emission region of the sample at the same shot by spatially resolved transmission grating spectrometer in which dispersed X-ray is recorded by X-ray CCD. The samples are low-Z CH foam with density of 0.042 g/cm 3 , thickness of 42 μm and mid-Z Al with density of 2.7 g/cm 3 , thickness of 0.5 μm or 1.0 μm. Mass absorption coefficients of the heated sample as function of the photon energy have been obtained experimentally in the same shot. The spectra line emitted from the heated CH foam has also been measured by OHM crystal spectrometer, which has been used to determine the temperature of the sample. The experimental results for opacity of carbon have been discussed

Opacity Build-up in Impulsive Relativistic Sources

International Nuclear Information System (INIS)

Granot, Jonathan; Cohen-Tanugi, Johann; Silva, Eduardo do Couto e

2007-01-01

Opacity effects in relativistic sources of high-energy gamma-rays, such as gamma-ray bursts (GRBs) or Blazars, can probe the Lorentz factor of the outflow as well as the distance of the emission site from the source, and thus help constrain the composition of the outflow (protons, pairs, magnetic field) and the emission mechanism. Most previous works consider the opacity in steady state. Here we study the effects of the time dependence of the opacity to pair production (γγ → e + e - ) in an impulsive relativistic source, which may be relevant for the prompt gamma-ray emission in GRBs or flares in Blazars. We present a simple, yet rich, semi-analytic model for the time and energy dependence of the optical depth, τγγ, in which a thin spherical shell expands ultra-relativistically and emits isotropically in its own rest frame over a finite range of radii, R 0 (le) R (le) R 0 +ΔR. This is particularly relevant for GRB internal shocks. We find that in an impulsive source (ΔR ∼ 0 ), while the instantaneous spectrum (which is typically hard to measure due to poor photon statistics) has an exponential cutoff above the photon energy (var e psilon)1(T) where tγγ((var e psilon)1) = 1, the time integrated spectrum (which is easier to measure) has a power-law high-energy tail above the photon energy (var e psilon)1* ∼ (var e psilon)1(ΔT) where ΔT is the duration of the emission episode. Furthermore, photons with energies (var e psilon) > (var e psilon)1* are expected to arrive mainly near the onset of the spike in the light curve or flare, which corresponds to the short emission episode. This arises since in such impulsive sources it takes time to build-up the (target) photon field, and thus the optical depth τγγ((var e psilon)) initially increases with time and (var e psilon)1(T) correspondingly decreases with time, so that photons of energy (var e psilon) > (var e psilon)1* are able to escape the source mainly very early on while (var e psilon)1(T) > (var

Gray and multigroup radiation transport models for two-dimensional binary stochastic media using effective opacities

International Nuclear Information System (INIS)

Olson, Gordon L.

2016-01-01

One-dimensional models for the transport of radiation through binary stochastic media do not work in multi-dimensions. Authors have attempted to modify or extend the 1D models to work in multidimensions without success. Analytic one-dimensional models are successful in 1D only when assuming greatly simplified physics. State of the art theories for stochastic media radiation transport do not address multi-dimensions and temperature-dependent physics coefficients. Here, the concept of effective opacities and effective heat capacities is found to well represent the ensemble averaged transport solutions in cases with gray or multigroup temperature-dependent opacities and constant or temperature-dependent heat capacities. In every case analyzed here, effective physics coefficients fit the transport solutions over a useful range of parameter space. The transport equation is solved with the spherical harmonics method with angle orders of n=1 and 5. Although the details depend on what order of solution is used, the general results are similar, independent of angular order. - Highlights: • Gray and multigroup radiation transport is done through 2D stochastic media. • Approximate models for the mean radiation field are found for all test problems. • Effective opacities are adjusted to fit the means of stochastic media transport. • Test problems include temperature dependent opacities and heat capacities • Transport solutions are done with angle orders n=1 and 5.

Studies of the experimental technologies of radiative opacity

International Nuclear Information System (INIS)

Zhang Jiyan; Yang Guohong; Ding Yaonan; Yang Jiamin; Li Jun; Zhang Wenhai; He Yingling; Wang Yaomei; Huang Haodong

2004-12-01

On the SHENGUANG-II laser facility, integrated experiment for opacity measurement was performed and related physical items were studies. In the experiment, some new-typed diagnosing device were also tested. The experiment includes three contents: (1) Investigation of the measurement technique of absorption spectra in the keV region; (2) Investigation of the measurement technique of dual point projection spectroscopy; (3) Investigation of the temperature and density parameters of the experimental samples. (authors)

Nonequilibrium Chromosome Looping via Molecular Slip Links

Science.gov (United States)

Brackley, C. A.; Johnson, J.; Michieletto, D.; Morozov, A. N.; Nicodemi, M.; Cook, P. R.; Marenduzzo, D.

2017-09-01

We propose a model for the formation of chromatin loops based on the diffusive sliding of molecular slip links. These mimic the behavior of molecules like cohesin, which, along with the CTCF protein, stabilize loops which contribute to organizing the genome. By combining 3D Brownian dynamics simulations and 1D exactly solvable nonequilibrium models, we show that diffusive sliding is sufficient to account for the strong bias in favor of convergent CTCF-mediated chromosome loops observed experimentally. We also find that the diffusive motion of multiple slip links along chromatin is rectified by an intriguing ratchet effect that arises if slip links bind to the chromatin at a preferred "loading site." This emergent collective behavior favors the extrusion of loops which are much larger than the ones formed by single slip links.

Corneal Opacity in Domestic Ducks Experimentally Infected With H5N1 Highly Pathogenic Avian Influenza Virus.

Science.gov (United States)

Yamamoto, Y; Nakamura, K; Yamada, M; Mase, M

2016-01-01

Domestic ducks can be a key factor in the regional spread of H5N1 highly pathogenic avian influenza (HPAI) virus in Asia. The authors performed experimental infections to examine the relationship between corneal opacity and H5N1 HPAI virus infection in domestic ducks (Anas platyrhyncha var domestica). A total of 99 domestic ducks, including 3 control birds, were used in the study. In experiment 1, when domestic ducks were inoculated intranasally with 2 H5N1 HPAI viruses, corneal opacity appeared more frequently than neurologic signs and mortality. Corneal ulceration and exophthalmos were rare findings. Histopathologic examinations of the eyes of domestic ducks in experiment 2 revealed that corneal opacity was due to the loss of corneal endothelial cells and subsequent keratitis with edema. Influenza viral antigen was detected in corneal endothelial cells and some other ocular cells by immunohistochemistry. Results suggest that corneal opacity is a characteristic and frequent finding in domestic ducks infected with the H5N1 HPAI virus. Confirming this ocular change may improve the detection rate of infected domestic ducks in the field. © The Author(s) 2015.

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.

Nuclear opacity for neutrinos at small Q2

International Nuclear Information System (INIS)

Kopeliovich, B.Z.

1989-01-01

The causes of nuclear screening of the vector and the weak axial currents are quite different. The hadronic fluctuations of neutrino in the nuclear matter live much longer than in the vacuum, due to interaction with nucleons. Nuclear opacity for neutrinos calculated using Glauber-Gribov theory, differs considerably from that given by the Bell optical model. A good agreement of the theory with the recent BEBC WA59 Collaboration measurements is found. 14 refs.; 4 figs

Designing the OPAC User Interface to Improve Access and Retrieval.

Science.gov (United States)

Basista, Thomas; And Others

1991-01-01

Discussion of problems with retrieval of records in library online public access catalogs (OPACs) focuses on an ongoing research project at the Indiana University of Pennsylvania (IUP) that has been trying to improve subject retrieval vocabulary control using natural and thesaural language and on the design of a good graphical user interface.…

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.

Epistemic Opacity, Confirmation Holism and Technical Debt: Computer Simulation in the Light of Empirical Software Engineering

OpenAIRE

Newman , Julian

2015-01-01

Epistemic opacity vis a vis human agents has been presented as an essential, ineliminable characteristic of computer simulation models resulting from the characteristics of the human cognitive agent. This paper argues, on the contrary, that such epistemic opacity as does occur in computer simulations is not a consequence of human limitations but of a failure on the part of model developers to adopt good software engineering practice for managing human error and ensuring the software artefact ...

A kinematic view of loop closure.

Science.gov (United States)

Coutsias, Evangelos A; Seok, Chaok; Jacobson, Matthew P; Dill, Ken A

2004-03-01

We consider the problem of loop closure, i.e., of finding the ensemble of possible backbone structures of a chain segment of a protein molecule that is geometrically consistent with preceding and following parts of the chain whose structures are given. We reduce this problem of determining the loop conformations of six torsions to finding the real roots of a 16th degree polynomial in one variable, based on the robotics literature on the kinematics of the equivalent rotator linkage in the most general case of oblique rotators. We provide a simple intuitive view and derivation of the polynomial for the case in which each of the three pair of torsional axes has a common point. Our method generalizes previous work on analytical loop closure in that the torsion angles need not be consecutive, and any rigid intervening segments are allowed between the free torsions. Our approach also allows for a small degree of flexibility in the bond angles and the peptide torsion angles; this substantially enlarges the space of solvable configurations as is demonstrated by an application of the method to the modeling of cyclic pentapeptides. We give further applications to two important problems. First, we show that this analytical loop closure algorithm can be efficiently combined with an existing loop-construction algorithm to sample loops longer than three residues. Second, we show that Monte Carlo minimization is made severalfold more efficient by employing the local moves generated by the loop closure algorithm, when applied to the global minimization of an eight-residue loop. Our loop closure algorithm is freely available at http://dillgroup. ucsf.edu/loop_closure/. Copyright 2004 Wiley Periodicals, Inc. J Comput Chem 25: 510-528, 2004

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.

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.

Studying DNA looping by single-molecule FRET.

Science.gov (United States)

Le, Tung T; Kim, Harold D

2014-06-28

Bending of double-stranded DNA (dsDNA) is associated with many important biological processes such as DNA-protein recognition and DNA packaging into nucleosomes. Thermodynamics of dsDNA bending has been studied by a method called cyclization which relies on DNA ligase to covalently join short sticky ends of a dsDNA. However, ligation efficiency can be affected by many factors that are not related to dsDNA looping such as the DNA structure surrounding the joined sticky ends, and ligase can also affect the apparent looping rate through mechanisms such as nonspecific binding. Here, we show how to measure dsDNA looping kinetics without ligase by detecting transient DNA loop formation by FRET (Fluorescence Resonance Energy Transfer). dsDNA molecules are constructed using a simple PCR-based protocol with a FRET pair and a biotin linker. The looping probability density known as the J factor is extracted from the looping rate and the annealing rate between two disconnected sticky ends. By testing two dsDNAs with different intrinsic curvatures, we show that the J factor is sensitive to the intrinsic shape of the dsDNA.

Soliton concepts and protein structure

Science.gov (United States)

Krokhotin, Andrei; Niemi, Antti J.; Peng, Xubiao

2012-03-01

Structural classification shows that the number of different protein folds is surprisingly small. It also appears that proteins are built in a modular fashion from a relatively small number of components. Here we propose that the modular building blocks are made of the dark soliton solution of a generalized discrete nonlinear Schrödinger equation. We find that practically all protein loops can be obtained simply by scaling the size and by joining together a number of copies of the soliton, one after another. The soliton has only two loop-specific parameters, and we compute their statistical distribution in the Protein Data Bank (PDB). We explicitly construct a collection of 200 sets of parameters, each determining a soliton profile that describes a different short loop. The ensuing profiles cover practically all those proteins in PDB that have a resolution which is better than 2.0 Å, with a precision such that the average root-mean-square distance between the loop and its soliton is less than the experimental B-factor fluctuation distance. We also present two examples that describe how the loop library can be employed both to model and to analyze folded proteins.

Experimental and Theoretical Study of the Movement of the Wpd Flexible Loop of Human Protein Tyrosine Phosphatase PTP1B in Complex with Halide Ions

Science.gov (United States)

Katz, Aline; Saenz-Méndez, Patricia; Cousido-Siah, Alexandra; Podjarny, Alberto D.; Ventura, Oscar N.

2012-11-01

Protein tyrosine phosphorylation is a post-translational modification mechanism, crucial for the regulation of nearly all aspects of cell life. This dynamic, reversible process is regulated by the balanced opposing activity of protein tyrosine kinases and protein tyrosine phosphatases. In particular, the protein tyrosine phosphatase 1B (PTP1B) is implicated in the regulation of the insulin-receptor activity, leptin-stimulated signal transduction pathways and other clinically relevant metabolic routes, and it has been found overexpressed or overregulated in human breasts, colon and ovary cancers. The WPD loop of the enzyme presents an inherent flexibility, and it plays a fundamental role in the enzymatic catalysis, turning it into a potential target in the design of new efficient PTP1B inhibitors. In order to determine the interactions that control the spatial conformation adopted by the WPD loop, complexes between the enzyme and halide ions (Br- and I- in particular) were crystallized and their crystallographic structure determined, and the collective movements of the aforementioned complexes were studied through Molecular Dynamics (MD) simulations. Both studies yielded concordant results, indicating the existence of a relationship between the identity of the ion present in the complex and the strength of the interactions it establishes with the surrounding protein residues.

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.

The soluble loop BC region guides, but not dictates, the assembly of the transmembrane cytochrome b6.

Directory of Open Access Journals (Sweden)

Lydia Tome-Stangl

Full Text Available Studying folding and assembly of naturally occurring α-helical transmembrane proteins can inspire the design of membrane proteins with defined functions. Thus far, most studies have focused on the role of membrane-integrated protein regions. However, to fully understand folding pathways and stabilization of α-helical membrane proteins, it is vital to also include the role of soluble loops. We have analyzed the impact of interhelical loops on folding, assembly and stability of the heme-containing four-helix bundle transmembrane protein cytochrome b6 that is involved in charge transfer across biomembranes. Cytochrome b6 consists of two transmembrane helical hairpins that sandwich two heme molecules. Our analyses strongly suggest that the loop connecting the helical hairpins is not crucial for positioning the two protein "halves" for proper folding and assembly of the holo-protein. Furthermore, proteolytic removal of any of the remaining two loops, which connect the two transmembrane helices of a hairpin structure, appears to also not crucially effect folding and assembly. Overall, the transmembrane four-helix bundle appears to be mainly stabilized via interhelical interactions in the transmembrane regions, while the soluble loop regions guide assembly and stabilize the holo-protein. The results of this study might steer future strategies aiming at designing heme-binding four-helix bundle structures, involved in transmembrane charge transfer reactions.

Statistical approach for calculating opacities of high-Z plasmas

International Nuclear Information System (INIS)

Nishikawa, Takeshi; Nakamura, Shinji; Takabe, Hideaki; Mima, Kunioki

1992-01-01

For simulating the X-ray radiation from laser produced high-Z plasma, an appropriate atomic modeling is necessary. Based on the average ion model, we have used a rather simple atomic model for opacity calculation in a hydrodynamic code and obtained a fairly good agreement with the experiment on the X-ray spectra from the laser-produced plasmas. We have investigated the accuracy of the atomic model used in the hydrodynamic code. It is found that transition energies of 4p-4d, 4d-4f, 4p-5d, 4d-5f and 4f-5g, which are important in laser produced high-Z plasma, can be given within an error of 15 % compared to the values by the Hartree-Fock-Slater (HFS) calculation and their oscillator strengths obtained by HFS calculation vary by a factor two according to the difference of charge state. We also propose a statistical method to carry out detail configuration accounting for electronic state by use of the population of bound electrons calculated with the average ion model. The statistical method is relatively simple and provides much improvement in calculating spectral opacities of line radiation, when we use the average ion model to determine electronic state. (author)

Ground-glass opacity in diffuse lung diseases: high-resolution computed tomography-pathology correlation

International Nuclear Information System (INIS)

Santos, Maria Lucia de Oliveira; Vianna, Alberto Domingues; Marchiori, Edson; Souza Junior, Arthur Soares; Moraes, Heleno Pinto de

2003-01-01

Ground-glass opacity is a finding frequently seen in high-resolution computed tomography examinations of the chest and is characterized by hazy increased attenuation of lung, however without blurring of bronchial and vascular margins. Due to its un specificity, association with other radiological, clinical and pathological findings must be considered for an accurate diagnostic interpretation. In this paper were reviewed 62 computed tomography examinations of patients with diffuse pulmonary diseases of 14 different etiologies in which ground-glass opacity was the only or the most remarkable finding, and correlated this findings with pathology abnormalities seen on specimens obtained from biopsies or necropsies. In pneumocystosis, ground-glass opacities correlated histologically with alveolar occupation by a foaming material containing parasites, in bronchiole alveolar cell carcinoma with thickening of the alveolar septa and occupation of the lumen by mucus and tumoral cells, in paracoccidioidomycosis with thickening of the alveolar septa, areas of fibrosis and alveolar bronchopneumonia exudate, in sarcoidosis with fibrosis or clustering of granulomas and in idiopathic pulmonary fibrosis with alveolar septa thickening due to fibrosis. Alveolar occupation by blood was found in cases of leptospirosis, idiopathic hemo siderosis, metastatic kidney tumor and invasive aspergillosis whereas oily vacuole were seen in lipoid pneumonia, proteinaceous and lipo proteinaceous material in silico proteinosis and pulmonary alveolar proteinosis, and edematous fluid in cardiac failure. (author)

Limb-darkening opacity experiment using a laser-heated plasma

International Nuclear Information System (INIS)

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

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

Science.gov (United States)

Kristensen, Tatjana P; Maria Cherian, Reeja; Gray, Fiona C; MacNeill, Stuart A

2014-01-01

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 studies.

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

Configuration interaction effect on open M shell Fe and Ni LTE spectral opacities, Rosseland and Planck means

International Nuclear Information System (INIS)

Gilles, D; Busquet, M; Gilleron, F; Pain, J-C; Klapisch, M

2016-01-01

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. (paper)

The Opacity of Russian-Ukrainian Energy Relations

International Nuclear Information System (INIS)

Dubien, A.

2007-01-01

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)

Analysis of irregular opacities of silicosis using computed tomography

International Nuclear Information System (INIS)

Maeda, Atsushi; Shida, Hisao; Chiyotani, Keizo; Saito, Kenichi; Mishina, Michihito

1983-01-01

Classification in used to codify Chest CT images of abnormalities of the lung in a simple reproducible manner. Simbols to record CT features of importance are listed. We applied CT to 92 cases of silicosis and roentgenological analysis was performed. Bullae, honeycombing, cavity, emphysema, pleural thickning and calcification were more clearly demonstrated in CT images than routine chest roentgenograms. Irregular opacities were considered to be a combined profusion of small round and streak or strand. (author)

IRAS associations with dark clouds of opacity class 6

International Nuclear Information System (INIS)

Parker, N.D.

1988-01-01

Accurate positions of the opacity class 6 clouds from the Lynds Catalog of Dark Nebulae have been measured on blue and red prints from the Polomar Observatory Sky Survey (POSS) plates. These revised positions and the dimensions of ellipses fitted to the clouds are listed. The IRAS point source catalog has been searched for sources lying within the boundaries of the 147 clouds in the sample. The distribution and properties of these IRAS sources are discussed briefly. (author)

Effect of cigarette smoking on the detection of small radiographic opacities in inorganic dust diseases

International Nuclear Information System (INIS)

Blanc, P.D.; Gamsu, G.

1988-01-01

Whether cigarette smoking can cause radiographic opacities indistinguishable from those due to pneumoconiosis remains controversial. The situation becomes clearer when one limits the abnormalities to those that can be standardized under the International Labour Office (ILO) classification system. The bulk of the evidence indicates that, using the ILO system, cigarette smoking alone is not associated with radiographic opacities that would be mistaken for pneumoconiosis with sufficient frequency to be of any practical importance. The effects of cigarette smoking, as a cofactor, in conjunction with occupational dust exposure depend on the type of dust. No relationship has been convincingly demonstrated for coal dust or silica. Only with asbestos exposure does there appear to be a significant cigarette smoking-associated increase in the frequency of irregular radiographic opacities. This increase does not appear to translate into a restrictive impairment in pulmonary function. The limited information available indicates that the features of asbestosis on high-resolution computed tomography are not similarly related to cigarette smoking. Additional research is needed to substantiate the relationship between smoking and occupational exposure to dust of many types, and also the possible imaging and pathophysiologic significance of their interactions. 47 references

Loop Transfer Matrix and Loop Quantum Mechanics

International Nuclear Information System (INIS)

Savvidy, George K.

2000-01-01

The gonihedric model of random surfaces on a 3d Euclidean lattice has equivalent representation in terms of transfer matrix K(Q i ,Q f ), which describes the propagation of loops Q. We extend the previous construction of the loop transfer matrix to the case of nonzero self-intersection coupling constant κ. We introduce the loop generalization of Fourier transformation which allows to diagonalize transfer matrices, that depend on symmetric difference of loops only and express all eigenvalues of 3d loop transfer matrix through the correlation functions of the corresponding 2d statistical system. The loop Fourier transformation allows to carry out the analogy with quantum mechanics of point particles, to introduce conjugate loop momentum P and to define loop quantum mechanics. We also consider transfer matrix on 4d lattice which describes propagation of memebranes. This transfer matrix can also be diagonalized by using the generalized Fourier transformation, and all its eigenvalues are equal to the correlation functions of the corresponding 3d statistical system. In particular the free energy of the 4d membrane system is equal to the free energy of 3d gonihedric system of loops and is equal to the free energy of 2d Ising model. (author)

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

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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.

A small stem-loop structure of the Ebola virus trailer is essential for replication and interacts with heat-shock protein A8.

Science.gov (United States)

Sztuba-Solinska, Joanna; Diaz, Larissa; Kumar, Mia R; Kolb, Gaëlle; Wiley, Michael R; Jozwick, Lucas; Kuhn, Jens H; Palacios, Gustavo; Radoshitzky, Sheli R; J Le Grice, Stuart F; Johnson, Reed F

2016-11-16

Ebola virus (EBOV) is a single-stranded negative-sense RNA virus belonging to the Filoviridae family. The leader and trailer non-coding regions of the EBOV genome likely regulate its transcription, replication, and progeny genome packaging. We investigated the cis-acting RNA signals involved in RNA-RNA and RNA-protein interactions that regulate replication of eGFP-encoding EBOV minigenomic RNA and identified heat shock cognate protein family A (HSC70) member 8 (HSPA8) as an EBOV trailer-interacting host protein. Mutational analysis of the trailer HSPA8 binding motif revealed that this interaction is essential for EBOV minigenome replication. Selective 2'-hydroxyl acylation analyzed by primer extension analysis of the secondary structure of the EBOV minigenomic RNA indicates formation of a small stem-loop composed of the HSPA8 motif, a 3' stem-loop (nucleotides 1868-1890) that is similar to a previously identified structure in the replicative intermediate (RI) RNA and a panhandle domain involving a trailer-to-leader interaction. Results of minigenome assays and an EBOV reverse genetic system rescue support a role for both the panhandle domain and HSPA8 motif 1 in virus replication. Published by Oxford University Press on behalf of Nucleic Acids Research 2016. This work is written by (a) US Government employee(s) and is in the public domain in the US.

A clickstream data analysis of Chinese academic library OPAC users' information behavior

NARCIS (Netherlands)

Jiang, Tingting; Chi, Yu; Gao, Huiqin

2017-01-01

Chinese academic libraries have been devoting great effort into introducing next-generation online public access catalogs (OPACs) in order to provide a better user experience. However, there is a lack of empirical research on their usage. In this study, a transaction log file from a typical

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

Loop-Loop Interactions Regulate KaiA-Stimulated KaiC Phosphorylation in the Cyanobacterial KaiABC Circadian Clock

Energy Technology Data Exchange (ETDEWEB)

Egli, Martin [Vanderbilt Univ., Nashville, TN (United States); Pattanayek, Rekha [Vanderbilt Univ., Nashville, TN (United States); Sheehan, Jonathan H. [Vanderbilt Univ., Nashville, TN (United States); Xu, Yao [Vanderbilt Univ., Nashville, TN (United States); Mori, Tetsuya [Vanderbilt Univ., Nashville, TN (United States); Smith, Jarrod A. [Vanderbilt Univ., Nashville, TN (United States); Johnson, Carl H. [Vanderbilt Univ., Nashville, TN (United States)

2013-01-25

We found that the Synechococcus elongatus KaiA, KaiB, and KaiC proteins in the presence of ATP generate a post-translational oscillator that runs in a temperature-compensated manner with a period of 24 h. KaiA dimer stimulates phosphorylation of KaiC hexamer at two sites per subunit, T432 and S431, and KaiB dimers antagonize KaiA action and induce KaiC subunit exchange. Neither the mechanism of KaiA-stimulated KaiC phosphorylation nor that of KaiB-mediated KaiC dephosphorylation is understood in detail at present. We demonstrate here that the A422V KaiC mutant sheds light on the former mechanism. It was previously reported that A422V is less sensitive to dark pulse-induced phase resetting and has a reduced amplitude of the KaiC phosphorylation rhythm in vivo. A422 maps to a loop (422-loop) that continues toward the phosphorylation sites. By pulling on the C-terminal peptide of KaiC (A-loop), KaiA removes restraints from the adjacent 422-loop whose increased flexibility indirectly promotes kinase activity. We found in the crystal structure that A422V KaiC lacks phosphorylation at S431 and exhibits a subtle, local conformational change relative to wild-type KaiC. Molecular dynamics simulations indicate higher mobility of the 422-loop in the absence of the A-loop and mobility differences in other areas associated with phosphorylation activity between wild-type and mutant KaiCs. Finally, the A-loop–422-loop relay that informs KaiC phosphorylation sites of KaiA dimer binding propagates to loops from neighboring KaiC subunits, thus providing support for a concerted allosteric mechanism of phosphorylation.

Random sampling technique for ultra-fast computations of molecular opacities for exoplanet atmospheres

Science.gov (United States)

Min, M.

2017-10-01

Context. Opacities of molecules in exoplanet atmospheres rely on increasingly detailed line-lists for these molecules. The line lists available today contain for many species up to several billions of lines. Computation of the spectral line profile created by pressure and temperature broadening, the Voigt profile, of all of these lines is becoming a computational challenge. Aims: We aim to create a method to compute the Voigt profile in a way that automatically focusses the computation time into the strongest lines, while still maintaining the continuum contribution of the high number of weaker lines. Methods: Here, we outline a statistical line sampling technique that samples the Voigt profile quickly and with high accuracy. The number of samples is adjusted to the strength of the line and the local spectral line density. This automatically provides high accuracy line shapes for strong lines or lines that are spectrally isolated. The line sampling technique automatically preserves the integrated line opacity for all lines, thereby also providing the continuum opacity created by the large number of weak lines at very low computational cost. Results: The line sampling technique is tested for accuracy when computing line spectra and correlated-k tables. Extremely fast computations ( 3.5 × 105 lines per second per core on a standard current day desktop computer) with high accuracy (≤1% almost everywhere) are obtained. A detailed recipe on how to perform the computations is given.

Arab Libraries’ Web-based OPACs: An evaluative study in the light of IFLA’s Guidelines For Online Public Access Catalogue (OPAC Displays

Directory of Open Access Journals (Sweden)

Sherif Kamel Shaheen

2005-03-01

Full Text Available The research aims at evaluating Arabic Libraries’ Web-based Catalogues in the light of Principles and Recommendations published in: IFLA’s Guidelines For OPAC Displays (September 30, 2003 Draft For Worldwide Review. The total No. Of Recommendations reached” 38 “were categorized under three main titles, as follows: User Needs (12 recommendations, Content and arrangement Principle (25 recommendations, Standardization Principle (one recommendation However that number increased to reach 88 elements when formulated as evaluative criteria and included in the study’s checklist.

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

International Nuclear Information System (INIS)

Furuita, Kyoko; Kataoka, Saori; Sugiki, Toshihiko; Hattori, Yoshikazu; Kobayashi, Naohiro; Ikegami, Takahisa; Shiozaki, Kazuhiro; Fujiwara, Toshimichi; Kojima, Chojiro

2015-01-01

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

Development of an Aerosol Opacity Retrieval Algorithm for Use with Multi-Angle Land Surface Images

Science.gov (United States)

Diner, D.; Paradise, S.; Martonchik, J.

