Science.gov

Sample records for acid loop extension

  1. Three-amino-acid-loop-extension homeodomain factor Meis3 regulates cell survival via PDK1

    PubMed Central

    Liu, Jiangying; Wang, You; Birnbaum, Morris J.; Stoffers, Doris A.

    2010-01-01

    Three-amino-acid-loop-extension (TALE) homeodomain proteins including Meis and Pbx families are generally recognized for their roles in growth and differentiation during vertebrate embryogenesis and tumorigenesis. Whereas genetic studies indicate that Pbx1 regulates the development and function of insulin-producing pancreatic β-cells, the role of Meis family members in β-cells is still unknown. Here we show that Meis3 is abundantly expressed in pancreatic islets and β-cells and that it regulates β-cell survival. We further identify the 3-phosphoinositide–dependent protein kinase 1 (PDK1), a well-known kinase involved in the PI3K–Akt signaling pathway, as a direct Meis3 target, which mediates its role in β-cell survival. This regulatory module appears to function broadly as we also identify Meis3 regulation of cell survival and PDK1 expression in ovarian carcinoma cells, suggesting a unique function for Meis3 beyond the traditional roles for TALE homeodomain factors during embryogenesis. PMID:21059917

  2. A loop group extension of the odd Chern character

    NASA Astrophysics Data System (ADS)

    Wilson, Scott O.

    2016-04-01

    We show that the universal odd Chern form, defined on the stable unitary group U, extends to the loop group LU as an equivariantly closed differential form. This provides an odd analogue to the Bismut-Chern form that appears in supersymmetric field theories. We also describe the associated transgression form, the so-called Bismut-Chern-Simons form, and explicate some properties it inherits as a differential form on the space of maps of a cylinder into the stable unitary group. As one corollary, we show that in a precise sense the spectral flow of a loop of self adjoint Fredholm operators equals the lowest degree component of the Bismut-Chern-Simons form, and the latter, when restricted to cylinders which are tori, is an equivariantly closed extension of spectral flow. As another corollary, we construct the Chern character homomorphism from odd K-theory to the periodic cohomology of the free loop space, represented geometrically on the level of differential forms.

  3. The three-loop cusp anomalous dimension in QCD and its supersymmetric extensions

    NASA Astrophysics Data System (ADS)

    Grozin, Andrey G.; Henn, Johannes M.; Korchemsky, Gregory P.; Marquard, Peter

    2016-01-01

    We present the details of the analytic calculation of the three-loop angle-dependent cusp anomalous dimension in QCD and its supersymmetric extensions, including the maximally supersymmetric N=4 super Yang-Mills theory. The three-loop result in the latter theory is new and confirms a conjecture made in our previous paper. We study various physical limits of the cusp anomalous dimension and discuss its relation to the quark-antiquark potential including the effects of broken conformal symmetry in QCD. We find that the cusp anomalous dimension viewed as a function of the cusp angle and the new effective coupling given by light-like cusp anomalous dimension reveals a remarkable universality property — it takes the same form in QCD and its supersymmetric extensions, to three loops at least. We exploit this universality property and make use of the known result for the three-loop quark-antiquark potential to predict the special class of nonplanar corrections to the cusp anomalous dimensions at four loops. Finally, we also discuss in detail the computation of all necessary Wilson line integrals up to three loops using the method of leading singularities and differential equations.

  4. Closed loop recycling of lead/acid batteries

    NASA Astrophysics Data System (ADS)

    Bied-Charreton, B.

    The traditional lead/acid battery is a recycleable product, irrespective whether it is of an automotive, traction or standby design. The product benefits from the traditional lead metallurgy that has been developed for both primary (mines) and secondary (recycling) smelting. Secondary smelting accounts for 60% of total lead production in Europe, and this market lead the most effectively metal. In secondary smelters, scrapped batteries are crushed and smelted. The polypropylene from the boxes is recycled to produce secondary plastic for battery, automotive, or other miscellaneous uses. The lead metal is refined to be re-used in the battery industry. The acid is retreated. Recycling requires a collection network. The lead/acid battery benefits from the traditional collection network that has been established for scrap-iron and non-ferrous metal scrap. In Western Europe, the recycling rate for scrapped batteries is estimated to be 80 to 90%. All participants in the battery recycling loop agree that the process must be a clean cycle for it to be credible. The collection organization is improving the quality of storage and transportation, especially with regard to the acid that can only be neutralized in correctly-controlled facilities, generally located at the smelters. The smelters themselves tend, through local regulations, to run at the optimum level of protection of the environment.

  5. Metabolism of hydroxy fatty acids in dogs with steatorrhea secondary to experimentally produced intestinal blind loops.

    PubMed

    Kim, Y S; Spritz, N

    1968-07-01

    Several aspects of the metabolism of hydroxy fatty acids were studied in dogs with steatorrhea resulting from an experimentally produced jejunal blind loop. In these animals hydroxy acids were present in the stool in amounts far above normal. These acids disappeared from the feces during tetracycline administration and after exclusion of the blind loop-both procedures that corrected the steatorrhea apparently by reducing bacterial overgrowth. Hydroxy acids persisted in higher than normal amounts, however, after administration of taurocholic acid, which also corrected the steatorrhea, but by a different mechanism. Both in normal dogs and in those with blind loops, hydroxy acid constituted a higher percentage of total fatty acids in the jejunum. A possible conclusion is that hydroxy fatty acids have an enterohepatic circulation via the portal system. When hydroxy acids were fed to normal dogs, steatorrhea was not produced and absorption in amounts similar to that of unsubstituted stearic acid was observed. Isotopic oleic and linoleic acids were converted to hydroxy acids both in vivo and during in vitro incubation with feces; stearic acid was not. These findings support the idea that hydroxy acids arise by the addition of water across double bonds, this addition being catalyzed by enzymes of intestinal bacteria. PMID:5725881

  6. Constraints on abelian extensions of the Standard Model from two-loop vacuum stability and U(1) B- L

    NASA Astrophysics Data System (ADS)

    Corianò, Claudio; Rose, Luigi Delle; Marzo, Carlo

    2016-02-01

    We present a renormalization group study of the scalar potential in a minimal U(1) B- L extension of the Standard Model involving one extra heavier Higgs and three heavy right-handed neutrinos with family universal B-L charge assignments. We implement a type-I seesaw for the masses of the light neutrinos of the Standard Model. In particular, compared to a previous study, we perform a two-loop extension of the evolution, showing that two-loop effects are essential for the study of the stability of the scalar potential up to the Planck scale. The analysis includes the contribution of the kinetic mixing between the two abelian gauge groups, which is radiatively generated by the evolution, and the one-loop matching conditions at the electroweak scale. By requiring the stability of the potential up to the Planck mass, significant constraints on the masses of the heavy neutrinos, on the gauge couplings and the mixing in the Higgs sector are identified.

  7. Data from extension trials: denosumab and zoledronic acid.

    PubMed

    Dore, Robin K

    2012-03-01

    Osteoporosis and fractures that occur as a result of this condition pose a huge public health problem to society and result in morbidity and mortality to individuals. Because osteoporosis is often a result of aging, many people are not aware that therapies exist to reduce the risk of fracture. Until recently, the most common therapies used to treat osteoporosis, the oral bisphosphonates, had an inconvenient and cumbersome mode of administration. Within the last 4 years, two new parenteral antiresorptive drugs to treat osteoporosis were approved by the US Food and Drug Administration. As treatment of osteoporosis may extend for many years, the collection of long-term efficacy and safety data is warranted. This paper discusses data from the extension trials of denosumab and zoledronic acid. PMID:22086442

  8. A unique loop extension in the serine protease domain of haptoglobin is essential for CD163 recognition of the haptoglobin-hemoglobin complex.

    PubMed

    Nielsen, Marianne Jensby; Petersen, Steen Vang; Jacobsen, Christian; Thirup, Søren; Enghild, Jan Johannes; Graversen, Jonas Heilskov; Moestrup, Søren Kragh

    2007-01-12

    Haptoglobin and haptoglobin-related protein are homologous hemoglobin-binding proteins consisting of a complement control repeat (alpha-chain) and a serine protease domain (beta-chain). Haptoglobin-hemoglobin complex formation promotes high affinity binding of hemoglobin to the macrophage scavenger receptor CD163 leading to endocytosis and degradation of the haptoglobin-hemoglobin complex. In contrast, complex formation between haptoglobin-related protein and hemoglobin does not promote high affinity interaction with CD163. To define structural components of haptoglobin important for CD163 recognition, we exploited this functional difference to design and analyze recombinant haptoglobin/haptoglobin-related protein chimeras complexed to hemoglobin. These data revealed that only the beta-chain of haptoglobin is involved in receptor recognition. Substitution of 4 closely spaced amino acid residues of the haptoglobin beta-chain (valine 259, glutamate 261, lysine 262, and threonine 264) abrogated the high affinity receptor binding. The 4 residues are encompassed by a part of the primary structure not present in other serine protease domain proteins. Structural modeling based on the well characterized serine protease domain fold suggests that this sequence represents a loop extension unique for haptoglobin and haptoglobin-related protein. A synthetic peptide representing the haptoglobin loop sequence exhibited a pronounced inhibitory effect on receptor binding of haptoglobin-hemoglobin. PMID:17102136

  9. Differential Ubiquitin Binding by the Acidic Loops of Ube2g1 and Ube2r1 Enzymes Distinguishes Their Lys-48-ubiquitylation Activities*

    PubMed Central

    Choi, Yun-Seok; Lee, Yun-Ju; Lee, Seo-Yeon; Shi, Lei; Ha, Jung-Hye; Cheong, Hae-Kap; Cheong, Chaejoon; Cohen, Robert E.; Ryu, Kyoung-Seok

    2015-01-01

    The ubiquitin E2 enzymes, Ube2g1 and Ube2r1, are able to synthesize Lys-48-linked polyubiquitins without an E3 ligase but how that is accomplished has been unclear. Although both E2s contain essential acidic loops, only Ube2r1 requires an additional C-terminal extension (184–196) for efficient Lys-48-ubiquitylation activity. The presence of Tyr-102 and Tyr-104 in the Ube2g1 acidic loop enhanced both ubiquitin binding and Lys-48-ubiquitylation and distinguished Ube2g1 from the otherwise similar truncated Ube2r11–183 (Ube2r1C). Replacement of Gln-105–Ser-106–Gly-107 in the acidic loop of Ube2r1C (Ube2r1CYGY) by the corresponding residues from Ube2g1 (Tyr-102–Gly-103–Tyr-104) increased Lys-48-ubiquitylation activity and ubiquitin binding. Two E2∼UB thioester mimics (oxyester and disulfide) were prepared to characterize the ubiquitin binding activity of the acidic loop. The oxyester but not the disulfide derivative was found to be a functional equivalent of the E2∼UB thioester. The ubiquitin moiety of the Ube2r1CC93S-[15N]UBK48R oxyester displayed two-state conformational exchange, whereas the Ube2r1CC93S/YGY-[15N]UBK48R oxyester showed predominantly one state. Together with NMR studies that compared UBK48R oxyesters of the wild-type and the acidic loop mutant (Y102G/Y104G) forms of Ube2g1, in vitro ubiquitylation assays with various mutation forms of the E2s revealed how the intramolecular interaction between the acidic loop and the attached donor ubiquitin regulates Lys-48-ubiquitylation activity. PMID:25471371

  10. Periodic acid-Schiff-positive loops and networks as a prognostic factor in oral mucosal melanoma.

    PubMed

    Song, Hao; Jing, Guangping; Wang, Lizhen; Guo, Wei; Ren, Guoxin

    2016-04-01

    The prognostic factors of oral mucosal melanoma (OMM), a rare and aggressive neoplasm, remain to be determined. The aim of this study is to investigate the prognostic significance of vasculogenic mimicry in OMM. The clinical data of 62 patients with primary OMM treated in Shanghai Ninth People's Hospital from April 2007 to April 2012 were retrieved and analyzed retrospectively. Staining of periodic acid-Schiff (PAS) and CD31 immunohistochemistry were performed to evaluate the prognostic value of PAS-positive patterns, blood lakes, and microvascular density. PAS-positive loops and networks (P<0.001) as well as blood lakes (P=0.040) were found to be predictors of overall survival (OS). The presence of PAS-positive loops and networks was an independent prognostic factor of poor OS in multivariate analysis (P=0.002). Although the presence of PAS-positive loops and networks was associated with hematogenous metastasis (P=0.041) and lymphogenous metastasis (P=0.041), it was not an independent predictor of both types of metastasis in multivariate analysis. Microvascular density was not associated with OS (P=0.627) and metastasis of OMM patients. PAS-positive loops and networks have a significant prognostic value in OMM. Detection of PAS-positive patterns may lead to better staging and serve as a prognostic parameter of OMM. PMID:26636907

  11. Long-term acid-induced wall extension in an in-vitro system

    NASA Technical Reports Server (NTRS)

    Cleland, R. E.; Cosgrove, D.; Tepfer, M.

    1987-01-01

    When frozen-thawed Avena sativa L. coleoptile and Cucumis sativa L. hypocotyl sections, under tension, are acid-treated, they undergo rapid elongation (acid-extension). The acid-extension response consists of two concurrent phases: a burst of extension which decays exponentially over 1-2 h (ExE), and a constant rate of extension (CE) which can persist for at least 6h. The extension (delta L) is closely represented by the equation: delta L = a-a e(-kt) + C t where a is the total extension of the exponential phase, k is the rate constant for ExE, and c is the rate of linear extension (CE). Low pH and high tension increased a and c, whereas temperature influenced k. The magnitude of the CE (over 50% extension/10 h), the similarity in its time course to auxin-induced growth, and the apparent yield threshold for CE indicate that CE is more likely than ExE to be the type of extension which cell walls undergo during normal auxin-induced growth.

  12. Hierarchical scale dependence associated with the extension of the nonlinear feedback loop in a seven-dimensional Lorenz model

    NASA Astrophysics Data System (ADS)

    Shen, Bo-Wen

    2016-07-01

    In this study, we construct a seven-dimensional Lorenz model (7DLM) to discuss the impact of an extended nonlinear feedback loop on solutions' stability and illustrate the hierarchical scale dependence of chaotic solutions. Compared to the 5DLM, the 7DLM includes two additional high wavenumber modes that are selected based on an analysis of the nonlinear temperature advection term, a Jacobian term (J(ψ, θ)), where, ψ and θ represent the streamfunction and temperature perturbations, respectively. Fourier modes that represent temperature in the 7DLM can be categorized into three major scales as the primary (the largest scale), secondary, and tertiary (the smallest scale) modes. Further extension of the nonlinear feedback loop within the 7DLM can provide negative nonlinear feedback to stabilize solutions, thus leading to a much larger critical value for the Rayleigh parameter (rc ˜ 116.9) for the onset of chaos, as compared to an rc of 42.9 for the 5DLM as well as an rc of 24.74 for the 3DLM. The rc is determined by an analysis of ensemble Lyapunov exponents (eLEs) with a Prandtl number (σ) of 10. To examine the dependence of rc on the value of the Prandtl number, a linear stability analysis is performed near the nontrivial critical point using a wide range of the Rayleigh parameter (40 ≤ r ≤ 195) and the Prandtl number (5 ≤ σ ≤ 25). Then an eLE analysis is conducted using selected values of the Prandtl number. The linear stability analysis is done by solving for the analytical solutions of the critical points, by linearizing the 7DLM with respect to the analytical solutions, and by calculating the eigenvalues of the linearized system. Within the range of (5 ≤ σ ≤ 25), the 7DLM requires a larger rc for the onset of chaos than the 5DLM. In addition to the negative nonlinear feedback illustrated and emulated by the quasi-equilibrium state solutions for high wavenumber modes, the 7DLM reveals the hierarchical scale dependence of chaotic solutions. For

  13. Protein loop compaction and the origin of the effect of arginine and glutamic acid mixtures on solubility, stability and transient oligomerization of proteins.

    PubMed

    Blobel, Jascha; Brath, Ulrika; Bernadó, Pau; Diehl, Carl; Ballester, Lidia; Sornosa, Alejandra; Akke, Mikael; Pons, Miquel

    2011-12-01

    Addition of a 50 mM mixture of L: -arginine and L: -glutamic acid (RE) is extensively used to improve protein solubility and stability, although the origin of the effect is not well understood. We present Small Angle X-ray Scattering (SAXS) and Nuclear Magnetic Resonance (NMR) results showing that RE induces protein compaction by collapsing flexible loops on the protein core. This is suggested to be a general mechanism preventing aggregation and improving resistance to proteases and to originate from the polyelectrolyte nature of RE. Molecular polyelectrolyte mixtures are expected to display long range correlation effects according to dressed interaction site theory. We hypothesize that perturbation of the RE solution by dissolved proteins is proportional to the volume occupied by the protein. As a consequence, loop collapse, minimizing the effective protein volume, is favored in the presence of RE. PMID:21390527

  14. NAIL: Nucleic Acid detection using Isotachophoresis and Loop-mediated isothermal amplification.

    PubMed

    Borysiak, Mark D; Kimura, Kevin W; Posner, Jonathan D

    2015-04-01

    Nucleic acid amplification tests are the gold standard for many infectious disease diagnoses due to high sensitivity and specificity, rapid operation, and low limits of detection. Despite the advantages of nucleic acid amplification tests, they currently offer limited point-of-care (POC) utility due to the need for complex instruments and laborious sample preparation. We report the development of the Nucleic Acid Isotachophoresis LAMP (NAIL) diagnostic device. NAIL uses isotachophoresis (ITP) and loop-mediated isothermal amplification (LAMP) to extract and amplify nucleic acids from complex matrices in less than one hour inside of an integrated chip. ITP is an electrokinetic separation technique that uses an electric field and two buffers to extract and purify nucleic acids in a single step. LAMP amplifies nucleic acids at constant temperature and produces large amounts of DNA that can be easily detected. A mobile phone images the amplification results to eliminate the need for laser fluorescent detection. The device requires minimal user intervention because capillary valves and heated air chambers act as passive valves and pumps for automated fluid actuation. In this paper, we describe NAIL device design and operation, and demonstrate the extraction and detection of pathogenic E. coli O157:H7 cells from whole milk samples. We use the Clinical and Laboratory Standards Institute (CLSI) limit of detection (LoD) definitions that take into account the variance from both positive and negative samples to determine the diagnostic LoD. According to the CLSI definition, the NAIL device has a limit of detection (LoD) of 1000 CFU mL(-1) for E. coli cells artificially inoculated into whole milk, which is two orders of magnitude improvement to standard tube-LAMP reactions with diluted milk samples and comparable to lab-based methods. The NAIL device potentially offers significant reductions in the complexity and cost of traditional nucleic acid diagnostics for POC applications

  15. Gibberellic Acid Regulates Cell Wall Extensibility in Wheat (Triticum aestivum L.) 1

    PubMed Central

    Keyes, Geoff; Sorrells, Mark E.; Setter, Tim L.

    1990-01-01

    Mutations (Rht genes) blocking sensitivity to gibberellic acid (GA) were used to examine phytohormone mediated cell wall expansion in wheat (Triticum aestivum L.). Irreversible extensibility of immature leaf segments, as determined by stress/strain (instron) measurements, declined with Rht gene dose. Exogenous GA3 significantly increased wall extensibility in the nonmutant controls but had no effect on the near-isogenic GA-insensitive genotypes. Furthermore, ancymidol, an inhibitor of gibberellin biosynthesis, diminished wall extensibility in the nonmutant control. Extensibility of immature segments was highly correlated with mature leaf sheath length (R = +0.95). The results indicate that wall yielding properties of expanding wheat leaves are associated with leaf cell expansion potential and that GA is involved in the determination of those properties. PMID:16667254

  16. Destabilization of pea lectin by substitution of a single amino acid in a surface loop.

    PubMed

    Hoedemaeker, F J; van Eijsden, R R; Díaz, C L; de Pater, B S; Kijne, J W

    1993-09-01

    Legume lectins are considered to be antinutritional factors (ANF) in the animal feeding industry. Inactivation of ANF is an important element in processing of food. In our study on the stability of Pisum sativum L. lectin (PSL), a conserved hydrophobic amino acid (Val103) in a surface loop was replaced with alanine. The mutant lectin, PSL V103A, showed a decrease in unfolding temperature (Tm) by some 10 degrees C in comparison with wild-type (wt) PSL, and the denaturation energy (delta H) is only about 55% of that of wt PSL. Replacement of an adjacent amino acid (Phe104) with alanine did not result in a significant difference in stability in comparison with wt PSL. Both mutations did not change the sugar-binding properties of the lectin, as compared with wt PSL and with PSL from pea seeds, at ambient temperatures. The double mutant, PSL V103A/F104A, was produced in Escherichia coli, but could not be isolated in an active (i.e. sugar-binding) form. Interestingly, the mutation in PSL V103A reversibly affected sugar-binding at 37 degrees C, as judged from haemagglutination assays. These results open the possibility of production of lectins that are active in planta at ambient temperatures, but are inactive and possibly non-toxic at 37 degrees C in the intestines of mammals. PMID:8400124

  17. Enzymatic recycling of ascorbic acid from dehydroascorbic acid by glutathione-like peptides in the extracellular loops of aminergic G-protein coupled receptors.

    PubMed

    Root-Bernstein, Robert; Fewins, Jenna; Rhinesmith, Tyler; Koch, Ariana; Dillon, Patrick F

    2016-07-01

    The intracellular recycling of ascorbic acid from dehydroascorbic acid by the glutathione-glutathione reductase system has been well-characterized. We propose that extracellular recycling of ascorbic acid is performed in a similar manner by cysteine-rich, glutathione-like regions of the first and second extracellular loops of some aminergic receptors including adrenergic, histaminergic, and dopaminergic receptors. Previous research in our laboratory demonstrated that ascorbic acid binds to these receptors at a site on their first or second extracellular loops, significantly enhancing ligand activity, and apparently recycling hundreds of times their own concentration of ascorbate in an enzymatic fashion. In this study, we have synthesized 25 peptides from the first and second extracellular loops of aminergic and insulin receptors and compared them directly to glutathione for their ability to prevent the oxidation of ascorbate and to regenerate ascorbate from dehydroascorbic acid. Peptide sequences that mimic glutathione in containing a cysteine and a glutamic acid-like amino acid also mimic glutathione activity in effects and in kinetics. Some (but not all) peptide sequences that contain one or more methionines instead of cysteine can significantly retard the oxidation of ascorbic acid but do not recycle it from dehydroascorbate into ascorbate. Peptides lacking both cysteines and methionines uniformly failed to alter significantly ascorbate or dehydroascorbate oxidation or reduction. We believe that this is the first proof that receptors may carry out both ligand binding and enzymatic activity extracellularly. Our results suggest the existence of a previously unknown extracellular system for recycling ascorbate. Copyright © 2016 John Wiley & Sons, Ltd. PMID:26749062

  18. The Lone Loop Radiative Corrections to W Pair Production in Electron Positron Annihilation in the Supersymmetric Extension of the Salam-Weinberg Model of the Electroweak Interactions.

    NASA Astrophysics Data System (ADS)

    Alam, S.

    1992-01-01

    The one loop radiative corrections to W pair production in e^+e^- annihilation in the supersymmetric extension of the Salam-Weinberg (SW) model of the electroweak interactions are calculated. Since our model contains the SW theory, and several calculations have been reported on the latter we compare these results with ours. In general agreement is found, a detailed comparison is not possible since the explicit details have not been published. However we have cross checked many of SW model results with Sundaresan and Kalyniak who have performed the calculation using the same renormalization scheme as ours. The virtual corrections are determined in the on-mass-shell renormalization scheme (OMRS) of Sakakibara. The OMRS scheme has several advantages, one being that it is a transparent (i.e. in terms of the physics) renormalization procedure. Moreover the fundamental set of input parameters of OMRS is well determined. By this we mean the accurate determination of the Z-boson mass at LEP I and the expected precise measurement of the W mass at LEP II, and the already well determined alpha value constitute a good set of the fundamental input parameters. Of course the Higgs boson mass and the fermion mass have also to be put in. So far the top quark and the Higgs boson have eluded detection and consequently their masses have to be put in as free parameters. One very important feature in determining how good the standard model (SM) is involves the measurement of the tri-boson coupling. Such a coupling occurs in e^+e^- to W^+W ^- in the SM, at the tree level. For a precision check, one must calculate one loop radiative corrections in SM, using the tri-boson coupling. We have also evaluated W pair production with non standard coupling to get an intuitive feel for deviations away from the SM. Supersymmetry has the effect of reducing the virtual corrections. The effect of supersymmetry is examined on the differential cross section of e^+e^- to W^+W^-, the 'A' term, the magnetic

  19. Point-of-care multiplexed assays of nucleic acids using microcapillary-based loop-mediated isothermal amplification.

    PubMed

    Zhang, Yi; Zhang, Lu; Sun, Jiashu; Liu, Yulei; Ma, Xingjie; Cui, Shangjin; Ma, Liying; Xi, Jianzhong Jeff; Jiang, Xingyu

    2014-07-15

    This report demonstrates a straightforward, robust, multiplexed and point-of-care microcapillary-based loop-mediated isothermal amplification (cLAMP) for assaying nucleic acids. This assay integrates capillaries (glass or plastic) to introduce and house sample/reagents, segments of water droplets to prevent contamination, pocket warmers to provide heat, and a hand-held flashlight for a visual readout of the fluorescent signal. The cLAMP system allows the simultaneous detection of two RNA targets of human immunodeficiency virus (HIV) from multiple plasma samples, and achieves a high sensitivity of two copies of standard plasmid. As few nucleic acid detection methods can be wholly independent of external power supply and equipment, our cLAMP holds great promise for point-of-care applications in resource-poor settings. PMID:24937125

  20. Disruption of a Nuclear NFATc2 Protein Stabilization Loop Confers Breast and Pancreatic Cancer Growth Suppression by Zoledronic Acid*

    PubMed Central

    Singh, Shiv K.; Baumgart, Sandra; Singh, Garima; König, Alexander O.; Reutlinger, Kristina; Hofbauer, Lorenz C.; Barth, Peter; Gress, Thomas M.; Lomberk, Gwen; Urrutia, Raul; Fernandez-Zapico, Martin E.; Ellenrieder, Volker

    2011-01-01

    The aminobisphosphonate zoledronic acid has elicited significant attention due to its remarkable anti-tumoral activity, although its detailed mechanism of action remains unclear. Here, we demonstrate the existence of a nuclear GSK-3β-NFATc2 stabilization pathway that promotes breast and pancreatic cancer growth in vitro and in vivo and serves as a bona fide target of zoledronic acid. Specifically, the serine/threonine kinase GSK-3β stabilizes nuclear NFATc2 through phosphorylation of the serine-rich SP2 domain, thus protecting the transcription factor from E3-ubiquitin ligase HDM2-mediated proteolysis. Zoledronic acid disrupts this NFATc2 stabilization pathway through two mechanisms, namely GSK-3β inhibition and induction of HDM2 activity. Upon nuclear accumulation, HDM2 targets unphosphorylated NFATc2 for ubiquitination at acceptor lysine residues Lys-684/Lys-897 and hence labels the factor for subsequent proteasomal degradation. Conversely, mutagenesis-induced constitutive serine phosphorylation (Ser-215, Ser-219, and Ser-223) of the SP2 domain prevents NFATc2 from HDM2-mediated ubiquitination and degradation and consequently rescues cancer cells from growth suppression by zoledronic acid. In conclusion, this study demonstrates a critical role of the GSK-3β-HDM2 signaling loop in the regulation of NFATc2 protein stability and growth promotion and suggests that double targeting of this pathway is responsible, at least to a significant part, for the potent and reliable anti-tumoral effects of zoledronic acid. PMID:21628454

  1. Interstrand loops CD and EF act as pH-dependent gates to regulate fatty acid ligand binding in tear lipocalin.

    PubMed

    Gasymov, Oktay K; Abduragimov, Adil R; Yusifov, Taleh N; Glasgow, Ben J

    2004-10-12

    Tear lipocalin (TL), a major component of human tears, shows pH-dependent endogenous ligand binding. The structural and conformational changes associated with ligand release in the pH range of 7.5-3.0 are monitored by circular dichroism spectroscopy and site-directed tryptophan fluorescence. In the transition from pH 7.5 to pH 5.5, the ligand affinity for 16-(9-anthroyloxy)palmitic acid (16AP) and 8-anilino-1-naphthalenesulfonic acid is reduced. At pH 4.0 these ligands no longer bind within the TL calyx. From pH 7.3 to pH 3.0, the residues on loops CD and EF, which overhang the calyx entrance, show reduced accessibility to acrylamide. In addition resonance energy transfer is enhanced between residues on the two loops; the distance between the loops narrows. These findings suggest that apposition of the loops at low pH excludes the ligand from the intracavitary binding site. The conformational changes observed in transition from pH 7.3 to pH 3.0 for loops CD and EF are quite different. The CD loop shows less population reshuffling than the EF loop with an acidic environment, probably because backbone motion is restrained by the adjacent disulfide bond. The Trp fluorescence wavelength maximum (lambda(max)) reflects internal electrostatic interactions for positions on loops CD and EF. The titration curves of lambda(max) for mutants on the EF loop fit the Hendersen-Hasselbalch equation for two apparent pK(a) values, while the CD loop positions fit satisfactorily with one pK(a) value. Midpoints of transition for the binding affinity of TL tryptophan mutants to 16AP occur at pH 5.5-6.1. Replacement of each amino acid on either loop by single tryptophan mutation does not disrupt the pH-dependent binding affinity to 16AP. Taken together the data suggest that pH-driven ligand release involves ionization changes in several titratable residues associated with CD and EF loop apposition and occlusion of the calyx. PMID:15461462

  2. Visual detection of Ebola virus using reverse transcription loop-mediated isothermal amplification combined with nucleic acid strip detection.

    PubMed

    Xu, Changping; Wang, Hualei; Jin, Hongli; Feng, Na; Zheng, Xuexing; Cao, Zengguo; Li, Ling; Wang, Jianzhong; Yan, Feihu; Wang, Lina; Chi, Hang; Gai, Weiwei; Wang, Chong; Zhao, Yongkun; Feng, Yan; Wang, Tiecheng; Gao, Yuwei; Lu, Yiyu; Yang, Songtao; Xia, Xianzhu

    2016-05-01

    Ebola virus (species Zaire ebolavirus) (EBOV) is highly virulent in humans. The largest recorded outbreak of Ebola hemorrhagic fever in West Africa to date was caused by EBOV. Therefore, it is necessary to develop a detection method for this virus that can be easily distributed and implemented. In the current study, we developed a visual assay that can detect EBOV-associated nucleic acids. This assay combines reverse transcription loop-mediated isothermal amplification and nucleic acid strip detection (RT-LAMP-NAD). Nucleic acid amplification can be achieved in a one-step process at a constant temperature (58 °C, 35 min), and the amplified products can be visualized within 2-5 min using a nucleic acid strip detection device. The assay is capable of detecting 30 copies of artificial EBOV glycoprotein (GP) RNA and RNA encoding EBOV GP from 10(2) TCID50 recombinant viral particles per ml with high specificity. Overall, the RT-LAMP-NAD method is simple and has high sensitivity and specificity; therefore, it is especially suitable for the rapid detection of EBOV in African regions. PMID:26831931

  3. A Complex Deoxyribonucleic Acid Looping Configuration Associated with the Silencing of the Maternal Igf2 Allele

    PubMed Central

    Qiu, Xinwen; Vu, Thanh H.; Lu, Qiucheng; Ling, Jian Qun; Li, Tao; Hou, Aiju; Wang, Shu Kui; Chen, Hui Ling; Hu, Ji Fan; Hoffman, Andrew R.

    2008-01-01

    Alternate interactions between the H19 imprinting control region (ICR) and one of the two Igf2 differentially methylated regions has been proposed as a model regulating the reciprocal imprinting of Igf2 and H19. To study the conformation of this imprint switch, we performed a systematic structural analysis across the 140 kb of the mouse Igf2-H19 region, which includes enhancers located both between the two genes as well as downstream of H19, by using a scanning chromosome conformation capture (3C) technique. Our results suggest that on the active paternal Igf2 allele, the various enhancers have direct access to the Igf2 promoters, whereas the imprinted silent maternal Igf2 allele assumes a complex three-dimensional knotted loop that keeps the enhancers away from the Igf2 promoters and allows them to interact with the H19 promoter. This complex DNA looping of the maternal allele is formed by interactions involving differentially methylated region 1, the ICR, and enhancers. Binding of CTC-binding factor to the maternal, unmethylated ICR in conjunction with the presence of multicomplex components including interchromosomal interactions, create a barrier blocking the access of all enhancers to Igf2, thereby silencing the maternal Igf2. This silencing configuration exists in newborn liver, mouse embryonic fibroblast, and embryonic stem cells and persists during mitosis, conferring a mechanism for epigenetic memory. PMID:18356289

  4. Acidic amino acids in the first intracellular loop contribute to voltage- and calcium- dependent gating of anoctamin1/TMEM16A.

    PubMed

    Xiao, Qinghuan; Cui, Yuanyuan

    2014-01-01

    Anoctamin1 (Ano1, or TMEM16A) is a Ca2+-activated chloride channel that is gated by both voltage and Ca2+. We have previously identified that the first intracellular loop that contains a high density of acidic residues mediates voltage- and calcium-dependent gating of Ano1. Mutation of the four consecutive glutamates (444EEEE447) inhibits the voltage-dependent activation of Ano1, whereas deletion of these residues decreases apparent Ca2+ sensitivity. In the present study, we further found that deletion of 444EEEEEAVKD452 produced a more than 40-fold decrease in the apparent Ca2+ sensitivity with altered activation kinetics. We then systematically mutated each acidic residue into alanine, and analyzed the voltage- and calcium dependent activation of each mutation. Activation kinetics of wild type Ano1 consisted of a fast component (τfast) that represented voltage-dependent mode, and a slow component (τslow) that reflected the Ca2+-dependent modal gating. E444A, E445A, E446A, E447A, E448A, and E457A mutations showed a decrease in the τfast, significantly inhibited voltage-dependent activation of Ano1 in the absence of Ca2+, and greatly shifted the G-V curve to the right, suggesting that these glutamates are involved in voltage-gating of Ano1. Furthermore, D452A, E464A, E470A, and E475A mutations that did not alter voltage-dependent activation of the channel, significantly decreased Ca2+ dependence of G-V curve, exhibited an increase in the τslow, and produced a 2-3 fold decrease in the apparent Ca2+ sensitivity, suggesting that these acidic residues are involved in Ca2+-dependent gating of the channel. Our data show that acidic residues in the first intracellular loop are the important structural determinant that couples the voltage and calcium dependent gating of Ano1. PMID:24901998

  5. 76 FR 17835 - Citric Acid and Certain Citrate Salts From the People's Republic of China: Extension of Time...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-31

    ... Administrative Review, 75 FR 37759 (June 30, 2010). On January 25, 2011, the Department published the extension... Time Limit for the Preliminary Results of the Antidumping Duty Administrative Review, 76 FR 4288... International Trade Administration A-570-937] Citric Acid and Certain Citrate Salts From the People's...

  6. A closed loop for municipal organic solid waste by lactic acid fermentation.

    PubMed

    Probst, Maraike; Walde, Janette; Pümpel, Thomas; Wagner, Andreas Otto; Insam, Heribert

    2015-01-01

    In order to investigate the feasibility of producing lactic acid from municipal organic solid waste different pH values (4-7) and temperatures (37°C and 55°C) were tested. For the evaluation of fermentation conditions the chemical, physical, and microbial characters were monitored over a period of 7days. Quantitative real time PCR, PCR-DGGE, and next generation sequencing of a 16S rRNA gene library were applied to identify the key players of the lactic acid production and their association. Lactobacillus acidophilus and its closest relatives were found to be efficient lactic acid producers (>300mM) under most suitable fermentation conditions tested in this study: 37°C with either uncontrolled pH or at a pH of 5. These data provide the first step in the realization of the idea "reuse, reduce, and recycle" of municipal organic solid waste. PMID:25459815

  7. Summary Report on Gamma Radiolysis of TBP/n-dodecane in the Presence of Nitric Acid Using the Radiolysis/Hydrolysis Test Loop

    SciTech Connect

    Dean R. Peterman; Bruce J. Mincher; Catherine L. Riddle; Richard D. Tillotson

    2010-08-01

    Design and installation has been completed for a state-of-the-art radiolysis/hydrolysis test loop system. The system is used to evaluate the effects of gamma radiolysis and acid hydrolysis on the stability and performance of solvent extraction process solvents. The test loop is comprised of two main sections; the solvent irradiation and hydrolysis loop and the solvent reconditioning loop. In the solvent irradiation and hydrolysis loop, aqueous and organic phases are mixed and circulated through a gamma irradiator until the desired absorbed dose is achieved. Irradiation of the mixed phases is more representative of actual conditions in a solvent extraction process. Additionally, the contact of the organic phase with the aqueous phase will subject the solvent components to hydrolysis. This hydrolysis can be accelerated by controlling the system at an elevated temperature. At defined intervals, the organic from the irradiation/hydrolysis loop will be transferred to the solvent reconditioning loop where the solvent is contacted with scrub, strip, and solvent wash solutions which simulate process flowsheet conditions. These two processes are repeated until the total desired dose is achieved. Since all viable solvent extraction components in an advanced fuel cycle must exhibit high radiolytic and hydrolytic stability, this test loop is not limited to any one solvent system but is applicable to all systems of interest. Also, the test loop is not limited to testing of process flowsheets. It is also a valuable tool in support of fundamental research on newly identified extractants/modifiers and the impact of gamma radiation on their stability in a dynamic environment. The investigation of the radiolysis of a TBP/n-dodecane process solvent in contact with aqueous nitric acid has been performed. These studies were intended to confirm/optimize the operability of the test loop system. Additionally, these data are directly applicable to numerous other solvent extraction

  8. Regulative Loops, Step Loops and Task Loops

    ERIC Educational Resources Information Center

    VanLehn, Kurt

    2016-01-01

    This commentary suggests a generalization of the conception of the behavior of tutoring systems, which the target article characterized as having an outer loop that was executed once per task and an inner loop that was executed once per step of the task. A more general conception sees these two loops as instances of regulative loops, which…

  9. Length and Amino Acid Sequence of Peptides Substituted for the 5-HT3A Receptor M3M4 Loop May Affect Channel Expression and Desensitization

    PubMed Central

    McKinnon, Nicole K.; Bali, Moez; Akabas, Myles H.

    2012-01-01

    5-HT3A receptors are pentameric neurotransmitter-gated ion channels in the Cys-loop receptor family. Each subunit contains an extracellular domain, four transmembrane segments (M1, M2, M3, M4) and a 115 residue intracellular loop between M3 and M4. In contrast, the M3M4 loop in prokaryotic homologues is <15 residues. To investigate the limits of M3M4 loop length and composition on channel function we replaced the 5-HT3A M3M4 loop with two to seven alanine residues (5-HT3A-An = 2–7). Mutants were expressed in Xenopus laevis oocytes and characterized using two electrode voltage clamp recording. All mutants were functional. The 5-HT EC50's were at most 5-fold greater than wild-type (WT). The desensitization rate differed significantly among the mutants. Desensitization rates for 5-HT3A-A2, 5-HT3A-A4, 5-HT3A-A6, and 5-HT3A-A7 were similar to WT. In contrast, 5-HT3A-A3 and 5-HT3A-A5 had desensitization rates at least an order of magnitude faster than WT. The one Ala loop construct, 5-HT3A-A1, entered a non-functional state from which it did not recover after the first 5-HT application. These results suggest that the large M3M4 loop of eukaryotic Cys-loop channels is not required for receptor assembly or function. However, loop length and amino acid composition can effect channel expression and desensitization. We infer that the cytoplasmic ends of the M3 and M4 segments may undergo conformational changes during channel gating and desensitization and/or the loop may influence the position and mobility of these segments as they undergo gating-induced conformational changes. Altering structure or conformational mobility of the cytoplasmic ends of M3 and M4 may be the basis by which phosphorylation or protein binding to the cytoplasmic loop alters channel function. PMID:22539982

  10. Multifunctional Pd/Ni-Co catalyst for hydrogen production by chemical looping coupled with steam reforming of acetic acid.

    PubMed

    Fermoso, Javier; Gil, María V; Rubiera, Fernando; Chen, De

    2014-11-01

    High yield of high-purity H2 from acetic acid, a model compound of bio-oil obtained from the fast pyrolysis of biomass, was produced by sorption-enhanced steam reforming (SESR). An oxygen carrier was introduced into a chemical loop (CL) coupled to the cyclical SESR process to supply heat in situ for the endothermic sorbent regeneration to increase the energy efficiency of the process. A new multifunctional 1 %Pd/20 %Ni-20 %Co catalyst was developed for use both as oxygen carrier in the CL and as reforming catalyst in the SESR whereas a CaO-based material was used as CO2 sorbent. In the sorbent-air regeneration step, the Ni-Co atoms in the catalyst undergo strong exothermic oxidation reactions that provide heat for the CaO decarbonation. The addition of Pd to the Ni-Co catalyst makes the catalyst active throughout the whole SESR-CL cycle. Pd significantly promotes the reduction of Ni-Co oxides to metallic Ni-Co during the reforming stage, which avoids the need for a reduction step after regeneration. H2 yield above 90 % and H2 purity above 99.2 vol % were obtained. PMID:25209388

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

    PubMed Central

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

    2015-01-01

    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. PMID:26490404

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

    NASA Astrophysics Data System (ADS)

    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.

  13. Roles of Amino Acids 161 to 179 in the PSE-4 Ω Loop in Substrate Specificity and in Resistance to Ceftazidime

    PubMed Central

    Therrien, Christian; Sanschagrin, Francois; Palzkill, Timothy; Levesque, Roger C.

    1998-01-01

    The PSE-4 enzyme is a prototype carbenicillin-hydrolyzing enzyme exhibiting high activity against penicillins and early cephalosporins. To understand the mechanism that modulates substrate profiles and to verify the ability of PSE-4 to extend its substrate specificity toward expanded-spectrum cephalosporins, we used random replacement mutagenesis to generate six random libraries from amino acids 162 to 179 in the Ω loop. This region is known from studies with TEM-1 to be implicated in substrate specificity. It was found that the mechanism modulating ceftazidime hydrolysis in PSE-4 was different from that in TEM-1. The specificity of class 2c carbenicillin-hydrolyzing enzymes could not be assigned to the Ω loop of PSE-4. Analysis of the percentage of functional enzymes revealed that the hydrolysis of ampicillin was more affected than hydrolysis of carbenicillin by amino acid substitutions at positions 162 to 164 and 165 to 167. PMID:9756758

  14. [Treatment of olive mill wastewater by a process combining an intensive treatment (Jet-Loop reactor) followed by an extensive treatment (stabilization ponds)].

    PubMed

    Jail, A; Boukhoubza, F; Nejmeddine, A; Duarte, J C; Sayadi, S; Hassani, L

    2010-04-14

    Olive oil mill wastewater (OMW) is generally recognized as an environmentally troublesome by-product of the olive oil industry as its disposal without any treatment is known to cause serious environmental problems. However, this effluent has a high fertilizing power and constitutes, with urban wastewater, an important low-cost source. Biological treatment of OMW, with a process combining an aerobic reactor, 'Jet-Loop', and waste stabilization ponds, was investigated for possible agricultural reuse. The focus of the present study was to evaluate the contribution and the complementarity of the two systems in the total OMW treatment. Bio-treatment was performed using a 100-litre Jet-Loop reactor working volume achieving a chemical oxygen demand (COD) and phenolic compounds maximum removal rate of 72% and 68%, respectively, at a hydraulic retention time of 10 days. Co-treatment of OMW and domestic wastewater in waste stabilization ponds, with a hydraulic retention time of 22 days, reached a global removal rate of 66% for COD while no trace of phenolic compounds was detected on this level during the entire treatment period. Dynamics of faecal coliforms in stabilization ponds showed a total removal rate of 99.9% (3 logarithmic units (Log.U)). Preliminary results of agronomic tests on the ray-grass have evaluated the fertilizing effect of the final effluent resulting from the co-treatment. PMID:20480828

  15. Three charged amino acids in extracellular loop 1 are involved in maintaining the outer pore architecture of CFTR

    PubMed Central

    Cui, Guiying; Rahman, Kazi S.; Infield, Daniel T.; Kuang, Christopher; Prince, Chengyu Z.

    2014-01-01

    The cystic fibrosis (CF) transmembrane conductance regulator (CFTR) bears six extracellular loops (ECL1–6); ECL1 is the site of several mutations associated with CF. Mutation R117H has been reported to reduce current amplitude, whereas D110H, E116K, and R117C/L/P may impair channel stability. We hypothesized that these amino acids might not be directly involved in ion conduction and permeation but may contribute to stabilizing the outer vestibule architecture in CFTR. We used cRNA injected oocytes combined with electrophysiological techniques to test this hypothesis. Mutants bearing cysteine at these sites were not functionally modified by extracellular MTS reagents and were blocked by GlyH-101 similarly to WT-CFTR. These results suggest that these three residues do not contribute directly to permeation in CFTR. In contrast, mutants D110R-, E116R-, and R117A-CFTR exhibited instability of the open state and significantly shortened burst duration compared with WT-CFTR and failed to be locked into the open state by AMP-PNP (adenosine 5′-(β,γ-imido) triphosphate); charge-retaining mutants showed mainly the full open state with comparably longer open burst duration. These interactions suggest that these ECL1 residues might be involved in maintaining the outer pore architecture of CFTR. A CFTR homology model suggested that E116 interacts with R104 in both the closed and open states, D110 interacts with K892 in the fully closed state, and R117 interacts with E1126 in the open state. These interactions were confirmed experimentally. The results suggest that D110, E116, and R117 may contribute to stabilizing the architecture of the outer pore of CFTR by interactions with other charged residues. PMID:25024266

  16. Three charged amino acids in extracellular loop 1 are involved in maintaining the outer pore architecture of CFTR.

    PubMed

    Cui, Guiying; Rahman, Kazi S; Infield, Daniel T; Kuang, Christopher; Prince, Chengyu Z; McCarty, Nael A

    2014-08-01

    The cystic fibrosis (CF) transmembrane conductance regulator (CFTR) bears six extracellular loops (ECL1-6); ECL1 is the site of several mutations associated with CF. Mutation R117H has been reported to reduce current amplitude, whereas D110H, E116K, and R117C/L/P may impair channel stability. We hypothesized that these amino acids might not be directly involved in ion conduction and permeation but may contribute to stabilizing the outer vestibule architecture in CFTR. We used cRNA injected oocytes combined with electrophysiological techniques to test this hypothesis. Mutants bearing cysteine at these sites were not functionally modified by extracellular MTS reagents and were blocked by GlyH-101 similarly to WT-CFTR. These results suggest that these three residues do not contribute directly to permeation in CFTR. In contrast, mutants D110R-, E116R-, and R117A-CFTR exhibited instability of the open state and significantly shortened burst duration compared with WT-CFTR and failed to be locked into the open state by AMP-PNP (adenosine 5'-(β,γ-imido) triphosphate); charge-retaining mutants showed mainly the full open state with comparably longer open burst duration. These interactions suggest that these ECL1 residues might be involved in maintaining the outer pore architecture of CFTR. A CFTR homology model suggested that E116 interacts with R104 in both the closed and open states, D110 interacts with K892 in the fully closed state, and R117 interacts with E1126 in the open state. These interactions were confirmed experimentally. The results suggest that D110, E116, and R117 may contribute to stabilizing the architecture of the outer pore of CFTR by interactions with other charged residues. PMID:25024266

  17. Signature amino acids enable the archaeal L7Ae box C/D RNP core protein to recognize and bind the K-loop RNA motif

    PubMed Central

    Gagnon, Keith T.; Zhang, Xinxin; Qu, Guosheng; Biswas, Shyamasri; Suryadi, Jimmy; Brown, Bernard A.; Maxwell, E. Stuart

    2010-01-01

    The archaeal L7Ae and eukaryotic 15.5kD protein homologs are members of the L7Ae/15.5kD protein family that characteristically recognize K-turn motifs found in both archaeal and eukaryotic RNAs. In Archaea, the L7Ae protein uniquely binds the K-loop motif found in box C/D and H/ACA sRNAs, whereas the eukaryotic 15.5kD homolog is unable to recognize this variant K-turn RNA. Comparative sequence and structural analyses, coupled with amino acid replacement experiments, have demonstrated that five amino acids enable the archaeal L7Ae core protein to recognize and bind the K-loop motif. These signature residues are highly conserved in the archaeal L7Ae and eukaryotic 15.5kD homologs, but differ between the two domains of life. Interestingly, loss of K-loop binding by archaeal L7Ae does not disrupt C′/D′ RNP formation or RNA-guided nucleotide modification. L7Ae is still incorporated into the C′/D′ RNP despite its inability to bind the K-loop, thus indicating the importance of protein–protein interactions for RNP assembly and function. Finally, these five signature amino acids are distinct for each of the L7Ae/L30 family members, suggesting an evolutionary continuum of these RNA-binding proteins for recognition of the various K-turn motifs contained in their cognate RNAs. PMID:19926724

  18. Impaired Acid Catalysis by Mutation of a Protein Loop Hinge Residue in a YopH Mutant Revealed by Crystal Structures

    SciTech Connect

    Brandao, T.; Robinson, H; Johnson, S; Hengge, A

    2009-01-01

    Catalysis by the Yersinia protein-tyrosine phosphatase YopH is significantly impaired by the mutation of the conserved Trp354 residue to Phe. Though not a catalytic residue, this Trp is a hinge residue in a conserved flexible loop (the WPD-loop) that must close during catalysis. To learn why this seemingly conservative mutation reduces catalysis by 2 orders of magnitude, we have solved high-resolution crystal structures for the W354F YopH in the absence and in the presence of tungstate and vanadate. Oxyanion binding to the P-loop in W354F is analogous to that observed in the native enzyme. However, the WPD-loop in the presence of oxyanions assumes a half-closed conformation, in contrast to the fully closed state observed in structures of the native enzyme. This observation provides an explanation for the impaired general acid catalysis observed in kinetic experiments with Trp mutants. A 1.4 Angstroms structure of the W354F mutant obtained in the presence of vanadate reveals an unusual divanadate species with a cyclic [VO]2 core, which has precedent in small molecules but has not been previously reported in a protein crystal structure.

  19. Atomistic Free Energy Model for Nucleic Acids: Simulations of Single-Stranded DNA and the Entropy Landscape of RNA Stem-Loop Structures.

    PubMed

    Mak, Chi H

    2015-11-25

    While single-stranded (ss) segments of DNAs and RNAs are ubiquitous in biology, details about their structures have only recently begun to emerge. To study ssDNA and RNAs, we have developed a new Monte Carlo (MC) simulation using a free energy model for nucleic acids that has the atomisitic accuracy to capture fine molecular details of the sugar-phosphate backbone. Formulated on the basis of a first-principle calculation of the conformational entropy of the nucleic acid chain, this free energy model correctly reproduced both the long and short length-scale structural properties of ssDNA and RNAs in a rigorous comparison against recent data from fluorescence resonance energy transfer, small-angle X-ray scattering, force spectroscopy and fluorescence correlation transport measurements on sequences up to ∼100 nucleotides long. With this new MC algorithm, we conducted a comprehensive investigation of the entropy landscape of small RNA stem-loop structures. From a simulated ensemble of ∼10(6) equilibrium conformations, the entropy for the initiation of different size RNA hairpin loops was computed and compared against thermodynamic measurements. Starting from seeded hairpin loops, constrained MC simulations were then used to estimate the entropic costs associated with propagation of the stem. The numerical results provide new direct molecular insights into thermodynaimc measurement from macroscopic calorimetry and melting experiments. PMID:26548372

  20. Sigma-1 receptor regulates Tau phosphorylation and axon extension by shaping p35 turnover via myristic acid

    PubMed Central

    Tsai, Shang-Yi A.; Pokrass, Michael J.; Klauer, Neal R.; Nohara, Hiroshi; Su, Tsung-Ping

    2015-01-01

    Dysregulation of cyclin-dependent kinase 5 (cdk5) per relative concentrations of its activators p35 and p25 is implicated in neurodegenerative diseases. P35 has a short t½ and undergoes rapid proteasomal degradation in its membrane-bound myristoylated form. P35 is converted by calpain to p25, which, along with an extended t½, promotes aberrant activation of cdk5 and causes abnormal hyperphosphorylation of tau, thus leading to the formation of neurofibrillary tangles. The sigma-1 receptor (Sig-1R) is an endoplasmic reticulum chaperone that is implicated in neuronal survival. However, the specific role of the Sig-1R in neurodegeneration is unclear. Here we found that Sig-1Rs regulate proper tau phosphorylation and axon extension by promoting p35 turnover through the receptor’s interaction with myristic acid. In Sig-1R–KO neurons, a greater accumulation of p35 is seen, which results from neither elevated transcription of p35 nor disrupted calpain activity, but rather to the slower degradation of p35. In contrast, Sig-1R overexpression causes a decrease of p35. Sig-1R–KO neurons exhibit shorter axons with lower densities. Myristic acid is found here to bind Sig-1R as an agonist that causes the dissociation of Sig-1R from its cognate partner binding immunoglobulin protein. Remarkably, treatment of Sig-1R–KO neurons with exogenous myristic acid mitigates p35 accumulation, diminishes tau phosphorylation, and restores axon elongation. Our results define the involvement of Sig-1Rs in neurodegeneration and provide a mechanistic explanation that Sig-1Rs help maintain proper tau phosphorylation by potentially carrying and providing myristic acid to p35 for enhanced p35 degradation to circumvent the formation of overreactive cdk5/p25. PMID:25964330

  1. Inhibition of non-templated nucleotide addition by DNA polymerases in primer extension using twisted intercalating nucleic acid modified templates.

    PubMed

    Güixens-Gallardo, Pedro; Hocek, Michal; Perlíková, Pavla

    2016-01-15

    A simple and elegant method for inhibition of non-templated nucleotide addition by DNA polymerases and for following DNA 3'-heterogeneity in enzymatic DNA synthesis by primer extension (PEX) is described. When template bearing ortho-twisted intercalating nucleic acid (ortho-TINA) at the 5'-end is used, non-templated nucleotide addition is reduced in both the A- and B-family DNA polymerases (KOD XL, KOD (exo-), Bst 2.0, Therminator, Deep Vent (exo-) and Taq). Formation of a single oligonucleotide product was observed with ortho-TINA modified template and KOD XL, KOD (exo-), Bst 2.0, Deep Vent (exo-) and Taq DNA polymerases. This approach can be applied to the synthesis of both unmodified and base-modified oligonucleotides. PMID:26707394

  2. The Effect of Surface Modification of Aligned Poly-L-Lactic Acid Electrospun Fibers on Fiber Degradation and Neurite Extension

    PubMed Central

    Schaub, Nicholas J.; Le Beux, Clémentine; Miao, Jianjun; Linhardt, Robert J.; Alauzun, Johan G.; Laurencin, Danielle; Gilbert, Ryan J.

    2015-01-01

    The surface of aligned, electrospun poly-L-lactic acid (PLLA) fibers was chemically modified to determine if surface chemistry and hydrophilicity could improve neurite extension from chick dorsal root ganglia. Specifically, diethylenetriamine (DTA, for amine functionalization), 2-(2-aminoethoxy)ethanol (AEO, for alcohol functionalization), or GRGDS (cell adhesion peptide) were covalently attached to the surface of electrospun fibers. Water contact angle measurements revealed that surface modification of electrospun fibers significantly improved fiber hydrophilicity compared to unmodified fibers (p < 0.05). Scanning electron microscopy (SEM) of fibers revealed that surface modification changed fiber topography modestly, with DTA modified fibers displaying the roughest surface structure. Degradation of chemically modified fibers revealed no change in fiber diameter in any group over a period of seven days. Unexpectedly, neurites from chick DRG were longest on fibers without surface modification (1651 ± 488 μm) and fibers containing GRGDS (1560 ± 107 μm). Fibers modified with oxygen plasma (1240 ± 143 μm) or DTA (1118 ± 82 μm) produced shorter neurites than the GRGDS or unmodified fibers, but were not statistically shorter than unmodified and GRGDS modified fibers. Fibers modified with AEO (844 ± 151 μm) were significantly shorter than unmodified and GRGDS modified fibers (p<0.05). Based on these results, we conclude that fiber hydrophilic enhancement alone on electrospun PLLA fibers does not enhance neurite outgrowth. Further work must be conducted to better understand why neurite extension was not improved on more hydrophilic fibers, but the results presented here do not recommend hydrophilic surface modification for the purpose of improving neurite extension unless a bioactive ligand is used. PMID:26340351

  3. NETL - Chemical Looping Reactor

    SciTech Connect

    2013-07-24

    NETL's Chemical Looping Reactor unit is a high-temperature integrated CLC process with extensive instrumentation to improve computational simulations. A non-reacting test unit is also used to study solids flow at ambient temperature. The CLR unit circulates approximately 1,000 pounds per hour at temperatures around 1,800 degrees Fahrenheit.

  4. NETL - Chemical Looping Reactor

    ScienceCinema

    None

    2014-06-26

    NETL's Chemical Looping Reactor unit is a high-temperature integrated CLC process with extensive instrumentation to improve computational simulations. A non-reacting test unit is also used to study solids flow at ambient temperature. The CLR unit circulates approximately 1,000 pounds per hour at temperatures around 1,800 degrees Fahrenheit.

  5. Electrostatic and potential cation-pi forces may guide the interaction of extracellular loop III with Na+ and bile acids for human apical Na+-dependent bile acid transporter.

    PubMed

    Banerjee, Antara; Hussainzada, Naissan; Khandelwal, Akash; Swaan, Peter W

    2008-03-01

    The hASBT (human apical Na(+)-dependent bile acid transporter) constitutes a key target of anti-hypercholesterolaemic therapies and pro-drug approaches; physiologically, hASBT actively reclaims bile acids along the terminal ileum via Na(+) co-transport. Previously, TM (transmembrane segment) 7 was identified as part of the putative substrate permeation pathway using SCAM (substitute cysteine accessibility mutagenesis). In the present study, SCAM was extended through EL3 (extracellular loop 3; residues Arg(254)-Val(286)) that leads into TM7 from the exofacial matrix. Activity of most EL3 mutants was significantly hampered upon cysteine substitution, whereas ten (out of 31) were functionally inactive (<10% activity). Since only E282C lacked plasma membrane expression, EL3 amino acids predominantly fulfill critical functional roles during transport. Oppositely charged membrane-impermeant MTS (methanethiosulfonate) reagents {MTSET [(2-trimethylammonium) ethyl MTS] and MTSES [(2-sulfonatoethyl) MTS]} produced mostly similar inhibition profiles wherein only middle and descending loop segments (residues Thr(267)-Val(286)) displayed significant MTS sensitivity. The presence of bile acid substrate significantly reduced the rates of MTS modification for all MTS-sensitive mutants, suggesting a functional association between EL3 residues and bile acids. Activity assessments at equilibrative [Na(+)] revealed numerous Na(+)-sensitive residues, possibly performing auxiliary functions during transport such as transduction of protein conformational changes during translocation. Integration of these data suggests ligand interaction points along EL3 via electrostatic interactions with Arg(256), Glu(261) and probably Glu(282) and a potential cation-pi interaction with Phe(278). We conclude that EL3 amino acids are essential for hASBT activity, probably as primary substrate interaction points using long-range electrostatic attractive forces. PMID:18028035

  6. Extensive cell migration, axon regeneration and improved function with polysialic acid-modified Schwann cells after spinal cord injury

    PubMed Central

    Ghosh, Mousumi; Tuesta, Luis M.; Puentes, Rocio; Patel, Samik; Melendez, Kiara; Maarouf, Abderrahman El; Rutishauser, Urs; Pearse, Damien Daniel

    2015-01-01

    Schwann cells (SC) implantation after spinal cord injury (SCI) promotes axonal regeneration, remyelination repair and functional recovery. Reparative efficacy, however, may be limited due to the inability of SCs to migrate outward from the lesion-implant site. Altering SC cell surface properties by over-expressing polysialic acid (PSA) has been shown to promote SC migration. In the current study, a SCI contusion was used to evaluate the migration, supraspinal axon growth support and functional recovery associated with polysialyltransferase (PST)-over-expressing SCs (PST-GFP SCs) or controls (GFP SCs). Compared to GFP SCs, which remained confined to the injection site at the injury center, PST-GFP SCs migrated across the lesion:host cord interface for distances of up to 4.4 mm within adjacent host tissue. In addition, with PST-GFP SCs, there was extensive serotonergic and corticospinal axon in-growth within the implants that was limited in the GFP SC controls. The enhanced migration of PST-GFP SCs was accompanied by significant growth of these axons caudal to lesion. Animals receiving PST-GFP SCs exhibited improved functional outcome, both in the open-field and on the gridwalk test, over modest improvements provided by GFP SC controls. The current study for the first time demonstrates that a lack of migration by SC may hinder their reparative benefits and that cell surface overexpression of PSA enhances the ability of implanted SCs to associate with and support the growth of corticospinal axons. These results provide further promise that PSA modified SCs will be a potent reparative approach for SCI. PMID:22460918

  7. Extensive cell migration, axon regeneration, and improved function with polysialic acid-modified Schwann cells after spinal cord injury.

