WorldWideScience

Sample records for partially unfolded states

  1. [Partially unfolded state of lysozyme with a developed secondary structure in dimethylsulfoxide].

    Science.gov (United States)

    Timchenko, A A; Kirkitadze, M D; Prokhorov, D A; Potekhin, S A; Serdiuk, I N

    1996-06-01

    The conformation of a chicken egg lysozyme molecule (dimensions, stoichiometry of its associates, and the degree of helicity) in DMSO was studied by small-angle neutron scattering, dynamic light scattering, and optical rotatory dispersion in the visible region of the spectrum. At high DMSO concentrations (70%), the protein was shown to exist as a dimer. The monomer molecules in the dimer adopt a partially unfolded conformation, with dimensions substantially greater than those in the native state and a high content of secondary structure (the degree of helicity is close to that of native lysozyme). This approach provides a unique possibility to assess the compactness of molecules in associates, which may be very useful in studying protein self-organization.

  2. Unfolding Simulations of Holomyoglobin from Four Mammals: Identification of Intermediates and β-Sheet Formation from Partially Unfolded States

    DEFF Research Database (Denmark)

    Dasmeh, Pouria; Kepp, Kasper Planeta

    2013-01-01

    simulations of holoMb and the first comparative study of unfolding of protein orthologs from different species (sperm whale, pig, horse, and harbor seal). We also provide new interpretations of experimental mean molecular ellipticities of myoglobin intermediates, notably correcting for random coil and number...... of helices in intermediates. The simulated holoproteins at 310 K displayed structures and dynamics in agreement with crystal structures (Rg ,1.48–1.51 nm, helicity ,75%). At 400 K, heme was not lost, but some helix loss was observed in pig and horse, suggesting that these helices are less stable......Myoglobin (Mb) is a centrally important, widely studied mammalian protein. While much work has investigated multi-step unfolding of apoMb using acid or denaturant, holomyoglobin unfolding is poorly understood despite its biological relevance. We present here the first systematic unfolding...

  3. Salt bridge as a gatekeeper against partial unfolding.

    Science.gov (United States)

    Hinzman, Mark W; Essex, Morgan E; Park, Chiwook

    2016-05-01

    Salt bridges are frequently observed in protein structures. Because the energetic contribution of salt bridges is strongly dependent on the environmental context, salt bridges are believed to contribute to the structural specificity rather than the stability. To test the role of salt bridges in enhancing structural specificity, we investigated the contribution of a salt bridge to the energetics of native-state partial unfolding in a cysteine-free version of Escherichia coli ribonuclease H (RNase H*). Thermolysin cleaves a protruding loop of RNase H(*) through transient partial unfolding under native conditions. Lys86 and Asp108 in RNase H(*) form a partially buried salt bridge that tethers the protruding loop. Investigation of the global stability of K86Q/D108N RNase H(*) showed that the salt bridge does not significantly contribute to the global stability. However, K86Q/D108N RNase H(*) is greatly more susceptible to proteolysis by thermolysin than wild-type RNase H(*) is. The free energy for partial unfolding determined by native-state proteolysis indicates that the salt bridge significantly increases the energy for partial unfolding by destabilizing the partially unfolded form. Double mutant cycles with single and double mutations of the salt bridge suggest that the partially unfolded form is destabilized due to a significant decrease in the interaction energy between Lys86 and Asp108 upon partial unfolding. This study demonstrates that, even in the case that a salt bridge does not contribute to the global stability, the salt bridge may function as a gatekeeper against partial unfolding that disturbs the optimal geometry of the salt bridge. © 2016 The Protein Society.

  4. The unfolding effects on the protein hydration shell and partial molar volume: a computational study.

    Science.gov (United States)

    Del Galdo, Sara; Amadei, Andrea

    2016-10-12

    In this paper we apply the computational analysis recently proposed by our group to characterize the solvation properties of a native protein in aqueous solution, and to four model aqueous solutions of globular proteins in their unfolded states thus characterizing the protein unfolded state hydration shell and quantitatively evaluating the protein unfolded state partial molar volumes. Moreover, by using both the native and unfolded protein partial molar volumes, we obtain the corresponding variations (unfolding partial molar volumes) to be compared with the available experimental estimates. We also reconstruct the temperature and pressure dependence of the unfolding partial molar volume of Myoglobin dissecting the structural and hydration effects involved in the process.

  5. Detection and characterization of partially unfolded oligomers of the SH3 domain of α-Spectrin

    NARCIS (Netherlands)

    Casares, S.; Sadqi, M.; López-Mayorga, O.; Conejero-Lara, F.; van Nuland, N.A.J.

    2004-01-01

    For the purpose of equilibrium and kinetic folding-unfolding studies, the SH3 domain of α-spectrin (spc-SH3) has long been considered a classic two-state folding protein. In this work we have indeed observed that the thermal unfolding curves of spc-SH3 measured at pH 3.0 by differential scanning

  6. Branches of Triangulated Origami Near the Unfolded State

    Directory of Open Access Journals (Sweden)

    Bryan Gin-ge Chen

    2018-02-01

    Full Text Available Origami structures are characterized by a network of folds and vertices joining unbendable plates. For applications to mechanical design and self-folding structures, it is essential to understand the interplay between the set of folds in the unfolded origami and the possible 3D folded configurations. When deforming a structure that has been folded, one can often linearize the geometric constraints, but the degeneracy of the unfolded state makes a linear approach impossible there. We derive a theory for the second-order infinitesimal rigidity of an initially unfolded triangulated origami structure and use it to study the set of nearly unfolded configurations of origami with four boundary vertices. We find that locally, this set consists of a number of distinct “branches” which intersect at the unfolded state, and that the number of these branches is exponential in the number of vertices. We find numerical and analytical evidence that suggests that the branches are characterized by choosing each internal vertex to either “pop up” or “pop down.” The large number of pathways along which one can fold an initially unfolded origami structure strongly indicates that a generic structure is likely to become trapped in a “misfolded” state. Thus, new techniques for creating self-folding origami are likely necessary; controlling the popping state of the vertices may be one possibility.

  7. Branches of Triangulated Origami Near the Unfolded State

    Science.gov (United States)

    Chen, Bryan Gin-ge; Santangelo, Christian D.

    2018-01-01

    Origami structures are characterized by a network of folds and vertices joining unbendable plates. For applications to mechanical design and self-folding structures, it is essential to understand the interplay between the set of folds in the unfolded origami and the possible 3D folded configurations. When deforming a structure that has been folded, one can often linearize the geometric constraints, but the degeneracy of the unfolded state makes a linear approach impossible there. We derive a theory for the second-order infinitesimal rigidity of an initially unfolded triangulated origami structure and use it to study the set of nearly unfolded configurations of origami with four boundary vertices. We find that locally, this set consists of a number of distinct "branches" which intersect at the unfolded state, and that the number of these branches is exponential in the number of vertices. We find numerical and analytical evidence that suggests that the branches are characterized by choosing each internal vertex to either "pop up" or "pop down." The large number of pathways along which one can fold an initially unfolded origami structure strongly indicates that a generic structure is likely to become trapped in a "misfolded" state. Thus, new techniques for creating self-folding origami are likely necessary; controlling the popping state of the vertices may be one possibility.

  8. A highly compliant protein native state with a spontaneous-like mechanical unfolding pathway

    DEFF Research Database (Denmark)

    Heiðarsson, Pétur Orri; Valpapuram, Immanuel; Camilloni, Carlo

    2012-01-01

    The mechanical properties of proteins and their force-induced structural changes play key roles in many biological processes. Previous studies have shown that natively folded proteins are brittle under tension, unfolding after small mechanical deformations, while partially folded intermediate...... states, such as molten globules, are compliant and can deform elastically a great amount before crossing the transition state barrier. Moreover, under tension proteins appear to unfold through a different sequence of events than during spontaneous unfolding. Here, we describe the response to force...... of the four-α-helix acyl-CoA binding protein (ACBP) in the low-force regime using optical tweezers and ratcheted molecular dynamics simulations. The results of our studies reveal an unprecedented mechanical behavior of a natively folded protein. ACBP displays an atypical compliance along two nearly orthogonal...

  9. Mechanism of Protein Denaturation: Partial Unfolding of the P22 Coat Protein I-Domain by Urea Binding

    Science.gov (United States)

    Newcomer, Rebecca L.; Fraser, LaTasha C.R.; Teschke, Carolyn M.; Alexandrescu, Andrei T.

    2015-01-01

    The I-domain is an insertion domain of the bacteriophage P22 coat protein that drives rapid folding and accounts for over half of the stability of the full-length protein. We sought to determine the role of hydrogen bonds (H-bonds) in the unfolding of the I-domain by examining 3JNC’ couplings transmitted through H-bonds, the temperature and urea-concentration dependence of 1HN and 15N chemical shifts, and native-state hydrogen exchange at urea concentrations where the domain is predominantly folded. The native-state hydrogen-exchange data suggest that the six-stranded β-barrel core of the I-domain is more stable against unfolding than a smaller subdomain comprised of a short α-helix and three-stranded β-sheet. H-bonds, separately determined from solvent protection and 3JNC’ H-bond couplings, are identified with an accuracy of 90% by 1HN temperature coefficients. The accuracy is improved to 95% when 15N temperature coefficients are also included. In contrast, the urea dependence of 1HN and 15N chemical shifts is unrelated to H-bonding. The protein segments with the largest chemical-shift changes in the presence of urea show curved or sigmoidal titration curves suggestive of direct urea binding. Nuclear Overhauser effects to urea for these segments are also consistent with specific urea-binding sites in the I-domain. Taken together, the results support a mechanism of urea unfolding in which denaturant binds to distinct sites in the I-domain. Disordered segments bind urea more readily than regions in stable secondary structure. The locations of the putative urea-binding sites correlate with the lower stability of the structure against solvent exchange, suggesting that partial unfolding of the structure is related to urea accessibility. PMID:26682823

  10. Guanidinium chloride induction of partial unfolding in amide proton exchange in RNase A.

    Science.gov (United States)

    Mayo, S L; Baldwin, R L

    1993-11-05

    Amide (NH) proton exchange rates were measured in 0.0 to 0.7 M guanidinium chloride (GdmCl) for 23 slowly exchanging peptide NH protons of ribonuclease A (RNase A) at pH* 5.5 (uncorrected pH measured in D2O), 34 degrees C. The purpose was to find out whether GdmCl induces exchange through binding to exchange intermediates that are partly or wholly unfolded. It was predicted that, when the logarithm of the exchange rate is plotted as a function of the molarity of GdmCl, the slope should be a measure of the amount of buried surface area exposed to GdmCl in the exchange intermediate. The results indicate that these concentrations of GdmCl do induce exchange by means of a partial unfolding mechanism for all 23 protons; this implies that exchange reactions can be used to study the unfolding and stability of local regions. Of the 23 protons, nine also show a second mechanism of exchange at lower concentrations of GdmCl, a mechanism that is nearly independent of GdmCl concentration and is termed "limited structural fluctuation."

  11. Antibody-Unfolding and Metastable-State Binding in Force Spectroscopy and Recognition Imaging

    Science.gov (United States)

    Kaur, Parminder; Qiang-Fu; Fuhrmann, Alexander; Ros, Robert; Kutner, Linda Obenauer; Schneeweis, Lumelle A.; Navoa, Ryman; Steger, Kirby; Xie, Lei; Yonan, Christopher; Abraham, Ralph; Grace, Michael J.; Lindsay, Stuart

    2011-01-01

    Force spectroscopy and recognition imaging are important techniques for characterizing and mapping molecular interactions. In both cases, an antibody is pulled away from its target in times that are much less than the normal residence time of the antibody on its target. The distribution of pulling lengths in force spectroscopy shows the development of additional peaks at high loading rates, indicating that part of the antibody frequently unfolds. This propensity to unfold is reversible, indicating that exposure to high loading rates induces a structural transition to a metastable state. Weakened interactions of the antibody in this metastable state could account for reduced specificity in recognition imaging where the loading rates are always high. The much weaker interaction between the partially unfolded antibody and target, while still specific (as shown by control experiments), results in unbinding on millisecond timescales, giving rise to rapid switching noise in the recognition images. At the lower loading rates used in force spectroscopy, we still find discrepancies between the binding kinetics determined by force spectroscopy and those determined by surface plasmon resonance—possibly a consequence of the short tethers used in recognition imaging. Recognition imaging is nonetheless a powerful tool for interpreting complex atomic force microscopy images, so long as specificity is calibrated in situ, and not inferred from equilibrium binding kinetics. PMID:21190677

  12. Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding

    Science.gov (United States)

    Nagpal, Suhani; Tiwari, Satyam; Mapa, Koyeli; Thukral, Lipi

    2015-01-01

    Many proteins comprising of complex topologies require molecular chaperones to achieve their unique three-dimensional folded structure. The E.coli chaperone, GroEL binds with a large number of unfolded and partially folded proteins, to facilitate proper folding and prevent misfolding and aggregation. Although the major structural components of GroEL are well defined, scaffolds of the non-native substrates that determine chaperone-mediated folding have been difficult to recognize. Here we performed all-atomistic and replica-exchange molecular dynamics simulations to dissect non-native ensemble of an obligate GroEL folder, DapA. Thermodynamics analyses of unfolding simulations revealed populated intermediates with distinct structural characteristics. We found that surface exposed hydrophobic patches are significantly increased, primarily contributed from native and non-native β-sheet elements. We validate the structural properties of these conformers using experimental data, including circular dichroism (CD), 1-anilinonaphthalene-8-sulfonic acid (ANS) binding measurements and previously reported hydrogen-deutrium exchange coupled to mass spectrometry (HDX-MS). Further, we constructed network graphs to elucidate long-range intra-protein connectivity of native and intermediate topologies, demonstrating regions that serve as central “hubs”. Overall, our results implicate that genomic variations (or mutations) in the distinct regions of protein structures might disrupt these topological signatures disabling chaperone-mediated folding, leading to formation of aggregates. PMID:26394388

  13. Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding.

    Science.gov (United States)

    Nagpal, Suhani; Tiwari, Satyam; Mapa, Koyeli; Thukral, Lipi

    2015-01-01

    Many proteins comprising of complex topologies require molecular chaperones to achieve their unique three-dimensional folded structure. The E.coli chaperone, GroEL binds with a large number of unfolded and partially folded proteins, to facilitate proper folding and prevent misfolding and aggregation. Although the major structural components of GroEL are well defined, scaffolds of the non-native substrates that determine chaperone-mediated folding have been difficult to recognize. Here we performed all-atomistic and replica-exchange molecular dynamics simulations to dissect non-native ensemble of an obligate GroEL folder, DapA. Thermodynamics analyses of unfolding simulations revealed populated intermediates with distinct structural characteristics. We found that surface exposed hydrophobic patches are significantly increased, primarily contributed from native and non-native β-sheet elements. We validate the structural properties of these conformers using experimental data, including circular dichroism (CD), 1-anilinonaphthalene-8-sulfonic acid (ANS) binding measurements and previously reported hydrogen-deutrium exchange coupled to mass spectrometry (HDX-MS). Further, we constructed network graphs to elucidate long-range intra-protein connectivity of native and intermediate topologies, demonstrating regions that serve as central "hubs". Overall, our results implicate that genomic variations (or mutations) in the distinct regions of protein structures might disrupt these topological signatures disabling chaperone-mediated folding, leading to formation of aggregates.

  14. Mapping of unfolding states of integral helical membrane proteins by GPS-NMR and scattering techniques

    DEFF Research Database (Denmark)

    Calcutta, Antonello; Jessen, Christian M; Behrens, Manja Annette

    2012-01-01

    induced by unfolding of an integral membrane protein, namely TFE-induced unfolding of KcsA solubilized by the n-dodecyl ß-d-maltoside (DDM) surfactant is investigated by the recently introduced GPS-NMR (Global Protein folding State mapping by multivariate NMR) (Malmendal et al., PlosONE 5, e10262 (2010......)) along with dynamic light scattering (DLS) and small-angle X-ray scattering (SAXS). GPS-NMR is used as a tool for fast analysis of the protein unfolding processes upon external perturbation, and DLS and SAXS are used for further structural characterization of the unfolding states. The combination allows...

  15. Non-leftmost Unfolding in Partial Evaluation of Logic Programs with Impure Predicates

    DEFF Research Database (Denmark)

    Albert, Elvira; Puebla, German; Gallagher, John Patrick

    2006-01-01

    -leftmost unfolding steps can result in incorrect results since the independence of the computation rule no longer holds in the presence of impure predicates. Existing proposals allow non-leftmost unfolding steps, but at the cost of accuracy: bindings and failure are not propagated backwards to predicates which...

  16. Application of long-range order to predict unfolding rates of two-state proteins.

    Science.gov (United States)

    Harihar, B; Selvaraj, S

    2011-03-01

    Predicting the experimental unfolding rates of two-state proteins and models describing the unfolding rates of these proteins is quite limited because of the complexity present in the unfolding mechanism and the lack of experimental unfolding data compared with folding data. In this work, 25 two-state proteins characterized by Maxwell et al. (Protein Sci 2005;14:602–616) using a consensus set of experimental conditions were taken, and the parameter long-range order (LRO) derived from their three-dimensional structures were related with their experimental unfolding rates ln(k(u)). From the total data set of 30 proteins used by Maxwell et al. (Protein Sci 2005;14:602–616), five slow-unfolding proteins with very low unfolding rates were considered to be outliers and were not included in our data set. Except all beta structural class, LRO of both the all-alpha and mixed-class proteins showed a strong inverse correlation of r = -0.99 and -0.88, respectively, with experimental ln(k(u)). LRO shows a correlation of -0.62 with experimental ln(k(u)) for all-beta proteins. For predicting the unfolding rates, a simple statistical method has been used and linear regression equations were developed for individual structural classes of proteins using LRO, and the results obtained showed a better agreement with experimental results. Copyright © 2010 Wiley-Liss, Inc.

  17. Highly Perturbed pKa Values in the Unfolded State of Hen Egg White Lysozyme

    OpenAIRE

    Bradley, John; O'Meara, Fergal; Farrell, Damien; Nielsen, Jens Erik

    2012-01-01

    The majority of pKa values in protein unfolded states are close to the amino acid model pKa values, thus reflecting the weak intramolecular interactions present in the unfolded ensemble of most proteins. We have carried out thermal denaturation measurements on the WT and eight mutants of HEWL from pH 1.5 to pH 11.0 to examine the unfolded state pKa values and the pH dependence of protein stability for this enzyme. The availability of accurate pKa values for the folded state of HEWL and separa...

  18. Conformational dynamics of a protein in the folded and the unfolded state

    Energy Technology Data Exchange (ETDEWEB)

    Fitter, Joerg

    2003-08-01

    In a quasielastic neutron scattering experiment, the picosecond dynamics of {alpha}-amylase was investigated for the folded and the unfolded state of the protein. In order to ensure a reasonable interpretation of the internal protein dynamics, the protein was measured in D{sub 2}O-buffer solution. The much higher structural flexibility of the pH induced unfolded state as compared to the native folded state was quantified using a simple analytical model, describing a local diffusion inside a sphere. In terms of this model the conformational volume, which is explored mainly by confined protein side-chain movements, is parameterized by the radius of a sphere (folded state, r=1.2 A; unfolded state, 1.8 A). Differences in conformational dynamics between the folded and the unfolded state of a protein are of fundamental interest in the field of protein science, because they are assumed to play an important role for the thermodynamics of folding/unfolding transition and for protein stability.

  19. Unfolding mechanism of thrombin-binding aptamer revealed by molecular dynamics simulation and Markov State Model.

    Science.gov (United States)

    Zeng, Xiaojun; Zhang, Liyun; Xiao, Xiuchan; Jiang, Yuanyuan; Guo, Yanzhi; Yu, Xinyan; Pu, Xuemei; Li, Menglong

    2016-04-05

    Thrombin-binding aptamer (TBA) with the sequence 5'GGTTGGTGTGGTTGG3' could fold into G-quadruplex, which correlates with functionally important genomic regionsis. However, unfolding mechanism involved in the structural stability of G-quadruplex has not been satisfactorily elucidated on experiments so far. Herein, we studied the unfolding pathway of TBA by a combination of molecular dynamics simulation (MD) and Markov State Model (MSM). Our results revealed that the unfolding of TBA is not a simple two-state process but proceeds along multiple pathways with multistate intermediates. One high flux confirms some observations from NMR experiment. Another high flux exhibits a different and simpler unfolding pathway with less intermediates. Two important intermediate states were identified. One is similar to the G-triplex reported in the folding of G-quadruplex, but lack of H-bonding between guanines in the upper plane. More importantly, another intermediate state acting as a connector to link the folding region and the unfolding one, was the first time identified, which exhibits higher population and stability than the G-triplex-like intermediate. These results will provide valuable information for extending our understanding the folding landscape of G-quadruplex formation.

  20. Reversibility and two state behaviour in the thermal unfolding of oligomeric TIM barrel proteins.

    Science.gov (United States)

    Romero-Romero, Sergio; Costas, Miguel; Rodríguez-Romero, Adela; Alejandro Fernández-Velasco, D

    2015-08-28

    Temperature is one of the main variables that modulate protein function and stability. Thermodynamic studies of oligomeric proteins, the dominant protein natural form, have been often hampered because irreversible aggregation and/or slow reactions are common. There are no reports on the reversible equilibrium thermal unfolding of proteins composed of (β/α)8 barrel subunits, albeit this "TIM barrel" topology is one of the most abundant and versatile in nature. We studied the eponymous TIM barrel, triosephosphate isomerase (TIM), belonging to five species of different bacterial taxa. All of them were found to be catalytically efficient dimers. The three-dimensional structure of four enzymes was solved at high/medium resolution. Irreversibility and kinetic control were observed in the thermal unfolding of two TIMs, while for the other three the thermal unfolding was found to follow a two-state equilibrium reversible process. Shifts in the global stability curves of these three proteins are related to the organismal temperature range of optimal growth and modulated by variations in maximum stability temperature and in the enthalpy change at that temperature. Reversibility appears to correlate with the low isoelectric point, the absence of a residual structure in the unfolded state, small cavity volume in the native state, low conformational stability and a low melting temperature. Furthermore, the strong coupling between dimer dissociation and monomer unfolding may reduce aggregation and favour reversibility. It is therefore very thought-provoking to find that a common topological ensemble, such as the TIM barrel, can unfold/refold in the Anfinsen way, i.e. without the help of the cellular machinery.

  1. Urea-temperature phase diagrams capture the thermodynamics of denatured state expansion that accompany protein unfolding

    Science.gov (United States)

    Tischer, Alexander; Auton, Matthew

    2013-01-01

    We have analyzed the thermodynamic properties of the von Willebrand factor (VWF) A3 domain using urea-induced unfolding at variable temperature and thermal unfolding at variable urea concentrations to generate a phase diagram that quantitatively describes the equilibrium between native and denatured states. From this analysis, we were able to determine consistent thermodynamic parameters with various spectroscopic and calorimetric methods that define the urea–temperature parameter plane from cold denaturation to heat denaturation. Urea and thermal denaturation are experimentally reversible and independent of the thermal scan rate indicating that all transitions are at equilibrium and the van't Hoff and calorimetric enthalpies obtained from analysis of individual thermal transitions are equivalent demonstrating two-state character. Global analysis of the urea–temperature phase diagram results in a significantly higher enthalpy of unfolding than obtained from analysis of individual thermal transitions and significant cross correlations describing the urea dependence of and that define a complex temperature dependence of the m-value. Circular dichroism (CD) spectroscopy illustrates a large increase in secondary structure content of the urea-denatured state as temperature increases and a loss of secondary structure in the thermally denatured state upon addition of urea. These structural changes in the denatured ensemble make up ∼40% of the total ellipticity change indicating a highly compact thermally denatured state. The difference between the thermodynamic parameters obtained from phase diagram analysis and those obtained from analysis of individual thermal transitions illustrates that phase diagrams capture both contributions to unfolding and denatured state expansion and by comparison are able to decipher these contributions. PMID:23813497

  2. Local Order in the Unfolded State: Conformational Biases and Nearest Neighbor Interactions

    Directory of Open Access Journals (Sweden)

    Siobhan Toal

    2014-07-01

    Full Text Available The discovery of Intrinsically Disordered Proteins, which contain significant levels of disorder yet perform complex biologically functions, as well as unwanted aggregation, has motivated numerous experimental and theoretical studies aimed at describing residue-level conformational ensembles. Multiple lines of evidence gathered over the last 15 years strongly suggest that amino acids residues display unique and restricted conformational preferences in the unfolded state of peptides and proteins, contrary to one of the basic assumptions of the canonical random coil model. To fully understand residue level order/disorder, however, one has to gain a quantitative, experimentally based picture of conformational distributions and to determine the physical basis underlying residue-level conformational biases. Here, we review the experimental, computational and bioinformatic evidence for conformational preferences of amino acid residues in (mostly short peptides that can be utilized as suitable model systems for unfolded states of peptides and proteins. In this context particular attention is paid to the alleged high polyproline II preference of alanine. We discuss how these conformational propensities may be modulated by peptide solvent interactions and so called nearest-neighbor interactions. The relevance of conformational propensities for the protein folding problem and the understanding of IDPs is briefly discussed.

  3. Photoinduced Partial Unfolding of Tubulin Bound to Meso-tetrakis(sulfonatophenyl) Porphyrin Leads to Inhibition of Microtubule Formation In Vitro

    Science.gov (United States)

    2013-07-30

    Bio- chemistry 44, 524–536 (2005). [4] M. Loweneck, A. G. Milbradt, C. Root , H. Satzger, W. Zinth, L. Moroder, and C. Renner, Biophys. J. 90, 2099–2108...H. Nettles , B. Cornett, K. H. Downing, and E. Nogales, Proc. Natl. Acad. Sci. 98, 5312–5316 (2001). B. McMicken et al.: Photoinduced unfolding of

  4. Overlaps of partial Néel states and Bethe states

    International Nuclear Information System (INIS)

    Foda, O; Zarembo, K

    2016-01-01

    Partial Néel states are generalizations of the ordinary Néel (classical anti-ferromagnet) state that can have arbitrary integer spin. We study overlaps of these states with Bethe states. We first identify this overlap with a partial version of reflecting-boundary domain-wall partition function, and then derive various determinant representations for off-shell and on-shell Bethe states. (paper: quantum statistical physics, condensed matter, integrable systems)

  5. Deterministic dense coding with partially entangled states

    Science.gov (United States)

    Mozes, Shay; Oppenheim, Jonathan; Reznik, Benni

    2005-01-01

    The utilization of a d -level partially entangled state, shared by two parties wishing to communicate classical information without errors over a noiseless quantum channel, is discussed. We analytically construct deterministic dense coding schemes for certain classes of nonmaximally entangled states, and numerically obtain schemes in the general case. We study the dependency of the maximal alphabet size of such schemes on the partially entangled state shared by the two parties. Surprisingly, for d>2 it is possible to have deterministic dense coding with less than one ebit. In this case the number of alphabet letters that can be communicated by a single particle is between d and 2d . In general, we numerically find that the maximal alphabet size is any integer in the range [d,d2] with the possible exception of d2-1 . We also find that states with less entanglement can have a greater deterministic communication capacity than other more entangled states.

  6. Unfolding Participation

    DEFF Research Database (Denmark)

    Saad-Sulonen, Joanna; Halskov, Kim; Eriksson, Eva

    2015-01-01

    The aim of the Unfolding Participation workshop is to outline an agenda for the next 10 years of participatory design (PD) and participatory human computer interaction (HCI) research. We will do that through a double strategy: 1) by critically interrogating the concept of participation (unfolding...... the concept itself), while at the same time, 2) reflecting on the way that participation unfolds across different participatory configurations. We invite researchers and practitioners from PD and HCI and fields in which information technology mediated participation is embedded (e.g. in political studies......, urban planning, participatory arts, business, science and technology studies) to bring a plurality of perspectives and expertise related to participation....

  7. Thermodynamic analysis of ANS binding to partially unfolded α-lactalbumin: correlation of endothermic to exothermic changeover with formation of authentic molten globules.

    Science.gov (United States)

    Kim, Ki Hyung; Yun, Soi; Mok, K H; Lee, E K

    2016-09-01

    A fluorescent reporter, 8-anilino-1-naphthalene sulfonic acid (ANS), can serve as a reference molecule for conformational transition of a protein because its aromatic carbons have strong affinity with hydrophobic cores of partially unfolded molten globules. Using a typical calcium-binding protein, bovine α-lactalbumin (BLA), as a model protein, we compared the ANS binding thermodynamics to the decalcified (10 mM EDTA treated) apo-BLA at two representative temperatures: 20 and 40 °C. This is because the authentic molten globule is known to form more heavily at an elevated temperature such as 40 °C. Isothermal titration calorimetry experiments revealed that the BLA-ANS interactions at both temperatures were entropy-driven, and the dissociation constants were similar on the order of 10(-4)  M, but there was a dramatic changeover in the binding thermodynamics from endothermic at 20 °C to exothermic at 40 °C. We believe that the higher subpopulation of authentic molten globules at 40 °C than 20 °C would be responsible for the results, which also indicate that weak binding is sufficient to alter the ANS binding mechanisms. We expect that the thermodynamic properties obtained from this study would serve as a useful reference for investigating the binding of other hydrophobic ligands such as oleic acid to apo-BLA, because oleic acid is known to have tumor-selective cytotoxicity when complexed with partially unfolded α-lactalbumin. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  8. The adsorption and unfolding kinetics determines the folding state of proteins at the air-water interface and thereby the equation of state

    NARCIS (Netherlands)

    Wierenga, P.A.; Egmond, M.R.; Voragen, A.G.J.; Jongh, H.H.J.de

    2006-01-01

    Unfolding of proteins has often been mentioned as an important factor during the adsorption process at air-water interfaces and in the increase of surface pressure at later stages of the adsorption process. This work focuses on the question whether the folding state of the adsorbed protein depends

  9. Characterization of the residual structure in the unfolded state of the Delta 131 Delta fragment of staphylococcal nuclease

    DEFF Research Database (Denmark)

    Francis, C. J.; Lindorff-Larsen, Kresten; Best, R. B.

    2006-01-01

    dynamics simulations to characterise the residual structure of the 131 fragment of staphylococcal nuclease under physiological conditions. Our findings indicate that 131 under these conditions shows a tendency to form transiently hydrophobic clusters similar to those present in the native state of wild......The determination of the conformational preferences in unfolded states of proteins constitutes an important challenge in structural biology. We use inter-residue distances estimated from site-directed spin-labeling NMR experimental measurements as ensemble-averaged restraints in all-atom molecular...

  10. Investigating the structural origin of trpzip2 temperature dependent unfolding fluorescence line shape based on a Markov state model simulation.

    Science.gov (United States)

    Song, Jian; Gao, Fang; Cui, Raymond Z; Shuang, Feng; Liang, Wanzhen; Huang, Xuhui; Zhuang, Wei

    2012-10-25

    Vibrationally resolved fluorescence spectra of the β-hairpin trpzip2 peptide at two temperatures as well as during a T-jump unfolding process are simulated on the basis of a combination of Markov state models and quantum chemistry schemes. The broad asymmetric spectral line shape feature is reproduced by considering the exciton-phonon couplings. The temperature dependent red shift observed in the experiment has been attributed to the state population changes of specific chromophores. Through further theoretical study, it is found that both the environment's electric field and the chromophores' geometry distortions are responsible for tryptophan fluorescence shift.

  11. Faithful teleportation with partially entangled states

    International Nuclear Information System (INIS)

    Gour, Gilad

    2004-01-01

    We write explicitly a general protocol for faithful teleportation of a d-state particle (qudit) via a partially entangled pair of (pure) n-state particles. The classical communication cost (CCC) of the protocol is log 2 (nd) bits, and it is implemented by a projective measurement performed by Alice, and a unitary operator performed by Bob (after receiving from Alice the measurement result). We prove the optimality of our protocol by a comparison with the concentrate and teleport strategy. We also show that if d>n/2, or if there is no residual entanglement left after the faithful teleportation, the CCC of any protocol is at least log 2 (nd) bits. Furthermore, we find a lower bound on the CCC in the process transforming one bipartite state to another by means of local operation and classical communication

  12. Probing the folded state and mechanical unfolding pathways of T4 lysozyme using all-atom and coarse-grained molecular simulation

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Wenjun, E-mail: wjzheng@buffalo.edu; Glenn, Paul [Department of Physics, University at Buffalo, Buffalo, New York 14260 (United States)

    2015-01-21

    The Bacteriophage T4 Lysozyme (T4L) is a prototype modular protein comprised of an N-terminal and a C-domain domain, which was extensively studied to understand the folding/unfolding mechanism of modular proteins. To offer detailed structural and dynamic insights to the folded-state stability and the mechanical unfolding behaviors of T4L, we have performed extensive equilibrium and steered molecular dynamics simulations of both the wild-type (WT) and a circular permutation (CP) variant of T4L using all-atom and coarse-grained force fields. Our all-atom and coarse-grained simulations of the folded state have consistently found greater stability of the C-domain than the N-domain in isolation, which is in agreement with past thermostatic studies of T4L. While the all-atom simulation cannot fully explain the mechanical unfolding behaviors of the WT and the CP variant observed in an optical tweezers study, the coarse-grained simulations based on the Go model or a modified elastic network model (mENM) are in qualitative agreement with the experimental finding of greater unfolding cooperativity in the WT than the CP variant. Interestingly, the two coarse-grained models predict different structural mechanisms for the observed change in cooperativity between the WT and the CP variant—while the Go model predicts minor modification of the unfolding pathways by circular permutation (i.e., preserving the general order that the N-domain unfolds before the C-domain), the mENM predicts a dramatic change in unfolding pathways (e.g., different order of N/C-domain unfolding in the WT and the CP variant). Based on our simulations, we have analyzed the limitations of and the key differences between these models and offered testable predictions for future experiments to resolve the structural mechanism for cooperative folding/unfolding of T4L.

  13. Decaying states as physically nonisolable partial systems

    International Nuclear Information System (INIS)

    Szasz, G.I.

    1976-01-01

    Presently the investigations of decaying quantum mechanical systems lack a well-founded concept, which is reflected by several formal difficulties of the corresponding mathematical treatment. In order to clarify in some respect the situation, it is investigated, within the framework of nonrelativistic quantum mechanics, the resonant scattering of an initially well localized partial wave packet. If the potential decreases sufficiently fast for r→infinite, the wave packet can be expressed at sufficiently long time after the scattering has taken place, as the sum of a term describing the direct scattering and a function of the resonant solution with complex 'momentum'. From such a heuristic relation one can deduce not only the probability for the creation of unstable particles but also obtain some hints to a connection between decaying states and physically nonisolable partial systems. On the other hand, this connection can perhaps display the inadequacy of attempts which suggest to solve the problem of decaying states within the usual Hilbert space methods. (author)

  14. Partial separability and entanglement criteria for multiqubit quantum states

    NARCIS (Netherlands)

    Seevinck, M.P.; Uffink, J.B.M.

    2008-01-01

    We explore the subtle relationships between partial separability and entanglement of subsystems in multiqubit quantum states and give experimentally accessible conditions that distinguish between various classes and levels of partial separability in a hierarchical order. These conditions take the

  15. Mechanics of collective unfolding

    Science.gov (United States)

    Caruel, M.; Allain, J.-M.; Truskinovsky, L.

    2015-03-01

    Mechanically induced unfolding of passive crosslinkers is a fundamental biological phenomenon encountered across the scales from individual macro-molecules to cytoskeletal actin networks. In this paper we study a conceptual model of athermal load-induced unfolding and use a minimalistic setting allowing one to emphasize the role of long-range interactions while maintaining full analytical transparency. Our model can be viewed as a description of a parallel bundle of N bistable units confined between two shared rigid backbones that are loaded through a series spring. We show that the ground states in this model correspond to synchronized, single phase configurations where all individual units are either folded or unfolded. We then study the fine structure of the wiggly energy landscape along the reaction coordinate linking the two coherent states and describing the optimal mechanism of cooperative unfolding. Quite remarkably, our study shows the fundamental difference in the size and the structure of the folding-unfolding energy barriers in the hard (fixed displacements) and soft (fixed forces) loading devices which persists in the continuum limit. We argue that both, the synchronization and the non-equivalence of the mechanical responses in hard and soft devices, have their origin in the dominance of long-range interactions. We then apply our minimal model to skeletal muscles where the power-stroke in acto-myosin crossbridges can be interpreted as passive folding. A quantitative analysis of the muscle model shows that the relative rigidity of myosin backbone provides the long-range interaction mechanism allowing the system to effectively synchronize the power-stroke in individual crossbridges even in the presence of thermal fluctuations. In view of the prototypical nature of the proposed model, our general conclusions pertain to a variety of other biological systems where elastic interactions are mediated by effective backbones.

  16. The introduction of hydrogen bond and hydrophobicity effects into the rotational isomeric states model for conformational analysis of unfolded peptides

    Science.gov (United States)

    Engin, Ozge; Sayar, Mehmet; Erman, Burak

    2009-03-01

    Relative contributions of local and non-local interactions to the unfolded conformations of peptides are examined by using the rotational isomeric states model which is a Markov model based on pairwise interactions of torsion angles. The isomeric states of a residue are well described by the Ramachandran map of backbone torsion angles. The statistical weight matrices for the states are determined by molecular dynamics simulations applied to monopeptides and dipeptides. Conformational properties of tripeptides formed from combinations of alanine, valine, tyrosine and tryptophan are investigated based on the Markov model. Comparison with molecular dynamics simulation results on these tripeptides identifies the sequence-distant long-range interactions that are missing in the Markov model. These are essentially the hydrogen bond and hydrophobic interactions that are obtained between the first and the third residue of a tripeptide. A systematic correction is proposed for incorporating these long-range interactions into the rotational isomeric states model. Preliminary results suggest that the Markov assumption can be improved significantly by renormalizing the statistical weight matrices to include the effects of the long-range correlations.

  17. The introduction of hydrogen bond and hydrophobicity effects into the rotational isomeric states model for conformational analysis of unfolded peptides

    International Nuclear Information System (INIS)

    Engin, Ozge; Sayar, Mehmet; Erman, Burak

    2009-01-01

    Relative contributions of local and non-local interactions to the unfolded conformations of peptides are examined by using the rotational isomeric states model which is a Markov model based on pairwise interactions of torsion angles. The isomeric states of a residue are well described by the Ramachandran map of backbone torsion angles. The statistical weight matrices for the states are determined by molecular dynamics simulations applied to monopeptides and dipeptides. Conformational properties of tripeptides formed from combinations of alanine, valine, tyrosine and tryptophan are investigated based on the Markov model. Comparison with molecular dynamics simulation results on these tripeptides identifies the sequence-distant long-range interactions that are missing in the Markov model. These are essentially the hydrogen bond and hydrophobic interactions that are obtained between the first and the third residue of a tripeptide. A systematic correction is proposed for incorporating these long-range interactions into the rotational isomeric states model. Preliminary results suggest that the Markov assumption can be improved significantly by renormalizing the statistical weight matrices to include the effects of the long-range correlations

  18. Many channel spectrum unfolding

    International Nuclear Information System (INIS)

    Najzer, M.; Glumac, B.; Pauko, M.

    1980-01-01

    The principle of the ITER unfolding code as used for the many channel spectrum unfolding is described. Its unfolding ability is tested on seven typical neutron spectra. The effect of the initial spectrum approximation upon the solution is discussed

  19. Reversible Unfolding of Rhomboid Intramembrane Proteases.

    Science.gov (United States)

    Panigrahi, Rashmi; Arutyunova, Elena; Panwar, Pankaj; Gimpl, Katharina; Keller, Sandro; Lemieux, M Joanne

    2016-03-29

    Denaturant-induced unfolding of helical membrane proteins provides insights into their mechanism of folding and domain organization, which take place in the chemically heterogeneous, anisotropic environment of a lipid membrane. Rhomboid proteases are intramembrane proteases that play key roles in various diseases. Crystal structures have revealed a compact helical bundle with a buried active site, which requires conformational changes for the cleavage of transmembrane substrates. A dimeric form of the rhomboid protease has been shown to be important for activity. In this study, we examine the mechanism of refolding for two distinct rhomboids to gain insight into their secondary structure-activity relationships. Although helicity is largely abolished in the unfolded states of both proteins, unfolding is completely reversible for HiGlpG but only partially reversible for PsAarA. Refolding of both proteins results in reassociation of the dimer, with a 90% regain of catalytic activity for HiGlpG but only a 70% regain for PsAarA. For both proteins, a broad, gradual transition from the native, folded state to the denatured, partly unfolded state was revealed with the aid of circular dichroism spectroscopy as a function of denaturant concentration, thus arguing against a classical two-state model as found for many globular soluble proteins. Thermal denaturation has irreversible destabilizing effects on both proteins, yet reveals important functional details regarding substrate accessibility to the buried active site. This concerted biophysical and functional analysis demonstrates that HiGlpG, with a simple six-transmembrane-segment organization, is more robust than PsAarA, which has seven predicted transmembrane segments, thus rendering HiGlpG amenable to in vitro studies of membrane-protein folding. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  20. Thermal unfolding of barstar and the properties of interfacial water around the unfolded forms

    Energy Technology Data Exchange (ETDEWEB)

    Pal, Somedatta; Bandyopadhyay, Sanjoy, E-mail: sanjoy@chem.iitkgp.ernet.in [Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur - 721302 (India)

    2013-12-21

    Identification of the intermediates along the folding-unfolding pathways and probing their interactions with surrounding solvent are two important but relatively unexplored issues in protein folding. In this work, we have carried out atomistic molecular dynamics simulations to study the thermal unfolding of barstar in aqueous solution from its folded native form at two different temperatures (400 K and 450 K). The calculations at 400 K reveal partial unfolding of two α-helices (helix-1 and helix-2) and their interconnecting loop. At 450 K, on the other hand, the entire protein attains an expanded flexible conformation due to disruption of a large fraction of tertiary contacts and breaking of almost all the secondary structures. These two disordered structures obtained at such high temperatures are then studied around room temperature to probe their influence on the properties of surrounding solvent. It is found that though the unfolding of the protein in general leads to increasingly hydrated interface, but new structural motifs with locally dehydrated interface may also form during the structural transition. Additionally, independent of the conformational state of the protein, its influence on surrounding solvent has been found to be restricted to the first hydration layer.

  1. The effect of a DeltaK280 mutation on the unfolded state of a microtubule-binding repeat in Tau.

    Directory of Open Access Journals (Sweden)

    Austin Huang

    Full Text Available Tau is a natively unfolded protein that forms intracellular aggregates in the brains of patients with Alzheimer's disease. To decipher the mechanism underlying the formation of tau aggregates, we developed a novel approach for constructing models of natively unfolded proteins. The method, energy-minima mapping and weighting (EMW, samples local energy minima of subsequences within a natively unfolded protein and then constructs ensembles from these energetically favorable conformations that are consistent with a given set of experimental data. A unique feature of the method is that it does not strive to generate a single ensemble that represents the unfolded state. Instead we construct a number of candidate ensembles, each of which agrees with a given set of experimental constraints, and focus our analysis on local structural features that are present in all of the independently generated ensembles. Using EMW we generated ensembles that are consistent with chemical shift measurements obtained on tau constructs. Thirty models were constructed for the second microtubule binding repeat (MTBR2 in wild-type (WT tau and a DeltaK280 mutant, which is found in some forms of frontotemporal dementia. By focusing on structural features that are preserved across all ensembles, we find that the aggregation-initiating sequence, PHF6*, prefers an extended conformation in both the WT and DeltaK280 sequences. In addition, we find that residue K280 can adopt a loop/turn conformation in WT MTBR2 and that deletion of this residue, which can adopt nonextended states, leads to an increase in locally extended conformations near the C-terminus of PHF6*. As an increased preference for extended states near the C-terminus of PHF6* may facilitate the propagation of beta-structure downstream from PHF6*, these results explain how a deletion at position 280 can promote the formation of tau aggregates.

  2. Superposing pure quantum states with partial prior information

    Science.gov (United States)

    Dogra, Shruti; Thomas, George; Ghosh, Sibasish; Suter, Dieter

    2018-05-01

    The principle of superposition is an intriguing feature of quantum mechanics, which is regularly exploited in many different circumstances. A recent work [M. Oszmaniec et al., Phys. Rev. Lett. 116, 110403 (2016), 10.1103/PhysRevLett.116.110403] shows that the fundamentals of quantum mechanics restrict the process of superimposing two unknown pure states, even though it is possible to superimpose two quantum states with partial prior knowledge. The prior knowledge imposes geometrical constraints on the choice of input states. We discuss an experimentally feasible protocol to superimpose multiple pure states of a d -dimensional quantum system and carry out an explicit experimental realization for two single-qubit pure states with partial prior information on a two-qubit NMR quantum information processor.

  3. Development of isothermal-isobaric replica-permutation method for molecular dynamics and Monte Carlo simulations and its application to reveal temperature and pressure dependence of folded, misfolded, and unfolded states of chignolin

    Science.gov (United States)

    Yamauchi, Masataka; Okumura, Hisashi

    2017-11-01

    We developed a two-dimensional replica-permutation molecular dynamics method in the isothermal-isobaric ensemble. The replica-permutation method is a better alternative to the replica-exchange method. It was originally developed in the canonical ensemble. This method employs the Suwa-Todo algorithm, instead of the Metropolis algorithm, to perform permutations of temperatures and pressures among more than two replicas so that the rejection ratio can be minimized. We showed that the isothermal-isobaric replica-permutation method performs better sampling efficiency than the isothermal-isobaric replica-exchange method and infinite swapping method. We applied this method to a β-hairpin mini protein, chignolin. In this simulation, we observed not only the folded state but also the misfolded state. We calculated the temperature and pressure dependence of the fractions on the folded, misfolded, and unfolded states. Differences in partial molar enthalpy, internal energy, entropy, partial molar volume, and heat capacity were also determined and agreed well with experimental data. We observed a new phenomenon that misfolded chignolin becomes more stable under high-pressure conditions. We also revealed this mechanism of the stability as follows: TYR2 and TRP9 side chains cover the hydrogen bonds that form a β-hairpin structure. The hydrogen bonds are protected from the water molecules that approach the protein as the pressure increases.

  4. Approximate thermodynamic state relations in partially ionized gas mixtures

    International Nuclear Information System (INIS)

    Ramshaw, John D.

    2004-01-01

    Thermodynamic state relations for mixtures of partially ionized nonideal gases are often approximated by artificially partitioning the mixture into compartments or subvolumes occupied by the pure partially ionized constituent gases, and requiring these subvolumes to be in temperature and pressure equilibrium. This intuitively reasonable procedure is easily shown to reproduce the correct thermal and caloric state equations for a mixture of neutral (nonionized) ideal gases. The purpose of this paper is to point out that (a) this procedure leads to incorrect state equations for a mixture of partially ionized ideal gases, whereas (b) the alternative procedure of requiring that the subvolumes all have the same temperature and free electron density reproduces the correct thermal and caloric state equations for such a mixture. These results readily generalize to the case of partially degenerate and/or relativistic electrons, to a common approximation used to represent pressure ionization effects, and to two-temperature plasmas. This suggests that equating the subvolume electron number densities or chemical potentials instead of pressures is likely to provide a more accurate approximation in nonideal plasma mixtures

  5. Reconsidering harmonic and anharmonic coherent states: Partial differential equations approach

    Energy Technology Data Exchange (ETDEWEB)

    Toutounji, Mohamad, E-mail: Mtoutounji@uaeu.ac.ae

    2015-02-15

    This article presents a new approach to dealing with time dependent quantities such as autocorrelation function of harmonic and anharmonic systems using coherent states and partial differential equations. The approach that is normally used to evaluate dynamical quantities involves formidable operator algebra. That operator algebra becomes insurmountable when employing Morse oscillator coherent states. This problem becomes even more complicated in case of Morse oscillator as it tends to exhibit divergent dynamics. This approach employs linear partial differential equations, some of which may be solved exactly and analytically, thereby avoiding the cumbersome noncommutative algebra required to manipulate coherent states of Morse oscillator. Additionally, the arising integrals while using the herein presented method feature stability and high numerical efficiency. The correctness, applicability, and utility of the above approach are tested by reproducing the partition and optical autocorrelation function of the harmonic oscillator. A closed-form expression for the equilibrium canonical partition function of the Morse oscillator is derived using its coherent states and partial differential equations. Also, a nonequilibrium autocorrelation function expression for weak electron–phonon coupling in condensed systems is derived for displaced Morse oscillator in electronic state. Finally, the utility of the method is demonstrated through further simplifying the Morse oscillator partition function or autocorrelation function expressions reported by other researchers in unevaluated form of second-order derivative exponential. Comparison with exact dynamics shows identical results.

  6. Unfolding Green Defense

    DEFF Research Database (Denmark)

    Larsen, Kristian Knus

    2015-01-01

    In recent years, many states have developed and implemented green solutions for defense. Building on these initiatives NATO formulated the NATO Green Defence Framework in 2014. The framework provides a broad basis for cooperation within the Alliance on green solutions for defense. This report aims...... to inform and support the further development of green solutions by unfolding how green technologies and green strategies have been developed and used to handle current security challenges. The report, initially, focuses on the security challenges that are being linked to green defense, namely fuel...... consumption in military operations, defense expenditure, energy security, and global climate change. The report then proceeds to introduce the NATO Green Defence Framework before exploring specific current uses of green technologies and green strategies for defense. The report concludes that a number...

  7. Partial transpose of random quantum states: Exact formulas and meanders

    Energy Technology Data Exchange (ETDEWEB)

    Fukuda, Motohisa [Zentrum Mathematik, M5, Technische Universitaet Muenchen, Boltzmannstrasse 3, 85748 Garching (Germany); Sniady, Piotr [Zentrum Mathematik, M5, Technische Universitaet Muenchen, Boltzmannstrasse 3, 85748 Garching (Germany); Institute of Mathematics, Polish Academy of Sciences, ul. Sniadeckich 8, 00-956 Warszawa (Poland); Institute of Mathematics, University of Wroclaw, pl. Grunwaldzki 2/4, 50-384 Wroclaw (Poland)

    2013-04-15

    We investigate the asymptotic behavior of the empirical eigenvalues distribution of the partial transpose of a random quantum state. The limiting distribution was previously investigated via Wishart random matrices indirectly (by approximating the matrix of trace 1 by the Wishart matrix of random trace) and shown to be the semicircular distribution or the free difference of two free Poisson distributions, depending on how dimensions of the concerned spaces grow. Our use of Wishart matrices gives exact combinatorial formulas for the moments of the partial transpose of the random state. We find three natural asymptotic regimes in terms of geodesics on the permutation groups. Two of them correspond to the above two cases; the third one turns out to be a new matrix model for the meander polynomials. Moreover, we prove the convergence to the semicircular distribution together with its extreme eigenvalues under weaker assumptions, and show large deviation bound for the latter.

  8. Partial transpose of random quantum states: Exact formulas and meanders

    Science.gov (United States)

    Fukuda, Motohisa; Śniady, Piotr

    2013-04-01

    We investigate the asymptotic behavior of the empirical eigenvalues distribution of the partial transpose of a random quantum state. The limiting distribution was previously investigated via Wishart random matrices indirectly (by approximating the matrix of trace 1 by the Wishart matrix of random trace) and shown to be the semicircular distribution or the free difference of two free Poisson distributions, depending on how dimensions of the concerned spaces grow. Our use of Wishart matrices gives exact combinatorial formulas for the moments of the partial transpose of the random state. We find three natural asymptotic regimes in terms of geodesics on the permutation groups. Two of them correspond to the above two cases; the third one turns out to be a new matrix model for the meander polynomials. Moreover, we prove the convergence to the semicircular distribution together with its extreme eigenvalues under weaker assumptions, and show large deviation bound for the latter.

  9. Cooperative unfolding of apolipoprotein A-1 induced by chemical denaturation.

    Science.gov (United States)

    Eckhardt, D; Li-Blatter, X; Schönfeld, H-J; Heerklotz, H; Seelig, J

    2018-05-25

    Apolipoprotein A-1 (Apo A-1) plays an important role in lipid transfer and obesity. Chemical unfolding of α-helical Apo A-1 is induced with guanidineHCl and monitored with differential scanning calorimetry (DSC) and CD spectroscopy. The unfolding enthalpy and the midpoint temperature of unfolding decrease linearly with increasing guanidineHCl concentration, caused by the weak binding of denaturant. At room temperature, binding of 50-60 molecules guanidineHCl leads to a complete Apo A-1 unfolding. The entropy of unfolding decreases to a lesser extent than the unfolding enthalpy. Apo A-1 chemical unfolding is a dynamic multi-state equilibrium that is analysed with the Zimm-Bragg theory modified for chemical unfolding. The chemical Zimm-Bragg theory predicts the denaturant binding constant K D and the protein cooperativity σ. Chemical unfolding of Apo A-1 is two orders of magnitude less cooperative than thermal unfolding. The free energy of thermal unfolding is ~0.2 kcal/mol per amino acid residue and ~1.0 kcal/mol for chemical unfolding at room temperature. The Zimm-Bragg theory calculates conformational probabilities and the chemical Zimm-Bragg theory predicts stretches of α-helical segments in dynamic equilibrium, unfolding and refolding independently and fast. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

  10. Partially coherent twisted states in arrays of coupled phase oscillators

    Energy Technology Data Exchange (ETDEWEB)

    Omel' chenko, Oleh E.; Wolfrum, Matthias [Weierstrass Institute, Mohrenstrasse 39, 10117 Berlin (Germany); Laing, Carlo R. [INMS, Massey University, Private Bag 102-904 NSMC, Auckland (New Zealand)

    2014-06-15

    We consider a one-dimensional array of phase oscillators with non-local coupling and a Lorentzian distribution of natural frequencies. The primary objects of interest are partially coherent states that are uniformly “twisted” in space. To analyze these, we take the continuum limit, perform an Ott/Antonsen reduction, integrate over the natural frequencies, and study the resulting spatio-temporal system on an unbounded domain. We show that these twisted states and their stability can be calculated explicitly. We find that stable twisted states with different wave numbers appear for increasing coupling strength in the well-known Eckhaus scenario. Simulations of finite arrays of oscillators show good agreement with results of the analysis of the infinite system.

  11. Partially coherent twisted states in arrays of coupled phase oscillators

    International Nuclear Information System (INIS)

    Omel'chenko, Oleh E.; Wolfrum, Matthias; Laing, Carlo R.

    2014-01-01

    We consider a one-dimensional array of phase oscillators with non-local coupling and a Lorentzian distribution of natural frequencies. The primary objects of interest are partially coherent states that are uniformly “twisted” in space. To analyze these, we take the continuum limit, perform an Ott/Antonsen reduction, integrate over the natural frequencies, and study the resulting spatio-temporal system on an unbounded domain. We show that these twisted states and their stability can be calculated explicitly. We find that stable twisted states with different wave numbers appear for increasing coupling strength in the well-known Eckhaus scenario. Simulations of finite arrays of oscillators show good agreement with results of the analysis of the infinite system

  12. Partial radiative recombination cross sections for excited states of hydrogen

    International Nuclear Information System (INIS)

    Fazio, P.M.

    1984-01-01

    In calculating the radiative recombination cross sections for interstellar H II regions, usually only the electric dipole term in the expansion of the interaction Hamiltonian is kept. The dipole and quadrupole transition strengths in closed analytical form are calculated here using the Coulomb wave functions because results for any electron energy and for recombination into any angular momentum state of hydrogen are needed. Several interesting effects are found. First, the transition probabilities are maximum for recombination into specific intermediate angular momentum states at low energies (w < 2eV) and where the free state angular momentum is greater than that of the bound state. Further, that specific intermediate angular momentum state depends on the kinetic energy of the free electron. This behavior is in contrast to the normal behavior of the transition strengths where recombination into s states is greatest and decreases with increasing angular momentum. Second, the quadrupole matrix elements vanish for certain velocities of the free electron. This leads to minima in the corresponding quadrupole cross sections when plotted as a function of the free electron's kinetic energy. Finally, the partial cross sections for highly excited states are greater than previously calculated because of the additional effects of the quadrupole transitions

  13. Protein unfolding with a steric trap.

    Science.gov (United States)

    Blois, Tracy M; Hong, Heedeok; Kim, Tae H; Bowie, James U

    2009-10-07

    The study of protein folding requires a method to drive unfolding, which is typically accomplished by altering solution conditions to favor the denatured state. This has the undesirable consequence that the molecular forces responsible for configuring the polypeptide chain are also changed. It would therefore be useful to develop methods that can drive unfolding without the need for destabilizing solvent conditions. Here we introduce a new method to accomplish this goal, which we call steric trapping. In the steric trap method, the target protein is labeled with two biotin tags placed close in space so that both biotin tags can only be bound by streptavidin when the protein unfolds. Thus, binding of the second streptavidin is energetically coupled to unfolding of the target protein. Testing the method on a model protein, dihydrofolate reductase (DHFR), we find that streptavidin binding can drive unfolding and that the apparent binding affinity reports on changes in DHFR stability. Finally, by employing the slow off-rate of wild-type streptavidin, we find that DHFR can be locked in the unfolded state. The steric trap method provides a simple method for studying aspects of protein folding and stability in native solvent conditions, could be used to specifically unfold selected domains, and could be applicable to membrane proteins.

  14. Equation of state of partially-ionized dense plasmas

    International Nuclear Information System (INIS)

    Rogers, F.J.

    1989-01-01

    This paper describes methods for calculating the equation of state of partially-ionized dense plasmas. The term dense plasma is used rather than strongly coupled plasma, since it is possible that at plasma conditions such that only a few levels can be observed spectroscopically the plasma coupling parameters are not large. Due mainly to their importance in theoretical astrophysics, the properties of partially ionized plasmas have been of interest for a long while. More recently, this interest has intensified due to the development of methods for producing partially ionized plasmas in the laboratory. This has opened up large programs of experimental investigation and of practical application. In this paper we consider detailed statistical mechanical methods that explicitly treat the distribution over ionic species and their energy level structure. These detailed approaches are generally characterized as being in the ''chemical picture'' when a free energy expression is minimized or in the ''physical picture'' when the starting point is the grand canonical ensemble. 52 refs., 2 tabs

  15. Bound states on the lattice with partially twisted boundary conditions

    International Nuclear Information System (INIS)

    Agadjanov, D.; Guo, F.-K.; Ríos, G.; Rusetsky, A.

    2015-01-01

    We propose a method to study the nature of exotic hadrons by determining the wave function renormalization constant Z from lattice simulations. It is shown that, instead of studying the volume-dependence of the spectrum, one may investigate the dependence of the spectrum on the twisting angle, imposing twisted boundary conditions on the fermion fields on the lattice. In certain cases, e.g., the case of the DK bound state which is addressed in detail, it is demonstrated that the partial twisting is equivalent to the full twisting up to exponentially small corrections.

  16. Lack of negative charge in the E46Q mutant of photoactive yellow protein prevents partial unfolding of the blue shifted intermediate

    NARCIS (Netherlands)

    Derix, N.M.; Wechselberger, R.W.|info:eu-repo/dai/nl/304829005; van der Horst, M.A.; Hellingwerf, K.J.; Boelens, R.|info:eu-repo/dai/nl/070151407; Kaptein, R.|info:eu-repo/dai/nl/074334603; van Nuland, N.A.J.

    2003-01-01

    The long-lived light-induced intermediate (pB) of the E46Q mutant (glutamic acid is replaced by glutamine at position 46) of photoactive yellow protein (PYP) has been investigated by NMR spectroscopy. The ground state of this mutant is very similar to that of wild-type PYP (WT), whereas the pB

  17. NMR of unfolded proteins

    Indian Academy of Sciences (India)

    Unknown

    2005-01-03

    Jan 3, 2005 ... covering all the systems, so far discovered.5,7,8,12. With the increasing ... Structural investigations on proteins by NMR are, currently ... rapid analysis of unfolded proteins. ...... and hence help in design of drugs against them.

  18. Evidence of non-coincidence of normalized sigmoidal curves of two different structural properties for two-state protein folding/unfolding

    International Nuclear Information System (INIS)

    Rahaman, Hamidur; Khan, Md. Khurshid Alam; Hassan, Md. Imtaiyaz; Islam, Asimul; Moosavi-Movahedi, Ali Akbar; Ahmad, Faizan

    2013-01-01

    Highlights: ► Non-coincidence of normalized sigmoidal curves of two different structural properties is consistence with the two-state protein folding/unfolding. ► DSC measurements of denaturation show a two-state behavior of g-cyt-c at pH 6.0. ► Urea-induced denaturation of g-cyt-c is a variable two- state process at pH 6.0. ► GdmCl-induced denaturation of g-cyt-c is a fixed two- state process at pH 6.0. -- Abstract: In practice, the observation of non-coincidence of normalized sigmoidal transition curves measured by two different structural properties constitutes a proof of existence of thermodynamically stable intermediate(s) on the folding ↔ unfolding pathway of a protein. Here we give first experimental evidence that this non-coincidence is also observed for a two-state protein denaturation. Proof of this evidence comes from our studies of denaturation of goat cytochrome-c (g-cyt-c) at pH 6.0. These studies involve differential scanning calorimetry (DSC) measurements in the absence of urea and measurements of urea-induced denaturation curves monitored by observing changes in absorbance at 405, 530, and 695 nm and circular dichroism (CD) at 222, 405, and 416 nm. DSC measurements showed that denaturation of the protein is a two-state process, for calorimetric and van’t Hoff enthalpy changes are, within experimental errors, identical. Normalization of urea-induced denaturation curves monitored by optical properties leads to noncoincident sigmoidal curves. Heat-induced transition of g-cyt-c in the presence of different urea concentrations was monitored by CD at 222 nm and absorption at 405 nm. It was observed that these two different structural probes gave not only identical values of T m (transition temperature), ΔH m (change in enthalpy at T m ) and ΔC p (constant-pressure heat capacity change), but these thermodynamic parameters in the absence of urea are also in agreement with those obtained from DSC measurements

  19. Thermal dissociation and unfolding of insulin

    DEFF Research Database (Denmark)

    Huus, Kasper; Havelund, Svend; Olsen, Helle B

    2005-01-01

    The thermal stability of human insulin was studied by differential scanning microcalorimetry and near-UV circular dichroism as a function of zinc/protein ratio, to elucidate the dissociation and unfolding processes of insulin in different association states. Zinc-free insulin, which is primarily...... dimeric at room temperature, unfolded at approximately 70 degrees C. The two monomeric insulin mutants Asp(B28) and Asp(B9),Glu(B27) unfolded at higher temperatures, but with enthalpies of unfolding that were approximately 30% smaller. Small amounts of zinc caused a biphasic thermal denaturation pattern...... of insulin. The biphasic denaturation is caused by a redistribution of zinc ions during the heating process and results in two distinct transitions with T(m)'s of approximately 70 and approximately 87 degrees C corresponding to monomer/dimer and hexamer, respectively. At high zinc concentrations (>or=5 Zn(2...

  20. Unfolding four-helix bundles

    Science.gov (United States)

    Gray, Harry B.; Winkler, Jay R.; Kozak, John J.

    2011-03-01

    A geometrical model has been developed to describe the early stages of unfolding of cytochromes c‧ and c-b562 . Calculations are based on a step-wise extension of the polypeptide chain subject to the constraint that the spatial relationship among the residues of each triplet is fixed by the native-state crystallographic data. The response of each protein to these structural perturbations allows the evolution of each of the four helices in these two proteins to be differentiated. It is found that the two external helices in c‧ unfold before its two internal helices, whereas exactly the opposite behaviour is demonstrated by c-b562 . Each of these cytochromes has an extended, internal, non-helical ('turning') region that initially lags behind the most labile helix but then, at a certain stage (identified for each cytochrome), unravels before any of the four helices present in the native structure. It is believed that these predictions will be useful in guiding future experimental studies on the unfolding of these two cytochromes.

  1. Partial phenotyping in voluntary blood donors of Gujarat State

    Directory of Open Access Journals (Sweden)

    Maitrey Gajjar

    2016-01-01

    Full Text Available Introduction: Partial phenotyping of voluntary blood donors has vital role in transfusion practice, population genetic study and in resolving legal issues.The Rh blood group is one of the most complex and highly immunogenic blood group known in humans. The Kell system, discovered in 1946, is the third most potent system at triggering hemolytic transfusion reactions and consists of 25 highly immunogenic antigens. Knowledge of Rh & Kell phenotypes in given population is relevant for better planning and management of blood bank; the main goal is to find compatible blood for patients needing multiple blood transfusions. The aim of this study was to evaluate the frequency of Rh & Kell phenotype of voluntary donors in Gujarat state. Materials and Methods: The present study was conducted by taking 5670 samples from random voluntary blood donors coming in blood donation camp. Written consent was taken for donor phenotyping. The antigen typing of donors was performed by Qwalys-3(manufacturer: Diagast by using electromagnetic technology on Duolys plates. Results: Out of 5670 donors, the most common Rh antigen observed in the study population was e (99.07% followed by D (95.40%, C (88.77%, c (55.89% and E (17.88%. The frequency of the Kell antigen (K was 1.78 %. Discussion: The antigen frequencies among blood donors from Gujarat were compared with those published for other Indian populations. The frequency of D antigen in our study (95.4% and north Indian donors (93.6 was significantly higher than in the Caucasians (85% and lower than in the Chinese (99%. The frequencies of C, c and E antigens were dissimilar to other ethnic groups while the ′e′ antigen was present in high frequency in our study as also in the other ethnic groups. Kell antigen (K was found in only 101 (1.78 % donors out of 5670. Frequency of Kell antigen in Caucasian and Black populations is 9% & 2% respectively. The most common Kell phenotype was K-k+, not just in Indians (96.5% but

  2. Monogamy relations of quantum entanglement for partially coherently superposed states

    Science.gov (United States)

    Shi, Xian

    2017-12-01

    Not Available Project partially supported by the National Key Research and Development Program of China (Grant No. 2016YFB1000902), the National Natural Science Foundation of China (Grant Nos. 61232015, 61472412, and 61621003), the Beijing Science and Technology Project (2016), Tsinghua-Tencent-AMSS-Joint Project (2016), and the Key Laboratory of Mathematics Mechanization Project: Quantum Computing and Quantum Information Processing.

  3. 78 FR 29292 - Partial Approval and Partial Disapproval of Air Quality State Implementation Plans; Arizona...

    Science.gov (United States)

    2013-05-20

    ... Smelter, American Smelting and Refining Company (ASARCO) Hayden Smelter, Catalyst Paper, and Arizona... Smelter, ASARCO Hayden Smelter, Catalyst Paper, and AEPCO Apache Generating Station. In summary, we propose to approve a revised set of BART-eligible units for the Miami and Hayden smelters; the State's...

  4. Heat, Acid and Chemically Induced Unfolding Pathways, Conformational Stability and Structure-Function Relationship in Wheat α-Amylase.

    Directory of Open Access Journals (Sweden)

    Kritika Singh

    Full Text Available Wheat α-amylase, a multi-domain protein with immense industrial applications, belongs to α+β class of proteins with native molecular mass of 32 kDa. In the present study, the pathways leading to denaturation and the relevant unfolded states of this multi-domain, robust enzyme from wheat were discerned under the influence of temperature, pH and chemical denaturants. The structural and functional aspects along with thermodynamic parameters for α-amylase unfolding were probed and analyzed using fluorescence, circular dichroism and enzyme assay methods. The enzyme exhibited remarkable stability up to 70°C with tendency to aggregate at higher temperature. Acid induced unfolding was also incomplete with respect to the structural content of the enzyme. Strong ANS binding at pH 2.0 suggested the existence of a partially unfolded intermediate state. The enzyme was structurally and functionally stable in the pH range 4.0-9.0 with 88% recovery of hydrolytic activity. Careful examination of biophysical properties of intermediate states populated in urea and GdHCl induced denaturation suggests that α-amylase unfolding undergoes irreversible and non-coincidental cooperative transitions, as opposed to previous reports of two-state unfolding. Our investigation highlights several structural features of the enzyme in relation to its catalytic activity. Since, α-amylase has been comprehensively exploited for use in a range of starch-based industries, in addition to its physiological significance in plants and animals, knowledge regarding its stability and folding aspects will promote its biotechnological applications.