1994-01-01

In 1998, the Multi-angle Imaging SpectroRadiometer (MISR) will fly aboard the EOS-AM1 spacecraft. MISR will enable unique methods for retrieving the properties of atmospheric aerosols, by providing global imagery of the Earth at nine viewing angles in four visible and near-IR spectral bands. As part of the MISR algorithm development, theoretical methods of analyzing multi-angle, multi-spectral data are being tested using images acquired by the airborne Advanced Solid-State Array Spectroradiometer (ASAS). In this paper we derive a method to be used over land surfaces for retrieving the change in opacity between spectral bands, which can then be used in conjunction with an aerosol model to derive a bound on absolute opacity.

TIPTOPbase: the Iron Project and the Opacity Project Atomic Database

Science.gov (United States)

Mendoza, Claudio; Nahar, Sultana; Pradhan, Anil; Seaton, Micheal; Zeippen, Claude

2001-05-01

The Opacity Project, the IRON Project, and the RmaX Network (The Opacity Project Team, Vol.1,2), IOPP, Bristol (1995,1996); Hummer et al., Astron. Astrophys. 279, 298 (1993) are international computational efforts concerned with the production of high quality atomic data for astrophysical applications. Research groups from Canada, France, Germany, UK, USA and Venezuela are involved. Extensive data sets containing accurate energy levels, f-values, A-values, photoionisation cross sections, collision strengths, recombination rates, and opacitites have been computed for cosmically abundant elements using state-of-the-art atomic physics codes. Their volume, completeness and overall accuracy are presently unmatched in the field of laboratory astrophysics. Some of the data sets have been available since 1993 from a public on-line database service referred to as TOPbase (Cunto et al Astron. Astrophys. 275), L5 (1993), ( http://cdsweb.u-strasbg.fr/OP.html at CDS France, and http://heasarc.gsfc.nasa.gov/topbase, at NSAS USA). We are currently involved in a major effort to scale the existing database services to develop a robust platform for the high-profile dissemination of atomic data to the scientific community within the next 12 months. (Partial support from the NSF and NASA is acknowledged.)

Loop residues and catalysis in OMP synthase

DEFF Research Database (Denmark)

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

2012-01-01

binding of OMP or PRPP in binary complexes was affected little by loop mutation, suggesting that the energetics of ground-state binding have little contribution from the catalytic loop, or that a favorable binding energy is offset by costs of loop reorganization. Pre-steady-state kinetics for mutants...... values for all four substrate molecules. The 20% (i.e., 1.20) intrinsic [1?-3H]OMP kinetic isotope effect (KIE) for WT is masked because of high forward and reverse commitment factors. K103A failed to express intrinsic KIEs fully (1.095 ± 0.013). In contrast, H105A, which has a smaller catalytic lesion...... (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...

Loop kinematics

International Nuclear Information System (INIS)

Migdal, A.A.

1982-01-01

Basic operators acting in the loop space are introduced. The topology of this space and properties of the Stokes type loop functionals are discussed. The parametrically invariant loop calculus developed here is used in the loop dynamics

Has the pelvic renal stone position inside the upper loop of JJ stent any influence on the extracorporeal shock wave lithotripsy results?

Science.gov (United States)

Pricop, Catalin; Serban, Dragomir N; Serban, Ionela Lacramioara; Cumpanas, Alin-Adrian; Gingu, Constantin-Virgil

2016-01-01

JJ stents are often encountered in patients with pelvic renal stones referred for shock wave lithotripsy, most of them being placed either for obstructive renal pelvic stones or for ureteric stones mobilized retrograde during the JJ stent insertion. The aim of the study was to determine whether the relative stone position in the upper loop of the JJ stent during extracorporeal shock wave lithotripsy (SWL) influences the efficiency of the procedure. The study was designed as a prospective cohort study on 162 patients addressing the same urological department, with single renal pelvic stone (primary or mobilized to the renal pelvis during the insertion of JJ stent), smaller than 15 mm, with JJ stent, treated by SWL using a second generation spark gap lithotripter, 18 kV, 3000 waves/session. Patients were divided in three groups according to the relative position of the stone to the upper loop of the JJ stent as appears on plain X-ray: stone-inside-loop, loop-crossing-stone and stone-outside the loop. The SWL success rate was the primary outcome of the study. p Value, Chi square and Kruskal-Wallis tests were used for statistical analysis. For stone-inside-loop cases, SWL efficiency was 22.7 versus 42 % for all the other cases (p = 0.002). Other factors for decreased SWL success rate were: higher stone radio-opacity, larger JJ of stent and obese patients. Study limitation is represented by the relative small study group and by the evaluation of stone density using plain X-ray instead of computer tomography. For pelvic renal stones having the same density characteristics studied by plain X-ray, the SWL efficiency is lower in stone-inside-loop cases comparing with the other positions. The overall stone free rate for renal pelvic stones could be explained by the second generation lithotripter used for all procedures.

Design for LTE EOS and opacity experiments using supersonic radiation waves

Science.gov (United States)

Tierney, T. E.; Peterson, R. R.; Tierney, H. E.

2007-11-01

Opacity and EOS at 100-200 eV are important physical parameters in ICF experiments. We describe an experiment design that uses the supersonic propagation of hohlraum radiation in foams to isochorically heat samples. Laser and Z-pinch experiments frequently use 150 to 220-eV quasi-blackbody emission from hohlraums to drive physics experiments. A foam target encapsulated in a gold-wall cylinder is placed next to the hohlraum. The low density and opacity foam captures some hohlraum emission and generates a supersonically-propagating radiation wave. The material heated by the wave is cooler towards the high-albedo gold wall. Modeling and past measurements show that core regions of the foam have small thermal gradients. We place a small, thin sample (e.g., Al, Si, or Fe) in the thermally-uniform region. X-ray emission of tracers and the sample as well as quasi-continuum x-ray absorption will be measured using time-resolved x-ray spectroscopy. The foam's EOS can be measured to ±5% by blast waves with a well characterized drive. This experiment could use the OMEGA, Z-Beamlet, and/or ZR facilities to explore temperature-dependent conditions.

Biodegradable X-ray markers of controlled radio-opacity. Temporary position measurements in bone

NARCIS (Netherlands)

Stallmann, H.P.; Faber, C.; Plokker, H.M.; Wuisman, P.I.J.M.

2005-01-01

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 × 10 mm markers containing different iodine concentrations (0,120, 240, 360

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.

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.

Lenticular opacities in proximally exposed A-bomb survivors and their lately significance

Energy Technology Data Exchange (ETDEWEB)

Sugimoto, S [Sugimoto Ophthalmological Clinic, Hiroshima (Japan)

1978-04-01

Five cases of lenticular opacities in proximally exposed A-bomb survivors (not published yet) were reported with some slides. From these experiment cases, following items were investigated. Significance of A-bomb radiation cataracts: Because cataract is the first manifistation of delayed hazard to a human body caused by A-bomb radiation and can be observed still now, cataract is regarded to be very important for recognizing A-bomb hazard. The manifestation of these findings of cataract is the reason for strong appeals that A-bomb hazard is still existing. Clinical findings of lenticular opacities was searched with reference to the literature. Several findings in experiment cases were described, and the importance of the study about changes of clinical findings was mentioned. It was pointed out that radiation cataract is closely related to the loss of hair in acute atomic radiation hazard. In case of radiation cataract, some difference between right and left eye was sometimes observed. Studies concerning this difference should be further developed in future. The importance of the factors of shielding was pointed out.

Improvement of chronic corneal opacity in ocular surface disease with prosthetic replacement of the ocular surface ecosystem (PROSE) treatment.

Science.gov (United States)

Cressey, Anna; Jacobs, Deborah S; Remington, Crystal; Carrasquillo, Karen G

2018-06-01

To demonstrate clearing of chronic corneal opacities and improvement of visual acuity with the use of BostonSight prosthetic replacement of the ocular surface ecosystem (PROSE) treatment in ocular surface disease. We undertook retrospective analysis of the medical records of a series of patients who underwent PROSE treatment from August 2006 to December 2014. Patients were referred for ocular surface disease of various etiologies. Primary inclusion criterion was corneal opacity that improved with PROSE treatment. Patients were excluded if topical steroids or adjuvant therapy used once PROSE treatment was initiated. Underlying disease, prior treatment, clinical presentation, and clinical course were extracted from the medical record. Four patients are included in this series. There were three females and one male; median age at time of treatment initiation was 30 years (range = 0.5-58 years). Median duration of PROSE treatment at time of retrospective analysis was 3.5 years (range = 1-8 years). Two cases had corneal opacification in the context of neurotrophic keratopathy: a unilateral case due to presumed herpes simplex keratitis and a bilateral case due to congenital corneal anesthesia associated with familial dysautonomia. One case had corneal opacity from exposure related to seventh nerve palsy, and one had corneal opacification associated with recurrent surface breakdown, neurotrophic keratopathy, and limbal stem deficiency of uncertain etiology. After consistent wear of prosthetic devices used in PROSE treatment for support of the ocular surface, visual acuity improved and clearing of the opacities was observed, without use of topical steroids or adjuvant therapy. These cases demonstrate clearing of chronic corneal opacity with PROSE treatment for ocular surface disease. This clearing can occur with no adjuvant therapy, suggesting that restoration of ocular surface function and integrity allows for corneal remodeling.

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

Two-loop polygon Wilson loops in N = 4 SYM

International Nuclear Information System (INIS)

Anastasiou, C.; Brandhuber, A.; Heslop, P.; Spence, B.; Travaglini, G.; Khoze, V.V.

2009-01-01

We compute for the first time the two-loop corrections to arbitrary n-gon lightlike Wilson loops in N = 4 supersymmetric Yang-Mills theory, using efficient numerical methods. The calculation is motivated by the remarkable agreement between the finite part of planar six-point MHV amplitudes and hexagon Wilson loops which has been observed at two loops. At n = 6 we confirm that the ABDK/BDS ansatz must be corrected by adding a remainder function, which depends only on conformally invariant ratios of kinematic variables. We numerically compute remainder functions for n = 7,8 and verify dual conformal invariance. Furthermore, we study simple and multiple collinear limits of the Wilson loop remainder functions and demonstrate that they have precisely the form required by the collinear factorisation of the corresponding two-loop n-point amplitudes. The number of distinct diagram topologies contributing to the n-gon Wilson loops does not increase with n, and there is a fixed number of 'master integrals', which we have computed. Thus we have essentially computed general polygon Wilson loops, and if the correspondence with amplitudes continues to hold, all planar n-point two-loop MHV amplitudes in the N = 4 theory.

Influence of the number of atomic levels on the spectral opacity of low temperature nickel and iron in the spectral range 50-300 eV

International Nuclear Information System (INIS)

Busquet, M.; Klapisch, M.; Gilles, D.

2013-01-01

Opacity is a fundamental ingredient for the secular evolution of stars. The calculation of the stellar plasma absorption coefficients is complex due to the composition of these plasmas, generally an H /He dominated mixture with a low concentration of partially ionized heavy ions (the iron group). The international collaboration OPAC recently presented extensive comparisons of spectral opacities of iron and nickel for temperatures between 15 and 40 eV and for densities of ∼ 3 mg/cm 3 , relevant to the stellar envelope conditions [1, 2]. The role of Configuration Interaction (CI) and the influence of the number of atomic levels on the opacity using the recently improved version of HULLAC atomic code [3, 4] are illustrated in this article. Comparisons with theoretical predictions already presented in [1] are discussed. (authors)

APLIKASI ONLINE PUBLIC ACCESS CATALOQUE (OPAC BERBASIS ANDROID SEBAGAI SARANA TEMU KEMBALI INFORMASI DI PERPUSTAKAAN UNIVERSITAS PENDIDIKAN GANESHA

Directory of Open Access Journals (Sweden)

Putu Tika Parmawati

2016-08-01

Full Text Available Abstrak Penelitian ini bertujuan untuk mengembangkan perangkat lunak aplikasi Online Public Access Cataloque (OPAC berbasis android. Jenis penelitian ini merupakan Research and Development (R & D dengan metode pengembangan menggunakan model prototyping. Pengembangan sistem informasi layanan audio visual berbasis video streaming dengan enam tahap, yaitu : 1 Tahap pengumpulan kebutuhan dan perbaikan, 2 Tahap perancangan desain cepat (desain awal, 3 Tahap membangun prototipe, 4 Tahap evaluasi prototype, 5 Tahap perbaikan prototype, dan 6 Tahap rekayasa produk. Penentuan tingkat kelayakan aplikasi Online Public Access Cataloque (OPAC berbasis android berdasarkan uji validasi ahli bidang teknologi informasi dan uji coba terbatas pada pengguna. Hasil uji coba sebagai berikut : 1 Pengembangan aplikasi Online Public Access Cataloque (OPAC berbasis android sudah sesuai dengan spesifikasi yang telah ditentukan sebagai aplikasi penelusuran informasi koleksi buku teks umum secara online melalui smartphone. 2 Indikator penilaian dari program ini adalah kebenaran atau ketepatan operasional sistem, ketegaran, keterluasan, keterpakaian ulang, efisiensi atau kinerja, portabilitas, integritas, modularitas, keterbacaan mendapat kualifikasi cukup baik, sedangkan verifikasi mendapat kualifikasi baik. 3 Secara umum dari hasil penilaian tersebut aplikasi OPAC berbasis android ini cukup layak untuk digunakan sebagai alternatif pelengkap pemberian layanan penelusuran informasi koleksi buku teks umum di Perpustakaan Undiksha. Kata Kunci: OPAC, android, dan temu kembali informasi Abstract Aim of this study to develop the software of Online Public Access Cataloque (OPAC based on android. Research and Development (R & D design was applied in this study which was developed through prototyping models. The software was constructed through six stages, namely: 1 needs analysis and repairment, 2 rapid design (preliminary design, 3 prototypes building, 4 prototype evaluation, 5

The Rosseland Mean Opacity in Dense Plasmas

Science.gov (United States)

van Horn, H. M.

1992-05-01

In post-main-sequence phases of stellar evolution, densities in the interiors of stars become large enough so that hbar omega_p /kT>1, where omega_p is the electron plasma frequency. The plasma is thus a strongly dispersive medium at frequencies near the peak of the Planck function, and only photons with frequencies omega >omega_p can propagate in the plasma. These effects must be taken into account in computing radiative transfer in stellar interiors. Here I first identify several late evolutionary stages in which these effects may be significant. Then I use the formalism Harris 1965 has developed to treat radiative transfer in a dispersive medium in order to derive the resulting modification of the Rosseland mean opacity kappa_R . The resulting expression is the same as that presented (without a full derivation) by Aharony & Opher 1979, who interpreted the frequency-dependent absorption coefficient kappa_ ω as that in vacuo. However, the absorption coefficient in a plasma scales from that in vacuum according to the relation kappa_ ω=n_ω(-1) kappa_ ω((vac)) (Bekefi 1966, p. 52), where n_ω equiv (kc/omega ) = [1-(omega_p (2/) omega (2)right ](1/2)) is the index of refraction of the plasma. With this correction, we find the Rosseland mean opacity to be given by the expression {1\\over \\kappa_R}={{\\int_{\\omega_p}^{\\infty} {n_{\\omega}^3 \\over \\kappa_{\\omega}^{(vac)}}{partial B_{\\omega} \\over partial T} \\bigg|_{\\omega} d\\omega} \\over{\\int_0^{\\infty}{partial B_{\\omega} \\over partial T} \\bigg|_{\\omega} d\\omega}}. This research has been supported in part by NASA grant NAGW-2444 and in part by NSF grant AST 91-15132. \\centerline{References} Aharony, U., and Opher, R. 1979, A&A, 79, 27. Bekefi, G. 1966, Radiation Processes in Plasmas, (John Wiley & Sons, Inc.: New York). Harris, E. G. 1965, Phys. Rev., 138, B479.

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

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

Opacity alterations of bovine crystalline proteins irradiated with 10 Co in vitro in the presence of sulfonate compounds

International Nuclear Information System (INIS)

Bernardes, D.M.L.; Mastro, N.L. del

1990-01-01

Sulfhydrilic compounds with a strong basic function separated from the SH group by no more than three C atoms, as amino ethyl iso thiourea (AET) and mercapto ethyl alanine (MEA) are exceptionally effective in competing with free radicals produced by water radiolysis. In a similar way, dimethyl sulfoxide (DMSO) is also effective in the removal of hydroxyl radicals. In the present work, aqueous solutions of crystalline removed surgically from bovine eyes were used. Crystalline were homogenized, the suspension centrifuged and the supernatant dialysed. From the dialysed supernatant a series of solutions was prepared that was 60 Co irradiated with different doses from 5,000 to 25,000 Gy in the presence of 10 mM AET, MEA and DMSO. The degree of opacification was read spectrophotometricaly at 600 nm. The results pointed out a decrease of the increment of opacity produced by the radiation in the presence of those free radical scavengers, showing a radioprotective action of them at the molecular level, that can be measured by this method that mimics the cataract formation in eye lens. (author)

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.

CLINICAL OUTCOME OF PENETRATING KERATOPLASTY IN CORNEAL OPACITIES OF DIFFERENT AETIOLOGY- A CLINICAL STUDY

Directory of Open Access Journals (Sweden)

Dipak Bhuyan

2017-01-01

Full Text Available BACKGROUND Corneal transplantation or grafting is an operation in which abnormal corneal host tissue is replaced by healthy donor cornea. According to the World Health Organization (WHO, corneal diseases are among the major causes of vision loss and blindness in the world today after cataract and glaucoma. The aim of the study is to- 1. Evaluate the different aetiology of corneal opacity including active infective aetiology as indicated for penetrating keratoplasty. 2. Determine the clinical outcome of penetrating keratoplasty in relation to graft survival, graft rejection and peri-operative complications in different aetiology groups. 3. Determine the final visual outcome. MATERIALS AND METHODS Candidates for keratoplasty were selected from- 1. Eye Bank of Regional Institute of Ophthalmology (R.I.O. 2. R.I.O OPD. The study period was from September 2014 to August 2015. 30 cases were taken in the study. Descriptive statistics were applied to analyse the data wherever necessary. RESULTS 34.6±19.73 yrs. (mean±SD was the mean age at which transplants were done in the study. Out of total 30 cases, 13 (43.33% and 17 (56.66% were male and female, respectively. The different indications for penetrating keratoplasty are- Post ulcer corneal opacity in 14 cases (46.66%, posttraumatic corneal opacity 9 cases (30%, pseudophakic bullous keratopathy 4 cases (13.33%, corneal dystrophy in 2 cases (6.66% and non-healing corneal ulcer in 1 case (3.33%. 16 cases (53.33% showed clear graft till the last follow up while 11 (33.33% cases showed partially clear graft resulting in improved visual outcome while 3 cases (10.00% of the grafts were opaque due to graft failure. CONCLUSION The major indications for penetrating keratoplasty in this part of the world are post ulcer and posttraumatic corneal opacity and majority of them are illiterate agricultural workers who failed to get adequate treatment on time. Graft survival rate is high, which can be attributed to the

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

Science.gov (United States)

2012-02-14

... with the opacity measurement/reference beam(s), spectrally selective optical filters, beam splitters... Monitor Manufacturers to Certify Conformance with Design and Performance Specifications, whereas the 2003... my COMS? Necessary components of the routine system checks will depend on the design details of your...

'Seeing the Dark': Grounding Phenomenal Transparency and Opacity in Precision Estimation for Active Inference.

Science.gov (United States)

Limanowski, Jakub; Friston, Karl

2018-01-01

One of the central claims of the Self-model Theory of Subjectivity is that the experience of being someone - even in a minimal form - arises through a transparent phenomenal self-model, which itself can in principle be reduced to brain processes. Here, we consider whether it is possible to distinguish between phenomenally transparent and opaque states in terms of active inference. We propose a relationship of phenomenal opacity to expected uncertainty or precision; i.e., the capacity for introspective attention and implicit mental action. Thus we associate introspective attention with the deployment of 'precision' that may render the perceptual evidence (for action) opaque, while treating transparency as a necessary aspect of beliefs about action, i.e., 'what I am' doing. We conclude by proposing how we may have to nuance our conception of minimal phenomenal selfhood and agency in light of this active inference conception of transparency-opacity.

Model of opacity and emissivity of non-equilibrium plasma

International Nuclear Information System (INIS)

Politov V Y

2008-01-01

In this work the model describing absorption and emission properties of the non-equilibrium plasma is presented. It is based on the kinetics equations for populations of the ground, singly and doubly excited states of multi-charged ions. After solving these equations, the states populations together with the spectroscopic data, supplied in the special database for a lot ionization stages, are used for building the spectral distributions of plasma opacity and emissivity in STA approximation. Results of kinetics simulation are performed for such important X-ray converter as gold, which is investigated intensively in ICF-experiments

Random walk loop soups and conformal loop ensembles

NARCIS (Netherlands)

van de Brug, T.; Camia, F.; Lis, M.

2016-01-01

The random walk loop soup is a Poissonian ensemble of lattice loops; it has been extensively studied because of its connections to the discrete Gaussian free field, but was originally introduced by Lawler and Trujillo Ferreras as a discrete version of the Brownian loop soup of Lawler and Werner, a

Renormalization of loop functions for all loops

International Nuclear Information System (INIS)

Brandt, R.A.; Neri, F.; Sato, M.

1981-01-01

It is shown that the vacuum expectation values W(C 1 ,xxx, C/sub n/) of products of the traces of the path-ordered phase factors P exp[igcontour-integral/sub C/iA/sub μ/(x)dx/sup μ/] are multiplicatively renormalizable in all orders of perturbation theory. Here A/sub μ/(x) are the vector gauge field matrices in the non-Abelian gauge theory with gauge group U(N) or SU(N), and C/sub i/ are loops (closed paths). When the loops are smooth (i.e., differentiable) and simple (i.e., non-self-intersecting), it has been shown that the generally divergent loop functions W become finite functions W when expressed in terms of the renormalized coupling constant and multiplied by the factors e/sup -K/L(C/sub i/), where K is linearly divergent and L(C/sub i/) is the length of C/sub i/. It is proved here that the loop functions remain multiplicatively renormalizable even if the curves have any finite number of cusps (points of nondifferentiability) or cross points (points of self-intersection). If C/sub γ/ is a loop which is smooth and simple except for a single cusp of angle γ, then W/sub R/(C/sub γ/) = Z(γ)W(C/sub γ/) is finite for a suitable renormalization factor Z(γ) which depends on γ but on no other characteristic of C/sub γ/. This statement is made precise by introducing a regularization, or via a loop-integrand subtraction scheme specified by a normalization condition W/sub R/(C-bar/sub γ/) = 1 for an arbitrary but fixed loop C-bar/sub γ/. Next, if C/sub β/ is a loop which is smooth and simple except for a cross point of angles β, then W(C/sub β/) must be renormalized together with the loop functions of associated sets S/sup i//sub β/ = ]C/sup i/ 1 ,xxx, C/sup i//sub p/i] (i = 2,xxx,I) of loops C/sup i//sub q/ which coincide with certain parts of C/sub β/equivalentC 1 1 . Then W/sub R/(S/sup i//sub β/) = Z/sup i/j(β)W(S/sup j//sub β/) is finite for a suitable matrix Z/sup i/j

Crescentic and ring-shaped opacities. CT features in two cases of bronchiolitis obliterans organizing pneumonia (BOOP)

International Nuclear Information System (INIS)

Voloudaki, A.E.; Bouros, D.E.; Froudarakis, M.E.; Datseris, G.E.; Apostolaki, E.G.; Gourtsoyiannis, N.C.

1996-01-01

Two cases of idiopathic bronchilitis obliterans organizing pneumonia (BOOP) with unusual CT findings are presented. On CT both cases exhibited crescentic and ring-shaped opacities, surrounding areas of groundglass attenuation, and associated with a nodular pattern in one patient and airspace consolidations in the second patient. CT-pathologic correlation dislosed that the central areas of groundglass attenuation corresponded to alveolar septal inflammation, in contrast to the denser periphery where granulomatous tissue in peripheral airspaces predominated. In the broad spectrum of CT findings, BOOP can exhibit specific CT features with regard to the crescentic or ring-shaped opacities with a central groundglass attenuation area. Since these features have not been described in any other disease, they might be characteristic features for the diagnosis of BOOP. (orig.)

DNA binding specificity of the basic-helix-loop-helix protein MASH-1.

Science.gov (United States)

Meierhan, D; el-Ariss, C; Neuenschwander, M; Sieber, M; Stackhouse, J F; Allemann, R K

1995-09-05

Despite the high degree of sequence similarity in their basic-helix-loop-helix (BHLH) domains, MASH-1 and MyoD are involved in different biological processes. In order to define possible differences between the DNA binding specificities of these two proteins, we investigated the DNA binding properties of MASH-1 by circular dichroism spectroscopy and by electrophoretic mobility shift assays (EMSA). Upon binding to DNA, the BHLH domain of MASH-1 underwent a conformational change from a mainly unfolded to a largely alpha-helical form, and surprisingly, this change was independent of the specific DNA sequence. The same conformational transition could be induced by the addition of 20% 2,2,2-trifluoroethanol. The apparent dissociation constants (KD) of the complexes of full-length MASH-1 with various oligonucleotides were determined from half-saturation points in EMSAs. MASH-1 bound as a dimer to DNA sequences containing an E-box with high affinity KD = 1.4-4.1 x 10(-14) M2). However, the specificity of DNA binding was low. The dissociation constant for the complex between MASH-1 and the highest affinity E-box sequence (KD = 1.4 x 10(-14) M2) was only a factor of 10 smaller than for completely unrelated DNA sequences (KD = approximately 1 x 10(-13) M2). The DNA binding specificity of MASH-1 was not significantly increased by the formation of an heterodimer with the ubiquitous E12 protein. MASH-1 and MyoD displayed similar binding site preferences, suggesting that their different target gene specificities cannot be explained solely by differential DNA binding. An explanation for these findings is provided on the basis of the known crystal structure of the BHLH domain of MyoD.

Primary Pulmonary Mucosa-Associated Lymphoid Tissue Lymphoma with a Nodular Opacity: Report of a Case.

Science.gov (United States)

Yoshino, Naoyuki; Hirata, Tomomi; Takeuchi, Chie; Usuda, Jitsuo; Hosone, Masaru

2017-01-01

Herein, we describe our experience in treating a case of primary pulmonary mucosa-associated lymphoid tissue lymphoma detected as a nodular opacity. A 79-year-old man was referred to our hospital. Computed tomography showed a nodular opacity measuring 20 mm in diameter with regular margins in segment 5 of the right middle lobe of the lung. Although the bronchoscopic brush cytology result was class III, the patient was tentatively diagnosed with suspected mucosa-associated lymphoid tissue lymphoma. A thoracoscopic right middle lobectomy was performed. The pathological findings showed nodular proliferation of small to medium-sized, mature-appearing atypical lymphoid cells, lymphoepithelial lesions, and vague follicles suggesting follicular colonization in some areas. The patient was diagnosed with low-grade small B-cell lymphoma and mucosa-associated lymphoid tissue lymphoma. He has remained well to date, 23 months after surgery, without evidence of recurrence.

Temperature dependence of looping rates in a short peptide.