    PubMed

    Ghosh, Mousumi; Tuesta, Luis M; Puentes, Rocio; Patel, Samik; Melendez, Kiara; El Maarouf, Abderrahman; Rutishauser, Urs; Pearse, Damien Daniel

    2012-05-01

    Schwann cell (SC) implantation after spinal cord injury (SCI) promotes axonal regeneration, remyelination repair, and functional recovery. Reparative efficacy, however, may be limited because of the inability of SCs to migrate outward from the lesion-implant site. Altering SC cell surface properties by overexpressing polysialic acid (PSA) has been shown to promote SC migration. In this study, a SCI contusion model was used to evaluate the migration, supraspinal axon growth support, and functional recovery associated with polysialyltransferase (PST)-overexpressing SCs [PST-green fluorescent protein (GFP) SCs] or controls (GFP SCs). Compared with GFP SCs, which remained confined to the injection site at the injury center, PST-GFP SCs migrated across the lesion:host cord interface for distances of up to 4.4 mm within adjacent host tissue. In addition, with PST-GFP SCs, there was extensive serotonergic and corticospinal axon in-growth within the implants that was limited in the GFP SC controls. The enhanced migration of PST-GFP SCs was accompanied by significant growth of these axons caudal to lesion. Animals receiving PST-GFP SCs exhibited improved functional outcome, both in the open-field and on the gridwalk test, beyond the modest improvements provided by GFP SC controls. This study for the first time demonstrates that a lack of migration by SCs may hinder their reparative benefits and that cell surface overexpression of PSA enhances the ability of implanted SCs to associate with and support the growth of corticospinal axons. These results provide further promise that PSA-modified SCs will be a potent reparative approach for SCI. © 2012 Wiley Periodicals, Inc. PMID:22460918

  8. Antibodies to Yeast Phenylalanine Transfer Ribonucleic Acid Are Specific for the Odd Nucleoside Y in the Anticodon Loop

    PubMed Central

    Fuchs, Sara; Aharonov, Aharon; Sela, Michael; Von Der Haar, Friedrich; Cramer, Friedrich

    1974-01-01

    Antibodies with specificity to a single species of tRNA were elicited in a goat by immunization with a glutaraldehyde conjugate of yeast phenylalanine transfer RNA with bovine gamma globulin. The specificity of the antibodies was studied by a radioimmunoassay measuring the direct binding of [3H]tRNAPhe or the inhibition of the binding. The antibodies formed are predominantly directed towards the characteristic highly modified nucleoside Y, which is located right next to the anticodon. The antibodies bind specifically to tRNAPhe, to oligonucleotides derived by enzymatic digestion from the anticodon loop of tRNAPhe, and to the Y nucleoside itself. tRNA species which do not contain Y in their sequences, or tRNAPhe from which the Y base has been excised, do not bind to the antibodies. Yeast tRNAPhe can be separated from other tRNA species with an immunoadsorbent of antibodies to tRNAPhe. PMID:4527666

  9. 77 FR 1455 - Citric Acid and Certain Citrate Salts From the People's Republic of China: Extension of Time...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-10

    ..., 76 FR 37781, 37785 (June 28, 2011). This review covers the period May 1, 2010, through April 30, 2011... International Trade Administration Citric Acid and Certain Citrate Salts From the People's Republic of China... acid and certain citrate salts (``citric acid'') from the People's Republic of China (``PRC'')....

  10. An amino acid residue in the second extracellular loop determines the agonist-dependent tolerance property of the human D3 dopamine receptor.

    PubMed

    Gil-Mast, Sara; Kortagere, Sandhya; Kota, Kokila; Kuzhikandathil, Eldo V

    2013-06-19

    The D3 dopamine receptor is a therapeutic target for treating various nervous system disorders such as schizophrenia, Parkinson's disease, depression, and addictive behaviors. The crystal structure of the D3 receptor bound to an antagonist was recently described; however, the structural features that contribute to agonist-induced conformational changes and signaling properties are not well understood. We have previously described the conformation-dependent tolerance and slow response termination (SRT) signaling properties of the D3 receptor and identified the C147 residue in the second intracellular loop (IL2) of the D3 receptor as important for the tolerance property. Interestingly, while IL2 and the C147 residue, in particular, were important for dopamine- and quinpirole-induced tolerance, this residue did not affect the severe tolerance induced by the high affinity, D3 receptor-selective agonist, PD128907. Here, we used D2/D3 receptor chimeras and site-specific D3 receptor mutants to identify another residue, D187, in the second extracellular loop (EC2) of the human D3 receptor that mediates the tolerance property induced by PD128907, quinpirole, pramipexole, and dopamine. Molecular dynamics simulations confirmed the distinct conformation adopted by D3 receptor during tolerance and suggested that in the tolerant D3 receptor the D187 residue in EC2 forms a salt bridge with the H354 residue in EC3. Indeed, site-directed mutation of the H354 residue resulted in loss of PD1287907-induced tolerance. The mapping of specific amino acid residues that contribute to agonist-dependent conformation changes and D3 receptor signaling properties refines the agonist-bound D3 receptor pharmacophore model which will help develop novel D3 receptor agonists. PMID:23477444

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

    PubMed

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

    2016-06-01

    Streptomycin, an antibiotic used against microbial infections, inhibits the protein synthesis by binding to ribosomal protein S12, encoded by rpsL12 gene, and associated mutations cause streptomycin resistance. A streptomycin resistant, Lysinibacillus sphaericus DSLS5 (MIC >300 µg/mL for streptomycin), was isolated from a marine sponge (Tedania anhelans). The characterisation of rpsL12 gene showed a region having similarity to long terminal repeat sequences of murine lukemia virus which added 13 amino acids for loop formation in RpsL12; in addition, a K56R mutation which corresponds to K43R mutation present in streptomycin-resistant Escherichia coli is also present. The RpsL12 protein was modelled and compared with that of Lysinibacillus boronitolerans, Escherichia coli and Mycobacterium tuberculosis. The modelled proteins docked with streptomycin indicate compound had less affinity. The effect of loop on streptomycin resistance was analysed by constructing three different models of RpsL12 by, (i) removing both loop and mutation, (ii) removing the loop alone while retaining the mutation and (iii) without mutation having loop. The results showed that the presence of loop causes streptomycin resistance (decreases the affinity), and it further enhanced in the presence of mutation at 56th codon. Further study will help in understanding the evolution of streptomycin resistance in organisms. PMID:26198082

  12. Loop-to-loop coupling.

    SciTech Connect

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

    2012-05-01

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

  13. Extension of microwave-accelerated residue-specific acid cleavage to proteins with carbohydrate side chains and disulfide linkages

    NASA Astrophysics Data System (ADS)

    Li, Jinxi; Shefcheck, Kevin; Callahan, John; Fenselau, Catherine

    2008-12-01

    This laboratory has introduced a chemical method for residue-specific protein cleavage and has provided a preliminary assessment of the suitability of microwave-accelerated acid cleavage as a proteomic tool. This report is a continuing assessment of the fate of common protein modifications in microwave-accelerated acid cleavage. We have examined the cleavage of ribonuclease A and the related N-linked glycoprotein ribonuclease B, and the O-linked glycoprotein alpha crystallin A chain, using MALDI-TOF and LC-ESI-MS to identify the peptide products. RNase A and B each contains four disulfide bonds, and the addition of a reducing reagent, such as dithiothreitol, was found to be required to achieve efficient acidic proteolysis. The linkage of the glycosidic group to the asparagine side chain in ribonuclease B was found not to be cleaved by brief microwave treatment in 12.5% acetic acid. The distribution of the heterogeneous carbohydrate side chain in the glycopeptide products of acid cleavage was compared to that of the glycopeptide products of tryptic digestion. Hydrolysis within the carbohydrate chain itself is minimal under the conditions used. The O-linked side chain on alpha crystalline A was found to be cleaved during acid cleavage of the protein.

  14. MYB elongation is regulated by the nucleic acid binding of NFκB p50 to the intronic stem-loop region.

    PubMed

    Pereira, Lloyd A; Hugo, Honor J; Malaterre, Jordane; Huiling, Xu; Sonza, Secondo; Cures, Alina; Purcell, Damian F J; Ramsland, Paul A; Gerondakis, Steven; Gonda, Thomas J; Ramsay, Robert G

    2015-01-01

    MYB transcriptional elongation is regulated by an attenuator sequence within intron 1 that has been proposed to encode a RNA stem loop (SLR) followed by a polyU tract. We report that NFκBp50 can bind the SLR polyU RNA and promote MYB transcriptional elongation together with NFκBp65. We identified a conserved lysine-rich motif within the Rel homology domain (RHD) of NFκBp50, mutation of which abrogated the interaction of NFκBp50 with the SLR polyU and impaired NFκBp50 mediated MYB elongation. We observed that the TAR RNA-binding region of Tat is homologous to the NFκBp50 RHD lysine-rich motif, a finding consistent with HIV Tat acting as an effector of MYB transcriptional elongation in an SLR dependent manner. Furthermore, we identify the DNA binding activity of NFκBp50 as a key component required for the SLR polyU mediated regulation of MYB. Collectively these results suggest that the MYB SLR polyU provides a platform for proteins to regulate MYB and reveals novel nucleic acid binding properties of NFκBp50 required for MYB regulation. PMID:25853889

  15. Effects of postweaning administration of conjugated linoleic acid on development of obesity in nescient basic helix-loop-helix 2 knockout mice.

    PubMed

    Kim, Yoo; Kim, Daeyoung; Good, Deborah J; Park, Yeonhwa

    2015-06-01

    Conjugated linoleic acid (CLA) has been reported to prevent body weight gain and fat accumulation in part by improving physical activity in mice. However, the effects of postweaning administration of CLA on the development of obesity later in life have not yet been demonstrated. The current study investigated the role of postweaning CLA treatment on skeletal muscle energy metabolism in genetically induced inactive adult-onset obese model, nescient basic helix-loop-helix 2 knockout (N2KO) mice. Four-week-old male N2KO and wild type mice were fed either control or a CLA-containing diet (0.5%) for 4 weeks, and then CLA was withdrawn and control diet provided to all mice for the following 8 weeks. Postweaning CLA supplementation in wild type animals, but not N2KO mice, may activate AMP-activated protein kinase (AMPK) and peroxisome proliferator-activated receptor-δ (PPARδ) as well as promote desensitization of phosphatase and tensin homologue (PTEN) and sensitization of protein kinase B (AKT) at threonine 308 in gastrocnemius skeletal muscle, improving voluntary activity and glucose homeostasis. We suggest that postweaning administration of CLA may in part stimulate the underlying molecular targets involved in muscle energy metabolism to reduce weight gain in normal animals, but not in the genetically induced inactive adult-onset animal model. PMID:25976059

  16. Shelf-life extension of vacuum-packaged meat from pheasant (Phasianus colchicus) by lactic acid treatment.

    PubMed

    Pfeifer, Agathe; Smulders, Frans J M; Paulsen, Peter

    2014-07-01

    We investigated the influence of lactic acid treatment of pheasant meat before vacuum-packaged storage of 3, 7, and 10 d at +6°C on microbiota and pH. Breast muscle samples were collected from carcasses of slaughtered as well as from hunted (shot) wild pheasants. Immersion of meat samples in 3% (wt/wt) lactic acid for 60 s effectuated a significant drop in pH of approximately 0.5 to 0.7 units, which remained during the entire storage period. In parallel, total aerobic counts of such treated and stored samples were on an average 1.5 to 1.7 log units lower than in non-acid-treated samples. Similar results were found for Enterobacteriaceae. A significant decrease in pH was measured at d 7 and 10 in the acid-treated samples in comparison with the untreated ones. In summary, the immersion of pheasant breast meat cuts in dilute lactic acid significantly reduced microbiota during vacuum-packed storage, even at slight temperature abuse conditions. PMID:24864290

  17. Single amino acid insertions in extracellular loop 2 of Bombyx mori ABCC2 disrupt its receptor function for Bacillus thuringiensis Cry1Ab and Cry1Ac but not Cry1Aa toxins.

    PubMed

    Tanaka, Shiho; Miyamoto, Kazuhisa; Noda, Hiroaki; Endo, Haruka; Kikuta, Shingo; Sato, Ryoichi

    2016-04-01

    In a previous report, seven Cry1Ab-resistant strains were identified in the silkworm, Bombyx mori; these strains were shown to have a tyrosine insertion at position 234 in extracellular loop 2 of the ABC transporter C2 (BmABCC2). This insertion was confirmed to destroy the receptor function of BmABCC2 and confer the strains resistance against Cry1Ab and Cry1Ac. However, these strains were susceptible to Cry1Aa. In this report, we examined the mechanisms of the loss of receptor function of the transporter by expressing mutations in Sf9 cells. After replacement of one or two of the five amino acid residues in loop 2 of the susceptible BmABCC2 gene [BmABCC2_S] with alanine, cells still showed susceptibility, retaining the receptor function. Five mutants with single amino acid insertions at position 234 in BmABCC2 were also generated, resulting in loop 2 having six amino acids, which corresponds to replacing the tyrosine insertion in the resistant BmABCC2 gene [BmABCC2_R(+(234)Y)] with another amino acid. All five mutants exhibited loss of function against Cry1Ab and Cry1Ac. These results suggest that the amino acid sequence in loop 2 is less important than the loop size (five vs. six amino acids) or loop structure for Cry1Ab and Cry1Ac activity. Several domain-swapped mutant toxins were then generated among Cry1Aa, Cry1Ab, and Cry1Ac, which are composed of three domains. Swapped mutants containing domain II of Cry1Ab or Cry1Ac did not kill Sf9 cells expressing BmABCC2_R(+(234)Y), suggesting that domain II of the Cry toxin is related to the interaction with the receptor function of BmABCC2. This also suggests that different reactions against Bt-toxins in some B. mori strains, that is, Cry1Ab resistance or Cry1Aa susceptibility, are attributable to structural differences in domain II of Cry1A toxins. PMID:26928903

  18. 76 FR 47146 - Citric Acid and Certain Citrate Salts From the People's Republic of China: Extension of Time...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-04

    ... Antidumping and Countervailing Duty Administrative Reviews and Deferral of Administrative Review, 75 FR 37759... of the Antidumping Duty Order; and Partial Rescission of Administrative Review, 76 FR 34048 (June 10... International Trade Administration Citric Acid and Certain Citrate Salts From the People's Republic of...

  19. 75 FR 74684 - 1-Hydroxyethylidene-1, 1-Diphosphonic Acid From the People's Republic of China: Extension of the...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-12-01

    ..., 2010. \\1\\ See Initiation of Antidumping and Countervailing Duty Administrative Reviews, 75 FR 29976... International Trade Administration 1-Hydroxyethylidene-1, 1-Diphosphonic Acid From the People's Republic of...: Effective Date: December 1, 2010. FOR FURTHER INFORMATION CONTACT: Shawn Higgins, AD/CVD Operations,...

  20. Extensive amino acid polymorphism at the pgm locus is consistent with adaptive protein evolution in Drosophila melanogaster.

    PubMed Central

    Verrelli, B C; Eanes, W F

    2000-01-01

    PGM plays a central role in the glycolytic pathway at the branch point leading to glycogen metabolism and is highly polymorphic in allozyme studies of many species. We have characterized the nucleotide diversity across the Pgm gene in Drosophila melanogaster and D. simulans to investigate the role that protein polymorphism plays at this crucial metabolic branch point shared with several other enzymes. Although D. melanogaster and D. simulans share common allozyme mobility alleles, we find these allozymes are the result of many different amino acid changes at the nucleotide level. In addition, specific allozyme classes within species contain several amino acid changes, which may explain the absence of latitudinal clines for PGM allozyme alleles, the lack of association of PGM allozymes with the cosmopolitan In(3L)P inversion, and the failure to detect differences between PGM allozymes in functional studies. We find a significant excess of amino acid polymorphisms within D. melanogaster when compared to the complete absence of fixed replacements with D. simulans. There is also strong linkage disequilibrium across the 2354 bp of the Pgm locus, which may be explained by a specific amino acid haplotype that is high in frequency yet contains an excess of singleton polymorphisms. Like G6pd, Pgm shows strong evidence for a branch point enzyme that exhibits adaptive protein evolution. PMID:11102370

  1. Trifluoracetic acid-assisted crystallization of vitamin B12 results in protonation of the phosphate group of the nucleotide loop: insight into the influence of crystal packing forces on vitamin B12 structures.

    PubMed

    Marino, Nadia; Rabideau, Amy E; Doyle, Robert P

    2011-01-01

    In the course of experiments concerning our ongoing project on the synthesis of vitamin B(12) (cyanocobalamin, CNCbl) bioconjugates for drug-delivery purposes, we observed the formation of well-shaped red parallelepipeds from a concentrated aqueous solution of the HPLC-purified vitamin. The X-ray structural investigation (MoK(α)) at 98 K on these crystals revealed a CNCbl-TFA salt of formula [CNCbl(H)](TFAc)·14H(2)O (1, where TFA = trifluoracetic acid; TFAc(-) = trifluoracetate anion), in which a proton transfer from the trifluoracetic acid to the phosphate-O4P oxygen atoms is observed. 1 crystallizes in the standard orthorhombic P2(1)2(1)2(1) space group, a = 16.069(2) Å, b = 20.818(2) Å, c = 24.081(2) Å, Z = 4. The final full-matrix least-squares refinements on F(2) converged with R(1) = 4.1% for the 18957 significant reflections, a very low crystallographic residual for cobalamins, which facilitated the analysis of the extensive network of hydrogen bonds within the lattice. To the best of our knowledge, this is the first cobalamin structure to show protonation of the phosphate group of the cobalamin nucleotide loop. In this work, the crystal structure of 1 is analyzed and compared to other CNCbls reported in the literature, namely, CNCbl·3PrOH·12H(2)O (2, PrOH = propyl alcohol), CNCbl·acetone·20H(2)O (3), CNCbl·2LiCl·10.2H(2)O (4), and CNCbl·2KCl·10.6H(2)O (5). The analysis confirmed that protonation of the phosphate leaves the major CNCbl structural parameters unaffected, so that 1 can be considered an "unmodified" Cbl solvate. However, comparison between 1-5 led to interesting findings. In fact, although the cobalt(III) coordination sphere in 1-5 is similar, significant differences could be noted in the upward fold angle of the corrin macrocycle, a parameter commonly related to the steric hindrance of the axial lower "α" nucleotide-base and the electronic trans influence of the upper "β" substituent. This suggests that crystal-packing forces may

  2. Effect of season on fatty acid and terpene profiles of milk from Greek sheep raised under a semi-extensive production system.

    PubMed

    Papaloukas, Loukas; Sinapis, Efthymios; Arsenos, George; Kyriakou, George; Basdagianni, Zoitsa

    2016-08-01

    The objective of the study was to investigate the effect of season on the fatty acid and terpene composition in ewe milk. A total of 760 samples of bulk sheep milk were collected during winter (147 samples), spring (314 samples) and summer (299 samples) of 2011, from 90 commercial farms of dairy sheep from the prefecture of Grevena, Greece. Regarding fatty acid composition, summer samples had higher concentrations of α-linolenic acid, cis-9, trans 11- CLA, trans-11, C18 : 1 and PUFAs but lower content of saturated fatty acids particularly C12 : 0, C14 : 0 and C16 : 0. The winter milk had the lowest content of terpenes, in particular sesquiterpenes, compared to spring and summer milk. The terpene profile of milk samples, in all three seasons, revealed the presence of monoterpenes: a-pinene, b-pinene and D-limonene, especially with a higher frequency of appearance in summer. The most common and abundant sesquiterpenes found in milk samples were β-caryophyllene and α-caryophyllene with a higher frequency of appearance in summer. In conclusion, the available pastures in semi-extensive farming systems can contribute to the production of high quality milk. PMID:27600974

  3. New Compstatin Peptides Containing N-Terminal Extensions and Non-Natural Amino Acids Exhibit Potent Complement Inhibition and Improved Solubility Characteristics

    PubMed Central

    2015-01-01

    Compstatin peptides are complement inhibitors that bind and inhibit cleavage of complement C3. Peptide binding is enhanced by hydrophobic interactions; however, poor solubility promotes aggregation in aqueous environments. We have designed new compstatin peptides derived from the W4A9 sequence (Ac-ICVWQDWGAHRCT-NH2, cyclized between C2 and C12), based on structural, computational, and experimental studies. Furthermore, we developed and utilized a computational framework for the design of peptides containing non-natural amino acids. These new compstatin peptides contain polar N-terminal extensions and non-natural amino acid substitutions at positions 4 and 9. Peptides with α-modified non-natural alanine analogs at position 9, as well as peptides containing only N-terminal polar extensions, exhibited similar activity compared to W4A9, as quantified via ELISA, hemolytic, and cell-based assays, and showed improved solubility, as measured by UV absorbance and reverse-phase HPLC experiments. Because of their potency and solubility, these peptides are promising candidates for therapeutic development in numerous complement-mediated diseases. PMID:25494040

  4. Involvement of hydrophobic amino acid residues in C7-C8 loop of Aspergillus oryzae hydrophobin RolA in hydrophobic interaction between RolA and a polyester.

    PubMed

    Tanaka, Takumi; Tanabe, Hiroki; Uehara, Kenji; Takahashi, Toru; Abe, Keietsu

    2014-01-01

    Hydrophobins are amphipathic secretory proteins with eight conserved cysteine residues and are ubiquitous among filamentous fungi. The Cys3-Cys4 and Cys7-Cys8 loops of hydrophobins are thought to form hydrophobic segments involved in adsorption of hydrophobins on hydrophobic surfaces. When the fungus Aspergillus oryzae is grown in a liquid medium containing the polyester polybutylene succinate-co-adipate (PBSA), A. oryzae produces hydrophobin RolA, which attaches to PBSA. Here, we analyzed the kinetics of RolA adsorption on PBSA by using a PBSA pull-down assay and a quartz crystal microbalance (QCM) with PBSA-coated electrodes. We constructed RolA mutants in which hydrophobic amino acids in the two loops were replaced with serine, and we examined the kinetics of mutant adsorption on PBSA. QCM analysis revealed that mutants with replacements in the Cys7-Cys8 loop had lower affinity than wild-type RolA for PBSA, suggesting that this loop is involved in RolA adsorption on PBSA. PMID:25273133

  5. Activity of Colistin in Combination with Meropenem, Tigecycline, Fosfomycin, Fusidic Acid, Rifampin or Sulbactam against Extensively Drug-Resistant Acinetobacter baumannii in a Murine Thigh-Infection Model

    PubMed Central

    Wang, Xiumei; Cong, Yulong

    2016-01-01

    Few effective therapeutic options are available for treating severe infections caused by extensively drug-resistant Acinetobacter baumannii (XDR-AB). Using a murine thigh-infection model, we examined the in vivo efficacy of colistin in combination with meropenem, tigecycline, fosfomycin, fusidic acid, rifampin, or sulbactam against 12 XDR-AB strains. Colistin, tigecycline, rifampin, and sulbactam monotherapy significantly decreased bacterial counts in murine thigh infections compared with those observed in control mice receiving no treatment. Colistin was the most effective agent tested, displaying bactericidal activity against 91.7% of strains at 48 h post-treatment. With strains showing a relatively low minimum inhibitory concentration (MIC) for meropenem (MIC ≤ 32 mg/L), combination therapy with colistin plus meropenem caused synergistic inhibition at both 24 h and 48 h post-treatment. However, when the meropenem MIC was ≥64 mg/L, meropenem did not significantly alter the efficacy of colistin. The addition of rifampin and fusidic acid significantly improved the efficacy of colistin, showing a synergistic effect in 100% and 58.3% of strains after 24 h of treatment, respectively, while the addition of tigecycline, fosfomycin, or sulbactam did not show obvious synergistic activity. No clear differences in activities were observed between colistin-rifampin and colistin-fusidic acid combination therapy with most strains. Overall, our in vivo study showed that administering colistin in combination with rifampin or fusidic acid is more efficacious in treating XDR-AB infections than other combinations. The colistin-meropenem combination may be another appropriate option if the MIC is ≤32 mg/L. Further clinical studies are urgently needed to confirm the relevance of these findings. PMID:27315107

  6. Rollercoaster Loop Shapes

    ERIC Educational Resources Information Center

    Pendrill, Ann-Marie

    2005-01-01

    Many modern rollercoasters feature loops. Although textbook loops are often circular, real rollercoaster loops are not. In this paper, we look into the mathematical description of various possible loop shapes, as well as their riding properties. We also discuss how a study of loop shapes can be used in physics education.

  7. Rollercoaster loop shapes

    NASA Astrophysics Data System (ADS)

    Pendrill, Ann-Marie

    2005-11-01

    Many modern rollercoasters feature loops. Although textbook loops are often circular, real rollercoaster loops are not. In this paper, we look into the mathematical description of various possible loop shapes, as well as their riding properties. We also discuss how a study of loop shapes can be used in physics education.

  8. The effect of 6 versus 9 years of zoledronic acid treatment in osteoporosis: a randomized second extension to the HORIZON-Pivotal Fracture Trial (PFT).

    PubMed

    Black, Dennis M; Reid, Ian R; Cauley, Jane A; Cosman, Felicia; Leung, Ping Chung; Lakatos, Peter; Lippuner, Kurt; Cummings, Steven R; Hue, Trisha F; Mukhopadhyay, Amitava; Tan, Monique; Aftring, R Paul; Eastell, Richard

    2015-05-01

    While bisphosphonates reduce fracture risk over 3 to 5 years, the optimal duration of treatment is uncertain. In a randomized extension study (E1) of the Health Outcomes and Reduced Incidence with Zoledronic Acid Once Yearly-Pivotal Fracture Trial (HORIZON-PFT), zoledronic acid (ZOL) 5 mg annually for 6 years showed maintenance of bone mineral density (BMD), decrease in morphometric vertebral fractures, and a modest reduction in bone turnover markers (BTMs) compared with discontinuation after 3 years. To investigate the longer-term efficacy and safety of ZOL, a second extension (E2) was conducted to 9 years in which women on ZOL for 6 years in E1 were randomized to either ZOL (Z9) or placebo (Z6P3) for 3 additional years. In this multicenter, randomized, double-blind study, 190 women were randomized to Z9 (n = 95) and Z6P3 (n = 95). The primary endpoint was change in total hip BMD at year 9 vs. year 6 in Z9 compared with Z6P3. Other secondary endpoints included fractures, BTMs, and safety. From year 6 to 9, the mean change in total hip BMD was -0.54% in Z9 vs. -1.31% in Z6P3 (difference 0.78%; 95% confidence interval [CI]: -0.37%, 1.93%; p = 0.183). BTMs showed small, non-significant increases in those who discontinued after 6 years compared with those who continued for 9 years. The number of fractures was low and did not significantly differ by treatment. While generally safe, there was a small increase in cardiac arrhythmias (combined serious and non-serious) in the Z9 group but no significant imbalance in other safety parameters. The results suggest almost all patients who have received six annual ZOL infusions can stop medication for up to 3 years with apparent maintenance of benefits. PMID:25545380

  9. Combined effects of thermosonication and slightly acidic electrolyzed water on the microbial quality and shelf life extension of fresh-cut kale during refrigeration storage.

    PubMed

    Mansur, Ahmad Rois; Oh, Deog-Hwan

    2015-10-01

    This study evaluated the efficacy of thermosonication combined with slightly acidic electrolyzed water (SAcEW) on the shelf life extension of fresh-cut kale during storage at 4 and 7 °C. Each kale (10 ± 0.2 g) was inoculated to contain approximately 6 log CFU/g of Listeria monocytogenes. Each inoculated or uninoculated samples was dip treated at 40 °C for 3 min with deionized water, thermosonication (400 W/L), SAcEW (5 mg/L), sodium chlorite (SC; 100 mg/L), sodium hypochlorite (SH; 100 mg/L), and thermosonication combined with SAcEW, SC, and SH (TS + SAcEW, TS + SC, and TS + SH, respectively). Growths of L. monocytogenes and spoilage microorganisms and changes in sensory (overall visual quality, browning, and off-odour) were evaluated. The results show that lag time and specific growth rate of each microorganism were not significantly (P > 0.05) affected by treatment and storage temperature. Exceeding the unacceptable counts of spoilage microorganisms did not always result in adverse effects on sensory attributes. This study suggests that TS + SAcEW was the most effective method to prolong the shelf life of kale with an extension of around 4 and 6 days at 4 and 7 °C, respectively, and seems to be a promising method for the shelf life extension of fresh produce. PMID:26187840

  10. Water Stream "Loop-the-Loop"

    ERIC Educational Resources Information Center

    Jefimenko, Oleg

    1974-01-01

    Discusses the design of a modified loop-the-loop apparatus in which a water stream is used to illustrate centripetal forces and phenomena of high-velocity hydrodynamics. Included are some procedures of carrying out lecture demonstrations. (CC)

  11. Extended loop representation of quantum gravity

    SciTech Connect

    Di Bartolo, C. ); Gambini, R.; Griego, J. )

    1995-01-15

    A new representation of quantum gravity is developed. This formulation is based on an extension of the group of loops. The enlarged group that we call the extended loop group behaves locally as an infinite dimensional Lie group. Quantum gravity can be realized on the state space of extended loop-dependent wave functions. The extended representation generalizes the loop representation and contains this representation as a particular case. The resulting diffeomorphism and Hamiltonian constraints take a very simple form and allow us to apply functional methods and simplify the loop calculus. In particular we show that the constraints are linear in the momenta. The nondegenerate solutions known in the loop representation are also solutions of the constraints in the new representation. An approach to the regularization problems associated with the formal calculus is performed. We show that the solutions are generalized knot invariants, smooth in the extended variables, and any framing is unnecessary.

  12. Gluing hexagons at three loops

    NASA Astrophysics Data System (ADS)

    Basso, Benjamin; Goncalves, Vasco; Komatsu, Shota; Vieira, Pedro

    2016-06-01

    We perform extensive three-loop tests of the hexagon bootstrap approach for structure constants in planar N = 4 SYM theory. We focus on correlators involving two BPS operators and one non-BPS operator in the so-called SL (2) sector. At three loops, such correlators receive wrapping corrections from mirror excitations flowing in either the adjacent or the opposing channel. Amusingly, we find that the first type of correction coincides exactly with the leading wrapping correction for the spectrum (divided by the one-loop anomalous dimension). We develop an efficient method for computing the second type of correction for operators with any spin. The results are in perfect agreement with the recently obtained three-loop perturbative data by Chicherin, Drummond, Heslop, Sokatchev [2] and by Eden [3]. We also derive the integrand for general multi-particle wrapping corrections, which turns out to take a remarkably simple form. As an application we estimate the loop order at which various new physical effects are expected to kick-in.

  13. OPE for super loops

    NASA Astrophysics Data System (ADS)

    Sever, Amit; Vieira, Pedro; Wang, Tianheng

    2011-11-01

    We extend the Operator Product Expansion for Null Polygon Wilson loops to the Mason-Skinner-Caron-Huot super loop dual to non MHV gluon amplitudes. We explain how the known tree level amplitudes can be promoted into an infinite amount of data at any loop order in the OPE picture. As an application, we re-derive all one loop NMHV six gluon amplitudes by promoting their tree level expressions. We also present some new all loops predictions for these amplitudes.

  14. The preprocessed doacross loop

    NASA Technical Reports Server (NTRS)

    Saltz, Joel H.; Mirchandaney, Ravi

    1990-01-01

    Dependencies between loop iterations cannot always be characterized during program compilation. Doacross loops typically make use of a-priori knowledge of inter-iteration dependencies to carry out required synchronizations. A type of doacross loop is proposed that allows the scheduling of iterations of a loop among processors without advance knowledge of inter-iteration dependencies. The method proposed for loop iterations requires that parallelizable preprocessing and postprocessing steps be carried out during program execution.

  15. Fast flux locked loop

    DOEpatents

    Ganther, Jr., Kenneth R.; Snapp, Lowell D.

    2002-09-10

    A flux locked loop for providing an electrical feedback signal, the flux locked loop employing radio-frequency components and technology to extend the flux modulation frequency and tracking loop bandwidth. The flux locked loop of the present invention has particularly useful application in read-out electronics for DC SQUID magnetic measurement systems, in which case the electrical signal output by the flux locked loop represents an unknown magnetic flux applied to the DC SQUID.

  16. Phenylacetic Acid Is ISR Determinant Produced by Bacillus fortis IAGS162, Which Involves Extensive Re-modulation in Metabolomics of Tomato to Protect against Fusarium Wilt

    PubMed Central

    Akram, Waheed; Anjum, Tehmina; Ali, Basharat

    2016-01-01

    Bacillus fortis IAGS162 has been previously shown to induce systemic resistance in tomato plants against Fusarium wilt disease. In the first phase of current study, the ISR determinant was isolated from extracellular metabolites of this bacterium. ISR bioassays combined with solvent extraction, column chromatography and GC/MS analysis proved that phenylacetic acid (PAA) was the potential ISR determinant that significantly ameliorated Fusarium wilt disease of tomato at concentrations of 0.1 and 1 mM. In the second phase, the biochemical basis of the induced systemic resistance (ISR) under influence of PAA was elucidated by performing non-targeted whole metabolomics through GC/MS analysis. Tomato plants were treated with PAA and fungal pathogen in various combinations. Exposure to PAA and subsequent pathogen challenge extensively re-modulated tomato metabolic networks along with defense related pathways. In addition, various phenylpropanoid precursors were significantly up-regulated in treatments receiving PAA. This work suggests that ISR elicitor released from B. fortis IAGS162 contributes to resistance against fungal pathogens through dynamic reprogramming of plant pathways that are functionally correlated with defense responses. PMID:27148321

  17. Phenylacetic Acid Is ISR Determinant Produced by Bacillus fortis IAGS162, Which Involves Extensive Re-modulation in Metabolomics of Tomato to Protect against Fusarium Wilt.

    PubMed

    Akram, Waheed; Anjum, Tehmina; Ali, Basharat

    2016-01-01

    Bacillus fortis IAGS162 has been previously shown to induce systemic resistance in tomato plants against Fusarium wilt disease. In the first phase of current study, the ISR determinant was isolated from extracellular metabolites of this bacterium. ISR bioassays combined with solvent extraction, column chromatography and GC/MS analysis proved that phenylacetic acid (PAA) was the potential ISR determinant that significantly ameliorated Fusarium wilt disease of tomato at concentrations of 0.1 and 1 mM. In the second phase, the biochemical basis of the induced systemic resistance (ISR) under influence of PAA was elucidated by performing non-targeted whole metabolomics through GC/MS analysis. Tomato plants were treated with PAA and fungal pathogen in various combinations. Exposure to PAA and subsequent pathogen challenge extensively re-modulated tomato metabolic networks along with defense related pathways. In addition, various phenylpropanoid precursors were significantly up-regulated in treatments receiving PAA. This work suggests that ISR elicitor released from B. fortis IAGS162 contributes to resistance against fungal pathogens through dynamic reprogramming of plant pathways that are functionally correlated with defense responses. PMID:27148321

  18. Analyses of inter- and intra-patient variation in the V3 loop of the HIV-1 envelope protein

    SciTech Connect

    Korber, B.; Myers, G. ); Wolinsky, S. . Medical School)

    1991-09-17

    The third hypervariable domain of the HIV-1 gp120 envelope protein (V3) has been the focus of intensive sequencing efforts. To date, nearly one thousand V3 loop sequences have been stored in the HIV sequence database. Studies have revealed that the V3 loop elicits potent type-specific immune responses, and that it plays a significant role in cell tropism and fusion . The immunogenic tip of the loop can serve as a type-specific neutralizing antibody epitope, as well as a cytotoxic T-cell epitope. A helper T-cell epitope that lies within the amino terminal half of the V3 loop has also been characterized. Despite the richness of the immunologic response to this region, its potential for variation makes it an elusive target for vaccine design. Analyses of sibling sequence sets (sets of viral sequences derived from one person) show that multiple forms of the immunogenic tip of the loop are found within most HIV-1 infected individuals. Viral V3 sequences obtained from epidemiologically unlinked individuals from North America and Europe show extensive variation. However, some amino acid positions distributed throughout the V3 loop are highly conserved, and there is also conservation of the charge class of amino acid able to occupy certain positions relative to the tip of the loop. By contrast, the sequences obtained from many countries throughout the African continent reveal that V3 is a remarkably fluid region with few absolute constraints on the nature of the amino acids that can occupy most positions in the loop. The high degree of heterogeneity in this region is particularly striking in view of its contribution to biologically important viral functions.

  19. The Effect of 3 Versus 6 Years of Zoledronic Acid Treatment of Osteoporosis: A Randomized Extension to the HORIZON-Pivotal Fracture Trial (PFT)

    PubMed Central

    Black, Dennis M; Reid, Ian R; Boonen, Steven; Bucci-Rechtweg, Christina; Cauley, Jane A; Cosman, Felicia; Cummings, Steven R; Hue, Trisha F; Lippuner, Kurt; Lakatos, Peter; Leung, Ping Chung; Man, Zulema; Martinez, Ruvie Lou Maria; Tan, Monique; Ruzycky, Mary Ellen; Su, Guoqin; Eastell, Richard

    2012-01-01

    Zoledronic acid 5 mg (ZOL) annually for 3 years reduces fracture risk in postmenopausal women with osteoporosis. To investigate long-term effects of ZOL on bone mineral density (BMD) and fracture risk, the Health Outcomes and Reduced Incidence with Zoledronic acid Once Yearly–Pivotal Fracture Trial (HORIZON-PFT) was extended to 6 years. In this international, multicenter, double-blind, placebo-controlled extension trial, 1233 postmenopausal women who received ZOL for 3 years in the core study were randomized to 3 additional years of ZOL (Z6, n = 616) or placebo (Z3P3, n = 617). The primary endpoint was femoral neck (FN) BMD percentage change from year 3 to 6 in the intent-to-treat (ITT) population. Secondary endpoints included other BMD sites, fractures, biochemical bone turnover markers, and safety. In years 3 to 6, FN-BMD remained constant in Z6 and dropped slightly in Z3P3 (between-treatment difference = 1.04%; 95% confidence interval 0.4 to 1.7; p = 0.0009) but remained above pretreatment levels. Other BMD sites showed similar differences. Biochemical markers remained constant in Z6 but rose slightly in Z3P3, remaining well below pretreatment levels in both. New morphometric vertebral fractures were lower in the Z6 (n = 14) versus Z3P3 (n = 30) group (odds ratio = 0.51; p = 0.035), whereas other fractures were not different. Significantly more Z6 patients had a transient increase in serum creatinine >0.5 mg/dL (0.65% versus 2.94% in Z3P3). Nonsignificant increases in Z6 of atrial fibrillation serious adverse events (2.0% versus 1.1% in Z3P3; p = 0.26) and stroke (3.1% versus 1.5% in Z3P3; p = 0.06) were seen. Postdose symptoms were similar in both groups. Reports of hypertension were significantly lower in Z6 versus Z3P3 (7.8% versus 15.1%, p < 0.001). Small differences in bone density and markers in those who continued versus those who stopped treatment suggest residual effects, and therefore, after 3 years of annual ZOL, many patients may discontinue

  20. AGRICULTURAL EXTENSION.

    ERIC Educational Resources Information Center

    FARQUHAR, R.N.

    AUSTRALIAN AGRICULTURAL EXTENSION HAS LONG EMPHASIZED TECHNICAL ADVISORY SERVICE AT THE EXPENSE OF THE SOCIOECONOMIC ASPECTS OF FARM PRODUCTION AND FARM LIFE. ONLY IN TASMANIA HAS FARM MANAGEMENT BEEN STRESSED. DEMANDS FOR THE WHOLE-FARM APPROACH HAVE PRODUCED A TREND TOWARD GENERALISM FOR DISTRICT OFFICERS IN MOST STATES. THE FEDERAL GOVERNMENT,…

  1. Blind loop syndrome

    MedlinePlus

    Blind loop syndrome occurs when digested food slows or stops moving through part of the intestines. This ... The name of this condition refers to the "blind loop" formed by part of the intestine that ...

  2. A study of FM threshold extension techniques

    NASA Technical Reports Server (NTRS)

    Arndt, G. D.; Loch, F. J.

    1972-01-01

    The characteristics of three postdetection threshold extension techniques are evaluated with respect to the ability of such techniques to improve the performance of a phase lock loop demodulator. These techniques include impulse-noise elimination, signal correlation for the detection of impulse noise, and delta modulation signal processing. Experimental results from signal to noise ratio data and bit error rate data indicate that a 2- to 3-decibel threshold extension is readily achievable by using the various techniques. This threshold improvement is in addition to the threshold extension that is usually achieved through the use of a phase lock loop demodulator.

  3. Diagnostic fragment-ion-based and extension strategy coupled to DFIs intensity analysis for identification of chlorogenic acids isomers in Flos Lonicerae Japonicae by HPLC-ESI-MS(n).

    PubMed

    Zhang, Jia-Yu; Zhang, Qian; Li, Ning; Wang, Zi-Jian; Lu, Jian-Qiu; Qiao, Yan-Jiang

    2013-01-30

    A method of modified diagnostic fragment-ion-based extension strategy (DFIBES) coupled to DFIs (diagnostic fragmentation ions) intensity analysis was successfully established to simultaneously screen and identify the chlorogenic acids (CGAs) in Flos Lonicerae Japonicae (FLJ) by HPLC-ESI-MS(n). DFIs, such as m/z 191 [quinic acid-H](-), m/z 179 [caffeic acid-H](-) and m/z 173 [quinic acid-H-H2O](-) were determined or proposed from the fragmentation patterns analysis of corresponding reference substances for every chemical family of CGAs. A "structure extension" method was then proposed based on the well-demonstrated fragmentation patterns and was successively applied into the rapid screening of CGAs in FLJ. Considering that substitution isomerism is a common phenomenon, a full ESI-MS(n) fragmentation analysis according to the intensity of DFIs has been performed to identify the CGA isomers. Based on the DFIs and intensity analysis, 41 peaks attributed to CGAs including 4 caffeoylquinic acids (CQA), 7 CQA glycosides, 6 dicaffeoylquinic acids (DiCQA), 10 DiCQA glycosides, 1 tricaffeoylquinic acids (TriCQA), 4p-coumaroylquinic acids (pCoQA), 3 feruloylquinic acids (FQA) and 6 caffeoylferuloylquinic acids (CFQA) were identified preliminarily in a 65-min chromatographic run. It was the first time to systematically report the presence of CGAs in FLJ, especially for CQA glycosides, DiCQA glycosides, TriCQA, pCoQA and CFQA. All the results indicated that the method of developed DFIBES coupled to DFIs analysis was feasible, reliable and universal for screening and identifying the constituents with the same carbon skeletons especially the isomeric compounds from the complex extract of TCMs. PMID:23597880

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

    PubMed

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

    2010-08-01

    Grapevine fanleaf virus (GFLV) and Arabis mosaic virus (ArMV) from the genus Nepovirus, family Secoviridae, cause a severe degeneration of grapevines. GFLV and ArMV have a bipartite RNA genome and are transmitted specifically by the ectoparasitic nematodes Xiphinema index and Xiphinema diversicaudatum, respectively. The transmission specificity of both viruses maps to their respective RNA2-encoded coat protein (CP). To further delineate the GFLV CP determinants of transmission specificity, three-dimensional (3D) homology structure models of virions and CP subunits were constructed based on the crystal structure of Tobacco ringspot virus, the type member of the genus Nepovirus. The 3D models were examined to predict amino acids that are exposed at the external virion surface, highly conserved among GFLV isolates but divergent between GFLV and ArMV. Five short amino acid stretches that matched these topographical and sequence conservation criteria were selected and substituted in single and multiple combinations by their ArMV counterparts in a GFLV RNA2 cDNA clone. Among the 21 chimeric RNA2 molecules engineered, transcripts of only three of them induced systemic plant infection in the presence of GFLV RNA1. Nematode transmission assays of the three viable recombinant viruses showed that swapping a stretch of (i) 11 residues in the betaB-betaC loop near the icosahedral 3-fold axis abolished transmission by X. index but was insufficient to restore transmission by X. diversicaudatum and (ii) 7 residues in the betaE-alphaB loop did not interfere with transmission by the two Xiphinema species. This study provides new insights into GFLV CP determinants of nematode transmission. PMID:20519403

  5. A tree-loop duality relation at two loops and beyond

    NASA Astrophysics Data System (ADS)

    Bierenbaum, Isabella; Catani, Stefano; Draggiotis, Petros; Rodrigo, Germán

    2010-10-01

    The duality relation between one-loop integrals and phase-space integrals, developed in a previous work, is extended to higher-order loops. The duality relation is realized by a modification of the customary + i0 prescription of the Feynman propagators, which compensates for the absence of the multiple-cut contributions that appear in the Feynman tree theorem. We rederive the duality theorem at one-loop order in a form that is more suitable for its iterative extension to higher-loop orders. We explicitly show its application to two-and three-loop scalar master integrals, and we discuss the structure of the occurring cuts and the ensuing results in detail.

  6. Kinematic calibration of manipulators with closed loop actuated joints

    NASA Technical Reports Server (NTRS)

    Everett, Louis J.; Lin, C. Y.

    1988-01-01

    A method for performing forward kinematic calibration of manipulators having one or more closed-loop-actuated joints is presented. The technique is an extension of algorithms designed for open-loop jointed manipulators. The calibration is equivalent to minimizing an objective function subject to constraints. The objective function is taken as the integral of end-effector position and orientation error. The constraints arise from the closed-loop mechanisms present in the manipulator.

  7. Loops and trees

    NASA Astrophysics Data System (ADS)

    Caron-Huot, S.

    2011-05-01

    We investigate relations between loop and tree amplitudes in quantum field theory that involve putting on-shell some loop propagators. This generalizes the so-called Feynman tree theorem which is satisfied at 1-loop. Exploiting retarded boundary conditions, we give a generalization to ℓ-loop expressing the loops as integrals over the on-shell phase space of exactly ℓ particles. We argue that the corresponding integrand for ℓ > 2 does not involve the forward limit of any physical tree amplitude, except in planar gauge theories. In that case we explicitly construct the relevant physical amplitude. Beyond the planar limit, abandoning direct integral representations, we propose that loops continue to be determined implicitly by the forward limit of physical connected trees, and we formulate a precise conjecture along this line. Finally, we set up technology to compute forward amplitudes in supersymmetric theories, in which specific simplifications occur.

  8. Monoclonal IgM rheumatoid factors bind IgG at a discontinuous epitope comprised of amino acid loops from heavy-chain constant-region domains 2 and 3.

    PubMed Central

    Artandi, S E; Calame, K L; Morrison, S L; Bonagura, V R

    1992-01-01

    A combination of site-directed mutagenesis and exon exchange has been used to further define the structure on IgG recognized by monoclonal IgM rheumatoid factors (RFs) from patients with Waldenstrom macroglobulinemia. Most of these RFs bound IgG1, -2, and -4 but not IgG3. For these RFs, His-435 is a critical residue for binding and replacing it with arginine, the residue present in IgG3, destroys or reduces RF binding. However, additional polymorphic sequences in both the heavy-chain constant-region domains (CH) 2 and 3 are important for RF binding. Among the important residues in CH2 are amino acids 252-254 and 309-311, which are conserved among IgG isotypes and comprise two loops of amino acids on the surface of the domain. Therefore, at least three regions, two from CH2 and one from CH3, contribute significantly to the epitope recognized by the RFs. Although this epitope contains many of the same residues as the staphylococcal protein A binding site on IgG, the binding specificities of staphylococcal protein A and monoclonal RFs are not identical. Sera from patients with rheumatoid arthritis contain antibodies directed not only at this epitope but also at other sites on IgG. Images PMID:1370358

  9. Laminated BEAM loops

    NASA Astrophysics Data System (ADS)

    Danisch, Lee A.

    1996-10-01

    BEAM sensors include treated loops of optical fiber that modulate optical throughput with great sensitivity and linearity, in response to curvature of the loop out of its plane. This paper describes BEAM sensors that have two loops treated in opposed fashion, hermetically sealed in flexible laminations. The sensors include an integrated optoelectronics package that extracts curvature information from the treated portion of the loops while rejecting common mode errors. The laminated structure is used to sense various parameters including displacement, force, pressure, flow, and acceleration.

  10. Observational Evidence for Loop-Loop Interaction

    NASA Astrophysics Data System (ADS)

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

    2004-01-01

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

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

    SciTech Connect

    CHERTKOV, MICHAEL; CHERNYAK, VLADIMIR

    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-Free energy variational approach of [3].

  12. The AP-3 adaptor complex mediates sorting of yeast and mammalian PQ-loop-family basic amino acid transporters to the vacuolar/lysosomal membrane

    PubMed Central

    Llinares, Elisa; Barry, Abdoulaye Oury; André, Bruno

    2015-01-01

    The limiting membrane of lysosomes in animal cells and that of the vacuole in yeast include a wide variety of transporters, but little is known about how these proteins reach their destination membrane. The mammalian PQLC2 protein catalyzes efflux of basic amino acids from the lysosome, and the similar Ypq1, −2, and −3 proteins of yeast perform an equivalent function at the vacuole. We here show that the Ypq proteins are delivered to the vacuolar membrane via the alkaline phosphatase (ALP) trafficking pathway, which requires the AP-3 adaptor complex. When traffic via this pathway is deficient, the Ypq proteins pass through endosomes from where Ypq1 and Ypq2 properly reach the vacuolar membrane whereas Ypq3 is missorted to the vacuolar lumen via the multivesicular body pathway. When produced in yeast, PQLC2 also reaches the vacuolar membrane via the ALP pathway, but tends to sort to the vacuolar lumen if AP-3 is defective. Finally, in HeLa cells, inhibiting the synthesis of an AP-3 subunit also impairs sorting of PQLC2 to lysosomes. Our results suggest the existence of a conserved AP-3-dependent trafficking pathway for proper delivery of basic amino acid exporters to the yeast vacuole and to lysosomes of human cells. PMID:26577948

  13. Fairy “tails”: flexibility and function of intrinsically disordered extensions in the photosynthetic world

    PubMed Central

    Thieulin-Pardo, Gabriel; Avilan, Luisana; Kojadinovic, Mila; Gontero, Brigitte

    2015-01-01

    Intrinsically Disordered Proteins (IDPs), or protein fragments also called Intrinsically Disordered Regions (IDRs), display high flexibility as the result of their amino acid composition. They can adopt multiple roles. In globular proteins, IDRs are usually found as loops and linkers between secondary structure elements. However, not all disordered fragments are loops: some proteins bear an intrinsically disordered extension at their C- or N-terminus, and this flexibility can affect the protein as a whole. In this review, we focus on the disordered N- and C-terminal extensions of globular proteins from photosynthetic organisms. Using the examples of the A2B2-GAPDH and the α Rubisco activase isoform, we show that intrinsically disordered extensions can help regulate their “host” protein in response to changes in light, thereby participating in photosynthesis regulation. As IDPs are famous for their large number of protein partners, we used the examples of the NAC, bZIP, TCP, and GRAS transcription factor families to illustrate the fact that intrinsically disordered extremities can allow a protein to have an increased number of partners, which directly affects its regulation. Finally, for proteins from the cryptochrome light receptor family, we describe how a new role for the photolyase proteins may emerge by the addition of an intrinsically disordered extension, while still allowing the protein to absorb blue light. This review has highlighted the diverse repercussions of the disordered extension on the regulation and function of their host protein and outlined possible future research avenues. PMID:26042223

  14. Arabidopsis triphosphate tunnel metalloenzyme2 is a negative regulator of the salicylic acid-mediated feedback amplification loop for defense responses.

    PubMed

    Ung, Huoi; Moeder, Wolfgang; Yoshioka, Keiko

    2014-10-01

    The triphosphate tunnel metalloenzyme (TTM) superfamily represents a group of enzymes that is characterized by their ability to hydrolyze a range of tripolyphosphate substrates. Arabidopsis (Arabidopsis thaliana) encodes three TTM genes, AtTTM1, AtTTM2, and AtTTM3. Although AtTTM3 has previously been reported to have tripolyphosphatase activity, recombinantly expressed AtTTM2 unexpectedly exhibited pyrophosphatase activity. AtTTM2 knockout mutant plants exhibit an enhanced hypersensitive response, elevated pathogen resistance against both virulent and avirulent pathogens, and elevated accumulation of salicylic acid (SA) upon infection. In addition, stronger systemic acquired resistance compared with wild-type plants was observed. These enhanced defense responses are dependent on SA, PHYTOALEXIN-DEFICIENT4, and NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1. Despite their enhanced pathogen resistance, ttm2 plants did not display constitutively active defense responses, suggesting that AtTTM2 is not a conventional negative regulator but a negative regulator of the amplification of defense responses. The transcriptional suppression of AtTTM2 by pathogen infection or treatment with SA or the systemic acquired resistance activator benzothiadiazole further supports this notion. Such transcriptional regulation is conserved among TTM2 orthologs in the crop plants soybean (Glycine max) and canola (Brassica napus), suggesting that TTM2 is involved in immunity in a wide variety of plant species. This indicates the possible usage of TTM2 knockout mutants for agricultural applications to generate pathogen-resistant crop plants. PMID:25185123

  15. Na(+),K(+)-ATPase isoform selectivity for digitalis-like compounds is determined by two amino acids in the first extracellular loop.

    PubMed

    Weigand, Karl M; Laursen, Mette; Swarts, Herman G P; Engwerda, Anthonius H J; Prüfert, Christian; Sandrock, Julia; Nissen, Poul; Fedosova, Natalya U; Russel, Frans G M; Koenderink, Jan B

    2014-12-15

    Digitalis-like compounds (DLCs) comprise a diverse group of molecules characterized by a cis-trans-cis ring-fused steroid core linked to a lactone. They have been used in the treatment of different medical problems including heart failure, where their inotropic effect on heart muscle is attributed to potent Na(+),K(+)-ATPase inhibition. Their application as drugs, however, has declined in recent past years due to their small safety margin. Since human Na(+),K(+)-ATPase is represented by four different isoforms expressed in a tissue-specific manner, one of the possibilities to improve the therapeutic index of DLCs is to exploit and amend their isoform selectivity. Here, we aimed to reveal the determinants of selectivity of the ubiquitously expressed α1 isoform and the more restricted α2 isoform toward several well-known DLCs and their hydrogenated forms. Using baculovirus to express various mutants of the α2 isoform, we were able to link residues Met(119) and Ser(124) to differences in affinity between the α1 and α2 isoforms to ouabain, dihydro-ouabain, digoxin, and dihydro-digoxin. We speculate that the interactions between these amino acids and DLCs affect the initial binding of these DLCs. Also, we observed isoform selectivity for DLCs containing no sugar groups. PMID:25361285

  16. The 5-amino acid N-terminal extension of non-sulfated drosulfakinin II is a unique target to generate novel agonists.

    PubMed

    Leander, M; Heimonen, J; Brocke, T; Rasmussen, M; Bass, C; Palmer, G; Egle, J; Mispelon, M; Berry, K; Nichols, R

    2016-09-01

    The ability to design agonists that target peptide signaling is a strategy to delineate underlying mechanisms and influence biology. A sequence that uniquely characterizes a peptide provides a distinct site to generate novel agonists. Drosophila melanogaster sulfakinin encodes non-sulfated drosulfakinin I (nsDSK I; FDDYGHMRF-NH2) and nsDSK II (GGDDQFDDYGHMRF-NH2). Drosulfakinin is typical of sulfakinin precursors, which are conserved throughout invertebrates. Non-sulfated DSK II is structurally related to DSK I, however, it contains a unique 5-residue N-terminal extension; drosulfakinins signal through G-protein coupled receptors, DSK-R1 and DSK-R2. Drosulfakinin II distinctly influences adult and larval gut motility and larval locomotion; yet, its structure-activity relationship was unreported. We hypothesized substitution of an N-terminal extension residue may alter nsDSK II activity. By targeting the extension we identified, not unexpectedly, analogs mimicking nsDSK II, yet, surprisingly, we also discovered novel agonists with increased (super) and opposite (protean) effects. We determined [A3] nsDSK II increased larval gut contractility rather than, like nsDSK II, decrease it. [N4] nsDSK II impacted larval locomotion, although nsDSK II was inactive. In adult gut, [A1] nsDSK II, [A2] nsDSKII, and [A3] nsDSK II mimicked nsDSK II, and [A4] nsDSK II and [A5] nsDSK II were more potent; [N3] nsDSK II and [N4] nsDSK II mimicked nsDSK II. This study reports nsDSK II signals through DSK-R2 to influence gut motility and locomotion, identifying a novel role for the N-terminal extension in sulfakinin biology and receptor activation; it also led to the discovery of nsDSK II structural analogs that act as super and protean agonists. PMID:27397853

  17. Extensive esterification of adrenal C19-delta 5-sex steroids to long-chain fatty acids in the ZR-75-1 human breast cancer cell line

    SciTech Connect

    Poulin, R.; Poirier, D.; Merand, Y.; Theriault, C.; Belanger, A.; Labrie, F.

    1989-06-05

    Estrogen-sensitive human breast cancer cells (ZR-75-1) were incubated with the 3H-labeled adrenal C19-delta 5-steroids dehydroepiandrosterone (DHEA) and its fully estrogenic derivative, androst-5-ene-3 beta,17 beta-diol (delta 5-diol) for various time intervals. When fractionated by solvent partition, Sephadex LH-20 column chromatography and silica gel TLC, the labeled cell components were largely present (40-75%) in three highly nonpolar, lipoidal fractions. Mild alkaline hydrolysis of these lipoidal derivatives yielded either free 3H-labeled DHEA or delta 5-diol. The three lipoidal fractions cochromatographed with the synthetic DHEA 3 beta-esters, delta 5-diol 3 beta (or 17 beta)-monoesters and delta 5-diol 3 beta,17 beta-diesters of long-chain fatty acids. DHEA and delta 5-diol were mainly esterified to saturated and mono-unsaturated fatty acids. For delta 5-diol, the preferred site of esterification of the fatty acids is the 3 beta-position while some esterification also takes place at the 17 beta-position. Time course studies show that ZR-75-1 cells accumulate delta 5-diol mostly (greater than 95%) as fatty acid mono- and diesters while DHEA is converted to delta 5-diol essentially as the esterified form. Furthermore, while free C19-delta 5-steroids rapidly diffuse out of the cells after removal of the precursor (3H)delta 5-diol, the fatty acid ester derivatives are progressively hydrolyzed, and DHEA and delta 5-diol thus formed are then sulfurylated prior to their release into the culture medium. The latter process however is rate-limited, since new steady-state levels of free steroids and fatty acid esters are rapidly reached and maintained for extended periods of time after removal of precursor, thus maintaining minimal concentrations of intracellular steroids.

  18. Extension of a PBPK model for ethylene glycol and glycolic acid to include the competitive formation and clearance of metabolites associated with kidney toxicity in rats and humans

    SciTech Connect

    Corley, R.A.; Saghir, S.A.; Bartels, M.J.; Hansen, S.C.; Creim, J.; McMartin, K.E.; Snellings, W.M.

    2011-02-01

    A previously developed PBPK model for ethylene glycol and glycolic acid was extended to include glyoxylic acid, oxalic acid, and the precipitation of calcium oxalate that is associated with kidney toxicity in rats and humans. The development and evaluation of the PBPK model was based upon previously published pharmacokinetic studies coupled with measured blood and tissue partition coefficients and rates of in vitro metabolism of glyoxylic acid to oxalic acid, glycine and other metabolites using primary hepatocytes isolated from male Wistar rats and humans. Precipitation of oxalic acid with calcium in the kidneys was assumed to occur only at concentrations exceeding the thermodynamic solubility product for calcium oxalate. This solubility product can be affected by local concentrations of calcium and other ions that are expressed in the model using an ion activity product estimated from toxicity studies such that calcium oxalate precipitation would be minimal at dietary exposures below the NOAEL for kidney toxicity in the sensitive male Wistar rat. The resulting integrated PBPK predicts that bolus oral or dietary exposures to ethylene glycol would result in typically 1.4-1.6-fold higher peak oxalate levels and 1.6-2-fold higher AUC's for calcium oxalate in kidneys of humans as compared with comparably exposed male Wistar rats over a dose range of 1-1000 mg/kg. The converse (male Wistar rats predicted to have greater oxalate levels in the kidneys than humans) was found for inhalation exposures although no accumulation of calcium oxalate is predicted to occur until exposures are well in excess of the theoretical saturated vapor concentration of 200 mg/m{sup 3}. While the current model is capable of such cross-species, dose, and route-of-exposure comparisons, it also highlights several areas of potential research that will improve confidence in such predictions, especially at low doses relevant for most human exposures.

  19. ZmPUMP encodes a fully functional monocot plant uncoupling mitochondrial protein whose affinity to fatty acid is increased with the introduction of a His pair at the second matrix loop

    SciTech Connect

    Favaro, Regiane Degan; Borecky, Jiri; Colombi, Debora; Maia, Ivan G. . E-mail: igmaia@ibb.unesp.br

    2006-05-26

    Uncoupling proteins (UCPs) are specialized mitochondrial transporter proteins that uncouple respiration from ATP synthesis. In this study, cDNA encoding maize uncoupling protein (ZmPUMP) was expressed in Escherichia coli and recombinant ZmPUMP reconstituted in liposomes. ZmPUMP activity was associated with a linoleic acid (LA)-mediated H{sup +} efflux with K {sub m} of 56.36 {+-} 0.27 {mu}M and V {sub max} of 66.9 {mu}mol H{sup +} min{sup -1} (mg prot){sup -1}. LA-mediated H{sup +} fluxes were sensitive to ATP inhibition with K {sub i} of 2.61 {+-} 0.36 mM (at pH 7.2), a value similar to those for dicot UCPs. ZmPUMP was also used to investigate the importance of a histidine pair present in the second matrix loop of mammalian UCP1 and absent in plant UCPs. ZmPUMP with introduced His pair (Lys155His and Ala157His) displayed a 1.55-fold increase in LA-affinity while its activity remained unchanged. Our data indicate conserved properties of plant UCPs and suggest an enhancing but not essential role of the histidine pair in proton transport mechanism.

  20. Thermal power loops

    NASA Technical Reports Server (NTRS)

    Gottschlich, Joseph M.; Richter, Robert

    1991-01-01

    The concept of a thermal power loop (TPL) to transport thermal power over relatively large distances is presented as an alternative to heat pipes and their derivatives. The TPL is compared to heat pipes, and capillary pumped loops with respect to size, weight, conservation of thermal potential, start-up, and 1-g testing capability. Test results from a proof of feasibility demonstrator at the NASA JPL are discussed. This analysis demonstrates that the development of specific thermal power loops will result in substantial weight and cost savings for many spacecraft.

  1. Extensive Reduction of Cell Viability and Enhanced Matrix Production in Pseudomonas aeruginosa PAO1 Flow Biofilms Treated with a d-Amino Acid Mixture

    PubMed Central

    Sanchez, Zoe; Tani, Akio

    2013-01-01

    Treatment of Pseudomonas aeruginosa PAO1 flow biofilms with a d-amino acid mixture caused significant reductions in cell biomass by 75% and cell viability by 71%. No biofilm disassembly occurred, and matrix production increased by 30%, thereby providing a thick protective cover for remaining viable or persister cells. PMID:23220960

  2. Natively Unstructured Loops Differ from Other Loops

    PubMed Central

    Schlessinger, Avner; Liu, Jinfeng; Rost, Burkhard

    2007-01-01

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

  3. Introduction to Loop Heat Pipes

    NASA Technical Reports Server (NTRS)

    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.