  5. Complete all-atom hydrodynamics of protein unfolding in uniform flow

    International Nuclear Information System (INIS)

    Wang, Guan M; Sandberg, William C

    2010-01-01

    The unfolding dynamics of a protein, ubiquitin, pinned in several uniform flows, was studied at low and high flow rates in an all-atom style through a non-equilibrium molecular dynamics approach with explicit water molecules included. Atomic hydrodynamic force components on individual amino acids, as a function of time, due to the collisional interactions with the flowing water molecules were calculated explicitly. The protein conformational change in response to those time-varying forces was computed completely at the high flow rate up to nanosecond until the fully stretched state was reached. The end-to-end length of the single ubiquitin protein molecule at high flow rate is smoothly increasing. The step-like jumps between metastable states that describe the μm ms -1 scale force pulling experiments conducted on polyubiquitins at low flow rates, are not seen at the high flow speeds necessary to computationally probe the ns nm -1 scale regime. No unfolding was observed in the low flow rate atomic computations at nanosecond scale while partial and complete unfolding was observed in the coarse-grained low flow rate computations at microsecond scale. Examination of the all-atom computation of the time variation of the hydrodynamic forces on, and the velocity components of, the protein molecule unveiled to some extent the details of the complexity of the hydrodynamic friction variation in the nm ns -1 regime of high rate flow-driven protein unfolding. This demonstrates quantitatively that all-atom computations are more suitable than the Langevin equation or Brownian dynamics methods for probing the interaction dynamics and resulting conformational dynamics of protein unfolding in strong flows on nm ns -1 time/length scales while the reverse is true for investigation of slow, diffusively driven systems.

  6. Numerical studies of entangled positive-partial-transpose states in composite quantum systems

    International Nuclear Information System (INIS)

    Leinaas, Jon Magne; Sollid, Per Oyvind; Myrheim, Jan

    2010-01-01

    We report here on the results of numerical searches for PPT states in a series of bipartite quantum systems of low dimensions. PPT states are represented by density matrices that remain positive semidefinite under partial transposition with respect to one of the subsystems, and our searches are for such states with specified ranks for the density matrix and its partial transpose. For a series of different ranks extremal PPT states and nonextremal entangled PPT states have been found. The results are listed in tables and charted in diagrams. Comparison of the results for systems of different dimensions reveals several regularities. We discuss lower and upper bounds on the ranks of extremal PPT states.

  7. Partial dissociative emission cross sections and product state distributions of the resulting photofragments

    Energy Technology Data Exchange (ETDEWEB)

    Picconi, David; Grebenshchikov, Sergy Yu., E-mail: Sergy.Grebenshchikov@ch.tum.de

    2016-12-20

    This paper relates the partial cross section of a continuous optical emission into a given scattering channel of the lower electronic state to the photofragment population. This allows one to infer partial emission cross sections ‘non-optically’ from product state distributions; in computations, explicit construction of exact scattering states is therefore avoided. Applications to the emission spectra of NaI, CO{sub 2}, and pyrrole are given. It is also demonstrated that a similar relationship holds between partial cross sections of dissociative photoionization and distributions of ionic fragments over final product channels.

  8. Classes of n-copy undistillable quantum states with negative partial transposition

    International Nuclear Information System (INIS)

    Bandyopadhyay, Somshubhro; Roychowdhury, Vwani

    2003-01-01

    The discovery of entangled quantum states from which one cannot distill pure entanglement constitutes a fundamental recent advance in the field of quantum information. Such bipartite bound-entangled (BE) quantum states could fall into two distinct categories: (1) Inseparable states with positive partial transposition (PPT), and (2) states with negative partial transposition (NPT). While the existence of PPT BE states has been confirmed, only one class of conjectured NPT BE states has been discovered so far. We provide explicit constructions of a variety of multicopy undistillable NPT states, and conjecture that they constitute families of NPT BE states. For example, we show that for every pure state of Schmidt rank greater than or equal to 3, one can construct n-copy undistillable NPT states, for any n≥1. The abundance of such conjectured NPT BE states, we believe, considerably strengthens the notion that being NPT is only a necessary condition for a state to be distillable

  9. Unfolding study of a trimeric membrane protein AcrB.

    Science.gov (United States)

    Ye, Cui; Wang, Zhaoshuai; Lu, Wei; Wei, Yinan

    2014-07-01

    The folding of a multi-domain trimeric α-helical membrane protein, Escherichia coli inner membrane protein AcrB, was investigated. AcrB contains both a transmembrane domain and a large periplasmic domain. Protein unfolding in sodium dodecyl sulfate (SDS) and urea was monitored using the intrinsic fluorescence and circular dichroism spectroscopy. The SDS denaturation curve displayed a sigmoidal profile, which could be fitted with a two-state unfolding model. To investigate the unfolding of separate domains, a triple mutant was created, in which all three Trp residues in the transmembrane domain were replaced with Phe. The SDS unfolding profile of the mutant was comparable to that of the wild type AcrB, suggesting that the observed signal change was largely originated from the unfolding of the soluble domain. Strengthening of trimer association through the introduction of an inter-subunit disulfide bond had little effect on the unfolding profile, suggesting that trimer dissociation was not the rate-limiting step in unfolding monitored by fluorescence emission. Under our experimental condition, AcrB unfolding was not reversible. Furthermore, we experimented with the refolding of a monomeric mutant, AcrBΔloop , from the SDS unfolded state. The CD spectrum of the refolded AcrBΔloop superimposed well onto the spectra of the original folded protein, while the fluorescence spectrum was not fully recovered. In summary, our results suggested that the unfolding of the trimeric AcrB started with a local structural rearrangement. While the refolding of secondary structure in individual monomers could be achieved, the re-association of the trimer might be the limiting factor to obtain folded wild-type AcrB. © 2014 The Protein Society.

  10. A statistical approach to the estimation of mechanical unfolding parameters from the unfolding patterns of protein heteropolymers

    International Nuclear Information System (INIS)

    Beddard, G S; Brockwell, D J

    2010-01-01

    A statistical calculation is described with which the saw-tooth-like unfolding patterns of concatenated heteropolymeric proteins can be used to estimate the forced unfolding parameters of a previously uncharacterized protein. The chance of observing the various sequences of unfolding events, such as ABAABBB or BBAAABB etc, for two proteins of types A and B is calculated using proteins with various ratios of A and B and at different values of effective unfolding rate constants. If the experimental rate constant for forced unfolding, k 0 , and distance to the transition state x u are known for one protein, then the calculation allows an estimation of values for the other. The predictions are compared with Monte Carlo simulations and experimental data. (communication)

  11. Osmolyte Effects on the Unfolding Pathway of β-Lactoglobulin

    International Nuclear Information System (INIS)

    Meng Wei; Pan Hai; Qin Meng; Cao Yi; Wang Wei

    2013-01-01

    There are large amounts of osmolytes inside cells, which impact many physiological processes by complicated mechanisms. The osmolyte effects on the stability and folding of proteins have been studied in detail using simple two-state folding proteins. However, many important functional proteins fold in complex pathways involving various intermediates. Little is known about the osmolyte effects on the folding and unfolding of these proteins. It is noted that β-lactoglobulin (BLG) is an example of such proteins, whose unfolding involves an obvious intermediate state. Using equilibrium chemical denaturation and stopped-flow kinetics, we investigate the unfolding of BLG in the presence of different osmolytes, e.g., glycerol, ethylene glycol (EG) and poly(ethylene glycol)400 (PEG400). It is found that all these osmolytes can stabilize the unfolding intermediate by modulating the relative unfolding kinetics of the native and the intermediate states. The stabilization effects are similar for EG and PEG400 but distinct for glycerol. Since the unfolding intermediates of many proteins are directly related to protein misfolding diseases, evaluation of the osmolyte effects for the unfolding of these proteins in vitro should be beneficial for the understanding of the occurrence of the related diseases in vivo

  12. Verification of unfold error estimates in the unfold operator code

    International Nuclear Information System (INIS)

    Fehl, D.L.; Biggs, F.

    1997-01-01

    Spectral unfolding is an inverse mathematical operation that attempts to obtain spectral source information from a set of response functions and data measurements. Several unfold algorithms have appeared over the past 30 years; among them is the unfold operator (UFO) code written at Sandia National Laboratories. In addition to an unfolded spectrum, the UFO code also estimates the unfold uncertainty (error) induced by estimated random uncertainties in the data. In UFO the unfold uncertainty is obtained from the error matrix. This built-in estimate has now been compared to error estimates obtained by running the code in a Monte Carlo fashion with prescribed data distributions (Gaussian deviates). In the test problem studied, data were simulated from an arbitrarily chosen blackbody spectrum (10 keV) and a set of overlapping response functions. The data were assumed to have an imprecision of 5% (standard deviation). One hundred random data sets were generated. The built-in estimate of unfold uncertainty agreed with the Monte Carlo estimate to within the statistical resolution of this relatively small sample size (95% confidence level). A possible 10% bias between the two methods was unresolved. The Monte Carlo technique is also useful in underdetermined problems, for which the error matrix method does not apply. UFO has been applied to the diagnosis of low energy x rays emitted by Z-pinch and ion-beam driven hohlraums. copyright 1997 American Institute of Physics

  13. Immobilized unfolded cytochrome c acts as a catalyst for dioxygen reduction.

    Science.gov (United States)

    Tavagnacco, Claudio; Monari, Stefano; Ranieri, Antonio; Bortolotti, Carlo Augusto; Peressini, Silvia; Borsari, Marco

    2011-10-21

    Unfolding turns immobilized cytochrome c into a His-His ligated form endowed with catalytic activity towards O(2), which is absent in the native protein. Dioxygen could be used by naturally occurring unfolded cytochrome c as a substrate for the production of partially reduced oxygen species (PROS) contributing to the cell oxidative stress.

  14. Comparison of intra-organellar chaperone capacity for dealing with stress-induced protein unfolding

    NARCIS (Netherlands)

    Hageman, Jurre; Vos, Michel J.; van Waarde, Maria A. W. H.; Kampinga, Harm H.

    2007-01-01

    Molecular chaperones are essential for cells to prevent that partially unfolded proteins form non-functional, toxic aggregates. This requirement is increased when cells experience protein unfolding stresses and such could affect all compartments in the eukaryotic cell. Whether all organelles are

  15. Stable intermediates determine proteins' primary unfolding sites in the presence of surfactants

    DEFF Research Database (Denmark)

    Petersen, Steen Vang; Andersen, Kell kleiner; Enghild, Jan J.

    2009-01-01

    Despite detailed knowledge of the overall structural changes and stoichiometries of surfactant binding, little is known about which protein regions constitute the preferred sites of attack for initial unfolding. Here we have exposed three proteins to limited proteolysis at anionic (SDS) and catio......Despite detailed knowledge of the overall structural changes and stoichiometries of surfactant binding, little is known about which protein regions constitute the preferred sites of attack for initial unfolding. Here we have exposed three proteins to limited proteolysis at anionic (SDS......) and cationic (DTAC) surfactant concentrations corresponding to specific conformational transitions, using the surfactant-robust broad-specificity proteases Savinase and Alcalase. Cleavage sites are identified by SDS-PAGE and N-terminal sequencing. We observe well-defined cleavage fragments, which suggest......, cleavage sites can be rationalized from the structure of the protein's folding transition state and the position of loops in the native state. Nevertheless, they are more sensitive to choice of surfactant and protease, probably reflecting a heterogeneous and fluctuating ensemble of partially unfolded...

  16. Inefficiency and classical communication bounds for conversion between partially entangled pure bipartite states

    International Nuclear Information System (INIS)

    Fortescue, Ben; Lo, H.-K.

    2005-01-01

    We derive lower limits on the inefficiency and classical communication costs of dilution between two-term bipartite pure states that are partially entangled. We first calculate explicit relations between the allowable error and classical communication costs of entanglement dilution using a previously described protocol, then consider a two-stage dilution from singlets with this protocol followed by some unknown protocol for conversion between partially entangled states. Applying overall lower bounds on classical communication and inefficiency to this two-stage protocol, we derive bounds for the unknown protocol. In addition we derive analogous (but looser) bounds for general pure states

  17. Temperature dependence of the partially localized state in a 2D molecular nanoporous network

    Energy Technology Data Exchange (ETDEWEB)

    Piquero-Zulaica, Ignacio, E-mail: ipiquerozulaica@gmail.com [Centro de Física de Materiales (CSIC/UPV-EHU)—Materials Physics Center, Manuel Lardizabal 5, 20018 San Sebastián (Spain); Nowakowska, Sylwia [Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel (Switzerland); Ortega, J. Enrique [Centro de Física de Materiales (CSIC/UPV-EHU)—Materials Physics Center, Manuel Lardizabal 5, 20018 San Sebastián (Spain); Donostia International Physics Center (DIPC), Manuel Lardizabal 4, 20018 San Sebastián (Spain); Departamento Física Aplicada I, Universidad del País Vasco, 20018 San Sebastián (Spain); Stöhr, Meike [Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen (Netherlands); Gade, Lutz H. [Anorganisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg (Germany); Jung, Thomas A. [Laboratory for Micro- and Nanotechnology, Paul Scherrer Institute, 5232 Villigen (Switzerland); Lobo-Checa, Jorge, E-mail: jorge.lobo@csic.es [Instituto de Ciencia de Materiales de Aragón (ICMA), CSIC-Universidad de Zaragoza, E-50009 Zaragoza (Spain); Departamento de Física de la Materia Condensada, Universidad de Zaragoza, E-50009 Zaragoza (Spain)

    2017-01-01

    Highlights: • A state of a 2D porous network is demonstrated to originate from the Shockley state. • The temperature evolution of both states is followed by means of ARPES. • Identical energy shifts are observed for both states, proving their common origin. - Abstract: Two-dimensional organic and metal-organic nanoporous networks can scatter surface electrons, leading to their partial localization. Such quantum states are related to intrinsic surface states of the substrate material. We further corroborate this relation by studying the thermally induced energy shifts of the electronic band stemming from coupled quantum states hosted in a metal-organic array formed by a perylene derivative on Cu(111). We observe by angle-resolved photoemission spectroscopy (ARPES), that both, the Shockley and the partially localized states, shift by the same amount to higher binding energies upon decreasing the sample temperature, providing evidence of their common origin. Our experimental approach and results further support the use of surface states for modelling these systems, which are expected to provide new insight into the physics concerning partially confined electronic states: scattering processes, potential barrier strengths, excited state lifetimes or the influence of guest molecules.

  18. Geometrical analysis of cytochrome c unfolding

    Science.gov (United States)

    Urie, Kristopher G.; Pletneva, Ekaterina; Gray, Harry B.; Winkler, Jay R.; Kozak, John J.

    2011-01-01

    A geometrical model has been developed to study the unfolding of iso-1 cytochrome c. The model draws on the crystallographic data reported for this protein. These data were used to calculate the distance between specific residues in the folded state, and in a sequence of extended states defined by n = 3, 5, 7, 9, 11, 13, and 15 residue units. Exact calculations carried out for each of the 103 residues in the polypeptide chain demonstrate that different regions of the chain have different unfolding histories. Regions where there is a persistence of compact structures can be identified, and this geometrical characterization is fully consistent with analyses of time-resolved fluorescence energy-transfer (TrFET) data using dansyl-derivatized cysteine side-chain probes at positions 39, 50, 66, 85, and 99. The calculations were carried out assuming that different regions of the polypeptide chain unfold synchronously. To test this assumption, lattice Monte Carlo simulations were performed to study systematically the possible importance of asynchronicity. Calculations show that small departures from synchronous dynamics can arise if displacements of residues in the main body of the chain are much more sluggish than near-terminal residues.

  19. Atomic-partial vibrational density of states of i-AlCuFe quasicrystals

    International Nuclear Information System (INIS)

    Parshin, P.P.; Zemlyanov, M.; Brand, R.A.; Dianoux, A.J.; Calvayrac, Y.

    2002-01-01

    We present new results on the separation of the atomic-partial vibrational density of states for the ternary quasicrystal i-Al 62 Cu 25.5 Fe 12.5 . The decomposition into three atomic-partial functions, Al-, Cu- and Fe-g(E), has been performed self-consistently with the calculation of the multi-phonon contributions. The results show the surprising result that both Cu- and Fe-g(E) are strongly peaked. The low-energy regions of Al- and Cu-g(E) show strong deviations from Debye behaviour due to the presence of non-propagating low-energy vibrational states. (orig.)

  20. Inactivation and unfolding of protein tyrosine phosphatase from Thermus thermophilus HB27 during urea and guanidine hydrochloride denaturation.

    Directory of Open Access Journals (Sweden)

    Yejing Wang

    Full Text Available The effects of urea and guanidine hydrochloride (GdnHCl on the activity, conformation and unfolding process of protein tyrosine phosphatase (PTPase, a thermostable low molecular weight protein from Thermus thermophilus HB27, have been studied. Enzymatic activity assays showed both urea and GdnHCl resulted in the inactivation of PTPase in a concentration and time-dependent manner. Inactivation kinetics analysis suggested that the inactivation of PTPase induced by urea and GdnHCl were both monophasic and reversible processes, and the effects of urea and GdnHCl on PTPase were similar to that of mixed-type reversible inhibitors. Far-ultraviolet (UV circular dichroism (CD, Tryptophan and 1-anilinonaphthalene -8-sulfonic acid (ANS fluorescence spectral analyses indicated the existence of a partially active and an inactive molten globule-like intermediate during the unfolding processes induced by urea and GdnHCl, respectively. Based on the sequence alignment and the homolog Tt1001 protein structure, we discussed the possible conformational transitions of PTPase induced by urea and GdnHCl and compared the conformations of these unfolding intermediates with the transient states in bovine PTPase and its complex structures in detail. Our results may be able to provide some valuable clues to reveal the relationship between the structure and enzymatic activity, and the unfolding pathway and mechanism of PTPase.

  1. Quantum communication for satellite-to-ground networks with partially entangled states

    International Nuclear Information System (INIS)

    Chen Na; Quan Dong-Xiao; Pei Chang-Xing; Yang-Hong

    2015-01-01

    To realize practical wide-area quantum communication, a satellite-to-ground network with partially entangled states is developed in this paper. For efficiency and security reasons, the existing method of quantum communication in distributed wireless quantum networks with partially entangled states cannot be applied directly to the proposed quantum network. Based on this point, an efficient and secure quantum communication scheme with partially entangled states is presented. In our scheme, the source node performs teleportation only after an end-to-end entangled state has been established by entanglement swapping with partially entangled states. Thus, the security of quantum communication is guaranteed. The destination node recovers the transmitted quantum bit with the help of an auxiliary quantum bit and specially defined unitary matrices. Detailed calculations and simulation analyses show that the probability of successfully transferring a quantum bit in the presented scheme is high. In addition, the auxiliary quantum bit provides a heralded mechanism for successful communication. Based on the critical components that are presented in this article an efficient, secure, and practical wide-area quantum communication can be achieved. (paper)

  2. Applied multidimensional scaling and unfolding

    CERN Document Server

    Borg, Ingwer; Mair, Patrick

    2018-01-01

    This book introduces multidimensional scaling (MDS) and unfolding as data analysis techniques for applied researchers. MDS is used for the analysis of proximity data on a set of objects, representing the data as distances between points in a geometric space (usually of two dimensions). Unfolding is a related method that maps preference data (typically evaluative ratings of different persons on a set of objects) as distances between two sets of points (representing the persons and the objects, resp.). This second edition has been completely revised to reflect new developments and the coverage of unfolding has also been substantially expanded. Intended for applied researchers whose main interests are in using these methods as tools for building substantive theories, it discusses numerous applications (classical and recent), highlights practical issues (such as evaluating model fit), presents ways to enforce theoretical expectations for the scaling solutions, and addresses the typical mistakes that MDS/unfoldin...

  3. Iterative nonlinear unfolding code: TWOGO

    International Nuclear Information System (INIS)

    Hajnal, F.

    1981-03-01

    a new iterative unfolding code, TWOGO, was developed to analyze Bonner sphere neutron measurements. The code includes two different unfolding schemes which alternate on successive iterations. The iterative process can be terminated either when the ratio of the coefficient of variations in terms of the measured and calculated responses is unity, or when the percentage difference between the measured and evaluated sphere responses is less than the average measurement error. The code was extensively tested with various known spectra and real multisphere neutron measurements which were performed inside the containments of pressurized water reactors

  4. Neutron spectrum unfolding: Pt. 2

    International Nuclear Information System (INIS)

    Matiullah; Wiyaja, D.S.; Berzonis, M.A.; Bondars, H.; Lapenas, A.A.; Kudo, K.; Majeed, A.; Durrani, S.A.

    1991-01-01

    In Part I of this paper, we described the use of the computer code SAIPS in neutron spectrum unfolding. Here in Part II, we present our experimental work carried out to study the shape of the neutron spectrum in different experimental channels of a 5 MW light-water cooled and moderated research reactor. The spectral neutron flux was determined using various fission foils (placed in close contact with mica track detectors) and activation detectors. From the measured activities, the neutron spectrum was unfolded by SAIPS. (author)

  5. Distribution, transition and thermodynamic stability of protein conformations in the denaturant-induced unfolding of proteins.

    Science.gov (United States)

    Bian, Liujiao; Ji, Xu

    2014-01-01

    Extensive and intensive studies on the unfolding of proteins require appropriate theoretical model and parameter to clearly illustrate the feature and characteristic of the unfolding system. Over the past several decades, four approaches have been proposed to describe the interaction between proteins and denaturants, but some ambiguity and deviations usually occur in the explanation of the experimental data. In this work, a theoretical model was presented to show the dependency of the residual activity ratio of the proteins on the molar denaturant concentration. Through the characteristic unfolding parameters ki and Δmi in this model, the distribution, transition and thermodynamic stability of protein conformations during the unfolding process can be quantitatively described. This model was tested with the two-state unfolding of bovine heart cytochrome c and the three-state unfolding of hen egg white lysozyme induced by both guanidine hydrochloride and urea, the four-state unfolding of bovine carbonic anhydrase b induced by guanidine hydrochloride and the unfolding of some other proteins induced by denaturants. The results illustrated that this model could be used accurately to reveal the distribution and transition of protein conformations in the presence of different concentrations of denaturants and to evaluate the unfolding tendency and thermodynamic stability of different conformations. In most denaturant-induced unfolding of proteins, the unfolding became increasingly hard in next transition step and the proteins became more unstable as they attained next successive stable conformation. This work presents a useful method for people to study the unfolding of proteins and may be used to describe the unfolding and refolding of other biopolymers induced by denaturants, inducers, etc.

  6. An Empirical Method to Fuse Partially Overlapping State Vectors for Distributed State Estimation

    NARCIS (Netherlands)

    Sijs, J.; Hanebeck, U.; Noack, B.

    2013-01-01

    State fusion is a method for merging multiple estimates of the same state into a single fused estimate. Dealing with multiple estimates is one of the main concerns in distributed state estimation, where an estimated value of the desired state vector is computed in each node of a networked system.

  7. Dry molten globule intermediates and the mechanism of protein unfolding.

    Science.gov (United States)

    Baldwin, Robert L; Frieden, Carl; Rose, George D

    2010-10-01

    New experimental results show that either gain or loss of close packing can be observed as a discrete step in protein folding or unfolding reactions. This finding poses a significant challenge to the conventional two-state model of protein folding. Results of interest involve dry molten globule (DMG) intermediates, an expanded form of the protein that lacks appreciable solvent. When an unfolding protein expands to the DMG state, side chains unlock and gain conformational entropy, while liquid-like van der Waals interactions persist. Four unrelated proteins are now known to form DMGs as the first step of unfolding, suggesting that such an intermediate may well be commonplace in both folding and unfolding. Data from the literature show that peptide amide protons are protected in the DMG, indicating that backbone structure is intact despite loss of side-chain close packing. Other complementary evidence shows that secondary structure formation provides a major source of compaction during folding. In our model, the major free-energy barrier separating unfolded from native states usually occurs during the transition between the unfolded state and the DMG. The absence of close packing at this barrier provides an explanation for why phi-values, derived from a Brønsted-Leffler plot, depend primarily on structure at the mutational site and not on specific side-chain interactions. The conventional two-state folding model breaks down when there are DMG intermediates, a realization that has major implications for future experimental work on the mechanism of protein folding. 2010 Wiley-Liss, Inc.

  8. Hacking on decoy-state quantum key distribution system with partial phase randomization

    Science.gov (United States)

    Sun, Shi-Hai; Jiang, Mu-Sheng; Ma, Xiang-Chun; Li, Chun-Yan; Liang, Lin-Mei

    2014-04-01

    Quantum key distribution (QKD) provides means for unconditional secure key transmission between two distant parties. However, in practical implementations, it suffers from quantum hacking due to device imperfections. Here we propose a hybrid measurement attack, with only linear optics, homodyne detection, and single photon detection, to the widely used vacuum + weak decoy state QKD system when the phase of source is partially randomized. Our analysis shows that, in some parameter regimes, the proposed attack would result in an entanglement breaking channel but still be able to trick the legitimate users to believe they have transmitted secure keys. That is, the eavesdropper is able to steal all the key information without discovered by the users. Thus, our proposal reveals that partial phase randomization is not sufficient to guarantee the security of phase-encoding QKD systems with weak coherent states.

  9. Hacking on decoy-state quantum key distribution system with partial phase randomization.

    Science.gov (United States)

    Sun, Shi-Hai; Jiang, Mu-Sheng; Ma, Xiang-Chun; Li, Chun-Yan; Liang, Lin-Mei

    2014-04-23

    Quantum key distribution (QKD) provides means for unconditional secure key transmission between two distant parties. However, in practical implementations, it suffers from quantum hacking due to device imperfections. Here we propose a hybrid measurement attack, with only linear optics, homodyne detection, and single photon detection, to the widely used vacuum + weak decoy state QKD system when the phase of source is partially randomized. Our analysis shows that, in some parameter regimes, the proposed attack would result in an entanglement breaking channel but still be able to trick the legitimate users to believe they have transmitted secure keys. That is, the eavesdropper is able to steal all the key information without discovered by the users. Thus, our proposal reveals that partial phase randomization is not sufficient to guarantee the security of phase-encoding QKD systems with weak coherent states.

  10. Atomic-partial vibrational density of states of i-AlCuFe quasicrystals

    CERN Document Server

    Parshin, P P; Brand, R A; Dianoux, A J; Calvayrac, Y

    2002-01-01

    We present new results on the separation of the atomic-partial vibrational density of states for the ternary quasicrystal i-Al sub 6 sub 2 Cu sub 2 sub 5 sub . sub 5 Fe sub 1 sub 2 sub . sub 5. The decomposition into three atomic-partial functions, Al-, Cu- and Fe-g(E), has been performed self-consistently with the calculation of the multi-phonon contributions. The results show the surprising result that both Cu- and Fe-g(E) are strongly peaked. The low-energy regions of Al- and Cu-g(E) show strong deviations from Debye behaviour due to the presence of non-propagating low-energy vibrational states. (orig.)

  11. Parabolic partial differential equations with discrete state-dependent delay: Classical solutions and solution manifold

    Czech Academy of Sciences Publication Activity Database

    Krisztin, T.; Rezunenko, Oleksandr

    2016-01-01

    Roč. 260, č. 5 (2016), s. 4454-4472 ISSN 0022-0396 R&D Projects: GA ČR GAP103/12/2431 Institutional support: RVO:67985556 Keywords : Parabolic partial differential equations * State dependent delay * Solution manifold Subject RIV: BC - Control Systems Theory Impact factor: 1.988, year: 2016 http://library.utia.cas.cz/separaty/2016/AS/rezunenko-0457879.pdf

  12. Enthalpy-entropy compensation in protein unfolding

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Enthalpy-entropy compensation was found to be a universal law in protein unfolding based on over 3 000 experimental data. Water molecular reorganization accompanying the protein unfolding was suggested as the origin of the enthalpy-entropy compensation in protein unfolding. It is indicated that the enthalpy-entropy compensation constitutes the physical foundation that satisfies the biological need of the small free energy changes in protein unfolding, without the sacrifice of the bio-diversity of proteins. The enthalpy-entropy compensation theory proposed herein also provides valuable insights into the Privalov's puzzle of enthalpy and entropy convergence in protein unfolding.

  13. Deep Unfolding for Topic Models.

    Science.gov (United States)

    Chien, Jen-Tzung; Lee, Chao-Hsi

    2018-02-01

    Deep unfolding provides an approach to integrate the probabilistic generative models and the deterministic neural networks. Such an approach is benefited by deep representation, easy interpretation, flexible learning and stochastic modeling. This study develops the unsupervised and supervised learning of deep unfolded topic models for document representation and classification. Conventionally, the unsupervised and supervised topic models are inferred via the variational inference algorithm where the model parameters are estimated by maximizing the lower bound of logarithm of marginal likelihood using input documents without and with class labels, respectively. The representation capability or classification accuracy is constrained by the variational lower bound and the tied model parameters across inference procedure. This paper aims to relax these constraints by directly maximizing the end performance criterion and continuously untying the parameters in learning process via deep unfolding inference (DUI). The inference procedure is treated as the layer-wise learning in a deep neural network. The end performance is iteratively improved by using the estimated topic parameters according to the exponentiated updates. Deep learning of topic models is therefore implemented through a back-propagation procedure. Experimental results show the merits of DUI with increasing number of layers compared with variational inference in unsupervised as well as supervised topic models.

  14. The effects of crowding agents Dextran-70k and PEG-8k on actin structure and unfolding reaction

    Science.gov (United States)

    Gagarskaia, Iuliia A.; Povarova, Olga I.; Uversky, Vladimir N.; Kuznetsova, Irina M.; Turoverov, Konstantin K.

    2017-07-01

    Recently, an increasing number of studies on proteins' structure, stability and folding are trying to bring the experimental conditions closer to those existing in a living cell, namely to the conditions of macromolecular crowding. In vitro such conditions are typically imitated by the ;inert; highly water-soluble polymers with different hydrodynamic dimensions. In this work, the effects of crowded milieu on the structure and conformational stability of actin, which is a key component of the muscle contraction system, was examined. The crowded milieu was simulated by high concentrations of PEG-8k or Dextran-70k. It was revealed that both crowding agents decelerated but not inhibited actin unfolding and made a compact state of inactivated actin thermodynamically more favorable in comparison with the unfolded state. At the same time, the high viscosity of the solution of crowding agents slowed down all processes and especially inactivated actin formation, since it involves the interaction of 14-16 partially unfolded actin molecules. The effects of crowding agent were larger when its hydrodynamic dimensions were closer to the size of globular actin.

  15. TFE-induced local unfolding and fibrillation of SOD1: bridging the experiment and simulation studies.

    Science.gov (United States)

    Kumar, Vijay; Prakash, Amresh; Pandey, Preeti; Lynn, Andrew M; Hassan, Md Imtaiyaz

    2018-05-18

    Misfolding and aggregation of Cu, Zn Superoxide dismutase (SOD1) is involved in the neurodegenerative disease, amyotrophic lateral sclerosis. Many studies have shown that metal-depleted, monomeric form of SOD1 displays substantial local unfolding dynamics and is the precursor for aggregation. Here, we have studied the structure and dynamics of different apo monomeric SOD1 variants associated with unfolding and aggregation in aqueous trifluoroethanol (TFE) through experiments and simulation. TFE induces partially unfolded β-sheet-rich extended conformations in these SOD1 variants, which subsequently develops aggregates with fibril-like characteristics. Fibrillation was achieved more easily in disulfide-reduced monomeric SOD1 when compared with wild-type and mutant monomeric SOD1. At higher concentrations of TFE, a native-like structure with the increase in α-helical content was observed. The molecular dynamics simulation results illustrate distinct structural dynamics for different regions of SOD1 variants and show uniform local unfolding of β-strands. The strands protected by the zinc-binding and electrostatic loops were found to unfold first in 20% (v/v) TFE, leading to a partial unfolding of β-strands 4, 5, and 6 which are prone to aggregation. Our results thus shed light on the role of local unfolding and conformational dynamics in SOD1 misfolding and aggregation. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

  16. Becoming a Peroxidase: Cardiolipin-Induced Unfolding of Cytochrome c

    Science.gov (United States)

    Muenzner, Julia; Toffey, Jason R.; Hong, Yuning; Pletneva, Ekaterina V.

    2014-01-01

    Interactions of cytochrome c (cyt c) with a unique mitochondrial glycerophospholipid cardiolipin (CL) are relevant for the protein’s function in oxidative phosphorylation and apoptosis. Binding to CL-containing membranes promotes cyt c unfolding and dramatically enhances the protein’s peroxidase activity, which is critical in early stages of apoptosis. We have employed a collection of seven dansyl variants of horse heart cyt c to probe the sequence of steps in this functional transformation. Kinetic measurements have unraveled four distinct processes during CL-induced cyt c unfolding: rapid protein binding to CL liposomes; rearrangements of protein substructures with small unfolding energies; partial insertion of the protein into the lipid bilayer; and extensive protein restructuring leading to “open” extended structures. While early rearrangements depend on a hierarchy of foldons in the native structure, the later process of large-scale unfolding is influenced by protein interactions with the membrane surface. The opening of the cyt c structure exposes the heme group, which enhances the protein’s peroxidase activity and also frees the C-terminal helix to aid in the translocation of the protein through CL membranes. PMID:23713573

  17. Partial radiative-recombination cross sections for excited states of hydrogen

    International Nuclear Information System (INIS)

    Fazio, P.M.; Copeland, G.E.

    1985-01-01

    The squares of the dipole and quadrupole matrix elements for the free-to-bound transitions of hydrogen up to bound states Vertical Barn = 20,l = 19> are derived in closed analytic form as a function of the kinetic energy of the free electron. Coulomb wave functions are used for the free as well as the bound states and, thus, the results are good for any electron energy. Several interesting effects are found. First, the transition probabilities are maximum for recombination into specific intermediate-angular-momentum states at low energies (w<1 eV) and where the free-state angular momentum is greater than that of the bound state. Further, that specific intermediate-angular-momentum state depends on the kinetic energy of the free electron. This behavior is in contrast to the ''normal'' behavior of the transition strengths where recombination into s states is greatest and decreases with increasing angular momentum. Second, the quadrupole matrix elements vanish for certain velocities of the free electron. These ''zeros'' produce minima in the corresponding quadrupole cross sections. Finally, the calculated partial cross sections for recombination into high-angular-momentum states are greater when quadrupole transitions are included

  18. Low-rank extremal positive-partial-transpose states and unextendible product bases

    International Nuclear Information System (INIS)

    Leinaas, Jon Magne; Sollid, Per Oyvind; Myrheim, Jan

    2010-01-01

    It is known how to construct, in a bipartite quantum system, a unique low-rank entangled mixed state with positive partial transpose (a PPT state) from an unextendible product basis (UPB), defined as an unextendible set of orthogonal product vectors. We point out that a state constructed in this way belongs to a continuous family of entangled PPT states of the same rank, all related by nonsingular unitary or nonunitary product transformations. The characteristic property of a state ρ in such a family is that its kernel Ker ρ has a generalized UPB, a basis of product vectors, not necessarily orthogonal, with no product vector in Im ρ, the orthogonal complement of Ker ρ. The generalized UPB in Ker ρ has the special property that it can be transformed to orthogonal form by a product transformation. In the case of a system of dimension 3x3, we give a complete parametrization of orthogonal UPBs. This is then a parametrization of families of rank 4 entangled (and extremal) PPT states, and we present strong numerical evidence that it is a complete classification of such states. We speculate that the lowest rank entangled and extremal PPT states also in higher dimensions are related to generalized, nonorthogonal UPBs in similar ways.

  19. BUMS--Bonner sphere Unfolding Made Simple an HTML based multisphere neutron spectrometer unfolding package

    CERN Document Server

    Sweezy, J; Veinot, K

    2002-01-01

    A new multisphere neutron spectrometer unfolding package, Bonner sphere Unfolding Made Simple (BUMS) has been developed that uses an HTML interface to simplify data input and code execution for the novice and the advanced user. This new unfolding package combines the unfolding algorithms contained in other popular unfolding codes under one easy to use interface. The interface makes use of web browsing software to provide a graphical user interface to the unfolding algorithms. BUMS integrates the SPUNIT, BON, MAXIET, and SAND-II unfolding algorithms into a single package. This package also includes a library of 14 response matrices, 58 starting spectra, and 24 dose and detector responses. BUMS has several improvements beyond the addition of unfolding algorithms. It has the ability to search for the most appropriate starting spectra. Also, plots of the unfolded neutron spectra are automatically generated. The BUMS package runs via a web server and may be accessed by any computer with access to the Internet at h...

  20. Stochastic simulations of conditional states of partially observed systems, quantum and classical

    International Nuclear Information System (INIS)

    Gambetta, Jay; Wiseman, H M

    2005-01-01

    In a partially observed quantum or classical system the information that we cannot access results in our description of the system becoming mixed, even if we have perfect initial knowledge. That is, if the system is quantum the conditional state will be given by a state matrix ρ r (t), and if classical, the conditional state will be given by a probability distribution P r (x,t), where r is the result of the measurement. Thus to determine the evolution of this conditional state, under continuous-in-time monitoring, requires a numerically expensive calculation. In this paper we demonstrate a numerical technique based on linear measurement theory that allows us to determine the conditional state using only pure states. That is, our technique reduces the problem size by a factor of N, the number of basis states for the system. Furthermore we show that our method can be applied to joint classical and quantum systems such as arise in modelling realistic (finite bandwidth, noisy) measurement

  1. Correlation functions for fully or partially state-resolved reactive scattering calculations

    International Nuclear Information System (INIS)

    Manthe, Uwe; Welsch, Ralph

    2014-01-01

    Flux correlation functions and the quantum transition state concept are important tools for the accurate description of polyatomic reaction processes. Combined with the multi-configurational time-dependent Hartree approach, they facilitate rigorous full-dimensional calculations of cumulative and initial-state selected reaction probabilities for six atom reactions. In recent work [R. Welsch, F. Huarte-Larrañaga, and U. Manthe, J. Chem. Phys. 136, 064117 (2012)], an approach which allows one to calculate also state-to-state reaction probabilities within the quantum transition state concept has been introduced. This article presents further developments. Alternative generalized flux correlation functions are introduced and discussed. Equations for the calculation of fully state-resolved differential cross section using arbitrary definitions of the body fixed frame are derived. An approach for the efficient calculation of partially state-resolved observables as a function of the collision energy is introduced. Finally, numerical test studying the D + H 2 reaction illustrate important aspects of the formalism

  2. Biomass hydrolysis inhibition at high hydrogen partial pressure in solid-state anaerobic digestion.

    Science.gov (United States)

    Cazier, E A; Trably, E; Steyer, J P; Escudie, R

    2015-08-01

    In solid-state anaerobic digestion, so-called ss-AD, biogas production is inhibited at high total solids contents. Such inhibition is likely caused by a slow diffusion of dissolved reaction intermediates that locally accumulate. In this study, we investigated the effect of H2 and CO2 partial pressure on ss-AD. Partial pressure of H2 and/or CO2 was artificially fixed, from 0 to 1 557mbars for H2 and from 0 to 427mbars for CO2. High partial pressure of H2 showed a significant effect on methanogenesis, while CO2 had no impact. At high [Formula: see text] , the overall substrate degradation decreased with no accumulation of metabolites from acidogenic bacteria, indicating that the hydrolytic activity was specifically impacted. Interestingly, such inhibition did not occur when CO2 was added with H2. This result suggests that CO2 gas transfer is probably a key factor in ss-AD from biomass. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Partial state feedback control of chaotic neural network and its application

    International Nuclear Information System (INIS)

    He Guoguang; Shrimali, Manish Dev; Aihara, Kazuyuki

    2007-01-01

    The chaos control in the chaotic neural network is studied using the partial state feedback with a control signal from a few control neurons. The controlled CNN converges to one of the stored patterns with a period which depends on the initial conditions, i.e., the set of control neurons and other control parameters. We show that the controlled CNN can distinguish between two initial patterns even if they have a small difference. This implies that such a controlled CNN can be feasibly applied to information processing such as pattern recognition

  4. Unfolding of cytochrome c immobilized on self-assembled monolayers. An electrochemical study

    International Nuclear Information System (INIS)

    Monari, Stefano; Ranieri, Antonio; Bortolotti, Carlo Augusto; Peressini, Silvia; Tavagnacco, Claudio; Borsari, Marco

    2011-01-01

    Highlights: → Denaturation involves intermediate and partially unfolded forms. → An unfolded species displaying the haem with Fe coordinated by two His is observed. → Under unfolding conditions the nature of the SAM influences conformation of protein. → Concentration of the unfolding agent affects redox properties of immobilized protein. - Abstract: The electron transfer (ET) process of progressively unfolded bovine cytochrome c immobilized on different self-assembled monolayers (SAMs) was investigated. Insight is gained on the role of the SAM surface on the functionality of the partially unfolded and non-native forms of the adsorbed protein. Direct electrochemical measurements were performed on cytochrome c adsorbed on mercaptopyridine (MP) and mixed 11-mercapto-1-undecanoic acid/11-mercapto-1-undecanol (MUA/MU) at varying temperature, in the presence of urea as unfolding agent. Under strongly unfolding conditions, a non-native form of cytochrome c, in which the methionine ligand is replaced by a histidine, was observed on both MP and MUA/MU SAMs. The E o ' of the native form, in which the haem is axially coordinated by methionine and histidine, slightly shifts to negative values upon increasing urea concentration. However, the non-native bis-histidinate species shows a much lower E o ' value (by approximately 0.4 V) which is by far enthalpic in origin and largely determined by axial ligand swapping. Analysis of the reduction enthalpies and entropies and of the ET rate constants indicate that the nature of the SAM (hydrophilic or anionic) results in changes in the conformational rearrangement of the cytochrome c under unfolding conditions.

  5. Unfolding of cytochrome c immobilized on self-assembled monolayers. An electrochemical study

    Energy Technology Data Exchange (ETDEWEB)

    Monari, Stefano; Ranieri, Antonio; Bortolotti, Carlo Augusto; Peressini, Silvia [Department of Chemistry, University of Modena and Reggio Emilia, via Campi 183, 41125 Modena (Italy); Tavagnacco, Claudio [Department of Chemistry, University of Trieste, via Giorgieri 1, 34127 Trieste (Italy); Borsari, Marco, E-mail: marco.borsari@unimore.it [Department of Chemistry, University of Modena and Reggio Emilia, via Campi 183, 41125 Modena (Italy)

    2011-08-01

    Highlights: > Denaturation involves intermediate and partially unfolded forms. > An unfolded species displaying the haem with Fe coordinated by two His is observed. > Under unfolding conditions the nature of the SAM influences conformation of protein. > Concentration of the unfolding agent affects redox properties of immobilized protein. - Abstract: The electron transfer (ET) process of progressively unfolded bovine cytochrome c immobilized on different self-assembled monolayers (SAMs) was investigated. Insight is gained on the role of the SAM surface on the functionality of the partially unfolded and non-native forms of the adsorbed protein. Direct electrochemical measurements were performed on cytochrome c adsorbed on mercaptopyridine (MP) and mixed 11-mercapto-1-undecanoic acid/11-mercapto-1-undecanol (MUA/MU) at varying temperature, in the presence of urea as unfolding agent. Under strongly unfolding conditions, a non-native form of cytochrome c, in which the methionine ligand is replaced by a histidine, was observed on both MP and MUA/MU SAMs. The E{sup o}' of the native form, in which the haem is axially coordinated by methionine and histidine, slightly shifts to negative values upon increasing urea concentration. However, the non-native bis-histidinate species shows a much lower E{sup o}' value (by approximately 0.4 V) which is by far enthalpic in origin and largely determined by axial ligand swapping. Analysis of the reduction enthalpies and entropies and of the ET rate constants indicate that the nature of the SAM (hydrophilic or anionic) results in changes in the conformational rearrangement of the cytochrome c under unfolding conditions.

  6. Influence of partial ionization and scattering states on the solar interior structure

    International Nuclear Information System (INIS)

    Ulrich, R.K.

    1982-01-01

    The equation of state for the solar interior is normally assumed to be a fully ionized gas corrected by the Debye-Hueckel Coulomb interaction, partial degeneracy, and radiation pressure. The assumption of full ionization is dropped in this paper, and the influence of scattering states is included. The theory of scattering states appears to be new to astrophysics. This theory has been developed by Larkin and is discussed thoroughly by Ebeling, Kraft, and Kremp. The effect of scattering states eliminates the need to invoke a process of ''pressure ionization'' for which no satisfactory theory exists. Six solar models which include varying forms of the equation of state are discussed. The Saha equation without scattering states gives a neutrino counting rate of 7.41 SNU for the 37 Cl experiment, while assumed ionization for T>3 x 10 5 K gives 8.87 SNU, and the Saha equation with the lowest order effect of scattering states (Planck-Larkin equation) gives 8.83 SNU. Inclusion of the second virial coefficient due to scattering states brings the result to 9.02 SNU. The changes of quantities such as central temperature and the temperature at the base of the convective envelope are small and bear a similar relationship among the models. The initial hydrogen abundance of the model including the second virial coefficient due to scattering states is in good agreement with that found for the Orion nebula and B stars, i.e., log (N/sub He//N/sub H/)+12 = 10.97

  7. Basis adaptation and domain decomposition for steady-state partial differential equations with random coefficients

    Energy Technology Data Exchange (ETDEWEB)

    Tipireddy, R.; Stinis, P.; Tartakovsky, A. M.

    2017-12-01

    We present a novel approach for solving steady-state stochastic partial differential equations (PDEs) with high-dimensional random parameter space. The proposed approach combines spatial domain decomposition with basis adaptation for each subdomain. The basis adaptation is used to address the curse of dimensionality by constructing an accurate low-dimensional representation of the stochastic PDE solution (probability density function and/or its leading statistical moments) in each subdomain. Restricting the basis adaptation to a specific subdomain affords finding a locally accurate solution. Then, the solutions from all of the subdomains are stitched together to provide a global solution. We support our construction with numerical experiments for a steady-state diffusion equation with a random spatially dependent coefficient. Our results show that highly accurate global solutions can be obtained with significantly reduced computational costs.

  8. Energy-Efficient Power Allocation for Fixed-Gain Amplify-and-Forward Relay Networks with Partial Channel State Information

    KAUST Repository

    Zafar, Ammar; Alouini, Mohamed-Slim; Chen, Yunfei; Radaydeh, Redha M.

    2012-01-01

    In this letter, energy-efficient transmission and power allocation for fixed-gain amplify-and-forward relay networks with partial channel state information (CSI) are studied. In the energy-efficiency problem, the total power consumed is minimized

  9. Solvent Effects on Protein Folding/Unfolding

    Science.gov (United States)

    García, A. E.; Hillson, N.; Onuchic, J. N.

    Pressure effects on the hydrophobic potential of mean force led Hummer et al. to postulate a model for pressure denaturation of proteins in which denaturation occurs by means of water penetration into the protein interior, rather than by exposing the protein hydrophobic core to the solvent --- commonly used to describe temperature denaturation. We study the effects of pressure in protein folding/unfolding kinetics in an off-lattice minimalist model of a protein in which pressure effects have been incorporated by means of the pair-wise potential of mean force of hydrophobic groups in water. We show that pressure slows down the kinetics of folding by decreasing the reconfigurational diffusion coefficient and moves the location of the folding transition state.

  10. Individual globular domains and domain unfolding visualized in overstretched titin molecules with atomic force microscopy.

    Directory of Open Access Journals (Sweden)

    Zsolt Mártonfalvi

    Full Text Available Titin is a giant elastomeric protein responsible for the generation of passive muscle force. Mechanical force unfolds titin's globular domains, but the exact structure of the overstretched titin molecule is not known. Here we analyzed, by using high-resolution atomic force microscopy, the structure of titin molecules overstretched with receding meniscus. The axial contour of the molecules was interrupted by topographical gaps with a mean width of 27.7 nm that corresponds well to the length of an unfolded globular (immunoglobulin and fibronectin domain. The wide gap-width distribution suggests, however, that additional mechanisms such as partial domain unfolding and the unfolding of neighboring domain multimers may also be present. In the folded regions we resolved globules with an average spacing of 5.9 nm, which is consistent with a titin chain composed globular domains with extended interdomain linker regions. Topographical analysis allowed us to allocate the most distal unfolded titin region to the kinase domain, suggesting that this domain systematically unfolds when the molecule is exposed to overstretching forces. The observations support the prediction that upon the action of stretching forces the N-terminal ß-sheet of the titin kinase unfolds, thus exposing the enzyme's ATP-binding site and hence contributing to the molecule's mechanosensory function.

  11. Improving the efficiency of single and multiple teleportation protocols based on the direct use of partially entangled states

    Energy Technology Data Exchange (ETDEWEB)

    Fortes, Raphael; Rigolin, Gustavo, E-mail: rigolin@ifi.unicamp.br

    2013-09-15

    We push the limits of the direct use of partially pure entangled states to perform quantum teleportation by presenting several protocols in many different scenarios that achieve the optimal efficiency possible. We review and put in a single formalism the three major strategies known to date that allow one to use partially entangled states for direct quantum teleportation (no distillation strategies permitted) and compare their efficiencies in real world implementations. We show how one can improve the efficiency of many direct teleportation protocols by combining these techniques. We then develop new teleportation protocols employing multipartite partially entangled states. The three techniques are also used here in order to achieve the highest efficiency possible. Finally, we prove the upper bound for the optimal success rate for protocols based on partially entangled Bell states and show that some of the protocols here developed achieve such a bound. -- Highlights: •Optimal direct teleportation protocols using directly partially entangled states. •We put in a single formalism all strategies of direct teleportation. •We extend these techniques for multipartite partially entangle states. •We give upper bounds for the optimal efficiency of these protocols.

  12. Imaging the equilibrium state and magnetization dynamics of partially built hard disk write heads

    Energy Technology Data Exchange (ETDEWEB)

    Valkass, R. A. J., E-mail: rajv202@ex.ac.uk; Yu, W.; Shelford, L. R.; Keatley, P. S.; Loughran, T. H. J.; Hicken, R. J. [School of Physics, University of Exeter, Stocker Road, Exeter EX4 4QL (United Kingdom); Cavill, S. A. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Department of Physics, University of York, Heslington, York YO10 5DD (United Kingdom); Laan, G. van der; Dhesi, S. S. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Bashir, M. A.; Gubbins, M. A. [Research and Development, Seagate Technology, 1 Disc Drive, Springtown Industrial Estate, Derry BT48 0BF (United Kingdom); Czoschke, P. J.; Lopusnik, R. [Recording Heads Operation, Seagate Technology, 7801 Computer Avenue South, Bloomington, Minnesota 55435 (United States)

    2015-06-08

    Four different designs of partially built hard disk write heads with a yoke comprising four repeats of NiFe (1 nm)/CoFe (50 nm) were studied by both x-ray photoemission electron microscopy (XPEEM) and time-resolved scanning Kerr microscopy (TRSKM). These techniques were used to investigate the static equilibrium domain configuration and the magnetodynamic response across the entire structure, respectively. Simulations and previous TRSKM studies have made proposals for the equilibrium domain configuration of similar structures, but no direct observation of the equilibrium state of the writers has yet been made. In this study, static XPEEM images of the equilibrium state of writer structures were acquired using x-ray magnetic circular dichroism as the contrast mechanism. These images suggest that the crystalline anisotropy dominates the equilibrium state domain configuration, but competition with shape anisotropy ultimately determines the stability of the equilibrium state. Dynamic TRSKM images were acquired from nominally identical devices. These images suggest that a longer confluence region may hinder flux conduction from the yoke into the pole tip: the shorter confluence region exhibits clear flux beaming along the symmetry axis, whereas the longer confluence region causes flux to conduct along one edge of the writer. The observed variations in dynamic response agree well with the differences in the equilibrium magnetization configuration visible in the XPEEM images, confirming that minor variations in the geometric design of the writer structure can have significant effects on the process of flux beaming.

  13. Iterative Observer-based Estimation Algorithms for Steady-State Elliptic Partial Differential Equation Systems

    KAUST Repository

    Majeed, Muhammad Usman

    2017-07-19

    Steady-state elliptic partial differential equations (PDEs) are frequently used to model a diverse range of physical phenomena. The source and boundary data estimation problems for such PDE systems are of prime interest in various engineering disciplines including biomedical engineering, mechanics of materials and earth sciences. Almost all existing solution strategies for such problems can be broadly classified as optimization-based techniques, which are computationally heavy especially when the problems are formulated on higher dimensional space domains. However, in this dissertation, feedback based state estimation algorithms, known as state observers, are developed to solve such steady-state problems using one of the space variables as time-like. In this regard, first, an iterative observer algorithm is developed that sweeps over regular-shaped domains and solves boundary estimation problems for steady-state Laplace equation. It is well-known that source and boundary estimation problems for the elliptic PDEs are highly sensitive to noise in the data. For this, an optimal iterative observer algorithm, which is a robust counterpart of the iterative observer, is presented to tackle the ill-posedness due to noise. The iterative observer algorithm and the optimal iterative algorithm are then used to solve source localization and estimation problems for Poisson equation for noise-free and noisy data cases respectively. Next, a divide and conquer approach is developed for three-dimensional domains with two congruent parallel surfaces to solve the boundary and the source data estimation problems for the steady-state Laplace and Poisson kind of systems respectively. Theoretical results are shown using a functional analysis framework, and consistent numerical simulation results are presented for several test cases using finite difference discretization schemes.

  14. A linear iterative unfolding method

    International Nuclear Information System (INIS)

    László, András

    2012-01-01

    A frequently faced task in experimental physics is to measure the probability distribution of some quantity. Often this quantity to be measured is smeared by a non-ideal detector response or by some physical process. The procedure of removing this smearing effect from the measured distribution is called unfolding, and is a delicate problem in signal processing, due to the well-known numerical ill behavior of this task. Various methods were invented which, given some assumptions on the initial probability distribution, try to regularize the unfolding problem. Most of these methods definitely introduce bias into the estimate of the initial probability distribution. We propose a linear iterative method (motivated by the Neumann series / Landweber iteration known in functional analysis), which has the advantage that no assumptions on the initial probability distribution is needed, and the only regularization parameter is the stopping order of the iteration, which can be used to choose the best compromise between the introduced bias and the propagated statistical and systematic errors. The method is consistent: 'binwise' convergence to the initial probability distribution is proved in absence of measurement errors under a quite general condition on the response function. This condition holds for practical applications such as convolutions, calorimeter response functions, momentum reconstruction response functions based on tracking in magnetic field etc. In presence of measurement errors, explicit formulae for the propagation of the three important error terms is provided: bias error (distance from the unknown to-be-reconstructed initial distribution at a finite iteration order), statistical error, and systematic error. A trade-off between these three error terms can be used to define an optimal iteration stopping criterion, and the errors can be estimated there. We provide a numerical C library for the implementation of the method, which incorporates automatic

  15. Uncertainty analysis of dosimetry spectrum unfolding

    International Nuclear Information System (INIS)

    Perey, F.G.

    1977-01-01

    The propagation of uncertainties in the input data is analyzed for the usual dosimetry unfolding solution. A new formulation of the dosimetry unfolding problem is proposed in which the most likely value of the spectrum is obtained. The relationship of this solution to the usual one is discussed

  16. History, rare, and multiple events of mechanical unfolding of repeat proteins

    Science.gov (United States)

    Sumbul, Fidan; Marchesi, Arin; Rico, Felix

    2018-03-01

    Mechanical unfolding of proteins consisting of repeat domains is an excellent tool to obtain large statistics. Force spectroscopy experiments using atomic force microscopy on proteins presenting multiple domains have revealed that unfolding forces depend on the number of folded domains (history) and have reported intermediate states and rare events. However, the common use of unspecific attachment approaches to pull the protein of interest holds important limitations to study unfolding history and may lead to discarding rare and multiple probing events due to the presence of unspecific adhesion and uncertainty on the pulling site. Site-specific methods that have recently emerged minimize this uncertainty and would be excellent tools to probe unfolding history and rare events. However, detailed characterization of these approaches is required to identify their advantages and limitations. Here, we characterize a site-specific binding approach based on the ultrastable complex dockerin/cohesin III revealing its advantages and limitations to assess the unfolding history and to investigate rare and multiple events during the unfolding of repeated domains. We show that this approach is more robust, reproducible, and provides larger statistics than conventional unspecific methods. We show that the method is optimal to reveal the history of unfolding from the very first domain and to detect rare events, while being more limited to assess intermediate states. Finally, we quantify the forces required to unfold two molecules pulled in parallel, difficult when using unspecific approaches. The proposed method represents a step forward toward more reproducible measurements to probe protein unfolding history and opens the door to systematic probing of rare and multiple molecule unfolding mechanisms.

  17. Group additivity calculations of the thermodynamic properties of unfolded proteins in aqueous solution: a critical comparison of peptide-based and HKF models.

    Science.gov (United States)

    Hakin, A W; Hedwig, G R

    2001-02-15

    A recent paper in this journal [Amend and Helgeson, Biophys. Chem. 84 (2000) 105] presented a new group additivity model to calculate various thermodynamic properties of unfolded proteins in aqueous solution. The parameters given for the revised Helgeson-Kirkham-Flowers (HKF) equations of state for all the constituent groups of unfolded proteins can be used, in principle, to calculate the partial molar heat capacity, C(o)p.2, and volume, V2(0), at infinite dilution of any polypeptide. Calculations of the values of C(o)p.2 and V2(0) for several polypeptides have been carried out to test the predictive utility of the HKF group additivity model. The results obtained are in very poor agreement with experimental data, and also with results calculated using a peptide-based group additivity model. A critical assessment of these two additivity models is presented.

  18. Probabilistic teleportation of an arbitrary three-particle state via a partial entangled four-particle state and a partial entangled pair

    Institute of Scientific and Technical Information of China (English)

    戴宏毅; 李承祖; 陈平行

    2003-01-01

    We present a scheme to probabilistically teleport an arbitrary and unknown three-particle state via a two-particle non-maximally entangled state and a four-particle non-maximally entangled state as the quantum channel. With the help of Bell-state measurements, an arbitrary three-particle state can be perfectly teleported if a receiver introduces a collective unitary transformation. All kinds of unitary transformations are given in greater detail. This scheme can be generalized to the teleportation of an arbitrary and unknown multiparticle state.

  19. Structure of Unsteady Partially Premixed Flames and the Existence of State Relationships

    Directory of Open Access Journals (Sweden)

    Suresh K. Aggarwal

    2009-09-01

    Full Text Available In this study, we examine the structure and existence of state relationships in unsteady partially premixed flames (PPFs subjected to buoyancy-induced and external perturbations. A detailed numerical model is employed to simulate the steady and unsteady two-dimensional PPFs established using a slot burner under normal and zero-gravity conditions. The coflow velocity is parametrically varied. The methane-air chemistry is modeled using a fairly detailed mechanism that contains 81 elementary reactions and 24 species. Validation of the computational model is provided through comparisons of predictions with nonintrusive measurements. The combustion proceeds in two reaction zones, one a rich premixed zone and the other a nonpremixed zone. These reaction zones are spatially separated, but involve strong interactions between them due to thermochemistry and scalar transport. The fuel is mostly consumed in the premixed zone to produce CO and H2, which are transported to and consumed in the nonpremixed zone. The nonpremixed zone in turn provides heat and H-atoms to the premixed zone. For the range of conditions investigated, the zero-g partially premixed flames exhibit a stable behavior and a remarkably strong resistance to perturbations. In contrast, the corresponding normal-gravity flames exhibit oscillatory behavior at low coflow velocities but a stable behavior at high coflow velocities, and the behavior can be explained in terms of a global and convective instabilities. The effects of coflow and gravity on the flames are characterized through a parameter VR, defined as the ratio of coflow velocity to jet velocity. For VR ≤ 1 (low coflow velocity regime, the structures of both 0- and 1-g flames are strongly sensitive to changes in VR, while they are only mildly affected by coflow in the high coflow velocity regime (VR > 1. In addition, the spatio-temporal characteristics of the 0- and 1-g flames are markedly different in the first regime, but are

  20. Experience with using unfolding procedures in ATLAS

    CERN Document Server

    Biondi, Silvia; The ATLAS collaboration

    2016-01-01

    In ATLAS, several unfolding methods are used to correct experimental measurements for detector effects, like acceptance and resolution. These methods use as input the raw experimental distributions, as well as Monte Carlo simulation for the description of the detector effects. The systematic uncertainties associated to the various unfolding methods are evaluated. The statistical and systematic uncertainties affecting the raw measurements and/or the simulation are propagated through the unfolding procedure. The resulting corrected measurements with their uncertainties can be directly compared with the corresponding theoretical predictions.

  1. Experience with using unfolding procedures in ATLAS

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00407321; The ATLAS collaboration

    2016-01-01

    In the ATLAS experiment, several unfolding methods are used to correct experimental measurements for detector effects, like acceptance and resolution. These methods use as input the raw experimental distributions, as well as Monte Carlo simulation for the description of the detector effects. The systematic uncertainties associated to the various unfolding methods are evaluated. The statistical and systematic uncertainties affecting the raw measurements and/or the simulation are propagated through the unfolding procedure. The resulting corrected measurements with their uncertainties can be directly compared with the corresponding theoretical predictions.

  2. UNFOLDED REGULAR AND SEMI-REGULAR POLYHEDRA

    Directory of Open Access Journals (Sweden)

    IONIŢĂ Elena

    2015-06-01

    Full Text Available This paper proposes a presentation unfolding regular and semi-regular polyhedra. Regular polyhedra are convex polyhedra whose faces are regular and equal polygons, with the same number of sides, and whose polyhedral angles are also regular and equal. Semi-regular polyhedra are convex polyhedra with regular polygon faces, several types and equal solid angles of the same type. A net of a polyhedron is a collection of edges in the plane which are the unfolded edges of the solid. Modeling and unfolding Platonic and Arhimediene polyhedra will be using 3dsMAX program. This paper is intended as an example of descriptive geometry applications.

  3. Semiclassical theory of the tunneling anomaly in partially spin-polarized compressible quantum Hall states

    Science.gov (United States)

    Chowdhury, Debanjan; Skinner, Brian; Lee, Patrick A.

    2018-05-01

    Electron tunneling into a system with strong interactions is known to exhibit an anomaly, in which the tunneling conductance vanishes continuously at low energy due to many-body interactions. Recent measurements have probed this anomaly in a quantum Hall bilayer of the half-filled Landau level, and shown that the anomaly apparently gets stronger as the half-filled Landau level is increasingly spin polarized. Motivated by this result, we construct a semiclassical hydrodynamic theory of the tunneling anomaly in terms of the charge-spreading action associated with tunneling between two copies of the Halperin-Lee-Read state with partial spin polarization. This theory is complementary to our recent work (D. Chowdhury, B. Skinner, and P. A. Lee, arXiv:1709.06091) where the electron spectral function was computed directly using an instanton-based approach. Our results show that the experimental observation cannot be understood within conventional theories of the tunneling anomaly, in which the spreading of the injected charge is driven by the mean-field Coulomb energy. However, we identify a qualitatively new regime, in which the mean-field Coulomb energy is effectively quenched and the tunneling anomaly is dominated by the finite compressibility of the composite Fermion liquid.

  4. A Solution Space for a System of Null-State Partial Differential Equations: Part 2

    Science.gov (United States)

    Flores, Steven M.; Kleban, Peter

    2015-01-01

    This article is the second of four that completely and rigorously characterize a solution space for a homogeneous system of 2 N + 3 linear partial differential equations in 2 N variables that arises in conformal field theory (CFT) and multiple Schramm-Löwner evolution (SLE). The system comprises 2 N null-state equations and three conformal Ward identities which govern CFT correlation functions of 2 N one-leg boundary operators. In the first article (Flores and Kleban, Commun Math Phys, arXiv:1212.2301, 2012), we use methods of analysis and linear algebra to prove that dim , with C N the Nth Catalan number. The analysis of that article is complete except for the proof of a lemma that it invokes. The purpose of this article is to provide that proof. The lemma states that if every interval among ( x 2, x 3), ( x 3, x 4),…,( x 2 N-1, x 2 N ) is a two-leg interval of (defined in Flores and Kleban, Commun Math Phys, arXiv:1212.2301, 2012), then F vanishes. Proving this lemma by contradiction, we show that the existence of such a nonzero function implies the existence of a non-vanishing CFT two-point function involving primary operators with different conformal weights, an impossibility. This proof (which is rigorous in spite of our occasional reference to CFT) involves two different types of estimates, those that give the asymptotic behavior of F as the length of one interval vanishes, and those that give this behavior as the lengths of two intervals vanish simultaneously. We derive these estimates by using Green functions to rewrite certain null-state PDEs as integral equations, combining other null-state PDEs to obtain Schauder interior estimates, and then repeatedly integrating the integral equations with these estimates until we obtain optimal bounds. Estimates in which two interval lengths vanish simultaneously divide into two cases: two adjacent intervals and two non-adjacent intervals. The analysis of the latter case is similar to that for one vanishing

  5. Mitigation of near-band balanced steady-state free precession through-plane flow artifacts using partial dephasing.

    Science.gov (United States)

    Datta, Anjali; Cheng, Joseph Y; Hargreaves, Brian A; Baron, Corey A; Nishimura, Dwight G

    2018-06-01

    To mitigate artifacts from through-plane flow at the locations of steady-state stopbands in balanced steady-state free precession (SSFP) using partial dephasing. A 60° range in the phase accrual during a TR was created over the voxel by slightly unbalancing the slice-select dephaser. The spectral profiles of SSFP with partial dephasing for various constant flow rates and during pulsatile flow were simulated to determine if partial dephasing decreases through-plane flow artifacts originating near SSFP dark bands while maintaining on-resonant signal. Simulations were then validated in a flow phantom. Lastly, phase-cycled SSFP cardiac cine images were acquired with and without partial dephasing in six subjects. Partial dephasing decreased the strength and non-linearity of the dependence of the signal at the stopbands on the through-plane flow rate. It thus mitigated hyper-enhancement from out-of-slice signal contributions and transient-related artifacts caused by variable flow both in the phantom and in vivo. In six volunteers, partial dephasing noticeably decreased artifacts in all of the phase-cycled cardiac cine datasets. Partial dephasing can mitigate the flow artifacts seen at the stopbands in balanced SSFP while maintaining the sequence's desired signal. By mitigating hyper-enhancement and transient-related artifacts originating from the stopbands, partial dephasing facilitates robust multiple-acquisition phase-cycled SSFP in the heart. Magn Reson Med 79:2944-2953, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  6. BUMS--Bonner sphere Unfolding Made Simple: an HTML based multisphere neutron spectrometer unfolding package

    International Nuclear Information System (INIS)

    Sweezy, Jeremy; Hertel, Nolan; Veinot, Ken

    2002-01-01

    A new multisphere neutron spectrometer unfolding package, Bonner sphere Unfolding Made Simple (BUMS) has been developed that uses an HTML interface to simplify data input and code execution for the novice and the advanced user. This new unfolding package combines the unfolding algorithms contained in other popular unfolding codes under one easy to use interface. The interface makes use of web browsing software to provide a graphical user interface to the unfolding algorithms. BUMS integrates the SPUNIT, BON, MAXIET, and SAND-II unfolding algorithms into a single package. This package also includes a library of 14 response matrices, 58 starting spectra, and 24 dose and detector responses. BUMS has several improvements beyond the addition of unfolding algorithms. It has the ability to search for the most appropriate starting spectra. Also, plots of the unfolded neutron spectra are automatically generated. The BUMS package runs via a web server and may be accessed by any computer with access to the Internet at http://nukeisit.gatech.edu/bums

  7. Mechanical unfolding reveals stable 3-helix intermediates in talin and α-catenin.

    Directory of Open Access Journals (Sweden)

    Vasyl V Mykuliak

    2018-04-01

    Full Text Available Mechanical stability is a key feature in the regulation of structural scaffolding proteins and their functions. Despite the abundance of α-helical structures among the human proteome and their undisputed importance in health and disease, the fundamental principles of their behavior under mechanical load are poorly understood. Talin and α-catenin are two key molecules in focal adhesions and adherens junctions, respectively. In this study, we used a combination of atomistic steered molecular dynamics (SMD simulations, polyprotein engineering, and single-molecule atomic force microscopy (smAFM to investigate unfolding of these proteins. SMD simulations revealed that talin rod α-helix bundles as well as α-catenin α-helix domains unfold through stable 3-helix intermediates. While the 5-helix bundles were found to be mechanically stable, a second stable conformation corresponding to the 3-helix state was revealed. Mechanically weaker 4-helix bundles easily unfolded into a stable 3-helix conformation. The results of smAFM experiments were in agreement with the findings of the computational simulations. The disulfide clamp mutants, designed to protect the stable state, support the 3-helix intermediate model in both experimental and computational setups. As a result, multiple discrete unfolding intermediate states in the talin and α-catenin unfolding pathway were discovered. Better understanding of the mechanical unfolding mechanism of α-helix proteins is a key step towards comprehensive models describing the mechanoregulation of proteins.