Science.gov (United States)

Roccatano, Danilo; Sahoo, Harekrushna; Zacharias, Martin; Nau, Werner M

2007-03-15

Knowledge of the influence of chain length and amino acid sequence on the structural and dynamic properties of small peptides in solution provides essential information on protein folding pathways. The combination of time-resolved optical spectroscopy and molecular dynamics (MD) simulation methods has become a powerful tool to investigate the kinetics of end-to-end collisions (looping rates) in short peptides, which are relevant in early protein folding events. We applied the combination of both techniques to study temperature-dependent (280-340 K) looping rates of the Dbo-AlaGlyGln-Trp-NH2 peptide, where Dbo represents a 2,3-diazabicyclo[2.2.2]oct-2-ene-labeled asparagine, which served as a fluorescent probe in the time-resolved spectroscopic experiments. The experimental looping rates increased from 4.8 x 10(7) s(-1) at 283 K to 2.0 x 10(8) s(-1) at 338 K in H2O. The corresponding Arrhenius plot provided as activation parameters Ea = 21.5 +/- 1.0 kJ mol(-1) and ln(A/s-1) = 26.8 +/- 0.2 in H2O. The results in D2O were consistent with a slight solvent viscosity effect, i.e., the looping rates were 10-20% slower. MD simulations were performed with the GROMOS96 force field in a water solvent model, which required first a parametrization of the synthetic amino acid Dbo. After corrections for solvent viscosity effects, the calculated looping rates varied from 1.5 x 10(8) s(-1) at 280 K to 8.2 x 10(8) s(-1) at 340 K in H2O, which was about four times larger than the experimental data. The calculated activation parameters were Ea = 24.7 +/- 1.5 kJ mol(-1) and ln(A/s(-1)) = 29.4 +/- 0.1 in H2O.

Rational Design of Nanobody80 Loop Peptidomimetics

DEFF Research Database (Denmark)

Martin, Charlotte; Moors, Samuel L C; Danielsen, Mia

2017-01-01

G protein-coupled receptors (GPCRs) play an important role in many cellular responses; as such, their mechanism of action is of utmost interest. To gain insight into the active conformation of GPCRs, the X-ray crystal structures of nanobody (Nb)-stabilized β2 -adrenergic receptor (β2 AR) have been......-hairpin conformation. Syntheses, conformational analysis, binding and functional in vitro assays, as well as internalization experiments, were performed. We demonstrate that peptidomimetics can structurally mimic the CDR3 loop of a nanobody and its function by inhibiting G protein coupling as measured by partial...

Plant proteins as binders in cellulosic paper composites.

Science.gov (United States)

Fahmy, Yehia; El-Wakil, Nahla A; El-Gendy, Ahmed A; Abou-Zeid, Ragab E; Youssef, M A

2010-07-01

Plant proteins are used - for the first time - in this work as bulk binders for cellulosic fibers in paper composites. Soy bean protein and wheat gluten were denatured by two methods, namely by: urea+NaOH and by urea+NaOH+acrylamide. Addition of increased amounts of the denatured proteins resulted in a significant increase in all paper strength properties. Soy protein led, in addition, to a remarkable enhancement in opacity. The use of proteins increased kaolin retention in the paper composites, while keeping the paper strength higher than the blank protein-free paper. The results show that plant proteins are favorable than synthetic adhesives; because they are biodegradable and do not cause troubles in paper recycling i.e. they are environmentally friendly. (c) 2010 Elsevier B.V. All rights reserved.

The Column Density Distribution and Continuum Opacity of the Intergalactic and Circumgalactic Medium at Redshift langzrang = 2.4

Science.gov (United States)

Rudie, Gwen C.; Steidel, Charles C.; Shapley, Alice E.; Pettini, Max

2013-06-01

We present new high-precision measurements of the opacity of the intergalactic and circumgalactic medium (IGM; CGM) at langzrang = 2.4. Using Voigt profile fits to the full Lyα and Lyβ forests in 15 high-resolution high-S/N spectra of hyperluminous QSOs, we make the first statistically robust measurement of the frequency of absorbers with H I column densities 14 \\lesssim log (N_H\\,\\scriptsize{ I}/ {cm}^{-2}) \\lesssim 17.2. We also present the first measurements of the frequency distribution of H I absorbers in the volume surrounding high-z galaxies (the CGM, 300 pkpc), finding that the incidence of absorbers in the CGM is much higher than in the IGM. In agreement with Rudie et al., we find that there are fractionally more high-N H I absorbers than low-N H I absorbers in the CGM compared to the IGM, leading to a shallower power law fit to the CGM frequency distribution. We use these new measurements to calculate the total opacity of the IGM and CGM to hydrogen-ionizing photons, finding significantly higher opacity than most previous studies, especially from absorbers with log (N_H\\,\\scriptsize{ I}/ {cm}^{-2}) law parameterization of the frequency distribution with a break near N H I ≈1015 cm-2. We compute new estimates of the mean free path (λmfp) to hydrogen-ionizing photons at z em = 2.4, finding λmfp = 147 ± 15 Mpc when considering only IGM opacity. If instead, we consider photons emanating from a high-z star-forming galaxy and account for the local excess opacity due to the surrounding CGM of the galaxy itself, the mean free path is reduced to λmfp = 121 ± 15 Mpc. These λmfp measurements are smaller than recent estimates and should inform future studies of the metagalactic UV background and of ionizing sources at z ≈ 2-3. Based on data obtained at the W. M. Keck Observatory, which is operated as a scientific partnership among the California Institute of Technology, the University of California, and the National Aeronautics and Space

Formation of Planetary Populations I: Metallicity & Envelope Opacity Effects

Science.gov (United States)

Alessi, Matthew; Pudritz, Ralph E.

2018-05-01

We present a comprehensive body of simulations of the formation of exoplanetary populations that incorporate the role of planet traps in slowing planetary migration. The traps we include in our model are the water ice line, the disk heat transition, and the dead zone outer edge. We reduce our model parameter set to two physical parameters: the opacity of the accreting planetary atmospheres (κenv) and a measure of the efficiency of planetary accretion after gap opening (fmax). We perform planet population synthesis calculations based on the initial observed distributions of host star and disk properties - their disk masses, lifetimes, and stellar metallicities. We find the frequency of giant planet formation scales with disk metallicity, in agreement with the observed Jovian planet frequency-metallicity relation. We consider both X-ray and cosmic ray disk ionization models, whose differing ionization rates lead to different dead zone trap locations. In both cases, Jovian planets form in our model out to 2-3 AU, with a distribution at smaller radii dependent on the disk ionization source and the setting of envelope opacity. We find that low values of κenv (0.001-0.002 cm2 g-1) and X-ray disk ionization are necessary to obtain a separation between hot Jupiters near 0.1 AU, and warm Jupiters outside 0.6 AU, a feature present in the data. Our model also produces a large number of super Earths, but the majority are outside of 2 AU. As our model assumes a constant dust to gas ratio, we suggest that radial dust evolution must be taken into account to reproduce the observed super Earth population.

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.

On the necessity of composition-dependent low-temperature opacity in models of metal-poor asymptotic giant branch stars

Energy Technology Data Exchange (ETDEWEB)

Constantino, Thomas; Campbell, Simon; Lattanzio, John [Monash Centre for Astrophysics, School of Mathematical Sciences, Monash University, Victoria 3800 (Australia); Gil-Pons, Pilar, E-mail: thomas.constantino@monash.edu [Department of Applied Physics, Polytechnic University of Catalonia, 08860 Barcelona (Spain)

2014-03-20

The vital importance of composition-dependent low-temperature opacity in low-mass (M ≤ 3 M {sub ☉}) asymptotic giant branch (AGB) stellar models of metallicity Z ≥ 0.001 has recently been demonstrated. Its significance to more metal-poor, intermediate-mass (M ≥ 2.5 M {sub ☉}) models has yet to be investigated. We show that its inclusion in lower-metallicity models ([Fe/H] ≤–2) is essential and that there exists no threshold metallicity below which composition-dependent molecular opacity may be neglected. We find it to be crucial in all intermediate-mass models investigated ([Fe/H] ≤–2 and 2.5 ≤ M/M {sub ☉} ≤ 5), because of the evolution of the surface chemistry, including the orders of magnitude increase in the abundance of molecule-forming species. Its effect on these models mirrors that previously reported for higher-metallicity models—increase in radius, decrease in T {sub eff}, faster mass loss, shorter thermally pulsing AGB lifetime, reduced enrichment in third dredge-up products (by a factor of 3-10), and an increase in the mass limit for hot bottom burning. We show that the evolution of low-metallicity models with composition-dependent low-temperature opacity is relatively independent of initial metal abundance because its contribution to the opacity is far outweighed by changes resulting from dredge-up. Our results imply a significant reduction in the expected number of nitrogen-enhanced metal-poor stars, which may help explain their observed paucity. We note that these findings are partially a product of the macrophysics adopted in our models, in particular, the Vassiliadis and Wood mass loss rate which is strongly dependent on radius.

The SH2 domain of Abl kinases regulates kinase autophosphorylation by controlling activation loop accessibility

Science.gov (United States)

Lamontanara, Allan Joaquim; Georgeon, Sandrine; Tria, Giancarlo; Svergun, Dmitri I.; Hantschel, Oliver

2014-11-01

The activity of protein kinases is regulated by multiple molecular mechanisms, and their disruption is a common driver of oncogenesis. A central and almost universal control element of protein kinase activity is the activation loop that utilizes both conformation and phosphorylation status to determine substrate access. In this study, we use recombinant Abl tyrosine kinases and conformation-specific kinase inhibitors to quantitatively analyse structural changes that occur after Abl activation. Allosteric SH2-kinase domain interactions were previously shown to be essential for the leukemogenesis caused by the Bcr-Abl oncoprotein. We find that these allosteric interactions switch the Abl activation loop from a closed to a fully open conformation. This enables the trans-autophosphorylation of the activation loop and requires prior phosphorylation of the SH2-kinase linker. Disruption of the SH2-kinase interaction abolishes activation loop phosphorylation. Our analysis provides a molecular mechanism for the SH2 domain-dependent activation of Abl that may also regulate other tyrosine kinases.

Opacity and gradients in aluminum wire array z-pinch implosions on the Z pulsed power facility

Energy Technology Data Exchange (ETDEWEB)

Ampleford, D. J., E-mail: damplef@sandia.gov; Hansen, S. B.; Jennings, C. A.; Jones, B.; Coverdale, C. A.; Harvey-Thompson, A. J.; Rochau, G. A.; Dunham, G.; Moore, N. W.; Harding, E. C.; Cuneo, M. E. [Sandia National Laboratories, Albuquerque, New Mexico 87185 (United States); Chong, Y.-K.; Clark, R. W.; Ouart, N.; Thornhill, J. W.; Giuliani, J.; Apruzese, J. P. [Naval Research Laboratory, Washington, DC 20375 (United States)

2014-03-15

Aluminum wire array z pinches imploded on the Z generator are an extremely bright source of 1–2 keV radiation, with close to 400 kJ radiated at photon energies >1 keV and more than 50 kJ radiated in a single line (Al Ly-α). Opacity plays a critical role in the dynamics and K-shell radiation efficiency of these pinches. Where significant structure is present in the stagnated pinch this acts to reduce the effective opacity of the system as demonstrated by direct analysis of spectra. Analysis of time-integrated broadband spectra (0.8–25 keV) indicates electron temperatures ranging from a few 100 eV to a few keV are present, indicative of substantial temperature gradients.

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.

SIRT1 promotes N-Myc oncogenesis through a positive feedback loop involving the effects of MKP3 and ERK on N-Myc protein stability.

Directory of Open Access Journals (Sweden)

Glenn M Marshall

2011-06-01

Full Text Available 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.

Proteins with Novel Structure, Function and Dynamics

Science.gov (United States)

Pohorille, Andrew

2014-01-01

Recently, a small enzyme that ligates two RNA fragments with the rate of 10(exp 6) above background was evolved in vitro (Seelig and Szostak, Nature 448:828-831, 2007). This enzyme does not resemble any contemporary protein (Chao et al., Nature Chem. Biol. 9:81-83, 2013). It consists of a dynamic, catalytic loop, a small, rigid core containing two zinc ions coordinated by neighboring amino acids, and two highly flexible tails that might be unimportant for protein function. In contrast to other proteins, this enzyme does not contain ordered secondary structure elements, such as alpha-helix or beta-sheet. The loop is kept together by just two interactions of a charged residue and a histidine with a zinc ion, which they coordinate on the opposite side of the loop. Such structure appears to be very fragile. Surprisingly, computer simulations indicate otherwise. As the coordinating, charged residue is mutated to alanine, another, nearby charged residue takes its place, thus keeping the structure nearly intact. If this residue is also substituted by alanine a salt bridge involving two other, charged residues on the opposite sides of the loop keeps the loop in place. These adjustments are facilitated by high flexibility of the protein. Computational predictions have been confirmed experimentally, as both mutants retain full activity and overall structure. These results challenge our notions about what is required for protein activity and about the relationship between protein dynamics, stability and robustness. We hypothesize that small, highly dynamic proteins could be both active and fault tolerant in ways that many other proteins are not, i.e. they can adjust to retain their structure and activity even if subjected to mutations in structurally critical regions. This opens the doors for designing proteins with novel functions, structures and dynamics that have not been yet considered.

Efficacy on chopping with lens loop-pad in the small incision extracapsular cataract surgery with intraocular lens implantation

Directory of Open Access Journals (Sweden)

Xiao-Ning Peng

2014-04-01

Full Text Available AIM: To study the clinical effects of chopping with lens loop-pad in the small incision extracapsular cataract surgery with intraocular lens implantation.METHODS:A total of 75 cases(80 eyes, in which loop-pad and chop knife were performed to chop nucleus before implanting intraocular lens. Visual acuity, postoperative astigmatism degree, intraoperative and postoperative complications were observed. The post-operative follow-up periods ranged from 3 to 12mo.RESULTS: The visual acuity was 0.3-0.5 in 37 eyes and 0.6 or better in 21 eyes at 1d, while was respectively in 43 eyes and in 26 eyes at 1mo. Compared with preoperative astigmatism(0.85±0.29D, there were significant difference at postoperative 1wk(1.75±0.55D(PP>0.05. Intraoperative posterior capsule rupture occurred in 4 eyes, which implantation was successful in 1 eye and 3 eyes was managed viaciliary sulcus. Two eyes had dermatoglyphic pattern edema in corneal endothelium which recovered after about 3d. Two eyes had local patchy opacities which recovered in 2wk. Two eyes had transient high intraocular pressure.CONCLUSION: The surgery is efficient, low cost, easy process and less complications, it is worth to be popularized.

Two-loop hard-thermal-loop thermodynamics with quarks

International Nuclear Information System (INIS)

Andersen, Jens O.; Petitgirard, Emmanuel; Strickland, Michael

2004-01-01

We calculate the quark contribution to the free energy of a hot quark-gluon plasma to two-loop order using hard-thermal-loop (HTL) perturbation theory. All ultraviolet divergences can be absorbed into renormalizations of the vacuum energy and the HTL quark and gluon mass parameters. The quark and gluon HTL mass parameters are determined self-consistently by a variational prescription. Combining the quark contribution with the two-loop HTL perturbation theory free energy for pure glue we obtain the total two-loop QCD free energy. Comparisons are made with lattice estimates of the free energy for N f =2 and with exact numerical results obtained in the large-N f limit

Penerapan Bahasa Alami Sederhana pada Online Public Access Catalog (Opac) Berbasis Web Semantik

OpenAIRE

Andri, Andri

2012-01-01

Online Public Access Catalog (OPAC) merupakan sistem katalog online yang memanfaatkan teknologi komputer dan internet sebagai media pengaksesan dan penyimpanan datanya. Sebuah katalog biasanya memberikan informasi mengenai koleksi yang disimpan dalam sebuah perpustakaan digital. Dalam penelitian ini akan dibuat sebuah prototipe aplikasi pencarian pada katalog online di perpustakaan Universitas Binadarma Palembang berbasis teknologi web semantik serta menerapkan pengolahan bahasa alami sederha...

Role of an Absolutely Conserved Tryptophan Pair in the Extracellular Domain of Cys-Loop Receptors

DEFF Research Database (Denmark)

Braun, Nina; Lynagh, Timothy; Yu, Rilei

2016-01-01

Cys-loop receptors mediate fast synaptic transmission in the nervous system, and their dysfunction is associated with a number of diseases. While some sequence variability is essential to ensure specific recognition of a chemically diverse set of ligands, other parts of the underlying amino acid...... sequences show a high degree of conservation, possibly to preserve the overall structural fold across the protein family. In this study, we focus on the only two absolutely conserved residues across the Cys-loop receptor family, two Trp side chains in the WXD motif of Loop D and in the WXPD motif of Loop A...

Research on Spectroscopy, Opacity, and Atmospheres

Science.gov (United States)

Kurucz, Robert L.

2005-01-01

I propose to continue providing observers with basic data for interpreting spectra from stars, novas, supernovas, clusters, and galaxies. These data will include allowed and forbidden line lists, both laboratory and computed, for the first five to ten ions of all atoms and for all relevant diatomic molecules. I will eventually expand to all ions of the first thirty elements to treat far UV and X-ray spectra, and for envelope opacities. I also include triatomic molecules provided by other researchers. I have also made CDs with Partridge and Schwenke's water data for work on UV stars. The line data also serve as input to my model atmosphere and synthesis programs that generate energy distributions, photometry, limb darkening, and spectra that can be used for planning observations and for fitting observed spectra. The spectrum synthesis programs produce detailed plots with the lines identified. Grids of stellar spectra can be used for radial velocity-, rotation-, or abundance templates and for population synthesis. I am fitting spectra of bright stars to test the data and to produce atlases to guide observers. For each star the whole spectrum is computed from the UV to the far IR. The line data, opacities, models, spectra, and programs are freely distributed on CDs and on my Web site and represent a unique resource for many NASA programs. I am now in full production of new line lists for atoms. I am computing all ions of all elements from H to Zn and the first 5 ions of all the heavier elements, about 800 ions. For each ion I treat as many as 61 even and 61 odd configurations, computing all energy levels and eigenvectors. The Hamiltonian is determined from a scaled-Hartree-Fock starting guess by least squares fitting the observed energy levels. The average energy of each configuration is used in computing scaled-Thomas-Fermi-Dirac wavefunctions for each configuration which in turn are used to compute allowed and forbidden transition integrals. These are multiplied

Digitisation of films and texture analysis for digital classification of pulmonary opacities

International Nuclear Information System (INIS)

Desaga, J.F.; Dengler, J.; Wolf, T.; Engelmann, U.; Scheppelmann, D.; Meinzer, H.P.

1988-01-01

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. (orig.) [de

Constraining the Dust Opacity Law in Three Small and Isolated Molecular Clouds

Energy Technology Data Exchange (ETDEWEB)

Webb, K. A.; Thanjavur, K. [Department of Physics and Astronomy, 3800 Finnerty Road, University of Victoria, Victoria, BC, V8P 5C2 (Canada); Di Francesco, J. [National Research Council of Canada, Herzberg Institute of Astrophysics, 5071 West Saanich Road, Victoria, BC, V9E 2E7 (Canada); Sadavoy, S. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Launhardt, R.; Vicente, J. Abreu; Kainulainen, J. [Max-Planck-Institut für Astronomy, Königstuhl 17, D-69117, Heidelberg (Germany); Shirley, Y. [Steward Observatory, 933 North Cherry Avenue, Tucson, AZ 85721 (United States); Stutz, A., E-mail: kawebb@uvic.ca [Departmento de Astronomìa, Facultad Ciencias Físicas y Matemáticas, Universidad de Concepción, Av. Esteban Iturra s/n Barro Universitario, Casilla 160-C, Concepción (Chile)

2017-11-01

Density profiles of isolated cores derived from thermal dust continuum emission rely on models of dust properties, such as mass opacity, that are poorly constrained. With complementary measures from near-infrared extinction maps, we can assess the reliability of commonly used dust models. In this work, we compare Herschel -derived maps of the optical depth with equivalent maps derived from CFHT WIRCAM near-infrared observations for three isolated cores: CB 68, L 429, and L 1552. We assess the dust opacities provided from four models: OH1a, OH5a, Orm1, and Orm4. Although the consistency of the models differs between the three sources, the results suggest that the optical properties of dust in the envelopes of the cores are best described by either silicate and bare graphite grains (e.g., Orm1) or carbonaceous grains with some coagulation and either thin or no ice mantles (e.g., OH5a). None of the models, however, individually produced the most consistent optical depth maps for every source. The results suggest that either the dust in the cores is not well-described by any one dust property model, the application of the dust models cannot be extended beyond the very center of the cores, or more complex SED fitting functions are necessary.

Zinc ion coordination as a modulating factor of the ZnuA histidine-rich loop flexibility: A molecular modeling and fluorescence spectroscopy study

Energy Technology Data Exchange (ETDEWEB)

Castelli, Silvia [Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome (Italy); Stella, Lorenzo [Department of Chemical Sciences and Technologies, University of Roma Tor Vergata, Via della Ricerca Scientifica, 00133 Rome (Italy); Neuromed, IRCCS, Pozzilli 86077 (Italy); Petrarca, Patrizia [Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome (Italy); Battistoni, Andrea [Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133 Rome (Italy); Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), Viale delle Medaglie D' Oro 305, 00136 Rome (Italy); Desideri, Alessandro [Department of Biology, University of Rome Tor Vergata and CIBB, Center of Biostatistics and Bioinformatics, Via della Ricerca Scientifica, 00133 Rome (Italy); Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), Viale delle Medaglie D' Oro 305, 00136 Rome (Italy); Falconi, Mattia, E-mail: falconi@uniroma2.it [Department of Biology, University of Rome Tor Vergata and CIBB, Center of Biostatistics and Bioinformatics, Via della Ricerca Scientifica, 00133 Rome (Italy); Interuniversity Consortium, National Institute Biostructure and Biosystem (INBB), Viale delle Medaglie D' Oro 305, 00136 Rome (Italy)

2013-01-11

Highlights: Black-Right-Pointing-Pointer Fluorescence data indicate that the His-loop of ZnuA interacts with Zn{sup +2} ions. Black-Right-Pointing-Pointer The ZnuA structural model proposed validates these spectroscopic findings. Black-Right-Pointing-Pointer It is proposed that a zinc loaded His-loop may facilitate the ZnuA-ZnuB recognition. -- Abstract: ZnuA is the soluble component of the high-affinity ZnuABC zinc transporter belonging to the ATP-binding cassette-type periplasmic Zn-binding proteins. The zinc transporter ZnuABC is composed by three proteins: ZnuB, the membrane permease, ZnuC, the ATPase component and ZnuA, the soluble periplasmic metal-binding protein which captures Zn and delivers it to ZnuB. The ZnuA protein contains a charged flexible loop, rich in histidines and acidic residues, showing significant species-specific differences. Various studies have established that this loop contributes to the formation of a secondary zinc binding site, which has been proposed to be important in the acquisition of periplasmic Zn for its delivery to ZnuB or for regulation of zinc uptake. Due to its high mobility the structure of the histidine-rich loop has never been solved by X-ray diffraction studies. In this paper, through a combined use of molecular modeling, mutagenesis and fluorescence spectroscopy, we confirm the presence of two zinc binding sites characterized by different affinities for the metal ion and show that the flexibility of the loop is modulated by the binding of the zinc ions to the protein. The data obtained by fluorescence spectroscopy have then be used to validate a 3D model including the unsolved histidine-rich loop.

RNA/DNA Hybrid Interactome Identifies DXH9 as a Molecular Player in Transcriptional Termination and R-Loop-Associated DNA Damage.

Science.gov (United States)

Cristini, Agnese; Groh, Matthias; Kristiansen, Maiken S; Gromak, Natalia

2018-05-08

R-loops comprise an RNA/DNA hybrid and displaced single-stranded DNA. They play important biological roles and are implicated in pathology. Even so, proteins recognizing these structures are largely undefined. Using affinity purification with the S9.6 antibody coupled to mass spectrometry, we defined the RNA/DNA hybrid interactome in HeLa cells. This consists of known R-loop-associated factors SRSF1, FACT, and Top1, and yet uncharacterized interactors, including helicases, RNA processing, DNA repair, and chromatin factors. We validate specific examples of these interactors and characterize their involvement in R-loop biology. A top candidate DHX9 helicase promotes R-loop suppression and transcriptional termination. DHX9 interacts with PARP1, and both proteins prevent R-loop-associated DNA damage. DHX9 and other interactome helicases are overexpressed in cancer, linking R-loop-mediated DNA damage and disease. Our RNA/DNA hybrid interactome provides a powerful resource to study R-loop biology in health and disease. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Influence of artificial accelerated aging on the color stability and opacity of composites of different shades.

Science.gov (United States)

Mundim, F M; Da Fonseca Roberti Garcia, L; Silva Sousa, A B; Cruvinel, D R; De Carvalho Panzeri Pires-De-Souza, F

2010-10-01

The aim of this study was to evaluate the influence of artificial accelerated aging on the color stability and opacity of composites of different shades. Four composites for direct use (Heliomolar, 4 Seasons, Tetric EvoCeram; QuiXfil) and one for indirect use (SR Adoro) in two shades were used: light (A2) and dark (C3 for direct, and D4 for indirect composite). QuiXfil was obtained in Universal shade. A Teflon matrix (12 X 2 mm) was used to obtain 54 specimens (N=6), which were submitted to color and opacity analysis (Spectrophotometer PCB 6807, Byk Gardner) before and after artificial accelerated aging for 384 hours. After the statistical analysis (2-way ANOVA - Bonferroni - PArtificial accelerated aging interfered in the optical properties assessed; however, the alterations seemed to be more related to the composites composition than to their shade.

Significance of lenticular opacity from the view point of the exposure dose of A-bomb radiation

Energy Technology Data Exchange (ETDEWEB)

Sugimoto, S [Sugimoto Hospital, Hiroshima (Japan)

1975-04-01

Two cases of lenticular opacity were discussed from the view point of exposure dose of A-bomb radiation. Case 1: female, 22 year and 5 months old when she was exposured to A-bomb radiation. The presumed exposure dose was 482.0 rad. Cataract due to A-bomb radiation. Case 2: female, 21 years and 6 months old when she was exposured to A-bomb radiation. The presumed exposure dose was more than 1,000 rad. Cataract due to A-bomb radiation and incipient cataract senilis. It was reported here that there was a marked difference in opacity findings of cataract due to A-bomb radiation in accordance with difference in exposure dose of radiation. It was also presumed from the findings of incipient cataract senilis that with increasing exposure dose, the aging phenomenon was promoted.

A mitosis-specific and R loop-driven ATR pathway promotes faithful chromosome segregation.

Science.gov (United States)

Kabeche, Lilian; Nguyen, Hai Dang; Buisson, Rémi; Zou, Lee

2018-01-05

The ataxia telangiectasia mutated and Rad3-related (ATR) kinase is crucial for DNA damage and replication stress responses. Here, we describe an unexpected role of ATR in mitosis. Acute inhibition or degradation of ATR in mitosis induces whole-chromosome missegregation. The effect of ATR ablation is not due to altered cyclin-dependent kinase 1 (CDK1) activity, DNA damage responses, or unscheduled DNA synthesis but to loss of an ATR function at centromeres. In mitosis, ATR localizes to centromeres through Aurora A-regulated association with centromere protein F (CENP-F), allowing ATR to engage replication protein A (RPA)-coated centromeric R loops. As ATR is activated at centromeres, it stimulates Aurora B through Chk1, preventing formation of lagging chromosomes. Thus, a mitosis-specific and R loop-driven ATR pathway acts at centromeres to promote faithful chromosome segregation, revealing functions of R loops and ATR in suppressing chromosome instability. Copyright © 2018, American Association for the Advancement of Science.

‘Seeing the Dark’: Grounding Phenomenal Transparency and Opacity in Precision Estimation for Active Inference

Science.gov (United States)

Limanowski, Jakub; Friston, Karl

2018-01-01

One of the central claims of the Self-model Theory of Subjectivity is that the experience of being someone – even in a minimal form – arises through a transparent phenomenal self-model, which itself can in principle be reduced to brain processes. Here, we consider whether it is possible to distinguish between phenomenally transparent and opaque states in terms of active inference. We propose a relationship of phenomenal opacity to expected uncertainty or precision; i.e., the capacity for introspective attention and implicit mental action. Thus we associate introspective attention with the deployment of ‘precision’ that may render the perceptual evidence (for action) opaque, while treating transparency as a necessary aspect of beliefs about action, i.e., ‘what I am’ doing. We conclude by proposing how we may have to nuance our conception of minimal phenomenal selfhood and agency in light of this active inference conception of transparency-opacity. PMID:29780343

TRF2 Recruits RTEL1 to Telomeres in S Phase to Promote T-Loop Unwinding

OpenAIRE

Sarek, Grzegorz; Vannier, Jean-Baptiste; Panier, Stephanie; Petrini, John?H.J.; Boulton, Simon?J.

