DEFF Research Database (Denmark)
Guglielmi, Michel; Johannesen, Hl
, Essex, Hertfordshire, Norfolk and Suffolk. Research found that there was a lack of identity or sense of belonging and nothing anchoring people to the region as a whole. Common affinity is somehow forced to the people of East England and thereby we came to the conclusion that a single landmark or a...... a sense of belonging to people sharing deterritorialized synchronic experiences. But at the same time, the immersion experience is highly low tech and desperately analog, mainly based on fabulation, cartoons, and mushrooms growing in local forests. It ultimately appeals to the experienced sense of...
J. Navarro; Sancho, C.; Sancho, P.
2009-01-01
A functor of sets $\\mathbb X$ over the category of $K$-commutative algebras is said to be an affine functor if its functor of functions, $\\mathbb A_{\\mathbb X}$, is reflexive and $\\mathbb X=\\Spec \\mathbb A_{\\mathbb X}$. We prove that affine functors are equal to a direct limit of affine schemes and that affine schemes, formal schemes, the completion of affine schemes along a closed subscheme, etc., are affine functors. Endowing an affine functor $\\mathbb X$ with a functor of monoids structure...
Meyer, Mathieu; Schuett, Carsten; Werner, Elisabeth M.
2013-01-01
An affine invariant point on the class of convex bodies in R^n, endowed with the Hausdorff metric, is a continuous map p which is invariant under one-to-one affine transformations A on R^n, that is, p(A(K))=A(p(K)). We define here the new notion of dual affine point q of an affine invariant point p by the formula q(K^{p(K)})=p(K) for every convex body K, where K^{p(K)} denotes the polar of K with respect to p(K). We investigate which affine invariant points do have a dual point, whether this ...
DEFF Research Database (Denmark)
Høholdt, Tom; Beelen, Peter; Ghorpade, Sudhir Ramakant
2010-01-01
We consider a new class of linear codes, called affine Grassmann codes. These can be viewed as a variant of generalized Reed-Muller codes and are closely related to Grassmann codes.We determine the length, dimension, and the minimum distance of any affine Grassmann code. Moreover, we show that...... affine Grassmann codes have a large automorphism group and determine the number of minimum weight codewords....
Affine and Projective Geometry
Bennett, M K
1995-01-01
An important new perspective on AFFINE AND PROJECTIVE GEOMETRY. This innovative book treats math majors and math education students to a fresh look at affine and projective geometry from algebraic, synthetic, and lattice theoretic points of view. Affine and Projective Geometry comes complete with ninety illustrations, and numerous examples and exercises, covering material for two semesters of upper-level undergraduate mathematics. The first part of the book deals with the correlation between synthetic geometry and linear algebra. In the second part, geometry is used to introduce lattice theory
Energy Technology Data Exchange (ETDEWEB)
Gueltekin, Kemal [Izmir Institute of Technology, Department of Physics, Izmir (Turkey)
2016-03-15
In this study, we give a thorough analysis of a general affine gravity with torsion. After a brief exposition of the affine gravities considered by Eddington and Schroedinger, we construct and analyze different affine gravities based on the determinants of the Ricci tensor, the torsion tensor, the Riemann tensor, and their combinations. In each case we reduce equations of motion to their simplest forms and give a detailed analysis of their solutions. Our analyses lead to the construction of the affine connection in terms of the curvature and torsion tensors. Our solutions of the dynamical equations show that the curvature tensors at different points are correlated via non-local, exponential rescaling factors determined by the torsion tensor. (orig.)
Affine and degenerate affine BMW algebras: Actions on tensor space
Daugherty, Zajj; Virk, Rahbar
2012-01-01
The affine and degenerate affine Birman-Murakami-Wenzl (BMW) algebras arise naturally in the context of Schur-Weyl duality for orthogonal and symplectic quantum groups and Lie algebras, respectively. Cyclotomic BMW algebras, affine and cyclotomic Hecke algebras, and their degenerate versions are quotients. In this paper we explain how the affine and degenerate affine BMW algebras are tantalizers (tensor power centralizer algebras) by defining actions of the affine braid group and the degenerate affine braid algebra on tensor space and showing that, in important cases, these actions induce actions of the affine and degenerate affine BMW algebras. We then exploit the connection to quantum groups and Lie algebras to determine universal parameters for the affine and degenerate affine BMW algebras. Finally, we show that the universal parameters are central elements--the higher Casimir elements for orthogonal and symplectic enveloping algebras and quantum groups.
DEFF Research Database (Denmark)
Skjødt, Mette Louise
Yeast surface display is an effective tool for antibody affinity maturation because yeast can be used as an all-in-one workhorse to assemble, display and screen diversified antibody libraries. By employing the natural ability of yeast Saccharomyces cerevisiae to efficiently recombine multiple DNA...
Affine and degenerate affine BMW algebras: The center
Daugherty, Zajj; Virk, Rahbar
2011-01-01
The degenerate affine and affine BMW algebras arise naturally in the context of Schur-Weyl duality for orthogonal and symplectic Lie algebras and quantum groups, respectively. Cyclotomic BMW algebras, affine Hecke algebras, cyclotomic Hecke algebras, and their degenerate versions are quotients. In this paper the theory is unified by treating the orthogonal and symplectic cases simultaneously; we make an exact parallel between the degenerate affine and affine cases via a new algebra which takes the role of the affine braid group for the degenerate setting. A main result of this paper is an identification of the centers of the affine and degenerate affine BMW algebras in terms of rings of symmetric functions which satisfy a "cancellation property" or "wheel condition" (in the degenerate case, a reformulation of a result of Nazarov). Miraculously, these same rings also arise in Schubert calculus, as the cohomology and K-theory of isotropic Grassmanians and symplectic loop Grassmanians. We also establish new inte...
Hierarchical Affinity Propagation
Givoni, Inmar; Frey, Brendan J
2012-01-01
Affinity propagation is an exemplar-based clustering algorithm that finds a set of data-points that best exemplify the data, and associates each datapoint with one exemplar. We extend affinity propagation in a principled way to solve the hierarchical clustering problem, which arises in a variety of domains including biology, sensor networks and decision making in operational research. We derive an inference algorithm that operates by propagating information up and down the hierarchy, and is efficient despite the high-order potentials required for the graphical model formulation. We demonstrate that our method outperforms greedy techniques that cluster one layer at a time. We show that on an artificial dataset designed to mimic the HIV-strain mutation dynamics, our method outperforms related methods. For real HIV sequences, where the ground truth is not available, we show our method achieves better results, in terms of the underlying objective function, and show the results correspond meaningfully to geographi...
Affinity driven social networks
Ruyú, B.; Kuperman, M. N.
2007-04-01
In this work we present a model for evolving networks, where the driven force is related to the social affinity between individuals of a population. In the model, a set of individuals initially arranged on a regular ordered network and thus linked with their closest neighbors are allowed to rearrange their connections according to a dynamics closely related to that of the stable marriage problem. We show that the behavior of some topological properties of the resulting networks follows a non trivial pattern.
Affine General Equilibrium Models
Bjørn Eraker
2008-01-01
No-arbitrage models are extremely flexible modelling tools but often lack economic motivation. This paper describes an equilibrium consumption-based CAPM framework based on Epstein-Zin preferences, which produces analytic pricing formulas for stocks and bonds under the assumption that macro growth rates follow affine processes. This allows the construction of equilibrium pricing formulas while maintaining the same flexibility of state dynamics as in no-arbitrage models. In demonstrating the a...
Gaussian Affine Feature Detector
Xu, Xiaopeng; Zhang, Xiaochun
2011-01-01
A new method is proposed to get image features' geometric information. Using Gaussian as an input signal, a theoretical optimal solution to calculate feature's affine shape is proposed. Based on analytic result of a feature model, the method is different from conventional iterative approaches. From the model, feature's parameters such as position, orientation, background luminance, contrast, area and aspect ratio can be extracted. Tested with synthesized and benchmark data, the method achieve...
On the Affine Isoperimetric Inequalities
Indian Academy of Sciences (India)
Wuyang Yu; Gangsong Leng
2011-11-01
We obtain an isoperimetric inequality which estimate the affine invariant -surface area measure on convex bodies. We also establish the reverse version of -Petty projection inequality and an affine isoperimetric inequality of $_{-p}K$.
Adjoint affine fusion and tadpoles
Urichuk, Andrew; Walton, Mark A.
2016-01-01
We study affine fusion with the adjoint representation. For simple Lie algebras, elementary and universal formulas determine the decomposition of a tensor product of an integrable highest-weight representation with the adjoint representation. Using the (refined) affine depth rule, we prove that equally striking results apply to adjoint affine fusion. For diagonal fusion, a coefficient equals the number of nonzero Dynkin labels of the relevant affine highest weight, minus 1. A nice lattice-pol...
Gaussian Affine Feature Detector
Xu, Xiaopeng
2011-01-01
A new method is proposed to get image features' geometric information. Using Gaussian as an input signal, a theoretical optimal solution to calculate feature's affine shape is proposed. Based on analytic result of a feature model, the method is different from conventional iterative approaches. From the model, feature's parameters such as position, orientation, background luminance, contrast, area and aspect ratio can be extracted. Tested with synthesized and benchmark data, the method achieves or outperforms existing approaches in term of accuracy, speed and stability. The method can detect small, long or thin objects precisely, and works well under general conditions, such as for low contrast, blurred or noisy images.
Affinity Purification of Insulin by Peptide-Ligand Affinity Chromatography
Institute of Scientific and Technical Information of China (English)
无
2007-01-01
The affinity heptapeptide (HWWWPAS) for insulin, selected from phage display library,was coupled to EAH Sepharose 4B gel and packed to a 1-mL column. The column was used for the affinity purification of insulin from protein mixture and commercial insulin preparation. It was observed that the minor impurity in the commercial insulin was removed by the affinity chromatography. Nearly 40 mg of insulin could be purified with the 1-mL affinity column. The results revealed the high specificity and capacity of the affinity column for insulin purification. Moreover, based on the analysis of the amino acids in the peptide sequence, shorter peptides were designed and synthesized for insulin chromatography. As a result, HWWPS was found to be a good alternative to HWWWPAS, while the other two peptides with three or four amino acids showed weak affinity for insulin. The results indicated that the peptide sequence of HWWWPAS was quite conservative for specific binding of insulin.
An affine framework for analytical mechanics
Urbanski, Pawel
2003-01-01
An affine Cartan calculus is developed. The concepts of special affine bundles and special affine duality are introduced. The canonical isomorphisms, fundamental for Lagrangian and Hamiltonian formulations of the dynamics in the affine setting are proved.
Adjoint affine fusion and tadpoles
Urichuk, Andrew; Walton, Mark A.
2016-06-01
We study affine fusion with the adjoint representation. For simple Lie algebras, elementary and universal formulas determine the decomposition of a tensor product of an integrable highest-weight representation with the adjoint representation. Using the (refined) affine depth rule, we prove that equally striking results apply to adjoint affine fusion. For diagonal fusion, a coefficient equals the number of nonzero Dynkin labels of the relevant affine highest weight, minus 1. A nice lattice-polytope interpretation follows and allows the straightforward calculation of the genus-1 1-point adjoint Verlinde dimension, the adjoint affine fusion tadpole. Explicit formulas, (piecewise) polynomial in the level, are written for the adjoint tadpoles of all classical Lie algebras. We show that off-diagonal adjoint affine fusion is obtained from the corresponding tensor product by simply dropping non-dominant representations.
Adjoint affine fusion and tadpoles
Urichuk, Andrew
2016-01-01
We study affine fusion with the adjoint representation. For simple Lie algebras, elementary and universal formulas determine the decomposition of a tensor product of an integrable highest-weight representation with the adjoint representation. Using the (refined) affine depth rule, we prove that equally striking results apply to adjoint affine fusion. For diagonal fusion, a coefficient equals the number of nonzero Dynkin labels of the relevant affine highest weight, minus 1. A nice lattice-polytope interpretation follows, and allows the straightforward calculation of the genus-1 1-point adjoint Verlinde dimension, the adjoint affine fusion tadpole. Explicit formulas, (piecewise) polynomial in the level, are written for the adjoint tadpoles of all classical Lie algebras. We show that off-diagonal adjoint affine fusion is obtained from the corresponding tensor product by simply dropping non-dominant representations.
Infinite transitivity on affine varieties
Arzhantsev, Ivan; Flenner, Hubert; Kaliman, Shulim; Kutzschebauch, Frank; ZAIDENBERG, MIKHAIL
2012-01-01
In this note we survey recent results on automorphisms of affine algebraic varieties, infinitely transitive group actions and flexibility. We present related constructions and examples, and discuss geometric applications and open problems.
Representations of affine Hecke algebras
Xi, Nanhua
1994-01-01
Kazhdan and Lusztig classified the simple modules of an affine Hecke algebra Hq (q E C*) provided that q is not a root of 1 (Invent. Math. 1987). Ginzburg had some very interesting work on affine Hecke algebras. Combining these results simple Hq-modules can be classified provided that the order of q is not too small. These Lecture Notes of N. Xi show that the classification of simple Hq-modules is essentially different from general cases when q is a root of 1 of certain orders. In addition the based rings of affine Weyl groups are shown to be of interest in understanding irreducible representations of affine Hecke algebras. Basic knowledge of abstract algebra is enough to read one third of the book. Some knowledge of K-theory, algebraic group, and Kazhdan-Lusztig cell of Cexeter group is useful for the rest
International Nuclear Information System (INIS)
In the theory of affine SL(2)-embeddings, which was constructed in 1973 by Popov, a locally transitive action of the group SL(2) on a normal affine three-dimensional variety X is determined by a pair (p/q,r), where 0GV//T-hat. In the substantiation of this result a key role is played by Cox's construction in toric geometry. Bibliography: 12 titles
Affine density in wavelet analysis
Kutyniok, Gitta
2007-01-01
In wavelet analysis, irregular wavelet frames have recently come to the forefront of current research due to questions concerning the robustness and stability of wavelet algorithms. A major difficulty in the study of these systems is the highly sensitive interplay between geometric properties of a sequence of time-scale indices and frame properties of the associated wavelet systems. This volume provides the first thorough and comprehensive treatment of irregular wavelet frames by introducing and employing a new notion of affine density as a highly effective tool for examining the geometry of sequences of time-scale indices. Many of the results are new and published for the first time. Topics include: qualitative and quantitative density conditions for existence of irregular wavelet frames, non-existence of irregular co-affine frames, the Nyquist phenomenon for wavelet systems, and approximation properties of irregular wavelet frames.
Protein isolation using affinity chromatography
Besselink, T.
2012-01-01
Many product or even waste streams in the food industry contain components that may have potential for e.g. functional foods. These streams are typically large in volume and the components of interest are only present at low concentrations. A robust and highly selective separation process should be developed for efficient isolation of the components. Affinity chromatography is such a selective method. Ligands immobilized to a stationary phase (e.g., a resin or membrane) are used to bind the c...
Inhomogeneous self-affine carpets
Fraser, Jonathan M.
2013-01-01
We investigate the dimension theory of inhomogeneous self-affine carpets. Through the work of Olsen, Snigireva and Fraser, the dimension theory of inhomogeneous self-similar sets is now relatively well-understood, however, almost no progress has been made concerning more general non-conformal inhomogeneous attractors. If a dimension is countably stable, then the results are immediate and so we focus on the upper and lower box dimensions and compute these explicitly for large classes of inhomo...
Alternative affinity tools: more attractive than antibodies?
Ruigrok, V.J.B.; Levisson, M.; Eppink, M.H.M.; Smidt, H.; Oost, van der J.
2011-01-01
Antibodies are the most successful affinity tools used today, in both fundamental and applied research (diagnostics, purification and therapeutics). Nonetheless, antibodies do have their limitations, including high production costs and low stability. Alternative affinity tools based on nucleic acids
Spectral affinity in protein networks
Directory of Open Access Journals (Sweden)
Teng Shang-Hua
2009-11-01
Full Text Available Abstract Background Protein-protein interaction (PPI networks enable us to better understand the functional organization of the proteome. We can learn a lot about a particular protein by querying its neighborhood in a PPI network to find proteins with similar function. A spectral approach that considers random walks between nodes of interest is particularly useful in evaluating closeness in PPI networks. Spectral measures of closeness are more robust to noise in the data and are more precise than simpler methods based on edge density and shortest path length. Results We develop a novel affinity measure for pairs of proteins in PPI networks, which uses personalized PageRank, a random walk based method used in context-sensitive search on the Web. Our measure of closeness, which we call PageRank Affinity, is proportional to the number of times the smaller-degree protein is visited in a random walk that restarts at the larger-degree protein. PageRank considers paths of all lengths in a network, therefore PageRank Affinity is a precise measure that is robust to noise in the data. PageRank Affinity is also provably related to cluster co-membership, making it a meaningful measure. In our experiments on protein networks we find that our measure is better at predicting co-complex membership and finding functionally related proteins than other commonly used measures of closeness. Moreover, our experiments indicate that PageRank Affinity is very resilient to noise in the network. In addition, based on our method we build a tool that quickly finds nodes closest to a queried protein in any protein network, and easily scales to much larger biological networks. Conclusion We define a meaningful way to assess the closeness of two proteins in a PPI network, and show that our closeness measure is more biologically significant than other commonly used methods. We also develop a tool, accessible at http://xialab.bu.edu/resources/pnns, that allows the user to
Manifolds with integrable affine shape operator
Directory of Open Access Journals (Sweden)
Daniel A. Joaquín
2005-05-01
Full Text Available This work establishes the conditions for the existence of vector fields with the property that theirs covariant derivative, with respect to the affine normal connection, be the affine shape operatorS in hypersurfaces. Some results are obtained from this property and, in particular, for some kind of affine decomposable hypersurfaces we explicitely get the actual vector fields.
Steiner, Wolfgang
2012-01-01
An integral self-affine tile is the solution of a set equation $\\mathbf{A} \\mathcal{T} = \\bigcup_{d \\in \\mathcal{D}} (\\mathcal{T} + d)$, where $\\mathbf{A}$ is an $n \\times n$ integer matrix and $\\mathcal{D}$ is a finite subset of $\\mathbb{Z}^n$. In the recent decades, these objects and the induced tilings have been studied systematically. We extend this theory to matrices $\\mathbf{A} \\in \\mathbb{Q}^{n \\times n}$. We define rational self-affine tiles as compact subsets of the open subring $\\mathbb{R}^n\\times \\prod_\\mathfrak{p} K_\\mathfrak{p}$ of the ad\\'ele ring $\\mathbb{A}_K$, where the factors of the (finite) product are certain $\\mathfrak{p}$-adic completions of a number field $K$ that is defined in terms of the characteristic polynomial of $\\mathbf{A}$. Employing methods from classical algebraic number theory, Fourier analysis in number fields, and results on zero sets of transfer operators, we establish a general tiling theorem for these tiles. We also associate a second kind of tiles with a rational matr...
The affine quantum gravity programme
International Nuclear Information System (INIS)
The central principle of affine quantum gravity is securing and maintaining the strict positivity of the matrix { g-hat ab(x)} composed of the spatial components of the local metric operator. On spectral grounds, canonical commutation relations are incompatible with this principle, and they must be replaced by noncanonical, affine commutation relations. Due to the partial second-class nature of the quantum gravitational constraints, it is advantageous to use the recently developed projection operator method, which treats all quantum constraints on an equal footing. Using this method, enforcement of regularized versions of the gravitational operator constraints is formulated quite naturally by means of a novel and relatively well-defined functional integral involving only the same set of variables that appears in the usual classical formulation. It is anticipated that skills and insight to study this formulation can be developed by studying special, reduced-variable models that still retain some basic characteristics of gravity, specifically a partial second-class constraint operator structure. Although perturbatively nonrenormalizable, gravity may possibly be understood nonperturbatively from a hard-core perspective that has proved valuable for specialized models. Finally, developing a procedure to pass to the genuine physical Hilbert space involves several interconnected steps that require careful coordination
Conformal field theory on affine Lie groups
International Nuclear Information System (INIS)
Working directly on affine Lie groups, we construct several new formulations of the WZW model, the gauged WZW model, and the generic affine-Virasoro action. In one formulation each of these conformal field theories (CFTs) is expressed as a one-dimensional mechanical system whose variables are coordinates on the affine Lie group. When written in terms of the affine group element, this formulation exhibits a two-dimensional WZW term. In another formulation each CFT is written as a two-dimensional field theory, with a three- dimensional WZW term, whose fields are coordinates on the affine group. On the basis of these equivalent formulations, we develop a translation dictionary in which the new formulations on the affine Lie group are understood as mode formulations of the conventional formulations on the Lie group. Using this dictionary, we also express each CFT as a three-dimensional field theory on the Lie group with a four-dimensional WZW term. 36 refs
Conformal field theory on affine Lie groups
Energy Technology Data Exchange (ETDEWEB)
Clubok, K.S.
1996-04-01
Working directly on affine Lie groups, we construct several new formulations of the WZW model, the gauged WZW model, and the generic affine-Virasoro action. In one formulation each of these conformal field theories (CFTs) is expressed as a one-dimensional mechanical system whose variables are coordinates on the affine Lie group. When written in terms of the affine group element, this formulation exhibits a two-dimensional WZW term. In another formulation each CFT is written as a two-dimensional field theory, with a three- dimensional WZW term, whose fields are coordinates on the affine group. On the basis of these equivalent formulations, we develop a translation dictionary in which the new formulations on the affine Lie group are understood as mode formulations of the conventional formulations on the Lie group. Using this dictionary, we also express each CFT as a three-dimensional field theory on the Lie group with a four-dimensional WZW term. 36 refs.
Maximin affinity learning of image segmentation
Turaga, Srinivas C; Helmstaedter, Moritz; Denk, Winfried; Seung, H Sebastian
2009-01-01
Images can be segmented by first using a classifier to predict an affinity graph that reflects the degree to which image pixels must be grouped together and then partitioning the graph to yield a segmentation. Machine learning has been applied to the affinity classifier to produce affinity graphs that are good in the sense of minimizing edge misclassification rates. However, this error measure is only indirectly related to the quality of segmentations produced by ultimately partitioning the affinity graph. We present the first machine learning algorithm for training a classifier to produce affinity graphs that are good in the sense of producing segmentations that directly minimize the Rand index, a well known segmentation performance measure. The Rand index measures segmentation performance by quantifying the classification of the connectivity of image pixel pairs after segmentation. By using the simple graph partitioning algorithm of finding the connected components of the thresholded affinity graph, we are ...
Methods for Improving Aptamer Binding Affinity
Hijiri Hasegawa; Nasa Savory; Koichi Abe; Kazunori Ikebukuro
2016-01-01
Aptamers are single stranded oligonucleotides that bind a wide range of biological targets. Although aptamers can be isolated from pools of random sequence oligonucleotides using affinity-based selection, aptamers with high affinities are not always obtained. Therefore, further refinement of aptamers is required to achieve desired binding affinities. The optimization of primary sequences and stabilization of aptamer conformations are the main approaches to refining the binding properties of a...
Covariant Functional Calculi from the Affine Groups
Gong, Yafang
2009-01-01
Invoking the Clifford-Hermite Wavelets from Clifford analysis, we use the covariances of affine groups to construct a kind of functional calculi for several non-commuting bounded operators. Functional calculi are the intertwining transforms between the representations of affine groups in the space $L^2(\\mathbb R^m)$ and in the space of bounded operators. It turns out that the Weyl calculus is the value of this new functional calculus at the identity of affine groups. Our app...
Multipole solutions in metric-affine gravity
Socorro, J; Macías, A; Mielke, E W; Socorro, José; Lämmerzahl, Claus; Macías, Alfredo; Mielke, Eckehard W.
1998-01-01
Above Planck energies, the spacetime might become non--Riemannian, as it is known fron string theory and inflation. Then geometries arise in which nonmetricity and torsion appear as field strengths, side by side with curvature. By gauging the affine group, a metric affine gauge theory emerges as dynamical framework. Here, by using the harmonic map ansatz, a new class of multipole like solutions in the metric affine gravity theory (MAG) is obtained.
Maximin affinity learning of image segmentation
Srinivas C Turaga; Briggman, Kevin L; Helmstaedter, Moritz; Denk, Winfried; Seung, H. Sebastian
2009-01-01
Images can be segmented by first using a classifier to predict an affinity graph that reflects the degree to which image pixels must be grouped together and then partitioning the graph to yield a segmentation. Machine learning has been applied to the affinity classifier to produce affinity graphs that are good in the sense of minimizing edge misclassification rates. However, this error measure is only indirectly related to the quality of segmentations produced by ultimately partitioning the a...
Discrete Affine Minimal Surfaces with Indefinite Metric
Craizer, Marcos; Anciaux, Henri; Lewiner, Thomas
2008-01-01
Inspired by the Weierstrass representation of smooth affine minimal surfaces with indefinite metric, we propose a constructive process producing a large class of discrete surfaces that we call discrete affine minimal surfaces. We show that they are critical points of an affine area functional defined on the space of quadrangular discrete surfaces. The construction makes use of asymptotic coordinates and allows defining the discrete analogs of some differential geometric objects, such as the n...
A Novel Vertex Affinity for Community Detection
Energy Technology Data Exchange (ETDEWEB)
Yoo, Andy [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Sanders, Geoffrey [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Henson, Van [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Vassilevski, Panayot [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2015-10-05
We propose a novel vertex affinity measure in this paper. The new vertex affinity quantifies the proximity between two vertices in terms of their clustering strength and is ideal for such graph analytics applications as community detection. We also developed a framework that combines simple graph searches and resistance circuit formulas to compute the vertex affinity efficiently. We study the properties of the new affinity measure empirically in comparison to those of other popular vertex proximity metrics. Our results show that the existing metrics are ill-suited for community detection due to their lack of fundamental properties that are essential for correctly capturing inter- and intra-cluster vertex proximity.
Compact noncontraction semigroups of affine operators
Voynov, A. S.; Protasov, V. Yu
2015-07-01
We analyze compact multiplicative semigroups of affine operators acting in a finite-dimensional space. The main result states that every such semigroup is either contracting, that is, contains elements of arbitrarily small operator norm, or all its operators share a common invariant affine subspace on which this semigroup is contracting. The proof uses functional difference equations with contraction of the argument. We look at applications to self-affine partitions of convex sets, the investigation of finite affine semigroups and the proof of a criterion of primitivity for nonnegative matrix families. Bibliography: 32 titles.
Protein Complex Purification by Affinity Capture.
LaCava, John; Fernandez-Martinez, Javier; Hakhverdyan, Zhanna; Rout, Michael P
2016-01-01
Affinity capture has become a powerful technique for consistently purifying endogenous protein complexes, facilitating biochemical and biophysical assays on otherwise inaccessible biological assemblies, and enabling broader interactomic exploration. For this procedure, cells are broken and their contents separated and extracted into a solvent, permitting access to target macromolecular complexes thus released in solution. The complexes are specifically enriched from the extract onto a solid medium coupled with an affinity reagent-usually an antibody-that recognizes the target either directly or through an appended affinity tag, allowing subsequent characterization of the complex. Here, we discuss approaches and considerations for purifying endogenous yeast protein complexes by affinity capture. PMID:27371601
Structural determinants of sigma receptor affinity
International Nuclear Information System (INIS)
The structural determinants of sigma receptor affinity have been evaluated by examining a wide range of compounds related to opioids, neuroleptics, and phenylpiperidine dopaminergic structures for affinity at sigma receptor-binding sites labeled with (+)-[3H]3-PPP. Among opioid compounds, requirements for sigma receptor affinity differ strikingly from the determinants of affinity for conventional opiate receptors. Sigma sites display reverse stereoselectivity to classical opiate receptors. Multi-ringed opiate-related compounds such as morphine and naloxone have negligible affinity for sigma sites, with the highest sigma receptor affinity apparent for benzomorphans which lack the C ring of opioids. Highest affinity among opioids and other compounds occurs with more lipophilic N-substituents. This feature is particularly striking among the 3-PPP derivatives as well as the opioids. The butyrophenone haloperidol is the most potent drug at sigma receptors we have detected. Among the series of butyrophenones, receptor affinity is primarily associated with the 4-phenylpiperidine moiety. Conformational calculations for various compounds indicate a fairly wide range of tolerance for distances between the aromatic ring and the amine nitrogen, which may account for the potency at sigma receptors of structures of considerable diversity. Among the wide range of structures that bind to sigma receptor-binding sites, the common pharmacophore associated with high receptor affinity is a phenylpiperidine with a lipophilic N-substituent
Structural determinants of sigma receptor affinity
Energy Technology Data Exchange (ETDEWEB)
Largent, B.L.; Wikstroem, H.G.; Gundlach, A.L.; Snyder, S.H.
1987-12-01
The structural determinants of sigma receptor affinity have been evaluated by examining a wide range of compounds related to opioids, neuroleptics, and phenylpiperidine dopaminergic structures for affinity at sigma receptor-binding sites labeled with (+)-(/sup 3/H)3-PPP. Among opioid compounds, requirements for sigma receptor affinity differ strikingly from the determinants of affinity for conventional opiate receptors. Sigma sites display reverse stereoselectivity to classical opiate receptors. Multi-ringed opiate-related compounds such as morphine and naloxone have negligible affinity for sigma sites, with the highest sigma receptor affinity apparent for benzomorphans which lack the C ring of opioids. Highest affinity among opioids and other compounds occurs with more lipophilic N-substituents. This feature is particularly striking among the 3-PPP derivatives as well as the opioids. The butyrophenone haloperidol is the most potent drug at sigma receptors we have detected. Among the series of butyrophenones, receptor affinity is primarily associated with the 4-phenylpiperidine moiety. Conformational calculations for various compounds indicate a fairly wide range of tolerance for distances between the aromatic ring and the amine nitrogen, which may account for the potency at sigma receptors of structures of considerable diversity. Among the wide range of structures that bind to sigma receptor-binding sites, the common pharmacophore associated with high receptor affinity is a phenylpiperidine with a lipophilic N-substituent.
Structure of classical affine and classical affine fractional W-algebras
International Nuclear Information System (INIS)
We introduce a classical BRST complex (See Definition 3.2.) and show that one can construct a classical affine W-algebra via the complex. This definition clarifies that classical affine W-algebras can be considered as quasi-classical limits of quantum affine W-algebras. We also give a definition of a classical affine fractional W-algebra as a Poisson vertex algebra. As in the classical affine case, a classical affine fractional W-algebra has two compatible λ-brackets and is isomorphic to an algebra of differential polynomials as a differential algebra. When a classical affine fractional W-algebra is associated to a minimal nilpotent, we describe explicit forms of free generators and compute λ-brackets between them. Provided some assumptions on a classical affine fractional W-algebra, we find an infinite sequence of integrable systems related to the algebra, using the generalized Drinfel’d and Sokolov reduction
Scaling analysis of affinity propagation.
Furtlehner, Cyril; Sebag, Michèle; Zhang, Xiangliang
2010-06-01
We analyze and exploit some scaling properties of the affinity propagation (AP) clustering algorithm proposed by Frey and Dueck [Science 315, 972 (2007)]. Following a divide and conquer strategy we setup an exact renormalization-based approach to address the question of clustering consistency, in particular, how many cluster are present in a given data set. We first observe that the divide and conquer strategy, used on a large data set hierarchically reduces the complexity O(N2) to O(N((h+2)/(h+1))) , for a data set of size N and a depth h of the hierarchical strategy. For a data set embedded in a d -dimensional space, we show that this is obtained without notably damaging the precision except in dimension d=2 . In fact, for d larger than 2 the relative loss in precision scales such as N((2-d)/(h+1)d). Finally, under some conditions we observe that there is a value s* of the penalty coefficient, a free parameter used to fix the number of clusters, which separates a fragmentation phase (for ss*) of the underlying hidden cluster structure. At this precise point holds a self-similarity property which can be exploited by the hierarchical strategy to actually locate its position, as a result of an exact decimation procedure. From this observation, a strategy based on AP can be defined to find out how many clusters are present in a given data set. PMID:20866473
Free C+ actions on affine threefolds
Kraft, H.
2005-01-01
We study algebraic actions of the additive group C+ on an affine threefold X and prove a smoothness property for the quotient morphism X -< X//C+. Then, following Shulim Kaliman, we give a proof of the conjecture that every free C+ action on affine 3-space C^3 is a translation.
Lectures on extended affine Lie algebras
Neher, Erhard
2010-01-01
We give an introduction to the structure theory of extended affine Lie algebras, which provide a common framework for finite-dimensional semisimple, affine and toroidal Lie algebras. The notes are based on a lecture series given during the Fields Institute summer school at the University of Ottawa in June 2009.
Affine Constellations Without Mutually Unbiased Counterparts
Weigert, Stefan
2010-01-01
It has been conjectured that a complete set of mutually unbiased bases in a space of dimension d exists if and only if there is an affine plane of order d. We introduce affine constellations and compare their existence properties with those of mutually unbiased constellations, mostly in dimension six. The observed discrepancies make a deeper relation between the two existence problems unlikely.
Affine constellations without mutually unbiased counterparts
Energy Technology Data Exchange (ETDEWEB)
Weigert, Stefan [Department of Mathematics, University of York, York YO10 5DD (United Kingdom); Durt, Thomas, E-mail: slow500@york.ac.u, E-mail: thomdurt@vub.ac.b [IR-TONA, VUB, BE-1050 Brussels (Belgium)
2010-10-08
It has been conjectured that a complete set of mutually unbiased bases in a space of dimension d exists if and only if there is an affine plane of order d. We introduce affine constellations and compare their existence properties with those of mutually unbiased constellations. The observed discrepancies make a deeper relation between the two existence problems unlikely. (fast track communication)
Dyes with high affinity for polylactide
Institute of Scientific and Technical Information of China (English)
Liang He; Shu Fen Zhang; Bing Tao Tang; Li Li Wang; Jin Zong Yang
2007-01-01
Attempts were made to develop dyes with high affinity for polylactide as an alternative to the existent commercial disperse dyes.The dyes synthesized according to the affinity concept of dye to polylactide exhibited excellent dyeing properties on polylactide compared with the commercial disperse dyes.
Institute of Scientific and Technical Information of China (English)
Lifeng XI
2008-01-01
In this paper,it is proved that any self-affine set satisfying the strong separation condition is uniformly porous.The author constructs a self-affine set which is not porous,although the open set condition holds.Besides,the author also gives a C1 iterated function system such that its invariant set is not porous.
Affine constellations without mutually unbiased counterparts
International Nuclear Information System (INIS)
It has been conjectured that a complete set of mutually unbiased bases in a space of dimension d exists if and only if there is an affine plane of order d. We introduce affine constellations and compare their existence properties with those of mutually unbiased constellations. The observed discrepancies make a deeper relation between the two existence problems unlikely. (fast track communication)
Improving image segmentation by learning region affinities
Energy Technology Data Exchange (ETDEWEB)
Prasad, Lakshman [Los Alamos National Laboratory; Yang, Xingwei [TEMPLE UNIV.; Latecki, Longin J [TEMPLE UNIV.
2010-11-03
We utilize the context information of other regions in hierarchical image segmentation to learn new regions affinities. It is well known that a single choice of quantization of an image space is highly unlikely to be a common optimal quantization level for all categories. Each level of quantization has its own benefits. Therefore, we utilize the hierarchical information among different quantizations as well as spatial proximity of their regions. The proposed affinity learning takes into account higher order relations among image regions, both local and long range relations, making it robust to instabilities and errors of the original, pairwise region affinities. Once the learnt affinities are obtained, we use a standard image segmentation algorithm to get the final segmentation. Moreover, the learnt affinities can be naturally unutilized in interactive segmentation. Experimental results on Berkeley Segmentation Dataset and MSRC Object Recognition Dataset are comparable and in some aspects better than the state-of-art methods.
Optimized Affinity Capture of Yeast Protein Complexes.
LaCava, John; Fernandez-Martinez, Javier; Hakhverdyan, Zhanna; Rout, Michael P
2016-01-01
Here, we describe an affinity isolation protocol. It uses cryomilled yeast cell powder for producing cell extracts and antibody-conjugated paramagnetic beads for affinity capture. Guidelines for determining the optimal extraction solvent composition are provided. Captured proteins are eluted in a denaturing solvent (sodium dodecyl sulfate polyacrylamide gel electrophoresis sample buffer) for gel-based proteomic analyses. Although the procedures can be modified to use other sources of cell extract and other forms of affinity media, to date we have consistently obtained the best results with the method presented. PMID:27371596
Affinity Proteomics in the mountains: Alpbach 2015.
Taussig, Michael J
2016-09-25
The 2015 Alpbach Workshop on Affinity Proteomics, organised by the EU AFFINOMICS consortium, was the 7th workshop in this series. As in previous years, the focus of the event was the current state of affinity methods for proteome analysis, including complementarity with mass spectrometry, progress in recombinant binder production methods, alternatives to classical antibodies as affinity reagents, analysis of proteome targets, industry focus on biomarkers, and diagnostic and clinical applications. The combination of excellent science with Austrian mountain scenery and winter sports engender an atmosphere that makes this series of workshops exceptional. The articles in this Special Issue represent a cross-section of the presentations at the 2015 meeting. PMID:27118167
Corner Transfer Matrices and Quantum Affine Algebras
Foda, O E; Foda, Omar; Miwa, Tetsuji
1992-01-01
Let H be the corner-transfer-matrix Hamiltonian for the six-vertex model in the anti-ferroelectric regime. It acts on the infinite tensor product W = V . V . V ....., where is the 2-dimensional irreducible representation of the quantum affine sl(2). We observe that H is the derivation of quantum affine sl(2), and conjecture that the eigenvectors of H form the level-1 vacuum representation of quantum affine sl(2). We report on checks in support of our conjecture.
Automorphisms in Birational and Affine Geometry
Ciliberto, Ciro; Flenner, Hubert; McKernan, James; Prokhorov, Yuri; Zaidenberg, Mikhail
2014-01-01
The main focus of this volume is on the problem of describing the automorphism groups of affine and projective varieties, a classical subject in algebraic geometry where, in both cases, the automorphism group is often infinite dimensional. The collection covers a wide range of topics and is intended for researchers in the fields of classical algebraic geometry and birational geometry (Cremona groups) as well as affine geometry with an emphasis on algebraic group actions and automorphism groups. It presents original research and surveys and provides a valuable overview of the current state of the art in these topics. Bringing together specialists from projective, birational algebraic geometry and affine and complex algebraic geometry, including Mori theory and algebraic group actions, this book is the result of ensuing talks and discussions from the conference “Groups of Automorphisms in Birational and Affine Geometry” held in October 2012, at the CIRM, Levico Terme, Italy. The talks at the conference high...
Synthesis of a New Series of Bone Affinity Compounds
Institute of Scientific and Technical Information of China (English)
无
2006-01-01
A new series of bone affinity compounds were synthesized by linking chrysophanol with 5-fluorouracil derivatives. Their bone affinity was established by hydroxyapafive (HA)affinity experiment in vitro, and their cytostatic effects were shown by the MTT assay.
Affine Moment Invariants Generated by Graph Method
Czech Academy of Sciences Publication Activity Database
Suk, Tomáš; Flusser, Jan
2011-01-01
Roč. 44, č. 9 (2011), 2047 – 2056. ISSN 0031-3203 R&D Projects: GA ČR(CZ) GA102/08/1593 Institutional research plan: CEZ:AV0Z10750506 Keywords : Image moments * Object recognition * Affine transformation * Affine moment invariants * Pseudoinvariants * Graph representation * Irreducibility * Independence Subject RIV: IN - Informatics, Computer Science Impact factor: 2.292, year: 2011 http://library.utia.cas.cz/separaty/2011/ZOI/suk-0359752.pdf
On Affine Fusion and the Phase Model
Walton, Mark A.
2012-01-01
A brief review is given of the integrable realization of affine fusion discovered recently by Korff and Stroppel. They showed that the affine fusion of the $su(n)$ Wess-Zumino-Novikov-Witten (WZNW) conformal field theories appears in a simple integrable system known as the phase model. The Yang-Baxter equation leads to the construction of commuting operators as Schur polynomials, with noncommuting hopping operators as arguments. The algebraic Bethe ansatz diagonalizes them, revealing a connec...
Purely affine elementary su(N) fusions
Rasmussen, Jorgen; Walton, Mark A.
2001-01-01
We consider three-point couplings in simple Lie algebras -- singlets in triple tensor products of their integrable highest weight representations. A coupling can be expressed as a linear combination of products of finitely many elementary couplings. This carries over to affine fusion, the fusion of Wess-Zumino-Witten conformal field theories, where the expressions are in terms of elementary fusions. In the case of su(4) it has been observed that there is a purely affine elementary fusion, i.e...
Complete algebraic vector fields on affine surfaces
Kaliman, Shulim; Kutzschebauch, Frank; Leuenberger, Matthias
2014-01-01
Let $\\AAutH (X)$ be the subgroup of the group $\\AutH (X)$ of holomorphic automorphisms of a normal affine algebraic surface $X$ generated by elements of flows associated with complete algebraic vector fields. Our main result is a classification of all normal affine algebraic surfaces $X$ quasi-homogeneous under $\\AAutH (X)$ in terms of the dual graphs of the boundaries $\\bX \\setminus X$ of their SNC-completions $\\bX$.
Fan affinity laws from a collision model
International Nuclear Information System (INIS)
The performance of a fan is usually estimated using hydrodynamical considerations. The calculations are long and involved and the results are expressed in terms of three affinity laws. In this paper we use kinetic theory to attack this problem. A hard sphere collision model is used, and subsequently a correction to account for the flow behaviour of air is incorporated. Our calculations prove the affinity laws and provide numerical estimates of the air delivery, thrust and drag on a rotating fan. (paper)
A MEMS Dielectric Affinity Glucose Biosensor
Xian HUANG; Li, SiQi; Davis, Erin; Li, Dachao; Wang, Qian; Lin, Qiao
2013-01-01
Continuous glucose monitoring (CGM) sensors based on affinity detection are desirable for long-term and stable glucose management. However, most affinity sensors contain mechanical moving structures and complex design in sensor actuation and signal readout, limiting their reliability in subcutaneously implantable glucose detection. We have previously demonstrated a proof-of-concept dielectric glucose sensor that measured pre-mixed glucose-sensitive polymer solutions at various glucose concent...
Affine modifications and affine hypersurfaces with a very transitive automorphism group
Kaliman, Shulim; ZAIDENBERG, MIKHAIL
1998-01-01
We study a kind of modification of an affine domain which produces another affine domain. First appeared in passing in the basic paper of O. Zariski (1942), it was further considered by E.D. Davis (1967). The first named author applied its geometric counterpart to construct contractible smooth affine varieties non-isomorphic to Euclidean spaces. Here we provide certain conditions which guarantee preservation of the topology under a modification. As an application, we show that the group of bi...
Affinity purification of aprotinin from bovine lung.
Xin, Yu; Liu, Lanhua; Chen, Beizhan; Zhang, Ling; Tong, Yanjun
2015-05-01
An affinity protocol for the purification of aprotinin from bovine lung was developed. To simulate the structure of sucrose octasulfate, a natural specific probe for aprotinin, the affinity ligand was composed of an acidic head and a hydrophobic stick, and was then linked with Sepharose. The sorbent was then subjected to adsorption analysis with pure aprotinin. The purification process consisted of one step of affinity chromatography and another step of ultrafiltration. Then purified aprotinin was subjected to sodium dodecyl sulfate polyacrylamide gel electrophoresis, trypsin inhibitor activity, gel-filtration, and thin-layer chromatography analysis. As calculated, the theoretical maximum adsorption (Qmax ) of the affinity sorbent was 25,476.0 ± 184.8 kallikrein inactivator unit/g wet gel; the dissociation constant of the complex "immobilized ligand-aprotinin" (Kd ) was 4.6 ± 0.1 kallikrein inactivator unit/mL. After the affinity separation of bovine lung aprotinin, reducing sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis and gel-filtration chromatography revealed that the protein was a single polypeptide, and the purities were ∼ 97 and 100%, respectively; the purified peptide was also confirmed with aprotinin standard by gel-filtration chromatography and thin-layer chromatography. After the whole purification process, protein, and bioactivity recoveries were 2.2 and 92.6%, respectively; and the specific activity was up to 15,907.1 ± 10.2 kallikrein inactivator unit/mg. PMID:25677462
DEFF Research Database (Denmark)
Heegaard, N H; Sen, J W; Nissen, Mogens Holst
2000-01-01
The amyloidogenic protein beta-microglobulin was characterized by affinity capillary electrophoresis (CE). CE could separate conformational variants of beta2-microglobulin and with the amyloid-specific dye Congo red as a buffer additive it was possible to measure different Congo red-affinities of...