  4. On a fractional representation approach to closed-loop experiment design

    NASA Technical Reports Server (NTRS)

    Hansen, Fred R.; Franklin, Gene F.

    1988-01-01

    A plant model, based on a fractional representation of the loop, which is uniquely suited to the closed-loop experiment design problem, is proposed. The advantage of this model is that it substitutes an open-loop problem (for which there has been extensive work) for the original-closed loop problem. The results of Monte Carlo simulations which support the utility of this approach are included.

  5. Mutational analysis of sclerostin shows importance of the flexible loop and the cystine-knot for Wnt-signaling inhibition.

    PubMed

    Boschert, Verena; van Dinther, Maarten; Weidauer, Stella; van Pee, Katharina; Muth, Eva-Maria; Ten Dijke, Peter; Mueller, Thomas D

    2013-01-01

    The cystine-knot containing protein Sclerostin is an important negative regulator of bone growth and therefore represents a promising therapeutic target. It exerts its biological task by inhibiting the Wnt (wingless and int1) signaling pathway, which participates in bone formation by promoting the differentiation of mesenchymal stem cells to osteoblasts. The core structure of Sclerostin consists of three loops with the first and third loop (Finger 1 and Finger 2) forming a structured β-sheet and the second loop being unstructured and highly flexible. Biochemical data showed that the flexible loop is important for binding of Sclerostin to Wnt co-receptors of the low-density lipoprotein related-protein family (LRP), by interacting with the Wnt co-receptors LRP5 or -6 it inhibits Wnt signaling. To further examine the structural requirements for Wnt inhibition, we performed an extensive mutational study within all three loops of the Sclerostin core domain involving single and multiple mutations as well as truncation of important regions. By this approach we could confirm the importance of the second loop and especially of amino acids Asn92 and Ile94 for binding to LRP6. Based on a Sclerostin variant found in a Turkish family suffering from Sclerosteosis we generated a Sclerostin mutant with cysteines 84 and 142 exchanged thereby removing the third disulfide bond of the cystine-knot. This mutant binds to LRP6 with reduced binding affinity and also exhibits a strongly reduced inhibitory activity against Wnt1 thereby showing that also elements outside the flexible loop are important for inhibition of Wnt by Sclerostin. Additionally, we examined the effect of the mutations on the inhibition of two different Wnt proteins, Wnt3a and Wnt1. We could detect clear differences in the inhibition of these proteins, suggesting that the mechanism by which Sclerostin antagonizes Wnt1 and Wnt3a is fundamentally different. PMID:24312339

  6. Combining Long-Term Watershed Monitoring at Buck Creek with Spatially Extensive Ecosystem Data to Understand the Processes of Acid Rain Effects and Recovery

    NASA Astrophysics Data System (ADS)

    Lawrence, G. B.; Ross, D. S.; Sullivan, T. J.; McDonnell, T. C.; Bailey, S. W.; Dukett, J. E.

    2014-12-01

    The Buck Creek Monitoring Watershed, in the western Adirondack Region of New York, has provided long-term data back to 1982 for tracking acid rain effects and recovery, and for supporting fundamental research on environmental change. At Buck Creek, monitoring acidic deposition effects as they worsened, then diminished, has advanced our understanding of key biogeochemical processes such as Al mobilization. Although Al mobilization has been one of the primary adverse effects of acidic deposition, in the recovery phase it is now affecting terrestrial and aquatic ecosystems in new ways that could be both positive and negative, as soils and surface waters respond to further declines in acidic deposition. Using stream Al measurements from Buck Creek over varying seasons and flows, a new index, the base cation surplus (BCS), was developed to account for dissolved organic carbon (DOC) effects on the relationship between ANC and inorganic Al. Mobilization of inorganic Al, the form toxic to biota, occurs below a BCS of zero, regardless of DOC concentrations. Soil and stream data from Adirondack surveys showed that a BCS value of zero corresponds to a soil base saturation value in the B horizon of approximately 12%. Additional Adirondack survey work indicated that, where sugar maple stands grew in soils with base saturation values below 12%, seedling regeneration was nearly zero, suggesting a link between Al mobilization and impairment of tree regeneration. In recovering Adirondack lakes, the BCS was also used to show that increasing trends in DOC were accelerating decreases of inorganic Al beyond what would be expected from the increasing trends of ANC. Similar decreases of inorganic Al in Buck Creek, were coupled with increases in organic Al concentrations, which resulted in no trend in total Al concentrations despite a strong increase in pH. Sampling of Buck Creek soils in 1997, and again in 2009-2010, indicated a substantial decrease in forest floor exchangeable Al, of

  7. Extensive impact of saturated fatty acids on metabolic and cardiovascular profile in rats with diet-induced obesity: a canonical analysis

    PubMed Central

    2013-01-01

    Background Although hypercaloric interventions are associated with nutritional, endocrine, metabolic, and cardiovascular disorders in obesity experiments, a rational distinction between the effects of excess adiposity and the individual roles of dietary macronutrients in relation to these disturbances has not previously been studied. This investigation analyzed the correlation between ingested macronutrients (including sucrose and saturated and unsaturated fatty acids) plus body adiposity and metabolic, hormonal, and cardiovascular effects in rats with diet-induced obesity. Methods Normotensive Wistar-Kyoto rats were submitted to Control (CD; 3.2 Kcal/g) and Hypercaloric (HD; 4.6 Kcal/g) diets for 20 weeks followed by nutritional evaluation involving body weight and adiposity measurement. Metabolic and hormonal parameters included glycemia, insulin, insulin resistance, and leptin. Cardiovascular analysis included systolic blood pressure profile, echocardiography, morphometric study of myocardial morphology, and myosin heavy chain (MHC) protein expression. Canonical correlation analysis was used to evaluate the relationships between dietary macronutrients plus adiposity and metabolic, hormonal, and cardiovascular parameters. Results Although final group body weights did not differ, HD presented higher adiposity than CD. Diet induced hyperglycemia while insulin and leptin levels remained unchanged. In a cardiovascular context, systolic blood pressure increased with time only in HD. Additionally, in vivo echocardiography revealed cardiac hypertrophy and improved systolic performance in HD compared to CD; and while cardiomyocyte size was unchanged by diet, nuclear volume and collagen interstitial fraction both increased in HD. Also HD exhibited higher relative β-MHC content and β/α-MHC ratio than their Control counterparts. Importantly, body adiposity was weakly associated with cardiovascular effects, as saturated fatty acid intake was directly associated with most

  8. Wilson-loop instantons

    NASA Technical Reports Server (NTRS)

    Lee, Kimyeong; Holman, Richard; Kolb, Edward W.

    1987-01-01

    Wilson-loop symmetry breaking is considered on a space-time of the form M4 x K, where M4 is a four-dimensional space-time and K is an internal space with nontrivial and finite fundamental group. It is shown in a simple model that the different vacua obtained by breaking a non-Abelian gauge group by Wilson loops are separated in the space of gauge potentials by a finite energy barrier. An interpolating gauge configuration is then constructed between these vacua and shown to have minimum energy. Finally some implications of this construction are discussed.

  9. Automatic one-loop calculations with Sherpa+OpenLoops

    NASA Astrophysics Data System (ADS)

    Cascioli, F.; Höche, S.; Krauss, F.; Maierhöfer, P.; Pozzorini, S.; Siegert, F.

    2014-06-01

    We report on the OpenLoops generator for one-loop matrix elements and its application to four-lepton production in association with up to one jet. The open loops algorithm uses a numerical recursion to construct the numerator of one-loop Feynman diagrams as functions of the loop momentum. In combination with tensor integrals this results in a highly efficient and numerically stable matrix element generator. In order to obtain a fully automated setup for the simulation of next-to-leading order scattering processes we interfaced OpenLoops to the Sherpa Monte Carlo event generator.

  10. Synergistic Effect of Slightly Acidic Electrolyzed Water and Ultrasound at Mild Heat Temperature in Microbial Reduction and Shelf-Life Extension of Fresh-Cut Bell Pepper.

    PubMed

    Luo, Ke; Oh, Deog-Hwan

    2015-09-01

    The objectives of this study were to evaluate the effect of combined treatments (slightly acidic electrolyzed water (SAEW), ultrasound (US), or mild heat (60°C)) on the growth of Listeria monocytogenes and Salmonella enterica serovar Typhimurium in fresh-cut bell pepper, and the shelf-life and sensory quality (color and texture) were followed during storage at 4°C and 25°C. An additional 0.65, 1.72, and 2.70 log CFU/g reduction was achieved by heat treatments at 60°C for 1 min for DW, SAEW, and SAEW+US, respectively. Regardless of the type of pathogen, the combined treatment (SAEW+US+60°C) achieved a significantly (p < 0.05) longer lag time in all treatment groups. This combined treatment also prolonged the shelf-life of bell pepper up to 8 days and 30 h for the storage at 4°C and 25°C, respectively. There was also no significant difference in the color and hardness of treated (SAEW+US+60°C) bell pepper from that of control during the storage. This new hurdle approach is thus expected to improve the microbial safety of bell peppers during storage and distribution. PMID:26032362

  11. Livermore Compiler Analysis Loop Suite

    2013-03-01

    LCALS is designed to evaluate compiler optimizations and performance of a variety of loop kernels and loop traversal software constructs. Some of the loop kernels are pulled directly from "Livermore Loops Coded in C", developed at LLNL (see item 11 below for details of earlier code versions). The older suites were used to evaluate floating-point performances of hardware platforms prior to porting larger application codes. The LCALS suite is geared toward assissing C++ compiler optimizationsmore » and platform performance related to SIMD vectorization, OpenMP threading, and advanced C++ language features. LCALS contains 20 of 24 loop kernels from the older Livermore Loop suites, plus various others representative of loops found in current production appkication codes at LLNL. The latter loops emphasize more diverse loop constructs and data access patterns than the others, such as multi-dimensional difference stencils. The loops are included in a configurable framework, which allows control of compilation, loop sampling for execution timing, which loops are run and their lengths. It generates timing statistics for analysis and comparing variants of individual loops. Also, it is easy to add loops to the suite as desired.« less

  12. Livermore Compiler Analysis Loop Suite

    SciTech Connect

    Hornung, R. D.

    2013-03-01

    LCALS is designed to evaluate compiler optimizations and performance of a variety of loop kernels and loop traversal software constructs. Some of the loop kernels are pulled directly from "Livermore Loops Coded in C", developed at LLNL (see item 11 below for details of earlier code versions). The older suites were used to evaluate floating-point performances of hardware platforms prior to porting larger application codes. The LCALS suite is geared toward assissing C++ compiler optimizations and platform performance related to SIMD vectorization, OpenMP threading, and advanced C++ language features. LCALS contains 20 of 24 loop kernels from the older Livermore Loop suites, plus various others representative of loops found in current production appkication codes at LLNL. The latter loops emphasize more diverse loop constructs and data access patterns than the others, such as multi-dimensional difference stencils. The loops are included in a configurable framework, which allows control of compilation, loop sampling for execution timing, which loops are run and their lengths. It generates timing statistics for analysis and comparing variants of individual loops. Also, it is easy to add loops to the suite as desired.

  13. [Prediction of short loops in the proteins with internal disorder].

    PubMed

    Deriusheva, E I; Galzitskaia, O V; Serdiuk, I N

    2008-01-01

    New possibility of the FoldUnfold program for prediction of short disordered regions (loops), which appears by using the short window width (3 amino acid residues), was described. For three representatives of the proteins G family the FoldUnfold program predicted almost all short loops and yield results are well compatible with the X-ray structure data. We have classified the loops predicted in the protein Ras-p21 structure in two types. In the first type, loops have high values of the Debye-Waller factor typical of the so-called functional loops (flexible loops). In the other type, loops have lower values of the Debye-Waller factor and can be considered as loops connecting secondary structure elements (rigid loops). When the results of prediction with the use of our program are compared with the results of other programs (PONDR, RONN, DisEMBL, PreLINK, IUPred, GlobPlot 2, FoldIndex), it is seen that the first enables far better prediction of short loop positions. Use of FoldUnfold for ubiquitin-like domain h-PLIC-2 allows to resolve such task as definition of boundary between the structured and unstructured regions in proteins with a big portion of disordered regions. The FoldUnfold program defines a clear boundary between the structured and unstructured regions at amino acid residues 30-31,whereas each of the other programs outlines the boundary from the 28-th amino acid residues through the 70th. PMID:19140328

  14. Loops: Twisting and Scaling

    NASA Astrophysics Data System (ADS)

    Walsh, R. W.

    2004-01-01

    Loop-like structures are the fundamental magnetic building blocks of the solar atmosphere. Recent space-based EUV and X-ray satellite observations (from Yohkoh SOHO and TRACE) have challenged the view that these features are simply static gravitationally stratified plasma pipes. Rather it is now surmised that each loop may consist of a bundle of fine plasma threads that are twisted around one another and can brighten independently. This invited review will outline the latest developments in ""untangling"" the topology of these features through three dimensional magnetohydrodynamic modelling and how their properties are being deduced through spectroscopic observations coupled to theoretical scaling laws. In particular recent interest has centred on how the observed thermal profile along loops can be employed as a tool to diagnose any localised energy input to the structure and hence constrain the presence of a particular coronal heating mechanism. The dynamic nature of loops will be highlighted and the implications of superior resolution plasma thread observations (whether spatial temporal or spectral) from future space missions (SolarB STEREO SDO and Solar Orbiter) will be discussed.

  15. RNA in the Loop

    PubMed Central

    Kung, Johnny T.Y.; Lee, Jeannie T.

    2013-01-01

    Long noncoding RNAs (lncRNAs) have been implicated in a variety of biological roles, particularly as cis or trans gene expression regulators. Reporting recently in Nature, Lai et al. (2013) show that a class of gene-activating lncRNAs combines two gene regulation paradigms: enhancer-directed chromosomal looping and RNA-mediated protein effector recruitment. PMID:23537627

  16. Closing the Loop Sampler.

    ERIC Educational Resources Information Center

    California Integrated Waste Management Board, Sacramento.

    Closing the Loop (CTL) is a science curriculum designed to introduce students to integrated waste management through awareness. This document presents five lesson plans focusing on developing an understanding of natural resources, solid wastes, conservation, and the life of landfills. Contents include: (1) "What Are Natural Resources?"; (2)…

  17. Taxonomy and conformational analysis of loops in proteins.

    PubMed

    Ring, C S; Kneller, D G; Langridge, R; Cohen, F E

    1992-04-01

    We propose a general classification scheme for loops, aperiodic segments of protein structure. In an effort to avoid the geometric complexity created by non-repeating phi psi angles, a morphologic definition that focuses upon the linearity and planarity of loops is utilized. Out of 432 loops (4 to 20 residues in length) extracted from 67 proteins, 205 are classified as linear (straps), 133 as non-linear and planar (omegas), and 86 as non-linear and non-planar (zetas). The remaining 8 are classified as compound loops because they contain a combination of strap, omega, and zeta morphologies. We introduce a structural alphabet as a shorthand notation for describing local conformation. The symbols of this alphabet are based on the virtual dihedral angle joining four consecutive alpha carbons. The notation is used to provide a compact description of loop motifs in phosphate binding and calcium binding proteins. Since similar loop conformations form similar "words", the structural sequence facilitates the search for common structural motifs in a family of loops. Contrary to the view of loops as "random coils", we find loops to have positional preferences for amino acid residues analogous to those previously described for beta-turns. PMID:1569550

  18. COLD TEST LOOP INTEGRATED TEST LOOP RESULTS

    SciTech Connect

    Abraham, TJ

    2003-10-22

    A testing facility (Cold Test Loop) was constructed and operated to demonstrate the efficacy of the Accelerated Waste Retrieval (AWR) Project's planned sluicing approach to the remediation of Silos 1 and 2 at the Fernald Environmental Management Project near Cincinnati, Ohio. The two silos contain almost 10,000 tons of radium-bearing low-level waste, which consists primarily of solids of raffinates from processing performed on ores from the Democratic Republic of Congo (commonly referred to as ''Belgium Congo ores'') for the recovery of uranium. These silos are 80 ft in diameter, 36 ft high to the center of the dome, and 26.75 ft to the top of the vertical side walls. The test facility contained two test systems, each designed for a specific purpose. The first system, the Integrated Test Loop (ITL), a near-full-scale plant including the actual equipment to be installed at the Fernald Site, was designed to demonstrate the sluicing operation and confirm the selection of a slurry pump, the optimal sluicing nozzle operation, and the preliminary design material balance. The second system, the Component Test Loop (CTL), was designed to evaluate many of the key individual components of the waste retrieval system over an extended run. The major results of the initial testing performed during July and August 2002 confirmed that the AWR approach to sluicing was feasible. The ITL testing confirmed the following: (1) The selected slurry pump (Hazleton 3-20 type SHW) performed well and is suitable for AWR application. However, the pump's motor should be upgraded to a 200-hp model and be driven by a 150-hp variable-frequency drive (VFD). A 200-hp VFD is not much more expensive and would allow the pump to operate at full speed. (2) The best nozzle performance was achieved by using 15/16-in. nozzles operated alternately. This configuration appeared to most effectively mine the surrogate. (3) The Solartron densitometer, which was tested as an alternative mass flow measurement

  19. Monte Carlo loop refinement and virtual screening of the thyroid-stimulating hormone receptor transmembrane domain

    PubMed Central

    Ali, M. Rejwan; Latif, Rauf; Davies, Terry F.; Mezei, Mihaly

    2015-01-01

    Metropolis Monte Carlo (MMC) loop refinement has been performed on the three extracellular loops (ECLs) of rhodopsin and opsin-based homology models of the thyroid-stimulating hormone receptor transmembrane domain, a class A type G protein-coupled receptor. The Monte Carlo sampling technique, employing torsion angles of amino acid side chains and local moves for the six consecutive backbone torsion angles, has previously reproduced the conformation of several loops with known crystal structures with accuracy consistently less than 2 Å. A grid-based potential map, which includes van der Waals, electrostatics, hydrophobic as well as hydrogen-bond potentials for bulk protein environment and the solvation effect, has been used to significantly reduce the computational cost of energy evaluation. A modified sigmoidal distance-dependent dielectric function has been implemented in conjunction with the desolvation and hydrogen-bonding terms. A long high-temperature simulation with 2 kcal/mol repulsion potential resulted in extensive sampling of the conformational space. The slow annealing leading to the low-energy structures predicted secondary structure by the MMC technique. Molecular docking with the reported agonist reproduced the binding site within 1.5 Å. Virtual screening performed on the three lowest structures showed that the ligand-binding mode in the inter-helical region is dependent on the ECL conformations. PMID:25012978

  20. A Novel Loop Domain in Superantigens Extends Their T Cell Receptor Recognition Site

    SciTech Connect

    Gunther,S.; Varma, A.; Moza, B.; Kasper, K.; Wyatt, A.; Zhu, P.; Nur-ur Rahman, A.; Li, Y.; Mariuzza, R.; et al.

    2007-01-01

    Superantigens (SAGs) interact with host immune receptors to induce a massive release of inflammatory cytokines that can lead to toxic shock syndrome and death. Bacterial SAGs can be classified into five distinct evolutionary groups. Group V SAGs are characterized by the {alpha}3-{beta}8 loop, a unique {approx}15 amino acid residue extension that is required for optimal T cell activation. Here, we report the X-ray crystal structures of the group V SAG staphylococcal enterotoxin K (SEK) alone and in complex with the TCR hV{beta}5.1 domain. SEK adopts a unique TCR binding orientation relative to other SAG-TCR complexes, which results in the {alpha}3-{beta}8 loop contacting the apical loop of framework region 4, thereby extending the known TCR recognition site of SAGs. These interactions are absolutely required for TCR binding and T cell activation by SEK, and dictate the TCR V{beta} domain specificity of SEK and other group V SAGs.

  1. Monte Carlo loop refinement and virtual screening of the thyroid-stimulating hormone receptor transmembrane domain.

    PubMed

    Ali, M Rejwan; Latif, Rauf; Davies, Terry F; Mezei, Mihaly

    2015-01-01

    Metropolis Monte Carlo (MMC) loop refinement has been performed on the three extracellular loops (ECLs) of rhodopsin and opsin-based homology models of the thyroid-stimulating hormone receptor transmembrane domain, a class A type G protein-coupled receptor. The Monte Carlo sampling technique, employing torsion angles of amino acid side chains and local moves for the six consecutive backbone torsion angles, has previously reproduced the conformation of several loops with known crystal structures with accuracy consistently less than 2 Å. A grid-based potential map, which includes van der Waals, electrostatics, hydrophobic as well as hydrogen-bond potentials for bulk protein environment and the solvation effect, has been used to significantly reduce the computational cost of energy evaluation. A modified sigmoidal distance-dependent dielectric function has been implemented in conjunction with the desolvation and hydrogen-bonding terms. A long high-temperature simulation with 2 kcal/mol repulsion potential resulted in extensive sampling of the conformational space. The slow annealing leading to the low-energy structures predicted secondary structure by the MMC technique. Molecular docking with the reported agonist reproduced the binding site within 1.5 Å. Virtual screening performed on the three lowest structures showed that the ligand-binding mode in the inter-helical region is dependent on the ECL conformations. PMID:25012978

  2. Fractional Loop Group and Twisted K-Theory

    NASA Astrophysics Data System (ADS)

    Hekmati, Pedram; Mickelsson, Jouko

    2010-11-01

    We study the structure of abelian extensions of the group L q G of q-differentiable loops (in the Sobolev sense), generalizing from the case of the central extension of the smooth loop group. This is motivated by the aim of understanding the problems with current algebras in higher dimensions. Highest weight modules are constructed for the Lie algebra. The construction is extended to the current algebra of the supersymmetric Wess-Zumino-Witten model. An application to the twisted K-theory on G is discussed.

  3. Generalized directed loop method for quantum Monte Carlo simulations.

    PubMed

    Alet, Fabien; Wessel, Stefan; Troyer, Matthias

    2005-03-01

    Efficient quantum Monte Carlo update schemes called directed loops have recently been proposed, which improve the efficiency of simulations of quantum lattice models. We propose to generalize the detailed balance equations at the local level during the loop construction by accounting for the matrix elements of the operators associated with open world-line segments. Using linear programming techniques to solve the generalized equations, we look for optimal construction schemes for directed loops. This also allows for an extension of the directed loop scheme to general lattice models, such as high-spin or bosonic models. The resulting algorithms are bounce free in larger regions of parameter space than the original directed loop algorithm. The generalized directed loop method is applied to the magnetization process of spin chains in order to compare its efficiency to that of previous directed loop schemes. In contrast to general expectations, we find that minimizing bounces alone does not always lead to more efficient algorithms in terms of autocorrelations of physical observables, because of the nonuniqueness of the bounce-free solutions. We therefore propose different general strategies to further minimize autocorrelations, which can be used as supplementary requirements in any directed loop scheme. We show by calculating autocorrelation times for different observables that such strategies indeed lead to improved efficiency; however, we find that the optimal strategy depends not only on the model parameters but also on the observable of interest. PMID:15903632

  4. Short loop length and high thermal stability determine genomic instability induced by G-quadruplex-forming minisatellites

    PubMed Central

    Piazza, Aurèle; Adrian, Michael; Samazan, Frédéric; Heddi, Brahim; Hamon, Florian; Serero, Alexandre; Lopes, Judith; Teulade-Fichou, Marie-Paule; Phan, Anh Tuân; Nicolas, Alain

    2015-01-01

    G-quadruplexes (G4) are polymorphic four-stranded structures formed by certain G-rich nucleic acids, with various biological roles. However, structural features dictating their formation and/or functionin vivo are unknown. InS. cerevisiae, the pathological persistency of G4 within the CEB1 minisatellite induces its rearrangement during leading-strand replication. We now show that several other G4-forming sequences remain stable. Extensive mutagenesis of the CEB25 minisatellite motif reveals that only variants with very short (≤ 4 nt) G4 loops preferentially containing pyrimidine bases trigger genomic instability. Parallel biophysical analyses demonstrate that shortening loop length does not change the monomorphic G4 structure of CEB25 variants but drastically increases its thermal stability, in correlation with thein vivo instability. Finally, bioinformatics analyses reveal that the threat for genomic stability posed by G4 bearing short pyrimidine loops is conserved inC. elegans and humans. This work provides a framework explanation for the heterogeneous instability behavior of G4-forming sequencesin vivo, highlights the importance of structure thermal stability, and questions the prevailing assumption that G4 structures with short or longer loops are as likely to formin vivo. PMID:25956747

  5. Breaking bad: R-loops and genome integrity.

    PubMed

    Sollier, Julie; Cimprich, Karlene A

    2015-09-01

    R-loops, nucleic acid structures consisting of an RNA-DNA hybrid and displaced single-stranded (ss) DNA, are ubiquitous in organisms from bacteria to mammals. First described in bacteria where they initiate DNA replication, it now appears that R-loops regulate diverse cellular processes such as gene expression, immunoglobulin (Ig) class switching, and DNA repair. Changes in R-loop regulation induce DNA damage and genome instability, and recently it was shown that R-loops are associated with neurodegenerative disorders. We discuss recent developments in the field; in particular, the regulation and effects of R-loops in cells, their effect on genomic and epigenomic stability, and their potential contribution to the origin of diseases including cancer and neurodegenerative disorders. PMID:26045257

  6. Inner mappings of Bruck loops

    NASA Astrophysics Data System (ADS)

    Kreuzer, Alexander

    1998-01-01

    K-loops have their origin in the theory of sharply 2-transitive groups. In this paper a proof is given that K-loops and Bruck loops are the same. For the proof it is necessary to show that in a (left) Bruck loop the left inner mappings L(b)L(a) L(ab)[minus sign]1 are automorphisms. This paper generalizes results of Glauberman [3], Kist [8] and Kreuzer [9].

  7. Loop Heat Pipes and Capillary Pumped Loops: An Applications Perspective

    NASA Technical Reports Server (NTRS)

    Butler, Dan; Ku, Jentung; Swanson, Theodore; Obenschain, Arthur F. (Technical Monitor)

    2001-01-01

    Capillary pumped loops (CPLS) and loop heat pipes (LHPS) are versatile two-phase heat transfer devices which have recently gained increasing acceptance in space applications. Both systems work based on the same principles and have very similar designs. Nevertheless, some differences exist in the construction of the evaporator and the hydro-accumulator, and these differences lead to very distinct operating characteristics for each loop. This paper presents comparisons of the two loops from an applications perspective, and addresses their impact on spacecraft design, integration, and test. Some technical challenges and issues for both loops are also addressed.

  8. Closed-loop anesthesia.

    PubMed

    LE Guen, Morgan; Liu, Ngai; Chazot, Thierry; Fischler, Marc

    2016-05-01

    Automated anesthesia which may offer to the physician time to control hemodynamic and to supervise neurological outcome and which may offer to the patient safety and quality was until recently consider as a holy grail. But this field of research is now increasing in every component of general anesthesia (hypnosis, nociception, neuromuscular blockade) and literature describes some successful algorithms - single or multi closed-loop controller. The aim of these devices is to control a predefined target and to continuously titrate anesthetics whatever the patients' co morbidities and surgical events to reach this target. Literature contains many randomized trials comparing manual and automated anesthesia and shows feasibility and safety of this system. Automation could quickly concern other aspects of anesthesia as fluid management and this review proposes an overview of closed-loop systems in anesthesia. PMID:26554614

  9. Separable Hilbert space in loop quantum gravity

    NASA Astrophysics Data System (ADS)

    Fairbairn, Winston; Rovelli, Carlo

    2004-07-01

    We study the separability of the state space of loop quantum gravity. In the standard construction, the kinematical Hilbert space of the diffeomorphism-invariant states is nonseparable. This is a consequence of the fact that the knot space of the equivalence classes of graphs under diffeomorphisms is noncountable. However, the continuous moduli labeling these classes do not appear to affect the physics of the theory. We investigate the possibility that these moduli could be only the consequence of a poor choice in the fine-tuning of the mathematical setting. We show that by simply choosing a minor extension of the functional class of the classical fields and coordinates, the moduli disappear, the knot classes become countable, and the kinematical Hilbert space of loop quantum gravity becomes separable.

  10. An Extensible Information Grid for Risk Management

    NASA Technical Reports Server (NTRS)

    Maluf, David A.; Bell, David G.

    2003-01-01

    This paper describes recent work on developing an extensible information grid for risk management at NASA - a RISK INFORMATION GRID. This grid is being developed by integrating information grid technology with risk management processes for a variety of risk related applications. To date, RISK GRID applications are being developed for three main NASA processes: risk management - a closed-loop iterative process for explicit risk management, program/project management - a proactive process that includes risk management, and mishap management - a feedback loop for learning from historical risks that escaped other processes. This is enabled through an architecture involving an extensible database, structuring information with XML, schemaless mapping of XML, and secure server-mediated communication using standard protocols.

  11. Verification of Loop Diagnostics

    NASA Technical Reports Server (NTRS)

    Winebarger, A.; Lionello, R.; Mok, Y.; Linker, J.; Mikic, Z.

    2014-01-01

    Many different techniques have been used to characterize the plasma in the solar corona: density-sensitive spectral line ratios are used to infer the density, the evolution of coronal structures in different passbands is used to infer the temperature evolution, and the simultaneous intensities measured in multiple passbands are used to determine the emission measure. All these analysis techniques assume that the intensity of the structures can be isolated through background subtraction. In this paper, we use simulated observations from a 3D hydrodynamic simulation of a coronal active region to verify these diagnostics. The density and temperature from the simulation are used to generate images in several passbands and spectral lines. We identify loop structures in the simulated images and calculate the loop background. We then determine the density, temperature and emission measure distribution as a function of time from the observations and compare with the true temperature and density of the loop. We find that the overall characteristics of the temperature, density, and emission measure are recovered by the analysis methods, but the details of the true temperature and density are not. For instance, the emission measure curves calculated from the simulated observations are much broader than the true emission measure distribution, though the average temperature evolution is similar. These differences are due, in part, to inadequate background subtraction, but also indicate a limitation of the analysis methods.

  12. Chemical Looping Combustion Kinetics

    SciTech Connect

    Edward Eyring; Gabor Konya

    2009-03-31

    One of the most promising methods of capturing CO{sub 2} emitted by coal-fired power plants for subsequent sequestration is chemical looping combustion (CLC). A powdered metal oxide such as NiO transfers oxygen directly to a fuel in a fuel reactor at high temperatures with no air present. Heat, water, and CO{sub 2} are released, and after H{sub 2}O condensation the CO{sub 2} (undiluted by N{sub 2}) is ready for sequestration, whereas the nickel metal is ready for reoxidation in the air reactor. In principle, these processes can be repeated endlessly with the original nickel metal/nickel oxide participating in a loop that admits fuel and rejects ash, heat, and water. Our project accumulated kinetic rate data at high temperatures and elevated pressures for the metal oxide reduction step and for the metal reoxidation step. These data will be used in computational modeling of CLC on the laboratory scale and presumably later on the plant scale. The oxygen carrier on which the research at Utah is focused is CuO/Cu{sub 2}O rather than nickel oxide because the copper system lends itself to use with solid fuels in an alternative to CLC called 'chemical looping with oxygen uncoupling' (CLOU).

  13. Loops of Jupiter

    NASA Astrophysics Data System (ADS)

    Opolski, Antoni

    2014-12-01

    Professor Antoni Opolski was actively interested in astronomy after his retirement in 1983. He especially liked to study the works of the famous astronomer Copernicus getting inspiration for his own work. Opolski started his work on planetary loops in 2011 continuing it to the end of 2012 . During this period calculations, drawings, tables, and basic descriptions of all the planets of the Solar System were created with the use of a piece of paper and a pencil only. In 2011 Antoni Opolski asked us to help him in editing the manuscript and preparing it for publication. We have been honored having the opportunity to work on articles on planetary loops with Antoni Opolski in his house for several months. In the middle of 2012 the detailed material on Jupiter was ready. However, professor Opolski improved the article by smoothing the text and preparing new, better drawings. Finally the article ''Loops of Jupiter'', written by the 99- year old astronomer, was published in the year of his 100th birthday.

  14. Force distribution in a semiflexible loop

    NASA Astrophysics Data System (ADS)

    Waters, James T.; Kim, Harold D.

    2016-04-01

    Loops undergoing thermal fluctuations are prevalent in nature. Ringlike or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category. Stability of these molecules are generally described in terms of free energy, an average quantity, but it may also be impacted by local fluctuating forces acting within these systems. The full distribution of these forces can thus give us insights into mechanochemistry beyond the predictive capability of thermodynamics. In this paper, we study the force exerted by an inextensible semiflexible polymer constrained in a looped state. By using a simulation method termed "phase-space sampling," we generate the equilibrium distribution of chain conformations in both position and momentum space. We compute the constraint forces between the two ends of the loop in this chain ensemble using Lagrangian mechanics, and show that the mean of these forces is equal to the thermodynamic force. By analyzing kinetic and potential contributions to the forces, we find that the mean force acts in the direction of increasing extension not because of bending stress, but in spite of it. Furthermore, we obtain a distribution of constraint forces as a function of chain length, extension, and stiffness. Notably, increasing contour length decreases the average force, but the additional freedom allows fluctuations in the constraint force to increase. The force distribution is asymmetric and falls off less sharply than a Gaussian distribution. Our work exemplifies a system where large-amplitude fluctuations occur in a way unforeseen by a purely thermodynamic framework, and offers computational tools useful for efficient, unbiased simulation of a constrained system.

  15. The Effects of Hairpin loops on Ligand-DNA Interactions

    PubMed Central

    Nguyen, Binh; Wilson, W. David

    2009-01-01

    Hairpin nucleic acids are frequently used in physical studies due to their greater thermal stability compared to their equivalent duplex structures. They are also good models for more complex loop-containing structures such as quadruplexes, i-motifs, cruciforms, and molecular beacons. Although a connecting loop can increase stability, there is little information on how the loop influences the interactions of small molecules with attached base-paired nucleic acid regions. In this study, the effects of different hairpin loops on the interactions of A/T specific DNA minor groove binding agents with a common stem sequence have been investigated by spectroscopic and surface plasmon resonance (SPR) biosensor methods. The results indicate that the hairpin loop has little influence on the specific site interactions on the stem but significantly affects nonspecific binding. The use of a non-nucleotide loop (with a reduced negative charge) not only enhances the thermal stability of the hairpin but also reduces the non-specific binding at the loop without compromising the primary binding affinity on the stem. PMID:19778070

  16. 40 CFR 72.42 - Phase I extension plans.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...) PERMITS REGULATION Acid Rain Compliance Plan and Compliance Options § 72.42 Phase I extension plans. (a... I extension plan from the requirement to comply with such unit's Acid Rain emissions limitations for... a.m. and 5 p.m. Eastern Standard Time at Acid Rain Division, Attn: Early Ranking, U.S....

  17. 40 CFR 72.42 - Phase I extension plans.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...) PERMITS REGULATION Acid Rain Compliance Plan and Compliance Options § 72.42 Phase I extension plans. (a... I extension plan from the requirement to comply with such unit's Acid Rain emissions limitations for... a.m. and 5 p.m. Eastern Standard Time at Acid Rain Division, Attn: Early Ranking, U.S....

  18. 40 CFR 72.42 - Phase I extension plans.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...) PERMITS REGULATION Acid Rain Compliance Plan and Compliance Options § 72.42 Phase I extension plans. (a... I extension plan from the requirement to comply with such unit's Acid Rain emissions limitations for... a.m. and 5 p.m. Eastern Standard Time at Acid Rain Division, Attn: Early Ranking, U.S....

  19. 40 CFR 72.42 - Phase I extension plans.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...) PERMITS REGULATION Acid Rain Compliance Plan and Compliance Options § 72.42 Phase I extension plans. (a... I extension plan from the requirement to comply with such unit's Acid Rain emissions limitations for... a.m. and 5 p.m. Eastern Standard Time at Acid Rain Division, Attn: Early Ranking, U.S....

  20. Loop Sequence Context Influences the Formation and Stability of the i-Motif for DNA Oligomers of Sequence (CCCXXX)4, where X = A and/or T, under Slightly Acidic Conditions.

    PubMed

    McKim, Mikeal; Buxton, Alexander; Johnson, Courtney; Metz, Amanda; Sheardy, Richard D

    2016-08-11

    The structure and stability of DNA is highly dependent upon the sequence context of the bases (A, G, C, and T) and the environment under which the DNA is prepared (e.g., buffer, temperature, pH, ionic strength). Understanding the factors that influence structure and stability of the i-motif conformation can lead to the design of DNA sequences with highly tunable properties. We have been investigating the influence of pH and temperature on the conformations and stabilities for all permutations of the DNA sequence (CCCXXX)4, where X = A and/or T, using spectroscopic approaches. All oligomers undergo transitions from single-stranded structures at pH 7.0 to i-motif conformations at pH 5.0 as evidenced by circular dichroism (CD) studies. These folded structures possess stacked C:CH(+) base pairs joined by loops of 5'-XXX-3'. Although the pH at the midpoint of the transition (pHmp) varies slightly with loop sequence, the linkage between pH and log K for the proton induced transition is highly loop sequence dependent. All oligomers also undergo the thermally induced i-motif to single-strand transition at pH 5.0 as the temperature is increased from 25 to 95 °C. The temperature at the midpoint of this transition (Tm) is also highly dependent on loop sequence context effects. For seven of eight possible permutations, the pH induced, and thermally induced transitions appear to be highly cooperative and two state. Analysis of the CD optical melting profiles via a van't Hoff approach reveals sequence-dependent thermodynamic parameters for the unfolding as well. Together, these data reveal that the i-motif conformation exhibits exquisite sensitivity to loop sequence context with respect to formation and stability. PMID:27438583

  1. Brief Review on Black Hole Loop Quantization

    NASA Astrophysics Data System (ADS)

    Olmedo, Javier

    2016-06-01

    Here, we present a review about the quantization of spherically-symmetric spacetimes adopting loop quantum gravity techniques. Several models that have been studied so far share similar properties: the resolution of the classical singularity and some of them an intrinsic discretization of the geometry. We also explain the extension to Reissner---Nordstr\\"om black holes. Besides, we review how quantum test fields on these quantum geometries allow us to study phenomena, like the Casimir effect or Hawking radiation. Finally, we briefly describe a recent proposal that incorporates spherically-symmetric matter, discussing its relevance for the understanding of black hole evolution.

  2. Structure of stem-loop IV of Tetrahymena telomerase RNA

    PubMed Central

    Chen, Yu; Fender, Jessica; Legassie, Jason D; Jarstfer, Michael B; Bryan, Tracy M; Varani, Gabriele

    2006-01-01

    Conserved domains within the RNA component of telomerase provide the template for reverse transcription, recruit protein components to the holoenzyme and are required for enzymatic activity. Among the functionally essential domains in ciliate telomerase RNA is stem-loop IV, which strongly stimulates telomerase activity and processivity even when provided in trans. The NMR structure of Tetrahymena thermophila stem-loop IV shows a highly structured distal stem-loop linked to a conformationally flexible template-proximal region by a bulge that severely kinks the entire RNA. Through extensive structure–function studies, we identify residues that contribute to both these structural features and to enzymatic activity, with no apparent effect on the binding of TERT protein. We propose that the bending induced by the GA bulge and the flexibility of the template-proximal region allow positioning of the prestructured apical loop during the catalytic cycle. PMID:16778765

  3. Coupled dual loop absorption heat pump

    DOEpatents

    Sarkisian, Paul H.; Reimann, Robert C.; Biermann, Wendell J.

    1985-01-01

    A coupled dual loop absorption system which utilizes two separate complete loops. Each individual loop operates at three temperatures and two pressures. This low temperature loop absorber and condenser are thermally coupled to the high temperature loop evaporator, and the high temperature loop condenser and absorber are thermally coupled to the low temperature generator.

  4. Closing the loop.

    PubMed

    Dassau, E; Atlas, E; Phillip, M

    2011-02-01

    Closed-loop algorithms can be found in every aspect of everyday modern life. Automation and control are used constantly to provide safety and to improve quality of life. Closed-loop systems and algorithms can be found in home appliances, automobiles, aviation and more. Can one imagine nowadays driving a car without ABS, cruise control or even anti-sliding control? Similar principles of automation and control can be used in the management of diabetes mellitus (DM). The idea of an algorithmic/technological way to control glycaemia is not new and has been researched for more than four decades. However, recent improvements in both glucose-sensing technology and insulin delivery together with advanced control and systems engineering made this dream of an artificial pancreas possible. The artificial pancreas may be the next big step in the treatment of DM since the use of insulin analogues. An artificial pancreas can be described as internal or external devices that use continuous glucose measurements to automatically manage exogenous insulin delivery with or without other hormones in an attempt to restore glucose regulation in individuals with DM using a control algorithm. This device as described can be internal or external; can use different types of control algorithms with bi-hormonal or uni-hormonal design; and can utilise different ways to administer them. The different designs and implementations have transitioned recently from in silico simulations to clinical evaluation stage with practical applications in mind. This may mark the beginning of a new era in diabetes management with the introduction of semi-closed-loop systems that can prevent or minimise nocturnal hypoglycaemia, to hybrid systems that will manage blood glucose (BG) levels with minimal user intervention to finally fully automated systems that will take the user out of the loop. More and more clinical trials will be needed for the artificial pancreas to become a reality but initial encouraging

  5. Response of an all digital phase-locked loop

    NASA Technical Reports Server (NTRS)

    Garodnick, J.; Greco, J.; Schilling, D. L.

    1974-01-01

    An all digital phase-locked loop (DPLL) is designed, analyzed, and tested. Three specific configurations are considered, generating first, second, and third order DPLL's; and it is found, using a computer simulation of a noise spike, and verified experimentally, that of these configurations the second-order system is optimum from the standpoint of threshold extension. This substantiates results obtained for analog PLL's.

  6. Systematic study of the d = 5 Weinberg operator at one-loop order

    NASA Astrophysics Data System (ADS)

    Bonnet, Florian; Hirsch, Martin; Ota, Toshihiko; Winter, Walter

    2012-07-01

    We perform a systematic study of the d = 5 Weinberg operator at the one-loop level. We identify three different categories of neutrino mass generation: (1) finite irreducible diagrams; (2) finite extensions of the usual seesaw mechanisms at one-loop and (3) divergent loop realizations of the seesaws. All radiative one-loop neutrino mass models must fall into one of these classes. Case (1) gives the leading contribution to neutrino mass naturally and a classic example of this class is the Zee model. We demonstrate that in order to prevent that a tree level contribution dominates in case (2), Majorana fermions running in the loop and an additional {Z_2} symmetry are needed for a genuinely leading one-loop contribution. In the type-II loop extensions, the Yukawa coupling will be generated at one loop, whereas the type-I/III extensions can be interpreted as loop-induced inverse or linear seesaw mechanisms. For the divergent diagrams in category (3), the tree level contribution cannot be avoided and is in fact needed as counter term to absorb the divergence.

  7. Ekpyrotic loop quantum cosmology

    SciTech Connect

    Wilson-Ewing, Edward

    2013-08-01

    We consider the ekpyrotic paradigm in the context of loop quantum cosmology. In loop quantum cosmology the classical big-bang singularity is resolved due to quantum gravity effects, and so the contracting ekpyrotic branch of the universe and its later expanding phase are connected by a smooth bounce. Thus, it is possible to explicitly determine the evolution of scalar perturbations, from the contracting ekpyrotic phase through the bounce and to the post-bounce expanding epoch. The possibilities of having either one or two scalar fields have been suggested for the ekpyrotic universe, and both cases will be considered here. In the case of a single scalar field, the constant mode of the curvature perturbations after the bounce is found to have a blue spectrum. On the other hand, for the two scalar field ekpyrotic model where scale-invariant entropy perturbations source additional terms in the curvature perturbations, the power spectrum in the post-bounce expanding cosmology is shown to be nearly scale-invariant and so agrees with observations.

  8. Accelerating the loop expansion

    SciTech Connect

    Ingermanson, R.

    1986-07-29

    This thesis introduces a new non-perturbative technique into quantum field theory. To illustrate the method, I analyze the much-studied phi/sup 4/ theory in two dimensions. As a prelude, I first show that the Hartree approximation is easy to obtain from the calculation of the one-loop effective potential by a simple modification of the propagator that does not affect the perturbative renormalization procedure. A further modification then susggests itself, which has the same nice property, and which automatically yields a convex effective potential. I then show that both of these modifications extend naturally to higher orders in the derivative expansion of the effective action and to higher orders in the loop-expansion. The net effect is to re-sum the perturbation series for the effective action as a systematic ''accelerated'' non-perturbative expansion. Each term in the accelerated expansion corresponds to an infinite number of terms in the original series. Each term can be computed explicitly, albeit numerically. Many numerical graphs of the various approximations to the first two terms in the derivative expansion are given. I discuss the reliability of the results and the problem of spontaneous symmetry-breaking, as well as some potential applications to more interesting field theories. 40 refs.

  9. Extensive quantities in thermodynamics

    NASA Astrophysics Data System (ADS)

    Mannaerts, Sebastiaan H.

    2014-05-01

    A literature survey shows little consistency in the definitions of the term ‘extensive quantity’ (a.k.a. extensive property) as used in thermodynamics. A majority assumes that extensive quantities are those that are proportional to mass. Taking the mathematical meaning of proportional and taking the ‘mass’ to be that of the system or subsystem, it is shown that the proportionality assumption is only correct for a few extensive quantities under condition of constant composition. A large subset of extensive quantities are completely independent of mass; for most systems extensive quantities are not proportional to mass, but mass is the (extensive) constant of proportionality. The definition by IUPAC, based on the additivity of extensive quantities, is the preferred baseline for discussing this subject. It is noted however, that two types of additivity need to be distinguished and that a few intensive quantities are also additive. This paper leaves several interesting questions open to further scrutiny.

  10. The double loop mattress suture

    PubMed Central

    Biddlestone, John; Samuel, Madan; Creagh, Terry; Ahmad, Tariq

    2014-01-01

    An interrupted stitch type with favorable tissue characteristics will reduce local wound complications. We describe a novel high-strength, low-tension repair for the interrupted closure of skin, cartilage, and muscle, the double loop mattress stitch, and compare it experimentally with other interrupted closure methods. The performance of the double loop mattress technique in porcine cartilage and skeletal muscle is compared with the simple, mattress, and loop mattress interrupted sutures in both a novel porcine loading chamber and mechanical model. Wound apposition is assessed by electron microscopy. The performance of the double loop mattress in vivo was confirmed using a series of 805 pediatric laparotomies/laparoscopies. The double loop mattress suture is 3.5 times stronger than the loop mattress in muscle and 1.6 times stronger in cartilage (p ≤ 0.001). Additionally, the double loop mattress reduces tissue tension by 66% compared with just 53% for the loop mattress (p ≤ 0.001). Wound gapping is equal, and wound eversion appears significantly improved (p ≤ 0.001) compared with the loop mattress in vitro. In vivo, the double loop mattress performs as well as the loop mattress and significantly better than the mattress stitch in assessments of wound eversion and dehiscence. There were no episodes of stitch extrusion in our series of patients. The mechanical advantage of its intrinsic pulley arrangement gives the double loop mattress its favorable properties. Wound dehiscence is reduced because this stitch type is stronger and exerts less tension on the tissue than the mattress stitch. We advocate the use of this novel stitch wherever a high-strength, low-tension repair is required. These properties will enhance wound repair, and its application will be useful to surgeons of all disciplines. PMID:24698436

  11. The Cooperative Extension Service.

    ERIC Educational Resources Information Center

    Sanders, H. C., Ed.

    Designed to stimulate and support training for Extension work and to orient new employees, this book covers the Cooperative Extension Service (CES) and its methods of operation. It begins by describing the status of rural extension in the United States and abroad; the history of the CES and its antecendents; the legal basis, scope, functions, and…

  12. Modeling of compact loop antennas

    SciTech Connect

    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 (CIT).

  13. Loop Heat Pipe Startup Behaviors

    NASA Technical Reports Server (NTRS)

    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.

  14. Heating Profiles of Coronal Loops

    NASA Astrophysics Data System (ADS)

    Plowman, Joseph; Kankelborg, Charles C.; Martens, Petrus C.

    2016-05-01

    We analyze the temperature and density profiles of coronal loops, as a function of their length, using data from SDO/AIA and Hinode/EIS. The analysis considers the location of the heating along the loop's length, and we conduct a more throrough investigation of our previous preliminary result that heating is concentrated near the loop footpoints. The work now features a larger selection of coronal loops, compared to our previous presentations, and examines their scale-height temperatures to ascertain the extent to which they are hydrostatic.

  15. Modeling of compact loop antennas

    NASA Astrophysics Data System (ADS)

    Baity, F. W.

    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 (CIT).

  16. Unstable anisotropic loop quantum cosmology

    SciTech Connect

    Nelson, William; Sakellariadou, Mairi

    2009-09-15

    We study stability conditions of the full Hamiltonian constraint equation describing the quantum dynamics of the diagonal Bianchi I model in the context of loop quantum cosmology. Our analysis has shown robust evidence of an instability in the explicit implementation of the difference equation, implying important consequences for the correspondence between the full loop quantum gravity theory and loop quantum cosmology. As a result, one may question the choice of the quantization approach, the model of lattice refinement, and/or the role of the ambiguity parameters; all these should, in principle, be dictated by the full loop quantum gravity theory.

  17. Cooled artery extension

    NASA Technical Reports Server (NTRS)

    Gernert, Nelson J. (Inventor)

    1990-01-01

    An artery vapor trap. A heat pipe artery is constructed with an extension protruding from the evaporator end of the heat pipe beyond the active area of the evaporator. The vapor migrates into the artery extension because of gravity or liquid displacement, and cooling the extension condenses the vapor to liquid, thus preventing vapor lock in the working portion of the artery by removing vapor from within the active artery. The condensed liquid is then transported back to the evaporator by the capillary action of the artery extension itself or by wick located within the extension.

  18. Loop-the-Loop: Bringing Theory into Practice

    ERIC Educational Resources Information Center

    Suwonjandee, N.; Asavapibhop, B.

    2012-01-01

    During the Thai high-school physics teacher training programme, we used an aluminum loop-the-loop system built by the Institute for the Promotion of Teaching Science and Technology (IPST) to demonstrate a circular motion and investigate the concept of the conservation of mechanical energy. There were 27 high-school teachers from three provinces,…

  19. Vortex loops and Majoranas

    SciTech Connect

    Chesi, Stefano; Jaffe, Arthur; Loss, Daniel; Pedrocchi, Fabio L.

    2013-11-15

    We investigate the role that vortex loops play in characterizing eigenstates of interacting Majoranas. We give some general results and then focus on ladder Hamiltonian examples as a test of further ideas. Two methods yield exact results: (i) A mapping of certain spin Hamiltonians to quartic interactions of Majoranas shows that the spectra of these two examples coincide. (ii) In cases with reflection-symmetric Hamiltonians, we use reflection positivity for Majoranas to characterize vortices in the ground states. Two additional methods suggest wider applicability of these results: (iii) Numerical evidence suggests similar behavior for certain systems without reflection symmetry. (iv) A perturbative analysis also suggests similar behavior without the assumption of reflection symmetry.

  20. Dynamic PID loop control

    SciTech Connect

    Pei, L.; Klebaner, A.; Theilacker, J.; Soyars, W.; Martinez, A.; Bossert, R.; DeGraff, B.; Darve, C.; /Fermilab

    2011-06-01

    The Horizontal Test Stand (HTS) SRF Cavity and Cryomodule 1 (CM1) of eight 9-cell, 1.3GHz SRF cavities are operating at Fermilab. For the cryogenic control system, how to hold liquid level constant in the cryostat by regulation of its Joule-Thompson JT-valve is very important after cryostat cool down to 2.0 K. The 72-cell cryostat liquid level response generally takes a long time delay after regulating its JT-valve; therefore, typical PID control loop should result in some cryostat parameter oscillations. This paper presents a type of PID parameter self-optimal and Time-Delay control method used to reduce cryogenic system parameters oscillation.

  1. Uranyl Nitrate Flow Loop

    SciTech Connect

    Ladd-Lively, Jennifer L

    2008-10-01

    The objectives of the work discussed in this report were to: (1) develop a flow loop that would simulate the purified uranium-bearing aqueous stream exiting the solvent extraction process in a natural uranium conversion plant (NUCP); (2) develop a test plan that would simulate normal operation and disturbances that could be anticipated in an NUCP; (3) use the flow loop to test commercially available flowmeters for use as safeguards monitors; and (4) recommend a flowmeter for production-scale testing at an NUCP. There has been interest in safeguarding conversion plants because the intermediate products [uranium dioxide (UO{sub 2}), uranium tetrafluoride (UF{sub 4}), and uranium hexafluoride (UF{sub 6})] are all suitable uranium feedstocks for producing special nuclear materials. Furthermore, if safeguards are not applied virtually any nuclear weapons program can obtain these feedstocks without detection by the International Atomic Energy Agency (IAEA). Historically, IAEA had not implemented safeguards until the purified UF{sub 6} product was declared as feedstock for enrichment plants. H. A. Elayat et al. provide a basic definition of a safeguards system: 'The function of a safeguards system on a chemical conversion plant is in general terms to verify that no useful nuclear material is being diverted to use in a nuclear weapons program'. The IAEA now considers all highly purified uranium compounds as candidates for safeguarding. DOE is currently interested in 'developing instruments, tools, strategies, and methods that could be of use to the IAEA in the application of safeguards' for materials found in the front end of the nuclear fuel cycle-prior to the production of the uranium hexafluoride or oxides that have been the traditional starting point for IAEA safeguards. Several national laboratories, including Oak Ridge, Los Alamos, Lawrence Livermore, and Brookhaven, have been involved in developing tools or techniques for safeguarding conversion plants. This study

  2. Loop-the-Loop: An Easy Experiment, A Challenging Explanation

    NASA Astrophysics Data System (ADS)

    Asavapibhop, B.; Suwonjandee, N.

    2010-07-01

    A loop-the-loop built by the Institute for the Promotion of Teaching Science and Technology (IPST) was used in Thai high school teachers training program to demonstrate a circular motion and investigate the concept of the conservation of mechanical energy. We took videos using high speed camera to record the motions of a spherical steel ball moving down the aluminum inclined track at different released positions. The ball then moved into the circular loop and underwent a projectile motion upon leaving the track. We then asked the teachers to predict the landing position of the ball if we changed the height of the whole loop-the-loop system. We also analyzed the videos using Tracker, a video analysis software. It turned out that most teachers did not realize the effect of the friction between the ball and the track and could not obtain the correct relationship hence their predictions were inconsistent with the actual landing positions of the ball.

  3. Large loop conformation sampling using the activation relaxation technique, ART-nouveau method.

    PubMed

    St-Pierre, Jean-François; Mousseau, Normand

    2012-07-01

    We present an adaptation of the ART-nouveau energy surface sampling method to the problem of loop structure prediction. This method, previously used to study protein folding pathways and peptide aggregation, is well suited to the problem of sampling the conformation space of large loops by targeting probable folding pathways instead of sampling exhaustively that space. The number of sampled conformations needed by ART nouveau to find the global energy minimum for a loop was found to scale linearly with the sequence length of the loop for loops between 8 and about 20 amino acids. Considering the linear scaling dependence of the computation cost on the loop sequence length for sampling new conformations, we estimate the total computational cost of sampling larger loops to scale quadratically compared to the exponential scaling of exhaustive search methods. PMID:22488731

  4. RCD+: Fast loop modeling server

    PubMed Central

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

    2016-01-01

    Modeling loops is a critical and challenging step in protein modeling and prediction. We have developed a quick online service (http://rcd.chaconlab.org) for ab initio loop modeling combining a coarse-grained conformational search with a full-atom refinement. Our original Random Coordinate Descent (RCD) loop closure algorithm has been greatly improved to enrich the sampling distribution towards near-native conformations. These improvements include a new workflow optimization, MPI-parallelization and fast backbone angle sampling based on neighbor-dependent Ramachandran probability distributions. The server starts by efficiently searching the vast conformational space from only the loop sequence information and the environment atomic coordinates. The generated closed loop models are subsequently ranked using a fast distance-orientation dependent energy filter. Top ranked loops are refined with the Rosetta energy function to obtain accurate all-atom predictions that can be interactively inspected in an user-friendly web interface. Using standard benchmarks, the average root mean squared deviation (RMSD) is 0.8 and 1.4 Å for 8 and 12 residues loops, respectively, in the challenging modeling scenario in where the side chains of the loop environment are fully remodeled. These results are not only very competitive compared to those obtained with public state of the art methods, but also they are obtained ∼10-fold faster. PMID:27151199

  5. RCD+: Fast loop modeling server.

    PubMed

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

    2016-07-01

    Modeling loops is a critical and challenging step in protein modeling and prediction. We have developed a quick online service (http://rcd.chaconlab.org) for ab initio loop modeling combining a coarse-grained conformational search with a full-atom refinement. Our original Random Coordinate Descent (RCD) loop closure algorithm has been greatly improved to enrich the sampling distribution towards near-native conformations. These improvements include a new workflow optimization, MPI-parallelization and fast backbone angle sampling based on neighbor-dependent Ramachandran probability distributions. The server starts by efficiently searching the vast conformational space from only the loop sequence information and the environment atomic coordinates. The generated closed loop models are subsequently ranked using a fast distance-orientation dependent energy filter. Top ranked loops are refined with the Rosetta energy function to obtain accurate all-atom predictions that can be interactively inspected in an user-friendly web interface. Using standard benchmarks, the average root mean squared deviation (RMSD) is 0.8 and 1.4 Å for 8 and 12 residues loops, respectively, in the challenging modeling scenario in where the side chains of the loop environment are fully remodeled. These results are not only very competitive compared to those obtained with public state of the art methods, but also they are obtained ∼10-fold faster. PMID:27151199

  6. Wilson Loop Diagrams and Positroids

    NASA Astrophysics Data System (ADS)

    Agarwala, Susama; Marin-Amat, Eloi

    2016-07-01

    In this paper, we study a new application of the positive Grassmannian to Wilson loop diagrams (or MHV diagrams) for scattering amplitudes in N= 4 Super Yang-Mill theory (N = 4 SYM). There has been much interest in studying this theory via the positive Grassmannians using BCFW recursion. This is the first attempt to study MHV diagrams for planar Wilson loop calculations (or planar amplitudes) in terms of positive Grassmannians. We codify Wilson loop diagrams completely in terms of matroids. This allows us to apply the combinatorial tools in matroid theory used to identify positroids (non-negative Grassmannians) to Wilson loop diagrams. In doing so, we find that certain non-planar Wilson loop diagrams define positive Grassmannians. While non-planar diagrams do not have physical meaning, this finding suggests that they may have value as an algebraic tool, and deserve further investigation.

  7. Higher dimensional loop quantum cosmology

    NASA Astrophysics Data System (ADS)

    Zhang, Xiangdong

    2016-07-01

    Loop quantum cosmology (LQC) is the symmetric sector of loop quantum gravity. In this paper, we generalize the structure of loop quantum cosmology to the theories with arbitrary spacetime dimensions. The isotropic and homogeneous cosmological model in n+1 dimensions is quantized by the loop quantization method. Interestingly, we find that the underlying quantum theories are divided into two qualitatively different sectors according to spacetime dimensions. The effective Hamiltonian and modified dynamical equations of n+1 dimensional LQC are obtained. Moreover, our results indicate that the classical big bang singularity is resolved in arbitrary spacetime dimensions by a quantum bounce. We also briefly discuss the similarities and differences between the n+1 dimensional model and the 3+1 dimensional one. Our model serves as a first example of higher dimensional loop quantum cosmology and offers the possibility to investigate quantum gravity effects in higher dimensional cosmology.

  8. Loop-bed combustion apparatus

    DOEpatents

    Shang, Jer-Yu; Mei, Joseph S.; Slagle, Frank D.; Notestein, John E.

    1984-01-01

    The present invention is directed to a combustion apparatus in the configuration of a oblong annulus defining a closed loop. Particulate coal together with a sulfur sorbent such as sulfur or dolomite is introduced into the closed loop, ignited, and propelled at a high rate of speed around the loop. Flue gas is withdrawn from a location in the closed loop in close proximity to an area in the loop where centrifugal force imposed upon the larger particulate material maintains these particulates at a location spaced from the flue gas outlet. Only flue gas and smaller particulates resulting from the combustion and innerparticle grinding are discharged from the combustor. This structural arrangement provides increased combustion efficiency due to the essentially complete combustion of the coal particulates as well as increased sulfur absorption due to the innerparticle grinding of the sorbent which provides greater particle surface area.

  9. Loop Heat Pipe Startup Behaviors

    NASA Technical Reports Server (NTRS)

    Ku, Jentung

    2014-01-01

    A loop heat pipe must start successfully before it can commence its service. The start-up transient represents one of the most complex phenomena in the loop heat pipe operation. This paper discusses various aspects of loop heat pipe start-up behaviors. Topics include the four start-up scenarios, the initial fluid distribution between the evaporator and reservoir that determines the start-up scenario, factors that affect the fluid distribution between the evaporator and reservoir, difficulties encountered during the low power start-up, and methods to enhance the start-up success. Also addressed are the thermodynamic constraint between the evaporator and reservoir in the loop heat pipe operation, the superheat requirement for nucleate boiling, pressure spike and pressure surge during the start-up transient, and repeated cycles of loop start-up andshutdown under certain conditions.

  10. On loop corrections to subleading soft behavior of gluons and gravitons

    NASA Astrophysics Data System (ADS)

    Bern, Zvi; Davies, Scott; Nohle, Josh

    2014-10-01

    Cachazo and Strominger recently proposed an extension of the soft-graviton theorem found by Weinberg. In addition, they proved the validity of their extension at tree level. This was motivated by a Virasoro symmetry of the gravity S-matrix related to Bondi, van der Burg, Metzner, and Sachs symmetry. As shown long ago by Weinberg, the leading behavior is not corrected by loops. In contrast, we show that with the standard definition of soft limits in dimensional regularization, the subleading behavior is anomalous and modified by loop effects. We argue that there are no new types of corrections to the first subleading behavior beyond one loop and to the second subleading behavior beyond two loops. To facilitate our investigation, we introduce a new momentum-conservation prescription for defining the subleading terms of the soft limit. We discuss the loop-level subleading soft behavior of gauge-theory amplitudes before turning to gravity amplitudes.