2015-01-01

Summary The helicase RTEL1 promotes t-loop unwinding and suppresses telomere fragility to maintain the integrity of vertebrate telomeres. An interaction between RTEL1 and PCNA is important to prevent telomere fragility, but how RTEL1 engages with the telomere to promote t-loop unwinding is unclear. Here, we establish that the shelterin protein TRF2 recruits RTEL1 to telomeres in S phase, which is required to?prevent catastrophic t-loop processing by structure-specific nucleases. We show that ...

Temporal differential proteomes of Clostridium difficile in the pig ileal-ligated loop model.

Directory of Open Access Journals (Sweden)

Tavan Janvilisri

Full Text Available The impact of Clostridium difficile infection (CDI on healthcare is becoming increasingly recognized as it represents a major cause of nosocomial diarrhea. A rising number of CDI cases and outbreaks have been reported worldwide. Here, we developed the pig ileal-ligated loop model for semi-quantitative analysis comparing temporal differential proteomes in C. difficile following in vivo incubation with in vitro growth using isobaric tags for relative and absolute quantification (iTRAQ. Proteins retrieved from the in vitro cultures and the loop contents after 4, 8, and 12 h in vivo incubation were subjected to in-solution digestion, iTRAQ labeling, two-dimensional liquid chromatography/tandem mass spectrometry and statistical analyses. From a total of 1152 distinct proteins identified in this study, 705 proteins were available for quantitative measures at all time points in both biological and technical replicates; 109 proteins were found to be differentially expressed. With analysis of clusters of orthologous group and protein-protein network interactions, we identified the proteins that might play roles in adaptive responses to the host environment, hence enhancing pathogenicity during CDI. This report represents the quantitative proteomic analysis of C. difficile that demonstrates time-dependent protein expression changes under conditions that mimic in vivo infection and identifies potential candidates for diagnostic or therapeutic measures.

The Belfast atomic data bank, recommended data, and the opacity project data base

International Nuclear Information System (INIS)

Berrington, K.A.; Kingston, A.E.; Sawey, P.M.J.

1991-01-01

The Belfast Atomic Data Bank holds data for the excitation and ionisation of atoms and ions by electrons and photons, and provides recommended data; electron excitation data recommended at regular Atomic Data Workshops is summarised. Photoabsorption data for all elements up to Fe have been calculated in the international Opacity Project, and a summary is given of the atomic data expected from the Project

Neocortical electrical stimulation for epilepsy : Closed-loop versus open-loop

NARCIS (Netherlands)

Vassileva, Albena; van Blooijs, Dorien; Leijten, Frans; Huiskamp, Geertjan

2018-01-01

The aim of this review is to evaluate whether open-loop or closed-loop neocortical electrical stimulation should be the preferred approach to manage seizures in intractable epilepsy. Twenty cases of open-loop neocortical stimulation with an implanted device have been reported, in 5 case studies.

From stellar plasmas to laboratory plasmas: application to X and XUV opacity measurements

International Nuclear Information System (INIS)

Loisel, G.

2011-01-01

The general context of this thesis is the one of radiative properties of high energy density matter. Energy densities involved (>10 11 J/cm 3 ) implies that a large part of energy exchange goes through radiation-matter interactions. My studies deal with spectral opacity, a fundamental parameter for modelling stellar interiors and constitute a propitious observable to experimental tests of theoretical descriptions of hot and dense plasmas physics. Although the main application of my work is stellar plasmas it can be useful for plasma diagnostics in inertial confinement fusion. My work activities are centred on the experimental study of opacities of plasmas at local thermodynamic equilibrium for temperature conditions of a few tens eV (a few 100000 K) and a few mg/cm 3 in matter density. Plasmas are obtained in conditions as homogenous as possible using the radiative heating of a laser-irradiated cavity. Heating is provided through a laser beam of high energy (100-300 J) and with relatively long pulse duration of a few nanosecond. For such measurements we could benefit from the LULI lasers configuration coupling the nanosecond beam with a picosecond one used to perform on a short duration the measurement of the plasma transmission. The use of short pulse laser to produce a short time radiography beam was a first achievement for this kind of experience. In the spectral range of keV photons, absorbing transitions 2p-3d or 3d-4f of elements of moderate or high atomic number have been probed. They present absorption structures which shape results mainly of the competition between spin-orbit splitting and statistical broadening effects. It appeared that this competition depends strongly on the atomic number Z. Thus for similar plasma parameters we explored opacities of Iron, Nickel, Copper and Germanium (Z around 30) in a first series of measurement and the one of Barium, Samarium and Gadolinium (Z around 60) in a second campaign

Exome Array Analysis of Nuclear Lens Opacity.

Science.gov (United States)

Loomis, Stephanie J; Klein, Alison P; Lee, Kristine E; Chen, Fei; Bomotti, Samantha; Truitt, Barbara; Iyengar, Sudha K; Klein, Ronald; Klein, Barbara E K; Duggal, Priya

2018-06-01

Nuclear cataract is the most common subtype of age-related cataract, the leading cause of blindness worldwide. It results from advanced nuclear sclerosis, or opacity in the center of the optic lens, and is affected by both genetic and environmental risk factors, including smoking. We sought to understand the genetic factors associated with nuclear sclerosis through interrogation of rare and low frequency coding variants using exome array data. We analyzed Illumina Human Exome Array data for 1,488 participants of European ancestry in the Beaver Dam Eye Study who were without cataract surgery for association with nuclear sclerosis grade, controlling for age and sex. We performed single-variant regression analysis for 32,138 variants with minor allele frequency (MAF) ≥0.003. In addition, gene-based analysis of 11,844 genes containing at least two variants with MAF nuclear sclerosis, the possible association with the RNF149 gene highlights a potential candidate gene for future studies that aim to understand the genetic architecture of nuclear sclerosis.

Delivering Electronic Resources with Web OPACs and Other Web-based Tools: Needs of Reference Librarians.

Science.gov (United States)

Bordeianu, Sever; Carter, Christina E.; Dennis, Nancy K.

2000-01-01

Describes Web-based online public access catalogs (Web OPACs) and other Web-based tools as gateway methods for providing access to library collections. Addresses solutions for overcoming barriers to information, such as through the implementation of proxy servers and other authentication tools for remote users. (Contains 18 references.)…

We Never Have to Say Goodbye: Finding a Place for OPACS in Discovery Environments

Science.gov (United States)

Matthews, J. Greg

2009-01-01

It is easy to lament the shortcomings of traditional online public access catalogs (OPACs) in the Google Age. Users cannot, for example, usually input a snippet of a long-forgotten pop song's chorus into an online library catalog and almost instantly retrieve a relevant result along with hundreds of other options. On the other hand, should OPACs…

Pierced Lasso Proteins

Science.gov (United States)

Jennings, Patricia

Entanglement and knots are naturally occurring, where, in the microscopic world, knots in DNA and homopolymers are well characterized. The most complex knots are observed in proteins which are harder to investigate, as proteins are heteropolymers composed of a combination of 20 different amino acids with different individual biophysical properties. As new-knotted topologies and new proteins containing knots continue to be discovered and characterized, the investigation of knots in proteins has gained intense interest. Thus far, the principle focus has been on the evolutionary origin of tying a knot, with questions of how a protein chain `self-ties' into a knot, what the mechanism(s) are that contribute to threading, and the biological relevance and functional implication of a knotted topology in vivo gaining the most insight. Efforts to study the fully untied and unfolded chain indicate that the knot is highly stable, remaining intact in the unfolded state orders of magnitude longer than first anticipated. The persistence of ``stable'' knots in the unfolded state, together with the challenge of defining an unfolded and untied chain from an unfolded and knotted chain, complicates the study of fully untied protein in vitro. Our discovery of a new class of knotted proteins, the Pierced Lassos (PL) loop topology, simplifies the knotting approach. While PLs are not easily recognizable by the naked eye, they have now been identified in many proteins in the PDB through the use of computation tools. PL topologies are diverse proteins found in all kingdoms of life, performing a large variety of biological responses such as cell signaling, immune responses, transporters and inhibitors (http://lassoprot.cent.uw.edu.pl/). Many of these PL topologies are secreted proteins, extracellular proteins, as well as, redox sensors, enzymes and metal and co-factor binding proteins; all of which provide a favorable environment for the formation of the disulphide bridge. In the PL

A multiple-pass ring oscillator based dual-loop phase-locked loop

International Nuclear Information System (INIS)

Chen Danfeng; Ren Junyan; Deng Jingjing; Li Wei; Li Ning

2009-01-01

A dual-loop phase-locked loop (PLL) for wideband operation is proposed. The dual-loop architecture combines a coarse-tuning loop with a fine-tuning one, enabling a wide tuning range and low voltage-controlled oscillator (VCO) gain without poisoning phase noise and reference spur suppression performance. An analysis of the phase noise and reference spur of the dual-loop PLL is emphasized. A novel multiple-pass ring VCO is designed for the dual-loop application. It utilizes both voltage-control and current-control simultaneously in the delay cell. The PLL is fabricated in Jazz 0.18-μm RF CMOS technology. The measured tuning range is from 4.2 to 5.9 GHz. It achieves a low phase noise of -99 dBc/Hz - 1 MHz offset from a 5.5 GHz carrier.

A multiple-pass ring oscillator based dual-loop phase-locked loop

Energy Technology Data Exchange (ETDEWEB)

Chen Danfeng; Ren Junyan; Deng Jingjing; Li Wei; Li Ning, E-mail: dfchen@fudan.edu.c [State Key Laboratory of ASIC and System, Fudan University, Shanghai 201203 (China)

2009-10-15

A dual-loop phase-locked loop (PLL) for wideband operation is proposed. The dual-loop architecture combines a coarse-tuning loop with a fine-tuning one, enabling a wide tuning range and low voltage-controlled oscillator (VCO) gain without poisoning phase noise and reference spur suppression performance. An analysis of the phase noise and reference spur of the dual-loop PLL is emphasized. A novel multiple-pass ring VCO is designed for the dual-loop application. It utilizes both voltage-control and current-control simultaneously in the delay cell. The PLL is fabricated in Jazz 0.18-{mu}m RF CMOS technology. The measured tuning range is from 4.2 to 5.9 GHz. It achieves a low phase noise of -99 dBc/Hz - 1 MHz offset from a 5.5 GHz carrier.

Sequence-structure relationships in RNA loops: establishing the basis for loop homology modeling.

Science.gov (United States)

Schudoma, Christian; May, Patrick; Nikiforova, Viktoria; Walther, Dirk

2010-01-01

The specific function of RNA molecules frequently resides in their seemingly unstructured loop regions. We performed a systematic analysis of RNA loops extracted from experimentally determined three-dimensional structures of RNA molecules. A comprehensive loop-structure data set was created and organized into distinct clusters based on structural and sequence similarity. We detected clear evidence of the hallmark of homology present in the sequence-structure relationships in loops. Loops differing by structures. Thus, our results support the application of homology modeling for RNA loop model building. We established a threshold that may guide the sequence divergence-based selection of template structures for RNA loop homology modeling. Of all possible sequences that are, under the assumption of isosteric relationships, theoretically compatible with actual sequences observed in RNA structures, only a small fraction is contained in the Rfam database of RNA sequences and classes implying that the actual RNA loop space may consist of a limited number of unique loop structures and conserved sequences. The loop-structure data sets are made available via an online database, RLooM. RLooM also offers functionalities for the modeling of RNA loop structures in support of RNA engineering and design efforts.

Interaction of the host protein NbDnaJ with Potato virus X minus-strand stem-loop 1 RNA and capsid protein affects viral replication and movement.

Science.gov (United States)

Cho, Sang-Yun; Cho, Won Kyong; Sohn, Seong-Han; Kim, Kook-Hyung

2012-01-06

Plant viruses must interact with host cellular components to replicate and move from cell to cell. In the case of Potato virus X (PVX), it carries stem-loop 1 (SL1) RNA essential for viral replication and movement. Using two-dimensional electrophoresis northwestern blot analysis, we previously identified several host proteins that bind to SL1 RNA. Of those, we further characterized a DnaJ-like protein from Nicotiana benthamiana named NbDnaJ. An electrophoretic mobility shift assay confirmed that NbDnaJ binds only to SL1 minus-strand RNA, and bimolecular fluorescence complementation (BiFC) indicated that NbDnaJ interacts with PVX capsid protein (CP). Using a series of deletion mutants, the C-terminal region of NbDnaJ was found to be essential for the interaction with PVX CP. The expression of NbDnaJ significantly changed upon infection with different plant viruses such as PVX, Tobacco mosaic virus, and Cucumber mosaic virus, but varied depending on the viral species. In transient experiments, both PVX replication and movement were inhibited in plants that over-expressed NbDnaJ but accelerated in plants in which NbDnaJ was silenced. In summary, we suggest that the newly identified NbDnaJ plays a role in PVX replication and movement by interacting with SL1(-) RNA and PVX CP. Copyright © 2011 Elsevier Inc. All rights reserved.

Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex.

OpenAIRE

Perederina, Anna; Nevskaya, Natalia; Nikonov, Oleg; Nikulin, Alexei; Dumas, Philippe; Yao, Min; Tanaka, Isao; Garber, Maria; Gongadze, George; Nikonov, Stanislav

2002-01-01

The crystal structure of ribosomal protein L5 from Thermus thermophilus complexed with a 34-nt fragment comprising helix III and loop C of Escherichia coli 5S rRNA has been determined at 2.5 A resolution. The protein specifically interacts with the bulged nucleotides at the top of loop C of 5S rRNA. The rRNA and protein contact surfaces are strongly stabilized by intramolecular interactions. Charged and polar atoms forming the network of conserved intermolecular hydrogen bonds are located in ...

Characterization of a Novel Association between Two Trypanosome-Specific Proteins and 5S rRNA

Science.gov (United States)

Ciganda, Martin; Williams, Noreen

2012-01-01

P34 and P37 are two previously identified RNA binding proteins in the flagellate protozoan Trypanosoma brucei. RNA interference studies have determined that the proteins are essential and are involved in ribosome biogenesis. Here, we show that these proteins interact in vitro with the 5S rRNA with nearly identical binding characteristics in the absence of other cellular factors. The T. brucei 5S rRNA has a complex secondary structure and presents four accessible loops (A to D) for interactions with RNA-binding proteins. In other eukaryotes, loop C is bound by the L5 ribosomal protein and loop A mainly by TFIIIA. The binding of P34 and P37 to T. brucei 5S rRNA involves the LoopA region of the RNA, but these proteins also protect the L5 binding site located on LoopC. PMID:22253864

Contribution of Topological Domains and Loop Formation to 3D Chromatin Organization

Directory of Open Access Journals (Sweden)

Vuthy Ea

2015-07-01

Full Text Available Recent investigations on 3D chromatin folding revealed that the eukaryote genomes are both highly compartmentalized and extremely dynamic. This review presents the most recent advances in topological domains’ organization of the eukaryote genomes and discusses the relationship to chromatin loop formation. CTCF protein appears as a central factor of these two organization levels having either a strong insulating role at TAD borders, or a weaker architectural role in chromatin loop formation. TAD borders directly impact on chromatin dynamics by restricting contacts within specific genomic portions thus confining chromatin loop formation within TADs. We discuss how sub-TAD chromatin dynamics, constrained into a recently described statistical helix conformation, can produce functional interactions by contact stabilization.

Split green fluorescent protein as a modular binding partner for protein crystallization

International Nuclear Information System (INIS)

Nguyen, Hau B.; Hung, Li-Wei; Yeates, Todd O.; Terwilliger, Thomas C.; Waldo, Geoffrey S.

2013-01-01

A strategy using a new split green fluorescent protein (GFP) as a modular binding partner to form stable protein complexes with a target protein is presented. The modular split GFP may open the way to rapidly creating crystallization variants. A modular strategy for protein crystallization using split green fluorescent protein (GFP) as a crystallization partner is demonstrated. Insertion of a hairpin containing GFP β-strands 10 and 11 into a surface loop of a target protein provides two chain crossings between the target and the reconstituted GFP compared with the single connection afforded by terminal GFP fusions. This strategy was tested by inserting this hairpin into a loop of another fluorescent protein, sfCherry. The crystal structure of the sfCherry-GFP(10–11) hairpin in complex with GFP(1–9) was determined at a resolution of 2.6 Å. Analysis of the complex shows that the reconstituted GFP is attached to the target protein (sfCherry) in a structurally ordered way. This work opens the way to rapidly creating crystallization variants by reconstituting a target protein bearing the GFP(10–11) hairpin with a variety of GFP(1–9) mutants engineered for favorable crystallization

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

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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.

Opacity calculations for laser plasma applications

International Nuclear Information System (INIS)

Magee, N.H. Jr.

1986-01-01

The Los Alamos LTE light element detailed configuration opacity code (LEDCOP) has been revised to provide more accurate absorption coefficients and group means for modern radiation-hydrodynamic codes. The new group means will be especially useful for computing the transport of thermal radiation from laser deposition. The principal improvement is the inclusion of a complete set of accurate and internally consistent LS term energies and oscillator strengths in both the EOS and absorption coefficients. Selected energies and oscillator strengths were calculated from a Hartree-Fock code, then fitted by a quantum defect method. This allowed transitions at all wavelengths to be treated consistently and accurately instead of being limited to wavelength regions covered by experimental observations or isolated theoretical calculations. A second improvement is the use of more accurate photoionization cross sections for excited as well as ground state configurations. These cross sections are now more consistent with the bound-bound oscillator strengths, leading to a smooth transition across the continuum limit. Results will be presented showing the agreement of the LS term energies and oscillator strengths with observed values. The new absorption coefficients will be compared with previous calculations. 5 refs., 9 figs., 1 tab

Geometrical criteria for characterizing open and closed states of WPD-loop in PTP1B

Science.gov (United States)

Shinde, Ranajit Nivrutti; Elizabeth Sobhia, M.

2012-06-01

Distinctive movement of WPD-loop occurs during the catalysis of phosphotyrosine by protein tyrosine phosphatase 1B (PTP1B). This loop is in the "open" state in apo-form whereas it is catalytically competent in the "closed" state. During the closure of this loop, unique hydrogen bond interactions are formed between different residues of the PTP1B. Present study examines such interactions from the available 118 crystal structures of PTP1B. It gives insights into the five novel hydrogen bonds essentially formed in the "closed" loop structures. Additionally, the study provides distance ranges between the atoms involved in the hydrogen bonds. This information can be used as a geometrical criterion in the characterization of conformational state of the WPD-loop especially in the molecular dynamics simulations.

Measuring the iron spectral opacity in solar conditions using a double ablation front scheme

Energy Technology Data Exchange (ETDEWEB)

Colaitis, A. [Centre Lasers Intenses et Applications, Talence (France); CEA/DRF/IRFU/DAp, CEA Saclay (France); Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Univ. of Rochester, NY (United States). Lab. for Laser Energetics; Ducret, J. E. [Centre Lasers Intenses et Applications, Talence (France); CEA/DRF/IRFU/DAp, CEA Saclay (France); Turck-Chieze, S [CEA/DRF/IRFU/DAp, CEA Saclay (France); Pennec, M L [CEA/DRF/IRFU/DAp, CEA Saclay (France); CEA/DIF, Arpajon (France); Blancard, C [CEA/DIF, Arpajon (France)

2018-01-22

We propose a new method to achieve hydrodynamic conditions relevant for the investigation of the radiation transport properties of the plasma at the base of the solar convection zone. The method is designed in the framework of opacity measurements with high-power lasers and exploits the temporal and spatial stability of hydrodynamic parameters in counter-propagating Double Ablation Front (DAF) structures.

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…

LOOP CALCULUS AND BELIEF PROPAGATION FOR Q-ARY ALPHABET: LOOP TOWER

Energy Technology Data Exchange (ETDEWEB)

CHERTKOV, MICHAEL [Los Alamos National Laboratory; CHERNYAK, VLADIMIR [Los Alamos National Laboratory

2007-01-10

Loop calculus introduced in [1], [2] constitutes a new theoretical tool that explicitly expresses symbol Maximum-A-Posteriori (MAP) solution of a general statistical inference problem via a solution of the Belief Propagation (BP) equations. This finding brought a new significance to the BP concept, which in the past was thought of as just a loop-free approximation. In this paper they continue a discussion of the Loop Calculus, partitioning the results into three Sections. In Section 1 they introduce a new formulation of the Loop Calculus in terms of a set of transformations (gauges) that keeping the partition function of the problem invariant. The full expression contains two terms referred to as the 'ground state' and 'excited states' contributions. The BP equations are interpreted as a special (BP) gauge fixing condition that emerges as a special orthogonality constraint between the ground state and excited states, which also selects loop contributions as the only surviving ones among the excited states. In Section 2 they demonstrate how the invariant interpretation of the Loop Calculus, introduced in Section 1, allows a natural extension to the case of a general q-ary alphabet, this is achieved via a loop tower sequential construction. The ground level in the tower is exactly equivalent to assigning one color (out of q available) to the 'ground state' and considering all 'excited' states colored in the remaining (q-1) colors, according to the loop calculus rule. Sequentially, the second level in the tower corresponds to selecting a loop from the previous step, colored in (q-1) colors, and repeating the same ground vs excited states splitting procedure into one and (q-2) colors respectively. The construction proceeds till the full (q-1)-levels deep loop tower (and the corresponding contributions to the partition function) are established. In Section 3 they discuss an ultimate relation between the loop calculus and the Bethe

Influence of Projection Operator on Oxygen Line Shapes and its effect on Rosseland-Mean Opacity in Stellar Interiors

Science.gov (United States)

Gomez, Thomas; Nagayama, Taisukue; Kilcrease, David; Hansen, Stephanie; Montgomery, Mike; Winget, Don

2018-01-01

The Rosseland-Mean opacity (RMO) is an important quantity in determining radiation transport through stars. The solar-convection-zone boundary predicted by the standard solar model disagrees with helioseismology measurements by many sigma; a 14% increase in the RMO would resolve this discrepancy. Experiments at Sandia National Laboratories are now measuring iron opacity at solar-interior conditions, and significant discrepancies are already observed. Highly-ionized oxygen is one of the dominant contributions to the RMO. The strongest line, Lyman alpha, is at the peak of the Rosseland weighting function. The accuracy of line-broadening calculations has been called into question due to various experimental results and comparisons between theory. We have developed an ab-initio calculation to explore different physical effects, our current focus is treating penetrating collisions explicitly. The equation of motion used to calculate line shapes within the relaxation and unified theories includes a projection operator, which performs an average over plasma electron states; this is neglected due to past calculations approximate treatment of penetrations. We now include this projection term explicitly, which results in a significant broadening of spectral lines from highly-charged ions (low-Z elements are not much affected). The additional broadening raises the O Ly-alpha wing opacity by a factor of 5; we examine the consequences of this additional broadening on the Rosseland mean.

Introduction of a proline residue into position 31 of the loop of the dimeric 4-alpha-helical protein ROP causes a drastic destabilization.

Science.gov (United States)

Peters, K; Hinz, H J; Cesareni, G

1997-10-01

The exchange of an alanine with a proline residue in position 31 of the loop region of the dimeric 4-alpha-helical-bundle protein ROP causes a reduction in the alpha-helix content of 7% and a reduction in stability of about 40% compared to the wild type parameters. The Gibbs energy of unfolding by denaturants extrapolated linearly to zero denaturant concentration, delta G0D (buffer, 25 degrees C), has been determined to be 43 kJ (mol dimer)-1. The corresponding ROPwt value is 72 kJ (mol dimer)-1 (Steif et al., 1993). The extrapolated delta G0D values obtained from urea and GdmHCI un- and refolding studies are identical within error limits. Deconvolution of the stability values into enthalpy and entropy terms resulted in the following parameters. At T1/2 = 43 degrees C (Cprotein = 0.05 mg.ml-1) the ROP A31P mutant is characterized by delta Hv.H.0 = 272 kJ (mol dimer)-1, delta Cp = 7.2 kJ (mol dimer)-1 K-1, delta S0 = 762 J (mol dimer)-1 K-1. These parameters are only approximately 50% as large as the corresponding values of ROPwt. We assume that the significant reduction in stability reflects the absence of at least one hydrogen bond as well as deformation of the protein structure. This interpretation is supported by the reduction in the change in heat capacity observed for the A31P mutant relative to ROPwt, by the increased aggregation tendency of the mutant and by the reduced specific CD absorption at 222 nm. All results support the view that in the case of ROP protein the loop region plays a significant role in the maintenance of native structure and conformational stability.

Third dredge-up in cluster AGB stars : observational constraints and improved opacity data for models

International Nuclear Information System (INIS)

Lederer, M. T.

2009-01-01

evolution calculations with our findings. The second part of the thesis deals with a new set of low-temperature mean opacity coefficients. Until recently, the change in chemistry due to the TDU in the cool layers of the star, where molecules are the dominant opacity source, has been neglected in almost all stellar evolution models. I show that already within a certain chemistry regime (i. e. an oxygen-rich or carbon-rich metal mixture) an alteration of the carbon abundance causes, due to the special role of the CO molecule, considerable changes in the Rosseland opacity which has distinct consequences for the stellar structure and evolution. In the stellar evolution models, the most pronounced effect can be expected when the TDU turns the initially oxygen-rich object into a carbon star. The new opacity database contains (beside a variation of the 12 C mass fraction) also tables with a varied abundance of 14 N. After describing the database as well as the tools and the data used for its computation, I point out the implications of the new opacity data for stellar evolution models. (author) [de

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.

The coat protein complex II, COPII, protein Sec13 directly interacts with presenilin-1

International Nuclear Information System (INIS)

Nielsen, Anders Lade

2009-01-01

Mutations in the human gene encoding presenilin-1, PS1, account for most cases of early-onset familial Alzheimer's disease. PS1 has nine transmembrane domains and a large loop orientated towards the cytoplasm. PS1 locates to cellular compartments as endoplasmic reticulum (ER), Golgi apparatus, vesicular structures, and plasma membrane, and is an integral member of γ-secretase, a protein protease complex with specificity for intra-membranous cleavage of substrates such as β-amyloid precursor protein. Here, an interaction between PS1 and the Sec13 protein is described. Sec13 takes part in coat protein complex II, COPII, vesicular trafficking, nuclear pore function, and ER directed protein sequestering and degradation control. The interaction maps to the N-terminal part of the large hydrophilic PS1 loop and the first of the six WD40-repeats present in Sec13. The identified Sec13 interaction to PS1 is a new candidate interaction for linking PS1 to secretory and protein degrading vesicular circuits.

The coat protein complex II, COPII, protein Sec13 directly interacts with presenilin-1

Energy Technology Data Exchange (ETDEWEB)

Nielsen, Anders Lade, E-mail: aln@humgen.au.dk [Department of Human Genetics, The Bartholin Building, University of Aarhus, DK-8000 Aarhus C (Denmark)

2009-10-23

Mutations in the human gene encoding presenilin-1, PS1, account for most cases of early-onset familial Alzheimer's disease. PS1 has nine transmembrane domains and a large loop orientated towards the cytoplasm. PS1 locates to cellular compartments as endoplasmic reticulum (ER), Golgi apparatus, vesicular structures, and plasma membrane, and is an integral member of {gamma}-secretase, a protein protease complex with specificity for intra-membranous cleavage of substrates such as {beta}-amyloid precursor protein. Here, an interaction between PS1 and the Sec13 protein is described. Sec13 takes part in coat protein complex II, COPII, vesicular trafficking, nuclear pore function, and ER directed protein sequestering and degradation control. The interaction maps to the N-terminal part of the large hydrophilic PS1 loop and the first of the six WD40-repeats present in Sec13. The identified Sec13 interaction to PS1 is a new candidate interaction for linking PS1 to secretory and protein degrading vesicular circuits.