On Affine Fusion and the Phase Model
Directory of Open Access Journals (Sweden)
Mark A. Walton
2012-11-01
Full Text Available A brief review is given of the integrable realization of affine fusion discovered recently by Korff and Stroppel. They showed that the affine fusion of the su(n Wess-Zumino-Novikov-Witten (WZNW conformal field theories appears in a simple integrable system known as the phase model. The Yang-Baxter equation leads to the construction of commuting operators as Schur polynomials, with noncommuting hopping operators as arguments. The algebraic Bethe ansatz diagonalizes them, revealing a connection to the modular S matrix and fusion of the su(n WZNW model. The noncommutative Schur polynomials play roles similar to those of the primary field operators in the corresponding WZNW model. In particular, their 3-point functions are the su(n fusion multiplicities. We show here how the new phase model realization of affine fusion makes obvious the existence of threshold levels, and how it accommodates higher-genus fusion.
On affine fusion and the phase model
Walton, Mark A
2012-01-01
A brief review is given of the integrable realization of affine fusion discovered recently by Korff and Stroppel. They showed that the affine fusion of the su(n) Wess-Zumino-Novikov-Witten (WZNW) conformal field theories appears in a simple integrable system known as the phase model. The algebraic Bethe ansatz constructs the commuting operators of the phase model as Schur polynomials, with non-commuting hopping operators as arguments. These non-commutative Schur polynomials play roles similar to those of the primary field operators in the corresponding WZNW model. In particular, their 3-point functions are the su(n) fusion multiplicities. We show here how the new phase model realization of affine fusion makes obvious the existence of threshold levels, and how it accommodates higher-genus fusion.
Affine Projection Algorithm Using Regressive Estimated Error
Zhang, Shu; Zhi, Yongfeng
2011-01-01
An affine projection algorithm using regressive estimated error (APA-REE) is presented in this paper. By redefining the iterated error of the affine projection algorithm (APA), a new algorithm is obtained, and it improves the adaptive filtering convergence rate. We analyze the iterated error signal and the stability for the APA-REE algorithm. The steady-state weights of the APA-REE algorithm are proved to be unbiased and consist. The simulation results show that the proposed algorithm has a f...
Control and estimation of piecewise affine systems
Xu, Jun
2014-01-01
As a powerful tool to study nonlinear systems and hybrid systems, piecewise affine (PWA) systems have been widely applied to mechanical systems. Control and Estimation of Piecewise Affine Systems presents several research findings relating to the control and estimation of PWA systems in one unified view. Chapters in this title discuss stability results of PWA systems, using piecewise quadratic Lyapunov functions and piecewise homogeneous polynomial Lyapunov functions. Explicit necessary and sufficient conditions for the controllability and reachability of a class of PWA systems are
Periodic cyclic homology of affine Hecke algebras
Solleveld, Maarten
2009-01-01
This is the author's PhD-thesis, which was written in 2006. The version posted here is identical to the printed one. Instead of an abstract, the short list of contents: Preface 5 1 Introduction 9 2 K-theory and cyclic type homology theories 13 3 Affine Hecke algebras 61 4 Reductive p-adic groups 103 5 Parameter deformations in affine Hecke algebras 129 6 Examples and calculations 169 A Crossed products 223 Bibliography 227 Index 237 Samenvatting 245 Curriculum vitae 253
Green, R. M.
1997-01-01
We introduce an analogue of the $q$-Schur algebra associated to Coxeter systems of type $\\hat A_{n-1}$. We give two constructions of this algebra. The first construction realizes the algebra as a certain endomorphism algebra arising from an affine Hecke algebra of type $\\hat A_{r-1}$, where $n \\geq r$. This generalizes the original $q$-Schur algebra as defined by Dipper and James, and the new algebra contains the ordinary $q$-Schur algebra and the affine Hecke algebra as subalgebras. Using th...
Crossing Chris: Some Markerian Affinities
Directory of Open Access Journals (Sweden)
Adrian Martin
2010-01-01
-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;}
Abstract (E: This essay creatively explores a group of artists, writers, and other special individuals whose work or life story can be described as having an intriguing affinity with the protean career of Chris Marker. Avoiding the ‘usual suspects’ (such as Godard or Sebald, it discusses gossip columnist Milt Machlin, record collector Harry Smith, painter Gianfranco Baruchello, writer-filmmaker Edgardo Cozarinsky, and several others. From this constellation, a particular view of Markerian poetics emerges, touching upon the meanings of anonymity, storytelling, history and archiving.
Abstract (F: Cet essai brosse de manière créative le portrait d’un groupe d'artistes, d'écrivains et d'autres personnes particulières dont le travail ou la biographie peuvent être décrits comme montrant une étrange mais certaine connivence avec la carrière protéiforme de Chris Marker. Evitant les lieux communs (comme Godard ou Sebald, cet article trace des références moins attendues :
Directory of Open Access Journals (Sweden)
Renhua Huang
2015-09-01
Full Text Available Often when generating recombinant affinity reagents to a target, one singles out an individual binder, constructs a secondary library of variants, and affinity selects a tighter or more specific binder. To enhance the throughput of this general approach, we have developed a more integrated strategy where the “affinity maturation” step is part of the phage-display pipeline, rather than a follow-on process. In our new schema, we perform two rounds of affinity selection, followed by error-prone PCR on the pools of recovered clones, generation of secondary libraries, and three additional rounds of affinity selection, under conditions of off-rate competition. We demonstrate the utility of this approach by generating low nanomolar fibronectin type III (FN3 monobodies to five human proteins: ubiquitin-conjugating enzyme E2 R1 (CDC34, COP9 signalosome complex subunit 5 (COPS5, mitogen-activated protein kinase kinase 5 (MAP2K5, Splicing factor 3A subunit 1 (SF3A1 and ubiquitin carboxyl-terminal hydrolase 11 (USP11. The affinities of the resulting monobodies are typically in the single-digit nanomolar range. We demonstrate the utility of two binders by pulling down the targets from a spiked lysate of HeLa cells. This integrated approach should be applicable to directed evolution of any phage-displayed affinity reagent scaffold.
Huang, Renhua; Gorman, Kevin T; Vinci, Chris R; Dobrovetsky, Elena; Gräslund, Susanne; Kay, Brian K
2015-01-01
Often when generating recombinant affinity reagents to a target, one singles out an individual binder, constructs a secondary library of variants, and affinity selects a tighter or more specific binder. To enhance the throughput of this general approach, we have developed a more integrated strategy where the "affinity maturation" step is part of the phage-display pipeline, rather than a follow-on process. In our new schema, we perform two rounds of affinity selection, followed by error-prone PCR on the pools of recovered clones, generation of secondary libraries, and three additional rounds of affinity selection, under conditions of off-rate competition. We demonstrate the utility of this approach by generating low nanomolar fibronectin type III (FN3) monobodies to five human proteins: ubiquitin-conjugating enzyme E2 R1 (CDC34), COP9 signalosome complex subunit 5 (COPS5), mitogen-activated protein kinase kinase 5 (MAP2K5), Splicing factor 3A subunit 1 (SF3A1) and ubiquitin carboxyl-terminal hydrolase 11 (USP11). The affinities of the resulting monobodies are typically in the single-digit nanomolar range. We demonstrate the utility of two binders by pulling down the targets from a spiked lysate of HeLa cells. This integrated approach should be applicable to directed evolution of any phage-displayed affinity reagent scaffold. PMID:26437402
General super Virasoro construction on affine G
International Nuclear Information System (INIS)
We consider a bosonic current algebra and a theory of free fermions and construct a general N = 1 super Virasoro current algebra. We obtain a master-set of equations which comprises the bosonic master equation for general Virasoro construction on affine G. As an illustration we study the case of the group SU(2). (author). 13 refs
Classification of neocortical interneurons using affinity propagation
Directory of Open Access Journals (Sweden)
Roberto eSantana
2013-12-01
Full Text Available In spite of over a century of research on cortical circuits, it is still unknown how many classes of cortical neurons exist. Neuronal classification has been a difficult problem because it is unclear what a neuronal cell class actually is and what are the best characteristics are to define them. Recently, unsupervised classifications using cluster analysis based on morphological, physiological or molecular characteristics, when applied to selected datasets, have provided quantitative and unbiased identification of distinct neuronal subtypes. However, better and more robust classification methods are needed for increasingly complex and larger datasets. We explored the use of affinity propagation, a recently developed unsupervised classification algorithm imported from machine learning, which gives a representative example or exemplar for each cluster. As a case study, we applied affinity propagation to a test dataset of 337 interneurons belonging to four subtypes, previously identified based on morphological and physiological characteristics. We found that affinity propagation correctly classified most of the neurons in a blind, non-supervised manner. In fact, using a combined anatomical/physiological dataset, our algorithm differentiated parvalbumin from somatostatin interneurons in 49 out of 50 cases. Affinity propagation could therefore be used in future studies to validly classify neurons, as a first step to help reverse engineer neural circuits.
Affinely Recursive Functions and Neural Networks
Czech Academy of Sciences Publication Activity Database
Kůrková, Věra; Kainen, P.C.
Atlanta : Georgia Institute of Technology, 1994 - ( Ames , W.), s. 776-779 [IMACS World Congress /14./. Atlanta (US), 11.07.1994-15.07.1994] R&D Projects: GA AV ČR IA23057; GA ČR GA201/93/0427 Keywords : neural networks * affinely recursive functions
Colliding waves in metric-affine gravity
García, A; Macías, A; Mielke, E W; Socorro, J; García, Alberto; Lämmerzahl, Claus; Macías, Alfredo; Mielke, Eckehard W.; Socorro, José
1998-01-01
We generalize the formulation of the colliding gravitational waves to metric-affine theories and present an example of such kind of exact solutions. The plane waves are equipped with five symmetries and the resulting geometry after the collision possesses two spacelike Killing vectors.
Artificial Affinity Proteins as Ligands of Immunoglobulins
Directory of Open Access Journals (Sweden)
Barbara Mouratou
2015-01-01
Full Text Available A number of natural proteins are known to have affinity and specificity for immunoglobulins. Some of them are widely used as reagents for detection or capture applications, such as Protein G and Protein A. However, these natural proteins have a defined spectrum of recognition that may not fit specific needs. With the development of combinatorial protein engineering and selection techniques, it has become possible to design artificial affinity proteins with the desired properties. These proteins, termed alternative scaffold proteins, are most often chosen for their stability, ease of engineering and cost-efficient recombinant production in bacteria. In this review, we focus on alternative scaffold proteins for which immunoglobulin binders have been identified and characterized.
Improved native affinity purification of RNA.
Batey, Robert T; Kieft, Jeffrey S
2007-08-01
RNA biochemical or structural studies often require an RNA sample that is chemically pure, and most protocols for its in vitro production use denaturing polyacrylamide gel electrophoresis to achieve this. Unfortunately, many RNAs do not quantitatively refold into an active conformation after denaturation, creating significant problems for downstream characterization or use. In addition, this traditional purification method is not amenable to studies demanding high-throughput RNA production. Recently, we presented the first general method for producing almost any RNA sequence that employs an affinity tag that is removed during the purification process. Because technical difficulties prevented application of this method to many RNAs, we have developed an improved version that utilizes a different activatable ribozyme and affinity tag that are considerably more robust, rapid, and broadly applicable. PMID:17548432
AFFINITY OF LIGNIN PREPARATIONS TOWARDS GENOTOXIC COMPOUNDS
Directory of Open Access Journals (Sweden)
Božena Košíková
2009-02-01
Full Text Available The carcinogenicity and mutagenicity of chemicals may be modulated by other chemicals, including those prepared by organic synthesis. Consid-ering the several drawbacks of synthetic compounds vis-a-vis the human organism, the lignin biomass component was examined for this purpose. The binding affinity of lignin samples prepared by chemical and biological modification of lignin products derived from chemical wood treatment towards for N-nitrosodiethylamine (NDA was examined. The protective role of the lignin samples against carcinogenesis was tested on a well-known model carcinogen, N-methyl-N´-nitro-N-nitrosoguanidine (MNNG. The observed ability of a series of lignin preparations to reduce alkylation damage of deoxyribonucleic acid (DNA on hamster cells in vitro could be explained by their affinity to bind N-nitrosoamines. The results indicate that lignin has potential to protect living organisms against damaging effects of different genotoxicants.
Phosphopeptide enrichment by immobilized metal affinity chromatography
DEFF Research Database (Denmark)
Thingholm, Tine E.; Larsen, Martin R.
2016-01-01
binding capacity. After binding, the enriched phosphopeptides are released from the metal ions using alkaline buffers of pH 10–11, EDTA, or phosphate-containing buffers. Here we describe a protocol for IMAC using Fe 3+ for phosphopeptide enrichment. The principles are illustrated on a semi-complex peptide......Immobilized metal affinity chromatography (IMAC) has been the method of choice for phosphopeptide enrichment prior to mass spectrometric analysis for many years and it is still used extensively in many laboratories. Using the affinity of negatively charged phosphate groups towards positively...... charged metal ions such as Fe3+, Ga3+, Al3+, Zr4+, and Ti4+ has made it possible to enrich phosphorylated peptides from peptide samples. However, the selectivity of most of the metal ions is limited, when working with highly complex samples, e.g., whole-cell extracts, resulting in contamination from...
High-affinity neuropeptide Y receptor antagonists.
Daniels, A J; Matthews, J. E.; Slepetis, R J; Jansen, M; Viveros, O. H.; Tadepalli, A.; Harrington, W; Heyer, D; Landavazo, A; Leban, J J
1995-01-01
Neuropeptide Y (NPY) is one of the most abundant peptide transmitters in the mammalian brain. In the periphery it is costored and coreleased with norepinephrine from sympathetic nerve terminals. However, the physiological functions of this peptide remain unclear because of the absence of specific high-affinity receptor antagonists. Three potent NPY receptor antagonists were synthesized and tested for their biological activity in in vitro, ex vivo, and in vivo functional assays. We describe he...
Staircase models from affine Toda field theory
International Nuclear Information System (INIS)
The authors propose a class of purely elastic scattering theories generalizing the staircase model of Al. B. Zamolodchikov, based on the affine Toda field theories for simply-laced Lie algebras g = A,D,E at suitable complex values of their coupling constants. Considering their Thermodynamic Bethe Ansatz equations, they give analytic arguments in support of a conjectured renormalization group flow visiting the neighborhood of each Wg minimal model in turn
AFFINE TRANSFORMATION IN RANDOM ITERATED FUNCTION SYSTEMS
Institute of Scientific and Technical Information of China (English)
熊勇; 史定华
2001-01-01
Random iterated function systems (IFSs) is discussed, which is one of the methods for fractal drawing. A certain figure can be reconstructed by a random IFS. One approach is presented to determine a new random IFS, that the figure reconstructed by the new random IFS is the image of the origin figure reconstructed by old IFS under a given affine transformation. Two particular examples are used to show this approach.
Homogeneous grading affine Toda quantum solitons
Czech Academy of Sciences Publication Activity Database
Zuevsky, Alexander
Vol. 563. Bristol : IOP Science, 2014 - (Burdik, C.; Navratil, O.; Posta, S.), 012036 ISSN 1742-6588. [International Conference on Integrable Systems and Quantum Symmetries (ISQS-22) /22./. Prague (CZ), 26.06.2014-29.06.-2014] Institutional support: RVO:67985840 Keywords : exactly solvable models * conformal and affine Toda systems * quantum groups Subject RIV: BA - General Mathematics http://iopscience.iop.org/1742-6596/563/1/012036
Denominators in cluster algebras of affine type
Buan, Aslak Bakke; Marsh, Robert J.
2008-01-01
The Fomin-Zelevinsky Laurent phenomenon states that every cluster variable in a cluster algebra can be expressed as a Laurent polynomial in the variables lying in an arbitrary initial cluster. We give representation-theoretic formulas for the denominators of cluster variables in cluster algebras of affine type. The formulas are in terms of the dimensions of spaces of homomorphisms in the corresponding cluster category, and hold for any choice of initial cluster.
Thermodynamics. Using Affinities to define reversible processes
Ritacco, Hernán A
2016-01-01
In this article a definition of reversible processes in terms of differences in intensive Thermodynamics properties (Affinities) is proposed. This definition makes it possible to both define reversible processes before introducing the concept of entropy and avoid the circularity problem that follows from the Clausius definition of entropy changes. The convenience of this new definition compared to those commonly found in textbooks is demonstrated with examples.
On constructing purely affine theories with matter
Cervantes-Cota, Jorge L.; Liebscher, D.-E.
2016-08-01
We explore ways to obtain the very existence of a space-time metric from an action principle that does not refer to it a priori. Although there are reasons to believe that only a non-local theory can viably achieve this goal, we investigate here local theories that start with Schrödinger's purely affine theory (Schrödinger in Space-time structure. Cambridge UP, Cambridge, 1950), where he gave reasons to set the metric proportional to the Ricci curvature aposteriori. When we leave the context of unified field theory, and we couple the non-gravitational matter using some weak equivalence principle, we can show that the propagation of shock waves does not define a lightcone when the purely affine theory is local and avoids the explicit use of the Ricci tensor in realizing the weak equivalence principle. When the Ricci tensor is substituted for the metric, the equations seem to have only a very limited set of solutions. This backs the conviction that viable purely affine theories have to be non-local.
On constructing purely affine theories with matter
Cervantes-Cota, Jorge L
2016-01-01
We explore ways to obtain the very existence of a space-time metric from an action principle that does not refer to it a priori. Although there are reasons to believe that only a non-local theory can viably achieve this goal, we investigate here local theories that start with Schroedinger's purely affine theory [21], where he gave reasons to set the metric proportional to the Ricci curvature aposteriori. When we leave the context of unified field theory, and we couple the non-gravitational matter using some weak equivalence principle, we can show that the propagation of shock waves does not define a lightcone when the purely affine theory is local and avoids the explicit use of the Ricci tensor in realizing the weak equivalence principle. When the Ricci tensor is substituted for the metric, the equations seem to have only a very limited set of solutions. This backs the conviction that viable purely affine theories have to be non-local.
Overview of affinity biosensors in food analysis.
Patel, Pradip D
2006-01-01
The 4 major driving forces that are expected to lead to increased use of affinity biosensors that meet crucial industrial test specifications, e.g., fast, reliable, cost-effective, and use of low-skilled personnel, are (1) strict legislative framework, e.g., recent changes proposed to the European food safety and hygiene legislation, EC No. 178/2002; (2) industrial shift from quality control to quality assurance procedures, e.g., Hazard Analysis Critical Control Point, ensuring effective positioning in the global competitive trade; (3) just-in-time production resulting in 'right' product every time; and (4) consumer demand for safe and wholesome products. The affinity biosensors field has expanded significantly over the past decade, with a projected global biosensors market growth from $6.1 billion in 2004 to $8.2 billion in 2009, representing major industrial sectors (e.g., Pharma, Medicare, and Food). This brief review is targeted to affinity biosensors developed for the food industry and includes research and development leading to biosensors for microbiological and chemical analytes of industrial concern, commercial biosensors products on the market, and examples of future prospects in this diagnostic field. PMID:16792079
A MEMS Dielectric Affinity Glucose Biosensor.
Huang, Xian; Li, Siqi; Davis, Erin; Li, Dachao; Wang, Qian; Lin, Qiao
2013-06-20
Continuous glucose monitoring (CGM) sensors based on affinity detection are desirable for long-term and stable glucose management. However, most affinity sensors contain mechanical moving structures and complex design in sensor actuation and signal readout, limiting their reliability in subcutaneously implantable glucose detection. We have previously demonstrated a proof-of-concept dielectric glucose sensor that measured pre-mixed glucose-sensitive polymer solutions at various glucose concentrations. This sensor features simplicity in sensor design, and possesses high specificity and accuracy in glucose detection. However, lack of glucose diffusion passage, this device is unable to fulfill real-time in-vivo monitoring. As a major improvement to this device, we present in this paper a fully implantable MEMS dielectric affinity glucose biosensor that contains a perforated electrode embedded in a suspended diaphragm. This capacitive-based sensor contains no moving parts, and enables glucose diffusion and real-time monitoring. The experimental results indicate that this sensor can detect glucose solutions at physiological concentrations and possesses good reversibility and reliability. This sensor has a time constant to glucose concentration change at approximately 3 min, which is comparable to commercial systems. The sensor has potential applications in fully implantable CGM that require excellent long-term stability and reliability. PMID:24511215
Phosphopeptide Enrichment by Immobilized Metal Affinity Chromatography.
Thingholm, Tine E; Larsen, Martin R
2016-01-01
Immobilized metal affinity chromatography (IMAC) has been the method of choice for phosphopeptide enrichment prior to mass spectrometric analysis for many years and it is still used extensively in many laboratories. Using the affinity of negatively charged phosphate groups towards positively charged metal ions such as Fe(3+), Ga(3+), Al(3+), Zr(4+), and Ti(4+) has made it possible to enrich phosphorylated peptides from peptide samples. However, the selectivity of most of the metal ions is limited, when working with highly complex samples, e.g., whole-cell extracts, resulting in contamination from nonspecific binding of non-phosphorylated peptides. This problem is mainly caused by highly acidic peptides that also share high binding affinity towards these metal ions. By lowering the pH of the loading buffer nonspecific binding can be reduced significantly, however with the risk of reducing specific binding capacity. After binding, the enriched phosphopeptides are released from the metal ions using alkaline buffers of pH 10-11, EDTA, or phosphate-containing buffers. Here we describe a protocol for IMAC using Fe(3+) for phosphopeptide enrichment. The principles are illustrated on a semi-complex peptide mixture. PMID:26584922
Quelques remarques sur la notion de modification affine
Dubouloz, Adrien
2005-01-01
in french We construct a global counterpart to the notion of affine modification due to Kaliman and Zaidenberg. This leads to a simple explicit description of the structure of birational affine morphisms between arbitrary quasi-projective varieties.
A multiscale framework for affine invariant pattern recognition and registration
Rahtu, E. (Esa)
2007-01-01
Abstract This thesis presents a multiscale framework for the construction of affine invariant pattern recognition and registration methods. The idea in the introduced approach is to extend the given pattern to a set of affine covariant versions, each carrying slightly different information, and then to apply known affine invariants to each of them separately. The key part of the framework is the construction of the affine covariant set, and this is done by combining several scaled represen...
The purification of affinity-labelled active-site peptides
International Nuclear Information System (INIS)
The isolation of the labelled peptide from the protein digest, following the affinity labelling of the active sites of enzymes or antibodies, is described. Single-step affinity chromatography utilises the affinity of the native enzymes or antibody for the ligand used to label the same protein. The labelled peptide is the only one in the digest that displays affinity for the immobilised protein and can be released with eluants that dissociate the protein-ligand complex. (Auth.)
Duals of Affine Grassmann Codes and Their Relatives
DEFF Research Database (Denmark)
Beelen, P.; Ghorpade, S. R.; Hoholdt, T.
2012-01-01
Affine Grassmann codes are a variant of generalized Reed-Muller codes and are closely related to Grassmann codes. These codes were introduced in a recent work by Beelen Here, we consider, more generally, affine Grassmann codes of a given level. We explicitly determine the dual of an affine Grassm...
Avoiding degenerate coframes in an affine gauge approach to quantum gravity
International Nuclear Information System (INIS)
This report discusses the following concepts on quantum gravity: The affine gauge approach; affine gauge transformations versus active differomorphisms; affine gauge approach to quantum gravity with topology change
On Metrizability of Invariant Affine Connections
Tanaka, Erico
2011-01-01
The metrizability problem for a symmetric affine connection on a manifold, invariant with respect to a group of diffeomorphisms G, is considered. We say that the connection is G-metrizable, if it is expressible as the Levi-Civita connection of a G-invariant metric field. In this paper we analyze the G-metrizability equations for the rotation group G = SO(3), acting canonically on three- and four-dimensional Euclidean spaces. We show that the property of the connection to be SO(3)-invariant allows us to find complete explicit description of all solutions of the SO(3)-metrizability equations.
Quantum affine symmetry in vertex models
Idzumi, M; Jimbo, M; Miwa, T; Nakashima, T; Tokihiro, T; Idzumi, Makoto; Iohara, Kenji; Jimbo, Michio; Miwa, Tetsuji; Nakashima, Toshiki; Tokihiro, Tetsuji
1993-01-01
We study the higher spin anologs of the six vertex model on the basis of its symmetry under the quantum affine algebra $U_q(\\slth)$. Using the method developed recently for the XXZ spin chain, we formulate the space of states, transfer matrix, vacuum, creation/annihilation operators of particles, and local operators, purely in the language of representation theory. We find that, regardless of the level of the representation involved, the particles have spin $1/2$, and that the $n$-particle space has an RSOS-type structure rather than a simple tensor product of the $1$-particle space. This agrees with the picture proposed earlier by Reshetikhin.
Connection between the Affine and conformal Affine Toda models and their Hirota's solution
International Nuclear Information System (INIS)
It is shown that the Affine Toda models (AT) constitute a gauge fixed version of the Conformal Affine Toda model (CAT). This result enables one to map every solution of the AT models into an infinite number of solutions of the corresponding CAT models, each one associated to a point of the orbit of the conformal group. The Hirota's τ-function are introduced and soliton solutions for the AT and CAT models associated to SL (r+1) and SP (r) are constructed. (author)
Aptamer Affinity Maturation by Resampling and Microarray Selection.
Kinghorn, Andrew B; Dirkzwager, Roderick M; Liang, Shaolin; Cheung, Yee-Wai; Fraser, Lewis A; Shiu, Simon Chi-Chin; Tang, Marco S L; Tanner, Julian A
2016-07-19
Aptamers have significant potential as affinity reagents, but better approaches are critically needed to discover higher affinity nucleic acids to widen the scope for their diagnostic, therapeutic, and proteomic application. Here, we report aptamer affinity maturation, a novel aptamer enhancement technique, which combines bioinformatic resampling of aptamer sequence data and microarray selection to navigate the combinatorial chemistry binding landscape. Aptamer affinity maturation is shown to improve aptamer affinity by an order of magnitude in a single round. The novel aptamers exhibited significant adaptation, the complexity of which precludes discovery by other microarray based methods. Honing aptamer sequences using aptamer affinity maturation could help optimize a next generation of nucleic acid affinity reagents. PMID:27346322
Induced Modules for Affine Lie Algebras
Directory of Open Access Journals (Sweden)
Vyacheslav Futorny
2009-03-01
Full Text Available We study induced modules of nonzero central charge with arbitrary multiplicities over affine Lie algebras. For a given pseudo parabolic subalgebra P of an affine Lie algebra G, our main result establishes the equivalence between a certain category of P-induced G-modules and the category of weight P-modules with injective action of the central element of G. In particular, the induction functor preserves irreducible modules. If P is a parabolic subalgebra with a finite-dimensional Levi factor then it defines a unique pseudo parabolic subalgebra P^{ps}, P subset P^{ps}. The structure of P-induced modules in this case is fully determined by the structure of P^{ps}-induced modules. These results generalize similar reductions in particular cases previously considered by V. Futorny, S. König, V. Mazorchuk [Forum Math. 13 (2001, 641-661], B. Cox [Pacific J. Math. 165 (1994, 269-294] and I. Dimitrov, V. Futorny, I. Penkov [Comm. Math. Phys. 250 (2004, 47-63].
Exploring Fluorous Affinity by Liquid Chromatography.
Catani, Martina; Guzzinati, Roberta; Marchetti, Nicola; Pasti, Luisa; Cavazzini, Alberto
2015-07-01
Terms such as "fluorous affinity" and "fluorophilicity" have been used to describe the unique partition and sorption properties often exhibited by highly fluorinated organic compounds, that is molecules rich in sp(3) carbon-fluorine bonds. In this work, we made use of a highly fluorinated stationary phase and a series of benzene derivatives to study the effect of one single perfluorinated carbon on the chromatographic behavior and adsorption properties of molecules. For this purpose, the adsorption equilibria of α,α,α-trifluorotoluene, toluene, and other alkylbenzenes have been studied by means of nonlinear chromatography in a variety of acetonitrile/water eluents. Our results reveal that one single perfluorinated carbon is already enough to induce a drastic change in the adsorption properties of molecules on the perfluorinated stationary phase. In particular, it has been found that adsorption is monolayer if the perfluoroalkyl carbon is present but that, when this unit is missing, molecules arrange as multilayer stack structures. These findings can contribute to the understanding of molecular mechanisms of fluorous affinity. PMID:26047527
Aspects of affine Toda field theory
International Nuclear Information System (INIS)
The report is devoted to properties of the affine Toda field theory, the intention being to highlight a selection of curious properties that should be explicable in terms of the underlying group theory but for which in most cases there are no explanation. The motivation for exploring the ideas contained in this report came principally from the recent work of Zamolodchikov concerning the two dimensional Ising model at critical temperature perturbed by a magnetic field. Hollowood and Mansfield pointed out that since Toda field theory is conformal the perturbation considered by Zamolodchikov might well be best regarded as a perturbation of a Toda field theory. This work made it seem plausible that the theory sought by Zamolodchikov was actually affine E8 Toda field theory. However, this connection required an imaginary value of the coupling constant. Investigations here concerning exact S-matrices use a perturbative approach based on real coupling and the results differ in various ways from those thought to correspond to perturbed conformal field theory. A further motivation is to explore the connection between conformal and perturbed conformal field theories in other contexts using similar ideas. (N.K.)
Data Stream Clustering With Affinity Propagation
Zhang, Xiangliang
2014-07-09
Data stream clustering provides insights into the underlying patterns of data flows. This paper focuses on selecting the best representatives from clusters of streaming data. There are two main challenges: how to cluster with the best representatives and how to handle the evolving patterns that are important characteristics of streaming data with dynamic distributions. We employ the Affinity Propagation (AP) algorithm presented in 2007 by Frey and Dueck for the first challenge, as it offers good guarantees of clustering optimality for selecting exemplars. The second challenging problem is solved by change detection. The presented StrAP algorithm combines AP with a statistical change point detection test; the clustering model is rebuilt whenever the test detects a change in the underlying data distribution. Besides the validation on two benchmark data sets, the presented algorithm is validated on a real-world application, monitoring the data flow of jobs submitted to the EGEE grid.
Generalized affine transformation monoids on Galois rings
Yonglin Cao
2006-01-01
Let A be a ring with identity. The generalized affine transformation monoid Gaff(A) is defined as the set of all transformations on A of the form xÃ¢Â†Â¦xu+a (for all xÃ¢ÂˆÂˆA), where u,aÃ¢ÂˆÂˆA. We study the algebraic structure of the monoid Gaff(A) on a finite Galois ring A. The following results are obtained: an explicit description of Green's relations on Gaff(A); and an explicit description of the SchÃƒÂ¼tzenberger group of every Ã°ÂÂ’ÂŸ-class, which is shown to be isomorphic to the aff...
Gravitational Goldstone fields from affine gauge theory
Tresguerres, R
2000-01-01
In order to facilitate the application of standard renormalization techniques, gravitation should be decribed, if possible, in pure connection formalism, as a Yang-Mills theory of a certain spacetime group, say the Poincare or the affine group. This embodies the translational as well as the linear connection. However, the coframe is not the standard Yang-Mills type gauge field of the translations, since it lacks the inhomogeneous gradient term in the gauge transformations. By explicitly restoring the "hidden" piece responsible for this behavior within the framework of nonlinear realizations, the usual geometrical interpretation of the dynamical theory becomes possible, and in addition one can avoid the metric or coframe degeneracy which would otherwise interfere with the integrations within the path integral. We claim that nonlinear realizations provide a general mathematical scheme clarifying the foundations of gauge theories of spacetime symmetries. When applied to construct the Yang-Mills theory of the aff...
Effectively nonlocal metric-affine gravity
Golovnev, Alexey; Sandstad, Marit
2015-01-01
In metric-affine theories of gravity such as the C-theories, the spacetime connection is associated to a metric that is nontrivially related to the physical metric. In this article, such theories are rewritten in terms of a single metric and it is shown that they can be recast as effectively nonlocal gravity. With some assumptions, known ghost-free theories with non-singular and cosmologically interesting properties may be recovered. Relations between different formulations are analysed at both perturbative and nonperturbative levels taking carefully into account subtleties with boundary conditions in the presence of integral operators in the action, and equivalences between theories related by nonlocal redefinitions of the fields are verified at the level of equations of motion. This suggests a possible geometrical interpretation of nonlocal gravity as an emergent property of non-Riemannian spacetime structure.
Effectively nonlocal metric-affine gravity
Golovnev, Alexey; Koivisto, Tomi; Sandstad, Marit
2016-03-01
In metric-affine theories of gravity such as the C-theories, the spacetime connection is associated to a metric that is nontrivially related to the physical metric. In this article, such theories are rewritten in terms of a single metric, and it is shown that they can be recast as effectively nonlocal gravity. With some assumptions, known ghost-free theories with nonsingular and cosmologically interesting properties may be recovered. Relations between different formulations are analyzed at both perturbative and nonperturbative levels, taking carefully into account subtleties with boundary conditions in the presence of integral operators in the action, and equivalences between theories related by nonlocal redefinitions of the fields are verified at the level of equations of motion. This suggests a possible geometrical interpretation of nonlocal gravity as an emergent property of non-Riemannian spacetime structure.
Affine connection form of Regge calculus
Khatsymovsky, V M
2015-01-01
Regge action is represented analogously to how the Palatini action for general relativity (GR) as some functional of the metric and a general connection as independent variables represents the Einstein-Hilbert action. The piecewise flat (or simplicial) spacetime of Regge calculus is equipped with some world coordinates and some piecewise affine metric which is completely defined by the set of edge lengths and the world coordinates of the vertices. The conjugate variables are the general nondegenerate matrices on the 3-simplices which play a role of a general discrete connection. Our previous result on some representation of the Regge calculus action in terms of the local Euclidean (Minkowsky) frame vectors and orthogonal connection matrices as independent variables is somewhat modified for the considered case of the general linear group GL(4,R) of the connection matrices. As a result, we have some action invariant w. r. t. arbitrary change of coordinates of the vertices (and related GL(4,R) transformations in...
Li, Bing; Fouts, Ashley E; Stengel, Katharina; Luan, Peng; Dillon, Michael; Liang, Wei-Ching; Feierbach, Becket; Kelley, Robert F; Hötzel, Isidro
2014-01-01
Antibodies isolated from human donors are increasingly being developed for anti-infective therapeutics. These antibodies undergo affinity maturation in vivo, minimizing the need for engineering of therapeutic leads for affinity. However, the affinities required for some therapeutic applications may be higher than the affinities of the leads obtained, requiring further affinity maturation in vitro. To improve the neutralization potency of natural human antibody MSL-109 targeting human cytomegalovirus (CMV), we affinity matured the antibody against the gH/gL glycoprotein complex. A phage display library where most of the six complementary-determining regions (CDRs) were allowed to vary in only one amino acid residue at a time was used to scan for mutations that improve binding affinity. A T55R mutation and multiple mutations in position 53 of the heavy chain were identified that, when present individually or in combination, resulted in higher apparent affinities to gH/gL and improved CMV neutralization potency of Fab fragments expressed in bacterial cells. Three of these mutations in position 53 introduced glycosylation sites in heavy chain CDR 2 (CDR H2) that impaired binding of antibodies expressed in mammalian cells. One high affinity (KD < 10 pM) variant was identified that combined the D53N and T55R mutations while avoiding glycosylation of CDR H2. However, all the amino acid substitutions identified by phage display that improved binding affinity without introducing glycosylation sites required between two and four simultaneous nucleotide mutations to avoid glycosylation. These results indicate that the natural human antibody MSL-109 is close to a local affinity optimum. We show that affinity maturation by phage display can be used to identify and bypass barriers to in vivo affinity maturation of antibodies imposed by glycosylation and codon usage. These constraints may be relatively prevalent in human antibodies due to the codon usage and the amino acid
Classical affine W-algebras associated to Lie superalgebras
International Nuclear Information System (INIS)
In this paper, we prove classical affine W-algebras associated to Lie superalgebras (W-superalgebras), which can be constructed in two different ways: via affine classical Hamiltonian reductions and via taking quasi-classical limits of quantum affine W-superalgebras. Also, we show that a classical finite W-superalgebra can be obtained by a Zhu algebra of a classical affine W-superalgebra. Using the definition by Hamiltonian reductions, we find free generators of a classical W-superalgebra associated to a minimal nilpotent. Moreover, we compute generators of the classical W-algebra associated to spo(2|3) and its principal nilpotent. In the last part of this paper, we introduce a generalization of classical affine W-superalgebras called classical affine fractional W-superalgebras. We show these have Poisson vertex algebra structures and find generators of a fractional W-superalgebra associated to a minimal nilpotent
Classical affine W-algebras associated to Lie superalgebras
Energy Technology Data Exchange (ETDEWEB)
Suh, Uhi Rinn, E-mail: uhrisu1@math.snu.ac.kr [Department of Mathematical Sciences, Seoul National University, GwanAkRo 1, Gwanak-Gu, Seoul 151-747 (Korea, Republic of)
2016-02-15
In this paper, we prove classical affine W-algebras associated to Lie superalgebras (W-superalgebras), which can be constructed in two different ways: via affine classical Hamiltonian reductions and via taking quasi-classical limits of quantum affine W-superalgebras. Also, we show that a classical finite W-superalgebra can be obtained by a Zhu algebra of a classical affine W-superalgebra. Using the definition by Hamiltonian reductions, we find free generators of a classical W-superalgebra associated to a minimal nilpotent. Moreover, we compute generators of the classical W-algebra associated to spo(2|3) and its principal nilpotent. In the last part of this paper, we introduce a generalization of classical affine W-superalgebras called classical affine fractional W-superalgebras. We show these have Poisson vertex algebra structures and find generators of a fractional W-superalgebra associated to a minimal nilpotent.
Non-affine displacements in flexible polymer networks
Basu, Anindita; Wen, Qi; Mao, Xiaoming; Lubensky, T. C.; Janmey, Paul A.; Yodh, A. G.
2010-01-01
The validity of the affine assumption in model flexible polymer networks is explored. To this end, the displacements of fluorescent tracer beads embedded in polyacrylamide gels are quantified by confocal microscopy under shear deformation, and the deviations of these displacements from affine responses are recorded. Non-affinity within the gels is quantified as a function of polymer chain density and cross-link concentration. Observations are in qualitative agreement with current theories of ...
Affine Vertex Operator Algebras and Modular Linear Differential Equations
Arike, Yusuke; Kaneko, Masanobu; Nagatomo, Kiyokazu; Sakai, Yuichi
2016-05-01
In this paper, we list all affine vertex operator algebras of positive integral levels whose dimensions of spaces of characters are at most 5 and show that a basis of the space of characters of each affine vertex operator algebra in the list gives a fundamental system of solutions of a modular linear differential equation. Further, we determine the dimensions of the spaces of characters of affine vertex operator algebras whose numbers of inequivalent simple modules are not exceeding 20.
Affine Vertex Operator Algebras and Modular Linear Differential Equations
Arike, Yusuke; Kaneko, Masanobu; Nagatomo, Kiyokazu; Sakai, Yuichi
2016-04-01
In this paper, we list all affine vertex operator algebras of positive integral levels whose dimensions of spaces of characters are at most 5 and show that a basis of the space of characters of each affine vertex operator algebra in the list gives a fundamental system of solutions of a modular linear differential equation. Further, we determine the dimensions of the spaces of characters of affine vertex operator algebras whose numbers of inequivalent simple modules are not exceeding 20.
Extended affine Weyl groups: Presentation by conjugation via integral collection
Azam, Saeid; Shahsanaei, Valiollah
2009-01-01
We give several necessary and sufficient conditions for the existence of {\\it the presentation by conjugation} for a non-simply laced extended affine Weyl group. We invent a computational tool by which one can determine simply the existence of the presentation by conjugation for an extended affine Weyl group. As an application, we determine the existence of the presentation by conjugation for a large class of extended affine Weyl groups.
Dirac cohomology for the degenerate affine Hecke Clifford algebra
Chan, Kei Yuen
2013-01-01
We define an analogue of the Dirac operator for the degenerate affine Hecke-Clifford algebra. A main result is to relate the central characters of the degenerate affine Hecke-Clifford algebra with the central characters of the Sergeev algebra via Dirac cohomology. The action of the Dirac operator on certain modules is also computed. Results in this paper could be viewed as a projective version of the Dirac cohomology of the degenerate affine Hecke algebra.
DECISION TREE ANALYSIS OF THE PREDICTORS OF INTERNET AFFINITY
BUBAŠ, Goran; Kliček, Božidar; Hutinski, Željko
2001-01-01
A recently developed model of Internet affinity was used for survey design and data collection on variables that have potential influence on affinity for Internet use. A total of 600 Croatian students with access to the Internet at their college participated in this survey. The collected data were used for investigation of the relation between decision tree analysis and regression analysis of predictor variables of Internet affinity. Different predictors were found to influence two distinct c...
Self-affine sets and the continuity of subadditive pressure
Shmerkin, Pablo
2013-01-01
The affinity dimension is a number associated to an iterated function system of affine maps, which is fundamental in the study of the fractal dimensions of self-affine sets. De-Jun Feng and the author recently solved a folklore open problem, by proving that the affinity dimension is a continuous function of the defining maps. The proof also yields the continuity of a topological pressure arising in the study of random matrix products. I survey the definition, motivation and main properties of...
On invariant measures of finite affine type tilings
Petite, S.
2004-01-01
In this paper, we consider tilings of the hyperbolic 2-space, built with a finite number of polygonal tiles, up to affine transformation. To such a tiling T, we associate a space of tilings: the continuous hull Omega(T) on which the affine group acts. This space Omega(T) inherits a solenoid structure whose leaves correspond to the orbits of the affine group. First we prove the finite harmonic measures of this laminated space correspond to finite invariant measures for the affine group action....
Smooth affine shear tight frames: digitization and applications
Zhuang, Xiaosheng
2015-08-01
In this paper, we mainly discuss one of the recent developed directional multiscale representation systems: smooth affine shear tight frames. A directional wavelet tight frame is generated by isotropic dilations and translations of directional wavelet generators, while an affine shear tight frame is generated by anisotropic dilations, shears, and translations of shearlet generators. These two tight frames are actually connected in the sense that the affine shear tight frame can be obtained from a directional wavelet tight frame through subsampling. Consequently, an affine shear tight frame indeed has an underlying filter bank from the MRA structure of its associated directional wavelet tight frame. We call such filter banks affine shear filter banks, which can be designed completely in the frequency domain. We discuss the digitization of affine shear filter banks and their implementations: the forward and backward digital affine shear transforms. Redundancy rate and computational complexity of digital affine shear transforms are also investigated in this paper. Numerical experiments and comparisons in image/video processing show the advantages of digital affine shear transforms over many other state-of-art directional multiscale representation systems.
International Nuclear Information System (INIS)
We further find the defining structure of a two-parameter quantum affine algebra Ur,s(sln-circumflex) (n > 2) in the sense of Benkart-Witherspoon [BW1] after the work of [BGH1], [HS] and [BH], which turns out to be a Drinfeld double. Of more importance for the 'affine' cases is that we work out the compatible two-parameter version of the Drinfeld realization as a quantum affinization of Ur,s(sln) and establish the Drinfeld isomorphism Theorem in the two-parameter setting via developing a new remarkable combinatorial approach - quantum 'affine' Lyndon basis with an explicit valid algorithm, based on the Drinfeld realization. (author)
Affinity of guanosine derivatives for polycytidylate revisited
Kanavarioti, A.; Hurley, T. B.; Baird, E. E.
1995-01-01
Evidence is presented for complexation of guanosine 5'-monophosphate 2-methylimidazolide (2-MeImpG) with polycytidylate (poly(C)) at pH 8.0 and 23 degrees C in the presence of 1.0 M NaCl2 and 0.2 M MgCl2 in water. The association of 2-MeImpG with poly(C) was investigated using UV-vis spectroscopy as well as by monitoring the kinetics of the nucleophilic substitution reaction of the imidazole moiety by amines. The results of both methods are consistent with moderately strong poly(C) 2-MeImpG complexation and the spectrophotometric measurements allowed the construction of a binding isotherm with a concentration of 2-MeImpG equal to 5.55 +/- 0.15 mM at half occupancy. UV spectroscopy was employed to establish the binding of other guanosine derivatives on poly(C). These derivatives are guanosine 5'-monophosphate (5'GMP), guanosine 5'-monophosphate imidazolide (ImpG), and guanosine 5'-monophosphate morpholidate (morpG). Within experimental error these guanosine derivatives exhibit the same affinity for poly(C) as 2-MeImpG.