  11. University of Wisconsin - Extension

    MedlinePlus

    ... Continuing and Online Education About Degree Programs Independent Learning School for Workers UW HELP UW System eCampus Cooperative Extension About Agriculture & Natural Resources Community, Natural Resource & ...

  12. Type Safe Extensible Programming

    NASA Astrophysics Data System (ADS)

    Chae, Wonseok

    2009-10-01

    Software products evolve over time. Sometimes they evolve by adding new features, and sometimes by either fixing bugs or replacing outdated implementations with new ones. When software engineers fail to anticipate such evolution during development, they will eventually be forced to re-architect or re-build from scratch. Therefore, it has been common practice to prepare for changes so that software products are extensible over their lifetimes. However, making software extensible is challenging because it is difficult to anticipate successive changes and to provide adequate abstraction mechanisms over potential changes. Such extensibility mechanisms, furthermore, should not compromise any existing functionality during extension. Software engineers would benefit from a tool that provides a way to add extensions in a reliable way. It is natural to expect programming languages to serve this role. Extensible programming is one effort to address these issues. In this thesis, we present type safe extensible programming using the MLPolyR language. MLPolyR is an ML-like functional language whose type system provides type-safe extensibility mechanisms at several levels. After presenting the language, we will show how these extensibility mechanisms can be put to good use in the context of product line engineering. Product line engineering is an emerging software engineering paradigm that aims to manage variations, which originate from successive changes in software.

  13. Digital phase-locked loop

    NASA Technical Reports Server (NTRS)

    Cliff, R. A. (Inventor)

    1975-01-01

    An digital phase-locked loop is provided for deriving a loop output signal from an accumulator output terminal. A phase detecting exclusive OR gate is fed by the loop digital input and output signals. The output of the phase detector is a bi-level digital signal having a duty cycle indicative of the relative phase of the input and output signals. The accumulator is incremented at a first rate in response to a first output level of the phase detector and at a second rate in response to a second output level of the phase detector.

  14. Structural and sequence patterns in the loops of beta alpha beta units.

    PubMed

    Edwards, M S; Sternberg, J E; Thornton, J M

    1987-06-01

    The conformation and sequences of the 129 loops of 70 beta alpha beta units from 17 alpha/beta proteins were analysed for patterns. Many different conformations of the loop regions were observed, but 18 of the loops could be classified into one of four loop families with distinctive conformation and sequence patterns. (i) Adjacent alpha beta loops with one residue between the alpha-helix and beta-strand. The residue is a glycine with conformationally restricted phi/psi angles; (ii) adjacent alpha beta loops of three residues with a conformationally restricted glycine as the first of the loop followed by an analine or histidine residue and a third residue with helical phi/psi angles; (iii) adjacent beta alpha loops of 3/4 residues previously reported to bind nucleotides and which have three glycine residues in the loop region; (iv) non-adjacent beta alpha loops of 0 residues with a serine or threonine as the last residue of the beta-strand. The analysis provides information for the model building of loops and prediction of secondary structure from amino acid sequences. PMID:3507703

  15. Asymmetric structure of five and six membered DNA hairpin loops

    NASA Technical Reports Server (NTRS)

    Baumann, U.; Chang, S.

    1995-01-01

    The tertiary structure of nucleic acid hairpins was elucidated by means of the accessibility of the single-strand-specific nuclease from mung bean. This molecular probe has proven especially useful in determining details of the structural arrangement of the nucleotides within a loop. In this study 3'-labeling is introduced to complement previously used 5'-labeling in order to assess and to exclude possible artifacts of the method. Both labeling procedures result in mutually consistent cleavage patterns. Therefore, methodological artifacts can be excluded and the potential of the nuclease as structural probe is increased. DNA hairpins with five and six membered loops reveal an asymmetric loop structure with a sharp bend of the phosphate-ribose backbone between the second and third nucleotide on the 3'-side of a loop. These hairpin structures differ from smaller loops with 3 or 4 members, which reveal this type of bend between the first and second 3' nucleotide, and resemble with respect to the asymmetry anticodon loops of tRNA.

  16. Loop-mediated amplification accelerated by stem primers.

    PubMed

    Gandelman, Olga; Jackson, Rebecca; Kiddle, Guy; Tisi, Laurence

    2011-01-01

    Isothermal nucleic acid amplifications (iNAATs) have become an important alternative to PCR for in vitro molecular diagnostics in all fields. Amongst iNAATs Loop-mediated amplification (LAMP) has gained much attention over the last decade because of the simplicity of hardware requirements. LAMP demonstrates performance equivalent to that of PCR, but its application has been limited by the challenging primer design. The design of six primers in LAMP requires a selection of eight priming sites with significant restrictions imposed on their respective positioning and orientation. In order to relieve primer design constraints we propose an alternative approach which uses Stem primers instead of Loop primers and demonstrate the application of STEM-LAMP in assaying for Clostridium difficile, Listeria monocytogenes and HIV. Stem primers used in LAMP in combination with loop-generating and displacement primers gave significant benefits in speed and sensitivity, similar to those offered by Loop primers, while offering additional options of forward and reverse orientations, multiplexing, use in conjunction with Loop primers or even omission of one or two displacement primers, where necessary. Stem primers represent a valuable alternative to Loop primers and an additional tool for IVD assay development by offering more choices for primer design at the same time increasing assay speed, sensitivity, and reproducibility. PMID:22272122

  17. A Computer Model of a Phase Lock Loop

    NASA Technical Reports Server (NTRS)

    Shelton, Ralph Paul

    1973-01-01

    A computer model is reported of a PLL (phase-lock loop), preceded by a bandpass filter, which is valid when the bandwidth of the bandpass filter is of the same order of magnitude as the natural frequency of the PLL. New results for the PLL natural frequency equal to the bandpass filter bandwidth are presented for a second order PLL operating with carrier plus noise as the input. However, it is shown that extensions to higher order loops, and to the case of a modulated carrier are straightforward. The new results presented give the cycle skipping rate of the PLL as a function of the input carrier to noise ratio when the PLL natural frequency is equal to the bandpass filter bandwidth. Preliminary results showing the variation of the output noise power and cycle skipping rates of the PLL as a function of the loop damping ratio for the PLL natural frequency equal to the bandpass filter bandwidth are also included.

  18. HIPK2 catalytic activity and subcellular localization are regulated by activation-loop Y354 autophosphorylation.

    PubMed

    Siepi, Francesca; Gatti, Veronica; Camerini, Serena; Crescenzi, Marco; Soddu, Silvia

    2013-06-01

    HIPK2 (homeodomain-interacting protein kinase-2) binds to and phosphorylates, at Ser and Thr residues, a large number of targets involved in cell division and cell fate decision in response to different physiological or stress stimuli. Inactivation of HIPK2 has been observed in human and mouse cancers supporting its role as a tumor suppressor. Despite the biological relevance of this kinase, very little is known on how HIPK2 becomes catalytically active. Based on sequence homologies, HIPK2 has been taxonomically classified as a subfamily member of the dual-specificity tyrosine-regulated kinases (DYRKs) and the activation-loop Y354 of HIPK2 has been found phosphorylated in different cells; however, the relevance of this Y phosphorylation is presently unknown. Here, we show that HIPK2, which is extensively phosphorylated at S/T sites throughout its functional domains, becomes catalytically active by autophosphorylation at the activation-loop Y354. In particular, we found that, in analogy to DYRKs, HIPK2-Y354 phosphorylation is an autocatalytic event and its prevention, through Y354 substitution with non-phosphorylatable amino acids or by using the kinase inhibitor purvalanol A, induces a strong reduction of the HIPK2 S/T-kinase activity on different substrates. Interestingly, at variance from DYRKs, inhibition of HIPK2-Y354 phosphorylation induces a strong out-of-target Y-kinase activity in cis and a strong cytoplasmic relocalization of the kinase. Together, these results demonstrate that the catalytic activity, substrate specificity, and subcellular localization of HIPK2 are regulated by autophosphorylation of its activation-loop Y354. PMID:23485397

  19. HIPK2 catalytic activity and subcellular localization are regulated by activation-loop Y354 autophosphorylation

    PubMed Central

    Siepi, Francesca; Gatti, Veronica; Camerini, Serena; Crescenzi, Marco; Soddu, Silvia

    2013-01-01

    HIPK2 (homeodomain-interacting protein kinase-2) binds to and phosphorylates, at Ser and Thr residues, a large number of targets involved in cell division and cell fate decision in response to different physiological or stress stimuli. Inactivation of HIPK2 has been observed in human and mouse cancers supporting its role as a tumor suppressor. Despite the biological relevance of this kinase, very little is known on how HIPK2 becomes catalytically active. Based on sequence homologies, HIPK2 has been taxonomically classified as a subfamily member of the dual-specificity tyrosine-regulated kinases (DYRKs) and the activation-loop Y354 of HIPK2 has been found phosphorylated in different cells; however, the relevance of this Y phosphorylation is presently unknown. Here, we show that HIPK2, which is extensively phosphorylated at S/T sites throughout its functional domains, becomes catalytically active by autophosphorylation at the activation-loop Y354. In particular, we found that, in analogy to DYRKs, HIPK2-Y354 phosphorylation is an autocatalytic event and its prevention, through Y354 substitution with non-phosphorylatable amino acids or by using the kinase inhibitor purvalanol A, induces a strong reduction of the HIPK2 S/T-kinase activity on different substrates. Interestingly, at variance from DYRKs, inhibition of HIPK2-Y354 phosphorylation induces a strong out-of-target Y-kinase activity in cis and a strong cytoplasmic relocalization of the kinase. Together, these results demonstrate that the catalytic activity, substrate specificity, and subcellular localization of HIPK2 are regulated by autophosphorylation of its activation-loop Y354. PMID:23485397

  20. SDO Sees Brightening Magnetic Loops

    NASA Video Gallery

    Two active regions sprouted arches of bundled magnetic loops in this video from NASA’s Solar Dynamics Observatory taken on Nov. 11-12, 2015. Charged particles spin along the magnetic field, tracing...

  1. Automatic blocking of nested loops

    NASA Technical Reports Server (NTRS)

    Schreiber, Robert; Dongarra, Jack J.

    1990-01-01

    Blocked algorithms have much better properties of data locality and therefore can be much more efficient than ordinary algorithms when a memory hierarchy is involved. On the other hand, they are very difficult to write and to tune for particular machines. The reorganization is considered of nested loops through the use of known program transformations in order to create blocked algorithms automatically. The program transformations used are strip mining, loop interchange, and a variant of loop skewing in which invertible linear transformations (with integer coordinates) of the loop indices are allowed. Some problems are solved concerning the optimal application of these transformations. It is shown, in a very general setting, how to choose a nearly optimal set of transformed indices. It is then shown, in one particular but rather frequently occurring situation, how to choose an optimal set of block sizes.

  2. SDO Sees Flourishing Magnetic Loops

    NASA Video Gallery

    A bright set of loops near the edge of the sun’s face grew and shifted quickly after the magnetic field was disrupted by a small eruption on Nov. 25, 2015. Charged particles emitting light in extre...

  3. Loop Electrosurgical Excision Procedure (LEEP)

    MedlinePlus

    ... that acts like a scalpel (surgical knife). An electric current is passed through the loop, which cuts away ... A procedure in which an instrument works with electric current to destroy tissue. Local Anesthesia: The use of ...

  4. Observations of loops and prominences

    NASA Technical Reports Server (NTRS)

    Strong, Keith T.

    1994-01-01

    We review recent observations by the Yohkoh-SXT (Soft X-ray Telescope) in collaboration with other spacecraft and ground-based observatories of coronal loops and prominences. These new results point to problems that SoHO will be able to address. With a unique combination of rapid-cadence digital imaging (greater than or equal to 32 s full-disk and greater than or equal to 2 s partial-frame images), high spatial resolution (greater than or equal to 2.5 arcsec pixels), high sensitivity (EM less than or equal to 10(exp 42) cm(exp -3)), a low-scatter mirror, and large dynamic range, SXT can observe a vast range of targets on the Sun. Over the first 21 months of Yohkoh operations SXT has taken over one million images of the corona and so is building up an invaluable long-term database on the large-scale corona and loop geometry. The most striking thing about the SXT images is the range of loop sizes and shapes. The active regions are a bright tangle of magnetic field lines, surrounded by a network of large-scale quiet-Sun loops stretching over distances in excess of 105 km. The cross-section of most loops seems to be constant. Loops displaying significant Gamma's are the exception, not the rule, implying the presence of widespread currents in the corona. All magnetic structures show changes. Time scales range from seconds to months. The question of how these structures are formed, become filled with hot plasma, and are maintained is still open. While we see the propagation of brightenings along the length of active-region loops and in X-ray jets with velocities of several hundred km/s, much higher velocities are seen in the quiet Sun. In XBP flares, for example, velocities of over 1000 km/s are common. Active-region loops seem to be in constant motion, moving slowly outward, carrying plasma with them. During flares, loops often produce localized brightenings at the base and later at the apex of the loop. Quiescent filaments and prominences have been observed regularly

  5. Dynamical behaviour in coronal loops

    NASA Technical Reports Server (NTRS)

    Haisch, Bernhard M.

    1986-01-01

    Rapid variability has been found in two active region coronal loops observed by the X-ray Polychromator (XRP) and the Hard X-ray Imaging Spectrometer (HXIS) onboard the Solar Maximum Mission (SMM). There appear to be surprisingly few observations of the short-time scale behavior of hot loops, and the evidence presented herein lends support to the hypothesis that coronal heating may be impulsive and driven by flaring.

  6. Signature extension studies

    NASA Technical Reports Server (NTRS)

    Vincent, R. K.; Thomas, G. S.; Nalepka, R. F.

    1974-01-01

    The importance of specific spectral regions to signature extension is explored. In the recent past, the signature extension task was focused on the development of new techniques. Tested techniques are now used to investigate this spectral aspect of the large area survey. Sets of channels were sought which, for a given technique, were the least affected by several sources of variation over four data sets and yet provided good object class separation on each individual data set. Using sets of channels determined as part of this study, signature extension was accomplished between data sets collected over a six-day period and over a range of about 400 kilometers.

  7. Pharmacokinetics of para-Aminosalicylic Acid in HIV-Uninfected and HIV-Coinfected Tuberculosis Patients Receiving Antiretroviral Therapy, Managed for Multidrug-Resistant and Extensively Drug-Resistant Tuberculosis

    PubMed Central

    de Kock, Lizanne; Sy, Sherwin K. B.; Diacon, Andreas H.; Prescott, Kim; Hernandez, Kenneth R.; Yu, Mingming; Derendorf, Hartmut; Donald, Peter R.

    2014-01-01

    The emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mycobacterium tuberculosis prompted the reintroduction of para-aminosalicylic acid (PAS) to protect companion anti-tuberculosis drugs from additional acquired resistance. In sub-Saharan Africa, MDR/XDR tuberculosis with HIV coinfection is common, and concurrent treatment of HIV infection and MDR/XDR tuberculosis is required. Out of necessity, patients receive multiple drugs, and PAS therapy is frequent; however, neither potential drug interactions nor the effects of HIV infection are known. Potential drug-drug interaction with PAS and the effect of HIV infection was examined in 73 pulmonary tuberculosis patients; 22 (30.1%) were HIV coinfected. Forty-one pulmonary MDR or XDR tuberculosis patients received 4 g PAS twice daily, and in a second crossover study, another 32 patients were randomized, receiving 4 g PAS twice daily or 8 g PAS once daily. A PAS population pharmacokinetic model in two dosing regimens was developed; potential covariates affecting its pharmacokinetics were examined, and Monte Carlo simulations were conducted evaluating the pharmacokinetic-pharmacodynamic index. The probability of target attainment (PTA) to maintain PAS levels above MIC during the dosing interval was estimated by simulation of once-, twice-, and thrice-daily dosing regimens not exceeding 12 g daily. Concurrent efavirenz (EFV) medication resulted in a 52% increase in PAS clearance and a corresponding >30% reduction in mean PAS area under the concentration curve in 19 of 22 HIV-M. tuberculosis-coinfected patients. Current practice recommends maintenance of PAS concentrations at ≥1 μg/ml (the MIC of M. tuberculosis), but the model predicts that at only a minimum dose of 4 g twice daily can this PTA be achieved in at least 90% of the population, whether or not EFV is concomitantly administered. Once-daily dosing of 12 g PAS will not provide PAS concentrations exceeding the MIC over the entire dosing

  8. The corrections from one loop and two-loop Barr-Zee type diagrams to muon MDM in BLMSSM

    NASA Astrophysics Data System (ADS)

    Zhao, Shu-Min; Feng, Tai-Fu; Zhang, Hai-Bin; Yan, Ben; Zhan, Xi-Jie

    2014-11-01

    In a supersymmetric extension of the standard model where baryon and lepton numbers are local gauge symmetries(BLMSSM) and the Yukawa couplings between Higgs doublets and exotic quarks are considered, we study the one loop diagrams and the two-loop Barr-Zee type diagrams with a closed Fermi(scalar) loop between the vector Boson and Higgs. Using the effective Lagrangian method, we deduce the Wilson coefficients of dimension 6 operators contributing to the anomalous magnetic moment of muon, which satisfies the electromagnetic gauge invariance. In the numerical analysis, we consider the experiment constraints from Higgs and neutrino data. In some parameter space, the new physics contribution is large and even reaches 24 × 10-10, which can remedy the deviation well.

  9. The Coronal Loop Inventory Project

    NASA Astrophysics Data System (ADS)

    Schmelz, J. T.; Pathak, S.; Christian, G. M.; Dhaliwal, R. S. S.; Paul, K. S.

    2015-11-01

    Most coronal physicists now seem to agree that loops are composed of tangled magnetic strands and have both isothermal and multithermal cross-field temperature distributions. As yet, however, there is no information on the relative importance of each of these categories, and we do not know how common one is with respect to the other. In this paper, we investigate these temperature properties for all loop segments visible in the 171-Å image of AR 11294, which was observed by the Atmospheric Imaging Assembly (AIA) on 2011 September 15. Our analysis revealed 19 loop segments, but only 2 of these were clearly isothermal. Six additional segments were effectively isothermal, that is, the plasma emission to which AIA is sensitive could not be distinguished from isothermal emission, within measurement uncertainties. One loop had both isothermal transition region and multithermal coronal solutions. Another five loop segments require multithermal plasma to reproduce the AIA observations. The five remaining loop segments could not be separated reliably from the background in the crucial non-171-Å AIA images required for temperature analysis. We hope that the direction of coronal heating models and the efforts modelers spend on various heating scenarios will be influenced by these results.

  10. The Structure of Coronal Loops

    NASA Technical Reports Server (NTRS)

    Antiochos, Spiro K.

    2009-01-01

    It is widely believed that the simple coronal loops observed by XUV imagers, such as EIT, TRACE, or XRT, actually have a complex internal structure consisting of many (perhaps hundreds) of unresolved, interwoven "strands". According to the nanoflare model, photospheric motions tangle the strands, causing them to reconnect and release the energy required to produce the observed loop plasma. Although the strands, themselves, are unresolved by present-generation imagers, there is compelling evidence for their existence and for the nanoflare model from analysis of loop intensities and temporal evolution. A problem with this scenario is that, although reconnection can eliminate some of the strand tangles, it cannot destroy helicity, which should eventually build up to observable scales. we consider, therefore, the injection and evolution of helicity by the nanoflare process and its implications for the observed structure of loops and the large-scale corona. we argue that helicity does survive and build up to observable levels, but on spatial and temporal scales larger than those of coronal loops. we discuss the implications of these results for coronal loops and the corona, in general .

  11. Geothermal Loop Experimental Facility. Final report

    SciTech Connect

    Not Available

    1980-04-01

    Research at the Geothermal Loop Experimental Facility was successfully concluded in September 1979. In 13,000 hours of operation over a three and one half year period, the nominal 10 megawatt electrical equivalent GLEF provided the opportunity to identify problems in working with highly saline geothermal fluids and to develop solutions that could be applied to a commercial geothermal power plant producing electricity. A seven and one half year period beginning in April 1972, with early well flow testing and ending in September 1979, with the completion of extensive facility and reservoir operations is covered. During this period, the facility was designed, constructed and operated in several configurations. A comprehensive reference document, addressing or referencing documentation of all the key areas investigated is presented.

  12. Loop quantum cosmology of Bianchi type I models

    SciTech Connect

    Ashtekar, Abhay; Wilson-Ewing, Edward

    2009-04-15

    The ''improved dynamics'' of loop quantum cosmology is extended to include anisotropies of the Bianchi type I model. As in the isotropic case, a massless scalar field serves as a relational time parameter. However, the extension is nontrivial because one has to face several conceptual subtleties as well as technical difficulties. These include a better understanding of the relation between loop quantum gravity and loop quantum cosmology, handling novel features associated with the nonlocal field strength operator in presence of anisotropies, and finding dynamical variables that make the action of the Hamiltonian constraint manageable. Our analysis provides a conceptually complete description that overcomes limitations of earlier works. We again find that the big-bang singularity is resolved by quantum geometry effects but, because of the presence of Weyl curvature, Planck scale physics is now much richer than in the isotropic case. Since the Bianchi I models play a key role in the Belinskii, Khalatnikov, Lifshitz conjecture on the nature of generic spacelike singularities in general relativity, the quantum dynamics of Bianchi I cosmologies is likely to provide considerable intuition about the fate of generic spacelike singularities in quantum gravity. Finally, we show that the quantum dynamics of Bianchi I cosmologies projects down exactly to that of the Friedmann model. This opens a new avenue to relate more complicated models to simpler ones, thereby providing a new tool to relate the quantum dynamics of loop quantum gravity to that of loop quantum cosmology.

  13. Loop quantum cosmology of Bianchi type I models

    NASA Astrophysics Data System (ADS)

    Ashtekar, Abhay; Wilson-Ewing, Edward

    2009-04-01

    The “improved dynamics” of loop quantum cosmology is extended to include anisotropies of the Bianchi type I model. As in the isotropic case, a massless scalar field serves as a relational time parameter. However, the extension is nontrivial because one has to face several conceptual subtleties as well as technical difficulties. These include a better understanding of the relation between loop quantum gravity and loop quantum cosmology, handling novel features associated with the nonlocal field strength operator in presence of anisotropies, and finding dynamical variables that make the action of the Hamiltonian constraint manageable. Our analysis provides a conceptually complete description that overcomes limitations of earlier works. We again find that the big-bang singularity is resolved by quantum geometry effects but, because of the presence of Weyl curvature, Planck scale physics is now much richer than in the isotropic case. Since the Bianchi I models play a key role in the Belinskii, Khalatnikov, Lifshitz conjecture on the nature of generic spacelike singularities in general relativity, the quantum dynamics of Bianchi I cosmologies is likely to provide considerable intuition about the fate of generic spacelike singularities in quantum gravity. Finally, we show that the quantum dynamics of Bianchi I cosmologies projects down exactly to that of the Friedmann model. This opens a new avenue to relate more complicated models to simpler ones, thereby providing a new tool to relate the quantum dynamics of loop quantum gravity to that of loop quantum cosmology.

  14. Run-time parallelization and scheduling of loops

    NASA Technical Reports Server (NTRS)

    Saltz, Joel H.; Mirchandaney, Ravi; Baxter, Doug

    1988-01-01

    The class of problems that can be effectively compiled by parallelizing compilers is discussed. This is accomplished with the doconsider construct which would allow these compilers to parallelize many problems in which substantial loop-level parallelism is available but cannot be detected by standard compile-time analysis. We describe and experimentally analyze mechanisms used to parallelize the work required for these types of loops. In each of these methods, a new loop structure is produced by modifying the loop to be parallelized. We also present the rules by which these loop transformations may be automated in order that they be included in language compilers. The main application area of the research involves problems in scientific computations and engineering. The workload used in our experiment includes a mixture of real problems as well as synthetically generated inputs. From our extensive tests on the Encore Multimax/320, we have reached the conclusion that for the types of workloads we have investigated, self-execution almost always performs better than pre-scheduling. Further, the improvement in performance that accrues as a result of global topological sorting of indices as opposed to the less expensive local sorting, is not very significant in the case of self-execution.

  15. Kalman Orbit Optimized Loop Tracking

    NASA Technical Reports Server (NTRS)

    Young, Lawrence E.; Meehan, Thomas K.

    2011-01-01

    Under certain conditions of low signal power and/or high noise, there is insufficient signal to noise ratio (SNR) to close tracking loops with individual signals on orbiting Global Navigation Satellite System (GNSS) receivers. In addition, the processing power available from flight computers is not great enough to implement a conventional ultra-tight coupling tracking loop. This work provides a method to track GNSS signals at very low SNR without the penalty of requiring very high processor throughput to calculate the loop parameters. The Kalman Orbit-Optimized Loop (KOOL) tracking approach constitutes a filter with a dynamic model and using the aggregate of information from all tracked GNSS signals to close the tracking loop for each signal. For applications where there is not a good dynamic model, such as very low orbits where atmospheric drag models may not be adequate to achieve the required accuracy, aiding from an IMU (inertial measurement unit) or other sensor will be added. The KOOL approach is based on research JPL has done to allow signal recovery from weak and scintillating signals observed during the use of GPS signals for limb sounding of the Earth s atmosphere. That approach uses the onboard PVT (position, velocity, time) solution to generate predictions for the range, range rate, and acceleration of the low-SNR signal. The low- SNR signal data are captured by a directed open loop. KOOL builds on the previous open loop tracking by including feedback and observable generation from the weak-signal channels so that the MSR receiver will continue to track and provide PVT, range, and Doppler data, even when all channels have low SNR.

  16. Fabrication techniques for superconducting readout loops

    NASA Technical Reports Server (NTRS)

    Payne, J. E.

    1982-01-01

    Procedures for the fabrication of superconducting readout loops out of niobium on glass substrates were developed. A computer program for an existing fabrication system was developed. Both positive and negative resist procedures for the production of the readout loops were investigated. Methods used to produce satisfactory loops are described and the various parameters affecting the performance of the loops are analyzed.

  17. Filter for third order phase locked loops

    NASA Technical Reports Server (NTRS)

    Crow, R. B.; Tausworthe, R. C. (Inventor)

    1973-01-01

    Filters for third-order phase-locked loops are used in receivers to acquire and track carrier signals, particularly signals subject to high doppler-rate changes in frequency. A loop filter with an open-loop transfer function and set of loop constants, setting the damping factor equal to unity are provided.

  18. Study of the Open Loop and Closed Loop Oscillator Techniques

    SciTech Connect

    Imel, George R.; Baker, Benjamin; Riley, Tony; Langbehn, Adam; Aryal, Harishchandra; Benzerga, M. Lamine

    2015-04-11

    This report presents the progress and completion of a five-year study undertaken at Idaho State University of the measurement of very small worth reactivity samples comparing open and closed loop oscillator techniques.The study conclusively demonstrated the equivalency of the two techniques with regard to uncertainties in reactivity values, i.e., limited by reactor noise. As those results are thoroughly documented in recent publications, in this report we will concentrate on the support work that was necessary. For example, we describe in some detail the construction and calibration of a pilot rod for the closed loop system. We discuss the campaign to measure the required reactor parameters necessary for inverse-kinetics. Finally, we briefly discuss the transfer of the open loop technique to other reactor systems.

  19. A single amino acid substitution in the C4 region in gp120 confers enhanced neutralization of HIV-1 by modulating CD4 binding sites and V3 loop.

    PubMed

    Ringe, Rajesh; Sharma, Deepak; Zolla-Pazner, Susan; Phogat, Sanjay; Risbud, Arun; Thakar, Madhuri; Paranjape, Ramesh; Bhattacharya, Jayanta

    2011-09-30

    Identification of vulnerability in the HIV-1 envelope (Env) will aid in Env-based vaccine design. We recently found an HIV-1 clade C Env clone (4-2.J45) amplified from a recently infected Indian patient showing exceptional neutralization sensitivity to autologous plasma in contrast to other autologous Envs obtained at the same time point. By constructing chimeric Envs and fine mapping between sensitive and resistant Env clones, we found that substitution of highly conserved isoleucine (I) with methionine (M) (ATA to ATG) at position 424 in the C4 domain conferred enhanced neutralization sensitivity of Env-pseudotyped viruses to autologous and heterologous plasma antibodies. When tested against monoclonal antibodies targeting different sites in gp120 and gp41, Envs expressing M424 showed significant sensitivity to anti-V3 monoclonal antibodies and modestly to sCD4 and b12. Substitution of I424M in unrelated Envs also showed similar neutralization phenotype, indicating that M424 in C4 region induces exposure of neutralizing epitopes particularly in CD4 binding sites and V3 loop. PMID:21851958

  20. Top3-Rmi1 dissolve Rad51-mediated D-loops by a topoisomerase-based mechanism

    PubMed Central

    Fasching, Clare L.; Cejka, Petr; Kowalczykowski, Stephen C.; Heyer, Wolf-Dietrich

    2015-01-01

    Summary The displacement loop (D-loop) is the DNA strand invasion product formed during homologous recombination. Disruption of nascent D-loops represents a mechanism of anti-recombination. During Synthesis-Dependent Strand Annealing D-loop disruption after extension of the invading strand is an integral step of the pathway and ensures a non-crossover outcome. The proteins implicated in D-loop disruption are DNA motor proteins/helicases acting by migrating DNA junctions. Here we report an unanticipated mechanism of D-loop dissolution mediated by DNA topoisomerase 3 (Top3) and dependent on its catalytic activity. D-loop dissolution catalyzed by yeast Top3 is highly specific for yeast Rad51/Rad54-mediated D-loops, whereas protein-free D-loops or D-loop mediated by bacterial RecA protein or human RAD51/RAD54 resist dissolution. Also the human Topoisomerase IIIα-RMI1–RMI2 complex is capable of dissolving D-loops. Consistent with genetic data, we suggest that the extreme growth defect and hyper-recombination phenotype of Top3-deficient yeast cells is in part a result of unprocessed D-loops. PMID:25699708

  1. Loop residues and catalysis in OMP synthase.

    PubMed

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

    2012-06-01

    Residue-to-alanine mutations and a two-amino acid deletion have been made in the highly conserved catalytic loop (residues 100-109) of Salmonella typhimurium OMP synthase (orotate phosphoribosyltransferase, EC 2.4.2.10). As described previously, the K103A mutant enzyme exhibited a 10(4)-fold decrease in k(cat)/K(M) for PRPP; the K100A enzyme suffered a 50-fold decrease. Alanine mutations at His105 and Glu107 produced 40- and 7-fold decreases in k(cat)/K(M), respectively, and E101A, D104A, and G106A were slightly faster than the wild-type (WT) in terms of k(cat), with minor effects on k(cat)/K(M). Equilibrium 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 showed that K103A and E107A had lost the burst of product formation in each direction that indicated rapid on-enzyme chemistry for WT, but that the burst was retained by H105A. Δ102Δ106, a loop-shortened enzyme with Ala102 and Gly106 deleted, showed a 10(4)-fold reduction of k(cat) but almost unaltered K(D) values for all four substrate molecules. The 20% (i.e., 1.20) intrinsic [1'-(3)H]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, gave a [1'-(3)H]OMP KIE of 1.21 ± 0.0005, and E107A (1.179 ± 0.0049) also gave high values. These results are interpreted in the context of the X-ray structure of the complete substrate complex for the enzyme [Grubmeyer, C., Hansen, M. R., Fedorov, A. A., and Almo, S. C. (2012) Biochemistry 51 (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

  2. Bandwidth controller for phase-locked-loop

    NASA Technical Reports Server (NTRS)

    Brockman, Milton H. (Inventor)

    1992-01-01

    A phase locked loop utilizing digital techniques to control the closed loop bandwidth of the RF carrier phase locked loop in a receiver provides high sensitivity and a wide dynamic range for signal reception. After analog to digital conversion, a digital phase locked loop bandwidth controller provides phase error detection with automatic RF carrier closed loop tracking bandwidth control to accommodate several modes of transmission.

  3. 40 CFR 76.12 - Phase I NOX compliance extension.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... (CONTINUED) ACID RAIN NITROGEN OXIDES EMISSION REDUCTION PROGRAM § 76.12 Phase I NOX compliance extension. (a... Administrator will approve the plan and revise the Acid Rain permit governing the unit in the plan in order to... the complete petition. The Acid Rain permit governing the unit will be revised in order to...

  4. 40 CFR 76.12 - Phase I NOX compliance extension.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... (CONTINUED) ACID RAIN NITROGEN OXIDES EMISSION REDUCTION PROGRAM § 76.12 Phase I NOX compliance extension. (a... Administrator will approve the plan and revise the Acid Rain permit governing the unit in the plan in order to... the complete petition. The Acid Rain permit governing the unit will be revised in order to...

  5. 40 CFR 76.12 - Phase I NOX compliance extension.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... (CONTINUED) ACID RAIN NITROGEN OXIDES EMISSION REDUCTION PROGRAM § 76.12 Phase I NOX compliance extension. (a... Administrator will approve the plan and revise the Acid Rain permit governing the unit in the plan in order to... the complete petition. The Acid Rain permit governing the unit will be revised in order to...

  6. 40 CFR 76.12 - Phase I NOX compliance extension.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... (CONTINUED) ACID RAIN NITROGEN OXIDES EMISSION REDUCTION PROGRAM § 76.12 Phase I NOX compliance extension. (a... Administrator will approve the plan and revise the Acid Rain permit governing the unit in the plan in order to... the complete petition. The Acid Rain permit governing the unit will be revised in order to...

  7. Digital phase-lock loop

    NASA Technical Reports Server (NTRS)

    Thomas, Jr., Jess B. (Inventor)

    1991-01-01

    An improved digital phase lock loop incorporates several distinctive features that attain better performance at high loop gain and better phase accuracy. These features include: phase feedback to a number-controlled oscillator in addition to phase rate; analytical tracking of phase (both integer and fractional cycles); an amplitude-insensitive phase extractor; a more accurate method for extracting measured phase; a method for changing loop gain during a track without loss of lock; and a method for avoiding loss of sampled data during computation delay, while maintaining excellent tracking performance. The advantages of using phase and phase-rate feedback are demonstrated by comparing performance with that of rate-only feedback. Extraction of phase by the method of modeling provides accurate phase measurements even when the number-controlled oscillator phase is discontinuously updated.

  8. Criteria for saturated magnetization loop

    NASA Astrophysics Data System (ADS)

    Harres, A.; Mikhov, M.; Skumryev, V.; Andrade, A. M. H. de; Schmidt, J. E.; Geshev, J.

    2016-03-01

    Proper estimation of magnetization curve parameters is vital in studying magnetic systems. In the present article, criteria for discrimination non-saturated (minor) from saturated (major) hysteresis loops are proposed. These employ the analysis of (i) derivatives of both ascending and descending branches of the loop, (ii) remanent magnetization curves, and (iii) thermomagnetic curves. Computational simulations are used in order to demonstrate their validity. Examples illustrating the applicability of these criteria to well-known real systems, namely Fe3O4 and Ni fine particles, are provided. We demonstrate that the anisotropy-field value estimated from a visual examination of an only apparently major hysteresis loop could be more than two times lower than the real one.

  9. Waves in Solar Coronal Loops

    NASA Astrophysics Data System (ADS)

    Wang, T. J.

    2016-02-01

    The corona is visible in the optical band only during a total solar eclipse or with a coronagraph. Coronal loops are believed to be plasma-filled closed magnetic flux anchored in the photosphere. Based on the temperature regime, they are generally classified into cool, warm, and hot loops. The magnetized coronal structures support propagation of various types of magnetohydrodynamics (MHD) waves. This chapter reviews the recent progress made in studies based on observations of four types of wave phenomena mainly occurring in coronal loops of active regions, including: flare-excited slow-mode waves; impulsively excited kink-mode waves; propagating slow magnetoacoustic waves; and ubiquitous propagating kink (Alfvénic) waves. This review not only comprehensively discusses these waves and coronal seismology but also topics that are newly emerging or hotly debated in order to provide the reader with useful guidance on further studies.

  10. All digital pulsewidth control loop

    NASA Astrophysics Data System (ADS)

    Huang, Hong-Yi; Jan, Shiun-Dian; Pu, Ruei-Iun

    2013-03-01

    This work presents an all-digital pulsewidth control loop (ADPWCL). The proposed system accepts a wide range of input duty cycles and performs a fast correction to the target output pulsewidth. An all-digital delay-locked loop (DLL) with fast locking time using a simplified time to digital converter and a new differential two-step delay element is proposed. The area of the delay element is much smaller than that in conventional designs, while having the same delay range. A test chip is verified in a 0.18-µm CMOS process. The measured duty cycle ranges from 4% to 98% with 7-bit resolution.

  11. Loop quantum cosmology: an overview

    NASA Astrophysics Data System (ADS)

    Ashtekar, Abhay

    2009-04-01

    A brief overview of loop quantum cosmology of homogeneous isotropic models is presented with emphasis on the origin of and subtleties associated with the resolution of big bang and big crunch singularities. These results bear out the remarkable intuition that John Wheeler had. Discussion is organized at two levels. The the main text provides a bird’s eye view of the subject that should be accessible to non-experts. Appendices address conceptual and technical issues that are often raised by experts in loop quantum gravity and string theory.

  12. Modeling of compact loop antennas

    NASA Astrophysics Data System (ADS)

    Baity, F. W.

    1987-09-01

    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 sub-tuned RDL antennas. Calculations using the model have been compared with measurements on full-scale mock-ups of RDL 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 the Compact Ignition Tokamak (CIT).

  13. Many Ways to Loop DNA

    PubMed Central

    Griffith, Jack D.

    2013-01-01

    In the 1960s, I developed methods for directly visualizing DNA and DNA-protein complexes using an electron microscope. This made it possible to examine the shape of DNA and to visualize proteins as they fold and loop DNA. Early applications included the first visualization of true nucleosomes and linkers and the demonstration that repeating tracts of adenines can cause a curvature in DNA. The binding of DNA repair proteins, including p53 and BRCA2, has been visualized at three- and four-way junctions in DNA. The trombone model of DNA replication was directly verified, and the looping of DNA at telomeres was discovered. PMID:24005675

  14. Force fluctuation in a semiflexible loop

    NASA Astrophysics Data System (ADS)

    Waters, James; Kim, Harold; Harold Kim Team

    DNA-binding proteins can regulate genetic expression by holding two sites in close proximity, forming a closed loop. Such complexes may require strong bending of DNA segments on the order of one persistence length or less. Both this elastic bending and the thermal fluctuations of the DNA molecule are necessary to describe the resulting behavior. To explore this problem, we consider a discrete model of a wormlike chain, kept in the fixed extension ensemble. By using a novel method to sample conformations in both position and momentum space, we can obtain a distribution of constraint forces as a function of chain length, extension, and flexibility. Our coarse-grained model allows us to explore the space of these parameters more efficiently than a detailed molecular dynamics approach. We find that increasing contour length decreases average force by relieving bending stress, but that the additional freedom allows fluctuations in the constraint force to increase. This implies that the probability of large forces may go up even as the mean goes down, impacting the lifetime of such bound states in a way unforeseen by purely equilibrium methods.

  15. Mobile Applications for Extension

    ERIC Educational Resources Information Center

    Drill, Sabrina L.

    2012-01-01

    Mobile computing devices (smart phones, tablets, etc.) are rapidly becoming the dominant means of communication worldwide and are increasingly being used for scientific investigation. This technology can further our Extension mission by increasing our power for data collection, information dissemination, and informed decision-making. Mobile…

  16. Extensions of Natural Hamiltonians

    NASA Astrophysics Data System (ADS)

    Rastelli, G.

    2014-03-01

    Given an n-dimensional natural Hamiltonian L on a Riemannian or pseudo-Riemannian manifold, we call "extension" of L the n+1 dimensional Hamiltonian H = ½p2u + α(u)L + β(u) with new canonically conjugated coordinates (u,pu). For suitable L, the functions α and β can be chosen depending on any natural number m such that H admits an extra polynomial first integral in the momenta of degree m, explicitly determined in the form of the m-th power of a differential operator applied to a certain function of coordinates and momenta. In particular, if L is maximally superintegrable (MS) then H is MS also. Therefore, the extension procedure allows the creation of new superintegrable systems from old ones. For m=2, the extra first integral generated by the extension procedure determines a second-order symmetry operator of a Laplace-Beltrami quantization of H, modified by taking in account the curvature of the configuration manifold. The extension procedure can be applied to several Hamiltonian systems, including the three-body Calogero and Wolfes systems (without harmonic term), the Tremblay-Turbiner-Winternitz system and n-dimensional anisotropic harmonic oscillators. We propose here a short review of the known results of the theory and some previews of new ones.

  17. Job Enrichment in Extension.

    ERIC Educational Resources Information Center

    Fourman, Louis S.; Jones, Jo

    1997-01-01

    Interviews with 10 participants in Ohio State University's job enrichment program for midcareer extension agents found that 5 returned to their same jobs after the experience but only 2 felt challenged/renewed. Part-time participation while working made it difficult to balance responsibilities. More information and a structured orientation were…

  18. Identifying High Extension Communicators

    ERIC Educational Resources Information Center

    Lionberger, Herbert F.; Pope, LaVern

    1978-01-01

    Reports results of a survey of social science faculty at the University of Missouri-Columbia to find the extent to which they engaged in communicating information to the public through university extension, with implications for changes in the university rewards system. (MF)

  19. Vocabulary Extension through Poetry.

    ERIC Educational Resources Information Center

    Surajlal, K. C.

    1986-01-01

    Based on the notion that teaching vocabulary extension in isolation makes little impact on students, a three-part exercise, designed to develop students' vocabulary through poetry while providing meaningful enjoyment, uses the poem "The Hawk" by A. C. Benson. In the first class period, students are introduced to both the exercise and the poem and…

  20. Extensive Reading in Japanese

    ERIC Educational Resources Information Center

    Hitosugi, Claire Ikumi; Day, Richard R.

    2004-01-01

    This article discusses how we incorporated an extensive reading (ER) program into a second semester Japanese course at the University of Hawai'i using Japanese children's literature. After summarizing the ten principles of ER, we describe how we addressed six critical issues faced while introducing ER into the course. We also discuss the outcomes…

  1. Extending Extensive Reading

    ERIC Educational Resources Information Center

    Day, Richard R.

    2015-01-01

    The April 2015 issue of "Reading in a Foreign Language" featured a discussion forum on extensive reading (ER). Most of the authors, recognized authorities on ER, discussed their views of the principles of ER, particularly in establishing and conducting ER programs. The purpose of this discussion is to review developments in the practice…

  2. Simulations of Solar Jets Confined by Coronal Loops

    NASA Astrophysics Data System (ADS)

    Wyper, P. F.; DeVore, C. R.

    2016-03-01

    Coronal jets are collimated, dynamic events that occur over a broad range of spatial scales in the solar corona. In the open magnetic field of coronal holes, jets form quasi-radial spires that can extend far out into the heliosphere, while in closed-field regions the jet outflows are confined to the corona. We explore the application of the embedded-bipole model to jets occurring in closed coronal loops. In this model, magnetic free energy is injected slowly by footpoint motions that introduce twist within the closed dome of the jet source region, and is released rapidly by the onset of an ideal kink-like instability. Two length scales characterize the system: the width (N) of the jet source region and the footpoint separation (L) of the coronal loop that envelops the jet source. We find that both the conditions for initiation and the subsequent dynamics are highly sensitive to the ratio L/N. The longest-lasting and most energetic jets occur along long coronal loops with large L/N ratios, and share many of the features of open-field jets, while smaller L/N ratios produce shorter-duration, less energetic jets that are affected by reflections from the far-loop footpoint. We quantify the transition between these behaviors and show that our model replicates key qualitative and quantitative aspects of both quiet Sun and active-region loop jets. We also find that the reconnection between the closed dome and surrounding coronal loop is very extensive: the cumulative reconnected flux at least matches the total flux beneath the dome for small L/N, and is more than double that value for large L/N.

  3. Role of connecting loop I in catalysis and allosteric regulation of human glucokinase

    PubMed Central

    Martinez, Juliana A; Larion, Mioara; Conejo, Maria S; Porter, Carol M; Miller, Brian G

    2014-01-01

    Glucokinase (GCK, hexokinase IV) is a monomeric enzyme with a single glucose binding site that displays steady-state kinetic cooperativity, a functional characteristic that affords allosteric regulation of GCK activity. Structural evidence suggests that connecting loop I, comprised of residues 47–71, facilitates cooperativity by dictating the rate and scope of motions between the large and small domains of GCK. Here we investigate the impact of varying the length and amino acid sequence of connecting loop I upon GCK cooperativity. We find that sequential, single amino acid deletions from the C-terminus of connecting loop I cause systematic decreases in cooperativity. Deleting up to two loop residues leaves the kcat value unchanged; however, removing three or more residues reduces kcat by 1000-fold. In contrast, the glucose K0.5 and KD values are unaffected by shortening the connecting loop by up to six residues. Substituting alanine or glycine for proline-66, which adopts a cis conformation in some GCK crystal structures, does not alter cooperativity, indicating that cis/trans isomerization of this loop residue does not govern slow conformational reorganizations linked to hysteresis. Replacing connecting loop I with the corresponding loop sequence from the catalytic domain of the noncooperative isozyme human hexokinase I (HK-I) eliminates cooperativity without impacting the kcat and glucose K0.5 values. Our results indicate that catalytic turnover requires a minimal length of connecting loop I, whereas the loop has little impact upon the binding affinity of GCK for glucose. We propose a model in which the primary structure of connecting loop I affects cooperativity by influencing conformational dynamics, without altering the equilibrium distribution of GCK conformations. PMID:24723372

  4. Role of connecting loop I in catalysis and allosteric regulation of human glucokinase.

    PubMed

    Martinez, Juliana A; Larion, Mioara; Conejo, Maria S; Porter, Carol M; Miller, Brian G

    2014-07-01

    Glucokinase (GCK, hexokinase IV) is a monomeric enzyme with a single glucose binding site that displays steady-state kinetic cooperativity, a functional characteristic that affords allosteric regulation of GCK activity. Structural evidence suggests that connecting loop I, comprised of residues 47-71, facilitates cooperativity by dictating the rate and scope of motions between the large and small domains of GCK. Here we investigate the impact of varying the length and amino acid sequence of connecting loop I upon GCK cooperativity. We find that sequential, single amino acid deletions from the C-terminus of connecting loop I cause systematic decreases in cooperativity. Deleting up to two loop residues leaves the kcat value unchanged; however, removing three or more residues reduces kcat by 1000-fold. In contrast, the glucose K0.5 and KD values are unaffected by shortening the connecting loop by up to six residues. Substituting alanine or glycine for proline-66, which adopts a cis conformation in some GCK crystal structures, does not alter cooperativity, indicating that cis/trans isomerization of this loop residue does not govern slow conformational reorganizations linked to hysteresis. Replacing connecting loop I with the corresponding loop sequence from the catalytic domain of the noncooperative isozyme human hexokinase I (HK-I) eliminates cooperativity without impacting the kcat and glucose K0.5 values. Our results indicate that catalytic turnover requires a minimal length of connecting loop I, whereas the loop has little impact upon the binding affinity of GCK for glucose. We propose a model in which the primary structure of connecting loop I affects cooperativity by influencing conformational dynamics, without altering the equilibrium distribution of GCK conformations. PMID:24723372

  5. Closed-Loop Neuromorphic Benchmarks

    PubMed Central

    Stewart, Terrence C.; DeWolf, Travis; Kleinhans, Ashley; Eliasmith, Chris

    2015-01-01

    Evaluating the effectiveness and performance of neuromorphic hardware is difficult. It is even more difficult when the task of interest is a closed-loop task; that is, a task where the output from the neuromorphic hardware affects some environment, which then in turn affects the hardware's future input. However, closed-loop situations are one of the primary potential uses of neuromorphic hardware. To address this, we present a methodology for generating closed-loop benchmarks that makes use of a hybrid of real physical embodiment and a type of “minimal” simulation. Minimal simulation has been shown to lead to robust real-world performance, while still maintaining the practical advantages of simulation, such as making it easy for the same benchmark to be used by many researchers. This method is flexible enough to allow researchers to explicitly modify the benchmarks to identify specific task domains where particular hardware excels. To demonstrate the method, we present a set of novel benchmarks that focus on motor control for an arbitrary system with unknown external forces. Using these benchmarks, we show that an error-driven learning rule can consistently improve motor control performance across a randomly generated family of closed-loop simulations, even when there are up to 15 interacting joints to be controlled. PMID:26696820

  6. Closed-Loop Neuromorphic Benchmarks.

    PubMed

    Stewart, Terrence C; DeWolf, Travis; Kleinhans, Ashley; Eliasmith, Chris

    2015-01-01

    Evaluating the effectiveness and performance of neuromorphic hardware is difficult. It is even more difficult when the task of interest is a closed-loop task; that is, a task where the output from the neuromorphic hardware affects some environment, which then in turn affects the hardware's future input. However, closed-loop situations are one of the primary potential uses of neuromorphic hardware. To address this, we present a methodology for generating closed-loop benchmarks that makes use of a hybrid of real physical embodiment and a type of "minimal" simulation. Minimal simulation has been shown to lead to robust real-world performance, while still maintaining the practical advantages of simulation, such as making it easy for the same benchmark to be used by many researchers. This method is flexible enough to allow researchers to explicitly modify the benchmarks to identify specific task domains where particular hardware excels. To demonstrate the method, we present a set of novel benchmarks that focus on motor control for an arbitrary system with unknown external forces. Using these benchmarks, we show that an error-driven learning rule can consistently improve motor control performance across a randomly generated family of closed-loop simulations, even when there are up to 15 interacting joints to be controlled. PMID:26696820

  7. Closing the Loop with Exercises

    ERIC Educational Resources Information Center

    Altizer, Andy

    2008-01-01

    Conducting exercises provides a critical bridge between the theory of an Emergency Action Plan and its effective implementation. When conducted properly, exercises can fill the gap between training and after-action review to close the preparedness loop--before an actual emergency occurs. Often exercises are planned and conducted on campus based on…

  8. Manchester transition tracking loop (MTTL)

    NASA Technical Reports Server (NTRS)

    Cellier, A.; Ma, L. N.; Huey, D. C.

    1977-01-01

    In new tracking loop, separate phase detection algorithm is incorporated for acquisition; programmed acquisition-to-track sequence includes automatic bandwidth switching. Additionally, system has very effective phase detection signal-to-noise ratio and can operate at any rate by changing master clock frequency. All system parameters remain constant.

  9. Bimodal loop-gap resonator

    NASA Astrophysics Data System (ADS)

    Piasecki, W.; Froncisz, W.; Hyde, James S.

    1996-05-01

    A bimodal loop-gap resonator for use in electron paramagnetic resonance (EPR) spectroscopy at S band is described. It consists of two identical one-loop-one-gap resonators in coaxial juxtaposition. In one mode, the currents in the two loops are parallel and in the other antiparallel. By introducing additional capacitors between the loops, the frequencies of the two modes can be made to coincide. Details are given concerning variable coupling to each mode, tuning of the resonant frequency of one mode to that of the other, and adjustment of the isolation between modes. An equivalent circuit is given and network analysis carried out both experimentally and theoretically. EPR applications are described including (a) probing of the field distributions with DPPH, (b) continuous wave (cw) EPR with a spin-label line sample, (c) cw electron-electron double resonance (ELDOR), (d) modulation of saturation, and (e) saturation-recovery (SR) EPR. Bloch induction experiments can be performed when the sample extends half way through the structure, but microwave signals induced by Mx and My components of magnetization cancel when it extends completely through. This latter situation is particularly favorable for SR, modulation of saturation, and ELDOR experiments, which depend on observing Mz indirectly using a second weak observing microwave source.

  10. Phase diagram and nucleation in the Polyakov-loop-extended quark-meson truncation of QCD with the unquenched Polyakov-loop potential

    NASA Astrophysics Data System (ADS)

    Stiele, Rainer; Schaffner-Bielich, Jürgen

    2016-05-01

    The unquenching of the Polyakov-loop potential has been shown to be an important improvement for the description of the phase structure and thermodynamics of strongly interacting matter at zero quark chemical potentials with Polyakov-loop-extended chiral models. This work constitutes the first application of the quark backreaction on the Polyakov-loop potential at nonzero density. The observation is that it links the chiral and deconfinement phase transitions also at small temperatures and large quark chemical potentials. The build-up of the surface tension in the Polyakov-loop-extended quark-meson model is explored by investigating the two- and 2 +1 -flavor quark-meson model and analyzing the impact of the Polyakov-loop extension. In general, the order of magnitude of the surface tension is given by the chiral phase transition. The coupling of the chiral and deconfinement transitions with the unquenched Polyakov-loop potential leads to the fact that the Polyakov loop contributes at all temperatures.

  11. Minimalist explicit solvation models for surface loops in proteins.

    PubMed

    White, Ronald P; Meirovitch, Hagai

    2006-01-01

    We have performed molecular dynamics simulations of protein surface loops solvated by explicit water, where a prime focus of the study is the small numbers (e.g., ~100) of explicit water molecules employed. The models include only part of the protein (typically 500 - 1000 atoms), and the water molecules are restricted to a region surrounding the loop. In this study, the number of water molecules (N(w)) is systematically varied, and convergence with large N(w) is monitored to reveal N(w)(min), the minimum number required for the loop to exhibit realistic (fully hydrated) behavior. We have also studied protein surface coverage, as well as diffusion and residence times for water molecules as a function of N(w). A number of other modeling parameters are also tested. These include the number of environmental protein atoms explicitly considered in the model, as well as two ways to constrain the water molecules to the vicinity of the loop (where we find one of these methods to perform better when N(w) is small). The results (for RMSD and its fluctuations for four loops) are further compared to much larger, fully solvated systems (using ~10,000 water molecules under periodic boundary conditions and Ewald electrostatics), and to results for the GBSA implicit solvation model. We find that the loop backbone can stabilize with a surprisingly small number of water molecules (as low as 5 molecules per amino acid residue). The side chains of the loop require somewhat larger N(w), where the atomic fluctuations become too small if N(w) is further reduced. Thus, in general, we find adequate hydration to occur at roughly 12 water molecules per residue. This is an important result, because at this hydration level, computational times are comparable to those required for GBSA. Therefore these "minimalist explicit models" can provide a viable and potentially more accurate alternative. The importance of protein loop modeling is discussed in the context of these, and other, loop models

  12. A conserved P-loop anchor limits the structural dynamics that mediate nucleotide dissociation in EF-Tu

    PubMed Central

    Mercier, Evan; Girodat, Dylan; Wieden, Hans-Joachim

    2015-01-01

    The phosphate-binding loop (P-loop) is a conserved sequence motif found in mononucleotide-binding proteins. Little is known about the structural dynamics of this region and its contribution to the observed nucleotide binding properties. Understanding the underlying design principles is of great interest for biomolecular engineering applications. We have used rapid-kinetics measurements in vitro and molecular dynamics (MD) simulations in silico to investigate the relationship between GTP-binding properties and P-loop structural dynamics in the universally conserved Elongation Factor (EF) Tu. Analysis of wild type EF-Tu and variants with substitutions at positions in or adjacent to the P-loop revealed a correlation between P-loop flexibility and the entropy of activation for GTP dissociation. The same variants demonstrate more backbone flexibility in two N-terminal amino acids of the P-loop during force-induced EF-Tu·GTP dissociation in Steered Molecular Dynamics simulations. Amino acids Gly18 and His19 are involved in stabilizing the P-loop backbone via interactions with the adjacent helix C. We propose that these P-loop/helix C interactions function as a conserved P-loop anchoring module and identify the presence of P-loop anchors within several GTPases and ATPases suggesting their evolutionary conservation. PMID:25566871

  13. Inherent directionality explains the lack of feedback loops in empirical networks

    PubMed Central

    Domínguez-García, Virginia; Pigolotti, Simone; Muñoz, Miguel A.

    2014-01-01

    We explore the hypothesis that the relative abundance of feedback loops in many empirical complex networks is severely reduced owing to the presence of an inherent global directionality. Aimed at quantifying this idea, we propose a simple probabilistic model in which a free parameter γ controls the degree of inherent directionality. Upon strengthening such directionality, the model predicts a drastic reduction in the fraction of loops which are also feedback loops. To test this prediction, we extensively enumerated loops and feedback loops in many empirical biological, ecological and socio-technological directed networks. We show that, in almost all cases, empirical networks have a much smaller fraction of feedback loops than network randomizations. Quite remarkably, this empirical finding is quantitatively reproduced, for all loop lengths, by our model by fitting its only parameter γ. Moreover, the fitted value of γ correlates quite well with another direct measurement of network directionality, performed by means of a novel algorithm. We conclude that the existence of an inherent network directionality provides a parsimonious quantitative explanation for the observed lack of feedback loops in empirical networks. PMID:25531727

  14. Inherent directionality explains the lack of feedback loops in empirical networks.

    PubMed

    Domínguez-García, Virginia; Pigolotti, Simone; Muñoz, Miguel A

    2014-01-01

    We explore the hypothesis that the relative abundance of feedback loops in many empirical complex networks is severely reduced owing to the presence of an inherent global directionality. Aimed at quantifying this idea, we propose a simple probabilistic model in which a free parameter γ controls the degree of inherent directionality. Upon strengthening such directionality, the model predicts a drastic reduction in the fraction of loops which are also feedback loops. To test this prediction, we extensively enumerated loops and feedback loops in many empirical biological, ecological and socio-technological directed networks. We show that, in almost all cases, empirical networks have a much smaller fraction of feedback loops than network randomizations. Quite remarkably, this empirical finding is quantitatively reproduced, for all loop lengths, by our model by fitting its only parameter γ. Moreover, the fitted value of γ correlates quite well with another direct measurement of network directionality, performed by means of a novel algorithm. We conclude that the existence of an inherent network directionality provides a parsimonious quantitative explanation for the observed lack of feedback loops in empirical networks. PMID:25531727

  15. Coronal Loop Mapping to Infer the Best Magnetic Field Models for Active Region Prominences

    NASA Astrophysics Data System (ADS)

    Gary, G. Allen; Hu, Qiang; Lee, Jong Kwan

    2014-01-01

    This article comments on the results of a new, rapid, and flexible manual method to map on-disk individual coronal loops of a two-dimensional EUV image into the three-dimensional coronal loops. The method by Gary, Hu, and Lee (2013) employs cubic Bézier splines to map coronal loops using only four free parameters per loop. A set of 2D splines for coronal loops is transformed to the best 3D pseudo-magnetic field lines for a particular coronal model. The results restrict the magnetic field models derived from extrapolations of magnetograms to those admissible and inadmissible via a fitness parameter. This method uses the minimization of the misalignment angles between the magnetic field model and the best set of 3D field lines that match a set of closed coronal loops. We comment on the implication of the fitness parameter in connection with the magnetic free energy and comment on extensions of our earlier work by considering the issues of employing open coronal loops or employing partial coronal loop.

  16. Evolution in a Braided Loop Ensemble

    NASA Video Gallery

    This braided loop has several loops near the 'base' that appear to be unwinding with significant apparent outflow. This is evidence of untwisting, and the braided structure also seeming to unwind w...

  17. The arrangement of disulfide loops in human alpha 2-HS glycoprotein. Similarity to the disulfide bridge structures of cystatins and kininogens.

    PubMed

    Kellermann, J; Haupt, H; Auerswald, E A; Müller-Ester, W

    1989-08-25

    The complete disulfide loop structure of human alpha 2-HS glycoprotein has been elucidated. alpha 2-HS glycoprotein isolated from human plasma was found to be a two-chain protein composed of a heavy and a light chain. The heavy chain comprises the A-chain of alpha 2-HS glycoprotein (Yoshioka, Y., Gejyo, F., Marti, T., Rickli, E. E., Bürgi, W., Offner, G. D., Troxler, R. F., and Schmid, K. (1986) J. Biol. Chem. 261, 1665-1676) and part of the connecting peptide which has been predicted from the corresponding cDNA sequence (Lee, C. C., Bowman, B. H., and Yang, F. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 4403-4407), whereas the light chain corresponds to the beta-chain of alpha 2-HS glycoprotein (Gejyo, F., Chang, J. L., Bürgi, W., Schmid, K., Offner, G. D., Troxler, R. F., Van Halbeek, H., Dorland, L., Gerwig, G. J., Vliegenthart, J. F. G. (1983) J. Biol. Chem. 258, 4966-4971). Twelve half-cystine residues are present in the alpha 2-HS glycoprotein molecule, and 11 of them are positioned in the heavy chain and a single one in the light chain of the molecule; they form six disulfide bridges. The first and the last half-cystine residues of the amino acid sequence of alpha 2-HS glycoprotein are engaged in the formation of a loop spanning the extreme NH2- and COOH-terminal portions of the molecule, thereby connecting the heavy and light chains. The other 10 half-cystines residues are linked consecutively in the heavy chain and form five loops which span 4-19 amino acid residues. Among them are two pairs of loops which are characterized by mutual sequence homology. The particular arrangement of disulfide loops in alpha 2-HS glycoprotein is similar to the patterns of linearly arranged and tandemly repeated disulfide loops of cysteine proteinase inhibitors, i.e. the cystatins and the kininogens. It is concluded that alpha 2-HS glycoprotein represents a structural prototype of a novel family among the cystatin superfamily, characterized by the presence of two cystatin

  18. Simultaneous determination of arsenic, cadmium, calcium, chromium, cobalt, copper, iron, lead, magnesium, manganese, molybdenum, nickel, selenium, and zinc in fertilizers by microwave acid digestion and inductively coupled plasma-optical emission spectrometry detection: single-laboratory validation of a modification and extension of AOAC 2006.03.