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.

Reactor loops at Chalk River

International Nuclear Information System (INIS)

Sochaski, R.O.

1962-07-01

This report describes broadly the nine in-reactor loops, and their components, located in and around the NRX and NRU reactors at Chalk River. First an introduction and general description is given of the loops and their function, supplemented with a table outlining some loop specifications and nine simplified flow sheets, one for each individual loop. The report then proceeds to classify each loop into two categories, the 'main loop circuit' and the 'auxiliary circuit', and descriptions are given of each circuit's components in turn. These components, in part, are comprised of the main loop pumps, the test section, loop heaters, loop coolers, delayed-neutron monitors, surge tank, Dowtherm coolers, loop piping. Here again photographs, drawings and tables are included to provide a clearer understanding of the descriptive literature and to include, in tables, some specifications of the more important components in each loop. (author)

The role of autolysis loop in determining the specificity of coagulation proteases.

Science.gov (United States)

Yang, L; Manithody, C; Rezaie, A R

2007-08-01

We recently demonstrated that the substitution of the autolysis loop (residues 143 to 154 in the chymotrypsin numbering system) of activated protein C (APC) with the corresponding loop of factor Xa (fXa) renders the APC mutant (APC/fX143-154) susceptible to inhibition by antithrombin (AT) in the presence of pentasaccharide. Our recent results further indicated, that in addition to an improvement in the reactivity of APC/fX143-154 with AT, both the amidolytic and anti-factor Va activities of the mutant APC have also been significantly increased. Since the autolysis loop of APC is five residues longer than the autolysis loop of fXa, it could not be ascertained whether this loop in the mutant APC specifically interacts with the activated conformation of AT or if a shorter autolysis loop is responsible for a global improvement in the catalytic activity of the mutant protease. To answer this question, we prepared another APC mutant in which the autolysis loop of the protease was replaced with the corresponding loop of trypsin (APC/Tryp143-154). Unlike an approximately 500-fold improvement in the reactivity of APC/fX143-154 with AT in the presence of pentasaccharide, the reactivity of APC/Tryp143-154 with the serpin was improved approximately 10-fold. These results suggest that both the length and structure of residues of the autolysis loop are critical for the specificity of the coagulation protease interaction with AT. Further factor Va inactivation studies with the APC mutants revealed a similar role for the autolysis loop of APC in the interaction with its natural substrate.

The role of autolysis loop in determining the specificity of coagulation proteases

Directory of Open Access Journals (Sweden)

L. Yang

2007-08-01

Full Text Available We recently demonstrated that the substitution of the autolysis loop (residues 143 to 154 in the chymotrypsin numbering system of activated protein C (APC with the corresponding loop of factor Xa (fXa renders the APC mutant (APC/fX143-154 susceptible to inhibition by antithrombin (AT in the presence of pentasaccharide. Our recent results further indicated, that in addition to an improvement in the reactivity of APC/fX143-154 with AT, both the amidolytic and anti-factor Va activities of the mutant APC have also been significantly increased. Since the autolysis loop of APC is five residues longer than the autolysis loop of fXa, it could not be ascertained whether this loop in the mutant APC specifically interacts with the activated conformation of AT or if a shorter autolysis loop is responsible for a global improvement in the catalytic activity of the mutant protease. To answer this question, we prepared another APC mutant in which the autolysis loop of the protease was replaced with the corresponding loop of trypsin (APC/Tryp143-154. Unlike an ~500-fold improvement in the reactivity of APC/fX143-154 with AT in the presence of pentasaccharide, the reactivity of APC/Tryp143-154 with the serpin was improved ~10-fold. These results suggest that both the length and structure of residues of the autolysis loop are critical for the specificity of the coagulation protease interaction with AT. Further factor Va inactivation studies with the APC mutants revealed a similar role for the autolysis loop of APC in the interaction with its natural substrate.

Influence of minor displacements in loops of the porcine parvovirus VP2 capsid on virus-like particles assembly and the induction of antibody responses.

Science.gov (United States)

Pan, Qunxing; He, Kongwang; Wang, Yongshan; Wang, Xiaoli; Ouyang, Wei

2013-06-01

An antigen-delivery system based on hybrid virus-like particles (VLPs) formed by the self-assembly of the capsid VP2 protein of porcine parvovirus (PPV) and expressing foreign peptides offers an alternative method for vaccination. In this study, the three-dimensional structure of the PPV capsid protein and surface loops deletion mutants were analyzed to define essential domains in PPV VP2 for the assembly of VLPs. Electron microscopic analysis and SDS-PAGE analysis confirmed the presence of abundant VLPs in a loop2 deletion mutant of expected size and appropriate morphology. Loop4 and loop2-loop4 deletion mutants, however, resulted in a lower number of particles and the morphology of the particles was not well preserved. Furthermore, the green fluorescent protein (gfp) gene was used as a model. GFP was observed at the same level in displacements mutants. However, GFP displacement mutants in loop2 construct allowed better adaptation for the fusion GFP to be further displayed on the surface of the capsid-like structure. Immunogenicity study showed that there is no obvious difference in mice inoculated with rAd-VP2(Δloop2), rAd-VP2(Δloop4), rAd-VP2(Δloop2-Δloop4), and PPV inactivated vaccine. The results suggested the possibility of inserting simultaneously B and T cell epitopes in the surface loop2 and the N-terminus. The combination of different types of epitopes (B, CD4+, and CD8+) in different positions of the PPV particles opens the way to the development of highly efficient vaccines, able to stimulate at the same time the different branches of the immune system.

Senataxin Mutation Reveals How R-Loops Promote Transcription by Blocking DNA Methylation at Gene Promoters.

Science.gov (United States)

Grunseich, Christopher; Wang, Isabel X; Watts, Jason A; Burdick, Joshua T; Guber, Robert D; Zhu, Zhengwei; Bruzel, Alan; Lanman, Tyler; Chen, Kelian; Schindler, Alice B; Edwards, Nancy; Ray-Chaudhury, Abhik; Yao, Jianhua; Lehky, Tanya; Piszczek, Grzegorz; Crain, Barbara; Fischbeck, Kenneth H; Cheung, Vivian G

2018-02-01

R-loops are three-stranded nucleic acid structures found abundantly and yet often viewed as by-products of transcription. Studying cells from patients with a motor neuron disease (amyotrophic lateral sclerosis 4 [ALS4]) caused by a mutation in senataxin, we uncovered how R-loops promote transcription. In ALS4 patients, the senataxin mutation depletes R-loops with a consequent effect on gene expression. With fewer R-loops in ALS4 cells, the expression of BAMBI, a negative regulator of transforming growth factor β (TGF-β), is reduced; that then leads to the activation of the TGF-β pathway. We uncovered that genome-wide R-loops influence promoter methylation of over 1,200 human genes. DNA methyl-transferase 1 favors binding to double-stranded DNA over R-loops. Thus, in forming R-loops, nascent RNA blocks DNA methylation and promotes further transcription. Hence, our results show that nucleic acid structures, in addition to sequences, influence the binding and activity of regulatory proteins. Copyright © 2017 Elsevier Inc. All rights reserved.

Extended Impact of Pin1 Catalytic Loop Phosphorylation Revealed by S71E Phosphomimetic.

Science.gov (United States)

Mahoney, Brendan J; Zhang, Meiling; Zintsmaster, John S; Peng, Jeffrey W

2018-03-02

Pin1 is a two-domain human protein that catalyzes the cis-trans isomerization of phospho-Ser/Thr-Pro (pS/T-P) motifs in numerous cell-cycle regulatory proteins. These pS/T-P motifs bind to Pin1's peptidyl-prolyl isomerase (PPIase) domain in a catalytic pocket, between an extended catalytic loop and the PPIase domain core. Previous studies showed that post-translational phosphorylation of S71 in the catalytic loop decreases substrate binding affinity and isomerase activity. To define the origins for these effects, we investigated a phosphomimetic Pin1 mutant, S71E-Pin1, using solution NMR. We find that S71E perturbs not only its host loop but also the nearby PPIase core. The perturbations identify a local network of hydrogen bonds and salt bridges that is more extended than previously thought, and includes interactions between the catalytic loop and the α2/α3 turn in the PPIase core. Explicit-solvent molecular dynamics simulations and phylogenetic analysis suggest that these interactions act as conserved "latches" between the loop and PPIase core that enhance binding of phosphorylated substrates, as they are absent in PPIases lacking pS/T-P specificity. Our results suggest that S71 is a hub residue within an electrostatic network primed for phosphorylation, and may illustrate a common mechanism of phosphorylation-mediated allostery. Copyright © 2018 Elsevier Ltd. All rights reserved.

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.

Distribution of sizes of erased loops for loop-erased random walks

OpenAIRE

Dhar, Deepak; Dhar, Abhishek

1997-01-01

We study the distribution of sizes of erased loops for loop-erased random walks on regular and fractal lattices. We show that for arbitrary graphs the probability $P(l)$ of generating a loop of perimeter $l$ is expressible in terms of the probability $P_{st}(l)$ of forming a loop of perimeter $l$ when a bond is added to a random spanning tree on the same graph by the simple relation $P(l)=P_{st}(l)/l$. On $d$-dimensional hypercubical lattices, $P(l)$ varies as $l^{-\\sigma}$ for large $l$, whe...

Reovirus FAST Proteins Drive Pore Formation and Syncytiogenesis Using a Novel Helix-Loop-Helix Fusion-Inducing Lipid Packing Sensor.

Directory of Open Access Journals (Sweden)

Jolene Read

2015-06-01

Full Text Available Pore formation is the most energy-demanding step during virus-induced membrane fusion, where high curvature of the fusion pore rim increases the spacing between lipid headgroups, exposing the hydrophobic interior of the membrane to water. How protein fusogens breach this thermodynamic barrier to pore formation is unclear. We identified a novel fusion-inducing lipid packing sensor (FLiPS in the cytosolic endodomain of the baboon reovirus p15 fusion-associated small transmembrane (FAST protein that is essential for pore formation during cell-cell fusion and syncytiogenesis. NMR spectroscopy and mutational studies indicate the dependence of this FLiPS on a hydrophobic helix-loop-helix structure. Biochemical and biophysical assays reveal the p15 FLiPS preferentially partitions into membranes with high positive curvature, and this partitioning is impeded by bis-ANS, a small molecule that inserts into hydrophobic defects in membranes. Most notably, the p15 FLiPS can be functionally replaced by heterologous amphipathic lipid packing sensors (ALPS but not by other membrane-interactive amphipathic helices. Furthermore, a previously unrecognized amphipathic helix in the cytosolic domain of the reptilian reovirus p14 FAST protein can functionally replace the p15 FLiPS, and is itself replaceable by a heterologous ALPS motif. Anchored near the cytoplasmic leaflet by the FAST protein transmembrane domain, the FLiPS is perfectly positioned to insert into hydrophobic defects that begin to appear in the highly curved rim of nascent fusion pores, thereby lowering the energy barrier to stable pore formation.

PHOTOSPHERIC PROPERTIES OF WARM EUV LOOPS AND HOT X-RAY LOOPS

Energy Technology Data Exchange (ETDEWEB)

Kano, R. [National Astronomical Observatory of Japan, 2-21-1 Osawa, Mitaka, Tokyo 181-8588 (Japan); Ueda, K. [Department of Astronomy, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Tsuneta, S., E-mail: ryouhei.kano@nao.ac.jp [Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency, 3-1-1 Yoshinodai, Chuo, Sagamihara, Kanagawa 252-5210 (Japan)

2014-02-20

We investigate the photospheric properties (vector magnetic fields and horizontal velocity) of a well-developed active region, NOAA AR 10978, using the Hinode Solar Optical Telescope specifically to determine what gives rise to the temperature difference between ''warm loops'' (1-2 MK), which are coronal loops observed in EUV wavelengths, and ''hot loops'' (>3 MK), coronal loops observed in X-rays. We found that outside sunspots, the magnetic filling factor in the solar network varies with location and is anti-correlated with the horizontal random velocity. If we accept that the observed magnetic features consist of unresolved magnetic flux tubes, this anti-correlation can be explained by the ensemble average of flux-tube motion driven by small-scale random flows. The observed data are consistent with a flux tube width of ∼77 km and horizontal flow at ∼2.6 km s{sup –1} with a spatial scale of ∼120 km. We also found that outside sunspots, there is no significant difference between warm and hot loops either in the magnetic properties (except for the inclination) or in the horizontal random velocity at their footpoints, which are identified with the Hinode X-Ray Telescope and the Transition Region and Coronal Explorer. The energy flux injected into the coronal loops by the observed photospheric motion of the magnetic fields is estimated to be 2 × 10{sup 6} erg s{sup –1} cm{sup –2}, which is the same for both warm and hot loops. This suggests that coronal properties (e.g., loop length) play a more important role in giving rise to temperature differences of active-region coronal loops than photospheric parameters.

"Garbage" In, "Refuse and Refuse Disposal" Out: Making the Most of the Subject Authority File in OPAC.

Science.gov (United States)

Horn, Marguerite E.

2002-01-01

Discusses the difference in subject access in OPACs (online public access catalogs) between subject searching (authority, alphabetic, or controlled vocabulary) versus keyword searching (uncontrolled, free text, natural language vocabulary). Compares a query on the term "garbage" in two online catalogs and discusses results. (Author/LRW)

Interplay of protein and DNA structure revealed in simulations of the lac operon.

Directory of Open Access Journals (Sweden)

Luke Czapla

Full Text Available The E. coli Lac repressor is the classic textbook example of a protein that attaches to widely spaced sites along a genome and forces the intervening DNA into a loop. The short loops implicated in the regulation of the lac operon suggest the involvement of factors other than DNA and repressor in gene control. The molecular simulations presented here examine two likely structural contributions to the in-vivo looping of bacterial DNA: the distortions of the double helix introduced upon association of the highly abundant, nonspecific nucleoid protein HU and the large-scale deformations of the repressor detected in low-resolution experiments. The computations take account of the three-dimensional arrangements of nucleotides and amino acids found in crystal structures of DNA with the two proteins, the natural rest state and deformational properties of protein-free DNA, and the constraints on looping imposed by the conformation of the repressor and the orientation of bound DNA. The predicted looping propensities capture the complex, chain-length-dependent variation in repression efficacy extracted from gene expression studies and in vitro experiments and reveal unexpected chain-length-dependent variations in the uptake of HU, the deformation of repressor, and the folding of DNA. Both the opening of repressor and the presence of HU, at levels approximating those found in vivo, enhance the probability of loop formation. HU affects the global organization of the repressor and the opening of repressor influences the levels of HU binding to DNA. The length of the loop determines whether the DNA adopts antiparallel or parallel orientations on the repressor, whether the repressor is opened or closed, and how many HU molecules bind to the loop. The collective behavior of proteins and DNA is greater than the sum of the parts and hints of ways in which multiple proteins may coordinate the packaging and processing of genetic information.

Interplay of protein and DNA structure revealed in simulations of the lac operon.

Science.gov (United States)

Czapla, Luke; Grosner, Michael A; Swigon, David; Olson, Wilma K

2013-01-01

The E. coli Lac repressor is the classic textbook example of a protein that attaches to widely spaced sites along a genome and forces the intervening DNA into a loop. The short loops implicated in the regulation of the lac operon suggest the involvement of factors other than DNA and repressor in gene control. The molecular simulations presented here examine two likely structural contributions to the in-vivo looping of bacterial DNA: the distortions of the double helix introduced upon association of the highly abundant, nonspecific nucleoid protein HU and the large-scale deformations of the repressor detected in low-resolution experiments. The computations take account of the three-dimensional arrangements of nucleotides and amino acids found in crystal structures of DNA with the two proteins, the natural rest state and deformational properties of protein-free DNA, and the constraints on looping imposed by the conformation of the repressor and the orientation of bound DNA. The predicted looping propensities capture the complex, chain-length-dependent variation in repression efficacy extracted from gene expression studies and in vitro experiments and reveal unexpected chain-length-dependent variations in the uptake of HU, the deformation of repressor, and the folding of DNA. Both the opening of repressor and the presence of HU, at levels approximating those found in vivo, enhance the probability of loop formation. HU affects the global organization of the repressor and the opening of repressor influences the levels of HU binding to DNA. The length of the loop determines whether the DNA adopts antiparallel or parallel orientations on the repressor, whether the repressor is opened or closed, and how many HU molecules bind to the loop. The collective behavior of proteins and DNA is greater than the sum of the parts and hints of ways in which multiple proteins may coordinate the packaging and processing of genetic information.

A Longitudinal Study of the Effects of OPAC Screen Changes on Searching Behavior and Searcher Success.

Science.gov (United States)

Blecic, Deborah D.; Dorsch, Josephine L.; Koenig, Melissa H.; Bangalore, Nimala S.

1999-01-01

Describes a longitudinal study of four sets of OPAC (online public access catalog) transaction logs that examined the effects of screen changes in helping searchers improve their search behavior. Results show that while screen changes initially had a positive impact on search behavior, they were not always sustained over time. (Author/LRW)

An Empirical Determination of the Intergalactic Background Light Using Near-Infrared Deep Galaxy Survey Data Out to 5 Micrometers and the Gamma-Ray Opacity of the Universe

Science.gov (United States)

Scully, Sean T.; Malkan, Matthew A.; Stecker, Floyd W.

2014-01-01

We extend our previous model-independent determination of the intergalactic background light, based purely on galaxy survey data, out to a wavelength of 5 micrometers. Our approach enables us to constrain the range of photon densities, based on the uncertainties from observationally determined luminosity densities and colors. We further determine a 68% confidence upper and lower limit on the opacity of the universe to gamma-rays up to energies of 1.6/(1 + z) terraelectron volts. A comparison of our lower limit redshift-dependent opacity curves to the opacity limits derived from the results of both ground-based air Cerenkov telescope and Fermi-LAT observations of PKS 1424+240 allows us to place a new upper limit on the redshift of this source, independent of IBL modeling.

Proving Opacity of Transactional Memory with Early Release

Directory of Open Access Journals (Sweden)

Siek Konrad

2015-12-01

Full Text Available Transactional Memory (TM is an alternative way of synchronizing concurrent accesses to shared memory by adopting the abstraction of transactions in place of low-level mechanisms like locks and barriers. TMs usually apply optimistic concurrency control to provide a universal and easy-to-use method of maintaining correctness. However, this approach performs a high number of aborts in high contention workloads, which can adversely affect performance. Optimistic TMs can cause problems when transactions contain irrevocable operations. Hence, pessimistic TMs were proposed to solve some of these problems. However, an important way of achieving efficiency in pessimistic TMs is to use early release. On the other hand, early release is seemingly at odds with opacity, the gold standard of TM safety properties, which does not allow transactions to make their state visible until they commit. In this paper we propose a proof technique that makes it possible to demonstrate that a TM with early release can be opaque as long as it prevents inconsistent views.

Disease-associated extracellular loop mutations in the adhesion G protein-coupled receptor G1 (ADGRG1; GPR56) differentially regulate downstream signaling.

Science.gov (United States)

Kishore, Ayush; Hall, Randy A

2017-06-09

Mutations to the adhesion G protein-coupled receptor ADGRG1 (G1; also known as GPR56) underlie the neurological disorder bilateral frontoparietal polymicrogyria. Disease-associated mutations in G1 studied to date are believed to induce complete loss of receptor function through disruption of either receptor trafficking or signaling activity. Given that N-terminal truncation of G1 and other adhesion G protein-coupled receptors has been shown to significantly increase the receptors' constitutive signaling, we examined two different bilateral frontoparietal polymicrogyria-inducing extracellular loop mutations (R565W and L640R) in the context of both full-length and N-terminally truncated (ΔNT) G1. Interestingly, we found that these mutations reduced surface expression of full-length G1 but not G1-ΔNT in HEK-293 cells. Moreover, the mutations ablated receptor-mediated activation of serum response factor luciferase, a classic measure of Gα 12/13 -mediated signaling, but had no effect on G1-mediated signaling to nuclear factor of activated T cells (NFAT) luciferase. Given these differential signaling results, we sought to further elucidate the pathway by which G1 can activate NFAT luciferase. We found no evidence that ΔNT activation of NFAT is dependent on Gα q/11 -mediated or β-arrestin-mediated signaling but rather involves liberation of Gβγ subunits and activation of calcium channels. These findings reveal that disease-associated mutations to the extracellular loops of G1 differentially alter receptor trafficking, depending on the presence of the N terminus, and differentially alter signaling to distinct downstream pathways. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

Chimeric microbial rhodopsins for optical activation of Gs-proteins

Science.gov (United States)

Yoshida, Kazuho; Yamashita, Takahiro; Sasaki, Kengo; Inoue, Keiichi; Shichida, Yoshinori; Kandori, Hideki

2017-01-01

We previously showed that the chimeric proteins of microbial rhodopsins, such as light-driven proton pump bacteriorhodopsin (BR) and Gloeobacter rhodopsin (GR) that contain cytoplasmic loops of bovine rhodopsin, are able to activate Gt protein upon light absorption. These facts suggest similar protein structural changes in both the light-driven proton pump and animal rhodopsin. Here we report two trials to engineer chimeric rhodopsins, one for the inserted loop, and another for the microbial rhodopsin template. For the former, we successfully activated Gs protein by light through the incorporation of the cytoplasmic loop of β2-adrenergic receptor (β2AR). For the latter, we did not observe any G-protein activation for the light-driven sodium pump from Indibacter alkaliphilus (IndiR2) or a light-driven chloride pump halorhodopsin from Natronomonas pharaonis (NpHR), whereas the light-driven proton pump GR showed light-dependent G-protein activation. This fact suggests that a helix opening motion is common to G protein coupled receptor (GPCR) and GR, but not to IndiR2 and NpHR. Light-induced difference FTIR spectroscopy revealed similar structural changes between WT and the third loop chimera for each light-driven pump. A helical structural perturbation, which was largest for GR, was further enhanced in the chimera. We conclude that similar structural dynamics that occur on the cytoplasmic side of GPCR are needed to design chimeric microbial rhodopsins. PMID:29362703

Multiple Flow Loop SCADA System Implemented on the Production Prototype Loop

Energy Technology Data Exchange (ETDEWEB)

Baily, Scott A. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Dalmas, Dale Allen [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Wheat, Robert Mitchell [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Woloshun, Keith Albert [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Dale, Gregory E. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2015-11-16

The following report covers FY 15 activities to develop supervisory control and data acquisition (SCADA) system for the Northstar Moly99 production prototype gas flow loop. The goal of this effort is to expand the existing system to include a second flow loop with a larger production-sized blower. Besides testing the larger blower, this system will demonstrate the scalability of our solution to multiple flow loops.

AKSES JENIS DOKUMEN PADA BASIS DATA TERPADU: SUATU TINJAUAN TERHADAP OPAC DI PDII-LIPI

Directory of Open Access Journals (Sweden)

Ade Kohar

2012-07-01

Full Text Available Integrated data base is a data base records bibliographic data of several types of document like textbook, periodicals, proceedings, research report, thesis, and article. Purposes of this study were to investigate document type description and searching strategy in integrated data base of online public access catalogs (OPAC in PDII-LIPI, and to know user opinion about that data base existence. It used observation and interviews to 100 data base users to collect data. Result of this study stated that document type description in OPAC was not indexed, so users couldn't do information searching of special type of document directly in the data base. There was only one method could be used to search information of special type of document. User could select it from some information records on the computer screen as the result of document title, author name or subject searching in the data base. This information access method was not efficient. So document type description and indexing was an important factor and should be done in information retrieval system using integrated data base. But respondent majority (84% in PDII-LIPI stated that they liked using separated data base to search information of special type of document.

Atomic data base and the U.K.-U.S. opacity project

Science.gov (United States)

Pradhan, A. K.

1988-08-01

With the primary aim of calculating stellar envelope opacities, a joint international collaboration is under way for the calculation of basic atomic data for radiative processes: oscillator strengths, photoionization cross sections, energy levels, radiative damping constants (including line broadening). Atomic calculations have been completed for the first ten isoelectronic sequences, H-like to Ne-like, going up to iron, and work is in progress on the third and fourth row atoms and isosequences. The close-coupling approximation is employed throughout using a new version of the R-matrix method. Particular emphasis is placed on the detailed resolution of the autoionization structures in the bound-free continuum.

The Response of Ω-Loop D Dynamics to Truncation of Trimethyllysine 72 of Yeast Iso-1-cytochrome c Depends on the Nature of Loop Deformation

Science.gov (United States)

McClelland, Levi J.; Seagraves, Sean M.; Khan, Khurshid Alam; Cherney, Melisa M.; Bandi, Swati; Culbertson, Justin E.; Bowler, Bruce E.

2015-01-01

Trimethyllysine 72 (tmK72) has been suggested to play a role in sterically constraining the heme crevice dynamics of yeast iso-1-cytochrome c mediated by the Ω-loop D cooperative substructure (residues 70 to 85). A tmK72A mutation causes a gain in peroxidase activity, a function of cytochrome c that is important early in apoptosis. More than one higher energy state is accessible for the Ω-loop D substructure via tier 0 dynamics. Two of these are alkaline conformers mediated by Lys73 and Lys79. In the current work, the effect of the tmK72A mutation on the thermodynamic and kinetic properties of wild type iso-1-cytochrome c (yWT versus WT*) and on variants carrying a K73H mutation (yWT/K73H versus WT*/K73H) is studied. Whereas the tmK72A mutation confers increased peroxidase activity in wild type yeast iso-1-cytochrome c and increased dynamics for formation of a previously studied His79-heme alkaline conformer, the tmK72A mutation speeds return of the His73-heme alkaline conformer to the native state through destabilization of the His73-heme alkaline conformer relative to the native conformer. These opposing behaviors demonstrate that the response of the dynamics of a protein substructure to mutation depends on the nature of the perturbation to the substructure. For a protein substructure which mediates more than one function of a protein through multiple non-native structures, a mutation could change the partitioning between these functions. The current results suggest that the tier 0 dynamics of Ω-loop D that mediates peroxidase activity has similarities to the tier 0 dynamics required to form the His79-heme alkaline conformer. PMID:25948392

Studying DNA Looping by Single-Molecule FRET

OpenAIRE

Le, Tung T.; Kim, Harold D.

2014-01-01

Bending of double-stranded DNA (dsDNA) is associated with many important biological processes such as DNA-protein recognition and DNA packaging into nucleosomes. Thermodynamics of dsDNA bending has been studied by a method called cyclization which relies on DNA ligase to covalently join short sticky ends of a dsDNA. However, ligation efficiency can be affected by many factors that are not related to dsDNA looping such as the DNA structure surrounding the joined sticky ends, and ligase can als...

On loop extensions and cohomology of loops

OpenAIRE

Benítez, Rolando Jiménez; Meléndez, Quitzeh Morales

2015-01-01

In this paper are defined cohomology-like groups that classify loop extensions satisfying a given identity in three variables for association identities, and in two variables for the case of commutativity. It is considered a large amount of identities. This groups generalize those defined in works of Nishigori [2] and of Jhonson and Leedham-Green [4]. It is computed the number of metacyclic extensions for trivial action of the quotient on the kernel in one particular case for left Bol loops a...

ABC transporter Cdr1p harbors charged residues in the intracellular loop and nucleotide-binding domain critical for protein trafficking and drug resistance.