Affine group formulation of the Standard Model coupled to gravity
International Nuclear Information System (INIS)
In this work we apply the affine group formalism for four dimensional gravity of Lorentzian signature, which is based on Klauder’s affine algebraic program, to the formulation of the Hamiltonian constraint of the interaction of matter and all forces, including gravity with non-vanishing cosmological constant Λ, as an affine Lie algebra. We use the hermitian action of fermions coupled to gravitation and Yang–Mills theory to find the density weight one fermionic super-Hamiltonian constraint. This term, combined with the Yang–Mills and Higgs energy densities, are composed with York’s integrated time functional. The result, when combined with the imaginary part of the Chern–Simons functional Q, forms the affine commutation relation with the volume element V(x). Affine algebraic quantization of gravitation and matter on equal footing implies a fundamental uncertainty relation which is predicated upon a non-vanishing cosmological constant. -- Highlights: •Wheeler–DeWitt equation (WDW) quantized as affine algebra, realizing Klauder’s program. •WDW formulated for interaction of matter and all forces, including gravity, as affine algebra. •WDW features Hermitian generators in spite of fermionic content: Standard Model addressed. •Constructed a family of physical states for the full, coupled theory via affine coherent states. •Fundamental uncertainty relation, predicated on non-vanishing cosmological constant
Synthesis of tetracycline analogs and their bone affinities
Institute of Scientific and Technical Information of China (English)
Wen Cai Huang; Hu Zheng; Ling Ling Weng
2008-01-01
Tetracycline analogs were designed and synthesized and their bone affinities were tested on hydroxyapatite. The results showedthat the carbonyl-amide-enol structure in A ring and phenol-ketone structure in BCD ring may be responsible for tetracycline's highbone affinity and either A ring or BCD ring has a planar conformation is essential.
Self-affine roughness influence on redox reaction charge admittance
Palasantzas, G
2005-01-01
In this work we investigate the influence of self-affine electrode roughness on the admittance of redox reactions during facile charge transfer kinetics. The self-affine roughness is characterized by the rms roughness amplitude w, the correlation length xi and the roughness exponent H (0
Striving for Empathy: Affinities, Alliances and Peer Sexuality Educators
Fields, Jessica; Copp, Martha
2015-01-01
Peer sexuality educators' accounts of their work reveal two approaches to empathy with their students: affinity and alliance. "Affinity-based empathy" rests on the idea that the more commonalities sexuality educators and students share (or perceive they share), the more they will be able to empathise with one another, while…
Tending to Change: Toward a Situated Model of Affinity Spaces
Bommarito, Dan
2014-01-01
The concept of affinity spaces, a theoretical construct used to analyze literate activity from a spatial perspective, has gained popularity among scholars of literacy studies and, particularly, video-game studies. This article seeks to expand current notions of affinity spaces by identifying key assumptions that have limited researchers'…
IMPLEMENTASI ENKRIPSI DEKRIPSI ALGORITMA AFFINE CIPHER BERBASIS ANDROID
Directory of Open Access Journals (Sweden)
Sasono Wibowo
2014-11-01
Full Text Available Perkembangan Teknologi Informasi yang cukup pesat khususnya dalam bidang komunikasi menjadikan komunikasi sangat mudah namun dalam implementasinya perlu adanya keamanan tentang informasi yang disampaikan. Dalam komunikasi antar orang pasti memiliki pembicaraan informasi yang bersifat privat atau orang lain tidak boleh tahu tentang pembicaraan yang terjadi. Diperlukannya keamanan untuk menjaga kerahasiaan informasi pada saat komunikasi. Masyarakat lebih sering menggunakan komunikasi dengan telepon seluler karena dinilai mudah dibawa dan tidak repot menggunakannya. Kriptografi yang biasa dikenal sebagai ilmu yang mempelajari bagaimana cara menyembunyikan pesan bisa diterapkan dalam aplikasi pada telepon seluler sebagai contoh smartphone android. Dengan mengimplementasikan algoritma affine cipher maka aplikasi yang akan dibuat bisa mengubah isi pesan yang ada dan dapat mengamankan informasi yang ada. Algoritma affine cipher merupakan perkembangan dari algoritma caesar dimana algoritma affine cipher menggunakan dua kunci. Dengan mengimplementasikan algoritma affine cipher ke dalam android maka diharapkan kita bisa menyimpan informasi dari siapapun tanpa terbaca. Kata Kunci : Kriptografi, Affine Cipher, android, Implementasi, Informasi
Chasing polys: Interdisciplinary affinity and its connection to physics identity
Scott, Tyler D.
This research is based on two motivations that merge by means of the frameworks of interdisciplinary affinity and physics identity. First, a goal of education is to develop interdisciplinary abilities in students' thinking and work. But an often ignored factor is students interests and beliefs about being interdisciplinary. Thus, this work develops and uses a framework called interdisciplinary affinity. It encompasses students interests in making connections across disciplines and their beliefs about their abilities to make those connections. The second motivation of this research is to better understand how to engage more students with physics. Physics identity describes how a student sees themselves in relation to physics. By understanding how physics identity is developed, researchers and educators can identify factors that increase interest and engagement in physics classrooms. Therefore, physics identity was used in conjunction with interdisciplinary affinity. Using a mixed methods approach, this research used quantitative data to identify the relationships interdisciplinary affinity has with physics identity and the physics classroom. These connections were explored in more detail using a case study of three students in a high school physics class. Results showed significant and positive relationships between interdisciplinary affinity and physics identity, including the individual interest and recognition components of identity. It also identified characteristics of physics classrooms that had a significant, positive relationship with interdisciplinary affinity. The qualitative case study highlighted the importance of student interest to the relationship between interdisciplinary affinity and physics identity. It also identified interest and mastery orientation as key to understanding the link between interdisciplinary affinity and the physics classroom. These results are a positive sign that by understanding interdisciplinary affinity and physics identity
Convulsant bicuculline modifies CNS muscarinic receptor affinity
Directory of Open Access Journals (Sweden)
Rodríguez de Lores Arnaiz Georgina
2006-04-01
Full Text Available Abstract Background Previous work from this laboratory has shown that the administration of the convulsant drug 3-mercaptopropionic acid (MP, a GAD inhibitor, modifies not only GABA synthesis but also binding of the antagonist [3H]-quinuclidinyl benzilate ([3H]-QNB to central muscarinic receptors, an effect due to an increase in affinity without modifications in binding site number. The cholinergic system has been implicated in several experimental epilepsy models and the ability of acetylcholine to regulate neuronal excitability in the neocortex is well known. To study the potential relationship between GABAergic and cholinergic systems with seizure activity, we analyzed the muscarinic receptor after inducing seizure by bicuculline (BIC, known to antagonize the GABA-A postsynaptic receptor subtype. Results We analyzed binding of muscarinic antagonist [3H]-QNB to rat CNS membranes after i.p. administration of BIC at subconvulsant (1.0 mg/kg and convulsant (7.5 mg/kg doses. Subconvulsant BIC dose failed to develop seizures but produced binding alteration in the cerebellum and hippocampus with roughly 40% increase and 10% decrease, respectively. After convulsant BIC dose, which invariably led to generalized tonic-clonic seizures, binding increased 36% and 15% to cerebellar and striatal membranes respectively, but decreased 12% to hippocampal membranes. Kd value was accordingly modified: with the subconvulsant dose it decreased 27% in cerebellum whereas it increased 61% in hippocampus; with the convulsant dose, Kd value decreased 33% in cerebellum but increased 85% in hippocampus. No change in receptor number site was found, and Hill number was invariably close to unity. Conclusion Results indicate dissimilar central nervous system area susceptibility of muscarinic receptor to BIC. Ligand binding was modified not only by a convulsant BIC dose but also by a subconvulsant dose, indicating that changes are not attributable to the seizure process
Electron affinities of atoms, molecules, and radicals
International Nuclear Information System (INIS)
We review briefly but comprehensively the theoretical, semiempirical and experimental methods employed to determine electron affinities (EAs) of atoms, molecules and radicals, and summarize the EA data obtained by these methods. The detailed processes underlying the principles of the experimental methods are discussed very briefly. It is, nonetheless, instructive to recapitulate the definition of EA and those of the related quantities, namely, the vertical detachment energy, VDE, and the vertical attachment energy, VAE. The EA of an atom is defined as the difference in total energy between the ground state of the neutral atom (plus the electron at rest at infinity) and its negative ion. The EA of a molecule is defined as the difference in energy between the neutral molecule plus an electron at rest at infinity and the molecular negative ion when both, the neutral molecules and the negative ion, are in their ground electronic, vibrational and rotational states. The VDE is defined as the minimum energy required to eject the electron from the negative ion (in its ground electronic and nuclear state) without changing the internuclear separation; since the vertical transition may leave the neutral molecule in an excited vibrational/rotational state, the VDE, although the same as the EA for atoms is, in general, different (larger than), from the EA for molecules. Similarly, the VAE is defined as the difference in energy between the neutral molecule in its ground electronic, vibrational and rotational states plus an electron at rest at infinity and the molecular negative ion formed by addition of an electron to the neutral molecule without allowing a change in the intermolecular separation of the constituent nuclei; it is a quantity appropriate to those cases where the lowest negative ion state lies above the ground states of the neutral species and is less or equal to EA
Tetrahydroprotoberberine alkaloids with dopamine and σ receptor affinity.
Gadhiya, Satishkumar; Madapa, Sudharshan; Kurtzman, Thomas; Alberts, Ian L; Ramsey, Steven; Pillarsetty, Nagavara-Kishore; Kalidindi, Teja; Harding, Wayne W
2016-05-01
Two series of analogues of the tetrahydroprotoberberine (THPB) alkaloid (±)-stepholidine that (a) contain various alkoxy substituents at the C10 position and, (b) were de-rigidified with respect to (±)-stepholidine, were synthesized and evaluated for affinity at dopamine and σ receptors in order to evaluate effects on D3 and σ2 receptor affinity and selectivity. Small n-alkoxy groups are best tolerated by D3 and σ2 receptors. Among all compounds tested, C10 methoxy and ethoxy analogues (10 and 11 respectively) displayed the highest affinity for σ2 receptors as well as σ2 versus σ1 selectivity and also showed the highest D3 receptor affinity. De-rigidification of stepholidine resulted in decreased affinity at all receptors evaluated; thus the tetracyclic THPB framework is advantageous for affinity at dopamine and σ receptors. Docking of the C10 analogues at the D3 receptor, suggest that an ionic interaction between the protonated nitrogen atom and Asp110, a H-bond interaction between the C2 phenol and Ser192, a H-bond interaction between the C10 phenol and Cys181 as well as hydrophobic interactions of the aryl rings to Phe106 and Phe345, are critical for high affinity of the compounds. PMID:27032890
Genetic Algorithm-based Affine Parameter Estimation for Shape Recognition
Directory of Open Access Journals (Sweden)
Yuxing Mao
2014-06-01
Full Text Available Shape recognition is a classically difficult problem because of the affine transformation between two shapes. The current study proposes an affine parameter estimation method for shape recognition based on a genetic algorithm (GA. The contributions of this study are focused on the extraction of affine- invariant features, the individual encoding scheme, and the fitness function construction policy for a GA. First, the affine-invariant characteristics of the centroid distance ratios (CDRs of any two opposite contour points to the barycentre are analysed. Using different intervals along the azimuth angle, the different numbers of CDRs of two candidate shapes are computed as representations of the shapes, respectively. Then, the CDRs are selected based on predesigned affine parameters to construct the fitness function. After that, a GA is used to search for the affine parameters with optimal matching between candidate shapes, which serve as actual descriptions of the affine transformation between the shapes. Finally, the CDRs are resampled based on the estimated parameters to evaluate the similarity of the shapes for classification. The experimental results demonstrate the robust performance of the proposed method in shape recognition with translation, scaling, rotation and distortion.
Einstein-Maxwell dynamics as a P(4) affine theory
International Nuclear Information System (INIS)
In Newtonian mechanics the energy of a particle is defined only up to an arbitrary additive constant. By using affine functions to model the Newtonian energy we show that it is possible to reformulate arbitrary time- and velocity-independent forces as R1 affine gauge potentials. Solutions of Newton's second law then define R1 affine energy geodesics, and the R1 flat gauge potentials are shown to correspond to conservative Newtonian forces. We generalize these ideas to relativistic mechanics by modeling the energy-momentum of classical particles as R4 affine four-vectors. If this R4 affine structure is to be compatible with the O(1,3) Riemannian structure of spacetime, then the R4 gauge potential must correspond to an antisymmetric tensor field on spacetime, and this field is identified with the electromagnetic field tensor. We are eventually led to a reformulation of the Einstein-Maxwell theory as a P(4) = O(1,3) x R4 affine gauge theory in which the timelike affine geodesics correspond to Lorentz-force-law trajectories, and the Einstein-Maxwell field equations are reformulated as gauge field equations in terms of the P(4) curvature
Affine deformation tensor - a necessary object in GRT
International Nuclear Information System (INIS)
Einstein notions about the nature of gravitation are refined. The geometric gravitation theory (GGT) grounds are discussed. It is noted that there is no one of the important geometrical object in the Einstein gravitation theory (EGT) i.e. background affinity, which along with the metric tensor determines the gravitational gield energy density. Considering that it is not necessary to introduce background metrics, the author has introduced the background affinity and affine deformation tensor. The theory of black holes is considered as an alternative of EGT. 53 refs
Synthesis and Image Matching On Structural Patterns Using Affine Transformation
Directory of Open Access Journals (Sweden)
S.Vandana
2012-06-01
Full Text Available This paper focuses in explaining a Fourier based affine estimator which is applied to the task of Image Synthesis. An affine transformation is an important class of linear 2-D geometric transformations which maps variables into new by applying a linear combination of translation, rotation, scaling and/or shearing operations. Conventional retrieval systems are very effective when knowledge information and query information are in a uniform orientation but fails in recognition when effects such as scaling, orientation exist. But as this technique is based on texture analysis, which is termed the affine estimator, it will even match the images with non-uniform orientation.
Affinity- and topology-dependent bound on current fluctuations
Pietzonka, Patrick; Seifert, Udo
2016-01-01
We provide a proof of a recently conjectured universal bound on current fluctuations in Markovian processes. This bound establishes a link between the fluctuations of an individual observable current, the cycle affinities driving the system into a non-equilibrium steady state, and the topology of the network. The proof is based on a decomposition of the network into independent cycles with both positive affinity and positive stationary cycle current. This formalism allows for a refinement of the bound for systems in equilibrium or with locally vanishing affinities.
Pepsin-modified chiral monolithic column for affinity capillary electrochromatography.
Hong, Tingting; Chi, Cuijie; Ji, Yibing
2014-11-01
Pepsin-modified affinity monolithic capillary electrochromatography, a novel microanalysis system, was developed by the covalent bonding of pepsin on silica monolith. The column was successfully applied in the chiral separation of (±)-nefopam. Furthermore, the electrochromatographic performance of the pepsin-functionalized monolith for enantiomeric analysis was evaluated in terms of protein content, pH of running buffer, sample volume, buffer concentration, applied voltage, and capillary temperature. The relative standard deviation (%RSD) values of retention time (intraday implied that the affinity monolith used in this research opens a new path of exploring particularly versatile class of enzymes to develop enzyme-modified affinity capillary monolith for enantioseparation. PMID:25146884
ODE/IM correspondence and modified affine Toda field equations
Ito, Katsushi
2014-01-01
We study the two-dimensional affine Toda field equations for affine Lie algebra $\\hat{\\mathfrak{g}}$ modified by a conformal transformation and the associated linear equations. In the conformal limit, the associated linear problem reduces to a (pseudo-)differential equation. For classical affine Lie algebra $\\hat{\\mathfrak{g}}$, we obtain a (pseudo-)differential equation corresponding to the Bethe equations for the Langlands dual of the Lie algebra $\\mathfrak{g}$, which were found by Dorey et al. in study of the ODE/IM correspondence.
Centro-affine hypersurface immersions with parallel cubic form
HILDEBRAND, Roland
2012-01-01
We consider non-degenerate centro-affine hypersurface immersions in R^n whose cubic form is parallel with respect to the Levi-Civita connection of the affine metric. There exists a bijective correspondence between homothetic families of proper affine hyperspheres with center in the origin and with parallel cubic form, and K\\"ochers conic omega-domains, which are the maximal connected sets consisting of invertible elements in a real semi-simple Jordan algebra. Every level surface of the omega ...
Roy, Ipsita; Mondal, Kalyani; Gupta, Munishwar N
2014-01-01
This chapter describes two simple interrelated non-chromatographic methods of protein purification. In the first method, called affinity precipitation, inherent affinity of reversibly soluble-insoluble polymers (also called stimuli-sensitive or smart polymers) is exploited to form an affinity complex in free solution with target protein. The affinity complex is precipitated by a suitable change in the medium. The desired protein is dissociated from the smart polymer. In the second method called macro (affinity ligand)-facilitated three phase partitioning (MLFTPP), the affinity complex is precipitated at an interface between upper t-butanol-rich phase and lower aqueous phase. These three phases are achieved by adding appropriate amounts of ammonium sulfate and t-butanol to the initial crude extract. In the first protocol, sequential MLFTPP is used with two different smart polymers to purify pectinase and cellulase from a single crude preparation. The second protocol illustrates the application of the affinity precipitation in simultaneous purification and refolding of a urea-denatured xylanase. PMID:24648072
Volatility Components, Affine Restrictions and Non-Normal Innovations
DEFF Research Database (Denmark)
Christoffersen, Peter; Jacobs, Kris; Dorian, Christian;
Recent work by Engle and Lee (1999) shows that allowing for long-run and short-run components greatly enhances a GARCH model's ability fit daily equity return dynamics. Using the risk-neutralization in Duan (1995), we assess the option valuation performance of the Engle-Lee model and compare it to...... GARCH models to four conditionally non-normal versions. As in Hsieh and Ritchken (2005), we find that non-affine models dominate affine models both in terms of fitting return and in terms of option valuation. For the affine models we find strong evidence in favor of the component structure for both...... returns and options, but for the non-affine models the evidence is much less strong in option valuation. The evidence in favor of the non-normal models is strong when fitting daily returns, but the non-normal models do not provide much improvement when valuing options....
Antibody Affinity Maturation in Fishes—Our Current Understanding
Magor, Brad G.
2015-01-01
It has long been believed that fish lack antibody affinity maturation, in part because they were thought to lack germinal centers. Recent research done on sharks and bony fishes indicates that these early vertebrates are able to affinity mature their antibodies. This article reviews the functionality of the fish homologue of the immunoglobulin (Ig) mutator enzyme activation-induced cytidine deaminase (AID). We also consider the protein and molecular evidence for Ig somatic hypermutation and antibody affinity maturation. In the context of recent evidence for a putative proto-germinal center in fishes we propose some possible reasons that observed affinity maturation in fishes often seems lacking and propose future work that might shed further light on this process in fishes. PMID:26264036
Antibody Affinity Maturation in Fishes-Our Current Understanding.
Magor, Brad G
2015-01-01
It has long been believed that fish lack antibody affinity maturation, in part because they were thought to lack germinal centers. Recent research done on sharks and bony fishes indicates that these early vertebrates are able to affinity mature their antibodies. This article reviews the functionality of the fish homologue of the immunoglobulin (Ig) mutator enzyme activation-induced cytidine deaminase (AID). We also consider the protein and molecular evidence for Ig somatic hypermutation and antibody affinity maturation. In the context of recent evidence for a putative proto-germinal center in fishes we propose some possible reasons that observed affinity maturation in fishes often seems lacking and propose future work that might shed further light on this process in fishes. PMID:26264036
Rigid affine surfaces with isomorphic A2-cylinders
Dubouloz, Adrien
2015-01-01
We construct families of smooth affine surfaces with pairwise non isomorphic A 1-cylinders but whose A 2-cylinders are all isomorphic. These arise as complements of cuspidal hyperplane sections of smooth projective cubic surfaces.
Note on Dilogarithm Identities from Nilpotent Double Affine Hecke Algebras
Directory of Open Access Journals (Sweden)
Tomoki Nakanishi
2012-12-01
Full Text Available Recently Cherednik and Feigin [arXiv:1209.1978] obtained several Rogers-Ramanujan type identities via the nilpotent double affine Hecke algebras (Nil-DAHA. These identities further led to a series of dilogarithm identities, some of which are known, while some are left conjectural. We confirm and explain all of them by showing the connection with Y-systems associated with (untwisted and twisted quantum affine Kac-Moody algebras.
An affine sphere equation associated to Einstein toric surfaces
Mabuchi, Toshiki
2007-01-01
As seen in the works of Calabi, Cheng-Yau and Loftin, affine sphere equations have a close relationship with Kaehler-Einstein metrics. The main purpose of this note is to show that an equation analogous to those of hyperbolic affine spheres arises naturally from Kaehler-Einstein metrics on Einstein toric surfaces. The case for the remaining toric surfaces with Kaehler-Ricci solitons will also be discussed.
The ABC's of affine Grassmannians and Hall-Littlewood polynomials
Dalal, Avinash J.; Morse, Jennifer
2016-01-01
We give a new description of the Pieri rule for k-Schur functions using the Bruhat order on the affine type-A Weyl group. In doing so, we prove a new combinatorial formula for representatives of the Schubert classes for the cohomology of affine Grassmannians. We show how new combinatorics involved in our formulas gives the Kostka-Foulkes polynomials and discuss how this can be applied to study the transition matrices between Hall-Littlewood and k-Schur functions.
Peculiarities of Matter Motion in Metric-Affine Gravitational Theory
Babourova, O. V.; Frolov, B. N.; Koroliov, M. Yu.
1995-01-01
On the basis of the Lie derivative method in a metric-affine space-time it is shown that in the metric-affine gravitational theory the energy-momentum conservation law and therefore the equations of the matter motion are the consequence (as in the GR) of the gravitational field equations. The possi- bility of the detection of the space-time non-metric properties is discussed.
Euclidean Reconstruction and Affine Camera Calibration Using Controlled Robot Motions
Horaud, Radu; Christy, Stéphane; Mohr, Roger
1997-01-01
We are addressing the problem of Euclidean reconstruction with an uncalibrated affine camera and the calibration of this camera. We investigate constraints under which the Euclidean shape and motion problem becomes linear. The theoretical study described in this paper leads us to impose some practical constraints that the camera is mounted onto a robot arm and that the robot is executing controlled motions whose parameters are known. The affine camera model considered here is just an approxim...
Algebraic volume density property of affine algebraic manifolds
Kaliman, Shulim; Kutzschebauch, Frank
2009-01-01
We introduce the notion of algebraic volume density property for affine algebraic manifolds and prove some important basic facts about it, in particular that it implies the volume density property. The main results of the paper are producing two big classes of examples of Stein manifolds with volume density property. One class consists of certain affine modifications of $\\C^n$ equipped with a canonical volume form, the other is the class of all Linear Algebraic Groups equipped with the left i...
Quantized gauge-affine gravity in the superfiber bundle approach
Meziane, A.; Tahiri, M
2004-01-01
The quantization of gauge-affine gravity within the superfiber bundle formalism is proposed. By introducing an even pseudotensorial 1-superform over a principal superfibre bundle with superconnection, we obtain the geometrical Becchi-Rouet-Stora-Tyutin (BRST) and anti-BRST transformations of the fields occurring in such a theory. Reducing the four-dimensional general affine group double-covering to the Poincare group double-covering we also find the BRST and anti-BRST transformations of the f...
Affine invariant texture analysis based on structural properties
Zhang, Jianguo; Tan, Tieniu
2002-01-01
This paper presents a new texture analysis method based on structural properties. The texture features extracted using this algorithm are invariant to affine transform (including rotation, translation, scaling, and skewing). Affine invariant structural properties are derived based on texel areas. An area-ratio map utilizing these properties is introduced to characterize texture images. Histogram based on this map is constructed for texture classification. Efficiency of this algorithm for affi...
Several Affinity Tags Commonly Used in Chromatographic Purification
Xinyu Zhao; Guoshun Li; Shufang Liang
2013-01-01
Affinity tags have become powerful tools from basic biological research to structural and functional proteomics. They were widely used to facilitate the purification and detection of proteins of interest, as well as the separation of protein complexes. Here, we mainly discuss the benefits and drawbacks of several affinity or epitope tags frequently used, including hexahistidine tag, FLAG tag, Strep II tag, streptavidin-binding peptide (SBP) tag, calmodulin-binding peptide (CBP), glutathione S...
Skein Modules from Skew Howe Duality and Affine Extensions
Queffelec, Hoel
2013-01-01
We show that we can release the rigidity of the skew Howe duality process for ${\\mathfrak sl}_n$ knot invariants by rescaling the quantum Weyl group action, and recover skein modules for web-tangles. This skew Howe duality phenomenon can be extended to the affine ${\\mathfrak sl}_m$ case, corresponding to looking at tangles embedded in a solid torus. We investigate the relations between the invariants constructed by evaluation representations (and affinization of them) and usual skein modules,...
Minimum information about a protein affinity reagent (MIAPAR).
Bourbeillon, Julie; Orchard, Sandra; Benhar, Itai; Borrebaeck, Carl; de Daruvar, Antoine; Dübel, Stefan; Frank, Ronald; Gibson, Frank; Gloriam, David; Haslam, Niall; Hiltker, Tara; Humphrey-Smith, Ian; Hust, Michael; Juncker, David; Koegl, Manfred
2010-01-01
We wish to alert your readers to MIAPAR, the minimum information about a protein affinity reagent. This is a proposal developed within the community as an important first step in formalizing standards in reporting the production and properties of protein binding reagents, such as antibodies, developed and sold for the identification and detection of specific proteins present in biological samples. It defines a checklist of required information, intended for use by producers of affinity reagen...
Affinity Solvents for Intensified Organics Extraction: Development Challenges and Prospects
Institute of Scientific and Technical Information of China (English)
无
2006-01-01
In most organics extraction processes, the commonly used solvents employ solely physical interactions. Therefore, for the recovery and purification of products from complex mixtures, the selectivity and/or capacity of classical solvents towards the desired solutes is usually insufficient, enforcing the need for complex and thus expensive separation schemes. Significant simplification and cost-reduction can be achieved when affinity solvents would be available that are able to recognize the solutes of interest by their molecular structure. The main development challenges to establish such affinity solvents are: Selection and incorporation of molecular recognition and complexation capabilities; Evaluation of extraction capabilities; Efficient recovery and recycling of the affinity solvents; Implementation in industrial extraction equipment. This paper presents how these development challenges are addressed at the University of Twente, going all the way from affinity solvent design and synthesis, via high throughput screening and characterization up to pilot plant evaluation. Essential in the successful development of affinity solvents are structural cooperations with molecular chemists and custom synthesis companies for their design and synthesis. The various aspects are illustrated by several examples where newly developed environmentally benign affinity solvents appeared able to create major breakthroughs. The applications addressed involve oxygenates, sugars, and pharmaceutical ingredients, such as optical isomers and biomolecules.
Kool, J.; N. Jonker; Irth, H.; Niessen, W.M.A.
2011-01-01
This review discusses the most important current methods employing mass spectrometry (MS) analysis for the study of protein affinity interactions. The methods are discussed in depth with particular reference to MS-based approaches for analyzing protein–protein and protein–immobilized ligand interactions, analyzed either directly or indirectly. First, we introduce MS methods for the study of intact protein complexes in the gas phase. Next, pull-down methods for affinity-based analysis of prote...
Increased hemoglobin O2 affinity protects during acute hypoxia.
Yalcin, Ozlem; Cabrales, Pedro
2012-08-01
Acclimatization to hypoxia requires time to complete the adaptation mechanisms that influence oxygen (O(2)) transport and O(2) utilization. Although decreasing hemoglobin (Hb) O(2) affinity would favor the release of O(2) to the tissues, increasing Hb O(2) affinity would augment arterial O(2) saturation during hypoxia. This study was designed to test the hypothesis that pharmacologically increasing the Hb O(2) affinity will augment O(2) transport during severe hypoxia (10 and 5% inspired O(2)) compared with normal Hb O(2) affinity. RBC Hb O(2) affinity was increased by infusion of 20 mg/kg of 5-hydroxymethyl-2-furfural (5HMF). Control animals received only the vehicle. The effects of increasing Hb O(2) affinity were studied in the hamster window chamber model, in terms of systemic and microvascular hemodynamics and partial pressures of O(2) (Po(2)). Pimonidazole binding to hypoxic areas of mice heart and brain was also studied. 5HMF decreased the Po(2) at which the Hb is 50% saturated with O(2) by 12.6 mmHg. During 10 and 5% O(2) hypoxia, 5HMF increased arterial blood O(2) saturation by 35 and 48% from the vehicle group, respectively. During 5% O(2) hypoxia, blood pressure and heart rate were 58 and 30% higher for 5HMF compared with the vehicle. In addition, 5HMF preserved microvascular blood flow, whereas blood flow decreased to 40% of baseline in the vehicle group. Consequently, perivascular Po(2) was three times higher in the 5HMF group compared with the control group at 5% O(2) hypoxia. 5HMF also reduced heart and brain hypoxic areas in mice. Therefore, increased Hb O(2) affinity resulted in hemodynamics and oxygenation benefits during severe hypoxia. This acute acclimatization process may have implications in survival during severe environmental hypoxia when logistic constraints prevent chronic acclimatization. PMID:22636677
Isotope shift in the electron affinity of beryllium
International Nuclear Information System (INIS)
The study of the isotope shift in the electron affinity is interesting for probing correlation effects. Experiments that allow this property to be measured are rare, being difficult to realize, while accurate calculations remain a challenge for atomic theory. The present work focuses on the theoretical estimation of the isotope shift in the electron affinity of Be (2s2p 3Po), using correlated electronic wavefunctions obtained from multiconfiguration Hartree-Fock and configuration interaction variational calculations. The reliability of the correlation models is assessed from a comparison between the observed and theoretical electron affinities, and between theoretical isotope shift values for the 2s2p 3Po 2s21S transition of neutral beryllium. The sign and the magnitude of the difference between the mass polarization term expectation values obtained for the neutral atom and the negative ion are such that the resulting isotope shift in the electron affinity is 'anomalous', corresponding to a smaller electron affinity for the heavier isotope
Coenzyme-like ligands for affinity isolation of cholesterol oxidase.
Xin, Yu; Lu, Liushen; Wang, Qing; Zhang, Ling; Tong, Yanjun; Wang, Wu
2016-05-15
Two coenzyme-like chemical ligands were designed and synthesized for affinity isolation of cholesterol oxidase (COD). To simulate the structure of natural coenzyme of COD (flavin adenine dinucleotide (FAD)), on Sepharose beads, 5-aminouracil, cyanuric chloride and 1, 4-butanediamine were composed and then modified. The COD gene from Brevibacterium sp. (DQ345780) was expressed in Escherichia coli BL21 (DE3), and then the sorbents were applied to adsorption analysis with the pure enzyme. Subsequently, the captured enzyme was applied to SDS-PAGE and activity analysis. As calculated, the theoretical maximum adsorption (Qmax) of the two affinity sorbents (RL-1 and RL-2) were ∼83.5 and 46.3mg/g wet gel; and the desorption constant Kd of the two sorbents were ∼6.02×10(-4) and 1.19×10(-4)μM. The proteins after cell lysis were applied to affinity isolation, and then after one step of affinity binding on the two sorbents, the protein recoveries of RL-1 and RL-2 were 9.2% and 9.7%; the bioactivity recoveries were 92.7% and 91.3%, respectively. SDS-PAGE analysis revealed that the purities of COD isolated with the two affinity sorbents were approximately 95%. PMID:26856529
Bulbeck, David
2013-01-01
Genetic research into Southeast Asia's "negritos" has revealed their deep-rooted ancestry, with time depth comparable to that of Southwest Pacific populations. This finding is often interpreted as evidence that negritos, in contrast to other Southeast Asians, can trace much of their ancestry directly back to the early dispersal of Homo sapiens in the order of 70 kya from Africa to Pleistocene New Guinea and Australia. One view on negritos is to lump them and Southwest Pacific peoples into an "Australoid" race whose geographic distribution had included Southeast Asia prior to the Neolithic incursion of "Mongoloid" farmers. Studies into Semang osteology have revealed some hints of Southwest Pacific affinities in cranial shape, dental morphology, and dental metrical "shape." On the other hand, the Andamanese have been shown to resemble Africans in their craniometrics and South Asians in their dental morphology, while Philippine negritos resemble Mongoloid Southeast Asians in these respects and also in their dental metrics. This study expands the scope of negrito cranial comparisons by including Melayu Malays and additional coverage of South Asians. It highlights the distinction between the Mongoloid-like Philippine negritos and the Andamanese and Semang (and Senoi of Malaya) with their non-Mongoloid associations. It proposes that the early/mid-Holocene dispersal of the B4a1a mitochondrial DNA clade across Borneo, the Philippines, and Taiwan may be important for understanding the distinction between Philippine and other negritos. PMID:24297222
k-Schur functions and affine Schubert calculus
Lam, Thomas; Morse, Jennifer; Schilling, Anne; Shimozono, Mark; Zabrocki, Mike
2014-01-01
This book gives an introduction to the very active field of combinatorics of affine Schubert calculus, explains the current state of the art, and states the current open problems. Affine Schubert calculus lies at the crossroads of combinatorics, geometry, and representation theory. Its modern development is motivated by two seemingly unrelated directions. One is the introduction of k-Schur functions in the study of Macdonald polynomial positivity, a mostly combinatorial branch of symmetric function theory. The other direction is the study of the Schubert bases of the (co)homology of the affine Grassmannian, an algebro-topological formulation of a problem in enumerative geometry. This is the first introductory text on this subject. It contains many examples in Sage, a free open source general purpose mathematical software system, to entice the reader to investigate the open problems. This book is written for advanced undergraduate and graduate students, as well as researchers, who want to become familiar with ...
Enhancing Community Detection By Affinity-based Edge Weighting Scheme
Energy Technology Data Exchange (ETDEWEB)
Yoo, Andy [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Sanders, Geoffrey [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Henson, Van [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Vassilevski, Panayot [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2015-10-05
Community detection refers to an important graph analytics problem of finding a set of densely-connected subgraphs in a graph and has gained a great deal of interest recently. The performance of current community detection algorithms is limited by an inherent constraint of unweighted graphs that offer very little information on their internal community structures. In this paper, we propose a new scheme to address this issue that weights the edges in a given graph based on recently proposed vertex affinity. The vertex affinity quantifies the proximity between two vertices in terms of their clustering strength, and therefore, it is ideal for graph analytics applications such as community detection. We also demonstrate that the affinity-based edge weighting scheme can improve the performance of community detection algorithms significantly.
Semisupervised Clustering for Networks Based on Fast Affinity Propagation
Directory of Open Access Journals (Sweden)
Mu Zhu
2013-01-01
Full Text Available Most of the existing clustering algorithms for networks are unsupervised, which cannot help improve the clustering quality by utilizing a small number of prior knowledge. We propose a semisupervised clustering algorithm for networks based on fast affinity propagation (SCAN-FAP, which is essentially a kind of similarity metric learning method. Firstly, we define a new constraint similarity measure integrating the structural information and the pairwise constraints, which reflects the effective similarities between nodes in networks. Then, taking the constraint similarities as input, we propose a fast affinity propagation algorithm which keeps the advantages of the original affinity propagation algorithm while increasing the time efficiency by passing only the messages between certain nodes. Finally, by extensive experimental studies, we demonstrate that the proposed algorithm can take fully advantage of the prior knowledge and improve the clustering quality significantly. Furthermore, our algorithm has a superior performance to some of the state-of-art approaches.
Single-cell measurement of red blood cell oxygen affinity
Caprio, Di; Higgins, John M; Schonbrun, Ethan
2015-01-01
Oxygen is transported throughout the body by hemoglobin in red blood cells. While the oxygen affinity of blood is well understood and is routinely assessed in patients by pulse oximetry, variability at the single-cell level has not been previously measured. In contrast, single-cell measurements of red blood cell volume and hemoglobin concentration are taken millions of times per day by clinical hematology analyzers and are important factors in determining the health of the hematologic system. To better understand the variability and determinants of oxygen affinity on a cellular level, we have developed a system that quantifies the oxygen saturation, cell volume and hemoglobin concentration for individual red blood cells in high-throughput. We find that the variability in single-cell saturation peaks at an oxygen partial pressure of 2.5%, which corresponds to the maximum slope of the oxygen-hemoglobin dissociation curve. In addition, single-cell oxygen affinity is positively correlated with hemoglobin concentr...
Properties of the Affine Invariant Ensemble Sampler in high dimensions
Huijser, David; Brewer, Brendon J
2015-01-01
We present theoretical and practical properties of the affine-invariant ensemble sampler Markov chain Monte Carlo method. In high dimensions the affine-invariant ensemble sampler shows unusual and undesirable properties. We demonstrate this with an $n$-dimensional correlated Gaussian toy problem with a known mean and covariance structure, and analyse the burn-in period. The burn-in period seems to be short, however upon closer inspection we discover the mean and the variance of the target distribution do not match the expected, known values. This problem becomes greater as $n$ increases. We therefore conclude that the affine-invariant ensemble sampler should be used with caution in high dimensional problems. We also present some theoretical results explaining this behaviour.
Evaluation Codes from an Affine Veriety Code Perspective
DEFF Research Database (Denmark)
Geil, Hans Olav
2008-01-01
Evaluation codes (also called order domain codes) are traditionally introduced as generalized one-point geometric Goppa codes. In the present paper we will give a new point of view on evaluation codes by introducing them instead as particular nice examples of affine variety codes. Our study...... includes a reformulation of the usual methods to estimate the minimum distances of evaluation codes into the setting of affine variety codes. Finally we describe the connection to the theory of one-pointgeometric Goppa codes. Contents 4.1 Introduction...... . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153 4.2 Affine variety codes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154 4.3 Some Gr¨obner basis theoretical tools . . . . . . . . . . . . . . . . . . . . . . . 155 4.4 A bound on the minimum distance of C(I,L) . . . . . . . . . . . . . . . . . . 157 4.5 The Feng-Rao bound for...
Ferromagnetic Levan Composite: An Affinity Matrix to Purify Lectin
Directory of Open Access Journals (Sweden)
Renata Angeli
2009-01-01
Full Text Available A simple and inexpensive procedure used magnetite and levan to synthesize a composite recovered by a magnetic field. Lectins from Canavalia ensiformis (Con A and Cratylia mollis (Cramoll 1 and Cramoll 1,4 did bind specifically to composite. The magnetic property of derivative favored washing out contaminating proteins and recovery of pure lectins with glucose elution. Cramoll 1 was purified by this affinity binding procedure in two steps instead of a previous three-step protocol with ammonium sulfate fractionation, affinity chromatography on Sephadex G-75, and ion exchange chromatography through a CM-cellulose column.
Ferromagnetic levan composite: an affinity matrix to purify lectin.
Angeli, Renata; da Paz, Nathalia V N; Maciel, Jackeline C; Araújo, Flávia F B; Paiva, Patrícia M G; Calazans, Glícia M T; Valente, Ana Paula; Almeida, Fábio C L; Coelho, Luana C B B; Carvalho, Luiz B; Silva, Maria da Paz C; dos Santos Correia, Maria Tereza
2009-01-01
A simple and inexpensive procedure used magnetite and levan to synthesize a composite recovered by a magnetic field. Lectins from Canavalia ensiformis (Con A) and Cratylia mollis (Cramoll 1 and Cramoll 1, 4) did bind specifically to composite. The magnetic property of derivative favored washing out contaminating proteins and recovery of pure lectins with glucose elution. Cramoll 1 was purified by this affinity binding procedure in two steps instead of a previous three-step protocol with ammonium sulfate fractionation, affinity chromatography on Sephadex G-75, and ion exchange chromatography through a CM-cellulose column. PMID:19547713
Extremely high negative electron affinity of diamond via magnesium adsorption
O'Donnell, Kane M.; Edmonds, Mark T.; Tadich, Anton; Thomsen, Lars; Stacey, Alastair; Schenk, Alex; Pakes, Chris I.; Ley, Lothar
2015-01-01
We report large negative electron affinity (NEA) on diamond (100) using magnesium adsorption on a previously oxygen-terminated surface. The measured NEA is up to $(-2.01\\pm0.05)$ eV, the largest reported negative electron affinity to date. Despite the expected close relationship between the surface chemistry of Mg and Li species on oxygen-terminated diamond, we observe differences in the adsorption properties between the two. Most importantly, a high-temperature annealing step is not required...
Combinatorial topology of three-dimensional self-affine tiles
Bandt, Christoph
2010-01-01
We develop tools to study the topology and geometry of self-affine fractals in dimension three and higher. We use the self-affine structure and obtain rather detailed information about the connectedness of interior and boundary sets, and on the dimensions and intersections of boundary sets. As an application, we describe in algebraic terms the polyhedral structure of the six fractal three-dimensional twindragons. Only two of them can be homeomorphic to a ball but even these have faces which are not homeomorphic to a disk.
and as Vertex Operator Extensionsof Dual Affine Algebras
Bowcock, P.; Feigin, B. L.; Semikhatov, A. M.; Taormina, A.
We discover a realisation of the affine Lie superalgebra and of the exceptional affine superalgebra as vertex operator extensions of two algebras with ``dual'' levels (and an auxiliary level-1 algebra). The duality relation between the levels is . We construct the representation of on a sum of tensor products of , , and modules and decompose it into a direct sum over the spectral flow orbit. This decomposition gives rise to character identities, which we also derive. The extension of the construction to is traced to the properties of embeddings into and their relation with the dual pairs. Conversely, we show how the representations are constructed from representations.
SMOOTH AFFINE SURFACES WITH NON-UNIQUE C*-ACTIONS
Flenner, Hubert; Kaliman, Shulim; ZAIDENBERG, MIKHAIL
2008-01-01
In this paper we complete the classification of effective C*-actions on smooth affine surfaces up to conjugation in the full automorphism group and up to inversion of C*. If a smooth affine surface V admits more than one C*-action then it is known to be Gizatullin i.e., it can be completed by a linear chain of smooth rational curves. In our previous paper we gave a sufficient condition, in terms of the Dolgachev- Pinkham-Demazure (or DPD) presentation, for the uniqueness of a C*-action on a G...
Algebraic volume density property of affine algebraic manifolds
Kaliman, Shulim
2009-01-01
We introduce the notion of algebraic volume density property for affine algebraic manifolds and prove some important basic facts about it, in particular that it implies the volume density property. The main results of the paper are producing two big classes of examples of Stein manifolds with volume density property. One class consists of certain affine modifications of $\\C^n$ equipped with a canonical volume form, the other is the class of all Linear Algebraic Groups equipped with the left invariant volume form.
Affine Moment Invariants Generated by Automated Solution of the Equations
Czech Academy of Sciences Publication Activity Database
Suk, Tomáš; Flusser, Jan
Los Alamitos : IEEE Press, 2008, s. 3270-3273. ISBN 978-1-4244-2174-9. [19th International Conference on Pattern Recognition. Tampa (US), 07.12.2008-11.12.2008] R&D Projects: GA ČR GA102/08/1593 Institutional research plan: CEZ:AV0Z10750506 Keywords : affine moment invariants * object recognition * Cayley-Aronhold differential equation Subject RIV: JD - Computer Applications, Robotics http://library.utia.cas.cz/separaty/2008/ZOI/suk-affine moment invariants generated by automated solution of the equations. pdf
Affine diffusions and related processes simulation, theory and applications
Alfonsi, Aurélien
2015-01-01
This book gives an overview of affine diffusions, from Ornstein-Uhlenbeck processes to Wishart processes and it considers some related diffusions such as Wright-Fisher processes. It focuses on different simulation schemes for these processes, especially second-order schemes for the weak error. It also presents some models, mostly in the field of finance, where these methods are relevant and provides some numerical experiments. The book explains the mathematical background to understand affine diffusions and analyze the accuracy of the schemes.
Double affine Hecke algebras and 2-dimensional local fields
Kapranov, M.
1998-01-01
We give an interpretation of the double affine Hecke algebra of Cherednik as the (suitably regularized) algebra of double cosets of a group G by a subgroup J, extending the well known interpretations of finite and affine Hecke algebras. In this interpretation, G consists of K-points of a split reductive group where K is a 2-dimensional local field such as Q_p((t)) or F_q((t_1))((t_2)), and J is a certain analog of the Iwahori subgroup.
Affinity based and molecularly imprinted cryogels: Applications in biomacromolecule purification.
Andaç, Müge; Galaev, Igor Yu; Denizli, Adil
2016-05-15
The publications in macro-molecularly imprinted polymers have increased drastically in recent years with the development of water-based polymer systems. The macroporous structure of cryogels has allowed the use of these materials within different applications, particularly in affinity purification and molecular imprinting based methods. Due to their high selectivity, specificity, efficient mass transfer and good reproducibility, molecularly imprinted cryogels (MICs) have become attractive for researchers in the separation and purification of proteins. In this review, the recent developments in affinity based cryogels and molecularly imprinted cryogels in protein purification are reviewed comprehensively. PMID:26454622
Kinetic controlled affinity labeling of target enzyme with thioester chemistry.