    PubMed

    Webb, Sharon; Bartos, James; Boles, Rhonda; Hasty, Elaine; Thuotte, Ethel; Thiex, Nancy J

    2014-01-01

    A single-laboratory validation study was conducted for the simultaneous determination of arsenic, cadmium, calcium, cobalt, copper, chromium, iron, lead, magnesium, manganese, molybdenum, nickel, selenium, and zinc in all major types of commercial fertilizer products by microwave digestion and inductively coupled plasma-optical emission spectroscopy analysis. This validation study proposes an extension and modification of AOAC 2006.03. The extension is the inclusion of calcium, copper, iron, magnesium, manganese, and zinc, and the modification is incorporation of hydrochloric acid in the digestion system. This dual acid digestion utilizes both hydrochloric and nitric acids in a 3 to 9 mL volume ratio/100 mL. In addition to 15 of the 30 original validation materials used in the 2006.03 collaborative study, National Institute of Standards and Technology Standard Reference Material 695 and Magruder 2009-06 were incorporated as accuracy materials. The main benefits of this proposed method are a significant increase in laboratory efficiency when compared to the use of both AOAC Methods 965.09 and 2006.03 to achieve the same objective and an enhanced recovery of several metals. PMID:25051614

  19. Fragmentation of cosmic-string loops

    NASA Technical Reports Server (NTRS)

    York, Thomas

    1989-01-01

    The fragmentation of cosmic string loops is discussed, and the results of a simulation of this process are presented. The simulation can evolve any of a large class of loops essentially exactly, including allowing fragments that collide to join together. Such reconnection enhances the production of small fragments, but not drastically. With or without reconnections, the fragmentation process produces a collection of nonself-intersecting loops whose typical length is on the order of the persistence length of the initial loop.

  20. Sea urchin egg mitochondrial DNA contains a short displacement loop (D-loop) in the replication origin region.

    PubMed Central

    Jacobs, H T; Herbert, E R; Rankine, J

    1989-01-01

    Based on solution hybridization using single-stranded probes, native mitochondrial DNA extracted from sea urchin eggs contains a displacement-loop (D-loop) of approximately 70-80 nt. This maps to the single extended unassigned sequence of the genome, between the genes for tRNA(thr) and tRNA(pro), which also appears to contain the origin of first-strand replication. The D-loop commences at or close to a site of supercoil-dependent S1 nuclease hypersensitivity, adjacent to a run of 20 consecutive C residues, terminates near to the boundary of tRNA(thr), and appears to be composed at least partly of RNA, based on the sensitivity of the assays to RNase H. These experiments imply that the mechanisms of replication initiation in sea urchin and vertebrate mtDNAs are very similar, and suggest that the developmental restriction on mtDNA synthesis in eggs and embryos is maintained at the level of D-loop extension. Images PMID:2555781

  1. Agricultural Extension: Who Uses It?

    ERIC Educational Resources Information Center

    Nolan, Michael; Lasley, Paul

    1979-01-01

    A Missouri study conducted to determine agricultural extension usage patterns found that heavy users of extension publications tended to be younger farmers, those with a relatively large amount of land, and pork producers. Extension meetings were a less frequent source of information than either publications or county extension office visits. (LRA)

  2. Chromosome Compaction by Active Loop Extrusion.

    PubMed

    Goloborodko, Anton; Marko, John F; Mirny, Leonid A

    2016-05-24

    During cell division, chromosomes are compacted in length by more than a 100-fold. A wide range of experiments demonstrated that in their compacted state, mammalian chromosomes form arrays of closely stacked consecutive ∼100 kb loops. The mechanism underlying the active process of chromosome compaction into a stack of loops is unknown. Here we test the hypothesis that chromosomes are compacted by enzymatic machines that actively extrude chromatin loops. When such loop-extruding factors (LEF) bind to chromosomes, they progressively bridge sites that are further away along the chromosome, thus extruding a loop. We demonstrate that collective action of LEFs leads to formation of a dynamic array of consecutive loops. Simulations and an analytically solved model identify two distinct steady states: a sparse state, where loops are highly dynamic but provide little compaction; and a dense state, where there are more stable loops and dramatic chromosome compaction. We find that human chromosomes operate at the border of the dense steady state. Our analysis also shows how the macroscopic characteristics of the loop array are determined by the microscopic properties of LEFs and their abundance. When the number of LEFs are used that match experimentally based estimates, the model can quantitatively reproduce the average loop length, the degree of compaction, and the general loop-array morphology of compact human chromosomes. Our study demonstrates that efficient chromosome compaction can be achieved solely by an active loop-extrusion process. PMID:27224481

  3. Hard thermal loops in static external fields

    SciTech Connect

    Frenkel, J.; Takahashi, N.; Pereira, S. H.

    2009-04-15

    We examine, in the imaginary-time formalism, the high temperature behavior of n-point thermal loops in static Yang-Mills and gravitational fields. We show that in this regime, any hard thermal loop gives the same leading contribution as the one obtained by evaluating the loop integral at zero external energies and momenta.

  4. LIMB demonstration project extension

    SciTech Connect

    Not Available

    1990-09-21

    The purpose of the DOE limestone injection multistage burner (LIMB) Demonstration Project Extension is to extend the data base on LIMB technology and to expand DOE's list of Clean Coal Technologies by demonstrating the Coolside process as part of the project. The main objectives of this project are: to demonstrate the general applicability of LIMB technology by testing 3 coals and 4 sorbents (total of 12 coal/sorbent combinations) at the Ohio Edison Edgewater plant; and to demonstrate that Coolside is a viable technology for improving precipitator performance and reducing sulfur dioxide emissions while acceptable operability is maintained. Progress is reported. 3 figs.

  5. Portable Extensible Viewer

    NASA Technical Reports Server (NTRS)

    Horowitz, Jay G.

    1997-01-01

    The use of Nonuniform Rational B-Splines (NURBS) to represent geometry and data offers a standard way to facilitate the multidisciplinary analysis and design of aeropropulsion products. Using standard geometry defined by NURBS throughout design, analysis, part definition, manufacture, and test processes saves money and time. The Portable Extensible Viewer (PEV) offers engineers of different disciplines a means to view and manipulate NURBS geometry and associated data. Under the guidance of a team of Lewis, Boeing Company, and Navy personnel, PEV was developed by NASA Lewis Research Center's Computer Services Division for Lewis' Interdisciplinary Technology Office. The aeropropulsion industry provided input to the design requirements.

  6. The Statistical Loop Analyzer (SLA)

    NASA Technical Reports Server (NTRS)

    Lindsey, W. C.

    1985-01-01

    The statistical loop analyzer (SLA) is designed to automatically measure the acquisition, tracking and frequency stability performance characteristics of symbol synchronizers, code synchronizers, carrier tracking loops, and coherent transponders. Automated phase lock and system level tests can also be made using the SLA. Standard baseband, carrier and spread spectrum modulation techniques can be accomodated. Through the SLA's phase error jitter and cycle slip measurements the acquisition and tracking thresholds of the unit under test are determined; any false phase and frequency lock events are statistically analyzed and reported in the SLA output in probabilistic terms. Automated signal drop out tests can be performed in order to trouble shoot algorithms and evaluate the reacquisition statistics of the unit under test. Cycle slip rates and cycle slip probabilities can be measured using the SLA. These measurements, combined with bit error probability measurements, are all that are needed to fully characterize the acquisition and tracking performance of a digital communication system.

  7. Microgyroscope with closed loop output

    NASA Technical Reports Server (NTRS)

    Challoner, A. Dorian (Inventor); Gutierrez, Roman C. (Inventor); Tang, Tony K. (Inventor); Cargille, Donald R. (Inventor)

    2002-01-01

    A micro-gyroscope (10) having closed loop operation by a control voltage (V.sub.TY), that is demodulated by an output signal of the sense electrodes (S1, S2), providing Coriolis torque rebalance to prevent displacement of the micro-gyroscope (10) on the output axis (y-axis). The present invention provides wide-band, closed-loop operation for a micro-gyroscope (10) and allows the drive frequency to be closely tuned to a high Q sense axis resonance. A differential sense signal (S1-S2) is compensated and fed back by differentially changing the voltage on the drive electrodes to rebalance Coriolis torque. The feedback signal is demodulated in phase with the drive axis signal (K.sub..omega..crclbar..sub.x) to produce a measure of the Coriolis force.

  8. Loop connectors in dentogenic diastema.

    PubMed

    Nayar, Sanjna; Jayesh, Raghevendra; Venkateshwaran; Dinakarsamy, V

    2015-04-01

    Patients with a missing tooth along with diastema have limited treatment options to restore the edentulous space. The use of a conventional fixed partial denture (FPD) to replace the missing tooth may result in too wide anterior teeth leading to poor esthetics. Loss of anterior teeth with existing diastema may result in excess space available for pontic. This condition presents great esthetic challenge for prosthodontist. If implant supported prosthesis is not possible because of inadequate bone support, FPD along with loop connector may be a treatment option to maintain the diastema and provide optimal esthetic restoration. Here, we report a clinical case where FPD along with loop connector was used to achieve esthetic rehabilitation in maxillary anterior region in which midline diastema has been maintained. PMID:26015732

  9. 40 CFR 72.44 - Phase II repowering extensions.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 16 2010-07-01 2010-07-01 false Phase II repowering extensions. 72.44 Section 72.44 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) PERMITS REGULATION Acid Rain Compliance Plan and Compliance Options § 72.44 Phase II repowering extensions. (a) Applicability. (1)...

  10. 40 CFR 76.12 - Phase I NOX compliance extension.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 16 2010-07-01 2010-07-01 false Phase I NOX compliance extension. 76.12 Section 76.12 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) ACID RAIN NITROGEN OXIDES EMISSION REDUCTION PROGRAM § 76.12 Phase I NOX compliance extension. (a) General provisions. (1) The...

  11. 40 CFR 72.42 - Phase I extension plans.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 16 2010-07-01 2010-07-01 false Phase I extension plans. 72.42 Section 72.42 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) PERMITS REGULATION Acid Rain Compliance Plan and Compliance Options § 72.42 Phase I extension plans. (a) Applicability. (1) This section shall...

  12. Responses of a triple mutant defective in three iron deficiency-induced Basic Helix-Loop-Helix genes of the subgroup Ib(2) to iron deficiency and salicylic acid.

    PubMed

    Maurer, Felix; Naranjo Arcos, Maria Augusta; Bauer, Petra

    2014-01-01

    Plants are sessile organisms that adapt to external stress by inducing molecular and physiological responses that serve to better cope with the adverse growth condition. Upon low supply of the micronutrient iron, plants actively increase the acquisition of soil iron into the root and its mobilization from internal stores. The subgroup Ib(2) BHLH genes function as regulators in this response, however their concrete functions are not fully understood. Here, we analyzed a triple loss of function mutant of BHLH39, BHLH100 and BHLH101 (3xbhlh mutant). We found that this mutant did not have any iron uptake phenotype if iron was provided. However, under iron deficiency the mutant displayed a more severe leaf chlorosis than the wild type. Microarray-based transcriptome analysis revealed that this mutant phenotype resulted in the mis-regulation of 198 genes, out of which only 15% were associated with iron deficiency regulation itself. A detailed analysis revealed potential targets of the bHLH transcription factors as well as genes reflecting an exaggerated iron deficiency response phenotype. Since the BHLH genes of this subgroup have been brought into the context of the plant hormone salicylic acid, we investigated whether the 3xbhlh mutant might have been affected by this plant signaling molecule. Although a very high number of genes responded to SA, also in a differential manner between mutant and wild type, we did not find any indication for an association of the BHLH gene functions in SA responses upon iron deficiency. In summary, our study indicates that the bHLH subgroup Ib(2) transcription factors do not only act in iron acquisition into roots but in other aspects of the adaptation to iron deficiency in roots and leaves. PMID:24919188

  13. Responses of a Triple Mutant Defective in Three Iron Deficiency-Induced BASIC HELIX-LOOP-HELIX Genes of the Subgroup Ib(2) to Iron Deficiency and Salicylic Acid

    PubMed Central

    Maurer, Felix; Naranjo Arcos, Maria Augusta; Bauer, Petra

    2014-01-01

    Plants are sessile organisms that adapt to external stress by inducing molecular and physiological responses that serve to better cope with the adverse growth condition. Upon low supply of the micronutrient iron, plants actively increase the acquisition of soil iron into the root and its mobilization from internal stores. The subgroup Ib(2) BHLH genes function as regulators in this response, however their concrete functions are not fully understood. Here, we analyzed a triple loss of function mutant of BHLH39, BHLH100 and BHLH101 (3xbhlh mutant). We found that this mutant did not have any iron uptake phenotype if iron was provided. However, under iron deficiency the mutant displayed a more severe leaf chlorosis than the wild type. Microarray-based transcriptome analysis revealed that this mutant phenotype resulted in the mis-regulation of 198 genes, out of which only 15% were associated with iron deficiency regulation itself. A detailed analysis revealed potential targets of the bHLH transcription factors as well as genes reflecting an exaggerated iron deficiency response phenotype. Since the BHLH genes of this subgroup have been brought into the context of the plant hormone salicylic acid, we investigated whether the 3xbhlh mutant might have been affected by this plant signaling molecule. Although a very high number of genes responded to SA, also in a differential manner between mutant and wild type, we did not find any indication for an association of the BHLH gene functions in SA responses upon iron deficiency. In summary, our study indicates that the bHLH subgroup Ib(2) transcription factors do not only act in iron acquisition into roots but in other aspects of the adaptation to iron deficiency in roots and leaves. PMID:24919188

  14. Two Loop Higgs Unitarity Constraints

    NASA Astrophysics Data System (ADS)

    Maher, Peter Noel

    The perturbative approximation in the Symmetry Breaking sector of the Standard Model is investigated to two loops. The breakdown of perturbative unitarity seen at one loop is only slightly postponed. Attention is restricted to the coupled elastic scattering matrix of the neutral channels W^+W ^-, ZZ, HH, ZH. The high energy limit s gg M_sp{H} {2} gg M_sp{W}{2} and the Equivalence Theorem are used to simplify the calculation. The theory is renormalized on mass shell, in a way that automatically sums the tadpole graphs. Calculation of the counterterms was the most difficult part of the entire work. The running coupling and anomalous dimensions are calculated. The Landau pole of the running coupling is not significantly affected by the two loop contributions unless the coupling is large. Similarly, the anomalous dimensions are small. The eigen-amplitudes of the partial wave projected scattering matrix are analysed for breakdown of perturbative unitarity using Argand diagrams, and for term-wise convergence. It is found that if the Standard Model is to hold true up to sqrt{s} ~ 2TeV, the theory is strongly coupled and perturbative approximations are no longer trustworthy if M_{H} _sp{~}{>} 350 - 450 GeV. If the Standard Model is embedded in a perturbative grand unified theory, and assumed to hold true up to sqrt{s} = 10^ {15} GeV, then the Higgs mass is bounded M_{H} _sp{~ }{<} 160 GeV.

  15. Polyhedra in loop quantum gravity

    SciTech Connect

    Bianchi, Eugenio; Speziale, Simone; Dona, Pietro

    2011-02-15

    Intertwiners are the building blocks of spin-network states. The space of intertwiners is the quantization of a classical symplectic manifold introduced by Kapovich and Millson. Here we show that a theorem by Minkowski allows us to interpret generic configurations in this space as bounded convex polyhedra in R{sup 3}: A polyhedron is uniquely described by the areas and normals to its faces. We provide a reconstruction of the geometry of the polyhedron: We give formulas for the edge lengths, the volume, and the adjacency of its faces. At the quantum level, this correspondence allows us to identify an intertwiner with the state of a quantum polyhedron, thus generalizing the notion of the quantum tetrahedron familiar in the loop quantum gravity literature. Moreover, coherent intertwiners result to be peaked on the classical geometry of polyhedra. We discuss the relevance of this result for loop quantum gravity. In particular, coherent spin-network states with nodes of arbitrary valence represent a collection of semiclassical polyhedra. Furthermore, we introduce an operator that measures the volume of a quantum polyhedron and examine its relation with the standard volume operator of loop quantum gravity. We also comment on the semiclassical limit of spin foams with nonsimplicial graphs.

  16. Two-loop quantum gravity

    NASA Astrophysics Data System (ADS)

    van de Ven, Anton E. M.

    1992-07-01

    We prove the existence of a nonrenormalizable infinity in the two-loop effective action of perturbative quantum gravity by means of an explicit calculation. Our final result agrees with that obtained by earlier authors. We use the background-field method in coordinate space, combined with dimensional regularization and a heat kernel representation for the propagators. General covariance is manifestly preserved. Only vacuum graphs in the presence of an on-shell background metric need to be calculated. We extend the background covariant harmonic gauge to include terms nonlinear in the quantum gravitational fields and allow for general reparametrizations of those fields. For a particular gauge choice and field parametrization only two three-graviton and six four-graviton vertices are present in the action. Calculational labor is further reduced by restricting to backgrounds, which are not only Ricci-flat, but satisfy an additional constraint bilinear in the Weyl tensor. To handle the still formidable amount of algebra, we use the symbolic manipulation program FORM. We checked that the on-shell two-loop effective action is in fact independent of all gauge and field redefinition parameters. A two-loop analysis for Yang-Mills fields is included as well, since in that case we can give full details as well as simplify earlier analyses.

  17. Polyhedra in loop quantum gravity

    NASA Astrophysics Data System (ADS)

    Bianchi, Eugenio; Doná, Pietro; Speziale, Simone

    2011-02-01

    Intertwiners are the building blocks of spin-network states. The space of intertwiners is the quantization of a classical symplectic manifold introduced by Kapovich and Millson. Here we show that a theorem by Minkowski allows us to interpret generic configurations in this space as bounded convex polyhedra in R3: A polyhedron is uniquely described by the areas and normals to its faces. We provide a reconstruction of the geometry of the polyhedron: We give formulas for the edge lengths, the volume, and the adjacency of its faces. At the quantum level, this correspondence allows us to identify an intertwiner with the state of a quantum polyhedron, thus generalizing the notion of the quantum tetrahedron familiar in the loop quantum gravity literature. Moreover, coherent intertwiners result to be peaked on the classical geometry of polyhedra. We discuss the relevance of this result for loop quantum gravity. In particular, coherent spin-network states with nodes of arbitrary valence represent a collection of semiclassical polyhedra. Furthermore, we introduce an operator that measures the volume of a quantum polyhedron and examine its relation with the standard volume operator of loop quantum gravity. We also comment on the semiclassical limit of spin foams with nonsimplicial graphs.

  18. Quantum reduced loop gravity and the foundation of loop quantum cosmology

    NASA Astrophysics Data System (ADS)

    Alesci, Emanuele; Cianfrani, Francesco

    2016-06-01

    Quantum reduced loop gravity is a promising framework for linking loop quantum gravity and the effective semiclassical dynamics of loop quantum cosmology. We review its basic achievements and its main perspectives, outlining how it provides a quantum description of the Universe in terms of a cuboidal graph which constitutes the proper framework for applying loop techniques in a cosmological setting.

  19. Seizure Suppression Efficacy of Closed-Loop Versus Open-Loop Deep Brain Stimulation in a Rodent Model of Epilepsy.

    PubMed

    Salam, M Tariqus; Perez Velazquez, Jose Luis; Genov, Roman

    2016-06-01

    We assess and compare the effects of both closed-loop and open-loop neurostimulation of the rat hippocampus by means of a custom low-power programmable therapeutic neurostimulation device on the suppression of spontaneous seizures in a rodent model of epilepsy. Chronic seizures were induced by intraperitoneal kainic acid injection. Two bipolar electrodes were implanted into the CA1 regions of both hippocampi. The electrodes were connected to the custom-built programmable therapeutic neurostimulation device that can trigger an electrical stimulation either in a periodic manner or upon detection of the intracerebral electroencephalographic (icEEE) seizure onset. This device includes a microchip consisting of a 256-channel icEEG recording system and a 64-channel stimulator, and a programmable seizure detector implemented in a field-programmable gate array (FPGA). The neurostimulator was used to evaluate seizure suppression efficacy in ten epileptic rats for a total of 240 subject-days (5760 subject-hours). For this purpose, all rats were randomly divided into two groups: the no-stimulation group and the stimulation group. The no-stimulation group did not receive stimulation. The stimulation group received, first, closed-loop stimulation and, next, open-loop stimulation. The no-stimulation and stimulation groups had a similar seizure frequency baseline, averaging five seizures per day. Closed-loop stimulation reduced seizure frequency by 90% and open-loop stimulation reduced seizure frequency by 17%, both in the stimulation group as compared to the no-stimulation group. PMID:26571534

  20. Premeasured Chordal Loops for Mitral Valve Repair.

    PubMed

    Gillinov, Marc; Quinn, Reed; Kerendi, Faraz; Gaudiani, Vince; Shemin, Richard; Barnhart, Glenn; Raines, Edward; Gerdisch, Marc W; Banbury, Michael

    2016-09-01

    Premeasured expanded polytetrafluoroethylene chordal loops with integrated sutures for attachment to the papillary muscle and leaflet edges facilitate correction of mitral valve prolapse. Configured as a group of 3 loops (length range 12 to 24 mm), the loops are attached to a pledget that is passed through the papillary muscle and tied. Each of the loops has 2 sutures with attached needles; these needles are passed through the free edge of the leaflet and then the sutures are tied to each other, securing the chordal loop to the leaflet. PMID:27549563

  1. Z-Sum approach to loop integrals

    NASA Astrophysics Data System (ADS)

    Rottmann, Paulo A.

    We study the applicability of the Z-Sum approach to multi-loop calculations with massive particles in perturbative quantum field theory. We systematically analyze the case of one-loop scalar integrals, which represent the building blocks of any higher-loop calculation. We focus in particular on triangle one-loop integrals and identify strengths and limitations of the Z-Sum approach, extending our results to the case of one-loop box integrals when appropriate. We conclude with the calculation of a specific physical example: the calculation of heavy flavor corrections to the renormalized scattering amplitude for deep inelastic scattering.

  2. Dynamic Aperture-based Solar Loop Segmentation

    NASA Technical Reports Server (NTRS)

    Lee, Jon Kwan; Newman, Timothy S.; Gary, G. Allen

    2006-01-01

    A new method to automatically segment arc-like loop structures from intensity images of the Sun's corona is introduced. The method constructively segments credible loop structures by exploiting the Gaussian-like shape of loop cross-sectional intensity profiles. The experimental results show that the method reasonably segments most of the well-defined loops in coronal images. The method is only the second published automated solar loop segmentation method. Its advantage over the other published method is that it operates independently of supplemental time specific data.

  3. Efficient Tiled Loop Generation: D-Tiling

    NASA Astrophysics Data System (ADS)

    Kim, Daegon; Rajopadhye, Sanjay

    Tiling is an important loop optimization for exposing coarse-grained parallelism and enhancing data locality. Tiled loop generation from an arbitrarily shaped polyhedron is a well studied problem. Except for the special case of a rectangular iteration space, the tiled loop generation problem has been long believed to require heavy machinery such as Fourier-Motzkin elimination and projection, and hence to have an exponential complexity. In this paper we propose a simple and efficient tiled loop generation technique similar to that for a rectangular iteration space. In our technique, each loop bound is adjusted only once, syntactically and independently. Therefore, our algorithm runs linearly with the number of loop bounds. Despite its simplicity, we retain several advantages of recent tiled code generation schemes - unified generation for fixed, parameterized and hybrid tiled loops, scalability for multi-level tiled loop generation with the ability to separate full tiles at any levels, and compact code. We also explore various schemes for multi-level tiled loop generation. We formally prove the correctness of our scheme and experimentally validate that the efficiency of our technique is comparable to existing parameterized tiled loop generation approaches. Our experimental results also show that multi-level tiled loop generation schemes have an impact on performance of generated code. The fact that our scheme can be implemented without sophisticated machinery makes it well suited for autotuners and production compilers.

  4. Prevalent, Dynamic, and Conserved R-Loop Structures Associate with Specific Epigenomic Signatures in Mammals.

    PubMed

    Sanz, Lionel A; Hartono, Stella R; Lim, Yoong Wearn; Steyaert, Sandra; Rajpurkar, Aparna; Ginno, Paul A; Xu, Xiaoqin; Chédin, Frédéric

    2016-07-01

    R-loops are three-stranded nucleic acid structures formed upon annealing of an RNA strand to one strand of duplex DNA. We profiled R-loops using a high-resolution, strand-specific methodology in human and mouse cell types. R-loops are prevalent, collectively occupying up to 5% of mammalian genomes. R-loop formation occurs over conserved genic hotspots such as promoter and terminator regions of poly(A)-dependent genes. In most cases, R-loops occur co-transcriptionally and undergo dynamic turnover. Detailed epigenomic profiling revealed that R-loops associate with specific chromatin signatures. At promoters, R-loops associate with a hyper-accessible state characteristic of unmethylated CpG island promoters. By contrast, terminal R-loops associate with an enhancer- and insulator-like state and define a broad class of transcription terminators. Together, this suggests that the retention of nascent RNA transcripts at their site of expression represents an abundant, dynamic, and programmed component of the mammalian chromatin that affects chromatin patterning and the control of gene expression. PMID:27373332

  5. Hyperstaticity and loops in frictional granular packings

    NASA Astrophysics Data System (ADS)

    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.

  6. Non-extensive radiobiology

    SciTech Connect

    Sotolongo-Grau, O.; Rodriguez-Perez, D.; Antoranz, J. C.; Sotolongo-Costa, O.

    2011-03-14

    The expression of survival factors for radiation damaged cells is based on probabilistic assumptions and experimentally fitted for each tumor, radiation and conditions. Here we show how the simplest of these radiobiological models can be derived from the maximum entropy principle of the classical Boltzmann-Gibbs expression. We extend this derivation using the Tsallis entropy and a cutoff hypothesis, motivated by clinical observations. A generalization of the exponential, the logarithm and the product to a non-extensive framework, provides a simple formula for the survival fraction corresponding to the application of several radiation doses on a living tissue. The obtained expression shows a remarkable agreement with the experimental data found in the literature, also providing a new interpretation of some of the parameters introduced anew. It is also shown how the presented formalism may have direct application in radiotherapy treatment optimization through the definition of the potential effect difference, simply calculated between the tumour and the surrounding tissue.

  7. Overlap extension PCR cloning.

    PubMed

    Bryksin, Anton; Matsumura, Ichiro

    2013-01-01

    Rising demand for recombinant proteins has motivated the development of efficient and reliable cloning methods. Here we show how a beginner can clone virtually any DNA insert into a plasmid of choice without the use of restriction endonucleases or T4 DNA ligase. Chimeric primers encoding plasmid sequence at the 5' ends and insert sequence at the 3' ends are designed and synthesized. Phusion(®) DNA polymerase is utilized to amplify the desired insert by PCR. The double-stranded product is subsequently employed as a pair of mega-primers in a PCR-like reaction with circular plasmids. The original plasmids are then destroyed in restriction digests with Dpn I. The product of the overlap extension PCR is used to transform competent Escherichia coli cells. Phusion(®) DNA polymerase is used for both the amplification and fusion reactions, so both steps can be monitored and optimized in the same way. PMID:23996437

  8. Non-extensive radiobiology

    NASA Astrophysics Data System (ADS)

    Sotolongo-Grau, O.; Rodriguez-Perez, D.; Antoranz, J. C.; Sotolongo-Costa, O.

    2011-03-01

    The expression of survival factors for radiation damaged cells is based on probabilistic assumptions and experimentally fitted for each tumor, radiation and conditions. Here we show how the simplest of these radiobiological models can be derived from the maximum entropy principle of the classical Boltzmann-Gibbs expression. We extend this derivation using the Tsallis entropy and a cutoff hypothesis, motivated by clinical observations. A generalization of the exponential, the logarithm and the product to a non-extensive framework, provides a simple formula for the survival fraction corresponding to the application of several radiation doses on a living tissue. The obtained expression shows a remarkable agreement with the experimental data found in the literature, also providing a new interpretation of some of the parameters introduced anew. It is also shown how the presented formalism may have direct application in radiotherapy treatment optimization through the definition of the potential effect difference, simply calculated between the tumour and the surrounding tissue.

  9. A molecular characterization of the agonist binding site of a nematode cys-loop GABA receptor

    PubMed Central

    Kaji, Mark D; Kwaka, Ariel; Callanan, Micah K; Nusrat, Humza; Desaulniers, Jean-Paul; Forrester, Sean G

    2015-01-01

    Background and Purpose Cys-loop GABA receptors represent important targets for human chemotherapeutics and insecticides and are potential targets for novel anthelmintics (nematicides). However, compared with insect and mammalian receptors, little is known regarding the pharmacological characteristics of nematode Cys-loop GABA receptors. Here we have investigated the agonist binding site of the Cys-loop GABA receptor UNC-49 (Hco-UNC-49) from the parasitic nematode Haemonchus contortus. Experimental Approach We used two-electrode voltage-clamp electrophysiology to measure channel activation by classical GABA receptor agonists on Hco-UNC-49 expressed in Xenopus laevis oocytes, along with site-directed mutagenesis and in silico homology modelling. Key Results The sulphonated molecules P4S and taurine had no effect on Hco-UNC-49. Other classical Cys-loop GABAA receptor agonists tested on the Hco-UNC-49B/C heteromeric channel had a rank order efficacy of GABA > trans-4-aminocrotonic acid > isoguvacine > imidazole-4-acetic acid (IMA) > (R)-(−)-4-amino-3-hydroxybutyric acid [R(−)-GABOB] > (S)-(+)-4-amino-3-hydroxybutyric acid [S(+)-GABOB] > guanidinoacetic acid > isonipecotic acid > 5-aminovaleric acid (DAVA) (partial agonist) > β-alanine (partial agonist). In silico ligand docking revealed some variation in binding between agonists. Mutagenesis of a key serine residue in binding loop C to threonine had minimal effects on GABA and IMA but significantly increased the maximal response to DAVA and decreased twofold the EC50 for R(−)- and S(+)-GABOB. Conclusions and Implications The pharmacological profile of Hco-UNC-49 differed from that of vertebrate Cys-loop GABA receptors and insect resistance to dieldrin receptors, suggesting differences in the agonist binding pocket. These findings could be exploited to develop new drugs that specifically target GABA receptors of parasitic nematodes. PMID:25850584

  10. Extensive modifications for methionine enhancement in the beta-barrels do not alter the structural stability of the bean seed storage protein phaseolin.

    PubMed

    Dyer, J M; Nelson, J W; Murai, N

    1995-11-01

    Common beans are widely utilized as a food source, yet are low in the essential amino acid methionine. As an initial step to overcome this defect the methionine content of the primary bean seed storage protein phaseolin was increased by replacing 20 evolutionarily variant hydrophobic residues with methionine and inserting short, methionine-rich sequences into turn and loop regions of the protein structure. Methionine enhancement ranged from 5 to 30 residues. An Escherichia coli expression system was developed to characterize the structural stability of the mutant proteins. Proteins of expected sizes were obtained for all constructs except for negative controls, which were rapidly degraded in E. coli. Thermal denaturation of the purified proteins demonstrated that both wild-type and mutant phaseolin proteins denatured reversibly at approximately 61 degrees C. In addition, urea denaturation experiments of the wild-type and a mutant protein (with 30 additional methionines) confirmed that the structural stability of the proteins was very similar. Remarkably, these results indicate that the phaseolin protein tolerates extensive modifications, including 20 substitutions and two loop inserts for methionine enhancement in the beta-barrel and loop structures, with extremely small effects on protein stability. PMID:8747427

  11. Turning an Extension Aide into an Extension Agent

    ERIC Educational Resources Information Center

    Seevers, Brenda; Dormody, Thomas J.

    2010-01-01

    For any organization to remain sustainable, a renewable source of faculty and staff needs to be available. The Extension Internship Program for Juniors and Seniors in High School is a new tool for recruiting and developing new Extension agents. Students get "hands on" experience working in an Extension office and earn college credit while in high…

  12. Closing the tau loop: the missing tau mutation.

    PubMed

    McCarthy, Allan; Lonergan, Roisin; Olszewska, Diana A; O'Dowd, Sean; Cummins, Gemma; Magennis, Brian; Fallon, Emer M; Pender, Niall; Huey, Edward D; Cosentino, Stephanie; O'Rourke, Killian; Kelly, Brendan D; O'Connell, Martin; Delon, Isabelle; Farrell, Michael; Spillantini, Maria Grazia; Rowland, Lewis P; Fahn, Stanley; Craig, Peter; Hutton, Michael; Lynch, Tim

    2015-10-01

    Frontotemporal lobar degeneration comprises a group of disorders characterized by behavioural, executive, language impairment and sometimes features of parkinsonism and motor neuron disease. In 1994 we described an Irish-American family with frontotemporal dementia linked to chromosome 17 associated with extensive tau pathology. We named this disinhibition-dementia-parkinsonism-amyotrophy complex. We subsequently identified mutations in the MAPT gene. Eleven MAPT gene splice site stem loop mutations were identified over time except for 5' splice site of exon 10. We recently identified another Irish family with autosomal dominant early amnesia and behavioural change or parkinsonism associated with the 'missing' +15 mutation at the intronic boundary of exon 10. We performed a clinical, neuropsychological and neuroimaging study on the proband and four siblings, including two affected siblings. We sequenced MAPT and performed segregation analysis. We looked for a biological effect of the tau variant by performing real-time polymerase chain reaction analysis of RNA extracted from human embryonic kidney cells transfected with exon trapping constructs. We found a c.915+15A>C exon 10/intron 10 stem loop mutation in all affected subjects but not in the unaffected. The c.915+15A>C variant caused a shift in tau splicing pattern to a predominantly exon 10+ pattern presumably resulting in predominant 4 repeat tau and little 3 repeat tau. This strongly suggests that the c.915+15A>C variant is a mutation and that it causes frontotemporal dementia linked to chromosome 17 in this pedigree by shifting tau transcription and translation to +4 repeat tau. Tau (MAPT) screening should be considered in families where amnesia or atypical parkinsonism coexists with behavioural disturbance early in the disease process. We describe the final missing stem loop tau mutation predicted 15 years ago. Mutations have now been identified at all predicted sites within the 'stem' when the stem-loop

  13. Functional Analysis of the Autographa californica Multiple Nucleopolyhedrovirus GP64 Terminal Fusion Loops and Interactions with Membranes

    PubMed Central

    Dong, Sicong

    2012-01-01

    The Autographa californica multiple nucleopolyhedrovirus (AcMNPV) glycoprotein GP64 is the major envelope protein of the budded virus (BV). GP64 is a class III fusion protein that mediates BV attachment to the cell surface and low-pH-triggered membrane fusion between the BV envelope and the endosome membrane during entry. Class III fusion proteins contain terminal looped structures that are believed to interact with membranes. To examine the functions of 3 loops found at the apex of the GP64 postfusion structure, we generated 2-alanine substitutions that scanned the two so-called fusion loops (loop 1 and loop 2) plus an adjacent loop structure (loop 3) that is closely attached to loop 2 and is also found at the apex of the GP64 postfusion structure. We identified essential residues from Y75 to T86 (loop 1) and N149 to H156 (loop 2) that are required for fusion activity, but no essential residues in loop 3. Further analysis revealed that critical fusion loop residues fall within two groups that are associated with either membrane merger (hemifusion) or fusion pore expansion. We next examined the interactions of soluble GP64 proteins and BV with membranes composed of various phospholipids. BV interacted directly with small unilamellar vesicles (SUVs) comprised of phospholipids phosphatidylcholine and phosphatidic acid (PC/PA) or phosphatidylcholine and phosphatidylserine (PC/PS) under neutral and acidic pH. We also examined the interactions of soluble GP64 constructs containing substitutions of the most hydrophobic residues within each of the two fusion loops. We found that a 2-residue substitution in either single loop (loop 1 [positions 81 and 82] or loop 2 [positions 153 and 154]) was not sufficient to substantially reduce the GP64-liposome interaction, but the same substitutions in both fusion loops severely reduced the GP64-liposome association at neutral pH. These results suggest that critical hydrophobic residues in both fusion loops may be involved in the

  14. The one loop corrections to the neutrino masses in BLMSSM

    NASA Astrophysics Data System (ADS)

    Zhao, Shu-Min; Feng, Tai-Fu; Dong, Xing-Xing; Zhang, Hai-Bin; Ning, Guo-Zhu; Guo, Tao

    2016-09-01

    The neutrino masses and mixings are studied in the model which is the supersymmetric extension of the standard model with local gauged baryon and lepton numbers (BLMSSM). At tree level the neutrinos can obtain tiny masses through the See-Saw mechanism in the BLMSSM. The one-loop corrections to the neutrino masses and mixings are important, and they are studied in this work with the mass insertion approximation. We study the numerical results and discuss the allowed parameter space of BLMSSM. It can contribute to study the neutrino masses and to explore the new physics beyond the standard model (SM).

  15. Development of Computational Approaches for Simulation and Advanced Controls for Hybrid Combustion-Gasification Chemical Looping

    SciTech Connect

    Joshi, Abhinaya; Lou, Xinsheng; Neuschaefer, Carl; Chaudry, Majid; Quinn, Joseph

    2012-07-31

    This document provides the results of the project through September 2009. The Phase I project has recently been extended from September 2009 to March 2011. The project extension will begin work on Chemical Looping (CL) Prototype modeling and advanced control design exploration in preparation for a scale-up phase. The results to date include: successful development of dual loop chemical looping process models and dynamic simulation software tools, development and test of several advanced control concepts and applications for Chemical Looping transport control and investigation of several sensor concepts and establishment of two feasible sensor candidates recommended for further prototype development and controls integration. There are three sections in this summary and conclusions. Section 1 presents the project scope and objectives. Section 2 highlights the detailed accomplishments by project task area. Section 3 provides conclusions to date and recommendations for future work.

  16. Probing the influence of hypermodified residues within the tRNA3(Lys) anticodon stem loop interacting with the A-loop primer sequence from HIV-1.

    PubMed

    Galindo-Murillo, Rodrigo; Davis, Darrell R; Cheatham, Thomas E

    2016-03-01

    Replication of the HIV-1 virus requires reverse transcription of the viral RNA genome, a process that is specifically initiated by human tRNA3(Lys) packaged within the infectious virion. The primary binding site for the tRNA involves the 3' 18 nucleotides with an additional interaction between an adenine rich loop (A-loop) in the template and the anticodon stem-loop region of the tRNA3(Lys). The loop of the tRNA primer contains two hypermodified base residues and a pseudouridine that are required for a proper binding and activity. Here, we investigate the influence on the structure, dynamics and binding stability of the three modified residues (mnm(5)s(2)U34, t(6)A37 and Ψ39) using extensive molecular dynamics and Quantum Theory of Atoms in Molecules (QTAIM) analysis. Consistent with experiment, the results suggest that the three modified residues are required for faithful binding. Residues mnm(5)s(2)U34 and Ψ39 have a major influence in stabilizing the anticodon loop whereas mnm(5)s(2)U34 and t(6)A37 appear to stabilize the formation of the complex of tRNA3(Lys) with the HIV-1 A-loop. PMID:26655694

  17. Loop Virasoro Lie conformal algebra

    SciTech Connect

    Wu, Henan Chen, Qiufan; Yue, Xiaoqing

    2014-01-15

    The Lie conformal algebra of loop Virasoro algebra, denoted by CW, is introduced in this paper. Explicitly, CW is a Lie conformal algebra with C[∂]-basis (L{sub i} | i∈Z) and λ-brackets [L{sub i} {sub λ} L{sub j}] = (−∂−2λ)L{sub i+j}. Then conformal derivations of CW are determined. Finally, rank one conformal modules and Z-graded free intermediate series modules over CW are classified.

  18. Loop-linker PCR: an advanced PCR technique for genome walking.

    PubMed

    Trinh, Quoclinh; Shi, Hui; Xu, Wentao; Hao, Junran; Luo, Yunbo; Huang, Kunlun

    2012-10-01

    In this article, we developed a novel PCR method, termed loop-linker PCR, to isolate flanking sequences in transgenic crops. The novelty of this approach is its use of a stem-loop structure to design a loop-linker adapter. The adapter is designed to form a nick site when ligated with restricted DNA. This modification not only can prevent the self-ligation of adapters but also promotes the elongation of the 3' end of the loop-linker adapter to generate a stem-loop structure in the ligation products. Moreover, the suppressive effect of the stem-loop structure decreases nonspecific amplification and increases the success rate of the approach; all extension products will suppress exponential amplification except from the ligation product that contains the specific primer binding site. Using this method, 442, 1830, 107, and 512 bp left border flanking sequences were obtained from the transgenic maizes LY038, DAS-59122-7, Event 3272, and the transgenic soybean MON89788, respectively. The experimental results demonstrated that loop-linker PCR is an efficient, reliable, and cost-effective method for identifying flanking sequences in transgenic crops and could be applied for other genome walking applications. PMID:23008115

  19. Testing of a Neon Loop Heat Pipe for Large Area Cryocooling

    NASA Technical Reports Server (NTRS)

    Ku, Jentung; Robinson, Franklin Lee

    2014-01-01

    Cryocooling of large areas such as optics, detector arrays, and cryogenic propellant tanks is required for future NASA missions. A cryogenic loop heat pipe (CLHP) can provide a closed-loop cooling system for this purpose and has many advantages over other devices in terms of reduced mass, reduced vibration, high reliability, and long life. A neon CLHP was tested extensively in a thermal vacuum chamber using a cryopump as the heat sink to characterize its transient and steady performance and verify its ability to cool large areas or components. Tests conducted included loop cool-down from the ambient temperature, startup, power cycle, heat removal capability, loop capillary limit and recovery from a dry-out, low power operation, and long duration steady state operation. The neon CLHP demonstrated robust operation. The loop could be cooled from the ambient temperature to subcritical temperatures very effectively, and could start successfully by applying power to both the pump and evaporator without any pre-conditioning. It could adapt to changes in the pump power andor evaporator power, and reach a new steady state very quickly. The evaporator could remove heat loads between 0.25W and 4W. When the pump capillary limit was exceeded, the loop could resume its normal function by reducing the pump power. Steady state operations were demonstrated for up to 6 hours. The ability of the neon loop to cool large areas was therefore successfully verified.

  20. Closed-Loop Neuroscience and Non-Invasive Brain Stimulation: A Tale of Two Loops.

    PubMed

    Zrenner, Christoph; Belardinelli, Paolo; Müller-Dahlhaus, Florian; Ziemann, Ulf

    2016-01-01

    Closed-loop neuroscience is receiving increasing attention with recent technological advances that enable complex feedback loops to be implemented with millisecond resolution on commodity hardware. We summarize emerging conceptual and methodological frameworks that are available to experimenters investigating a "brain in the loop" using non-invasive brain stimulation and briefly review the experimental and therapeutic implications. We take the view that closed-loop neuroscience in fact deals with two conceptually quite different loops: a "brain-state dynamics" loop, used to couple with and modulate the trajectory of neuronal activity patterns, and a "task dynamics" loop, that is the bidirectional motor-sensory interaction between brain and (simulated) environment, and which enables goal-directed behavioral tasks to be incorporated. Both loops need to be considered and combined to realize the full experimental and therapeutic potential of closed-loop neuroscience. PMID:27092055

  1. Thermal Analysis of CDS Coronal Loops

    NASA Astrophysics Data System (ADS)

    Kimble, J. A.; Schmelz, J. T.; Nasraoui, K.; Rightmire, L. A.; Andrews, J. M.; Cirtain, J. W.

    2008-05-01

    The coronal loop data used for this analysis was obtained using the Coronal Diagnostic Spectrometer (CDS) aboard the Solar and Heliospheric Observatory on 2003 January 17 at 14:24:43 UT. We use the Chianti atomic physics database and the hybrid coronal abundances to determine temperatures and densities for positions along several loops. We chose six pixels along each loop as well as background pixels. The intensities of the background pixels are subtracted from each loop pixel to isolate the emission from the loop pixel, and then spectral lines with significant contributions to the loop intensities are selected. The loops were then analyzed with a forward folding process to produce differential emission measure (DEM) curves. Emission measure loci plots and DEM automatic inversions are then used to verify those conclusions. We find different results for each of these loops. One appears to be isothermal at each loop position, and the temperature does not change with height. The second appears to be multithermal at each position and the third seems to be consistent with two DEM spikes, which might indicate that there are two isothermal loops so close together, that they are not resolved by CDS. Solar physics research at the University of Memphis is supported by a Hinode subcontract from NASA/SAO as well as NSF ATM-0402729.

  2. Multidimensional smooth loops with universal elasticity

    NASA Astrophysics Data System (ADS)

    Dzhukashev, K. R.; Shelekhov, A. M.

    2015-05-01

    Let \\widetilde E be a universal (isotopically invariant) identity that is derived from the elasticity identity E\\colon (xy)x=x(yx). One of the authors has previously shown that a) each local loop of dimension r with identity \\widetilde E (briefly, a loop \\widetilde E) is a smooth middle Bol loop of dimension r; b) smooth two-dimensional loops \\widetilde E are Lie groups; c) up to isotopy, there exist only two three-dimensional loops \\widetilde E: the loops E_1 and E_2. In this paper, the loops E_1 and E_2 are extended to the multidimensional case. The fact that each smooth loop \\widetilde E of dimension r corresponds to a unique multidimensional three-web on a manifold of dimension 2r is key to our work. In addition, the class of loops under investigation is characterized by the fact that the torsion tensor of the corresponding web has rank 1 (that is, the algebra generated by this tensor has a one-dimensional derived algebra). This enables us to express the differential equations of the problem in an invariant form. The system of equations thus obtained was found to be amenable to integration in the most general case, and the equations of the required loops have been obtained in local coordinates. Bibliography: 17 titles.

  3. The BGAN extension programme

    NASA Astrophysics Data System (ADS)

    Rivera, Juan J.; Trachtman, Eyal; Richharia, Madhavendra

    2005-11-01

    Mobile satellite telecommunications systems have undergone an enormous evolution in the last decades, with the interest in having advanced telecommunications services available on demand, anywhere and at any time, leading to incredible advances. The demand for braodband data is therefore rapidly gathering pace, but current solutions are finding it increasingly difficult to combine large bandwidth with ubiquitous coverage, reliability and portability. The BGAN (Broadband Global Area Network) system, designed to operate with the Inmarsat-4 satellites, provides breakthrough services that meet all of these requirements. It will enable broadband connection on the move, delivering all the key tools of the modern office. Recognising the great impact that Inmarsat's BGAN system will have on the European satellite communications industry, and the benefits that it will bring to a wide range of European industries, in 2003 ESA initiated the "BGAN Extension" project. Its primary goals are to provide the full range of BGAN services to truly mobile platforms, operating in aeronautical, vehicular and maritime environments, and to introduce a multicast service capability. The project is supported by the ARTES Programme which establishes a collaboration agreement between ESA, Inmarsat and a group of key industrial and academic institutions which includes EMS, Logica, Nera and the University of Surrey (UK).

  4. Extensible Wind Towers

    NASA Astrophysics Data System (ADS)

    Sinagra, Marco; Tucciarelli, Tullio

    The diffusion of wind energy generators is restricted by their strong landscape impact. The PERIMA project is about the development of an extensible wind tower able to support a wind machine for several hundred kW at its optimal working height, up to more than 50 m. The wind tower has a telescopic structure, made by several tubes located inside each other with their axis in vertical direction. The lifting force is given by a jack-up system confined inside a shaft, drilled below the ground level. In the retracted tower configuration, at rest, tower tubes are hidden in the foundation of the telescopic structure, located below the ground surface, and the wind machine is the only emerging part of the system. The lifting system is based on a couple of oleodynamic cylinders that jack-up a central tube connected to the top of the tower by a spring, with a diameter smaller than the minimum tower diameter and with a length a bit greater than the length of the extended telescopic structure. The central tube works as plunger and lifts all telescopic elements. The constraint between the telescopic elements is ensured by special parts, which are kept in traction by the force of the spring and provide the resisting moment. The most evident benefit of the proposed system is attained with the use of a two-blade propeller, which can be kept horizontal in the retracted tower configuration.

  5. Transcription of potato spindle tuber viroid by RNA polymerase II starts in the left terminal loop

    SciTech Connect

    Kolonko, Nadine; Bannach, Oliver; Aschermann, Katja; Hu, Kang-Hong; Moors, Michaela; Schmitz, Michael; Steger, Gerhard; Riesner, Detlev . E-mail: riesner@biophys.uni-duesseldorf.de

    2006-04-10

    Viroids are single-stranded, circular RNAs of 250 to 400 bases, that replicate autonomously in their host plants but do not code for a protein. Viroids of the family Pospiviroidae, of which potato spindle tuber viroid (PSTVd) is the type strain, are replicated by the host's DNA-dependent RNA polymerase II in the nucleus. To analyze the initiation site of transcription from the (+)-stranded circles into (-)-stranded replication intermediates, we used a nuclear extract from a non-infected cell culture of the host plant S. tuberosum. The (-)-strands, which were de novo-synthesized in the extract upon addition of circular (+)-PSTVd, were purified by affinity chromatography. This purification avoided contamination by host nucleic acids that had resulted in a misassignment of the start site in an earlier study. Primer-extension analysis of the de novo-synthesized (-)-strands revealed a single start site located in the hairpin loop of the left terminal region in circular PSTVd's secondary structure. This start site is supported further by analysis of the infectivity and replication behavior of site-directed mutants in planta.

  6. The Logical Extension

    NASA Technical Reports Server (NTRS)

    2003-01-01

    The same software controlling autonomous and crew-assisted operations for the International Space Station (ISS) is enabling commercial enterprises to integrate and automate manual operations, also known as decision logic, in real time across complex and disparate networked applications, databases, servers, and other devices, all with quantifiable business benefits. Auspice Corporation, of Framingham, Massachusetts, developed the Auspice TLX (The Logical Extension) software platform to effectively mimic the human decision-making process. Auspice TLX automates operations across extended enterprise systems, where any given infrastructure can include thousands of computers, servers, switches, and modems that are connected, and therefore, dependent upon each other. The concept behind the Auspice software spawned from a computer program originally developed in 1981 by Cambridge, Massachusetts-based Draper Laboratory for simulating tasks performed by astronauts aboard the Space Shuttle. At the time, the Space Shuttle Program was dependent upon paper-based procedures for its manned space missions, which typically averaged 2 weeks in duration. As the Shuttle Program progressed, NASA began increasing the length of manned missions in preparation for a more permanent space habitat. Acknowledging the need to relinquish paper-based procedures in favor of an electronic processing format to properly monitor and manage the complexities of these longer missions, NASA realized that Draper's task simulation software could be applied to its vision of year-round space occupancy. In 1992, Draper was awarded a NASA contract to build User Interface Language software to enable autonomous operations of a multitude of functions on Space Station Freedom (the station was redesigned in 1993 and converted into the international venture known today as the ISS)

  7. Two loop correction to interference in gg → ZZ

    NASA Astrophysics Data System (ADS)

    Campbell, John M.; Ellis, R. Keith; Czakon, Michal; Kirchner, Sebastian

    2016-08-01

    We present results for the production of a pair of on-shell Z bosons via gluon-gluon fusion. This process occurs both through the production and decay of the Higgs boson, and through continuum production where the Z boson couples to a loop of massless quarks or to a massive quark. We calculate the interference of the two processes and its contribution to the cross section up to and including order O( α s 3 ). The two-loop contributions to the amplitude are all known analytically, except for the continuum production through loops of top quarks of mass m. The latter contribution is important for the invariant mass of the two Z bosons, (as measured by the mass of their leptonic decay products, m 4 l ), in a regime where m 4 l ≥ 2 m because of the contributions of longitudinal bosons. We examine all the contributions to the virtual amplitude involving top quarks, as expansions about the heavy top quark limit combined with a conformal mapping and Padé approximants. Comparison with the analytic results, where known, allows us to assess the validity of the heavy quark expansion, and it extensions. We give results for the NLO corrections to this interference, including both real and virtual radiation.

  8. Two loop correction to interference in $$gg \\to ZZ$$

    DOE PAGESBeta

    Campbell, John M.; Ellis, R. Keith; Czakon, Michal; Kirchner, Sebastian

    2016-08-01

    Here, we present results for the production of a pair of on-shell Z bosons via gluon-gluon fusion. This process occurs both through the production and decay of the Higgs boson, and through continuum production where the Z boson couples to a loop of massless quarks or to a massive quark. We calculate the interference of the two processes and its contribution to the cross section up to and including order O(αmore » $$_{s}^{3}$$ ). The two-loop contributions to the amplitude are all known analytically, except for the continuum production through loops of top quarks of mass m. The latter contribution is important for the invariant mass of the two Z bosons, (as measured by the mass of their leptonic decay products, m$$_{4l}$$), in a regime where m$$_{4l}$$ ≥ 2m because of the contributions of longitudinal bosons. We examine all the contributions to the virtual amplitude involving top quarks, as expansions about the heavy top quark limit combined with a conformal mapping and Padé approximants. Comparison with the analytic results, where known, allows us to assess the validity of the heavy quark expansion, and it extensions. We give results for the NLO corrections to this interference, including both real and virtual radiation.« less

  9. Analysis of the loop length distribution for the negative-weight percolation problem in dimensions d=2 through d=6.

    PubMed

    Claussen, G; Apolo, L; Melchert, O; Hartmann, A K

    2012-11-01

    We consider the negative weight percolation (NWP) problem on hypercubic lattice graphs with fully periodic boundary conditions in all relevant dimensions from d=2 to the upper critical dimension d=6. The problem exhibits edge weights drawn from disorder distributions that allow for weights of either sign. We are interested in the full ensemble of loops with negative weight, i.e., nontrivial (system spanning) loops as well as topologically trivial ("small") loops. The NWP phenomenon refers to the disorder driven proliferation of system spanning loops of total negative weight. While previous studies where focused on the latter loops, we here put under scrutiny the ensemble of small loops. Our aim is to characterize-using this extensive and exhaustive numerical study-the loop length distribution of the small loops right at and below the critical point of the hypercubic setups by means of two independent critical exponents. These can further be related to the results of previous finite-size scaling analyses carried out for the system spanning loops. For the numerical simulations, we employed a mapping of the NWP model to a combinatorial optimization problem that can be solved exactly by using sophisticated matching algorithms. This allowed us to study here numerically exact very large systems with high statistics. PMID:23214907

  10. Magnetic monopole in the loop representation

    SciTech Connect

    Leal, Lorenzo; Lopez, Alexander

    2006-01-15

    We quantize, within the Loop Representation formalism, the electromagnetic field in the presence of a static magnetic pole. It is found that the loop-dependent physical wave functionals of the quantum Maxwell theory become multivalued, through a topological phase factor depending on the solid angle subtended at the monopole by a surface bounded by the loop. It is discussed how this fact generalizes what occurs in ordinary quantum mechanics in multiply connected spaces.

  11. Biopolymer hairpin loops sustained by polarons

    NASA Astrophysics Data System (ADS)

    Chakrabarti, B.; Piette, B. M. A. G.; Zakrzewski, W. J.

    2012-08-01

    We show that polarons can sustain looplike configurations in flexible biopolymers and that the size of the loops depend on both the flexural rigidity of the polymer and the electron-phonon coupling constant. In particular we show that for single stranded DNA (ssDNA) and polyacetylene such loops can have as few as seven monomers. We also show that these configurations are very stable under thermal fluctuations and so could facilitate the formation of hairpin loops of ssDNA.

  12. LMFBR with booster pump in pumping loop

    DOEpatents

    Rubinstein, H.J.

    1975-10-14

    A loop coolant circulation system is described for a liquid metal fast breeder reactor (LMFBR) utilizing a low head, high specific speed booster pump in the hot leg of the coolant loop with the main pump located in the cold leg of the loop, thereby providing the advantages of operating the main pump in the hot leg with the reliability of cold leg pump operation.

  13. Loop anomalies in the causal approach

    NASA Astrophysics Data System (ADS)

    Grigore, Dan-Radu

    2015-01-01

    We consider gauge models in the causal approach and study one-loop contributions to the chronological products and the anomalies they produce. We prove that in order greater than 4 there are no one-loop anomalies. Next we analyze one-loop anomalies in the second- and third-order of the perturbation theory. We prove that the even parity contributions (with respect to parity) do not produce anomalies; for the odd parity contributions we reobtain the well-known result.

  14. Binary phase locked loops for Omega receivers

    NASA Technical Reports Server (NTRS)

    Chamberlin, K.

    1974-01-01

    An all-digital phase lock loop (PLL) is considered because of a number of problems inherent in an employment of analog PLL. The digital PLL design presented solves these problems. A single loop measures all eight Omega time slots. Memory-aiding leads to the name of this design, the memory-aided phase lock loop (MAPLL). Basic operating principles are discussed and the superiority of MAPLL over the conventional digital phase lock loop with regard to the operational efficiency for Omega applications is demonstrated.

  15. Loop statistics in polymers in crowded environment

    NASA Astrophysics Data System (ADS)

    Haydukivska, K.; Blavatska, V.

    2016-02-01

    We analyze the probability to find a single loop in a long flexible polymer chain in disordered environment in d dimensions. The structural defects are considered to be correlated on large distances r according to a power law ˜r-a. Working within the frames of continuous chain model and applying the direct polymer renormalization scheme, we obtain the values of critical exponents governing the scaling of probabilities to find the loops of various positions along the chain as function of loops' length. Our results quantitatively reveal that the presence of structural defects in environment decreases the probability of loop formation in polymer macromolecules.

  16. Multi-instrument observations of coronal loops

    NASA Astrophysics Data System (ADS)

    Scott, Jason Terrence

    This document exhibits results of analysis from data collected with multiple EUV satellites (SOHO, TRACE, STEREO, Hinode, and SDO). The focus is the detailed observation of coronal loops using multiple instruments, i.e. filter imagers and spectrometers. Techniques for comparing the different instruments and deriving loop parameters are demonstrated. Attention is given to the effects the different instruments may introduce into the data and their interpretation. The assembled loop parameters are compared to basic energy balance equations and scaling laws. Discussion of the blue-shifted, asymmetric, and line broadened spectral line profiles near the footpoints of coronal loops is made. The first quantitative analysis of the anti-correlation between intensity and spectral line broadening for isolated regions along loops and their footpoints is presented. A magnetic model of an active region shows where the separatrices meet the photospheric boundary. At the boundary, the spectral data reveal concentrated regions of increased blue-shifted outflows, blue wing asymmetry, and line broadening. This is found just outside the footpoints of bright loops. The intensity and line broadening in this region are anti-correlated. A comparison of the similarities in the spectroscopic structure near the footpoints of the arcade loops and more isolated loops suggests the notion of consistent structuring for the bright loops forming an apparent edge of an active region core.

  17. Closed-Loop Neuroscience and Non-Invasive Brain Stimulation: A Tale of Two Loops

    PubMed Central

    Zrenner, Christoph; Belardinelli, Paolo; Müller-Dahlhaus, Florian; Ziemann, Ulf

    2016-01-01

    Closed-loop neuroscience is receiving increasing attention with recent technological advances that enable complex feedback loops to be implemented with millisecond resolution on commodity hardware. We summarize emerging conceptual and methodological frameworks that are available to experimenters investigating a “brain in the loop” using non-invasive brain stimulation and briefly review the experimental and therapeutic implications. We take the view that closed-loop neuroscience in fact deals with two conceptually quite different loops: a “brain-state dynamics” loop, used to couple with and modulate the trajectory of neuronal activity patterns, and a “task dynamics” loop, that is the bidirectional motor-sensory interaction between brain and (simulated) environment, and which enables goal-directed behavioral tasks to be incorporated. Both loops need to be considered and combined to realize the full experimental and therapeutic potential of closed-loop neuroscience. PMID:27092055

  18. UWB communication receiver feedback loop

    DOEpatents

    Spiridon, Alex; Benzel, Dave; Dowla, Farid U.; Nekoogar, Faranak; Rosenbury, Erwin T.

    2007-12-04

    A novel technique and structure that maximizes the extraction of information from reference pulses for UWB-TR receivers is introduced. The scheme efficiently processes an incoming signal to suppress different types of UWB as well as non-UWB interference prior to signal detection. Such a method and system adds a feedback loop mechanism to enhance the signal-to-noise ratio of reference pulses in a conventional TR receiver. Moreover, sampling the second order statistical function such as, for example, the autocorrelation function (ACF) of the received signal and matching it to the ACF samples of the original pulses for each transmitted bit provides a more robust UWB communications method and system in the presence of channel distortions.

  19. Closed loop steam cooled airfoil

    SciTech Connect

    Widrig, Scott M.; Rudolph, Ronald J.; Wagner, Gregg P.

    2006-04-18

    An airfoil, a method of manufacturing an airfoil, and a system for cooling an airfoil is provided. The cooling system can be used with an airfoil located in the first stages of a combustion turbine within a combined cycle power generation plant and involves flowing closed loop steam through a pin array set within an airfoil. The airfoil can comprise a cavity having a cooling chamber bounded by an interior wall and an exterior wall so that steam can enter the cavity, pass through the pin array, and then return to the cavity to thereby cool the airfoil. The method of manufacturing an airfoil can include a type of lost wax investment casting process in which a pin array is cast into an airfoil to form a cooling chamber.

  20. Delay locked loop integrated circuit.

    SciTech Connect

    Brocato, Robert Wesley

    2007-10-01

    This report gives a description of the development of a Delay Locked Loop (DLL) integrated circuit (IC). The DLL was developed and tested as a stand-alone IC test chip to be integrated into a larger application specific integrated circuit (ASIC), the Quadrature Digital Waveform Synthesizer (QDWS). The purpose of the DLL is to provide a digitally programmable delay to enable synchronization between an internal system clock and external peripherals with unknown clock skew. The DLL was designed and fabricated in the IBM 8RF process, a 0.13 {micro}m CMOS process. It was designed to operate with a 300MHz clock and has been tested up to 500MHz.