  8. The fluorescence intensities ratio is not a reliable parameter for evaluation of protein unfolding transitions.

    Science.gov (United States)

    Žoldák, Gabriel; Jancura, Daniel; Sedlák, Erik

    2017-06-01

    Monitoring the fluorescence of proteins, particularly the fluorescence of intrinsic tryptophan residues, is a popular method often used in the analysis of unfolding transitions (induced by temperature, chemical denaturant, and pH) in proteins. The tryptophan fluorescence provides several suitable parameters, such as steady-state fluorescence intensity, apparent quantum yield, mean fluorescence lifetime, position of emission maximum that are often utilized for the observation of the conformational/unfolding transitions of proteins. In addition, the fluorescence intensities ratio at different wavelengths (usually at 330 nm and 350 nm) is becoming an increasingly popular parameter for the evaluation of thermal transitions. We show that, under certain conditions, the use of this parameter for the analysis of unfolding transitions leads to the incorrect determination of thermodynamic parameters characterizing unfolding transitions in proteins (e.g., melting temperature) and, hence, can compromise the hit identification during high-throughput drug screening campaigns. © 2017 The Protein Society.

  9. High rate partial-state-of-charge operation of VRLA batteries

    Science.gov (United States)

    Moseley, Patrick T.

    The world market for 12 V SLI batteries currently stands at around US$ 12 billion. The lack of a serious challenge from other battery types has allowed lead-acid products to serve this market exclusively, with minimal demand for product improvement through research and development, and a sharp competition has, over time, cut sales prices to commodity levels. The electrochemical storage of energy in automobiles now faces the possibility of a major change, in the form of the proposed 36/42 V electrical systems for vehicles that remain primarily powered by internal combustion engines, and of the hybrid electric vehicle. The duty cycle for these two applications sees the battery held at a partial-state-of-charge (PSoC) for most of its life and required to supply, and to accept, charge at unprecedented rates. The remarkable advances achieved with VRLA battery technology for electric vehicles during the past 8-10 years will be of only passing value in overcoming the challenges posed by high rate PSoC service in 36/42 V and HEV duty. This is because the failure modes seen in PSoC are quite different from those faced in EV (deep cycle) use. The replacement of the 12 V SLI will not take place rapidly. However, if the applications which take its place are to be satisfied by a lead-acid product (probably VRLA), rather than by a battery of a different chemistry, a program of development as successful as that mounted for deep cycle duty will be required. The present phase of the Advanced Lead-Acid Battery Consortium (ALABC) R&D program has begun to shed light on those aspects of the function of a VRLA battery which currently limit its life in high rate PSoC duty. The program is also pursuing the several technologies which show promise of overcoming those limits, including multiple tab plate design, mass transport facilitation and minor component (both beneficial and detrimental impurity) management. This paper presents a brief review of the changes which are taking place in

  10. A Solution Space for a System of Null-State Partial Differential Equations: Part 1

    Science.gov (United States)

    Flores, Steven M.; Kleban, Peter

    2015-01-01

    This article is the first of four that completely and rigorously characterize a solution space for a homogeneous system of 2 N + 3 linear partial differential equations (PDEs) in 2 N variables that arises in conformal field theory (CFT) and multiple Schramm-Löwner evolution (SLE). In CFT, these are null-state equations and conformal Ward identities. They govern partition functions for the continuum limit of a statistical cluster or loop-gas model, such as percolation, or more generally the Potts models and O( n) models, at the statistical mechanical critical point. (SLE partition functions also satisfy these equations.) For such a lattice model in a polygon with its 2 N sides exhibiting a free/fixed side-alternating boundary condition , this partition function is proportional to the CFT correlation function where the w i are the vertices of and where is a one-leg corner operator. (Partition functions for "crossing events" in which clusters join the fixed sides of in some specified connectivity are linear combinations of such correlation functions.) When conformally mapped onto the upper half-plane, methods of CFT show that this correlation function satisfies the system of PDEs that we consider. In this first article, we use methods of analysis to prove that the dimension of this solution space is no more than C N , the Nth Catalan number. While our motivations are based in CFT, our proofs are completely rigorous. This proof is contained entirely within this article, except for the proof of Lemma 14, which constitutes the second article (Flores and Kleban, in Commun Math Phys, arXiv:1404.0035, 2014). In the third article (Flores and Kleban, in Commun Math Phys, arXiv:1303.7182, 2013), we use the results of this article to prove that the solution space of this system of PDEs has dimension C N and is spanned by solutions constructed with the CFT Coulomb gas (contour integral) formalism. In the fourth article (Flores and Kleban, in Commun Math Phys, arXiv:1405

  11. A Solution Space for a System of Null-State Partial Differential Equations: Part 4

    Science.gov (United States)

    Flores, Steven M.; Kleban, Peter

    2015-01-01

    This article is the last of four that completely and rigorously characterize a solution space for a homogeneous system of 2 N + 3 linear partial differential equations in 2 N variables that arises in conformal field theory (CFT) and multiple Schramm-Löwner evolution (SLE). The system comprises 2 N null-state equations and three conformal Ward identities that govern CFT correlation functions of 2 N one-leg boundary operators. In the first two articles (Flores and Kleban in Commun Math Phys, 2012; Flores and Kleban, in Commun Math Phys, 2014), we use methods of analysis and linear algebra to prove that dim , with C N the Nth Catalan number. Using these results in the third article (Flores and Kleban, in Commun Math Phys, 2013), we prove that dim and is spanned by (real-valued) solutions constructed with the Coulomb gas (contour integral) formalism of CFT. In this article, we use these results to prove some facts concerning the solution space . First, we show that each of its elements equals a sum of at most two distinct Frobenius series in powers of the difference between two adjacent points (unless is odd, in which case a logarithmic term may appear). This establishes an important element in the operator product expansion for one-leg boundary operators, assumed in CFT. We also identify particular elements of , which we call connectivity weights, and exploit their special properties to conjecture a formula for the probability that the curves of a multiple-SLE process join in a particular connectivity. This leads to new formulas for crossing probabilities of critical lattice models inside polygons with a free/fixed side-alternating boundary condition, which we derive in Flores et al. (Partition functions and crossing probabilities for critical systems inside polygons, in preparation). Finally, we propose a reason for why the exceptional speeds [certain values that appeared in the analysis of the Coulomb gas solutions in Flores and Kleban (Commun Math Phys, 2013)] and

  12. A Solution Space for a System of Null-State Partial Differential Equations: Part 3

    Science.gov (United States)

    Flores, Steven M.; Kleban, Peter

    2015-01-01

    This article is the third of four that completely and rigorously characterize a solution space for a homogeneous system of 2 N + 3 linear partial differential equations (PDEs) in 2 N variables that arises in conformal field theory (CFT) and multiple Schramm-Löwner evolution (SLE κ ). The system comprises 2 N null-state equations and three conformal Ward identities that govern CFT correlation functions of 2 N one-leg boundary operators. In the first two articles (Flores and Kleban, in Commun Math Phys, arXiv:1212.2301, 2012; Commun Math Phys, arXiv:1404.0035, 2014), we use methods of analysis and linear algebra to prove that dim , with C N the Nth Catalan number. Extending these results, we prove in this article that dim and entirely consists of (real-valued) solutions constructed with the CFT Coulomb gas (contour integral) formalism. In order to prove this claim, we show that a certain set of C N such solutions is linearly independent. Because the formulas for these solutions are complicated, we prove linear independence indirectly. We use the linear injective map of Lemma 15 in Flores and Kleban (Commun Math Phys, arXiv:1212.2301, 2012) to send each solution of the mentioned set to a vector in , whose components we find as inner products of elements in a Temperley-Lieb algebra. We gather these vectors together as columns of a symmetric matrix, with the form of a meander matrix. If the determinant of this matrix does not vanish, then the set of C N Coulomb gas solutions is linearly independent. And if this determinant does vanish, then we construct an alternative set of C N Coulomb gas solutions and follow a similar procedure to show that this set is linearly independent. The latter situation is closely related to CFT minimal models. We emphasize that, although the system of PDEs arises in CFT in away that is typically non-rigorous, our treatment of this system here and in Flores and Kleban (Commun Math Phys, arXiv:1212.2301, 2012; Commun Math Phys, arXiv:1404

  13. NEUPAC, Experimental Neutron Spectra Unfolding with Sensitivities

    International Nuclear Information System (INIS)

    Sasaki, Makoto; Nakazawa, Masaharu

    1986-01-01

    1 - Description of problem or function: The code is able to determine the integral quantities and their sensitivities, together with an estimate of the unfolded spectrum and integral quantities. The code also performs a chi-square test of the input/output data, and contains many options for the calculational routines. 2 - Method of solution: The code is based on the J1-type unfolding method, and the estimated neutron flux spectrum is obtained as its solution. 3 - Restrictions on the complexity of the problem: The maximum number of energy groups used for unfolding is 620. The maximum number of reaction rates and the window functions given as input is 20. The total storage requirement depends on the amount of input data

  14. Unfolding energetics and stability of banana lectin.

    Science.gov (United States)

    Gupta, Garima; Sinha, Sharmistha; Surolia, Avadhesha

    2008-08-01

    The unfolding pathway of banana lectin from Musa paradisiaca was determined by isothermal denaturation induced by the chaotrope GdnCl. The unfolding was found to be a reversible process. The data obtained by isothermal denaturation provided information on conformational stability of banana lectin. The high values of DeltaG of unfolding at various temperatures indicated the strength of intersubunit interactions. It was found that banana lectin is a very stable and denatures at high chaotrope concentrations only. The basis of the stability may be attributed to strong hydrogen bonds of the order 2.5-3.1 A at the dimeric interface along with the presence of water bridges. This is perhaps very unique example in proteins where subunit association is not a consequence of the predominance of hydrophobic interactions. (c) 2008 Wiley-Liss, Inc.

  15. Routing protocol for wireless quantum multi-hop mesh backbone network based on partially entangled GHZ state

    Science.gov (United States)

    Xiong, Pei-Ying; Yu, Xu-Tao; Zhang, Zai-Chen; Zhan, Hai-Tao; Hua, Jing-Yu

    2017-08-01

    Quantum multi-hop teleportation is important in the field of quantum communication. In this study, we propose a quantum multi-hop communication model and a quantum routing protocol with multihop teleportation for wireless mesh backbone networks. Based on an analysis of quantum multi-hop protocols, a partially entangled Greenberger-Horne-Zeilinger (GHZ) state is selected as the quantum channel for the proposed protocol. Both quantum and classical wireless channels exist between two neighboring nodes along the route. With the proposed routing protocol, quantum information can be transmitted hop by hop from the source node to the destination node. Based on multi-hop teleportation based on the partially entangled GHZ state, a quantum route established with the minimum number of hops. The difference between our routing protocol and the classical one is that in the former, the processes used to find a quantum route and establish quantum channel entanglement occur simultaneously. The Bell state measurement results of each hop are piggybacked to quantum route finding information. This method reduces the total number of packets and the magnitude of air interface delay. The deduction of the establishment of a quantum channel between source and destination is also presented here. The final success probability of quantum multi-hop teleportation in wireless mesh backbone networks was simulated and analyzed. Our research shows that quantum multi-hop teleportation in wireless mesh backbone networks through a partially entangled GHZ state is feasible.

  16. Regularization and error assignment to unfolded distributions

    CERN Document Server

    Zech, Gunter

    2011-01-01

    The commonly used approach to present unfolded data only in graphical formwith the diagonal error depending on the regularization strength is unsatisfac-tory. It does not permit the adjustment of parameters of theories, the exclusionof theories that are admitted by the observed data and does not allow the com-bination of data from different experiments. We propose fixing the regulariza-tion strength by a p-value criterion, indicating the experimental uncertaintiesindependent of the regularization and publishing the unfolded data in additionwithout regularization. These considerations are illustrated with three differentunfolding and smoothing approaches applied to a toy example.

  17. Equilibrium unfolding of A. niger RNase: pH dependence of chemical and thermal denaturation.

    Science.gov (United States)

    Kumar, Gundampati Ravi; Sharma, Anurag; Kumari, Moni; Jagannadham, Medicherla V; Debnath, Mira

    2011-08-01

    Equilibrium unfolding of A. niger RNase with chemical denaturants, for example GuHCl and urea, and thermal unfolding have been studied as a function of pH using fluorescence, far-UV, near-UV, and absorbance spectroscopy. Because of their ability to affect electrostatic interactions, pH and chemical denaturants have a marked effect on the stability, structure, and function of many globular proteins. ANS binding studies have been conducted to enable understanding of the folding mechanism of the protein in the presence of the denaturants. Spectroscopic studies by absorbance, fluorescence, and circular dichroism and use of K2D software revealed that the enzyme has α + β type secondary structure with approximately 29% α-helix, 24% β-sheet, and 47% random coil. Under neutral conditions the enzyme is stable in urea whereas GuHCl-induced equilibrium unfolding was cooperative. A. niger RNase has little ANS binding even under neutral conditions. Multiple intermediates were populated during the pH-induced unfolding of A. niger RNase. Urea and temperature-induced unfolding of A. niger RNase into the molten globule-like state is non-cooperative, in contrast to the cooperativity seen with the native protein, suggesting the presence of two parts/domains, in the molecular structure of A. niger RNase, with different stability that unfolds in steps. Interestingly, the GuHCl-induced unfolding of the A state (molten globule state) of A. niger RNase is unique, because a low concentration of denaturant not only induces structural change but also facilitates transition from one molten globule like state (A(MG1)) into another (I(MG2)).

  18. Iterative Observer-based Estimation Algorithms for Steady-State Elliptic Partial Differential Equation Systems

    KAUST Repository

    Majeed, Muhammad Usman

    2017-01-01

    the problems are formulated on higher dimensional space domains. However, in this dissertation, feedback based state estimation algorithms, known as state observers, are developed to solve such steady-state problems using one of the space variables as time

  19. Motional properties of unfolded ubiquitin: a model for a random coil protein

    Energy Technology Data Exchange (ETDEWEB)

    Wirmer, Julia [Johann Wolfgang GoeUniversityFrankfurt, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (Germany); Peti, Wolfgang [Brown University, Department of Molecular Pharmacology, Physiology and Biotechnology (United States); Schwalbe, Harald [Johann Wolfgang GoeUniversityFrankfurt, Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (Germany)], E-mail: schwalbe@nmr.uni-frankfurt.de

    2006-07-15

    The characterization of unfolded states of proteins has recently attracted considerable interest, as the residual structure present in these states may play a crucial role in determining their folding and misfolding behavior. Here, we investigated the dynamics in the denatured state of ubiquitin in 8 M urea at pH2. Under these conditions, ubiquitin does not have any detectable local residual structure, and uniform {sup 15}N relaxation rates along the sequence indicate the absence of motional restrictions caused by residual secondary structure and/or long-range interactions. A comparison of different models to predict relaxation data in unfolded proteins suggests that the subnanosecond dynamics in unfolded states depend on segmental motions only and do not show a dependence on the residue type but for proline and glycine residues.

  20. Deciphering hierarchical features in the energy landscape of adenylate kinase folding/unfolding

    Science.gov (United States)

    Taylor, J. Nicholas; Pirchi, Menahem; Haran, Gilad; Komatsuzaki, Tamiki

    2018-03-01

    Hierarchical features of the energy landscape of the folding/unfolding behavior of adenylate kinase, including its dependence on denaturant concentration, are elucidated in terms of single-molecule fluorescence resonance energy transfer (smFRET) measurements in which the proteins are encapsulated in a lipid vesicle. The core in constructing the energy landscape from single-molecule time-series across different denaturant concentrations is the application of rate-distortion theory (RDT), which naturally considers the effects of measurement noise and sampling error, in combination with change-point detection and the quantification of the FRET efficiency-dependent photobleaching behavior. Energy landscapes are constructed as a function of observation time scale, revealing multiple partially folded conformations at small time scales that are situated in a superbasin. As the time scale increases, these denatured states merge into a single basin, demonstrating the coarse-graining of the energy landscape as observation time increases. Because the photobleaching time scale is dependent on the conformational state of the protein, possible nonequilibrium features are discussed, and a statistical test for violation of the detailed balance condition is developed based on the state sequences arising from the RDT framework.

  1. Prediction-based control for LTI systems with uncertain time-varying delays and partial state knowledge

    Science.gov (United States)

    Léchappé, V.; Moulay, E.; Plestan, F.

    2018-06-01

    The stability of a prediction-based controller for linear time-invariant (LTI) systems is studied in the presence of time-varying input and output delays. The uncertain delay case is treated as well as the partial state knowledge case. The reduction method is used in order to prove the convergence of the closed-loop system including the state observer, the predictor and the plant. Explicit conditions that guarantee the closed-loop stability are given, thanks to a Lyapunov-Razumikhin analysis. Simulations illustrate the theoretical results.

  2. Comparison of neutron spectrum unfolding codes

    International Nuclear Information System (INIS)

    Zijp, W.

    1979-02-01

    This final report contains a set of four ECN-reports. The first is dealing with the comparison of the neutron spectrum unfolding codes CRYSTAL BALL, RFSP-JUL, SAND II and STAY'SL. The other three present the results of calculations about the influence of statistical weights in CRYSTAL BALL, SAND II and RFSP-JUL

  3. FERD and FERDOR type unfolding codes

    International Nuclear Information System (INIS)

    Burrus, W.R.

    1976-01-01

    FERD and FERDO are unfolding codes which were developed at the Neutron Physics Division of Oak Ridge National Laboratory in 1965 and 1966. FERDO variants such as FERDOR and FORIST have been widely used, and many useful supplementary procedures have been developed for neutron and gamma-ray spectroscopy and other diverse applications. Algorithms for the codes are discussed

  4. Peripheral Protein Unfolding Drives Membrane Bending.

    Science.gov (United States)

    Siaw, Hew Ming Helen; Raghunath, Gokul; Dyer, R Brian

    2018-06-20

    Dynamic modulation of lipid membrane curvature can be achieved by a number of peripheral protein binding mechanisms such as hy-drophobic insertion of amphipathic helices and membrane scaffolding. Recently, an alternative mechanism was proposed in which crowding of peripherally bound proteins induces membrane curvature through steric pressure generated by lateral collisions. This effect was enhanced using intrinsically disordered proteins that possess high hydrodynamic radii, prompting us to explore whether membrane bending can be triggered by the folding-unfolding transition of surface-bound proteins. We utilized histidine-tagged human serum albumin bound to Ni-NTA-DGS containing liposomes as our model system to test this hypothesis. We found that reduction of the disulfide bonds in the protein resulted in unfolding of HSA, which subsequently led to membrane tubule formation. The frequency of tubule formation was found to be significantly higher when the proteins were unfolded while being localized to a phase-separated domain as opposed to randomly distributed in fluid phase liposomes, indicating that the steric pressure generated from protein unfolding is directly responsible for membrane deformation. Our results are critical for the design of peripheral membrane protein-immobilization strategies and open new avenues for exploring mechanisms of membrane bending driven by conformational changes of peripheral membrane proteins.

  5. Practical purification scheme for decohered coherent-state superpositions via partial homodyne detection

    International Nuclear Information System (INIS)

    Suzuki, Shigenari; Takeoka, Masahiro; Sasaki, Masahide; Andersen, Ulrik L.; Kannari, Fumihiko

    2006-01-01

    We present a simple protocol to purify a coherent-state superposition that has undergone a linear lossy channel. The scheme constitutes only a single beam splitter and a homodyne detector, and thus is experimentally feasible. In practice, a superposition of coherent states is transformed into a classical mixture of coherent states by linear loss, which is usually the dominant decoherence mechanism in optical systems. We also address the possibility of producing a larger amplitude superposition state from decohered states, and show that in most cases the decoherence of the states are amplified along with the amplitude

  6. Unfolding of Vortices into Topological Stripes in a Multiferroic Material

    Science.gov (United States)

    Wang, X.; Mostovoy, M.; Han, M. G.; Horibe, Y.; Aoki, T.; Zhu, Y.; Cheong, S.-W.

    2014-06-01

    Multiferroic hexagonal RMnO3 (R =rare earths) crystals exhibit dense networks of vortex lines at which six domain walls merge. While the domain walls can be readily moved with an applied electric field, the vortex cores so far have been impossible to control. Our experiments demonstrate that shear strain induces a Magnus-type force pulling vortices and antivortices in opposite directions and unfolding them into a topological stripe domain state. We discuss the analogy between this effect and the current-driven dynamics of vortices in superconductors and superfluids.

  7. Considerably Unfolded Transthyretin Monomers Preceed and Exchange with Dynamically Structured Amyloid Protofibrils

    DEFF Research Database (Denmark)

    Groenning, Minna; Campos, Raul I; Hirschberg, Daniel

    2015-01-01

    describe an unexpectedly dynamic TTR protofibril structure which exchanges protomers with highly unfolded monomers in solution. The protofibrils only grow to an approximate final size of 2,900 kDa and a length of 70 nm and a comparative HXMS analysis of native and aggregated samples revealed a much higher...... average solvent exposure of TTR upon fibrillation. With SAXS, we reveal the continuous presence of a considerably unfolded TTR monomer throughout the fibrillation process, and show that a considerable fraction of the fibrillating protein remains in solution even at a late maturation state. Together......, these data reveal that the fibrillar state interchanges with the solution state. Accordingly, we suggest that TTR fibrillation proceeds via addition of considerably unfolded monomers, and the continuous presence of amyloidogenic structures near the protofibril surface offers a plausible explanation...

  8. 78 FR 48326 - Partial Disapproval of State Implementation Plan; Arizona; Regional Haze Requirements

    Science.gov (United States)

    2013-08-08

    ... Disapproval of State Implementation Plan; Arizona; Regional Haze Requirements AGENCY: Environmental Protection... behalf of National Parks Conservation Association, Sierra Club, Physicians for Social Responsibility... Haze State Implementation Plan Revision submitted by the Arizona Department of Environmental Quality on...

  9. Ground-state properties of ordered, partially ordered, and random Cu-Au and Ni-Pt alloys

    DEFF Research Database (Denmark)

    Ruban, Andrei; Abrikosov, I. A.; Skriver, Hans Lomholt

    1995-01-01

    We have studied the ground-state properties of ordered, partially ordered, and random Cu-Au and Ni-Pt alloys at the stoichiometric 1/4, 1/2, and 3/4 compositions in the framework of the multisublattice single-site (SS) coherent potential approximation (CPA). Charge-transfer effects in the random ...... for the ordered alloys are in good agreement with experimental data. For all the alloys the calculated ordering energy and the equilibrium lattices parameters are found to be almost exact quadratic functions of the long-range-order parameter....... and the partially ordered alloys are included in the screened impurity model. The prefactor in the Madelung energy is determined by the requirement that the total energy obtained in direct SS CPA calculations should equal the total energy given by the Connolly-Williams expansion based on Green’s function...

  10. Energy-Efficient Power Allocation for Fixed-Gain Amplify-and-Forward Relay Networks with Partial Channel State Information

    KAUST Repository

    Zafar, Ammar

    2012-06-01

    In this report, energy-efficient transmission and power allocation for fixed-gain amplify-and-forward relay networks with partial channel state information (CSI) are studied. In the energy-efficiency problem, the total power consumed is minimized while keeping the signal-to-noise-ratio (SNR) above a certain threshold. In the dual problem of power allocation, the end-to-end SNR is maximized under individual and global power constraints. Closed-form expressions for the optimal source and relay powers and the Lagrangian multiplier are obtained. Numerical results show that the optimal power allocation with partial CSI provides comparable performance as optimal power allocation with full CSI at low SNR.

  11. Energy-Efficient Power Allocation for Fixed-Gain Amplify-and-Forward Relay Networks with Partial Channel State Information

    KAUST Repository

    Zafar, Ammar

    2012-09-16

    In this letter, energy-efficient transmission and power allocation for fixed-gain amplify-and-forward relay networks with partial channel state information (CSI) are studied. In the energy-efficiency problem, the total power consumed is minimized while keeping the signal-to-noise-ratio (SNR) above a certain threshold. In the dual problem of power allocation, the end-to-end SNR is maximized under individual and global power constraints. Closed-form expressions for the optimal source and relay powers and the Lagrangian multiplier are obtained. Numerical results show that the optimal power allocation with partial CSI provides comparable performance as optimal power allocation with full CSI at low SNR. © 2012 IEEE.

  12. Partial Evaluation of the Euclidian Algorithm

    DEFF Research Database (Denmark)

    Danvy, Olivier; Goldberg, Mayer

    1997-01-01

    -like behavior. Each of them presents a challenge for partial evaluation. The Euclidian algorithm is one of them, and in this article, we make it amenable to partial evaluation. We observe that the number of iterations in the Euclidian algorithm is bounded by a number that can be computed given either of the two...... arguments. We thus rephrase this algorithm using bounded recursion. The resulting program is better suited for automatic unfolding and thus for partial evaluation. Its specialization is efficient....

  13. Thermal unfolding of a Ca- and Lanthanide-binding protein

    Energy Technology Data Exchange (ETDEWEB)

    Fahmy, Karim [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Biophysics; Goettfert, M. [Technische Univ. Dresden (Germany); Knoeppel, J.

    2017-06-01

    The MIIA (metal ion-induced autocleavage)-domain of the protein Vic001052 from the pathogen Vibrio coralliilyticus, comprises 173 amino acids and exhibits Ca-dependent autoproteolytic activity. It shows homology to nodulation proteins which are secreted by Rhizobiacea into plant host cells where they exert Ca-dependent functions. We have studied the structural and energetic aspects of metal protein interactions of the MIIA domain which appear attractive for engineering metal-binding synthetic peptides. Using a non-cleavable MIIA domain construct, we detected very similar structural changes upon binding to Ca{sup 2+} and Eu{sup 3+}. The thermal denaturation of the Ca-bound state was studied by circular dichroism spectroscopy. The metal-bound folded state unfolds reversibly into an unstructured metal-free state similar to the metal-free state at room temperature.

  14. Dysregulation of the unfolded protein response in db/db mice with diet induced steatohepatitis

    OpenAIRE

    Rinella, Mary E.; Siddiqui, M. Shaddab; Gardikiotes, Konstantina; Gottstein, Jeanne; Elias, Marc; Green, Richard M.

    2011-01-01

    In humans with non-alcoholic fatty liver, diabetes is associated with more advanced disease. We have previously shown that diabetic db/db mice are highly susceptible to methionine choline deficient diet (MCD) induced hepatic injury. Since activation of the unfolded protein response (UPR) is an important adaptive cellular mechanism in diabetes, obesity and fatty liver, we hypothesized that dysregulation of the UPR may partially explain how diabetes could promote liver injury.

  15. Relationship between the partial molar and molar quantity of a thermodynamic state function in a multicomponent mixture – revisited

    International Nuclear Information System (INIS)

    Näfe, H.

    2013-01-01

    As far as a multicomponent mixture is concerned, different versions exist in the literature for the relationship between the partial molar and molar quantity of a thermodynamic state function with the most prominent example of the two quantities being the activity coefficient of an arbitrary component and the excess Gibbs free energy of a mixture comprising this component. Since the relationships published so far have to a large degree been derived independently of each other and result from apparently conflicting approaches, they are still considered as separate subjects in the literature. It is demonstrated that despite this curious situation all relationships are equivalent to each other from a mathematical point of view

  16. Construction of carrier state viruses with partial genomes of the segmented dsRNA bacteriophages

    International Nuclear Information System (INIS)

    Sun Yang; Qiao Xueying; Mindich, Leonard

    2004-01-01

    The cystoviridae are bacteriophages with genomes of three segments of dsRNA enclosed within a polyhedral capsid. Two members of this family, PHI6 and PHI8, have been shown to form carrier states in which the virus replicates as a stable episome in the host bacterium while expressing reporter genes such as kanamycin resistance or lacα. The carrier state does not require the activity of all the genes necessary for phage production. It is possible to generate carrier states by infecting cells with virus or by electroporating nonreplicating plasmids containing cDNA copies of the viral genomes into the host cells. We have found that carrier states in both PHI6 and PHI8 can be formed at high frequency with all three genomic segments or with only the large and small segments. The large genomic segment codes for the proteins that constitute the inner core of the virus, which is the structure responsible for the packaging and replication of the genome. In PHI6, a carrier state can be formed with the large and middle segment if mutations occur in the gene for the major structural protein of the inner core. In PHI8, carrier state formation requires the activity of genes 8 and 12 of segment S

  17. Bosonic Fradkin-Tseytlin equations unfolded

    Energy Technology Data Exchange (ETDEWEB)

    Shaynkman, O.V. [I.E.Tamm Theory Department, Lebedev Physical Institute,Leninski prospect 53, 119991, Moscow (Russian Federation)

    2016-12-22

    We test infinite-dimensional extension of algebra su(k,k) proposed by Fradkin and Linetsky as the candidate for conformal higher spin algebra. Adjoint and twisted-adjoint representations of su(k,k) on the space of this algebra are carefully explored. For k=2 corresponding unfolded system is analyzed and it is shown to encode Fradkin-Tseytlin equations for the set of all integer spins 1,2,… with infinite multiplicity.

  18. Effective electrochemical method for investigation of hemoglobin unfolding based on the redox property of heme groups at glassy carbon electrodes.

    Science.gov (United States)

    Li, Xianchan; Zheng, Wei; Zhang, Limin; Yu, Ping; Lin, Yuqing; Su, Lei; Mao, Lanqun

    2009-10-15

    This study demonstrates a facile and effective electrochemical method for investigation of hemoglobin (Hb) unfolding based on the electrochemical redox property of heme groups in Hb at bare glassy carbon (GC) electrodes. In the native state, the heme groups are deeply buried in the hydrophobic pockets of Hb with a five-coordinate high-spin complex and thus show a poor electrochemical property at bare GC electrodes. Upon the unfolding of Hb induced by the denaturant of guanidine hydrochloride (GdnHCl), the fifth coordinative bond between the heme groups and the residue of the polypeptides (His-F8) is broken, and as a result, the heme groups initially buried deeply in the hydrophobic pockets dissociate from the polypeptide chains and are reduced electrochemically at GC electrodes, which can be used to probe the unfolding of Hb. The results on the GdnHCl-induced Hb unfolding obtained with the electrochemical method described here well coincide with those studied with other methods, such as UV-vis spectroscopy, fluorescence, and circular dichroism. The application of the as-established electrochemical method is illustrated to study the kinetics of GdnHCl-induced Hb unfolding, the GdnHCl-induced unfolding of another kind of hemoprotein, catalase, and the pH-induced Hb unfolding/refolding.

  19. Production and partial characterisation of feruloyl esterase by Sporotrichum thermophile in solid-state fermentation

    DEFF Research Database (Denmark)

    Topakas, E.; Kalogeris, E.; Kekos, D.

    2003-01-01

    A number of factors affecting production of feruloyl esterase an enzyme that hydrolyse ester linkages of ferulic acid (FA) in plant cell walls, by the thermophylic fungus Sporotrichum thermophile under solid state fermentation (SSF) were investigated. Initial moisture content and type of carbon...

  20. Partial purification and characterization of amylase enzyme under solid state fermentation from Monascus sanguineus

    Directory of Open Access Journals (Sweden)

    Padmavathi Tallapragada

    2017-06-01

    It can be concluded that the fungus M. sanguineus is a good source of amylase production under solid state fermentation. Application of amylase produced by M. sanguineus in detergent industry was also carried out and it was proven very effective in stain removal from the fabrics.

  1. Dynamic coarse-graining fills the gap between atomistic simulations and experimental investigations of mechanical unfolding

    Science.gov (United States)

    Knoch, Fabian; Schäfer, Ken; Diezemann, Gregor; Speck, Thomas

    2018-01-01

    We present a dynamic coarse-graining technique that allows one to simulate the mechanical unfolding of biomolecules or molecular complexes on experimentally relevant time scales. It is based on Markov state models (MSMs), which we construct from molecular dynamics simulations using the pulling coordinate as an order parameter. We obtain a sequence of MSMs as a function of the discretized pulling coordinate, and the pulling process is modeled by switching among the MSMs according to the protocol applied to unfold the complex. This way we cover seven orders of magnitude in pulling speed. In the region of rapid pulling, we additionally perform steered molecular dynamics simulations and find excellent agreement between the results of the fully atomistic and the dynamically coarse-grained simulations. Our technique allows the determination of the rates of mechanical unfolding in a dynamical range from approximately 10-8/ns to 1/ns thus reaching experimentally accessible time regimes without abandoning atomistic resolution.

  2. Spectrum unfolding by the least-squares methods

    International Nuclear Information System (INIS)

    Perey, F.G.

    1977-01-01

    The method of least squares is briefly reviewed, and the conditions under which it may be used are stated. From this analysis, a least-squares approach to the solution of the dosimetry neutron spectrum unfolding problem is introduced. The mathematical solution to this least-squares problem is derived from the general solution. The existence of this solution is analyzed in some detail. A chi 2 -test is derived for the consistency of the input data which does not require the solution to be obtained first. The fact that the problem is technically nonlinear, but should be treated in general as a linear one, is argued. Therefore, the solution should not be obtained by iteration. Two interpretations are made for the solution of the code STAY'SL, which solves this least-squares problem. The relationship of the solution to this least-squares problem to those obtained currently by other methods of solving the dosimetry neutron spectrum unfolding problem is extensively discussed. It is shown that the least-squares method does not require more input information than would be needed by current methods in order to estimate the uncertainties in their solutions. From this discussion it is concluded that the proposed least-squares method does provide the best complete solution, with uncertainties, to the problem as it is understood now. Finally, some implications of this method are mentioned regarding future work required in order to exploit its potential fully

  3. Nuclear magnetic resonance characterization of the stationary dynamics of partially saturated media during steady-state infiltration flow

    Science.gov (United States)

    Rassi, Erik M.; Codd, Sarah L.; Seymour, Joseph D.

    2011-01-01

    Flow in porous media and the resultant hydrodynamics are important in fields including but not limited to the hydrology, chemical, medical and petroleum industries. The observation and understanding of the hydrodynamics in porous media are critical to the design and optimal utilization of porous media, such as those seen in trickle-bed reactors, medical filters, subsurface flows and carbon sequestration. Magnetic resonance (MR) provides for a non-invasive technique that can probe the hydrodynamics on pore and bulk scale lengths; many previous works have characterized fully saturated porous media, while rapid MR imaging (MRI) methods in particular have previously been applied to partially saturated flows. We present time- and ensemble-averaged MR measurements to observe the effects on a bead pack partially saturated with air under flowing water conditions. The 10 mm internal diameter bead pack was filled with 100 μm borosilicate glass beads. Air was injected into the bead pack as water flowed simultaneously through the sample at 25 ml h-1. The initial partially saturated state was characterized with MRI density maps, free induction decay (FID) experiments, propagators and velocity maps before the water flow rate was increased incrementally from 25 to 500 ml h-1. After the maximum flow rate of 500 ml h-1, the MRI density maps, FID experiments, propagators and velocity maps were repeated and compared to the data taken before the maximum flow rate. This work shows that a partially saturated single-phase flow has global flow dynamics that return to characteristic flow statistics once a steady-state high flow rate has been reached. This high flow rate pushed out a significant amount of the air in the bead pack and caused the return of a preferential flow pattern. Velocity maps indicated that local flow statistics were not the same for the before and after blow out conditions. It has been suggested and shown previously that a flow pattern can return to

  4. Nuclear magnetic resonance characterization of the stationary dynamics of partially saturated media during steady-state infiltration flow

    International Nuclear Information System (INIS)

    Rassi, Erik M; Codd, Sarah L; Seymour, Joseph D

    2011-01-01

    Flow in porous media and the resultant hydrodynamics are important in fields including but not limited to the hydrology, chemical, medical and petroleum industries. The observation and understanding of the hydrodynamics in porous media are critical to the design and optimal utilization of porous media, such as those seen in trickle-bed reactors, medical filters, subsurface flows and carbon sequestration. Magnetic resonance (MR) provides for a non-invasive technique that can probe the hydrodynamics on pore and bulk scale lengths; many previous works have characterized fully saturated porous media, while rapid MR imaging (MRI) methods in particular have previously been applied to partially saturated flows. We present time- and ensemble-averaged MR measurements to observe the effects on a bead pack partially saturated with air under flowing water conditions. The 10 mm internal diameter bead pack was filled with 100 μm borosilicate glass beads. Air was injected into the bead pack as water flowed simultaneously through the sample at 25 ml h -1 . The initial partially saturated state was characterized with MRI density maps, free induction decay (FID) experiments, propagators and velocity maps before the water flow rate was increased incrementally from 25 to 500 ml h -1 . After the maximum flow rate of 500 ml h -1 , the MRI density maps, FID experiments, propagators and velocity maps were repeated and compared to the data taken before the maximum flow rate. This work shows that a partially saturated single-phase flow has global flow dynamics that return to characteristic flow statistics once a steady-state high flow rate has been reached. This high flow rate pushed out a significant amount of the air in the bead pack and caused the return of a preferential flow pattern. Velocity maps indicated that local flow statistics were not the same for the before and after blow out conditions. It has been suggested and shown previously that a flow pattern can return to similar

  5. Probabilistic teleportation via multi-parameter measurements and partially entangled states

    Science.gov (United States)

    Wei, Jiahua; Shi, Lei; Han, Chen; Xu, Zhiyan; Zhu, Yu; Wang, Gang; Wu, Hao

    2018-04-01

    In this paper, a novel scheme for probabilistic teleportation is presented with multi-parameter measurements via a non-maximally entangled state. This is in contrast to the fact that the measurement kinds for quantum teleportation are usually particular in most previous schemes. The detail implementation producers for our proposal are given by using of appropriate local unitary operations. Moreover, the total success probability and classical information of this proposal are calculated. It is demonstrated that the success probability and classical cost would be changed with the multi-measurement parameters and the entanglement factor of quantum channel. Our scheme could enlarge the research range of probabilistic teleportation.

  6. Troponin C Mutations Partially Stabilize the Active State of Regulated Actin and Fully Stabilize the Active State When Paired with Δ14 TnT.

    Science.gov (United States)

    Baxley, Tamatha; Johnson, Dylan; Pinto, Jose R; Chalovich, Joseph M

    2017-06-13

    Striated muscle contraction is regulated by the actin-associated proteins tropomyosin and troponin. The extent of activation of myosin ATPase activity is lowest in the absence of both Ca 2+ and activating cross-bridges (i.e., S1-ADP or rigor S1). Binding of activating species of myosin to actin at a saturating Ca 2+ concentration stabilizes the most active state (M state) of the actin-tropomyosin-troponin complex (regulated actin). Ca 2+ binding alone produces partial stabilization of the active state. The extent of stabilization at a saturating Ca 2+ concentration depends on the isoform of the troponin subunits, the phosphorylation state of troponin, and, in the case of cardiac muscle, the presence of hypertrophic cardiomyopathy-producing mutants of troponin T and troponin I. Cardiac dysfunction is also associated with mutations of troponin C (TnC). Troponin C mutants A8V, C84Y, and D145E increase the Ca 2+ sensitivity of ATPase activity. We show that these mutants change the distribution of regulated actin states. The A8V and C84Y TnC mutants decreased the inactive B state distribution slightly at low Ca 2+ concentrations, but the D145E mutants had no effect on that state. All TnC mutants increased the level of the active M state compared to that of the wild type, at a saturating Ca 2+ concentration. Troponin complexes that contained two mutations that stabilize the active M state, A8V TnC and Δ14 TnT, appeared to be completely in the active state in the presence of only Ca 2+ . Because Ca 2+ gives full activation, in this situation, troponin must be capable of positioning tropomyosin in the active M state without the need for rigor myosin binding.

  7. Production and Partial Purification of Alpha Amylase from Bacillus subtilis (MTCC 121 Using Solid State Fermentation

    Directory of Open Access Journals (Sweden)

    Dibyangana Raul

    2014-01-01

    Full Text Available Amylase is an enzyme that catalyzes the breakdown of starch into sugars and plays a pivotal role in a variety of areas like use as digestives, for the production of ethanol and high fructose corn syrup, detergents, desiring of textiles, modified starches, hydrolysis of oil-field drilling fluids, and paper recycling. In the present work, solid state fermentation (SSF for α-amylase production has been used in lieu of submerged fermentation (SmF due to its simple technique, low capital investment, lower levels of catabolite repression, and better product recovery. Bacillus subtilis has been well known as producer of alpha amylase and was tested using solid state fermentation for 48 hours at 37°C with wheat bran as substrate. Comparison between different fermentation hours demonstrated high yield of alpha amylase after 48 hours. This alpha amylase has optimum pH and temperature at 7.1 and 40°C, respectively. With the goal to purify alpha amylase, 30–70% (NH42SO4 cut concentrated the amylase activity threefold with respect to crude fermented extract. This was verified in quantitative DNS assay method as well as in zymogram gel profile. The exact molecular weight of the amylase is yet to be determined with the aid of other protein purification techniques.

  8. Calculations on charge state and energy loss of argon ions in partially and fully ionized carbon plasmas.

    Science.gov (United States)

    Barriga-Carrasco, Manuel D; Casas, David; Morales, Roberto

    2016-03-01

    The energy loss of argon ions in a target depends on their velocity and charge density. At the energies studied in this work, it depends mostly on the free and bound electrons in the target. Here the random-phase approximation is used for analyzing free electrons at any degeneracy. For the plasma-bound electrons, an interpolation between approximations for low and high energies is applied. The Brandt-Kitagawa (BK) model is employed to depict the projectile charge space distribution, and the stripping criterion of Kreussler et al. is used to determine its equilibrium charge state Q(eq). This latter criterion implies that the equilibrium charge state depends slightly on the electron density and temperature of the plasma. On the other hand, the effective charge Q(eff) is obtained as the ratio between the energy loss of the argon ion and that of the proton for the same plasma conditions. This effective charge Q(eff) is larger than the equilibrium charge state Q(eq) due to the incorporation of the BK charge distribution. Though our charge-state estimations are not exactly the same as the experimental values, our energy loss agrees quite well with the experiments. It is noticed that the energy loss in plasmas is higher than that in the same cold target of about, ∼42-62.5% and increases with carbon plasma ionization. This confirms the well-known enhanced plasma stopping. It is also observed that only a small part of this energy loss enhancement is due to an increase of the argon charge state, namely only ∼2.2 and 5.1%, for the partially and the fully ionized plasma, respectively. The other contribution is connected with a better energy transfer to the free electrons at plasma state than to the bound electrons at solid state of about, ∼38.8-57.4%, where higher values correspond to a fully ionized carbon plasma.

  9. A Mechanistic Neural Field Theory of How Anesthesia Suppresses Consciousness: Synaptic Drive Dynamics, Bifurcations, Attractors, and Partial State Equipartitioning.

    Science.gov (United States)

    Hou, Saing Paul; Haddad, Wassim M; Meskin, Nader; Bailey, James M

    2015-12-01

    With the advances in biochemistry, molecular biology, and neurochemistry there has been impressive progress in understanding the molecular properties of anesthetic agents. However, there has been little focus on how the molecular properties of anesthetic agents lead to the observed macroscopic property that defines the anesthetic state, that is, lack of responsiveness to noxious stimuli. In this paper, we use dynamical system theory to develop a mechanistic mean field model for neural activity to study the abrupt transition from consciousness to unconsciousness as the concentration of the anesthetic agent increases. The proposed synaptic drive firing-rate model predicts the conscious-unconscious transition as the applied anesthetic concentration increases, where excitatory neural activity is characterized by a Poincaré-Andronov-Hopf bifurcation with the awake state transitioning to a stable limit cycle and then subsequently to an asymptotically stable unconscious equilibrium state. Furthermore, we address the more general question of synchronization and partial state equipartitioning of neural activity without mean field assumptions. This is done by focusing on a postulated subset of inhibitory neurons that are not themselves connected to other inhibitory neurons. Finally, several numerical experiments are presented to illustrate the different aspects of the proposed theory.

  10. A computational formalization for partial evaluation

    DEFF Research Database (Denmark)

    Hatcliff, John; Danvy, Olivier

    1997-01-01

    We formalize a partial evaluator for Eugenio Moggi's computational metalanguage. This formalization gives an evaluation-order independent view of binding-time analysis and program specialization, including a proper treatment of call unfolding. It also enables us to express the essence of `control...

  11. On the Partial-Wave Analysis of Mesonic Resonances Decaying to Multiparticle Final States Produced by Polarized Photons

    Energy Technology Data Exchange (ETDEWEB)

    Salgado, Carlos W. [Norfolk State University, Norfolk, VA (United States) and Thomas Jefferson National Accelerator Facility, Newport News, VA (United States); Weygand, Dennis P. [Thomas Jefferson National Accelerator Facility, Newport News, VA (United States)

    2014-04-01

    Meson spectroscopy is going through a revival with the advent of high statistics experiments and new advances in the theoretical predictions. The Constituent Quark Model (CQM) is finally being expanded considering more basic principles of field theory and using discrete calculations of Quantum Chromodynamics (lattice QCD). These new calculations are approaching predictive power for the spectrum of hadronic resonances and decay modes. It will be the task of the new experiments to extract the meson spectrum from the data and compare with those predictions. The goal of this report is to describe one particular technique for extracting resonance information from multiparticle final states. The technique described here, partial wave analysis based on the helicity formalism, has been used at Brookhaven National Laboratory (BNL) using pion beams, and Jefferson Laboratory (Jlab) using photon beams. In particular this report broaden this technique to include production experiments using linearly polarized real photons or quasi-real photons. This article is of a didactical nature. We describe the process of analysis, detailing assumptions and formalisms, and is directed towards people interested in starting partial wave analysis.

  12. Improvements in the equation of state for the partially ionized plasmas of the solar interior

    Science.gov (United States)

    Liang, Aihua

    2005-11-01

    The three major material properties relevant for solar and stellar modeling are the equation of state (EOS), opacity and the nuclear reaction rate. Due to the nature of the equations of stellar structure and evolution, in most parts of a stars interior, the three material properties are entangled, and it is difficult to use astrophysics to constrain a single one. Luckily, thanks to the adiabatic stratification of the convection zone, there the structure only depends on the EOS, which is therefore largely disentangled from the other quantities. Our research, which aims at constraining the EOS using information from the Sun, is therefore most successful when data from the convection zone are used. Among the many solar equations of state that are being currently used there are two popular ones: Mihalas-Däppen-Hummer (MHD) EOS and OPAL EOS. Helioseismic inversion procedures, which have become standard to evaluate the accuracy of different solar models with respect to the real Sun, have revealed that except for the top 2%, the OPAL EOS matches the solar observations better than the MHD EOS. For this reason we have set our research goal to find a modification of the MHD EOS that can, in a first step, simulate the OPAL EOS, and ultimately, the real Sun. This goal has been attained. By construction, the OPAL EOS contains higher order correlation terms which are missing in the MHD EOS. Through an inversion procedure from the activity series expansion (ACTEX), upon which the OPAL EOS is based to the free energy expression of the MHD EOS, we have found out that the free particle assumption, used in the original version of the MHD EOS has indeed to be abandoned. We show that the two-body scattering terms of the Coulomb interaction, as well as electron degeneracy play a significant role in the difference between the original version of the MHD and OPAL EOS. During our interdisciplinary investigation, aiming at seeking an improved MHD EOS under the guidance of the OPAL EOS, we

  13. Configuration model of partial repairable spares under batch ordering policy based on inventory state

    Institute of Scientific and Technical Information of China (English)

    Ruan Minzhi; Luo Yi; Li Hua

    2014-01-01

    Rational planning of spares configuration project is an effective approach to improve equipment availability as well as reduce life cycle cost (LCC). With an analysis of various impacts on support system, the spares demand rate forecast model is constructed. According to systemic analysis method, spares support effectiveness evaluation indicators system is built, and then, initial spares configuration and optimization method is researched. To the issue of discarding and con-sumption for incomplete repairable items, its expected backorders function is approximated by Laplace demand distribution. Combining the (s-1, s) and (R, Q) inventory policy, the spares resup-ply model is established under the batch ordering policy based on inventory state, and the optimi-zation analysis flow for spares configuration is proposed. Through application on shipborne equipment spares configuration, the given scenarios are analyzed under two constraint targets:one is the support effectiveness, and the other is the spares cost. Analysis reveals that the result is consistent with practical regulation;therefore, the model’s correctness, method’s validity as well as optimization project’s rationality are proved to a certain extent.

  14. Partial-Wave Analysis of Centrally Produced Two-Pseudoscalar Final States in pp Reactions at COMPASS

    CERN Document Server

    Austregesilo, Alexander

    2014-01-01

    COMPASS is a fixed-target experiment at the CERN SPS which focused on light-quark hadron spectroscopy during the data taking periods in 2008 and 2009. A world-leading data set was collected with a 190GeV/c hadron beam impinging on a liquid hydrogen target in order to study, inter alia, the central exclusive production of glueball candidates in the light-meson sector. Especially the double-Pomeron exchange mechanism is well suited for the production of mesons without valence quark content. We select centrally produced systems with two pseudo-scalar mesons in the final state from the COMPASS data set recorded with an incoming proton. The decay of this system is decomposed in terms of partial waves, where particular attention is paid to the inherent mathematical ambiguities of the amplitude analysis. Furthermore, we show that simple parametrisations are able to describe the mass dependence of the fit results with sensible Breit-Wigner parameters.

  15. Thermal, chemical and pH induced unfolding of turmeric root lectin: modes of denaturation.

    Directory of Open Access Journals (Sweden)

    Himadri Biswas

    Full Text Available Curcuma longa rhizome lectin, of non-seed origin having antifungal, antibacterial and α-glucosidase inhibitory activities, forms a homodimer with high thermal stability as well as acid tolerance. Size exclusion chromatography and dynamic light scattering show it to be a dimer at pH 7, but it converts to a monomer near pH 2. Circular dichroism spectra and fluorescence emission maxima are virtually indistinguishable from pH 7 to 2, indicating secondary and tertiary structures remain the same in dimer and monomer within experimental error. The tryptophan environment as probed by acrylamide quenching data yielded very similar data at pH 2 and pH 7, implying very similar folding for monomer and dimer. Differential scanning calorimetry shows a transition at 350.3 K for dimer and at 327.0 K for monomer. Thermal unfolding and chemical unfolding induced by guanidinium chloride for dimer are both reversible and can be described by two-state models. The temperatures and the denaturant concentrations at which one-half of the protein molecules are unfolded, are protein concentration-dependent for dimer but protein concentration-independent for monomer. The free energy of unfolding at 298 K was found to be 5.23 Kcal mol-1 and 14.90 Kcal mol-1 for the monomer and dimer respectively. The value of change in excess heat capacity upon protein denaturation (ΔCp is 3.42 Kcal mol-1 K-1 for dimer. The small ΔCp for unfolding of CLA reflects a buried hydrophobic core in the folded dimeric protein. These unfolding experiments, temperature dependent circular dichroism and dynamic light scattering for the dimer at pH 7 indicate its higher stability than for the monomer at pH 2. This difference in stability of dimeric and monomeric forms highlights the contribution of inter-subunit interactions in the former.

  16. RPA-mediated unfolding of systematically varying G-quadruplex structures.

    Science.gov (United States)

    Ray, Sujay; Qureshi, Mohammad H; Malcolm, Dominic W; Budhathoki, Jagat B; Celik, Uğur; Balci, Hamza

    2013-05-21

    G-quadruplex (GQ) is a noncanonical nucleic acid structure that is formed by guanine rich sequences. Unless it is destabilized by proteins such as replication protein A (RPA), GQ could interfere with DNA metabolic functions, such as replication or repair. We studied RPA-mediated GQ unfolding using single-molecule FRET on two groups of GQ structures that have different loop lengths and different numbers of G-tetrad layers. We observed a linear increase in the steady-state stability of the GQ against RPA-mediated unfolding with increasing number of layers or decreasing loop length. The stability demonstrated by different GQ structures varied by at least three orders of magnitude. Those with shorter loops (less than three nucleotides long) or a greater number of layers (more than three layers) maintained a significant folded population even at physiological RPA concentration (≈1 μM), raising the possibility of physiological viability of such GQ structures. Finally, we measured the transition time between the start and end of the RPA-mediated GQ unfolding process to be 0.35 ± 0.10 s for all GQ constructs we studied, despite significant differences in their steady-state stabilities. We propose a two-step RPA-mediated GQ unfolding mechanism that is consistent with our observations. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  17. Combined and controlled remote implementations of partially unknown quantum operations of multiqubits using Greenberger-Horne-Zeilinger states

    International Nuclear Information System (INIS)

    Wang Anmin

    2007-01-01

    We propose and prove protocols of combined and controlled remote implementations of partially unknown quantum operations belonging to the restricted sets [A. M. Wang, Phys. Rev. A 74, 032317 (2006)] using Greenberger-Horne-Zeilinger (GHZ) states. We present the protocols in detail in the cases of one qubit, with two senders and with one controller, respectively. Then we study the variations of protocols with many senders, or with many controllers, or with both many senders and controllers using a multipartite GHZ state. Furthermore, we extend these protocols to the cases of multiqubits. Because our protocols have to request that the senders work together and transfer the information in turn or receive the repertoire of extra supercontrollers, or/and the controller(s) open the quantum channel and distribute the passwords in different ways, they definitely have the strong security in remote quantum information processing and communications. Moreover, the combined protocol with many senders is helpful to arrive at the power of remote implementations of quantum operations to the utmost extent in theory, since the different senders may have different operational resources and different operational rights in practice, and the controlled protocol with many controllers is able to enhance security and increase applications of remote implementations of quantum operations in engineering, since it has some common features in a controlled process

  18. Neutron spectrum unfolding using computer code SAIPS

    International Nuclear Information System (INIS)

    Karim, S.

    1999-01-01

    The main objective of this project was to study the neutron energy spectrum at rabbit station-1 in Pakistan Research Reactor (PARR-I). To do so, multiple foils activation method was used to get the saturated activities. The computer code SAIPS was used to unfold the neutron spectra from the measured reaction rates. Of the three built in codes in SAIPS, only SANDI and WINDOWS were used. Contribution of thermal part of the spectra was observed to be higher than the fast one. It was found that the WINDOWS gave smooth spectra while SANDII spectra have violet oscillations in the resonance region. The uncertainties in the WINDOWS results are higher than those of SANDII. The results show reasonable agreement with the published results. (author)

  19. Kinetics of protein unfolding at interfaces

    International Nuclear Information System (INIS)

    Yano, Yohko F

    2012-01-01

    The conformation of protein molecules is determined by a balance of various forces, including van der Waals attraction, electrostatic interaction, hydrogen bonding, and conformational entropy. When protein molecules encounter an interface, they are often adsorbed on the interface. The conformation of an adsorbed protein molecule strongly depends on the interaction between the protein and the interface. Recent time-resolved investigations have revealed that protein conformation changes during the adsorption process due to the protein-protein interaction increasing with increasing interface coverage. External conditions also affect the protein conformation. This review considers recent dynamic observations of protein adsorption at various interfaces and their implications for the kinetics of protein unfolding at interfaces. (topical review)

  20. Unfolding in particle physics: A window on solving inverse problems

    International Nuclear Information System (INIS)

    Spano, F.

    2013-01-01

    Unfolding is the ensemble of techniques aimed at resolving inverse, ill-posed problems. A pedagogical introduction to the origin and main problems related to unfolding is presented and used as the the stepping stone towards the illustration of some of the most common techniques that are currently used in particle physics experiments. (authors)

  1. Review of unfolding methods for neutron flux dosimetry

    International Nuclear Information System (INIS)

    Stallmann, F.W.; Kam, F.B.K.

    1975-01-01

    The primary method in reactor dosimetry is the foil activation technique. To translate the activation measurements into neutron fluxes, a special data processing technique called unfolding is needed. Some general observations about the problems and the reliability of this approach to reactor dosimetry are presented. Current unfolding methods are reviewed. 12 references. (auth)

  2. The ribosome can prevent aggregation of partially folded protein intermediates: studies using the Escherichia coli ribosome.

    Directory of Open Access Journals (Sweden)

    Bani Kumar Pathak

    Full Text Available BACKGROUND: Molecular chaperones that support de novo folding of proteins under non stress condition are classified as chaperone 'foldases' that are distinct from chaperone' holdases' that provide high affinity binding platform for unfolded proteins and prevent their aggregation specifically under stress conditions. Ribosome, the cellular protein synthesis machine can act as a foldase chaperone that can bind unfolded proteins and release them in folding competent state. The peptidyl transferase center (PTC located in the domain V of the 23S rRNA of Escherichia coli ribosome (bDV RNA is the chaperoning center of the ribosome. It has been proposed that via specific interactions between the RNA and refolding proteins, the chaperone provides information for the correct folding of unfolded polypeptide chains. RESULTS: We demonstrate using Escherichia coli ribosome and variants of its domain V RNA that the ribosome can bind to partially folded intermediates of bovine carbonic anhydrase II (BCAII and lysozyme and suppress aggregation during their refolding. Using mutants of domain V RNA we demonstrate that the time for which the chaperone retains the bound protein is an important factor in determining its ability to suppress aggregation and/or support reactivation of protein. CONCLUSION: The ribosome can behave like a 'holdase' chaperone and has the ability to bind and hold back partially folded intermediate states of proteins from participating in the aggregation process. Since the ribosome is an essential organelle that is present in large numbers in all living cells, this ability of the ribosome provides an energetically inexpensive way to suppress cellular aggregation. Further, this ability of the ribosome might also be crucial in the context that the ribosome is one of the first chaperones to be encountered by a large nascent polypeptide chains that have a tendency to form partially folded intermediates immediately following their synthesis.

  3. Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage mini protein

    Science.gov (United States)

    Day, Ryan; Paschek, Dietmar; Garcia, Angel E.

    2012-01-01

    We study the unbiased folding/unfolding thermodynamics of the Trp-cage miniprotein using detailed molecular dynamics simulations of an all-atom model of the protein in explicit solvent, using the Amberff99SB force field. Replica-exchange molecular dynamics (REMD) simulations are used to sample the protein ensembles over a broad range of temperatures covering the folded and unfolded states, and at two densities. The obtained ensembles are shown to reach equilibrium in the 1 μs per replica timescale. The total simulation time employed in the calculations exceeds 100 μs. Ensemble averages of the fraction folded, pressure, and energy differences between the folded and unfolded states as a function of temperature are used to model the free energy of the folding transition, ΔG(P,T), over the whole region of temperature and pressures sampled in the simulations. The ΔG(P,T) diagram describes an ellipse over the range of temperatures and pressures sampled, predicting that the system can undergo pressure induced unfolding and cold denaturation at low temperatures and high pressures, and unfolding at low pressures and high temperatures. The calculated free energy function exhibits remarkably good agreement with the experimental folding transition temperature (Tf = 321 K), free energy and specific heat changes. However, changes in enthalpy and entropy are significantly different than the experimental values. We speculate that these differences may be due to the simplicity of the semi-empirical force field used in the simulations and that more elaborate force fields may be required to describe appropriately the thermodynamics of proteins. PMID:20408169

  4. Defining a methodology for benchmarking spectrum unfolding codes

    International Nuclear Information System (INIS)

    Meyer, W.; Kirmser, P.G.; Miller, W.H.; Hu, K.K.

    1976-01-01

    It has long been recognized that different neutron spectrum unfolding codes will produce significantly different results when unfolding the same measured data. In reviewing the results of such analyses it has been difficult to determine which result if any is the best representation of what was measured by the spectrometer detector. A proposal to develop a benchmarking procedure for spectrum unfolding codes is presented. The objective of the procedure will be to begin to develop a methodology and a set of data with a well established and documented result that could be used to benchmark and standardize the various unfolding methods and codes. It is further recognized that development of such a benchmark must involve a consensus of the technical community interested in neutron spectrum unfolding

  5. The Unfolding MD Simulations of Cyclophilin: Analyzed by Surface Contact Networks and Their Associated Metrics

    Science.gov (United States)

    Roy, Sourav; Basu, Sankar; Dasgupta, Dipak; Bhattacharyya, Dhananjay; Banerjee, Rahul

    2015-01-01

    Currently, considerable interest exists with regard to the dissociation of close packed aminoacids within proteins, in the course of unfolding, which could result in either wet or dry moltenglobules. The progressive disjuncture of residues constituting the hydrophobic core ofcyclophilin from L. donovani (LdCyp) has been studied during the thermal unfolding of the molecule, by molecular dynamics simulations. LdCyp has been represented as a surface contactnetwork (SCN) based on the surface complementarity (Sm) of interacting residues within themolecular interior. The application of Sm to side chain packing within proteins make it a very sensitive indicator of subtle perturbations in packing, in the thermal unfolding of the protein. Network based metrics have been defined to track the sequential changes in the disintegration ofthe SCN spanning the hydrophobic core of LdCyp and these metrics prove to be highly sensitive compared to traditional metrics in indicating the increased conformational (and dynamical) flexibility in the network. These metrics have been applied to suggest criteria distinguishing DMG, WMG and transition state ensembles and to identify key residues involved in crucial conformational/topological events during the unfolding process. PMID:26545107

  6. Average State IQ, State Wealth and Racial Composition as Predictors of State Health Statistics: Partial Support for "g" as a Fundamental Cause of Health Disparities

    Science.gov (United States)

    Reeve, Charlie L.; Basalik, Debra

    2010-01-01

    This study examined the degree to which differences in average IQ across the 50 states was associated with differences in health statistics independent of differences in wealth, health care expenditures and racial composition. Results show that even after controlling for differences in state wealth and health care expenditures, average IQ had…

  7. Converting partially-stocked aspen stands to fully-stocked stands in the Lake States: an economic analysis.

    Science.gov (United States)

    Jeffrey T. Olson; Allen L. Lundgren

    1978-01-01

    The 1968 Wisconsin Forest Survey showed large areas of aspen type that are not considered fully stocked. The economic feasibility of converting partially-stocked stands to full stocking is examined, and a rule presented for determining when a partially-stocked stand should be harvested to maximize its present value.

  8. Exploring the Unfolding Pathway of Maltose Binding Proteins: An Integrated Computational Approach

    KAUST Repository

    Guardiani, Carlo; Marino, Daniele Di; Tramontano, Anna; Chinappi, Mauro; Cecconi, Fabio

    2014-01-01

    © 2014 American Chemical Society. Recent single-molecule force spectroscopy experiments on the Maltose Binding Proteins (MBPs) identified four stable structural units, termed unfoldons, that resist mechanical stress and determine the intermediates of the unfolding pathway. In this work, we analyze the topological origin and the dynamical role of the unfoldons using an integrated approach which combines a graph-theoretical analysis of the interaction network of the MBP native-state with steered molecular dynamics simulations. The topological analysis of the native state, while revealing the structural nature of the unfoldons, provides a framework to interpret the MBP mechanical unfolding pathway. Indeed, the experimental pathway can be effectively predicted by means of molecular dynamics simulations with a simple topology-based and low-resolution model of the MBP. The results obtained from the coarse-grained approach are confirmed and further refined by all-atom molecular dynamics.

  9. Exploring the Unfolding Pathway of Maltose Binding Proteins: An Integrated Computational Approach

    KAUST Repository

    Guardiani, Carlo

    2014-09-09

    © 2014 American Chemical Society. Recent single-molecule force spectroscopy experiments on the Maltose Binding Proteins (MBPs) identified four stable structural units, termed unfoldons, that resist mechanical stress and determine the intermediates of the unfolding pathway. In this work, we analyze the topological origin and the dynamical role of the unfoldons using an integrated approach which combines a graph-theoretical analysis of the interaction network of the MBP native-state with steered molecular dynamics simulations. The topological analysis of the native state, while revealing the structural nature of the unfoldons, provides a framework to interpret the MBP mechanical unfolding pathway. Indeed, the experimental pathway can be effectively predicted by means of molecular dynamics simulations with a simple topology-based and low-resolution model of the MBP. The results obtained from the coarse-grained approach are confirmed and further refined by all-atom molecular dynamics.

  10. A genetic algorithm based method for neutron spectrum unfolding

    International Nuclear Information System (INIS)

    Suman, Vitisha; Sarkar, P.K.

    2013-03-01

    An approach to neutron spectrum unfolding based on a stochastic evolutionary search mechanism - Genetic Algorithm (GA) is presented. It is tested to unfold a set of simulated spectra, the unfolded spectra is compared to the output of a standard code FERDOR. The method was then applied to a set of measured pulse height spectrum of neutrons from the AmBe source as well as of emitted neutrons from Li(p,n) and Ag(C,n) nuclear reactions carried out in the accelerator environment. The unfolded spectra compared to the output of FERDOR show good agreement in the case of AmBe spectra and Li(p,n) spectra. In the case of Ag(C,n) spectra GA method results in some fluctuations. Necessity of carrying out smoothening of the obtained solution is also studied, which leads to approximation of the solution yielding an appropriate solution finally. Few smoothing techniques like second difference smoothing, Monte Carlo averaging, combination of both and gaussian based smoothing methods are also studied. Unfolded results obtained after inclusion of the smoothening criteria are in close agreement with the output obtained from the FERDOR code. The present method is also tested on a set of underdetermined problems, the outputs of which is compared to the unfolded spectra obtained from the FERDOR applied to a completely determined problem, shows a good match. The distribution of the unfolded spectra is also studied. Uncertainty propagation in the unfolded spectra due to the errors present in the measurement as well as the response function is also carried out. The method appears to be promising for unfolding the completely determined as well as underdetermined problems. It also has provisions to carry out the uncertainty analysis. (author)

  11. Assessing the suitability of a partial water reuse system for rearing juvenile Chinook salmon Oncorhynchus tshawytscha for stocking in Washington State

    Science.gov (United States)

    Health and welfare of juvenile Chinook salmon Oncorhynchus tshawytsha reared in a pilot circular tank-based partial water reuse system in Washington State were evaluated in comparison to fish from the same spawn reared in a flow-through raceway, in order to assess the suitability of using water reus...