Tomohiro, Takenori; Nakabayashi, Masahiro; Sugita, Yuka; Morimoto, Shota
2016-08-01
High specificity has been an important feature in affinity labeling for target profiling. Especially, to label targets via rapidly progressing reactions with consumption of ligand (probe), high specificity of reaction with common functional groups of target protein should be achieved without reactions with similar groups of non-target proteins. Herein, we demonstrate the kinetic controlled affinity labeling of acyl CoA synthetase using a fatty acid analogue containing a phenylthioester linkage. High specificity was attained by accelerating the labeling rate in the binding pocket. This approach could be useful for profiling a series of target enzymes and transporters in signal transduction pathways. PMID:27298000
Affine Hecke algebras associated to Kac-Moody groups
Garland, H
1995-01-01
In this paper we give a geometric construction of Cherednik's double affine Hecke algebra. We construct the algebra as the equivariant K-theory of the Lagrangian subvariety of the cotangent variety of the square of the flag variety of G, the variety being given by the union of the conormal bundles to the G-orbits on \\flag\\times\\flag. This is a generalisation of work of Kazhdan and Lusztig to the Kac-Moody case, and is suitable for describing a certain class of modules for this algebra. In a paper in preparation we will do this, in the case G is affine (Cherednik's case).
Multiple poes and other features of affine Toda field theory
International Nuclear Information System (INIS)
Some perturbative features of affine Toda field theory are explored, in particular the mechanisms responsible for the first-, second- and third-order poles in the conjectured exact factorisable S-matrices in the ADE series of models. It is found that generic collections of Feynman diagrams are responsible for the leading order poles in any of the theories. However, the complexity is such that it has not yet proved possible to analyse all the singularities that occur up to order twelve. Some comments are made on an associated tiling problem and on an interesting connection between the affine Toda couplings and the Clebsch-Gordan decomposition of tensor products. (orig.)
A Comment on a Novel Approach for the Registration of Weak Affine Images
Czech Academy of Sciences Publication Activity Database
Flusser, Jan; Zitová, Barbara
2013-01-01
Roč. 34, č. 12 (2013), s. 1381-1385. ISSN 0167-8655 R&D Projects: GA ČR GAP103/11/1552 Keywords : Image registration * Affine transform * Affine subgroups * Weak affine transform * Area-preserving affine transform Subject RIV: JD - Computer Applications, Robotics Impact factor: 1.062, year: 2013 http://library.utia.cas.cz/separaty/2013/ZOI/flusser-a comment on a novel approach for the registration of weak affine images.pdf
A molecular determinant of phosphoinositide affinity in mammalian TRPV channels.
Velisetty, Phanindra; Borbiro, Istvan; Kasimova, Marina A; Liu, Luyu; Badheka, Doreen; Carnevale, Vincenzo; Rohacs, Tibor
2016-01-01
Phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] is an important cofactor for ion channels. Affinity for this lipid is a major determinant of channel inhibition by depletion of PI(4,5)P2 upon phospholipase C (PLC) activation. Little is known about what determines PI(4,5)P2 affinity in mammalian ion channels. Here we report that two members of the Transient Receptor Potential Vanilloid (TRPV) ion channel family, TRPV5 and TRPV6 lack a positively charged residue in the TM4-TM5 loop that was shown to interact with PI(4,5)P2 in TRPV1, which shows high affinity for this lipid. When this positively charged residue was introduced to either TRPV6 or TRPV5, they displayed markedly higher affinities for PI(4,5)P2, and were largely resistant to inhibition by PI(4,5)P2 depletion. Furthermore, Ca(2+)-induced inactivation of TRPV6 was essentially eliminated in the G488R mutant, showing the importance of PLC-mediated PI(4,5)P2 depletion in this process. Computational modeling shows that the introduced positive charge interacts with PI(4,5)P2 in TRPV6. PMID:27291418
Affine Toda Solitons and Systems of Calogero-Moser Type
Braden, H. W.; Hone, Andrew N. W.
1996-01-01
The solitons of affine Toda field theory are related to the spin-generalised Ruijsenaars-Schneider (or relativistic Calogero-Moser) models. This provides the sought after extension of the correspondence between the sine-Gordon solitons and the Ruijsenaars-Schneider model.
On representation theory of affine Hecke algebras of type B
Miemietz, Vanessa
2007-01-01
Ariki's and Grojnowski's approach to the representation theory of affine Hecke algebras of type $A$ is applied to type $B$ with unequal parameters to obtain -- under certain restrictions on the eigenvalues of the lattice operators -- analogous multiplicity-one results and a classification of irreducibles with partial branching rules as in type $A$.
Soliton solutions for higher grading affine Toda from quantum algebras
Czech Academy of Sciences Publication Activity Database
Zuevsky, Alexander
Bristol: IOP, 2015, 012001. ISSN 1755-1307. [2nd International Conference on Geological, Geographical, Aerospace and Earth Sciences 2014 (AeroEarth 2014). Bali (ID), 11.10.2014-12.10.2014] Institutional support: RVO:67985840 Keywords : Lie algebra s * integrable models * affine Toda model Subject RIV: BA - General Mathematics http://iopscience.iop.org/1755-1315/23/1/012001
PP-waves with torsion and metric-affine gravity
Pasic, Vedad; Vassiliev, Dmitri
2005-01-01
A classical pp-wave is a 4-dimensional Lorentzian spacetime which admits a nonvanishing parallel spinor field; here the connection is assumed to be Levi-Civita. We generalise this definition to metric compatible spacetimes with torsion and describe basic properties of such spacetimes. We use our generalised pp-waves for constructing new explicit vacuum solutions of quadratic metric-affine gravity.
Electrochemical affinity biosensors for detection of mycotoxins: A review.
Vidal, Juan C; Bonel, Laura; Ezquerra, Alba; Hernández, Susana; Bertolín, Juan R; Cubel, Carlota; Castillo, Juan R
2013-11-15
This review discusses the current state of electrochemical biosensors in the determination of mycotoxins in foods. Mycotoxins are highly toxic secondary metabolites produced by molds. The acute toxicity of these results in serious human and animal health problems, although it has been only since early 1960s when the first studied aflatoxins were found to be carcinogenic. Mycotoxins affect a broad range of agricultural products, most important cereals and cereal-based foods. A majority of countries, mentioning especially the European Union, have established preventive programs to control contamination and strict laws of the permitted levels in foods. Official methods of analysis of mycotoxins normally requires sophisticated instrumentation, e.g. liquid chromatography with fluorescence or mass detectors, combined with extraction procedures for sample preparation. For about sixteen years, the use of simpler and faster analytical procedures based on affinity biosensors has emerged in scientific literature as a very promising alternative, particularly electrochemical (i.e., amperometric, impedance, potentiometric or conductimetric) affinity biosensors due to their simplicity and sensitivity. Typically, electrochemical biosensors for mycotoxins use specific antibodies or aptamers as affinity ligands, although recombinant antibodies, artificial receptors and molecular imprinted polymers show potential utility. This article deals with recent advances in electrochemical affinity biosensors for mycotoxins and covers complete literature from the first reports about sixteen years ago. PMID:23743326
Canonical bases and affine Hecke algebras of type B
Varagnolo, Michela
2009-01-01
We prove a series of conjectures of Enomoto and Kashiwara on canonical bases and branching rules of affine Hecke algebras of type B. The main ingredient of the proof is a new graded Ext-algebra associated with quiver with involutions that we compute explicitly.
Immobilized metal affinity chromatography of phosphorylated proteins using highperformance sorbents
Czech Academy of Sciences Publication Activity Database
Novotná, L.; Hrubý, Martin; Beneš, Milan J.; Kučerová, Z.
2008-01-01
Roč. 68, 5-6 (2008), s. 381-386. ISSN 0009-5893 Grant ostatní: GA MŠk(CZ) LC06044 Institutional research plan: CEZ:AV0Z40500505 Keywords : immobilized metal affinity chromatography * phosphorylation * metal ions Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.312, year: 2008
Study of pepsin phosphorylation using immobilized metal affinity chromatography
Czech Academy of Sciences Publication Activity Database
Novotná, L.; Hrubý, Martin; Beneš, Milan J.; Kučerová, Z.
2008-01-01
Roč. 31, č. 10 (2008), s. 1662-1668. ISSN 1615-9306 Institutional research plan: CEZ:AV0Z40500505 Keywords : Fe(III) * Ga(III) * immobilized metal affinity chromatography * modification of carboxyl groups Subject RIV: CD - Macromolecular Chemistry Impact factor: 2.746, year: 2008
Several Affinity Tags Commonly Used in Chromatographic Purification
Directory of Open Access Journals (Sweden)
Xinyu Zhao
2013-01-01
Full Text Available Affinity tags have become powerful tools from basic biological research to structural and functional proteomics. They were widely used to facilitate the purification and detection of proteins of interest, as well as the separation of protein complexes. Here, we mainly discuss the benefits and drawbacks of several affinity or epitope tags frequently used, including hexahistidine tag, FLAG tag, Strep II tag, streptavidin-binding peptide (SBP tag, calmodulin-binding peptide (CBP, glutathione S-transferase (GST, maltose-binding protein (MBP, S-tag, HA tag, and c-Myc tag. In some cases, a large-size affinity tag, such as GST or MBP, can significantly impact on the structure and biological activity of the fusion partner protein. So it is usually necessary to excise the tag by protease. The most commonly used endopeptidases are enterokinase, factor Xa, thrombin, tobacco etch virus, and human rhinovirus 3C protease. The proteolysis features of these proteases are described in order to provide a general guidance on the proteolytic removal of the affinity tags.
Toward an Affinity Space Methodology: Considerations for Literacy Research
Lammers, Jayne C.; Curwood, Jen Scott; Magnifico, Alecia Marie
2012-01-01
As researchers seek to make sense of young people's online literacy practices and participation, questions of methodology are important to consider. In our work to understand the culture of physical, virtual and blended spheres that adolescents inhabit, we find it necessary to expand Gee's (2004) notion of affinity spaces. In this article, we draw…
Self-Affine Sets with Positive Lebesgue Measure
Dajani, Karma; Jiang, Kan; Kempton, Tom
2014-01-01
Using techniques introduced by C. G ̈unt ̈urk, we prove that the attractors of a family of overlapping self-affine iterated function systems contain a neighbourhood of zero for all parameters in a certain range. This corresponds to giving conditions under which a single sequence may serve as a ‘simu
Native Elution of Yeast Protein Complexes Obtained by Affinity Capture.
LaCava, John; Fernandez-Martinez, Javier; Rout, Michael P
2016-01-01
This protocol describes two options for the native (nondenaturing) elution of protein complexes obtained by affinity capture. The first approach involves the elution of complexes purified through a tag that includes a human rhinovirus 3C protease (PreScission protease) cleavage site sequence between the protein of interest and the tag. Incubation with the protease cleaves immobilized complexes from the affinity medium. The second approach involves the release of protein A-tagged protein complexes using a competitive elution reagent called PEGylOx. The degree of purity of the native assemblies eluted is sample dependent and strongly influenced by the affinity capture. It should be noted that the efficiency of native elution is commonly lower than that of elution by a denaturing agent (e.g., SDS) and the release of the complex will be limited by the activity of the protease or the inhibition constant (Ki) of the competitive release agent. However, an advantage of native release is that some nonspecifically bound materials tend to stay adsorbed to the affinity medium, providing an eluted fraction of higher purity. Finally, keep in mind that the presence of the protease or elution peptide could potentially affect downstream applications; thus, their removal should be considered. PMID:27371597
Harmonic fusion and pitch affinity: Is there a direct link?
Bonnard, Damien; Dauman, René; Semal, Catherine; Demany, Laurent
2016-03-01
Simultaneous pure tones approximately one octave apart tend to be fused perceptually and to evoke a single pitch sensation. Besides, sequentially presented pure tones show a subjective "affinity" or similarity in pitch when their frequency ratio is close to one octave. The aim of the study reported here was to determine if these two perceptual phenomena are directly related. Each stimulus was a triplet of simultaneous or successive pure tones forming frequency ratios varying across stimuli between 0.96 and 1.04 octaves. The tones were presented at a low sensation level (15 dB) within broadband threshold-equalizing noise, in order to prevent them from interacting in the cochlea when they were simultaneous. A large set of stimulus comparisons made by 18 listeners indicated that: (1) when the tones were simultaneous, maximal fusion was obtained for a mean frequency ratio deviating by less than 0.2% from one octave, and fusion decreased less rapidly above this frequency ratio than below it; (2) when the tones were presented successively, maximal pitch affinity was obtained for a mean frequency ratio significantly larger than one octave, and pitch affinity decreased more rapidly above this frequency ratio than below it. The differences between the results obtained for simultaneous and successive tones suggest that harmonic fusion and pitch affinity are unrelated phenomena. PMID:26341475
Soliton-preserving boundary condition in affine Toda field theories
Delius, Gustav W
1998-01-01
We give a new integrable boundary condition in affine Toda theory which is soliton-preserving in the sense that a soliton hitting the boundary is reflected as a soliton. All previously known integrable boundary conditions forced a soliton to be converted into an antisoliton upon reflection. We prove integrability of our boundary condition using a generalization of Sklyanin's formalism.
Demazure modules and vertex models the affine sl(2) case
Foda, O E; Okado, M; Foda, Omar; Misra, Kailash C; Okado, Masato
1996-01-01
We characterize, in the case of affine sl(2), the crystal base of the Demazure module E_w(\\La) in terms of extended Young diagrams or paths for any dominant integral weight \\La and Weyl group element w. Its character is evaluated via two expressions, 'bosonic' and 'fermionic'.
Demazure modules and vertex models: the affine sl(2) case
Foda, Omar; Misra, Kailash C.; Okado, Masato
1996-01-01
We characterize, in the case of affine sl(2), the crystal base of the Demazure module E_w(\\La) in terms of extended Young diagrams or paths for any dominant integral weight \\La and Weyl group element w. Its character is evaluated via two expressions, 'bosonic' and 'fermionic'.
Soliton solutions for higher grading affine Toda from quantum algebras
Czech Academy of Sciences Publication Activity Database
Zuevsky, Alexander
Bristol : IOP, 2015, 012001. ISSN 1755-1307. [2nd International Conference on Geological, Geographical, Aerospace and Earth Sciences 2014 (AeroEarth 2014). Bali (ID), 11.10.2014-12.10.2014] Institutional support: RVO:67985840 Keywords : Lie algebra s * integrable models * affine Toda model Subject RIV: BA - General Mathematics http://iopscience.iop.org/1755-1315/23/1/012001
Combinatorial Vector Fields for Piecewise Affine Control Systems
DEFF Research Database (Denmark)
Wisniewski, Rafal; Larsen, Jesper Abildgaard
2008-01-01
This paper is intended to be a continuation of Habets and van Schuppen (2004) and Habets, Collins and van Schuppen (2006), which address the control problem for piecewise-affine systems on an arbitrary polytope or a family of these. Our work deals with the underlying combinatorics of the underlyi...
Linear independence measure of logarithms over affine groups
Huicochea, Mario
2015-01-01
Linear forms in logarithms over connected commutative algebraic groups over the algebraic numbers field have been studied widely. However, the theory of linear forms in logarithms over noncommutative algebraic groups have not been developed as the one of the commutative algebraic groups and in this paper we start studying linear forms in logarithms over affine groups.
An Affine Invariant $k$-Nearest Neighbor Regression Estimate
Biau, Gérard; Dujmovic, Vida; Krzyzak, Adam
2012-01-01
We design a data-dependent metric in $\\mathbb R^d$ and use it to define the $k$-nearest neighbors of a given point. Our metric is invariant under all affine transformations. We show that, with this metric, the standard $k$-nearest neighbor regression estimate is asymptotically consistent under the usual conditions on $k$, and minimal requirements on the input data.
Smooth surfaces from bilinear patches: Discrete affine minimal surfaces
Käferböck, Florian
2013-06-01
Motivated by applications in freeform architecture, we study surfaces which are composed of smoothly joined bilinear patches. These surfaces turn out to be discrete versions of negatively curved affine minimal surfaces and share many properties with their classical smooth counterparts. We present computational design approaches and study special cases which should be interesting for the architectural application. 2013 Elsevier B.V.
Myoglobin oxygen affinity in aquatic and terrestrial birds and mammals.
Wright, Traver J; Davis, Randall W
2015-07-01
Myoglobin (Mb) is an oxygen binding protein found in vertebrate skeletal muscle, where it facilitates intracellular transport and storage of oxygen. This protein has evolved to suit unique physiological needs in the muscle of diving vertebrates that express Mb at much greater concentrations than their terrestrial counterparts. In this study, we characterized Mb oxygen affinity (P50) from 25 species of aquatic and terrestrial birds and mammals. Among diving species, we tested for correlations between Mb P50 and routine dive duration. Across all species examined, Mb P50 ranged from 2.40 to 4.85 mmHg. The mean P50 of Mb from terrestrial ungulates was 3.72±0.15 mmHg (range 3.70-3.74 mmHg). The P50 of cetaceans was similar to terrestrial ungulates ranging from 3.54 to 3.82 mmHg, with the exception of the melon-headed whale, which had a significantly higher P50 of 4.85 mmHg. Among pinnipeds, the P50 ranged from 3.23 to 3.81 mmHg and showed a trend for higher oxygen affinity in species with longer dive durations. Among diving birds, the P50 ranged from 2.40 to 3.36 mmHg and also showed a trend of higher affinities in species with longer dive durations. In pinnipeds and birds, low Mb P50 was associated with species whose muscles are metabolically active under hypoxic conditions associated with aerobic dives. Given the broad range of potential globin oxygen affinities, Mb P50 from diverse vertebrate species appears constrained within a relatively narrow range. High Mb oxygen affinity within this range may be adaptive for some vertebrates that make prolonged dives. PMID:25987728
Novel trends in affinity biosensors: current challenges and perspectives
International Nuclear Information System (INIS)
Molecular biorecognition processes facilitate physical and biochemical interactions between molecules in all crucial metabolic pathways. Perhaps the target analyte and the biorecognition element interactions have the most impactful use in biosensing applications. Traditional analytical sensing systems offer excellent biorecognition elements with the ability to detect and determine the presence of analytes. High affinity antibodies and DNA play an important role in the development of affinity biosensors based on electrochemical, optical and mass sensitive approaches. Advancements in this area routinely employ labels, label free, nanoparticles, multifunctional matrices, carbon nanotubes and other methods to meet the requirements of its own application. However, despite increasing affinity ceilings for conventional biosensors, the field draws back in meeting specifically important demands, such as long-term stability, ultrasensitivity, rapid detection, extreme selectivity, strong biological base, calibration, in vivo measurements, regeneration, satisfactory performance and ease of production. Nevertheless, recent efforts through this line have produced novel high-tech nanosensing systems such as ‘aptamers’ and ‘phages’ which exhibit high-throughput sensing. Aptamers and phages are powerful tools that excel over antibodies in sensibility, stability, multi-detection, in vivo measurements and regeneration. Phages are superior in stability, screening for affinity-based target molecules ranging from small to proteins and even cells, and easy production. In this review, we focus mainly on recent developments in affinity-based biosensors such as immunosensors, DNA sensors, emphasizing aptasensors and phage-based biosensors basing on novel electrochemical, optical and mass sensitive detection techniques. We also address enzyme inhibition-based biosensors and the current problems associated with the above sensors and their future perspectives. (topical review)
Chou, Beverly; Mirau, Peter; Jiang, Tian; Wang, Szu-Wen; Shea, Kenneth J
2016-05-01
Hydrophobic interactions often dominate the associative forces between biomacromolecules. A synthetic affinity reagent must be able to exploit and optimize these interactions. We describe synthesis of abiotic affinity reagents that sequester biomacromolecules with lipid-like domains. NIPAm-based copolymer nanoparticles (NPs) containing C4-C8 hydrophobic groups were evaluated for their affinity for lipopolysaccharides (LPS), the lipophilic component of the outer membrane of Gram-negative bacteria. Optimal affinity was found for NPs incorporating a linear C4 hydrocarbon group. 1D and 2D (1)H NMR studies revealed that in water, the longer chain (C6 and C8) alkyl groups in the hydrogel NPs were engaged in intrachain association, rendering them less available to interact with LPS. Optimal LPS-NP interaction requires maximizing hydrophobicity, while avoiding side chain aggregation. Polymer compositions with high LPS binding were grafted onto agarose beads and evaluated for LPS clearance from solution; samples containing linear C4 groups also showed the highest LPS clearance capacity. PMID:27064286
The Weyl-Cartan Space Problem in Purely Affine Theory
von Borzeszkowski, Horst-Heino; Treder, Hans-Jürgen
1997-04-01
According to Poincaré, only the ``epistemological sum of geometry and physics is measurable". Of course, there are requirements of measurement to be imposed on geometry because otherwise the theory resting on this geometry cannot be physically interpreted. In particular, the Weyl--Cartan space problem must be solved, i.e., it must be guaranteed that the comparison of distances is compatible with the Levi-Civita transport. In the present paper, we discuss these requirements of measurement and show that in the (purely affine) Einstein-Schrödinger unified field theory the solution of the Weyl-Cartan space problem simultaneously determines the matter via Einstein's equations. Here the affine field $\\Gamma^ikl$ represents Poincaré's sum, and the solution of the space problem means its splitting in a metrical space and in matter fields, where the latter are given by the torsion tensor $\\Gamma^i_{[kl]}$.
Improved Energy-Momentum Currents in Metric-Affine Spacetime
Hecht, R D; McCrea, J D; Mielke, E W; Ne'eman, Yuval; Hecht, Ralf; Hehl, Friedrich W.; Mielke, Eckehard W.; Ne'eman, Yuval
1992-01-01
In Minkowski spacetime it is well-known that the canonical energy-momentum current is involved in the construction of the globally conserved currents of energy-momentum and total angular momentum. For the construction of conserved currents corresponding to (approximate) scale and proper conformal symmetries, however, an improved energy-momentum current is needed. By extending the Minkowskian framework to a genuine metric-affine spacetime, we find that the affine Noether identities and the conformal Killing equations enforce this improvement in a rather natural way. So far, no gravitational dynamics is involved in our construction. The resulting dilation and proper conformal currents are conserved provided the trace of the energy-momentum current satisfies a (mild) scaling relation or even vanishes.
The affine theory of gravitation and electromagnetism I
Poplawski, N J
2006-01-01
The affine variational principle of Eddington generates the Einstein field equations of general relativity in vacuum with a non-zero cosmological constant. We generalize this principle to include electromagnetism, obtaining the Einstein--Maxwell field equations and the Lorentz equation of motion. We vary the action with respect to the quantities that appear in the definition of the electromagnetic covariant derivative: the affine (nonsymmetric) connection and the electromagnetic potential, while the Lagrangian density is taken to be the square root of the determinant of a linear combination of the symmetrized Ricci tensor and the electromagnetic field tensor. This construction generates a symmetric metric tensor and a connection with torsion that depends only on the torsion vector. The whole formulation is valid only for very weak electromagnetic fields on the order of the magnetic field in interstellar space.
An angular momentum conserving Affine-Particle-In-Cell method
Jiang, Chenfanfu; Teran, Joseph
2016-01-01
We present a new technique for transferring momentum and velocity between particles and grid with Particle-In-Cell (PIC) calculations which we call Affine-Particle-In-Cell (APIC). APIC represents particle velocities as locally affine, rather than locally constant as in traditional PIC. We show that this representation allows APIC to conserve linear and angular momentum across transfers while also dramatically reducing numerical diffusion usually associated with PIC. Notably, conservation is achieved with lumped mass, as opposed to the more commonly used Fluid Implicit Particle (FLIP) transfers which require a 'full' mass matrix for exact conservation. Furthermore, unlike FLIP, APIC retains a filtering property of the original PIC and thus does not accumulate velocity modes on particles as FLIP does. In particular, we demonstrate that APIC does not experience velocity instabilities that are characteristic of FLIP in a number of Material Point Method (MPM) hyperelasticity calculations. Lastly, we demonstrate th...
Affinity of four polar neurotransmitters for lipid bilayer membranes
DEFF Research Database (Denmark)
Wang, Chunhua; Ye, Fengbin; Valardez, Gustavo F.;
2011-01-01
Weak interactions of neurotransmitters and the lipid matrix in the synaptic membrane have been hypothesized to play a role in synaptic transmission of nerve signals, particularly with respect to receptor desensitization (Cantor, R. S. Biochemistry 2003, 42, 11891). The strength of such interactions......, however, was not measured, and this is an obvious impediment for further evaluation and understanding of a possible role for desensitization. We have used dialysis equilibrium to directly measure the net affinity of selected neurotransmitters for lipid membranes and analyzed this affinity data with...... respect to calorimetric measurements and molecular dynamics simulations. We studied an anionic (glutamate), a cationic (acetylcholine), and two zwitterionic (-aminobutyric acid and glycine) neurotransmitters, and membranes of pure dimyristoyl phosphatidylcholine (DMPC), DMPC doped with 10% anionic lipid...
On purely transmitting defects in affine Toda field theory
Corrigan, E
2007-01-01
Affine Toda field theories with a purely transmitting integrable defect are considered and the model based on a_2 is analysed in detail. After providing a complete characterization of the problem in a classical framework, a suitable quantum transmission matrix, able to describe the interaction between an integrable defect and solitons, is found. Two independent paths are taken to reach the result. One is an investigation of the triangle equations using the S-matrix for the imaginary coupling bulk affine Toda field theories proposed by Hollowood, and the other uses a functional integral approach together with a bootstrap procedure. Evidence to support the results is collected in various ways: for instance, through the calculation of the transmission factors for the lightest breathers. While previous discoveries within the sine-Gordon model motivated this study, there are several new phenomena displayed in the a_2 model including intriguing disparities between the classical and the quantum pictures. For example...
Del Pezzo surfaces and affine 7-brane backgrounds
Hauer, T; Hauer, Tamas; Iqbal, Amer
2000-01-01
A map between string junctions in the affine 7-brane backgrounds and vector bundles on del Pezzo surfaces is constructed using mirror symmetry. It is shown that the lattice of string junctions with support on an affine 7-brane configuration is isomorphic to the K-theory group of the corresponding del Pezzo surface. This isomorphism allows us to construct a map between the states of the N=2, D=4 theories with E_N global symmetry realized in two different ways in Type IIB and Type IIA string theory. A subgroup of the SL(2,Z) symmetry of the \\hat{E}_9 7-brane background appears as the Fourier-Mukai transform acting on the D-brane configurations realizing vector bundles on elliptically fibered B_9.
Evolution based on chromosome affinity from a network perspective
Monteiro, R. L. S.; Fontoura, J. R. A.; Carneiro, T. K. G.; Moret, M. A.; Pereira, H. B. B.
2014-06-01
Recent studies have focused on models to simulate the complex phenomenon of evolution of species. Several studies have been performed with theoretical models based on Darwin's theories to associate them with the actual evolution of species. However, none of the existing models include the affinity between individuals using network properties. In this paper, we present a new model based on the concept of affinity. The model is used to simulate the evolution of species in an ecosystem composed of individuals and their relationships. We propose an evolutive algorithm that incorporates the degree centrality and efficiency network properties to perform the crossover process and to obtain the network topology objective, respectively. Using a real network as a starting point, we simulate its evolution and compare its results with the results of 5788 computer-generated networks.
Affinity purification of proteins binding to GST fusion proteins.
Swaffield, J C; Johnston, S A
2001-05-01
This unit describes the use of proteins fused to glutathione-S-transferase (GST fusion proteins) to affinity purify other proteins, a technique also known as GST pulldown purification. The describes a strategy in which a GST fusion protein is bound to agarose affinity beads and the complex is then used to assay the binding of a specific test protein that has been labeled with [35S]methionine by in vitro translation. However, this method can be adapted for use with other types of fusion proteins; for example, His6, biotin tags, or maltose-binding protein fusions (MBP), and these may offer particular advantages. A describes preparation of an E. coli extract that is added to the reaction mixture with purified test protein to reduce nonspecific binding. PMID:18265191
Craniomandibular morphology and phylogenetic affinities of panthera atrox
DEFF Research Database (Denmark)
Christiansen, Per; Harris, J.M.
2009-01-01
The great North American Pleistocene pantherine felid Panthera atrox has had a turbulent phylogenetic history, and has been claimed to show affinities to both the jaguar and the tiger; currently, it is most often regarded as a subspecies of the extant lion. The cranial, mandibular, and dental...... morphology of Panthera atrox was compared with those of extant lions, jaguars, and tigers using bivariate, multivariate, and shape analyses. Results indicate that the skull of Panthera atrox shows lion affinities, but also deviates from lions in numerous aspects. Mandibular morphology is more similar to...... jaguars and tigers and, as with cranial morphology, the mandible shows a number of traits not present among extant pantherines. Multivariate analyses grouped Panthera atrox separately from other pantherines. Panthera atrox was no lion, and cannot be assigned to any of the extant pantherines; it...
Theoretical Estimate of Hydride Affinities of Aromatic Carbonyl Compounds
Institute of Scientific and Technical Information of China (English)
AI Teng; ZHU Xiao-Qing; CHENG Jin-Pei
2003-01-01
@@ Aromatic carbonyl compounds are one type of the most important organic compounds, and the reductions ofthem by hydride agents such as LiAlH4 or NaBH4 are widely used in organic synthesis. The reactivity of carbonyl compounds generally increases in the following order: ketone ＜ aldehyde, and amide ＜ acid ＜ ester ＜ acid halide, which could be related to their hydride affinities (HA). In the previous paper, Robert[1] calculated the absolute HAof a series of small non-aromatic carbonyl compounds. In this paper, we use DFT method at B3LYP/6-311 + + G (2d, 2p)∥B3LYP/6-31 + G* level to estimate hydride affinities of five groups of aromatic carbonyl compounds. The detailed results are listed in Table 1.
Nonspectrality of Certain Self-Affine Measures on ℝ3
Directory of Open Access Journals (Sweden)
Gui-Bao Gao
2014-01-01
Full Text Available We will determine the nonspectrality of self-affine measure μB,D corresponding to B=diag[p1,p2,p3] (p1∈(2ℤ+1∖{±1}, p2∈2ℤ∖{0}, and D={0,e1,e2,e3} in the space ℝ3 is supported on T(B,D, where e1, e2, and e3 are the standard basis of unit column vectors in ℝ3, and there exist at most 4 mutually orthogonal exponential functions in L2(μB,D, where the number 4 is the best. This generalizes the known results on the spectrality of self-affine measures.
Black Hole Singularity and Generalized Quantum Affine Parameter
Hosoya, Akio; Oda, Ichiro
1996-01-01
We study a behavior of quantum generalized affine parameter (QGAP), which has been recently proposed by one of the present authors, near the singularity and the event horizon in three and four spacetime dimensions in terms of a minisuperspace model of quantum gravity. It is shown that the QGAP is infinite to the singularity while it remains finite to the event horizon. This fact indicates a possible interpretation that the singularity is wiped out in quantum gravity in this particular model o...
Affinity chromatography based on a combinatorial strategy for rerythropoietin purification.
Martínez-Ceron, María C; Marani, Mariela M; Taulés, Marta; Etcheverrigaray, Marina; Albericio, Fernando; Cascone, Osvaldo; Camperi, Silvia A
2011-05-01
Small peptides containing fewer than 10 amino acids are promising ligand candidates with which to build affinity chromatographic systems for industrial protein purification. The application of combinatorial peptide synthesis strategies greatly facilitates the discovery of suitable ligands for any given protein of interest. Here we sought to identify peptide ligands with affinity for recombinant human erythropoietin (rhEPO), which is used for the treatment of anemia. A combinatorial library containing the octapeptides X-X-X-Phe-X-X-Ala-Gly, where X = Ala, Asp, Glu, Phe, His, Leu, Asn, Pro, Ser, or Thr, was synthesized on HMBA-ChemMatrix resin by the divide-couple-recombine method. For the library screening, rhEPO was coupled to either Texas Red or biotin. Fluorescent beads or beads showing a positive reaction with streptavidin-peroxidase were isolated. After cleavage, peptides were sequenced by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Fifty-seven beads showed a positive reaction. Peptides showing more consensuses were synthesized, and their affinity to rhEPO was assessed using a plasma resonance biosensor. Dissociation constant values in the range of 1-18 μM were obtained. The best two peptides were immobilized on Sepharose, and the resultant chromatographic matrixes showed affinity for rhEPO with dissociation constant values between 1.8 and 2.7 μM. Chinese hamster ovary (CHO) cell culture supernatant was spiked with rhEPO, and the artificial mixture was loaded on Peptide-Sepharose columns. The rhEPO was recovered in the elution fraction with a yield of 90% and a purity of 95% and 97% for P1-Sepharose and P2-Sepharose, respectively. PMID:21495625
Symbolic Dynamics for a Piecewise-Affine System with Hysteresis
Sella, Lorenzo; Collins, Pieter
2008-01-01
In this paper we present the computation of symbolic dynamics of a one dimensional return map of a piecewise-affine hybrid system. The system arises as a simple electrical circuit with hysteresis switching, and exhibits chaotic dynamics. Our method allows us to rigorously obtain a qualitative description of the discrete behaviour of the system. We show how the discrete dynamics changes as a parameter is varied, and we compute bounds for the topological entropy to provide a measure of the comp...
PREPARATION OF CHITOSAN COATED METAL AFFINITY CHROMATOGRAPHY ADSORBENT
Institute of Scientific and Technical Information of China (English)
AanTianwei; XuWeijiang; 等
1998-01-01
A new and an inexpensive adsorbent of chitosan coated silica for immobilized metal affinity chromatography(IMAC) was studied.After a double coating,the chitosan coated on silica beads could be up to 53.4mg/g silica beads.When pH>3.8,the metal ligand Cu2+ was chelated on the coated chitosan with a bound capacity of 14.6mg/g chitosan without introducing iminodiacetic acid(IDA).
Chitinolytic activity of the rumen ciliates Diploplastron affine
Czech Academy of Sciences Publication Activity Database
Belzecki, G.; Miltko, R.; Michalowski, T.; Šimůnek, Jiří; Kopečný, Jan
2008-01-01
Roč. 53, č. 3 (2008), s. 201-203. ISSN 0015-5632 R&D Projects: GA ČR GA525/05/2584 Grant ostatní: Ministry of Scientific Research and Information Technology Poland(PL) 2 P06Z 052 30 Institutional research plan: CEZ:AV0Z50450515 Keywords : Diploplastron affine Subject RIV: EE - Microbiology, Virology Impact factor: 1.172, year: 2008
Affine Correlation Method for Direct Vorticity, Skew and Displacement Estimation
Czech Academy of Sciences Publication Activity Database
Gronát, Petr
Praha : Ústav termomechaniky, AV ČR, v. v. i., 2010 - (Příhoda, J.; Kozel, K.), s. 59-62 ISBN 978-80-87012-25-3. [Topical Problems of Fluid Mechanics 2010. Praha (CZ), 10.02.2010-11.02.2010] R&D Projects: GA ČR GA101/08/1112 Institutional research plan: CEZ:AV0Z20760514 Keywords : normalized cross correlation * affine correlation Subject RIV: BK - Fluid Dynamics
Proton Affinities of Organocatalysts Derived from Pyridine N-oxide
Czech Academy of Sciences Publication Activity Database
Váňa, J.; Roithová, J.; Kotora, Martin; Beran, Pavel; Rulíšek, Lubomír; Kočovský, Pavel
2014-01-01
Roč. 87, č. 4 (2014), s. 349-356. ISSN 0011-1643 R&D Projects: GA ČR(CZ) GA14-31419S Grant ostatní: GA ČR(CZ) GAP207/11/0587 Institutional support: RVO:61388963 Keywords : density functional theory * isodesmic reactions * kinetic method * mass spectrometry * organocatalysis * proton affinity * superbases Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 0.728, year: 2014
Communication: Revised electron affinity of SF6 from kinetic data.
Troe, J.; Miller, T; Viggiano, A.
2012-01-01
Previously determined experimental data for thermal attachment of electrons to SF 6 and thermal detachment from SF 6 − over the range 590–670 K are reevaluated by a third-law analysis. Recent high precision calculations of SF 6 − harmonic frequences and anharmonicities (for several of the modes) lead to considerable changes in modeled vibrational partition functions which then have to be accommodated for by a smaller value of the derived adiabatic electron affinity EA of SF 6 . The previously...
An Early Cambrian problematic fossil: Vetustovermis and its possible affinities
Chen, Jun-Yuan; Huang, Di-Ying; Bottjer, David J.
2005-01-01
The Early Cambrian problematic fossil Vetustovermis (Glaessner 1979 Alcheringa 3, 21–31) was described as an annelid or arthropod. Anatomical analysis of 17 new specimens from the Lower Cambrian Maotianshan Shale at Anning, Kunming (South China) does not support its affinities with annelids or arthropods. Anatomical features instead resemble other animal groups including modern flatworms, nemertines and molluscs. The presence of a pelagic slug-like form and ventral foot, as well as a head wit...
Agonist binding to high-affinity dopamine sites
Energy Technology Data Exchange (ETDEWEB)
Tedesco, J.L.
1985-01-01
The authors have characterized the dopamine D/sub 3/ site and its binding requirements. The dopamine D/sub 3/ site in calf caudate crude homogenate has a site density of 214-230 fmoles/mg. protein by both /sup 3/H-apomorphine (/sup 3/H-AOP) and /sup 3/H-dopamine (/sup 3/H-DA) Scatchard analysis of specific binding (SB). Stereospecific subsets of /sup 3/H-APO and /sup 3/H-DA sites were defined by the use of agonist and antagonist enantiomer-pairs as a rigorous test for D/sub 3/ site heterogeneity. IC/sub 50/ values for both /sup 3/H-APO and /sup 3/H-DA SB sites were assessed for 55 agonist ligands and an excellent correlation was obtained. The authors conclude that both /sup 3/H-ligands label the same D/sub 3/ site. The D/sub 3/ site affinities of 105 dopamine-agonist ligands, in particular 2-aminotetralins,, aporphines and flexible dopamine analogues were measured. Low D/sub 3/-site affinities of N-quaternary analogues confirm the need for a lone pair. Subadditivity of substituents' effects in semi-flexible DA analogues confirms their postulate that sidechain conformation is the critical determinant of affinity. They conclude that there are at least two high-affinity ligand conformations of the DA sidechain pharmacophore. These binding requirements are presented as two interface-Geometry tetrahedral models of the double H-bond interface between the D/sub 3/ site and the ideal ligand.
Ferromagnetic Levan Composite: An Affinity Matrix to Purify Lectin
Renata Angeli; da Paz, Nathalia V. N.; Maciel, Jackeline C.; Flávia F. B. Araújo; Paiva, Patrícia M. G.; Glícia M. T. Calazans; Ana Paula Valente; Almeida, Fábio C. L.; Coelho, Luana C. B. B.; Carvalho, Luiz B; Silva, Maria da Paz C.; Maria Tereza dos Santos Correia
2009-01-01
A simple and inexpensive procedure used magnetite and levan to synthesize a composite recovered by a magnetic field. Lectins from Canavalia ensiformis (Con A) and Cratylia mollis (Cramoll 1 and Cramoll 1, 4) did bind specifically to composite. The magnetic property of derivative favored washing out contaminating proteins and recovery of pure lectins with glucose elution. Cramoll 1 was purified by this affinity binding procedure in two steps instead of a previous three-step protocol with ammon...
Families of Dirac operators and quantum affine groups
Mickelsson, Jouko
2010-01-01
Twisted K-theory classes over compact Lie groups can be realized as families of Fredholm operators using the representation theory of loop groups. In this talk I want to show how to deform the Fredholm family, in the sense of quantum groups. The family of Dirac type operators is parametrized by vectors in the adjoint module for a quantum affine algebra and transform covariantly under a (central extension of) the algebra.
Macro factors and the affine term structure of interest rates
Tao Wu
2001-01-01
I formulate an affine term structure model of bond yields from a general equilibrium business-cycle model, with observable macro state variables of the structural economy as the factors. The factor representing monetary policy is strongly mean-reverting, and its influence on the term structure is primarily through changing the slope of the yield curve. The factor representing technology is more persistent, and it affects the term structure by shifting the level of the yield curve. The dynamic...
The relation of morphology and affinity maturation in germinal centers
Meyer-Hermann, M
2002-01-01
The specific morphology of germinal centers is analyzed in the context of the optimization of the humoral immune response. The relevance of dark and light zones for the affinity maturation process is investigated in the framework of a theoretical model for the germinal center reaction. Especially, it is shown that an intermediate appearance of dark zones in germinal center reactions is advantageous for the process of antibody optimization.
Affinity purification of polysaccharide degrading enzymes with crosslinked substrates.
Rozie, H.J.
1992-01-01
The aim of this work was to find economically favourable, affinity based, purification methods for several polysaccharide splitting bulk enzymes. The framework in which this study is done is described in Chapter 1.Chapter 2 describes the adsorption of endo-polygalacturonase (endoPG) from a commercial enzyme preparation (Rapidase) to calcium alginate beads. Approximately 75% of the various polygalacturonase activities from Rapidase can be adsorbed at pH 4.4 by calcium alginate beads as well as...
Term premia and interest rate forecasts in affine models
Duffee, Gregory R.
2000-01-01
I find that the standard class of affine models produces poor forecasts of future changes in Treasury yields. Better forecasts are generated by assuming that yields follow random walks. The failure of these models is driven by one of their key features: the compensation that investors receive for facing risk is a multiple of the variance of the risk. This means that risk compensation cannot vary independently of interest rate volatility. I also describe and empirically estimate a class of mod...
Responding Bodies and Partial Affinities in Human–Animal Worlds
Despret, Vinciane
2013-01-01
The aim of this paper is to explore the different manners in which scientists’ bodies are actively engaged when interacting with the animals they observe in the field. Bodies are multiple, as are the practices that involve them: sharing the same diet, feeling similar affects, acting the same, inhabiting the same world of perceptions, constructing empathic affinities, etc. Some scientists aim to embody the animals’ experiences. Some are willing to empathetically experience situations “from ins...
TALMRS: Time-Affinity Linked Medical Record System
Langer, Robert D.
1987-01-01
Use of relational data base techniques allows the development of a three dimensional medical record system in which data relevant to multiple problems need only be entered once, but may be presented in an essentially unlimited number of contexts. This Time-Affinity Linked Medical Record System (TALMRS) builds upon and extends the concepts of the Problem Oriented Medical Record (POMR). Links which enable the user to view the data in many different ways make it possible for the same record to b...
Affine extensions of functions with a closed graph
Marek Wójtowicz; Waldemar Sieg
2015-01-01
Let \\(A\\) be a closed \\(G_{\\delta}\\)-subset of a normal space \\(X\\). We prove that every function \\(f_0: A\\to\\mathbb{R}\\) with a closed graph can be extended to a function \\(f: X\\to\\mathbb{R}\\) with a closed graph, too. This is a consequence of a more general result which gives an affine and constructive method of obtaining such extensions.
Affine-Detection Loophole in Quantum Data Processing
Vlasov, Alexander Yu.
2002-01-01
Here is considered a specific detection loophole, that is relevant not only to testing of quantum nonlocality, but also to some other applications of quantum computations and communications. It is described by a simple affine relation between different quantum "data structures" like pure and mixed state, separable and inseparable one. It is shown also, that due to such relations imperfect device for a classical model may mimic measurements of quantum correlations on ideal equipment.
Identification and Estimation of Gaussian Affine Term Structure Models
Hamilton, James D.; Jing Cynthia Wu
2012-01-01
This paper develops new results for identification and estimation of Gaussian affine term structure models. We establish that three popular canonical representations are unidentified, and demonstrate how unidentified regions can complicate numerical optimization. A separate contribution of the paper is the proposal of minimum-chi-square estimation as an alternative to MLE. We show that, although it is asymptotically equivalent to MLE, it can be much easier to compute. In some cases, MCSE allo...
A pulse radiolysis study on electron affinity of piperonal
Institute of Scientific and Technical Information of China (English)
MA; Jianhua; LIN; Weizhen; WANG; Wenfeng; YAO; Side
2005-01-01
The piperonal electron affinity was studied using pulse radiolysis technique. The electron transfer reaction process between piperonal and anthraquinone-2-sulfate was observed in the pH 7 phosphoric acid salt buffer. The transient absorption spectra of electron transfer reaction between piperonal and anthraquinone-2-sulfate were obtained, and the initial proof of the electron transfer between electron donor and acceptor was provided directly. The one-electron reduction potential of piperonal was determined to be -0.457 V.
Affitins for protein purification by affinity magnetic fishing.