Science.gov (United States)

Shah, Abdul Haseeb; Banerjee, Atanu; Rawal, Manpreet Kaur; Saxena, Ajay Kumar; Mondal, Alok Kumar; Prasad, Rajendra

2015-08-01

The ABC transporter Cdr1 protein of Candida albicans, which plays a major role in antifungal resistance, has two transmembrane domains (TMDs) and two nucleotide-binding domains (NBDs). The 12 transmembrane helices of TMDs that are interconnected by extracellular and intracellular loops (ICLs) mainly harbor substrate recognition sites where drugs bind while cytoplasmic NBDs hydrolyze ATP which powers drug efflux. The coupling of ATP hydrolysis to drug transport requires proper communication between NBDs and TMDs typically accomplished by ICLs. This study examines the role of cytoplasmic ICLs of Cdr1p by rationally predicting the critical residues on the basis of their interatomic distances. Among nine pairs that fall within a proximity of trafficking. These results point to a new role for ICL/NBD interacting residues in PDR ABC transporters in protein folding and trafficking. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Resistance of Subtype C HIV-1 Strains to Anti-V3 Loop Antibodies

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David Almond

2012-01-01

Full Text Available HIV-1’s subtype C V3 loop consensus sequence exhibits increased resistance to anti-V3 antibody-mediated neutralization as compared to the subtype B consensus sequence. The dynamic 3D structure of the consensus C V3 loop crown, visualized by ab initio folding, suggested that the resistance derives from structural rigidity and non-β-strand secondary protein structure in the N-terminal strand of the β-hairpin of the V3 loop crown, which is where most known anti-V3 loop antibodies bind. The observation of either rigidity or non-β-strand structure in this region correlated with observed resistance to antibody-mediated neutralization in a series of chimeric pseudovirus (psV mutants. The results suggest the presence of an epitope-independent, neutralization-relevant structural difference in the antibody-targeted region of the V3 loop crown between subtype C and subtype B, a difference that we hypothesize may contribute to the divergent pattern of global spread between these subtypes. As antibodies to a variable loop were recently identified as an inverse correlate of risk for HIV infection, the structure-function relationships discussed in this study may have relevance to HIV vaccine research.

Rapid Simulation of Flat Knitting Loops Based On the Yarn Texture and Loop Geometrical Model

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Lu Zhiwen

2017-06-01

Full Text Available In order to create realistic loop primitives suitable for the fast computer-aided design (CAD of the flat knitted fabric, we have a research on the geometric model of the loop as well as the variation of the loop surface. Establish the texture variation model based on the changing process from the normal yarn to loop that provides the realistic texture of the simulative loop. Then optimize the simulative loop based on illumination variation. This paper develops the computer program with the optimization algorithm and achieves the loop simulation of different yarns to verify the feasibility of the proposed algorithm. Our work provides a fast CAD of the flat knitted fabric with loop simulation, and it is not only more realistic but also material adjustable. Meanwhile it also provides theoretical value for the flat knitted fabric computer simulation.

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...

Structures of Gate Loop Variants of the AcrB Drug Efflux Pump Bound by Erythromycin Substrate.

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Abdessamad Ababou

Full Text Available Gram-negative bacteria such as E. coli use tripartite efflux pumps such as AcrAB-TolC to expel antibiotics and noxious compounds. A key feature of the inner membrane transporter component, AcrB, is a short stretch of residues known as the gate/switch loop that divides the proximal and distal substrate binding pockets. Amino acid substitutions of the gate loop are known to decrease antibiotic resistance conferred by AcrB. Here we present two new AcrB gate loop variants, the first stripped of its bulky side chains, and a second in which the gate loop is removed entirely. By determining the crystal structures of the variant AcrB proteins in the presence and absence of erythromycin and assessing their ability to confer erythromycin tolerance, we demonstrate that the gate loop is important for AcrB export activity but is not required for erythromycin binding.

Multi-loop PWR modeling and hardware-in-the-loop testing using ACSL

International Nuclear Information System (INIS)

Thomas, V.M.; Heibel, M.D.; Catullo, W.J.

1989-01-01

Westinghouse has developed an Advanced Digital Feedwater Control System (ADFCS) which is aimed at reducing feedwater related reactor trips through improved control performance for pressurized water reactor (PWR) power plants. To support control system setpoint studies and functional design efforts for the ADFCS, an ACSL based model of the nuclear steam supply system (NSSS) of a Westinghouse (PWR) was generated. Use of this plant model has been extended from system design to system testing through integration of the model into a Hardware-in-Loop test environment for the ADFCS. This integration includes appropriate interfacing between a Gould SEL 32/87 computer, upon which the plant model executes in real time, and the Westinghouse Distributed Processing family (WDPF) test hardware. A development program has been undertaken to expand the existing ACSL model to include capability to explicitly model multiple plant loops, steam generators, and corresponding feedwater systems. Furthermore, the program expands the ADFCS Hardware-in-Loop testing to include the multi-loop plant model. This paper provides an overview of the testing approach utilized for the ADFCS with focus on the role of Hardware-in-Loop testing. Background on the plant model, methodology and test environment is also provided. Finally, an overview is presented of the program to expand the model and associated Hardware-in-Loop test environment to handle multiple loops

Random walk loop soup

OpenAIRE

Lawler, Gregory F.; Ferreras, José A. Trujillo

2004-01-01

The Brownian loop soup introduced in Lawler and Werner (2004) is a Poissonian realization from a sigma-finite measure on unrooted loops. This measure satisfies both conformal invariance and a restriction property. In this paper, we define a random walk loop soup and show that it converges to the Brownian loop soup. In fact, we give a strong approximation result making use of the strong approximation result of Koml\\'os, Major, and Tusn\\'ady. To make the paper self-contained, we include a proof...

An Extended Surface Loop on Toxoplasma gondii Apical Membrane Antigen 1 (AMA1 Governs Ligand Binding Selectivity.

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Michelle L Parker

Full Text Available Apicomplexan parasites are the causative agents of globally prevalent diseases including malaria and toxoplasmosis. These obligate intracellular pathogens have evolved a sophisticated host cell invasion strategy that relies on a parasite-host cell junction anchored by interactions between apical membrane antigens (AMAs on the parasite surface and rhoptry neck 2 (RON2 proteins discharged from the parasite and embedded in the host cell membrane. Key to formation of the AMA1-RON2 complex is displacement of an extended surface loop on AMA1 called the DII loop. While conformational flexibility of the DII loop is required to expose the mature RON2 binding groove, a definitive role of this substructure has not been elucidated. To establish a role of the DII loop in Toxoplasma gondii AMA1, we engineered a form of the protein where the mobile portion of the loop was replaced with a short Gly-Ser linker (TgAMA1ΔDIIloop. Isothermal titration calorimetry measurements with a panel of RON2 peptides revealed an influential role for the DII loop in governing selectivity. Most notably, an Eimeria tenella RON2 (EtRON2 peptide that showed only weak binding to TgAMA1 bound with high affinity to TgAMA1ΔDIIloop. To define the molecular basis for the differential binding, we determined the crystal structure of TgAMA1ΔDIIloop in complex with the EtRON2 peptide. When analyzed in the context of existing AMA1-RON2 structures, spatially distinct anchor points in the AMA1 groove were identified that, when engaged, appear to provide the necessary traction to outcompete the DII loop. Collectively, these data support a model where the AMA1 DII loop serves as a structural gatekeeper to selectively filter out ligands otherwise capable of binding with high affinity in the AMA1 apical groove. These data also highlight the importance of considering the functional implications of the DII loop in the ongoing development of therapeutic intervention strategies targeting the AMA1-RON

Lens Opacity and Hydrogen Sulfide in a New Zealand Geothermal Area.

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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.

All-atom normal-mode analysis reveals an RNA-induced allostery in a bacteriophage coat protein.

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Dykeman, Eric C; Twarock, Reidun

2010-03-01

Assembly of the T=3 bacteriophage MS2 is initiated by the binding of a 19 nucleotide RNA stem loop from within the phage genome to a symmetric coat protein dimer. This binding event effects a folding of the FG loop in one of the protein subunits of the dimer and results in the formation of an asymmetric dimer. Since both the symmetric and asymmetric forms of the dimer are needed for the assembly of the protein container, this allosteric switch plays an important role in the life cycle of the phage. We provide here details of an all-atom normal-mode analysis of this allosteric effect. The results suggest that asymmetric contacts between the A -duplex RNA phosphodiester backbone of the stem loop with the EF loop in one coat protein subunit results in an increased dynamic behavior of its FG loop. The four lowest-frequency modes, which encompass motions predominantly on the FG loops, account for over 90% of the increased dynamic behavior due to a localization of the vibrational pattern on a single FG loop. Finally, we show that an analysis of the allosteric effect using an elastic network model fails to predict this localization effect, highlighting the importance of using an all-atom full force field method for this problem.

Scanning a DNA molecule for bound proteins using hybrid magnetic and optical tweezers.

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Marijn T J van Loenhout

Full Text Available The functional state of the genome is determined by its interactions with proteins that bind, modify, and move along the DNA. To determine the positions and binding strength of proteins localized on DNA we have developed a combined magnetic and optical tweezers apparatus that allows for both sensitive and label-free detection. A DNA loop, that acts as a scanning probe, is created by looping an optically trapped DNA tether around a DNA molecule that is held with magnetic tweezers. Upon scanning the loop along the λ-DNA molecule, EcoRI proteins were detected with ~17 nm spatial resolution. An offset of 33 ± 5 nm for the detected protein positions was found between back and forwards scans, corresponding to the size of the DNA loop and in agreement with theoretical estimates. At higher applied stretching forces, the scanning loop was able to remove bound proteins from the DNA, showing that the method is in principle also capable of measuring the binding strength of proteins to DNA with a force resolution of 0.1 pN/[Formula: see text]. The use of magnetic tweezers in this assay allows the facile preparation of many single-molecule tethers, which can be scanned one after the other, while it also allows for direct control of the supercoiling state of the DNA molecule, making it uniquely suitable to address the effects of torque on protein-DNA interactions.

Neutron transport in irradiation loops (IRENE loop)

International Nuclear Information System (INIS)

Sarsam, Maher.

1980-09-01

This thesis is composed of two parts with different aspects. Part one is a technical description of the loop and its main ancillary facilities as well as of the safety and operational regulations. The measurement methods on the model of the ISIS reactor and on the loop in the OSIRIS reactor are described. Part two deals with the possibility of calculating the powers dissipated by each rod of the fuel cluster, using appropriate computer codes, not only in the reflector but also in the core and to suggest a method of calculation [fr

Loop Replacement Enhances the Ancestral Antibacterial Function of a Bifunctional Scorpion Toxin

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Shangfei Zhang

2018-06-01

Full Text Available On the basis of the evolutionary relationship between scorpion toxins targeting K+ channels (KTxs and antibacterial defensins (Zhu S., Peigneur S., Gao B., Umetsu Y., Ohki S., Tytgat J. Experimental conversion of a defensin into a neurotoxin: Implications for origin of toxic function. Mol. Biol. Evol. 2014, 31, 546–559, we performed protein engineering experiments to modify a bifunctional KTx (i.e., weak inhibitory activities on both K+ channels and bacteria via substituting its carboxyl loop with the structurally equivalent loop of contemporary defensins. As expected, the engineered peptide (named MeuTXKα3-KFGGI remarkably improved the antibacterial activity, particularly on some Gram-positive bacteria, including several antibiotic-resistant opportunistic pathogens. Compared with the unmodified toxin, its antibacterial spectrum also enlarged. Our work provides a new method to enhance the antibacterial activity of bifunctional scorpion venom peptides, which might be useful in engineering other proteins with an ancestral activity.

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.

Loop space representation of quantum general relativity and the group of loops

International Nuclear Information System (INIS)

Gambini, R.

1991-01-01

The action of the constraints of quantum general relativity on a general state in the loop representation is coded in terms of loop derivatives. These differential operators are related to the infinitesimal generators of the group of loops and generalize the area derivative first considered by Mandelstam. A new sector of solutions of the physical states space of nonperturbative quantum general relativity is found. (orig.)

Fermions and loops on graphs: I. Loop calculus for determinants

International Nuclear Information System (INIS)

Chernyak, Vladimir Y; Chertkov, Michael

2008-01-01

This paper is the first in a series devoted to evaluation of the partition function in statistical models on graphs with loops in terms of the Berezin/fermion integrals. The paper focuses on a representation of the determinant of a square matrix in terms of a finite series, where each term corresponds to a loop on the graph. The representation is based on a fermion version of the loop calculus, previously introduced by the authors for graphical models with finite alphabets. Our construction contains two levels. First, we represent the determinant in terms of an integral over anti-commuting Grassmann variables, with some reparametrization/gauge freedom hidden in the formulation. Second, we show that a special choice of the gauge, called the BP (Bethe–Peierls or belief propagation) gauge, yields the desired loop representation. The set of gauge fixing BP conditions is equivalent to the Gaussian BP equations, discussed in the past as efficient (linear scaling) heuristics for estimating the covariance of a sparse positive matrix

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

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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.

Dechanneling by dislocation loops

International Nuclear Information System (INIS)

Chalant, Gerard.

1976-09-01

Ion implantation always induces the creation of dislocation loops. When the damage profile is determined by a backscattering technique, the dechanneling by these loops is implicitely at the origin of these measurements. The dechanneling of alpha particles by dislocation loops produced by the coalescence of quenched-in vacancies in aluminium is studied. The dechanneling and the concentration of loops were determined simultaneously. The dechanneling width around dislocation was found equal to lambda=6A, both for perfect and imperfect loops having a mean diameter d=250A. In the latter case, a dechanneling probability chi=0.34 was determined for the stacking fault, in good agreement with previous determination in gold. A general formula is proposed which takes into account the variation of lambda with the curvature (or the diameter d) of the loops. Finally, by a series of isothermal anneals, the self-diffusion energy ΔH of aluminium was measured. The value obtained ΔH=1.32+-0.10eV is in good agreement with the values obtained by other methods [fr

The Brownian loop soup

OpenAIRE

Lawler, Gregory F.; Werner, Wendelin

2003-01-01

We define a natural conformally invariant measure on unrooted Brownian loops in the plane and study some of its properties. We relate this measure to a measure on loops rooted at a boundary point of a domain and show how this relation gives a way to ``chronologically add Brownian loops'' to simple curves in the plane.

The Impact of Lens Opacity on SD-OCT Retinal Nerve Fiber Layer and Bruch's Membrane Opening Measurements Using the Anatomical Positioning System (APS).

Science.gov (United States)

Mauschitz, Matthias M; Roth, Felix; Holz, Frank G; Breteler, Monique M B; Finger, Robert P

2017-05-01

To evaluate the impact of lens opacity on retinal nerve fiber layer thickness (RNFLT) and Bruch's membrane opening (BMO) measurements. Fifty-nine randomly selected patients without any other relevant ocular pathology undergoing elective routine cataract surgery in two specialized eye clinics were enrolled. RNFLT, BMO area, and BMO minimum rim width (BMO-MRW) were assessed with the Heidelberg Engineering Spectralis OCT using the anatomical positioning system (APS) prior to and 1 day after cataract surgery using a ring scan at different eccentricities of the disc (3.5, 4.1 and 4.7 mm). Lens opacity was quantified using densitometry based on Scheimpflug images (Oculus Pentacam AXL). RNFLT, BMO area, and BMO-MRW were virtually identical before and following removal of the cataractous lens. This held when assessed overall, within the six sectors for the 3.5-mm scan, or at any other eccentricity. Baseline RNFLT was not associated with lens opacity. Using the APS, RNFLT remained unchanged following cataract surgery, contrary to results reported by previous studies. Our results imply that the APS may have contributed to more precise spectral-domain optical coherence measurements, minimizing the influence of cataract on RNFLT and BMO assessments in our cohort.

Mediator binds to boundaries of chromosomal interaction domains and to proteins involved in DNA looping, RNA metabolism, chromatin remodeling, and actin assembly.

Science.gov (United States)

Chereji, Razvan V; Bharatula, Vasudha; Elfving, Nils; Blomberg, Jeanette; Larsson, Miriam; Morozov, Alexandre V; Broach, James R; Björklund, Stefan

2017-09-06

Mediator is a multi-unit molecular complex that plays a key role in transferring signals from transcriptional regulators to RNA polymerase II in eukaryotes. We have combined biochemical purification of the Saccharomyces cerevisiae Mediator from chromatin with chromatin immunoprecipitation in order to reveal Mediator occupancy on DNA genome-wide, and to identify proteins interacting specifically with Mediator on the chromatin template. Tandem mass spectrometry of proteins in immunoprecipitates of mediator complexes revealed specific interactions between Mediator and the RSC, Arp2/Arp3, CPF, CF 1A and Lsm complexes in chromatin. These factors are primarily involved in chromatin remodeling, actin assembly, mRNA 3'-end processing, gene looping and mRNA decay, but they have also been shown to enter the nucleus and participate in Pol II transcription. Moreover, we have found that Mediator, in addition to binding Pol II promoters, occupies chromosomal interacting domain (CID) boundaries and that Mediator in chromatin associates with proteins that have been shown to interact with CID boundaries, such as Sth1, Ssu72 and histone H4. This suggests that Mediator plays a significant role in higher-order genome organization. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Reactor recirculation pump test loop

International Nuclear Information System (INIS)

Taka, Shusei; Kato, Hiroyuki

1979-01-01

A test loop for a reactor primary loop recirculation pumps (PLR pumps) has been constructed at Ebara's Haneda Plant in preparation for production of PLR pumps under license from Byron Jackson Pump Division of Borg-Warner Corporation. This loop can simulate operating conditions for test PLR pumps with 130 per cent of the capacity of pumps for a 1100 MWe BWR plant. A main loop, primary cooling system, water demineralizer, secondary cooling system, instrumentation and control equipment and an electric power supply system make up the test loop. This article describes the test loop itself and test results of two PLR pumps for Fukushima No. 2 N.P.S. Unit 1 and one main circulation pump for HAZ Demonstration Test Facility. (author)

Relaxing the Small Particle Approximation for Dust-grain opacities in Carbon-star Wind Models

OpenAIRE

Mattsson, Lars; Höfner, Susanne

2010-01-01

We have computed wind models with time-dependent dust formation and grain-size dependent opacities, where (1) the problem is simplified by assuming a fixed dust-grain size, and where (2) the radiation pressure efficiency is approximated using grain sizes based on various means of the actual grain size distribution. It is shown that in critical cases, the effect of grain sizes can be significant. For well-developed winds, however, the effects on the mass-loss rate and the wind speed are small.

Plant STAND P-loop NTPases: a current perspective of genome distribution, evolution, and function : Plant STAND P-loop NTPases: genomic organization, evolution, and molecular mechanism models contribute broadly to plant pathogen defense.

Science.gov (United States)

Arya, Preeti; Acharya, Vishal

2018-02-01

STAND P-loop NTPase is the common weapon used by plant and other organisms from all three kingdoms of life to defend themselves against pathogen invasion. The purpose of this study is to review comprehensively the latest finding of plant STAND P-loop NTPase related to their genomic distribution, evolution, and their mechanism of action. Earlier, the plant STAND P-loop NTPase known to be comprised of only NBS-LRRs/AP-ATPase/NB-ARC ATPase. However, recent finding suggests that genome of early green plants comprised of two types of STAND P-loop NTPases: (1) mammalian NACHT NTPases and (2) NBS-LRRs. Moreover, YchF (unconventional G protein and members of P-loop NTPase) subfamily has been reported to be exceptionally involved in biotic stress (in case of Oryza sativa), thereby a novel member of STAND P-loop NTPase in green plants. The lineage-specific expansion and genome duplication events are responsible for abundance of plant STAND P-loop NTPases; where "moderate tandem and low segmental duplication" trajectory followed in majority of plant species with few exception (equal contribution of tandem and segmental duplication). Since the past decades, systematic research is being investigated into NBS-LRR function supported the direct recognition of pathogen or pathogen effectors by the latest models proposed via 'integrated decoy' or 'sensor domains' model. Here, we integrate the recently published findings together with the previous literature on the genomic distribution, evolution, and distinct models proposed for functional molecular mechanism of plant STAND P-loop NTPases.

Wilson loops in minimal surfaces

International Nuclear Information System (INIS)

Drukker, Nadav; Gross, David J.; Ooguri, Hirosi

1999-01-01

The AdS/CFT correspondence suggests that the Wilson loop of the large N gauge theory with N = 4 supersymmetry in 4 dimensions is described by a minimal surface in AdS 5 x S 5 . The authors examine various aspects of this proposal, comparing gauge theory expectations with computations of minimal surfaces. There is a distinguished class of loops, which the authors call BPS loops, whose expectation values are free from ultra-violet divergence. They formulate the loop equation for such loops. To the extent that they have checked, the minimal surface in AdS 5 x S 5 gives a solution of the equation. The authors also discuss the zig-zag symmetry of the loop operator. In the N = 4 gauge theory, they expect the zig-zag symmetry to hold when the loop does not couple the scalar fields in the supermultiplet. They will show how this is realized for the minimal surface

Wilson loops and minimal surfaces

International Nuclear Information System (INIS)

Drukker, Nadav; Gross, David J.; Ooguri, Hirosi

1999-01-01

The AdS-CFT correspondence suggests that the Wilson loop of the large N gauge theory with N=4 supersymmetry in four dimensions is described by a minimal surface in AdS 5 xS 5 . We examine various aspects of this proposal, comparing gauge theory expectations with computations of minimal surfaces. There is a distinguished class of loops, which we call BPS loops, whose expectation values are free from ultraviolet divergence. We formulate the loop equation for such loops. To the extent that we have checked, the minimal surface in AdS 5 xS 5 gives a solution of the equation. We also discuss the zigzag symmetry of the loop operator. In the N=4 gauge theory, we expect the zigzag symmetry to hold when the loop does not couple the scalar fields in the supermultiplet. We will show how this is realized for the minimal surface. (c) 1999 The American Physical Society

BPS Wilson loops and Bremsstrahlung function in ABJ(M): a two loop analysis

Energy Technology Data Exchange (ETDEWEB)

Bianchi, Marco S. [Institut für Physik, Humboldt-Universität zu Berlin,Newtonstraße 15, 12489 Berlin (Germany); Griguolo, Luca [Dipartimento di Fisica e Scienze della Terra, Università di Parmaand INFN Gruppo Collegato di Parma,Viale G.P. Usberti 7/A, 43100 Parma (Italy); Leoni, Matias [Physics Department, FCEyN-UBA & IFIBA-CONICETCiudad Universitaria, Pabellón I, 1428, Buenos Aires (Argentina); Penati, Silvia [Dipartimento di Fisica, Università di Milano-Bicoccaand INFN, Sezione di Milano-Bicocca,Piazza della Scienza 3, I-20126 Milano (Italy); Seminara, Domenico [Dipartimento di Fisica, Università di Firenzeand INFN Sezione di Firenze,via G. Sansone 1, 50019 Sesto Fiorentino (Italy)

2014-06-19

We study a family of circular BPS Wilson loops in N=6 super Chern-Simons-matter theories, generalizing the usual 1/2-BPS circle. The scalar and fermionic couplings depend on two deformation parameters and these operators can be considered as the ABJ(M) counterpart of the DGRT latitudes defined in N=4 SYM. We perform a complete two-loop analysis of their vacuum expectation value, discuss the appearance of framing-like phases and propose a general relation with cohomologically equivalent bosonic operators. We make an all-loop proposal for computing the Bremsstrahlung function associated to the 1/2-BPS cusp in terms of these generalized Wilson loops. When applied to our two-loop result it reproduces the known expression. Finally, we comment on the generalization of this proposal to the bosonic 1/6-BPS case.

Effects of Silicone Hydrogel Contact Lens Application on Corneal High-order Aberration and Visual Guality in Patients with Corneal Opacities

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Sevda Aydın Kurna

2012-03-01

Full Text Available Pur po se: Evaluation of the corneal high-order aberrations and visual quality changes after application of silicone hydrogel contact lenses in patients with corneal opacities due to various etiologies. Ma te ri al and Met hod: Fifteen eyes of 13 patients with corneal opacities were included in the study. During the ophthalmologic examination before and after contact lens application, visual acuity was measured with Snellen acuity chart and contrast sensitivity - with Bailey-Lowie Charts in letters. Aberrations were measured with corneal aberrometer (NIDEK Magellan Mapper under a naturally dilated pupil. Spherical aberration, coma, trefoil, irregular astigmatism and total high-order root mean square (RMS values were recorded. Measurements were repeated with balafilcon A lenses (PureVision 2 HD, B&L on all patients. Re sults: Patient age varied between 23 and 50 years. Two eyes had subepithelial infiltrates due to adenoviral keratitis, 1 had nebulae due to previous infections or trauma, and 2 had Salzmann’s nodular degeneration. We observed a mean increase of 1 line in visual acuity and 5 letters in contrast sensitivity with contact lenses versus glasses in the patients. Mean RMS values of spherical aberration, irregular astigmatism and total high-order aberrations decreased significantly with contact lenses. Dis cus si on: Silicone hydrogel soft contact lenses may improve visual quality by decreasing the corneal aberrations in patients with corneal opacities. (Turk J Ophthalmol 2012; 42: 97-102

A Loop Region in the N-Terminal Domain of Ebola Virus VP40 Is Important in Viral Assembly, Budding, and Egress

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Emmanuel Adu-Gyamfi

2014-10-01

Full Text Available Ebola virus (EBOV causes viral hemorrhagic fever in humans and can have clinical fatality rates of ~60%. The EBOV genome consists of negative sense RNA that encodes seven proteins including viral protein 40 (VP40. VP40 is the major Ebola virus matrix protein and regulates assembly and egress of infectious Ebola virus particles. It is well established that VP40 assembles on the inner leaflet of the plasma membrane of human cells to regulate viral budding where VP40 can produce virus like particles (VLPs without other Ebola virus proteins present. The mechanistic details, however, of VP40 lipid-interactions and protein-protein interactions that are important for viral release remain to be elucidated. Here, we mutated a loop region in the N-terminal domain of VP40 (Lys127, Thr129, and Asn130 and find that mutations (K127A, T129A, and N130A in this loop region reduce plasma membrane localization of VP40. Additionally, using total internal reflection fluorescence microscopy and number and brightness analysis we demonstrate these mutations greatly reduce VP40 oligomerization. Lastly, VLP assays demonstrate these mutations significantly reduce VLP release from cells. Taken together, these studies identify an important loop region in VP40 that may be essential to viral egress.

Opacity calculations and Saha's equation for high Z elements

International Nuclear Information System (INIS)

Godwal, B.K.; Sikka, S.K.

1977-01-01

Opacity calculations are needed for energy transport by radiation for high Z element plasmas as these have been suggested as temper materials in laser, electron beam and heavy ion fusion schemes. The pressure ionised modified form of Saha's ionisation equation has been used to obtain the free electron density, populations of various ionic species and the populations of various energy states for a given ion. Results are presented for two typical elements; tungsten and uranium. The ionisation potential have been evaluated using the Bohr's formula with suitable effective screened charges for ions. The results show that for uranium, even at a temperature of 10 kev, the K shell is intact. The reliability of the Saha's equation solution has been checked by comparing the equation of state (total pressure vs total energy curve) with that given by the Thomas-Fermi-Dirac equation of state. The agreement between the two is good from temperature upwards of 0.2 kev. (author)

Unusual loop-sequence flexibility of the proximal RNA replication element in EMCV.

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Jan Zoll

Full Text Available Picornaviruses contain stable RNA structures at the 5' and 3' ends of the RNA genome, OriL and OriR involved in viral RNA replication. The OriL RNA element found at the 5' end of the enterovirus genome folds into a cloverleaf-like configuration. In vivo SELEX experiments revealed that functioning of the poliovirus cloverleaf depends on a specific structure in this RNA element. Little is known about the OriL of cardioviruses. Here, we investigated structural aspects and requirements of the apical loop of proximal stem-loop SL-A of mengovirus, a strain of EMCV. Using NMR spectroscopy, we showed that the mengovirus SL-A apical loop consists of an octaloop. In vivo SELEX experiments demonstrated that a large number of random sequences are tolerated in the apical octaloop that support virus replication. Mutants in which the SL-A loop size and the length of the upper part of the stem were varied showed that both stem-length and stability of the octaloop are important determinants for viral RNA replication and virus reproduction. Together, these data show that stem-loop A plays an important role in virus replication. The high degree of sequence flexibility and the lack of selective pressure on the octaloop argue against a role in sequence specific RNA-protein or RNA-RNA interactions in which octaloop nucleotides are involved.