  12. Neutron spectrum unfolding using neural networks

    International Nuclear Information System (INIS)

    Vega C, H.R.; Hernandez D, V.M.; Manzanares A, E.

    2004-01-01

    An artificial neural network has been designed to obtain the neutron spectra from the Bonner spheres spectrometer's count rates. The neural network was trained using a large set of neutron spectra compiled by the International Atomic Energy Agency. These include spectra from iso- topic neutron sources, reference and operational neutron spectra obtained from accelerators and nuclear reactors. The spectra were transformed from lethargy to energy distribution and were re-binned to 31 energy groups using the MCNP 4C code. Re-binned spectra and UTA4 matrix were used to calculate the expected count rates in Bonner spheres spectrometer. These count rates were used as input and correspondent spectrum was used as output during neural network training. The network has 7 input nodes, 56 neurons as hidden layer and 31 neurons in the output layer. After training the network was tested with the Bonner spheres count rates produced by twelve neutron spectra. The network allows unfolding the neutron spectrum from count rates measured with Bonner spheres. Good results are obtained when testing count rates belong to neutron spectra used during training, acceptable results are obtained for count rates obtained from actual neutron fields; however the network fails when count rates belong to monoenergetic neutron sources. (Author)

  13. Folding and unfolding phylogenetic trees and networks.

    Science.gov (United States)

    Huber, Katharina T; Moulton, Vincent; Steel, Mike; Wu, Taoyang

    2016-12-01

    Phylogenetic networks are rooted, labelled directed acyclic graphswhich are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any phylogenetic network N can be "unfolded" to obtain a MUL-tree U(N) and, conversely, a MUL-tree T can in certain circumstances be "folded" to obtain aphylogenetic network F(T) that exhibits T. In this paper, we study properties of the operations U and F in more detail. In particular, we introduce the class of stable networks, phylogenetic networks N for which F(U(N)) is isomorphic to N, characterise such networks, and show that they are related to the well-known class of tree-sibling networks. We also explore how the concept of displaying a tree in a network N can be related to displaying the tree in the MUL-tree U(N). To do this, we develop aphylogenetic analogue of graph fibrations. This allows us to view U(N) as the analogue of the universal cover of a digraph, and to establish a close connection between displaying trees in U(N) and reconciling phylogenetic trees with networks.

  14. Unfolding Visual Lexical Decision in Time

    Science.gov (United States)

    Barca, Laura; Pezzulo, Giovanni

    2012-01-01

    Visual lexical decision is a classical paradigm in psycholinguistics, and numerous studies have assessed the so-called “lexicality effect" (i.e., better performance with lexical than non-lexical stimuli). Far less is known about the dynamics of choice, because many studies measured overall reaction times, which are not informative about underlying processes. To unfold visual lexical decision in (over) time, we measured participants' hand movements toward one of two item alternatives by recording the streaming x,y coordinates of the computer mouse. Participants categorized four kinds of stimuli as “lexical" or “non-lexical:" high and low frequency words, pseudowords, and letter strings. Spatial attraction toward the opposite category was present for low frequency words and pseudowords. Increasing the ambiguity of the stimuli led to greater movement complexity and trajectory attraction to competitors, whereas no such effect was present for high frequency words and letter strings. Results fit well with dynamic models of perceptual decision-making, which describe the process as a competition between alternatives guided by the continuous accumulation of evidence. More broadly, our results point to a key role of statistical decision theory in studying linguistic processing in terms of dynamic and non-modular mechanisms. PMID:22563419

  15. The identification of unfolding facial expressions.

    Science.gov (United States)

    Fiorentini, Chiara; Schmidt, Susanna; Viviani, Paolo

    2012-01-01

    We asked whether the identification of emotional facial expressions (FEs) involves the simultaneous perception of the facial configuration or the detection of emotion-specific diagnostic cues. We recorded at high speed (500 frames s-1) the unfolding of the FE in five actors, each expressing six emotions (anger, surprise, happiness, disgust, fear, sadness). Recordings were coded every 10 frames (20 ms of real time) with the Facial Action Coding System (FACS, Ekman et al 2002, Salt Lake City, UT: Research Nexus eBook) to identify the facial actions contributing to each expression, and their intensity changes over time. Recordings were shown in slow motion (1/20 of recording speed) to one hundred observers in a forced-choice identification task. Participants were asked to identify the emotion during the presentation as soon as they felt confident to do so. Responses were recorded along with the associated response times (RTs). The RT probability density functions for both correct and incorrect responses were correlated with the facial activity during the presentation. There were systematic correlations between facial activities, response probabilities, and RT peaks, and significant differences in RT distributions for correct and incorrect answers. The results show that a reliable response is possible long before the full FE configuration is reached. This suggests that identification is reached by integrating in time individual diagnostic facial actions, and does not require perceiving the full apex configuration.

  16. Two-terminal charge tunneling: Disentangling Majorana zero modes from partially separated Andreev bound states in semiconductor-superconductor heterostructures

    Science.gov (United States)

    Moore, Christopher; Stanescu, Tudor D.; Tewari, Sumanta

    2018-04-01

    We show that a pair of overlapping Majorana bound states (MBSs) forming a partially separated Andreev bound state (ps-ABS) represents a generic low-energy feature in spin-orbit-coupled semiconductor-superconductor (SM-SC) hybrid nanowire in the presence of a Zeeman field. The ps-ABS interpolates continuously between the "garden variety" ABS, which consists of two MBSs sitting on top of each other, and the topologically protected Majorana zero modes (MZMs), which are separated by a distance given by the length of the wire. The really problematic ps-ABSs consist of component MBSs separated by a distance of the order of the characteristic Majorana decay length ξ , and have nearly zero energy in a significant range of control parameters, such as the Zeeman field and chemical potential, within the topologically trivial phase. Despite being topologically trivial, such ps-ABSs can generate signatures identical to MZMs in local charge tunneling experiments. In particular, the height of the zero-bias conductance peak (ZBCP) generated by ps-ABSs has the quantized value 2 e2/h , and it can remain unchanged in an extended range of experimental parameters, such as Zeeman field and the tunnel barrier height. We illustrate the formation of such low-energy robust ps-ABSs in two experimentally relevant situations: a hybrid SM-SC system consisting of a proximitized nanowire coupled to a quantum dot and the SM-SC system in the presence of a spatially varying inhomogeneous potential. We then show that, unlike local measurements, a two-terminal experiment involving charge tunneling at both ends of the wire is capable of distinguishing between the generic ps-ABSs and the non-Abelian MZMs. While the MZMs localized at the opposite ends of the wire generate correlated differential conduction spectra, including correlations in energy splittings and critical Zeeman fields associated with the emergence of the ZBCPs, such correlations are absent if the ZBCPs are due to ps-ABSs emerging in the

  17. Multistage unfolding of an SH3 domain: an initial urea-filled dry molten globule precedes a wet molten globule with non-native structure.

    Science.gov (United States)

    Dasgupta, Amrita; Udgaonkar, Jayant B; Das, Payel

    2014-06-19

    The unfolding of the SH3 domain of the PI3 kinase in aqueous urea has been studied using a synergistic experiment-simulation approach. The experimental observation of a transient wet molten globule intermediate, IU, with an unusual non-native burial of the sole Trp residue, W53, provides the benchmark for the unfolding simulations performed (eight in total, each at least 0.5 μs long). The simulations reveal that the partially unfolded IU ensemble is preceded by an early native-like molten globule intermediate ensemble I*. In the very initial stage of unfolding, dry globule conformations with the protein core filled with urea instead of water are transiently observed within the I* ensemble. Water penetration into the urea-filled core of dry globule conformations is frequently accompanied by very transient burial of W53. Later during gradual unfolding, W53 is seen to again become transiently buried in the IU ensemble for a much longer time. In the structurally heterogeneous IU ensemble, conformational flexibility of the C-terminal β-strands enables W53 burial by the formation of non-native, tertiary contacts with hydrophobic residues, which could serve to protect the protein from aggregation during unfolding.

  18. Unfolding intermediates of the mutant His-107-Tyr of human ...

    Indian Academy of Sciences (India)

    Srabani Taraphder

    We present in this article a detailed analysis of representative structures and proton transfer activity of .... cal molecular dynamics simulations to identify potential unfolding ... clustering parameters to carry out K-means cluster- ing of different ...

  19. Catalogue to select the initial guess spectrum during unfolding

    CERN Document Server

    Vega-Carrillo, H R

    2002-01-01

    A new method to select the initial guess spectrum is presented. Neutron spectra unfolded from Bonner sphere data are dependent on the initial guess spectrum used in the unfolding code. The method is based on a catalogue of detector count rates calculated from a set of reported neutron spectra. The spectra of three isotopic neutron sources sup 2 sup 5 sup 2 Cf, sup 2 sup 3 sup 9 PuBe and sup 2 sup 5 sup 2 Cf/D sub 2 O, were measured to test the method. The unfolding was carried out using the three initial guess options included in the BUNKIUT code. Neutron spectra were also calculated using MCNP code. Unfolded spectra were compared with those calculated; in all the cases our method gives the best results.

  20. Unfolding methods in high-energy physics experiments

    International Nuclear Information System (INIS)

    Blobel, V.

    1985-01-01

    Distributions measured in high-energy physics experiments are often distorted or transformed by limited acceptance and finite resolution of the detectors. The unfolding of measured distributions is an important, but due to inherent instabilities a very difficult problem. Methods for unfolding, applicable for the analysis of high-energy physics experiments, and their properties are discussed. An introduction is given to the method of regularization. (orig.)

  1. Unfolding methods in high-energy physics experiments

    International Nuclear Information System (INIS)

    Blobel, V.

    1984-12-01

    Distributions measured in high-energy physics experiments are often distorted or transformed by limited acceptance and finite resolution of the detectors. The unfolding of measured distributions is an important, but due to inherent instabilities a very difficult problem. Methods for unfolding, applicable for the analysis of high-energy physics experiments, and their properties are discussed. An introduction is given to the method of regularization. (orig.)

  2. Partial Correlation-Based Retinotopically Organized Resting-State Functional Connectivity Within and Between Areas of the Visual Cortex Reflects More Than Cortical Distance.

    Science.gov (United States)

    Dawson, Debra Ann; Lam, Jack; Lewis, Lindsay B; Carbonell, Felix; Mendola, Janine D; Shmuel, Amir

    2016-02-01

    Numerous studies have demonstrated functional magnetic resonance imaging (fMRI)-based resting-state functional connectivity (RSFC) between cortical areas. Recent evidence suggests that synchronous fluctuations in blood oxygenation level-dependent fMRI reflect functional organization at a scale finer than that of visual areas. In this study, we investigated whether RSFCs within and between lower visual areas are retinotopically organized and whether retinotopically organized RSFC merely reflects cortical distance. Subjects underwent retinotopic mapping and separately resting-state fMRI. Visual areas V1, V2, and V3, were subdivided into regions of interest (ROIs) according to quadrants and visual field eccentricity. Functional connectivity (FC) was computed based on Pearson's linear correlation (correlation), and Pearson's linear partial correlation (correlation between two time courses after the time courses from all other regions in the network are regressed out). Within a quadrant, within visual areas, all correlation and nearly all partial correlation FC measures showed statistical significance. Consistently in V1, V2, and to a lesser extent in V3, correlation decreased with increasing eccentricity separation. Consistent with previously reported monkey anatomical connectivity, correlation/partial correlation values between regions from adjacent areas (V1-V2 and V2-V3) were higher than those between nonadjacent areas (V1-V3). Within a quadrant, partial correlation showed consistent significance between regions from two different areas with the same or adjacent eccentricities. Pairs of ROIs with similar eccentricity showed higher correlation/partial correlation than pairs distant in eccentricity. Between dorsal and ventral quadrants, partial correlation between common and adjacent eccentricity regions within a visual area showed statistical significance; this extended to more distant eccentricity regions in V1. Within and between quadrants, correlation decreased

  3. OPERATOR NORM INEQUALITIES BETWEEN TENSOR UNFOLDINGS ON THE PARTITION LATTICE.

    Science.gov (United States)

    Wang, Miaoyan; Duc, Khanh Dao; Fischer, Jonathan; Song, Yun S

    2017-05-01

    Interest in higher-order tensors has recently surged in data-intensive fields, with a wide range of applications including image processing, blind source separation, community detection, and feature extraction. A common paradigm in tensor-related algorithms advocates unfolding (or flattening) the tensor into a matrix and applying classical methods developed for matrices. Despite the popularity of such techniques, how the functional properties of a tensor changes upon unfolding is currently not well understood. In contrast to the body of existing work which has focused almost exclusively on matricizations, we here consider all possible unfoldings of an order- k tensor, which are in one-to-one correspondence with the set of partitions of {1, …, k }. We derive general inequalities between the l p -norms of arbitrary unfoldings defined on the partition lattice. In particular, we demonstrate how the spectral norm ( p = 2) of a tensor is bounded by that of its unfoldings, and obtain an improved upper bound on the ratio of the Frobenius norm to the spectral norm of an arbitrary tensor. For specially-structured tensors satisfying a generalized definition of orthogonal decomposability, we prove that the spectral norm remains invariant under specific subsets of unfolding operations.

  4. Molecular origin of urea driven hydrophobic polymer collapse and unfolding depending on side chain chemistry.

    Science.gov (United States)

    Nayar, Divya; Folberth, Angelina; van der Vegt, Nico F A

    2017-07-19

    Osmolytes affect hydrophobic collapse and protein folding equilibria. The underlying mechanisms are, however, not well understood. We report large-scale conformational sampling of two hydrophobic polymers with secondary and tertiary amide side chains using extensive molecular dynamics simulations. The calculated free energy of unfolding increases with urea for the secondary amide, yet decreases for the tertiary amide, in agreement with experiment. The underlying mechanism is rooted in opposing entropic driving forces: while urea screens the hydrophobic macromolecular interface and drives unfolding of the tertiary amide, urea's concomitant loss in configurational entropy drives collapse of the secondary amide. Only at sufficiently high urea concentrations bivalent urea hydrogen bonding interactions with the secondary amide lead to further stabilisation of its collapsed state. The observations provide a new angle on the interplay between side chain chemistry, urea hydrogen bonding, and the role of urea in attenuating or strengthening the hydrophobic effect.

  5. Solvent-Exposed Salt Bridges Influence the Kinetics of α-Helix Folding and Unfolding.

    Science.gov (United States)

    Meuzelaar, Heleen; Tros, Martijn; Huerta-Viga, Adriana; van Dijk, Chris N; Vreede, Jocelyne; Woutersen, Sander

    2014-03-06

    Salt bridges are known to play an essential role in the thermodynamic stability of the folded conformation of many proteins, but their influence on the kinetics of folding remains largely unknown. Here, we investigate the effect of Glu-Arg salt bridges on the kinetics of α-helix folding using temperature-jump transient-infrared spectroscopy and steady-state UV circular dichroism. We find that geometrically optimized salt bridges (Glu - and Arg + are spaced four peptide units apart, and the Glu/Arg order is such that the side-chain rotameric preferences favor salt-bridge formation) significantly speed up folding and slow down unfolding, whereas salt bridges with unfavorable geometry slow down folding and slightly speed up unfolding. Our observations suggest a possible explanation for the surprising fact that many biologically active proteins contain salt bridges that do not stabilize the native conformation: these salt bridges might have a kinetic rather than a thermodynamic function.

  6. A computational formalization for partial evaluation

    DEFF Research Database (Denmark)

    Hatcliff, John; Danvy, Olivier

    1996-01-01

    We formalize a partial evaluator for Eugenio Moggi's computational metalanguage. This formalization gives an evaluation-order independent view of binding-time analysis and program specialization, including a proper treatment of call unfolding. It also enables us to express the essence of `control......-based binding-time improvements' for let expressions. Specically, we prove that the binding-time improvements given by `continuation-based specialization' can be expressed in the metalanguage via monadic laws....

  7. When structure affects function--the need for partial volume effect correction in functional and resting state magnetic resonance imaging studies.

    Science.gov (United States)

    Dukart, Juergen; Bertolino, Alessandro

    2014-01-01

    Both functional and also more recently resting state magnetic resonance imaging have become established tools to investigate functional brain networks. Most studies use these tools to compare different populations without controlling for potential differences in underlying brain structure which might affect the functional measurements of interest. Here, we adapt a simulation approach combined with evaluation of real resting state magnetic resonance imaging data to investigate the potential impact of partial volume effects on established functional and resting state magnetic resonance imaging analyses. We demonstrate that differences in the underlying structure lead to a significant increase in detected functional differences in both types of analyses. Largest increases in functional differences are observed for highest signal-to-noise ratios and when signal with the lowest amount of partial volume effects is compared to any other partial volume effect constellation. In real data, structural information explains about 25% of within-subject variance observed in degree centrality--an established resting state connectivity measurement. Controlling this measurement for structural information can substantially alter correlational maps obtained in group analyses. Our results question current approaches of evaluating these measurements in diseased population with known structural changes without controlling for potential differences in these measurements.

  8. Analysis of Partial Discharge Activity for Evaluation of the State of High Power Electric Generators Stator Windings

    Directory of Open Access Journals (Sweden)

    Dumitrescu Sorin

    2016-08-01

    Full Text Available The paper shows the importance of trending of partial discharge activity in assessing the insulation condition. It is presented the principle of the measurement method and the quantities that characterize partial discharges and also the criteria utilized for the assessement of the insulation condition of the hydrogenerators. Results of the measurements made on several hydrogenerators are presented, like the variation with time of the two main quantities that characterize the partial discharges, maximum magnitude, Qm and the normalized quantity, NQN over a period of about 10 years. Further, a classification of the insulation condition by 3 main and 2 intermediary categories and the definition of these categories are given. The criteria used for the assessment of the insulation condition are presented in the form of a table: quantitative criteria by the ± NQN and ± Qm values and qualitative criteria for the analysis of the 2D and 3D diagrams. At the end of each set of measurements, an analyze of the insulation condition annual evaluation is made, also a verdict is put, and of course, the recommendations made relating to the maintenance and the decisions that have been taken. The paper ends with several considerations on the method of on-line partial discharges and especially, on the conditions for valid trending activity in time.

  9. Partially folded intermediates during trypsinogen denaturation

    Directory of Open Access Journals (Sweden)

    Martins N.F.

    1999-01-01

    Full Text Available The equilibrium unfolding of bovine trypsinogen was studied by circular dichroism, differential spectra and size exclusion HPLC. The change in free energy of denaturation was = 6.99 ± 1.40 kcal/mol for guanidine hydrochloride and = 6.37 ± 0.57 kcal/mol for urea. Satisfactory fits of equilibrium unfolding transitions required a three-state model involving an intermediate in addition to the native and unfolded forms. Size exclusion HPLC allowed the detection of an intermediate population of trypsinogen whose Stokes radii varied from 24.1 ± 0.4 Å to 26.0 ± 0.3 Å for 1.5 M and 2.5 M guanidine hydrochloride, respectively. During urea denaturation, the range of Stokes radii varied from 23.9 ± 0.3 Å to 25.7 ± 0.6 Å for 4.0 M and 6.0 M urea, respectively. Maximal intrinsic fluorescence was observed at about 3.8 M urea with 8-aniline-1-naphthalene sulfonate (ANS binding. These experimental data indicate that the unfolding of bovine trypsinogen is not a simple transition and suggest that the equilibrium intermediate population comprises one intermediate that may be characterized as a molten globule. To obtain further insight by studying intermediates representing different stages of unfolding, we hope to gain a better understanding of the complex interrelations between protein conformation and energetics.

  10. Circuit topology of self-interacting chains: implications for folding and unfolding dynamics.

    Science.gov (United States)

    Mugler, Andrew; Tans, Sander J; Mashaghi, Alireza

    2014-11-07

    Understanding the relationship between molecular structure and folding is a central problem in disciplines ranging from biology to polymer physics and DNA origami. Topology can be a powerful tool to address this question. For a folded linear chain, the arrangement of intra-chain contacts is a topological property because rearranging the contacts requires discontinuous deformations. Conversely, the topology is preserved when continuously stretching the chain while maintaining the contact arrangement. Here we investigate how the folding and unfolding of linear chains with binary contacts is guided by the topology of contact arrangements. We formalize the topology by describing the relations between any two contacts in the structure, which for a linear chain can either be in parallel, in series, or crossing each other. We show that even when other determinants of folding rate such as contact order and size are kept constant, this 'circuit' topology determines folding kinetics. In particular, we find that the folding rate increases with the fractions of parallel and crossed relations. Moreover, we show how circuit topology constrains the conformational phase space explored during folding and unfolding: the number of forbidden unfolding transitions is found to increase with the fraction of parallel relations and to decrease with the fraction of series relations. Finally, we find that circuit topology influences whether distinct intermediate states are present, with crossed contacts being the key factor. The approach presented here can be more generally applied to questions on molecular dynamics, evolutionary biology, molecular engineering, and single-molecule biophysics.

  11. Contribution of long-range interactions to the secondary structure of an unfolded globin.

    Science.gov (United States)

    Fedyukina, Daria V; Rajagopalan, Senapathy; Sekhar, Ashok; Fulmer, Eric C; Eun, Ye-Jin; Cavagnero, Silvia

    2010-09-08

    This work explores the effect of long-range tertiary contacts on the distribution of residual secondary structure in the unfolded state of an alpha-helical protein. N-terminal fragments of increasing length, in conjunction with multidimensional nuclear magnetic resonance, were employed. A protein representative of the ubiquitous globin fold was chosen as the model system. We found that, while most of the detectable alpha-helical population in the unfolded ensemble does not depend on the presence of the C-terminal region (corresponding to the native G and H helices), specific N-to-C long-range contacts between the H and A-B-C regions enhance the helical secondary structure content of the N terminus (A-B-C regions). The simple approach introduced here, based on the evaluation of N-terminal polypeptide fragments of increasing length, is of general applicability to identify the influence of long-range interactions in unfolded proteins. Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  12. Identification of an Unfolding Intermediate for a DNA Lesion Bypass Polymerase

    Science.gov (United States)

    Sherrer, Shanen M.; Maxwell, Brian A.; Pack, Lindsey R.; Fiala, Kevin A.; Fowler, Jason D.; Zhang, Jun; Suo, Zucai

    2012-01-01

    Sulfolobus solfataricusDNA Polymerase IV (Dpo4), a prototype Y-family DNA polymerase, has been well characterized biochemically and biophysically at 37 °C or lower temperatures. However, the physiological temperature of the hyperthermophile S. solfataricus is approximately 80 °C. With such a large discrepancy in temperature, the in vivo relevance of these in vitro studies of Dpo4 has been questioned. Here, we employed circular dichroism spectroscopy and fluorescence-based thermal scanning to investigate the secondary structural changes of Dpo4 over a temperature range from 26 to 119 °C. Dpo4 was shown to display a high melting temperature characteristic of hyperthermophiles. Unexpectedly, the Little Finger domain of Dpo4, which is only found in the Y-family DNA polymerases, was shown to be more thermostable than the polymerase core. More interestingly, Dpo4 exhibited a three-state cooperative unfolding profile with an unfolding intermediate. The linker region between the Little Finger and Thumb domains of Dpo4 was found to be a source of structural instability. Through site-directed mutagenesis, the interactions between the residues in the linker region and the Palm domain were identified to play a critical role in the formation of the unfolding intermediate. Notably, the secondary structure of Dpo4 was not altered when the temperature was increased from 26 to 87.5 °C. Thus, in addition to providing structural insights into the thermal stability and an unfolding intermediate of Dpo4, our work also validated the relevance of the in vitro studies of Dpo4 performed at temperatures significantly lower than 80 °C. PMID:22667759

  13. High-energy intermediates in protein unfolding characterized by thiol labeling under nativelike conditions.

    Science.gov (United States)

    Malhotra, Pooja; Udgaonkar, Jayant B

    2014-06-10

    A protein unfolding reaction usually appears to be so dominated by a large free energy barrier that identifying and characterizing high-energy intermediates and, hence, dissecting the unfolding reaction into multiple structural transitions have proven to be a challenge. In particular, it has been difficult to identify any detected high-energy intermediate with the dry (DMG) and wet (WMG) molten globules that have been implicated in the unfolding reactions of at least some proteins. In this study, a native-state thiol labeling methodology was used to identify high-energy intermediates, as well as to delineate the barriers to the disruption of side chain packing interactions and to site-specific solvent exposure in different regions of the small protein, single-chain monellin (MNEI). Labeling studies of four single-cysteine-containing variants of MNEI have identified three high-energy intermediates, populated to very low extents under nativelike conditions. A significant dispersion in the opening rates of the cysteine side chains has allowed multiple steps, leading to the loss of side chain packing, to be resolved temporally. A detailed structural analysis of the positions of the four cysteine residue positions, which are buried to different depths within the protein, has suggested a direct correlation with the structure of a DMG, detected in previous studies. It is observed that side chain packing within the core of the protein is maintained, while that at the surface is disrupted, in the DMG. The core of the protein becomes solvent-exposed only in a WMG populated after the rate-limiting step of unfolding at high denaturant concentrations.

  14. Unfolding code for neutron spectrometry based on neural nets technology

    International Nuclear Information System (INIS)

    Ortiz R, J. M.; Vega C, H. R.

    2012-10-01

    The most delicate part of neutron spectrometry, is the unfolding process. The derivation of the spectral information is not simple because the unknown is not given directly as a result of the measurements. The drawbacks associated with traditional unfolding procedures have motivated the need of complementary approaches. Novel methods based on Artificial Neural Networks have been widely investigated. In this work, a neutron spectrum unfolding code based on neural nets technology is presented. This unfolding code called Neutron Spectrometry and Dosimetry by means of Artificial Neural Networks was designed in a graphical interface under LabVIEW programming environment. The core of the code is an embedded neural network architecture, previously optimized by the R obust Design of Artificial Neural Networks Methodology . The main features of the code are: is easy to use, friendly and intuitive to the user. This code was designed for a Bonner Sphere System based on a 6 Lil(Eu) neutron detector and a response matrix expressed in 60 energy bins taken from an International Atomic Energy Agency compilation. The main feature of the code is that as entrance data, only seven rate counts measurement with a Bonner spheres spectrometer are required for simultaneously unfold the 60 energy bins of the neutron spectrum and to calculate 15 dosimetric quantities, for radiation protection porpoises. This code generates a full report in html format with all relevant information. (Author)

  15. Influence of cross-section structure on unfolded neutron spectra

    International Nuclear Information System (INIS)

    Ertek, C.; Vlasov, M.F.; Cross, B.; Smith, P.M.

    1979-01-01

    The influence of cross-section structure on neutron spectra unfolded by multiple foil activation technique, SAND-II case, has been studied. For three reactions with evident structure in neutron cross-section above threshold: 27Al(n,α)24Na, 31P(n,p)31Si and 32S(n,p)32P, two remarkably different sets of evaluated data were selected from the available evaluations; one set of data was ''smooth'', the structure having been averaged over by a smooth curve; the other set was ''sharp'' with structure given in detail. These data were used in unfolding procedure together with other reactions, the same in both cases (as well as input spectra and measured reaction rates). It was found that during unfolding calculations less iteration steps were needed to unfold the neutron flux spectrum with the set of ''sharp'' data. In case of ''smooth'' data it was difficult to obtain an agreement between measured and calculated activity values even by increasing the number of iteration steps. Contrary to expectations, considerable deformation of unfolded neutron flux spectrum has been observed in the case of the ''smooth'' data set. (author)

  16. Unfolding code for neutron spectrometry based on neural nets technology

    Energy Technology Data Exchange (ETDEWEB)

    Ortiz R, J. M.; Vega C, H. R., E-mail: morvymm@yahoo.com.mx [Universidad Autonoma de Zacatecas, Unidad Academica de Ingenieria Electrica, Apdo. Postal 336, 98000 Zacatecas (Mexico)

    2012-10-15

    The most delicate part of neutron spectrometry, is the unfolding process. The derivation of the spectral information is not simple because the unknown is not given directly as a result of the measurements. The drawbacks associated with traditional unfolding procedures have motivated the need of complementary approaches. Novel methods based on Artificial Neural Networks have been widely investigated. In this work, a neutron spectrum unfolding code based on neural nets technology is presented. This unfolding code called Neutron Spectrometry and Dosimetry by means of Artificial Neural Networks was designed in a graphical interface under LabVIEW programming environment. The core of the code is an embedded neural network architecture, previously optimized by the {sup R}obust Design of Artificial Neural Networks Methodology{sup .} The main features of the code are: is easy to use, friendly and intuitive to the user. This code was designed for a Bonner Sphere System based on a {sup 6}Lil(Eu) neutron detector and a response matrix expressed in 60 energy bins taken from an International Atomic Energy Agency compilation. The main feature of the code is that as entrance data, only seven rate counts measurement with a Bonner spheres spectrometer are required for simultaneously unfold the 60 energy bins of the neutron spectrum and to calculate 15 dosimetric quantities, for radiation protection porpoises. This code generates a full report in html format with all relevant information. (Author)

  17. [Unfolding item response model using best-worst scaling].

    Science.gov (United States)

    Ikehara, Kazuya

    2015-02-01

    In attitude measurement and sensory tests, the unfolding model is typically used. In this model, response probability is formulated by the distance between the person and the stimulus. In this study, we proposed an unfolding item response model using best-worst scaling (BWU model), in which a person chooses the best and worst stimulus among repeatedly presented subsets of stimuli. We also formulated an unfolding model using best scaling (BU model), and compared the accuracy of estimates between the BU and BWU models. A simulation experiment showed that the BWU modell performed much better than the BU model in terms of bias and root mean square errors of estimates. With reference to Usami (2011), the proposed models were apllied to actual data to measure attitudes toward tardiness. Results indicated high similarity between stimuli estimates generated with the proposed models and those of Usami (2011).

  18. Comparison of intra-organellar chaperone capacity for dealing with stress-induced protein unfolding.

    Science.gov (United States)

    Hageman, Jurre; Vos, Michel J; van Waarde, Maria A W H; Kampinga, Harm H

    2007-11-23

    Molecular chaperones are essential for cells to prevent that partially unfolded proteins form non-functional, toxic aggregates. This requirement is increased when cells experience protein unfolding stresses and such could affect all compartments in the eukaryotic cell. Whether all organelles are equipped with comparable chaperone capacities is largely unknown, mainly due to the lack of suitable reporters that allow such a comparison. Here we describe the development of fluorescent luciferase reporters that are sorted to various cellular locations (nucleus, cytoplasm, endoplasmic reticulum, and peroxisomes) and that differ minimally in their intrinsic thermal stability properties. When heating living cells, the rate of inactivation was most rapid for the nuclear-targeted luciferase, indicating that the nucleus is the most sensitive organelle toward heat-induced denaturing stress. Post-heat re-activation, however, occurred at equal kinetics irrespective of luciferase localization. Also, induction of thermotolerance by a priming heat treatment, that coordinately up-regulates all heat-inducible chaperones, resulted in a transient heat resistance of the luciferase in all organelles in a comparable manner. Overexpression of the main heat-inducible Hsp70 family member, HspA1A, protected only the cytosolic and nuclear, but not the other luciferases. Together, our data suggest that in each compartment investigated, including the peroxisome in which so far no chaperones could be detected, chaperone machines are present and can be induced with activities similar to those present in the cytosolic/nuclear compartment.

  19. Unfolded protein response is required for Aspergillus oryzae growth under conditions inducing secretory hydrolytic enzyme production.

    Science.gov (United States)

    Tanaka, Mizuki; Shintani, Takahiro; Gomi, Katsuya

    2015-12-01

    Unfolded protein response (UPR) is an intracellular signaling pathway for adaptation to endoplasmic reticulum (ER) stress. In yeast UPR, Ire1 cleaves the unconventional intron of HAC1 mRNA, and the functional Hac1 protein translated from the spliced HAC1 mRNA induces the expression of ER chaperone genes and ER-associated degradation genes for the refolding or degradation of unfolded proteins. In this study, we constructed an ireA (IRE1 ortholog) conditionally expressing strain of Aspergillus oryzae, a filamentous fungus producing a large amount of amylolytic enzymes, and examined the contribution of UPR to ER stress adaptation under physiological conditions. Repression of ireA completely blocked A. oryzae growth under conditions inducing the production of hydrolytic enzymes, such as amylases and proteases. This growth defect was restored by the introduction of unconventional intronless hacA (hacA-i). Furthermore, UPR was observed to be induced by amylolytic gene expression, and the disruption of the transcriptional activator for amylolytic genes resulted in partial growth restoration of the ireA-repressing strain. In addition, a homokaryotic ireA disruption mutant was successfully generated using the strain harboring hacA-i as a parental host. These results indicated that UPR is required for A. oryzae growth to alleviate ER stress induced by excessive production of hydrolytic enzymes. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Conformational fluctuation dynamics of domain I of human serum albumin in the course of chemically and thermally induced unfolding using fluorescence correlation spectroscopy.

    Science.gov (United States)

    Yadav, Rajeev; Sengupta, Bhaswati; Sen, Pratik

    2014-05-22

    The present study elucidates the involvement of conformational fluctuation dynamics during chemically and thermally induced unfolding of human serum albumin (HSA) by fluorescence correlation spectroscopic (FCS) study, time-resolved fluorescence measurements, and circular dichroism (CD) spectroscopic methods. Two fluorescent probes, tetramethylrhodamine-5-maleimide (TMR) and N-(7-dimethylamino-4-methylcoumarin-3-yl) iodoacetamide (DACIA) were used to selectively label the domain I of HSA through the reaction with cys-34 for these studies. The guanidine hydrochloride (GnHCl) induced global structural change of HSA is monitored through its hydrodynamic radius (r(H)) and CD response, which is found to be two step in nature. In FCS experiment, along with the diffusion time component we have observed an exponential relaxation time component (τ(R)) that has been ascribed to the concerted chain dynamics of HSA. Unlike in the global structural change, we found that the τ(R) value changes in a different manner in the course of the unfolding. The dependence of τ(R) on the concentration of GnHCl was best fitted with a four state model, indicating the involvement of two intermediate states during the unfolding process, which were not observed through the CD response and r(H) data. The fluorescence lifetime measurement also supports our observation of intermediate states during the unfolding of HSA. However, no such intermediate states were observed during thermally induced unfolding of HSA.

  1. One Peptide Reveals the Two Faces of α-Helix Unfolding-Folding Dynamics.

    Science.gov (United States)

    Jesus, Catarina S H; Cruz, Pedro F; Arnaut, Luis G; Brito, Rui M M; Serpa, Carlos

    2018-04-12

    The understanding of fast folding dynamics of single α-helices comes mostly from studies on rationally designed peptides displaying sequences with high helical propensity. The folding/unfolding dynamics and energetics of α-helix conformations in naturally occurring peptides remains largely unexplored. Here we report the study of a protein fragment analogue of the C-peptide from bovine pancreatic ribonuclease-A, RN80, a 13-amino acid residue peptide that adopts a highly populated helical conformation in aqueous solution. 1 H NMR and CD structural studies of RN80 showed that α-helix formation displays a pH-dependent bell-shaped curve, with a maximum near pH 5, and a large decrease in helical content in alkaline pH. The main forces stabilizing this short α-helix were identified as a salt bridge formed between Glu-2 and Arg-10 and the cation-π interaction involving Tyr-8 and His-12. Thus, deprotonation of Glu-2 or protonation of His-12 are essential for the RN80 α-helix stability. In the present study, RN80 folding and unfolding were triggered by laser-induced pH jumps and detected by time-resolved photoacoustic calorimetry (PAC). The photoacid proton release, amino acid residue protonation, and unfolding/folding events occur at different time scales and were clearly distinguished using time-resolved PAC. The partial unfolding of the RN80 α-helix, due to protonation of Glu-2 and consequent breaking of the stabilizing salt bridge between Glu-2 and Arg-10, is characterized by a concentration-independent volume expansion in the sub-microsecond time range (0.8 mL mol -1 , 369 ns). This small volume expansion reports the cost of peptide backbone rehydration upon disruption of a solvent-exposed salt bridge, as well as backbone intrinsic expansion. On the other hand, RN80 α-helix folding triggered by His-12 protonation and subsequent formation of a cation-π interaction leads to a microsecond volume contraction (-6.0 mL mol -1 , ∼1.7 μs). The essential role of two

  2. Folding and unfolding of large-size shell construction for application in Earth orbit

    Science.gov (United States)

    Kondyurin, Alexey; Pestrenina, Irena; Pestrenin, Valery; Rusakov, Sergey

    2016-07-01

    A future exploration of space requires a technology of large module for biological, technological, logistic and other applications in Earth orbits [1-3]. This report describes the possibility of using large-sized shell structures deployable in space. Structure is delivered to the orbit in the spaceship container. The shell is folded for the transportation. The shell material is either rigid plastic or multilayer prepreg comprising rigid reinforcements (such as reinforcing fibers). The unfolding process (bringing a construction to the unfolded state by loading the internal pressure) needs be considered at the presence of both stretching and bending deformations. An analysis of the deployment conditions (the minimum internal pressure bringing a construction from the folded state to the unfolded state) of large laminated CFRP shell structures is formulated in this report. Solution of this mechanics of deformable solids (MDS) problem of the shell structure is based on the following assumptions: the shell is made of components whose median surface has a reamer; in the separate structural element relaxed state (not stressed and not deformed) its median surface coincides with its reamer (this assumption allows choose the relaxed state of the structure correctly); structural elements are joined (sewn together) by a seam that does not resist rotation around the tangent to the seam line. The ways of large shell structures folding, whose median surface has a reamer, are suggested. Unfolding of cylindrical, conical (full and truncated cones), and large-size composite shells (cylinder-cones, cones-cones) is considered. These results show that the unfolding pressure of such large-size structures (0.01-0.2 atm.) is comparable to the deploying pressure of pneumatic parts (0.001-0.1 atm.) [3]. It would be possible to extend this approach to investigate the unfolding process of large-sized shells with ruled median surface or for non-developable surfaces. This research was

  3. 75 FR 54116 - Notice of Intent To Grant Partially Exclusive License of the United States Patent Application No...

    Science.gov (United States)

    2010-09-03

    ... coatings, side dressing, lawn application and starter ground cover) and applications in the fields of soil... announcement. ADDRESSES: United States Army Engineer Research and Development Center, Attn: CEERD-OT (Ms. Bea...

  4. Nonintegrability of the unfolding of the fold-Hopf bifurcation

    Science.gov (United States)

    Yagasaki, Kazuyuki

    2018-02-01

    We consider the unfolding of the codimension-two fold-Hopf bifurcation and prove its meromorphic nonintegrability in the meaning of Bogoyavlenskij for almost all parameter values. Our proof is based on a generalized version of the Morales-Ramis-Simó theory for non-Hamiltonian systems and related variational equations up to second order are used.

  5. Redox Thermodynamics of Cytochromes c Subjected to Urea Induced Unfolding

    NARCIS (Netherlands)

    Monari, S.; Ranieri, A.; Di Rocco, G.; van der Zwan, G.; Peressini, S.; Tavagnacco, C.; Millo, D.; Borsari, M.

    2009-01-01

    The thermodynamics of the electron transfer (ET) process for beef heart and yeast cytochromes c and the Lys72Ala/Lys73Ala/Lys79Ala mutant of the latter species subjected to progressive urea-induced unfolding was determined electrochemically. The results indicate the presence of at least three

  6. Unfolding the phenomenon of inter-rater agreement

    DEFF Research Database (Denmark)

    Slaug, Bjørn; Schilling, Oliver; Helle, Tina

    2011-01-01

    Objective: The overall objective was to unfold the phenomenon of inter-rater agreement: to identify potential sources of variation in agreement data and to explore how they can be statistically accounted for. The ultimate aim was to propose recommendations for in-depth examination of agreement, i...

  7. PPARγ Ligand-Induced Unfolded Protein Responses in Monocytes

    African Journals Online (AJOL)

    High levels of oxLDL lead to cell dysfunction and apoptosis, a phenomenon known as lipotoxicity. Disturbing endoplasmic reticulum (ER) function results in ER stress and unfolded protein response (UPR), which tends to restore ER homeostasis but switches to apoptosis when ER stress is prolonged. In the present study the ...

  8. Dante-unfolding code for energy spectra evaluation

    International Nuclear Information System (INIS)

    Petilli, M.

    1979-01-01

    The code DANTE, using the last square method in unfolding for dosimetry purpose, solves the neutron spectra evaluation problem starting by activity measurements. The code DANTE introduced for the first time the correlation between available data by mean of flux and activity variance-covariance matrices and the error propagation. In the present report the solution method is detailed described

  9. PPARγ Ligand-Induced Unfolded Protein Responses in Monocytes ...

    African Journals Online (AJOL)

    acer

    Disturbing endoplasmic reticulum (ER) function results in ER stress and unfolded protein response. (UPR), which tends to ... in mnocyte/macrophage cell lines as evident of the activation/up-regulation of ER stress/UPR genes. Cholesterol does not seem to exert ... inflammation (Tiwari et al., 2008). One prominent feature of ...

  10. Structural changes during the unfolding of Bovine serum albumin

    Indian Academy of Sciences (India)

    The native form of serum albumin is the most important soluble protein in the body plasma. In order to investigate the structural changes of Bovine serum albumin (BSA) during its unfolding in the presence of urea, a small-angle neutron scattering (SANS) study was performed. The scattering curves of dilute solutions of BSA ...

  11. Towards data warehousing and mining of protein unfolding simulation data.

    Science.gov (United States)

    Berrar, Daniel; Stahl, Frederic; Silva, Candida; Rodrigues, J Rui; Brito, Rui M M; Dubitzky, Werner

    2005-10-01

    The prediction of protein structure and the precise understanding of protein folding and unfolding processes remains one of the greatest challenges in structural biology and bioinformatics. Computer simulations based on molecular dynamics (MD) are at the forefront of the effort to gain a deeper understanding of these complex processes. Currently, these MD simulations are usually on the order of tens of nanoseconds, generate a large amount of conformational data and are computationally expensive. More and more groups run such simulations and generate a myriad of data, which raises new challenges in managing and analyzing these data. Because the vast range of proteins researchers want to study and simulate, the computational effort needed to generate data, the large data volumes involved, and the different types of analyses scientists need to perform, it is desirable to provide a public repository allowing researchers to pool and share protein unfolding data. To adequately organize, manage, and analyze the data generated by unfolding simulation studies, we designed a data warehouse system that is embedded in a grid environment to facilitate the seamless sharing of available computer resources and thus enable many groups to share complex molecular dynamics simulations on a more regular basis. To gain insight into the conformational fluctuations and stability of the monomeric forms of the amyloidogenic protein transthyretin (TTR), molecular dynamics unfolding simulations of the monomer of human TTR have been conducted. Trajectory data and meta-data of the wild-type (WT) protein and the highly amyloidogenic variant L55P-TTR represent the test case for the data warehouse. Web and grid services, especially pre-defined data mining services that can run on or 'near' the data repository of the data warehouse, are likely to play a pivotal role in the analysis of molecular dynamics unfolding data.

  12. Development of the unfolding procedures in fast neutron scintillation spectrometry; Razvoj unfolding procedura u scintilacionoj spektrometriji brzih neutrona

    Energy Technology Data Exchange (ETDEWEB)

    Marinkovic, P [Elektrotehnicki fakultet, Belgrade (Yugoslavia)

    1988-07-01

    Two unfolding procedures have been developed for obtaining fast neutron spectrum from proton-recoil spectrum assigned for spectrometry with organic scintillators. First is the method of differentiation of proton-recoil spectrum, and the second is the method based on solution of integral equation of Fredholm of first kind. (author)

  13. Production and partial characterization of arabinoxylan-degrading enzymes by Penicillium brasilianum under solid-state fermentation

    DEFF Research Database (Denmark)

    Panagiotou, Gianni; Granouillet, P.; Olsson, Lisbeth

    2006-01-01

    The production of a battery of arabinoxylan-degrading enzymes by the fungus Penicillium brasilianum grown on brewer's spent grain (BSG) under solid-state fermentation was investigated. Initial moisture content, initial pH, temperature, and nitrogen source content were optimized to achieve maximum...

  14. Rock-Mechanics Research. A Survey of United States Research to 1965, with a Partial Survey of Canadian Universities.

    Science.gov (United States)

    National Academy of Sciences - National Research Council, Washington, DC.

    The results of a survey, conducted by the Committee on Rock Mechanics, to determine the status of training and research in rock mechanics in presented in this publication. In 1964 and 1965 information was gathered by questionnaires sent to industries, selected federal agencies, and universities in both the United States and Canada. Results are…

  15. 76 FR 35425 - Notice of Intent to Grant Partially Exclusive License of the United States Patent Application No...

    Science.gov (United States)

    2011-06-17

    ... by the fluid in which the sample is incorporated determines the gap without need of a spacer. To... States Army Engineer Research and Development Center, Attn: CEERD-OT (Ms. Bea Shahin), 2902 Newmark Drive... each of two silicon wafers abutting to contain the sample in a small uniform gap formed between the...

  16. Solving binary-state multi-objective reliability redundancy allocation series-parallel problem using efficient epsilon-constraint, multi-start partial bound enumeration algorithm, and DEA

    International Nuclear Information System (INIS)

    Khalili-Damghani, Kaveh; Amiri, Maghsoud

    2012-01-01

    In this paper, a procedure based on efficient epsilon-constraint method and data envelopment analysis (DEA) is proposed for solving binary-state multi-objective reliability redundancy allocation series-parallel problem (MORAP). In first module, a set of qualified non-dominated solutions on Pareto front of binary-state MORAP is generated using an efficient epsilon-constraint method. In order to test the quality of generated non-dominated solutions in this module, a multi-start partial bound enumeration algorithm is also proposed for MORAP. The performance of both procedures is compared using different metrics on well-known benchmark instance. The statistical analysis represents that not only the proposed efficient epsilon-constraint method outperform the multi-start partial bound enumeration algorithm but also it improves the founded upper bound of benchmark instance. Then, in second module, a DEA model is supplied to prune the generated non-dominated solutions of efficient epsilon-constraint method. This helps reduction of non-dominated solutions in a systematic manner and eases the decision making process for practical implementations. - Highlights: ► A procedure based on efficient epsilon-constraint method and DEA was proposed for solving MORAP. ► The performance of proposed procedure was compared with a multi-start PBEA. ► Methods were statistically compared using multi-objective metrics.

  17. Partial correlation analysis method in ultrarelativistic heavy-ion collisions

    Science.gov (United States)

    Olszewski, Adam; Broniowski, Wojciech

    2017-11-01

    We argue that statistical data analysis of two-particle longitudinal correlations in ultrarelativistic heavy-ion collisions may be efficiently carried out with the technique of partial covariance. In this method, the spurious event-by-event fluctuations due to imprecise centrality determination are eliminated via projecting out the component of the covariance influenced by the centrality fluctuations. We bring up the relationship of the partial covariance to the conditional covariance. Importantly, in the superposition approach, where hadrons are produced independently from a collection of sources, the framework allows us to impose centrality constraints on the number of sources rather than hadrons, that way unfolding of the trivial fluctuations from statistical hadronization and focusing better on the initial-state physics. We show, using simulated data from hydrodynamics followed with statistical hadronization, that the technique is practical and very simple to use, giving insight into the correlations generated in the initial stage. We also discuss the issues related to separation of the short- and long-range components of the correlation functions and show that in our example the short-range component from the resonance decays is largely reduced by considering pions of the same sign. We demonstrate the method explicitly on the cases where centrality is determined with a single central control bin or with two peripheral control bins.

  18. Partial Cancellation

    Indian Academy of Sciences (India)

    First page Back Continue Last page Overview Graphics. Partial Cancellation. Full Cancellation is desirable. But complexity requirements are enormous. 4000 tones, 100 Users billions of flops !!! Main Idea: Challenge: To determine which cross-talker to cancel on what “tone” for a given victim. Constraint: Total complexity is ...

  19. Coexisting synchronous and asynchronous states in locally coupled array of oscillators by partial self-feedback control

    Science.gov (United States)

    Bera, Bidesh K.; Ghosh, Dibakar; Parmananda, Punit; Osipov, G. V.; Dana, Syamal K.

    2017-07-01

    We report the emergence of coexisting synchronous and asynchronous subpopulations of oscillators in one dimensional arrays of identical oscillators by applying a self-feedback control. When a self-feedback is applied to a subpopulation of the array, similar to chimera states, it splits into two/more sub-subpopulations coexisting in coherent and incoherent states for a range of self-feedback strength. By tuning the coupling between the nearest neighbors and the amount of self-feedback in the perturbed subpopulation, the size of the coherent and the incoherent sub-subpopulations in the array can be controlled, although the exact size of them is unpredictable. We present numerical evidence using the Landau-Stuart system and the Kuramoto-Sakaguchi phase model.

  20. The secondary structure and the thermal unfolding parameters of the S-layer protein from Lactobacillus salivarius.

    Science.gov (United States)

    Lighezan, Liliana; Georgieva, Ralitsa; Neagu, Adrian

    2016-09-01

    Surface layer (S-layer) proteins have been identified in the cell envelope of many organisms, such as bacteria and archaea. They self-assemble, forming monomolecular crystalline arrays. Isolated S-layer proteins are able to recrystallize into regular lattices, which proved useful in biotechnology. Here we investigate the structure and thermal unfolding of the S-layer protein isolated from Lactobacillus salivarius 16 strain of human origin. Using circular dichroism (CD) spectroscopy, and the software CDSSTR from DICHROWEB, CONTINLL from CDPro, as well as CDNN, we assess the fractions of the protein's secondary structural elements at temperatures ranging between 10 and 90 °C, and predict the tertiary class of the protein. To study the thermal unfolding of the protein, we analyze the temperature dependence of the CD signal in the far- and near-UV domains. Fitting the experimental data by two- and three-state models of thermal unfolding, we infer the midpoint temperatures, the temperature dependence of the changes in Gibbs free energy, enthalpy, and entropy of the unfolding transitions in standard conditions, and the temperature dependence of the equilibrium constant. We also estimate the changes in heat capacity at constant pressure in standard conditions. The results indicate that the thermal unfolding of the S-layer protein from L. salivarius is highly cooperative, since changes in the secondary and tertiary structures occur simultaneously. The thermodynamic analysis predicts a "cold" transition, at about -3 °C, of both the secondary and tertiary structures. Our findings may be important for the use of S-layer proteins in biotechnology and in biomedical applications.

  1. Partial processing

    International Nuclear Information System (INIS)

    1978-11-01

    This discussion paper considers the possibility of applying to the recycle of plutonium in thermal reactors a particular method of partial processing based on the PUREX process but named CIVEX to emphasise the differences. The CIVEX process is based primarily on the retention of short-lived fission products. The paper suggests: (1) the recycle of fission products with uranium and plutonium in thermal reactor fuel would be technically feasible; (2) it would, however, take ten years or more to develop the CIVEX process to the point where it could be launched on a commercial scale; (3) since the majority of spent fuel to be reprocessed this century will have been in storage for ten years or more, the recycling of short-lived fission products with the U-Pu would not provide an effective means of making refabrication fuel ''inaccessible'' because the radioactivity associated with the fission products would have decayed. There would therefore be no advantage in partial processing

  2. Partial gigantism

    Directory of Open Access Journals (Sweden)

    М.М. Karimova

    2017-05-01

    Full Text Available A girl with partial gigantism (the increased I and II fingers of the left foot is being examined. This condition is a rare and unresolved problem, as the definite reason of its development is not determined. Wait-and-see strategy is recommended, as well as correcting operations after closing of growth zones, and forming of data pool for generalization and development of schemes of drug and radial therapeutic methods.

  3. One-Step Partially Purified Lipases (ScLipA and ScLipB from Schizophyllum commune UTARA1 Obtained via Solid State Fermentation and Their Applications

    Directory of Open Access Journals (Sweden)

    Yew Chee Kam

    2017-12-01

    Full Text Available Lipases with unique characteristics are of value in industrial applications, especially those targeting cost-effectiveness and less downstream processes. The aims of this research were to: (i optimize the fermentation parameters via solid state fermentation (SSF; and (ii study the performance in hydrolysis and esterification processes of the one-step partially purified Schizophyllum commune UTARA1 lipases. Lipase was produced by cultivating S. commune UTARA1 on sugarcane bagasse (SB with used cooking oil (UCO via SSF and its production was optimized using Design-Expert® 7.0.0. Fractions 30% (ScLipA and 70% (ScLipB which contained high lipase activity were obtained by stepwise (NH42SO4 precipitation. Crude fish oil, coconut oil and butter were used to investigate the lipase hydrolysis capabilities by a free glycerol assay. Results showed that ScLipA has affinities for long, medium and short chain triglycerides, as all the oils investigated were degraded, whereas ScLipB has affinities for long chain triglycerides as it only degrades crude fish oil. During esterification, ScLipA was able to synthesize trilaurin and triacetin. Conversely, ScLipB was specific towards the formation of 2-mono-olein and triacetin. From the results obtained, it was determined that ScLipA and ScLipB are sn-2 regioselective lipases. Hence, the one-step partial purification strategy proved to be feasible for partial purification of S. commune UTARA1 lipases that has potential use in industrial applications.

  4. An unfolding method for high energy physics experiments

    International Nuclear Information System (INIS)

    Blobel, V.

    2002-06-01

    Finite detector resolution and limited acceptance require one to apply unfolding methods in high energy physics experiments. Information on the detector resolution is usually given by a set of Monte Carlo events. Based on the experience with a widely used unfolding program (RUN) a modified method has been developed. The first step of the method is a maximum likelihood fit of the Monte Carlo distributions to the measured distribution in one, two or three dimensions; the finite statistics of the Monte Carlo events is taken into account by the use of Barlow's method with a new method of solution. A clustering method is used before combining bins in sparsely populated areas. In the second step a regularization is applied to the solution, which introduces only a small bias. The regularization parameter is determined from the data after a diagonalization and rotation procedure. (orig.)

  5. Amyloid protein unfolding and insertion kinetics on neuronal membrane mimics

    Science.gov (United States)

    Qiu, Liming; Buie, Creighton; Vaughn, Mark; Cheng, Kwan

    2010-03-01

    Atomistic details of beta-amyloid (Aβ ) protein unfolding and lipid interaction kinetics mediated by the neuronal membrane surface are important for developing new therapeutic strategies to prevent and cure Alzheimer's disease. Using all-atom MD simulations, we explored the early unfolding and insertion kinetics of 40 and 42 residue long Aβ in binary lipid mixtures with and without cholesterol that mimic the cholesterol-depleted and cholesterol-enriched lipid nanodomains of neurons. The protein conformational transition kinetics was evaluated from the secondary structure profile versus simulation time plot. The extent of membrane disruption was examined by the calculated order parameters of lipid acyl chains and cholesterol fused rings as well as the density profiles of water and lipid headgroups at defined regions across the lipid bilayer from our simulations. Our results revealed that both the cholesterol content and the length of the protein affect the protein-insertion and membrane stability in our model lipid bilayer systems.

  6. FERDO/FERD, Unfolding of Pulse-Height Spectrometer Spectra

    International Nuclear Information System (INIS)

    Rust, B.W.; Ingersoll, D.T.; Burrus, W.R.

    1985-01-01

    1 - Description of problem or function: FERDO and FERD are unfolding codes which can be used to correct observed pulse-height distributions for the non-ideal response of a pulse-height spectrometer or to solve poorly conditioned linear equations. 2 - Method of solution: It is assumed that the response of the spectrometer is given by Ax = b, where A is the spectrometer response function matrix, x is the unknown spectrum, and b is the pulse-height distribution. FERDO does not resolve directly for x but instead solves for p = Wx, where W is a 'window function matrix'. Typically, W is the resolution function of an ideal spectrometer which has a single Gaussian response. The effective resolution of the unfolding solution may be varied by the choice of W. Confidence intervals are found for each element of the solution p

  7. Plant transducers of the endoplasmic reticulum unfolded protein response

    KAUST Repository

    Iwata, Yuji; Koizumi, Nozomu

    2012-01-01

    The unfolded protein response (UPR) activates a set of genes to overcome accumulation of unfolded proteins in the endoplasmic reticulum (ER), a condition termed ER stress, and constitutes an essential part of ER protein quality control that ensures efficient maturation of secretory and membrane proteins in eukaryotes. Recent studies on Arabidopsis and rice identified the signaling pathway in which the ER membrane-localized ribonuclease IRE1 (inositol-requiring enzyme 1) catalyzes unconventional cytoplasmic splicing of mRNA, thereby producing the active transcription factor Arabidopsis bZIP60 (basic leucine zipper 60) and its ortholog in rice. Here we review recent findings identifying the molecular components of the plant UPR, including IRE1/bZIP60 and the membrane-bound transcription factors bZIP17 and bZIP28, and implicating its importance in several physiological phenomena such as pathogen response. © 2012 Elsevier Ltd.

  8. Plant transducers of the endoplasmic reticulum unfolded protein response

    KAUST Repository

    Iwata, Yuji

    2012-12-01

    The unfolded protein response (UPR) activates a set of genes to overcome accumulation of unfolded proteins in the endoplasmic reticulum (ER), a condition termed ER stress, and constitutes an essential part of ER protein quality control that ensures efficient maturation of secretory and membrane proteins in eukaryotes. Recent studies on Arabidopsis and rice identified the signaling pathway in which the ER membrane-localized ribonuclease IRE1 (inositol-requiring enzyme 1) catalyzes unconventional cytoplasmic splicing of mRNA, thereby producing the active transcription factor Arabidopsis bZIP60 (basic leucine zipper 60) and its ortholog in rice. Here we review recent findings identifying the molecular components of the plant UPR, including IRE1/bZIP60 and the membrane-bound transcription factors bZIP17 and bZIP28, and implicating its importance in several physiological phenomena such as pathogen response. © 2012 Elsevier Ltd.

  9. Unfolding education for sustainable development as didactic thinking and practice

    DEFF Research Database (Denmark)

    Madsen, Katrine Dahl

    2013-01-01

    This article’s primary objective is to unfold how teachers translate education for sustainable development (ESD) in a school context. The article argues that exploring tensions, ruptures and openings apparent in this meeting is crucial for the development of existing teaching practices in relatio...... the analytical foundation; thus it is the practices as seen from the ‘inside’. Furthermore, ESD practices are considered in a broader societal perspective, pointing to the critical power of the practice lens....

  10. STRUCTURAL ANALYSIS, GEOMETRY AND STATICS OF A COACH UNFOLDING MECHANISM

    Directory of Open Access Journals (Sweden)

    Ovidiu ANTONESCU

    2016-05-01

    Full Text Available Starting from the constructive scheme of the mechanism, the kinematic scheme is drawn in three distinct positions (folded, middle and unfolded. By means of this scheme the mobility of the mechanism is calculated and the structural-topological formula of it is obtained. In the last section of the paper an algorithm of geometric calculus has been elaborated, starting from a kinematic link articulated to the base, element which is considered the driving component.

  11. Joint mapping of genes and conditions via multidimensional unfolding analysis

    Directory of Open Access Journals (Sweden)

    Engelen Kristof

    2007-06-01

    Full Text Available Abstract Background Microarray compendia profile the expression of genes in a number of experimental conditions. Such data compendia are useful not only to group genes and conditions based on their similarity in overall expression over profiles but also to gain information on more subtle relations between genes and conditions. Getting a clear visual overview of all these patterns in a single easy-to-grasp representation is a useful preliminary analysis step: We propose to use for this purpose an advanced exploratory method, called multidimensional unfolding. Results We present a novel algorithm for multidimensional unfolding that overcomes both general problems and problems that are specific for the analysis of gene expression data sets. Applying the algorithm to two publicly available microarray compendia illustrates its power as a tool for exploratory data analysis: The unfolding analysis of a first data set resulted in a two-dimensional representation which clearly reveals temporal regulation patterns for the genes and a meaningful structure for the time points, while the analysis of a second data set showed the algorithm's ability to go beyond a mere identification of those genes that discriminate between different patient or tissue types. Conclusion Multidimensional unfolding offers a useful tool for preliminary explorations of microarray data: By relying on an easy-to-grasp low-dimensional geometric framework, relations among genes, among conditions and between genes and conditions are simultaneously represented in an accessible way which may reveal interesting patterns in the data. An additional advantage of the method is that it can be applied to the raw data without necessitating the choice of suitable genewise transformations of the data.

  12. Directional Unfolded Source Term (DUST) for Compton Cameras.

    Energy Technology Data Exchange (ETDEWEB)

    Mitchell, Dean J.; Mitchell, Dean J.; Horne, Steven M.; O' Brien, Sean; Thoreson, Gregory G

    2018-03-01

    A Directional Unfolded Source Term (DUST) algorithm was developed to enable improved spectral analysis capabilities using data collected by Compton cameras. Achieving this objective required modification of the detector response function in the Gamma Detector Response and Analysis Software (GADRAS). Experimental data that were collected in support of this work include measurements of calibration sources at a range of separation distances and cylindrical depleted uranium castings.

  13. High-Temperature unfolding of a trp-Cage mini-protein: a molecular dynamics simulation study

    Directory of Open Access Journals (Sweden)

    Seshasayee Aswin Sai Narain

    2005-03-01

    Full Text Available Abstract Background Trp cage is a recently-constructed fast-folding miniprotein. It consists of a short helix, a 3,10 helix and a C-terminal poly-proline that packs against a Trp in the alpha helix. It is known to fold within 4 ns. Results High-temperature unfolding molecular dynamics simulations of the Trp cage miniprotein have been carried out in explicit water using the OPLS-AA force-field incorporated in the program GROMACS. The radius of gyration (Rg and Root Mean Square Deviation (RMSD have been used as order parameters to follow the unfolding process. Distributions of Rg were used to identify ensembles. Conclusion Three ensembles could be identified. While the native-state ensemble shows an Rg distribution that is slightly skewed, the second ensemble, which is presumably the Transition State Ensemble (TSE, shows an excellent fit. The denatured ensemble shows large fluctuations, but a Gaussian curve could be fitted. This means that the unfolding process is two-state. Representative structures from each of these ensembles are presented here.

  14. Pre-steady-state kinetic analysis of 1-deoxy-D-xylulose-5-phosphate reductoisomerase from Mycobacterium tuberculosis reveals partially rate-limiting product release by parallel pathways.

    Science.gov (United States)

    Liu, Juan; Murkin, Andrew S

    2012-07-03

    As part of the non-mevalonate pathway for the biosynthesis of the isoprenoid precursor isopentenyl pyrophosphate, 1-deoxy-D-xylulose-5-phosphate (DXP) reductoisomerase (DXR) catalyzes the conversion of DXP into 2-C-methyl-D-erythritol 4-phosphate (MEP) by consecutive isomerization and NADPH-dependent reduction reactions. Because this pathway is essential to many infectious organisms but is absent in humans, DXR is a target for drug discovery. In an attempt to characterize its kinetic mechanism and identify rate-limiting steps, we present the first complete transient kinetic investigation of DXR. Stopped-flow fluorescence measurements with Mycobacterium tuberculosis DXR (MtDXR) revealed that NADPH and MEP bind to the free enzyme and that the two bind together to generate a nonproductive ternary complex. Unlike the Escherichia coli orthologue, MtDXR exhibited a burst in the oxidation of NADPH during pre-steady-state reactions, indicating a partially rate-limiting step follows chemistry. By monitoring NADPH fluorescence during these experiments, the transient generation of MtDXR·NADPH·MEP was observed. Global kinetic analysis supports a model involving random substrate binding and ordered release of NADP(+) followed by MEP. The partially rate-limiting release of MEP occurs via two pathways--directly from the binary complex and indirectly via the MtDXR·NADPH·MEP complex--the partitioning being dependent on NADPH concentration. Previous mechanistic studies, including kinetic isotope effects and product inhibition, are discussed in light of this kinetic mechanism.

  15. Measurement of the unfolded protein response (UPR) in monocytes.

    LENUS (Irish Health Repository)

    Carroll, Tomás P

    2011-01-01

    In mammalian cells, the primary function of the endoplasmic reticulum (ER) is to synthesize and assemble membrane and secreted proteins. As the main site of protein folding and posttranslational modification in the cell, the ER operates a highly conserved quality control system to ensure only correctly assembled proteins exit the ER and misfolded and unfolded proteins are retained for disposal. Any disruption in the equilibrium of the ER engages a multifaceted intracellular signaling pathway termed the unfolded protein response (UPR) to restore normal conditions in the cell. A variety of pathological conditions can induce activation of the UPR, including neurodegenerative disorders such as Parkinson\\'s disease, metabolic disorders such as atherosclerosis, and conformational disorders such as cystic fibrosis. Conformational disorders are characterized by mutations that modify the final structure of a protein and any cells that express abnormal protein risk functional impairment. The monocyte is an important and long-lived immune cell and acts as a key immunological orchestrator, dictating the intensity and duration of the host immune response. Monocytes expressing misfolded or unfolded protein may exhibit UPR activation and this can compromise the host immune system. Here, we describe in detail methods and protocols for the examination of UPR activation in peripheral blood monocytes. This guide should provide new investigators to the field with a broad understanding of the tools required to investigate the UPR in the monocyte.

  16. Measurement of the unfolded protein response (UPR) in monocytes.

    LENUS (Irish Health Repository)

    Carroll, Tomas P

    2012-02-01

    In mammalian cells, the primary function of the endoplasmic reticulum (ER) is to synthesize and assemble membrane and secreted proteins. As the main site of protein folding and posttranslational modification in the cell, the ER operates a highly conserved quality control system to ensure only correctly assembled proteins exit the ER and misfolded and unfolded proteins are retained for disposal. Any disruption in the equilibrium of the ER engages a multifaceted intracellular signaling pathway termed the unfolded protein response (UPR) to restore normal conditions in the cell. A variety of pathological conditions can induce activation of the UPR, including neurodegenerative disorders such as Parkinson\\'s disease, metabolic disorders such as atherosclerosis, and conformational disorders such as cystic fibrosis. Conformational disorders are characterized by mutations that modify the final structure of a protein and any cells that express abnormal protein risk functional impairment. The monocyte is an important and long-lived immune cell and acts as a key immunological orchestrator, dictating the intensity and duration of the host immune response. Monocytes expressing misfolded or unfolded protein may exhibit UPR activation and this can compromise the host immune system. Here, we describe in detail methods and protocols for the examination of UPR activation in peripheral blood monocytes. This guide should provide new investigators to the field with a broad understanding of the tools required to investigate the UPR in the monocyte.

  17. Neutron spectra unfolding in Bonner spheres spectrometry using neural networks

    International Nuclear Information System (INIS)

    Kardan, M.R.; Setayeshi, S.; Koohi-Fayegh, R.; Ghiassi-Nejad, M.

    2003-01-01

    The neural network method has been used for the unfolding of neutron spectra in neutron spectrometry by Bonner spheres. A back propagation algorithm was used for training of neural networks 4mm x 4 mm bare LiI(Eu) and in a polyethylene sphere set: 2, 3, 4, 5, 6, 7, 8, 10, 12, 18 inch diameter have been used for unfolding of neutron spectra. Neural networks were trained by 199 sets of neutron spectra, which were subdivided into 6, 8, 10, 12, 15 and 20 energy bins and for each of them an appropriate neural network was designed and trained. The validation was performed by the 21 sets of neutron spectra. A neural network with 10 energy bins which had a mean value of error of 6% for dose equivalent estimation of spectra in the validation set showed the best results. The obtained results show that neural networks can be applied as an effective method for unfolding neutron spectra especially when the main target is neutron dosimetry. (author)

  18. Prediction of clinical depression scores and detection of changes in whole-brain using resting-state functional MRI data with partial least squares regression.