Fernandes, Cláudia S M; Dos Santos, Raquel; Ottengy, Stella; Viecinski, Aline Canani; Béhar, Ghislaine; Mouratou, Barbara; Pecorari, Frédéric; Roque, A Cecília A
2016-07-29
Currently most economical and technological bottlenecks in protein production are placed in the downstream processes. With the aim of increasing the efficiency and reducing the associated costs, various affinity ligands have been developed. Affitins are small, yet robust and easy to produce, proteins derived from the archaeal extremophilic "7kDa DNA-binding" protein family. By means of combinatorial protein engineering and ribosome display selection techniques, Affitins have shown to bind a diversity of targets. In this work, two previously developed Affitins (anti-lysozyme and anti-IgG) were immobilized onto magnetic particles to assess their potential for protein purification by magnetic fishing. The optimal lysozyme and human IgG binding conditions yielded 58mg lysozyme/g support and 165mgIgG/g support, respectively. The recovery of proteins was possible in high yield (≥95%) and with high purity, namely ≥95% and 81%, when recovering lysozyme from Escherichia coli supernatant and IgG from human plasma, respectively. Static binding studies indicated affinity constants of 5.0×10(4)M(-1) and 9.3×10(5)M(-1) for the anti-lysozyme and anti-IgG magnetic supports. This work demonstrated that Affitins, which can be virtually evolved for any protein of interest, can be coupled onto magnetic particles creating novel affinity adsorbents for purification by magnetic fishing. PMID:27342136
Supramolecular Affinity Chromatography for Methylation-Targeted Proteomics.
Garnett, Graham A E; Starke, Melissa J; Shaurya, Alok; Li, Janessa; Hof, Fraser
2016-04-01
Proteome-wide studies of post-translationally methylated species using mass spectrometry are complicated by high sample diversity, competition for ionization among peptides, and mass redundancies. Antibody-based enrichment has powered methylation proteomics until now, but the reliability, pan-specificity, polyclonal nature, and stability of the available pan-specific antibodies are problematic and do not provide a standard, reliable platform for investigators. We have invented an anionic supramolecular host that can form host-guest complexes selectively with methyllysine-containing peptides and used it to create a methylysine-affinity column. The column resolves peptides on the basis of methylation-a feat impossible with a comparable commercial cation-exchange column. A proteolyzed nuclear extract was separated on the methyl-affinity column prior to standard proteomics analysis. This experiment demonstrates that such chemical methyl-affinity columns are capable of enriching and improving the analysis of methyllysine residues from complex protein mixtures. We discuss the importance of this advance in the context of biomolecule-driven enrichment methods. PMID:26973166
A Quick and Affine Invariance Matching Method for Oblique Images
Directory of Open Access Journals (Sweden)
XIAO Xiongwu
2015-04-01
Full Text Available This paper proposed a quick, affine invariance matching method for oblique images. It calculated the initial affine matrix by making full use of the two estimated camera axis orientation parameters of an oblique image, then recovered the oblique image to a rectified image by doing the inverse affine transform, and left over by the SIFT method. We used the nearest neighbor distance ratio(NNDR, normalized cross correlation(NCC measure constraints and consistency check to get the coarse matches, then used RANSAC method to calculate the fundamental matrix and the homography matrix. And we got the matches that they were interior points when calculating the homography matrix, then calculated the average value of the matches' principal direction differences. During the matching process, we got the initial matching features by the nearest neighbor(NN matching strategy, then used the epipolar constrains, homography constrains, NCC measure constrains and consistency check of the initial matches' principal direction differences with the calculated average value of the interior matches' principal direction differences to eliminate false matches. Experiments conducted on three pairs of typical oblique images demonstrate that our method takes about the same time as SIFT to match a pair of oblique images with a plenty of corresponding points distributed evenly and an extremely low mismatching rate.
Crystal structures of fusion proteins with large-affinity tags.
Smyth, Douglas R; Mrozkiewicz, Marek K; McGrath, William J; Listwan, Pawel; Kobe, Bostjan
2003-07-01
The fusion of a protein of interest to a large-affinity tag, such as the maltose-binding protein (MBP), thioredoxin (TRX), or glutathione-S-transferase (GST), can be advantageous in terms of increased expression, enhanced solubility, protection from proteolysis, improved folding, and protein purification via affinity chromatography. Unfortunately, crystal growth is hindered by the conformational heterogeneity induced by the fusion tag, requiring that the tag is removed by a potentially problematic cleavage step. The first three crystal structures of fusion proteins with large-affinity tags have been reported recently. All three structures used a novel strategy to rigidly fuse the protein of interest to MBP via a short three- to five-amino acid spacer. This strategy has the potential to aid structure determination of proteins that present particular experimental challenges and are not conducive to more conventional crystallization strategies (e.g., membrane proteins). Structural genomics initiatives may also benefit from this approach as a way to crystallize problematic proteins of significant interest. PMID:12824478
Exact deformations of quantum groups; applications to the affine case
Frønsdal, Christian
1996-01-01
This paper continues our investigation of a class of generalized quantum groups. The ``standard" R-matrix was shown to be the unique solution of a very simple, linear recursion relation and the classical limit was obtained in the case of quantized Kac-Moody algebras of finite type. Here the standard R-matrix for generalized quantum groups is first examined in the case of quantized affine Kac-Moody algebras. The classical limit yields the standard affine r-matrices of Belavin and Drinfeld. Then, turning to the general case, we study the exact deformations of the standard R-matrix and the associated Hopf algebras. They are described as a generalized twist, R_\\epsilon = (F^t)^{-1}RF, where R is the standard R-matrix and F (a power series in the deformation parameter \\epsilon) is the solution of a linear recursion relation of the same type as that which determines R. Specializing again, to the case of quantized, affine Kac-Moody algebras, and taking the classical limit of these esoteric quantum groups, one re-dis...
[Fractionation of lymphocytes using affinity chromatography with 9 lectins].
de Dios, I; Manso, M; López-Borrasca, A
1983-12-01
Lymphocyte subclasses from normal peripheral blood have been fractionated by affinity chromatography with lectins. Concanavalin A (Con A), Lens culinaris lectin (LC), Pisum sativum lectin (PS), Phaseolus vulgaris lectin (PHA), Dolichos biflours lectin (DB), Glicine max lectin (SBA), Ricinus communis lectin (RCA II), Tetragonolobus purpureus lectin (TP) and Triticum vulgaris lectin (WGA), were coupled to Sepharose 6MB, and lymphocytes labelled with 125I were eluted through the chromatographic columns. The binding of lymphocytes to WGA and SBA lectins was 32% and 13% respectively. The binding to the other lectins tested were found to be between 32% and 13%. When solutions of increasing concentrations of specific sugar were added to the columns a progressive elution of bound lymphocytes was observed. These results indicate the existence of a large range of lymphocyte subclasses, with different binding capacity to lectins, which was a function of the receptor number or/and receptor affinity to each lectin. Furthermore, these two parameters were found to vary in each functional population. Even though all the lymphocytes had lectin receptors, T lymphocytes showed higher affinity for Con A, PHA and TP lectins, while B lymphocytes appeared to be more specific for LC, PS, SBA, DB, RCAII and WGA lectins. PMID:6675094
Affinity approaches in RNAi-based therapeutics purification.
Pereira, Patrícia; Queiroz, João A; Figueiras, Ana; Sousa, Fani
2016-05-15
The recent investigation on RNA interference (RNAi) related mechanisms and applications led to an increased awareness of the importance of RNA in biology. Nowadays, RNAi-based technology has emerged as a potentially powerful tool for silencing gene expression, being exploited to develop new therapeutics for treating a vast number of human disease conditions, as it is expected that this technology can be translated onto clinical applications in a near future. This approach makes use of a large number of small (namely short interfering RNAs, microRNAs and PIWI-interacting RNAs) and long non-coding RNAs (ncRNAs), which are likely to have a crucial role as the next generation therapeutics. The commercial and biomedical interest in these RNAi-based therapy applications have fostered the need to develop innovative procedures to easily and efficiently purify RNA, aiming to obtain the final product with high purity degree, good quality and biological activity. Recently, affinity chromatography has been applied to ncRNAs purification, in view of the high specificity. Therefore, this article intends to review the biogenesis pathways of regulatory ncRNAs and also to discuss the most significant and recent developments as well as applications of affinity chromatography in the challenging task of purifying ncRNAs. In addition, the importance of affinity chromatography in ncRNAs purification is addressed and prospects for what is forthcoming are presented. PMID:26830537
Con A affinity glycoproteomics of normal human liver tissue
Institute of Scientific and Technical Information of China (English)
2007-01-01
In order to establish the novel high throughput, high efficiency and low cost technological platform for the research of N-glycoproteomics, to resolve the significance of characteristic expression profile of glycoprotein and to find the proteins with biological functional importance, the glycoproteins with high-mannose core and the two antennary types were purified and enriched by the Con A affinity chromatography. Con A affinity protein expression profiles of normal human liver tissue were gener- ated by using SDS-PAGE, two-dimensional electrophoresis (2-DE) followed by fast fluorescence stain- ing based on multiplexed proteomics (MP) technology. 301 visible protein spots on the gel were de- tected and 85 of glycoproteins were further successfully identified via peptide mass fingerprinting (PMF) by a matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF- MS/MS) and annotated to IPI databases. Identified glycoproteins definitely take part in the regulation of cell cycle and metabolic processes. The glycosylation sites were predicted with NetNGlyc 1.0 and NetOGlyc 3.1 software, meanwhile they were classified according to the geneontology methods. The construction of Con A affinity glycoprotein database of normal human liver tissue would contribute to the subsequent research.
Relative Binding Affinities of Monolignols to Horseradish Peroxidase.
Sangha, Amandeep K; Petridis, Loukas; Cheng, Xiaolin; Smith, Jeremy C
2016-08-11
Monolignol binding to the peroxidase active site is the first step in lignin polymerization in plant cell walls. Using molecular dynamics, docking, and free energy perturbation calculations, we investigate the binding of monolignols to horseradish peroxidase C. Our results suggest that p-coumaryl alcohol has the strongest binding affinity followed by sinapyl and coniferyl alcohol. Stacking interactions between the monolignol aromatic rings and nearby phenylalanine residues play an important role in determining the calculated relative binding affinities. p-Coumaryl and coniferyl alcohols bind in a pose productive for reaction in which a direct H-bond is formed between the phenolic -OH group and a water molecule (W2) that may facilitate proton transfer during oxidation. In contrast, in the case of sinapyl alcohol there is no such direct interaction, the phenolic -OH group instead interacting with Pro139. Since proton and electron transfer is the rate-limiting step in monolignol oxidation by peroxidase, the binding pose (and thus the formation of near attack conformation) appears to play a more important role than the overall binding affinity in determining the oxidation rate. PMID:27447548
Structure of Greyhound hemoglobin: origin of high oxygen affinity.
Bhatt, Veer S; Zaldívar-López, Sara; Harris, David R; Couto, C Guillermo; Wang, Peng G; Palmer, Andre F
2011-05-01
This study presents the crystal structure of Greyhound hemoglobin (GrHb) determined to 1.9 Å resolution. GrHb was found to crystallize with an α₁β₁ dimer in the asymmetric unit and belongs to the R2 state. Oxygen-affinity measurements combined with the fact that GrHb crystallizes in the R2 state despite the high-salt conditions used for crystallization strongly indicate that GrHb can serve as a model high-oxygen-affinity hemoglobin (Hb) for higher mammals, especially humans. Structural analysis of GrHb and its comparison with the R2-state of human Hb revealed several regions that can potentially contribute to the high oxygen affinity of GrHb and serve to rationalize the additional stability of the R2-state of GrHb. A previously well studied hydrophobic cluster of bar-headed goose Hb near α119 was also incorporated in the comparison between GrHb and human Hb. Finally, a structural comparison with generic dog Hb and maned wolf Hb was conducted, revealing that in contrast to GrHb these structures belong to the R state of Hb and raising the intriguing possibility of an additional allosteric factor co-purifying with GrHb that can modulate its quaternary structure. PMID:21543841
Virtual-real spatial information visualization registration using affine representations
Wu, Xueling; Ren, Fu; Du, Qingyun
2009-10-01
Virtual-real registration in Outdoor Augmented Reality is committed to enhance user's spatial cognition by overlaying virtual geographical objects on real scene. According to analyze fiducial detection registration method in indoor AR, for the purpose of avoiding complex and tedious process of position tracking and camera calibration in traditional registration methods, it puts forward and practices a virtual-real spatial information visualization registration method using affine representations. Based on the observation from Koenderink and van Doorn, Ullman and Basri in 1991 which is given a set of four or more non-coplanar 3D points, the projection of all points in the set can be computed as a linear combination of the projection of just four of the points, it sets up global affine coordinate system in light of world coordinates, camera coordinates and virtual coordinates and extracts four feature points from scene image and calculates the global affine coordinates of key points of virtual objects. Then according to a linear homogeneous coordinates of the four feature point's projection, it calculates projection pixel coordinates of key points of virtual objects. In addition, it proposes an approach to obtain pixel relative depth for hidden surface removal. Finally, by a case study, it verifies the feasibility and efficiency of the registration methods. The method would not only explore a new research direction for Geographical Information Science, but also would provide location-based information and services for outdoor AR.
The Purification of a Blood Group A Glycoprotein: An Affinity Chromatography Experiment.
Estelrich, J.; Pouplana, R.
1988-01-01
Describes a purification process through affinity chromatography necessary to obtain specific blood group glycoproteins from erythrocytic membranes. Discusses the preparation of erythrocytic membranes, extraction of glycoprotein from membranes, affinity chromatography purification, determination of glycoproteins, and results. (CW)
Zhao, Shitie; Gao, Xianwen
2016-08-01
A robust adaptive control is proposed for a class of single-input single-output non-affine nonlinear systems. In order to approximate the unknown nonlinear function, a novel affine-type neural network is used, and then to compensate the approximation error and external disturbance a robust control term is employed. By Lyapunov stability analysis for the closed-loop system, it is proved that tracking errors asymptotically converge to zero. Moreover, an observer is designed to estimate the system states because all the states may not be available for measurements. Furthermore, the adaptation laws of neural networks and the robust controller are given out based on the Lyapunov stability theory. Finally, two simulation examples are presented to demonstrate the effectiveness of the proposed control method.
Zheng, Xiwei; Podariu, Maria; Matsuda, Ryan; Hage, David S
2016-01-01
Ultrafast affinity extraction and a two-dimensional high performance affinity chromatographic system were used to measure the free fractions for various drugs in serum and at typical therapeutic concentrations. Pooled samples of normal serum or serum from diabetic patients were utilized in this work. Several drug models (i.e., quinidine, diazepam, gliclazide, tolbutamide, and acetohexamide) were examined that represented a relatively wide range of therapeutic concentrations and affinities for human serum albumin (HSA). The two-dimensional system consisted of an HSA microcolumn for the extraction of a free drug fraction, followed by a larger HSA analytical column for the further separation and measurement of this fraction. Factors that were optimized in this method included the flow rates, column sizes, and column switching times that were employed. The final extraction times used for isolating the free drug fractions were 333-665 ms or less. The dissociation rate constants for several of the drugs with soluble HSA were measured during system optimization, giving results that agreed with reference values. In the final system, free drug fractions in the range of 0.7-9.5% were measured and gave good agreement with values that were determined by ultrafiltration. Association equilibrium constants or global affinities were also estimated by this approach for the drugs with soluble HSA. The results for the two-dimensional system were obtained in 5-10 min or less and required only 1-5 μL of serum per injection. The same approach could be adapted for work with other drugs and proteins in clinical samples or for biomedical research. PMID:26462924
Sarah D. Alison-Youel
2008-01-01
Liquefied gas reaction turbines are subject to the hydraulic affinity laws. Particularly for liquefied hydrocarbon gas-driven turbines, deviations from the affinity laws are encountered. In the case of reaction turbines, where the geometry is fixed, the affinity law relationships between flow, head, and rotational speed are relevant. Field experience confirms that the affinity law relationships are adequate, but that the predictions made also tend to deviate from real turbine performance. Par...
Koszul duality of affine Kac-Moody algebras and cyclotomic rational DAHA
Shan, Peng; Vasserot, Eric
2011-01-01
We give a proof of the parabolic/singular Koszul duality for the category O of affine Kac-Moody algebras. The main new tool is a relation between moment graphs and finite codimensional affine Schubert varieties. We apply this duality to q-Schur algebras and to cyclotomic rational double affine Hecke algebras.
Surface affinity role in graphoepitaxy of lamellar block copolymers
Claveau, G.; Quemere, P.; Argoud, M.; Hazart, J.; Pimenta Barros, P.; Sarrazin, A.; Posseme, N.; Tiron, R.; Chevalier, X.; Nicolet, C.; Navarro, C.
2016-03-01
Overcoming the optical limitations of 193nm immersion lithography can be achieved using Directed Self Assembly (DSA) of block-copolymers (BCPs) as a low-cost and versatile complementary technique. The goal of this paper is to investigate the potential of DSA to address line and space (L/S) high resolution patterning by performing the density multiplication of lines with the graphoepitaxy approach. As surface affinity is a key parameter in self-assembly, three variations, or "flavors", of DSA template affinity are investigated regarding several success criteria such as morphology control or defectivity. More precisely, both the methodology to register DSA defects and the impact of process parameters on defectivity are detailed. Using the 300mm pilot line available in LETI and Arkema's advanced materials, we investigate process optimization of DSA line/space patterning of a 38nm period lamellar PS-b-PMMA BCP (L38). For this study, our integration scheme, depicted in figure 2-1, is based on BCP self-assembly inside organic hard mask guiding patterns obtained using 193i nm lithography. Defect analysis coupled with the fine tuning of process parameters (annealing, brush material) provided the optimum conditions for the L38 self-assembly. Using such conditions, DSA using the three affinity flavors is investigated by means of SEM top-view and cross-section review. Lithographic performances of one selected flavor are then evaluated with the comparison of Process Windows (PWs) function of either commensurability, morphology or LWR. This work is a first step in finding the best process for an industrial graphoepitaxy approach.
Presentation by conjugation for $A_1$-type extended affine Weyl groups
Azam, Saeid; Sahsanaei, Valiollah
2006-01-01
There is a well-known presentation for finite and affine Weyl groups called the {\\it presentation by conjugation}. Recently, it has been proved that this presentation holds for certain sub-classes of extended affine Weyl groups, the Weyl groups of extended affine root systems. In particular, it is shown that if nullity is $\\leq 2$, an $A_1$-type extended affine Weyl group has the presentation by conjugation. We set up a general framework for the study of simply laced extended affine Weyl grou...
Cohomology of various completions of quasicoherent sheaves on affines.
Laudal, O A
1972-09-01
Let O be a complete discrete valuation ring and let A be a commutative O-algebra. Let M be any A-module. In this paper, a class of completions M on the affine X corresponding to A, which includes, e.g., the Washnitzer-Monsky completion [1], and the full completion is studied. We then prove that for all of these completions we have, H(i)(X,M(+)) = O for i >/= 1, H degrees (X,M(+)) = M(+). PMID:16592014
Rotating Black Holes in Metric-Affine Gravity
Baekler, P; Baekler, Peter; Hehl, Friedrich W.
2006-01-01
Within the framework of metric-affine gravity (MAG, metric and an independent linear connection constitute spacetime), we find, for a specific gravitational Lagrangian and by using {\\it prolongation} techniques, a stationary axially symmetric exact solution of the vacuum field equations. This black hole solution embodies a Kerr-deSitter metric and the post-Riemannian structures of torsion and nonmetricity. The solution is characterized by mass, angular momentum, and shear charge, the latter of which is a measure for violating Lorentz invariance.
Enrichment of Phosphopeptides via Immobilized Metal Affinity Chromatography.
Swaney, Danielle L; Villén, Judit
2016-01-01
Immobilized metal affinity chromatography (IMAC) is a frequently used method for the enrichment of phosphorylated peptides from complex, cellular lysate-derived peptide mixtures. Here we outline an IMAC protocol that uses iron-chelated magnetic beads to selectively isolate phosphorylated peptides for mass spectrometry-based proteomic analysis. Under acidic conditions, negatively charged phosphoryl modifications preferentially bind to positively charged metal ions (e.g., Fe(3+), Ga(3+)) on the beads. After washing away nonphosphorylated peptides, a pH shift to basic conditions causes the elution of bound phosphopeptides from the metal ion. Under optimal conditions, very high specificity for phosphopeptides can be achieved. PMID:26933247
Corner detectors for affine invariant salient regions: is color important?
Sebe, Nicu; Gevers, Theo; Van De Weijer, Joost; Dijkstra, Sietse
2006-01-01
Recently, a lot of research has been done on the matching of images and their structures. Although the approaches are very different, most methods use some kind of point selection from which descriptors or a hierarchy are derived. We focus here on the methods that are related to the detection of points and regions that can be detected in an affine invariant way. Most of the previous research concentrated on intensity based methods. However, we show in this work that color information can make...
Telonemia, a new protist phylum with affinity to chromist lineages
DEFF Research Database (Denmark)
Shalchian-Tabrizi, K.; Eikrem, W.; Klaveness, D.; Vaulot, D.; Minge, M.A.; Le Gall, F.; Romari, K.; Throndsen, J.; Botnen, A.; Massana, R.; Thomsen, Helge Abildhauge; Jakobsen, K.
2006-01-01
the alveolates and heterokonts. Using the same approach on coastal samples, we have identified a novel group of protist small subunit (SSU) rDNA sequences that do not correspond to any phylogenetic group previously identified. Comparison with other sequences obtained from cultures of heterotrophic...... protists showed that the environmental sequences grouped together with Telonema, a genus known since 1913 but of uncertain taxonomic affinity. Phylogenetic analyses using four genes (SSU, Hsp90, alpha-tubulin and beta-tubulin), and accounting for gamma- and covarion-distributed substitution rates, revealed...
Affine and nonaffine motions in sheared polydisperse emulsions.
Clara-Rahola, J; Brzinski, T A; Semwogerere, D; Feitosa, K; Crocker, J C; Sato, J; Breedveld, V; Weeks, Eric R
2015-01-01
We study dense and highly polydisperse emulsions at droplet volume fractions ϕ≥0.65. We apply oscillatory shear and observe droplet motion using confocal microscopy. The presence of droplets with sizes several times the mean size dramatically changes the motion of smaller droplets. Both affine and nonaffine droplet motions are observed, with the more nonaffine motion exhibited by the smaller droplets which are pushed around by the larger droplets. Droplet motions are correlated over length scales from one to four times the mean droplet diameter, with larger length scales corresponding to higher strain amplitudes (up to strains of about 6%). PMID:25679553
Nine switch-affine neurons suffice for Turing universality.
Siegelmann, H T.; Margenstern, M
1999-06-01
In a previous work Pollack showed that a particular type of heterogeneous processor network is Turing universal. Siegelmann and Sontag (1991) showed the universality of homogeneous networks of first-order neurons having piecewise-linear activation functions. Their result was generalized by Kilian and Siegelmann (1996) to include various sigmoidal activation functions. Here we focus on a type of high-order neurons called switch-affine neurons, with piecewise-linear activation functions, and prove that nine such neurons suffice for simulating universal Turing machines. PMID:12662670
Algebraic (Volume) Density Property for Affine Homogeneous Spaces
Kaliman, Shulim; Kutzschebauch, Frank
2015-01-01
Let $X$ be a connected affine homogenous space of a linear algebraic group $G$ over $\\C$. (1) If $X$ is different from a line or a torus we show that the space of all algebraic vector fields on $X$ coincides with the Lie algebra generated by complete algebraic vector fields on $X$. (2) Suppose that $X$ has a $G$-invariant volume form $\\omega$. We prove that the space of all divergence-free (with respect to $\\omega$) algebraic vector fields on $X$ coincides with the Lie algebra generated by di...
Poisson bivectors and Poisson brackets on affine derived stacks
Melani, Valerio
2014-01-01
Let Spec(A) be an affine derived stack. We give two proofs of the existence of a canonical map from the moduli space of shifted Poisson structures (in the sense of Pantev-To\\"en-Vaqui\\'e-Vezzosi, see http://arxiv.org/abs/1111.3209 ) on Spec(A) to the moduli space of homotopy (shifted) Poisson algebra structures on A. The first makes use of a more general description of the Poisson operad and of its cofibrant models, while the second in more computational and involves an explicit resolution of...
Affinity and Hostility in Divided Communities: a Mathematical Model
Thron, Christopher
2015-01-01
We propose, develop, and analyze a mathematical model of intergroup attitudes in a community that is divided between two distinct social groups (which may be distinguished by religion, ethnicity, or some other socially distinguishing factor). The model is based on very simple premises that are both intuitive and justified by sociological research. We investigate the behavior of the model in various special cases, for various model configurations. We discuss the stability of the model, and the continuous or discontinuous dependence of model behavior on various parameters. Finally, we discuss possible implications for strategies to improve intergroup affinity, and to defuse tension and prevent deterioration of intergroup relationships.
Standard Bases for Affine SL(n)-Modules
Kreiman, V.; Lakshmibai, V.; Magyar, P.; Weyman, J.
2004-01-01
We give an elementary and easily computable basis for the Demazure modules in the basic representation of the affine Lie algebra sl(n)-hat (and the loop group SL(n)-hat). A novel feature is that we define our basis ``bottom-up'' by raising each extremal weight vector, rather than ``top-down'' by lowering the highest weight vector. Our basis arises naturally from the combinatorics of its indexing set, which consists of certain subsets of the integers first specified by the Kyoto school in term...
Lateral Casimir force between self-affine rough surfaces
Tajik, Fatemeh; Masoudi, Amir Ali; Khorrami, Mohammad
2016-03-01
The effect of self-affine roughness on the lateral Casimir force between two plates is studied using a perturbative expansion method. The PWS (pairwise summation) method is applicable only at lateral correlation lengths much larger than the separation between two plates. The effect of the roughness parameters on the lateral Casimir force is investigated, and it is seen that this effect is significant, enabling one to tailor roughness parameters so that to obtain the desirable Casimir force and increase the yield of micro- or nano-electromechanical devices based on the vacuum fluctuations.
Jumps and twists in affine Toda field theories
Energy Technology Data Exchange (ETDEWEB)
Doikou, Anastasia, E-mail: A.Doikou@hw.ac.uk [Department of Mathematics, Heriot–Watt University, EH14 4AS, Edinburgh (United Kingdom); Department of Computer Engineering & Informatics, University of Patras, GR-Patras 26500 (Greece)
2015-04-15
The concept of point-like “jump” defects is investigated in the context of affine Toda field theories. The Hamiltonian formulation is employed for the analysis of the problem. The issue is also addressed when integrable boundary conditions ruled by the classical twisted Yangian are present. In both periodic and boundary cases explicit expressions of conserved quantities as well as the relevant Lax pairs and sewing conditions are extracted. It is also observed that in the case of the twisted Yangian the bulk behavior is not affected by the presence of the boundaries.
Understanding proton affinity of tyrosine sidechain in hydrophobic confinement
Indian Academy of Sciences (India)
T G Abi; T Karmakar; S Taraphder
2012-01-01
Tyrosine is an important amino acid residue that plays a key role in several biochemical transformations such as, abstraction/donation of proton from/by its sidechain. We present here a density functional study on the proton affinity of tyrosine sidechain suspended inside the core of a single walled carbon nanotube that mimics the environment of protein structural pores and molecular channels. Tyrosine is found to exhibit a lower reactivity on confinement and unlike several other polar amino acid sidechains, its reactivity does not respond to hydrogen bonding with neighbouring hydroxyl groups.
Feedback control design for discrete-time piecewise affine systems
Institute of Scientific and Technical Information of China (English)
XU Jun; XIE Li-hua
2007-01-01
This paper investigates the design of state feedback and dynamic output feedback stabilizing controllers for discrete-time piecewise affine (PWA) systems. The main objective is to derive design methods that will incorporate the partition information of the PWA systems so as to reduce the design conservatism embedded in existing design methods. We first introduce a transformation that converts the feedback control design problem into a bilinear matrix inequality (BMI) problem. Then, two iterative algorithms are proposed to compute the feedback controllers characterized by the BMI. Several simulation examples are given to demonstrate the advantages of the proposed design.
Realization of parking task based on affine system modeling
International Nuclear Information System (INIS)
This paper presents a motion control system of an unmanned vehicle, where parallel parking task is realized based on a self-organizing affine system modeling and a quadratic programming based robust controller. Because of non-linearity of the vehicle system and complexity of the task to realize, control objective is not always realized with a single algorithm or control mode. This paper presents a hybrid model for parallel parking task in which seven modes for describing sub-tasks constitute an entire model
Tubular algebras and affine Kac-Moody algebras
Institute of Scientific and Technical Information of China (English)
Zheng-xin CHEN; Ya-nan LIN
2007-01-01
The purpose of this paper is to construct quotient algebras L(A)C1/I(A) of complex degenerate composition Lie algebras L(A)C1 by some ideals, where L(A)C1 is defined via Hall algebras of tubular algebras A, and to prove that the quotient algebras L(A)C1/I(A) are isomorphic to the corresponding affine Kac-Moody algebras. Moreover, it is shown that the Lie algebra Lre(A)C1 generated by A-modules with a real root coincides with the degenerate composition Lie algebra L(A)C1 generated by simple A-modules.
Tubular algebras and affine Kac-Moody algebras
Institute of Scientific and Technical Information of China (English)
2007-01-01
The purpose of this paper is to construct quotient algebras L(A)1C/I(A) of complex degenerate composition Lie algebras L(A)1C by some ideals, where L(A)1C is defined via Hall algebras of tubular algebras A, and to prove that the quotient algebras L(A)1C/I(A) are isomorphic to the corresponding affine Kac-Moody algebras. Moreover, it is shown that the Lie algebra Lre(A)1C generated by A-modules with a real root coincides with the degenerate composition Lie algebra L(A)1C generated by simple A-modules.
Two measured completely different electron affinities for atomic Eu?
Msezane, A. Z.; Felfli, Z.
2016-05-01
Recently, the electron affinity (EA) of atomic Eu was measured to be 0.116?eV. This value is in outstanding agreement with the theoretically calculated values using the Regge pole and MCDF-RCI methods. Previously, the EA of Eu was measured to be 1.053 eV. In an attempt to resolve the discrepancy between the two measured values, we have adopted the complex angular momentum (CAM) method and investigated in the electron energy range 0.11 eV methane to methanol without CO2 emission. These new results call for immediate experimental and theoretical verification.
Determinants of benzodiazepine brain uptake: lipophilicity versus binding affinity.
Arendt, R M; Greenblatt, D J; Liebisch, D C; Luu, M D; Paul, S M
1987-01-01
Factors influencing brain uptake of benzodiazepine derivatives were evaluated in adult Sprague Dawley rats (n = 8-10 per drug). Animals received single intraperitoneal doses of alprazolam, triazolam, lorazepam, flunitrazepam, diazepam, midazolam, desmethyldiazepam, or clobazam. Concentrations of each drug (and metabolites) in whole brain and serum 1 h after dosage were determined by gas chromatography. Serum free fraction was measured by equilibrium dialysis. In vitro binding affinity (apparent Ki) of each compound was estimated based on displacement of tritiated flunitrazepam in washed membrane preparations from rat cerebral cortex. Lipid solubility of each benzodiazepine was estimated using the reverse-phase liquid chromatographic (HPLC) retention index at physiologic pH. There was no significant relation between brain:total serum concentration ratio and either HPLC retention (r = 0.18) or binding Ki (r = -0.34). Correction of uptake ratios for free as opposed to total serum concentration yielded a highly significant correlation with HPLC retention (r = 0.78, P less than 0.005). However, even the corrected ratio was not correlated with binding Ki (r = -0.22). Thus a benzodiazepine's capacity to diffuse from systemic blood into brain tissue is much more closely associated with the physicochemical property of lipid solubility than with specific affinity. Unbound rather than total serum or plasma concentration most accurately reflects the quantity of drug available for diffusion. PMID:2888155
Altered catecholamine receptor affinity in rabbit aortic intimal hyperplasia
International Nuclear Information System (INIS)
Intimal thickening is a universal response to endothelial denudation and is also thought to be a precursor of atherosclerosis. The authors have demonstrated selective supersensitivity in arterial intimal hyperplasia to norepinephrine and they now report a possible mechanism for this. Binding studies in rabbit aorta with the selective alpha 1-adrenergic radioligand 125I-HEAT demonstrated that there was no change in receptor density (20 ± 4 fmole/10(6) cells) in intact vascular smooth muscle cells at either 5 or 14 days after denudation. However, competition studies showed a 2.6-fold increase in alpha 1-adrenergic receptor affinity for norepinephrine in intimal hyperplastic tissue (P less than 0.05). This increased affinity for norepinephrine was associated with a greater increase in 32P-labeled phosphatidylinositol (148% intimal thickening versus 76% control) and phosphatidic acid (151% intimal thickening versus 56% control) following norepinephrine stimulation of free floating rings of intimal hyperplastic aorta. These data suggest that the catecholamine supersensitivity in rabbit aortic intimal hyperplasia is receptor mediated and may be linked to the phosphatidylinositol cycle
Theory of affine projection algorithms for adaptive filtering
Ozeki, Kazuhiko
2016-01-01
This book focuses on theoretical aspects of the affine projection algorithm (APA) for adaptive filtering. The APA is a natural generalization of the classical, normalized least-mean-squares (NLMS) algorithm. The book first explains how the APA evolved from the NLMS algorithm, where an affine projection view is emphasized. By looking at those adaptation algorithms from such a geometrical point of view, we can find many of the important properties of the APA, e.g., the improvement of the convergence rate over the NLMS algorithm especially for correlated input signals. After the birth of the APA in the mid-1980s, similar algorithms were put forward by other researchers independently from different perspectives. This book shows that they are variants of the APA, forming a family of APAs. Then it surveys research on the convergence behavior of the APA, where statistical analyses play important roles. It also reviews developments of techniques to reduce the computational complexity of the APA, which are important f...
Altered catecholamine receptor affinity in rabbit aortic intimal hyperplasia
Energy Technology Data Exchange (ETDEWEB)
O' Malley, M.K.; Cotecchia, S.; Hagen, P.O. (Duke University Medical Center, Durham, NC (USA))
1991-08-01
Intimal thickening is a universal response to endothelial denudation and is also thought to be a precursor of atherosclerosis. The authors have demonstrated selective supersensitivity in arterial intimal hyperplasia to norepinephrine and they now report a possible mechanism for this. Binding studies in rabbit aorta with the selective alpha 1-adrenergic radioligand 125I-HEAT demonstrated that there was no change in receptor density (20 {plus minus} 4 fmole/10(6) cells) in intact vascular smooth muscle cells at either 5 or 14 days after denudation. However, competition studies showed a 2.6-fold increase in alpha 1-adrenergic receptor affinity for norepinephrine in intimal hyperplastic tissue (P less than 0.05). This increased affinity for norepinephrine was associated with a greater increase in 32P-labeled phosphatidylinositol (148% intimal thickening versus 76% control) and phosphatidic acid (151% intimal thickening versus 56% control) following norepinephrine stimulation of free floating rings of intimal hyperplastic aorta. These data suggest that the catecholamine supersensitivity in rabbit aortic intimal hyperplasia is receptor mediated and may be linked to the phosphatidylinositol cycle.
Impact of crystalline quality on neuronal affinity of pristine graphene.
Veliev, Farida; Briançon-Marjollet, Anne; Bouchiat, Vincent; Delacour, Cécile
2016-04-01
Due to its outstanding mechanical and electrical properties as well as chemical inertness, graphene has attracted a growing interest in the field of bioelectric interfacing. Herein, we investigate the suitability of pristine, i.e. without a cell adhesive coating, chemical vapor deposition (CVD) grown monolayer graphene to act as a platform for neuronal growth. We study the development of primary hippocampal neurons grown on bare graphene (transferred on glass coverslip) for up to 5 days and show that pristine graphene significantly improves the neurons adhesion and outgrowth at the early stage of culture (1-2 days in vitro). At the later development stage, neurons grown on coating free graphene (untreated with poly-L-lysine) show remarkably well developed neuritic architecture similar to those cultured on conventional poly-L-lysine coated glass coverslips. This exceptional possibility to bypass the adhesive coating allows a direct electrical contact of graphene to the cells and reveals its great potential for chronic medical implants and tissue engineering. Moreover, regarding the controversial results obtained on the neuronal affinity of pristine graphene and its ability to support neuronal growth without the need of polymer or protein coating, we found that the crystallinity of CVD grown graphene plays an important role in neuronal attachment, outgrowth and axonal specification. In particular, we show that the decreasing crystalline quality of graphene tunes the neuronal affinity from highly adhesive to fully repellent. PMID:26878439
Subband Affine Projection Algorithm for Acoustic Echo Cancellation System
Directory of Open Access Journals (Sweden)
Choi Hun
2007-01-01
Full Text Available We present a new subband affine projection (SAP algorithm for the adaptive acoustic echo cancellation with long echo path delay. Generally, the acoustic echo canceller suffers from the long echo path and large computational complexity. To solve this problem, the proposed algorithm combines merits of the affine projection (AP algorithm and the subband filtering. Convergence speed of the proposed algorithm is improved by the signal-decorrelating property of the orthogonal subband filtering and the weight updating with the prewhitened input signal of the AP algorithm. Moreover, in the proposed algorithms, as applying the polyphase decomposition, the noble identity, and the critical decimation to subband the adaptive filter, the sufficiently decomposed SAP updates the weights of adaptive subfilters without a matrix inversion. Therefore, computational complexity of the proposed method is considerably reduced. In the SAP, the derived weight updating formula for the subband adaptive filter has a simple form as ever compared with the normalized least-mean-square (NLMS algorithm. The efficiency of the proposed algorithm for the colored signal and speech signal was evaluated experimentally.
Affinity sensor using 3-aminophenylboronic acid for bacteria detection.
Wannapob, Rodtichoti; Kanatharana, Proespichaya; Limbut, Warakorn; Numnuam, Apon; Asawatreratanakul, Punnee; Thammakhet, Chongdee; Thavarungkul, Panote
2010-10-15
Boronic acid that can reversibly bind to diols was used to detect bacteria through its affinity binding reaction with diol-groups on bacterial cell walls. 3-aminophenylboronic acid (3-APBA) was immobilized on a gold electrode via a self-assembled monolayer. The change in capacitance of the sensing surface caused by the binding between 3-APBA and bacteria in a flow system was detected by a potentiostatic step method. Under optimal conditions the linear range of 1.5×10(2)-1.5×10(6) CFU ml(-1) and the detection limit of 1.0×10(2) CFU ml(-1) was obtained. The sensing surface can be regenerated and reused up to 58 times. The method was used for the analysis of bacteria in several types of water, i.e., bottled, well, tap, reservoir and wastewater. Compared with the standard plate count method, the results were within one standard deviation of each other. The proposed method can save both time and cost of analysis. The electrode modified with 3-APBA would also be applicable to the detection of other cis-diol-containing analytes. The concept could be extended to other chemoselective ligands, offering less expensive and more robust affinity sensors for a wide range of compounds. PMID:20801635
Finite-sided deformation spaces of complete affine 3-manifolds
Charette, Virginie; Goldman, William M
2011-01-01
A Margulis spacetime is a complete affine 3-manifold M with nonsolvable fundamental group. Associated to every Margulis spacetime is a noncompact complete hyperbolic surface S. We show that every Margulis spacetime is orientable, even though S may be nonorientable. We classify Margulis spacetimes when S is homeomorphic to a two-holed cross-surface, that is, the complement of two disjoint discs in the real projective plane. We show that every such manifold is homeomorphic to a solid handlebody of genus two, and admits a fundamental polyhedron bounded by crooked planes. Furthermore, the deformation space is a bundle of convex quadrilateral cones over the space of marked hyperbolic structures. The sides of each quadrilateral cone are defined by invariants of the two boundary components and the two orientation-reversing simple curves. The two-holed cross-surface, together with the three-holed sphere, are the only topologies for which the deformation space of complete affine structures is finite-sided.
Fundamentals and application of ordered molecular assemblies to affinity biosensing.
Matharu, Zimple; Bandodkar, Amay Jairaj; Gupta, Vinay; Malhotra, Bansi Dhar
2012-02-01
Organization of biomolecules in two/three dimensional assemblies has recently aroused much interest in nanobiotechnology. In this context, the development of techniques for controlling spatial arrangement and orientation of the desired molecules to generate highly-ordered nanostructures in the form of a mono/multi layer is considered highly significant. The studies of monolayer films to date have focused on three distinct methods of preparation: (i) the Langmuir-Blodgett (LB) technique, involving the transfer of a monolayer assembled at the gas-liquid interface; (ii) self-assembly at the liquid-solid interface, based on spontaneous adsorption of desired molecules from a solution directly onto a solid surface; and (iii) Layer-by-layer (LBL) self-assembly at a liquid-solid interface, based on inter-layer electrostatic attractions for fabrication of multilayers. A variety of monolayers have been utilized to fabricate biomolecular electronic devices including biosensors. The composition of a monolayer based matrix has been found to influence the activity(ies) of biomolecule(s). We present comprehensive and critical analysis of ordered molecular assemblies formed by LB and self-assembly with potential applications to affinity biosensing. This critical review on fundamentals and application of ordered molecular assemblies to affinity biosensing is likely to benefit researchers working in this as well as related fields of research (401 references). PMID:22105315
Flexible Molybdenum Electrodes towards Designing Affinity Based Protein Biosensors.
Kamakoti, Vikramshankar; Panneer Selvam, Anjan; Radha Shanmugam, Nandhinee; Muthukumar, Sriram; Prasad, Shalini
2016-01-01
Molybdenum electrode based flexible biosensor on porous polyamide substrates has been fabricated and tested for its functionality as a protein affinity based biosensor. The biosensor performance was evaluated using a key cardiac biomarker; cardiac Troponin-I (cTnI). Molybdenum is a transition metal and demonstrates electrochemical behavior upon interaction with an electrolyte. We have leveraged this property of molybdenum for designing an affinity based biosensor using electrochemical impedance spectroscopy. We have evaluated the feasibility of detection of cTnI in phosphate-buffered saline (PBS) and human serum (HS) by measuring impedance changes over a frequency window from 100 mHz to 1 MHz. Increasing changes to the measured impedance was correlated to the increased dose of cTnI molecules binding to the cTnI antibody functionalized molybdenum surface. We achieved cTnI detection limit of 10 pg/mL in PBS and 1 ng/mL in HS medium. The use of flexible substrates for designing the biosensor demonstrates promise for integration with a large-scale batch manufacturing process. PMID:27438863
The eyes of Tullimonstrum reveal a vertebrate affinity.
Clements, Thomas; Dolocan, Andrei; Martin, Peter; Purnell, Mark A; Vinther, Jakob; Gabbott, Sarah E
2016-04-28
Tullimonstrum gregarium is an iconic soft-bodied fossil from the Carboniferous Mazon Creek Lagerstätte (Illinois, USA). Despite a large number of specimens and distinct anatomy, various analyses over the past five decades have failed to determine the phylogenetic affinities of the 'Tully monster', and although it has been allied to such disparate phyla as the Mollusca, Annelida or Chordata, it remains enigmatic. The nature and phylogenetic affinities of Tullimonstrum have defied confident systematic placement because none of its preserved anatomy provides unequivocal evidence of homology, without which comparative analysis fails. Here we show that the eyes of Tullimonstrum possess ultrastructural details indicating homology with vertebrate eyes. Anatomical analysis using scanning electron microscopy reveals that the eyes of Tullimonstrum preserve a retina defined by a thick sheet comprising distinct layers of spheroidal and cylindrical melanosomes. Time-of-flight secondary ion mass spectrometry and multivariate statistics provide further evidence that these microbodies are melanosomes. A range of animals have melanin in their eyes, but the possession of melanosomes of two distinct morphologies arranged in layers, forming retinal pigment epithelium, is a synapomorphy of vertebrates. Our analysis indicates that in addition to evidence of colour patterning, ecology and thermoregulation, fossil melanosomes can also carry a phylogenetic signal. Identification in Tullimonstrum of spheroidal and cylindrical melanosomes forming the remains of retinal pigment epithelium indicates that it is a vertebrate; considering its body parts in this new light suggests it was an anatomically unusual member of total group Vertebrata. PMID:27074512
Braided affine geometry and q-analogs of wave operators
International Nuclear Information System (INIS)
The main goal of this review is to compare different approaches to constructing the geometry associated with a Hecke type braiding (in particular, with that related to the quantum group Uq(sl(n))). We place emphasis on the affine braided geometry related to the so-called reflection equation algebra (REA). All objects of such a type of geometry are defined in the spirit of affine algebraic geometry via polynomial relations on generators. We begin by comparing the Poisson counterparts of 'quantum varieties' and describe different approaches to their quantization. Also, we exhibit two approaches to introducing q-analogs of vector bundles and defining the Chern-Connes index for them on quantum spheres. In accordance with the Serre-Swan approach, the q-vector bundles are treated as finitely generated projective modules over the corresponding quantum algebras. Besides, we describe the basic properties of the REA used in this construction and compare different ways of defining q-analogs of partial derivatives and differentials on the REA and algebras close to them. In particular, we present a way of introducing a q-differential calculus via Koszul type complexes. The elements of the q-calculus are applied to defining q-analogs of some relativistic wave operators. (topical review)
Innate immunity probed by lipopolysaccharides affinity strategy and proteomics.