  1. Closing the loop with blur

    NASA Astrophysics Data System (ADS)

    Tani, Jacopo

    A great variety of systems use image sensors to provide measurements for closed loop operation. A drawback of using image sensors in real-time feedback is that they provide measurements at slower sampling rates as compared to the actuators, typically around 30 Hz for CCD cameras, hence acting as the bottleneck for closed loop control bandwidths. While high speed cameras exist, higher frame rates imply an upper bound on exposures which lowers the signal-to-noise-ratio (SNR), reducing measurements accuracy. The integrative nature of image sensors though offers the opportunity to prolong the exposure window and collect motion blurred measurements. This research describes how to exploit the dynamic information of observed system outputs, encoded in motion blur, to control fast systems at the fast rate through slow rate image sensors. In order to achieve this objective it is necessary to (a) design a controller providing fast rate input to the system based on the slow image measurements. Ideally such a controller would require a fast rate estimate of the system's state variables in order to provide the necessary control action, therefore an (b) image blur based estimator is to be developed. State estimators typically need a model of the system in order to provide their estimates, so (c) a system identification problem has to be addressed, where a reliable model describing the frequency content of the system, up to frequencies corresponding to the fast rate, has to be determined through slow rate image sensor measurements. Alternatively when such a procedure is not possible for lack, e.g., of knowledge of the input to the system, then (d) a method to reconstruct the output signal frequency content up to frequencies above those set by the limitations of the sampling theorem is to be devised. Therefore in order to "close the loop with blur", this work describes how to pose and solve the problems of, namely: system identification , state estimation, closed loop control and

  2. Multiple LacI-mediated loops revealed by Bayesian statistics and tethered particle motion

    PubMed Central

    Johnson, Stephanie; van de Meent, Jan-Willem; Phillips, Rob; Wiggins, Chris H.; Lindén, Martin

    2014-01-01

    The bacterial transcription factor LacI loops DNA by binding to two separate locations on the DNA simultaneously. Despite being one of the best-studied model systems for transcriptional regulation, the number and conformations of loop structures accessible to LacI remain unclear, though the importance of multiple coexisting loops has been implicated in interactions between LacI and other cellular regulators of gene expression. To probe this issue, we have developed a new analysis method for tethered particle motion, a versatile and commonly used in vitro single-molecule technique. Our method, vbTPM, performs variational Bayesian inference in hidden Markov models. It learns the number of distinct states (i.e. DNA–protein conformations) directly from tethered particle motion data with better resolution than existing methods, while easily correcting for common experimental artifacts. Studying short (roughly 100 bp) LacI-mediated loops, we provide evidence for three distinct loop structures, more than previously reported in single-molecule studies. Moreover, our results confirm that changes in LacI conformation and DNA-binding topology both contribute to the repertoire of LacI-mediated loops formed in vitro, and provide qualitatively new input for models of looping and transcriptional regulation. We expect vbTPM to be broadly useful for probing complex protein–nucleic acid interactions. PMID:25120267

  3. Three-loop cusp anomalous dimension and a conjecture for n loops

    NASA Astrophysics Data System (ADS)

    Kidonakis, Nikolaos

    2016-05-01

    I present analytical expressions for the massive cusp anomalous dimension in QCD through three loops, first calculated in 2014, in terms of elementary functions and ordinary polylogarithms. I observe interesting relations between the results at different loops and provide a conjecture for the n-loop cusp anomalous dimension in terms of the lower-loop results. I also present numerical results and simple approximate formulas for the cusp anomalous dimension relevant to top-quark production.

  4. Improved methods for the formation and stabilization of R-loops

    PubMed Central

    Kaback, David B.; Angerer, Lynne M.; Davidson, Norman

    1979-01-01

    Improved methods for the formation and stabilization of R-loops for visualization in the electron microscope are presented. The two complementary strands of a duplex DNA are photochemically crosslinked once every 1 to 3 kb using 4, 5', 8 trimethylpsoralen. R-loops are then formed by incubation with RNA in 70% formamide at a temperature above the DNA melting temperature. Finally, the R-loops are stabilized by modifying the free single strand of DNA with glyoxal, thus minimizing the displacement of the hybridized RNA by branch migration. In this manner R-loops can be formed and visualized at a high frequency irrespective of the base composition of the nucleic acid of interest. Images PMID:379821

  5. Dihedral-like constructions of automorphic loops

    NASA Astrophysics Data System (ADS)

    Aboras, Mouna

    In this dissertation we study dihedral-like constructions of automorphic loops. Automorphic loops are loops in which all inner mappings are automorphisms. We start by describing a generalization of the dihedral construction for groups. Namely, if (G, +) is an abelian group, m > 1 and alpha ∈2 Aut(G), let Dih(m, G, alpha) on Zm x G be defined by. (i, u)(j, v) = (i + j, ((--1)ju + v)alpha ij). We prove that the resulting loop is automorphic if and only if m = 2 or (alpha2 = 1 and m is even) or (m is odd, alpha = 1 and exp(G) ≤ 2). In the last case, the loop is a group. The case m = 2 was introduced by Kinyon, Kunen, Phillips, and Vojtechovsky. We study basic structural properties of dihedral-like automorphic loops. We describe certain subloops, including: nucleus, commutant, center, associator subloop and derived subloop. We prove theorems for dihedral-like automorphic loops analogous to the Cauchy and Lagrange theorems for groups, and further we discuss the coset decomposition in dihedral-like automorphic loops. We show that two finite dihedral-like automorphic loops Dih( m, G, alpha) and Dih(m¯, G¯, [special character omitted]) are isomorphic if and only if m = m¯, G ≅ G¯ and alpha is conjugate to [special character omitted] in Aut(G). We describe the automorphism group of Q and its subgroup consisting of inner mappings of Q. Finally, due to the solution to the isomorphism problem, we are interested in studying conjugacy classes of automorphism groups of finite abelian groups. Then we describe all dihedral-like automorphic loops of order < 128 up to isomorphism. We conclude with a description of all dihedral-like automorphic loops of order < 64 up to isotopism.

  6. Magnetic loop emergence within a granule

    NASA Astrophysics Data System (ADS)

    Gömöry, P.; Beck, C.; Balthasar, H.; Rybák, J.; Kučera, A.; Koza, J.; Wöhl, H.

    2010-02-01

    Aims: We investigate the temporal evolution of magnetic flux emerging within a granule in the quiet-Sun internetwork at disk center. Methods: We combined IR spectropolarimetry of high angular resolution performed in two Fe i lines at 1565 nm with speckle-reconstructed G-band imaging. We determined the magnetic field parameters by a LTE inversion of the full Stokes vector using the SIR code, and followed their evolution in time. To interpret the observations, we created a geometrical model of a rising loop in 3D. The relevant parameters of the loop were matched to the observations where possible. We then synthesized spectra from the 3D model for a comparison to the observations. Results: We found signatures of magnetic flux emergence within a growing granule. In the early phases, a horizontal magnetic field with a distinct linear polarization signal dominated the emerging flux. Later on, two patches of opposite circular polarization signal appeared symmetrically on either side of the linear polarization patch, indicating a small loop-like structure. The mean magnetic flux density of this loop was roughly 450 G, with a total magnetic flux of around 3 × 1017 Mx. During the ~12 min episode of loop occurrence, the spatial extent of the loop increased from about 1 to 2 arcsec. The middle part of the appearing feature was blueshifted during its occurrence, supporting the scenario of an emerging loop. There is also clear evidence for the interaction of one loop footpoint with a preexisting magnetic structure of opposite polarity. The temporal evolution of the observed spectra is reproduced to first order by the spectra derived from the geometrical model. During the phase of clearest visibility of the loop in the observations, the observed and synthetic spectra match quantitatively. Conclusions: The observed event can be explained as a case of flux emergence in the shape of a small-scale loop. The fast disappearance of the loop at the end could possibly be due to magnetic

  7. Quantitation of interactions between two DNA loops demonstrates loop domain insulation in E. coli cells.

    PubMed

    Priest, David G; Kumar, Sandip; Yan, Yan; Dunlap, David D; Dodd, Ian B; Shearwin, Keith E

    2014-10-21

    Eukaryotic gene regulation involves complex patterns of long-range DNA-looping interactions between enhancers and promoters, but how these specific interactions are achieved is poorly understood. Models that posit other DNA loops--that aid or inhibit enhancer-promoter contact--are difficult to test or quantitate rigorously in eukaryotic cells. Here, we use the well-characterized DNA-looping proteins Lac repressor and phage λ CI to measure interactions between pairs of long DNA loops in E. coli cells in the three possible topological arrangements. We find that side-by-side loops do not affect each other. Nested loops assist each other's formation consistent with their distance-shortening effect. In contrast, alternating loops, where one looping element is placed within the other DNA loop, inhibit each other's formation, thus providing clear support for the loop domain model for insulation. Modeling shows that combining loop assistance and loop interference can provide strong specificity in long-range interactions. PMID:25288735

  8. 34. PLAN, PROPOSED EXTENSION OF COAL HOUSE, EXTENSIONS OF ENGINE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    34. PLAN, PROPOSED EXTENSION OF COAL HOUSE, EXTENSIONS OF ENGINE AND COAL HOUSES, DEER ISLAND PUMPING STATION, METROPOLITAN WATER AND SEWERAGE BOARD, METROPOLITAN SEWARAGE WORKS, JANUARY 1909, SHEET NO. 11. Aperture card 6498-11. - Deer Island Pumping Station, Boston, Suffolk County, MA

  9. 35. WEST END ELEVATION, PROPOSED EXTENSION OF COAL HOUSE, EXTENSIONS ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    35. WEST END ELEVATION, PROPOSED EXTENSION OF COAL HOUSE, EXTENSIONS OF ENGINE AND COAL HOUSES, DEER ISLAND PUMPING STATION, METROPOLITAN WATER AND SEWERAGE BOARD, METROPOLITAN SEWERAGE WORKS, JANUARY 1908, SHEET NO. 7. Aperture card 6498-7. - Deer Island Pumping Station, Boston, Suffolk County, MA

  10. Welding torch gas cup extension

    NASA Technical Reports Server (NTRS)

    Gordon, Stephen S. (Inventor)

    1988-01-01

    The invention relates to a gas shielded electric arc welding torch having a detachable gas cup extension which may be of any desired configuration or length. The gas cup extension assembly is mounted on a standard electric welding torch gas cup to enable welding in areas with limited access. The gas cup assembly has an upper tubular insert that fits within the gas cup such that its lower portion protrudes thereform and has a lower tubular extension that is screwed into the lower portion. The extension has a rim to define the outer perimeter of the seat edge about its entrance opening so a gasket may be placed to effect an airtight seal between the gas cup and extension. The tubular extension may be made of metal or cermaic material that can be machined. The novelty lies in the use of an extension assembly for a standard gas cup of an electric arc welding torch which extension assembly is detachable permitting the use of a number of extensions which may be of different configurations and materials and yet fit the standard gas cup.

  11. Robotic hand with modular extensions

    DOEpatents

    Salisbury, Curt Michael; Quigley, Morgan

    2015-01-20

    A robotic device is described herein. The robotic device includes a frame that comprises a plurality of receiving regions that are configured to receive a respective plurality of modular robotic extensions. The modular robotic extensions are removably attachable to the frame at the respective receiving regions by way of respective mechanical fuses. Each mechanical fuse is configured to trip when a respective modular robotic extension experiences a predefined load condition, such that the respective modular robotic extension detaches from the frame when the load condition is met.

  12. Loop calculus for lattice gauge theories

    SciTech Connect

    Gambini, R.; Leal, L.; Trias, A.

    1989-05-15

    Hamiltonian calculations are performed using a loop-labeled basis where the full set of identities for the SU(/ital N/) gauge models has been incorporated. The loops are classified as clusterlike structures and the eigenvalue problem leads to a linear set of finite-difference equations easily amenable to numerical treatment. Encouraging results are reported for SU(2) at spatial dimension 2.

  13. Feedback loop compensates for rectifier nonlinearity

    NASA Technical Reports Server (NTRS)

    1966-01-01

    Signal processing circuit with two negative feedback loops rectifies two sinusoidal signals which are 180 degrees out of phase and produces a single full-wave rectified output signal. Each feedback loop incorporates a feedback rectifier to compensate for the nonlinearity of the circuit.

  14. The Cygnus Loop: An Older Supernova Remnant.

    ERIC Educational Resources Information Center

    Straka, William

    1987-01-01

    Describes the Cygnus Loop, one of brightest and most easily studied of the older "remnant nebulae" of supernova outbursts. Discusses some of the historical events surrounding the discovery and measurement of the Cygnus Loop and makes some projections on its future. (TW)

  15. Loop substitution as a tool to identify active sites of interleukin-1 beta.

    PubMed

    Palla, E; Bensi, G; Solito, E; Buonamassa, D T; Fassina, G; Raugei, G; Spano, F; Galeotti, C; Mora, M; Domenighini, M

    1993-06-25

    By computer analysis of the amino acid sequence of human interleukin-1 beta (IL-1 beta) and of the human type I IL-1 receptor (IL-1RI), we have identified two hydropathically complementary peptides (Fassina, G., Roller, P. P., Olson, A. D., Thorgeirsson, S. S., and Omichinski, J. G. (1989) J. Biol. Chem. 264, 11252-11257) capable of binding to each other. The sequence of the IL-1 beta peptide corresponds to that of residues 88-99 (loop 7 of the crystal structure of mature IL-1 beta) of mature IL-1 beta, one of the exposed and highly charged regions of the molecule. The substitution of this loop with an amino acid sequence of the same length but different hydropathic profile generates a mutant with drastically reduced binding activity to IL-1RI. In contrast, the binding affinity to the type II IL-1R (IL-1RII) is the same as that of wild type IL-1 beta. The results show that 1) loop 7 is part of the binding site of IL-1 beta to IL-1RI, but not to IL-1RII. 2) The structure of the mutant protein is not grossly altered except locally at the position of the substituted loop. 3) The substitution of amino acids by site-directed mutagenesis of the loop 7 region generates mutants with binding affinity constants slightly lower than that of wild type IL-1 beta and not comparable to that of the loop substitution analogue. 4. All mutants analyzed, including the loop substitutions, are biologically active, confirming the structural integrity of the proteins. We propose a binding site in which the cooperation of several low energy bonds extended over a wide area results in a high affinity complex between IL-1 and the type I receptor. PMID:7685764

  16. Contrasting HIV phylogenetic relationships and V3 loop protein similarities

    SciTech Connect

    Korber, B. |; Myers, G.

    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.

  17. Contrasting HIV phylogenetic relationships and V3 loop protein similarities

    SciTech Connect

    Korber, B. Santa Fe Inst., NM ); Myers, G. )

    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.

  18. Intrachain diffusion in a protein loop fragment from carp parvalbumin

    NASA Astrophysics Data System (ADS)

    Krieger, Florian; Fierz, Beat; Axthelm, Fabian; Joder, Karin; Meyer, Dominique; Kiefhaber, Thomas

    2004-12-01

    During protein folding a polypeptide chain has to form specific intrachain interactions starting from an ensemble of unfolded conformation. Thus, intrachain diffusion in unfolded polypeptide chains can be regarded as an elementary step in protein folding, which should determine the dynamics of the early stages in the folding process. We have previously applied exothermic triplet-triplet energy transfer from xanthone to naphthalene to determine rate constants for intrachain end-to-end contact formation in unstructured homo-polypeptide chains. Here we show that the method can be applied to determine absolute rate constants for intrachain diffusion in natural loop sequences, if they are free of methionine, tryptophan and tyrosine. We measured the rate of loop formation in an 18 amino acid polypeptide chain corresponding to a natural loop sequence from carp muscle β-parvalbumin (residues 85-102). Contact formation shows single exponential kinetics with a time constant ( τ=1/ k) of 53 ± 3 ns at 22.5 °C in water. Comparison with the results on homo-polypeptide chains shows that this value agrees well with rates obtained earlier for a polyserine chain of the same length.

  19. Loop polymer brushes from polymer single crystals

    NASA Astrophysics Data System (ADS)

    Zhou, Tian; Li, Christopher

    2014-03-01

    Loop polymer brushes represent a category of polymer brushes with both chain ends being tethered to a surface or interface with sufficiently high density. Due to this morphological difference, loop brushes exhibit distinct properties compared with traditional polymer brushes with single chain end being tethered. In our study, α, ω-functionalized polycaprolactone (PCL) single crystals were prepared as templates for polymer brush synthesis. By carefully controlling crystallization condition and immobilization, looped polymer brushes were successfully prepared. Comprehensive studies on the morphology and physical properties of these polymer brushes were carried out using Atomic Force Microscopy and FTIR. Advantages of using this method include exclusive loop morphology, high grafting density, controlled tethering sites and tunable loop size.

  20. DNA looping increases the range of bistability in a stochastic model of the lac genetic switch.

    PubMed

    Earnest, Tyler M; Roberts, Elijah; Assaf, Michael; Dahmen, Karin; Luthey-Schulten, Zaida

    2013-04-01

    Conditions and parameters affecting the range of bistability of the lac genetic switch in Escherichia coli are examined for a model which includes DNA looping interactions with the lac repressor and a lactose analogue. This stochastic gene-mRNA-protein model of the lac switch describes DNA looping using a third transcriptional state. We exploit the fast bursting dynamics of mRNA by combining a novel geometric burst extension with the finite state projection method. This limits the number of protein/mRNA states, allowing for an accelerated search of the model's parameter space. We evaluate how the addition of the third state changes the bistability properties of the model and find a critical region of parameter space where the phenotypic switching occurs in a range seen in single molecule fluorescence studies. Stochastic simulations show induction in the looping model is preceded by a rare complete dissociation of the loop followed by an immediate burst of mRNA rather than a slower build up of mRNA as in the two-state model. The overall effect of the looped state is to allow for faster switching times while at the same time further differentiating the uninduced and induced phenotypes. Furthermore, the kinetic parameters are consistent with free energies derived from thermodynamic studies suggesting that this minimal model of DNA looping could have a broader range of application. PMID:23406725

  1. Fast, vacancy-free climb of prismatic dislocation loops in bcc metals

    PubMed Central

    Swinburne, Thomas D.; Arakawa, Kazuto; Mori, Hirotaro; Yasuda, Hidehiro; Isshiki, Minoru; Mimura, Kouji; Uchikoshi, Masahito; Dudarev, Sergei L.

    2016-01-01

    Vacancy-mediated climb models cannot account for the fast, direct coalescence of dislocation loops seen experimentally. An alternative mechanism, self climb, allows prismatic dislocation loops to move away from their glide surface via pipe diffusion around the loop perimeter, independent of any vacancy atmosphere. Despite the known importance of self climb, theoretical models require a typically unknown activation energy, hindering implementation in materials modeling. Here, extensive molecular statics calculations of pipe diffusion processes around irregular prismatic loops are used to map the energy landscape for self climb in iron and tungsten, finding a simple, material independent energy model after normalizing by the vacancy migration barrier. Kinetic Monte Carlo simulations yield a self climb activation energy of 2 (2.5) times the vacancy migration barrier for 1/2〈111〉 (〈100〉) dislocation loops. Dislocation dynamics simulations allowing self climb and glide show quantitative agreement with transmission electron microscopy observations of climbing prismatic loops in iron and tungsten, confirming that this novel form of vacancy-free climb is many orders of magnitude faster than what is predicted by traditional climb models. Self climb significantly influences the coarsening rate of defect networks, with important implications for post-irradiation annealing. PMID:27549928

  2. DNA looping increases the range of bistability in a stochastic model of the lac genetic switch

    NASA Astrophysics Data System (ADS)

    Earnest, Tyler M.; Roberts, Elijah; Assaf, Michael; Dahmen, Karin; Luthey-Schulten, Zaida

    2013-04-01

    Conditions and parameters affecting the range of bistability of the lac genetic switch in Escherichia coli are examined for a model which includes DNA looping interactions with the lac repressor and a lactose analogue. This stochastic gene-mRNA-protein model of the lac switch describes DNA looping using a third transcriptional state. We exploit the fast bursting dynamics of mRNA by combining a novel geometric burst extension with the finite state projection method. This limits the number of protein/mRNA states, allowing for an accelerated search of the model's parameter space. We evaluate how the addition of the third state changes the bistability properties of the model and find a critical region of parameter space where the phenotypic switching occurs in a range seen in single molecule fluorescence studies. Stochastic simulations show induction in the looping model is preceded by a rare complete dissociation of the loop followed by an immediate burst of mRNA rather than a slower build up of mRNA as in the two-state model. The overall effect of the looped state is to allow for faster switching times while at the same time further differentiating the uninduced and induced phenotypes. Furthermore, the kinetic parameters are consistent with free energies derived from thermodynamic studies suggesting that this minimal model of DNA looping could have a broader range of application.

  3. Fast, vacancy-free climb of prismatic dislocation loops in bcc metals.

    PubMed

    Swinburne, Thomas D; Arakawa, Kazuto; Mori, Hirotaro; Yasuda, Hidehiro; Isshiki, Minoru; Mimura, Kouji; Uchikoshi, Masahito; Dudarev, Sergei L

    2016-01-01

    Vacancy-mediated climb models cannot account for the fast, direct coalescence of dislocation loops seen experimentally. An alternative mechanism, self climb, allows prismatic dislocation loops to move away from their glide surface via pipe diffusion around the loop perimeter, independent of any vacancy atmosphere. Despite the known importance of self climb, theoretical models require a typically unknown activation energy, hindering implementation in materials modeling. Here, extensive molecular statics calculations of pipe diffusion processes around irregular prismatic loops are used to map the energy landscape for self climb in iron and tungsten, finding a simple, material independent energy model after normalizing by the vacancy migration barrier. Kinetic Monte Carlo simulations yield a self climb activation energy of 2 (2.5) times the vacancy migration barrier for 1/2〈111〉 (〈100〉) dislocation loops. Dislocation dynamics simulations allowing self climb and glide show quantitative agreement with transmission electron microscopy observations of climbing prismatic loops in iron and tungsten, confirming that this novel form of vacancy-free climb is many orders of magnitude faster than what is predicted by traditional climb models. Self climb significantly influences the coarsening rate of defect networks, with important implications for post-irradiation annealing. PMID:27549928

  4. Transient brightenings of interconnecting loops. II - Dynamics of the brightened loops

    NASA Technical Reports Server (NTRS)

    Svestka, Z.; Howard, R.

    1981-01-01

    Three different kinds of dynamic events related to interconnecting loops observed in soft X-rays aboard Skylab are discussed: (1) a newly born transequatorial loop that was either emerging from subphotospheric layers or gradually filled in with hot plasma; (2) large-scale twists of interconnecting loops which never relax, and often only form after the loop brightenings, and (3) three events where the loop that later interconnected two active regions had been visible long before one of the interconnecting regions was born. Several impacts this observation might have upon the understanding of the process of flux emergence are suggested.

  5. A communication scheme for the distrubted execution of loop nests with while loops

    SciTech Connect

    Griebl, M.; Lengauer, C.

    1995-10-01

    The mathematical model for the parallelization, or {open_quotes}space-time mapping,{close_quotes} of loop nests is the polyhedron model. The presence of while loops in the nest complicates matters for two reasons: (1) the parallelized loop nest does not correspond to a polyhedron but instead to a subset that resembles a (multi-dimensional) comb and (2) it is not clear when the entire loop nest has terminated. We describe a communication scheme which can deal with both problems and which can be added to the parallel target loop nest by a compiler.

  6. Loop heat pipes and capillary pumped loops-an applications perspective

    NASA Astrophysics Data System (ADS)

    Butler, Dan; Ku, Jentung; Swanson, Theodore

    2002-01-01

    Capillary pumped loops (CPLs) and loop heat pipes (LHPs) are versatile two-phase heat transfer devices which have recently gained increasing acceptance in space applications. Both systems work based on the same principles and have very similar designs. Nevertheless, some differences exist in the construction of the evaporator and the hydro-accumulator, and these differences lead to very distinct operating characteristics for each loop. This paper presents comparisons of the two loops from an applications perspective, and addresses their impact on spacecraft design, integration, and test. Some technical challenges and issues for both loops are also addressed. .

  7. Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis.

    PubMed

    Wang, Dong; Bushnell, David A; Westover, Kenneth D; Kaplan, Craig D; Kornberg, Roger D

    2006-12-01

    New structures of RNA polymerase II (pol II) transcribing complexes reveal a likely key to transcription. The trigger loop swings beneath a correct nucleoside triphosphate (NTP) in the nucleotide addition site, closing off the active center and forming an extensive network of interactions with the NTP base, sugar, phosphates, and additional pol II residues. A histidine side chain in the trigger loop, precisely positioned by these interactions, may literally "trigger" phosphodiester bond formation. Recognition and catalysis are thus coupled, ensuring the fidelity of transcription. PMID:17129781

  8. Two-loop Higgs mass calculations in supersymmetric models beyond the MSSM with SARAH and SPheno

    NASA Astrophysics Data System (ADS)

    Goodsell, Mark D.; Nickel, Kilian; Staub, Florian

    2015-01-01

    We present an extension to the Mathematica package SARAH which allows for Higgs mass calculations at the two-loop level in a wide range of supersymmetric (SUSY) models beyond the MSSM. These calculations are based on the effective potential approach and include all two-loop corrections which are independent of electroweak gauge couplings. For the numerical evaluation Fortran code for SPheno is generated by SARAH. This allows the prediction of the Higgs mass in more complicated SUSY models with the same precision that most state-of-the-art spectrum generators provide for the MSSM.

  9. Cygnus Loop Supernova Blast Wave

    NASA Technical Reports Server (NTRS)

    1993-01-01

    This is an image of a small portion of the Cygnus Loop supernova remnant, which marks the edge of a bubble-like, expanding blast wave from a colossal stellar explosion, occurring about 15,000 years ago. The HST image shows the structure behind the shock waves, allowing astronomers for the first time to directly compare the actual structure of the shock with theoretical model calculations. Besides supernova remnants, these shock models are important in understanding a wide range of astrophysical phenomena, from winds in newly-formed stars to cataclysmic stellar outbursts. The supernova blast is slamming into tenuous clouds of insterstellar gas. This collision heats and compresses the gas, causing it to glow. The shock thus acts as a searchlight revealing the structure of the interstellar medium. The detailed HST image shows the blast wave overrunning dense clumps of gas, which despite HST's high resolution, cannot be resolved. This means that the clumps of gas must be small enough to fit inside our solar system, making them relatively small structures by interstellar standards. A bluish ribbon of light stretching left to right across the picture might be a knot of gas ejected by the supernova; this interstellar 'bullet' traveling over three million miles per hour (5 million kilometres) is just catching up with the shock front, which has slowed down by ploughing into interstellar material. The Cygnus Loop appears as a faint ring of glowing gases about three degrees across (six times the diameter of the full Moon), located in the northern constellation, Cygnus the Swan. The supernova remnant is within the plane of our Milky Way galaxy and is 2,600 light-years away. The photo is a combination of separate images taken in three colors, oxygen atoms (blue) emit light at temperatures of 30,000 to 60,000 degrees Celsius (50,000 to 100,000 degrees Farenheit). Hydrogen atoms (green) arise throughout the region of shocked gas. Sulfur atoms (red) form when the gas cools to

  10. Quantitation of interactions between two DNA loops demonstrates loop domain insulation in E. coli cells

    PubMed Central

    Priest, David G.; Kumar, Sandip; Yan, Yan; Dunlap, David D.; Dodd, Ian B.; Shearwin, Keith E.

    2014-01-01

    Eukaryotic gene regulation involves complex patterns of long-range DNA-looping interactions between enhancers and promoters, but how these specific interactions are achieved is poorly understood. Models that posit other DNA loops—that aid or inhibit enhancer–promoter contact—are difficult to test or quantitate rigorously in eukaryotic cells. Here, we use the well-characterized DNA-looping proteins Lac repressor and phage λ CI to measure interactions between pairs of long DNA loops in E. coli cells in the three possible topological arrangements. We find that side-by-side loops do not affect each other. Nested loops assist each other’s formation consistent with their distance-shortening effect. In contrast, alternating loops, where one looping element is placed within the other DNA loop, inhibit each other’s formation, thus providing clear support for the loop domain model for insulation. Modeling shows that combining loop assistance and loop interference can provide strong specificity in long-range interactions. PMID:25288735

  11. Why Do Extension Agents Resign?

    ERIC Educational Resources Information Center

    Manton, Linda Nunes; van Es, J. C.

    1985-01-01

    Past and current Illinois extension agents were surveyed via mail questionnaires as to reasons for staying or leaving extension programs. Reasons for leaving included family changes, family moves, opportunity to advance, better salary/benefits, dissatisfaction with administration, and too much time away from family. (CT)

  12. GNU Fortran Cray Pointer Extension

    2005-07-27

    The gfortran compiler is a Fortran front end to the GNU Compiler Collection. The Cray Pointer extension adds to this existing compiler support for Cray-style integer pointers. This non-standard but widely used extension adds the functionality of C-like pointers to the Fortran language.

  13. Extension and the Practicing Veterinarian

    ERIC Educational Resources Information Center

    Meyerholz, G. W.

    1974-01-01

    In order for Extension programs of veterinary medicine to succeed, good relationships are needed among university veterinarians, practicing local veterinarians, county Extension agents and the clientele. This author attempts to define some roles and relationships and offer some suggestions for the improvement of relationships to increase…

  14. Extensive Reading Coursebooks in China

    ERIC Educational Resources Information Center

    Renandya, Willy A.; Hu, Guangwei; Xiang, Yu

    2015-01-01

    This article reports on a principle-based evaluation of eight dedicated extensive reading coursebooks published in mainland China and used in many universities across the country. The aim is to determine the extent to which these coursebooks reflect a core set of nine second language acquisition and extensive reading principles. Our analysis shows…

  15. Repeat Customer Success in Extension

    ERIC Educational Resources Information Center

    Bess, Melissa M.; Traub, Sarah M.

    2013-01-01

    Four multi-session research-based programs were offered by two Extension specialist in one rural Missouri county. Eleven participants who came to multiple Extension programs could be called "repeat customers." Based on the total number of participants for all four programs, 25% could be deemed as repeat customers. Repeat customers had…

  16. Energy Crisis vs. Extension Opportunities

    ERIC Educational Resources Information Center

    Liles, Harold R.

    1978-01-01

    Discusses what steps were taken by the Cooperative Extension Service in Oklahoma, after the energy crisis began, to help landowners make better decisions regarding oil and gas leases. Oklahoma's Extension educational efforts in mineral rights management have been successful because they met the needs of the people. (EM)

  17. Presence of mitochondrial D-loop DNA in scrapie-infected brain preparations enriched for the prion protein.

    PubMed Central

    Aiken, J M; Williamson, J L; Borchardt, L M; Marsh, R F

    1990-01-01

    The prion preparation has, in recent years, been the focal point of scrapie research. The inability to identify agent-specific nucleic acids in this sample has led to the formulation of the infectious protein or prion hypothesis. In this study, we analyzed three different prion protein-enriched preparations and found all to contain significant amounts of mitochondrial nucleic acid. Southern blot analyses indicated that they are enriched for a specific component of the mitochondrial genome, the single-stranded displacement loop fragment. Our results suggest that if mitochondrial nucleic acids are involved in scrapie infection, it is the displacement loop fragment that is specifically responsible. Images PMID:1972202

  18. Towards conformal loop quantum gravity

    NASA Astrophysics Data System (ADS)

    H-T Wang, Charles

    2006-03-01

    A discussion is given of recent developments in canonical gravity that assimilates the conformal analysis of gravitational degrees of freedom. The work is motivated by the problem of time in quantum gravity and is carried out at the metric and the triad levels. At the metric level, it is shown that by extending the Arnowitt-Deser-Misner (ADM) phase space of general relativity (GR), a conformal form of geometrodynamics can be constructed. In addition to the Hamiltonian and Diffeomorphism constraints, an extra first class constraint is introduced to generate conformal transformations. This phase space consists of York's mean extrinsic curvature time, conformal three-metric and their momenta. At the triad level, the phase space of GR is further enlarged by incorporating spin-gauge as well as conformal symmetries. This leads to a canonical formulation of GR using a new set of real spin connection variables. The resulting gravitational constraints are first class, consisting of the Hamiltonian constraint and the canonical generators for spin-gauge and conformorphism transformations. The formulation has a remarkable feature of being parameter-free. Indeed, it is shown that a conformal parameter of the Barbero-Immirzi type can be absorbed by the conformal symmetry of the extended phase space. This gives rise to an alternative approach to loop quantum gravity that addresses both the conceptual problem of time and the technical problem of functional calculus in quantum gravity.

  19. Direct Demonstration That Loop1 of Scap Binds to Loop7: A CRUCIAL EVENT IN CHOLESTEROL HOMEOSTASIS.

    PubMed

    Zhang, Yinxin; Lee, Kwang Min; Kinch, Lisa N; Clark, Lindsay; Grishin, Nick V; Rosenbaum, Daniel M; Brown, Michael S; Goldstein, Joseph L; Radhakrishnan, Arun

    2016-06-10

    Cholesterol homeostasis is mediated by Scap, a polytopic endoplasmic reticulum (ER) protein that transports sterol regulatory element-binding proteins from the ER to Golgi, where they are processed to forms that activate cholesterol synthesis. Scap has eight transmembrane helices and two large luminal loops, designated Loop1 and Loop7. We earlier provided indirect evidence that Loop1 binds to Loop7, allowing Scap to bind COPII proteins for transport in coated vesicles. When ER cholesterol rises, it binds to Loop1. We hypothesized that this causes dissociation from Loop7, abrogating COPII binding. Here we demonstrate direct binding of the two loops when expressed as isolated fragments or as a fusion protein. Expressed alone, Loop1 remained intracellular and membrane-bound. When Loop7 was co-expressed, it bound to Loop1, and the soluble complex was secreted. A Loop1-Loop7 fusion protein was also secreted, and the two loops remained bound when the linker between them was cleaved by a protease. Point mutations that disrupt the Loop1-Loop7 interaction prevented secretion of the Loop1-Loop7 fusion protein. These data provide direct documentation of intramolecular Loop1-Loop7 binding, a central event in cholesterol homeostasis. PMID:27068746

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

    PubMed Central

    Ababou, Abdessamad; Koronakis, Vassilis

    2016-01-01

    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. PMID:27403665

  1. Mitotic chromosome compaction via active loop extrusion

    NASA Astrophysics Data System (ADS)

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

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

  2. Microfluidic Continuous Flow Digital Loop-Mediated Isothermal Amplification (LAMP)

    PubMed Central

    Rane, Tushar D.; Chen, Liben; Zec, Helena C.; Wang, Tza-Huei

    2015-01-01

    Digital nucleic acid detection is rapidly becoming a popular technique for ultra-sensitive and quantitative detection of nucleic acid molecules in a wide range of biomedical studies. Digital polymerase chain reaction (PCR) remains the most popular way of conducting digital nucleic acid detection. However, due to the need for thermocycling, digital PCR is difficult to implement in a streamlined manner on a single microfluidic device, leading to complex fragmented workflows and multiple separate devices and instruments. Loop-mediated isothermal amplification (LAMP) is an excellent isothermal alternative to PCR with potentially better specificity than PCR through the use of multiple primer sets for a nucleic acid target. Here we report a microfluidic droplet device implementing all the steps required for digital nucleic acid detection including droplet generation, incubation and in-line detection for digital LAMP. As compared to microchamber or droplet array-based digital assays, continuous flow operation of this device eliminates the constraints on the number of total reactions by the footprint of the device and the analysis throughput by the time for lengthy incubation and transfers of materials between instruments. PMID:25431886

  3. The ionospheric outflow feedback loop

    NASA Astrophysics Data System (ADS)

    Moore, T. E.; Fok, M.-C.; Garcia-Sage, K.

    2014-08-01

    Following a long period of observation and investigation beginning in the early 1970s, it has been firmly established that Earth's magnetosphere is defined as much by the geogenic plasma within it as by the geomagnetic field. This plasma is not confined to the ionosphere proper, defined as the region within a few density scale heights of the F-region plasma density peak. Rather, it fills the flux tubes on which it is created, and circulates throughout the magnetosphere in a pattern driven by solar wind plasma that becomes magnetically connected to the ionosphere by reconnection through the dayside magnetopause. Under certain solar wind conditions, plasma and field energy is stored in the magnetotail rather than being smoothly recirculated back to the dayside. Its release into the downstream solar wind is produced by magnetotail disconnection of stored plasma and fields both continuously and in the form of discrete plasmoids, with associated generation of energetic Earthward-moving bursty bulk flows and injection fronts. A new generation of global circulation models is showing us that outflowing ionospheric plasmas, especially O+, load the system in a different way than the resistive F-region load of currents dissipating energy in the plasma and atmospheric neutral gas. The extended ionospheric load is reactive to the primary dissipation, forming a time-delayed feedback loop within the system. That sets up or intensifies bursty transient behaviors that would be weaker or absent if the ionosphere did not “strike back” when stimulated. Understanding this response appears to be a necessary, if not sufficient, condition for us to gain accurate predictive capability for space weather. However, full predictive understanding of outflow and incorporation into global simulations requires a clear observational and theoretical identification of the causal mechanisms of the outflows. This remains elusive and requires a dedicated mission effort.

  4. Boosted Fast Flux Loop Alternative Cooling Assessment

    SciTech Connect

    Glen R. Longhurst; Donna Post Guillen; James R. Parry; Douglas L. Porter; Bruce W. Wallace

    2007-08-01

    The Gas Test Loop (GTL) Project was instituted to develop the means for conducting fast neutron irradiation tests in a domestic radiation facility. It made use of booster fuel to achieve the high neutron flux, a hafnium thermal neutron absorber to attain the high fast-to-thermal flux ratio, a mixed gas temperature control system for maintaining experiment temperatures, and a compressed gas cooling system to remove heat from the experiment capsules and the hafnium thermal neutron absorber. This GTL system was determined to provide a fast (E > 0.1 MeV) flux greater than 1.0E+15 n/cm2-s with a fast-to-thermal flux ratio in the vicinity of 40. However, the estimated system acquisition cost from earlier studies was deemed to be high. That cost was strongly influenced by the compressed gas cooling system for experiment heat removal. Designers were challenged to find a less expensive way to achieve the required cooling. This report documents the results of the investigation leading to an alternatively cooled configuration, referred to now as the Boosted Fast Flux Loop (BFFL). This configuration relies on a composite material comprised of hafnium aluminide (Al3Hf) in an aluminum matrix to transfer heat from the experiment to pressurized water cooling channels while at the same time providing absorption of thermal neutrons. Investigations into the performance this configuration might achieve showed that it should perform at least as well as its gas-cooled predecessor. Physics calculations indicated that the fast neutron flux averaged over the central 40 cm (16 inches) relative to ATR core mid-plane in irradiation spaces would be about 1.04E+15 n/cm2-s. The fast-to-thermal flux ratio would be in excess of 40. Further, the particular configuration of cooling channels was relatively unimportant compared with the total amount of water in the apparatus in determining performance. Thermal analyses conducted on a candidate configuration showed the design of the water coolant and

  5. Tertiary structure-dependence of misfolding substitutions in loops of the maltose-binding protein.

    PubMed

    Raffy, S; Sassoon, N; Hofnung, M; Betton, J M

    1998-10-01

    We previously identified and characterized amino acid substitutions in a loop connecting helix I to strand B, the alphaI/betaB loop, of the N-domain that are critical for in vivo folding of the maltose-binding protein (MalE31). The tertiary context-dependence of this mutation in MalE folding was assessed by probing the tolerance of an equivalent alphabeta loop of the C-domain to the same amino acid substitutions (MalE219). Moving the loop mutation from the N- to the C-domain eliminated the in vivo misfolding step that led to the formation of inclusion bodies. In vitro, both loop variants exhibited an important decrease of stability, but their intrinsic tendency to aggregate was well correlated with their periplasmic fates in Escherichia coli. Furthermore, the noncoincidence of the unfolding and refolding transition curves and increase of light scattering during the refolding of MalE31 indicate that a competing off-pathway reaction could occurs on the folding pathway of this variant. These results strongly support the notion that the formation of super-secondary structures of the N-domain is a rate-limiting step in the folding pathway of MalE. PMID:9792100

  6. System description of the ANL (Argonne National Laboratory) Slurry Loop Testing facility (SLTF)

    SciTech Connect

    Porges, K.G.; Cox, S.A.; Brewer, W.E.; Hacker, D.S.

    1986-09-01

    This report describes a test loop specifically designed for dense slurries. The loop provides flow velocity and medium composition calibrations within 1%, as well as online rheometric characterization in non-Newtonian, laminar flow, by means of several unique calibration facilities developed at Argonne National Laboratory. Two horizontal test sections of 6 and 12 m length, as well as a vertical test section of 6 m length, are provided for flowmeter calibration; up to 5 flowmeters can be accommodated simultaneously. In addition to the online calibration schemes, which rank this test loop among the most accurate facilities currently existing, extensive laboratory characterization of grab samples is available. Initial work with coal/oil and coal/water slurries ranged over 60% solids. 18 refs., 26 figs., 1 tab.

  7. Picrotoxin dramatically speeds the mammalian circadian clock independent of Cys-loop receptors

    PubMed Central

    Freeman, G. Mark; Nakajima, Masato; Ueda, Hiroki R.

    2013-01-01

    Picrotoxin is extensively and specifically used to inhibit GABAA receptors and other members of the Cys-loop receptor superfamily. We find that picrotoxin acts independently of known Cys-loop receptors to shorten the period of the circadian clock markedly by specifically advancing the accumulation of PERIOD2 protein. We show that this mechanism is surprisingly tetrodotoxin-insensitive, and the effect is larger than any known chemical or genetic manipulation. Notably, our results indicate that the circadian target of picrotoxin is common to a variety of human and rodent cell types but not Drosophila, thereby ruling out all conserved Cys-loop receptors and known regulators of mammalian PERIOD protein stability. Given that the circadian clock modulates significant aspects of cell physiology including synaptic plasticity, these results have immediate and broad experimental implications. Furthermore, our data point to the existence of an important and novel target within the mammalian circadian timing system. PMID:23576702

  8. A design method for closed loop solar energy systems with concentrating collectors

    NASA Astrophysics Data System (ADS)

    Ryan, W. A.

    1982-01-01

    A method of performance prediction and design for closed loop concentrating solar collector systems is presented, along with a comparison of prediction with results using a compound parabolic concentrating collector. The numerical model is an extension of Collares-Pereira and Rabl (1978) model for concentrating collectors to a closed-loop scenario, using a monthly average utilizability factor and the f-chart technique. The predictions were compared with simulations using the TRNSYS program, considering 1.5, 3.0, and 5.0 concentration factors, and a sensible heat storage system. Performance predictions were found to depart from the simulations by an average of 14.04% for all cases, with the predictions giving consistently lower results. The method is concluded to be useful for optimizing collector areas and concentration ratios in closed-loop systems.

  9. Sensitivity of the blue loops of intermediate-mass stars to nuclear reactions

    SciTech Connect

    Halabi, Ghina M.; El Eid, Mounib

    2012-11-20

    We investigate the effects of a modification of the {sup 14}N(p,{gamma}){sup 15}O reaction rate, as suggested by recent evaluations, on the formation and extension of the blue loops encountered during the evolution of the stars in the mass range 5M{sub Circled-Dot-Operator} to 12M{sub Circled-Dot-Operator }. We show that the blue loops of stars in the mass range 5M{sub Circled-Dot-Operator} to 8M{sub Circled-Dot-Operator }, that is the range of super ABG stars, are severely affected by a modification of the important {sup 14}N(p,{gamma}){sup 15}O reaction rate. We also show that the blue loops can be restored if envelope overshooting is included, which is necessary to explain the observations of the Cepheid stars.

  10. Putting Extension on a Spot

    ERIC Educational Resources Information Center

    Lawrence, James E.

    1970-01-01

    Between and during television programs from WNBF-TV, Binghamton, New York, the Extension Service is providing public service announcements giving information on nutrition, food stamps, forage pests, outdoor recreation, farm safety, environmental quality, and many other subjects. (EB)

  11. Decentralizing Agricultural Extension: Alternative Strategies.

    ERIC Educational Resources Information Center

    Rivera, William M.

    1997-01-01

    Examines government strategies for decentralizing agricultural extension, concluding that such changes are largely determined by the country's constitutional status. Reviews decentralization guidelines for structural and fiscal reforms and participatory management systems. (SK)

  12. Open-loop digital frequency multiplier

    NASA Technical Reports Server (NTRS)

    Moore, R. C.

    1977-01-01

    Monostable multivibrator is implemented by using digital integrated circuits where multiplier constant is too large for conventional phase-locked-loop integrated circuit. A 400 Hz clock is generated by divide-by-N counter from 1 Hz timing reference.

  13. The universal one-loop effective action

    NASA Astrophysics Data System (ADS)

    Drozd, Aleksandra; Ellis, John; Quevillon, Jérémie; You, Tevong

    2016-03-01

    We present the universal one-loop effective action for all operators of dimension up to six obtained by integrating out massive, non-degenerate multiplets. Our general expression may be applied to loops of heavy fermions or bosons, and has been checked against partial results available in the literature. The broad applicability of this approach simplifies one-loop matching from an ultraviolet model to a lower-energy effective field theory (EFT), a procedure which is now reduced to the evaluation of a combination of matrices in our universal expression, without any loop integrals to evaluate. We illustrate the relationship of our results to the Standard Model (SM) EFT, using as an example the supersymmetric stop and sbottom squark Lagrangian and extracting from our universal expression the Wilson coefficients of dimension-six operators composed of SM fields.

  14. Loop Diuretics in the Treatment of Hypertension.

    PubMed

    Malha, Line; Mann, Samuel J

    2016-04-01

    Loop diuretics are not recommended in current hypertension guidelines largely due to the lack of outcome data. Nevertheless, they have been shown to lower blood pressure and to offer potential advantages over thiazide-type diuretics. Torsemide offers advantages of longer duration of action and once daily dosing (vs. furosemide and bumetanide) and more reliable bioavailability (vs. furosemide). Studies show that the previously employed high doses of thiazide-type diuretics lower BP more than furosemide. Loop diuretics appear to have a preferable side effect profile (less hyponatremia, hypokalemia, and possibly less glucose intolerance). Studies comparing efficacy and side effect profiles of loop diuretics with the lower, currently widely prescribed, thiazide doses are needed. Research is needed to fill gaps in knowledge and common misconceptions about loop diuretic use in hypertension and to determine their rightful place in the antihypertensive arsenal. PMID:26951244

  15. Mathematical Modeling of Loop Heat Pipes

    NASA Technical Reports Server (NTRS)

    Kaya, Tarik; Ku, Jentung; Hoang, Triem T.; Cheung, Mark L.

    1998-01-01

    The primary focus of this study is to model steady-state performance of a Loop Heat Pipe (LHP). The mathematical model is based on the steady-state energy balance equations at each component of the LHP. The heat exchange between each LHP component and the surrounding is taken into account. Both convection and radiation environments are modeled. The loop operating temperature is calculated as a function of the applied power at a given loop condition. Experimental validation of the model is attempted by using two different LHP designs. The mathematical model is tested at different sink temperatures and at different elevations of the loop. Tbc comparison of the calculations and experimental results showed very good agreement (within 3%). This method proved to be a useful tool in studying steady-state LHP performance characteristics.

  16. A magnetohydrodynamic theory of coronal loop transients

    NASA Technical Reports Server (NTRS)

    Yeh, T.

    1982-01-01

    The physical and geometrical characteristics of solar coronal loop transients are described in an MHD model based on Archimedes' MHD buoyancy force. The theory was developed from interpretation of coronagraphic data, particularly from Skylab. The brightness of a loop is taken to indicate the electron density, and successive pictures reveal the electron enhancement in different columns. The forces which lift the loop off the sun surface are analyzed as an MHD buoyancy force affecting every mass element by imparting an inertial force necessary for heliocentrifugal motion. Thermal forces are responsible for transferring the ambient stress to the interior of the loop to begin the process. The kinematic and hydrostatic buoyancy overcome the gravitational force, and a flux rope can then curve upward, spiralling like a corkscrew with varying cross section around the unwinding solar magnetic field lines.

  17. Boiler-turbine life extension

    SciTech Connect

    Natzkov, S.; Nikolov, M.

    1995-12-01

    The design life of the main power equipment-boilers and turbines is about 105 working hours. The possibilities for life extension are after normatively regulated control tests. The diagnostics and methodology for Boilers and Turbines Elements Remaining Life Assessment using up to date computer programs, destructive and nondestructive control of metal of key elements of units equipment, metal creep and low cycle fatigue calculations. As well as data for most common damages and some technical decisions for elements life extension are presented.

  18. μ →e γ decay in an MSSM extension

    NASA Astrophysics Data System (ADS)

    Ibrahim, Tarek; Itani, Ahmad; Nath, Pran

    2015-07-01

    An analysis is given of the decay μ →e +γ in an minimal supersymmetric standard model extension with a vectorlike generation. Here mixing with the mirrors allows the possibility of this decay. The analysis is done at the one-loop level with the exchange of charginos and neutralinos and of sleptons and mirror sleptons in the loops. A one-loop analysis with W- and Z-boson exchange and mirror leptons and neutrinos is also considered. The effects of C P -violating phases from the new sector on the decay μ →e γ are analyzed in detail. The constraints arising from the current upper limit on the branching ratio B (μ →e γ ) from the MEG experiment of 2.4 ×10-12 (at 90% C.L.) on the parameter space of supersymmetry (SUSY) models and on vectorlike models are explored. Further, the MEG experiment is likely to improve the upper limit by an order of magnitude in the coming years. The improved limits will allow one to probe a much larger domain of the parameter space of the extended models.

  19. Looping through the Lamb Shift

    SciTech Connect

    Hazi, A U

    2007-02-06

    Sometimes in science, a small measurement can have big ramifications. For a team of Livermore scientists, such was the case when they measured a small shift in the spectrum of extremely ionized atoms of uranium. The measurement involves the Lamb shift, a subtle change in the energy of an electron orbiting an atom's nucleus. The precision of the Livermore result was 10 times greater than that of existing measurements, making it the best measurement to date of a complicated correction to the simplest quantum description of how atoms behave. The measurement introduces a new realm in the search for deviations between the theory of quantum electrodynamics (QED), which is an extension of quantum mechanics, and the real world. Such deviations, if discovered, would have far-reaching consequences, indicating that QED is not a fundamental theory of nature.

  20. Extension of the model of the magnetic characteristics of anisotropic metallic glasses

    NASA Astrophysics Data System (ADS)

    Szewczyk, Roman

    2007-07-01

    This paper presents an extension of the Jiles-Atherton model, applied for modelling the magnetic characteristics of anisotropic amorphous material. The presented extension of the model takes into account changes in the parameter k during the magnetization process. Such an extension is physically judged. Moreover, the extended model shows the possibility of a novel achievement of good agreement between experimental data and modelled hysteresis loops. As a result, the extended Jiles-Atherton model may be applied for both technical applications and fundamental research focused on understanding the physical aspects of the magnetization process of anisotropic soft magnetic materials.

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

    NASA Astrophysics Data System (ADS)

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

    2009-10-01

    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.

  2. A molecular mechanism of P-loop pliability of Rho-kinase investigated by molecular dynamic simulation.

    PubMed

    Gohda, Keigo; Hakoshima, Toshio

    2008-11-01

    Rho-kinase is a leading player in the regulation of cytoskeletal events involving smooth muscle contraction and neurite growth-cone collapse and retraction, and is a promising drug target in the treatment of both vascular and neurological disorders. Recent crystal structure of Rho-kinase complexed with a small-molecule inhibitor fasudil has revealed structural details of the ATP-binding site, which represents the target site for the inhibitor, and showed that the conserved phenylalanine on the P-loop occupies the pocket, resulting in an increase of protein-ligand contacts. Thus, the P-loop pliability is considered to play an important role in inhibitor binding affinity and specificity. In this study, we carried out a molecular dynamic simulation for Rho-kinase-fasudil complexes with two different P-loop conformations, i.e., the extended and folded conformations, in order to understand the P-loop pliability and dynamics at atomic level. A PKA-fasudil complex was also used for comparison. In the MD simulation, the flip-flop movement of the P-loop conformation starting either from the extended or folded conformation was not able to be observed. However, a significant conformational change in a long loop region covering over the P-loop, and also alteration of ionic interaction-manner of fasudil with acidic residues in the ATP binding site were shown only in the Rho-kinase-fasudil complex with the extended P-loop conformation, while Rho-kinase with the folded P-loop conformation and PKA complexes did not show large fluctuations, suggesting that the Rho-kinase-fasudil complex with the extended P-loop conformation represents a meta-stable state. The information of the P-loop pliability at atomic level obtained in this study could provide valuable clues to designing potent and/or selective inhibitors for Rho-kinase. PMID:18415022

  3. Loop quantum cosmology in 2 +1 dimension

    NASA Astrophysics Data System (ADS)

    Zhang, Xiangdong

    2014-12-01

    As a first step to generalize the structure of loop quantum cosmology to the theories with the spacetime dimension other than four, the isotropic model of loop quantum cosmology in 2 +1 dimension is studied in this paper. We find that the classical big bang singularity is again replaced by a quantum bounce in the model. The similarities and differences between the (2 +1 )-dimensional model and the (3 +1 )-dimensional one are also discussed.

  4. Onset of inflation in loop quantum cosmology

    SciTech Connect

    Germani, Cristiano; Nelson, William; Sakellariadou, Mairi

    2007-08-15

    Using a Liouville measure, similar to the one proposed recently by Gibbons and Turok, we investigate the probability that single-field inflation with a polynomial potential can last long enough to solve the shortcomings of the standard hot big bang model, within the semiclassical regime of loop quantum cosmology. We conclude that, for such a class of inflationary models and for natural values of the loop quantum cosmology parameters, a successful inflationary scenario is highly improbable.

  5. Deployable radiator with flexible line loop

    NASA Technical Reports Server (NTRS)

    Keeler, Bryan V. (Inventor); Lehtinen, Arthur Mathias (Inventor); McGee, Billy W. (Inventor)

    2003-01-01

    Radiator assembly (10) for use on a spacecraft (12) is provided including at least one radiator panel assembly (26) repeatably movable between a panel stowed position (28) and a panel deployed position (36), at least two flexible lines (40) in fluid communication with the at least one radiator panel assembly (26) and repeatably movable between a stowage loop (42) and a flattened deployed loop (44).

  6. Bonus symmetry for super Wilson loops

    NASA Astrophysics Data System (ADS)

    Münkler, Hagen

    2016-05-01

    The Yangian level-one hypercharge generator for the super Wilson loop in { N }=4 supersymmetric Yang-Mills theory is constructed. Moreover, evidence for the presence of a corresponding symmetry generator at all higher levels is provided. The derivation is restricted to the strong-coupling description of the super Wilson loop and based on the construction of novel conserved charges for type IIB superstrings on {{AdS}}5× {{{S}}}5.

  7. Cyclic universe from Loop Quantum Gravity

    NASA Astrophysics Data System (ADS)

    Cianfrani, Francesco; Kowalski-Glikman, Jerzy; Rosati, Giacomo

    2016-02-01

    We discuss how a cyclic model for the flat universe can be constructively derived from Loop Quantum Gravity. This model has a lower bounce, at small values of the scale factor, which shares many similarities with that of Loop Quantum Cosmology. We find that Quantum Gravity corrections can be also relevant at energy densities much smaller than the Planckian one and that they can induce an upper bounce at large values of the scale factor.

  8. Tachyon matter in loop quantum cosmology

    NASA Astrophysics Data System (ADS)

    Sen, A. A.

    2006-08-01

    An analytical approach for studying the cosmological scenario with a homogeneous tachyon field within the framework of loop quantum gravity is developed. Our study is based on the semiclassical regime where space time can be approximated as a continuous manifold, but matter Hamiltonian gets nonperturbative quantum corrections. A formal correspondence between classical and loop quantum cosmology is also established. The Hamilton-Jacobi method for getting exact solutions is constructed and some exact power law as well as bouncing solutions are presented.

  9. Can Chemical Looping Combustion Use CFB Technology?

    SciTech Connect

    Gamwo, I.K.

    2006-11-01

    Circulating Fluidized Bed (CFB) technology has demonstrated an unparalleled ability to achieve low SO2 and NOx emissions for coal-fired power plants without CO2 capture. Chemical Looping combustion (CLC) is a novel fuel combustion technology which appears as a leading candidate in terms of competitiveness for CO2 removal from flue gas. This presentaion deals with the adaptation of circulating fluidized bed technology to Chemical looping combustion

  10. Conceptual Design of Forced Convection Molten Salt Heat Transfer Testing Loop

    SciTech Connect

    Manohar S. Sohal; Piyush Sabharwall; Pattrick Calderoni; Alan K. Wertsching; S. Brandon Grover

    2010-09-01

    This report develops a proposal to design and construct a forced convection test loop. A detailed test plan will then be conducted to obtain data on heat transfer, thermodynamic, and corrosion characteristics of the molten salts and fluid-solid interaction. In particular, this report outlines an experimental research and development test plan. The most important initial requirement for heat transfer test of molten salt systems is the establishment of reference coolant materials to use in the experiments. An earlier report produced within the same project highlighted how thermophysical properties of the materials that directly impact the heat transfer behavior are strongly correlated to the composition and impurities concentration of the melt. It is therefore essential to establish laboratory techniques that can measure the melt composition, and to develop purification methods that would allow the production of large quantities of coolant with the desired purity. A companion report describes the options available to reach such objectives. In particular, that report outlines an experimental research and development test plan that would include following steps: •Molten Salts: The candidate molten salts for investigation will be selected. •Materials of Construction: Materials of construction for the test loop, heat exchangers, and fluid-solid corrosion tests in the test loop will also be selected. •Scaling Analysis: Scaling analysis to design the test loop will be performed. •Test Plan: A comprehensive test plan to include all the tests that are being planned in the short and long term time frame will be developed. •Design the Test Loop: The forced convection test loop will be designed including extensive mechanical design, instrument selection, data acquisition system, safety requirements, and related precautionary measures. •Fabricate the Test Loop. •Perform the Tests. •Uncertainty Analysis: As a part of the data collection, uncertainty analysis will

  11. Surface loops of extracellular phospholipase A1 determine both substrate specificity and preference for lysophospholipids[S

    PubMed Central

    Arima, Naoaki; Inoue, Asuka; Makide, Kumiko; Nonaka, Takamasa; Aoki, Junken

    2012-01-01

    Members of the pancreatic lipase family exhibit both lipase activity toward triacylglycerol and/or phospholipase A1 (PLA1) activity toward certain phospholipids. Some members of the pancreatic lipase family exhibit lysophospholipase activity in addition to their lipase and PLA1 activities. Two such enzymes, phosphatidylserine (PS)-specific PLA1 (PS-PLA1) and phosphatidic acid (PA)-selective PLA1α (PA-PLA1α, also known as LIPH) specifically hydrolyze PS and PA, respectively. However, little is known about the mechanisms that determine their substrate specificities. Crystal structures of lipases and mutagenesis studies have suggested that three surface loops, namely, β5, β9, and lid, have roles in determining substrate specificity. To determine roles of these loop structures in the substrate recognition of these PLA1 enzymes, we constructed a number of PS-PLA1 mutants in which the three surface loops are replaced with those of PA-PLA1α. The results indicate that the surface loops, especially the β5 loop, of PA-PLA1α play important roles in the recognition of PA, whereas other structure(s) in PS-PLA1 is responsible for PS preference. In addition, β5 loop of PS-PLA1 has a crucial role in lysophospholipase activity toward lysophosphatidylserine. The present study revealed the critical role of lipase surface loops, especially the β5 loop, in determining substrate specificities of PLA1 enzymes. PMID:22172514

  12. Multiple Flow Loop SCADA System Implemented on the Production Prototype Loop

    SciTech Connect

    Baily, Scott A.; Dalmas, Dale Allen; Wheat, Robert Mitchell; Woloshun, Keith Albert; Dale, Gregory E.

    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.

  13. Space Station evolution study oxygen loop closure

    NASA Technical Reports Server (NTRS)

    Wood, M. G.; Delong, D.

    1993-01-01

    In the current Space Station Freedom (SSF) Permanently Manned Configuration (PMC), physical scars for closing the oxygen loop by the addition of oxygen generation and carbon dioxide reduction hardware are not included. During station restructuring, the capability for oxygen loop closure was deferred to the B-modules. As such, the ability to close the oxygen loop in the U.S. Laboratory module (LAB A) and the Habitation A module (HAB A) is contingent on the presence of the B modules. To base oxygen loop closure of SSF on the funding of the B-modules may not be desirable. Therefore, this study was requested to evaluate the necessary hooks and scars in the A-modules to facilitate closure of the oxygen loop at or subsequent to PMC. The study defines the scars for oxygen loop closure with impacts to cost, weight and volume and assesses the effects of byproduct venting. In addition, the recommended scenarios for closure with regard to topology and packaging are presented.

  14. Flare Half-Loops: What Are They?

    NASA Astrophysics Data System (ADS)

    McKenzie, David Eugene; Guidoni, S. E.; Longcope, D. W.; Yoshimura, K.

    2012-05-01

    The M1.4 flare of 28 January 2011 has a remarkable resemblance to the famous "Tsuneta candle-flame" flare of 1992. It was observed with Hinode/XRT, SDO/AIA, and STEREO (A)/EUVI, resulting in higher resolution, greater temperature coverage, and stereoscopic views of this iconic structure. The high temperature images reveal a brightening that grows in size to form a tower-like structure at the top of the arcade. They also show that loops which are successively connected to this tower develop a density increase in one of their legs that can exceed twice the density of the other leg, giving the appearance of "half loops". These jumps in density last for an extended period of time. On the other hand, XRT filter ratios suggest that temperature is approximately uniform along the entire loop. XRT filter-ratio density maps corroborate that the brighter legs have higher density than the fainter halves. The tower is associated with a localized density increase, with even higher densities than either leg of the loop. This spatial variation of density may correspond to a shock at the top of the loops. We use STEREO images to show that the half loop brightening is not a line-of-sight projection effect of the type suggested by Forbes & Acton. This work is supported under contract SP02H3901R from Lockheed-Martin to MSU, and under contract NNM07AB07C with the Harvard-Smithsonian Astrophysical Observatory.

  15. Agricultural extension and mass media.

    PubMed

    Perraton, H

    1983-12-01

    To learn more about the use of the mass media for agricultural extension, the World Bank has considered the efforts of 2 units: INADES-formation in West Africa and the Extension Aids Branch of Malawi. The INADES-formation study focuses on Cameroon but also considers work in Rwanda and the Ivory Coast. Some general conclusions emerge from a comparison of the 2 organizations. Malawi operates an extension service which reaches farmers through extension agents, through farmer training centers, and through mass media. The Extension Aids Branch (EAB) has responsibility for its media work and broadcasts 4 1/2 hours of radio each week. Its 6 regular radio programs include a general program which interviews farmers, a music request program in which the music is interspersed with farming advice, a farming family serial, and a daily broadcast of agricultural news and information. The 17 cinema vans show some agricultural films, made by EAB, some entertainment films, and some government information films from departments other than the ministry of agriculture. EAB also has a well-developed program of research and evaluation of its own work. INADES-formation, the training section of INADES, works towards social and economic development of the population. It teaches peasant farmers and extension agents and does this through running face-to-face seminars, by publishing a magazine, "Agripromo," and through correspondence courses. In 1978-79 INADES-formation enrolled some 4500 farmers and extension agents as students. Both of these organizations work to teach farmers better agriculture techniques, and both were created in response to the fact that agricultural extension agents cannot meet all the farmers in their area. Despite the similarity of objective, there are differences in methods and philosophy. The EAB works in a single country and uses a variety of mass media, with print playing a minor role. INADES-formation is an international and nongovernmental organization and its

  16. Hybrid Combustion-Gasification Chemical Looping

    SciTech Connect

    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

  17. Consistency of loop regularization method and divergence structure of QFTs Beyond one-loop order

    NASA Astrophysics Data System (ADS)

    Huang, Da; Li, Ling-Fong; Wu, Yue-Liang

    2013-04-01

    We study the problem how to deal with tensor-type two-loop integrals in the Loop Regularization (LORE) scheme. We use the two-loop photon vacuum polarization in the massless Quantum Electrodynamics (QED) as the example to present the general procedure. In the processes, we find a new divergence structure: the regulated result for each two-loop diagram contains a gauge-violating quadratic harmful divergent term even combined with their corresponding counterterm insertion diagrams. Only when we sum up over all the relevant diagrams do these quadratic harmful divergences cancel, recovering the gauge invariance and locality.