    Directory of Open Access Journals (Sweden)

    Kosuke Yoshida

    Full Text Available In diagnostic applications of statistical machine learning methods to brain imaging data, common problems include data high-dimensionality and co-linearity, which often cause over-fitting and instability. To overcome these problems, we applied partial least squares (PLS regression to resting-state functional magnetic resonance imaging (rs-fMRI data, creating a low-dimensional representation that relates symptoms to brain activity and that predicts clinical measures. Our experimental results, based upon data from clinically depressed patients and healthy controls, demonstrated that PLS and its kernel variants provided significantly better prediction of clinical measures than ordinary linear regression. Subsequent classification using predicted clinical scores distinguished depressed patients from healthy controls with 80% accuracy. Moreover, loading vectors for latent variables enabled us to identify brain regions relevant to depression, including the default mode network, the right superior frontal gyrus, and the superior motor area.

  19. Production and partial characterization of serine and metallo peptidases secreted by Aspergillus fumigatus Fresenius in submerged and solid state fermentation.

    Science.gov (United States)

    da Silva, Ronivaldo Rodrigues; de Freitas Cabral, Tatiana Pereira; Rodrigues, André; Cabral, Hamilton

    2013-01-01

    Enzyme production varies in different fermentation systems. Enzyme expression in different fermentation systems yields important information for improving our understanding of enzymatic production induction. Comparative studies between solid-state fermentation (SSF) using agro-industrial waste wheat bran and submerged fermentation (SmF) using synthetic media were carried out to determinate the best parameters for peptidase production by the fungus Aspergillus fumigatus Fresen. Variables tested include: the concentration of carbon and protein nitrogen sources, the size of the inoculum, the pH of the media, temperature, and the length of the fermentation process. The best peptidase production during SSF was obtained after 96 hours using wheat bran at 30 °C with an inoculum of 1 × 10(6) spores and yielded 1500 active units (U/mL). The best peptidase production using SmF was obtained after periods of 72 and 96 hours of fermentation in media containing 0.5% and 0.25% of casein, respectively, at a pH of 6.0 and at 30 °C and yielded 40 U/mL. We also found examples of catabolite repression of peptidase production under SmF conditions. Biochemical characterization of the peptidases produced by both fermentative processes showed optimum activity at pH 8.0 and 50 °C, and also showed that their proteolytic activity is modulated by surfactants. The enzymatic inhibition profile using phenylmethylsulfonyl fluoride (PMSF) in SmF and SSF indicated that both fermentative processes produced a serine peptidase. Additionally, the inhibitory effect of the ethylene-diaminetetraacetic acid (EDTA) chelating agent on the peptidase produced by SmF indicated that this fermentative process also produced a metallopeptidase.

  20. Partially Hidden Markov Models

    DEFF Research Database (Denmark)

    Forchhammer, Søren Otto; Rissanen, Jorma

    1996-01-01

    Partially Hidden Markov Models (PHMM) are introduced. They differ from the ordinary HMM's in that both the transition probabilities of the hidden states and the output probabilities are conditioned on past observations. As an illustration they are applied to black and white image compression where...

  1. Two-dimensional partial-wave analysis of exclusive 190 GeV π-p scattering into the π-π-π+ final state at COMPASS (CERN)

    International Nuclear Information System (INIS)

    Haas, Florian

    2014-01-01

    The dynamics of strong interaction in the regime of low energies, i.e. large distances, is still not understood. Given its simplicity the non-relativistic simple quark model (SQM) describes successfully the observed hadronic spectra. QCD-inspired models, however, predict hadronic states where the gluonic content contributes to the hadron quantum numbers. These so-called hybrids cannot be explained within the SQM. A solid experimental proof of the existence of such systems would be the observation of spin-exotic states, with spin-parity quantum numbers, not allowed in the SQM. The study of mesons, the simplest hadrons, permits to gain insight into the realm of strong interaction where hadrons are the relevant degrees of freedom. The most promising spin-exotic meson candidate is the π 1 (1600), which was claimed in several experiments and in particular in data taken during a previous hadron campaign of the COMPASS experiment. The hadron spectroscopy program of the COMPASS experiment at CERN focuses on the investigation of the light-meson spectrum in order to enlighten this rarely understood regime of strong interaction. During the 2008 data taking an unprecedented statistical precision has been reached in peripheral interactions of 190 GeV/c pions with a proton target leading to the π - π - π + final state. A spin-parity analysis in the kinematical region of the squared fourmomentum transfer 0.1≤t'0≤1.0 GeV 2 /c 2 was carried out based on a model of 88 partial waves up to a total angular momentum of 6. Besides the precise determination of properties of known resonances, a new axial-vector state, the a 1 (1420), was observed for the first time in a mass region where neither model nor lattice calculations predict mesons with this quantum numbers. Noteworthy is the very small intensity of this signal and that it only couples to the f 0 (980) isobar which is assumed to have a large strangeness content. The spin-exotic π 1 (1600) was observed albeit as a

  2. Alpha-lactalbumin unfolding is not sufficient to cause apoptosis, but is required for the conversion to HAMLET (human alpha-lactalbumin made lethal to tumor cells).

    Science.gov (United States)

    Svensson, Malin; Fast, Jonas; Mossberg, Ann-Kristin; Düringer, Caroline; Gustafsson, Lotta; Hallgren, Oskar; Brooks, Charles L; Berliner, Lawrence; Linse, Sara; Svanborg, Catharina

    2003-12-01

    HAMLET (human alpha-lactalbumin made lethal to tumor cells) is a complex of human alpha-lactalbumin and oleic acid (C18:1:9 cis) that kills tumor cells by an apoptosis-like mechanism. Previous studies have shown that a conformational change is required to form HAMLET from alpha-lactalbumin, and that a partially unfolded conformation is maintained in the HAMLET complex. This study examined if unfolding of alpha-lactalbumin is sufficient to induce cell death. We used the bovine alpha-lactalbumin Ca(2+) site mutant D87A, which is unable to bind Ca(2+), and thus remains partially unfolded regardless of solvent conditions. The D87A mutant protein was found to be inactive in the apoptosis assay, but could readily be converted to a HAMLET-like complex in the presence of oleic acid. BAMLET (bovine alpha-lactalbumin made lethal to tumor cells) and D87A-BAMLET complexes were both able to kill tumor cells. This activity was independent of the Ca(2+)site, as HAMLET maintained a high affinity for Ca(2+) but D87A-BAMLET was active with no Ca(2+) bound. We conclude that partial unfolding of alpha-lactalbumin is necessary but not sufficient to trigger cell death, and that the activity of HAMLET is defined both by the protein and the lipid cofactor. Furthermore, a functional Ca(2+)-binding site is not required for conversion of alpha-lactalbumin to the active complex or to cause cell death. This suggests that the lipid cofactor stabilizes the altered fold without interfering with the Ca(2+)site.

  3. 32 CFR 751.13 - Partial payments.

    Science.gov (United States)

    2010-07-01

    ... voucher and all other information related to the partial payment shall be placed in the claim file. Action... 32 National Defense 5 2010-07-01 2010-07-01 false Partial payments. 751.13 Section 751.13 National... Claims Against the United States § 751.13 Partial payments. (a) Partial payments when hardship exists...

  4. Soft-x-ray emission and the local p-type partial density of electronic states in Y2O3: Experiment and theory

    International Nuclear Information System (INIS)

    Mueller, D.R.; Ederer, D.L.; van Ek, J.; OBrien, W.L.; Dong, Q.Y.; Jia, J.; Callcott, T.A.

    1996-01-01

    Photon-excited yttrium M IV,V , and electron-excited oxygen K x-ray emission spectra for yttrium oxide are presented. It is shown that, as in the case of yttrium metal, the decay of M IV vacancies does not contribute substantially to the oxide M IV,V emission. The valence emission is interpreted in a one-electron picture as a measure of the local p-type partial density of states. The yttrium and oxygen valence emission bands are very similar and strongly resemble published photoelectron spectra. Using local-density approximation electronic structure calculations, we show that the broadening of the Y-4p signal in yttrium oxide relative to Y metal are due to two inequivalent yttrium sites in Y 2 O 3 . Features present in the oxide, but not the metal spectrum, are the result of overlap (hybridization) between the Y-4p wave function and states in the oxygen 2s subband. copyright 1996 The American Physical Society

  5. Redox Thermodynamics of Cytochromes c Subjected to Urea Induced Unfolding

    OpenAIRE

    Monari, S.; Ranieri, A.; Di Rocco, G.; van der Zwan, G.; Peressini, S.; Tavagnacco, C.; Millo, D.; Borsari, M.

    2009-01-01

    The thermodynamics of the electron transfer (ET) process for beef heart and yeast cytochromes c and the Lys72Ala/Lys73Ala/Lys79Ala mutant of the latter species subjected to progressive urea-induced unfolding was determined electrochemically. The results indicate the presence of at least three protein forms which were assigned to a low-temperature and a high-temperature His-Met intermediate species and a bis-histidinate form (although the presence of a His-Lys form cannot be excluded). The muc...

  6. Evaluation of spectral unfolding techniques for neutron spectroscopy

    International Nuclear Information System (INIS)

    Sunden, Erik Andersson; Conroy, S.; Ericsson, G.; Johnson, M. Gatu; Giacomelli, L.; Hellesen, C.; Hjalmarsson, A.; Ronchi, E.; Sjoestrand, H.; Weiszflog, M.; Kaellne, J.; Gorini, G.; Tardocchi, M.

    2008-01-01

    The precision of the JET installations of MAXED, GRAVEL and the L-curve version of MAXED has been evaluated by using synthetic neutron spectra. We have determined the number of counts needed for the detector systems NE213 and MPR to get an error below 10% of the MAXED unfolded neutron spectra is determined to be ∼10 6 and ∼10 4 , respectively. For GRAVEL the same number is ∼10 7 and ∼3·10 4 for NE213 and MPR, respectively

  7. Unfolding of neutron spectra from Godiva type critical assemblies

    International Nuclear Information System (INIS)

    Harvey, J.T.; Meason, J.L.; Wright, H.L.

    1976-01-01

    The results from three experiments conducted at the White Sands Missile Range Fast Burst Reactor Facility are discussed. The experiments were designed to measure the ''free-field'' neutron leakage spectrum and the neutron spectra from mildly perturbed environments. SAND-II was used to calculate the neutron spectrum utilizing several different trial input spectra for each experiment. Comparisons are made between the unfolded neutron spectrum for each trial input on the basis of the following parameters: average neutron energy (above 10 KeV), integral fluence (above 10 KeV), spectral index and the hardness parameter, phi/sub eq//phi

  8. Uncertainties related to numerical methods for neutron spectra unfolding

    International Nuclear Information System (INIS)

    Glodic, S.; Ninkovic, M.; Adarougi, N.A.

    1987-10-01

    One of the often used techniques for neutron detection in radiation protection utilities is the Bonner multisphere spectrometer. Besides its advantages and universal applicability for evaluating integral parameters of neutron fields in health physics practices, the outstanding problems of the method are data analysis and the accuracy of the results. This paper briefly discusses some numerical problems related to neutron spectra unfolding, such as uncertainty of the response matrix as a source of error, and the possibility of real time data reduction using spectrometers. (author)

  9. Solving inverse problems with the unfolding program TRUEE: Examples in astroparticle physics

    International Nuclear Information System (INIS)

    Milke, N.; Doert, M.; Klepser, S.; Mazin, D.; Blobel, V.; Rhode, W.

    2013-01-01

    The unfolding program TRUEE is a software package for the numerical solution of inverse problems. The algorithm was first applied in the FORTRAN 77 program RUN. RUN is an event-based unfolding algorithm which makes use of the Tikhonov regularization. It has been tested and compared to different unfolding applications and stood out with notably stable results and reliable error estimation. TRUEE is a conversion of RUN to C++, which works within the powerful ROOT framework. The program has been extended for more user-friendliness and delivers unfolding results which are identical to RUN. Beside the simplicity of the installation of the software and the generation of graphics, there are new functions, which facilitate the choice of unfolding parameters and observables for the user. In this paper, we introduce the new unfolding program and present its performance by applying it to two exemplary data sets from astroparticle physics, taken with the MAGIC telescopes and the IceCube neutrino detector, respectively.

  10. CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function.

    Science.gov (United States)

    Krüger, Dennis M; Rathi, Prakash Chandra; Pfleger, Christopher; Gohlke, Holger

    2013-07-01

    The Constraint Network Analysis (CNA) web server provides a user-friendly interface to the CNA approach developed in our laboratory for linking results from rigidity analyses to biologically relevant characteristics of a biomolecular structure. The CNA web server provides a refined modeling of thermal unfolding simulations that considers the temperature dependence of hydrophobic tethers and computes a set of global and local indices for quantifying biomacromolecular stability. From the global indices, phase transition points are identified where the structure switches from a rigid to a floppy state; these phase transition points can be related to a protein's (thermo-)stability. Structural weak spots (unfolding nuclei) are automatically identified, too; this knowledge can be exploited in data-driven protein engineering. The local indices are useful in linking flexibility and function and to understand the impact of ligand binding on protein flexibility. The CNA web server robustly handles small-molecule ligands in general. To overcome issues of sensitivity with respect to the input structure, the CNA web server allows performing two ensemble-based variants of thermal unfolding simulations. The web server output is provided as raw data, plots and/or Jmol representations. The CNA web server, accessible at http://cpclab.uni-duesseldorf.de/cna or http://www.cnanalysis.de, is free and open to all users with no login requirement.

  11. Structural dynamics of the MecA-ClpC complex: a type II AAA+ protein unfolding machine.

    Science.gov (United States)

    Liu, Jing; Mei, Ziqing; Li, Ningning; Qi, Yutao; Xu, Yanji; Shi, Yigong; Wang, Feng; Lei, Jianlin; Gao, Ning

    2013-06-14

    The MecA-ClpC complex is a bacterial type II AAA(+) molecular machine responsible for regulated unfolding of substrates, such as transcription factors ComK and ComS, and targeting them to ClpP for degradation. The six subunits of the MecA-ClpC complex form a closed barrel-like structure, featured with three stacked rings and a hollow passage, where substrates are threaded and translocated through successive pores. Although the general concepts of how polypeptides are unfolded and translocated by internal pore loops of AAA(+) proteins have long been conceived, the detailed mechanistic model remains elusive. With cryoelectron microscopy, we captured four different structures of the MecA-ClpC complexes. These complexes differ in the nucleotide binding states of the two AAA(+) rings and therefore might presumably reflect distinctive, representative snapshots from a dynamic unfolding cycle of this hexameric complex. Structural analysis reveals that nucleotide binding and hydrolysis modulate the hexameric complex in a number of ways, including the opening of the N-terminal ring, the axial and radial positions of pore loops, the compactness of the C-terminal ring, as well as the relative rotation between the two nucleotide-binding domain rings. More importantly, our structural and biochemical data indicate there is an active allosteric communication between the two AAA(+) rings and suggest that concerted actions of the two AAA(+) rings are required for the efficiency of the substrate unfolding and translocation. These findings provide important mechanistic insights into the dynamic cycle of the MecA-ClpC unfoldase and especially lay a foundation toward the complete understanding of the structural dynamics of the general type II AAA(+) hexamers.

  12. Correcting human heart 31P NMR spectra for partial saturation. Evidence that saturation factors for PCr/ATP are homogeneous in normal and disease states

    Science.gov (United States)

    Bottomley, Paul A.; Hardy, Christopher J.; Weiss, Robert G.

    Heart PCr/ATP ratios measured from spatially localized 31P NMR spectra can be corrected for partial saturation effects using saturation factors derived from unlocalized chest surface-coil spectra acquired at the heart rate and approximate Ernst angle for phosphor creatine (PCr) and again under fully relaxed conditions during each 31P exam. To validate this approach in studies of normal and disease states where the possibility of heterogeneity in metabolite T1 values between both chest muscle and heart and normal and disease states exists, the properties of saturation factors for metabolite ratios were investigated theoretically under conditions applicable in typical cardiac spectroscopy exams and empirically using data from 82 cardiac 31P exams in six study groups comprising normal controls ( n = 19) and patients with dilated ( n = 20) and hypertrophic ( n = 5) cardiomyopathy, coronary artery disease ( n = 16), heart transplants ( n = 19), and valvular heart disease ( n = 3). When TR ≪ T1,(PCr), with T1(PCr) ⩾ T1(ATP), the saturation factor for PCr/ATP lies in the range 1.5 ± 0.5, regardless of the T1 values. The precise value depends on the ratio of metabolite T1 values rather than their absolute values and is insensitive to modest changes in TR. Published data suggest that the metabolite T1 ratio is the same in heart and muscle. Our empirical data reveal that the saturation factors do not vary significantly with disease state, nor with the relative fractions of muscle and heart contributing to the chest surface-coil spectra. Also, the corrected myocardial PCr/ATP ratios in each normal or disease state bear no correlation with the corresponding saturation factors nor the fraction of muscle in the unlocalized chest spectra. However, application of the saturation correction (mean value, 1.36 ± 0.03 SE) significantly reduced scatter in myocardial PCr/ATP data by 14 ± 11% (SD) ( p ⩽ 0.05). The findings suggest that the relative T1 values of PCr and ATP are

  13. Model based rib-cage unfolding for trauma CT

    Science.gov (United States)

    von Berg, Jens; Klinder, Tobias; Lorenz, Cristian

    2018-03-01

    A CT rib-cage unfolding method is proposed that does not require to determine rib centerlines but determines the visceral cavity surface by model base segmentation. Image intensities are sampled across this surface that is flattened using a model based 3D thin-plate-spline registration. An average rib centerline model projected onto this surface serves as a reference system for registration. The flattening registration is designed so that ribs similar to the centerline model are mapped onto parallel lines preserving their relative length. Ribs deviating from this model appear deviating from straight parallel ribs in the unfolded view, accordingly. As the mapping is continuous also the details in intercostal space and those adjacent to the ribs are rendered well. The most beneficial application area is Trauma CT where a fast detection of rib fractures is a crucial task. Specifically in trauma, automatic rib centerline detection may not be guaranteed due to fractures and dislocations. The application by visual assessment on the large public LIDC data base of lung CT proved general feasibility of this early work.

  14. Constrained Unfolding of a Helical Peptide: Implicit versus Explicit Solvents.

    Directory of Open Access Journals (Sweden)

    Hailey R Bureau

    Full Text Available Steered Molecular Dynamics (SMD has been seen to provide the potential of mean force (PMF along a peptide unfolding pathway effectively but at significant computational cost, particularly in all-atom solvents. Adaptive steered molecular dynamics (ASMD has been seen to provide a significant computational advantage by limiting the spread of the trajectories in a staged approach. The contraction of the trajectories at the end of each stage can be performed by taking a structure whose nonequilibrium work is closest to the Jarzynski average (in naive ASMD or by relaxing the trajectories under a no-work condition (in full-relaxation ASMD--namely, FR-ASMD. Both approaches have been used to determine the energetics and hydrogen-bonding structure along the pathway for unfolding of a benchmark peptide initially constrained as an α-helix in a water environment. The energetics are quite different to those in vacuum, but are found to be similar between implicit and explicit solvents. Surprisingly, the hydrogen-bonding pathways are also similar in the implicit and explicit solvents despite the fact that the solvent contact plays an important role in opening the helix.

  15. Understanding how biodiversity unfolds through time under neutral theory.

    Science.gov (United States)

    Missa, Olivier; Dytham, Calvin; Morlon, Hélène

    2016-04-05

    Theoretical predictions for biodiversity patterns are typically derived under the assumption that ecological systems have reached a dynamic equilibrium. Yet, there is increasing evidence that various aspects of ecological systems, including (but not limited to) species richness, are not at equilibrium. Here, we use simulations to analyse how biodiversity patterns unfold through time. In particular, we focus on the relative time required for various biodiversity patterns (macroecological or phylogenetic) to reach equilibrium. We simulate spatially explicit metacommunities according to the Neutral Theory of Biodiversity (NTB) under three modes of speciation, which differ in how evenly a parent species is split between its two daughter species. We find that species richness stabilizes first, followed by species area relationships (SAR) and finally species abundance distributions (SAD). The difference in timing of equilibrium between these different macroecological patterns is the largest when the split of individuals between sibling species at speciation is the most uneven. Phylogenetic patterns of biodiversity take even longer to stabilize (tens to hundreds of times longer than species richness) so that equilibrium predictions from neutral theory for these patterns are unlikely to be relevant. Our results suggest that it may be unwise to assume that biodiversity patterns are at equilibrium and provide a first step in studying how these patterns unfold through time. © 2016 The Author(s).

  16. Inhibition of the Unfolded Protein Response Mechanism Prevents Cardiac Fibrosis.

    Directory of Open Access Journals (Sweden)

    Jody Groenendyk

    Full Text Available Cardiac fibrosis attributed to excessive deposition of extracellular matrix proteins is a major cause of heart failure and death. Cardiac fibrosis is extremely difficult and challenging to treat in a clinical setting due to lack of understanding of molecular mechanisms leading to cardiac fibrosis and effective anti-fibrotic therapies. The objective in this study was to examine whether unfolded protein response (UPR pathway mediates cardiac fibrosis and whether a pharmacological intervention to modulate UPR can prevent cardiac fibrosis and preserve heart function.We demonstrate here that the mechanism leading to development of fibrosis in a mouse with increased expression of calreticulin, a model of heart failure, stems from impairment of endoplasmic reticulum (ER homeostasis, transient activation of the unfolded protein response (UPR pathway and stimulation of the TGFβ1/Smad2/3 signaling pathway. Remarkably, sustained pharmacologic inhibition of the UPR pathway by tauroursodeoxycholic acid (TUDCA is sufficient to prevent cardiac fibrosis, and improved exercise tolerance.We show that the mechanism leading to development of fibrosis in a mouse model of heart failure stems from transient activation of UPR pathway leading to persistent remodelling of cardiac tissue. Blocking the activation of the transiently activated UPR pathway by TUDCA prevented cardiac fibrosis, and improved prognosis. These findings offer a window for additional interventions that can preserve heart function.

  17. Network Unfolding Map by Vertex-Edge Dynamics Modeling.

    Science.gov (United States)

    Verri, Filipe Alves Neto; Urio, Paulo Roberto; Zhao, Liang

    2018-02-01

    The emergence of collective dynamics in neural networks is a mechanism of the animal and human brain for information processing. In this paper, we develop a computational technique using distributed processing elements in a complex network, which are called particles, to solve semisupervised learning problems. Three actions govern the particles' dynamics: generation, walking, and absorption. Labeled vertices generate new particles that compete against rival particles for edge domination. Active particles randomly walk in the network until they are absorbed by either a rival vertex or an edge currently dominated by rival particles. The result from the model evolution consists of sets of edges arranged by the label dominance. Each set tends to form a connected subnetwork to represent a data class. Although the intrinsic dynamics of the model is a stochastic one, we prove that there exists a deterministic version with largely reduced computational complexity; specifically, with linear growth. Furthermore, the edge domination process corresponds to an unfolding map in such way that edges "stretch" and "shrink" according to the vertex-edge dynamics. Consequently, the unfolding effect summarizes the relevant relationships between vertices and the uncovered data classes. The proposed model captures important details of connectivity patterns over the vertex-edge dynamics evolution, in contrast to the previous approaches, which focused on only vertex or only edge dynamics. Computer simulations reveal that the new model can identify nonlinear features in both real and artificial data, including boundaries between distinct classes and overlapping structures of data.

  18. A neutron spectrum unfolding code based on iterative procedures

    International Nuclear Information System (INIS)

    Ortiz R, J. M.; Vega C, H. R.

    2012-10-01

    In this work, the version 3.0 of the neutron spectrum unfolding code called Neutron Spectrometry and Dosimetry from Universidad Autonoma de Zacatecas (NSDUAZ), is presented. This code was designed in a graphical interface under the LabVIEW programming environment and it is based on the iterative SPUNIT iterative algorithm, using as entrance data, only the rate counts obtained with 7 Bonner spheres based on a 6 Lil(Eu) neutron detector. The main features of the code are: it is intuitive and friendly to the user; it has a programming routine which automatically selects the initial guess spectrum by using a set of neutron spectra compiled by the International Atomic Energy Agency. Besides the neutron spectrum, this code calculates the total flux, the mean energy, H(10), h(10), 15 dosimetric quantities for radiation protection porpoises and 7 survey meter responses, in four energy grids, based on the International Atomic Energy Agency compilation. This code generates a full report in html format with all relevant information. In this work, the neutron spectrum of a 241 AmBe neutron source on air, located at 150 cm from detector, is unfolded. (Author)

  19. Experimental parameterization of an energy function for the simulation of unfolded proteins

    DEFF Research Database (Denmark)

    Norgaard, A.B.; Ferkinghoff-Borg, Jesper; Lindorff-Larsen, K.

    2008-01-01

    The determination of conformational preferences in unfolded and disordered proteins is an important challenge in structural biology. We here describe an algorithm to optimize energy functions for the simulation of unfolded proteins. The procedure is based on the maximum likelihood principle and e...... and can be applied to a range of experimental data and energy functions including the force fields used in molecular dynamics simulations.......The determination of conformational preferences in unfolded and disordered proteins is an important challenge in structural biology. We here describe an algorithm to optimize energy functions for the simulation of unfolded proteins. The procedure is based on the maximum likelihood principle...

  20. Partially composite Higgs models

    DEFF Research Database (Denmark)

    Alanne, Tommi; Buarque Franzosi, Diogo; Frandsen, Mads T.

    2018-01-01

    We study the phenomenology of partially composite-Higgs models where electroweak symmetry breaking is dynamically induced, and the Higgs is a mixture of a composite and an elementary state. The models considered have explicit realizations in terms of gauge-Yukawa theories with new strongly...... interacting fermions coupled to elementary scalars and allow for a very SM-like Higgs state. We study constraints on their parameter spaces from vacuum stability and perturbativity as well as from LHC results and find that requiring vacuum stability up to the compositeness scale already imposes relevant...... constraints. A small part of parameter space around the classically conformal limit is stable up to the Planck scale. This is however already strongly disfavored by LHC results. in different limits, the models realize both (partially) composite-Higgs and (bosonic) technicolor models and a dynamical extension...

  1. Two states or not two states: Single-molecule folding studies of protein L

    Science.gov (United States)

    Aviram, Haim Yuval; Pirchi, Menahem; Barak, Yoav; Riven, Inbal; Haran, Gilad

    2018-03-01

    Experimental tools of increasing sophistication have been employed in recent years to study protein folding and misfolding. Folding is considered a complex process, and one way to address it is by studying small proteins, which seemingly possess a simple energy landscape with essentially only two stable states, either folded or unfolded. The B1-IgG binding domain of protein L (PL) is considered a model two-state folder, based on measurements using a wide range of experimental techniques. We applied single-molecule fluorescence resonance energy transfer (FRET) spectroscopy in conjunction with a hidden Markov model analysis to fully characterize the energy landscape of PL and to extract the kinetic properties of individual molecules of the protein. Surprisingly, our studies revealed the existence of a third state, hidden under the two-state behavior of PL due to its small population, ˜7%. We propose that this minority intermediate involves partial unfolding of the two C-terminal β strands of PL. Our work demonstrates that single-molecule FRET spectroscopy can be a powerful tool for a comprehensive description of the folding dynamics of proteins, capable of detecting and characterizing relatively rare metastable states that are difficult to observe in ensemble studies.

  2. Communication: Role of explicit water models in the helix folding/unfolding processes

    Science.gov (United States)

    Palazzesi, Ferruccio; Salvalaglio, Matteo; Barducci, Alessandro; Parrinello, Michele

    2016-09-01

    In the last years, it has become evident that computer simulations can assume a relevant role in modelling protein dynamical motions for their ability to provide a full atomistic image of the processes under investigation. The ability of the current protein force-fields in reproducing the correct thermodynamics and kinetics systems behaviour is thus an essential ingredient to improve our understanding of many relevant biological functionalities. In this work, employing the last developments of the metadynamics framework, we compare the ability of state-of-the-art all-atom empirical functions and water models to consistently reproduce the folding and unfolding of a helix turn motif in a model peptide. This theoretical study puts in evidence that the choice of the water models can influence the thermodynamic and the kinetics of the system under investigation, and for this reason cannot be considered trivial.

  3. S-Adenosylmethionine metabolism and its relation to polyamine synthesis in rat liver. Effect of nutritional state, adrenal function, some drugs and partial hepatectomy

    Science.gov (United States)

    Eloranta, Terho O.; Raina, Aarne M.

    1977-01-01

    S-Adenosylmethionine metabolism and its relation to the synthesis and accumulation of polyamines was studied in rat liver under various nutritional conditions, in adrenalectomized or partially hepatectomized animals and after treatment with cortisol, thioacetamide or methylglyoxal bis(guanylhydrazone) {1,1′-[(methylethanediylidine)dinitrilo]diguanidine}. Starvation for 2 days only slightly affected S-adenosylmethionine metabolism. The ratio of spermidine/spermine decreased markedly, but the concentration of total polyamines did not change significantly. The activity of S-adenosylmethionine decarboxylase initially decreased and then increased during prolonged starvation. This increase was dependent on intact adrenals. Re-feeding of starved animals caused a rapid but transient stimulation of polyamine synthesis and also increased the concentrations of S-adenosylmethionine and S-adenosylhomocysteine. Similarly, cortisol treatment enhanced the synthesis of polyamines, S-adenosylmethionine and S-adenosylhomocysteine. Feeding with a methionine-deficient diet for 7–14 days profoundly increased the concentration of spermidine, whereas the concentrations of total polyamines and of S-adenosylmethionine showed no significant changes. The results show that nutritional state and adrenal function play a significant role in the regulation of hepatic metabolism of S-adenosylmethionine and polyamines. They further indicate that under a variety of physiological and experimental conditions the concentrations of S-adenosylmethionine and of total polyamines remain fairly constant and that changes in polyamine metabolism are not primarily connected with changes in the accumulation of S-adenosylmethionine or S-adenosylhomocysteine. PMID:597268

  4. Micro-hybrid electric vehicle application of valve-regulated lead-acid batteries in absorbent glass mat technology: Testing a partial-state-of-charge operation strategy

    Energy Technology Data Exchange (ETDEWEB)

    Schaeck, S.; Stoermer, A.O.; Hockgeiger, E. [BMW Group, Powertrain Development, Energy Storage, Hufelandstrasse 4, 80788 Muenchen (Germany)

    2009-05-01

    The BMW Group has launched two micro-hybrid functions in high volume models in order to contribute to reduction of fuel consumption in modern passenger cars. Both the brake energy regeneration (BER) and the auto-start-stop function (ASSF) are based on the conventional 14 V vehicle electrical system and current series components with only little modifications. An intelligent control algorithm of the alternator enables recuperative charging in braking and coasting phases, known as BER. By switching off the internal combustion engine at a vehicle standstill the idling fuel consumption is effectively reduced by ASSF. By reason of economy and package a lead-acid battery is used as electrochemical energy storage device. The BMW Group assembles valve-regulated lead-acid (VRLA) batteries in absorbent glass mat (AGM) technology in the micro-hybrid electrical power system since special challenges arise for the batteries. By field data analysis a lower average state-of-charge (SOC) due to partial state-of-charge (PSOC) operation and a higher cycling rate due to BER and ASSF are confirmed in this article. Similar to a design of experiment (DOE) like method we present a long-term lab investigation. Two types of 90 Ah VRLA AGM batteries are operated with a test bench profile that simulates the micro-hybrid vehicle electrical system under varying conditions. The main attention of this lab testing is focused on capacity loss and charge acceptance over cycle life. These effects are put into context with periodically refresh charging the batteries in order to prevent accelerated battery aging due to hard sulfation. We demonstrate the positive effect of refresh chargings concerning preservation of battery charge acceptance. Furthermore, we observe moderate capacity loss over 90 full cycles both at 25 C and at 3 C battery temperature. (author)

  5. Micro-hybrid electric vehicle application of valve-regulated lead-acid batteries in absorbent glass mat technology: Testing a partial-state-of-charge operation strategy

    Science.gov (United States)

    Schaeck, S.; Stoermer, A. O.; Hockgeiger, E.

    The BMW Group has launched two micro-hybrid functions in high volume models in order to contribute to reduction of fuel consumption in modern passenger cars. Both the brake energy regeneration (BER) and the auto-start-stop function (ASSF) are based on the conventional 14 V vehicle electrical system and current series components with only little modifications. An intelligent control algorithm of the alternator enables recuperative charging in braking and coasting phases, known as BER. By switching off the internal combustion engine at a vehicle standstill the idling fuel consumption is effectively reduced by ASSF. By reason of economy and package a lead-acid battery is used as electrochemical energy storage device. The BMW Group assembles valve-regulated lead-acid (VRLA) batteries in absorbent glass mat (AGM) technology in the micro-hybrid electrical power system since special challenges arise for the batteries. By field data analysis a lower average state-of-charge (SOC) due to partial state-of-charge (PSOC) operation and a higher cycling rate due to BER and ASSF are confirmed in this article. Similar to a design of experiment (DOE) like method we present a long-term lab investigation. Two types of 90 Ah VRLA AGM batteries are operated with a test bench profile that simulates the micro-hybrid vehicle electrical system under varying conditions. The main attention of this lab testing is focused on capacity loss and charge acceptance over cycle life. These effects are put into context with periodically refresh charging the batteries in order to prevent accelerated battery aging due to hard sulfation. We demonstrate the positive effect of refresh chargings concerning preservation of battery charge acceptance. Furthermore, we observe moderate capacity loss over 90 full cycles both at 25 °C and at 3 °C battery temperature.

  6. Regeneration in United States Department of Agriculture Forest Service mixed conifer partial cuttings in the Blue Mountains of Oregon and Washington.

    Science.gov (United States)

    K.W. Seidel; S. Conrade. Head

    1983-01-01

    A survey in the Blue Mountains of north-eastern Oregon and southeastern Washington showed that, on the average, partial cuts in the grand fir/big huckleberry community were well stocked with a mixture of advance, natural post-harvest, and planted reproduction of a number of species. Partial cuts in the mixed conifer/pinegrass community had considerably fewer seedlings...

  7. Evolution and thermodynamics of the slow unfolding of hyperstable monomeric proteins

    Directory of Open Access Journals (Sweden)

    Koga Yuichi

    2010-07-01

    Full Text Available Abstract Background The unfolding speed of some hyperthermophilic proteins is dramatically lower than that of their mesostable homologs. Ribonuclease HII from the hyperthermophilic archaeon Thermococcus kodakaraensis (Tk-RNase HII is stabilized by its remarkably slow unfolding rate, whereas RNase HI from the thermophilic bacterium Thermus thermophilus (Tt-RNase HI unfolds rapidly, comparable with to that of RNase HI from Escherichia coli (Ec-RNase HI. Results To clarify whether the difference in the unfolding rate is due to differences in the types of RNase H or differences in proteins from archaea and bacteria, we examined the equilibrium stability and unfolding reaction of RNases HII from the hyperthermophilic bacteria Thermotoga maritima (Tm-RNase HII and Aquifex aeolicus (Aa-RNase HII and RNase HI from the hyperthermophilic archaeon Sulfolobus tokodaii (Sto-RNase HI. These proteins from hyperthermophiles are more stable than Ec-RNase HI over all the temperature ranges examined. The observed unfolding speeds of all hyperstable proteins at the different denaturant concentrations studied are much lower than those of Ec-RNase HI, which is in accordance with the familiar slow unfolding of hyperstable proteins. However, the unfolding rate constants of these RNases H in water are dispersed, and the unfolding rate constant of thermophilic archaeal proteins is lower than that of thermophilic bacterial proteins. Conclusions These results suggest that the nature of slow unfolding of thermophilic proteins is determined by the evolutionary history of the organisms involved. The unfolding rate constants in water are related to the amount of buried hydrophobic residues in the tertiary structure.

  8. The impact of urea-induced unfolding on the redox process of immobilised cytochrome c.

    Science.gov (United States)

    Monari, Stefano; Millo, Diego; Ranieri, Antonio; Di Rocco, Giulia; van der Zwan, Gert; Gooijer, Cees; Peressini, Silvia; Tavagnacco, Claudio; Hildebrandt, Peter; Borsari, Marco

    2010-11-01

    We have studied the effect of urea-induced unfolding on the electron transfer process of yeast iso-1-cytochrome c and its mutant K72AK73AK79A adsorbed on electrodes coated by mixed 11-mercapto-1-undecanoic acid/11-mercapto-1-undecanol self-assembled monolayers. Electrochemical measurements, complemented by surface enhanced resonance Raman studies, indicate two distinct states of the adsorbed proteins that mainly differ with respect to the ligation pattern of the haem. The native state, in which the haem is axially coordinated by Met80 and His18, displays a reduction potential that slightly shifts to negative values with increasing urea concentration. At urea concentrations higher than 6 M, a second state prevails in which the Met80 ligand is replaced by an additional histidine residue. This structural change in the haem pocket is associated with an approximately 0.4 V shift of the reduction potential to negative values. These two states were found for both the wild-type protein and the mutant in which lysine residues 72, 73 and 79 had been substituted by alanines. The analysis of the reduction potentials, the reaction enthalpies and entropies as well as the rate constants indicates that these three lysine residues have an important effect on stabilising the protein structure in the adsorbed state and facilitating the electron transfer dynamics.

  9. Unfolding and Refolding Embodiment into the Landscape of Ubiquitous Computing

    DEFF Research Database (Denmark)

    Schick, Lea; Malmborg, Lone

    2009-01-01

    This paper advocates the future of the body as a distributed and shared embodiment; an unfolded body that doesn’t end at one's skin, but emerges as intercorporeality between bodies and the technological environment. Looking at new tendencies within interaction design and ubiquitous computing to see...... how these are to an increasing extent focusing on sociality, context-awareness, relations, affects, connectedness, and collectivity we will examine how these new technological movements can change our perception of embodiment towards a distributed and shared one. By examining interactive textiles...... as part of a future rising landscape of multi-sensory networks we will exemplify how the new technologies can shutter dichotomies and challenge traditional notions of embodiment and the subject. Finally, we show how this ‘new embodiment’ manifests Deleuze’s philosophy of the body as something unstable...

  10. Neutron spectra unfolding with maximum entropy and maximum likelihood

    International Nuclear Information System (INIS)

    Itoh, Shikoh; Tsunoda, Toshiharu

    1989-01-01

    A new unfolding theory has been established on the basis of the maximum entropy principle and the maximum likelihood method. This theory correctly embodies the Poisson statistics of neutron detection, and always brings a positive solution over the whole energy range. Moreover, the theory unifies both problems of overdetermined and of underdetermined. For the latter, the ambiguity in assigning a prior probability, i.e. the initial guess in the Bayesian sense, has become extinct by virtue of the principle. An approximate expression of the covariance matrix for the resultant spectra is also presented. An efficient algorithm to solve the nonlinear system, which appears in the present study, has been established. Results of computer simulation showed the effectiveness of the present theory. (author)

  11. DANTE, Activation Analysis Neutron Spectra Unfolding by Covariance Matrix Method

    International Nuclear Information System (INIS)

    Petilli, M.

    1981-01-01

    1 - Description of problem or function: The program evaluates activation measurements of reactor neutron spectra and unfolds the results for dosimetry purposes. Different evaluation options are foreseen: absolute or relative fluxes and different iteration algorithms. 2 - Method of solution: A least-square fit method is used. A correlation between available data and their uncertainties has been introduced by means of flux and activity variance-covariance matrices. Cross sections are assumed to be constant, i.e. with variance-covariance matrix equal to zero. The Lagrange multipliers method has been used for calculating the solution. 3 - Restrictions on the complexity of the problem: 9 activation experiments can be analyzed. 75 energy groups are accepted

  12. The Unfolded Protein Response and Cell Fate Control.

    Science.gov (United States)

    Hetz, Claudio; Papa, Feroz R

    2018-01-18

    The secretory capacity of a cell is constantly challenged by physiological demands and pathological perturbations. To adjust and match the protein-folding capacity of the endoplasmic reticulum (ER) to changing secretory needs, cells employ a dynamic intracellular signaling pathway known as the unfolded protein response (UPR). Homeostatic activation of the UPR enforces adaptive programs that modulate and augment key aspects of the entire secretory pathway, whereas maladaptive UPR outputs trigger apoptosis. Here, we discuss recent advances into how the UPR integrates information about the intensity and duration of ER stress stimuli in order to control cell fate. These findings are timely and significant because they inform an evolving mechanistic understanding of a wide variety of human diseases, including diabetes mellitus, neurodegeneration, and cancer, thus opening up the potential for new therapeutic modalities to treat these diverse diseases. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Emerging Role of the Unfolded Protein Response in Tumor Immunosurveillance.

    Science.gov (United States)

    Vanacker, Hélène; Vetters, Jessica; Moudombi, Lyvia; Caux, Christophe; Janssens, Sophie; Michallet, Marie-Cécile

    2017-07-01

    Disruption of endoplasmic reticulum (ER) homeostasis results in ER stress and activation of the unfolded protein response (UPR). This response alleviates cell stress, and is activated in both tumor cells and tumor infiltrating immune cells. The UPR plays a dual function in cancer biology, acting as a barrier to tumorigenesis at the premalignant stage, while fostering cancer maintenance in established tumors. In infiltrating immune cells, the UPR has been involved in both immunosurveillance and immunosuppressive functions. This review aims to decipher the role of the UPR at different stages of tumorigenesis and how the UPR shapes the balance between immunosurveillance and immune escape. This knowledge may improve existing UPR-targeted therapies and the design of novel strategies for cancer treatment. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. The Unfolded Protein Response in Chronic Obstructive Pulmonary Disease.

    Science.gov (United States)

    Kelsen, Steven G

    2016-04-01

    Accumulation of nonfunctional and potentially cytotoxic, misfolded proteins in chronic obstructive pulmonary disease (COPD) is believed to contribute to lung cell apoptosis, inflammation, and autophagy. Because of its fundamental role as a quality control system in protein metabolism, the "unfolded protein response" (UPR) is of potential importance in the pathogenesis of COPD. The UPR comprises a series of transcriptional, translational, and post-translational processes that decrease protein synthesis while enhancing protein folding capacity and protein degradation. Several studies have suggested that the UPR contributes to lung cell apoptosis and lung inflammation in at least some subjects with human COPD. However, information on the prevalence of the UPR in subjects with COPD, the lung cells that manifest a UPR, and the role of the UPR in the pathogenesis of COPD is extremely limited and requires additional study.

  15. Arctigenin suppresses unfolded protein response and sensitizes glucose deprivation-mediated cytotoxicity of cancer cells.

    Science.gov (United States)

    Sun, Shengrong; Wang, Xiong; Wang, Changhua; Nawaz, Ahmed; Wei, Wen; Li, Juanjuan; Wang, Lijun; Yu, De-Hua

    2011-01-01

    The involvement of unfolded protein response (UPR) activation in tumor survival and resistance to chemotherapies suggests a new anticancer strategy targeting UPR pathway. Arctigenin, a natural product, has been recently identified for its antitumor activity with selective toxicity against cancer cells under glucose starvation with unknown mechanism. Here we found that arctigenin specifically blocks the transcriptional induction of two potential anticancer targets, namely glucose-regulated protein-78 (GRP78) and its analog GRP94, under glucose deprivation, but not by tunicamycin. The activation of other UPR pathways, e.g., XBP-1 and ATF4, by glucose deprivation was also suppressed by arctigenin. A further transgene experiment showed that ectopic expression of GRP78 at least partially rescued arctigenin/glucose starvation-mediated cell growth inhibition, suggesting the causal role of UPR suppression in arctigenin-mediated cytotoxicity under glucose starvation. These observations bring a new insight into the mechanism of action of arctigenin and may lead to the design of new anticancer therapeutics. © Georg Thieme Verlag KG Stuttgart · New York.

  16. Resveratrol-induced cytotoxicity in human Burkitt's lymphoma cells is coupled to the unfolded protein response

    Directory of Open Access Journals (Sweden)

    Yan Ying

    2010-08-01

    Full Text Available Abstract Background Resveratrol (RES, a natural phytoalexin found at high levels in grapes and red wine, has been shown to induce anti-proliferation and apoptosis of human cancer cell lines. However, the underlying molecular mechanisms are at present only partially understood. Method The effects of RES on activation of unfolded protein responses (UPR were evaluated using Western blotting, semi-quantitative and real-time RT-PCR. Cell death was evaluated using Annexin V/PI staining and subsequent FACS. Results Similar as tunicamycin, treatment with RES lead to the activation of all 3 branches of the UPR, with early splicing of XBP-1 indicative of IRE1 activation, phosphorylation of eIF2α consistent with ER resident kinase (PERK activation, activating transcription factor 6 (ATF6 splicing, and increase in expression levels of the downstream molecules GRP78/BiP, GRP94 and CHOP/GADD153 in human Burkitt's lymphoma Raji and Daudi cell lines. RES was shown to induce cell death, which could be attenuated by thwarting upregulation of CHOP. Conclusions Our data suggest that activation of the apoptotic arm of the UPR and its downstream effector CHOP/GADD153 is involved, at least in part, in RES-induced apoptosis in Burkitt's lymphoma cells.

  17. The Unfolding of Value Sources During Online Business Model Transformation

    Directory of Open Access Journals (Sweden)

    Nadja Hoßbach

    2016-12-01

    Full Text Available Purpose: In the magazine publishing industry, viable online business models are still rare to absent. To prepare for the ‘digital future’ and safeguard their long-term survival, many publishers are currently in the process of transforming their online business model. Against this backdrop, this study aims to develop a deeper understanding of (1 how the different building blocks of an online business model are transformed over time and (2 how sources of value creation unfold during this transformation process. Methodology: To answer our research question, we conducted a longitudinal case study with a leading German business magazine publisher (called BIZ. Data was triangulated from multiple sources including interviews, internal documents, and direct observations. Findings: Based on our case study, we nd that BIZ used the transformation process to differentiate its online business model from its traditional print business model along several dimensions, and that BIZ’s online business model changed from an efficiency- to a complementarity- to a novelty-based model during this process. Research implications: Our findings suggest that different business model transformation phases relate to different value sources, questioning the appropriateness of value source-based approaches for classifying business models. Practical implications: The results of our case study highlight the need for online-offline business model differentiation and point to the important distinction between service and product differentiation. Originality: Our study contributes to the business model literature by applying a dynamic and holistic perspective on the link between online business model changes and unfolding value sources.

  18. The construction of periodic unfolding operators on some compact Riemannian manifolds

    DEFF Research Database (Denmark)

    Dobberschütz, Sören; Böhm, Michael

    2014-01-01

    The notion of periodic unfolding has become a standard tool in the theory of periodic homogenization. However, all the results obtained so far are only applicable to the "flat" Euclidean space R n. In this paper, we present a generalization of the method of periodic unfolding applicable to struct...

  19. The criteria for selecting a method for unfolding neutron spectra based on the information entropy theory

    International Nuclear Information System (INIS)

    Zhu, Qingjun; Song, Fengquan; Ren, Jie; Chen, Xueyong; Zhou, Bin

    2014-01-01

    To further expand the application of an artificial neural network in the field of neutron spectrometry, the criteria for choosing between an artificial neural network and the maximum entropy method for the purpose of unfolding neutron spectra was presented. The counts of the Bonner spheres for IAEA neutron spectra were used as a database, and the artificial neural network and the maximum entropy method were used to unfold neutron spectra; the mean squares of the spectra were defined as the differences between the desired and unfolded spectra. After the information entropy of each spectrum was calculated using information entropy theory, the relationship between the mean squares of the spectra and the information entropy was acquired. Useful information from the information entropy guided the selection of unfolding methods. Due to the importance of the information entropy, the method for predicting the information entropy using the Bonner spheres' counts was established. The criteria based on the information entropy theory can be used to choose between the artificial neural network and the maximum entropy method unfolding methods. The application of an artificial neural network to unfold neutron spectra was expanded. - Highlights: • Two neutron spectra unfolding methods, ANN and MEM, were compared. • The spectrum's entropy offers useful information for selecting unfolding methods. • For the spectrum with low entropy, the ANN was generally better than MEM. • The spectrum's entropy was predicted based on the Bonner spheres' counts

  20. Unfolding Semantics of the Untyped λ-Calculus with lectrec-Calculus with letrec

    NARCIS (Netherlands)

    Rochel, J.

    2016-01-01

    We investigate the relationship between finite terms in lambda-letrec, the lambda calculus with letrec, and the infinite lambda terms they express. We say that a lambda-letrec term expresses a lambda term if the latter can be obtained as an infinite unfolding of the former. Unfolding is the process

  1. Activation of the unfolded protein response during anoxia exposure in the turtle Trachemys scripta elegans.

    Science.gov (United States)

    Krivoruchko, Anastasia; Storey, Kenneth B

    2013-02-01

    Red-eared slider turtles, Trachemys scripta elegans, can survive for several weeks without oxygen when submerged in cold water. We hypothesized that anaerobiosis is aided by adaptive up-regulation of the unfolded protein response (UPR), a stress-responsive pathway that is activated by accumulation of unfolded proteins in the endoplasmic reticulum (ER) and functions to restore ER homeostasis. RT-PCR, western immunoblotting and DNA-binding assays were used to quantify the responses and/or activation status of UPR-responsive genes and proteins in turtle tissues after animal exposure to 5 or 20 h of anoxic submergence at 4 °C. The phosphorylation state of protein kinase-like ER kinase (PERK) (a UPR-regulated kinase) and eukaryotic initiation factor 2 (eIF2α) increased by 1.43-2.50 fold in response to anoxia in turtle heart, kidney, and liver. Activation of the PERK-regulated transcription factor, activating transcription factor 4 (ATF4), during anoxia was documented by elevated atf4 transcripts and total ATF4 protein (1.60-2.43 fold), increased nuclear ATF4 content, and increased DNA-binding activity (1.44-2.32 fold). ATF3 and GADD34 (downstream targets of ATF4) also increased by 1.38-3.32 fold in heart and liver under anoxia, and atf3 transcripts were also elevated in heart. Two characteristic chaperones of the UPR, GRP78, and GRP94, also responded positively to anoxia with strong increases in both the transcript and protein levels. The data demonstrate that the UPR is activated in turtle heart, kidney, and liver in response to anoxia, suggesting that this pathway mediates an integrated stress response to protect tissues during oxygen deprivation.

  2. The unfolded protein response has a protective role in yeast models of classic galactosemia

    Directory of Open Access Journals (Sweden)

    Evandro A. De-Souza

    2014-01-01

    Full Text Available Classic galactosemia is a human autosomal recessive disorder caused by mutations in the GALT gene (GAL7 in yeast, which encodes the enzyme galactose-1-phosphate uridyltransferase. Here we show that the unfolded protein response pathway is triggered by galactose in two yeast models of galactosemia: lithium-treated cells and the gal7Δ mutant. The synthesis of galactose-1-phosphate is essential to trigger the unfolded protein response under these conditions because the deletion of the galactokinase-encoding gene GAL1 completely abolishes unfolded protein response activation and galactose toxicity. Impairment of the unfolded protein response in both yeast models makes cells even more sensitive to galactose, unmasking its cytotoxic effect. These results indicate that endoplasmic reticulum stress is induced under galactosemic conditions and underscores the importance of the unfolded protein response pathway to cellular adaptation in these models of classic galactosemia.

  3. Folding and unfolding pathway of chaperonin GroEL monomer and elucidation of thermodynamic parameters.

    Science.gov (United States)

    Puri, Sarita; Chaudhuri, Tapan K

    2017-03-01

    The conformation and thermodynamic stability of monomeric GroEL were studied by CD and fluorescence spectroscopy. GroEL denaturation with urea and dilution in buffer leads to formation of a folded GroEL monomer. The monomeric nature of this protein was verified by size-exclusion chromatography and native PAGE. It has a well-defined secondary and tertiary structure, folding activity (prevention of aggregation) for substrate protein and is resistant to proteolysis. Being a properly folded and reversibly refoldable, monomeric GroEL is amenable for the study of thermodynamic stability by unfolding transition methods. We present the equilibrium unfolding of monomeric GroEL as studied by urea and heat mediated unfolding processes. The urea mediated unfolding shows two transitions and a single transition in the heat mediated unfolding process. In the case of thermal unfolding, some residual structure unfolds at a higher temperature (70-75°C). The process of folding/unfolding is reversible in both cases. Analysis of folding/unfolding data provides a measure of ΔG NU H 2 O , T m , ΔH van and ΔS van of monomeric GroEL. The thermodynamic stability parameter ΔG NU H 2 O is similar with both CD and intrinsic fluorescence i.e. 7.10±1.0kcal/mol. The calculated T m , ΔH van and ΔS van from the thermal unfolding transition is 46±0.5°C, 43.3±0.1kcal/mol and 143.9±0.1cal/mol/k respectively. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Partial twisting for scalar mesons

    International Nuclear Information System (INIS)

    Agadjanov, Dimitri; Meißner, Ulf-G.; Rusetsky, Akaki

    2014-01-01

    The possibility of imposing partially twisted boundary conditions is investigated for the scalar sector of lattice QCD. According to the commonly shared belief, the presence of quark-antiquark annihilation diagrams in the intermediate state generally hinders the use of the partial twisting. Using effective field theory techniques in a finite volume, and studying the scalar sector of QCD with total isospin I=1, we however demonstrate that partial twisting can still be performed, despite the fact that annihilation diagrams are present. The reason for this are delicate cancellations, which emerge due to the graded symmetry in partially quenched QCD with valence, sea and ghost quarks. The modified Lüscher equation in case of partial twisting is given

  5. Medical Comorbidity of Full and Partial Posttraumatic Stress Disorder in United States Adults: Results from Wave 2 of the National Epidemiologic Survey on Alcohol and Related Conditions

    Science.gov (United States)

    Pietrzak, Robert H.; Goldstein, Risë B.; Southwick, Steven M.; Grant, Bridget F.

    2011-01-01

    Objective This study examined associations between lifetime trauma exposures, PTSD and partial PTSD, and past-year medical conditions in a nationally representative sample of U.S. adults. Methods Face-to-face interviews were conducted with 34,653 participants in the Wave 2 National Epidemiologic Survey on Alcohol and Related Conditions. Logistic regression analyses evaluated associations of trauma exposure, PTSD and partial PTSD with respondent-reported medical diagnoses. Results After adjustment for sociodemographic characteristics and comorbid Axis I and II disorders, respondents with full PTSD were more likely than traumatized respondents without full or partial PTSD (comparison group) to report diagnoses of diabetes mellitus, noncirrhotic liver disease, angina pectoris, tachycardia, hypercholesterolemia, other heart disease, stomach ulcer, HIV seropositivity, gastritis, and arthritis (odds ratios [ORs]=1.2-2.5). Respondents with partial PTSD were more likely than the comparison group to report past-year diagnoses of stomach ulcer, angina pectoris, tachycardia, and arthritis (ORs=1.3-1.6). Men with full and partial PTSD were more likely than controls to report diagnoses of hypertension (both ORs=1.6), and both men and women with PTSD (ORs=1.8 and 1.6, respectively), and men with partial PTSD (OR=2.0) were more likely to report gastritis. Total number of lifetime traumatic event types was associated with many assessed medical conditions (ORs=1.04-1.16), reducing the magnitudes and rendering non-significant some of the associations between PTSD status and medical conditions. Conclusions Greater lifetime trauma exposure and PTSD are associated with numerous medical conditions, many of which are stress-related and chronic, in U.S. adults. Partial PTSD is associated with intermediate odds of some of these conditions. PMID:21949429

  6. Psychiatric Comorbidity of Full and Partial Posttraumatic Stress Disorder among Older Adults in the United States: Results from Wave 2 of the National Epidemiologic Survey on Alcohol and Related Conditions

    Science.gov (United States)

    Pietrzak, Robert H.; Goldstein, Risë B.; Southwick, Steven M.; Grant, Bridget F.

    2011-01-01

    Objectives To present findings on the prevalence, correlates, and psychiatric comorbidity of DSM-IV posttraumatic stress disorder (PTSD) and partial PTSD in a nationally representative sample of U.S. older adults. Design, Setting, and Participants Face-to-face interviews with 9,463 adults aged 60 years and older in the Wave 2 National Epidemiologic Survey on Alcohol and Related Conditions. Measurements Sociodemographic correlates, worst stressful experiences, comorbid lifetime mood, anxiety, substance use, and personality disorders, psychosocial functioning, and suicide attempts. Results Lifetime prevalences±standard errors of PTSD and partial PTSD were 4.5%±0.25 and 5.5%±0.27, respectively. Rates were higher in women (5.7%±0.37 and 6.5%±0.39) than men (3.1%±0.31 and 4.3%±0.37). Older adults with PTSD most frequently identified unexpected death of someone close, serious illness or injury to someone close, and own serious or life-threatening illness as their worst stressful events. Older adults exposed to trauma but without full or partial PTSD and respondents with partial PTSD most often identified unexpected death of someone close, serious illness or injury to someone close, and indirect experience of 9/11 as their worst events. PTSD was associated with elevated odds of lifetime mood, anxiety, drug use, and borderline and narcissistic personality disorders, and decreased psychosocial functioning. Partial PTSD was associated with elevated odds of mood, anxiety, and narcissistic and schizotypal personality disorders, and poorer psychosocial functioning relative to older adults exposed to trauma but without full or partial PTSD. Conclusions PTSD among older adults in the United States is slightly more prevalent than previously reported and associated with considerable psychiatric comorbidity and psychosocial dysfunction. Partial PTSD is associated with significant psychiatric comorbidity, particularly with mood and other anxiety disorders. PMID:22522959

  7. Partial differential equations

    CERN Document Server

    Agranovich, M S

    2002-01-01

    Mark Vishik's Partial Differential Equations seminar held at Moscow State University was one of the world's leading seminars in PDEs for over 40 years. This book celebrates Vishik's eightieth birthday. It comprises new results and survey papers written by many renowned specialists who actively participated over the years in Vishik's seminars. Contributions include original developments and methods in PDEs and related fields, such as mathematical physics, tomography, and symplectic geometry. Papers discuss linear and nonlinear equations, particularly linear elliptic problems in angles and gener

  8. Guanidine hydrochloride denaturation of human serum albumin originates by local unfolding of some stable loops in domain III.

    Science.gov (United States)

    Ahmad, Basir; Ahmed, Md Zulfazal; Haq, Soghra Khatun; Khan, Rizwan Hasan

    2005-06-15

    The effect of guanidine hydrochloride (GnHCl) on the global stability of human serum albumin (HSA) has been studied by fluorescence and circular dichroism spectroscopic measurements. The differential stability of native conformation of three HSA domains were explored by using domain-specific ligands, hemin (domain I), chloroform (domain II), bilirubin (at domain I/domain II interface) and diazepam (domain III). GnHCl induced unfolding transition curves as monitored by probes for secondary and tertiary structures were cooperative but noncoincidental. A strong ANS binding to the protein was observed around 1.8 M GnHCl, suggesting existence of intermediate states in the unfolding pathway of HSA. A gradual decrease (in the GnHCl concentration range 0.0-1.8 M) in the binding of diazepam indicates that domain III is the most labile to GnHCl denaturation. A significant increase in the binding of bilirubin up to 1.4 M GnHCl and decrease thereafter leading to complete abolishment of bilirubin binding at around 2.0 M GnHCl suggest favorable rearrangement and separation of domains I and II at 1.4 and 2.0 M GnHCl concentration, respectively. Above 1.6 M GnHCl, decrease of the binding of hemin, a ligand for domain I, chloroform, which binds in domain II and lone tryptophanyl fluorescence (Trp-214 located in domain II) indicate that at higher concentration of GnHCl domains I and II start unfolding simultaneously but the stability of domain I (7.4 Kcal/mol) is much more than domain II (4.3 Kcal/mol). A pictorial model for the unfolding of HSA domains, consistent with all these results, has been formulated, suggesting that domain III is the most labile followed by domain II while domain I is the most stable. A molten globule like state of domain III around 1.8 M GnHCl has also been identified and characterized.

  9. NSDUAZ unfolding package for neutron spectrometry and dosimetry with Bonner spheres

    Energy Technology Data Exchange (ETDEWEB)

    Vega C, H. R.; Martinez B, M. R. [Universidad Autonoma de Zacatecas, Unidad Academica de Estudios Nucleares, Calle Cipres No. 10, Fracc. La Penuela, 98068 Zacatecas (Mexico); Ortiz R, J. M., E-mail: fermineutron@yahoo.com [Universidad Autonoma de Zacatecas, Unidad Academica de Ingenieria Electrica, Av. Ramon Lopez Velarde 801, Col. Centro, 98000 Zacatecas (Mexico)

    2011-10-15

    NSDUAZ (Neutron Spectrometry and Dosimetry for the Universidad Autonoma de Zacatecas) is a user friendly neutron unfolding package for Bonner sphere spectrometer with {sup 6}Lil(Eu) developed under Lab View environment. Unfolding is carried out using a recursive iterative procedure with the SPUNIT algorithm, where the starting spectrum is obtained from a library initial guess spectrum to start the iterations, the package include a statistical procedure based on the count rates relative to the count rate in the 8 inches-diameter sphere to select the initial spectrum. Neutron spectrum is unfolded in 32 energy groups ranging from 10{sup -8} up to 231.2 MeV. (Author)

  10. Unfolded equations for massive higher spin supermultiplets in AdS{sub 3}

    Energy Technology Data Exchange (ETDEWEB)

    Buchbinder, I.L. [Department of Theoretical Physics, Tomsk State Pedagogical University,60 Kievskaya Str., Tomsk, 634061 (Russian Federation); National Research Tomsk State University,36 Lenina Ave., Tomsk, 634050 (Russian Federation); Snegirev, T.V. [Department of Theoretical Physics, Tomsk State Pedagogical University,60 Kievskaya Str., Tomsk, 634061 (Russian Federation); Department of Higher Mathematics and Mathematical Physics,National Research Tomsk Polytechnic University, 30 Lenina Ave., Tomsk, 634050 (Russian Federation); Zinoviev, Yu.M. [Department of Theoretical Physics,Institute for High Energy Physics of National Research Center “Kurchatov Institute”, 1 Pobedy Str., Protvino, Moscow Region, 142280 (Russian Federation)

    2016-08-10

    In this paper we give an explicit construction of unfolded equations for massive higher spin supermultiplets of the minimal (1,0) supersymmetry in AdS{sub 3} space. For that purpose we use an unfolded formulation for massive bosonic and fermionic higher spins and find supertransformations leaving appropriate set of unfolded equations invariant. We provide two general supermultiplets (s,s+1/2) and (s,s−1/2) with arbitrary integer s, as well as a number of lower spin examples.

  11. Multiscale unfolding of real networks by geometric renormalization

    Science.gov (United States)

    García-Pérez, Guillermo; Boguñá, Marián; Serrano, M. Ángeles

    2018-06-01

    Symmetries in physical theories denote invariance under some transformation, such as self-similarity under a change of scale. The renormalization group provides a powerful framework to study these symmetries, leading to a better understanding of the universal properties of phase transitions. However, the small-world property of complex networks complicates application of the renormalization group by introducing correlations between coexisting scales. Here, we provide a framework for the investigation of complex networks at different resolutions. The approach is based on geometric representations, which have been shown to sustain network navigability and to reveal the mechanisms that govern network structure and evolution. We define a geometric renormalization group for networks by embedding them into an underlying hidden metric space. We find that real scale-free networks show geometric scaling under this renormalization group transformation. We unfold the networks in a self-similar multilayer shell that distinguishes the coexisting scales and their interactions. This in turn offers a basis for exploring critical phenomena and universality in complex networks. It also affords us immediate practical applications, including high-fidelity smaller-scale replicas of large networks and a multiscale navigation protocol in hyperbolic space, which betters those on single layers.

  12. Effects of ubiquilin 1 on the unfolded protein response.

    Science.gov (United States)

    Lu, Alice; Hiltunen, Mikko; Romano, Donna M; Soininen, Hilkka; Hyman, Bradley T; Bertram, Lars; Tanzi, Rudolph E

    2009-05-01

    Previous studies have implicated the unfolded protein response (UPR) in the pathogenesis of Alzheimer's disease (AD). We previously reported that DNA variants in the ubiquilin 1 (UBQLN1) gene increase the risk for AD. Since UBQLN1 has been shown to play a role in the UPR, we assessed the effects of overexpression and downregulation of UBQLN1 splice variants during tunicamycin-induced ER stress. In addition to previously described transcript variants, TV1 and TV2, we identified two novel transcript variants of UBQLN1 in brain: TV3 (lacking exons 2-4) and TV4 (lacking exon 4). Overexpression of TV1-3, but not TV4 significantly decreased the mRNA induction of UPR-inducible genes, C/EBP homologous protein (CHOP), BiP/GRP78, and protein disulfide isomerase (PDI) during the UPR. Stable overexpression of TV1-3, but not TV4, also significantly decreased the induction of CHOP protein and increased cell viability during the UPR. In contrast, downregulation of UBQLN1 did not affect CHOP mRNA induction, but instead increased PDI mRNA levels. These findings suggest that overexpression UBQLN1 transcript variants TV1-3, but not TV4, exert a protective effect during the UPR by attenuating CHOP induction and potentially increasing cell viability.

  13. An Expansion Method to Unfold Proton Recoil Spectra

    Energy Technology Data Exchange (ETDEWEB)

    Kockum, J

    1970-07-01

    A method is given to obtain a good estimate of the input neutron spectrum from a pulse-height distribution measured with proportional counters filled with a hydrogenous gas. The method consists of expanding the sought estimate as a product of two functions where one is obtained by differentiating the pulse-height distribution and the other is a power series of the neutron energy. The coefficients of this series are determined by a least-squares fit of the calculated pulse-height distribution to the measured one. The method has been tested on pulse-height distributions obtained by calculations from a realistic neutron spectrum and response functions for a spherical counter 3. 94 cm in diameter and filled with 7 atm. of methane and 1 atm. of hydrogen, respectively. In the former case it is possible with the method described, to unfold pulse-height distributions up to a neutron energy of about 3 MeV to within 10 % of the input spectrum. The differentiating procedure included in the method ensures that all spectral details not smoothed out by the finite resolution of the counter, are kept in the spectrum estimate. A realistic estimate of the statistical uncertainty of each neutron spectrum value is given. Some of the possible systematical errors caused by uncertainties in input data have been investigated.

  14. Endoplasmic Reticulum Stress, Unfolded Protein Response, and Cancer Cell Fate

    Directory of Open Access Journals (Sweden)

    Marco Corazzari

    2017-04-01

    Full Text Available Perturbation of endoplasmic reticulum (ER homeostasis results in a stress condition termed “ER stress” determining the activation of a finely regulated program defined as unfolded protein response (UPR and whose primary aim is to restore this organelle’s physiological activity. Several physiological and pathological stimuli deregulate normal ER activity causing UPR activation, such as hypoxia, glucose shortage, genome instability, and cytotoxic compounds administration. Some of these stimuli are frequently observed during uncontrolled proliferation of transformed cells, resulting in tumor core formation and stage progression. Therefore, it is not surprising that ER stress is usually induced during solid tumor development and stage progression, becoming an hallmark of such malignancies. Several UPR components are in fact deregulated in different tumor types, and accumulating data indicate their active involvement in tumor development/progression. However, although the UPR program is primarily a pro-survival process, sustained and/or prolonged stress may result in cell death induction. Therefore, understanding the mechanism(s regulating the cell survival/death decision under ER stress condition may be crucial in order to specifically target tumor cells and possibly circumvent or overcome tumor resistance to therapies. In this review, we discuss the role played by the UPR program in tumor initiation, progression and resistance to therapy, highlighting the recent advances that have improved our understanding of the molecular mechanisms that regulate the survival/death switch.