Giangrande, Chiara; Colarusso, Lucia; Lanzetta, Rosa; Molinaro, Antonio; Pucci, Piero; Amoresano, Angela
2013-01-01
Lipopolysaccharides (LPSs) are ubiquitous and vital components of the cell surface of Gram-negative bacteria that have been shown to play a relevant role in the induction of the immune-system response. In animal and plant cells, innate immune defenses toward microorganisms are triggered by the perception of pathogen associated molecular patterns. These are conserved and generally indispensable microbial structures such as LPSs that are fundamental in the Gram-negative immunity recognition. This paper reports the development of an integrated strategy based on lipopolysaccharide affinity methodology that represents a new starting point to elucidate the molecular mechanisms elicited by bacterial LPS and involved in the different steps of innate immunity response. Biotin-tagged LPS was immobilized on streptavidin column and used as a bait in an affinity capture procedure to identify protein partners from human serum specifically interacting with this effector. The complex proteins/lipopolysaccharide was isolated and the protein partners were fractionated by gel electrophoresis and identified by mass spectrometry. This procedure proved to be very effective in specifically binding proteins functionally correlated with the biological role of LPS. Proteins specifically bound to LPS essentially gathered within two functional groups, regulation of the complement system (factor H, C4b, C4BP, and alpha 2 macroglobulin) and inhibition of LPS-induced inflammation (HRG and Apolipoproteins). The reported strategy might have important applications in the elucidation of biological mechanisms involved in the LPSs-mediated molecular recognition and anti-infection responses. PMID:22752448
Influence of affinity on antibody determination in microtiter ELISA systems
International Nuclear Information System (INIS)
Theoretically, all immunoassays are affinity (Ka) dependent when the product of the antibody (Ab) Ka and the free epitope concentration is less than 10. Thus, the degree of dependence on Ka depends on the concentration of available antigen in the system. The authors examined the binding of 125I-anti-fluorescein (a-FLU) monoclonal antibodies of different affinities to FLU-gelatin adsorbed on Immunlon 2 microtiter plates. Data obtained were in general agreement with our theoretical predictions; the percent of 125I-a-FLU which bound correlated with Ka, as did the shape of the titration curves. Measurement of 5 a-FLU monoclonals by the ELISA showed that the determination of Ab concentrations depends on the FLU-gelatin concentration, epitope density, and on the relationship between the Kas of test samples and the reference standard Ab preparation. Thus the ELISA is Ka dependent and should not be used routinely to estimate the absolute amount to Ab in unknown samples. However, the Ka dependency of the ELISA might provide a convenient assay for the estimation of the relative functional Ka (rfKa) of antibody preparations
Study on Removal of Bilirubin with Magnetic Affinity Separation Technique
Institute of Scientific and Technical Information of China (English)
张凤宝; 王淑兰; 徐辉; 张国亮
2003-01-01
An affinity adsorbent, Cibacron Blue 3GA immobilized magnetic polyvinyl alcohol (PVA) microspheres was used for bilirubin removal taking the advantage of easy separation of magnetic sorbent from the biosystem.Fe3 O4 superparamagnetic particles was synthesized with hydrothermal reaction of ferrous chloride (FeC12) and ferric chloride (FeCl3). Such magnetic particles are then encapsulated in biocompatible PVA to form magnetic polymer microspheres sized from 2 to 15 nm with hydroxyl groups on its surface. Cibacron Blue 3GA, a dye-ligand, was covalently coupled with the polyvinyl alcohol through the nucleophilic reaction between the chloride of its triazine ring and the hydroxyl groups of PVA molecules under alkaline condition. The affinity adsorbent carried 21.1μmol Cibacron Blue 3GA per gram magnetic polymer microspheres was used to remove unconjugated and conjugated bilirubin from the solution which was composed of bilirubin or bilirubin and protein. After the adsorption, the adsorbent loaded with bilirubin was removed easily in the magnetic field.
01-ERD-111 - The Development of Synthetic High Affinity Ligands
Energy Technology Data Exchange (ETDEWEB)
Perkins, J; Balhorn, R; Cosman, M; Lightstone, F; Zeller, L
2004-02-05
The aim of this project was to develop Synthetic High-Affinity Ligands (SHALs), which bind with high affinity and specificity to proteins of interest for national security and cancer therapy applications. The aim of producing synthetic ligands for sensory devices as an alternative to antibody-based detection assays and therapeutic agents is to overcome the drawbacks associated with antibody-based in next-generation sensors and systems. The focus area of the project was the chemical synthesis of the SHALs. The project concentrated on two different protein targets. (a) The C fragment of tetanus and botulinum toxin, potential biowarfare agents. A SHAL for tetanus or botulinum toxin would be incorporated into a sensory device for the toxins. (b) HLA-DR10, a protein found in high abundance on the surface of Non-Hodgkins Lymphoma. A SHAL specific to a tumor marker, labeled with a radionuclide, would enable the targeted delivery of radiation therapy to metastatic disease. The technical approach used to develop a SHAL for each protein target will be described in more detail below. However, in general, the development of a SHAL requires a combination of computational modeling techniques, modern nuclear magnetic resonance spectroscopy (NMR) and synthetic chemistry.
Weak Affine Light Typing: Polytime intensional expressivity, soundness and completeness
Roversi, Luca
2007-01-01
Weak affine light typing (WALT) assigns light affine linear formulae as types to a subset of lambda-terms in System F. WALT is poly-time sound: if a lambda-term M has type in WALT, M can be evaluated with a polynomial cost in the dimension of the derivation that gives it a type. In particular, the evaluation can proceed under any strategy of a rewriting relation, obtained as a mix of both call-by-name/call-by-value beta-reductions. WALT is poly-time complete since it can represent any poly-time Turing machine. WALT weakens, namely generalizes, the notion of stratification of deductions common to some Light Systems -- we call as such those logical systems, derived from Linear logic, to characterize FP, the set of Polynomial functions -- . A weaker stratification allows to define a compositional embedding of the Quasi-linear fragment QlSRN of Safe recursion on notation (SRN) into WALT. QlSRN is SRN, which is a recursive-theoretical system characterizing FP, where only the composition scheme is restricted to lin...
International Nuclear Information System (INIS)
An exact S-matrix is conjectured for the imaginary coupled d4(3) affine Toda field theory, using the Uq(g2(1)) symmetry. It is shown that this S-matrix is consistent with the results for the case of real coupling using the breather-particle correspondence. For q a root of unity it is argued that the theory can be restricted to yield Φ(11 vertical stroke 14) perturbations of WA2 minimal models and the restriction is performed for the (3,p') minimal models. (orig.)
A thermal responsive affinity ligand for precipitation of sialylated proteins
Directory of Open Access Journals (Sweden)
Lindsay Arnold
2016-01-01
Full Text Available We report here the development of a thermal responsive affinity ligand specific to sialic acid, sialic acid containing oligosaccharides, glycoproteins, and other sialylated glycoconjugates. The ligand is a fusion protein of 40 repeats of pentapeptide of an elastin like polymer (ELP and the 21 kD sialic acid binding domain of a Vibrio cholera neuraminidase (VCNA. For cost-effective synthesis, the fusion protein was targeted to the periplasmic space of an E. coli lpp deletion mutant, resulting in its secretion to the growth medium. A pre-induction heat-shock step at 42 ˚C for 20 minutes was necessary to achieve high level expression of the ligand. Under optimized induction condition (18 ˚C, 0.1 mM IPTG and 48 hours of post-induction cultivation, the ligand was produced to about 100 mg/L. The ligand exhibited a transition temperature of 52 ˚C, which could be depressed to 37 ˚C with the addition of 0.5 M NaCl. Using fetuin as a model sialylated protein, the ligand was applied in an affinity precipitation process to illustrate its potential application in glycoprotein isolation. The ligand captured 100% fetuin from an aqueous solution when the molar ratio of ligand to fetuin was 10 to 1, which was lower than the expected for full titration of sialic acid on the glycoprotein by the lectin. Elution of fetuin from ligand was achieved with PBS buffer containing 2 mM sialic acid. To evaluate how protein and other contaminants influence the recovery of sialylated proteins, CHO medium was spiked into the fetuin solution. The predominant protein species in CHO medium was found to be albumin. Although its removal of over 94% was evident, purified fetuin contained some albumin due to its over-abundance. Additional experiments with albumin contaminant of varying concentrations showed that below 1 mg/L, albumin had no impact on the affinity precipitation, whereas above 10 mg/L, some albumin was co-purified with fetuin. However, even at 50 mg/ml, fetuin
Reconfigurable Control of Input Affine Nonlinear Systems under Actuator Fault
DEFF Research Database (Denmark)
Tabatabaeipour, Mojtaba; Galeazzi, Roberto
2015-01-01
This paper proposes a fault tolerant control method for input-affine nonlinear systems using a nonlinear reconfiguration block (RB). The basic idea of the method is to insert the RB between the plant and the nominal controller such that fault tolerance is achieved without re-designing the nominal...... controller. The role of the RB is twofold: on one hand it transforms the output of the faulty system such that its behaviour is similar to that of the nominal one from the controller’s viewpoint; on the other hand it modifies the control input to the faulty system such that the stability of the reconfigured...... need any knowledge of the nominal controller and only assumes that the nominal closed-loop system is ISS. The method is demonstrated on a dynamic positioning system for an offshore supply vessel, where the virtual actuator is designed using backstepping....
A novel affinity purification method to isolate peptide specific antibodies
DEFF Research Database (Denmark)
Karlsen, Alan E; Lernmark, A; Kofod, Hans; Dyrberg, T
1990-01-01
affinity-purify anti-peptide antibodies. To test our system, rabbits were immunized with model peptides representing sequences of the putative rabbit growth hormone receptor and several HLA-DQ beta-chain molecules. Polystyrene plastic beads were coated with peptides. Immune serum was incubated with the...... beads and after a wash step the bound antibodies were eluted in 1 M acetic acid. The eluted material was composed predominantly of intact immunoglobulin as evidenced by the presence of heavy and light chain bands in SDS-PAGE. The eluted antibodies were peptide specific in ELISA and bound only to intact......, antigenic protein in immunoblot analyses. The sequence-specific nature of the eluted antibodies was confirmed since binding to the antigenic proteins could be displaced by the immunizing but not by unrelated peptides....
Universal vertex-IRF transformation for quantum affine algebras
Energy Technology Data Exchange (ETDEWEB)
Buffenoir, E.; Roche, Ph. [Universite Montpellier 2, CNRS, LPTA, UMR 5207 (France); Terras, V. [Universite de Lyon, ENS Lyon, CNRS, Laboratoire de Physique, UMR 5672, France, on leave of absence from Universite Montpellier 2, CNRS, LPTA, UMR 5207 (France)
2012-10-15
We construct a universal solution of the generalized coboundary equation in the case of quantum affine algebras, which is an extension of our previous work to U{sub q}(A{sub r}{sup (1)}). This universal solution has a simple Gauss decomposition which is constructed using Sevostyanov's characters of twisted quantum Borel algebras. We show that in the evaluation representations it gives a vertex-face transformation between a vertex type solution and a face type solution of the quantum dynamical Yang-Baxter equation. In particular, in the evaluation representation of U{sub q}(A{sub 1}{sup (1)}), it gives Baxter's well-known transformation between the 8-vertex model and the interaction-round-faces (IRF) height model.
Electron Affinities of the Early Lanthanide Monoxide Molecules
Institute of Scientific and Technical Information of China (English)
Chao-xian Chi; Hua Xie; Ran Cong; Zi-chao Tang; Ming-fei Zhou
2011-01-01
The photoelectron imagings of LaO-,CeO-,PRO-,and NdO- at 1064 nm are reported.The well resolved photoelectron spectra allow the electron affinities to be determined as 0.99(1) eV for LaO,1.00(1) eV for CeO,1.00(1) eV for PrO,and 1.01(1) eV for NdO,respectively.Density functional calculations and natural atomic orbital analyses show that the 4f electrons tend to be localized and suffer little from the charge states of the molecules.The photodetached electron mainly originates from the 6s orbital of the metals.The ligand field theory with the δ=2 assumption is still an effective method to analyze the ground states of the neutral and anionic lanthanide monoxides.
The metric-affine formalism of f(R) gravity
International Nuclear Information System (INIS)
Recently a class of alternative theories of gravity which goes under the name f(R) gravity, has received considerable attention, mainly due to its interesting applications in cosmology. However, the phenomenology of such theories is not only relevant to cosmological scales, especially when it is treated within the framework of the so called Palatini variation, an independent variation with respect to the metric and the connection, which is not considered a priori to be the Levi-Civita connection of the metric. If this connection has its standard geometrical meaning the resulting theory will be a metric-affine theory of gravity, as will be discussed in this talk. The general formalism will be presented and several aspects of the theory will be covered, mainly focusing on the enriched phenomenology that such theories exhibit with respect to General Relativity, relevant not only to large scales (cosmology) but also to small scales (e.g. torsion)
Political ideology: its structure, functions, and elective affinities.
Jost, John T; Federico, Christopher M; Napier, Jaime L
2009-01-01
Ideology has re-emerged as an important topic of inquiry among social, personality, and political psychologists. In this review, we examine recent theory and research concerning the structure, contents, and functions of ideological belief systems. We begin by defining the construct and placing it in historical and philosophical context. We then examine different perspectives on how many (and what types of) dimensions individuals use to organize their political opinions. We investigate (a) how and to what extent individuals acquire the discursive contents associated with various ideologies, and (b) the social-psychological functions that these ideologies serve for those who adopt them. Our review highlights "elective affinities" between situational and dispositional needs of individuals and groups and the structure and contents of specific ideologies. Finally, we consider the consequences of ideology, especially with respect to attitudes, evaluations, and processes of system justification. PMID:19035826
Boundaries of Disk-like Self-affine Tiles
Leung, King-Shun
2012-01-01
Let $T:= T(A, {\\mathcal D})$ be a disk-like self-affine tile generated by an integral expanding matrix $A$ and a consecutive collinear digit set ${\\mathcal D}$, and let $f(x)=x^{2}+px+q$ be the characteristic polynomial of $A$. By investigating the neighbors of $T$, we construct a neighbor graph and show that any point on the boundary $\\partial T$ can be identified with a one-sided infinite path of the graph. Also we derive certain equivalent conditions for the pair $(A,{\\mathcal D})$ to be a number system. From the neighbor graph we can deduce a family of graph-directed sets, which gives a second description of $\\partial T$. When $A$ is a similarity, we obtain $\\dim_H (\\partial T)=2\\log \\rho/\\log |q|$ where $\\rho$ is the largest positive zero of the cubic polynomial $x^{3}-(|p|-1)x^{2}-(|q|-|p|)x-|q|$.
Higher Order Kernels and Locally Affine LDDMM Registration
Sommer, Stefan; Darkner, Sune; Pennec, Xavier
2011-01-01
To achieve sparse description that allows intuitive analysis, we aim to represent deformation with a basis containing interpretable elements, and we wish to use elements that have the description capacity to represent the deformation compactly. We accomplish this by introducing higher order kernels in the LDDMM registration framework. The kernels allow local description of affine transformations and subsequent compact description of non-translational movement and of the entire non-rigid deformation. This is obtained with a representation that contains directly interpretable information from both mathematical and modeling perspectives. We develop the mathematical construction behind the higher order kernels, we show the implications for sparse image registration and deformation description, and we provide examples of how the capacity of the kernels enables registration with a very low number of parameters. The capacity and interpretability of the kernels lead to natural modeling of articulated movement, and th...
Affinity sensor based on immobilized molecular imprinted synthetic recognition elements.
Lenain, Pieterjan; De Saeger, Sarah; Mattiasson, Bo; Hedström, Martin
2015-07-15
An affinity sensor based on capacitive transduction was developed to detect a model compound, metergoline, in a continuous flow system. This system simulates the monitoring of low-molecular weight organic compounds in natural flowing waters, i.e. rivers and streams. During operation in such scenarios, control of the experimental parameters is not possible, which poses a true analytical challenge. A two-step approach was used to produce a sensor for metergoline. Submicron spherical molecularly imprinted polymers, used as recognition elements, were obtained through emulsion polymerization and subsequently coupled to the sensor surface by electropolymerization. This way, a robust and reusable sensor was obtained that regenerated spontaneously under the natural conditions in a river. Small organic compounds could be analyzed in water without manipulating the binding or regeneration conditions, thereby offering a viable tool for on-site application. PMID:25703726
Vibrational photodetachment spectroscopy near the electron affinity of S2
Barrick, J. B.; Yukich, J. N.
2016-02-01
We have conducted laser photodetachment spectroscopy near the detachment threshold of the electron affinity of S2 in a 1.8-T field. The ions are prepared by dissociative electron attachment to carbonyl sulfide. The experiment is conducted in a Penning ion trap and with a narrow-band, tunable, Ti:sapphire laser. A hybrid model for photodetachment in an ion trap is fit to the data using the appropriate Franck-Condon factors. The observations reveal detachment from and to the first few vibrational levels of the anion and the neutral molecule, respectively. Evaporative cooling of the anion ensemble condenses the thermal distribution to the lowest initial vibrational states. The subsequent detachment spectroscopy yields results consistent with a vibrationally cooled anion population.
Deformation of supersymmetric and conformal quantum mechanics through affine transformations
Spiridonov, Vyacheslav
1993-01-01
Affine transformations (dilatations and translations) are used to define a deformation of one-dimensional N = 2 supersymmetric quantum mechanics. Resulting physical systems do not have conserved charges and degeneracies in the spectra. Instead, superpartner Hamiltonians are q-isospectral, i.e. the spectrum of one can be obtained from another (with possible exception of the lowest level) by q(sup 2)-factor scaling. This construction allows easily to rederive a special self-similar potential found by Shabat and to show that for the latter a q-deformed harmonic oscillator algebra of Biedenharn and Macfarlane serves as the spectrum generating algebra. A general class of potentials related to the quantum conformal algebra su(sub q)(1,1) is described. Further possibilities for q-deformation of known solvable potentials are outlined.
Local Structural Alignment of RNA with Affine Gap Model
Wong, Thomas K. F.; Cheung, Brenda W. Y.; Lam, T. W.; Yiu, S. M.
Predicting new non-coding RNAs (ncRNAs) of a family can be done by aligning the potential candidate with a member of the family with known sequence and secondary structure. Existing tools either only consider the sequence similarity or cannot handle local alignment with gaps. In this paper, we consider the problem of finding the optimal local structural alignment between a query RNA sequence (with known secondary structure) and a target sequence (with unknown secondary structure) with the affine gap penalty model. We provide the algorithm to solve the problem. Based on a preliminary experiment, we show that there are ncRNA families in which considering local structural alignment with gap penalty model can identify real hits more effectively than using global alignment or local alignment without gap penalty model.
Optimal growth for linear processes with affine control
Calvez, Vincent
2012-01-01
We analyse an optimal control with the following features: the dynamical system is linear, and the dependence upon the control parameter is affine. More precisely we consider $\\dot x_\\alpha(t) = (G + \\alpha(t) F)x_\\alpha(t)$, where $G$ and $F$ are $3\\times 3$ matrices with some prescribed structure. In the case of constant control $\\alpha(t)\\equiv \\alpha$, we show the existence of an optimal Perron eigenvalue with respect to varying $\\alpha$ under some assumptions. Next we investigate the Floquet eigenvalue problem associated to time-periodic controls $\\alpha(t)$. Finally we prove the existence of an eigenvalue (in the generalized sense) for the optimal control problem. The proof is based on the results by [Arisawa 1998, Ann. Institut Henri Poincar\\'e] concerning the ergodic problem for Hamilton-Jacobi equations. We discuss the relations between the three eigenvalues. Surprisingly enough, the three eigenvalues appear to be numerically the same.
Affine generalizations of gravity in the light of modern cosmology
Filippov, A T
2010-01-01
We discuss new models of an `affine' theory of gravity in multidimensional space-times with symmetric connections. We use and develop ideas of Weyl, Eddington, and Einstein, in particular, Einstein's proposal to specify the space - time geometry by use of the Hamilton principle. More specifically, the connection coefficients are determined using a `geometric' Lagrangian that is an arbitrary function of the generalized (non-symmetric) Ricci curvature tensor (and, possibly, of other fundamental tensors) expressed in terms of the connection coefficients regarded as independent variables. Such a theory supplements the standard Einstein gravity with dark energy (the cosmological constant, in the first approximation), a neutral massive (or tachyonic) vector field (vecton), and massive (or tachyonic) scalar fields. These fields couple only to gravity and can generate dark matter and/or inflation. The new field masses (real or imaginary) have a geometric origin and must appear in any concrete model. The concrete choi...
Affine Lie algebraic origin of constrained KP hierarchies
International Nuclear Information System (INIS)
It is presented an affine sl(n+1) algebraic construction of the basic constrained KP hierarchy. This hierarchy is analyzed using two approaches, namely linear matrix eigenvalue problem on hermitian symmetric space and constrained KP Lax formulation and we show that these approaches are equivalent. The model is recognized to be generalized non-linear Schroedinger (GNLS) hierarchy and it is used as a building block for a new class of constrained KP hierarchies. These constrained KP hierarchies are connected via similarity-Backlund transformations and interpolate between GNLS and multi-boson KP-Toda hierarchies. The construction uncovers origin of the Toda lattice structure behind the latter hierarchy. (author). 23 refs
A High-Affinity Adenosine Kinase from Anopheles Gambiae
Energy Technology Data Exchange (ETDEWEB)
M Cassera; M Ho; E Merino; E Burgos; A Rinaldo-Matthis; S Almo; V Schramm
2011-12-31
Genome analysis revealed a mosquito orthologue of adenosine kinase in Anopheles gambiae (AgAK; the most important vector for the transmission of Plasmodium falciparum in Africa). P. falciparum are purine auxotrophs and do not express an adenosine kinase but rely on their hosts for purines. AgAK was kinetically characterized and found to have the highest affinity for adenosine (K{sub m} = 8.1 nM) of any known adenosine kinase. AgAK is specific for adenosine at the nucleoside site, but several nucleotide triphosphate phosphoryl donors are tolerated. The AgAK crystal structure with a bound bisubstrate analogue Ap{sub 4}A (2.0 {angstrom} resolution) reveals interactions for adenosine and ATP and the geometry for phosphoryl transfer. The polyphosphate charge is partly neutralized by a bound Mg{sup 2+} ion and an ion pair to a catalytic site Arg. The AgAK structure consists of a large catalytic core in a three-layer {alpha}/{beta}/{alpha} sandwich, and a small cap domain in contact with adenosine. The specificity and tight binding for adenosine arise from hydrogen bond interactions of Asn14, Leu16, Leu40, Leu133, Leu168, Phe168, and Thr171 and the backbone of Ile39 and Phe168 with the adenine ring as well as through hydrogen bond interactions between Asp18, Gly64, and Asn68 and the ribosyl 2'- and 3'-hydroxyl groups. The structure is more similar to that of human adenosine kinase (48% identical) than to that of AK from Toxoplasma gondii (31% identical). With this extraordinary affinity for AgAK, adenosine is efficiently captured and converted to AMP at near the diffusion limit, suggesting an important role for this enzyme in the maintenance of the adenine nucleotide pool. mRNA analysis verifies that AgAK transcripts are produced in the adult insects.
Electron affinity of cubic boron nitride terminated with vanadium oxide
Energy Technology Data Exchange (ETDEWEB)
Yang, Yu; Sun, Tianyin; Shammas, Joseph; Hao, Mei; Nemanich, Robert J. [Department of Physics, Arizona State University, Tempe, Arizona 85287-1504 (United States); Kaur, Manpuneet [School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, Arizona 85287-6106 (United States)
2015-10-28
A thermally stable negative electron affinity (NEA) for a cubic boron nitride (c-BN) surface with vanadium-oxide-termination is achieved, and its electronic structure was analyzed with in-situ photoelectron spectroscopy. The c-BN films were prepared by electron cyclotron resonance plasma-enhanced chemical vapor deposition employing BF{sub 3} and N{sub 2} as precursors. Vanadium layers of ∼0.1 and 0.5 nm thickness were deposited on the c-BN surface in an electron beam deposition system. Oxidation of the metal layer was achieved by an oxygen plasma treatment. After 650 °C thermal annealing, the vanadium oxide on the c-BN surface was determined to be VO{sub 2}, and the surfaces were found to be thermally stable, exhibiting an NEA. In comparison, the oxygen-terminated c-BN surface, where B{sub 2}O{sub 3} was detected, showed a positive electron affinity of ∼1.2 eV. The B{sub 2}O{sub 3} evidently acts as a negatively charged layer introducing a surface dipole directed into the c-BN. Through the interaction of VO{sub 2} with the B{sub 2}O{sub 3} layer, a B-O-V layer structure would contribute a dipole between the O and V layers with the positive side facing vacuum. The lower enthalpy of formation for B{sub 2}O{sub 3} is favorable for the formation of the B-O-V layer structure, which provides a thermally stable surface dipole and an NEA surface.
Electron affinity of cubic boron nitride terminated with vanadium oxide
International Nuclear Information System (INIS)
A thermally stable negative electron affinity (NEA) for a cubic boron nitride (c-BN) surface with vanadium-oxide-termination is achieved, and its electronic structure was analyzed with in-situ photoelectron spectroscopy. The c-BN films were prepared by electron cyclotron resonance plasma-enhanced chemical vapor deposition employing BF3 and N2 as precursors. Vanadium layers of ∼0.1 and 0.5 nm thickness were deposited on the c-BN surface in an electron beam deposition system. Oxidation of the metal layer was achieved by an oxygen plasma treatment. After 650 °C thermal annealing, the vanadium oxide on the c-BN surface was determined to be VO2, and the surfaces were found to be thermally stable, exhibiting an NEA. In comparison, the oxygen-terminated c-BN surface, where B2O3 was detected, showed a positive electron affinity of ∼1.2 eV. The B2O3 evidently acts as a negatively charged layer introducing a surface dipole directed into the c-BN. Through the interaction of VO2 with the B2O3 layer, a B-O-V layer structure would contribute a dipole between the O and V layers with the positive side facing vacuum. The lower enthalpy of formation for B2O3 is favorable for the formation of the B-O-V layer structure, which provides a thermally stable surface dipole and an NEA surface
Spectra of quantum KdV Hamiltonians, Langlands duality, and affine opers
Frenkel, Edward
2016-01-01
We prove a system of relations in the Grothendieck ring of the category O of representations of the Borel subalgebra of an untwisted quantum affine algebra U_q(g^) introduced in [HJ]. This system was discovered in [MRV1, MRV2], where it was shown that solutions of this system can be attached to certain affine opers for the Langlands dual affine Kac-Moody algebra of g^, introduced in [FF5]. Together with the results of [BLZ3, BHK], which enable one to associate quantum g^-KdV Hamiltonians to representations from the category O, this provides strong evidence for the conjecture of [FF5] linking the spectra of quantum g^-KdV Hamiltonians and affine opers for the Langlands dual affine algebra. As a bonus, we obtain a direct and uniform proof of the Bethe Ansatz equations for a large class of quantum integrable models associated to arbitrary untwisted quantum affine algebras, under a mild genericity condition.
S\\lawianowski, J J; Martens, A; Go\\lubowska, B; zko, E E Ro\\
2010-01-01
In the present paper we investigate the mechanics of systems of affinely-rigid bodies, i.e., bodies rigid in the sense of affine geometry. Certain physical applications are possible in modelling of molecular crystals, granular media, and other physical objects. Particularly interesting are dynamical models invariant under the group underlying geometry of degrees of freedom. In contrary to the single body case there exist nontrivial potentials invariant under this group (left and right acting). The concept of relative (mutual) deformation tensors of pairs of affine bodies is discussed. Scalar invariants built of such tensors are constructed. There is an essential novelty in comparison to deformation scalars of single affine bodies, i.e., there exist affinely-invariant scalars of mutual deformations. Hence, the hierarchy of interaction models according to their invariance group, from Euclidean to affine ones, can be considered.
APPLICATION OF IMMUNOGLOBULIN-BINDING PROTEINS A, G, L IN THE AFFINITY CHROMATOGRAPHY
Sviatenko, О.; Gorbatiuk, O.; Vasylchenko, О.
2014-01-01
Proteins A, G and L are native or recombinant proteins of microbial origin that bind to mammalian immunoglobulins. Preferably recombinant variants of proteins A, G, L are used in biotechnology for affinity sorbents production. Сomparative characteristics of proteins A, G, L and affinity sorbents on the basis of them, advantages and disadvantages of these proteins application as ligands in the affinity chromatography are done. Analysis of proteins A, G, L properties is presented. Binding speci...
Affine symmetry in mechanics of collective and internal modes. Part I. Classical models
SÅawianowski, J J; SÅawianowska, A; GoÅubowska, B; Martens, A; zko, E E Ro\\; Zawistowski, Z J
2008-01-01
Discussed is a model of collective and internal degrees of freedom with kinematics based on affine group and its subgroups. The main novelty in comparison with the previous attempts of this kind is that it is not only kinematics but also dynamics that is affinely-invariant. The relationship with the dynamics of integrable one-dimensional lattices is discussed. It is shown that affinely-invariant geodetic models may encode the dynamics of something like elastic vibrations.
Is a `hadronic' shear current one of the sources in metric-affine gravity?
Hehl, Friedrich W.; Obukhov, Yuri N.
1997-01-01
The Minkowski space of special relativity can be understood as a flat 4-dimensional affine space enriched by a constant Minkowski metric. If we gauge the general affine group and `superimpose' the metric, then we arrive at the metric-affine theory of gravity (MAG). The gravitational potentials are the spacetime coframe, the metric, and the linear connection. The material energy-momentum is coupled to the coframe (and the metric), a hypothetical hypermomentum current to the connection. The hyp...
The classical origin of quantum affine algebra in squashed sigma models
Kawaguchi, Io; Matsumoto, Takuya; Yoshida, Kentaroh
2012-01-01
We consider a quantum affine algebra realized in two-dimensional non-linear sigma models with target space three-dimensional squashed sphere. Its affine generators are explicitly constructed and the Poisson brackets are computed. The defining relations of quantum affine algebra in the sense of the Drinfeld first realization are satisfied at classical level. The relation to the Drinfeld second realization is also discussed including higher conserved charges. Finally we comment on a semiclassic...
Guo, Haixun; Hathaway, Helen; Royce, Melanie E.; Prossnitz, Eric R.; Miao, Yubin
2013-01-01
Three new DOTA-conjugated GnRH peptides with various hydrocarbon linkers were synthesized to evaluate the influences of the linkers on their receptor binding affinities. The hydrocarbon linker displayed a profound impact on the receptor binding affinities of DOTA-conjugated GnRH peptides. The Aun linker was better than Gaba, Ahx and Aoc linkers in retaining strong receptor binding affinity of the GnRH peptide. DOTA-Aun-(D-Lys6-GnRH) displayed 22.8 nM GnRH receptor binding affinity. 111In-DOTA...
Synthesis and receptor binding affinity of new selective GluR5 ligands
DEFF Research Database (Denmark)
Bunch, L; Johansen, T H; Bräuner-Osborne, Hans;
2001-01-01
Two hybrid analogues of the kainic acid receptor agonists, 2-amino-3-(5-tert-butyl-3-hydroxy-4-isoxazolyl)propionic acid (ATPA) and (2S,4R)-4-methylglutamic acid ((2S,4R)-4-Me-Glu), were designed, synthesized, and characterized in radioligand binding assays using cloned ionotropic and metabotropi.......0 and 2.0 microM. respectively. Their affinities in the [3H]AMPA binding assay on native cortical receptors were shown to correlate with their GluR2 affinity rather than their GluR5 affinity. No affinity for GluR6 was detected (IC50 > 100 microM)....
Indian Academy of Sciences (India)
Namita Mukherjee; Mitashree Mitra; Madan Chakraborty; Partha P. Majumder
2000-08-01
The central Indian state of Madhya Pradesh is home to a large number of tribal populations of diverse linguistic and ethnic backgrounds. With a view to examining how well genomic affinities among tribal populations of this state correspond with their ethnic and linguistic affinities, we analysed DNA samples of individuals drawn from five tribes with diverse, but reasonably well-documented, ethnohistorical and linguistic backgrounds. Each DNA sample was scored at 16 biallelic DNA marker loci. On the basis of these data, genomic affinities among these populations were estimated. We have found an extremely good correspondence between the genomic and ethnolinguistic affinities.
Na+,K+-ATPase Na+ affinity in rat skeletal muscle fiber types
DEFF Research Database (Denmark)
Kristensen, Michael; Juel, Carsten
2010-01-01
Previous studies in expression systems have found different ion activation of the Na(+)/K(+)-ATPase isozymes, which suggest that different muscles have different ion affinities. The rate of ATP hydrolysis was used to quantify Na(+),K(+)-ATPase activity, and the Na(+) affinity of Na(+),K(+)-ATPase......Previous studies in expression systems have found different ion activation of the Na(+)/K(+)-ATPase isozymes, which suggest that different muscles have different ion affinities. The rate of ATP hydrolysis was used to quantify Na(+),K(+)-ATPase activity, and the Na(+) affinity of Na...
DFT study on the effect of exocyclic substituents on the proton affinity of 1-methylimidazole
Energy Technology Data Exchange (ETDEWEB)
Liu, Haining; Bara, Jason E.; Turner, C. Heath, E-mail: hturner@eng.ua.edu
2013-04-18
Highlights: • DFT calculations are used to predict the proton affinity of 1-methylimidazoles. • The electron-withdrawing groups dominate the predicted proton affinity. • The effects of multiple substituents on the proton affinity can be accurately predicted. • Large compound libraries can be screened for imidazoles with tailored reactivity. - Abstract: A deeper understanding of the acid/base properties of imidazole derivatives will aid the development of solvents, polymer membranes and other materials that can be used for CO{sub 2} capture and acid gas removal. In this study, we employ density functional theory calculations to investigate the effect of various electron-donating and electron-withdrawing groups on the proton affinity of 1-methylimidazole. We find that electron-donating groups are able to increase the proton affinity relative to 1-methylimidazole, i.e., making the molecule more basic. In contrast, electron-withdrawing groups cause a decrease of the proton affinity. When multiple substituents are present, their effects on the proton affinity were found to be additive. This finding offers a quick approach for predicting and targeting the proton affinities of this series of molecules, and we show the strong correlation between the calculated proton affinities and experimental pK{sub a} values.
High Affinity Binding of Indium and Ruthenium Ions by Gastrins.
Directory of Open Access Journals (Sweden)
Graham S Baldwin
Full Text Available The peptide hormone gastrin binds two ferric ions with high affinity, and iron binding is essential for the biological activity of non-amidated forms of the hormone. Since gastrins act as growth factors in gastrointestinal cancers, and as peptides labelled with Ga and In isotopes are increasingly used for cancer diagnosis, the ability of gastrins to bind other metal ions was investigated systematically by absorption spectroscopy. The coordination structures of the complexes were characterized by extended X-ray absorption fine structure (EXAFS spectroscopy. Changes in the absorption of gastrin in the presence of increasing concentrations of Ga3+ were fitted by a 2 site model with dissociation constants (Kd of 3.3 x 10-7 and 1.1 x 10-6 M. Although the absorption of gastrin did not change upon the addition of In3+ ions, the changes in absorbance on Fe3+ ion binding in the presence of indium ions were fitted by a 2 site model with Kd values for In3+ of 6.5 x 10-15 and 1.7 x 10-7 M. Similar results were obtained with Ru3+ ions, although the Kd values for Ru3+ of 2.6 x 10-13 and 1.2 x 10-5 M were slightly larger than observed for In3+. The structures determined by EXAFS all had metal:gastrin stoichiometries of 2:1 but, while the metal ions in the Fe, Ga and In complexes were bridged by a carboxylate and an oxygen with a metal-metal separation of 3.0-3.3 Å, the Ru complex clearly demonstrated a short range Ru-Ru separation, which was significantly shorter, at 2.4 Å, indicative of a metal-metal bond. We conclude that gastrin selectively binds two In3+ or Ru3+ ions, and that the affinity of the first site for In3+ or Ru3+ ions is higher than for ferric ions. Some of the metal ion-gastrin complexes may be useful for cancer diagnosis and therapy.
Hemoglobin oxygen affinity in patients with cystic fibrosis.
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Dieter Böning
Full Text Available In patients with cystic fibrosis lung damages cause arterial hypoxia. As a typical compensatory reaction one might expect changes in oxygen affinity of hemoglobin. Therefore position (standard half saturation pressure P50st and slope (Hill's n of the O2 dissociation curve as well as the Bohr coefficients (BC for CO2 and lactic acid were determined in blood of 14 adult patients (8 males, 6 females and 14 healthy controls (6 males, 8 females. While Hill's n amounted to approximately 2.6 in all subjects, P50st was slightly increased by 1 mmHg in both patient groups (controls male 26.7 ± 0.2, controls female 27.0 ± 0.1, patients male 27.7 ± 0.5, patients female 28.0 ± 0.3 mmHg; mean and standard error, overall p<0.01. Main cause was a rise of 1-2 µmol/g hemoglobin in erythrocytic 2,3-biphosphoglycerate concentration. One patient only, clearly identified as an outlier and with the mutation G551D, showed a reduction of both P50st (24.5 mmHg and [2,3-biphosphoglycerate] (9.8 µmol/g hemoglobin. There were no differences in BCCO2, but small sex differences in the BC for lactic acid in the controls which were not detectable in the patients. Causes for the right shift of the O2 dissociation curve might be hypoxic stimulation of erythrocytic glycolysis and an increased red cell turnover both causing increased [2,3-biphosphoglycerate]. However, for situations with additional hypercapnia as observed in exercising patients a left shift seems to be a more favourable adaptation in cystic fibrosis. Additionally when in vivo PO2 values were corrected to the standard conditions they mostly lay left of the in vitro O2 dissociation curve in both patients and controls. This hints to unknown fugitive factors influencing oxygen affinity.
Genetic affinities between endogamous and inbreeding populations of Uttar Pradesh
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Borkar Minal
2007-04-01
Full Text Available Abstract Background India has experienced several waves of migration since the Middle Paleolithic. It is believed that the initial demic movement into India was from Africa along the southern coastal route, approximately 60,000–85,000 years before present (ybp. It has also been reported that there were two other major colonization which included eastward diffusion of Neolithic farmers (Elamo Dravidians from Middle East sometime between 10,000 and 7,000 ybp and a southern dispersal of Indo Europeans from Central Asia 3,000 ybp. Mongol entry during the thirteenth century A.D. as well as some possible minor incursions from South China 50,000 to 60,000 ybp may have also contributed to cultural, linguistic and genetic diversity in India. Therefore, the genetic affinity and relationship of Indians with other world populations and also within India are often contested. In the present study, we have attempted to offer a fresh and immaculate interpretation on the genetic relationships of different North Indian populations with other Indian and world populations. Results We have first genotyped 20 tetra-nucleotide STR markers among 1800 north Indian samples of nine endogamous populations belonging to three different socio-cultural strata. Genetic distances (Nei's DA and Reynold's Fst were calculated among the nine studied populations, Caucasians and East Asians. This analysis was based upon the allelic profile of 20 STR markers to assess the genetic similarity and differences of the north Indian populations. North Indians showed a stronger genetic relationship with the Europeans (DA 0.0341 and Fst 0.0119 as compared to the Asians (DA 0.1694 and Fst – 0.0718. The upper caste Brahmins and Muslims were closest to Caucasians while middle caste populations were closer to Asians. Finally, three phylogenetic assessments based on two different NJ and ML phylogenetic methods and PC plot analysis were carried out using the same panel of 20 STR markers and 20
International Nuclear Information System (INIS)
The effects of brief incubation with carbamylcholine on subsequent binding of [3H]N-methylscopolamine were investigated in mouse neuroblastoma cells (clone N1E-115). This treatment demonstrated that the muscarinic receptors in this neuronal clone can be divided into two types; one which is readily susceptible to regulation by receptor agonists, whereas the other is resistant in this regard. In control cells, both pirenzepine and carbamylcholine interacted with high- and low-affinity subsets of muscarinic receptors. Computer-assisted analysis of the competition between pirenzepine and carbamylcholine with [3H]N-methylscopolamine showed that the receptor sites remaining upon desensitization are composed mainly of pirenzepine low-affinity and agonist high-affinity binding sites. Furthermore, there was an excellent correlation between the ability of various muscarinic receptor agonists to induce a decrease in consequent [3H]N-methylscopolamine binding and their efficacy in stimulating cyclic GMP synthesis in these cells. Thus, only the agonists that are known to recognize the receptor's low-affinity conformation in order to elicit increases in cyclic GMP levels were capable of diminishing ligand binding. Taken together, our present results suggest that the receptor population that is sensitive to regulation by agonists includes both the pirenzepine high-affinity and the agonist low-affinity receptor binding states. In addition, the sensitivity of these receptor subsets to rapid regulation by agonists further implicates their involvement in desensitization of muscarinic receptor-mediated cyclic GMP formation
Surface Plasmon Resonance for Rapid Screening of Uranyl Affine Proteins
International Nuclear Information System (INIS)
A sensitive immunoassay based on SPR analysis was developed to measure uranyl cation (UO22+) affinity for any protein in a free state under physiological conditions. The technique involves immobilization of a specific monoclonal antibody (mAb) raised against UO22+ and 1, 10-phenanthroline-2, 9-dicarboxylic acid (DCP) used as a probe of UO22+ captured by the mAb. Calibration curves were established for accurate determination of UO22+ concentrations with a detection limit of 7 nM. The remaining free UO22+ could be accurately quantified from the different protein-metal equilibrium and a dose-response curve established for KD determination. This generic method was applied not only to proteins such as transferrin and albumin but also to small phosphonated ligands. Its robustness allows the fast UO22+ KD determination of any kind of macromolecules and small ligands using very few amount of compounds, thus opening new prospects in the field of uranium toxicity. (authors)
Experimental Immunization Based on Plasmodium Antigens Isolated by Antibody Affinity
Kamali, Ali N.; Marín-García, Patricia; Azcárate, Isabel G.; Puyet, Antonio; Diez, Amalia; Bautista, José M.
2015-01-01
Vaccines blocking malaria parasites in the blood-stage diminish mortality and morbidity caused by the disease. Here, we isolated antigens from total parasite proteins by antibody affinity chromatography to test an immunization against lethal malaria infection in a murine model. We used the sera of malaria self-resistant ICR mice to lethal Plasmodium yoelii yoelii 17XL for purification of their IgGs which were subsequently employed to isolate blood-stage parasite antigens that were inoculated to immunize BALB/c mice. The presence of specific antibodies in vaccinated mice serum was studied by immunoblot analysis at different days after vaccination and showed an intensive immune response to a wide range of antigens with molecular weight ranging between 22 and 250 kDa. The humoral response allowed delay of the infection after the inoculation to high lethal doses of P. yoelii yoelii 17XL resulting in a partial protection against malaria disease, although final survival was managed in a low proportion of challenged mice. This approach shows the potential to prevent malaria disease with a set of antigens isolated from blood-stage parasites. PMID:26539558
Methods for determining the genetic affinity of microorganisms and viruses
Fox, George E. (Inventor); Willson, III, Richard C. (Inventor); Zhang, Zhengdong (Inventor)
2012-01-01
Selecting which sub-sequences in a database of nucleic acid such as 16S rRNA are highly characteristic of particular groupings of bacteria, microorganisms, fungi, etc. on a substantially phylogenetic tree. Also applicable to viruses comprising viral genomic RNA or DNA. A catalogue of highly characteristic sequences identified by this method is assembled to establish the genetic identity of an unknown organism. The characteristic sequences are used to design nucleic acid hybridization probes that include the characteristic sequence or its complement, or are derived from one or more characteristic sequences. A plurality of these characteristic sequences is used in hybridization to determine the phylogenetic tree position of the organism(s) in a sample. Those target organisms represented in the original sequence database and sufficient characteristic sequences can identify to the species or subspecies level. Oligonucleotide arrays of many probes are especially preferred. A hybridization signal can comprise fluorescence, chemiluminescence, or isotopic labeling, etc.; or sequences in a sample can be detected by direct means, e.g. mass spectrometry. The method's characteristic sequences can also be used to design specific PCR primers. The method uniquely identifies the phylogenetic affinity of an unknown organism without requiring prior knowledge of what is present in the sample. Even if the organism has not been previously encountered, the method still provides useful information about which phylogenetic tree bifurcation nodes encompass the organism.