RNA polymerase gate loop guides the nontemplate DNA strand in transcription complexes.

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NandyMazumdar, Monali; Nedialkov, Yuri; Svetlov, Dmitri; Sevostyanova, Anastasia; Belogurov, Georgiy A; Artsimovitch, Irina

2016-12-27

Upon RNA polymerase (RNAP) binding to a promoter, the σ factor initiates DNA strand separation and captures the melted nontemplate DNA, whereas the core enzyme establishes interactions with the duplex DNA in front of the active site that stabilize initiation complexes and persist throughout elongation. Among many core RNAP elements that participate in these interactions, the β' clamp domain plays the most prominent role. In this work, we investigate the role of the β gate loop, a conserved and essential structural element that lies across the DNA channel from the clamp, in transcription regulation. The gate loop was proposed to control DNA loading during initiation and to interact with NusG-like proteins to lock RNAP in a closed, processive state during elongation. We show that the removal of the gate loop has large effects on promoter complexes, trapping an unstable intermediate in which the RNAP contacts with the nontemplate strand discriminator region and the downstream duplex DNA are not yet fully established. We find that although RNAP lacking the gate loop displays moderate defects in pausing, transcript cleavage, and termination, it is fully responsive to the transcription elongation factor NusG. Together with the structural data, our results support a model in which the gate loop, acting in concert with initiation or elongation factors, guides the nontemplate DNA in transcription complexes, thereby modulating their regulatory properties.

Akt kinase C-terminal modifications control activation loop dephosphorylation and enhance insulin response.

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Chan, Tung O; Zhang, Jin; Tiegs, Brian C; Blumhof, Brian; Yan, Linda; Keny, Nikhil; Penny, Morgan; Li, Xue; Pascal, John M; Armen, Roger S; Rodeck, Ulrich; Penn, Raymond B

2015-10-01

The Akt protein kinase, also known as protein kinase B, plays key roles in insulin receptor signalling and regulates cell growth, survival and metabolism. Recently, we described a mechanism to enhance Akt phosphorylation that restricts access of cellular phosphatases to the Akt activation loop (Thr(308) in Akt1 or protein kinase B isoform alpha) in an ATP-dependent manner. In the present paper, we describe a distinct mechanism to control Thr(308) dephosphorylation and thus Akt deactivation that depends on intramolecular interactions of Akt C-terminal sequences with its kinase domain. Modifications of amino acids surrounding the Akt1 C-terminal mTORC2 (mammalian target of rapamycin complex 2) phosphorylation site (Ser(473)) increased phosphatase resistance of the phosphorylated activation loop (pThr(308)) and amplified Akt phosphorylation. Furthermore, the phosphatase-resistant Akt was refractory to ceramide-dependent dephosphorylation and amplified insulin-dependent Thr(308) phosphorylation in a regulated fashion. Collectively, these results suggest that the Akt C-terminal hydrophobic groove is a target for the development of agents that enhance Akt phosphorylation by insulin. © 2015 Authors; published by Portland Press Limited.

Computational stability appraisal of rectangular natural circulation loop: Effect of loop inclination

International Nuclear Information System (INIS)

Krishnani, Mayur; Basu, Dipankar N.

2017-01-01

Highlights: • Computational model developed for single-phase rectangular natural circulation loop. • Role of loop inclination to vertical on thermalhydraulic stability is explored. • Inclination has strong stabilizing effect due to lower effective gravitation force. • Increase in tilt angle reduces settling time and highest amplitude of oscillation. • An angle of 15° is suggested for the selected loop geometry. - Abstract: Controlling stability behavior of single-phase natural circulation loops, without significantly affecting its steady-state characteristics, is a topic of wide research interest. Present study explores the role of loop inclination on a particular loop geometry. Accordingly a 3D computational model of a rectangular loop is developed and transient conservation equations are solved to obtain the temporal variation in flow parameters. Starting from the quiescent state, simulations are performed for selected sets of operating conditions and also with a few selected inclination angles. System experiences instability at higher heater powers and also with higher sink temperatures. Inclination is found to have a strong stabilizing influence owing to the reduction in the effective gravitational acceleration and subsequent decline in local buoyancy effects. The settling time and highest amplitude of oscillations substantially reduces for a stable system with a small inclination. Typically-unstable systems can also suppress the oscillations, when subjected to tilting, within a reasonable period of time. It is possible to stabilize the loop within shorter time span by increasing the tilt angle, but at the expense of reduction in steady-state flow rate. Overall a tilt angle of 15° is suggested for the selected geometry. Results from the 3D model is compared with the predictions from an indigenous 1D code. While similar qualitative influence of inclination is observed, the 1D model predicts early appearance of the stability threshold and hence hints

Diffusion of Wilson loops

International Nuclear Information System (INIS)

Brzoska, A.M.; Lenz, F.; Thies, M.; Negele, J.W.

2005-01-01

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

Recognition and Binding of a Helix-Loop-Helix Peptide to Carbonic Anhydrase Occurs via Partly Folded Intermediate Structures

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Lignell, Martin; Becker, Hans-Christian

2010-01-01

Abstract We have studied the association of a helix-loop-helix peptide scaffold carrying a benzenesulfonamide ligand to carbonic anhydrase using steady-state and time-resolved fluorescence spectroscopy. The helix-loop-helix peptide, developed for biosensing applications, is labeled with the fluorescent probe dansyl, which serves as a polarity-sensitive reporter of the binding event. Using maximum entropy analysis of the fluorescence lifetime of dansyl at 1:1 stoichiometry reveals three characteristic fluorescence lifetime groups, interpreted as differently interacting peptide/protein structures. We characterize these peptide/protein complexes as mostly bound but unfolded, bound and partly folded, and strongly bound and folded. Furthermore, analysis of the fluorescence anisotropy decay resulted in three different dansyl rotational correlation times, namely 0.18, 1.2, and 23 ns. Using the amplitudes of these times, we can correlate the lifetime groups with the corresponding fluorescence anisotropy component. The 23-ns rotational correlation time, which appears with the same amplitude as a 17-ns fluorescence lifetime, shows that the dansyl fluorophore follows the rotational diffusion of carbonic anhydrase when it is a part of the folded peptide/protein complex. A partly folded and partly hydrated interfacial structure is manifested in an 8-ns dansyl fluorescence lifetime and a 1.2-ns rotational correlation time. This structure, we believe, is similar to a molten-globule-like interfacial structure, which allows segmental movement and has a higher degree of solvent exposure of dansyl. Indirect excitation of dansyl on the helix-loop-helix peptide through Förster energy transfer from one or several tryptophans in the carbonic anhydrase shows that the helix-loop-helix scaffold binds to a tryptophan-rich domain of the carbonic anhydrase. We conclude that binding of the peptide to carbonic anhydrase involves a transition from a disordered to an ordered structure of the

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

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Sanborn, Adrian; Rao, Suhas; Huang, Su-Chen; Durand, Neva; Huntley, Miriam; Jewett, Andrew; Bochkov, Ivan; Chinnappan, Dharmaraj; Cutkosky, Ashok; Li, Jian; Geeting, Kristopher; McKenna, Doug; Stamenova, Elena; Gnirke, Andreas; Melnikov, Alexandre; Lander, Eric; Aiden, Erez

Our recent kilobase-resolution genome-wide maps of DNA self-contacts demonstrated that mammalian genomes are organized into domains and loops demarcated by the DNA-binding protein CTCF. Here, we combine these maps with new Hi-C, microscopy, and genome-editing experiments to study the physical structure of chromatin fibers, domains, and loops. We find that domains are inconsistent with equilibrium and fractal models. Instead, we use physical simulations to study two models of genome folding. In one, intermonomer attraction during condensation leads to formation of an anisotropic ``tension globule.'' In the other, CTCF and cohesin act together to extrude unknotted loops. Both models are consistent with the observed domains and loops. However, the extrusion model explains a far wider array of observations, such as why the CTCF-binding motifs at pairs of loop anchors lie in the convergent orientation. Finally, we perform 13 genome-editing experiments examining the effect of altering CTCF-binding sites on chromatin folding. The extrusion model predicts in silico the experimental maps using only CTCF-binding sites. Thus, we show that it is possible to disrupt, restore, and move loops and domains using targeted mutations as small as a single base pair.

Study of Opacity Effects on Emission Lines at EXTRAP T2R RFP

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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.

On some properties of conjugacy closed loops

International Nuclear Information System (INIS)

Adeniran, John Olusola

2002-07-01

It is shown that central loops are not conjugacy closed loops but instead are loops of units in their loop algebras that are conjugacy closed. It is also shown that certain inner mappings of a conjugacy closed loop are nuclear. Some invariants of left conjugacy closed loops are obtained. (author)

The relative frequencies of causes of widespread ground-glass opacity: A retrospective cohort

International Nuclear Information System (INIS)

Hewitt, Michael G.; Miller, Wallace T.; Reilly, Thomas J.; Simpson, Scott

2014-01-01

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

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

Mirror symmetry and loop operators

Energy Technology Data Exchange (ETDEWEB)

Assel, Benjamin [Department of Mathematics, King’s College London,The Strand, London WC2R 2LS (United Kingdom); Gomis, Jaume [Perimeter Institute for Theoretical Physics,Waterloo, Ontario, N2L 2Y5 (Canada)

2015-11-09

Wilson loops in gauge theories pose a fundamental challenge for dualities. Wilson loops are labeled by a representation of the gauge group and should map under duality to loop operators labeled by the same data, yet generically, dual theories have completely different gauge groups. In this paper we resolve this conundrum for three dimensional mirror symmetry. We show that Wilson loops are exchanged under mirror symmetry with Vortex loop operators, whose microscopic definition in terms of a supersymmetric quantum mechanics coupled to the theory encode in a non-trivial way a representation of the original gauge group, despite that the gauge groups of mirror theories can be radically different. Our predictions for the mirror map, which we derive guided by branes in string theory, are confirmed by the computation of the exact expectation value of Wilson and Vortex loop operators on the three-sphere.

A Protective Eye Shield for Prevention of Media Opacities during Small Animal Ocular Imaging

Science.gov (United States)

Bell, Brent A.; Kaul, Charles; Hollyfield, Joe G.

2014-01-01

Optical coherence tomography (OCT), scanning laser ophthalmoscopy (SLO) and other non-invasive imaging techniques are increasingly used in eye research to document disease-related changes in rodent eyes. Corneal dehydration is a major contributor to the formation of ocular opacities that can limit the repeated application of these techniques to individual animals. General anesthesia is usually required for imaging, which is accompanied by the loss of the blink reflex. As a consequence, the tear film cannot be maintained, drying occurs and the cornea becomes dehydrated. Without supplemental hydration, structural damage to the cornea quickly follows. Soon thereafter, anterior lens opacities can also develop. Collectively these changes ultimately compromise image quality, especially for studies involving repeated use of the same animal over several weeks or months. To minimize these changes, a protective shield was designed for mice and rats that prevent ocular dehydration during anesthesia. The eye shield, along with a semi-viscous ophthalmic solution, is placed over the corneas as soon as the anesthesia immobilizes the animal. Eye shields are removed for only the brief periods required for imaging and then reapplied before the fellow eye is examined. As a result, the corneal surface of each eye is exposed only for the time required for imaging. The device and detailed methods described here minimize the corneal and lens changes associated with ocular surface desiccation. When these methods are used consistently, high quality images can be obtained repeatedly from individual animals. PMID:25245081

Sp1-CD147 positive feedback loop promotes the invasion ability of ovarian cancer.

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Zhao, Jing; Ye, Wei; Wu, Juan; Liu, Lijuan; Yang, Lina; Gao, Lu; Chen, Biliang; Zhang, Fanglin; Yang, Hong; Li, Yu

2015-07-01

CD147 is a novel cancer biomarker that has been confirmed to be overexpressed in ovarian carcinoma, which is significantly associated with poor prognosis. Although the Sp1 protein regulates the expression level of CD147, it remains unclear whether Sp1 phosphorylation plays a role in this regulation. A dual-luciferase assay revealed that T453 and T739 mutations decreased the activity of Sp1 binding to the promoter of CD147, followed by a decrease in CD147 mRNA and protein expression. Western blot analysis showed that CD147 promoted Sp1 phosphorylation at T453 and T739 through the PI3K/AKT and MAPK/ERK pathways. In addition, blocking the Sp1-CD147 positive feedback loop reduced the invasion ability of HO-8910pm cells. Immunohistochemical staining showed that the components of the feedback loop were overexpressed in ovarian cancer tissues. The correlation analysis revealed a significant correlation between phospho-Sp1 (T453), phospho-Sp1 (T739) and CD147 expression levels, with correlation coefficients of r=0.477 and r=0.461, respectively. Collectively, our results suggest that a Sp1-CD147 positive feedback loop plays a critical role in the invasion ability of ovarian cancer cells.

Small, synthetic, GC-rich mRNA stem-loop modules 5' proximal to the AUG start-codon predictably tune gene expression in yeast.

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Lamping, Erwin; Niimi, Masakazu; Cannon, Richard D

2013-07-29

A large range of genetic tools has been developed for the optimal design and regulation of complex metabolic pathways in bacteria. However, fewer tools exist in yeast that can precisely tune the expression of individual enzymes in novel metabolic pathways suitable for industrial-scale production of non-natural compounds. Tuning expression levels is critical for reducing the metabolic burden of over-expressed proteins, the accumulation of toxic intermediates, and for redirecting metabolic flux from native pathways involving essential enzymes without negatively affecting the viability of the host. We have developed a yeast membrane protein hyper-expression system with critical advantages over conventional, plasmid-based, expression systems. However, expression levels are sometimes so high that they adversely affect protein targeting/folding or the growth and/or phenotype of the host. Here we describe the use of small synthetic mRNA control modules that allowed us to predictably tune protein expression levels to any desired level. Down-regulation of expression was achieved by engineering small GC-rich mRNA stem-loops into the 5' UTR that inhibited translation initiation of the yeast ribosomal 43S preinitiation complex (PIC). Exploiting the fact that the yeast 43S PIC has great difficulty scanning through GC-rich mRNA stem-loops, we created yeast strains containing 17 different RNA stem-loop modules in the 5' UTR that expressed varying amounts of the fungal multidrug efflux pump reporter Cdr1p from Candida albicans. Increasing the length of mRNA stem-loops (that contained only GC-pairs) near the AUG start-codon led to a surprisingly large decrease in Cdr1p expression; ~2.7-fold for every additional GC-pair added to the stem, while the mRNA levels remained largely unaffected. An mRNA stem-loop of seven GC-pairs (∆G = -15.8 kcal/mol) reduced Cdr1p expression levels by >99%, and even the smallest possible stem-loop of only three GC-pairs (∆G = -4.4 kcal/mol) inhibited

WWER type reactor primary loop imitation on large test loop facility in MARIA reactor

International Nuclear Information System (INIS)

Moldysh, A.; Strupchevski, A.; Kmetek, Eh.; Spasskov, V.P.; Shumskij, A.M.

1982-01-01

At present in Poland in cooperation with USSR a nuclear water loop test facility (WL) in 'MARIA' reactor in Sverke is under construction. The program objective is to investigate processes occuring in WWER reactor under emergency conditions, first of all after the break of the mainprimary loop circulation pipe-line. WL with the power of about 600 kW consists of three major parts: 1) an active loop, imitating the undamaged loops of the WWER reactor; 2) a passive loop assignedfor modelling the broken loop of the WWER reactor; 3) the emergency core cooling system imitating the corresponding full-scale system. The fuel rod bundle consists of 18 1 m long rods. They were fabricated according to the standard WWER fuel technology. In the report some general principles of WWERbehaviour imitation under emergency conditions are given. They are based on the operation experience obtained from 'SEMISCALE' and 'LOFT' test facilities in the USA. A description of separate modelling factors and criteria effects on the development of 'LOCA'-type accident is presented (the break cross-section to the primary loop volume ratio, the pressure differential between inlet and outlet reactor chambers, the pressure drop rate in the loop, the coolant flow rate throuh the core etc.). As an example a comparison of calculated flow rate variations for the WWER-1000 reactor and the model during the loss-of-coolant accident with the main pipe-line break at the core inlet is given. Calculations have been carried out with the use of TECH'-M code [ru

Functional characteristics of a double positive feedback loop coupled with autorepression

International Nuclear Information System (INIS)

Banerjee, Subhasis; Bose, Indrani

2008-01-01

We study the functional characteristics of a two-gene motif consisting of a double positive feedback loop and an autoregulatory negative feedback loop. The motif appears in the gene regulatory network controlling the functional activity of pancreatic β-cells. The model exhibits bistability and hysteresis in appropriate parameter regions. The two stable steady states correspond to low (OFF state) and high (ON state) protein levels, respectively. Using a deterministic approach, we show that the region of bistability increases in extent when the copy number of one of the genes is reduced from 2 to 1. The negative feedback loop has the effect of reducing the size of the bistable region. Loss of a gene copy, brought about by mutations, hampers the normal functioning of the β-cells giving rise to the genetic disorder, maturity-onset diabetes of the young (MODY). The diabetic phenotype makes its appearance when a sizable fraction of the β-cells is in the OFF state. Using stochastic simulation techniques we show that, on reduction of the gene copy number, there is a transition from the monostable ON to the ON state in the bistable region of the parameter space. Fluctuations in the protein levels, arising due to the stochastic nature of gene expression, can give rise to transitions between the ON and OFF states. We show that as the strength of autorepression increases, the ON → OFF state transitions become less probable whereas the reverse transitions are more probable. The implications of the results in the context of the occurrence of MODY are pointed out

Functional characteristics of a double positive feedback loop coupled with autorepression

Science.gov (United States)

Banerjee, Subhasis; Bose, Indrani

2008-12-01

We study the functional characteristics of a two-gene motif consisting of a double positive feedback loop and an autoregulatory negative feedback loop. The motif appears in the gene regulatory network controlling the functional activity of pancreatic β-cells. The model exhibits bistability and hysteresis in appropriate parameter regions. The two stable steady states correspond to low (OFF state) and high (ON state) protein levels, respectively. Using a deterministic approach, we show that the region of bistability increases in extent when the copy number of one of the genes is reduced from 2 to 1. The negative feedback loop has the effect of reducing the size of the bistable region. Loss of a gene copy, brought about by mutations, hampers the normal functioning of the β-cells giving rise to the genetic disorder, maturity-onset diabetes of the young (MODY). The diabetic phenotype makes its appearance when a sizable fraction of the β-cells is in the OFF state. Using stochastic simulation techniques we show that, on reduction of the gene copy number, there is a transition from the monostable ON to the ON state in the bistable region of the parameter space. Fluctuations in the protein levels, arising due to the stochastic nature of gene expression, can give rise to transitions between the ON and OFF states. We show that as the strength of autorepression increases, the ON → OFF state transitions become less probable whereas the reverse transitions are more probable. The implications of the results in the context of the occurrence of MODY are pointed out.

MicroRNA miR-308 regulates dMyc through a negative feedback loop in Drosophila

Directory of Open Access Journals (Sweden)

Kaveh Daneshvar

2012-10-01

The abundance of Myc protein must be exquisitely controlled to avoid growth abnormalities caused by too much or too little Myc. An intriguing mode of regulation exists in which Myc protein itself leads to reduction in its abundance. We show here that dMyc binds to the miR-308 locus and increases its expression. Using our gain-of-function approach, we show that an increase in miR-308 causes a destabilization of dMyc mRNA and reduced dMyc protein levels. In vivo knockdown of miR-308 confirmed the regulation of dMyc levels in embryos. This regulatory loop is crucial for maintaining appropriate dMyc levels and normal development. Perturbation of the loop, either by elevated miR-308 or elevated dMyc, caused lethality. Combining elevated levels of both, therefore restoring balance between miR-308 and dMyc levels, resulted in lower apoptotic activity and suppression of lethality. These results reveal a sensitive feedback mechanism that is crucial to prevent the pathologies caused by abnormal levels of dMyc.

Physicochemical and microstructural characterization of gum tragacanth added whey protein based films.

Science.gov (United States)

Tonyali, Bade; Cikrikci, Sevil; Oztop, Mecit Halil

2018-03-01

Edible films of gum tragacanth (GT) with whey protein were fabricated to see how the incorporation of GT influenced whey protein based film properties. Whey protein isolate (WPI) was replaced with GT at different ratios as 0.5, 1, 1.5 and 2% of WPI. Optical, mechanical, permeability and microstructural properties, as well as moisture sorption and solubility behavior of films were measured. The findings indicated that combination of WPI and GT in film formulation led to less strength, more flexible, less soluble films with lower permeability to water and with higher opacity. The results suggested that the addition of GT to WPI could lead to obtain modified WPI based edible films with desirable properties. Copyright © 2017 Elsevier Ltd. All rights reserved.

A type of loop algebra and the associated loop algebras

International Nuclear Information System (INIS)

Tam Honwah; Zhang Yufeng

2008-01-01

A higher-dimensional twisted loop algebra is constructed. As its application, a new Lax pair is presented, whose compatibility gives rise to a Liouville integrable hierarchy of evolution equations by making use of Tu scheme. One of the reduction cases of the hierarchy is an analogous of the well-known AKNS system. Next, the twisted loop algebra, furthermore, is extended to another higher dimensional loop algebra, from which a hierarchy of evolution equations with 11-potential component functions is obtained, whose reduction is just standard AKNS system. Especially, we prove that an arbitrary linear combination of the four Hamiltonian operators directly obtained from the recurrence relations is still a Hamiltonian operator. Therefore, the hierarchy with 11-potential functions possesses 4-Hamiltonian structures. Finally, an integrable coupling of the hierarchy is worked out

Small interfering RNA targeted to stem-loop II of the 5' untranslated region effectively inhibits expression of six HCV genotypes

Directory of Open Access Journals (Sweden)

Dash Srikanta

2006-11-01

Full Text Available Abstract Background The antiviral action of interferon alpha targets the 5' untranslated region (UTR used by hepatitis C virus (HCV to translate protein by an internal ribosome entry site (IRES mechanism. Although this sequence is highly conserved among different clinical strains, approximately half of chronically infected hepatitis C patients do not respond to interferon therapy. Therefore, development of small interfering RNA (siRNA targeted to the 5'UTR to inhibit IRES mediated translation may represent an alternative approach that could circumvent the problem of interferon resistance. Results Four different plasmid constructs were prepared for intracellular delivery of siRNAs targeting the stem loop II-III of HCV 5' UTR. The effect of siRNA production on IRES mediated translation was investigated using chimeric clones between the gene for green fluorescence protein (GFP and IRES sequences of six different HCV genotypes. The siRNA targeted to stem loop II effectively mediated degradation of HCV IRES mRNA and inhibited GFP expression in the case of six different HCV genotypes, where as siRNAs targeted to stem loop III did not. Furthermore, intracytoplasmic expression of siRNA into transfected Huh-7 cells efficiently degraded HCV genomic RNA and inhibited core protein expression from infectious full-length infectious clones HCV 1a and HCV 1b strains. Conclusion These in vitro studies suggest that siRNA targeted to stem-loop II is highly effective inhibiting IRES mediated translation of the major genotypes of HCV. Stem-loop II siRNA may be a good target for developing an intracellular immunization strategy based antiviral therapy to inhibit hepatitis C virus strains that are not inhibited by interferon.

TRF2 recruits RTEL1 to telomeres in S phase to promote t-loop unwinding.

Science.gov (United States)

Sarek, Grzegorz; Vannier, Jean-Baptiste; Panier, Stephanie; Petrini, John H J; Boulton, Simon J

2015-02-19

The helicase RTEL1 promotes t-loop unwinding and suppresses telomere fragility to maintain the integrity of vertebrate telomeres. An interaction between RTEL1 and PCNA is important to prevent telomere fragility, but how RTEL1 engages with the telomere to promote t-loop unwinding is unclear. Here, we establish that the shelterin protein TRF2 recruits RTEL1 to telomeres in S phase, which is required to prevent catastrophic t-loop processing by structure-specific nucleases. We show that the TRF2-RTEL1 interaction is mediated by a metal-coordinating C4C4 motif in RTEL1, which is compromised by the Hoyeraal-Hreidarsson syndrome (HHS) mutation, RTEL1(R1264H). Conversely, we define a TRF2(I124D) substitution mutation within the TRFH domain of TRF2, which eliminates RTEL1 binding and phenocopies the RTEL1(R1264H) mutation, giving rise to aberrant t-loop excision, telomere length heterogeneity, and loss of the telomere as a circle. These results implicate TRF2 in the recruitment of RTEL1 to facilitate t-loop disassembly at telomeres in S phase. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

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

... curtain incinerators that burn 100 percent yard waste? 62.15380 Section 62.15380 Protection of Environment... Combustion Units Constructed on or Before August 30, 1999 Air Curtain Incinerators That Burn 100 Percent Yard Waste § 62.15380 How must I monitor opacity for air curtain incinerators that burn 100 percent yard...

Neutrino opacities in kaon condensation and evolution of neutron stars

Energy Technology Data Exchange (ETDEWEB)

Muto, Takumi [Chiba Institute of Technology, Dept. of Physics, Narashino, Chiba (Japan); Yasuhira, Masatomi [Kyoto Univ., Yukawa Institute for Theoretical Physics, Kyoto (Japan); Tatsumi, Toshitaka [Kyoto Univ., Dept. of Physics, Kyoto (Japan); Iwamoto, Naoki [Kagawa Univ., Faculty of Engineering, Takamatsu, Kagawa (Japan)

2002-09-01

The neutrino mean free paths are obtained in kaon condensates realized from hot neutron-star matter. Kaon-induced neutrino absorption processes (KA), {nu}{sub e}N {yields} e{sup -}N (N stands for the nucleon), which are unique in the presence of kaon condensates, are mainly considered in nondegenerate neutrino case. The mean free paths for the KA processes are compared with the neutrino scatterings (S), {nu}{sub e}N {yields} {nu}{sub e}N. It is shown that the mean free paths for KA are shorter than the ordinary two-nucleon processes, {nu}{sub e}nN {yields} e{sup -}pN by several orders of magnitude when the temperature is not very high. However, the scattering processes have a dominant contribution to the neutrino opacities as compared with KA, so that KA has a minor effect on the thermal and dynamical evolution of protoneutron stars. (author)

Modeling of compact loop antennas

International Nuclear Information System (INIS)

Baity, F.W.

1987-01-01

A general compact loop antenna model which treats all elements of the antenna as lossy transmission lines has been developed. In addition to capacitively-tuned resonant double loop (RDL) antennas the model treats stub-tuned resonant double loop antennas. Calculations using the model have been compared with measurements on full-scale mockups of resonant double loop antennas for ATF and TFTR in order to refine the transmission line parameters. Results from the model are presented for RDL antenna designs for ATF, TFTR, Tore Supra, and for the Compact Ignition Tokamak

Rogowski Loop design for NSTX

International Nuclear Information System (INIS)

McCormack, B.; Kaita, R.; Kugel, H.; Hatcher, R.

2000-01-01

The Rogowski Loop is one of the most basic diagnostics for tokamak operations. On the National Spherical Torus Experiment (NSTX), the plasma current Rogowski Loop had the constraints of the very limited space available on the center stack, 5,000 volt isolation, flexibility requirements as it remained a part of the Center Stack assembly after the first phase of operation, and a +120 C temperature requirement. For the second phase of operation, four Halo Current Rogowski Loops under the Center Stack tiles will be installed having +600 C and limited space requirements. Also as part of the second operational phase, up to ten Rogowski Loops will installed to measure eddy currents in the Passive Plate support structures with +350 C, restricted space, and flexibility requirements. This presentation will provide the details of the material selection, fabrication techniques, testing, and installation results of the Rogowski Loops that were fabricated for the high temperature operational and bakeout requirements, high voltage isolation requirements, and the space and flexibility requirements imposed upon the Rogowski Loops. In the future operational phases of NSTX, additional Rogowski Loops could be anticipated that will measure toroidal plasma currents in the vacuum vessel and in the Passive Plate assemblies

The effect of design and scale on the mixing and mass transfer in U-loop bioreactors

DEFF Research Database (Denmark)

Petersen, Leander Adrian Haaning; Villadsen, John; Jørgensen, Sten Bay

is altered? In this study we have investigated the mixing time and mass transfer capabilities of U-loop reactors of different geometries (high vs. diameter ratio) in pilot (0.15m3) and semi-industrial scales (2.2m3). A new expression for the mechanical power input into the system is also proposed, which......A system capable of handling a large volumetric gas fraction while providing a high gas to liquid mass transfer is a necessity if the metanotrophic bacterium Methylococcus capsulatus is to be used in single cell protein (SCP) production. Previous studies have proven that a U-loop fermenter, a novel...... indicates that an even more favorable relationship between power input and mass transfer rate (compared to previous literature) applies to U-loop fermenters....