  15. The Myocardial Unfolded Protein Response during Ischemic Cardiovascular Disease

    Directory of Open Access Journals (Sweden)

    Edward B. Thorp

    2012-01-01

    Full Text Available Heart failure is a progressive and disabling disease. The incidence of heart failure is also on the rise, particularly in the elderly of industrialized societies. This is in part due to an increased ageing population, whom initially benefits from improved, and life-extending cardiovascular therapy, yet ultimately succumb to myocardial failure. A major cause of heart failure is ischemia secondary to the sequence of events that is dyslipidemia, atherosclerosis, and myocardial infarction. In the case of heart failure postmyocardial infarction, ischemia can lead to myocardial cell death by both necrosis and apoptosis. The extent of myocyte death postinfarction is associated with adverse cardiac remodeling that can contribute to progressive heart chamber dilation, ventricular wall thinning, and the onset of loss of cardiac function. In cardiomyocytes, recent studies indicate that myocardial ischemic injury activates the unfolded protein stress response (UPR and this is associated with increased apoptosis. This paper focuses on the intersection of ischemia, the UPR, and cell death in cardiomyocytes. Targeting of the myocardial UPR may prove to be a viable target for the prevention of myocyte cell loss and the progression of heart failure due to ischemic injury.

  16. Unfolded protein response in filamentous fungi-implications in biotechnology.

    Science.gov (United States)

    Heimel, Kai

    2015-01-01

    The unfolded protein response (UPR) represents a mechanism to preserve endoplasmic reticulum (ER) homeostasis that is conserved in eukaryotes. ER stress caused by the accumulation of potentially toxic un- or misfolded proteins in the ER triggers UPR activation and the induction of genes important for protein folding in the ER, ER expansion, and transport from and to the ER. Along with this adaptation, the overall capacity for protein secretion is markedly increased by the UPR. In filamentous fungi, various approaches to employ the UPR for improved production of homologous and heterologous proteins have been investigated. As the effects on protein production were strongly dependent on the expressed protein, generally applicable strategies have to be developed. A combination of transcriptomic approaches monitoring secretion stress and basic research on the UPR mechanism provided novel and important insight into the complex regulatory cross-connections between UPR signalling, cellular physiology, and developmental processes. It will be discussed how this increasing knowledge on the UPR might stimulate the development of novel strategies for using the UPR as a tool in biotechnology.

  17. Resolution unfolding with limits imposed by statistical experimental errors

    International Nuclear Information System (INIS)

    Lang, D.W.

    1977-02-01

    A typical form of the resolution equation is derived by considering the physical measurement of an energy dependent spectrum. It is shown that the information contained in a data set may be expressed by writing the spectrum as a linear combination of a set of resolution functions. Introduction of other functions to describe the spectrum involves extra physical information. An iterative conjugate gradient technique to obtain a spectrum consistent with the data is described. At each iteration the residual discrepancy between the currently predicted yield and the measured data is used to generate the form and mangitude of the next term to be added to the spectrum. Other unfolding techniques are described and analysed, some faster than the conjugate gradient technique in special cases, but restricted in usefulness by implicit assumptions about the resolution functions. The nature of residual errors is considered. The variations of independently measured data sets are discussed, and hence, the variations of the sequence of terms appearing in a consequent conjugate gradient analysis. An approximate measure is obtained for the expected variation of independently obtained spectra. Refinements are briefly considered which apply to a resolution function that is not known precisely or which make use of a requirement that the spectrum be positive throughout its range. It is concluded that a conjugate gradient technique is best if sufficient computer facilities are available, and that, of the less demanding techniques, the best is one that is essentially a more slowly convergent version of a conjugate gradient method. (author)

  18. The unfolded protein response is required for dendrite morphogenesis

    Science.gov (United States)

    Wei, Xing; Howell, Audrey S; Dong, Xintong; Taylor, Caitlin A; Cooper, Roshni C; Zhang, Jianqi; Zou, Wei; Sherwood, David R; Shen, Kang

    2015-01-01

    Precise patterning of dendritic fields is essential for the formation and function of neuronal circuits. During development, dendrites acquire their morphology by exuberant branching. How neurons cope with the increased load of protein production required for this rapid growth is poorly understood. Here we show that the physiological unfolded protein response (UPR) is induced in the highly branched Caenorhabditis elegans sensory neuron PVD during dendrite morphogenesis. Perturbation of the IRE1 arm of the UPR pathway causes loss of dendritic branches, a phenotype that can be rescued by overexpression of the ER chaperone HSP-4 (a homolog of mammalian BiP/ grp78). Surprisingly, a single transmembrane leucine-rich repeat protein, DMA-1, plays a major role in the induction of the UPR and the dendritic phenotype in the UPR mutants. These findings reveal a significant role for the physiological UPR in the maintenance of ER homeostasis during morphogenesis of large dendritic arbors. DOI: http://dx.doi.org/10.7554/eLife.06963.001 PMID:26052671

  19. The Unfolded Protein Response in Amelogenesis and Enamel Pathologies

    Directory of Open Access Journals (Sweden)

    Steven J. Brookes

    2017-09-01

    Full Text Available During the secretory phase of their life-cycle, ameloblasts are highly specialized secretory cells whose role is to elaborate an extracellular matrix that ultimately confers both form and function to dental enamel, the most highly mineralized of all mammalian tissues. In common with many other “professional” secretory cells, ameloblasts employ the unfolded protein response (UPR to help them cope with the large secretory cargo of extracellular matrix proteins transiting their ER (endoplasmic reticulum/Golgi complex and so minimize ER stress. However, the UPR is a double-edged sword, and, in cases where ER stress is severe and prolonged, the UPR switches from pro-survival to pro-apoptotic mode. The purpose of this review is to consider the role of the ameloblast UPR in the biology and pathology of amelogenesis; specifically in respect of amelogenesis imperfecta (AI and fluorosis. Some forms of AI appear to correspond to classic proteopathies, where pathological intra-cellular accumulations of protein tip the UPR toward apoptosis. Fluorosis also involves the UPR and, while not of itself a classic proteopathic disease, shares some common elements through the involvement of the UPR. The possibility of therapeutic intervention by pharmacological modulation of the UPR in AI and fluorosis is also discussed.

  20. The Unfolded Protein Response in Amelogenesis and Enamel Pathologies.

    Science.gov (United States)

    Brookes, Steven J; Barron, Martin J; Dixon, Michael J; Kirkham, Jennifer

    2017-01-01

    During the secretory phase of their life-cycle, ameloblasts are highly specialized secretory cells whose role is to elaborate an extracellular matrix that ultimately confers both form and function to dental enamel, the most highly mineralized of all mammalian tissues. In common with many other "professional" secretory cells, ameloblasts employ the unfolded protein response (UPR) to help them cope with the large secretory cargo of extracellular matrix proteins transiting their ER (endoplasmic reticulum)/Golgi complex and so minimize ER stress. However, the UPR is a double-edged sword, and, in cases where ER stress is severe and prolonged, the UPR switches from pro-survival to pro-apoptotic mode. The purpose of this review is to consider the role of the ameloblast UPR in the biology and pathology of amelogenesis; specifically in respect of amelogenesis imperfecta (AI) and fluorosis. Some forms of AI appear to correspond to classic proteopathies, where pathological intra-cellular accumulations of protein tip the UPR toward apoptosis. Fluorosis also involves the UPR and, while not of itself a classic proteopathic disease, shares some common elements through the involvement of the UPR. The possibility of therapeutic intervention by pharmacological modulation of the UPR in AI and fluorosis is also discussed.

  1. Partial Transposition on Bipartite System

    International Nuclear Information System (INIS)

    Xi-Jun, Ren; Yong-Jian, Han; Yu-Chun, Wu; Guang-Can, Guo

    2008-01-01

    Many properties of partial transposition are unclear as yet. Here we carefully consider the number of the negative eigenvalues of ρ T (ρ's partial transposition) when ρ is a two-partite state. There is strong evidence to show that the number of negative eigenvalues of ρ T is N(N − 1)/2 at most when ρ is a state in Hilbert space C N C N . For the special case, the 2 × 2 system, we use this result to give a partial proof of the conjecture |ρ T | T ≥ 0. We find that this conjecture is strongly connected with the entanglement of the state corresponding to the negative eigenvalue of ρ T or the negative entropy of ρ

  2. Action adaptation during natural unfolding social scenes influences action recognition and inferences made about actor beliefs.

    Science.gov (United States)

    Keefe, Bruce D; Wincenciak, Joanna; Jellema, Tjeerd; Ward, James W; Barraclough, Nick E

    2016-07-01

    When observing another individual's actions, we can both recognize their actions and infer their beliefs concerning the physical and social environment. The extent to which visual adaptation influences action recognition and conceptually later stages of processing involved in deriving the belief state of the actor remains unknown. To explore this we used virtual reality (life-size photorealistic actors presented in stereoscopic three dimensions) to see how visual adaptation influences the perception of individuals in naturally unfolding social scenes at increasingly higher levels of action understanding. We presented scenes in which one actor picked up boxes (of varying number and weight), after which a second actor picked up a single box. Adaptation to the first actor's behavior systematically changed perception of the second actor. Aftereffects increased with the duration of the first actor's behavior, declined exponentially over time, and were independent of view direction. Inferences about the second actor's expectation of box weight were also distorted by adaptation to the first actor. Distortions in action recognition and actor expectations did not, however, extend across different actions, indicating that adaptation is not acting at an action-independent abstract level but rather at an action-dependent level. We conclude that although adaptation influences more complex inferences about belief states of individuals, this is likely to be a result of adaptation at an earlier action recognition stage rather than adaptation operating at a higher, more abstract level in mentalizing or simulation systems.

  3. Spontaneous Unfolding-Refolding of Fibronectin Type III Domains Assayed by Thiol Exchange: THERMODYNAMIC STABILITY CORRELATES WITH RATES OF UNFOLDING RATHER THAN FOLDING.

    Science.gov (United States)

    Shah, Riddhi; Ohashi, Tomoo; Erickson, Harold P; Oas, Terrence G

    2017-01-20

    Globular proteins are not permanently folded but spontaneously unfold and refold on time scales that can span orders of magnitude for different proteins. A longstanding debate in the protein-folding field is whether unfolding rates or folding rates correlate to the stability of a protein. In the present study, we have determined the unfolding and folding kinetics of 10 FNIII domains. FNIII domains are one of the most common protein folds and are present in 2% of animal proteins. FNIII domains are ideal for this study because they have an identical seven-strand β-sandwich structure, but they vary widely in sequence and thermodynamic stability. We assayed thermodynamic stability of each domain by equilibrium denaturation in urea. We then assayed the kinetics of domain opening and closing by a technique known as thiol exchange. For this we introduced a buried Cys at the identical location in each FNIII domain and measured the kinetics of labeling with DTNB over a range of urea concentrations. A global fit of the kinetics data gave the kinetics of spontaneous unfolding and refolding in zero urea. We found that the folding rates were relatively similar, ∼0.1-1 s -1 , for the different domains. The unfolding rates varied widely and correlated with thermodynamic stability. Our study is the first to address this question using a set of domains that are structurally homologous but evolved with widely varying sequence identity and thermodynamic stability. These data add new evidence that thermodynamic stability correlates primarily with unfolding rate rather than folding rate. The study also has implications for the question of whether opening of FNIII domains contributes to the stretching of fibronectin matrix fibrils. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  4. Moessbauer spectroscopic evidence on the heme binding to the proximal histidine in unfolded carbonmonoxy myoglobin by guanidine hydrochloride

    Energy Technology Data Exchange (ETDEWEB)

    Harami, Taikan, E-mail: harami.taikan@jaea.go.jp [Japan Atomic Energy Agency (Japan); Kitao, Shinji; Kobayashi, Yasuhiro [Kyoto University, Research Reactor Institute (Japan); Mitsui, Takaya [Japan Atomic Energy Agency (Japan)

    2008-01-15

    The unfolded heme structure in myoglobin is controversial because of no chance of direct X-ray structure analyses. The unfolding of carbonmonoxy myoglobin (MbCO) by guanidine hydrochloride (GdnHCl) was studied by the Moessbauer spectroscopy. The spectra show the presence of a sort of spectrum in the unfolded MbCO, independent on the concentration of GdnHCl from 1 to 6 M and the increase of the fraction of unfolded MbCO, depending on the GdnHCl concentration. The isomer shift of the iron of heme in the unfolded MbCO was identified to be different from that of the native MbCO as the globin structure in Mb collapses under the unfolded conditions. This result and the existing related Moessbauer data proved that the heme in the unfolded MbCO may remain coordinated to the proximal histidine.

  5. Physics of partially ionized plasmas

    CERN Document Server

    Krishan, Vinod

    2016-01-01

    Plasma is one of the four fundamental states of matter; the other three being solid, liquid and gas. Several components, such as molecular clouds, diffuse interstellar gas, the solar atmosphere, the Earth's ionosphere and laboratory plasmas, including fusion plasmas, constitute the partially ionized plasmas. This book discusses different aspects of partially ionized plasmas including multi-fluid description, equilibrium and types of waves. The discussion goes on to cover the reionization phase of the universe, along with a brief description of high discharge plasmas, tokomak plasmas and laser plasmas. Various elastic and inelastic collisions amongst the three particle species are also presented. In addition, the author demonstrates the novelty of partially ionized plasmas using many examples; for instance, in partially ionized plasma the magnetic induction is subjected to the ambipolar diffusion and the Hall effect, as well as the usual resistive dissipation. Also included is an observation of kinematic dynam...

  6. BONDI-97 A novel neutron energy spectrum unfolding tool using a genetic algorithm

    CERN Document Server

    Mukherjee, B

    1999-01-01

    The neutron spectrum unfolding procedure using the count rate data obtained from a set of Bonner sphere neutron detectors requires the solution of the Fredholm integral equation of the first kind by using complex mathematical methods. This paper reports a new approach for the unfolding of neutron spectra using the Genetic Algorithm tool BONDI-97 (BOnner sphere Neutron DIfferentiation). The BONDI-97 was used as the input for Genetic Algorithm engine EVOLVER to search for a globally optimised solution vector from a population of randomly generated solutions. This solution vector corresponds to the unfolded neutron energy spectrum. The Genetic Algorithm engine emulates the Darwinian 'Survival of the Fittest' strategy, the key ingredient of the 'Theory of Evolution'. The spectra of sup 2 sup 4 sup 1 Am/Be (alpha,n) and sup 2 sup 3 sup 9 Pu/Be (alpha,n) neutron sources were unfolded using the BONDI-97 tool. (author)

  7. Genetic algorithms - A new technique for solving the neutron spectrum unfolding problem

    International Nuclear Information System (INIS)

    Freeman, David W.; Edwards, D. Ray; Bolon, Albert E.

    1999-01-01

    A new technique utilizing genetic algorithms has been applied to the Bonner sphere neutron spectrum unfolding problem. Genetic algorithms are part of a relatively new field of 'evolutionary' solution techniques that mimic living systems with computer-simulated 'chromosome' solutions. Solutions mate and mutate to create better solutions. Several benchmark problems, considered representative of radiation protection environments, have been evaluated using the newly developed UMRGA code which implements the genetic algorithm unfolding technique. The results are compared with results from other well-established unfolding codes. The genetic algorithm technique works remarkably well and produces solutions with relatively high spectral qualities. UMRGA appears to be a superior technique in the absence of a priori data - it does not rely on 'lucky' guesses of input spectra. Calculated personnel doses associated with the unfolded spectra match benchmark values within a few percent

  8. Inter-regulation of the unfolded protein response and auxin signaling

    Czech Academy of Sciences Publication Activity Database

    Chen, Y.N.; Aung, K.; Rolčík, Jakub; Walicki, K.; Friml, J.; Brandizzi, F.

    2014-01-01

    Roč. 77, č. 1 (2014), s. 97-107 ISSN 0960-7412 Institutional support: RVO:61389030 Keywords : endoplasmic reticulum stress * unfolded protein response * auxin response Subject RIV: ED - Physiology Impact factor: 5.972, year: 2014

  9. Protein unfolding versus β-sheet separation in spider silk nanocrystals

    International Nuclear Information System (INIS)

    Alam, Parvez

    2014-01-01

    In this communication a mechanism for spider silk strain hardening is proposed. Shear failure of β-sheet nanocrystals is the first failure mode that gives rise to the creation of smaller nanocrystals, which are of higher strength and stiffness. β-sheet unfolding requires more energy than nanocrystal separation in a shear mode of failure. As a result, unfolding occurs after the nanocrystals separate in shear. β-sheet unfolding yields a secondary strain hardening effect once the β-sheet conformation is geometrically stable and acts like a unidirectional fibre in a fibre reinforced composite. The mechanism suggested herein is based on molecular dynamics calculations of residual inter-β-sheet separation strengths against residual intra-β-sheet unfolding strengths. (paper)

  10. Partial wave analysis of the reaction p(3.5 GeV) + p -> pK(+) Lambda to search for the "ppK(-)" bound state

    Czech Academy of Sciences Publication Activity Database

    Agakishiev, G.; Arnold, O.; Belver, D.; Belyaev, A.; Krása, Antonín; Křížek, Filip; Kugler, Andrej; Sobolev, Yuri, G.; Tlustý, Pavel; Wagner, Vladimír

    2015-01-01

    Roč. 742, MAR (2015), s. 242-248 ISSN 0370-2693 R&D Projects: GA MŠk LG12007; GA ČR GA13-06759S Institutional support: RVO:61389005 Keywords : kaonic nuclei * anti-kaon-nucleon physics * ppK(-) * low energy * QCD * partial wave analysis Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders Impact factor: 4.787, year: 2015

  11. Long-term dynamic and pseudo-state modeling of complete partial nitrification process at high nitrogen loading rates in a sequential batch reactor (SBR).

    Science.gov (United States)

    Soliman, Moomen; Eldyasti, Ahmed

    2017-06-01

    Recently, partial nitrification has been adopted widely either for the nitrite shunt process or intermediate nitrite generation step for the Anammox process. However, partial nitrification has been hindered by the complexity of maintaining stable nitrite accumulation at high nitrogen loading rates (NLR) which affect the feasibility of the process for high nitrogen content wastewater. Thus, the operational data of a lab scale SBR performing complete partial nitrification as a first step of nitrite shunt process at NLRs of 0.3-1.2kg/(m 3 d) have been used to calibrate and validate a process model developed using BioWin® in order to describe the long-term dynamic behavior of the SBR. Moreover, an identifiability analysis step has been introduced to the calibration protocol to eliminate the needs of the respirometric analysis for SBR models. The calibrated model was able to predict accurately the daily effluent ammonia, nitrate, nitrite, alkalinity concentrations and pH during all different operational conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Antiviral activity of a small molecule deubiquitinase inhibitor occurs via induction of the unfolded protein response.

    Directory of Open Access Journals (Sweden)

    Jeffrey W Perry

    Full Text Available Ubiquitin (Ub is a vital regulatory component in various cellular processes, including cellular responses to viral infection. As obligate intracellular pathogens, viruses have the capacity to manipulate the ubiquitin (Ub cycle to their advantage by encoding Ub-modifying proteins including deubiquitinases (DUBs. However, how cellular DUBs modulate specific viral infections, such as norovirus, is poorly understood. To examine the role of DUBs during norovirus infection, we used WP1130, a small molecule inhibitor of a subset of cellular DUBs. Replication of murine norovirus in murine macrophages and the human norovirus Norwalk virus in a replicon system were significantly inhibited by WP1130. Chemical proteomics identified the cellular DUB USP14 as a target of WP1130 in murine macrophages, and pharmacologic inhibition or siRNA-mediated knockdown of USP14 inhibited murine norovirus infection. USP14 is a proteasome-associated DUB that also binds to inositol-requiring enzyme 1 (IRE1, a critical mediator of the unfolded protein response (UPR. WP1130 treatment of murine macrophages did not alter proteasome activity but activated the X-box binding protein-1 (XBP-1 through an IRE1-dependent mechanism. In addition, WP1130 treatment or induction of the UPR also reduced infection of other RNA viruses including encephalomyocarditis virus, Sindbis virus, and La Crosse virus but not vesicular stomatitis virus. Pharmacologic inhibition of the IRE1 endonuclease activity partially rescued the antiviral effect of WP1130. Taken together, our studies support a model whereby induction of the UPR through cellular DUB inhibition blocks specific viral infections, and suggest that cellular DUBs and the UPR represent novel targets for future development of broad spectrum antiviral therapies.

  13. Cigarette smoke induces an unfolded protein response in the human lung: a proteomic approach.

    Science.gov (United States)

    Kelsen, Steven G; Duan, Xunbao; Ji, Rong; Perez, Oscar; Liu, Chunli; Merali, Salim

    2008-05-01

    Cigarette smoking, which exposes the lung to high concentrations of reactive oxidant species (ROS) is the major risk factor for chronic obstructive pulmonary disease (COPD). Recent studies indicate that ROS interfere with protein folding in the endoplasmic reticulum and elicit a compensatory response termed the "unfolded protein response" (UPR). The importance of the UPR lies in its ability to alter expression of a variety of genes involved in antioxidant defense, inflammation, energy metabolism, protein synthesis, apoptosis, and cell cycle regulation. The present study used comparative proteomic technology to test the hypothesis that chronic cigarette smoking induces a UPR in the human lung. Studies were performed on lung tissue samples obtained from three groups of human subjects: nonsmokers, chronic cigarette smokers, and ex-smokers. Proteomes of lung samples from chronic cigarette smokers demonstrated 26 differentially expressed proteins (20 were up-regulated, 5 were down-regulated, and 1 was detected only in the smoking group) compared with nonsmokers. Several UPR proteins were up-regulated in smokers compared with nonsmokers and ex-smokers, including the chaperones, glucose-regulated protein 78 (GRP78) and calreticulin; a foldase, protein disulfide isomerase (PDI); and enzymes involved in antioxidant defense. In cultured human airway epithelial cells, GRP78 and the UPR-regulated basic leucine zipper, transcription factors, ATF4 and Nrf2, which enhance expression of important anti-oxidant genes, increased rapidly (< 24 h) with cigarette smoke extract. These data indicate that cigarette smoke induces a UPR response in the human lung that is rapid in onset, concentration dependent, and at least partially reversible with smoking cessation. We speculate that activation of a UPR by cigarette smoke may protect the lung from oxidant injury and the development of COPD.

  14. Ethanol cellular defense induce unfolded protein response in yeast

    Directory of Open Access Journals (Sweden)

    Elisabet eNavarro-Tapia

    2016-02-01

    Full Text Available Ethanol is a valuable industrial product and a common metabolite used by many cell types. However, this molecule produces high levels of cytotoxicity affecting cellular performance at several levels. In the presence of ethanol, cells must adjust some of their components, such as the membrane lipids to maintain homeostasis. In the case of microorganism as Saccharomyces cerevisiae, ethanol is one of the principal products of their metabolism and is the main stress factor during fermentation. Although many efforts have been made, mechanisms of ethanol tolerance are not fully understood and very little evidence is available to date for specific signaling by ethanol in the cell. This work studied two Saccharomyces cerevisiae strains, CECT10094 and Temohaya-MI26, isolated from flor wine and agave fermentation (a traditional fermentation from Mexico respectively, which differ in ethanol tolerance, in order to understand the molecular mechanisms underlying the ethanol stress response and the reasons for different ethanol tolerance. The transcriptome was analyzed after ethanol stress and, among others, an increased activation of genes related with the unfolded protein response (UPR and its transcription factor, Hac1p, was observed in the tolerant strain CECT10094. We observed that this strain also resist more UPR agents than Temohaya-MI26 and the UPR-ethanol stress correlation was corroborated observing growth of 15 more strains and discarding UPR correlation with other stresses as thermal or oxidative stress. Furthermore, higher activation of UPR pathway in the tolerant strain CECT10094 was observed using a UPR mCherry reporter. Finally, we observed UPR activation in response to ethanol stress in other S. cerevisiae ethanol tolerant strains as the wine strains T73 and EC1118. This work demonstrates that the UPR pathway is activated under ethanol stress occurring in a standard fermentation and links this response to an enhanced ethanol tolerance. Thus

  15. Application of LEPRICON methodology to the unfolding of neutron fluxes in the Arkansas Nuclear One-Unit 1 reactor

    International Nuclear Information System (INIS)

    Maerker, R.E.; Broadhead, B.L.; Williams, M.L.

    1985-01-01

    The LEPRICON (Least-squares EPRI CONsolidation) methodology has been gradually developed over the past few years. The system predicts the absolute neutron fluence levels as a function of energy at specified locations within the pressure vessel of an LWR from the analysis of dosimetry measurements performed at some other readily accessible surveillance location(s). LEPRICON is unique in the field of few-group spectral unfolding in that (1) it solves the extrapolation problem necessitated by the ex-situ measurements; (2) it has the capability of simultaneously unfolding a large number of spectral fluences; (3) it has the capability of simultaneously analyzing a series of benchmark experiments, along with measurements performed in an LWR; (4) it provides state-of-the-art methods for calculating the surveillance dosimeter activities and pressure vessel spectral fluences; (5) it incorporates the basic sensitivity and covariance information necessary for estimates of the uncertainties in the original calculated quantities; and (6) it produces adjustments to the calculated quantities with uncertainties that can be significantly reduced from the original values

  16. Novel insights into the unfolded protein response using Pichia pastoris specific DNA microarrays

    Directory of Open Access Journals (Sweden)

    Kreil David P

    2008-08-01

    Full Text Available Abstract Background DNA Microarrays are regarded as a valuable tool for basic and applied research in microbiology. However, for many industrially important microorganisms the lack of commercially available microarrays still hampers physiological research. Exemplarily, our understanding of protein folding and secretion in the yeast Pichia pastoris is presently widely dependent on conclusions drawn from analogies to Saccharomyces cerevisiae. To close this gap for a yeast species employed for its high capacity to produce heterologous proteins, we developed full genome DNA microarrays for P. pastoris and analyzed the unfolded protein response (UPR in this yeast species, as compared to S. cerevisiae. Results By combining the partially annotated gene list of P. pastoris with de novo gene finding a list of putative open reading frames was generated for which an oligonucleotide probe set was designed using the probe design tool TherMODO (a thermodynamic model-based oligoset design optimizer. To evaluate the performance of the novel array design, microarrays carrying the oligo set were hybridized with samples from treatments with dithiothreitol (DTT or a strain overexpressing the UPR transcription factor HAC1, both compared with a wild type strain in normal medium as untreated control. DTT treatment was compared with literature data for S. cerevisiae, and revealed similarities, but also important differences between the two yeast species. Overexpression of HAC1, the most direct control for UPR genes, resulted in significant new understanding of this important regulatory pathway in P. pastoris, and generally in yeasts. Conclusion The differences observed between P. pastoris and S. cerevisiae underline the importance of DNA microarrays for industrial production strains. P. pastoris reacts to DTT treatment mainly by the regulation of genes related to chemical stimulus, electron transport and respiration, while the overexpression of HAC1 induced many genes

  17. Alpha-fetoprotein is a biomarker of unfolded protein response and altered proteostasis in hepatocellular carcinoma cells exposed to sorafenib.

    Science.gov (United States)

    Houessinon, Aline; Gicquel, Albane; Bochereau, Flora; Louandre, Christophe; Nyga, Rémy; Godin, Corinne; Degonville, James; Fournier, Emma; Saidak, Zuzana; Drullion, Claire; Barbare, Jean-Claude; Chauffert, Bruno; François, Catherine; Pluquet, Olivier; Galmiche, Antoine

    2016-01-28

    Sorafenib is the treatment of reference for advanced hepatocellular carcinoma (HCC). A decrease in the serum levels of Alpha-fetoprotein (AFP) is reported to be the biological parameter that is best associated with disease control by sorafenib. In order to provide a biological rationale for the variations of AFP, we analyzed the various steps of AFP production in human HCC cell lines exposed to sorafenib. Sorafenib dramatically reduced the levels of AFP produced by HCC cells independently of its effect on cell viability. The mRNA levels of AFP decreased upon sorafenib treatment, while the AFP protein remained localized in the Golgi apparatus. Sorafenib activated the Regulated Inositol-Requiring Enzyme-1α (IRE-1α) and the PKR-like ER Kinase (PERK)-dependent arms of the Unfolded Protein Response (UPR). The inhibition of IRE-1α partially restored the mRNA levels of AFP upon treatment with sorafenib. The inhibition of both pathways partially prevented the drop in the production of AFP induced by sorafenib. The findings provide new insights on the regulation of AFP, and identify it as a biomarker suitable for the exploration of HCC cell proteostasis in the context of therapeutic targeting. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  18. Spectroscopic and MD simulation studies on unfolding processes of mitochondrial carbonic anhydrase VA induced by urea.

    Science.gov (United States)

    Idrees, Danish; Prakash, Amresh; Haque, Md Anzarul; Islam, Asimul; Ahmad, Faizan; Hassan, Md Imtaiyaz

    2016-09-01

    Carbonic anhydrase VA (CAVA) is primarily expressed in the mitochondria and involved in numerous physiological processes including lipogenesis, insulin secretion from pancreatic cells, ureagenesis, gluconeogenesis and neuronal transmission. To understand the biophysical properties of CAVA, we carried out a reversible urea-induced isothermal denaturation at pH 7.0 and 25°C. Spectroscopic probes, [θ]222 (mean residue ellipticity at 222 nm), F344 (Trp-fluorescence emission intensity at 344 nm) and Δε280 (difference absorption at 280 nm) were used to monitor the effect of urea on the structure and stability of CAVA. The urea-induced reversible denaturation curves were used to estimate [Formula: see text], Gibbs free energy in the absence of urea; Cm, the mid-point of the denaturation curve, i.e. molar urea concentration ([urea]) at which ΔGD = 0; and m, the slope (=∂ΔGD/∂[urea]). Coincidence of normalized transition curves of all optical properties suggests that unfolding/refolding of CAVA is a two-state process. We further performed 40 ns molecular dynamics simulation of CAVA to see the dynamics at different urea concentrations. An excellent agreement was observed between in silico and in vitro studies.

  19. Unfolding Studies of the Cysteine Protease Baupain, a Papain-Like Enzyme from Leaves of Bauhinia forficata: Effect of pH, Guanidine Hydrochloride and Temperature

    Directory of Open Access Journals (Sweden)

    Rosemeire A. Silva-Lucca

    2013-12-01

    Full Text Available Baupain belongs to the α+β class of proteins with a secondary structure-content of 44% α-helix, 16% β-sheet and 12% β-turn. The structural transition induced by pH was found to be noncooperative, with no important differences observed in the pH range from 3.0 to 10.5. At pH 2.0 the protein presented substantial non-native structure with strong ANS binding. Guanidine hydrochloride (GdnHCl-induced unfolding did not change the protein structure significantly until 4.0 M, indicating the high rigidity of the molecule. The unfolding was cooperative, as seen by the sigmoidal transition curves with midpoints at 4.7 ± 0.2 M and 5.0 ± 0.2 M GdnHCl, as measured by CD and fluorescence spectroscopy. A red shift of 7 nm in intrinsic fluorescence was observed with 6.0 M GdnHCl. Temperature-induced unfolding of baupain was incomplete, and at least 35% of the native structure of the protein was retained, even at high temperature (90 °C. Baupain showed characteristics of a molten globule state, due to preferential ANS binding at pH 2.0 in comparison to the native form (pH 7.0 and completely unfolded (6.0 M GdnHCl state. Combined with information about N-terminal sequence similarity, these results allow us to include baupain in the papain superfamily.

  20. Unfolding studies of the cysteine protease baupain, a papain-like enzyme from leaves of Bauhinia forficata: effect of pH, guanidine hydrochloride and temperature.

    Science.gov (United States)

    Silva-Lucca, Rosemeire A; Andrade, Sheila S; Ferreira, Rodrigo Silva; Sampaio, Misako U; Oliva, Maria Luiza V

    2013-12-24

    Baupain belongs to the α+β class of proteins with a secondary structure-content of 44% α-helix, 16% β-sheet and 12% β-turn. The structural transition induced by pH was found to be noncooperative, with no important differences observed in the pH range from 3.0 to 10.5. At pH 2.0 the protein presented substantial non-native structure with strong ANS binding. Guanidine hydrochloride (GdnHCl)-induced unfolding did not change the protein structure significantly until 4.0 M, indicating the high rigidity of the molecule. The unfolding was cooperative, as seen by the sigmoidal transition curves with midpoints at 4.7±0.2 M and 5.0±0.2 M GdnHCl, as measured by CD and fluorescence spectroscopy. A red shift of 7 nm in intrinsic fluorescence was observed with 6.0 M GdnHCl. Temperature-induced unfolding of baupain was incomplete, and at least 35% of the native structure of the protein was retained, even at high temperature (90 °C). Baupain showed characteristics of a molten globule state, due to preferential ANS binding at pH 2.0 in comparison to the native form (pH 7.0) and completely unfolded (6.0 M GdnHCl) state. Combined with information about N-terminal sequence similarity, these results allow us to include baupain in the papain superfamily.

  1. Timed Testing under Partial Observability

    DEFF Research Database (Denmark)

    David, Alexandre; Larsen, Kim Guldstrand; Li, Shuhao

    2009-01-01

    observability of SUT using a set of predicates over the TGA state space, and specify the test purposes in Computation Tree Logic (CTL) formulas. A recently developed partially observable timed game solver is used to generate winning strategies, which are used as test cases. We propose a conformance testing...

  2. Fundamental partial compositeness

    CERN Document Server

    Sannino, Francesco

    2016-11-07

    We construct renormalizable Standard Model extensions, valid up to the Planck scale, that give a composite Higgs from a new fundamental strong force acting on fermions and scalars. Yukawa interactions of these particles with Standard Model fermions realize the partial compositeness scenario. Successful models exist because gauge quantum numbers of Standard Model fermions admit a minimal enough 'square root'. Furthermore, right-handed SM fermions have an SU(2)$_R$-like structure, yielding a custodially-protected composite Higgs. Baryon and lepton numbers arise accidentally. Standard Model fermions acquire mass at tree level, while the Higgs potential and flavor violations are generated by quantum corrections. We further discuss accidental symmetries and other dynamical features stemming from the new strongly interacting scalars. If the same phenomenology can be obtained from models without our elementary scalars, they would reappear as composite states.

  3. Fundamental partial compositeness

    International Nuclear Information System (INIS)

    Sannino, Francesco; Strumia, Alessandro; Tesi, Andrea; Vigiani, Elena

    2016-01-01

    We construct renormalizable Standard Model extensions, valid up to the Planck scale, that give a composite Higgs from a new fundamental strong force acting on fermions and scalars. Yukawa interactions of these particles with Standard Model fermions realize the partial compositeness scenario. Under certain assumptions on the dynamics of the scalars, successful models exist because gauge quantum numbers of Standard Model fermions admit a minimal enough ‘square root’. Furthermore, right-handed SM fermions have an SU(2)_R-like structure, yielding a custodially-protected composite Higgs. Baryon and lepton numbers arise accidentally. Standard Model fermions acquire mass at tree level, while the Higgs potential and flavor violations are generated by quantum corrections. We further discuss accidental symmetries and other dynamical features stemming from the new strongly interacting scalars. If the same phenomenology can be obtained from models without our elementary scalars, they would reappear as composite states.

  4. Instability-induced ordering, universal unfolding and the role of gravity in granular Couette flow

    Science.gov (United States)

    Alam, Meheboob; Arakeri, V. H.; Nott, P. R.; Goddard, J. D.; Herrmann, H. J.

    2005-01-01

    Linear stability theory and bifurcation analysis are used to investigate the role of gravity in shear-band formation in granular Couette flow, considering a kinetic-theory rheological model. We show that the only possible state, at low shear rates, corresponds to a "plug" near the bottom wall, in which the particles are densely packed and the shear rate is close to zero, and a uniformly sheared dilute region above it. The origin of such plugged states is shown to be tied to the spontaneous symmetry-breaking instabilities of the gravity-free uniform shear flow, leading to the formation of ordered bands of alternating dilute and dense regions in the transverse direction, via an infinite hierarchy of pitchfork bifurcations. Gravity plays the role of an "imperfection", thus destroying the "perfect" bifurcation structure of uniform shear. The present bifurcation problem admits universal unfolding of pitchfork bifurcations which subsequently leads to the formation of a sequence of a countably infinite number of "isolas", with the solution structures being a modulated version of their gravity-free counterpart. While the solution with a plug near the bottom wall looks remarkably similar to the shear-banding phenomenon in dense slow granular Couette flows, a "floating" plug near the top wall is also a solution of these equations at high shear rates. A two-dimensional linear stability analysis suggests that these floating plugged states are unstable to long-wave travelling disturbances.The unique solution having a bottom plug can also be unstable to long waves, but remains stable at sufficiently low shear rates. The implications and realizability of the present results are discussed in the light of shear-cell experiments under "microgravity" conditions.

  5. A neutron spectrum unfolding computer code based on artificial neural networks

    Science.gov (United States)

    Ortiz-Rodríguez, J. M.; Reyes Alfaro, A.; Reyes Haro, A.; Cervantes Viramontes, J. M.; Vega-Carrillo, H. R.

    2014-02-01

    The Bonner Spheres Spectrometer consists of a thermal neutron sensor placed at the center of a number of moderating polyethylene spheres of different diameters. From the measured readings, information can be derived about the spectrum of the neutron field where measurements were made. Disadvantages of the Bonner system are the weight associated with each sphere and the need to sequentially irradiate the spheres, requiring long exposure periods. Provided a well-established response matrix and adequate irradiation conditions, the most delicate part of neutron spectrometry, is the unfolding process. The derivation of the spectral information is not simple because the unknown is not given directly as a result of the measurements. The drawbacks associated with traditional unfolding procedures have motivated the need of complementary approaches. Novel methods based on Artificial Intelligence, mainly Artificial Neural Networks, have been widely investigated. In this work, a neutron spectrum unfolding code based on neural nets technology is presented. This code is called Neutron Spectrometry and Dosimetry with Artificial Neural networks unfolding code that was designed in a graphical interface. The core of the code is an embedded neural network architecture previously optimized using the robust design of artificial neural networks methodology. The main features of the code are: easy to use, friendly and intuitive to the user. This code was designed for a Bonner Sphere System based on a 6LiI(Eu) neutron detector and a response matrix expressed in 60 energy bins taken from an International Atomic Energy Agency compilation. The main feature of the code is that as entrance data, for unfolding the neutron spectrum, only seven rate counts measured with seven Bonner spheres are required; simultaneously the code calculates 15 dosimetric quantities as well as the total flux for radiation protection purposes. This code generates a full report with all information of the unfolding in

  6. Microscopic dynamics of water around unfolded structures of barstar at room temperature

    Energy Technology Data Exchange (ETDEWEB)

    Pal, Somedatta; Chakraborty, Kaushik; Khatua, Prabir; Bandyopadhyay, Sanjoy, E-mail: sanjoy@chem.iitkgp.ernet.in [Molecular Modeling Laboratory, Department of Chemistry, Indian Institute of Technology, Kharagpur 721302 (India)

    2015-02-07

    The breaking of the native structure of a protein and its influences on the dynamic response of the surrounding solvent is an important issue in protein folding. In this work, we have carried out atomistic molecular dynamics simulations to unfold the protein barstar at two different temperatures (400 K and 450 K). The two unfolded forms obtained at such high temperatures are further studied at room temperature to explore the effects of nonuniform unfolding of the protein secondary structures along two different pathways on the microscopic dynamical properties of the surface water molecules. It is demonstrated that though the structural transition of the protein in general results in less restricted water motions around its segments, but there are evidences of formation of new conformational motifs upon unfolding with increasingly confined environment around them, thereby resulting in further restricted water mobility in their hydration layers. Moreover, it is noticed that the effects of nonuniform unfolding of the protein segments on the relaxation times of the protein–water (PW) and the water–water (WW) hydrogen bonds are correlated with hindered hydration water motions. However, the kinetics of breaking and reformation of such hydrogen bonds are found to be influenced differently at the interface. It is observed that while the effects of unfolding on the PW hydrogen bond kinetics seem to be minimum, but the kinetics involving the WW hydrogen bonds around the protein segments exhibit noticeably heterogeneous characteristics. We believe that this is an important observation, which can provide valuable insights on the origin of heterogeneous influence of unfolding of a protein on the microscopic properties of its hydration water.

  7. Partial tooth gear bearings

    Science.gov (United States)

    Vranish, John M. (Inventor)

    2010-01-01

    A partial gear bearing including an upper half, comprising peak partial teeth, and a lower, or bottom, half, comprising valley partial teeth. The upper half also has an integrated roller section between each of the peak partial teeth with a radius equal to the gear pitch radius of the radially outwardly extending peak partial teeth. Conversely, the lower half has an integrated roller section between each of the valley half teeth with a radius also equal to the gear pitch radius of the peak partial teeth. The valley partial teeth extend radially inwardly from its roller section. The peak and valley partial teeth are exactly out of phase with each other, as are the roller sections of the upper and lower halves. Essentially, the end roller bearing of the typical gear bearing has been integrated into the normal gear tooth pattern.

  8. Partial dynamical systems, fell bundles and applications

    CERN Document Server

    Exel, Ruy

    2017-01-01

    Partial dynamical systems, originally developed as a tool to study algebras of operators in Hilbert spaces, has recently become an important branch of algebra. Its most powerful results allow for understanding structural properties of algebras, both in the purely algebraic and in the C*-contexts, in terms of the dynamical properties of certain systems which are often hiding behind algebraic structures. The first indication that the study of an algebra using partial dynamical systems may be helpful is the presence of a grading. While the usual theory of graded algebras often requires gradings to be saturated, the theory of partial dynamical systems is especially well suited to treat nonsaturated graded algebras which are in fact the source of the notion of "partiality". One of the main results of the book states that every graded algebra satisfying suitable conditions may be reconstructed from a partial dynamical system via a process called the partial crossed product. Running in parallel with partial dynamica...

  9. Essays on partial retirement

    NARCIS (Netherlands)

    Kantarci, T.

    2012-01-01

    The five essays in this dissertation address a range of topics in the micro-economic literature on partial retirement. The focus is on the labor market behavior of older age groups. The essays examine the economic and non-economic determinants of partial retirement behavior, the effect of partial

  10. Quantification accuracy and partial volume effect in dependence of the attenuation correction of a state-of-the-art small animal PET scanner

    International Nuclear Information System (INIS)

    Mannheim, Julia G; Judenhofer, Martin S; Schmid, Andreas; Pichler, Bernd J; Tillmanns, Julia; Stiller, Detlef; Sossi, Vesna

    2012-01-01

    Quantification accuracy and partial volume effect (PVE) of the Siemens Inveon PET scanner were evaluated. The influence of transmission source activities (40 and 160 MBq) on the quantification accuracy and the PVE were determined. Dynamic range, object size and PVE for different sphere sizes, contrast ratios and positions in the field of view (FOV) were evaluated. The acquired data were reconstructed using different algorithms and correction methods. The activity level of the transmission source and the total emission activity in the FOV strongly influenced the attenuation maps. Reconstruction algorithms, correction methods, object size and location within the FOV had a strong influence on the PVE in all configurations. All evaluated parameters potentially influence the quantification accuracy. Hence, all protocols should be kept constant during a study to allow a comparison between different scans. (paper)

  11. Replica exchange simulation of reversible folding/unfolding of the Trp-cage miniprotein in explicit solvent: on the structure and possible role of internal water.

    Science.gov (United States)

    Paschek, Dietmar; Nymeyer, Hugh; García, Angel E

    2007-03-01

    We simulate the folding/unfolding equilibrium of the 20-residue miniprotein Trp-cage. We use replica exchange molecular dynamics simulations of the AMBER94 atomic detail model of the protein explicitly solvated by water, starting from a completely unfolded configuration. We employ a total of 40 replicas, covering the temperature range between 280 and 538 K. Individual simulation lengths of 100 ns sum up to a total simulation time of about 4 micros. Without any bias, we observe the folding of the protein into the native state with an unfolding-transition temperature of about 440 K. The native state is characterized by a distribution of root mean square distances (RMSD) from the NMR data that peaks at 1.8A, and is as low as 0.4A. We show that equilibration times of about 40 ns are required to yield convergence. A folded configuration in the entire extended ensemble is found to have a lifetime of about 31 ns. In a clamp-like motion, the Trp-cage opens up during thermal denaturation. In line with fluorescence quenching experiments, the Trp-residue sidechain gets hydrated when the protein opens up, roughly doubling the number of water molecules in the first solvation shell. We find the helical propensity of the helical domain of Trp-cage rather well preserved even at very high temperatures. In the folded state, we can identify states with one and two buried internal water molecules interconnecting parts of the Trp-cage molecule by hydrogen bonds. The loss of hydrogen bonds of these buried water molecules in the folded state with increasing temperature is likely to destabilize the folded state at elevated temperatures.

  12. Probing force-induced unfolding intermediates of a single staphylococcal nuclease molecule and the effect of ligand binding

    International Nuclear Information System (INIS)

    Ishii, Takaaki; Murayama, Yoshihiro; Katano, Atsuto; Maki, Kosuke; Kuwajima, Kunihiro; Sano, Masaki

    2008-01-01

    Single-molecule manipulation techniques have given experimental access to unfolding intermediates of proteins that are inaccessible in conventional experiments. A detailed characterization of the intermediates is a challenging problem that provides new possibilities for directly probing the energy landscape of proteins. We investigated single-molecule mechanical unfolding of a small globular protein, staphylococcal nuclease (SNase), using atomic force microscopy. The unfolding trajectories of the protein displayed sub-molecular and stochastic behavior with typical lengths corresponding to the size of the unfolded substructures. Our results support the view that the single protein unfolds along multiple pathways as suggested in recent theoretical studies. Moreover, we found the drastic change, caused by the ligand and inhibitor bindings, in the mechanical unfolding dynamics

  13. A neutron spectrum unfolding computer code based on artificial neural networks

    International Nuclear Information System (INIS)

    Ortiz-Rodríguez, J.M.; Reyes Alfaro, A.; Reyes Haro, A.; Cervantes Viramontes, J.M.; Vega-Carrillo, H.R.

    2014-01-01

    The Bonner Spheres Spectrometer consists of a thermal neutron sensor placed at the center of a number of moderating polyethylene spheres of different diameters. From the measured readings, information can be derived about the spectrum of the neutron field where measurements were made. Disadvantages of the Bonner system are the weight associated with each sphere and the need to sequentially irradiate the spheres, requiring long exposure periods. Provided a well-established response matrix and adequate irradiation conditions, the most delicate part of neutron spectrometry, is the unfolding process. The derivation of the spectral information is not simple because the unknown is not given directly as a result of the measurements. The drawbacks associated with traditional unfolding procedures have motivated the need of complementary approaches. Novel methods based on Artificial Intelligence, mainly Artificial Neural Networks, have been widely investigated. In this work, a neutron spectrum unfolding code based on neural nets technology is presented. This code is called Neutron Spectrometry and Dosimetry with Artificial Neural networks unfolding code that was designed in a graphical interface. The core of the code is an embedded neural network architecture previously optimized using the robust design of artificial neural networks methodology. The main features of the code are: easy to use, friendly and intuitive to the user. This code was designed for a Bonner Sphere System based on a 6 LiI(Eu) neutron detector and a response matrix expressed in 60 energy bins taken from an International Atomic Energy Agency compilation. The main feature of the code is that as entrance data, for unfolding the neutron spectrum, only seven rate counts measured with seven Bonner spheres are required; simultaneously the code calculates 15 dosimetric quantities as well as the total flux for radiation protection purposes. This code generates a full report with all information of the unfolding

  14. Spectrum unfolding in X-ray spectrometry using the maximum entropy method

    International Nuclear Information System (INIS)

    Fernandez, Jorge E.; Scot, Viviana; Di Giulio, Eugenio

    2014-01-01

    The solution of the unfolding problem is an ever-present issue in X-ray spectrometry. The maximum entropy technique solves this problem by taking advantage of some known a priori physical information and by ensuring an outcome with only positive values. This method is implemented in MAXED (MAXimum Entropy Deconvolution), a software code contained in the package UMG (Unfolding with MAXED and GRAVEL) developed at PTB and distributed by NEA Data Bank. This package contains also the code GRAVEL (used to estimate the precision of the solution). This article introduces the new code UMESTRAT (Unfolding Maximum Entropy STRATegy) which applies a semi-automatic strategy to solve the unfolding problem by using a suitable combination of MAXED and GRAVEL for applications in X-ray spectrometry. Some examples of the use of UMESTRAT are shown, demonstrating its capability to remove detector artifacts from the measured spectrum consistently with the model used for the detector response function (DRF). - Highlights: ► A new strategy to solve the unfolding problem in X-ray spectrometry is presented. ► The presented strategy uses a suitable combination of the codes MAXED and GRAVEL. ► The applied strategy provides additional information on the Detector Response Function. ► The code UMESTRAT is developed to apply this new strategy in a semi-automatic mode

  15. Unfolding neutron spectra obtained from BS–TLD system using genetic algorithm

    International Nuclear Information System (INIS)

    Santos, J.A.L.; Silva, E.R.; Ferreira, T.A.E; Vilela, E.C.

    2012-01-01

    Due to the variability of neutron spectrum within the same environment, it is essential that the spectral distribution as a function of energy should be characterized. The precise information allows radiological quantities establishment related to that spectrum, but it is necessary that a spectrometric system covers a large interval of energy and an unfolding process is appropriate. This paper proposes use of a technique of Artificial Intelligence (AI) called genetic algorithm (GA), which uses bio-inspired mathematical models with the implementation of a specific matrix to unfolding data obtained from a combination of TLDs embedded in a BS system to characterize the neutron spectrum as a function of energy. The results obtained with this method were in accordance with reference spectra, thus enabling this technique to unfold neutron spectra with the BS–TLD system. - Highlights: ► The unfolding code used the artificial intelligence technique called genetic algorithms. ► A response matrix specific to the unfolding data obtained with the BS–TLD system is used by the AGLN. ► The observed results demonstrate the potential use of genetic algorithms in solving complex nuclear problems.

  16. Clinical evaluation of coronary territory map by using unfolded map of Tl-201 myocardial SPECT

    International Nuclear Information System (INIS)

    Uehara, Toshiisa; Nishimura, Tsunehiko; Katafuchi, Tetsuro; Yamagami, Hidetoshi; Kumita, Shinichirou; Hayashida, Kohei; Hayashi, Makoto

    1990-01-01

    Coronary territory map was developed on unfolded map of exercise Tl-201 myocardial SPECT. Each coronary territory was determined by summing the each unfolded map of 54 cases of single vessel disease respectively, and standardizing with normal pattern obtained from normal patients. The diagnostic accuracy of coronary territory map to identify the diseased coronary artery was analyzed in 104 clinical cases and was compared with that of planar and SPECT visual diagnosis, simple unfolded map (raw map) and extent and severity map. The results were as follows. (1) Territory map showed excellent diagnostic accuracy in single or double vessel disease, especially in diagnosis of left circumflex coronary artery lesion. (2) In triple vessel disease, the diagnostic accuracy of territory map or other unfolded maps was 30% at best, and was inferior to planar or SPECT visual analysis. The cause of this inferiority seemed that the quantitatively analyzed map had no information about the degree of Tl-uptake into lung or myocardium, which give useful information in visual diagnosis. (3) The diagnostic agreement ratio in two observers was the highest in territory map diagnosis, so that the territory map diagnosis seemed to be the most objective one. (4) The unfolded map diagnosis with apical display obtained from long-axis tomogram was useful to diagnose left anteior descending coronary (LAD) lesion, which improve not only the sensitivity of LAD but also specificity of right coronary artery single vessel disease. (author)

  17. Partially composite Goldstone Higgs boson

    DEFF Research Database (Denmark)

    Alanne, Tommi; Franzosi, Diogo Buarque; Frandsen, Mads T.

    2017-01-01

    We consider a model of dynamical electroweak symmetry breaking with a partially composite Goldstone Higgs boson. The model is based on a strongly interacting fermionic sector coupled to a fundamental scalar sector via Yukawa interactions. The SU(4)×SU(4) global symmetry of these two sectors...... is broken to a single SU(4) via Yukawa interactions. Electroweak symmetry breaking is dynamically induced by condensation due to the strong interactions in the new fermionic sector which further breaks the global symmetry SU(4)→Sp(4). The Higgs boson arises as a partially composite state which is an exact...... Goldstone boson in the limit where SM interactions are turned off. Terms breaking the SU(4) global symmetry explicitly generate a mass for the Goldstone Higgs boson. The model realizes in different limits both (partially) composite Higgs and (bosonic) technicolor models, thereby providing a convenient...

  18. Recurrent Partial Words

    Directory of Open Access Journals (Sweden)

    Francine Blanchet-Sadri

    2011-08-01

    Full Text Available Partial words are sequences over a finite alphabet that may contain wildcard symbols, called holes, which match or are compatible with all letters; partial words without holes are said to be full words (or simply words. Given an infinite partial word w, the number of distinct full words over the alphabet that are compatible with factors of w of length n, called subwords of w, refers to a measure of complexity of infinite partial words so-called subword complexity. This measure is of particular interest because we can construct partial words with subword complexities not achievable by full words. In this paper, we consider the notion of recurrence over infinite partial words, that is, we study whether all of the finite subwords of a given infinite partial word appear infinitely often, and we establish connections between subword complexity and recurrence in this more general framework.

  19. Molten Globule-Like Partially Folded State of Bacillus licheniformis α-Amylase at Low pH Induced by 1,1,1,3,3,3-Hexafluoroisopropanol

    Directory of Open Access Journals (Sweden)

    Adyani Azizah Abd Halim

    2014-01-01

    Full Text Available Effect of 1,1,1,3,3,3-hexafluoroisopropanol (HFIP on acid-denatured Bacillus licheniformis α-amylase (BLA at pH 2.0 was investigated by far-UV CD, intrinsic fluorescence, and ANS fluorescence measurements. Addition of increasing HFIP concentrations led to an increase in the mean residue ellipticity at 222 nm (MRE222 nm up to 1.5 M HFIP concentration beyond which it sloped off. A small increase in the intrinsic fluorescence and a marked increase in the ANS fluorescence were also observed up to 0.4 M HFIP concentration, both of which decreased thereafter. Far- and near-UV CD spectra of the HFIP-induced state observed at 0.4 M HFIP showed significant retention of the secondary structures closer to native BLA but a disordered tertiary structure. Increase in the ANS fluorescence intensity was also observed with the HFIP-induced state, suggesting exposure of the hydrophobic clusters to the solvent. Furthermore, thermal denaturation of HFIP-induced state showed a non-cooperative transition. Taken together, all these results suggested that HFIP-induced state of BLA represented a molten globule-like state at pH 2.0.

  20. Study of small partial-wave contributions in the neighbourhood of dominating resonance states of the proton by linearly polarized photons

    International Nuclear Information System (INIS)

    Elsner, D.

    2007-04-01

    The reaction p(e, e'p)π 0 has been studied at Q 2 =0.2 (GeV/c) 2 in the region of W=1232 MeV. From measurements left and right of vector q cross section asymmetries ρ LT have been obtained in forward ρ LT (θ π 0 cm =20 )=(-11.68±2.36 stat ±2.36 sys ) and backward ρ LT (θ π 0 cm =160 )=(12.18±0.27 stat ±0.82 sys ) π 0 kinematics, from which R{S 1+ * M 1+ }/ vertical stroke M 1+ vertical stroke 2 and R{S 0+ * M 1+ }/ vertical stroke M 1+ vertical stroke 2 could be determined. Using linear polarised tagged photon beams of energy up to E γ ≅1.5 GeV the photon beam asymmetry Σ has been measured in the reaction p(vector γ, η)p. Based on coherent bremsstrahlung off a diamond crystal a maximum polarisation of P γ =49% has been achieved at E γ =1305 MeV. The beam asymmetry has been extracted from the azimuthal modulation of the cross section using both decay modes of the η into two photons and 3π 0 . Large asymmetries up to 80% are observed, in agreement with previous measurements where already available. There is also agreement with standard model calculations. However, the required partial waves to describe the measurements differ significantly. (orig.)

  1. Mathematical Modelling of Intraretinal Oxygen Partial Pressure ...

    African Journals Online (AJOL)

    Purpose: The aim of our present work is to develop a simple steady state model for intraretinal oxygen partial pressure distribution and to investigate the effect of various model parameters on the partial pressure distribution under adapted conditions of light and darkness.. Method: A simple eight-layered mathematical model ...

  2. An Auto sequence Code to Integrate a Neutron Unfolding Code with thePC-MCA Accuspec

    International Nuclear Information System (INIS)

    Darsono

    2000-01-01

    In a neutron spectrometry using proton recoil method, the neutronunfolding code is needed to unfold the measured proton spectrum to become theneutron spectrum. The process of the unfolding neutron in the existingneutron spectrometry which was successfully installed last year was doneseparately. This manuscript reports that the auto sequence code to integratethe neutron unfolding code UNFSPEC.EXE with the software facility of thePC-MCA Accuspec has been made and run successfully so that the new neutronspectrometry become compact. The auto sequence code was written based on therules in application program facility of PC-MCA Accuspec and then it wascompiled using AC-EXE. Result of the test of the auto sequence code showedthat for binning width 20, 30, and 40 giving a little different spectrumshape. The binning width around 30 gives a better spectrum in mean of givingsmall error compared to the others. (author)

  3. A high-resolution neutron spectra unfolding method using the Genetic Algorithm technique

    CERN Document Server

    Mukherjee, B

    2002-01-01

    The Bonner sphere spectrometers (BSS) are commonly used to determine the neutron spectra within various nuclear facilities. Sophisticated mathematical tools are used to unfold the neutron energy distribution from the output data of the BSS. This paper highlights a novel high-resolution neutron spectra-unfolding method using the Genetic Algorithm (GA) technique. The GA imitates the biological evolution process prevailing in the nature to solve complex optimisation problems. The GA method was utilised to evaluate the neutron energy distribution, average energy, fluence and equivalent dose rates at important work places of a DIDO class research reactor and a high-energy superconducting heavy ion cyclotron. The spectrometer was calibrated with a sup 2 sup 4 sup 1 Am/Be (alpha,n) neutron standard source. The results of the GA method agreed satisfactorily with the results obtained by using the well-known BUNKI neutron spectra unfolding code.

  4. Proving the correctness of unfold/fold program transformations using bisimulation

    DEFF Research Database (Denmark)

    Hamilton, Geoff W.; Jones, Neil

    2011-01-01

    by a labelled transition system whose bisimilarity relation is a congruence that coincides with contextual equivalence. Labelled transition systems are well-suited to represent global program behaviour. On the other hand, unfold/fold program transformations use generalization and folding, and neither is easy......This paper shows that a bisimulation approach can be used to prove the correctness of unfold/fold program transformation algorithms. As an illustration, we show how our approach can be use to prove the correctness of positive supercompilation (due to Sørensen et al). Traditional program equivalence...... to describe contextually, due to use of non-local information. We show that weak bisimulation on labelled transition systems gives an elegant framework to prove contextual equivalence of original and transformed programs. One reason is that folds can be seen in the context of corresponding unfolds....

  5. On unfolding counting-rate spectra of recoil-proton neutron detectors

    International Nuclear Information System (INIS)

    Yeivin, Yehuda

    1983-01-01

    This note proposes a possible scheme for unfolding recoil-proton neutron detector data, in which at first the undistorted proton source spectrum is derived. The main argument in favour of this scheme is that, compared with the conventional scheme, it necessitates somewhat weaker assumptions with respect to the unknown spectrum above the detector's upper energy cutoff, and would therefore be more reliable. We also demonstrate a simple, elementary proof of the wall effect correction for spherical detectors, and, in order to gain insight of the potential merits of the proposed unfolding scheme, illustrate our main argument by considering a hypothetic linear range-energy relation, in which case complete unfolding becomes possible with no assumptions at all on the proton spectrum above the cutoff energy. (author)

  6. Performance of artificial neural networks and genetical evolved artificial neural networks unfolding techniques

    International Nuclear Information System (INIS)

    Ortiz R, J. M.; Martinez B, M. R.; Vega C, H. R.; Gallego D, E.; Lorente F, A.; Mendez V, R.; Los Arcos M, J. M.; Guerrero A, J. E.

    2011-01-01

    With the Bonner spheres spectrometer neutron spectrum is obtained through an unfolding procedure. Monte Carlo methods, Regularization, Parametrization, Least-squares, and Maximum Entropy are some of the techniques utilized for unfolding. In the last decade methods based on Artificial Intelligence Technology have been used. Approaches based on Genetic Algorithms and Artificial Neural Networks (Ann) have been developed in order to overcome the drawbacks of previous techniques. Nevertheless the advantages of Ann still it has some drawbacks mainly in the design process of the network, vg the optimum selection of the architectural and learning Ann parameters. In recent years the use of hybrid technologies, combining Ann and genetic algorithms, has been utilized to. In this work, several Ann topologies were trained and tested using Ann and Genetically Evolved Artificial Neural Networks in the aim to unfold neutron spectra using the count rates of a Bonner sphere spectrometer. Here, a comparative study of both procedures has been carried out. (Author)

  7. Unfolding, aggregation, and seeded amyloid formation of lysine-58-cleaved beta(2)-microglobulin

    DEFF Research Database (Denmark)

    Heegaard, N.H.H.; Jørgensen, T.J.D.; Rozlosnik, N.

    2005-01-01

    . Using amide hydrogen/deuterium exchange monitored by mass spectrometry, we show that Delta K58-beta(2)m has increased unfolding rates compared to wt-beta(2)m and that unfolding is highly temperature dependent. The unfolding rate is I order of magnitude faster in Delta K58-beta(2)M than in wt-beta(2)m...... in the circulation of dialysis patients. This beta(2)M variant, Delta K58-beta(2)m, is a disulfide-linked two-chain molecule consisting of amino acid residues 1-57 and 59-99 of intact beta(2)m, and we here demonstrate and characterize its decreased conformational stability as compared to wild-type (wt) beta(2)M...

  8. Declining global warming effects on the phenology of spring leaf unfolding.

    Science.gov (United States)

    Fu, Yongshuo H; Zhao, Hongfang; Piao, Shilong; Peaucelle, Marc; Peng, Shushi; Zhou, Guiyun; Ciais, Philippe; Huang, Mengtian; Menzel, Annette; Peñuelas, Josep; Song, Yang; Vitasse, Yann; Zeng, Zhenzhong; Janssens, Ivan A

    2015-10-01

    Earlier spring leaf unfolding is a frequently observed response of plants to climate warming. Many deciduous tree species require chilling for dormancy release, and warming-related reductions in chilling may counteract the advance of leaf unfolding in response to warming. Empirical evidence for this, however, is limited to saplings or twigs in climate-controlled chambers. Using long-term in situ observations of leaf unfolding for seven dominant European tree species at 1,245 sites, here we show that the apparent response of leaf unfolding to climate warming (ST, expressed in days advance of leaf unfolding per °C warming) has significantly decreased from 1980 to 2013 in all monitored tree species. Averaged across all species and sites, ST decreased by 40% from 4.0 ± 1.8 days °C(-1) during 1980-1994 to 2.3 ± 1.6 days °C(-1) during 1999-2013. The declining ST was also simulated by chilling-based phenology models, albeit with a weaker decline (24-30%) than observed in situ. The reduction in ST is likely to be partly attributable to reduced chilling. Nonetheless, other mechanisms may also have a role, such as 'photoperiod limitation' mechanisms that may become ultimately limiting when leaf unfolding dates occur too early in the season. Our results provide empirical evidence for a declining ST, but also suggest that the predicted strong winter warming in the future may further reduce ST and therefore result in a slowdown in the advance of tree spring phenology.

  9. UNFOLDINGS OF THE CYLINDRICA L SURFACES USED IN THE INDUSTRIAL INSTALLATIONS

    Directory of Open Access Journals (Sweden)

    VASILE GHEORGHITA

    2013-02-01

    Full Text Available The connections in the construction of the various industrial installations: pipes, boilers, joints elements and fittings have a cylindrical configuration, or similar cylindrical shape. The execution and their installation require knowledge of the unfolding and intersection curves, which compose them. The graphical solving of the problems of tech nical representation has enabled the formation of abstract geometric of the pieces forms and the ability to see into space. The paper proposes to establish the unfolding of a connection, used in the industrial equipments, by the classical method of the des criptive geometry and mathematics, using appropriate software

  10. Neutron response matrix for unfolding NE-213 measurements to 21 MeV

    International Nuclear Information System (INIS)

    Ingersoll, D.T.; Wehring, B.W.; Johnson, R.H.

    1976-01-01

    A neutron response matrix from measured neutron responses of NE-213 in the energy range of 0.2 to 22 MeV is presented. An interpolation scheme was used to construct an 81-column matrix from the data of Verbinski, Burrus, Love, Zobel, and Hill. As a test of the new response matrix, the Cf-252 neutron spectrum was measured and unfolded using the new response matrix and the FORIST unfolding code. The spectrum agrees well with previous measurements at lower energies, while providing new information above 8 MeV

  11. THE SURFACE-MEDIATED UNFOLDING KINETICS OF GLOBULAR PROTEINS IS DEPENDENT ON MOLECULAR WEIGHT AND TEMPERATURE

    Energy Technology Data Exchange (ETDEWEB)

    Patananan, A.N.; Goheen, S.C.

    2008-01-01

    The adsorption and unfolding pathways of proteins on rigid surfaces are essential in numerous complex processes associated with biomedical engineering, nanotechnology, and chromatography. It is now well accepted that the kinetics of unfolding are characterized by chemical and physical interactions dependent on protein deformability and structure, as well as environmental pH, temperature, and surface chemistry. Although this fundamental process has broad implications in medicine and industry, little is known about the mechanism because of the atomic lengths and rapid time scales involved. Therefore, the unfolding kinetics of myoglobin, β-glucosidase, and ovalbumin were investigated by adsorbing the globular proteins to non-porous cationic polymer beads. The protein fractions were adsorbed at different residence times (0, 9, 10, 20, and 30 min) at near-physiological conditions using a gradient elution system similar to that in high-performance liquid chromatography. The elution profi les and retention times were obtained by ultraviolet/visible spectrophotometry. A decrease in recovery was observed with time for almost all proteins and was attributed to irreversible protein unfolding on the non-porous surfaces. These data, and those of previous studies, fi t a positively increasing linear trend between percent unfolding after a fi xed (9 min) residence time (71.8%, 31.1%, and 32.1% of myoglobin, β-glucosidase, and ovalbumin, respectively) and molecular weight. Of all the proteins examined so far, only myoglobin deviated from this trend with higher than predicted unfolding rates. Myoglobin also exhibited an increase in retention time over a wide temperature range (0°C and 55°C, 4.39 min and 5.74 min, respectively) whereas ovalbumin and β-glucosidase did not. Further studies using a larger set of proteins are required to better understand the physiological and physiochemical implications of protein unfolding kinetics. This study confi rms that surface

  12. RDANN a new methodology to solve the neutron spectra unfolding problem

    International Nuclear Information System (INIS)

    Ortiz R, J.M.; Martinez B, M.R.; Vega C, H.R.