Displacement affinity chromatography of protein phosphatase one (PP1 complexes
Directory of Open Access Journals (Sweden)
Gourlay Robert
2008-11-01
Full Text Available Abstract Background Protein phosphatase one (PP1 is a ubiquitously expressed, highly conserved protein phosphatase that dephosphorylates target protein serine and threonine residues. PP1 is localized to its site of action by interacting with targeting or regulatory proteins, a majority of which contains a primary docking site referred to as the RVXF/W motif. Results We demonstrate that a peptide based on the RVXF/W motif can effectively displace PP1 bound proteins from PP1 retained on the phosphatase affinity matrix microcystin-Sepharose. Subsequent co-immunoprecipitation experiments confirmed that each identified binding protein was either a direct PP1 interactor or was in a complex that contains PP1. Our results have linked PP1 to numerous new nuclear functions and proteins, including Ki-67, Rif-1, topoisomerase IIα, several nuclear helicases, NUP153 and the TRRAP complex. Conclusion This modification of the microcystin-Sepharose technique offers an effective means of purifying novel PP1 regulatory subunits and associated proteins and provides a simple method to uncover a link between PP1 and additional cellular processes.
High-throughput analysis of protein-DNA binding affinity.
Franco-Zorrilla, José M; Solano, Roberto
2014-01-01
Sequence-specific protein-DNA interactions mediate most regulatory processes underlying gene expression, such as transcriptional regulation by transcription factors (TFs) or chromatin organization. Current knowledge about DNA-binding specificities of TFs is based mostly on low- to medium-throughput methodologies that are time-consuming and often fail to identify DNA motifs recognized by a TF with lower affinity but retaining biological relevance. The use of protein-binding microarrays (PBMs) offers a high-throughput alternative for the identification of protein-DNA specificities. PBM consists in an array of pseudorandomized DNA sequences that are optimized to include all the possible 10- or 11-mer DNA sequences, allowing the determination of binding specificities of most eukaryotic TFs. PBMs that can be synthesized by several manufacturing companies as single-stranded DNA are converted into double-stranded in a simple primer extension reaction. The protein of interest fused to an epitope tag is then incubated onto the PBM, and specific DNA-protein complexes are revealed in a series of immunological reactions coupled to a fluorophore. After scanning and quantifying PBMs, specific DNA motifs recognized by the protein are identified with ready-to-use scripts, generating comprehensive but accessible information about the DNA-binding specificity of the protein. This chapter describes detailed procedures for preparation of double-stranded PBMs, incubation with recombinant protein, and detection of protein-DNA complexes. Finally, we outline some cues for evaluating the biological role of DNA motifs obtained in vitro. PMID:24057393
Surface-modified magnetic colloids for affinity adsorption of immunoglobulins
Energy Technology Data Exchange (ETDEWEB)
Martins, Fernanda [School of Chemical Engineering, State University of Campinas, C.P. 6066, 13083-970 Campinas-SP (Brazil); Pinho, Samantha C. [School of Chemical Engineering, State University of Campinas, C.P. 6066, 13083-970 Campinas-SP (Brazil)], E-mail: samantha@usp.br; Zollner, Terezinha C.A. [School of Chemical Engineering, State University of Campinas, C.P. 6066, 13083-970 Campinas-SP (Brazil); Zollner, Ricardo L. [School of Medical Sciences, State University of Campinas, Campinas-SP (Brazil)], E-mail: zollner@unicamp.br; Cuyper, Marcel de [Interdisciplinary Research Centre, Katholieke Universiteit Leuven-Campus Kortrijk, B-8500 Kortrijk (Belgium)], E-mail: Marcel.DeCuyper@kulak.ac.be; Santana, Maria Helena A. [School of Chemical Engineering, State University of Campinas, C.P. 6066, 13083-970 Campinas-SP (Brazil)], E-mail: lena@feq.unicamp.br
2008-07-15
This work describes the preparation, characterization and in vitro adsorption tests of surface-modified magnetoliposomes for affinity binding of (i) anticardiolipin (isotype G) antibodies and (ii) specific isotype E antibodies generated by hypersensitivity reactions in humans with respiratory allergy. In the first case, cardiolipin embedded in the bilayer of magnetoliposomes was used as specific ligand. In the second case, antigenic proteins present in an extract of Dermatophagoids pteronyssinus and Blomia tropicalis mites were covalently coupled on the surface of magnetoliposomes via a diglycolic spacer arm, and used as specific ligands for IgE. Antibody adsorption was performed in a high-gradient magnetophoresis system, using either sera of healthy individuals or a pool of sera from autoimmune or allergic patients. The selectivity and capacity of the system were quantified by a frontal analysis in a capillary column, and by constructing breakthrough curves. The results show that the highest yield and selectivity were obtained if the ligand was extended into the aqueous layer surrounding the magnetoliposome surface. A 100% selectivity was obtained for adsorption of specific IgE, and 8% for IgG. These results demonstrate the potentialities of both types of surface-modified magnetic biocolloids in the field of in vitro diagnosis tests for allergic or autoimmune conditions.
Surface-modified magnetic colloids for affinity adsorption of immunoglobulins
International Nuclear Information System (INIS)
This work describes the preparation, characterization and in vitro adsorption tests of surface-modified magnetoliposomes for affinity binding of (i) anticardiolipin (isotype G) antibodies and (ii) specific isotype E antibodies generated by hypersensitivity reactions in humans with respiratory allergy. In the first case, cardiolipin embedded in the bilayer of magnetoliposomes was used as specific ligand. In the second case, antigenic proteins present in an extract of Dermatophagoids pteronyssinus and Blomia tropicalis mites were covalently coupled on the surface of magnetoliposomes via a diglycolic spacer arm, and used as specific ligands for IgE. Antibody adsorption was performed in a high-gradient magnetophoresis system, using either sera of healthy individuals or a pool of sera from autoimmune or allergic patients. The selectivity and capacity of the system were quantified by a frontal analysis in a capillary column, and by constructing breakthrough curves. The results show that the highest yield and selectivity were obtained if the ligand was extended into the aqueous layer surrounding the magnetoliposome surface. A 100% selectivity was obtained for adsorption of specific IgE, and 8% for IgG. These results demonstrate the potentialities of both types of surface-modified magnetic biocolloids in the field of in vitro diagnosis tests for allergic or autoimmune conditions
Surface-modified magnetic colloids for affinity adsorption of immunoglobulins
Martins, Fernanda; Pinho, Samantha C.; Zollner, Terezinha C. A.; Zollner, Ricardo L.; de Cuyper, Marcel; Santana, Maria Helena A.
This work describes the preparation, characterization and in vitro adsorption tests of surface-modified magnetoliposomes for affinity binding of (i) anticardiolipin (isotype G) antibodies and (ii) specific isotype E antibodies generated by hypersensitivity reactions in humans with respiratory allergy. In the first case, cardiolipin embedded in the bilayer of magnetoliposomes was used as specific ligand. In the second case, antigenic proteins present in an extract of Dermatophagoids pteronyssinus and Blomia tropicalis mites were covalently coupled on the surface of magnetoliposomes via a diglycolic spacer arm, and used as specific ligands for IgE. Antibody adsorption was performed in a high-gradient magnetophoresis system, using either sera of healthy individuals or a pool of sera from autoimmune or allergic patients. The selectivity and capacity of the system were quantified by a frontal analysis in a capillary column, and by constructing breakthrough curves. The results show that the highest yield and selectivity were obtained if the ligand was extended into the aqueous layer surrounding the magnetoliposome surface. A 100% selectivity was obtained for adsorption of specific IgE, and 8% for IgG. These results demonstrate the potentialities of both types of surface-modified magnetic biocolloids in the field of in vitro diagnosis tests for allergic or autoimmune conditions.
Affinity chromatography of native and irradiated lactate dehydrogenase
International Nuclear Information System (INIS)
LDH V was irradiated in aqueous solution at a concentration of 1mg/ml in the presence of nitrogen or oxygen. The dose given was 1700 Gy. The irradiated enzyme was separated on 5'AMP Sepharose 4B. The NADH-gradient-eluted fraction was then further studied by determinations of activity, protein, and SH-groups. Gel electrophoresis was also performed on some of the samples. It could be shown that radiation-damaged protein was, overall, less firmly specificially bound. Completely inactivated protein was not bound at all and could be eluted with a buffer immediately after spreading. A wide flat peak was shown in activity determinations of NADH-gradient eluted samples. Radiosensitivity was increased by the presence of oxygen. With the aid of SH-group determination, three further peaks could be identified whereby peaks I and II were bound less strongly, and peak III more strongly than native enzyme. These three peaks are thought to represent different modifications of irradiated LDH. A detailed analysis could be the subject of further investigation. The presence of protein fragments was established by electrophoresis for samples irradiated under oxygen but were not found for samples irradiated under nitrogen. Affinity chromatography is an elegant and safe method for establishing the purity of substances from mixtures. It is, however, only of limited value for studying irradiated proteins. (orig.)
Magnetic particles as affinity matrix for purification of antithrombin
Mercês, A. A. D.; Maciel, J. C.; Carvalho Júnior, L. B.
2015-11-01
Immobilization of biomolecules onto insoluble supports is an important tool for the fabrication of a diverse range of functional materials. It provides advantages: enhanced stability and easy separation. In this work two different magnetic composites were synthesized (MAG-PANI-HS and mDAC-HS) to human antithrombin purification. The magnetic particles (MAG) were obtained by co-precipitation method of iron salts II and III and subsequently coated with polyaniline (MAG-PANI particles). Dacron (polyethylene terephthalate) suffered a hydrazinolysis reaction to obtain a powder (Dacron hydrazide) which was subsequently magnetized (mDAC particles) also by co-precipitation method. Heparan sulfate (HS) was immobilized to MAG-PANI and mDAC retained respectively 35μg and 38.6μg per of support. The magnetic composite containing HS immobilized (MAG-PANI-HS and mDAC-HS) was incubated with human blood plasma (1mL) and then washed with NaCl gradients. Electrophoresis of proteins present in eluates showed bands of antithrombin (58kDa). A reduction in the antithrombin activity was detected in plasma that were incubated in the composites magnetic with HS immobilized, suggesting that the antithrombin was removed of the human blood plasma and then purified. Therefore, the above results suggest that both preparations: MAG-PANI-HS and mDAC-HS are able to affinity purify antithrombin, an important component of blood coagulation.
Isomorphism of two realizations of quantum affine algebra Uq(gl(n))
International Nuclear Information System (INIS)
We establish an explicit isomorphism between two realizations of the quantum affine algebra Uq(gl(n)) given previously by Drinfeld and Reshetikhin-Semenov-Tian-Shansky. Our result can be considered as an affine version of the isomorphism between the Drinfield/Jimbo and the Faddeev-Reshetikhin-Takhtajan constructions of the quantum algebra Uq(gl(n)). (orig.)
DEFF Research Database (Denmark)
Domanski, Michal; Molloy, Kelly; Jiang, Hua;
2012-01-01
An efficient and reliable procedure for the capture of affinity-tagged proteins and associated complexes from human cell lines is reported. Through multiple optimizations, high yield and low background affinity-purifications are achieved from modest quantities of human cells expressing endogenous......-level tagged proteins. Isolations of triple-FLAG and GFP-tagged fusion proteins involved in RNA metabolism are presented....
A recurrence relation for characters of highest weight integrable modules for affine Lie algebras
Cook, William J; Li, Haisheng; Misra, Kailash C.
2005-01-01
Using certain results for the vertex operator algebras associated with affine Lie algebras we obtain recurrence relations for the characters of integrable highest weight irreducible modules for an affine Lie algebra. As an application we show that in the simply-laced level 1 case, these recurrence relations give the known characters, whose principal specializations naturally give rise to some multisum Macdonald identities.
A Piecewise Affine Hybrid Systems Approach to Fault Tolerant Satellite Formation Control
DEFF Research Database (Denmark)
Grunnet, Jacob Deleuran; Larsen, Jesper Abildgaard; Bak, Thomas;
2008-01-01
In this paper a procedure for modelling satellite formations including failure dynamics as a piecewise-affine hybrid system is shown. The formulation enables recently developed methods and tools for control and analysis of piecewise-affine systems to be applied leading to synthesis of fault...
Affinity for Quantitative Tools: Undergraduate Marketing Students Moving beyond Quantitative Anxiety
Tarasi, Crina O.; Wilson, J. Holton; Puri, Cheenu; Divine, Richard L.
2013-01-01
Marketing students are known as less likely to have an affinity for the quantitative aspects of the marketing discipline. In this article, we study the reasons why this might be true and develop a parsimonious 20-item scale for measuring quantitative affinity in undergraduate marketing students. The scale was administered to a sample of business…
International Nuclear Information System (INIS)
A new method has been developed for measuring the binding affinity of phage displayed peptides and a target protein using magnetic particles. The specific interaction between the phage displayed peptides and the target protein was subject to a force generated by the magnetic particle. The binding affinity was obtained by analyzing the force-bond lifetime
Relative binding affinity of steroids for the corticosterone receptor system in rat hippocampus
De Kloet, E R; Veldhuis, H D; Wagenaars, J L; Bergink, E W
1984-01-01
In cytosol of the hippocampus corticosterone displays highest affinity for the sites that remain available for binding in the presence of excess RU 26988, which is shown to be a "pure" glucocorticoid. A rather high affinity (greater than or equal to 25%) was found for 11 beta-hydroxyprogesterone, 21
Directory of Open Access Journals (Sweden)
Sarah D. Alison-Youel
2008-11-01
Full Text Available Liquefied gas reaction turbines are subject to the hydraulic affinity laws. Particularly for liquefied hydrocarbon gas-driven turbines, deviations from the affinity laws are encountered. In the case of reaction turbines, where the geometry is fixed, the affinity law relationships between flow, head, and rotational speed are relevant. Field experience confirms that the affinity law relationships are adequate, but that the predictions made also tend to deviate from real turbine performance. Part of the deviations seen may be attributed to the nonideal fluid; however, further examination is warranted. This paper presents an investigation into the affinity law relationships between head, flow, and rotational speed in conjunction with actual turbine performance. The three basic affinity law relationships are combined to form the most general performance equation. This equation subsequently incorporates both the affinity law relationships and the conservation of energy principal. Application of real turbine test data shows that this general performance equation presents a more accurate representation of turbine performance than the affinity law relationships alone.
Affine equivariant rank-weighted L-estimation of multivariate location
Sen, Pranab Kumar; Jureckova, Jana; Picek, Jan
2015-01-01
In the multivariate one-sample location model, we propose a class of flexible robust, affine-equivariant L-estimators of location, for distributions invoking affine-invariance of Mahalanobis distances of individual observations. An involved iteration process for their computation is numerically illustrated.
The Quantum Affine Origin of the AdS/CFT Secret Symmetry
de Leeuw, Marius; Torrielli, Alessandro
2011-01-01
We find a new quantum affine symmetry of the S-matrix of the one-dimensional Hubbard chain. We show that this symmetry originates from the quantum affine superalgebra U_q(gl(2|2)), and in the rational limit exactly reproduces the secret symmetry of the AdS/CFT worldsheet S-matrix.
Structural insights into the affinity of Cel7A carbohydrate-binding module for lignin.
Strobel, Kathryn L; Pfeiffer, Katherine A; Blanch, Harvey W; Clark, Douglas S
2015-09-11
The high cost of hydrolytic enzymes impedes the commercial production of lignocellulosic biofuels. High enzyme loadings are required in part due to their non-productive adsorption to lignin, a major component of biomass. Despite numerous studies documenting cellulase adsorption to lignin, few attempts have been made to engineer enzymes to reduce lignin binding. In this work, we used alanine-scanning mutagenesis to elucidate the structural basis for the lignin affinity of Trichoderma reesei Cel7A carbohydrate binding module (CBM). T. reesei Cel7A CBM mutants were produced with a Talaromyces emersonii Cel7A catalytic domain and screened for their binding to cellulose and lignin. Mutation of aromatic and polar residues on the planar face of the CBM greatly decreased binding to both cellulose and lignin, supporting the hypothesis that the cellulose-binding face is also responsible for lignin affinity. Cellulose and lignin affinity of the 31 mutants were highly correlated, although several mutants displayed selective reductions in lignin or cellulose affinity. Four mutants with increased cellulose selectivity (Q2A, H4A, V18A, and P30A) did not exhibit improved hydrolysis of cellulose in the presence of lignin. Further reduction in lignin affinity while maintaining a high level of cellulose affinity is thus necessary to generate an enzyme with improved hydrolysis capability. This work provides insights into the structural underpinnings of lignin affinity, identifies residues amenable to mutation without compromising cellulose affinity, and informs engineering strategies for family one CBMs. PMID:26209638
Multi-Dimensional Piece-Wise Self-Affine Fractal Interpolation Model
Institute of Scientific and Technical Information of China (English)
ZHANG Tong; ZHUANG Zhuo
2007-01-01
Iterated function system (IFS) models have been used to represent discrete sequences where the attractor of the IFS is piece-wise self-affine in R2 or R3 (R is the set of real numbers). In this paper, the piece-wise self-affine IFS model is extended from R3 to Rn (n is an integer greater than 3), which is called the multi-dimensional piece-wise self-affine fractal interpolation model. This model uses a "mapping partial derivative", and a constrained inverse algorithm to identify the model parameters. The model values depend continuously on all the model parameters, and represent most data which are not multi-dimensional self-affine in Rn. Therefore, the result is very general. The class of functions obtained is much more diverse because their values depend continuously on all of the variables, with all the coefficients of the possible multi-dimensional affine maps determining the functions.
Importance of non-affine viscoelastic response in disordered fibre networks.
Rizzi, L G; Auer, S; Head, D A
2016-05-11
Disordered fibre networks are ubiquitous in nature and have a wide range of industrial applications as novel biomaterials. Predicting their viscoelastic response is straightforward for affine deformations that are uniform over all length scales, but when affinity fails, as has been observed experimentally, modelling becomes challenging. Here we present a numerical methodology, related to an existing framework for amorphous packings, to predict the steady-state viscoelastic spectra and degree of affinity for disordered fibre networks driven at arbitrary frequencies. Applying this method to a peptide gel model reveals a monotonic increase of the shear modulus as the soft, non-affine normal modes are successively suppressed as the driving frequency increases. In addition to being dominated by fibril bending, these low frequency network modes are also shown to be delocalised. The presented methodology provides insights into the importance of non-affinity in the viscoelastic response of peptide gels, and is easily extendible to all types of fibre networks. PMID:27079274
A combinatorial description of the affine Gindikin-Karpelevich formula of type A_n^(1)
Kang, Seok-Jin; Ryu, Hansol; Salisbury, Ben
2012-01-01
The classical Gindikin-Karpelevich formula appears in Langlands' calculation of the constant terms of Eisenstein series on reductive groups and in Macdonald's work on p-adic groups and affine Hecke algebras. The formula has been generalized in the work of Garland to the affine Kac-Moody case, and the affine case has been geometrically constructed in a recent paper of Braverman, Finkelberg, and Kazhdan. On the other hand, there have been efforts to write the formula as a sum over Kashiwara's crystal basis or Lusztig's canonical basis, initiated by Brubaker, Bump, and Friedberg. In this paper, we write the affine Gindikin-Karpelevich formula as a sum over the crystal of generalized Young walls when the underlying Kac-Moody algebra is of affine type A_n^(1). The coefficients of the terms in the sum are determined explicitly by the combinatorial data from Young walls.
Genetic affinities of the central Indian tribal populations.
Directory of Open Access Journals (Sweden)
Gunjan Sharma
Full Text Available BACKGROUND: The central Indian state Madhya Pradesh is often called as 'heart of India' and has always been an important region functioning as a trinexus belt for three major language families (Indo-European, Dravidian and Austroasiatic. There are less detailed genetic studies on the populations inhabited in this region. Therefore, this study is an attempt for extensive characterization of genetic ancestries of three tribal populations, namely; Bharia, Bhil and Sahariya, inhabiting this region using haploid and diploid DNA markers. METHODOLOGY/PRINCIPAL FINDINGS: Mitochondrial DNA analysis showed high diversity, including some of the older sublineages of M haplogroup and prominent R lineages in all the three tribes. Y-chromosomal biallelic markers revealed high frequency of Austroasiatic-specific M95-O2a haplogroup in Bharia and Sahariya, M82-H1a in Bhil and M17-R1a in Bhil and Sahariya. The results obtained by haploid as well as diploid genetic markers revealed strong genetic affinity of Bharia (a Dravidian speaking tribe with the Austroasiatic (Munda group. The gene flow from Austroasiatic group is further confirmed by their Y-STRs haplotype sharing analysis, where we determined their founder haplotype from the North Munda speaking tribe, while, autosomal analysis was largely in concordant with the haploid DNA results. CONCLUSIONS/SIGNIFICANCE: Bhil exhibited largely Indo-European specific ancestry, while Sahariya and Bharia showed admixed genetic package of Indo-European and Austroasiatic populations. Hence, in a landscape like India, linguistic label doesn't unequivocally follow the genetic footprints.
Synthesis and binding affinity of an iodinated juvenile hormone
International Nuclear Information System (INIS)
The synthesis of the first iodinated juvenile hormone (JH) in enantiomerically enriched form is reported. This chiral compound, 12-iodo-JH I, has an iodine atom replacing a methyl group of the natural insect juvenile hormone, JH I, which is important in regulating morphogenesis and reproduction in the Lepidoptera. The unlabeled compound shows approximately 10% of the relative binding affinity for the larval hemolymph JH binding protein (JHBP) of Manduca sexta, which specifically binds natural 3H-10R,11S-JH I (labeled at 58 Ci/mmol) with a KD of 8 X 10(-8) M. It is also approximately one-tenth as biologically active as JH I in the black Manduca and epidermal commitment assays. The 12-hydroxy and 12-oxo compounds are poor competitors and are also biologically inactive. The radioiodinated [125I]12-iodo-JH I can be prepared in low yield at greater than 2500 Ci/mmol by nucleophilic displacement using no-carrier-added 125I-labeled sodium iodide in acetone; however, synthesis using sodium iodide carrier to give the approximately 50 Ci/mmol radioiodinated ligand proceeds in higher radiochemical yield with fewer by-products and provides a radioligand which is more readily handled in binding assays. The KD of [125I]12-iodo-JH I was determined for hemolymph JHBP of three insects: M. sexta, 795 nM; Galleria mellonella, 47 nM; Locusta migratoria, 77 nM. The selectivity of 12-iodo-JH I for the 32-kDa JHBP of M. sexta was demonstrated by direct autoradiography of a native polyacrylamide gel electrophoresis gel of larval hemolymph incubated with the radioiodinated ligand. Thus, the in vitro and in vivo activity of 12-iodo-JH I indicate that it can serve as an important new gamma-emitting probe in the search for JH receptor proteins in target tissues
Binding Affinity and Capacity for the Uremic Toxin Indoxyl Sulfate
Directory of Open Access Journals (Sweden)
Eric Devine
2014-01-01
Full Text Available Protein binding prevents uremic toxins from removal by conventional extracorporeal therapies leading to accumulation in maintenance dialysis patients. Weakening of the protein binding may enhance the dialytic elimination of these toxins. In ultrafiltration and equilibrium dialysis experiments, different measures to modify the plasma binding affinity and capacity were tested: (i, increasing the sodium chloride (NaCl concentration to achieve a higher ionic strength; (ii, increasing the temperature; and (iii, dilution. The effects on the dissociation constant KD and the protein bound fraction of the prototypical uremic toxin indoxyl sulfate (IS in plasma of healthy and uremic individuals were studied. Binding of IS corresponded to one site binding in normal plasma. KD increased linearly with the NaCl concentration between 0.15 (KD = 13.2 ± 3.7 µM and 0.75 M (KD = 56.2 ± 2.0 µM. Plasma dilution further reduced the protein bound toxin fraction by lowering the protein binding capacity of the plasma. Higher temperatures also decreased the protein bound fraction of IS in human plasma. Increasing the NaCl concentration was effective to weaken the binding of IS also in uremic plasma: the protein bound fraction decreased from 89% ± 3% to 81% ± 3% at 0.15 and 0.75 M NaCl, respectively. Dilution and increasing the ionic strength and temperature enhance the free fraction of IS allowing better removal of the substance during dialysis. Applied during clinical dialysis, this may have beneficial effects on the long-term outcome of maintenance dialysis patients.
Differential affinity of mammalian histone H1 somatic subtypes for DNA and chromatin
Directory of Open Access Journals (Sweden)
Mora Xavier
2007-05-01
Full Text Available Abstract Background Histone H1 is involved in the formation and maintenance of chromatin higher order structure. H1 has multiple isoforms; the subtypes differ in timing of expression, extent of phosphorylation and turnover rate. In vertebrates, the amino acid substitution rates differ among subtypes by almost one order of magnitude, suggesting that each subtype might have acquired a unique function. We have devised a competitive assay to estimate the relative binding affinities of histone H1 mammalian somatic subtypes H1a-e and H1° for long chromatin fragments (30–35 nucleosomes in physiological salt (0.14 M NaCl at constant stoichiometry. Results The H1 complement of native chromatin was perturbed by adding an additional amount of one of the subtypes. A certain amount of SAR (scaffold-associated region DNA was present in the mixture to avoid precipitation of chromatin by excess H1. SAR DNA also provided a set of reference relative affinities, which were needed to estimate the relative affinities of the subtypes for chromatin from the distribution of the subtypes between the SAR and the chromatin. The amounts of chromatin, SAR and additional H1 were adjusted so as to keep the stoichiometry of perturbed chromatin similar to that of native chromatin. H1 molecules freely exchanged between the chromatin and SAR binding sites. In conditions of free exchange, H1a was the subtype of lowest affinity, H1b and H1c had intermediate affinities and H1d, H1e and H1° the highest affinities. Subtype affinities for chromatin differed by up to 19-fold. The relative affinities of the subtypes for chromatin were equivalent to those estimated for a SAR DNA fragment and a pUC19 fragment of similar length. Avian H5 had an affinity ~12-fold higher than H1e for both DNA and chromatin. Conclusion H1 subtypes freely exchange in vitro between chromatin binding sites in physiological salt (0.14 M NaCl. The large differences in relative affinity of the H1 subtypes for
Directory of Open Access Journals (Sweden)
Xiakun Chu
2014-08-01
Full Text Available Flexibility in biomolecular recognition is essential and critical for many cellular activities. Flexible recognition often leads to moderate affinity but high specificity, in contradiction with the conventional wisdom that high affinity and high specificity are coupled. Furthermore, quantitative understanding of the role of flexibility in biomolecular recognition is still challenging. Here, we meet the challenge by quantifying the intrinsic biomolecular recognition energy landscapes with and without flexibility through the underlying density of states. We quantified the thermodynamic intrinsic specificity by the topography of the intrinsic binding energy landscape and the kinetic specificity by association rate. We found that the thermodynamic and kinetic specificity are strongly correlated. Furthermore, we found that flexibility decreases binding affinity on one hand, but increases binding specificity on the other hand, and the decreasing or increasing proportion of affinity and specificity are strongly correlated with the degree of flexibility. This shows more (less flexibility leads to weaker (stronger coupling between affinity and specificity. Our work provides a theoretical foundation and quantitative explanation of the previous qualitative studies on the relationship among flexibility, affinity and specificity. In addition, we found that the folding energy landscapes are more funneled with binding, indicating that binding helps folding during the recognition. Finally, we demonstrated that the whole binding-folding energy landscapes can be integrated by the rigid binding and isolated folding energy landscapes under weak flexibility. Our results provide a novel way to quantify the affinity and specificity in flexible biomolecular recognition.
Fridman, Yearit; Gur, Eyal; Fleishman, Sarel J; Aharoni, Amir
2013-02-01
Increasing the affinity of binding proteins is invaluable for basic and applied biological research. Currently, directed protein evolution experiments are the main approach for generating such proteins through the construction and screening of large mutant libraries. Proliferating cell nuclear antigen (PCNA) is an essential hub protein that interacts with many different partners to tightly regulate DNA replication and repair in all eukaryotes. Here, we used computational design to generate human PCNA mutants with enhanced affinity for several different partners. We identified double mutations in PCNA, outside the main partner binding site, that were predicted to increase PCNA-partner binding affinities compared to the wild-type protein by forming additional hydrophobic interactions with conserved residues in the PCNA partners. Affinity increases were experimentally validated with four different PCNA partners, demonstrating that computational design can reveal unexpected regions where affinity enhancements in natural systems are possible. The designed PCNA mutants can be used as a valuable tool for further examination of the regulation of PCNA-partner interactions during DNA replication and repair both in vitro and in vivo. More broadly, the ability to engineer affinity increases toward several PCNA partners suggests that interaction affinity is not an evolutionarily optimized trait of this system. PMID:23011891
Proton Affinity of Isomeric Dipeptides Containing Lysine and Non-Proteinogenic Lysine Homologues.
Batoon, Patrick; Ren, Jianhua
2016-08-18
Conformational effects on the proton affinity of oligopeptides have been studied using six alanine (A)-based acetylated dipeptides containing a basic probe that is placed closest to either the C- or the N-terminus. The basic probe includes Lysine (Lys) and two nonproteinogenic Lys-homologues, ornithine (Orn) and 2,3-diaminopropionic acid (Dap). The proton affinities of the peptides have been determined using the extended Cooks kinetic method in a triple quadrupole mass spectrometer. Computational studies have been carried out to search for the lowest energy conformers and to calculate theoretical proton affinities as well as various molecular properties using the density functional theory. The dipeptides containing a C-terminal probe, ALys, AOrn, and ADap, were determined to have a higher proton affinity by 1-4 kcal/mol than the corresponding dipeptides containing an N-terminal probe, LysA, OrnA, and DapA. For either the C-probe peptides or the N-probe peptides, the proton affinity reduces systematically as the side-chain of the probe residue is shortened. The difference in the proton affinities between isomeric peptides is largely associated with the variation of the conformations. The peptides with higher values of the proton affinity adopt a relatively compact conformation such that the protonated peptides can be stabilized through more efficient internal solvation. PMID:27459294
Energy Technology Data Exchange (ETDEWEB)
Mo, Kai-For; Dai, Ziyu; Wunschel, David S.
2016-05-27
Siderophores are Fe binding secondary metabolites that have been investigated for their uranium binding properties. Much of the previous work has focused on characterizing hydroxamate types of siderophores, such as desferrioxamine B, for their uranyl binding affinity. Carboxylate forms of these metabolites hold potential to be more efficient chelators of uranyl, yet they have not been widely studied and are more difficult to obtain. Desmalonichrome is a carboxylate siderophore which is not commercially available and so was obtained from the ascomycete fungus Fusarium oxysporum cultivated under Fe depleted conditions. The relative affinity for uranyl binding of desmalonichrome was investigated using a competitive analysis of binding affinities between uranyl acetate and different concentrations of iron(III) chloride using electrospray ionization mass spectrometry (ESI-MS). In addition to desmalonichrome, three other siderophores, including two hydroxamates (desferrioxamine B and desferrichrome) and one carboxylate (desferrichrome A) were studied to understand their relative affinities for the uranyl ion at two pH values. The binding affinities of hydroxymate siderophores to uranyl ion were found to decrease to a greater degree at lower pH as the concentration of Fe (III) ion increases. On the other hand, lowering pH has little impact on the binding affinities between carboxylate siderophores and uranyl ion. Desmalonichrome was shown to have the greatest relative affinity for uranyl at any pH and Fe(III) concentration. These results suggest that acidic functional groups in the ligands are critical for strong chelation with uranium at lower pH.
Affinity Induced Surface Functionalization of Liposomes Using Cu-Free Click Chemistry
DEFF Research Database (Denmark)
Bak, Martin; Jølck, Rasmus Irming; Eliasen, Rasmus;
2016-01-01
be used for functionalization of other nanoparticles or solid surfaces. The method exploits a synergistic effect of having both affinity and covalent anchoring tags on the surface of the liposome. This was achieved by synthesizing a peptide linker system that uses Cu-free strain-promoted click...... chemistry in combination with histidine affinity tags. The investigation of post-functionalization of PEGylated liposomes was performed with a cyclic RGDfE peptide. By exploring both affinity and covalent tags a 98 ± 2.0% coupling efficiency was achieved, even a diluted system showed a coupling efficiency...
Li, Peng; He, Tingting; Hu, Xiaohua; Zhao, Junmin; Shen, Xianjun; Zhang, Ming; Wang, Yan
2014-06-01
A novel algorithm based on Connected Affinity Clique Extension (CACE) for mining overlapping functional modules in protein interaction network is proposed in this paper. In this approach, the value of protein connected affinity which is inferred from protein complexes is interpreted as the reliability and possibility of interaction. The protein interaction network is constructed as a weighted graph, and the weight is dependent on the connected affinity coefficient. The experimental results of our CACE in two test data sets show that the CACE can detect the functional modules much more effectively and accurately when compared with other state-of-art algorithms CPM and IPC-MCE. PMID:24803142
Institute of Scientific and Technical Information of China (English)
无
2000-01-01
The synthesis route was investigated and optimized for the preparation of iminodiacetic acid polyethylene glycol (IDA-PEG) for immobilized metal ion affinity partitioning in aqueous two-phaze systems. IDA PEG was synthesized from PEG in two steps by the reaction of iminodiacetic acid with a monosubetituted derivative of epichlorohydrin-activated PEG. The Cu2+ content combined with IDA-PEG was determined by atomic absorp tion spectrometry as 0.5 mol.mol-1 (PEG). Furthermore, the affinity partitioning behavior of lactate dehydrogenase in polyethylene glycol/hydroxypropyl starch aqueous two-phaze systems was studied to clarify the affinity effect of the Cu(Ⅱ)-IDA-PEG.
Hausdorff dimension of boundaries of self-affine tiles in R^n
Veerman, J. J. P.
1997-01-01
We present a new method to calculate the Hausdorff dimension of a certain class of fractals: boundaries of self-affine tiles. Among the interesting aspects are that even if the affine contraction underlying the iterated function system is not conjugated to a similarity we obtain an upper- and lower-bounds for its Hausdorff dimension. In fact, we obtain the exact value for the dimension if the moduli of the eigenvalues of the underlying affine contraction are all equal (this includes Jordan bl...
Canonical factorization of the quotient morphism for an affine $\\mathbb{G}_a$-variety
Freudenburg, Gene
2016-01-01
Working over a ground field of characteristic zero, this paper studies the quotient morphism $\\pi :X\\to Y$ for an affine $\\mathbb{G}_a$-variety $X$ with affine quotient $Y$. We show that the degree modules associated to the $\\mathbb{G}_a$-action give a uniquely determined sequence of dominant $\\mathbb{G}_a$-equivariant morphisms, $X=X_r\\to X_{r-1}\\to\\cdots\\to X_1\\to X_0=Y$, where $X_i$ is an affine variety and $X_{i+1}\\to X_i$ is birational for each $i\\ge 1$. This is the canonical factorizati...
Identification of Thioredoxin Target Disulfides Using Isotope-Coded Affinity Tags
DEFF Research Database (Denmark)
Hägglund, Per; Bunkenborg, Jakob; Maeda, Kenji; Finnie, Christine; Svensson, Birte
extracts is described. The procedure utilizes the isotope-coded affinity tag (ICAT) reagents containing a thiol reactive iodoacetamide group and a biotin affinity tag to target peptides containing reduced cysteine residues. The identification of substrates for Trx and the extent of target disulfide......Thioredoxins (Trx) are small redox proteins that reduce disulfide bonds in various target proteins and maintain cellular thiol redox control. Here, a thiol-specific labeling and affinity enrichment approach for identification and relative quantification of Trx target disulfides in complex protein...
Institute of Scientific and Technical Information of China (English)
无
2002-01-01
B3LYP/6-31+g (d, p) method was used to calculate the lithium and sodium affinities of n-alkyl fluoride. These affinities were found to obey the Holmes relationship, i.e. they correlate linearly with the quotient n/(n+1), where n is the number of carbon atoms in the alkyl chain. From the correlation the limiting values of lithium and sodium affinities for very long alkyl chain were predicted to be -153.3 kJ/mol and -108.4 kJ/mol, respectively.
Dimension theory and fractal constructions based on self-affine carpets
Fraser, Jonathan M.
2013-01-01
The aim of this thesis is to develop the dimension theory of self-affine carpets in several directions. Self-affine carpets are an important class of planar self-affine sets which have received a great deal of attention in the literature on fractal geometry over the last 30 years. These constructions are important for several reasons. In particular, they provide a bridge between the relatively well-understood world of self-similar sets and the far from understood world of general self-affi...
Gini covariance matrix and its affine equivariant version
Weatherall, Lauren Anne
Gini's mean difference (GMD) and its derivatives such as Gini index have been widely used as alternative measures of variability over one century in many research fields especially in finance, economics and social welfare. In this dissertation, we generalize the univariate GMD to the multivariate case and propose a new covariance matrix so called the Gini covariance matrix (GCM). The extension is natural, which is based on the covariance representation of GMD with the notion of multivariate spatial rank function. In order to gain the affine equivariance property for GCM, we utilize the transformation-retransformation (TR) technique and obtain TR version GCM that turns out to be a symmetrized M-functional. Indeed, both GCMs are symmetrized approaches based on the difference of two independent variables without reference of a location, hence avoiding some arbitrary definition of location for non-symmetric distributions. We study the properties of both GCMs. They possess the so-called independence property, which is highly important, for example, in independent component analysis. Influence functions of two GCMs are derived to assess their robustness. They are found to be more robust than the regular covariance matrix but less robust than Tyler and Dumbgen M-functional. Under elliptical distributions, the relationship between the scatter parameter and the two GCM are obtained. With this relationship, principal component analysis (PCA) based on GCM is possible. Estimation of two GCMs is presented. We study asymptotical behavior of the estimators. √n-consistency and asymptotical normality of estimators are established. Asymptotic relative efficiency (ARE) of TR-GCM estimator with respect to sample covariance matrix is compared to that of Tyler and Dumbgen M-estimators. With little loss on efficiency (gains high efficiency for heavy-tailed distributions. Finite sample behavior of Gini estimators is explored under various models using two criteria. As a by-product, a
Development of an aptamer-based affinity purification method for vascular endothelial growth factor
Directory of Open Access Journals (Sweden)
Maren Lönne
2015-12-01
Full Text Available Since aptamers bind their targets with high affinity and specificity, they are promising alternative ligands in protein affinity purification. As aptamers are chemically synthesized oligonucleotides, they can be easily produced in large quantities regarding GMP conditions allowing their application in protein production for therapeutic purposes. Several advantages of aptamers compared to antibodies are described in general within this paper. Here, an aptamer directed against the human Vascular Endothelial Growth Factor (VEGF was used as affinity ligand for establishing a purification platform for VEGF in small scale. The aptamer was covalently immobilized on magnetic beads in a controlled orientation resulting in a functional active affinity matrix. Target binding was optimized by introduction of spacer molecules and variation of aptamer density. Further, salt-induced target elution was demonstrated as well as VEGF purification from a complex protein mixture proving the specificity of protein-aptamer binding.
Classification of curves in 2D and 3D via affine integral signatures
Feng, S; Krim, H
2008-01-01
We propose a robust classification algorithm for curves in 2D and 3D, under the special and full groups of affine transformations. To each plane or spatial curve we assign a plane signature curve. Curves, equivalent under an affine transformation, have the same signature. The signatures introduced in this paper are based on integral invariants, which behave much better on noisy images than classically known differential invariants. The comparison with other types of invariants is given in the introduction. Though the integral invariants for planar curves were known before, the affine integral invariants for spatial curves are proposed here for the first time. Using the inductive variation of the moving frame method we compute affine invariants in terms of Euclidean invariants. We present two types of signatures, the global signature and the local signature. Both signatures are independent of parameterization (curve sampling). The global signature depends on the choice of the initial point and does not allow u...
Synthesis of Tetracycline Analogues and Test of Their Affinity of Synthetic Hydroxyapatite
Institute of Scientific and Technical Information of China (English)
LingLingWENG; GangLIN; 等
2002-01-01
Eight of new 5-oxo[1] benzopyrano [2,3-b] pyridines as the analogues of tetracycline, were designed and synthesized, and their affinity to the hydroxyapatite-the inorganic composition of bone were tested.
Synthesis of Tetracycline Analogues and Test of Their Affinity on Synthetic Hydroxyapatite
Institute of Scientific and Technical Information of China (English)
无
2002-01-01
Eight of new 5-oxo-[1]benzopyrano[2,3-b]pyridines as the analogues of tetracycline, were designed and synthesized, and their affinity to the hydroxyapatite - the inorganic composition of bone were tested.
Deer mouse hemoglobin exhibits a lowered oxygen affinity owing to mobility of the E helix
Inoguchi, Noriko; Oshlo, Jake R.; Natarajan, Chandrasekhar; Weber, Roy E.; Fago, Angela; Storz, Jay F.; Moriyama, Hideaki
2013-01-01
The deer mouse, Peromyscus maniculatus, exhibits altitude-associated variation in hemoglobin oxygen affinity. To examine the structural basis of this functional variation, the structure of the hemoglobin has been solved.
Preparation of Affinity Column Based on Zr{sup 4+} Ion for Phosphoproteins Isolation
Energy Technology Data Exchange (ETDEWEB)
Lee, Seon Mi; Bae, In Ae; Park, Jung Hyen; Kim, Tae Dong; Choi, Seong Ho [Hannam University, Daejeon (Korea, Republic of)
2009-06-15
This paper has described about preparation of Zr{sup 4+} affinity column based on the poly(styreneco- glycidyl methacrylate) prepared by emulsion polymerization of styrene and glycidyl methacrylate in order to isolate phosphopeptide. The Zr{sup 4+} ions were introduced after the phophonation of an epoxy group on polymeric microspheres. The successful preparation of Zr{sup 4+}-immobilized polymeric microsphere stationary phase was confirmed through Fourier transform infrared spectra, optical microscopy, scanning electron microscopy, X-ray photoelectron spectra and inductively coupled plasma-atomic emission spectrometer. The separation efficiency for Zr{sup 4+} affinity column prepared by slurry packing was tested to phosphonated casein and dephosphonated casein. The resolution time (min) of the phosphonated casein was higher than that of dephosphated casein for Zr{sup 4+} affinity polymeric microsphere by liquid chromatography. This Zr{sup 4+} affinity column can be used for isolation of phosphonated casein from casein using liquid chromatography.
Preparation of Affinity Column Based on Zr4+ Ion for Phosphoproteins Isolation
International Nuclear Information System (INIS)
This paper has described about preparation of Zr4+ affinity column based on the poly(styreneco- glycidyl methacrylate) prepared by emulsion polymerization of styrene and glycidyl methacrylate in order to isolate phosphopeptide. The Zr4+ ions were introduced after the phophonation of an epoxy group on polymeric microspheres. The successful preparation of Zr4+-immobilized polymeric microsphere stationary phase was confirmed through Fourier transform infrared spectra, optical microscopy, scanning electron microscopy, X-ray photoelectron spectra and inductively coupled plasma-atomic emission spectrometer. The separation efficiency for Zr4+ affinity column prepared by slurry packing was tested to phosphonated casein and dephosphonated casein. The resolution time (min) of the phosphonated casein was higher than that of dephosphated casein for Zr4+ affinity polymeric microsphere by liquid chromatography. This Zr4+ affinity column can be used for isolation of phosphonated casein from casein using liquid chromatography
Biochemical method for fast affinity diagnosis in grape-vine transplantation
International Nuclear Information System (INIS)
Long term experiments have proved the affinity of cv. Mavroud in transplantations on various root stocks. Best affinity was observed in the combination cv. Mavroud X Riparia tomanteau, followed, in a descending order, by the combinations Mavroud X Mavroud (autotransplantation), Mavroud X Berlandieri X Riparia Kobber SBB and Mavroud X Riparia 33 EM. In view to establish indices for predicting the transplantation affinity a great number of physiological-biochemical and morphological-anatomical studies were carried out. The results obtained showed that a most clearly expressed positive, statistically significant correlation exists between the amount of 15N transported from the root stock to the scions, shoots and leaves. As a result, a biochemical method for fast affinity diagnosis in grape-vine transplantation has been developed. The reliability of the method has been checked up also with other cultivars. Up to the present no such method was known in grape-vine science and practice. (author)
Quantum image encryption based on generalized affine transform and logistic map
Liang, Hao-Ran; Tao, Xiang-Yang; Zhou, Nan-Run
2016-07-01
Quantum circuits of the generalized affine transform are devised based on the novel enhanced quantum representation of digital images. A novel quantum image encryption algorithm combining the generalized affine transform with logistic map is suggested. The gray-level information of the quantum image is encrypted by the XOR operation with a key generator controlled by the logistic map, while the position information of the quantum image is encoded by the generalized affine transform. The encryption keys include the independent control parameters used in the generalized affine transform and the logistic map. Thus, the key space is large enough to frustrate the possible brute-force attack. Numerical simulations and analyses indicate that the proposed algorithm is realizable, robust and has a better performance than its classical counterpart in terms of computational complexity.