Hybrid Combustion-Gasification Chemical Looping

Energy Technology Data Exchange (ETDEWEB)

Herbert Andrus; Gregory Burns; John Chiu; Gregory Lijedahl; Peter Stromberg; Paul Thibeault

2009-01-07

For the past several years Alstom Power Inc. (Alstom), a leading world-wide power system manufacturer and supplier, has been in the initial stages of developing an entirely new, ultra-clean, low cost, high efficiency power plant for the global power market. This new power plant concept is based on a hybrid combustion-gasification process utilizing high temperature chemical and thermal looping technology The process consists of the oxidation, reduction, carbonation, and calcination of calcium-based compounds, which chemically react with coal, biomass, or opportunity fuels in two chemical loops and one thermal loop. The chemical and thermal looping technology can be alternatively configured as (i) a combustion-based steam power plant with CO{sub 2} capture, (ii) a hybrid combustion-gasification process producing a syngas for gas turbines or fuel cells, or (iii) an integrated hybrid combustion-gasification process producing hydrogen for gas turbines, fuel cells or other hydrogen based applications while also producing a separate stream of CO{sub 2} for use or sequestration. In its most advanced configuration, this new concept offers the promise to become the technology link from today's Rankine cycle steam power plants to tomorrow's advanced energy plants. The objective of this work is to develop and verify the high temperature chemical and thermal looping process concept at a small-scale pilot facility in order to enable AL to design, construct and demonstrate a pre-commercial, prototype version of this advanced system. In support of this objective, Alstom and DOE started a multi-year program, under this contract. Before the contract started, in a preliminary phase (Phase 0) Alstom funded and built the required small-scale pilot facility (Process Development Unit, PDU) at its Power Plant Laboratories in Windsor, Connecticut. Construction was completed in calendar year 2003. The objective for Phase I was to develop the indirect combustion loop with CO{sub 2

Thermal-hydraulic analyses for in-pile SCWR fuel qualification test loops and SCWR material loop

Energy Technology Data Exchange (ETDEWEB)

Vojacek, A.; Mazzini, G.; Zmitkova, J.; Ruzickova, M. [Research Centre Rez (Czech Republic)

2014-07-01

One of the R&D directions of Research Centre Rez is dedicated to the supercritical water-cooled reactor concept (SCWR). Among the developed experimental facilities and infrastructure in the framework of the SUSEN project (SUStainable ENergy) is construction and experimental operation of the supercritical water loop SCWL focusing on material tests. At the first phase, this SCWL loop is assembled and operated out-of-pile in the dedicated loop facilities hall. At this out-of-pile operation various operational conditions are tested and verified. After that, in the second phase, the SCWL loop will be situated in-pile, in the core of the research reactor LVR-15, operated at CVR. Furthermore, it is planned to carry out a test of a small scale fuel assembly within the SuperCritical Water Reactor Fuel Qualification Test (SCWR-FQT) loop, which is now being designed. This paper presents the results of the thermal-hydraulic analyses of SCWL loop out-of-pile operation using the RELAP5/MOD3.3. The thermal-hydraulic modeling and the performed analyses are focused on the SCWL loop model validation through a comparison of the calculation results with the experimental results obtained at various operation conditions. Further, the present paper focuses on the transient analyses for start-up and shut-down of the FQT loop, particularly to explore the ability of system codes ATHLET 3.0A to simulate the transient between subcritical conditions and supercritical conditions. (author)

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.

Algorithm for counting large directed loops

Energy Technology Data Exchange (ETDEWEB)

Bianconi, Ginestra [Abdus Salam International Center for Theoretical Physics, Strada Costiera 11, 34014 Trieste (Italy); Gulbahce, Natali [Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, NM 87545 (United States)

2008-06-06

We derive a Belief-Propagation algorithm for counting large loops in a directed network. We evaluate the distribution of the number of small loops in a directed random network with given degree sequence. We apply the algorithm to a few characteristic directed networks of various network sizes and loop structures and compare the algorithm with exhaustive counting results when possible. The algorithm is adequate in estimating loop counts for large directed networks and can be used to compare the loop structure of directed networks and their randomized counterparts.

Oscillation damping of chiral string loops

International Nuclear Information System (INIS)

Babichev, Eugeny; Dokuchaev, Vyacheslav

2002-01-01

Chiral cosmic string loops tend to the stationary (vorton) configuration due to energy loss into gravitational and electromagnetic radiation. We describe the asymptotic behavior of near stationary chiral loops and their fading to vortons. General limits on the gravitational and electromagnetic energy losses by near stationary chiral loops are found. For these loops we estimate the oscillation damping time. We present solvable examples of gravitational radiation energy loss by some chiral loop configurations. The analytical dependence of string energy with time is found in the case of the chiral ring with small amplitude radial oscillations

Small, synthetic, GC-rich mRNA stem-loop modules 5′ proximal to the AUG start-codon predictably tune gene expression in yeast

Science.gov (United States)

2013-01-01

Background A large range of genetic tools has been developed for the optimal design and regulation of complex metabolic pathways in bacteria. However, fewer tools exist in yeast that can precisely tune the expression of individual enzymes in novel metabolic pathways suitable for industrial-scale production of non-natural compounds. Tuning expression levels is critical for reducing the metabolic burden of over-expressed proteins, the accumulation of toxic intermediates, and for redirecting metabolic flux from native pathways involving essential enzymes without negatively affecting the viability of the host. We have developed a yeast membrane protein hyper-expression system with critical advantages over conventional, plasmid-based, expression systems. However, expression levels are sometimes so high that they adversely affect protein targeting/folding or the growth and/or phenotype of the host. Here we describe the use of small synthetic mRNA control modules that allowed us to predictably tune protein expression levels to any desired level. Down-regulation of expression was achieved by engineering small GC-rich mRNA stem-loops into the 5′ UTR that inhibited translation initiation of the yeast ribosomal 43S preinitiation complex (PIC). Results Exploiting the fact that the yeast 43S PIC has great difficulty scanning through GC-rich mRNA stem-loops, we created yeast strains containing 17 different RNA stem-loop modules in the 5′ UTR that expressed varying amounts of the fungal multidrug efflux pump reporter Cdr1p from Candida albicans. Increasing the length of mRNA stem-loops (that contained only GC-pairs) near the AUG start-codon led to a surprisingly large decrease in Cdr1p expression; ~2.7-fold for every additional GC-pair added to the stem, while the mRNA levels remained largely unaffected. An mRNA stem-loop of seven GC-pairs (∆G = −15.8 kcal/mol) reduced Cdr1p expression levels by >99%, and even the smallest possible stem-loop of only three GC-pairs (�

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 of...

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) Use...

Calculation of opacities and emissivities for carbon plasmas under NLTE and LTE conditions

International Nuclear Information System (INIS)

Gil, J.M.; Rodriguez, R.; Florido, R.; Rubiano, J.G.; Martel, P.; Sauvan, P.; Minguez, E.

2006-01-01

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)

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)

Multiple roles of mobile active center loops in the E1 component of the Escherichia coli pyruvate dehydrogenase complex - Linkage of protein dynamics to catalysis

Science.gov (United States)

Jordan, Frank; Arjunan, Palaniappa; Kale, Sachin; Nemeria, Natalia S.; Furey, William

2009-01-01

The region encompassing residues 401–413 on the E1 component of the pyruvate dehydrogenase multienzyme complex from Escherichia coli comprises a loop (the inner loop) which was not seen in the X-ray structure in the presence of thiamin diphosphate, the required cofactor for the enzyme. This loop is seen in the presence of a stable analogue of the pre-decarboxylation intermediate, the covalent adduct between the substrate analogue methyl acetylphosphonate and thiamin diphosphate, C2α-phosphonolactylthiamin diphosphate. It has been shown that the residue H407 and several other residues on this loop are required to reduce the mobility of the loop so electron density corresponding to it can be seen once the pre-decarboxylation intermediate is formed. Concomitantly, the loop encompassing residues 541–557 (the outer loop) appears to work in tandem with the inner loop and there is a hydrogen bond between the two loops ensuring their correlated motion. The inner loop was shown to: a) sequester the active center from carboligase side reactions; b) assist the interaction between the E1 and the E2 components, thereby affecting the overall reaction rate of the entire multienzyme complex; c) control substrate access to the active center. Using viscosity effects on kinetics it was shown that formation of the pre-decarboxylation intermediate is specifically affected by loop movement. A cysteine-less variant was created for the E1 component, onto which cysteines were substituted at selected loop positions. Introducing an electron spin resonance spin label and an 19F NMR label onto these engineered cysteines, the loop mobility was examined: a) both methods suggested that in the absence of ligand, the loop exists in two conformations; b) line-shape analysis of the NMR signal at different temperatures, enabled estimation of the rate constant for loop movement, and this rate constant was found to be of the same order of magnitude as the turnover number for the enzyme under the

Effect of tobacco smoking on the presence of asbestosis at postmortem and on the reading of irregular opacities on roentgenograms in asbestos-exposed workers

International Nuclear Information System (INIS)

Hnizdo, E.; Sluis-Cremer, G.K.

1988-01-01

A statistically significant association between cigarette smoking and radiologic readings of irregular opacities was observed in a case-control study of 430 South African asbestos miners (OR = 3.03; 95% confidence interval, 1.50; 6.11). In another case-control study of 487 dead South African asbestos miners, no positive association between smoking and autopsy findings for asbestosis was observed (OR = 0.50; 95% confidence interval, 0.20; 1.29). The association between greater than slight asbestosis (moderate and marked) and smoking (yes/no) was not significant (Fisher's exact test, p = 0.44), and the adjusted odds ratio was 1.25 with 95% confidence interval (0.20; 7.78). In addition, the certification in life for asbestosis, based on chest roentgenogram readings for irregular opacities, was also found to have a tendency to be related to smoking. Thus, the findings of these studies do not support the hypothesis that smoking is associated with the presence of asbestosis at autopsy or that smoking and asbestos dust act synergistically in producing asbestosis at autopsy. But the findings of this and other studies suggest that smoking does produce some change in the lung structure that can be visible on the roentgenogram and can be wrongly interpreted as irregular opacities caused by asbestosis

Expression of the helix-loop-helix protein inhibitor of DNA binding-1 (ID-1) is activated by all-trans retinoic acid in normal human keratinocytes

International Nuclear Information System (INIS)

Villano, C.M.; White, L.A.

2006-01-01

The ID (inhibitor of differentiation or DNA binding) helix-loop-helix proteins are important mediators of cellular differentiation and proliferation in a variety of cell types through regulation of gene expression. Overexpression of the ID proteins in normal human keratinocytes results in extension of culture lifespan, indicating that these proteins are important for epidermal differentiation. Our hypothesis is that the ID proteins are targets of the retinoic acid signaling pathway in keratinocytes. Retinoids, vitamin A analogues, are powerful regulators of cell growth and differentiation and are widely used in the prevention and treatment of a variety of cancers in humans. Furthermore, retinoic acid is necessary for the maintenance of epithelial differentiation and demonstrates an inhibitory action on skin carcinogenesis. We examined the effect of all-trans retinoic acid on expression of ID-1, -2, -3, and -4 in normal human keratinocytes and found that exposure of these cells to all-trans retinoic acid causes an increase in both ID-1 and ID-3 gene expression. Furthermore, our data show that this increase is mediated by increased transcription involving several cis-acting elements in the distal portion of the promoter, including a CREB-binding site, an Egr1 element, and an YY1 site. These data demonstrate that the ID proteins are direct targets of the retinoic acid signaling pathway. Given the importance of the ID proteins to epidermal differentiation, these results suggest that IDs may be mediating some of the effects of all-trans retinoic acid in normal human keratinocytes

Repeatability of pachymetric mapping using fourier domain optical coherence tomography in corneas with opacities.

Science.gov (United States)

Samy El Gendy, Nehal M; Li, Yan; Zhang, Xinbo; Huang, David

2012-04-01

To evaluate the repeatability of Fourier domain optical coherence tomography (OCT) pachymetric mapping in patients with corneal opacities and to assess the reliability of Fourier domain OCT with 830 nm wavelength as a pachymetric measurement tool in opaque corneas. A Fourier domain OCT system was used to map the corneal thickness of patients with corneal scars or dystrophy. A retrospective study of a consecutive series was conducted. The repeatability was measured using pooled standard deviation of repeated measurements. A slit-scanning tomography device provided pachymetric mapping for comparison. Seventeen eyes of 12 patients with corneal scars (7 trauma and 3 post infection) or dystrophy (2 Reis-Bucklers and 5 granular dystrophy) were included. The posterior corneal boundary was detectable in all cases. The average corneal thickness measured by OCT was 536 ± 89 μm in central 2 mm area, 553 ± 76 μm in pericentral 2- to 5-mm area, and 508 ± 93 μm for the minimum corneal thickness. The slit-scanning tomography central corneal thickness, 433 ± 111 μm, was significantly lower than OCT readings (mean difference -91.1 ± 33.3 μm, P = 0.002). Repeatability of the OCT measurements was 2.1 μm centrally and 1.2 μm pericentrally. Pachymetric mapping with Fourier domain OCT was highly repeatable. Fourier domain OCT is a reliable pachymetric tool in opaque corneas. In comparison, corneal thickness measured by the slit-scanning tomography is significantly thinner than those measured by the Fourier domain OCT in the presence of corneal opacities.

Different roles of eukaryotic MutS and MutL complexes in repair of small insertion and deletion loops in yeast.

Directory of Open Access Journals (Sweden)

Nina V Romanova

2013-10-01

Full Text Available DNA mismatch repair greatly increases genome fidelity by recognizing and removing replication errors. In order to understand how this fidelity is maintained, it is important to uncover the relative specificities of the different components of mismatch repair. There are two major mispair recognition complexes in eukaryotes that are homologues of bacterial MutS proteins, MutSα and MutSβ, with MutSα recognizing base-base mismatches and small loop mispairs and MutSβ recognizing larger loop mispairs. Upon recognition of a mispair, the MutS complexes then interact with homologues of the bacterial MutL protein. Loops formed on the primer strand during replication lead to insertion mutations, whereas loops on the template strand lead to deletions. We show here in yeast, using oligonucleotide transformation, that MutSα has a strong bias toward repair of insertion loops, while MutSβ has an even stronger bias toward repair of deletion loops. Our results suggest that this bias in repair is due to the different interactions of the MutS complexes with the MutL complexes. Two mutants of MutLα, pms1-G882E and pms1-H888R, repair deletion mispairs but not insertion mispairs. Moreover, we find that a different MutL complex, MutLγ, is extremely important, but not sufficient, for deletion repair in the presence of either MutLα mutation. MutSβ is present in many eukaryotic organisms, but not in prokaryotes. We suggest that the biased repair of deletion mispairs may reflect a critical eukaryotic function of MutSβ in mismatch repair.

On the loop-loop scattering amplitudes in Abelian and non-Abelian gauge theories

International Nuclear Information System (INIS)

Meggiolaro, Enrico

2005-01-01

The high-energy elastic scattering amplitude of two colour-singlet qq-bar pairs is governed by the correlation function of two Wilson loops, which follow the classical straight lines for quark (antiquark) trajectories. This quantity is expected to be free of IR divergences, differently from what happens for the parton-parton elastic scattering amplitude, described, in the high-energy limit, by the expectation value of two Wilson lines. We shall explicitly test this IR finiteness by a direct non-perturbative computation of the loop-loop scattering amplitudes in the (pedagogic, but surely physically interesting) case of quenched QED. The results obtained for the Abelian case will be generalized to the case of a non-Abelian gauge theory with Nc colours, but stopping to the order O(g4) in perturbation theory. In connection with the above-mentioned IR finiteness, we shall also discuss some analytic properties of the loop-loop scattering amplitudes in both Abelian and non-Abelian gauge theories, when going from Minkowskian to Euclidean theory, which can be relevant to the still unsolved problem of the s-dependence of hadron-hadron total cross-sections

Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex.

Science.gov (United States)

Perederina, Anna; Nevskaya, Natalia; Nikonov, Oleg; Nikulin, Alexei; Dumas, Philippe; Yao, Min; Tanaka, Isao; Garber, Maria; Gongadze, George; Nikonov, Stanislav

2002-12-01

The crystal structure of ribosomal protein L5 from Thermus thermophilus complexed with a 34-nt fragment comprising helix III and loop C of Escherichia coli 5S rRNA has been determined at 2.5 A resolution. The protein specifically interacts with the bulged nucleotides at the top of loop C of 5S rRNA. The rRNA and protein contact surfaces are strongly stabilized by intramolecular interactions. Charged and polar atoms forming the network of conserved intermolecular hydrogen bonds are located in two narrow planar parallel layers belonging to the protein and rRNA, respectively. The regions, including these atoms conserved in Bacteria and Archaea, can be considered an RNA-protein recognition module. Comparison of the T. thermophilus L5 structure in the RNA-bound form with the isolated Bacillus stearothermophilus L5 structure shows that the RNA-recognition module on the protein surface does not undergo significant changes upon RNA binding. In the crystal of the complex, the protein interacts with another RNA molecule in the asymmetric unit through the beta-sheet concave surface. This protein/RNA interface simulates the interaction of L5 with 23S rRNA observed in the Haloarcula marismortui 50S ribosomal subunit.

Scoring functions for protein-protein interactions.

Science.gov (United States)

Moal, Iain H; Moretti, Rocco; Baker, David; Fernández-Recio, Juan

2013-12-01

The computational evaluation of protein-protein interactions will play an important role in organising the wealth of data being generated by high-throughput initiatives. Here we discuss future applications, report recent developments and identify areas requiring further investigation. Many functions have been developed to quantify the structural and energetic properties of interacting proteins, finding use in interrelated challenges revolving around the relationship between sequence, structure and binding free energy. These include loop modelling, side-chain refinement, docking, multimer assembly, affinity prediction, affinity change upon mutation, hotspots location and interface design. Information derived from models optimised for one of these challenges can be used to benefit the others, and can be unified within the theoretical frameworks of multi-task learning and Pareto-optimal multi-objective learning. Copyright © 2013 Elsevier Ltd. All rights reserved.

A sequence predicted to form a stem–loop is proposed to be required for formation of an RNA–protein complex involving the 3'UTR of beta-subunit F0F1-ATPase mRNA

Czech Academy of Sciences Publication Activity Database

Kramarova, T. V.; Antonická, Hana; Houštěk, Josef; Cannon, B.; Nedergaard, J.

2008-01-01

Roč. 1777, 7-8 (2008), s. 747-757 ISSN 0005-2728 R&D Projects: GA MZd(CZ) NR7790; GA MŠk(CZ) 1M0520 Grant - others:Univerzita Karlova(CZ) 97807 Institutional research plan: CEZ:AV0Z50110509 Keywords : ATPase * RNA-protein komplex * stem-loop secondary structure Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.447, year: 2008

Lethality Index 2008-2014: Less shootings, same lethality, more opacity

Directory of Open Access Journals (Sweden)

Carlos Silva Forné

2017-11-01

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.

Higher dimensional loop quantum cosmology

International Nuclear Information System (INIS)

Zhang, Xiangdong

2016-01-01

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. (orig.)

Insulators form gene loops by interacting with promoters in Drosophila.

Science.gov (United States)

Erokhin, Maksim; Davydova, Anna; Kyrchanova, Olga; Parshikov, Alexander; Georgiev, Pavel; Chetverina, Darya

2011-09-01

Chromatin insulators are regulatory elements involved in the modulation of enhancer-promoter communication. The 1A2 and Wari insulators are located immediately downstream of the Drosophila yellow and white genes, respectively. Using an assay based on the yeast GAL4 activator, we have found that both insulators are able to interact with their target promoters in transgenic lines, forming gene loops. The existence of an insulator-promoter loop is confirmed by the fact that insulator proteins could be detected on the promoter only in the presence of an insulator in the transgene. The upstream promoter regions, which are required for long-distance stimulation by enhancers, are not essential for promoter-insulator interactions. Both insulators support basal activity of the yellow and white promoters in eyes. Thus, the ability of insulators to interact with promoters might play an important role in the regulation of basal gene transcription.

Hyperstaticity and loops in frictional granular packings

Science.gov (United States)

Tordesillas, Antoinette; Lam, Edward; Metzger, Philip T.

2009-06-01

The hyperstatic nature of granular packings of perfectly rigid disks is analyzed algebraically and through numerical simulation. The elementary loops of grains emerge as a fundamental element in addressing hyperstaticity. Loops consisting of an odd number of grains behave differently than those with an even number. For odd loops, the latent stresses are exterior and are characterized by the sum of frictional forces around each loop. For even loops, the latent stresses are interior and are characterized by the alternating sum of frictional forces around each loop. The statistics of these two types of loop sums are found to be Gibbsian with a "temperature" that is linear with the friction coefficient μ when μ<1.

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.

Conformal boundary loop models

International Nuclear Information System (INIS)

Jacobsen, Jesper Lykke; Saleur, Hubert

2008-01-01

We study a model of densely packed self-avoiding loops on the annulus, related to the Temperley-Lieb algebra with an extra idempotent boundary generator. Four different weights are given to the loops, depending on their homotopy class and whether they touch the outer rim of the annulus. When the weight of a contractible bulk loop x≡q+q -1 element of (-2,2], this model is conformally invariant for any real weight of the remaining three parameters. We classify the conformal boundary conditions and give exact expressions for the corresponding boundary scaling dimensions. The amplitudes with which the sectors with any prescribed number and types of non-contractible loops appear in the full partition function Z are computed rigorously. Based on this, we write a number of identities involving Z which hold true for any finite size. When the weight of a contractible boundary loop y takes certain discrete values, y r ≡([r+1] q )/([r] q ) with r integer, other identities involving the standard characters K r,s of the Virasoro algebra are established. The connection with Dirichlet and Neumann boundary conditions in the O(n) model is discussed in detail, and new scaling dimensions are derived. When q is a root of unity and y=y r , exact connections with the A m type RSOS model are made. These involve precise relations between the spectra of the loop and RSOS model transfer matrices, valid in finite size. Finally, the results where y=y r are related to the theory of Temperley-Lieb cabling

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.

Large lithium loop experience

International Nuclear Information System (INIS)

Kolowith, R.; Owen, T.J.; Berg, J.D.; Atwood, J.M.

1981-10-01

An engineering design and operating experience of a large, isothermal, lithium-coolant test loop are presented. This liquid metal coolant loop is called the Experimental Lithium System (ELS) and has operated safely and reliably for over 6500 hours through September 1981. The loop is used for full-scale testing of components for the Fusion Materials Irradiation Test (FMIT) Facility. Main system parameters include coolant temperatures to 430 0 C and flow to 0.038 m 3 /s (600 gal/min). Performance of the main pump, vacuum system, and control system is discussed. Unique test capabilities of the ELS are also discussed

Modular invariance and covariant loop calculus

International Nuclear Information System (INIS)

Petersen, J.L.; Roland, K.O.; Sidenius, J.R.

1988-01-01

The covariant loop calculus provides an efficient technique for computing explicit expressions for the density on moduli space corresponding to arbitrary (bosonic string) loop diagrams. Since modular invariance is not manifest, however, we carry out a detailed comparison with known explicit two- and three-loop results derived using analytic geometry (one loop is known to be okay). We establish identity to 'high' order in some moduli and exactly in others. Agreement is found as a result of various nontrivial cancellations, in part related to number theory. We feel our results provide very strong support for the correctness of the covariant loop calculus approach. (orig.)

Modular invariance and covariant loop calculus

International Nuclear Information System (INIS)

Petersen, J.L.; Roland, K.O.; Sidenius, J.R.

1988-01-01

The covariant loop calculus provides and efficient technique for computing explicit expressions for the density on moduli space corresponding to arbitrary (bosonic string) loop diagrams. Since modular invariance is not manifest, however, we carry out a detailed comparison with known explicit 2- and 3- loop results derived using analytic geometry (1 loop is known to be ok). We establish identity to 'high' order in some moduli and exactly in others. Agreement is found as a result of various non-trivial cancellations, in part related to number theory. We feel our results provide very strong support for the correctness of the covariant loop calculus approach. (orig.)

Transcription-factor-mediated DNA looping probed by high-resolution, single-molecule imaging in live E. coli cells.

Directory of Open Access Journals (Sweden)

Zach Hensel

Full Text Available DNA looping mediated by transcription factors plays critical roles in prokaryotic gene regulation. The "genetic switch" of bacteriophage λ determines whether a prophage stays incorporated in the E. coli chromosome or enters the lytic cycle of phage propagation and cell lysis. Past studies have shown that long-range DNA interactions between the operator sequences O(R and O(L (separated by 2.3 kb, mediated by the λ repressor CI (accession number P03034, play key roles in regulating the λ switch. In vitro, it was demonstrated that DNA segments harboring the operator sequences formed loops in the presence of CI, but CI-mediated DNA looping has not been directly visualized in vivo, hindering a deep understanding of the corresponding dynamics in realistic cellular environments. We report a high-resolution, single-molecule imaging method to probe CI-mediated DNA looping in live E. coli cells. We labeled two DNA loci with differently colored fluorescent fusion proteins and tracked their separations in real time with ∼40 nm accuracy, enabling the first direct analysis of transcription-factor-mediated DNA looping in live cells. Combining looping measurements with measurements of CI expression levels in different operator mutants, we show quantitatively that DNA looping activates transcription and enhances repression. Further, we estimated the upper bound of the rate of conformational change from the unlooped to the looped state, and discuss how chromosome compaction may impact looping kinetics. Our results provide insights into transcription-factor-mediated DNA looping in a variety of operator and CI mutant backgrounds in vivo, and our methodology can be applied to a broad range of questions regarding chromosome conformations in prokaryotes and higher organisms.

The architecture of metal coordination groups in proteins.

Science.gov (United States)

Harding, Marjorie M

2004-05-01

A set of tables is presented and a survey given of the architecture of metal coordination groups in a representative set of protein structures from the Protein Data Bank [Bernstein et al. (1977), J. Mol. Biol. 112, 535-542; Berman et al. (2000), Nucleic Acids Res. 28, 235-242]. The structures have been determined to a resolution of 2.5 A or better; the metals considered are Ca, Mg, Mn, Fe, Cu, Zn, Na and K, with particular emphasis on Ca and Zn and the exclusion of haem groups and Fe/S clusters; the proteins are a representative set in which none has more than 30% sequence identity with any other. In them the metal is coordinated by several donor groups from different amino-acid residues in the protein chain and often also by water or other small molecules. The tables, for approximately 600 metal coordination groups, include information on the conformations of the protein chain in the region around the metal and reliability indicators. They illustrate the wide variety of coordination numbers, chelate-loop sizes and other properties and the different characteristics of different metals. They show that glycine has a particular significance in the position adjacent to a donor residue, especially in Ca coordination groups. They also show that metal coordination does not appear to lead to significant distortions of the torsion angles phi, psi from their normally allowed values. Very few metal coordination groups occur more than once in the representative set and when they do they are usually related in fold and function; they have similar but not necessarily identical conformations. However, individual chelate loops, for example Zn(-C-X-X'-C-), in which both cysteines are coordinated to Zn through S, and X and X' are any amino acids, are repeated frequently in many different and unrelated proteins. Not all chelate loops with the same composition have the same conformation, but for smaller loops there are usually one or two strongly preferred and well defined