    2006-01-01

    The optimization processes known as Taguchi method and DOE methodology are applied to the design, training and testing of Artificial Neural Networks in the neutron spectrometry field, which offer potential benefits in the evaluation of the behavior of the net as well as the ability to examine the interaction of the weights and neurons inside the same one. In this work, the Robust Design of Artificial Neural Networks methodology is used to solve the neutron spectra unfolding problem, designing, training and testing an ANN using a set of 187 neutron spectra compiled by the International Atomic Energy Agency, to obtain the better neutron spectra unfolded from the Bonner spheres spectrometer's count rates. (Author)

  13. UMG 3.3, Analysis of data measured with spectrometers using unfolding techniques

    International Nuclear Information System (INIS)

    Reginatto, Marcel; Wiegel, Burkhard; Zimbal, Andreas; Langner, Frank

    2004-01-01

    1 - Description of program or function: UMG (Unfolding with MAXED and GRAVEL) is a package of seven programs written for the analysis of data measured with spectrometers that require the use of unfolding techniques. The program MAXED applies the maximum entropy principle to the unfolding problem, and the program GRAVEL uses a modified SAND-II algorithm to do the unfolding. There are two versions of each: MXD F C33 and GRV F C33 for 'few-channel' unfolding (e.g., Bonner sphere spectrometers) and MXD M C33 and GRV M C33 for 'multi-channel' unfolding (e.g., NE-213). The program IQU can be used to calculate integral quantities for both MAXED and GRAVEL solution spectra and, in the case of MAXED solutions, it can also be used to calculate the uncertainty in these values as well as the uncertainty in the solution spectrum. The uncertainty calculation is handled in the following way: given a solution spectrum generated by MAXED, the program IQU considers variations in the measured data and in the default spectrum and uses standard Methods to do sensitivity analysis and uncertainty propagation. There are two versions: IQU F C33 for 'few-channel' unfolding and IQU M C33 for 'multi-channel' unfolding. The program UMGPlot can be used to display the results from the unfolding programs MAXED and GRAVEL in graphical form in a quick and easy way. 2 - Methods: MAXED is based on the maximum entropy principle. The solution to the unfolding problem is obtained by maximisation of the relative entropy (used here in the form due to Skilling, which is a generalisation of the usual expression to distributions that are not necessarily normalized) subject to constraints imposed by the measurements. This approach permits the inclusion of prior information in a well-defined and mathematically consistent way, and it leads to a solution spectrum that is a non-negative function which can be written in closed form. This last feature permits the use of standard Methods for sensitivity analysis and

  14. Network Organization Unfolds over Time during Periods of Anxious Anticipation

    OpenAIRE

    McMenamin, Brenton W.; Langeslag, Sandra J.E.; Sirbu, Mihai; Padmala, Srikanth; Pessoa, Luiz

    2014-01-01

    Entering a state of anxious anticipation triggers widespread changes across large-scale networks in the brain. The temporal aspects of this transition into an anxious state are poorly understood. To address this question, an instructed threat of shock paradigm was used while recording functional MRI in humans to measure how activation and functional connectivity change over time across the salience, executive, and task-negative networks and how they interact with key regions implicated in emo...

  15. The partial-birth stratagem.

    Science.gov (United States)

    1998-06-01

    In Wisconsin, physicians stopped performing abortions when a Federal District Court Judge refused to issue a temporary restraining order against the state's newly enacted "partial birth" abortion ban that was couched in such vague language it actually covered all abortions. While ostensibly attempting to ban late-term "intact dilation and extraction," the language of the law did not refer to that procedure or to late terms. Instead, it prohibited all abortions in which a physician "partially vaginally delivers a living child, causes the death of the partially delivered child with the intent to kill the child and then completes the delivery of the child." The law also defined "child" as "a human being from the time of fertilization" until birth. It is clear that this abortion ban is unconstitutional under Row v. Wade, and this unconstitutionality is compounded by the fact that the law allowed no exception to protect a woman's health, which is required by Roe for abortion bans after fetal viability. Wisconsin is only one of about 28 states that have enacted similar laws, and only two have restricted the ban to postviability abortions. Many of these laws have been struck down in court, and President Clinton has continued to veto the Federal partial-birth bill. The Wisconsin Judge acknowledged that opponents of the ban will likely prevail when the case is heard, but his action in denying the temporary injunction means that many women in Wisconsin will not receive timely medical care. The partial birth strategy is really only another anti-abortion strategy.

  16. Partial differential equation for the idempotent Dirac density matrix characterized solely by the exact non-relativistic ground-state electron density for spherical atomic ions

    International Nuclear Information System (INIS)

    March, N.H.

    2009-08-01

    In this Journal, March and Suhai have earlier set up a first-order Dirac idempotent density matrix theory for one- and two-level occupancy in which the only input required is the nonrelativistic ground-state electron density. Here, an analytic generalization is provided for the case of spherical electron densities for arbitrary level occupancy. Be-like atomic ions are referred to as an example, but 'almost spherical' molecules like SiH 4 and GeH 4 also become accessible. (author)

  17. Resveratrol-induced cytotoxicity in human Burkitt's lymphoma cells is coupled to the unfolded protein response

    International Nuclear Information System (INIS)

    Yan, Ying; Gao, Yan-Yan; Liu, Bao-Qin; Niu, Xiao-Fang; Zhuang, Ying; Wang, Hua-Qin

    2010-01-01

    Resveratrol (RES), a natural phytoalexin found at high levels in grapes and red wine, has been shown to induce anti-proliferation and apoptosis of human cancer cell lines. However, the underlying molecular mechanisms are at present only partially understood. The effects of RES on activation of unfolded protein responses (UPR) were evaluated using Western blotting, semi-quantitative and real-time RT-PCR. Cell death was evaluated using Annexin V/PI staining and subsequent FACS. Similar as tunicamycin, treatment with RES lead to the activation of all 3 branches of the UPR, with early splicing of XBP-1 indicative of IRE1 activation, phosphorylation of eIF2α consistent with ER resident kinase (PERK) activation, activating transcription factor 6 (ATF6) splicing, and increase in expression levels of the downstream molecules GRP78/BiP, GRP94 and CHOP/GADD153 in human Burkitt's lymphoma Raji and Daudi cell lines. RES was shown to induce cell death, which could be attenuated by thwarting upregulation of CHOP. Our data suggest that activation of the apoptotic arm of the UPR and its downstream effector CHOP/GADD153 is involved, at least in part, in RES-induced apoptosis in Burkitt's lymphoma cells

  18. Two-Dimensional Partial-Wave Analysis of Exclusive 190 GeV $\\pi^- p$ Scattering into the $\\pi^-\\pi^-\\pi^+$ Final State at COMPASS (CERN)}

    CERN Document Server

    Haas, Florian

    2014-02-19

    The dynamics of strong interaction in the regime of low energies, i.e. large distances, is still not understood. Given its simplicity the non-relativistic simple quark model (SQM) describes successfully the observed hadronic spectra. QCD-inspired models, however, predict hadronic states where the gluonic content contributes to the hadron quantum numbers. These so-called hybrids cannot be explained within the SQM. A solid experimental proof of the existence of such systems would be the observation of spin-exotic states, with spin-parity quantum numbers, not allowed in the SQM. The study of mesons, the simplest hadrons, permits to gain insight into the realm of strong interaction where hadrons are the relevant degrees of freedom. The most promising spin-exotic meson candidate is the $\\pi_1(1600)$, which was claimed in several experiments and in particular in data taken during a previous hadron campaign of the COMPASS experiment. The hadron spectroscopy program of the COMPASS experiment at CER...

  19. Partial transposition on bi-partite system

    OpenAIRE

    Han, Y. -J.; Ren, X. J.; Wu, Y. C.; Guo, G. -C.

    2006-01-01

    Many of the properties of the partial transposition are not clear so far. Here the number of the negative eigenvalues of K(T)(the partial transposition of K) is considered carefully when K is a two-partite state. There are strong evidences to show that the number of negative eigenvalues of K(T) is N(N-1)/2 at most when K is a state in Hilbert space N*N. For the special case, 2*2 system(two qubits), we use this result to give a partial proof of the conjecture sqrt(K(T))(T)>=0. We find that thi...

  20. Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins

    Directory of Open Access Journals (Sweden)

    J. M. Dick

    2006-01-01

    Full Text Available Thermodynamic calculations can be used to quantify environmental constraints on the speciation of proteins, such as the pH and temperature dependence of ionization state, and the relative chemical stabilities of proteins in different biogeochemical settings. These calculations depend in part on values of the standard molal Gibbs energies of proteins and their ionization reactions as a function of temperature and pressure. Because these values are not generally available, we calculated values of the standard molal thermodynamic properties at 25°C and 1 bar as well as the revised Helgeson-Kirkham-Flowers equations of state parameters of neutral and charged zwitterionic reference model compounds including aqueous amino acids, polypeptides, and unfolded proteins. The experimental calorimetric and volumetric data for these species taken from the literature were combined with group additivity algorithms to calculate the properties and parameters of neutral and ionized sidechain and backbone groups in unfolded proteins. The resulting set of group contributions enables the calculation of the standard molal Gibbs energy, enthalpy, entropy, isobaric heat capacity, volume, and isothermal compressibility of unfolded proteins in a range of proton ionization states to temperatures and pressures exceeding 100°C and 1000 bar. This approach provides a useful frame of reference for thermodynamic studies of protein folding and complexation reactions. It can also be used to assign provisional values of the net charge and Gibbs energy of ionized proteins as a function of temperature and pH. Using these values, an Eh-pH diagram for a reaction representing the speciation of extracellular proteins from Pyrococcus furiosus and Bacillus subtilis was generated. The predicted predominance limits of these proteins correspond with the different electrochemical conditions of hydrothermal vents and soils. More comprehensive calculations of this kind may reveal pervasive

  1. The impact of urea-induced unfolding on the redox process of immobilised cytochrome c

    NARCIS (Netherlands)

    Monari, S.; Millo, D.; Ranieri, A.; di Rocco, G.; van der Zwan, G.; Gooijer, C.; Peressini, S.; Tavagnacco, C.; Hildebrandt, P.; Borsari, M.

    2010-01-01

    We have studied the effect of urea-induced unfolding on the electron transfer process of yeast iso-1-cytochrome c and its mutant K72AK73AK79A adsorbed on electrodes coated by mixed 11-mercapto-1-undecanoic acid/11-mercapto-1-undecanol self-assembled monolayers. Electrochemical measurements,

  2. Sequence-dependent unfolding kinetics of DNA hairpins studied by nanopore force spectroscopy

    International Nuclear Information System (INIS)

    Renner, Stephan; Bessonov, Andrey; Simmel, Friedrich C; Gerland, Ulrich

    2010-01-01

    Nanopore force spectroscopy is used to study the unzipping kinetics of two DNA hairpin molecules with a 12 base pair long stem containing two contiguous stretches of six GC and six AT base pairs in interchanged order. Even though the thermodynamic stabilities of the two structures are nearly the same, they differ greatly in their unzipping kinetics. When the GC segment has to be broken before the AT segment, the unfolding rate is orders of magnitude smaller than in the opposite case. We also investigated hairpins with stem regions consisting only of AT or GC base pairs. The pure AT hairpins translocate much faster than the other hairpins, whereas the pure GC hairpins translocate on similar timescales to the hairpins with only an initial GC segment. For each hairpin, nanopore force spectroscopy is performed for different loading rates and the resulting unzipping distributions are mathematically transformed to a master curve that yields the unfolding rate as a function of applied voltage. This is compared with a stochastic model of the unfolding process for the two sequences for different voltages. The results can be rationalized in terms of the different natures of the free energy landscapes for the unfolding process.

  3. A novel neutron energy spectrum unfolding code using particle swarm optimization

    International Nuclear Information System (INIS)

    Shahabinejad, H.; Sohrabpour, M.

    2017-01-01

    A novel neutron Spectrum Deconvolution using Particle Swarm Optimization (SDPSO) code has been developed to unfold the neutron spectrum from a pulse height distribution and a response matrix. The Particle Swarm Optimization (PSO) imitates the bird flocks social behavior to solve complex optimization problems. The results of the SDPSO code have been compared with those of the standard spectra and recently published Two-steps Genetic Algorithm Spectrum Unfolding (TGASU) code. The TGASU code have been previously compared with the other codes such as MAXED, GRAVEL, FERDOR and GAMCD and shown to be more accurate than the previous codes. The results of the SDPSO code have been demonstrated to match well with those of the TGASU code for both under determined and over-determined problems. In addition the SDPSO has been shown to be nearly two times faster than the TGASU code. - Highlights: • Introducing a novel method for neutron spectrum unfolding. • Implementation of a particle swarm optimization code for neutron unfolding. • Comparing results of the PSO code with those of recently published TGASU code. • Match results of the PSO code with those of TGASU code. • Greater convergence rate of implemented PSO code than TGASU code.

  4. Seeking Educational Quality in the Unfolding of Classroom Discourse: A Focus on Microtransitions

    Science.gov (United States)

    Mameli, Consuelo; Molinari, Luisa

    2014-01-01

    In this paper, we argue the importance of conceptualizing educational quality as located in everyday talk, and to search for it in the unfolding of classroom discourse and interactions. More specifically, we argue that for the discursive classroom process to be qualitatively effective it should be open and accessible by a series of…

  5. Statistical energy as a tool for binning-free, multivariate goodness-of-fit tests, two-sample comparison and unfolding

    International Nuclear Information System (INIS)

    Aslan, B.; Zech, G.

    2005-01-01

    We introduce the novel concept of statistical energy as a statistical tool. We define statistical energy of statistical distributions in a similar way as for electric charge distributions. Charges of opposite sign are in a state of minimum energy if they are equally distributed. This property is used to check whether two samples belong to the same parent distribution, to define goodness-of-fit tests and to unfold distributions distorted by measurement. The approach is binning-free and especially powerful in multidimensional applications

  6. Prediction and analysis of structure, stability and unfolding of thermolysin-like proteases

    Science.gov (United States)

    Vriend, Gert; Eijsink, Vincent

    1993-08-01

    Bacillus neutral proteases (NPs) form a group of well-characterized homologous enzymes, that exhibit large differences in thermostability. The three-dimensional (3D) structures of several of these enzymes have been modelled on the basis of the crystal structures of the NPs of B. thermoproteolyticus (thermolysin) and B. cercus. Several new techniques have been developed to improve the model-building procedures. Also a model-building by mutagenesis' strategy was used, in which mutants were designed just to shed light on parts of the structures that were particularly hard to model. The NP models have been used for the prediction of site-directed mutations aimed at improving the thermostability of the enzymes. Predictions were made using several novel computational techniques, such as position-specific rotamer searching, packing quality analysis and property-profile database searches. Many stabilizing mutations were predicted and produced: improvement of hydrogen bonding, exclusion of buried water molecules, capping helices, improvement of hydrophobic interactions and entropic stabilization have been applied successfully. At elevated temperatures NPs are irreversibly inactivated as a result of autolysis. It has been shown that this denaturation process is independent of the protease activity and concentration and that the inactivation follows first-order kinetics. From this it has been conjectured that local unfolding of (surface) loops, which renders the protein susceptible to autolysis, is the rate-limiting step. Despite the particular nature of the thermal denaturation process, normal rules for protein stability can be applied to NPs. However, rather than stabilizing the whole protein against global unfolding, only a small region has to be protected against local unfolding. In contrast to proteins in general, mutational effects in proteases are not additive and their magnitude is strongly dependent on the location of the mutation. Mutations that alter the stability

  7. Structural changes during the unfolding of Bovine serum albumin in ...

    Indian Academy of Sciences (India)

    Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400 085, India. E-mail: ... The protein samples were equilibrated in D2O for 24 h for the ... This assumption is true as the BSA solutions used in the experiments were suffi-.

  8. Computing rates of Markov models of voltage-gated ion channels by inverting partial differential equations governing the probability density functions of the conducting and non-conducting states.

    Science.gov (United States)

    Tveito, Aslak; Lines, Glenn T; Edwards, Andrew G; McCulloch, Andrew

    2016-07-01

    Markov models are ubiquitously used to represent the function of single ion channels. However, solving the inverse problem to construct a Markov model of single channel dynamics from bilayer or patch-clamp recordings remains challenging, particularly for channels involving complex gating processes. Methods for solving the inverse problem are generally based on data from voltage clamp measurements. Here, we describe an alternative approach to this problem based on measurements of voltage traces. The voltage traces define probability density functions of the functional states of an ion channel. These probability density functions can also be computed by solving a deterministic system of partial differential equations. The inversion is based on tuning the rates of the Markov models used in the deterministic system of partial differential equations such that the solution mimics the properties of the probability density function gathered from (pseudo) experimental data as well as possible. The optimization is done by defining a cost function to measure the difference between the deterministic solution and the solution based on experimental data. By evoking the properties of this function, it is possible to infer whether the rates of the Markov model are identifiable by our method. We present applications to Markov model well-known from the literature. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  9. Comparison of two equation-of-state models for partially ionized aluminum: Zel'dovich and Raizer's model versus the activity expansion code

    Science.gov (United States)

    Harrach, Robert J.; Rogers, Forest J.

    1981-09-01

    Two equation-of-state (EOS) models for multipy ionized matter are evaluated for the case of an aluminum plasma in the temperature range from about one eV to several hundred eV, spanning conditions of weak to strong ionization. Specifically, the simple analytical mode of Zel'dovich and Raizer and the more comprehensive model comprised by Rogers' plasma physics avtivity expansion code (ACTEX) are used to calculate the specific internal energy ɛ and average degree of ionization Z¯*, as functons of temperature T and density ρ. In the absence of experimental data, these results are compared against each other, covering almost five orders-of-magnitude variation in ɛ and the full range of Z¯* We find generally good agreement between the two sets of results, especially for low densities and for temperatures near the upper end of the rage. Calculated values of ɛ(T) agree to within ±30% over nearly the full range in T for densities below about 1 g/cm3. Similarly, the two models predict values of Z¯*(T) which track each other fairly well; above 20 eV the discrepancy is less than ±20% fpr ρ≲1 g/cm3. Where the calculations disagree, we expect the ACTEX code to be more accurate than Zel'dovich and Raizer's model, by virtue of its more detailed physics content.

  10. Comparison of two equation-of-state models for partially ionized aluminum: Zel'dovich and Raizer's model versus the activity expansion code

    Energy Technology Data Exchange (ETDEWEB)

    Harrach, R.J.; Rogers, F.J.

    1981-09-01

    Two equation-of-state (EOS) models for multipy ionized matter are evaluated for the case of an aluminum plasma in the temperature range from about one eV to several hundred eV, spanning conditions of weak to strong ionization. Specifically, the simple analytical mode of Zel'dovich and Raizer and the more comprehensive model comprised by Rogers' plasma physics avtivity expansion code (ACTEX) are used to calculate the specific internal energy epsilon and average degree of ionization Z-bar*, as functons of temperature T and density rho. In the absence of experimental data, these results are compared against each other, covering almost five orders-of-magnitude variation in epsilon and the full range of Z-bar* We find generally good agreement between the two sets of results, especially for low densities and for temperatures near the upper end of the rage. Calculated values of epsilon(T) agree to within +- 30% over nearly the full range in T for densities below about 1 g/cm/sup 3/. Similarly, the two models predict values of Z-bar*(T) which track each other fairly well; above 20 eV the discrepancy is less than +- 20% fpr rho< or approx. =1 g/cm/sup 3/. Where the calculations disagree, we expect the ACTEX code to be more accurate than Zel'dovich and Raizer's model, by virtue of its more detailed physics content.

  11. Hyperbolic partial differential equations

    CERN Document Server

    Witten, Matthew

    1986-01-01

    Hyperbolic Partial Differential Equations III is a refereed journal issue that explores the applications, theory, and/or applied methods related to hyperbolic partial differential equations, or problems arising out of hyperbolic partial differential equations, in any area of research. This journal issue is interested in all types of articles in terms of review, mini-monograph, standard study, or short communication. Some studies presented in this journal include discretization of ideal fluid dynamics in the Eulerian representation; a Riemann problem in gas dynamics with bifurcation; periodic M

  12. Successful removable partial dentures.

    Science.gov (United States)

    Lynch, Christopher D

    2012-03-01

    Removable partial dentures (RPDs) remain a mainstay of prosthodontic care for partially dentate patients. Appropriately designed, they can restore masticatory efficiency, improve aesthetics and speech, and help secure overall oral health. However, challenges remain in providing such treatments, including maintaining adequate plaque control, achieving adequate retention, and facilitating patient tolerance. The aim of this paper is to review the successful provision of RPDs. Removable partial dentures are a successful form of treatment for replacing missing teeth, and can be successfully provided with appropriate design and fabrication concepts in mind.

  13. Beginning partial differential equations

    CERN Document Server

    O'Neil, Peter V

    2011-01-01

    A rigorous, yet accessible, introduction to partial differential equations-updated in a valuable new edition Beginning Partial Differential Equations, Second Edition provides a comprehensive introduction to partial differential equations (PDEs) with a special focus on the significance of characteristics, solutions by Fourier series, integrals and transforms, properties and physical interpretations of solutions, and a transition to the modern function space approach to PDEs. With its breadth of coverage, this new edition continues to present a broad introduction to the field, while also addres

  14. Partial deletion of eNOS gene causes hyperinsulinemic state, unbalance of cardiac insulin signaling pathways and coronary dysfunction independently of high fat diet.

    Directory of Open Access Journals (Sweden)

    Cecilia Vecoli

    Full Text Available Abnormalities in eNOS gene, possibly interacting with high fat diet (HFD, affect peripheral vascular function and glucose metabolism. The relative role of eNOS gene, HFD and metabolic derangement on coronary function has not been fully elucidated. We test whether eNOS gene deficiency per se or in association with HFD modulates coronary function through mechanisms involving molecular pathways related to insulin signaling. Wild type (WT, eNOS-/- and eNOS+/- mice were studied. WT and eNOS+/- mice were fed with either standard or HF diet for 16 weeks and compared with standard diet fed eNOS-/-. Glucose and insulin tolerance tests were performed during the last week of diet. Coronary resistance (CR was measured at baseline and during infusions of acetylcholine (Ach or sodium-nitroprusside (SNP to evaluate endothelium-dependent or independent vasodilation, in the Langendorff isolated hearts. Cardiac expression of Akt and ERK genes as evaluation of two major insulin-regulated signaling pathways involved in the control of vascular tone were assessed by western blot. HFD-fed mice developed an overt diabetic state. Conversely, chow-fed genetically modified mice (in particular eNOS-/- showed a metabolic pattern characterized by normoglycemia and hyperinsulinemia with a limited degree of insulin resistance. CR was significantly higher in animals with eNOS gene deletions than in WT, independently of diet. Percent decrease in CR, during Ach infusion, was significantly lower in both eNOS-/- and eNOS+/- mice than in WT, independently of diet. SNP reduced CR in all groups except eNOS-/-. The cardiac ERK1-2/Akt ratio, increased in animals with eNOS gene deletions compared with WT, independently of diet. These results suggest that the eNOS genetic deficiency, associated or not with HFD, has a relevant effect on coronary vascular function, possibly mediated by increase in blood insulin levels and unbalance in insulin-dependent signaling in coronary vessels

  15. Dynamics of partial differential equations

    CERN Document Server

    Wayne, C Eugene

    2015-01-01

    This book contains two review articles on the dynamics of partial differential equations that deal with closely related topics but can be read independently. Wayne reviews recent results on the global dynamics of the two-dimensional Navier-Stokes equations. This system exhibits stable vortex solutions: the topic of Wayne's contribution is how solutions that start from arbitrary initial conditions evolve towards stable vortices. Weinstein considers the dynamics of localized states in nonlinear Schrodinger and Gross-Pitaevskii equations that describe many optical and quantum systems. In this contribution, Weinstein reviews recent bifurcations results of solitary waves, their linear and nonlinear stability properties, and results about radiation damping where waves lose energy through radiation.   The articles, written independently, are combined into one volume to showcase the tools of dynamical systems theory at work in explaining qualitative phenomena associated with two classes of partial differential equ...

  16. Partial knee replacement - slideshow

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/presentations/100225.htm Partial knee replacement - series—Normal anatomy To use the sharing ... A.M. Editorial team. Related MedlinePlus Health Topics Knee Replacement A.D.A.M., Inc. is accredited ...

  17. Beginning partial differential equations

    CERN Document Server

    O'Neil, Peter V

    2014-01-01

    A broad introduction to PDEs with an emphasis on specialized topics and applications occurring in a variety of fields Featuring a thoroughly revised presentation of topics, Beginning Partial Differential Equations, Third Edition provides a challenging, yet accessible,combination of techniques, applications, and introductory theory on the subjectof partial differential equations. The new edition offers nonstandard coverageon material including Burger's equation, the telegraph equation, damped wavemotion, and the use of characteristics to solve nonhomogeneous problems. The Third Edition is or

  18. India's tryst with the atom: unfolding the nuclear story

    International Nuclear Information System (INIS)

    Sabherwal, O.P.

    2004-01-01

    India's tryst with the atom is the story of a nuclear dream come true. All nuclear weapons states (as per NPT definition) launched their nuclear programmes by acquiring weapon capacity first, and later moved on to peaceful nuclear technologies. India took the reverse route: First building capacity for nuclear power generation and other areas of peaceful application, then having built a nuclear infrastructure and R and D base, moving on to nuclear weapon deterrence. Spectacular results followed. As this book notes: That India with minuscule investment in the weapon programme had jumped into the league of nuclear weapon powers-all of whom had years been throwing a good chunk of their fortune into nuclear weapon making was amazing

  19. Catastrophic shifts in vegetation-soil systems may unfold rapidly or slowly independent of the rate of change in the system driver

    Science.gov (United States)

    Karssenberg, Derek; Bierkens, Marc

    2014-05-01

    Complex systems may switch between contrasting stable states under gradual change of a driver. Such critical transitions often result in considerable long-term damage because strong hysteresis impedes reversion, and the transition becomes catastrophic. Critical transitions largely reduce our capability of forecasting future system states because it is hard to predict the timing of their occurrence [2]. Moreover, for many systems it is unknown how rapidly the critical transition unfolds when the tipping point has been reached. The rate of change during collapse, however, is important information because it determines the time available to take action to reverse a shift [1]. In this study we explore the rate of change during the degradation of a vegetation-soil system on a hillslope from a state with considerable vegetation cover and large soil depths, to a state with sparse vegetation and a bare rock or negligible soil depths. Using a distributed, stochastic model coupling hydrology, vegetation, weathering and water erosion, we derive two differential equations describing the vegetation and the soil system, and their interaction. Two stable states - vegetated and bare - are identified by means of analytical investigation, and it is shown that the change between these two states is a critical transition as indicated by hysteresis. Surprisingly, when the tipping point is reached under a very slow increase of grazing pressure, the transition between the vegetated and the bare state can either unfold rapidly, over a few years, or gradually, occurring over decennia up to millennia. These differences in the rate of change during the transient state are explained by differences in bedrock weathering rates. This finding emphasizes the considerable uncertainty associated with forecasting catastrophic shifts in ecosystems, which is due to both difficulties in forecasting the timing of the tipping point and the rate of change when the transition unfolds. References [1] Hughes

  20. Partial synchronization and spontaneous spatial ordering in coupled chaotic systems

    International Nuclear Information System (INIS)

    Ying Zhang; Gang Hu; Cerdeira, Hilda A.; Shigang Chen; Braun, Thomas; Yugui Yao

    2000-11-01

    A model of many symmetrically and locally coupled chaotic oscillators is studied. Partial chaotic synchronizations associated with spontaneous spatial ordering are demonstrated. Very rich patterns of the system are revealed, based on partial synchronization analysis. The stabilities of different partially synchronous spatiotemporal structures and some novel dynamical behaviors of these states are discussed both numerically and analytically. (author)

  1. North American natural gas : the future is unfolding

    International Nuclear Information System (INIS)

    Dominy, D.M.

    1997-01-01

    The imbalance between natural gas supply and demand and the demand for pipeline capacity was discussed. TransCanada Pipelines (TCPL) has supplied about 60 per cent of the incremental capacity between 1990 and 1995. Between 1996 and 1998 TransCanada will be adding another 532 million cubic feet per day of capacity. There is a need for additional capacity out of the Western Canada Sedimentary Basin to eastern markets. TCPL's answer to the demand is the multi-year NEXUS pipeline expansion project, designed to expand TransCanada's system from Empress to Emerson, and further into eastern Canada. It will be built on the high-pressure 'header' concept comprising a 42 inch pipe with 1440 psig technology. Through six major interconnects, TransCanada will provide access for shippers to all major markets for Canadian gas: (1) Portland to New England, (2) Iroquois to New York state, (3) Millennium to the Northeast pipeline grid, (4) NFG/Tennessee to Ellisburg/Leidy, and (5) Viking Voyageur to Minnesota, Wisconsin and Illinois. The imbalance between supply and demand is expected to decrease over the next 10 years. NEXUS not only offers shippers a portfolio of markets and a wide choice of interconnections; it is also the lowest cost alternative. 22 figs

  2. West Nile virus and North America: an unfolding story.

    Science.gov (United States)

    Glaser, A

    2004-08-01

    Before the introduction of the West Nile virus (WNV) into the United States of America (USA) in 1999, conditions in North America were ideal for an arboviral epidemic. Such factors as the large, susceptible and non-immune animal and human populations, the presence of competent vectors, increasing international travel and commerce, existing methods for rapid dissemination and an ill-prepared animal and public health infrastructure all combined to create the essential elements for a severe animal and public health crisis--the 'perfect microbial storm'. The introduction of WNV into New York City was the final factor, serving as the catalyst to initiate one of the most significant epidemics in the USA. The spread of WNV across the country resulted in very large populations of wildlife, equines and people being exposed and infected. The epidemic is still not fully understood and its character continues to change and adapt. The recent recognition of a number of non-vector modes of transmission has revealed the disease as a greater threat and more difficult to control than first thought. West Nile virus gives every indication that it will become a permanent part of the 'medical landscape' of the USA, continuing to threaten wildlife, domestic animals and humans as a now endemic disease. This paper discusses the features of this extraordinary epidemic, and emphasises the need for an integrated surveillance system, greater diagnostic capacity and improved control strategies.

  3. A Model for Partial Kantian Cooperation

    OpenAIRE

    Kordonis, Ioannis

    2016-01-01

    This work presents a game theoretic model to describe game situations in which there is a partial cooperation among the players. Specifically, we assume that the players partially follow Kant's "Categorical Imperative". The model is stated for games with a continuum of players and the basic assumption made is that the participants consider that they belong to virtual groups in which they optimize their actions as if they were bound to follow the same strategy. The relation with the Nash, (Ben...

  4. Pancharatnam geometric phase originating from successive partial ...

    Indian Academy of Sciences (India)

    Pancharatnam connection [1,2] dictates that ψp is in phase ψ0. The partial projection effects a ... up to a real multiplier. Here again, ψf is in phase with ψp but relative to ψ0, has a .... For the third partial projection of strength t3 and an azimuth angle φ13 to effect a triangle closure for both initial states |z〉 and | − z〉, we derive ...

  5. Experience – Information – Image: A Historiography of Unfolding. Arab Cinema as Example

    Directory of Open Access Journals (Sweden)

    Laura U. Marks

    2011-04-01

    Many artworks can be illuminated by this process. My examples will be drawn from contemporary Arab cinema. In the heavily politicized Arab milieu, the Image world is constructed as a selective unfolding of only those aspects of Experience that are deemed to be useful or profitable. Some Arab filmmakers, rather than deconstruct the resulting ideological images, prefer to carry out their own unfoldings:  explicating hitherto latent events, knowledges, and sensations. Thus what official history deems merely personal, absurd, micro-events, or no events at all, becomes the stuff of a rich alternative historiography. This process characterizes the work of, among others, Joana Hadjithomas and Khalil Joreige, Nisrine Khodr, Mohammed Soueid, and Akram Zaatari (Lebanon, Azza El-Hassan, Elia Suleiman, and Sobhi Al-Zobaidi (Palestine, and Mohamad Khan (Egypt.

  6. Simulation study on unfolding methods for diagnostic X-rays and mixed gamma rays

    International Nuclear Information System (INIS)

    Hashimoto, Makoto; Ohtaka, Masahiko; Ara, Kuniaki; Kanno, Ikuo; Imamura, Ryo; Mikami, Kenta; Nomiya, Seiichiro; Onabe, Hideaki

    2009-01-01

    A photon detector operating in current mode that can sense X-ray energy distribution has been reported. This detector consists of a row of several segment detectors. The energy distribution is derived using an unfolding technique. In this paper, comparisons of the unfolding techniques among error reduction, spectrum surveillance, and neural network methods are discussed through simulation studies on the detection of diagnostic X-rays and gamma rays emitted by a mixture of 137 Cs and 60 Co. For diagnostic X-ray measurement, the spectrum surveillance and neural network methods appeared promising, while the error reduction method yielded poor results. However, in the case of measuring mixtures of gamma rays, the error reduction method was both sufficient and effective. (author)

  7. Exploring the role of internal friction in the dynamics of unfolded proteins using simple polymer models

    Science.gov (United States)

    Cheng, Ryan R.; Hawk, Alexander T.; Makarov, Dmitrii E.

    2013-02-01

    Recent experiments showed that the reconfiguration dynamics of unfolded proteins are often adequately described by simple polymer models. In particular, the Rouse model with internal friction (RIF) captures internal friction effects as observed in single-molecule fluorescence correlation spectroscopy (FCS) studies of a number of proteins. Here we use RIF, and its non-free draining analog, Zimm model with internal friction, to explore the effect of internal friction on the rate with which intramolecular contacts can be formed within the unfolded chain. Unlike the reconfiguration times inferred from FCS experiments, which depend linearly on the solvent viscosity, the first passage times to form intramolecular contacts are shown to display a more complex viscosity dependence. We further describe scaling relationships obeyed by contact formation times in the limits of high and low internal friction. Our findings provide experimentally testable predictions that can serve as a framework for the analysis of future studies of contact formation in proteins.

  8. Spectrum unfolding, sensitivity analysis and propagation of uncertainties with the maximum entropy deconvolution code MAXED

    CERN Document Server

    Reginatto, M; Neumann, S

    2002-01-01

    MAXED was developed to apply the maximum entropy principle to the unfolding of neutron spectrometric measurements. The approach followed in MAXED has several features that make it attractive: it permits inclusion of a priori information in a well-defined and mathematically consistent way, the algorithm used to derive the solution spectrum is not ad hoc (it can be justified on the basis of arguments that originate in information theory), and the solution spectrum is a non-negative function that can be written in closed form. This last feature permits the use of standard methods for the sensitivity analysis and propagation of uncertainties of MAXED solution spectra. We illustrate its use with unfoldings of NE 213 scintillation detector measurements of photon calibration spectra, and of multisphere neutron spectrometer measurements of cosmic-ray induced neutrons at high altitude (approx 20 km) in the atmosphere.

  9. Unfolding measurement of the atmospheric muon neutrino spectrum using IceCube

    Energy Technology Data Exchange (ETDEWEB)

    Boerner, Mathis; Ruhe, Tim; Meier, Maximilian; Schlunder, Philipp; Menne, Thorben; Fuchs, Tomasz [Dept. of Physics, Technical University of Dortmund, 44227 Dortmund (Germany); Collaboration: IceCube-Collaboration

    2016-07-01

    IceCube is a cubic kilometer neutrino observatory located at the geographic South Pole. With its huge volume, the detector is well suited for measurements of the atmospheric muon neutrino energy spectrum. Over the last years, several unfolding analyses for single years were able to provide model independent measurements for the northern hemisphere in an energy region between 200 GeV and 3.2 PeV. In this talk, the extension of the analyses to four additional years of data is presented. With this significant enlargement of the data basis, it is possible to reanalyze the full northern hemisphere with smaller statistical errors. Moreover, the spectrum can be unfolded in several small zenith bands. Measurements of the energy spectrum for different zenith regions provide further information on the composition and the shape of the flux.

  10. On the unfolding of the fundamental region in integrals of modular invariant amplitudes

    International Nuclear Information System (INIS)

    Trapletti, Michele

    2003-01-01

    We study generic one-loop (string) amplitudes where an integration over the fundamental region F of the modular group is needed. We show how the known lattice-reduction technique used to unfold F to a more suitable region S can be modified to rearrange generic modular invariant amplitudes. The main aim is to unfold F to the strip and, at the same time, to simplify the form of the integrand when it is a sum over a finite number of terms, like in one-loop amplitudes for closed strings compactified on orbifolds. We give a general formula and a recipe to compute modular invariant amplitudes. As an application of the technique we compute the one-loop vacuum energy ρ n for a generic Z n freely acting orbifold, generalizing the result that this energy is less than zero and drives the system to a tachyonic divergence, and that ρ n m if n>m. (author)

  11. Situated peer coaching and unfolding cases in the fundamentals skills laboratory.

    Science.gov (United States)

    Himes, Deborah O; Ravert, Patricia K

    2012-09-03

    Using unfolding case studies and situated peer coaching for the Fundamentals Skills Laboratory provides students with individualized feedback and creates a realistic clinical learning experience. A quasi-experimental design with pre- and post-intervention data was used to evaluate changes in student ratings of the course. An instrument was used to examine students' self-ratings and student comments about each lab. We found that students' ratings of the lab remained high with the new method and self-evaluations of their performance were higher as the semester progressed. Students appreciated the personalized feedback associated with peer coaching and demonstrated strong motivation and self-regulation in learning. By participating in unfolding case studies with situated peer coaching, students focus on safety issues, practice collaborative communication, and critical thinking in addition to performing psychomotor skills.

  12. NEWSPEC: A computer code to unfold neutron spectra from Bonner sphere data

    International Nuclear Information System (INIS)

    Lemley, E.C.; West, L.

    1996-01-01

    A new computer code, NEWSPEC, is in development at the University of Arkansas. The NEWSPEC code allows a user to unfold, fold, rebin, display, and manipulate neutron spectra as applied to Bonner sphere measurements. The SPUNIT unfolding algorithm, a new rebinning algorithm, and the graphical capabilities of Microsoft (MS) Windows and MS Excel are utilized to perform these operations. The computer platform for NEWSPEC is a personal computer (PC) running MS Windows 3.x or Win95, while the code is written in MS Visual Basic (VB) and MS VB for Applications (VBA) under Excel. One of the most useful attributes of the NEWSPEC software is the link to Excel allowing additional manipulation of program output or creation of program input

  13. RDANN a new methodology to solve the neutron spectra unfolding problem

    Energy Technology Data Exchange (ETDEWEB)

    Ortiz R, J.M.; Martinez B, M.R.; Vega C, H.R. [UAZ, Av. Ramon Lopez Velarde No. 801, 98000 Zacatecas (Mexico)

    2006-07-01

    The optimization processes known as Taguchi method and DOE methodology are applied to the design, training and testing of Artificial Neural Networks in the neutron spectrometry field, which offer potential benefits in the evaluation of the behavior of the net as well as the ability to examine the interaction of the weights and neurons inside the same one. In this work, the Robust Design of Artificial Neural Networks methodology is used to solve the neutron spectra unfolding problem, designing, training and testing an ANN using a set of 187 neutron spectra compiled by the International Atomic Energy Agency, to obtain the better neutron spectra unfolded from the Bonner spheres spectrometer's count rates. (Author)

  14. Descriptive and Computer Aided Drawing Perspective on an Unfolded Polyhedral Projection Surface

    Science.gov (United States)

    Dzwierzynska, Jolanta

    2017-10-01

    The aim of the herby study is to develop a method of direct and practical mapping of perspective on an unfolded prism polyhedral projection surface. The considered perspective representation is a rectilinear central projection onto a surface composed of several flat elements. In the paper two descriptive methods of drawing perspective are presented: direct and indirect. The graphical mapping of the effects of the representation is realized directly on the unfolded flat projection surface. That is due to the projective and graphical connection between points displayed on the polyhedral background and their counterparts received on the unfolded flat surface. For a significant improvement of the construction of line, analytical algorithms are formulated. They draw a perspective image of a segment of line passing through two different points determined by their coordinates in a spatial coordinate system of axis x, y, z. Compared to other perspective construction methods that use information about points, for computer vision and the computer aided design, our algorithms utilize data about lines, which are applied very often in architectural forms. Possibility of drawing lines in the considered perspective enables drawing an edge perspective image of an architectural object. The application of the changeable base elements of perspective as a horizon height and a station point location enable drawing perspective image from different viewing positions. The analytical algorithms for drawing perspective images are formulated in Mathcad software, however, they can be implemented in the majority of computer graphical packages, which can make drawing perspective more efficient and easier. The representation presented in the paper and the way of its direct mapping on the flat unfolded projection surface can find application in presentation of architectural space in advertisement and art.

  15. Unfolding of true distributions from experimental data distorted by detectors with finite resolutions

    International Nuclear Information System (INIS)

    Gagunashvili, N.D.

    1993-01-01

    A new procedure for unfolding the true distribution from experimental data distorted by a detector is proposed. For the given detector a result can be found by the least squares method, hence, without bias and involving minimal statistical errors. Stability of the result is achieved at the expense of its information content and/or using additional information on the shape of the distributions to be measured. The method may be applied for detectors with linear or nonlinear distortions. 8 refs.; 5 figs

  16. Unfolded Protein Response Signaling and MAP Kinase Pathways Underlie Pathogenesis of Arsenic-induced Cutaneous Inflammation

    OpenAIRE

    Li, Changzhao; Xu, Jianmin; Li, Fugui; Chaudhary, Sandeep C.; Weng, Zhiping; Wen, Jianming; Elmets, Craig A.; Ahsan, Habibul; Athar, Mohammad

    2011-01-01

    Arsenic exposure through drinking water is a major global public health problem and is associated with an enhanced risk of various cancers including skin cancer. In human skin, arsenic induces precancerous melanosis and keratosis, which may progress to basal cell and squamous cell carcinoma. However, the mechanism by which these pathophysiological alterations occur remains elusive. In this study, we showed that sub-chronic arsenic exposure to SKH-1 mice induced unfolded protein response (UPR)...

  17. STRANGE ATTRACTORS IN SYMMETRIC UNFOLDINGS OF A SINGULARITY WITH THREE-FOLD ZERO EIGENVALUE

    Institute of Scientific and Technical Information of China (English)

    Qinghua Zhou

    2009-01-01

    In this paper, we study the Sil'nikov heteroclinic bifurcations, which display strange attractors, for the symmetric versal unfoldings of the singularity at the origin with a nilpotent Linear part and 3-jet, using the normal form, the blow-up and the ge-neralized Mel'nikov methods of heteroclinic orbits to two hyperbolic or nonhyperbolic equilibria in a high-dimensional space.

  18. Thermal- and urea-induced unfolding processes of glutathione S-transferase by molecular dynamics simulation.

    Science.gov (United States)

    Li, Jiahuang; Chen, Yuan; Yang, Jie; Hua, Zichun

    2015-05-01

    The Schistosoma juponicum 26 kDa glutathione S-transferase (sj26GST) consists of the N-terminal domain (N-domain), containing three alpha-helices (named H1-H3) and four anti-parallel beta-strands (S1-S4), and the C-terminal domain (C-domain), comprising five alpha-helices (named H4-H8). In present work, molecular dynamics simulations and fluorescence spectroscopic were used to gain insights into the unfolding process of sj26GST. The molecular dynamics simulations on sj26GST subunit both in water and in 8 M urea were carried out at 300 K, 400 K and 500 K, respectively. Spectroscopic measurements were employed to monitor structural changes. Molecular dynamics simulations of sj26GST subunit induced by urea and temperature showed that the initial unfolding step of sj26GST both in water and urea occurred on N-domain, involving the disruption of helices H2, H3 and strands S3 and S4, whereas H6 was the last region exposed to solution and was the last helix to unfold. Moreover, simulations analyses combining with fluorescence and circular dichroism spectra indicated that N-domain could not fold independent, suggesting that correct folding of N-domain depended on its interactions with C-domain. We further proposed that the folding of GSTs could begin with the hydrophobic collapse of C-domain whose H4, H5, H6 and H7 could move close to each other and form a hydrophobic core, especially H6 wrapped in the hydrophobic center and beginning spontaneous formation of the helix. S3, S4, H3, and H2 could form in the wake of the interaction between C-domain and N-domain. The paper can offer insights into the molecular mechanism of GSTs unfolding. © 2014 Wiley Periodicals, Inc.

  19. Unfolding neutron spectra with BS-TLD system using genetic algorithms

    International Nuclear Information System (INIS)

    Santos, Joelan A.L.; Silva, Everton R.; Vilela, Eudice C.

    2011-01-01

    Due to the variability of neutron spectrum within the same environment, it is essential that the spectral distribution as function of energy to be characterized. To perform this task, the neutron spectrometer has a primary role in determining the neutron flux (Φ E (E)). Precise information allows radiological quantities establishment related to that spectrum but it is necessary, however, a series of steps with a spectrometric system that can cover a large interval of energy and whose answer is isotropic. The most widely used for accomplishing this task is the spectrometric Bonner spheres system. One of the biggest problems related to neutron spectrometry is the process of data analysis, known as unfolding. Most of the work undertaken to implement new techniques of this process, using data obtained with the scintillator 6 LiI(I). However, characteristics related to the dead time make it not be so effective when used in high flow neutron fields. An alternative to this problem is the use of thermoluminescent detectors (TLD), but the codes used do not provide a more specific response matrix to unfolding the information obtained through these materials, which makes the development of a specific response matrix important to adequately characterize the response obtained by them. This paper proposes using a technique of artificial intelligence called genetic algorithm, which uses bio-inspired mathematical models and through the implementation of a specific matrix to unfolding data obtained from a combination of TLDs embedded in a system of Bonner spheres, such as thermal neutron detectors, to characterize the neutron spectrum as a function of energy. The results obtained with this method were in accordance with reference spectra, thus enables of this technique to unfolding neutrons spectra with BS-TLD system. (author)

  20. Unfolding and smoothing applied to the quality enhancement of neutron tomographic images

    International Nuclear Information System (INIS)

    Almeida, Gevaldo L. de; Silvani, Maria I.; Lopes, Ricardo T.

    2008-01-01

    Resolution and contrast are the major parameters defining the quality of a computer-aided tomographic image. These parameters depend upon several features of the image acquisition system, such as detector resolution, geometrical arrangement of the source-object-detector, beam divergence, source strength, detector efficiency and counting time. Roughly, the detector finite resolution is the main source of systematic errors affecting the separation power of the image acquisition system, while the electronic noise and statistical fluctuation are responsible for the data dispersion, which spoils the contrast. An algorithm has been developed in this work aiming at the improvement of the image quality through the minimization of both types of errors. The systematic ones are reduced by a mathematical unfolding of the position spectra - used as projections to reconstruct the 2D-images - using the Line Spread Function - LSF of the neutron tomographic system. The principle behind this technique is that every single channel contains information about all channels of the spectrum, but it is concealed due to the automatic integration carried out by the detector. Therefore, knowing the shape of this curve, it is possible to retrieve the original spectra. These spectra are unfortunately corrupted by the unavoidable statistical fluctuation, and by oscillations arising from the unfolding process, which strongly affects the quality of the final unfolded image. In order to reduce this impact, the spectra have been filtered by a Fourier transform technique or smoothed with a least square fitting procedure. The algorithm has been applied to spectra of some test-bodies generated by an earlier developed tomographic simulator, which reproduces the spectra furnished by a thermal neutron tomographic system employing a position sensitive detector. The obtained results have shown that the unfolded spectra produce final images capable to resolve features otherwise not achievable with the

  1. Unfolding neutron spectra with BS-TLD system using genetic algorithms

    Energy Technology Data Exchange (ETDEWEB)

    Santos, Joelan A.L., E-mail: jasantos@cnen.gov.br [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Dept. de Energia Nuclear; Centro Regional de Ciencias Nucleares do Nordeste (CRCN-NE/CNEN-PE), Recife, PE (Brazil); Silva, Everton R. [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Centro de Informatica; Ferreira, Tiago A.E. [Universidade Federal Rural de Pernambuco (UFRPE), Recife, PE (Brazil). Dept. de Estatistica e Informatica; Fonseca, Evaldo S. [Instituto de Radioprotecao e Dosimetria (IRD/CNEN-RJ), Rio de Janeiro, RJ (Brazil); Vilela, Eudice C., E-mail: ecvilela@cnen.gov.br [Centro Regional de Ciencias Nucleares do Nordeste (CRCN-NE/CNEN-PE), Recife, PE (Brazil)

    2011-07-01

    Due to the variability of neutron spectrum within the same environment, it is essential that the spectral distribution as function of energy to be characterized. To perform this task, the neutron spectrometer has a primary role in determining the neutron flux ({Phi}{sub E}(E)). Precise information allows radiological quantities establishment related to that spectrum but it is necessary, however, a series of steps with a spectrometric system that can cover a large interval of energy and whose answer is isotropic. The most widely used for accomplishing this task is the spectrometric Bonner spheres system. One of the biggest problems related to neutron spectrometry is the process of data analysis, known as unfolding. Most of the work undertaken to implement new techniques of this process, using data obtained with the scintillator {sup 6}LiI(I). However, characteristics related to the dead time make it not be so effective when used in high flow neutron fields. An alternative to this problem is the use of thermoluminescent detectors (TLD), but the codes used do not provide a more specific response matrix to unfolding the information obtained through these materials, which makes the development of a specific response matrix important to adequately characterize the response obtained by them. This paper proposes using a technique of artificial intelligence called genetic algorithm, which uses bio-inspired mathematical models and through the implementation of a specific matrix to unfolding data obtained from a combination of TLDs embedded in a system of Bonner spheres, such as thermal neutron detectors, to characterize the neutron spectrum as a function of energy. The results obtained with this method were in accordance with reference spectra, thus enables of this technique to unfolding neutrons spectra with BS-TLD system. (author)

  2. The l z ( p ) * Person-Fit Statistic in an Unfolding Model Context.

    Science.gov (United States)

    Tendeiro, Jorge N

    2017-01-01

    Although person-fit analysis has a long-standing tradition within item response theory, it has been applied in combination with dominance response models almost exclusively. In this article, a popular log likelihood-based parametric person-fit statistic under the framework of the generalized graded unfolding model is used. Results from a simulation study indicate that the person-fit statistic performed relatively well in detecting midpoint response style patterns and not so well in detecting extreme response style patterns.

  3. Regulation of Cytokine Production by the Unfolded Protein Response; Implications for Infection and Autoimmunity

    OpenAIRE

    Judith A. Smith; Judith A. Smith

    2018-01-01

    Protein folding in the endoplasmic reticulum (ER) is an essential cell function. To safeguard this process in the face of environmental threats and internal stressors, cells mount an evolutionarily conserved response known as the unfolded protein response (UPR). Invading pathogens induce cellular stress that impacts protein folding, thus the UPR is well situated to sense danger and contribute to immune responses. Cytokines (inflammatory cytokines and interferons) critically mediate host defen...

  4. Partial differential equations

    CERN Document Server

    Evans, Lawrence C

    2010-01-01

    This text gives a comprehensive survey of modern techniques in the theoretical study of partial differential equations (PDEs) with particular emphasis on nonlinear equations. The exposition is divided into three parts: representation formulas for solutions; theory for linear partial differential equations; and theory for nonlinear partial differential equations. Included are complete treatments of the method of characteristics; energy methods within Sobolev spaces; regularity for second-order elliptic, parabolic, and hyperbolic equations; maximum principles; the multidimensional calculus of variations; viscosity solutions of Hamilton-Jacobi equations; shock waves and entropy criteria for conservation laws; and, much more.The author summarizes the relevant mathematics required to understand current research in PDEs, especially nonlinear PDEs. While he has reworked and simplified much of the classical theory (particularly the method of characteristics), he primarily emphasizes the modern interplay between funct...

  5. Partial Synchronization Manifolds for Linearly Time-Delay Coupled Systems

    OpenAIRE

    Steur, Erik; van Leeuwen, Cees; Michiels, Wim

    2014-01-01

    Sometimes a network of dynamical systems shows a form of incomplete synchronization characterized by synchronization of some but not all of its systems. This type of incomplete synchronization is called partial synchronization. Partial synchronization is associated with the existence of partial synchronization manifolds, which are linear invariant subspaces of C, the state space of the network of systems. We focus on partial synchronization manifolds in networks of system...

  6. An FCS study of unfolding and refolding of CPM-labeled human serum albumin: role of ionic liquid.

    Science.gov (United States)

    Sasmal, Dibyendu Kumar; Mondal, Tridib; Sen Mojumdar, Supratik; Choudhury, Aparajita; Banerjee, Rajat; Bhattacharyya, Kankan

    2011-11-10

    The effect of a room temperature ionic liquid (RTIL) on the conformational dynamics of a protein, human serum albumin (HSA), is studied by fluorescence correlation spectroscopy (FCS). For this, the protein was covalently labeled by a fluorophore, 7-dimethylamino-3-(4-maleimidophenyl)-4-methylcoumarin (CPM). On addition of a RTIL ([pmim][Br]) to the native protein, the diffusion coefficient (D(t)) decreases and the hydrodynamic radius (R(h)) increases. This suggests that the RTIL ([pmim][Br]) acts as a denaturant when the protein is in the native state. However, addition of [pmim][Br] to a protein denatured by GdnHCl causes an increases in D(t) and decrease in R(h). This suggests that in the presence of GdnHCl addition of RTIL helps the protein to refold. In the native state, the conformational dynamics of protein is described by three distinct time constants: ~3.6 ± 0.7, ~29 ± 4.5, and 133 ± 23 μs. The faster components (~3.6 ± 0.7 and ~29 ± 4.5 μs) are ascribed to chain dynamics of the protein, while the slowest component (133 μs) is responsible for interchain interaction or concerted motion. On addition of [pmim][Br], the conformational dynamics of HSA becomes slower (~5.1 ± 1, ~43.5 ± 2.8, and ~311 ± 2.3 μs in the presence of 1.5 M [pmim][Br]). The time constants for the protein denatured by 6 M GdnHCl are 3.2 ± 0.4, 34 ± 6, and 207 ± 38 μs. When 1.5 M [pmim][Br] is added to the denatured protein (in 6 M GdnHCl), the time constants become ~5 ± 1, ~41 ± 10, and ~230 ± 45 μs. The lifetime histogram shows that, on addition of GdnHCl to HSA, the contribution of the shorter lifetime component decreases and vanishes at 6 M GdnHCl. The shorter lifetime component immediately reappears after addition of RTIL to unfolded HSA. This suggests recoiling of the unfolded protein by RTIL.

  7. The Unfolded Protein Response in Homeostasis and Modulation of Mammalian Immune Cells.

    Science.gov (United States)

    Martins, Ana Sofia; Alves, Inês; Helguero, Luisa; Domingues, Maria Rosário; Neves, Bruno Miguel

    2016-11-01

    The endoplasmic reticulum (ER) plays important roles in eukaryotic protein folding and lipid biosynthesis. Several exogenous and endogenous cellular sources of stress can perturb ER homeostasis leading to the accumulation of unfolded proteins in the lumen. Unfolded protein accumulation triggers a signal-transduction cascade known as the unfolded protein response (UPR), an adaptive mechanism which aims to protect cells from protein aggregates and to restore ER functions. Further to this protective mechanism, in immune cells, UPR molecular effectors have been shown to participate in a wide range of biological processes such as cell differentiation, survival and immunoglobulin and cytokine production. Recent findings also highlight the involvement of the UPR machinery in the maturational program and antigen presentation capacities of dendritic cells. UPR is therefore a key element in immune system homeostasis with direct implications on both adaptive and innate immune responses. The present review summarizes the knowledge on the emerging roles of UPR signaling cascades in mammalian immune cells as well as the consequences of their dysregulation in relation to the pathogenesis of several diseases.

  8. β-sheet-like formation during the mechanical unfolding of prion protein

    International Nuclear Information System (INIS)

    Tao, Weiwei; Cao, Penghui; Park, Harold S.; Yoon, Gwonchan; Eom, Kilho

    2015-01-01

    Single molecule experiments and simulations have been widely used to characterize the unfolding and folding pathways of different proteins. However, with few exceptions, these tools have not been applied to study prion protein, PrP C , whose misfolded form PrP Sc can induce a group of fatal neurodegenerative diseases. Here, we apply novel atomistic modeling based on potential energy surface exploration to study the constant force unfolding of human PrP at time scales inaccessible with standard molecular dynamics. We demonstrate for forces around 100 pN, prion forms a stable, three-stranded β-sheet-like intermediate configuration containing residues 155-214 with a lifetime exceeding hundreds of nanoseconds. A mutant without the disulfide bridge shows lower stability during the unfolding process but still forms the three-stranded structure. The simulations thus not only show the atomistic details of the mechanically induced structural conversion from the native α-helical structure to the β-rich-like form but also lend support to the structural theory that there is a core of the recombinant PrP amyloid, a misfolded form reported to induce transmissible disease, mapping to C-terminal residues ≈160-220

  9. Characteristics of SiC neutron sensor spectrum unfolding process based on Bayesian inference

    Energy Technology Data Exchange (ETDEWEB)

    Cetnar, Jerzy; Krolikowski, Igor [Faculty of Energy and Fuels AGH - University of Science and Technology, Al. Mickiewicza 30, 30-059 Krakow (Poland); Ottaviani, L. [IM2NP, UMR CNRS 7334, Aix-Marseille University, Case 231 -13397 Marseille Cedex 20 (France); Lyoussi, A. [CEA, DEN, DER, Instrumentation Sensors and Dosimetry Laboratory, Cadarache, F-13108 St-Paul-Lez-Durance (France)

    2015-07-01

    This paper deals with SiC detector signal interpretation in neutron radiation measurements in mixed neutron gamma radiation fields, which is called the detector inverse problem or the spectrum unfolding, and it aims in finding a representation of the primary radiation, based on the measured detector signals. In our novel methodology we resort to Bayesian inference approach. In the developed procedure the resultant spectra is unfolded form detector channels reading, where the estimated neutron fluence in a group structure is obtained with its statistical characteristic comprising of standard deviation and correlation matrix. In the paper we present results of unfolding process for case of D-T neutron source in neutron moderating environment. Discussions of statistical properties of obtained results are presented as well as of the physical meaning of obtained correlation matrix of estimated group fluence. The presented works has been carried out within the I-SMART project, which is part of the KIC InnoEnergy R and D program. (authors)

  10. Neutron spectrum unfolding using genetic algorithm in a Monte Carlo simulation

    Energy Technology Data Exchange (ETDEWEB)

    Suman, Vitisha [Health Physics Division, Bhabha Atomic Research Centre, Mumbai 400085 (India); Sarkar, P.K., E-mail: pksarkar02@gmail.com [Manipal Centre for Natural Sciences, Manipal University, Manipal 576104 (India)

    2014-02-11

    A spectrum unfolding technique GAMCD (Genetic Algorithm and Monte Carlo based spectrum Deconvolution) has been developed using the genetic algorithm methodology within the framework of Monte Carlo simulations. Each Monte Carlo history starts with initial solution vectors (population) as randomly generated points in the hyper dimensional solution space that are related to the measured data by the response matrix of the detection system. The transition of the solution points in the solution space from one generation to another are governed by the genetic algorithm methodology using the techniques of cross-over (mating) and mutation in a probabilistic manner adding new solution points to the population. The population size is kept constant by discarding solutions having lesser fitness values (larger differences between measured and calculated results). Solutions having the highest fitness value at the end of each Monte Carlo history are averaged over all histories to obtain the final spectral solution. The present method shows promising results in neutron spectrum unfolding for both under-determined and over-determined problems with simulated test data as well as measured data when compared with some existing unfolding codes. An attractive advantage of the present method is the independence of the final spectra from the initial guess spectra.

  11. β-sheet-like formation during the mechanical unfolding of prion protein

    Energy Technology Data Exchange (ETDEWEB)

    Tao, Weiwei; Cao, Penghui; Park, Harold S., E-mail: parkhs@bu.edu [Department of Mechanical Engineering, Boston University, Boston, Massachusetts 02215 (United States); Yoon, Gwonchan [Department of Mechanical Engineering, Boston University, Boston, Massachusetts 02215 (United States); Department of Mechanical Engineering, Korea University, Seoul 136-701 (Korea, Republic of); Eom, Kilho [Biomechanics Laboratory, College of Sport Science, Sungkyunkwan University, Suwon 16419 (Korea, Republic of)

    2015-09-28

    Single molecule experiments and simulations have been widely used to characterize the unfolding and folding pathways of different proteins. However, with few exceptions, these tools have not been applied to study prion protein, PrP{sup C}, whose misfolded form PrP{sup Sc} can induce a group of fatal neurodegenerative diseases. Here, we apply novel atomistic modeling based on potential energy surface exploration to study the constant force unfolding of human PrP at time scales inaccessible with standard molecular dynamics. We demonstrate for forces around 100 pN, prion forms a stable, three-stranded β-sheet-like intermediate configuration containing residues 155-214 with a lifetime exceeding hundreds of nanoseconds. A mutant without the disulfide bridge shows lower stability during the unfolding process but still forms the three-stranded structure. The simulations thus not only show the atomistic details of the mechanically induced structural conversion from the native α-helical structure to the β-rich-like form but also lend support to the structural theory that there is a core of the recombinant PrP amyloid, a misfolded form reported to induce transmissible disease, mapping to C-terminal residues ≈160-220.

  12. β-sheet-like formation during the mechanical unfolding of prion protein

    Science.gov (United States)

    Tao, Weiwei; Yoon, Gwonchan; Cao, Penghui; Eom, Kilho; Park, Harold S.

    2015-09-01

    Single molecule experiments and simulations have been widely used to characterize the unfolding and folding pathways of different proteins. However, with few exceptions, these tools have not been applied to study prion protein, PrPC, whose misfolded form PrPSc can induce a group of fatal neurodegenerative diseases. Here, we apply novel atomistic modeling based on potential energy surface exploration to study the constant force unfolding of human PrP at time scales inaccessible with standard molecular dynamics. We demonstrate for forces around 100 pN, prion forms a stable, three-stranded β-sheet-like intermediate configuration containing residues 155-214 with a lifetime exceeding hundreds of nanoseconds. A mutant without the disulfide bridge shows lower stability during the unfolding process but still forms the three-stranded structure. The simulations thus not only show the atomistic details of the mechanically induced structural conversion from the native α-helical structure to the β-rich-like form but also lend support to the structural theory that there is a core of the recombinant PrP amyloid, a misfolded form reported to induce transmissible disease, mapping to C-terminal residues ≈160-220.

  13. Induction of the unfolded protein response by constitutive G-protein signaling in rod photoreceptor cells.

    Science.gov (United States)

    Wang, Tian; Chen, Jeannie

    2014-10-17

    Phototransduction is a G-protein signal transduction cascade that converts photon absorption to a change in current at the plasma membrane. Certain genetic mutations affecting the proteins in the phototransduction cascade cause blinding disorders in humans. Some of these mutations serve as a genetic source of "equivalent light" that activates the cascade, whereas other mutations lead to amplification of the light response. How constitutive phototransduction causes photoreceptor cell death is poorly understood. We showed that persistent G-protein signaling, which occurs in rod arrestin and rhodopsin kinase knock-out mice, caused a rapid and specific induction of the PERK pathway of the unfolded protein response. These changes were not observed in the cGMP-gated channel knock-out rods, an equivalent light condition that mimics light-stimulated channel closure. Thus transducin signaling, but not channel closure, triggers rapid cell death in light damage caused by constitutive phototransduction. Additionally, we show that in the albino light damage model cell death was not associated with increase in global protein ubiquitination or unfolded protein response induction. Taken together, these observations provide novel mechanistic insights into the cell death pathway caused by constitutive phototransduction and identify the unfolded protein response as a potential target for therapeutic intervention. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  14. Warhead verification as inverse problem: Applications of neutron spectrum unfolding from organic-scintillator measurements

    Science.gov (United States)

    Lawrence, Chris C.; Febbraro, Michael; Flaska, Marek; Pozzi, Sara A.; Becchetti, F. D.

    2016-08-01

    Verification of future warhead-dismantlement treaties will require detection of certain warhead attributes without the disclosure of sensitive design information, and this presents an unusual measurement challenge. Neutron spectroscopy—commonly eschewed as an ill-posed inverse problem—may hold special advantages for warhead verification by virtue of its insensitivity to certain neutron-source parameters like plutonium isotopics. In this article, we investigate the usefulness of unfolded neutron spectra obtained from organic-scintillator data for verifying a particular treaty-relevant warhead attribute: the presence of high-explosive and neutron-reflecting materials. Toward this end, several improvements on current unfolding capabilities are demonstrated: deuterated detectors are shown to have superior response-matrix condition to that of standard hydrogen-base scintintillators; a novel data-discretization scheme is proposed which removes important detector nonlinearities; and a technique is described for re-parameterizing the unfolding problem in order to constrain the parameter space of solutions sought, sidestepping the inverse problem altogether. These improvements are demonstrated with trial measurements and verified using accelerator-based time-of-flight calculation of reference spectra. Then, a demonstration is presented in which the elemental compositions of low-Z neutron-attenuating materials are estimated to within 10%. These techniques could have direct application in verifying the presence of high-explosive materials in a neutron-emitting test item, as well as other for treaty verification challenges.

  15. Neutron spectrum unfolding using genetic algorithm in a Monte Carlo simulation

    International Nuclear Information System (INIS)

    Suman, Vitisha; Sarkar, P.K.

    2014-01-01

    A spectrum unfolding technique GAMCD (Genetic Algorithm and Monte Carlo based spectrum Deconvolution) has been developed using the genetic algorithm methodology within the framework of Monte Carlo simulations. Each Monte Carlo history starts with initial solution vectors (population) as randomly generated points in the hyper dimensional solution space that are related to the measured data by the response matrix of the detection system. The transition of the solution points in the solution space from one generation to another are governed by the genetic algorithm methodology using the techniques of cross-over (mating) and mutation in a probabilistic manner adding new solution points to the population. The population size is kept constant by discarding solutions having lesser fitness values (larger differences between measured and calculated results). Solutions having the highest fitness value at the end of each Monte Carlo history are averaged over all histories to obtain the final spectral solution. The present method shows promising results in neutron spectrum unfolding for both under-determined and over-determined problems with simulated test data as well as measured data when compared with some existing unfolding codes. An attractive advantage of the present method is the independence of the final spectra from the initial guess spectra

  16. Geometrically engineering the standard model: Locally unfolding three families out of E8

    International Nuclear Information System (INIS)

    Bourjaily, Jacob L.

    2007-01-01

    This paper extends and builds upon the results of [J. L. Bourjaily, arXiv:0704.0444.], in which we described how to use the tools of geometrical engineering to deform geometrically engineered grand unified models into ones with lower symmetry. This top-down unfolding has the advantage that the relative positions of singularities giving rise to the many 'low-energy' matter fields are related by only a few parameters which deform the geometry of the unified model. And because the relative positions of singularities are necessary to compute the superpotential, for example, this is a framework in which the arbitrariness of geometrically engineered models can be greatly reduced. In [J. L. Bourjaily, arXiv:0704.0444.], this picture was made concrete for the case of deforming the representations of an SU 5 model into their standard model content. In this paper we continue that discussion to show how a geometrically engineered 16 of SO 10 can be unfolded into the standard model, and how the three families of the standard model uniquely emerge from the unfolding of a single, isolated E 8 singularity

  17. The unfolding effects of transfer functions and processing of the pulse height distributions

    Directory of Open Access Journals (Sweden)

    Avdić Senada

    2010-01-01

    Full Text Available This paper deals with the improvements of the linear artificial neural network unfolding approach aimed at accurately determining the incident neutron spectrum. The effects of the transfer functions and pre-processing of the simulated pulse height distributions from liquid scintillation detectors on the artificial neural networks performance have been studied. A better energy resolution and higher reliability of the linear artificial neural network technique have been achieved after implementation of the results of this study. The optimized structure of the network was used to unfold both monoenergetic and continuous neutron energy spectra, such as the spectra of 252Cf and 241Am-Be sources, traditionally used in the nuclear safeguards experiments. We have demonstrated that the artificial neural network energy resolution of 0.1 MeV is comparable with the one obtained by the reference maximum likelihood expectation-maximization method which was implemented by using the one step late algorithm. Although the maximum likelihood algorithm provides the unfolded results of higher accuracy, especially for continuous neutron sources, the artificial neural network approach with the improved performances is more suitable for fast and robust determination of the neutron spectra with sufficient accuracy.