  18. Structure of a cardiotoxic phospholipase A(2) from Ophiophagus hannah with the "pancreatic loop".

    PubMed

    Zhang, Hai-Long; Xu, Su-Juan; Wang, Qiu-Yan; Song, Shi-Ying; Shu, Yu-Yan; Lin, Zheng-Jiong

    2002-06-01

    The crystal structure of an acidic phospholipase A(2) from Ophiophagus hannah (king cobra) has been determined by molecular replacement at 2.6-A resolution to a crystallographic R factor of 20.5% (R(free)=23.3%) with reasonable stereochemistry. The venom enzyme contains an unusual "pancreatic loop." The conformation of the loop is well defined and different from those in pancreas PLA(2), showing its structural variability. This analysis provides the first structure of a PLA(2)-type cardiotoxin. The sites related to the cardiotoxic and myotoxic activities are explored and the oligomer observed in the crystalline state is described. PMID:12217659

  19. An experimental investigation of a natural convection solar air loop

    SciTech Connect

    Mastrullo, R.; Mazzei, P.; Vanoli, R.

    1983-12-01

    The interest that has been shown in the use of solar energy to heat dwellings following the ''passive'' design criteria does not correspond to the development of accurate theoretical and experimental analysis. This is particularly true for natural circulation solar air heaters. A significant application of these components is wall panel to complement south-facing windows in supplying solar heat directly to buildings. This idea, formerly suggested by Trombe et al., leads to various realizations, one of which was theoretically investigated by present authors. A convective loop panel consists of a glass layer and a black absorber that is backed by insulation. In the configuration shown the air flows in the channel in front of the absorber and the deflecting panel allows cool air to settle to the bottom of the U channel, preventing reverse thermocirculation during night or very low insolation periods. Since thermocirculation is the primary mode of heat transfer for the solar air heaters, the definition of an accurate convection model for the channel is essential for performance predictions. Studies on this subject - free convection between asymmetrically heated vertical planes - deal mainly with theoretical solutions for laminar flow, with the two usual boundary conditions. As the heat transfer process in the solar air loop cannot be expected to follow this model, there is the need of extensive experimental investigation.

  20. Supervisory control of a pilot-scale cooling loop

    SciTech Connect

    Kris Villez; Venkat Venkatasubramanian; Humberto Garcia

    2011-08-01

    We combine a previously developed strategy for Fault Detection and Identification (FDI) with a supervisory controller in closed loop. The combined method is applied to a model of a pilot-scale cooling loop of a nuclear plant, which includes Kalman filters and a model-based predictive controller as part of normal operation. The system has two valves available for flow control meaning that some redundancy is available. The FDI method is based on likelihood ratios for different fault scenarios which in turn are derived from the application of the Kalman filter. A previously introduced extension of the FDI method is used here to enable detection and identification of non-linear faults like stuck valve problems and proper accounting of the time of fault introduction. The supervisory control system is designed so to take different kinds of actions depending on the status of the fault diagnosis task and on the type of identified fault once diagnosis is complete. Some faults, like sensor bias and drift, are parametric in nature and can be adjusted without need for reconfiguration of the regulatory control system. Other faults, like a stuck valve problem, require reconfiguration of the regulatory control system. The whole strategy is demonstrated for several scenarios.

  1. Gravitational Two-Loop Counterterm Is Asymptotically Safe.

    PubMed

    Gies, Holger; Knorr, Benjamin; Lippoldt, Stefan; Saueressig, Frank

    2016-05-27

    Weinberg's asymptotic safety scenario provides an elegant mechanism to construct a quantum theory of gravity within the framework of quantum field theory based on a non-Gaussian fixed point of the renormalization group flow. In this work we report novel evidence for the validity of this scenario, using functional renormalization group techniques to determine the renormalization group flow of the Einstein-Hilbert action supplemented by the two-loop counterterm found by Goroff and Sagnotti. The resulting system of beta functions comprises three scale-dependent coupling constants and exhibits a non-Gaussian fixed point which constitutes the natural extension of the one found at the level of the Einstein-Hilbert action. The fixed point exhibits two ultraviolet attractive and one repulsive direction supporting a low-dimensional UV-critical hypersurface. Our result vanquishes the long-standing criticism that asymptotic safety will not survive once a "proper perturbative counterterm" is included in the projection space. PMID:27284643

  2. Inflation with the Starobinsky potential in loop quantum cosmology

    NASA Astrophysics Data System (ADS)

    Bonga, Béatrice; Gupt, Brajesh

    2016-06-01

    A self-consistent pre-inflationary extension of the inflationary scenario with the Starobinsky potential, favored by Planck data, is studied using techniques from loop quantum cosmology (LQC). The results are compared with the quadratic potential previously studied. Planck scale completion of the inflationary paradigm and observable signatures of LQC are found to be robust under the change of the inflation potential. The entire evolution, from the quantum bounce all the way to the end of inflation, is compatible with observations. Occurrence of desired slow-roll phase is almost inevitable and natural initial conditions exist for both the background and perturbations for which the resulting power spectrum agrees with recent observations. There exist initial data for which the quantum gravitational corrections to the power spectrum are potentially observable.

  3. Gravitational Two-Loop Counterterm Is Asymptotically Safe

    NASA Astrophysics Data System (ADS)

    Gies, Holger; Knorr, Benjamin; Lippoldt, Stefan; Saueressig, Frank

    2016-05-01

    Weinberg's asymptotic safety scenario provides an elegant mechanism to construct a quantum theory of gravity within the framework of quantum field theory based on a non-Gaussian fixed point of the renormalization group flow. In this work we report novel evidence for the validity of this scenario, using functional renormalization group techniques to determine the renormalization group flow of the Einstein-Hilbert action supplemented by the two-loop counterterm found by Goroff and Sagnotti. The resulting system of beta functions comprises three scale-dependent coupling constants and exhibits a non-Gaussian fixed point which constitutes the natural extension of the one found at the level of the Einstein-Hilbert action. The fixed point exhibits two ultraviolet attractive and one repulsive direction supporting a low-dimensional UV-critical hypersurface. Our result vanquishes the long-standing criticism that asymptotic safety will not survive once a "proper perturbative counterterm" is included in the projection space.

  4. Performance evaluation of the time delay digital tanlock loop architectures

    NASA Astrophysics Data System (ADS)

    Al-Kharji Al-Ali, Omar; Anani, Nader; Al-Qutayri, Mahmoud; Al-Araji, Saleh; Ponnapalli, Prasad

    2016-01-01

    This article presents the architectures, theoretical analyses and testing results of modified time delay digital tanlock loop (TDTLs) system. The modifications to the original TDTL architecture were introduced to overcome some of the limitations of the original TDTL and to enhance the overall performance of the particular systems. The limitations addressed in this article include the non-linearity of the phase detector, the restricted width of the locking range and the overall system acquisition speed. Each of the modified architectures was tested by subjecting the system to sudden positive and negative frequency steps and comparing its response with that of the original TDTL. In addition, the performance of all the architectures was evaluated under noise-free as well as noisy environments. The extensive simulation results using MATLAB/SIMULINK demonstrate that the new architectures overcome the limitations they addressed and the overall results confirmed significant improvements in performance compared to the conventional TDTL system.

  5. Highlighting chromosome loops in DNA-picked chromatin (DPC).

    PubMed

    Abbondanza, Ciro; De Rosa, Caterina; Ombra, Maria Neve; Aceto, Fabiana; Medici, Nicola; Altucci, Lucia; Moncharmont, Bruno; Puca, Giovanni Alfredo; Porcellini, Antonio; Avvedimento, Enrico Vittorio; Perillo, Bruno

    2011-08-01

    Growing evidence supports the concept that dynamic intra- and inter-chromosomal links between specific loci contribute to the creation of cell-type specific gene expression profiles. Therefore, analysis of the establishment of peculiar functional correlations between sites, also distant on linear DNA, that govern the transcriptional process appears to be of fundamental relevance. We propose here an experimental approach showing that 17β-estradiol-induced transcription associates to formation of loops between the promoter and termination regions of hormone-responsive genes. This strategy reveals as a tool to be also suitably used, in conjunction with automated techniques, for an extensive analysis of sites shared by multiple genes for induced expression. PMID:21725198

  6. TRUEX Radiolysis Testing Using the INL Radiolysis Test Loop: FY-2012 Status Report

    SciTech Connect

    Dean R. Peterman; Lonnie G. Olson; Richard D. Tillotson; Rocklan G. McDowell; Jack D. Law

    2012-09-01

    The INL radiolysis test loop has been used to evaluate the affect of radiolytic degradation upon the efficacy of the strip section of the TRUEX flowsheet for the recovery of trivalent actinides and lanthanides from acidic solution. The nominal composition of the TRUEX solvent used in this study is 0.2 M CMPO and 1.4 M TBP dissolved in n-dodecane and the nominal composition of the TRUEX strip solution is 1.5 M lactic acid and 0.050 M diethylenetriaminepentaacetic acid. Gamma irradiation of a mixture of TRUEX process solvent and stripping solution in the test loop does not adversely impact flowsheet performance as measured by stripping americium ratios. The observed increase in americium stripping distribution ratios with increasing absorbed dose indicates the radiolytic production of organic soluble degradation compounds.

  7. ENTHALPY-BASED THERMAL EVOLUTION OF LOOPS. II. IMPROVEMENTS TO THE MODEL

    SciTech Connect

    Cargill, P. J.; Bradshaw, S. J.; Klimchuk, J. A.

    2012-06-20

    This paper develops the zero-dimensional (0D) hydrodynamic coronal loop model 'Enthalpy-based Thermal Evolution of Loops' (EBTEL) proposed by Klimchuk et al., which studies the plasma response to evolving coronal heating, especially impulsive heating events. The basis of EBTEL is the modeling of mass exchange between the corona and transition region (TR) and chromosphere in response to heating variations, with the key parameter being the ratio of the TR to coronal radiation. We develop new models for this parameter that now include gravitational stratification and a physically motivated approach to radiative cooling. A number of examples are presented, including nanoflares in short and long loops, and a small flare. The new features in EBTEL are important for accurate tracking of, in particular, the density. The 0D results are compared to a 1D hydro code (Hydrad) with generally good agreement. EBTEL is suitable for general use as a tool for (1) quick-look results of loop evolution in response to a given heating function, (2) extensive parameter surveys, and (3) situations where the modeling of hundreds or thousands of elemental loops is needed. A single run takes a few seconds on a contemporary laptop.

  8. Facilitation of polymer looping and giant polymer diffusivity in crowded solutions of active particles

    NASA Astrophysics Data System (ADS)

    Shin, Jaeoh; Cherstvy, Andrey G.; Kim, Won Kyu; Metzler, Ralf

    2015-11-01

    We study the dynamics of polymer chains in a bath of self-propelled particles (SPP) by extensive Langevin dynamics simulations in a two-dimensional model system. Specifically, we analyse the polymer looping properties versus the SPP activity and investigate how the presence of the active particles alters the chain conformational statistics. We find that SPPs tend to extend flexible polymer chains, while they rather compactify stiffer semiflexible polymers, in agreement with previous results. Here we show that higher activities of SPPs yield a higher effective temperature of the bath and thus facilitate the looping kinetics of a passive polymer chain. We explicitly compute the looping probability and looping time in a wide range of the model parameters. We also analyse the motion of a monomeric tracer particle and the polymer’s centre of mass in the presence of the active particles in terms of the time averaged mean squared displacement, revealing a giant diffusivity enhancement for the polymer chain via SPP pooling. Our results are applicable to rationalising the dimensions and looping kinetics of biopolymers at constantly fluctuating and often actively driven conditions inside biological cells or in suspensions of active colloidal particles or bacteria cells.

  9. KD loop for increasing arch perimeter in cleft and noncleft cases.

    PubMed

    Dholakia, Kartik D; Bhat, Shweta R

    2012-01-01

    One of the many indications for dental arch expansion in treating malocclusion is to achieve arch compatibility, especially in surgical cases with severe Bolton discrepancies or collapsed arches due to congenitally missing anterior teeth. These cases usually require expansion in both the sagittal and transverse plane to achieve normal arch compatibility. Arch compatibility can be achieved by either dentoalveolar or skeletal expansion or both. Orthodontically, dentoalveolar expansion can be achieved by means of expanded arch form, vertical loops, or an added assembly such as a quad helix or Ni-Ti expander from the palatal or lingual aspect of the arch. However, these modalities normally provide expansion along transverse plane. If any expansion along sagittal plane is required, then additional appliances such as TransForce or modifications in the appliance system (eg, a quad helix with extension on anterior teeth) are necessary. Vertical loops do overcome these drawbacks to a certain extent; however, at the expense of generating moments during preactivation, which may lead to tipping of segments adjacent to the loop and precludes its use for larger changes of arch dimension. This article describes a new loop design--the KD loop--that increases the arch perimeter by sagittal and transverse expansion without generating significant moments along vertical plane. PMID:22567644

  10. Dangling bond deflection model: Growth of gel network with loop structure

    NASA Astrophysics Data System (ADS)

    Ma, Hang-Shing; Jullien, Rémi; Scherer, George W.

    2002-04-01

    It has been shown that the closed-loop structure in the model gel networks is responsible for their stiffness. However, the creation of loops has been underestimated in most of the existing kinetic aggregation models [e.g., DLCA (diffusion-limited cluster-cluster aggregation) and derivatives]. A dangling bond deflection (DEF) mechanism is proposed to model the fluctuation of dangling branches or dead ends under thermal excitation. The random deflections of the dangling branches can create loops in the network by forming intracluster bonds, and proceed during both the gelling and aging processes. The resulting DLCADEF networks have extensive loop structure with a negligible number of dangling branches. Its growth kinetics and fractal behavior resemble those of real gels, including volume-invariant gel time and fractal dimension of about 2. The DLCADEF model is the first attempt to model the gel growth with loop formation by the physically realistic fluctuation mechanism. The mechanical properties of the resulting networks will be studied and verified by comparison with real gels.

  11. An Antibody Loop Replacement Design Feasibility Study and a Loop-Swapped Dimer Structure

    SciTech Connect

    Clark, L.; Boriack-Sjodin, P; Day, E; Eldredge, J; Fitch, C; Jarpe, M; Miller, S; Li, Y; Simon, K; van Vlijmen, H

    2009-01-01

    A design approach was taken to investigate the feasibility of replacing single complementarity determining region (CDR) antibody loops. This approach may complement simpler mutation-based strategies for rational antibody design by expanding conformation space. Enormous crystal structure diversity is available, making CDR loops logical targets for structure-based design. A detailed analysis for the L1 loop shows that each loop length takes a distinct conformation, thereby allowing control on a length scale beyond that accessible to simple mutations. The L1 loop in the anti-VLA1 antibody was replaced with the L2 loop residues longer in an attempt to add an additional hydrogen bond and fill space on the antibody-antigen interface. The designs expressed well, but failed to improve affinity. In an effort to learn more, one design was crystallized and data were collected at 1.9 {angstrom} resolution. The designed L1 loop takes the qualitatively desired conformation; confirming that loop replacement by design is feasible. The crystal structure also shows that the outermost loop (residues Leu51-Ser68) is domain swapped with another monomer. Tryptophan fluorescence measurements were used to monitor unfolding as a function of temperature and indicate that the loop involved in domain swapping does not unfold below 60C. The domain-swapping is not directly responsible for the affinity loss, but is likely a side-effect of the structural instability which may contribute to affinity loss. A second round of design was successful in eliminating the dimerization through mutation of a residue (Leu51Ser) at the joint of the domain-swapped loop.

  12. Mechanics of Protein-Mediated DNA Looping

    NASA Astrophysics Data System (ADS)

    Meiners, Jens-Christian

    2009-03-01

    The formation of looped DNA-protein complexes in which a protein or protein assembly binds to multiple distant operator sites on the DNA is a common feature for many regulatory schemes on the transcriptional level. In a living cell, a multitude of mechanical forces and constraints act on these complexes, and it is imperative to understand their effects on biological function. For this aim, we study the lactose repressor as a model system for protein-mediated DNA looping in single-molecule experiments. Using a novel axial constant-force optical trapping scheme that allows us to manipulate sub-micron DNA fragments with well-controlled forces down to the 10 fN range, we show that mechanical tension in the substrate DNA of hundred femtonewton is sufficient to disrupt the loop formation process, which suggests that such mechanical tension may provide a mechanical pathway to controlling gene expression in vivo. From the force sensitivity of the loop formation process, we can also infer the topology of the looped complex; in our case an antiparallel conformation. In addition, we will present new tethered-particle microscopy data that shows lifetimes of the looped complexes that are two to three orders of magnitude shorter than those measured in biochemical competition assays and discuss possible interpretations, including the suggestion that operator binding of the lactose repressor tetramer leads to a destabilization of the dimer-dimer interface and that thus the loop breakdown process is mostly a dissociation of the tetramer into two dimers, instead, as widely assumed, an unbinding of the tetramer from the DNA.

  13. An extended loop in CE7 carbohydrate esterase family is dispensable for oligomerization but required for activity and thermostability.

    PubMed

    Singh, Mrityunjay K; Manoj, Narayanan

    2016-06-01

    The carbohydrate esterase family 7 (CE7) belonging to the α/β hydrolase superfamily contains a structurally conserved loop extension element relative to the canonical α/β hydrolase fold. This element called the β-interface loop contributes 20-30% of the total buried surface area at intersubunit interfaces of the functional hexameric state. To test whether this loop is an enabling region for the structure and function of the oligomeric assembly, we designed a truncation variant of the thermostable CE7 acetyl esterase from Thermotoga maritima (TmAcE). Although deletion of 26 out of 40 residues in the loop had little impact on the hexamer formation, the variant exhibited altered dynamics of the oligomeric assembly and a loss of thermal stability. Furthermore, the mutant lacked catalytic activity. Crystal structures of the variant and a new crystal form of the wild type protein determined at 2.75Å and 1.76Å, respectively, provide a rationale for the properties of the variant. The hexameric assembly in the variant is identical to that of the wild type and differed only in the lack of buried surface area interactions at the original intersubunit interfaces. This is accompanied by disorder in an extended region of the truncated loop that consequently induces disorder in the neighboring oxyanion hole loop. Overall, the results suggest that the β-interface loop in CE7 enzymes is dispensable for the oligomeric assembly. Rather, the loop extension event was evolutionarily selected to regulate activity, conformational flexibility and thermal stability. PMID:27085421

  14. Three determinants in ezrin are responsible for cell extension activity.

    PubMed Central

    Martin, M; Roy, C; Montcourrier, P; Sahuquet, A; Mangeat, P

    1997-01-01

    The ERM proteins--ezrin, radixin, and moesin--are key players in membrane-cytoskeleton interactions. In insect cells infected with recombinant baculoviruses, amino acids 1-115 of ezrin were shown to inhibit an actin- and tubulin-dependent cell-extension activity located in ezrin C-terminal domain (ezrin310-586), whereas full-length ezrin1-586 did not induce any morphological change. To refine the mapping of functional domains of ezrin, 30 additional constructs were overexpressed in Sf9 cells, and the resulting effect of each was qualitatively and semiquantitatively compared. The removal of amino acids 13-30 was sufficient to release a cell-extension phenotype. This effect was abrogated if the 21 distal-most C-terminal amino acids were subsequently deleted (ezrin31-565), confirming the existence of a head-to-tail regulation in the whole molecule. Surprisingly, the deletion in full-length ezrin of the same 21 amino acids provided strong cell-extension competence to ezrin1-565, and this property was recovered in N-terminal constructs as short as ezrin1-310. Within ezrin1-310, amino acid sequences 13-30 and 281-310 were important determinants and acted in cooperation to induce cytoskeleton mobilization. In addition, these same residues are part of a new actin-binding site characterized in vitro in ezrin N-terminal domain. Images PMID:9285824

  15. Extension for prevention: margin placement.

    PubMed

    Larson, Thomas D

    2012-01-01

    This article will review the concept of extension for prevention popularized by G.V. Black around the early 1900s. Concepts of extension and prevention have changed over the years with a more informed knowledge of the caries process, improved materials, cutting instruments, and techniques. The reasons for placement of the outline form relative to the tooth morphology, gingival tissue, relationship to adjacent teeth, and the choice of material will be described for all of the materials used in restorative dentistry. Research will be cited to support the scientific basis for outline form placement. PMID:22662468

  16. TRANSVERSE OSCILLATIONS OF A COOLING CORONAL LOOP

    SciTech Connect

    Morton, R. J.; Erdelyi, R. E-mail: Robertus@sheffield.ac.u

    2009-12-10

    Here we present an investigation into how cooling of the plasma influences the oscillation properties (e.g., eigenfunctions and eigenfrequencies) of transverse (i.e., kink) magnetohydrodynamic (MHD) waves in a compressible magnetic flux tube embedded in a gravitationally stratified and uniformly magnetized atmosphere. The cooling is introduced via a temperature-dependent density profile. A time-dependent governing equation is derived and an approximate zeroth-order solution is then obtained. From this the influence of cooling on the behavior of the eigenfrequencies and eigenfunctions of the transverse MHD waves is determined for representative cooling timescales. It is shown analytically, as the loop cools, how the amplitude of the perturbations is found to decrease as time increases. For cooling timescales of 900-2000 s (as observed in typical EUV loops), it is shown that the cooling has important and relevant influence on the damping times of loop oscillations. Next, the theory is put to the test. The damping due to cooling is fitted to a representative observation of standing kink oscillation of EUV loops. It is also shown with an explicit approximate analytical form, how the period of the fundamental and first harmonic of the kink mode changes with time as the loop cools. A consequence of this is that the value of the period ratio P {sub 1}/P {sub 2}, a tool that is popular in magneto-seismological studies in coronal diagnostics, decreases from the value of a uniform loop, 2, as the temperature decreases. The rate of change in P {sub 1}/P {sub 2} is dependent upon the cooling timescale and is well within the observable range for typical EUV loops. Further to this, the magnitude of the anti-node shift of the eigenfunctions of the first harmonic is shown to continually increase as the loop cools, giving additional impetus to the use of spatial magneto-seismology of the solar atmosphere. Finally, we suggest that measurements of the rate of change in the

  17. Students' Understanding of Loops and Nested Loops in Computer Programming: An APOS Theory Perspective

    ERIC Educational Resources Information Center

    Cetin, Ibrahim

    2015-01-01

    The purpose of this study is to explore students' understanding of loops and nested loops concepts. Sixty-three mechanical engineering students attending an introductory programming course participated in the study. APOS (Action, Process, Object, Schema) is a constructivist theory developed originally for mathematics education. This study is the…

  18. Teachers' Attitudes and Perceptions of Looping and the Effect of Looping on Students' Academic Achievement

    ERIC Educational Resources Information Center

    Williams-Wright, Vera

    2013-01-01

    The purpose of this research study was two-fold. The first purpose was to investigate the impact of looping on academic achievement of students in selected public schools in Mississippi. The students' results on the 2010 and 2011 Mississippi Curriculum Test, Second Edition (MCT2) were used to determine whether looping students score differently in…

  19. Multithermal Analysis of EIS Coronal Loops

    NASA Astrophysics Data System (ADS)

    Worley, Brian T.; Schmelz, J. T.; Pathak, S.

    2012-05-01

    Four separate active regions containing multiple coronal loops were selected for Differential Emission Measure (DEM) analysis from Hinode Extreme ultraviolet Imaging Spectrometer (EIS) data. Each loop was chosen based on its location and our ability to find a clean nearby area for background subtraction. Our analysis uses iron lines with ionization stages from Fe VIII to Fe XVI in the wavelength ranges 170 - 210 and 250 - 290 A. The twelve selected loops were then analyzed to determine if their cross-field temperature was isothermal or multithermal. This was accomplished by averaging the intensities of ten individual pixels along the length of each loop and subtracting the average intensity of ten nearby background pixels. We then used these background-subtracted values, the density from a density-sensitive line ratio, and the atomic data from the CHIANTI database to create a DEM curve for each loop. Solar physics research at the University of Memphis is supported by NSF ATM-0402729 as well as a Hinode subcontract from NASA/SAO.

  20. Modeling of protein loops by simulated annealing.

    PubMed Central

    Collura, V.; Higo, J.; Garnier, J.

    1993-01-01

    A method is presented to model loops of protein to be used in homology modeling of proteins. This method employs the ESAP program of Higo et al. (Higo, J., Collura, V., & Garnier, J., 1992, Biopolymers 32, 33-43) and is based on a fast Monte Carlo simulation and a simulated annealing algorithm. The method is tested on different loops or peptide segments from immunoglobulin, bovine pancreatic trypsin inhibitor, and bovine trypsin. The predicted structure is obtained from the ensemble average of the coordinates of the Monte Carlo simulation at 300 K, which exhibits the lowest internal energy. The starting conformation of the loop prior to modeling is chosen to be completely extended, and a closing harmonic potential is applied to N, CA, C, and O atoms of the terminal residues. A rigid geometry potential of Robson and Platt (1986, J. Mol. Biol. 188, 259-281) with a united atom representation is used. This we demonstrate to yield a loop structure with good hydrogen bonding and torsion angles in the allowed regions of the Ramachandran map. The average accuracy of the modeling evaluated on the eight modeled loops is 1 A root mean square deviation (rmsd) for the backbone atoms and 2.3 A rmsd for all heavy atoms. PMID:8401234

  1. Coronal loops - Current-based heating processes

    NASA Technical Reports Server (NTRS)

    Beaufume, P.; Coppi, B.; Golub, L.

    1992-01-01

    Based on new observations, a theoretical model of magnetic-field related heating processes in the solar corona is given. In this model, field-aligned currents are induced along coronal loops in thin current sheaths. Excitation of instabilities involving magnetic reconnection converts the energy associated with the current-related magnetic field directly into particle energy, where the heating process proceeds via short bursts corresponding to an intermittent disruption of the current sheath configuration. Because of the relatively low transverse thermal conduction, only a small fraction of the loop volume is heated to a much higher temperature than the average value. This is consistent with experimental observations of low filling factors of hot plasmas in coronal loops. Thus the model involves a repeated sequence of dynamic events taking into account the observed loop topology, the differential emission measure distribution in the 10 exp 6 - 10 exp 7 K range, the energy balance requirements in the loop, and the probable duty cycles involved in the heating processes.

  2. Crack interaction with 3-D dislocation loops

    NASA Astrophysics Data System (ADS)

    Gao, Huajian

    CRACKS in a solid often interact with other crystal defects such as dislocation loops. The interaction effects are of 3-D character yet their analytical treatment has been mostly limited to the 2-D regime due to mathematical complications. This paper shows that distribution of the stress intensity factors along a crack front due to arbitrary dislocation loops may be expressed as simple line integrals along the loop contours. The method of analysis is based on the 3-D Bueckner-Rice weight function theory for elastic crack analysis. Our results have significantly simplified the calculations for 3-D dislocation loops produced in the plastic processes at the crack front due to highly concentrated crack tip stress fields. Examples for crack-tip 3-D loops and 2-D straight dislocations emerging from the crack tip are given to demonstrate applications of the derived formulae. The results are consistent with some previous analytical solutions existing in the literature. As further applications we also analyse straight dislocations that are parallel or perpendicular to the crack plane but are not parallel to the crack front.

  3. Bootstrapping the Three-Loop Hexagon

    SciTech Connect

    Dixon, Lance J.; Drummond, James M.; Henn, Johannes M.; /Humboldt U., Berlin /Santa Barbara, KITP

    2011-11-08

    We consider the hexagonal Wilson loop dual to the six-point MHV amplitude in planar N = 4 super Yang-Mills theory. We apply constraints from the operator product expansion in the near-collinear limit to the symbol of the remainder function at three loops. Using these constraints, and assuming a natural ansatz for the symbol's entries, we determine the symbol up to just two undetermined constants. In the multi-Regge limit, both constants drop out from the symbol, enabling us to make a non-trivial confirmation of the BFKL prediction for the leading-log approximation. This result provides a strong consistency check of both our ansatz for the symbol and the duality between Wilson loops and MHV amplitudes. Furthermore, we predict the form of the full three-loop remainder function in the multi-Regge limit, beyond the leading-log approximation, up to a few constants representing terms not detected by the symbol. Our results confirm an all-loop prediction for the real part of the remainder function in multi-Regge 3 {yields} 3 scattering. In the multi-Regge limit, our result for the remainder function can be expressed entirely in terms of classical polylogarithms. For generic six-point kinematics other functions are required.

  4. Wilson loops in supersymmetric gauge theories

    NASA Astrophysics Data System (ADS)

    Pestun, Vasily

    This thesis is devoted to several exact computations in four-dimensional supersymmetric gauge field theories. In the first part of the thesis we prove conjecture due to Erickson-Semenoff-Zarembo and Drukker-Gross which relates supersymmetric circular Wilson loop operators in the N = 4 supersymmetric Yang-Mills theory with a Gaussian matrix model. We also compute the partition function and give a new matrix model formula for the expectation value of a supersymmetric circular Wilson loop operator for the pure N = 2 and the N* = 2 supersymmetric Yang-Mills theory on a four-sphere. Circular supersymmetric Wilson loops in four-dimensional N = 2 superconformal gauge theory are treated similarly. In the second part we consider supersymmetric Wilson loops of arbitrary shape restricted to a two-dimensional sphere in the four-dimensional N = 4 supersymmetric Yang-Mills theory. We show that expectation value for these Wilson loops can be exactly computed using a two-dimensional theory closely related to the topological two-dimensional Higgs-Yang-Mills theory, or two-dimensional Yang-Mills theory for the complexified gauge group.

  5. Unusual ganglioglioma with extensive calcification and ossification.

    PubMed

    Kavishwar, Vikas Shashikant; Chadha, Kirti G; Barodawala, Shaikhali Moiz; Murthy, Anuradha Krishna

    2016-01-01

    Ganglioglioma is a slow-growing relatively low-grade mixed glioneuronal tumor with most cases corresponding to the WHO Grade I category. It frequently presents with seizures. The temporal lobe is the most common location followed by frontal, parietal, and occipital lobes. These generally behave in a benign fashion and have a favorable prognosis. We describe a case of a 24-year-old male presenting with convulsions and a calcified parieto-occipital mass. This mass removed from the parietal lobe showed neoplastic glial and dysplastic neuronal tissue amidst extensive areas of calcification and foci of ossification. On immunohistochemistry, the glial component expressed glial fibrillary acidic protein whereas the dysplastic neuronal component expressed synaptophysin and CD34. Epithelial membrane antigen was negative and Ki-67 showed a low proliferative index. After the surgery, the patient is free of neurological symptoms. Widespread calcification and ossification are very unusual in ganglioglioma, which prompted us to report this case. PMID:27510688

  6. Fatigue-Resistant Metal Hook-And-Loop Fastener

    NASA Technical Reports Server (NTRS)

    Sawaf, Bernard

    1994-01-01

    Proposed metal hook-and-loop fastener engaged and disengaged many hundreds of times without breaking. Fastener opens by mechanical action. Translation moves hooks out of loops or pushes loops away from hooks. Hooks not required to flex and, therefore, do not fail by fatigue. Lifetime much greater than that of other metal hook-and-loop fasteners, depending on flexure for disengagement such as article, "Hook-and-Loop Metal Fastener" (MSC-21586).

  7. A numerical study of the thermal stability of solar loops

    NASA Technical Reports Server (NTRS)

    Klimchuk, J. A.; Antiochos, S. K.; Mariska, J. T.

    1987-01-01

    An important property of all loops is their thermal stability. If low lying hot loops were thermally unstable, for example, a great majority of the low loops on the Sun might be expected to be cool. How small perturbations evolve in low lying, linearly unstable hot loops was determined and how high lying, linearly stable hot loops respond to large amplitude disturbances such as might be expected on the Sun were examined. Only general descriptions and results are given.

  8. Linear phase demodulator including a phase locked loop with auxiliary feedback loop

    NASA Technical Reports Server (NTRS)

    Rippy, R. R. (Inventor)

    1976-01-01

    A phase modulated wave that may have no carrier power is demodulated by a phase locked loop including a phase detector for deriving an A.C. data output signal having a magnitude and a phase indicative of the phase of the modulated wave. A feedback loop responsive to the data output signal restores power to the carrier frequency component to the loop. In one embodiment, the feedback loop includes a phase modulator responsive to the phase modulated wave and the data output signal. In a second embodiment, carrier frequency power is restored by differentiating the data output signal and supplying the differentiated signal to an input of a voltage controlled oscillator included in the phase locked loop.

  9. Three-loop hard-thermal-loop free energy for QED

    SciTech Connect

    Andersen, Jens O.; Strickland, Michael; Su, Nan

    2009-10-15

    We calculate the free energy of a hot gas of electrons and photons to three loops using the hard-thermal-loop perturbation theory reorganization of finite-temperature perturbation theory. We calculate the free energy through three loops by expanding in a power series in m{sub D}/T, m{sub f}/T, and e{sup 2}, where m{sub D} and m{sub f} are thermal masses and e is the coupling constant. We demonstrate that the hard-thermal-loop perturbation reorganization improves the convergence of the successive approximations to the QED free energy at large coupling, e{approx}2. The reorganization is gauge invariant by construction, and due to cancellation among various contributions, we obtain a completely analytic result for the resummed thermodynamic potential at three loops. Finally, we compare our result with similar calculations that use the {phi}-derivable approach.

  10. Hot topic, warm loops, cooling plasma? Multithermal analysis of active region loops

    SciTech Connect

    Schmelz, J. T.; Pathak, S.; Christian, G. M.; Dhaliwal, R. S.; Brooks, D. H.

    2014-11-10

    We have found indications of a relationship between the differential emission measure (DEM) weighted temperature and the cross-field DEM width for coronal loops. The data come from the Hinode X-ray Telescope, the Hinode EUV Imaging Spectrometer, and the Solar Dynamics Observatory Atmospheric Imaging Assembly. These data show that cooler loops tend to have narrower DEM widths. If most loops observed by these instruments are composed of bundles of unresolved magnetic strands and are only observed in their cooling phase, as some studies have suggested, then this relationship implies that the DEM of a coronal loop narrows as it cools. This could imply that fewer strands are seen emitting in the later cooling phase, potentially resolving the long standing controversy of whether the cross-field temperatures of coronal loops are multithermal or isothermal.

  11. Structural Study of a Flexible Active Site Loop in Human Indoleamine 2,3-Dioxygenase and Its Functional Implications.

    PubMed

    Álvarez, Lucía; Lewis-Ballester, Ariel; Roitberg, Adrián; Estrin, Darío A; Yeh, Syun-Ru; Marti, Marcelo A; Capece, Luciana

    2016-05-17

    Human indoleamine 2,3-dioxygenase catalyzes the oxidative cleavage of tryptophan to N-formyl kynurenine, the initial and rate-limiting step in the kynurenine pathway. Additionally, this enzyme has been identified as a possible target for cancer therapy. A 20-amino acid protein segment (the JK loop), which connects the J and K helices, was not resolved in the reported hIDO crystal structure. Previous studies have shown that this loop undergoes structural rearrangement upon substrate binding. In this work, we apply a combination of replica exchange molecular dynamics simulations and site-directed mutagenesis experiments to characterize the structure and dynamics of this protein region. Our simulations show that the JK loop can be divided into two regions: the first region (JK loop(C)) displays specific and well-defined conformations and is within hydrogen bonding distance of the substrate, while the second region (JK loop(N)) is highly disordered and exposed to the solvent. The peculiar flexible nature of JK loop(N) suggests that it may function as a target for post-translational modifications and/or a mediator for protein-protein interactions. In contrast, hydrogen bonding interactions are observed between the substrate and Thr379 in the highly conserved "GTGG" motif of JK loop(C), thereby anchoring JK loop(C) in a closed conformation, which secures the appropriate substrate binding mode for catalysis. Site-directed mutagenesis experiments confirm the key role of this residue, highlighting the importance of the JK loop(C) conformation in regulating the enzymatic activity. Furthermore, the existence of the partially and totally open conformations in the substrate-free form suggests a role of JK loop(C) in controlling substrate and product dynamics. PMID:27112409

  12. Rule Induction with Extension Matrices.

    ERIC Educational Resources Information Center

    Wu, Xindong

    1998-01-01

    Presents a heuristic, attribute-based, noise-tolerant data mining program, HCV (Version 2.0) based on the newly-developed extension matrix approach. Outlines some techniques implemented in the HCV program for noise handling and discretization of continuous domains; an empirical comparison shows that rules generated by HCV are more compact than the…

  13. Effective Public Relations in Extension.

    ERIC Educational Resources Information Center

    Hogan, Mike

    1994-01-01

    Public relations efforts of the Carroll County (Ohio) extension office included periodic reports to legislators, a toll-free number distributed on refrigerator magnets, annual calendar/report to the public, newspaper supplements, and town meetings. Long-term effects were a 116% increase in funding, used to upgrade staff, programs, and…

  14. Removing the Tension from Extension

    ERIC Educational Resources Information Center

    Bradley, Lucy; Driscoll, Elizabeth; Bardon, Robert

    2012-01-01

    Job burnout and stress begin with day-to-day frustrations, roadblocks, and unmet expectations. These can transform job satisfaction and, ultimately, career choices, affecting the quality of programs, expense to universities, and relationships with the community. A series of innovative statewide workshops involving 97 agents and Extension directors…

  15. Strategic Opportunities for Cooperative Extension

    ERIC Educational Resources Information Center

    National Association of State Universities and Land-Grant Colleges, 2007

    2007-01-01

    In this new century, opportunities exist to help advance America's greatness in the midst of many challenges. Energy, water, food, environment, health, economic productivity, global competitiveness, and the quality of the living environments are all paramount to the future. Extension is, as a part of higher education, prepared to create new…

  16. Slope Extensions to ASL Library

    2010-03-31

    Extensions to the AMPL/solver interface library (http://netlib.sandia.gov/ampl/solvers) to compute bounds on algebraic expressions, plus a test program. use in uncertainty quantification and global optimization algorithms. This software is not primarily for military applications.

  17. Teaching Structured Fortran without Structured Extensions.

    ERIC Educational Resources Information Center

    Worland, Peter B.

    Six control structures are used in teaching a college Fortran programing course: (1) simple sequences of instruction without any control statement, (2) IF-THEN selection, (3) IF-THEN-ELSE selection, (4) definite loop, (5) indefinite loop, and (6) generalized IF-THEN-ELSE case structure. Outlines, instead of flowcharts, are employed for algorithm…

  18. Loop quantum Brans-Dicke cosmology

    NASA Astrophysics Data System (ADS)

    Zhang, Xiangdong; Artymowski, Michal; Ma, Yongge

    2013-04-01

    The spatially flat and isotropic cosmological model of Brans-Dicke theory with coupling parameter ω≠-(3)/(2) is quantized by the approach of loop quantum cosmology. An interesting feature of this model is that although the Brans-Dicke scalar field is nonminimally coupled with curvature, it can still play the role of an emergent time variable. In the quantum theory, the classical differential equation which represents cosmological evolution is replaced by a quantum difference equation. The effective Hamiltonian and modified dynamical equations of loop quantum Brans-Dicke cosmology are also obtained, which lay a foundation for the phenomenological investigation to possible quantum gravity effects in cosmology. The effective equations indicate that the classical big bang singularity is again replaced by a quantum bounce in loop quantum Brans-Dicke cosmology.

  19. Double reference pulsed phase locked loop

    NASA Technical Reports Server (NTRS)

    Heyman, J. S. (Inventor)

    1986-01-01

    A double reference pulse phase locked loop is described which measures the phase shift between tone burst signals initially derived from the same periodic signal source (voltage controlled oscillator) and delayed by different amounts because of two different paths. A first path is from the transducer to the surface of a sample and back. A second path is from the transducer to the opposite surface and back. A first pulse phase locked loop including a phase detector and a phase shifter forces the tone burst signal delayed by the second path in phase quadrature with the periodic signal source. A second pulse phase locked loop including a second phase detector forces the tone burst signals delayed by the first path into phase quadrature with the phase shifted periodic signal source.

  20. Torus Knot Polynomials and Susy Wilson Loops

    NASA Astrophysics Data System (ADS)

    Giasemidis, Georgios; Tierz, Miguel

    2014-12-01

    We give, using an explicit expression obtained in (Jones V, Ann Math 126:335, 1987), a basic hypergeometric representation of the HOMFLY polynomial of ( n, m) torus knots, and present a number of equivalent expressions, all related by Heine's transformations. Using this result, the symmetry and the leading polynomial at large N are explicit. We show the latter to be the Wilson loop of 2d Yang-Mills theory on the plane. In addition, after taking one winding to infinity, it becomes the Wilson loop in the zero instanton sector of the 2d Yang-Mills theory, which is known to give averages of Wilson loops in = 4 SYM theory. We also give, using matrix models, an interpretation of the HOMFLY polynomial and the corresponding Jones-Rosso representation in terms of q-harmonic oscillators.

  1. Hierarchical curiosity loops and active sensing.

    PubMed

    Gordon, Goren; Ahissar, Ehud

    2012-08-01

    A curious agent acts so as to optimize its learning about itself and its environment, without external supervision. We present a model of hierarchical curiosity loops for such an autonomous active learning agent, whereby each loop selects the optimal action that maximizes the agent's learning of sensory-motor correlations. The model is based on rewarding the learner's prediction errors in an actor-critic reinforcement learning (RL) paradigm. Hierarchy is achieved by utilizing previously learned motor-sensory mapping, which enables the learning of other mappings, thus increasing the extent and diversity of knowledge and skills. We demonstrate the relevance of this architecture to active sensing using the well-studied vibrissae (whiskers) system, where rodents acquire sensory information by virtue of repeated whisker movements. We show that hierarchical curiosity loops starting from optimally learning the internal models of whisker motion and then extending to object localization result in free-air whisking and object palpation, respectively. PMID:22386787

  2. Coronal Loops: New Insights from EIS Observations

    NASA Astrophysics Data System (ADS)

    Del Zanna, G.; Bradshaw, S. J.

    2009-12-01

    Multi-instrument observations of coronal loops of different active regions have been studied. The general features discussed in Del Zanna (2003) and Del Zanna and Mason (2003) based on SOHO/CDS are confirmed. Hinode/EIS high-cadence observations clearly show how dynamic loops are at all temperatures. This clearly reflects the fast changes in the photospheric magnetic fields measured by SOT over a minute timescale. Despite that, persistent patterns are present. In particular, the pattern of Doppler shifts and non-thermal widths, found for the first time in NOAA 10926 (cf. Del Zanna 2007, 2008), is actually a common feature in all active regions. It is likely that the majority of cool (0.5--1 MK) loops are observed during their radiatively cooling phase.

  3. Current loop signal conditioning: Practical applications

    NASA Technical Reports Server (NTRS)

    Anderson, Karl F.

    1995-01-01

    This paper describes a variety of practical application circuits based on the current loop signal conditioning paradigm. Equations defining the circuit response are also provided. The constant current loop is a fundamental signal conditioning circuit concept that can be implemented in a variety of configurations for resistance-based transducers, such as strain gages and resistance temperature detectors. The circuit features signal conditioning outputs which are unaffected by extremely large variations in lead wire resistance, direct current frequency response, and inherent linearity with respect to resistance change. Sensitivity of this circuit is double that of a Wheatstone bridge circuit. Electrical output is zero for resistance change equals zero. The same excitation and output sense wires can serve multiple transducers. More application arrangements are possible with constant current loop signal conditioning than with the Wheatstone bridge.

  4. Coronal Loops: Evolving Beyond the Isothermal Approximation

    NASA Astrophysics Data System (ADS)

    Schmelz, J. T.; Cirtain, J. W.; Allen, J. D.

    2002-05-01

    Are coronal loops isothermal? A controversy over this question has arisen recently because different investigators using different techniques have obtained very different answers. Analysis of SOHO-EIT and TRACE data using narrowband filter ratios to obtain temperature maps has produced several key publications that suggest that coronal loops may be isothermal. We have constructed a multi-thermal distribution for several pixels along a relatively isolated coronal loop on the southwest limb of the solar disk using spectral line data from SOHO-CDS taken on 1998 Apr 20. These distributions are clearly inconsistent with isothermal plasma along either the line of sight or the length of the loop, and suggested rather that the temperature increases from the footpoints to the loop top. We speculated originally that these differences could be attributed to pixel size -- CDS pixels are larger, and more `contaminating' material would be expected along the line of sight. To test this idea, we used CDS iron line ratios from our data set to mimic the isothermal results from the narrowband filter instruments. These ratios indicated that the temperature gradient along the loop was flat, despite the fact that a more complete analysis of the same data showed this result to be false! The CDS pixel size was not the cause of the discrepancy; rather, the problem lies with the isothermal approximation used in EIT and TRACE analysis. These results should serve as a strong warning to anyone using this simplistic method to obtain temperature. This warning is echoed on the EIT web page: ``Danger! Enter at your own risk!'' In other words, values for temperature may be found, but they may have nothing to do with physical reality. Solar physics research at the University of Memphis is supported by NASA grant NAG5-9783. This research was funded in part by the NASA/TRACE MODA grant for Montana State University.

  5. Quasi-periodic processes in the flare loop generated by sudden temperature enhancements at loop footpoints

    NASA Astrophysics Data System (ADS)

    Karlický, M.; Jelínek, P.

    2016-05-01

    Aims: During the impulsive flare phase, the plasma at the flare loop footpoints is rapidly heated by particle beams. In the present paper, we study processes that occur after this sudden heating in a two-dimensional magnetic loop. Methods: We adopt a 2D magnetohydrodynamic (MHD) model, in which we solve a full set of the ideal time-dependent MHD equations by means of the FLASH code, using the adaptive mesh refinement (AMR) method. Periods in the processes are estimated by the wavelet analysis technique. Results: We consider a model of the solar atmosphere with a symmetric magnetic loop. The length of this loop in the corona is approximately 21.5 Mm. At both loop footpoints, at the transition region, we initiate the Gaussian temperature (pressure) perturbation with the maximum temperature 14, 7, or 3.5 times higher than the unperturbed temperature. In the corona, the perturbations produce supersonic blast shocks with the Mach number of about 1.1, but well below Alfvén velocities. We consider cases with the same perturbations at both footpoints (symmetric case) and one with different perturbations (asymmetric case). In the symmetric case, the shocks move along both loop legs upwards to the top of the loop, where they interact and form a transient compressed region. Then they continue in their motion to the transition region at the opposite side of the loop, where they are reflected upwards, and so on. At the top of the loop, the shock appears periodically with the period of about 170 s. In the loop legs during this period, a double peak of the plasma parameters, which is connected with two arrivals of shocks, is detected: firstly, when the shock moves up and then when the shock, propagating from the opposite loop leg, moves down. Increasing the distance of the detection point in the loop leg from the top of the loop, the time interval between these shock arrivals increases. Thus, at these detection points, the processes with shorter periods can be detected. After

  6. Similarity Metrics for Closed Loop Dynamic Systems

    NASA Technical Reports Server (NTRS)

    Whorton, Mark S.; Yang, Lee C.; Bedrossian, Naz; Hall, Robert A.

    2008-01-01

    To what extent and in what ways can two closed-loop dynamic systems be said to be "similar?" This question arises in a wide range of dynamic systems modeling and control system design applications. For example, bounds on error models are fundamental to the controller optimization with modern control design methods. Metrics such as the structured singular value are direct measures of the degree to which properties such as stability or performance are maintained in the presence of specified uncertainties or variations in the plant model. Similarly, controls-related areas such as system identification, model reduction, and experimental model validation employ measures of similarity between multiple realizations of a dynamic system. Each area has its tools and approaches, with each tool more or less suited for one application or the other. Similarity in the context of closed-loop model validation via flight test is subtly different from error measures in the typical controls oriented application. Whereas similarity in a robust control context relates to plant variation and the attendant affect on stability and performance, in this context similarity metrics are sought that assess the relevance of a dynamic system test for the purpose of validating the stability and performance of a "similar" dynamic system. Similarity in the context of system identification is much more relevant than are robust control analogies in that errors between one dynamic system (the test article) and another (the nominal "design" model) are sought for the purpose of bounding the validity of a model for control design and analysis. Yet system identification typically involves open-loop plant models which are independent of the control system (with the exception of limited developments in closed-loop system identification which is nonetheless focused on obtaining open-loop plant models from closed-loop data). Moreover the objectives of system identification are not the same as a flight test and

  7. Pressure structure of solar coronal loops

    NASA Technical Reports Server (NTRS)

    Krishan, V.

    1987-01-01

    The steady state pressure structure of a coronal loop is discussed in terms of the MHD global invariants of an incompressible plasma. The steady state is represented by the superposition of two Chandrasekhar-Kendall functions corresponding to (n=m=0) and (n=m=1) modes. The relative contribution of the two modes (epsilon) is found to depend on the surface pressure of the coronal loop which is also the pressure of the external medium. The mixed mode state does not exist for high values of the external pressure because epsilon becomes complex.

  8. Loop transformations to prevent false sharing

    SciTech Connect

    Granston, E.D.; Montaut, T.; Bodin, F.

    1995-08-01

    To date, page management in shared virtual memory (SVM) systems has been primarily the responsibility of the run-time system. However, there are some problems that are difficult to resolve efficiently at run time. Chief among these is false sharing. In this paper, a loop transformation theory is developed for identifying and eliminating potential sources of multiple-writer false sharing and other sources of page migration resulting from regular references in numerical applications. Loop nests of one and two dimensions (before blocking) with single-level, DOALL-style parallelism are covered. The potential of these transformations is demonstrated experimentally.

  9. Slipping magnetic reconnection in coronal loops.

    PubMed

    Aulanier, Guillaume; Golub, Leon; Deluca, Edward E; Cirtain, Jonathan W; Kano, Ryouhei; Lundquist, Loraine L; Narukage, Noriyuki; Sakao, Taro; Weber, Mark A

    2007-12-01

    Magnetic reconnection of solar coronal loops is the main process that causes solar flares and possibly coronal heating. In the standard model, magnetic field lines break and reconnect instantaneously at places where the field mapping is discontinuous. However, another mode may operate where the magnetic field mapping is continuous but shows steep gradients: The field lines may slip across each other. Soft x-ray observations of fast bidirectional motions of coronal loops, observed by the Hinode spacecraft, support the existence of this slipping magnetic reconnection regime in the Sun's corona. This basic process should be considered when interpreting reconnection, both on the Sun and in laboratory-based plasma experiments. PMID:18063789

  10. How current loops and solenoids curve spacetime

    NASA Astrophysics Data System (ADS)

    Füzfa, André

    2016-01-01

    The curved spacetime around current loops and solenoids carrying arbitrarily large steady electric currents is obtained from the numerical resolution of the coupled Einstein-Maxwell equations in cylindrical symmetry. The artificial gravitational field associated to the generation of a magnetic field produces gravitational redshift of photons and deviation of light. Null geodesics in the curved spacetime of current loops and solenoids are also presented. We finally propose an experimental setup achievable with current technology of superconducting coils, that produces a phase shift of light of the same order of magnitude as astrophysical signals in ground-based gravitational wave observatories.

  11. Temperature Oscillations in Loop Heat Pipe Operation

    NASA Technical Reports Server (NTRS)

    Ku, Jentung; Ottenstein, Laura; Kobel, Mark; Rogers, Paul; Kaya, Tarik; Paquin, Krista C. (Technical Monitor)

    2000-01-01

    Loop heat pipes (LHPs) are versatile two-phase heat transfer devices that have gained increasing acceptance for space and terrestrial applications. The operating temperature of an LHP is a function of its operating conditions. The LHP usually reaches a steady operating temperature for a given heat load and sink temperature. The operating temperature will change when the heat load and/or the sink temperature changes, but eventually reaches another steady state in most cases. Under certain conditions, however, the loop operating temperature never really reaches a true steady state, but instead becomes oscillatory. This paper discusses the temperature oscillation phenomenon using test data from a miniature LHP.

  12. A double-loop tracking system.

    NASA Technical Reports Server (NTRS)

    Yuen, J. H.

    1972-01-01

    A nonlinear analysis which can be used to assess certain statistical characteristics of double-loop tracking systems is presented. It takes into account the mutual coupling effects of the loops in the system. Two approaches are taken to obtain steady-state probability density functions (pdf's) of the system phase errors. From these pdf's, important system performance statistics, e.g., the phase-error variances, can be calculated, thus illustrating the application and usefulness of the analysis. The analysis is applied to a satellite transponder as an example.

  13. Stabilizing gene regulatory networks through feedforward loops

    NASA Astrophysics Data System (ADS)

    Kadelka, C.; Murrugarra, D.; Laubenbacher, R.

    2013-06-01

    The global dynamics of gene regulatory networks are known to show robustness to perturbations in the form of intrinsic and extrinsic noise, as well as mutations of individual genes. One molecular mechanism underlying this robustness has been identified as the action of so-called microRNAs that operate via feedforward loops. We present results of a computational study, using the modeling framework of stochastic Boolean networks, which explores the role that such network motifs play in stabilizing global dynamics. The paper introduces a new measure for the stability of stochastic networks. The results show that certain types of feedforward loops do indeed buffer the network against stochastic effects.

  14. Coronal Loops: Observations and Modeling of Confined Plasma

    NASA Astrophysics Data System (ADS)

    Reale, Fabio

    2014-07-01

    Coronal loops are the building blocks of the X-ray bright solar corona. They owe their brightness to the dense confined plasma, and this review focuses on loops mostly as structures confining plasma. After a brief historical overview, the review is divided into two separate but not independent parts: the first illustrates the observational framework, the second reviews the theoretical knowledge. Quiescent loops and their confined plasma are considered and, therefore, topics such as loop oscillations and flaring loops (except for non-solar ones, which provide information on stellar loops) are not specifically addressed here. The observational section discusses the classification, populations, and the morphology of coronal loops, its relationship with the magnetic field, and the loop stranded structure. The section continues with the thermal properties and diagnostics of the loop plasma, according to the classification into hot, warm, and cool loops. Then, temporal analyses of loops and the observations of plasma dynamics, hot and cool flows, and waves are illustrated. In the modeling section, some basics of loop physics are provided, supplying fundamental scaling laws and timescales, a useful tool for consultation. The concept of loop modeling is introduced and models are divided into those treating loops as monolithic and static, and those resolving loops into thin and dynamic strands. More specific discussions address modeling the loop fine structure and the plasma flowing along the loops. Special attention is devoted to the question of loop heating, with separate discussion of wave (AC) and impulsive (DC) heating. Large-scale models including atmosphere boxes and the magnetic field are also discussed. Finally, a brief discussion about stellar coronal loops is followed by highlights and open questions.

  15. Quantum mechanics in non-inertial reference frames: Time-dependent rotations and loop prolongations

    SciTech Connect

    Klink, W.H.; Wickramasekara, S.

    2013-09-15

    This is the fourth in a series of papers on developing a formulation of quantum mechanics in non-inertial reference frames. This formulation is grounded in a class of unitary cocycle representations of what we have called the Galilean line group, the generalization of the Galilei group to include transformations amongst non-inertial reference frames. These representations show that in quantum mechanics, just as the case in classical mechanics, the transformations to accelerating reference frames give rise to fictitious forces. In previous work, we have shown that there exist representations of the Galilean line group that uphold the non-relativistic equivalence principle as well as representations that violate the equivalence principle. In these previous studies, the focus was on linear accelerations. In this paper, we undertake an extension of the formulation to include rotational accelerations. We show that the incorporation of rotational accelerations requires a class of loop prolongations of the Galilean line group and their unitary cocycle representations. We recover the centrifugal and Coriolis force effects from these loop representations. Loops are more general than groups in that their multiplication law need not be associative. Hence, our broad theoretical claim is that a Galilean quantum theory that holds in arbitrary non-inertial reference frames requires going beyond groups and group representations, the well-established framework for implementing symmetry transformations in quantum mechanics. -- Highlights: •A formulation of Galilean quantum mechanics in non-inertial reference frames is presented. •The Galilei group is generalized to infinite dimensional Galilean line group. •Loop prolongations of Galilean line group contain central extensions of Galilei group. •Unitary representations of the loops are constructed. •These representations lead to terms in the Hamiltonian corresponding to fictitious forces, including centrifugal and Coriolis

  16. An analysis of DREO's (Defence Research Establishment Ottawa) analog rebalance loops for the CSG-2 (Canadian Strapdown Gyroscope) tuned-rotor gyroscope

    NASA Astrophysics Data System (ADS)

    Bird, Jeffrey S.

    1987-07-01

    A high performance analog rebalance loop was designed for the Canadian Strapdown Gyroscope (CSG-2). This instrument is a potentially low cost, near inertial grade, two degree-of-freedom, tuned-rotor gyro designed and manufactured by Litton Systems Canada Ltd. under contract to DREO. The resulting loops are analyzed extensively from a control systems point of view with the examination of such properties as closed-loop stability, frequency and time responses and, to some extent, stability margin, as interpreted from multivariable generalizations of classical control-theoretic notions of Nyguist plots and root locii. The results indicate that the loops will provide sufficient closed loop performance to achieve the desired goals of bandwidth, maximum input rate, low cross-axis coupling and acceleration compensation.

  17. Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes

    PubMed Central

    Szczelkun, Mark D.; Tikhomirova, Maria S.; Sinkunas, Tomas; Gasiunas, Giedrius; Karvelis, Tautvydas; Pschera, Patrizia; Siksnys, Virginijus; Seidel, Ralf

    2014-01-01

    Clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems protect bacteria and archaea from infection by viruses and plasmids. Central to this defense is a ribonucleoprotein complex that produces RNA-guided cleavage of foreign nucleic acids. In DNA-targeting CRISPR-Cas systems, the RNA component of the complex encodes target recognition by forming a site-specific hybrid (R-loop) with its complement (protospacer) on an invading DNA while displacing the noncomplementary strand. Subsequently, the R-loop structure triggers DNA degradation. Although these reactions have been reconstituted, the exact mechanism of R-loop formation has not been fully resolved. Here, we use single-molecule DNA supercoiling to directly observe and quantify the dynamics of torque-dependent R-loop formation and dissociation for both Cascade- and Cas9-based CRISPR-Cas systems. We find that the protospacer adjacent motif (PAM) affects primarily the R-loop association rates, whereas protospacer elements distal to the PAM affect primarily R-loop stability. Furthermore, Cascade has higher torque stability than Cas9 by using a conformational locking step. Our data provide direct evidence for directional R-loop formation, starting from PAM recognition and expanding toward the distal protospacer end. Moreover, we introduce DNA supercoiling as a quantitative tool to explore the sequence requirements and promiscuities of orthogonal CRISPR-Cas systems in rapidly emerging gene-targeting applications. PMID:24912165

  18. A Conserved Surface Loop in Type I Dehydroquinate Dehydratases Positions an Active Site Arginine and Functions in Substrate Binding

    SciTech Connect

    Light, Samuel H.; Minasov, George; Shuvalova, Ludmilla; Peterson, Scott N.; Caffrey, Michael; Anderson, Wayne F.; Lavie, Arnon

    2012-04-18

    Dehydroquinate dehydratase (DHQD) catalyzes the third step in the biosynthetic shikimate pathway. We present three crystal structures of the Salmonella enterica type I DHQD that address the functionality of a surface loop that is observed to close over the active site following substrate binding. Two wild-type structures with differing loop conformations and kinetic and structural studies of a mutant provide evidence of both direct and indirect mechanisms of involvement of the loop in substrate binding. In addition to allowing amino acid side chains to establish a direct interaction with the substrate, closure of the loop necessitates a conformational change of a key active site arginine, which in turn positions the substrate productively. The absence of DHQD in humans and its essentiality in many pathogenic bacteria make the enzyme a target for the development of nontoxic antimicrobials. The structures and ligand binding insights presented here may inform the design of novel type I DHQD inhibiting molecules.

  19. Radiation Enhanced Absorption of Frank Loops by Nanovoids in Cu

    NASA Astrophysics Data System (ADS)

    Chen, Y.; Zhang, X.; Wang, J.

    2016-01-01

    Neutron and heavy ion irradiations generally induce voids in metallic materials, and continuous radiations typically result in void swelling and mechanical failure of the irradiated materials. Recent experiments showed that nanovoids in nanotwinned copper could act as sinks for radiation-induced Frank loops, significantly mitigating radiation damage. In this paper, we report on structural evolution of Frank loops under cascades and address the role of nanovoids in absorbing Frank loops in detail by using molecular dynamics simulations. Results show that a stand-alone Frank loop is stable under cascades. When Frank loops are adjacent to nanovoids, the diffusion of a group of atoms from the loop into nanovoids is accomplished via the formation and propagation of dislocation loops. The loop-nanovoid interactions result in the shrinkage of the nanovoids and the Frank loops.

  20. Run-time parallelization and scheduling of loops

    NASA Technical Reports Server (NTRS)

    Saltz, Joel H.; Mirchandaney, Ravi; Crowley, Kay

    1990-01-01

    Run time methods are studied to automatically parallelize and schedule iterations of a do loop in certain cases, where compile-time information is inadequate. The methods presented involve execution time preprocessing of the loop. At compile-time, these methods set up the framework for performing a loop dependency analysis. At run time, wave fronts of concurrently executable loop iterations are identified. Using this wavefront information, loop iterations are reordered for increased parallelism. Symbolic transformation rules are used to produce: inspector procedures that perform execution time preprocessing and executors or transformed versions of source code loop structures. These transformed loop structures carry out the calculations planned in the inspector procedures. Performance results are presented from experiments conducted on the Encore Multimax. These results illustrate that run time reordering of loop indices can have a significant impact on performance. Furthermore, the overheads associated with this type of reordering are amortized when the loop is executed several times with the same dependency structure.