  18. Characteristic Investigation of Unfolded Neutron Spectra with Different Priori Information and Gamma Radiation Interference

    International Nuclear Information System (INIS)

    Kim, Bong Hwan

    2006-01-01

    Neutron field spectrometry using multi spheres such as Bonner Spheres (BS) has been almost essential in radiation protection dosimetry for a long time at workplace in spite of poor energy resolution because it is not asking the fine energy resolution but requiring easy operation and measurement performance over a wide range of energy interested. KAERI has developed and used extended BS system based on a LiI(Eu) scintillator as the representative neutron spectrometry system for workplace monitoring as well as for the quantification of neutron calibration fields such as those recommended by ISO 8529. Major topics in using BS are how close the unfolded spectra is the real one and to minimize the interference of gamma radiation in neutron/gamma mixed fields in case of active instrument such as a BS with a LiI(Eu) scintillator. The former is related with choosing a priori information when unfolding the measured data and the latter is depend on how to discriminate it in intense gamma radiation fields. Influence of a priori information in unfolding and effect of counting loss due to pile-up of signals for the KAERI BS system were investigated analyzing the spectral measurement results of Scattered Neutron Calibration Fields (SNCF)

  19. Improved spectral data unfolding for radiochromic film imaging spectroscopy of laser-accelerated proton beams

    Energy Technology Data Exchange (ETDEWEB)

    Schollmeier, M.; Geissel, M.; Sefkow, A. B. [Sandia National Laboratories, Albuquerque, New Mexico 87185 (United States); Flippo, K. A. [Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States)

    2014-04-15

    An improved method to unfold the space-resolved proton energy distribution function of laser-accelerated proton beams using a layered, radiochromic film (RCF) detector stack has been developed. The method takes into account the reduced RCF response near the Bragg peak due to a high linear energy transfer (LET). This LET dependence of the active RCF layer has been measured, and published data have been re-interpreted to find a nonlinear saturation scaling of the RCF response with stopping power. Accounting for the LET effect increased the integrated particle yield by 25% after data unfolding. An iterative, analytical, space-resolved deconvolution of the RCF response functions from the measured dose was developed that does not rely on fitting. After the particle number unfold, three-dimensional interpolation is performed to determine the spatial proton beam distribution for proton energies in-between the RCF data points. Here, image morphing has been implemented as a novel interpolation method that takes into account the energy-dependent, changing beam topology.

  20. Optimization of partial search

    International Nuclear Information System (INIS)

    Korepin, Vladimir E

    2005-01-01

    A quantum Grover search algorithm can find a target item in a database faster than any classical algorithm. One can trade accuracy for speed and find a part of the database (a block) containing the target item even faster; this is partial search. A partial search algorithm was recently suggested by Grover and Radhakrishnan. Here we optimize it. Efficiency of the search algorithm is measured by the number of queries to the oracle. The author suggests a new version of the Grover-Radhakrishnan algorithm which uses a minimal number of such queries. The algorithm can run on the same hardware that is used for the usual Grover algorithm. (letter to the editor)

  1. Mutant uromodulin expression leads to altered homeostasis of the endoplasmic reticulum and activates the unfolded protein response.

    Directory of Open Access Journals (Sweden)

    Céline Schaeffer

    Full Text Available Uromodulin is the most abundant urinary protein in physiological conditions. It is exclusively produced by renal epithelial cells lining the thick ascending limb of Henle's loop (TAL and it plays key roles in kidney function and disease. Mutations in UMOD, the gene encoding uromodulin, cause autosomal dominant tubulointerstitial kidney disease uromodulin-related (ADTKD-UMOD, characterised by hyperuricemia, gout and progressive loss of renal function. While the primary effect of UMOD mutations, retention in the endoplasmic reticulum (ER, is well established, its downstream effects are still largely unknown. To gain insight into ADTKD-UMOD pathogenesis, we performed transcriptional profiling and biochemical characterisation of cellular models (immortalised mouse TAL cells of robust expression of wild type or mutant GFP-tagged uromodulin. In this model mutant uromodulin accumulation in the ER does not impact on cell viability and proliferation. Transcriptional profiling identified 109 genes that are differentially expressed in mutant cells relative to wild type ones. Up-regulated genes include several ER resident chaperones and protein disulphide isomerases. Consistently, pathway enrichment analysis indicates that mutant uromodulin expression affects ER function and protein homeostasis. Interestingly, mutant uromodulin expression induces the Unfolded Protein Response (UPR, and specifically the IRE1 branch, as shown by an increased splicing of XBP1. Consistent with UPR induction, we show increased interaction of mutant uromodulin with ER chaperones Bip, calnexin and PDI. Using metabolic labelling, we also demonstrate that while autophagy plays no role, mutant protein is partially degraded by the proteasome through ER-associated degradation. Our work demonstrates that ER stress could play a central role in ADTKD-UMOD pathogenesis. This sets the bases for future work to develop novel therapeutic strategies through modulation of ER homeostasis and

  2. Using lattice tools and unfolding methods for hpge detector efficiency simulation with the Monte Carlo code MCNP5

    International Nuclear Information System (INIS)

    Querol, A.; Gallardo, S.; Ródenas, J.; Verdú, G.

    2015-01-01

    In environmental radioactivity measurements, High Purity Germanium (HPGe) detectors are commonly used due to their excellent resolution. Efficiency calibration of detectors is essential to determine activity of radionuclides. The Monte Carlo method has been proved to be a powerful tool to complement efficiency calculations. In aged detectors, efficiency is partially deteriorated due to the dead layer increasing and consequently, the active volume decreasing. The characterization of the radiation transport in the dead layer is essential for a realistic HPGe simulation. In this work, the MCNP5 code is used to calculate the detector efficiency. The F4MESH tally is used to determine the photon and electron fluence in the dead layer and the active volume. The energy deposited in the Ge has been analyzed using the ⁎F8 tally. The F8 tally is used to obtain spectra and to calculate the detector efficiency. When the photon fluence and the energy deposition in the crystal are known, some unfolding methods can be used to estimate the activity of a given source. In this way, the efficiency is obtained and serves to verify the value obtained by other methods. - Highlights: • The MCNP5 code is used to estimate the dead layer thickness of an HPGe detector. • The F4MESH tally is applied to verify where interactions occur into the Ge crystal. • PHD and the energy deposited are obtained with F8 and ⁎F8 tallies, respectively. • An average dead layer between 70 and 80 µm is obtained for the HPGe studied. • The efficiency is calculated applying the TSVD method to the response matrix.

  3. Characterization and error analysis of an N×N unfolding procedure applied to filtered, photoelectric x-ray detector arrays. II. Error analysis and generalization

    Directory of Open Access Journals (Sweden)

    D. L. Fehl

    2010-12-01

    Full Text Available A five-channel, filtered-x-ray-detector (XRD array has been used to measure time-dependent, soft-x-ray flux emitted by z-pinch plasmas at the Z pulsed-power accelerator (Sandia National Laboratories, Albuquerque, New Mexico, USA. The preceding, companion paper [D. L. Fehl et al., Phys. Rev. ST Accel. Beams 13, 120402 (2010PRABFM1098-4402] describes an algorithm for spectral reconstructions (unfolds and spectrally integrated flux estimates from data obtained by this instrument. The unfolded spectrum S_{unfold}(E,t is based on (N=5 first-order B-splines (histograms in contiguous unfold bins j=1,…,N; the recovered x-ray flux F_{unfold}(t is estimated as ∫S_{unfold}(E,tdE, where E is x-ray energy and t is time. This paper adds two major improvements to the preceding unfold analysis: (a Error analysis.—Both data noise and response-function uncertainties are propagated into S_{unfold}(E,t and F_{unfold}(t. Noise factors ν are derived from simulations to quantify algorithm-induced changes in the noise-to-signal ratio (NSR for S_{unfold} in each unfold bin j and for F_{unfold} (ν≡NSR_{output}/NSR_{input}: for S_{unfold}, 1≲ν_{j}≲30, an outcome that is strongly spectrally dependent; for F_{unfold}, 0.6≲ν_{F}≲1, a result that is less spectrally sensitive and corroborated independently. For nominal z-pinch experiments, the combined uncertainty (noise and calibrations in F_{unfold}(t at peak is estimated to be ∼15%. (b Generalization of the unfold method.—Spectral sensitivities (called here passband functions are constructed for S_{unfold} and F_{unfold}. Predicting how the unfold algorithm reconstructs arbitrary spectra is thereby reduced to quadratures. These tools allow one to understand and quantitatively predict algorithmic distortions (including negative artifacts, to identify potentially troublesome spectra, and to design more useful response functions.

  4. Auxiliary partial liver transplantation

    NARCIS (Netherlands)

    C.B. Reuvers (Cornelis Bastiaan)

    1986-01-01

    textabstractIn this thesis studies on auxiliary partial liver transplantation in the dog and the pig are reported. The motive to perform this study was the fact that patients with acute hepatic failure or end-stage chronic liver disease are often considered to form too great a risk for successful

  5. Partial Remission Definition

    DEFF Research Database (Denmark)

    Andersen, Marie Louise Max; Hougaard, Philip; Pörksen, Sven

    2014-01-01

    OBJECTIVE: To validate the partial remission (PR) definition based on insulin dose-adjusted HbA1c (IDAA1c). SUBJECTS AND METHODS: The IDAA1c was developed using data in 251 children from the European Hvidoere cohort. For validation, 129 children from a Danish cohort were followed from the onset...

  6. Fundamental partial compositeness

    DEFF Research Database (Denmark)

    Sannino, Francesco; Strumia, Alessandro; Tesi, Andrea

    2016-01-01

    We construct renormalizable Standard Model extensions, valid up to the Planck scale, that give a composite Higgs from a new fundamental strong force acting on fermions and scalars. Yukawa interactions of these particles with Standard Model fermions realize the partial compositeness scenario. Unde...

  7. Partially ordered models

    NARCIS (Netherlands)

    Fernandez, R.; Deveaux, V.

    2010-01-01

    We provide a formal definition and study the basic properties of partially ordered chains (POC). These systems were proposed to model textures in image processing and to represent independence relations between random variables in statistics (in the later case they are known as Bayesian networks).

  8. Honesty in partial logic

    NARCIS (Netherlands)

    W. van der Hoek (Wiebe); J.O.M. Jaspars; E. Thijsse

    1995-01-01

    textabstractWe propose an epistemic logic in which knowledge is fully introspective and implies truth, although truth need not imply epistemic possibility. The logic is presented in sequential format and is interpreted in a natural class of partial models, called balloon models. We examine the

  9. Inclusive neutral current ep cross sections with HERA II and two-dimensional unfolding

    International Nuclear Information System (INIS)

    Fischer, David-Johannes

    2011-06-01

    In this thesis, the inclusive neutral current ep → eX cross section at small e - scattering angles has been measured using the electromagnetic SpaCal calorimeter in the backward region of the H1 detector. This calorimeter constructed of lead and scintillating fiber was designed to measure the scattered electron with high resolution in both energy and polar angle. The analysis comprises the kinematic range of 0.06 e 2 e 2 2 for the squared momentum exchange. The data sample consists of positron proton collisions of the years 2006 and 2007, adding up to an integrated luminosity of ∝141 pb -1 . Due to the high luminosity of the HERA II run phase the accuracy is no longer limited by the data statistics but rather by the detector resolution and systematics. The migration becomes increasingly influential; an effect which leads to distortions of the measured distribution as well as to statistical correlations between adjacent data points. At this stage, the correction of detector effects as well as the precise determination of statistical correlations become important features of a rigorous error treatment. In this analysis two-dimensional unfolding has been applied. This is a novel approach to H1 inclusive cross section measurements, which are usually based on a bin-by-bin efficiency correction (bin-by-bin method). With unfolding, the detector effect to the measurements is modelled by a linear transformation (''response matrix'') which is used to correct any distortion of the data. The inclusion of off-diagonal elements results in a coherent assessment of the statistical uncertainties and correlations. The model dependence can be optimally evaluated. In this context, the bin-by-bin method can be viewed as an approximation based on a diagonal response matrix. In a scenario of limited detector resolution, the unfolded data distributions will typically exhibit strong fluctuations and correlations between the data points. This issue can be addressed by smoothing

  10. Inclusive neutral current ep cross sections with HERA II and two-dimensional unfolding

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, David-Johannes

    2011-06-15

    In this thesis, the inclusive neutral current ep {yields} eX cross section at small e{sup -} scattering angles has been measured using the electromagnetic SpaCal calorimeter in the backward region of the H1 detector. This calorimeter constructed of lead and scintillating fiber was designed to measure the scattered electron with high resolution in both energy and polar angle. The analysis comprises the kinematic range of 0.06 < y{sub e} < 0.6 for the inelasticity and 14 GeV{sup 2} < Q{sub e}{sup 2} < 110 GeV{sup 2} for the squared momentum exchange. The data sample consists of positron proton collisions of the years 2006 and 2007, adding up to an integrated luminosity of {proportional_to}141 pb{sup -1}. Due to the high luminosity of the HERA II run phase the accuracy is no longer limited by the data statistics but rather by the detector resolution and systematics. The migration becomes increasingly influential; an effect which leads to distortions of the measured distribution as well as to statistical correlations between adjacent data points. At this stage, the correction of detector effects as well as the precise determination of statistical correlations become important features of a rigorous error treatment. In this analysis two-dimensional unfolding has been applied. This is a novel approach to H1 inclusive cross section measurements, which are usually based on a bin-by-bin efficiency correction (bin-by-bin method). With unfolding, the detector effect to the measurements is modelled by a linear transformation (''response matrix'') which is used to correct any distortion of the data. The inclusion of off-diagonal elements results in a coherent assessment of the statistical uncertainties and correlations. The model dependence can be optimally evaluated. In this context, the bin-by-bin method can be viewed as an approximation based on a diagonal response matrix. In a scenario of limited detector resolution, the unfolded data distributions will

  11. Algebraic partial Boolean algebras

    International Nuclear Information System (INIS)

    Smith, Derek

    2003-01-01

    Partial Boolean algebras, first studied by Kochen and Specker in the 1960s, provide the structure for Bell-Kochen-Specker theorems which deny the existence of non-contextual hidden variable theories. In this paper, we study partial Boolean algebras which are 'algebraic' in the sense that their elements have coordinates in an algebraic number field. Several of these algebras have been discussed recently in a debate on the validity of Bell-Kochen-Specker theorems in the context of finite precision measurements. The main result of this paper is that every algebraic finitely-generated partial Boolean algebra B(T) is finite when the underlying space H is three-dimensional, answering a question of Kochen and showing that Conway and Kochen's infinite algebraic partial Boolean algebra has minimum dimension. This result contrasts the existence of an infinite (non-algebraic) B(T) generated by eight elements in an abstract orthomodular lattice of height 3. We then initiate a study of higher-dimensional algebraic partial Boolean algebras. First, we describe a restriction on the determinants of the elements of B(T) that are generated by a given set T. We then show that when the generating set T consists of the rays spanning the minimal vectors in a real irreducible root lattice, B(T) is infinite just if that root lattice has an A 5 sublattice. Finally, we characterize the rays of B(T) when T consists of the rays spanning the minimal vectors of the root lattice E 8

  12. Study of Different Unfolding Methods of Kinematic Distributions of the WZ$\\,\\to\\,$WZ Scattering with Data and Simulations of the ATLAS Detector at the LHC

    CERN Document Server

    AUTHOR|(CDS)2101612; Siegert, Frank

    It is analyzed in this work which unfolding methods are suited for the P-value calculation in statistical tests. It is analyzed for distributions of Vector Boson Scattering in the channel WZ$\\,\\to\\,$WZ for fully leptonic final states. WZ$\\,\\to\\,$WZ scattering is predicted by the most successful model of particle physics, the Standard Model of Particle Physics - but was not measured yet. It is scheduled to record $100~\\mathrm{fb}^{-1}$ with the ATLAS detector in Run$~$2 at LHC. With that integrated luminosity an observation of that process, via a cross section measurement, is expected. The distributions of the transverse mass of the WZ system $M_T(WZ)$ and the transverse momentum of the Z boson $p_T^Z$ which are sensitive to deviations of the WZ$\\,\\to\\,$WZ scattering from the Standard Model are analyzed in this work. For comparisons between data and theory predictions detector effect have to be considered, for which the theory has to be folded or the data has to be unfolded. In this study, no significant advan...

  13. An activated unfolded protein response promotes retinal degeneration and triggers an inflammatory response in the mouse retina.

    Science.gov (United States)

    Rana, T; Shinde, V M; Starr, C R; Kruglov, A A; Boitet, E R; Kotla, P; Zolotukhin, S; Gross, A K; Gorbatyuk, M S

    2014-12-18

    Recent studies on the endoplasmic reticulum stress have shown that the unfolded protein response (UPR) is involved in the pathogenesis of inherited retinal degeneration caused by mutant rhodopsin. However, the main question of whether UPR activation actually triggers retinal degeneration remains to be addressed. Thus, in this study, we created a mouse model for retinal degeneration caused by a persistently activated UPR to assess the physiological and morphological parameters associated with this disease state and to highlight a potential mechanism by which the UPR can promote retinal degeneration. We performed an intraocular injection in C57BL6 mice with a known unfolded protein response (UPR) inducer, tunicamycin (Tn) and examined animals by electroretinography (ERG), spectral domain optical coherence tomography (SD-OCT) and histological analyses. We detected a significant loss of photoreceptor function (over 60%) and retinal structure (35%) 30 days post treatment. Analysis of retinal protein extracts demonstrated a significant upregulation of inflammatory markers including interleukin-1β (IL-1β), IL-6, tumor necrosis factor-α (TNF-α), monocyte chemoattractant protein-1 (MCP-1) and IBA1. Similarly, we detected a strong inflammatory response in mice expressing either Ter349Glu or T17M rhodopsin (RHO). These mutant rhodopsin species induce severe retinal degeneration and T17M rhodopsin elicits UPR activation when expressed in mice. RNA and protein analysis revealed a significant upregulation of pro- and anti-inflammatory markers such as IL-1β, IL-6, p65 nuclear factor kappa B (NF-kB) and MCP-1, as well as activation of F4/80 and IBA1 microglial markers in both the retinas expressing mutant rhodopsins. We then assessed if the Tn-induced inflammatory marker IL-1β was capable of inducing retinal degeneration by injecting C57BL6 mice with a recombinant IL-1β. We observed ~19% reduction in ERG a-wave amplitudes and a 29% loss of photoreceptor cells compared with

  14. Partial Actions, Paradoxicality and Topological full Groups

    DEFF Research Database (Denmark)

    Scarparo, Eduardo

    uniform Roe algebra is finite. In Article C, we analyze the C*-algebra generated by the Koopman representation of a topological full group, showing, in particular, that it is not AF andhas real rank zero. We also prove that if G is a finitely generated, elementary amenable group, and C*(G) has real rank......We study how paradoxicality properties affect the way groups partially acton topological spaces and C*-algebras. We also investigate the real rank zero and AF properties for certain classes of group C*-algebras. Specifically, in article A, we characterize supramenable groups in terms of existence...... of invariant probability measures for partial actions on compact Hausdorff spaces and existence of tracial states on partial crossed products. These characterizations show that, in general, one cannot decompose a partial crossed product of a C*-algebra by a semidirect product of groups as two iterated...

  15. Unfolding Utzon

    DEFF Research Database (Denmark)

    Kirkegaard, Poul Henning; Hvejsel, Marie Frier

    2014-01-01

    The Danish architect Jørn Utzon's architecture is a fusion of form and structure inspired by nature and the visual universe of different cultures. The organic conception of form is clearly evoked in much of Utzon’s architecture following his genesis idea of an “Additive Architecture” founded in h...... of the Sydney Opera House....

  16. Unfolding Utzon

    DEFF Research Database (Denmark)

    Kirkegaard, Poul Henning

    2013-01-01

    For many, the architecture by j0rn Utzon is synonymous with the design of the Sydney Opera House (1973) that was made a UNESCO World Heritage Site in 2007, being one of the 20th century's most distinctive buildings and one of the most famous concert halls in the world.......For many, the architecture by j0rn Utzon is synonymous with the design of the Sydney Opera House (1973) that was made a UNESCO World Heritage Site in 2007, being one of the 20th century's most distinctive buildings and one of the most famous concert halls in the world....

  17. Sunshine Unfolding.

    Science.gov (United States)

    Holdrege, Craig; And Others

    Hinduism, yoga, transcendental meditation, traditional American Indian philosophies, far-Eastern philosophies (Taoism, Zen Buddhism, and Zen concepts), macrobiotics, and Judeo-Christian teachings are the topics discussed in this student developed book. Designed for use by both elementary and high school students, it was written with two major…

  18. Universe unfolding

    International Nuclear Information System (INIS)

    King, I.R.

    1976-01-01

    Topics covered the setting; looking at the stars; the earth; time, place and the sky; our satellite, the moon; orbits and motion; the motions of the planets; the Copernican revolution; the planets; the other bodies of the solar system; ages, origins, and life; introducing the stars; sorting out the stars; binary stars--two are better than one; variable stars--inconstancy as a virtue; the secrets of starlight--unraveling the spectrum; the sun--our own star; the structure of a star; interstellar material; the Milky Way, our home galaxy; galaxies--the stellar continents; cosmic violence--from radio galaxies to quasars; the universe; and epilogue. The primary emphasis is on how we have come to know what we know about the universe. Star maps are included

  19. Absolute partial photoionization cross sections of ethylene

    Science.gov (United States)

    Grimm, F. A.; Whitley, T. A.; Keller, P. R.; Taylor, J. W.

    1991-07-01

    Absolute partial photoionization cross sections for ionization out of the first four valence orbitals to the X 2B 3u, A 2B 3g, B 2A g and C 2B 2u states of the C 2H 4+ ion are presented as a function of photon energy over the energy range from 12 to 26 eV. The experimental results have been compared to previously published relative partial cross sections for the first two bands at 18, 21 and 24 eV. Comparison of the experimental data with continuum multiple scattering Xα calculations provides evidence for extensive autoionization to the X 2B 3u state and confirms the predicted shape resonances in ionization to the A 2B 3g and B 2A g states. Identification of possible transitions for the autoionizing resonances have been made using multiple scattering transition state calculations on Rydberg excited states.

  20. The inverted chevron plot measured by NMR relaxation reveals a native-like unfolding intermediate in acyl-CoA binding protein

    DEFF Research Database (Denmark)

    Teilum, Kaare; Poulsen, F. M.; Akke, M.

    2006-01-01

    those from stopped-flow kinetics and define an "inverted chevron" plot. The combination of NMR relaxation and stopped-flow kinetic measurements allowed determination of k f and k u in the range from 0.48 M GuHCl to 1.28 M GuHCl. Individually, the stopped-flow and NMR data fit two-state models...... for folding. However, although the values of k f determined by the two methods agree, the values of k u do not. As a result, a combined analysis of all data does not comply with a two-state model but indicates that an unfolding intermediate exists on the native side of the dominant energy barrier...

  1. The stability and formation of native proteins from unfolded monomers is increased through interactions with unrelated proteins.

    Directory of Open Access Journals (Sweden)

    Claudia Rodríguez-Almazán

    Full Text Available The intracellular concentration of protein may be as high as 400 mg per ml; thus it seems inevitable that within the cell, numerous protein-protein contacts are constantly occurring. A basic biochemical principle states that the equilibrium of an association reaction can be shifted by ligand binding. This indicates that if within the cell many protein-protein interactions are indeed taking place, some fundamental characteristics of proteins would necessarily differ from those observed in traditional biochemical systems. Accordingly, we measured the effect of eight different proteins on the formation of homodimeric triosephosphate isomerase from Trypanosoma brucei (TbTIM from guanidinium chloride unfolded monomers. The eight proteins at concentrations of micrograms per ml induced an important increase on active dimer formation. Studies on the mechanism of this phenomenon showed that the proteins stabilize the dimeric structure of TbTIM, and that this is the driving force that promotes the formation of active dimers. Similar data were obtained with TIM from three other species. The heat changes that occur when TbTIM is mixed with lysozyme were determined by isothermal titration calorimetry; the results provided direct evidence of the weak interaction between apparently unrelated proteins. The data, therefore, are strongly suggestive that the numerous protein-protein interactions that occur in the intracellular space are an additional control factor in the formation and stability of proteins.

  2. Photogenic partial seizures.

    Science.gov (United States)

    Hennessy, M J; Binnie, C D

    2000-01-01

    To establish the incidence and symptoms of partial seizures in a cohort of patients investigated on account of known sensitivity to intermittent photic stimulation and/or precipitation of seizures by environmental visual stimuli such as television (TV) screens or computer monitors. We report 43 consecutive patients with epilepsy, who had exhibited a significant EEG photoparoxysmal response or who had seizures precipitated by environmental visual stimuli and underwent detailed assessment of their photosensitivity in the EEG laboratory, during which all were questioned concerning their ictal symptoms. All patients were considered on clinical grounds to have an idiopathic epilepsy syndrome. Twenty-eight (65%) patients reported visually precipitated attacks occurring initially with maintained consciousness, in some instances evolving to a period of confusion or to a secondarily generalized seizure. Visual symptoms were most commonly reported and included positive symptoms such as coloured circles or spots, but also blindness and subjective symptoms such as "eyes going funny." Other symptoms described included nonspecific cephalic sensations, deja-vu, auditory hallucinations, nausea, and vomiting. No patient reported any clear spontaneous partial seizures, and there were no grounds for supposing that any had partial epilepsy excepting the ictal phenomenology of some or all of the visually induced attacks. These findings provide clinical support for the physiological studies that indicate that the trigger mechanism for human photosensitivity involves binocularly innervated cells located in the visual cortex. Thus the visual cortex is the seat of the primary epileptogenic process, and the photically triggered discharges and seizures may be regarded as partial with secondary generalization.

  3. Arthroscopic partial medial meniscectomy

    Directory of Open Access Journals (Sweden)

    Dašić Žarko

    2011-01-01

    Full Text Available Background/Aim. Meniscal injuries are common in professional or recreational sports as well as in daily activities. If meniscal lesions lead to physical impairment they usually require surgical treatment. Arthroscopic treatment of meniscal injuries is one of the most often performed orthopedic operative procedures. Methods. The study analyzed the results of arthroscopic partial medial meniscectomy in 213 patients in a 24-month period, from 2006, to 2008. Results. In our series of arthroscopically treated medial meniscus tears we noted 78 (36.62% vertical complete bucket handle lesions, 19 (8.92% vertical incomplete lesions, 18 (8.45% longitudinal tears, 35 (16.43% oblique tears, 18 (8.45% complex degenerative lesions, 17 (7.98% radial lesions and 28 (13.14% horisontal lesions. Mean preoperative International Knee Documentation Committee (IKDC score was 49.81%, 1 month after the arthroscopic partial medial meniscectomy the mean IKDC score was 84.08%, and 6 months after mean IKDC score was 90.36%. Six months after the procedure 197 (92.49% of patients had good or excellent subjective postoperative clinical outcomes, while 14 (6.57% patients subjectively did not notice a significant improvement after the intervention, and 2 (0.93% patients had no subjective improvement after the partial medial meniscectomy at all. Conclusion. Arthroscopic partial medial meniscetomy is minimally invasive diagnostic and therapeutic procedure and in well selected cases is a method of choice for treatment of medial meniscus injuries when repair techniques are not a viable option. It has small rate of complications, low morbidity and fast rehabilitation.

  4. Hierarchical partial order ranking

    International Nuclear Information System (INIS)

    Carlsen, Lars

    2008-01-01

    Assessing the potential impact on environmental and human health from the production and use of chemicals or from polluted sites involves a multi-criteria evaluation scheme. A priori several parameters are to address, e.g., production tonnage, specific release scenarios, geographical and site-specific factors in addition to various substance dependent parameters. Further socio-economic factors may be taken into consideration. The number of parameters to be included may well appear to be prohibitive for developing a sensible model. The study introduces hierarchical partial order ranking (HPOR) that remedies this problem. By HPOR the original parameters are initially grouped based on their mutual connection and a set of meta-descriptors is derived representing the ranking corresponding to the single groups of descriptors, respectively. A second partial order ranking is carried out based on the meta-descriptors, the final ranking being disclosed though average ranks. An illustrative example on the prioritisation of polluted sites is given. - Hierarchical partial order ranking of polluted sites has been developed for prioritization based on a large number of parameters

  5. Unfolded protein response and activated degradative pathways regulation in GNE myopathy.

    Directory of Open Access Journals (Sweden)

    Honghao Li

    Full Text Available Although intracellular beta amyloid (Aβ accumulation is known as an early upstream event in the degenerative course of UDP-N-acetylglucosamine 2-epimerase/N-acetylmannosamine kinase (GNE myopathy, the process by which Aβdeposits initiate various degradative pathways, and their relationship have not been fully clarified. We studied the possible secondary responses after amyloid beta precursor protein (AβPP deposition including unfolded protein response (UPR, ubiquitin proteasome system (UPS activation and its correlation with autophagy system. Eight GNE myopathy patients and five individuals with normal muscle morphology were included in this study. We performed immunofluorescence and immunoblotting to investigate the expression of AβPP, phosphorylated tau (p-tau and endoplasmic reticulum molecular chaperones. Proteasome activities were measured by cleavage of fluorogenic substrates. The expression of proteasome subunits and linkers between proteasomal and autophagy systems were also evaluated by immunoblotting and relative quantitative real-time RT-PCR. Four molecular chaperones, glucose-regulated protein 94 (GRP94, glucose-regulated protein 78 (GRP78, calreticulin and calnexin and valosin containing protein (VCP were highly expressed in GNE myopathy. 20S proteasome subunits, three main proteasome proteolytic activities, and the factors linking UPS and autophagy system were also increased. Our study suggests that AβPP deposition results in endoplasmic reticulum stress (ERS and highly expressed VCP deliver unfolded proteins from endoplasmic reticulum to proteosomal system which is activated in endoplasmic reticulum associated degradation (ERAD in GNE myopathy. Excessive ubiquitinated unfolded proteins are exported by proteins that connect UPS and autophagy to autophagy system, which is activated as an alternative pathway for degradation.

  6. Glioblastoma and chemoresistance to alkylating agents: Involvement of apoptosis, autophagy, and unfolded protein response.

    Science.gov (United States)

    Hombach-Klonisch, Sabine; Mehrpour, Maryam; Shojaei, Shahla; Harlos, Craig; Pitz, Marshall; Hamai, Ahmed; Siemianowicz, Krzysztof; Likus, Wirginia; Wiechec, Emilia; Toyota, Brian D; Hoshyar, Reyhane; Seyfoori, Amir; Sepehri, Zahra; Ande, Sudharsana R; Khadem, Forough; Akbari, Mohsen; Gorman, Adrienne M; Samali, Afshin; Klonisch, Thomas; Ghavami, Saeid

    2018-04-01

    Despite advances in neurosurgical techniques and radio-/chemotherapy, the treatment of brain tumors remains a challenge. This is particularly true for the most frequent and fatal adult brain tumor, glioblastoma (GB). Upon diagnosis, the average survival time of GB patients remains only approximately 15months. The alkylating drug temozolomide (TMZ) is routinely used in brain tumor patients and induces apoptosis, autophagy and unfolded protein response (UPR). Here, we review these cellular mechanisms and their contributions to TMZ chemoresistance in brain tumors, with a particular emphasis on TMZ chemoresistance in glioma stem cells and GB. Copyright © 2017 Elsevier Inc. All rights reserved.

  7. The effect of the neutron spectra unfolding method on the fast neutron dose determination

    International Nuclear Information System (INIS)

    Marinkovic, P.; Zavaljevski, N.

    1992-01-01

    Based on Shanon's information theory, a new unfolding method which gives non-negative spectrum values and a relatively low variance, is proposed, and a numerical code suitable for application in fast neutron spectroscopy based on proton recoil is developed. The principles of maximum entropy and maximum likelihood are jointly applied. According to the principle of maximum likelihood, the distribution functions around the mean value of the counts in the MCA channels are assumed to be Gaussians. The Lagrange parameter method is applied in the search for an optimal non-negative solution. The nonlinear system of equations is solved using the gradient and Newton iterative algorithms. (orig.)

  8. Bacteria, the endoplasmic reticulum and the unfolded protein response: friends or foes?

    Science.gov (United States)

    Celli, Jean; Tsolis, Renée M

    2015-02-01

    The unfolded protein response (UPR) is a cytoprotective response that is aimed at restoring cellular homeostasis following physiological stress exerted on the endoplasmic reticulum (ER), which also invokes innate immune signalling in response to invading microorganisms. Although it has been known for some time that the UPR is modulated by various viruses, recent evidence indicates that it also has multiple roles during bacterial infections. In this Review, we describe how bacteria interact with the ER, including how bacteria induce the UPR, how subversion of the UPR promotes bacterial proliferation and how the UPR contributes to innate immune responses against invading bacteria.

  9. Study of chemically unfolded {beta}-casein by means of small-angle neutron scattering

    Energy Technology Data Exchange (ETDEWEB)

    Aschi, Adel [Laboratoire de Physique de la Matiere Molle, Faculte des Sciences de Tunis, Campus Universitaire, 1060, Tunis (Tunisia)]. E-mail: aschi13@yahoo.fr; Gharbi, Abdelhafidh [Laboratoire de Physique de la Matiere Molle, Faculte des Sciences de Tunis, Campus Universitaire, 1060, Tunis (Tunisia); Daoud, Mohamed [Service de Physique de l' Etat Condense. CEA Saclay. 91191 Gif-sur-Yvette cedex (France); Douillard, Roger [Equipe de Biochimie des Macromolecules Vegetales, Centre de Recherche Agronomique, 2Esplanade R. Garros, BP 224, 51686 Reims cedex 2 (France); Calmettes, Patrick [Laboratoire Leon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette cedex (France)

    2007-01-01

    {beta}-casein is a flexible amphiphilic milk protein which forms an unfolded conformation in presence of very high denaturant concentrations. The structure of {beta}-casein formed at the bulk was studied by small-angle neutron scattering (SANS). The value of the second virial coefficient of the protein solutions indicates that the interactions between the polypeptide chain and solvent are repulsive. The protein conformation is similar to an excluded volume chain. The corresponding values of the contour length, L, the statistical length, b and the apparent radius of the chain cross-section, R{sub c} are given.

  10. Studying the applicability of densities mixture unfolding for heavy ion jet spectra in the ALICE experiment

    CERN Document Server

    Hackstock, Philip

    2016-01-01

    The results of a three months summer project from July 4th 2016 to September 23rd are presented in this summer student report.\\\\ The method presented in the paper\\footnote{\\url{http://www.sciencedirect.com/science/article/pii/S0168900215000406}} on densities mixture unfolding by Nikolay Gagunashvili and its software implementation were studied. A mind map flowchart, plotting macros and documentation were produced and while an 18 fold performance boost trough parallelization could be achieved, the verdict on the applicability of this method for heavy ion jet spectra in the ALICE experiment remains inconclusive. This is mainly due to a lack of time and complexity of the method and its implementation.

  11. Spectrum unfolding from activation measurements in a CTR-model blanket experiment

    International Nuclear Information System (INIS)

    Kuijpers, L.J.M.

    1977-07-01

    Neutron spectra in a lithium fusion reactor model blanket are determined experimentally by performing SAND II unfolding runs from measured activities. The principles of the iterative SAND II method are given and characteristics of the output are described. The spectra are calculated from available data with the aid of a Monte Carlo program, of which procedure numerical results are given. Both kinds of spectra are compared; when number of input data is varied or different cross section data sets are chosen, inconsistencies in activities or cross section data may be detected. (orig./WL) [de

  12. Unfolding and effective bandstructure calculations as discrete real- and reciprocal-space operations

    Energy Technology Data Exchange (ETDEWEB)

    Boykin, Timothy B., E-mail: boykin@ece.uah.edu [Department of Electrical and Computer Engineering, The University of Alabama in Huntsville, Huntsville, AL 35899 (United States); Ajoy, Arvind [School of Electrical and Computer Engineering, Cornell University, Ithaca, NY 14853 (United States); Ilatikhameneh, Hesameddin; Povolotskyi, Michael; Klimeck, Gerhard [Network for Computational Nanotechnology, School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907 (United States)

    2016-06-15

    In recent years, alloy electronic structure calculations based on supercell Brillouin zone unfolding have become popular. There are a number of formulations of the method which on the surface might appear different. Here we show that a discrete real-space description, based on discrete Fourier transforms, is fully general. Furthermore, such an approach can more easily show the effects of alloy scattering. We present such a method for treating the random alloy problem. This treatment features straightforward mathematics and a transparent physical interpretation of the calculated effective (i.e., approximate) energy bands.

  13. Catalogue of response spectra for unfolding in situ gamma-ray pulse-height distributions

    International Nuclear Information System (INIS)

    Dymke, N.

    1982-01-01

    To unfold in situ gamma-ray pulse-height distributions by means of a response matrix technique, the matrix must be in keeping with the measurement geometry, detector size, and energy range to be covered by the measurements. A methodology has been described for determination of standard gamma-ray spectra needed in deriving response matrices and a spectrum catalogue compiled containing graphs and data for the 0-3 MeV (4 x 4 in. NaI(Tl)) and 0-8 MeV (1.5 x 1.5 in. NaI(Tl)) ranges. (author)

  14. The effect of the neutron spectra unfolding method on the fast neutron dose determination

    International Nuclear Information System (INIS)

    Marinkovic, P.; Avdic, S.; Pesic, M.; Zavaljevski, N

    1992-09-01

    Based on Shanon's information theory, a new unfolding method which gives non-negative spectrum values and a relatively low variance, is proposed, and a numerical code suitable for application in fast neutron spectroscopy based on proton recoil is developed. The principles of maximum entropy and maximum likelihood are jointly applied. According to the principle of maximum likelihood, the distribution functions around the mean value of the counts in the MCA channels are assumed to be Gaussians. The Lagrange parameter method is applied in the search for an optimal non-negative solution. The nonlinear system of equations is solved using the gradient and Newton iterative algorithms. (author)

  15. Study of chemically unfolded β-casein by means of small-angle neutron scattering

    International Nuclear Information System (INIS)

    Aschi, Adel; Gharbi, Abdelhafidh; Daoud, Mohamed; Douillard, Roger; Calmettes, Patrick

    2007-01-01

    β-casein is a flexible amphiphilic milk protein which forms an unfolded conformation in presence of very high denaturant concentrations. The structure of β-casein formed at the bulk was studied by small-angle neutron scattering (SANS). The value of the second virial coefficient of the protein solutions indicates that the interactions between the polypeptide chain and solvent are repulsive. The protein conformation is similar to an excluded volume chain. The corresponding values of the contour length, L, the statistical length, b and the apparent radius of the chain cross-section, R c are given

  16. Unfolding of Ubiquitin Studied by Picosecond Time-Resolved Fluorescence of the Tyrosine Residue

    OpenAIRE

    Noronha, Melinda; Lima, João C.; Bastos, Margarida; Santos, Helena; Maçanita, António L.

    2004-01-01

    The photophysics of the single tyrosine in bovine ubiquitin (UBQ) was studied by picosecond time-resolved fluorescence spectroscopy, as a function of pH and along thermal and chemical unfolding, with the following results: First, at room temperature (25°C) and below pH 1.5, native UBQ shows single-exponential decays. From pH 2 to 7, triple-exponential decays were observed and the three decay times were attributed to the presence of tyrosine, a tyrosine-carboxylate hydrogen-bonded complex, and...

  17. Design of multistable systems via partial synchronization

    Indian Academy of Sciences (India)

    Mohammad Ali Khan

    2017-07-05

    Jul 5, 2017 ... The basic idea of the scheme is to design partial synchronization of states between the coupled systems and ... Numerical simulation results consisting of ... systems of the same order via active control is discussed. In §3, the ...

  18. Optimization studies of carbon additives to negative active material for the purpose of extending the life of VRLA batteries in high-rate partial-state-of-charge operation

    Energy Technology Data Exchange (ETDEWEB)

    Boden, D.P.; Loosemore, D.V.; Spence, M.A.; Wojcinski, T.D. [Hammond Expanders Division, Hammond Group, Inc., 6544 Osborn Avenue, Hammond, IN 46320 (United States)

    2010-07-15

    The negative plates of lead-acid batteries subjected to partial-state-of-charge (PSOC) operation fail because of the development of an electrically inert film of lead sulfate on their surfaces. It has been found that carbon additives to the negative active material can significantly increase their cycle life in this type of operation. In this paper we show that various types of carbon, including graphite, carbon black eliminate the surface development of lead sulfate and that, in their presence, the lead sulfate becomes homogeneously distributed throughout the active material. Examination of active material by energy dispersive spectroscopy after extensive cycling shows that lead formed during charge of lead sulfate preferentially deposits on the carbon particles that have been embedded in the active material. Electrochemical studies have been carried out on a number of types of carbon additives having a wide range of properties. These included flake, expanded and synthetic graphite, isotropically graphitized carbon, carbon black and activated carbon. We have investigated their effect on the resistivity and surface areas of the negative active material and also on such electrochemical properties as active material utilization and cycle life. Most of the carbon additives increase the utilization of the active material and impressive increases in cycle life have been obtained with over 6000 capacity turnovers having been achieved. However, at this time, we have not been able to correlate either the type or the properties of the carbon with capacity or cycle life. Further work is needed in this area. The increases that have been achieved in cycle life provide evidence that the lead-acid battery is a viable low cost option for hybrid-electric vehicle use. (author)

  19. Tempo de protrombina e de tromboplastina parcial ativada em caprinos criados extensivamente no Estado do Rio Grande do Norte Prothrombin time and activated partial thromboplastin time in goats raised extensively at Rio Grande do Norte State, Brazil

    Directory of Open Access Journals (Sweden)

    Benito Soto-Blanco

    2009-03-01

    Full Text Available Neste trabalho objetivou-se estabelecer os padrões de normalidade para tempo de protrombina (TP e tempo de tromboplastina parcial ativada (TTPA em caprinos criados extensivamente no estado do Rio Grande do Norte. Foram utilizados 40 caprinos SRD, 13 machos e 27 fêmeas, adultos, com idades entre 1 e 6 anos, todos clinicamente sadios. As amostras sanguíneas foram coletadas por venopunção jugular em tubos contendo citrato de sódio a 3,8%. O plasma foi imediatamente separado por centrifugação e refrigerado a ± 4ºC e, posteriormente, submetido às determinações de TP e TTPA por meio de métodos manuais utilizando kits comerciais. Os valores obtidos para caprinos da região, de 25,4 ± 0,90 e 39,5 ± 1,41 segundos para TP e TTPA, respectivamente, estavam dentro da normalidade.This study aimed to establish normal pattern for the prothrombin time (PT and activated partial thromboplastin time (APTT in goats extensively raised at Rio Grande do Norte state, Brazil. A total of 40 clinically healthy adult goats (13 males and 27 females aged 1 to 6 years-old was used. Blood samples were collected from jugular vein in tubes containing 3.8% of sodium citrate. The plasma was immediately separated by centrifugation and refrigerated at ± 4ºC and after submitted to PT e APTT determinations through manual methods using commercial kits. The results for goats in the region of 25.4 ± 0.90 and 39.5 ± 1.41 seconds, respectively, for PT and APTT were in an adequate range.

  20. Social determinants and lifestyle risk factors only partially explain the higher prevalence of food insecurity among Aboriginal and Torres Strait Islanders in the Australian state of Victoria: a cross-sectional study

    Science.gov (United States)

    2014-01-01

    Background The prevalence of food insecurity is substantially higher among Australians of Aboriginal or Torres Strait Islander descent. The purpose of this study is to explain the relationship between food insecurity and Aboriginal and Torres Islander status in the state of Victoria. Methods Data were obtained from the 2008 Victorian Population Health Survey; a cross-sectional landline computer-assisted telephone interview survey of 34,168 randomly selected Victorians aged 18 years and older; including 339 Aboriginal and Torres Strait Islanders. We categorised a respondent as food insecure, if in the previous 12 months, they reported having run out of food and not being able to afford to buy more. We used multivariable logistic regression to adjust for age, sex, socioeconomic status (household income), lifestyle risk factors (smoking, alcohol consumption and obesity), social support (ability to get help from family, friends or neighbours), household composition (lone parent status, household with a child, and household size), and geographic location (rurality). Results Aboriginal and Torres Strait Islanders (20.3%) were more likely than their non-Aboriginal and Torres Strait Islander counterparts (5.4%) to have experienced food insecurity; odds ratio (OR) = 4.5 (95% CI; 2.7-7.4). Controlling for age, SES, smoking, obesity and inability to get help from family or friends reduced the odds ratio by 38%; ORadjusted = 2.8 (1.6-5.0). Conclusions Social determinants and lifestyle risk factors only partially explained the higher prevalence of food insecurity among Aboriginal and Torres Strait Islanders in Victoria. Further research is needed to explain the disparity in food insecurity between the two populations in order to inform and guide corrective action. PMID:24924598

  1. Partially ordered algebraic systems

    CERN Document Server

    Fuchs, Laszlo

    2011-01-01

    Originally published in an important series of books on pure and applied mathematics, this monograph by a distinguished mathematician explores a high-level area in algebra. It constitutes the first systematic summary of research concerning partially ordered groups, semigroups, rings, and fields. The self-contained treatment features numerous problems, complete proofs, a detailed bibliography, and indexes. It presumes some knowledge of abstract algebra, providing necessary background and references where appropriate. This inexpensive edition of a hard-to-find systematic survey will fill a gap i

  2. Infinite partial summations

    International Nuclear Information System (INIS)

    Sprung, D.W.L.

    1975-01-01

    This paper is a brief review of those aspects of the effective interaction problem that can be grouped under the heading of infinite partial summations of the perturbation series. After a brief mention of the classic examples of infinite summations, the author turns to the effective interaction problem for two extra core particles. Their direct interaction is summed to produce the G matrix, while their indirect interaction through the core is summed in a variety of ways under the heading of core polarization. (orig./WL) [de

  3. On universal partial words

    OpenAIRE

    Chen, Herman Z. Q.; Kitaev, Sergey; Mütze, Torsten; Sun, Brian Y.

    2016-01-01

    A universal word for a finite alphabet $A$ and some integer $n\\geq 1$ is a word over $A$ such that every word in $A^n$ appears exactly once as a subword (cyclically or linearly). It is well-known and easy to prove that universal words exist for any $A$ and $n$. In this work we initiate the systematic study of universal partial words. These are words that in addition to the letters from $A$ may contain an arbitrary number of occurrences of a special `joker' symbol $\\Diamond\

  4. Partial differential equations

    CERN Document Server

    Levine, Harold

    1997-01-01

    The subject matter, partial differential equations (PDEs), has a long history (dating from the 18th century) and an active contemporary phase. An early phase (with a separate focus on taut string vibrations and heat flow through solid bodies) stimulated developments of great importance for mathematical analysis, such as a wider concept of functions and integration and the existence of trigonometric or Fourier series representations. The direct relevance of PDEs to all manner of mathematical, physical and technical problems continues. This book presents a reasonably broad introductory account of the subject, with due regard for analytical detail, applications and historical matters.

  5. Partial differential equations

    CERN Document Server

    Sloan, D; Süli, E

    2001-01-01

    /homepage/sac/cam/na2000/index.html7-Volume Set now available at special set price ! Over the second half of the 20th century the subject area loosely referred to as numerical analysis of partial differential equations (PDEs) has undergone unprecedented development. At its practical end, the vigorous growth and steady diversification of the field were stimulated by the demand for accurate and reliable tools for computational modelling in physical sciences and engineering, and by the rapid development of computer hardware and architecture. At the more theoretical end, the analytical insight in

  6. Elliptic partial differential equations

    CERN Document Server

    Han, Qing

    2011-01-01

    Elliptic Partial Differential Equations by Qing Han and FangHua Lin is one of the best textbooks I know. It is the perfect introduction to PDE. In 150 pages or so it covers an amazing amount of wonderful and extraordinary useful material. I have used it as a textbook at both graduate and undergraduate levels which is possible since it only requires very little background material yet it covers an enormous amount of material. In my opinion it is a must read for all interested in analysis and geometry, and for all of my own PhD students it is indeed just that. I cannot say enough good things abo

  7. Generalized Partial Volume

    DEFF Research Database (Denmark)

    Darkner, Sune; Sporring, Jon

    2011-01-01

    Mutual Information (MI) and normalized mutual information (NMI) are popular choices as similarity measure for multimodal image registration. Presently, one of two approaches is often used for estimating these measures: The Parzen Window (PW) and the Generalized Partial Volume (GPV). Their theoret...... of view as well as w.r.t. computational complexity. Finally, we present algorithms for both approaches for NMI which is comparable in speed to Sum of Squared Differences (SSD), and we illustrate the differences between PW and GPV on a number of registration examples....

  8. Predictors of natively unfolded proteins: unanimous consensus score to detect a twilight zone between order and disorder in generic datasets

    Directory of Open Access Journals (Sweden)

    Deiana Antonio

    2010-04-01

    Full Text Available Abstract Background Natively unfolded proteins lack a well defined three dimensional structure but have important biological functions, suggesting a re-assignment of the structure-function paradigm. To assess that a given protein is natively unfolded requires laborious experimental investigations, then reliable sequence-only methods for predicting whether a sequence corresponds to a folded or to an unfolded protein are of interest in fundamental and applicative studies. Many proteins have amino acidic compositions compatible both with the folded and unfolded status, and belong to a twilight zone between order and disorder. This makes difficult a dichotomic classification of protein sequences into folded and natively unfolded ones. In this work we propose an operational method to identify proteins belonging to the twilight zone by combining into a consensus score good performing single predictors of folding. Results In this methodological paper dichotomic folding indexes are considered: hydrophobicity-charge, mean packing, mean pairwise energy, Poodle-W and a new global index, that is called here gVSL2, based on the local disorder predictor VSL2. The performance of these indexes is evaluated on different datasets, in particular on a new dataset composed by 2369 folded and 81 natively unfolded proteins. Poodle-W, gVSL2 and mean pairwise energy have good performance and stability in all the datasets considered and are combined into a strictly unanimous combination score SSU, that leaves proteins unclassified when the consensus of all combined indexes is not reached. The unclassified proteins: i belong to an overlap region in the vector space of amino acidic compositions occupied by both folded and unfolded proteins; ii are composed by approximately the same number of order-promoting and disorder-promoting amino acids; iii have a mean flexibility intermediate between that of folded and that of unfolded proteins. Conclusions Our results show that

  9. Development of unfolding method to obtain pin-wise source strength distribution from PWR spent fuel assembly measurement

    International Nuclear Information System (INIS)

    Sitompul, Yos Panagaman; Shin, Hee-Sung; Park, Se-Hwan; Oh, Jong Myeong; Seo, Hee; Kim, Ho Dong

    2013-01-01

    An unfolding method has been developed to obtain a pin-wise source strength distribution of a 14 × 14 pressurized water reactor (PWR) spent fuel assembly. Sixteen measured gamma dose rates at 16 control rod guide tubes of an assembly are unfolded to 179 pin-wise source strengths of the assembly. The method calculates and optimizes five coefficients of the quadratic fitting function for X-Y source strength distribution, iteratively. The pin-wise source strengths are obtained at the sixth iteration, with a maximum difference between two sequential iterations of about 0.2%. The relative distribution of pin-wise source strength from the unfolding is checked using a comparison with the design code (Westinghouse APA code). The result shows that the relative distribution from the unfolding and design code is consistent within a 5% difference. The absolute value of the pin-wise source strength is also checked by reproducing the dose rates at the measurement points. The result shows that the pin-wise source strengths from the unfolding reproduce the dose rates within a 2% difference. (author)

  10. A broadband gamma-ray spectrometry using novel unfolding algorithms for characterization of laser wakefield-generated betatron radiation

    Energy Technology Data Exchange (ETDEWEB)

    Jeon, Jong Ho, E-mail: jhjeon07@ibs.re.kr; Nakajima, Kazuhisa, E-mail: naka115@dia-net.ne.jp; Pathak, Vishwa Bandhu; Cho, Myung Hoon; Yoo, Byung Ju; Shin, Kang Woo [Center for Relativistic Laser Science, Institute for Basic Science (IBS), Gwangju 500-712 (Korea, Republic of); Kim, Hyung Taek; Sung, Jae Hee; Lee, Seung Ku; Choi, Il Woo [Center for Relativistic Laser Science, Institute for Basic Science (IBS), Gwangju 500-712 (Korea, Republic of); Advanced Photonics Research Institute, GIST, Gwangju 500-712 (Korea, Republic of); Rhee, Yong Joo [Nuclear Data Center, Korea Atomic Energy Research Institute, Daejeon 305-353 (Korea, Republic of); Shin, Jung Hun; Jo, Sung Ha [Advanced Photonics Research Institute, GIST, Gwangju 500-712 (Korea, Republic of); Hojbota, Calin; Cho, Byeoung Ick; Nam, Chang Hee [Center for Relativistic Laser Science, Institute for Basic Science (IBS), Gwangju 500-712 (Korea, Republic of); Department of Physics and Photon Science, GIST, Gwangju 500-712 (Korea, Republic of)

    2015-12-15

    We present a high-flux, broadband gamma-ray spectrometry capable of characterizing the betatron radiation spectrum over the photon energy range from 10 keV to 20 MeV with respect to the peak photon energy, spectral bandwidth, and unique discrimination from background radiations, using a differential filtering spectrometer and the unfolding procedure based on the Monte Carlo code GEANT4. These properties are experimentally verified by measuring betatron radiation from a cm-scale laser wakefield accelerator (LWFA) driven by a 1-PW laser, using a differential filtering spectrometer consisting of a 15-filter and image plate stack. The gamma-ray spectra were derived by unfolding the photostimulated luminescence (PSL) values recorded on the image plates, using the spectrometer response matrix modeled with the Monte Carlo code GEANT4. The accuracy of unfolded betatron radiation spectra was assessed by unfolding the test PSL data simulated with GEANT4, showing an ambiguity of less than 20% and clear discrimination from the background radiation with less than 10%. The spectral analysis of betatron radiation from laser wakefield-accelerated electron beams with energies up to 3 GeV revealed radiation spectra characterized by synchrotron radiation with the critical photon energy up to 7 MeV. The gamma-ray spectrometer and unfolding method presented here facilitate an in-depth understanding of betatron radiation from LWFA process and a novel radiation source of high-quality photon beams in the MeV regime.

  11. An approach to unfold the response of a multi-element system using an artificial neural network

    International Nuclear Information System (INIS)

    Cordes, E.; Fehrenbacher, G.; Schuetz, R.; Sprunck, M.; Hahn, K.; Hofmann, R.; Wahl, W.

    1998-01-01

    An unfolding procedure is proposed which aims at obtaining spectral information of a neutron radiation field by the analysis of the response of a multi-element system consisting of converter type semiconductors. For the unfolding procedure an artificial neural network (feed forward network), trained by the back-propagation method, was used. The response functions of the single elements to neutron radiation were calculated by application of a computational model for an energy range from 10 -2 eV to 10 MeV. The training of the artificial neural network was based on the computation of responses of a six-element system for a set of 300 neutron spectra and the application of the back-propagation method. The validation was performed by the unfolding of 100 computed responses. Two unfolding examples were pointed out for the determination of the neutron spectra. The spectra resulting from the unfolding procedure agree well with the original spectra used for the response computation

  12. Time-dependent, x-ray spectral unfolds and brightness temperatures for intense Li+ ion beam-driven hohlraums

    International Nuclear Information System (INIS)

    Fehl, D.L.; Chandler, G.A.; Biggs, F.; Dukart, R.J.; Moats, A.R.; Leeper, R.J.

    1996-01-01

    X-ray-producing hohlraums are being studied as indirect drives for Inertial Confinement Fusion targets. In a 1994 target series on the PBFAII accelerator, cylindrical hohlraum targets were heated by an intense Li + ion beam and viewed by an array of 13 time-resolved, filtered x-ray detectors (XRDs). The UFO unfold code and its suite of auxiliary functions were used extensively in obtaining time- resolved x-ray spectra and radiation temperatures from this diagnostic. UFO was also used to obtain fitted response functions from calibration data, to simulate data from blackbody x-ray spectra of interest, to determine the suitability of various unfolding parameters (e.g., energy domain, energy partition, smoothing conditions, and basis functions), to interpolate the XRD signal traces, and to unfold experimental data. The simulation capabilities of the code were useful in understanding an anomalous feature in the unfolded spectra at low photon energies (≤ 100 eV). Uncertainties in the differential and energy-integrated unfolded spectra were estimated from uncertainties in the data. The time-history of the radiation temperature agreed well with independent calculations of the wall temperature in the hohlraum

  13. Time-dependent, x-ray spectral unfolds and brightness temperatures for intense Li+ ion beam-driven hohlraums

    International Nuclear Information System (INIS)

    Fehl, D.L.; Chandler, G.A.; Biggs, F.; Dukart, R.J.; Moats, A.R.; Leeper, R.J.

    1997-01-01

    X-ray-producing hohlraums are being studied as indirect drives for inertial confinement fusion targets. In a 1994 target series on the PBFAII accelerator, cylindrical hohlraum targets were heated by an intense Li + ion beam and viewed by an array of 13 time-resolved, filtered x-ray detectors (XRDs). The unfold operator (UFO) code and its suite of auxiliary functions were used extensively in obtaining time-resolved x-ray spectra and radiation temperatures from this diagnostic. The UFO was also used to obtain fitted response functions from calibration data, to simulate data from blackbody x-ray spectra of interest, to determine the suitability of various unfolding parameters (e.g., energy domain, energy partition, smoothing conditions, and basis functions), to interpolate the XRD signal traces, and to unfold experimental data. The simulation capabilities of the code were useful in understanding an anomalous feature in the unfolded spectra at low photon energies (≤100 eV). Uncertainties in the differential and energy-integrated unfolded spectra were estimated from uncertainties in the data. The time endash history of the radiation temperature agreed well with independent calculations of the wall temperature in the hohlraum. copyright 1997 American Institute of Physics

  14. Unilateral removable partial dentures.

    Science.gov (United States)

    Goodall, W A; Greer, A C; Martin, N

    2017-01-27

    Removable partial dentures (RPDs) are widely used to replace missing teeth in order to restore both function and aesthetics for the partially dentate patient. Conventional RPD design is frequently bilateral and consists of a major connector that bridges both sides of the arch. Some patients cannot and will not tolerate such an extensive appliance. For these patients, bridgework may not be a predictable option and it is not always possible to provide implant-retained restorations. This article presents unilateral RPDs as a potential treatment modality for such patients and explores indications and contraindications for their use, including factors relating to patient history, clinical presentation and patient wishes. Through case examples, design, material and fabrication considerations will be discussed. While their use is not widespread, there are a number of patients who benefit from the provision of unilateral RPDs. They are a useful treatment to have in the clinician's armamentarium, but a highly-skilled dental team and a specific patient presentation is required in order for them to be a reasonable and predictable prosthetic option.

  15. The structural basis of urea-induced protein unfolding in β-catenin

    Science.gov (United States)

    Wang, Chao; Chen, Zhongzhou; Hong, Xia; Ning, Fangkun; Liu, Haolin; Zang, Jianye; Yan, Xiaoxue; Kemp, Jennifer; Musselman, Catherine A.; Kutateladze, Tatinna G.; Zhao, Rui; Jiang, Chengyu; Zhang, Gongyi

    2014-01-01

    Although urea and guanidine hydrochloride are commonly used to denature proteins, the molecular underpinnings of this process have remained unclear for a century. To address this question, crystal structures of β-catenin were determined at various urea concentrations. These structures contained at least 105 unique positions that were occupied by urea molecules, each of which interacted with the protein primarily via hydrogen bonds. Hydrogen-bond competition experiments showed that the denaturing effects of urea were neutralized when polyethylene glycol was added to the solution. These data suggest that urea primarily causes proteins to unfold by competing and disrupting hydrogen bonds in proteins. Moreover, circular-dichroism spectra and nuclear magnetic resonance (NMR) analysis revealed that a similar mechanism caused protein denaturation in the absence of urea at pH levels greater than 12. Taken together, the results led to the conclusion that the disruption of hydrogen bonds is a general mechanism of unfolding induced by urea, high pH and potentially other denaturing agents such as guanidine hydrochloride. Traditionally, the disruption of hydrophobic inter­actions instead of hydrogen bonds has been thought to be the most important cause of protein denaturation. PMID:25372676

  16. Influence of Neutron Spectra Unfolding Method on Fast Neutron Dose Determination

    International Nuclear Information System (INIS)

    Marinkovic, P.

    1991-01-01

    Full text: Accuracy of knowing the fast neutron spectra has great influence on equivalent dose determination. In usual fast neutron spectrum measurements with scintillation detectors based on proton recoil, the main difficulty is confidence of unfolding method. In former ones variance of obtained result is usually great and negative values are possible too, which does means that we don't now exactly is obtained neutron spectrum real one. The new unfolding method based on Shanon's information theory, which gives non-negative spectrum and relative low variance, is obtained and appropriate numerical code for application in fast neutron spectrometry based on proton recoil is realized. In this method principle of maximum entropy and maximum likelihood are used together. Unknown group density distribution functions, which are considered as desired normalized mean neutron group flux, are constl u cted using only constrain of knowing mean value. Obtained distributions are consistent to available information (counts in NCA from proton recoil), while being maximally noncommittal with respect to all other unknown circumstances. For maximum likelihood principle, distribution functions around mean value of counts in the channels of MCA are taken to be Gauss function shape. Optimal non-negative solution is searched by means of Lagrange parameter method. Nonlinear system of equations, is solved using gradient and Newton iterative algorithm. Error covariance matrix is obtained too. (author)

  17. Optimization of expression and purification of human mortalin (Hsp70): Folding/unfolding analysis

    Science.gov (United States)

    Khan, Mohd Shahnawaz; Ahmed, Anwar; Tabrez, Shams; Islam, Badar ul; Rabbani, Nayyar; Malik, Ajamaluddin; Ismael, Mohamad A.; Alsenaidy, Mohammad A.; Alsenaidy, Abdulrahman M.

    2017-12-01

    Human mortalin is a Hsp70 mitochondrial protein that plays an essential role in the biogenesis of mitochondria. The deregulation of mortalin expression and its functions could lead to several age-associated disorders and some types of cancers. In the present study, we optimized the expression and purification of recombinant human mortalin by the use of two-step chromatography. Low temperature (18 °C) and 0.5 mM (IPTG) was required for optimum mortalin expression. Chaperone activity of mortalin was assessed by the citrate synthase and insulin protection assay, which suggested their protective role in mitochondria. Folding and unfolding assessments of mortalin were carried out in the presence of guanidine hydrochloride (GdnHCl) by intrinsic fluorescence measurement, ANS (8-analino 1-nephthlene sulfonic acid) binding and CD (circular dichroism) analysis. Under denaturing conditions, mortalin showed decrease in tryptophan fluorescence intensity along with a red shift of 11 nm. Moreover, ANS binding studies illustrated decrease in hydrophobicity. CD measurement of mortalin showed a predominant helical structure. However, the secondary structure was lost at low concentration of GdnHCl (1 M). We present a simple and robust method to produce soluble mortalin and warranted that chaperones are also susceptible to unfolding and futile to maintain protein homeostasis.

  18. Advances and New Concepts in Alcohol-Induced Organelle Stress, Unfolded Protein Responses and Organ Damage

    Directory of Open Access Journals (Sweden)

    Cheng Ji

    2015-06-01

    Full Text Available Alcohol is a simple and consumable biomolecule yet its excessive consumption disturbs numerous biological pathways damaging nearly all organs of the human body. One of the essential biological processes affected by the harmful effects of alcohol is proteostasis, which regulates the balance between biogenesis and turnover of proteins within and outside the cell. A significant amount of published evidence indicates that alcohol and its metabolites directly or indirectly interfere with protein homeostasis in the endoplasmic reticulum (ER causing an accumulation of unfolded or misfolded proteins, which triggers the unfolded protein response (UPR leading to either restoration of homeostasis or cell death, inflammation and other pathologies under severe and chronic alcohol conditions. The UPR senses the abnormal protein accumulation and activates transcription factors that regulate nuclear transcription of genes related to ER function. Similarly, this kind of protein stress response can occur in other cellular organelles, which is an evolving field of interest. Here, I review recent advances in the alcohol-induced ER stress response as well as discuss new concepts on alcohol-induced mitochondrial, Golgi and lysosomal stress responses and injuries.

  19. Digital force-feedback for protein unfolding experiments using atomic force microscopy

    Science.gov (United States)

    Bippes, Christian A.; Janovjak, Harald; Kedrov, Alexej; Muller, Daniel J.

    2007-01-01

    Since its invention in the 1990s single-molecule force spectroscopy has been increasingly applied to study protein (un-)folding, cell adhesion, and ligand-receptor interactions. In most force spectroscopy studies, the cantilever of an atomic force microscope (AFM) is separated from a surface at a constant velocity, thus applying an increasing force to folded bio-molecules or bio-molecular bonds. Recently, Fernandez and co-workers introduced the so-called force-clamp technique. Single proteins were subjected to a defined constant force allowing their life times and life time distributions to be directly measured. Up to now, the force-clamping was performed by analogue PID controllers, which require complex additional hardware and might make it difficult to combine the force-feedback with other modes such as constant velocity. These points may be limiting the applicability and versatility of this technique. Here we present a simple, fast, and all-digital (software-based) PID controller that yields response times of a few milliseconds in combination with a commercial AFM. We demonstrate the performance of our feedback loop by force-clamp unfolding of single Ig27 domains of titin and the membrane proteins bacteriorhodopsin (BR) and the sodium/proton antiporter NhaA.

  20. Digital force-feedback for protein unfolding experiments using atomic force microscopy

    International Nuclear Information System (INIS)

    Bippes, Christian A; Janovjak, Harald; Kedrov, Alexej; Muller, Daniel J

    2007-01-01

    Since its invention in the 1990s single-molecule force spectroscopy has been increasingly applied to study protein (un-)folding, cell adhesion, and ligand-receptor interactions. In most force spectroscopy studies, the cantilever of an atomic force microscope (AFM) is separated from a surface at a constant velocity, thus applying an increasing force to folded bio-molecules or bio-molecular bonds. Recently, Fernandez and co-workers introduced the so-called force-clamp technique. Single proteins were subjected to a defined constant force allowing their life times and life time distributions to be directly measured. Up to now, the force-clamping was performed by analogue PID controllers, which require complex additional hardware and might make it difficult to combine the force-feedback with other modes such as constant velocity. These points may be limiting the applicability and versatility of this technique. Here we present a simple, fast, and all-digital (software-based) PID controller that yields response times of a few milliseconds in combination with a commercial AFM. We demonstrate the performance of our feedback loop by force-clamp unfolding of single Ig27 domains of titin and the membrane proteins bacteriorhodopsin (BR) and the sodium/proton antiporter NhaA