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

    SciTech Connect

    Kano, R.; Ueda, K.; Tsuneta, S.

    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.

  2. Photospheric Properties of Warm EUV Loops and Hot X-Ray Loops

    NASA Astrophysics Data System (ADS)

    Kano, R.; Ueda, K.; Tsuneta, S.

    2014-02-01

    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-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 × 106 erg s-1 cm-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.

  3. Mechanical heterogeneities and lithospheric extension

    NASA Astrophysics Data System (ADS)

    Duretz, Thibault; Petri, Benoit; Mohn, Geoffroy; Schenker, Filippo L.; Schmalholz, Stefan

    2016-04-01

    Detailed geological and geophysical studies of passive margins have highlighted the multi-stage and depth-dependent aspect of lithospheric thinning. Lithospheric thinning involves a variety of structures (normal faults, low angle detachments, extensional shear zones, extraction faults) and leads to a complex architecture of passive margins (with e.g. necking zone, mantle exhumation, continental allochthons). The processes controlling the generation and evolution of these structures as well as the impact of pre-rift inheritance are so far incompletely understood. In this study, we investigate the impact of pre-rift inheritance on the development of rifted margins using two-dimensional thermo-mechanical models of lithospheric thinning. To first order, we represent the pre-rift mechanical heterogeneities with lithological layering. The rheologies are kept simple (visco-plastic) and do not involve any strain softening mechanism. Our models show that mechanical layering causes multi-stage and depth-dependent extension. In the initial rifting phase, lithospheric extension is decoupled: as the crust undergoes thinning by brittle (frictional-plastic) faults, the lithospheric mantle accommodates extension by symmetric ductile necking. In a second rifting phase, deformation in the crust and lithospheric mantle is coupled and marks the beginning of an asymmetric extension stage. Low angle extensional shear zones develop across the lithosphere and exhume subcontinental mantle. Furthemore, crustal allochthons and adjacent basins develop coevally. We describe as well the thermal evolution predicted by the numerical models and discuss the first-order implications of our results in the context of the Alpine geological history.

  4. Ductile extension in alpine Corsica

    NASA Astrophysics Data System (ADS)

    Jolivet, Laurent; Dubois, Roland; Fournier, Marc; Goffé, Bruno; Michard, André; Jourdan, Claudie

    1990-10-01

    Ductile deformation in high-pressure (P)-low temperature (T) conditions due to the westward thrusting of oceanic material onto a continental basement in alpine Corsica is overprinted by a late deformation event with a reverse shear sense (eastward) that took place in less severe P-T conditions. We show that the late deformation can be linked to extension during rifting and spreading of the Liguro Provençal basin from late Oligocene to late-middle Miocene time. Major compressive thrust contacts were reactivated as ductile normal faults and, in some units, only a penetrative eastward shear can be observed. This extension following the thickening of the crust brought tectonic units which underwent very different P- T conditions during the earlier stage into close contact. The Balagne nappe, which shows neither significant ductile deformation nor metamorphism, directly overlies the high-P units. The extensional deformation is distributed through the entire thickness of the nappe stack but is more important along the major thrust contacts, which localize the strain. The geometry of the crustal extension is controlled by that of the early compressive thrusts. The latest structures are east-dipping brittle normal faults which bound the early to middle Miocene Saint Florent half graben.

  5. Thermal criteria to compare fast reactors coolants for the intermediate loop

    SciTech Connect

    Saez, Manuel; Rodriguez, Gilles

    2007-07-01

    Fast Breeder Reactors (FBR) are typically using a liquid metal as the primary coolant. Up to now, sodium is the referenced coolant for all large-scale FBR, but lead and sodium-potassium alloy have both also been used successfully for smaller rigs. The French Atomic Energy Commission (CEA) has an extensive experience and significant expertise in Sodium cooled Fast Reactors (SFR) over the past 40 years of R and D and feedback experiments. Some improvements are needed on the SFR to meet the Generation IV goals, and in particular the safety and the reliability through the intermediate loop coolant. As sodium reacts exo-thermically with air and water and to eliminate the drawback of the water-sodium interaction when a steam generator tube is ruptured, CEA is involved in a substantial effort in order to investigate the interest to use an alternative coolant than sodium in the intermediate loop. This paper presents the main thermal criteria to compare Fast Reactors coolants for the intermediate loop under natural and forced convection. Neutronics considerations are not taken into account for the intermediate loop coolant. Transport, transfer and energetic criteria are analysed in the field of turbulent flows. Criteria are applied to the following potential coolant candidates: sodium, lithium, tin, bismuth, lead, lead-bismuth alloy, lead-lithium alloy, gallium, indium, potassium and sodium-potassium alloy. According to this thermal analysis, the gallium as heat transfer agent for the intermediate loop is considered as a promising candidate. For the discussion of the applicability of the gallium as heat transfer agent for the intermediate loop, a limited thermal hydraulic pre-sizing of a steam generator is undertaken using simple engineering methods implemented in COPERNIC code, a CEA tool dedicated to reactor systems pre-sizing. (authors)

  6. Sensory feedback in prosthetics: a standardized test bench for closed-loop control.

    PubMed

    Dosen, Strahinja; Markovic, Marko; Hartmann, Cornelia; Farina, Dario

    2015-03-01

    Closing the control loop by providing sensory feedback to the user of a prosthesis is an important challenge, with major impact on the future of prosthetics. Developing and comparing closed-loop systems is a difficult task, since there are many different methods and technologies that can be used to implement each component of the system. Here, we present a test bench developed in Matlab Simulink for configuring and testing the closed-loop human control system in standardized settings. The framework comprises a set of connected generic blocks with normalized inputs and outputs, which can be customized by selecting specific implementations from a library of predefined components. The framework is modular and extensible and it can be used to configure, compare and test different closed-loop system prototypes, thereby guiding the development towards an optimal system configuration. The use of the test bench was demonstrated by investigating two important aspects of closed-loop control: performance of different electrotactile feedback interfaces (spatial versus intensity coding) during a pendulum stabilization task and feedforward methods (joystick versus myocontrol) for force control. The first experiment demonstrated that in the case of trained subjects the intensity coding might be superior to spatial coding. In the second experiment, the control of force was rather poor even with a stable and precise control interface (joystick), demonstrating that inherent characteristics of the prosthesis can be an important limiting factor when considering the overall effectiveness of the closed-loop control. The presented test bench is an important instrument for investigating different aspects of human manual control with sensory feedback. PMID:25420268

  7. Time loops in a gravitational theory

    SciTech Connect

    Choudhury, A.L.

    1993-06-01

    We demonstrate here that time loops can be constructed by pasting different wormhole solutions with higher order perturbative terms in a model originated by Gidding and Strominger and subsequently improved by Coule and Maeda. In this model a scalar field interacts with a gravitational axion in Euclidean space. 6 refs., 2 figs.

  8. Lorentz invariance in loop quantum gravity

    NASA Astrophysics Data System (ADS)

    Pullin, Jorge; Rastgoo, Saeed; Gambini, Rodolfo

    2011-04-01

    We reconsider the argument of Collins, Perez, Sudarsky, Urrutia and Vucetich concerning violations of Lorentz invariance in the context of loop quantum gravity. We show that even if one introduces a lattice that violates Lorentz invariance at the Planck scale, this does not translate itself into large violations that would conflict with experiment.

  9. Extrasensitive phase-locked-loop circuit

    NASA Technical Reports Server (NTRS)

    Nyiri, E. J.

    1977-01-01

    Modified phase-locked loop (PLL) generates clock from incoming data signal. To minimize effects of threshold phase-detector gain variations, the PLL uses a dither oscillator, a dither band-pass filter, and correlator instead of coherent amplitude detector.

  10. Interstitial loop transformations in FeCr

    DOE PAGESBeta

    Béland, Laurent Karim; Osetsky, Yuri N.; Stoller, Roger E.; Xu, Haixuan

    2015-03-27

    Here, we improve the Self-Evolving Atomistic Kinetic Monte Carlo (SEAKMC) algorithm by integrating the Activation Relaxation Technique nouveau (ARTn), a powerful open-ended saddle-point search method, into the algorithm. We use it to investigate the reaction of 37-interstitial 1/2[1 1 1] and 1/2[View the MathML source] loops in FeCr at 10 at.% Cr. They transform into 1/2[1 1 1], 1/2[View the MathML source], [1 0 0] and [0 1 0] 74-interstitial clusters with an overall barrier of 0.85 eV. We find that Cr decoration locally inhibits the rotation of crowdions, which dictates the final loop orientation. Moreover, the final loop orientationmore » depends on the details of the Cr decoration. Generally, a region of a given orientation is favored if Cr near its interface with a region of another orientation is able to inhibit reorientation at this interface more than the Cr present at the other interfaces. Also, we find that substitutional Cr atoms can diffuse from energetically unfavorable to energetically favorable sites within the interlocked 37-interstitial loops conformation with barriers of less than 0.35 eV.« less

  11. Interstitial loop transformations in FeCr

    SciTech Connect

    Béland, Laurent Karim; Osetsky, Yuri N.; Stoller, Roger E.; Xu, Haixuan

    2015-03-27

    Here, we improve the Self-Evolving Atomistic Kinetic Monte Carlo (SEAKMC) algorithm by integrating the Activation Relaxation Technique nouveau (ARTn), a powerful open-ended saddle-point search method, into the algorithm. We use it to investigate the reaction of 37-interstitial 1/2[1 1 1] and 1/2[View the MathML source] loops in FeCr at 10 at.% Cr. They transform into 1/2[1 1 1], 1/2[View the MathML source], [1 0 0] and [0 1 0] 74-interstitial clusters with an overall barrier of 0.85 eV. We find that Cr decoration locally inhibits the rotation of crowdions, which dictates the final loop orientation. Moreover, the final loop orientation depends on the details of the Cr decoration. Generally, a region of a given orientation is favored if Cr near its interface with a region of another orientation is able to inhibit reorientation at this interface more than the Cr present at the other interfaces. Also, we find that substitutional Cr atoms can diffuse from energetically unfavorable to energetically favorable sites within the interlocked 37-interstitial loops conformation with barriers of less than 0.35 eV.

  12. BIOREACTOR DESIGN - OUTER LOOP LANDFILL, LOUISVILLE, KY

    EPA Science Inventory

    Bioreactor field demonstration projects are underway at the Outer Loop Landfill in Louisville, KY, USA. The research effort is a cooperative research effort between US EPA and Waste Management Inc. Two primary kinds of municipal waste bioreactors are under study at this site. ...

  13. Numerical multi-loop integrals and applications

    NASA Astrophysics Data System (ADS)

    Freitas, A.

    2016-09-01

    Higher-order radiative corrections play an important role in precision studies of the electroweak and Higgs sector, as well as for the detailed understanding of large backgrounds to new physics searches. For corrections beyond the one-loop level and involving many independent mass and momentum scales, it is in general not possible to find analytic results, so that one needs to resort to numerical methods instead. This article presents an overview of a variety of numerical loop integration techniques, highlighting their range of applicability, suitability for automatization, and numerical precision and stability. In a second part of this article, the application of numerical loop integration methods in the area of electroweak precision tests is illustrated. Numerical methods were essential for obtaining full two-loop predictions for the most important precision observables within the Standard Model. The theoretical foundations for these corrections will be described in some detail, including aspects of the renormalization, resummation of leading log contributions, and the evaluation of the theory uncertainty from missing higher orders.

  14. Can Thermal Nonequilibrium Explain Coronal Loops?

    NASA Technical Reports Server (NTRS)

    Klimchuk, James A.; Karpen, Judy T.; Antiochos, Spiro K.

    2010-01-01

    Any successful model of coronal loops must explain a number of observed properties. For warm (approx. 1 MK) loops, these include: 1. excess density, 2. flat temperature profile, 3. super-hydrostatic scale height, 4. unstructured intensity profile, and 5. 1000-5000 s lifetime. We examine whether thermal nonequilibrium can reproduce the observations by performing hydrodynamic simulations based on steady coronal heating that decreases exponentially with height. We consider both monolithic and multi-stranded loops. The simulations successfully reproduce certain aspects of the observations, including the excess density, but each of them fails in at least one critical way. -Xonolithic models have far too much intensity structure, while multi-strand models are either too structured or too long-lived. Storms of nanoflares remain the only viable explanation for warm loops that has been proposed so far. Our results appear to rule out the widespread existence of heating that is both highly concentrated low in the corona and steady or quasi-steady (slowly varying or impulsive with a rapid cadence). Active regions would have a very different appearance if the dominant heating mechanism had these properties. Thermal nonequilibrium may nonetheless play an important role in prominences and catastrophic cooling e(veen.gts..,coronal rain) that occupy a small fraction of the coronal volume. However, apparent inconsistencies between the models and observations of cooling events have yet to be understood.

  15. Mars Pathfinder mechanically pumped cooling loop

    NASA Technical Reports Server (NTRS)

    Birur, G. C.

    2001-01-01

    A mechanically pumped single-phase cooling loop was successfully flown on the Mars Pathfinder (MPF) Spacecraft which safely landed on the Martian surface on July 4, 1997. One of the key technologies that enabled the mission to succeed was an active heat rejection system (HRS) used to cool the electronics on the spacecraft during its seven-month cruise from Earth to Mars.

  16. Magnetic reconnection and solar flare loops

    NASA Technical Reports Server (NTRS)

    Forbes, T. G.

    1987-01-01

    Reconnection models of the main phase of large solar flares are used to explain the energetics and the motions of the large flare loops that occur during this phase. Correct predictions for the density and temperature of the X-ray emitting loops are obtained by coupling magnetic reconnection with chromospheric ablation. In the reconnection models the ablation is driven by the thermal conduction of heat along magnetic field lines connecting the reconnection shocks in the corona with the flare ribbons in the chromosphere. Combining the compressible reconnection theory of Soward and Priest (1982) with the magnetohydrodynamic (MHD) subshock criteria of Coroniti (1970) shows that the Petschek-type slow-mode shocks in the vicinity of the x-line always dissociate into pairs of isothermal slow-mode subshocks and thermal conduction fronts. The rate of expansion of the loops is a function of the reconnection rate, and loops can be evolving self-similarly in time with their height increasing as sq root t and the reconnection rate decreasing as t to the minus 1.

  17. Selective purge for hydrogenation reactor recycle loop

    DOEpatents

    Baker, Richard W.; Lokhandwala, Kaaeid A.

    2001-01-01

    Processes and apparatus for providing improved contaminant removal and hydrogen recovery in hydrogenation reactors, particularly in refineries and petrochemical plants. The improved contaminant removal is achieved by selective purging, by passing gases in the hydrogenation reactor recycle loop or purge stream across membranes selective in favor of the contaminant over hydrogen.

  18. Warm inflationary model in loop quantum cosmology

    SciTech Connect

    Herrera, Ramon

    2010-06-15

    A warm inflationary universe model in loop quantum cosmology is studied. In general we discuss the condition of inflation in this framework. By using a chaotic potential, V({phi}){proportional_to}{phi}{sup 2}, we develop a model where the dissipation coefficient {Gamma}={Gamma}{sub 0}=constant. We use recent astronomical observations for constraining the parameters appearing in our model.

  19. Closed Loop System Identification with Genetic Algorithms

    NASA Technical Reports Server (NTRS)

    Whorton, Mark S.

    2004-01-01

    High performance control design for a flexible space structure is challenging since high fidelity plant models are di.cult to obtain a priori. Uncertainty in the control design models typically require a very robust, low performance control design which must be tuned on-orbit to achieve the required performance. Closed loop system identi.cation is often required to obtain a multivariable open loop plant model based on closed-loop response data. In order to provide an accurate initial plant model to guarantee convergence for standard local optimization methods, this paper presents a global parameter optimization method using genetic algorithms. A minimal representation of the state space dynamics is employed to mitigate the non-uniqueness and over-parameterization of general state space realizations. This control-relevant system identi.cation procedure stresses the joint nature of the system identi.cation and control design problem by seeking to obtain a model that minimizes the di.erence between the predicted and actual closed-loop performance.

  20. Loop realizations of quantum affine algebras

    SciTech Connect

    Cautis, Sabin; Licata, Anthony

    2012-12-15

    We give a simplified description of quantum affine algebras in their loop presentation. This description is related to Drinfeld's new realization via halves of vertex operators. We also define an idempotent version of the quantum affine algebra which is suitable for categorification.

  1. Coal Combustion Products Extension Program

    SciTech Connect

    Tarunjit S. Butalia; William E. Wolfe

    2004-12-31

    The primary objective of the CCP Extension Program is to promote the responsible uses of Ohio CCPs that are technically sound, environmentally safe, and commercially competitive. A secondary objective is to assist other CCP generating states (particularly neighboring states) in establishing CCP use programs within their states. The goal of the CCP extension program at OSU is to work with CCP stakeholders to increase the overall CCP state utilization rate to more than 30% by the year 2005. The program aims to increase FGD utilization for Ohio to more than 20% by the year 2005. The increased utilization rates are expected to be achieved through increased use of CCPs for highway, mine reclamation, agricultural, manufacturing, and other civil engineering uses. In order to accomplish these objectives and goals, the highly successful CCP pilot extension program previously in place at the university has been expanded and adopted by the university as a part of its outreach and engagement mission. The extension program is an innovative technology transfer program with multiple sponsors. The program is a collaborative effort between The Ohio State University (College of Engineering and University Extension Service), United States Department of Energy's National Energy Technology Laboratory, Ohio Department of Development's Coal Development Office, and trade associations such as the American Coal Ash Association as well as the Midwest Coal Ash Association. Industry co-sponsors include American Electric Power, Dravo Lime Company, and ISG Resources. Implementation of the proposed project results in both direct and indirect as well as societal benefits. These benefits include (1) increased utilization of CCPs instead of landfilling, (2) development of proper construction and installation procedures, (3) education of regulators, specification-writers, designers, construction contractors, and the public, (4) emphasis on recycling and decrease in the need for landfill space, (5

  2. COAL COMBUSTION PRODUCTS EXTENSION PROGRAM

    SciTech Connect

    Tarunjit S. Butalia; William E. Wolfe

    2005-05-15

    The primary objective of the CCP Extension Program is to promote the responsible uses of Ohio CCPs that are technically sound, environmentally safe, and commercially competitive. A secondary objective is to assist other CCP generating states (particularly neighboring states) in establishing CCP use programs within their states. The goal of the CCP extension program at OSU is to work with CCP stakeholders to increase the overall CCP state utilization rate to more than 30% by the year 2005. The program aims to increase FGD utilization for Ohio to more than 20% by the year 2005. The increased utilization rates are expected to be achieved through increased use of CCPs for highway, mine reclamation, agricultural, manufacturing, and other civil engineering uses. In order to accomplish these objectives and goals, the highly successful CCP pilot extension program previously in place at the university has been expanded and adopted by the university as a part of its outreach and engagement mission. The extension program is an innovative technology transfer program with multiple sponsors. The program is a collaborative effort between The Ohio State University (College of Engineering and University Extension Service), United States Department of Energy's National Energy Technology Laboratory, Ohio Department of Development's Coal Development Office, and trade associations such as the American Coal Ash Association as well as the Midwest Coal Ash Association. Industry co-sponsors include American Electric Power, Dravo Lime Company, and ISG Resources. Implementation of the proposed project results in both direct and indirect as well as societal benefits. These benefits include (1) increased utilization of CCPs instead of landfilling, (2) development of proper construction and installation procedures, (3) education of regulators, specification-writers, designers, construction contractors, and the public, (4) emphasis on recycling and decrease in the need for landfill space, (5

  3. Coal Combustion Products Extension Program

    SciTech Connect

    Tarunjit S. Butalia; William E. Wolfe

    2003-12-31

    The primary objective of the CCP Extension Program is to promote the responsible uses of Ohio CCPs that are technically sound, environmentally safe, and commercially competitive. A secondary objective is to assist other CCP generating states (particularly neighboring states) in establishing CCP use programs within their states. The goal of the CCP extension program at OSU is to work with CCP stakeholders to increase the overall CCP state utilization rate to more than 30% by the year 2005. The program aims to increase FGD utilization for Ohio to more than 20% by the year 2005. The increased utilization rates are expected to be achieved through increased use of CCPs for highway, mine reclamation, agricultural, manufacturing, and other civil engineering uses. In order to accomplish these objectives and goals, the highly successful CCP pilot extension program previously in place at the university has been expanded and adopted by the university as a part of its outreach and engagement mission. The extension program is an innovative technology transfer program with multiple sponsors. The program is a collaborative effort between The Ohio State University (College of Engineering and University Extension Service), United States Department of Energy's National Energy Technology Laboratory, Ohio Department of Development's Coal Development Office, and trade associations such as the American Coal Ash Association as well as the Midwest Coal Ash Association. Industry co-sponsors include American Electric Power, Dravo Lime Company, and ISG Resources. Implementation of the proposed project results in both direct and indirect as well as societal benefits. These benefits include (1) increased utilization of CCPs instead of landfilling, (2) development of proper construction and installation procedures, (3) education of regulators, specification-writers, designers, construction contractors, and the public, (4) emphasis on recycling and decrease in the need for landfill space, (5

  4. Human METTL20 Methylates Lysine Residues Adjacent to the Recognition Loop of the Electron Transfer Flavoprotein in Mitochondria*

    PubMed Central

    Rhein, Virginie F.; Carroll, Joe; He, Jiuya; Ding, Shujing; Fearnley, Ian M.; Walker, John E.

    2014-01-01

    In mammalian mitochondria, protein methylation is a relatively uncommon post-transcriptional modification, and the extent of the mitochondrial protein methylome, the modifying methyltransferases, and their substrates have been little studied. As shown here, the β-subunit of the electron transfer flavoprotein (ETF) is one such methylated protein. The ETF is a heterodimer of α- and β-subunits. Lysine residues 199 and 202 of mature ETFβ are almost completely trimethylated in bovine heart mitochondria, whereas ETFα is not methylated. The enzyme responsible for the modifications was identified as methyltransferase-like protein 20 (METTL20). In human 143B cells, the methylation of ETFβ is less extensive and is diminished further by suppression of METTL20. Tagged METTL20 expressed in HEK293T cells specifically associates with the ETF and promotes the trimethylation of ETFβ lysine residues 199 and 202. ETF serves as a mobile electron carrier linking dehydrogenases involved in fatty acid oxidation and one-carbon metabolism to the membrane-associated ubiquinone pool. The methylated residues in ETFβ are immediately adjacent to a protein loop that recognizes and binds to the dehydrogenases. Suppression of trimethylation of ETFβ in mouse C2C12 cells oxidizing palmitate as an energy source reduced the consumption of oxygen by the cells. These experiments suggest that the oxidation of fatty acids in mitochondria and the passage of electrons via the ETF may be controlled by modulating the protein-protein interactions between the reduced dehydrogenases and the β-subunit of the ETF by trimethylation of lysine residues. METTL20 is the first lysine methyltransferase to be found to be associated with mitochondria. PMID:25023281

  5. Human METTL20 methylates lysine residues adjacent to the recognition loop of the electron transfer flavoprotein in mitochondria.

    PubMed

    Rhein, Virginie F; Carroll, Joe; He, Jiuya; Ding, Shujing; Fearnley, Ian M; Walker, John E

    2014-08-29

    In mammalian mitochondria, protein methylation is a relatively uncommon post-transcriptional modification, and the extent of the mitochondrial protein methylome, the modifying methyltransferases, and their substrates have been little studied. As shown here, the β-subunit of the electron transfer flavoprotein (ETF) is one such methylated protein. The ETF is a heterodimer of α- and β-subunits. Lysine residues 199 and 202 of mature ETFβ are almost completely trimethylated in bovine heart mitochondria, whereas ETFα is not methylated. The enzyme responsible for the modifications was identified as methyltransferase-like protein 20 (METTL20). In human 143B cells, the methylation of ETFβ is less extensive and is diminished further by suppression of METTL20. Tagged METTL20 expressed in HEK293T cells specifically associates with the ETF and promotes the trimethylation of ETFβ lysine residues 199 and 202. ETF serves as a mobile electron carrier linking dehydrogenases involved in fatty acid oxidation and one-carbon metabolism to the membrane-associated ubiquinone pool. The methylated residues in ETFβ are immediately adjacent to a protein loop that recognizes and binds to the dehydrogenases. Suppression of trimethylation of ETFβ in mouse C2C12 cells oxidizing palmitate as an energy source reduced the consumption of oxygen by the cells. These experiments suggest that the oxidation of fatty acids in mitochondria and the passage of electrons via the ETF may be controlled by modulating the protein-protein interactions between the reduced dehydrogenases and the β-subunit of the ETF by trimethylation of lysine residues. METTL20 is the first lysine methyltransferase to be found to be associated with mitochondria. PMID:25023281

  6. Loop Evolution Observed with AIA and Hi-C

    NASA Technical Reports Server (NTRS)

    Mulu-Moore, Fana; Winebarger, Amy R.; Cirtain, Jonathan W.; Kobayashi, Ken; Korreck, Kelly E.; Golub, Leon; Kuzin, Sergei; Walsh, Robert William; DeForest, Craig E.; De Pontieu, Bart; Title, Alan M.; Weber, Mark

    2012-01-01

    In the past decade, the evolution of EUV loops has been used to infer the loop substructure. With the recent launch of High Resolution Coronal Imager (Hi-C), this inference can be validated. In this presentation we discuss the first results of loop analysis comparing AIA and Hi-C data. In the past decade, the evolution of EUV loops has been used to infer the loop substructure. With the recent launch of High Resolution Coronal Imager (Hi-C), this inference can be validated. In this presentation we discuss the first results of loop analysis comparing AIA and Hi-C data.

  7. Program to justify life extension of older nuclear piping systems

    SciTech Connect

    Burr, T.K.; Dwight, J.E. Jr.; Morton, D.K.

    1991-01-01

    The Idaho National Engineering Laboratory (INEL) has a history of more than 40 years devoted to the operation of nuclear reactors designed for research and experiments. The Advanced Test Reactor (ATR) is one such operating reactor whose mission requires continued operation for an additional 25 years or more. Since the ATR is approaching its design life of twenty years, life extension evaluations have been initiated. Of particular importance are the associated high temperature, high pressure loop piping system supporting in--reactor experiments. Failure of this piping could challenge core safety margins. Since regulatory rules for nuclear power plant life extension are only in the formulation stage, the current technical guidance on this subject provided by the Department of Energy (DOE) or the commercial nuclear industry is incomplete. In the interim, order to assure continued safe operation of this piping beyond its initial design life, a program has been developed to provide the necessary technical justification for life extension. This paper describes a program that establishes Section 11 of the ASME Boiler and Pressure Vessel Code as the governing criteria document, retains B31.1 as the Code of record for Section 11 activities, specifies additional inservice inspection requirements more strict than Section 11, and relies heavily on flaw detection and fracture mechanics evaluations. 18 refs., 2 figs.

  8. DYNAMICS OF THE FLARING LOOP SYSTEM OF 2005 AUGUST 22 OBSERVED IN MICROWAVES AND HARD X-RAYS

    SciTech Connect

    Reznikova, V. E.; Melnikov, V. F.; Shibasaki, K.

    2010-11-20

    We studied the spatial dynamics of the flaring loop in the 2005 August 22 event using microwave (NoRH) and hard X-ray (RHESSI) observations together with complementary data from SOHO/MDI, SMART at Hida, SOHO/EIT, and TRACE. We have found that (1) the pre-flare morphology of the active region exhibits a strongly sheared arcade seen in H{alpha} and the J-shape filament seen in EUV; (2) energy release and high-energy electron acceleration occur in a sequence along the extensive arcade; (3) the shear angle and the parallel (to the magnetic neutral line) component of the footpoint (FP) distance steadily decrease during the flare process; (4) the radio loop shrinks in length and height during the first emission peak, and later it grows; after the fourth peak the simultaneous descending of the brightest loop and formation of a new microwave loop at a higher altitude occur; (5) the hard X-ray coronal source is located higher than the microwave loop apex and shows faster upward motion; (6) the first peak on microwave time profiles is present in both the loop top and FP regions. However, the emission peaks that follow are present only in the FP regions. We conclude that after the first emission peak the acceleration site is located over the flaring arcade and particles are accelerated along magnetic field lines. We make use of the collapsing magnetic trap model to understand some observational effects.

  9. Io: Mountains and crustal extension

    NASA Technical Reports Server (NTRS)

    Heath, M. J.

    1985-01-01

    It is argued that there is good reason to conclude that mountains on Io, like those on Earth, are subject to growth and decay. The decay of mountains will be assisted by the ability of SO sub 2 to rot silicate rock and by explosive escape of sub-surface SO sub 2 from aquifers (Haemus Mons is seen to be covered by bright material, presumably fallout from a SO sub 2 rich plume which had been active on the mountain flanks). On the west side of the massif at 10 degrees S, 270 degrees W a rugged surface consists of long ridges running perpendicular to the downslope direction, suggesting tectonic denudation with crustal blocks sliding down the mountain flank. Tectonic denudation may be assisted, as in the case of the Bearpaw Mountains, Montana by overloading mountain flanks with volcanic products. The surfaces of some massifs exhibit a well developed, enigmatic corrugated terrain, consisting of complex ridge systems. Ridges may bifurcate, anastomose to form closed depressions and form concentric loops. Taken together, observations of morphology, heat flux, surface deposits and styles of volcanism may point to the existence of lithosphere domains with distinct compositions and tectonic regimes.

  10. Scalable extensions of HEVC for next generation services

    NASA Astrophysics Data System (ADS)

    Misra, Kiran; Segall, Andrew; Zhao, Jie; Kim, Seung-Hwan

    2013-02-01

    The high efficiency video coding (HEVC) standard being developed by ITU-T VCEG and ISO/IEC MPEG achieves a compression goal of reducing the bitrate by half for the same visual quality when compared with earlier video compression standards such as H.264/AVC. It achieves this goal with the use of several new tools such as quad-tree based partitioning of data, larger block sizes, improved intra prediction, the use of sophisticated prediction of motion information, inclusion of an in-loop sample adaptive offset process etc. This paper describes an approach where the HEVC framework is extended to achieve spatial scalability using a multi-loop approach. The enhancement layer inter-predictive coding efficiency is improved by including within the decoded picture buffer multiple up-sampled versions of the decoded base layer picture. This approach has the advantage of achieving significant coding gains with a simple extension of the base layer tools such as inter-prediction, motion information signaling etc. Coding efficiency of the enhancement layer is further improved using adaptive loop filter and internal bit-depth increment. The performance of the proposed scalable video coding approach is compared to simulcast transmission of video data using high efficiency model version 6.1 (HM-6.1). The bitrate savings are measured using Bjontegaard Delta (BD) rate for a spatial scalability factor of 2 and 1.5 respectively when compared with simulcast anchors. It is observed that the proposed approach provides an average luma BD rate gains of 33.7% and 50.5% respectively.

  11. Sfermion loop contribution to the two-loop level fermion electric dipole moment in R-parity violating supersymmetric models

    NASA Astrophysics Data System (ADS)

    Yamanaka, Nodoka

    2012-10-01

    We evaluate the Barr-Zee-type two-loop level contribution to the fermion electric and chromo-electric dipole moments with sfermion loop in R-parity violating supersymmetric models. It is found that the Barr-Zee-type fermion dipole moment with sfermion loop acts destructively to the currently known fermion loop contribution, and that it has small effect when the mass of squarks or charged sleptons in the loop is larger than or comparable to that of the sneutrinos, but cannot be neglected if the sneutrinos are much heavier than loop sfermions.

  12. Direct measurement of loop gain and bandwidth of phase-locked loop for mode-locked laser.

    PubMed

    Hou, Dong; Tian, Jie; Sun, Fuyu; Huang, Xianhe

    2016-07-25

    A simple and robust technique for measuring the loop gain and bandwidth of a phase-locking loop (PLL) for mode-locked laser is proposed. This technique can be used for the real-time measurement of the PLL's real loop gain and bandwidth in a closed loop without breaking its locking state. The agreement of the experimental result and theoretical calculation proves the validity of the proposed technique for measuring the loop gain and bandwidth. This technique with a simple configuration can be easily expanded to other laser's locking system whose loop gain and bandwidth should be measured in advance. PMID:27464173

  13. General University Extension. Bulletin, 1926, No. 5

    ERIC Educational Resources Information Center

    Shelby, Thomas H.

    1926-01-01

    This report concerns itself with the growth and progress of "general" university extension for the biennial period 1922-1924. By general university extension is meant extension activities of universities and colleges in the fields not covered by agricultural and home economics extension under the Federal subsidy acts through the Federal land-grant…

  14. 48 CFR 570.405 - Lease extensions.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 48 Federal Acquisition Regulations System 4 2010-10-01 2010-10-01 false Lease extensions. 570.405... Requirements 570.405 Lease extensions. (a) This section applies to extension of the term of a lease to provide for continued occupancy on a short-term basis. (b) If the value of a lease extension will exceed...

  15. 10 CFR 903.23 - Rate extensions.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Rate Adjustments and Extensions for the Alaska, Southeastern, Southwestern, and Western Area Power Administrations § 903.23 Rate extensions. (a) The following regulations shall apply to the extension of rates... 10 Energy 4 2010-01-01 2010-01-01 false Rate extensions. 903.23 Section 903.23 Energy...

  16. Spreading the Word about Extension's Public Value

    ERIC Educational Resources Information Center

    Kalambokidis, Laura

    2011-01-01

    In recent years, the idea that Extension can build support for its programs by highlighting how they benefit people who have no contact with the programs has taken root in the Extension system. Providing Extension program teams with resources, training, and leadership can lead to a body of public value messages that can infuse Extension's…

  17. Simple Analytic Expressions for the Magnetic Field of a Circular Current Loop

    NASA Technical Reports Server (NTRS)

    Simpson, James C.; Lane, John E.; Immer, Christopher D.; Youngquist, Robert C.

    2001-01-01

    Analytic expressions for the magnetic induction (magnetic flux density, B) of a simple planar circular current loop have been published in Cartesian and cylindrical coordinates [1,2], and are also known implicitly in spherical coordinates [3]. In this paper, we present explicit analytic expressions for B and its spatial derivatives in Cartesian, cylindrical, and spherical coordinates for a filamentary current loop. These results were obtained with extensive use of Mathematica "TM" and are exact throughout all space outside of the conductor. The field expressions reduce to the well-known limiting cases and satisfy V · B = 0 and V x B = 0 outside the conductor. These results are general and applicable to any model using filamentary circular current loops. Solenoids of arbitrary size may be easily modeled by approximating the total magnetic induction as the sum of those for the individual loops. The inclusion of the spatial derivatives expands their utility to magnetohydrodynamics where the derivatives are required. The equations can be coded into any high-level programming language. It is necessary to numerically evaluate complete elliptic integrals of the first and second kind, but this capability is now available with most programming packages.

  18. Revealing a Two-Loop Transcriptional Feedback Mechanism in the Cyanobacterial Circadian Clock

    PubMed Central

    Hertel, Stefanie; Brettschneider, Christian; Axmann, Ilka M.

    2013-01-01

    Molecular genetic studies in the circadian model organism Synechococcus have revealed that the KaiC protein, the central component of the circadian clock in cyanobacteria, is involved in activation and repression of its own gene transcription. During 24 hours, KaiC hexamers run through different phospho-states during daytime. So far, it has remained unclear which phospho-state of KaiC promotes kaiBC expression and which opposes transcriptional activation. We systematically analyzed various combinations of positive and negative transcriptional feedback regulation by introducing a combined TTFL/PTO model consisting of our previous post-translational oscillator that considers all four phospho-states of KaiC and a transcriptional/translational feedback loop. Only a particular two-loop feedback mechanism out of 32 we have extensively tested is able to reproduce existing experimental observations, including the effects of knockout or overexpression of kai genes. Here, threonine and double phosphorylated KaiC hexamers activate and unphosphorylated KaiC hexamers suppress kaiBC transcription. Our model simulations suggest that the peak expression ratio of the positive and the negative component of kaiBC expression is the main factor for how the different two-loop feedback models respond to removal or to overexpression of kai genes. We discuss parallels between our proposed TTFL/PTO model and two-loop feedback structures found in the mammalian clock. PMID:23516349

  19. A combined NLP-differential evolution algorithm approach for the optimization of looped water distribution systems

    NASA Astrophysics Data System (ADS)

    Zheng, Feifei; Simpson, Angus R.; Zecchin, Aaron C.

    2011-08-01

    This paper proposes a novel optimization approach for the least cost design of looped water distribution systems (WDSs). Three distinct steps are involved in the proposed optimization approach. In the first step, the shortest-distance tree within the looped network is identified using the Dijkstra graph theory algorithm, for which an extension is proposed to find the shortest-distance tree for multisource WDSs. In the second step, a nonlinear programming (NLP) solver is employed to optimize the pipe diameters for the shortest-distance tree (chords of the shortest-distance tree are allocated the minimum allowable pipe sizes). Finally, in the third step, the original looped water network is optimized using a differential evolution (DE) algorithm seeded with diameters in the proximity of the continuous pipe sizes obtained in step two. As such, the proposed optimization approach combines the traditional deterministic optimization technique of NLP with the emerging evolutionary algorithm DE via the proposed network decomposition. The proposed methodology has been tested on four looped WDSs with the number of decision variables ranging from 21 to 454. Results obtained show the proposed approach is able to find optimal solutions with significantly less computational effort than other optimization techniques.

  20. Shifting the closed-loop spectrum in the optimal linear quadratic regulator problem for hereditary systems

    NASA Technical Reports Server (NTRS)

    Gibson, J. S.; Rosen, I. G.

    1985-01-01

    In the optimal linear quadratic regulator problem for finite dimensional systems, the method known as an alpha-shift can be used to produce a closed-loop system whose spectrum lies to the left of some specified vertical line; that is, a closed-loop system with a prescribed degree of stability. This paper treats the extension of the alpha-shift to hereditary systems. As infinite dimensions, the shift can be accomplished by adding alpha times the identity to the open-loop semigroup generator and then solving an optimal regulator problem. However, this approach does not work with a new approximation scheme for hereditary control problems recently developed by Kappel and Salamon. Since this scheme is among the best to date for the numerical solution of the linear regulator problem for hereditary systems, an alternative method for shifting the closed-loop spectrum is needed. An alpha-shift technique that can be used with the Kappel-Salamon approximation scheme is developed. Both the continuous-time and discrete-time problems are considered. A numerical example which demonstrates the feasibility of the method is included.

  1. Shifting the closed-loop spectrum in the optimal linear quadratic regulator problem for hereditary systems

    NASA Technical Reports Server (NTRS)

    Gibson, J. S.; Rosen, I. G.

    1987-01-01

    In the optimal linear quadratic regulator problem for finite dimensional systems, the method known as an alpha-shift can be used to produce a closed-loop system whose spectrum lies to the left of some specified vertical line; that is, a closed-loop system with a prescribed degree of stability. This paper treats the extension of the alpha-shift to hereditary systems. As infinite dimensions, the shift can be accomplished by adding alpha times the identity to the open-loop semigroup generator and then solving an optimal regulator problem. However, this approach does not work with a new approximation scheme for hereditary control problems recently developed by Kappel and Salamon. Since this scheme is among the best to date for the numerical solution of the linear regulator problem for hereditary systems, an alternative method for shifting the closed-loop spectrum is needed. An alpha-shift technique that can be used with the Kappel-Salamon approximation scheme is developed. Both the continuous-time and discrete-time problems are considered. A numerical example which demonstrates the feasibility of the method is included.

  2. Depression as a systemic syndrome: mapping the feedback loops of major depressive disorder

    PubMed Central

    Wittenborn, A. K.; Rahmandad, H.; Rick, J.; Hosseinichimeh, N.

    2016-01-01

    Background Depression is a complex public health problem with considerable variation in treatment response. The systemic complexity of depression, or the feedback processes among diverse drivers of the disorder, contribute to the persistence of depression. This paper extends prior attempts to understand the complex causal feedback mechanisms that underlie depression by presenting the first broad boundary causal loop diagram of depression dynamics. Method We applied qualitative system dynamics methods to map the broad feedback mechanisms of depression. We used a structured approach to identify candidate causal mechanisms of depression in the literature. We assessed the strength of empirical support for each mechanism and prioritized those with support from validation studies. Through an iterative process, we synthesized the empirical literature and created a conceptual model of major depressive disorder. Results The literature review and synthesis resulted in the development of the first causal loop diagram of reinforcing feedback processes of depression. It proposes candidate drivers of illness, or inertial factors, and their temporal functioning, as well as the interactions among drivers of depression. The final causal loop diagram defines 13 key reinforcing feedback loops that involve nine candidate drivers of depression. Conclusions Future research is needed to expand upon this initial model of depression dynamics. Quantitative extensions may result in a better understanding of the systemic syndrome of depression and contribute to personalized methods of evaluation, prevention and intervention. PMID:26621339

  3. Testing of a Loop Heat Pipe with Two Evaporators and Two Condensers

    NASA Technical Reports Server (NTRS)

    Ku, Jentung; Birur, Gaj; Powers, Edward I. (Technical Monitor)

    2001-01-01

    Most existing Loop Heat Pipes (LHPs) consist of one single evaporator and one single condenser. LHPs with multiple evaporators will be very desirable for cooling multiple heat sources or a heat source with large thermal footprints. Extending the LHP technology to include multiple evaporators and multiple condensers faces some challenges, including the interaction between individual compensation chambers, operating temperature stability, and adaptability to rapid power and sink temperature transients. This paper describe extensive testing of an LHP with two evaporators and two condensers. Tests performed include start-up, power cycle, sink temperature cycle, reservoir temperature cycle, and capillary limit. Test results showed that the loop could operate successfully under various heat load and sink conditions. The loop operating temperature is a function of the total heat load, the heat load distribution between the two evaporators, and temperatures of the two condenser sinks. Under most conditions, only one reservoir contained two-phase fluid and the other reservoir was completely liquid filled. Moreover, control of the loop operating temperature could shift from one reservoir to the other as the test condition changed.

  4. Coal Combustion Products Extension Program

    SciTech Connect

    Tarunjit S. Butalia; William E. Wolfe

    2006-01-11

    This final project report presents the activities and accomplishments of the ''Coal Combustion Products Extension Program'' conducted at The Ohio State University from August 1, 2000 to June 30, 2005 to advance the beneficial uses of coal combustion products (CCPs) in highway and construction, mine reclamation, agricultural, and manufacturing sectors. The objective of this technology transfer/research program at The Ohio State University was to promote the increased use of Ohio CCPs (fly ash, FGD material, bottom ash, and boiler slag) in applications that are technically sound, environmentally benign, and commercially competitive. The project objective was accomplished by housing the CCP Extension Program within The Ohio State University College of Engineering with support from the university Extension Service and The Ohio State University Research Foundation. Dr. Tarunjit S. Butalia, an internationally reputed CCP expert and registered professional engineer, was the program coordinator. The program coordinator acted as liaison among CCP stakeholders in the state, produced information sheets, provided expertise in the field to those who desired it, sponsored and co-sponsored seminars, meetings, and speaking at these events, and generally worked to promote knowledge about the productive and proper application of CCPs as useful raw materials. The major accomplishments of the program were: (1) Increase in FGD material utilization rate from 8% in 1997 to more than 20% in 2005, and an increase in overall CCP utilization rate of 21% in 1997 to just under 30% in 2005 for the State of Ohio. (2) Recognition as a ''voice of trust'' among Ohio and national CCP stakeholders (particularly regulatory agencies). (3) Establishment of a national and international reputation, especially for the use of FGD materials and fly ash in construction applications. It is recommended that to increase Ohio's CCP utilization rate from 30% in 2005 to 40% by 2010, the CCP Extension Program be

  5. On the extensible viscoelastic beam

    NASA Astrophysics Data System (ADS)

    Giorgi, Claudio; Pata, Vittorino; Vuk, Elena

    2008-04-01

    This work is focused on the equation \\[ \\begin{eqnarray*}\\fl {\\partial_{tt}} u+\\partial_{xxxx}u +\\int_0^\\infty \\mu(s) \\partial_{xxxx}[u(t)-u(t-s)]\\,\\rmd s\\\\ - \\big(\\beta+\\|\\partial_x u\\|_{L^2(0,1)}^2\\big)\\partial_{xx}u= f\\end{eqnarray*} \\] describing the motion of an extensible viscoelastic beam. Under suitable boundary conditions, the related dynamical system in the history space framework is shown to possess a global attractor of optimal regularity. The result is obtained by exploiting an appropriate decomposition of the solution semigroup, together with the existence of a Lyapunov functional.

  6. Chiral Extensions of the Mssm

    NASA Astrophysics Data System (ADS)

    Ferretti, Gabriele; Karateev, Denis

    2013-03-01

    We present a class of extensions of the MSSM characterized by a fully chiral field content (no μ-terms) and no baryon or lepton number violating term in the superpotential due to an extra U‧(1) gauge symmetry. The minimal model consists of the usual matter sector with family dependent U‧(1) charges, six Higgs weak doublets, and three singlets required to give masses to the Higgsinos and cancel anomalies. We discuss its main features such as the tree level mass spectrum and the constraints on flavor changing processes.

  7. Rhinomaxillary mucormycosis with cerebral extension

    PubMed Central

    Goel, Shikha; Palaskar, Sangeeta; Shetty, Vishwa Parkash; Bhushan, Anju

    2009-01-01

    Mucormycosis is a rare opportunistic infection caused by fungus belonging to the order Mucorales. A case of a controlled diabetic male with rhino maxillary mucormycosis, with cerebral extension, is described. The patient presented with hemifacial swelling, a nasal twang in his voice, fever, ocular signs, gross tissue destruction, and was sluggish. Early recognition of mucormycosis is necessary to limit the spread of infection, which can lead to high morbidity and mortality. Therefore, health practitioners should be familiar with the signs and symptoms of the disease. PMID:21886991

  8. Polyakov loop and correlator of Polyakov loops at next-to-next-to-leading order

    SciTech Connect

    Brambilla, Nora; Vairo, Antonio; Ghiglieri, Jacopo; Petreczky, Peter

    2010-10-01

    We study the Polyakov loop and the correlator of two Polyakov loops at finite temperature in the weak-coupling regime. We calculate the Polyakov loop at order g{sup 4}. The calculation of the correlator of two Polyakov loops is performed at distances shorter than the inverse of the temperature and for electric screening masses larger than the Coulomb potential. In this regime, it is accurate up to order g{sup 6}. We also evaluate the Polyakov-loop correlator in an effective field theory framework that takes advantage of the hierarchy of energy scales in the problem and makes explicit the bound-state dynamics. In the effective field theory framework, we show that the Polyakov-loop correlator is at leading order in the multipole expansion the sum of a color-singlet and a color-octet quark-antiquark correlator, which are gauge invariant, and compute the corresponding color-singlet and color-octet free energies.

  9. Application of loop analysis for evaluation of malaria control interventions

    PubMed Central

    2014-01-01

    Background Despite continuous efforts and recent rapid expansion in the financing and implementation of malaria control interventions, malaria still remains one of the most devastating global health issues. Even in countries that have been successful in reducing the incidence of malaria, malaria control is becoming more challenging because of the changing epidemiology of malaria and waning community participation in control interventions. In order to improve the effectiveness of interventions and to promote community understanding of the necessity of continued control efforts, there is an urgent need to develop new methodologies that examine the mechanisms by which community-based malaria interventions could reduce local malaria incidence. Methods This study demonstrated how the impact of community-based malaria control interventions on malaria incidence can be examined in complex systems by qualitative analysis combined with an extensive review of literature. First, sign digraphs were developed through loop analysis to analyse seven interventions: source reduction, insecticide/larvicide use, biological control, treatment with anti-malarials, insecticide-treated mosquito net/long-lasting insecticidal net, non-chemical personal protection measures, and educational intervention. Then, for each intervention, the sign digraphs and literature review were combined to analyse a variety of pathways through which the intervention can influence local malaria incidence as well as interactions between variables involved in the system. Through loop analysis it is possible to see whether increases in one variable qualitatively increases or decreases other variables or leaves them unchanged and the net effect of multiple, interacting variables. Results Qualitative analysis, specifically loop analysis, can be a useful tool to examine the impact of community-based malaria control interventions. Without relying on numerical data, the analysis was able to describe pathways through

  10. Extensions to PIFCGT: Multirate output feedback and optimal disturbance suppression

    NASA Technical Reports Server (NTRS)

    Broussard, J. R.

    1986-01-01

    New control synthesis procedures for digital flight control systems were developed. The theoretical developments are the solution to the problem of optimal disturbance suppression in the presence of windshear. Control synthesis is accomplished using a linear quadratic cost function, the command generator tracker for trajectory following and the proportional-integral-filter control structure for practical implementation. Extensions are made to the optimal output feedback algorithm for computing feedback gains so that the multirate and optimal disturbance control designs are computed and compared for the advanced transport operating system (ATOPS). The performance of the designs is demonstrated by closed-loop poles, frequency domain multiinput sigma and eigenvalue plots and detailed nonlinear 6-DOF aircraft simulations in the terminal area in the presence of windshear.

  11. Convexity at finite temperature and non-extensive thermodynamics

    NASA Astrophysics Data System (ADS)

    Alexandre, J.

    2016-09-01

    Assuming that tunnel effect between two degenerate bare minima occurs, in a scalar field theory at finite volume, this article studies the consequences for the effective potential, to all loop orders. Convexity is achieved only if the two bare minima are taken into account in the path integral, and a new derivation of the effective potential is given, in the large volume limit. The effective potential then has a universal form, it is suppressed by the space time volume, and does not feature spontaneous symmetry breaking as long as the volume is finite. The finite temperature analysis leads to surprising thermal properties, following from the non-extensive expression for the free energy. Although the physical relevance of these results is not clear, the potential application to ultra-light scalar particles is discussed.

  12. Parametric Multi-Level Tiling of Imperfectly Nested Loops

    SciTech Connect

    Hartono, Albert; Baskaran, Muthu M.; Bastoul, Cedric; Cohen, Albert; Krishnamoorthy, Sriram; Norris, Boyana; Ramanujam, J.; Sadayappan, Ponnuswamy

    2009-05-18

    Tiling is a critical loop transformation for generating high-performance code on modern architectures. Efficient generation of multilevel tiled code is essential to exploit several levels of parallelism and/or to maximize data reuse in deep memory hierarchies. Tiled loops with parameterized tile sizes (not compile time constants) facilitate runtime feedback and dynamic optimizations used in iterative compilation and automatic tuning. The existing parametric multilevel tiling approach has focused on transformation for perfectly nested loops, where all assignment statements are contained inside the innermost loop of a loop nest. Previous solutions to tiling for imperfect loop nests are limited to the case where tile sizes are fixed. In this paper, we present an approach to parameterized multilevel tiling for imperfectly nested loops. Our tiling algorithm generates loops that iterate over full rectangular tiles that are amenable for potential compiler optimizations such as register tiling. Experimental results using a number of computational benchmarks demonstrate the effectiveness of our tiling approach.

  13. The Seasonality Of The Loop Current

    NASA Astrophysics Data System (ADS)

    Hall, Cody Alan

    A total of 20 Loop Current eddy separation event dates were derived from Seasat and ERS-1 satellite altimetry, Coastal Zone Color Scanner chlorophyll-a images, Advanced Very High Resolution Radiometer sea surface temperature images, Horizon Marine, Inc. EddyWatch(TM) reports, and Climatology and Simulation of Eddies Eddy Joint Industry Project Gulf Eddy Model analyses spanning mid-1978 - 1992. There were many inconsistencies between the new "pre-altimetry" reanalysis dates derived from mostly non-altimeter data and dates published in past literature based on earlier versions of the pre-altimetry record. The reanalysis dates were derived from a larger compilation of data types and, consequently, were not as affected by intermittent and seasonal data outages common with past records. Therefore, the reanalysis dates are likely more accurate. About 30 Loop Current eddy separation dates were derived from altimetry data spanning 1993 -- 2012. The pre-altimetry and altimetry reanalysis dates along with similar altimetry dates published in other literature exhibit statistically significant seasonality. Eddy separation events are more likely in the months March, August, and September, and less likely in December. Reanalysis event dates were objectively divided into "spring" and "fall" seasons using a k-means clustering algorithm. The estimated spring and fall season centers are March 2nd and August 23 rd, respectively, with seasonal boundaries on May 22nd and December 3rd. The altimetry data suggest that Loop Current intrusion/retreat is dominantly an annual process. Loop Current metrics such as maximum northern boundary latitude and area are relatively high from January through about July and low in September and October. February metrics are statistically different than metrics in either October or November or both. This annual process is primarily driven by and dynamically linked to geostrophic currents seaward of the Campeche Bank shelf break forced by Kelvin waves

  14. On Harnack's theorem and extensions

    NASA Astrophysics Data System (ADS)

    Costa, Antonio F.; Parlier, Hugo

    Harnack's theorem states that the fixed points of an orientation reversing involution of a compact orientable surface of genus g are a set of k disjoint simple closed geodesic where 0≤ k≤ g+1 . The first goal of this article is to give a purely geometric, complete and self-contained proof of this fact. In the case where the fixed curves of the involution do not separate the surface, we prove an extension of this theorem, by exhibiting the existence of auxiliary invariant curves with interesting properties. Although this type of extension is well known (see, for instance, Comment. Math. Helv. 57(4): 603-626 (1982) and Transl. Math. Monogr., vol. 225, Amer. Math. Soc., Providence, RI, 2004), our method also extends the theorem in the case where the surface has boundary. As a byproduct, we obtain a geometric method on how to obtain these auxiliary curves. As a consequence of these constructions, we obtain results concerning presentations of Non-Euclidean crystallographic groups and a new proof of a result on the set of points corresponding to real algebraic curves in the compactification of the Moduli space of complex curves of genus g , overline{M_{g}} . More concretely, we establish that given two real curves there is a path in overline{M_{g}} which passes through at most two singular curves, a result of M. Seppaelae (Ann. Sci. Ecole Norm. Sup. (4), 24(5), 519-544 (1991)).

  15. The C-terminal loop of aldehyde reductase determines the substrate and inhibitor specificity.

    PubMed

    Barski, O A; Gabbay, K H; Bohren, K M

    1996-11-12

    Human aldehyde reductase has a preference for carboxyl group-containing negatively charged substrates. It belongs to the NADPH-dependent aldo-keto reductase superfamily whose members are in part distinguished by unique C-terminal loops. To probe the role of the C-terminal loops in determining substrate specificities in these enzymes, two arginine residues, Arg308 and Arg311, located in the C-terminal loop of aldehyde reductase, and not found in any other C-terminal loop, were replaced with alanine residues. The catalytic efficiency of the R311A mutant for aldehydes containing a carboxyl group is reduced 150-250-fold in comparison to that of the wild-type enzyme, while substrates not containing a negative charge are unaffected. The R311A mutant is also significantly less sensitive to inhibition by dicarboxylic acids, indicating that Arg311 interacts with one of the carboxyl groups. The inhibition pattern indicates that the other carboxyl group binds to the anion binding site formed by Tyr49, His112, and the nicotinamide moiety of NADP+. The correlation between inhibitor potency and the length of the dicarboxylic acid molecules suggests a distance of approximately 10 A between the amino group of Arg311 and the anion binding site in the aldehyde reductase molecule. The sensitivity of inhibition of the R311A mutant by several commercially available aldose reductase inhibitors (ARIs) was variable, with tolrestat and zopolrestat becoming more potent inhibitors (30- and 5-fold, respectively), while others remained the same or became less potent. The catalytic properties, substrate specificity, and susceptibility to inhibition of the R308A mutant remained similar to that of the wild-type enzyme. The data provide direct evidence for C-terminal loop participation in determining substrate and inhibitor specificity of aldo-keto reductases and specifically identifies Arg311 as the basis for the carboxyl-containing substrate preference of aldehyde reductase. PMID:8916913

  16. Typing and surface charges of the variable loop regions of PorB from Neisseria meningitidis.

    PubMed

    Stefanelli, Paola; Neri, Arianna; Tanabe, Mikio; Fazio, Cecilia; Massari, Paola

    2016-06-01

    PorB is a pan-Neisserial major outer membrane protein with a trimeric β-barrel structure. Each monomer presents eight periplasmic turns and eight surface exposed loop regions with sequence variability. PorB induces activation of host cell responses via a TLR2-dependent mechanism likely mediated by electrostatic interactions between TLR2 and PorB surface exposed loops. Variability in the loop amino acid sequence is known to influence cell responses to PorB in vitro, particularly for the residues in L5 and L7. In this work, the sequence of the porB gene and the electrostatic surface charges of PorB from 35 invasive meningococcal isolates belonging to the main clonal complexes identified in Italy and from five carriage genomes available on the website http://pubmlst.org/neisseria/ were examined. Analysis of the porB encoding regions from the invasive meningococci has identified four new alleles and a potential association between porB alleles, serogroup, and clonal complexes. Through computer-based modeling and analysis of the electrostatic surface charges of PorB from these strains, loop charge segregation between PorB from invasive serogroups B and C was observed. Specifically, loops 1, 4, and 7 were negatively charged and L2 and L8 were mostly neutral in serogroup B isolates, while an overall homogeneous positive surface charge was present in PorB from invasive serogroup C strains. A higher PorB sequence variability was observed among carriage genomes, and a general prevalence of negative loop surface charges. The surface charge differences in PorB from serogroups B and C invasive and carriage strains may, in part, influence the outcomes of Neisseriae interactions with host cells. © 2016 IUBMB Life, 68(6):488-495, 2016. PMID:27156582

  17. Loop A is critical for the functional interaction of two Beta vulgaris PIP aquaporins.

    PubMed

    Jozefkowicz, Cintia; Rosi, Pablo; Sigaut, Lorena; Soto, Gabriela; Pietrasanta, Lía Isabel; Amodeo, Gabriela; Alleva, Karina

    2013-01-01

    Research done in the last years strongly support the hypothesis that PIP aquaporin can form heterooligomeric assemblies, specially combining PIP2 monomers with PIP1 monomers. Nevertheless, the structural elements involved in the ruling of homo versus heterooligomeric organization are not completely elucidated. In this work we unveil some features of monomer-monomer interaction in Beta vulgaris PIP aquaporins. Our results show that while BvPIP2;2 is able to interact with BvPIP1;1, BvPIP2;1 shows no functional interaction. The lack of functional interaction between BvPIP2;1 and BvPIP1;1 was further corroborated by dose-response curves of water permeability due to aquaporin activity exposed to different acidic conditions. We also found that BvPIP2;1 is unable to translocate BvPIP1;1-ECFP from an intracellular position to the plasma membrane when co-expressed, as BvPIP2;2 does. Moreover we postulate that the first extracellular loop (loop A) of BvPIP2;1, could be relevant for the functional interaction with BvPIP1;1. Thus, we investigate BvPIP2;1 loop A at an atomic level by Molecular Dynamics Simulation (MDS) and by direct mutagenesis. We found that, within the tetramer, each loop A presents a dissimilar behavior. Besides, BvPIP2;1 loop A mutants restore functional interaction with BvPIP1;1. This work is a contribution to unravel how PIP2 and PIP1 interact to form functional heterooligomeric assemblies. We postulate that BvPIP2;1 loop A is relevant for the lack of functional interaction with BvPIP1;1 and that the monomer composition of PIP assemblies determines their functional properties. PMID:23483963

  18. Loop A Is Critical for the Functional Interaction of Two Beta vulgaris PIP Aquaporins

    PubMed Central

    Jozefkowicz, Cintia; Rosi, Pablo; Sigaut, Lorena; Soto, Gabriela; Pietrasanta, Lía Isabel; Amodeo, Gabriela; Alleva, Karina

    2013-01-01

    Research done in the last years strongly support the hypothesis that PIP aquaporin can form heterooligomeric assemblies, specially combining PIP2 monomers with PIP1 monomers. Nevertheless, the structural elements involved in the ruling of homo versus heterooligomeric organization are not completely elucidated. In this work we unveil some features of monomer-monomer interaction in Beta vulgaris PIP aquaporins. Our results show that while BvPIP2;2 is able to interact with BvPIP1;1, BvPIP2;1 shows no functional interaction. The lack of functional interaction between BvPIP2;1 and BvPIP1;1 was further corroborated by dose-response curves of water permeability due to aquaporin activity exposed to different acidic conditions. We also found that BvPIP2;1 is unable to translocate BvPIP1;1-ECFP from an intracellular position to the plasma membrane when co-expressed, as BvPIP2;2 does. Moreover we postulate that the first extracellular loop (loop A) of BvPIP2;1, could be relevant for the functional interaction with BvPIP1;1. Thus, we investigate BvPIP2;1 loop A at an atomic level by Molecular Dynamics Simulation (MDS) and by direct mutagenesis. We found that, within the tetramer, each loop A presents a dissimilar behavior. Besides, BvPIP2;1 loop A mutants restore functional interaction with BvPIP1;1. This work is a contribution to unravel how PIP2 and PIP1 interact to form functional heterooligomeric assemblies. We postulate that BvPIP2;1 loop A is relevant for the lack of functional interaction with BvPIP1;1 and that the monomer composition of PIP assemblies determines their functional properties. PMID:23483963

  19. Digital simulation of hybrid loop operation in RFI backgrounds.

    NASA Technical Reports Server (NTRS)

    Ziemer, R. E.; Nelson, D. R.

    1972-01-01

    A digital computer model for Monte-Carlo simulation of an imperfect second-order hybrid phase-locked loop (PLL) operating in radio-frequency interference (RFI) and Gaussian noise backgrounds has been developed. Characterization of hybrid loop performance in terms of cycle slipping statistics and phase error variance, through computer simulation, indicates that the hybrid loop has desirable performance characteristics in RFI backgrounds over the conventional PLL or the costas loop.

  20. An estimator-predictor approach to PLL loop filter design

    NASA Technical Reports Server (NTRS)

    Statman, Joseph I.; Hurd, William J.

    1990-01-01

    The design of digital phase locked loops (DPLL) using estimation theory concepts in the selection of a loop filter is presented. The key concept, that the DPLL closed-loop transfer function is decomposed into an estimator and a predictor, is discussed. The estimator provides recursive estimates of phase, frequency, and higher-order derivatives, and the predictor compensates for the transport lag inherent in the loop.