Effective Levi-Civita Dilaton theory from Metric Affine Dilaton Gravity
Scipioni, R.
1999-01-01
We show how a Metric Affine theory of Dilaton gravity can be reduced to an effective Riemannian Dilaton gravity model. A simple generalization of the Obukhov-Tucker-Wang theorem to Dilaton gravity is then presented.
Landman, A. D.; Landman, N. N.
1976-01-01
Describes a biochemistry experiment that illustrates the methodology of affinity chromatography by attaching avidin, a glycoprotein in egg white, to a Sepharose matrix in order to bind biotin-containing proteins. (MLH)
On the domain wall partition functions of level-1 affine so(n) vertex models
Dow, A.; Foda, O.
2006-01-01
We derive determinant expressions for domain wall partition functions of level-1 affine so(n) vertex models, n >= 4, at discrete values of the crossing parameter lambda = m pi / 2(n-3), m in Z, in the critical regime.
Institute of Scientific and Technical Information of China (English)
LIUYong-Qiang; WUXi-Rui
1989-01-01
With radioligand binding assays, the receptor binding affmities of mifepristone and lilopristone to the rabbit uterus cytosol progesterone receptor and the rat fiver cytosol glucocorticoid receptor have been measured. The relative binding affinities ( RBA ) of
Quantum image encryption based on generalized affine transform and logistic map
Liang, Hao-Ran; Tao, Xiang-Yang; Zhou, Nan-Run
2016-03-01
Quantum circuits of the generalized affine transform are devised based on the novel enhanced quantum representation of digital images. A novel quantum image encryption algorithm combining the generalized affine transform with logistic map is suggested. The gray-level information of the quantum image is encrypted by the XOR operation with a key generator controlled by the logistic map, while the position information of the quantum image is encoded by the generalized affine transform. The encryption keys include the independent control parameters used in the generalized affine transform and the logistic map. Thus, the key space is large enough to frustrate the possible brute-force attack. Numerical simulations and analyses indicate that the proposed algorithm is realizable, robust and has a better performance than its classical counterpart in terms of computational complexity.
ODE/IM correspondence and Bethe ansatz for affine Toda field equations
Ito, Katsushi
2015-01-01
We study the linear problem associated with modified affine Toda field equation for the Langlands dual $\\hat{\\mathfrak{g}}^\\vee$, where $\\hat{\\mathfrak{g}}$ is an untwisted affine Lie algebra. The connection coefficients for the asymptotic solutions of the linear problem correspond to the Q-functions for $\\mathfrak{g}$-type quantum integrable models. The $\\psi$-system for the solutions associated with the fundamental representations of $\\mathfrak{g}$ leads to Bethe ansatz equations associated with the affine Lie algebra $\\hat{\\mathfrak{g}}$. We also study the $A^{(2)}_{2r}$ affine Toda field equation in massless limit in detail and find its Bethe ansatz equations as well as T-Q relations.
ODE/IM correspondence and Bethe ansatz for affine Toda field equations
Directory of Open Access Journals (Sweden)
Katsushi Ito
2015-07-01
Full Text Available We study the linear problem associated with modified affine Toda field equation for the Langlands dual gˆ∨, where gˆ is an untwisted affine Lie algebra. The connection coefficients for the asymptotic solutions of the linear problem are found to correspond to the Q-functions for g-type quantum integrable models. The ψ-system for the solutions associated with the fundamental representations of g leads to Bethe ansatz equations associated with the affine Lie algebra gˆ. We also study the A2r(2 affine Toda field equation in massless limit in detail and find its Bethe ansatz equations as well as T–Q relations.
sprotocols
2014-01-01
Authors: Romain Legrand, Kuniko Takagi & Sergueï Fetissov ### Abstract Circulating peptide hormones such as ghrelin physiologically bind plasma immunoglobulins (Ig) which protect hormone from degradation and modulate its biological activity depending on affinity of hormone / IgG binding. Because the IgG set of each individual is unique, measuring affinity kinetics of human or animal plasma IgG binding to a specific peptide hormone may provide useful information towards understandi...
Use of Intrinsic Viscosity for evaluation of polymer-solvent affinity
DEFF Research Database (Denmark)
Marani, Debora; Hjelm, Johan; Wandel, Marie
2013-01-01
The objective of the current paper was to define a rheological method for the study of the solvent/binder affinity. The adopted strategy involves the study of the intrinsic viscosity [η] of polymer solutions. [η] was estimated via an extrapolation procedure using the Huggins and Kramer equations....... The intrinsic viscosity and the Mark-Houwink shape parameter were estimated for the three polymers and used as criteria for estimating the polymer/solvent affinity....
Particle Display: A Quantitative Screening Method for Generating High-Affinity Aptamers**
Wang, J.; Gong, Q; N Maheshwari; Eisenstein, M; Arcila, ML; Kosik, KS; Soh, HT
2014-01-01
We report an aptamer discovery technology that reproducibly yields higher affinity aptamers in fewer rounds compared to conventional selection. Our method (termed particle display) transforms libraries of solution-phase aptamers into "aptamer particles", each displaying many copies of a single sequence on its surface. We then use fluorescence-activated cell sorting (FACS) to individually measure the relative affinities of >108 aptamer particles and sort them in a high-throughput manner. Throu...
Brian H. Carrick; Linxuan Hao; Smaldino, Philip J.; Engelke, David R.
2016-01-01
Isolation of endogenous proteins from Saccharomyces cerevisiae has been facilitated by inserting encoding polypeptide affinity tags at the C-termini of chromosomal open reading frames (ORFs) using homologous recombination of DNA fragments. Tagged protein isolation is limited by a number of factors, including high cost of affinity resins for bulk isolation and low concentration of ligands on the resin surface, leading to low isolation efficiencies and trapping of contaminants. To address this,...
Seeger, N.J.; Rodrigues, P.J.M.; Ignatieva, K.
2015-01-01
This paper investigates several crucial issues that arise when modeling equity returns with stochastic variance. (i) Does the model need to include jumps even when using a nonaffine variance specification? We find that jump models clearly outperform pure stochastic volatility models. (ii) How do affine variance specifications perform when compared to nonaffine models in a jump diffusion setup? We find that nonaffine specifications outperform affine models, even after including jumps.
Blind prediction of host-guest binding affinities: A new SAMPL3 challenge
Muddana, Hari S.; Varnado, C. Daniel; Bielawski, Christopher W.; Urbach, Adam R.; Isaacs, Lyle; Geballe, Matthew T; Gilson, Michael K.
2012-01-01
The computational prediction of protein-ligand binding affinities is of central interest in early-stage drug-discovery, and there is a widely recognized need for improved methods. Low molecular weight receptors and their ligands—i.e. host-guest systems – represent valuable test-beds for such affinity prediction methods, because their small size makes for fast calculations and relatively facile numerical convergence. The SAMPL3 community exercise included the first ever blind prediction challe...
Calculation of Host-Guest Binding Affinities Using a Quantum-Mechanical Energy Model
Muddana, Hari S.; Gilson, Michael K.
2012-01-01
The prediction of protein-ligand binding affinities is of central interest in computer-aided drug discovery, but it is still difficult to achieve a high degree of accuracy. Recent studies suggesting that available force fields may be a key source of error motivate the present study, which reports the first mining minima (M2) binding affinity calculations based on a quantum mechanical energy model, rather than an empirical force field. We apply a semi-empirical quantum-mechanical energy functi...
Single Bead Affinity Detection (SINBAD) for the Analysis of Protein-Protein Interactions
Schulte, Roberta; Talamas, Jessica; Doucet, Christine; Hetzer, Martin W.
2008-01-01
We present a miniaturized pull-down method for the detection of protein-protein interactions using standard affinity chromatography reagents. Binding events between different proteins, which are color-coded with quantum dots (QDs), are visualized on single affinity chromatography beads by fluorescence microscopy. The use of QDs for single molecule detection allows the simultaneous analysis of multiple protein-protein binding events and reduces the amount of time and material needed to perform...
An Analysis of a Transport System Using Non-Affine Transformations
Directory of Open Access Journals (Sweden)
Péter Ficzer
2011-09-01
Full Text Available The authors investigated the transformation possibilities and particularly the usage of non-affine transformations of maps in order to analyse the current status and development possibilities of the Hungarian railway system. In the introduction, the authors overview the theoretical background of map transformations and then present the detailed description of the non-parameter affine transformations and their applicability to the evaluation of railway networks.
DEFF Research Database (Denmark)
Østergaard, Jesper; Jensen, Henrik; Holm, Rene
2012-01-01
influence on the ionic strength of the background electrolyte when the cyclodextrin is used in capillary electrophoresis. Mobility-shift affinity capillary methods for investigation of the complexation of taurocholate and taurochenodeoxycholate with the negatively charged cyclodextrin derivative applying...... constant power and ionic strength conditions as well as constant voltage and varying ionic strength were investigated. A new approach for the correction of background electrolyte ionic strength was developed. Mobility-shift affinity capillary electrophoresis experiments obtained at constant voltage and...
Tame Fréchet structures for affine Kac-Moody groups
Freyn, Walter
2014-01-01
We construct holomorphic loop groups and their associated affine Kac-Moody groups and prove that they are tame Fréchet manifolds; furthermore we study the adjoint action of these groups. These results form the functional analytic core for a theory of affine Kac-Moody symmetric spaces, that will be developed in forthcoming papers. Our construction also solves the problem of complexification of completed Kac-Moody groups: we obtain a description of complex completed Kac-Moody groups and, ...
Recruiting abroad: The role of foreign affinity and labour market scarcity
Bossler, Mario
2013-01-01
"I study the recruiting behaviour of German establishments with regard to the use of foreign labour markets. Applying instrumental variable strategies, I find foreign affinity and labour market scarcity to stimulate the use of foreign markets. Regional labour market scarcity is particularly relevant to small firms, and the effect of foreign affinity is largely driven by the share of foreigners in leading positions in large establishments. The results indicate that shortages are functional and...
Protein-ligand binding affinities from large-scale quantum mechanical simulations
Fox, Stephen J.
2012-01-01
The accurate prediction of protein-drug binding affinities is a major aim of computational drug optimisation and development. A quantitative measure of binding affinity is provided by the free energy of binding, and such calculations typically require extensive configurational sampling of entities such as proteins with thousands of atoms. Current binding free energy methods use force fields to perform the configurational sampling and to compute interaction energies. Due to the empirical natur...
Vergis, James M.; Michael C. Wiener
2011-01-01
Recombinant proteins typically include one or more affinity tags to facilitate purification and/or detection. Expression constructs with affinity tags often include an engineered protease site for tag removal. Like other enzymes, the activities of proteases can be affected by buffer conditions. The buffers used for integral membrane proteins contain detergents, which are required to maintain protein solubility. We examined the detergent sensitivity of six commonly-used proteases (Enterokinase...
The Protein-Protein Interface Evolution Acts in a Similar Way to Antibody Affinity Maturation*
Li, Bohua; Zhao, Lei; Wang, Chong; Guo, Huaizu; Wu, Lan; Zhang, Xunming; Qian, Weizhu; Wang, Hao; Guo, Yajun
2009-01-01
Understanding the evolutionary mechanism that acts at the interfaces of protein-protein complexes is a fundamental issue with high interest for delineating the macromolecular complexes and networks responsible for regulation and complexity in biological systems. To investigate whether the evolution of protein-protein interface acts in a similar way as antibody affinity maturation, we incorporated evolutionary information derived from antibody affinity maturation with common simulation techniq...
Algorithm for prediction of tumour suppressor p53 affinity for binding sites in DNA
Veprintsev, Dmitry B.; Fersht, Alan R.
2008-01-01
The tumour suppressor p53 is a transcription factor that binds DNA in the vicinity of the genes it controls. The affinity of p53 for specific binding sites relative to other DNA sequences is an inherent driving force for specificity, all other things being equal. We measured the binding affinities of systematically mutated consensus p53 DNA-binding sequences using automated fluorescence anisotropy titrations. Based on measurements of the effects of every possible single base-pair substitution...
No isomorphism between the affine $\\hat sl(2)$ algebra and the N=2 superconformal algebras
Gato-Rivera, Beatriz
2008-01-01
Since 1999 it became obvious that the would be `isomorphism' between the affine $\\hat sl(2)$ algebra and the N=2 superconformal algebras, proposed by some authors, simply does not work. However, this issue was never properly discussed in the literature and, as a result, some confusion still remains. In this article we finally settle down, clearly and unambiguously, the true facts: there is no isomorphism between the affine $\\hat sl(2)$ algebra and the N=2 superconformal algebras.
Hage, David S.; Anguizola, Jeanethe A.; Bi, Cong; Li, Rong; Matsuda, Ryan; Papastavros, Efthimia; Pfaunmiller, Erika; Vargas, John; Zheng, Xiwei
2012-01-01
Affinity chromatography is a separation technique that has become increasingly important in work with biological samples and pharmaceutical agents. This method is based on the use of a biologically-related agent as a stationary phase to selectively retain analytes or to study biological interactions. This review discusses the basic principles behind affinity chromatography and examines recent developments that have occurred in the use of this method for biomedical and pharmaceutical analysis....
Affinity profiles of hexahydro-sila-difenidol analogues at muscarinic receptor subtypes
Lambrecht, G.; Feifel, R.; Wagner-Röder, M.; Strohmann, C.; Zilch, H.; Tacke, Reinhold; Waelbroeck, M.; Christophe, J; Boddeke, H.; Mutschler, E.
2012-01-01
In an attempt to assess the structural requirements of hexahydro-sila-difenidol for potency and selectivity, a series of analogues modified in the amino group and the phenyl ring were investigated for their affinity to muscarinic M1- (rabbit vas deferens), Mr (guinea-pig atria) and Mr (guinea-pig ileum) receptors. All compounds were competitive antagonists in the three tissues. Their affinities to the three muscarinic receptor subtypes differed by more than two orders of magnitude and the obs...
Binding energies and electron affinities of small silicon clusters (n=2--5)
International Nuclear Information System (INIS)
The Gaussian-2 (G2) theoretical procedure, based on ab initio molecular orbital theory, is used to calculate the energies of Sin and Si-n (n=1--5) clusters. The G2 energies are used to derive accurate binding energies and electron affinities of these clusters. The calculated electron affinities of Si2--Si4 are in agreement to within 0.1 eV with results from recent photoelectron spectroscopic measurements
Separation and Purification of Thrombin-like Enzymes by Affinity Adsorbents
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
An affinity adsorbent, benzamidineSepharose 4B, was used to separate and purify thrombinlike enzymes. The paminobenzamidine as a specific ligand was coupled to the matrix-Sepharose 4B. The recombinant thrombinlike enzyme-defibrase was used as a model in order to evaluate the efficiency of this biospecific affinity adsorbent. The homogeneity of the enzyme preparation was comfirmed as one band on sodium dodecyl sulfatepolyacrylamide gel electrophoresis.
Affine Transformations of Loop Nests for Parallel Execution and Distribution of Data over Processors
Adutskevich, E. V.; Bakhanovich, S. V.; Likhoded, N. A.
2006-01-01
The paper is devoted to the problem of mapping affine loop nests onto distributed memory parallel computers. A method to find affine transformations of loop nests for parallel execution and distribution of data over processors is presented. The method tends to minimize the number of communications between processors and to improve locality of data within one processor. A problem of determination of data exchange sequence is investigated. Conditions to determine the ability to arrange broadcas...
Isotope-coded ATP Probe for Quantitative Affinity Profiling of ATP-binding Proteins
Xiao, Yongsheng; Guo, Lei; Wang, Yinsheng
2013-01-01
ATP-binding proteins play significant roles in numerous cellular processes. Here, we introduced a novel isotope-coded ATP-affinity probe (ICAP) as acylating agent to simultaneously enrich and incorporate isotope label to ATP-binding proteins. By taking advantage of the quantitative capability of this isotope-coded probe, we devised an affinity profiling strategy to comprehensively characterize ATP-protein interactions at the entire proteome scale. False-positive identification of ATP-binding ...
Synthetic Polymer Nanoparticles with Antibody-Like Affinity for a Hydrophilic Peptide
Zeng, Zhiyang; Hoshino, Yu; Rodriguez, Andy; Yoo, Hoseong; Shea, Kenneth J
2010-01-01
Synthetic polymer nanoparticles with antibody-like affinity for a hydrophilic peptide have been prepared by inverse microemulsion polymerization. Peptide affinity was achieved in part by incorporating the target (imprint) peptide in the polymerization reaction mixture. Incorporation of the imprint peptide assists in the creation of complementary binding sites in the resulting polymer nanoparticle (NP). To orient the imprint peptide at the interface of the water and oil domains during polymeri...
Preparation of Chitosan-coated Nylon Membranes and their Application as Affinity Membranes
Institute of Scientific and Technical Information of China (English)
Wei SHI; Feng Bao ZHANG; Guo Liang ZHANG
2005-01-01
Chitosan-coated nylon membranes which possess a large number of reactive groups of-CH2OH and -NH2 were prepared by coupling chitosan onto the nylon membrane. Then polylysine as ligand was also immobilized onto the composite membranes by 1, l′-carbonyldiimidazole activation to prepare affinity membranes for bilirubin adsorption. The results showed that these membranes exhibited high binding affinity capacities for bilirubin and the adsorption isotherm fitted the Freundlich model well.
Ikegami Toru; Yanagishita Hiroshi; Nakane Takashi; Im Jae Hong; Kitamoto Dai
2001-01-01
Abstract Background There have been many attempts to develop new materials with stability and high affinity towards immunoglobulins. Some of glycolipids such as gangliosides exhibit a high affinity toward immunoglobulins. However, it is considerably difficult to develop these glycolipids into the practical separation ligand due to their limited amounts. We thus focused our attention on the feasible use of "mannosylerythritol lipid A", a yeast glycolipid biosurfactant, as an alternative ligand...
Assessment of Solvated Interaction Energy Function for Ranking Antibody-Antigen Binding Affinities.
Sulea, Traian; Vivcharuk, Victor; Corbeil, Christopher R; Deprez, Christophe; Purisima, Enrico O
2016-07-25
Affinity modulation of antibodies and antibody fragments of therapeutic value is often required in order to improve their clinical efficacies. Virtual affinity maturation has the potential to quickly focus on the critical hotspot residues without the combinatorial explosion problem of conventional display and library approaches. However, this requires a binding affinity scoring function that is capable of ranking single-point mutations of a starting antibody. We focus here on assessing the solvated interaction energy (SIE) function that was originally developed for and is widely applied to scoring of protein-ligand binding affinities. To this end, we assembled a structure-function data set called Single-Point Mutant Antibody Binding (SiPMAB) comprising several antibody-antigen systems suitable for this assessment, i.e., based on high-resolution crystal structures for the parent antibodies and coupled with high-quality binding affinity measurements for sets of single-point antibody mutants in each system. Using this data set, we tested the SIE function with several mutation protocols based on the popular methods SCWRL, Rosetta, and FoldX. We found that the SIE function coupled with a protocol limited to sampling only the mutated side chain can reasonably predict relative binding affinities with a Spearman rank-order correlation coefficient of about 0.6, outperforming more aggressive sampling protocols. Importantly, this performance is maintained for each of the seven system-specific component subsets as well as for other relevant subsets including non-alanine and charge-altering mutations. The transferability and enrichment in affinity-improving mutants can be further enhanced using consensus ranking over multiple methods, including the SIE, Talaris, and FOLDEF energy functions. The knowledge gained from this study can lead to successful prospective applications of virtual affinity maturation. PMID:27367467
Role of the T cell receptor ligand affinity in T cell activation by bacterial superantigens
DEFF Research Database (Denmark)
Andersen, P S; Geisler, C; Buus, S; Mariuzza, R A; Karjalainen, K
2001-01-01
the SEC3 variants correlated with enhanced binding without any optimum in the binding range covered by native TCR ligands. Comparable studies using anti-TCR antibodies of known affinity confirmed these observations. By comparing the biological potency of the two sets of ligands, we found a significant...... correlation between ligand affinity and ligand potency indicating that it is the density of receptor-ligand complexes in the T cell contact area that determines TCR signaling strength....
Measuring the sequence-affinity landscape of antibodies with massively parallel titration curves
Adams, Rhys M.; Kinney, Justin B.; Mora, Thierry; Walczak, Aleksandra M.
2016-01-01
Despite the central role that antibodies play in the adaptive immune system and in biotechnology, much remains unknown about the quantitative relationship between an antibody's amino acid sequence and its antigen binding affinity. Here we describe a new experimental approach, called Tite-Seq, that is capable of measuring binding titration curves and corresponding affinities for thousands of variant antibodies in parallel. The measurement of titration curves eliminates the confounding effects ...
Cyclization strategies of meditopes: affinity and diffraction studies of meditope–Fab complexes
Energy Technology Data Exchange (ETDEWEB)
Bzymek, Krzysztof P.; Ma, Yuelong; Avery, Kendra A.; Horne, David A.; Williams, John C., E-mail: jcwilliams@coh.org [Beckman Research Institute of City of Hope, 1710 Flower Street, Duarte, CA 91010 (United States)
2016-05-23
An overview of cyclization strategies of a Fab-binding peptide to maximize affinity. Recently, a unique binding site for a cyclic 12-residue peptide was discovered within a cavity formed by the light and heavy chains of the cetuximab Fab domain. In order to better understand the interactions that drive this unique complex, a number of variants including the residues within the meditope peptide and the antibody, as well as the cyclization region of the meditope peptide, were created. Here, multiple crystal structures of meditope peptides incorporating different cyclization strategies bound to the central cavity of the cetuximab Fab domain are presented. The affinity of each cyclic derivative for the Fab was determined by surface plasmon resonance and correlated to structural differences. Overall, it was observed that the disulfide bond used to cyclize the peptide favorably packs against a hydrophobic ‘pocket’ and that amidation and acetylation of the original disulfide meditope increased the overall affinity ∼2.3-fold. Conversely, replacing the terminal cysteines with serines and thus creating a linear peptide reduced the affinity over 50-fold, with much of this difference being reflected in a decrease in the on-rate. Other cyclization methods, including the formation of a lactam, reduced the affinity but not to the extent of the linear peptide. Collectively, the structural and kinetic data presented here indicate that small perturbations introduced by different cyclization strategies can significantly affect the affinity of the meditope–Fab complex.
Only high-affinity receptors for interleukin 2 mediate internalization of ligand
International Nuclear Information System (INIS)
Interleukin 2 (IL-2) receptors are expressed on activated T cells and in select T-cell leukemias. Recently, it has been demonstrated that at least two classes of receptor for IL-2 exist with markedly different affinities for ligand. All known biological actions of IL-2 have been correlated with occupancy of high-affinity sites; the function of the low-affinity sites remains unknown. Receptor-mediated endocytosis is the primary means of internalization of cell-surface receptors and their ligands. The internalization of IL-2 bound to high- and low-affinity receptor sites was studied in a human T-cell lymphotrophic virus type 1 (HTLV-1)-infected human T-cell leukemia cell line and in a cloned murine cytotoxic T-cell line (CTLL). Internalization of IL-2 occurred only when bound to high-affinity sites. In addition, an anti-receptor antibody (anti-Tac), which binds equally well to high- and low-affinity sites, demonstrated no detectable internalization. The implications of these findings as they relate to IL-2 receptor structure and function are discussed
Binding affinities of anti-acetylcholine receptor autoantibodies in myasthenia gravis
International Nuclear Information System (INIS)
Antibodies directed against acetylcholine (ACh) receptors are present in the sera of nearly 90% of patients with myasthenia gravis (MG), and are involved in the pathogenesis of this autoimmune disease. However, the antibody titers measured by the standard radioimmunoassay correspond poorly with the clinical severity of the disease. To determine whether this disparity could be accounted for by differences in the binding affinities of anti-ACh receptor antibodies in different patients, we have measured the binding affinities of these autoantibodies in 15 sera from MG patients. The affinity constants (K/sub o/), as determined by Scatchard analysis, were all in the range of 1010 M-1, comparable to the highest values reported in immunized animals. The affinity constants were truly representative of the population of autoantibodies detected by the radioimmunoassay, as shown by the remarkable linearity of the Scatchard plots (r2>0.90) and the close correlation between the antibody titers determined by extrapolation of the Scatchard plots and by saturation analysis (r = 0.99; p < 0.001). There was only a 6-fold variation in affinity constants measured in this series of patients despite widely differing antibody titers and severity of the disease. Factors other than the titer and affinity of anti-ACh receptor antibodies may correlate better with the clinical manifestations of MG
Binding affinities of anti-acetylcholine receptor autoantibodies in myasthenia gravis
Energy Technology Data Exchange (ETDEWEB)
Bray, J.J.; Drachman, D.B.
1982-01-01
Antibodies directed against acetylcholine (ACh) receptors are present in the sera of nearly 90% of patients with myasthenia gravis (MG), and are involved in the pathogenesis of this autoimmune disease. However, the antibody titers measured by the standard radioimmunoassay correspond poorly with the clinical severity of the disease. To determine whether this disparity could be accounted for by differences in the binding affinities of anti-ACh receptor antibodies in different patients, we have measured the binding affinities of these autoantibodies in 15 sera from MG patients. The affinity constants (K/sub o/), as determined by Scatchard analysis, were all in the range of 10/sup 10/ M/sup -1/, comparable to the highest values reported in immunized animals. The affinity constants were truly representative of the population of autoantibodies detected by the radioimmunoassay, as shown by the remarkable linearity of the Scatchard plots (r/sup 2/>0.90) and the close correlation between the antibody titers determined by extrapolation of the Scatchard plots and by saturation analysis (r = 0.99; p < 0.001). There was only a 6-fold variation in affinity constants measured in this series of patients despite widely differing antibody titers and severity of the disease. Factors other than the titer and affinity of anti-ACh receptor antibodies may correlate better with the clinical manifestations of MG.
Food and value motivation: Linking consumer affinities to different types of food products.
de Boer, Joop; Schösler, Hanna
2016-08-01
This study uses the consumer affinity concept to examine the multiple motives that may shape consumers' relationships with food. The concept was applied in a study on four broad product types in the Netherlands, which cover a wide range of the market and may each appeal to consumers with different affinities towards foods. These product types may be denoted as 'conventional', 'efficient', 'gourmet' and 'pure'. A comparative analysis, based on Higgins' Regulatory Focus Theory, was performed to examine whether food-related value motivations could explain different consumer affinities for these product types. The affinities of consumers were measured by means of a non-verbal, visual presentation of four samples of food products in a nationwide survey (n = 742) among consumers who were all involved in food purchasing and/or cooking. The affinities found could be predicted fairly well from a number of self-descriptions relating to food and eating, which expressed different combinations of type of value motivation and involvement with food. The analysis demonstrated the contrasting role of high and low involvement as well as the potential complementarity of promotion- and prevention-focused value motivation. It is suggested that knowledge of the relationships between product types, consumer affinities and value motivation can help improve the effectiveness of interventions that seek to promote healthy and sustainable diets in developed countries. PMID:27046434
DEFF Research Database (Denmark)
Rosenberg, Martin; Ottosson, Henrik; Kilså, Kristine
2010-01-01
aromatic and those with 4n+2 pi-electrons are antiaromatic, opposite to Huckel's rule for aromaticity in S(0). Our hypothesis is now that the relative magnitudes of proton and hydride affinities of annulenyl anions and cations reverts systematically as one goes from S(0) to T(1) as a result of the opposite...
Mo, Kai-For; Dai, Ziyu; Wunschel, David S
2016-06-24
Siderophores are iron (Fe)-binding secondary metabolites that have been investigated for their uranium-binding properties. Previous work has focused on characterizing hydroxamate types of siderophores, such as desferrioxamine B, for their uranyl (UO2)-binding affinity. Carboxylate forms of these metabolites hold potential to be more efficient chelators of UO2, yet they have not been widely studied. Desmalonichrome is a carboxylate siderophore that is not commercially available and so was obtained from the fungus Fusarium oxysporum cultivated under Fe-depleted conditions. The relative affinity for UO2 binding of desmalonichrome was investigated using a competitive analysis of binding affinities between UO2 acetate and different concentrations of Fe(III) chloride using electrospray ionization mass spectrometry. In addition to desmalonichrome, three other siderophores, including two hydroxamates (desferrioxamine B and desferrichrome) and one carboxylate (desferrichrome A), were studied to understand their relative affinities for the UO2(2+) ion at two pH values. The binding affinities of hydroxamate siderophores to UO2(2+) ions were observed to decrease with increasing Fe(III)Cl3 concentration at the lower pH. On the other hand, decreasing the pH has a smaller impact on the binding affinities between carboxylate siderophores and the UO2(2+) ion. Desmalonichrome in particular was shown to have the greatest relative affinity for UO2 at all pH and Fe(III) concentrations examined. These results suggest that acidic functional groups in the ligands are important for strong chelation with UO2 at lower pH. PMID:27232848
Rational development of high-affinity T-cell receptor-like antibodies.
Stewart-Jones, Guillaume; Wadle, Andreas; Hombach, Anja; Shenderov, Eugene; Held, Gerhard; Fischer, Eliane; Kleber, Sascha; Nuber, Natko; Stenner-Liewen, Frank; Bauer, Stefan; McMichael, Andrew; Knuth, Alexander; Abken, Hinrich; Hombach, Andreas A; Cerundolo, Vincenzo; Jones, E Yvonne; Renner, Christoph
2009-04-01
T-cell interaction with a target cell is a key event in the adaptive immune response and primarily driven by T-cell receptor (TCR) recognition of peptide-MHC (pMHC) complexes. TCR avidity for a given pMHC is determined by number of MHC molecules, availability of coreceptors, and TCR affinity for MHC or peptide, respectively, with peptide recognition being the most important factor to confer target specificity. Here we present high-resolution crystal structures of 2 Fab antibodies in complex with the immunodominant NY-ESO-1(157-165) peptide analogue (SLLMWITQV) presented by HLA-A*0201 and compare them with a TCR recognizing the same pMHC. Binding to the central methionine-tryptophan peptide motif and orientation of binding were almost identical for Fabs and TCR. As the MW "peg" dominates the contacts between Fab and peptide, we estimated the contributions of individual amino acids between the Fab and peptide to provide the rational basis for a peptide-focused second-generation, high-affinity antibody library. The final Fab candidate achieved better peptide binding by 2 light-chain mutations, giving a 20-fold affinity improvement to 2-4 nM, exceeding the affinity of the TCR by 1,000-fold. The high-affinity Fab when grafted as recombinant TCR on T cells conferred specific killing of HLA-A*0201/NY-ESO-1(157-165) target cells. In summary, we prove that affinity maturation of antibodies mimicking a TCR is possible and provide a strategy for engineering high-affinity antibodies that can be used in targeting specific pMHC complexes for diagnostic and therapeutic purposes. PMID:19307587
Bishop, S A; Bailey, M; Lucke, V M; Stokes, C R
1992-07-01
An experimental model of proliferative glomerulonephritis (GN) in the cat, which closely resembles human proliferative forms of GN, has been used to study the role of antibody and antibody affinity in the development of immune complex-mediated renal disease. The serum IgG and IgM antibody response to antigen, average antibody affinity (avidity) and affinity heterogeneity of the IgG and IgM populations was assessed at varying times after commencement of chronic immunization with the antigen, human serum albumin (HSA), by enzyme immunoassay. Cats could be classified according to whether they were "low", "intermediate" or "high" IgG responders, by quantification of serum IgG values. Cats with the lowest serum IgG values failed to develop glomerulonephritis. However, there was no relationship between actual IgG values and the severity of the induced disease. In contrast to IgG, there was no division of cats into low or high IgM anti-HSA responders. Again, cats with the lowest IgM values failed to develop GN, but, more interestingly, a late, marked increase in serum IgM anti-HSA occurred only in cats that developed clinical signs of GN (anterior uveitis and nephrotic syndrome). Maturation of average, functional IgG affinity (avidity) for HSA following chronic immunization was clearly demonstrated for all cats. At the end of the experiment, all cats had IgG of high affinity for HSA and the average affinity heterogeneity of the IgG populations was less than in measurements taken earlier. Values of IgG affinity at the end of the experiment were very similar both in cats which developed GN and in those which remained clinically, biochemically and pathologically normal. In contrast to IgG antibody, some cats developed IgM of increased affinity, whilst others produced antibody of reduced affinity, following chronic immunization. There was no correlation between the development of disease and the production of either low or high affinity IgM antibody. Data indicated that an
O'Brien, Jeffrey; Shea, Kenneth J
2016-06-21
Nanomaterials, when introduced into a complex, protein-rich environment, rapidly acquire a protein corona. The type and amount of proteins that constitute the corona depend significantly on the synthetic identity of the nanomaterial. For example, hydrogel nanoparticles (NPs) such as poly(N-isopropylacrylamide) (NIPAm) have little affinity for plasma proteins; in contrast, carboxylated poly(styrene) NPs acquire a dense protein corona. This range of protein adsorption suggests that the protein corona might be "tuned" by controlling the chemical composition of the NP. In this Account, we demonstrate that small libraries of synthetic polymer NPs incorporating a diverse pool of functional monomers can be screened for candidates with high affinity and selectivity to targeted biomacromolecules. Through directed synthetic evolution of NP compositions, one can tailor the protein corona to create synthetic organic hydrogel polymer NPs with high affinity and specificity to peptide toxins, enzymes, and other functional proteins, as well as to specific domains of large proteins. In addition, many NIPAm NPs undergo a change in morphology as a function of temperature. This transformation often correlates with a significant change in NP-biomacromolecule affinity, resulting in a temperature-dependent protein corona. This temperature dependence has been used to develop NP hydrogels with autonomous affinity switching for the protection of proteins from thermal stress and as a method of biomacromolecule purification through a selective thermally induced catch and release. In addition to temperature, changes in pH or buffer can also alter a NP protein corona composition, a property that has been exploited for protein purification. Finally, synthetic polymer nanoparticles with low nanomolar affinity for a peptide toxin were shown to capture and neutralize the toxin in the bloodstream of living mice. While the development of synthetic polymer alternatives to protein affinity reagents is
Detection-Guided Fast Affine Projection Channel Estimator for Speech Applications
Directory of Open Access Journals (Sweden)
Yan Wu Jennifer
2007-04-01
Full Text Available In various adaptive estimation applications, such as acoustic echo cancellation within teleconferencing systems, the input signal is a highly correlated speech. This, in general, leads to extremely slow convergence of the NLMS adaptive FIR estimator. As a result, for such applications, the affine projection algorithm (APA or the low-complexity version, the fast affine projection (FAP algorithm, is commonly employed instead of the NLMS algorithm. In such applications, the signal propagation channel may have a relatively low-dimensional impulse response structure, that is, the number m of active or significant taps within the (discrete-time modelled channel impulse response is much less than the overall tap length n of the channel impulse response. For such cases, we investigate the inclusion of an active-parameter detection-guided concept within the fast affine projection FIR channel estimator. Simulation results indicate that the proposed detection-guided fast affine projection channel estimator has improved convergence speed and has lead to better steady-state performance than the standard fast affine projection channel estimator, especially in the important case of highly correlated speech input signals.
Co-evolution of affinity and stability of grafted amyloid-motif domain antibodies.
Julian, Mark C; Lee, Christine C; Tiller, Kathryn E; Rabia, Lilia A; Day, Evan K; Schick, Arthur J; Tessier, Peter M
2015-10-01
An attractive approach for designing lead antibody candidates is to mimic natural protein interactions by grafting peptide recognition motifs into the complementarity-determining regions (CDRs). We are using this approach to generate single-domain (VH) antibodies specific for amyloid-forming proteins such as the Alzheimer's Aβ peptide. Here, we use random mutagenesis and yeast surface display to improve the binding affinity of a lead VH domain grafted with Aβ residues 33-42 in CDR3. Interestingly, co-selection for improved Aβ binding and VH display on the surface of yeast yields antibody domains with improved affinity and reduced stability. The highest affinity VH domains were strongly destabilized on the surface of yeast as well as unfolded when isolated as autonomous domains. In contrast, stable VH domains with improved affinity were reliably identified using yeast surface display by replacing the display antibody that recognizes a linear epitope tag at the terminus of both folded and unfolded VH domains with a conformational ligand (Protein A) that recognizes a discontinuous epitope on the framework of folded VH domains. Importantly, we find that selection for improved stability using Protein A without simultaneous co-selection for improved Aβ binding leads to strong enrichment for stabilizing mutations that reduce antigen binding. Our findings highlight the importance of simultaneously optimizing affinity and stability to improve the rapid isolation of well-folded and specific antibody fragments. PMID:26386257
Role of T cell receptor affinity in the efficacy and specificity of adoptive T cell therapies
Directory of Open Access Journals (Sweden)
Jennifer D. Stone
2013-08-01
Full Text Available Over the last several years, there has been considerable progress in the treatment of cancer using gene modified adoptive T cell therapies. Two approaches have been used, one involving the introduction of a conventional alpha-beta T cell receptor (TCR against a pepMHC cancer antigen, and the second involving introduction of a chimeric antigen receptor (CAR consisting of a single-chain antibody as an Fv fragment (scFv linked to transmembrane and signaling domains. In this review, we focus on one aspect of TCR-mediated adoptive T cell therapies, the impact of the affinity of the alpha-beta TCR for the pepMHC cancer antigen on both efficacy and specificity. We discuss the advantages of higher affinity TCRs in mediating potent activity of CD4 T cells. This is balanced with the potential disadvantage of higher affinity TCRs in mediating greater self-reactivity against a wider range of structurally similar antigenic peptides, especially in synergy with the CD8 co-receptor. Both TCR affinity and target selection will influence potential safety issues. We suggest pre-clinical strategies that might be used to examine each TCR for possible on-target and off-target side effects due to self-reactivities, and to adjust TCR affinities accordingly.
Gaussian and Affine Approximation of Stochastic Diffusion Models for Interest and Mortality Rates
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Marcus C. Christiansen
2013-10-01
Full Text Available In the actuarial literature, it has become common practice to model future capital returns and mortality rates stochastically in order to capture market risk and forecasting risk. Although interest rates often should and mortality rates always have to be non-negative, many authors use stochastic diffusion models with an affine drift term and additive noise. As a result, the diffusion process is Gaussian and, thus, analytically tractable, but negative values occur with positive probability. The argument is that the class of Gaussian diffusions would be a good approximation of the real future development. We challenge that reasoning and study the asymptotics of diffusion processes with affine drift and a general noise term with corresponding diffusion processes with an affine drift term and an affine noise term or additive noise. Our study helps to quantify the error that is made by approximating diffusive interest and mortality rate models with Gaussian diffusions and affine diffusions. In particular, we discuss forward interest and forward mortality rates and the error that approximations cause on the valuation of life insurance claims.
Interplay between binding affinity and kinetics in protein-protein interactions.
Cao, Huaiqing; Huang, Yongqi; Liu, Zhirong
2016-07-01
To clarify the interplay between the binding affinity and kinetics of protein-protein interactions, and the possible role of intrinsically disordered proteins in such interactions, molecular simulations were carried out on 20 protein complexes. With bias potential and reweighting techniques, the free energy profiles were obtained under physiological affinities, which showed that the bound-state valley is deep with a barrier height of 12 - 33 RT. From the dependence of the affinity on interface interactions, the entropic contribution to the binding affinity is approximated to be proportional to the interface area. The extracted dissociation rates based on the Arrhenius law correlate reasonably well with the experimental values (Pearson correlation coefficient R = 0.79). For each protein complex, a linear free energy relationship between binding affinity and the dissociation rate was confirmed, but the distribution of the slopes for intrinsically disordered proteins showed no essential difference with that observed for ordered proteins. A comparison with protein folding was also performed. Proteins 2016; 84:920-933. © 2016 Wiley Periodicals, Inc. PMID:27018856
Cyclization strategies of meditopes: affinity and diffraction studies of meditope-Fab complexes.
Bzymek, Krzysztof P; Ma, Yuelong; Avery, Kendra A; Horne, David A; Williams, John C
2016-06-01
Recently, a unique binding site for a cyclic 12-residue peptide was discovered within a cavity formed by the light and heavy chains of the cetuximab Fab domain. In order to better understand the interactions that drive this unique complex, a number of variants including the residues within the meditope peptide and the antibody, as well as the cyclization region of the meditope peptide, were created. Here, multiple crystal structures of meditope peptides incorporating different cyclization strategies bound to the central cavity of the cetuximab Fab domain are presented. The affinity of each cyclic derivative for the Fab was determined by surface plasmon resonance and correlated to structural differences. Overall, it was observed that the disulfide bond used to cyclize the peptide favorably packs against a hydrophobic `pocket' and that amidation and acetylation of the original disulfide meditope increased the overall affinity ∼2.3-fold. Conversely, replacing the terminal cysteines with serines and thus creating a linear peptide reduced the affinity over 50-fold, with much of this difference being reflected in a decrease in the on-rate. Other cyclization methods, including the formation of a lactam, reduced the affinity but not to the extent of the linear peptide. Collectively, the structural and kinetic data presented here indicate that small perturbations introduced by different cyclization strategies can significantly affect the affinity of the meditope-Fab complex. PMID:27303895
Parameterization of an effective potential for protein-ligand binding from host-guest affinity data.
Wickstrom, Lauren; Deng, Nanjie; He, Peng; Mentes, Ahmet; Nguyen, Crystal; Gilson, Michael K; Kurtzman, Tom; Gallicchio, Emilio; Levy, Ronald M
2016-01-01
Force field accuracy is still one of the "stalemates" in biomolecular modeling. Model systems with high quality experimental data are valuable instruments for the validation and improvement of effective potentials. With respect to protein-ligand binding, organic host-guest complexes have long served as models for both experimental and computational studies because of the abundance of binding affinity data available for such systems. Binding affinity data collected for cyclodextrin (CD) inclusion complexes, a popular model for molecular recognition, is potentially a more reliable resource for tuning energy parameters than hydration free energy measurements. Convergence of binding free energy calculations on CD host-guest systems can also be obtained rapidly, thus offering the opportunity to assess the robustness of these parameters. In this work, we demonstrate how implicit solvent parameters can be developed using binding affinity experimental data and the binding energy distribution analysis method (BEDAM) and validated using the Grid Inhomogeneous Solvation Theory analysis. These new solvation parameters were used to study protein-ligand binding in two drug targets against the HIV-1 virus and improved the agreement between the calculated and the experimental binding affinities. This work illustrates how benchmark sets of high quality experimental binding affinity data and physics-based binding free energy models can be used to evaluate and optimize force fields for protein-ligand systems. Copyright © 2015 John Wiley & Sons, Ltd. PMID:26256816
Crystal structure of the plant dual-affinity nitrate transporter NRT1.1
Sun, Ji; Bankston, John R.; Payandeh, Jian; Hinds, Thomas R.; Zagotta, William N.; Zheng, Ning
2014-03-01
Nitrate is a primary nutrient for plant growth, but its levels in soil can fluctuate by several orders of magnitude. Previous studies have identified Arabidopsis NRT1.1 as a dual-affinity nitrate transporter that can take up nitrate over a wide range of concentrations. The mode of action of NRT1.1 is controlled by phosphorylation of a key residue, Thr 101 however, how this post-translational modification switches the transporter between two affinity states remains unclear. Here we report the crystal structure of unphosphorylated NRT1.1, which reveals an unexpected homodimer in the inward-facing conformation. In this low-affinity state, the Thr 101 phosphorylation site is embedded in a pocket immediately adjacent to the dimer interface, linking the phosphorylation status of the transporter to its oligomeric state. Using a cell-based fluorescence resonance energy transfer assay, we show that functional NRT1.1 dimerizes in the cell membrane and that the phosphomimetic mutation of Thr 101 converts the protein into a monophasic high-affinity transporter by structurally decoupling the dimer. Together with analyses of the substrate transport tunnel, our results establish a phosphorylation-controlled dimerization switch that allows NRT1.1 to uptake nitrate with two distinct affinity modes.
Ngo, That T; Narinesingh, Dyer
2008-01-01
The yield of antibody purified using affinity chromatography on immobilized Protein A or Protein G was increased up to 5-fold (500%) by including kosmotropic salts in the binding buffer. The binding buffer is used to equilibrate the affinity column before applying a sample to the column and also to dilute the sample prior to loading onto the affinity column to optimize conditions for a maximal binding of antibodies to affinity gels. In this study, the kosmotropic salts that were effective in greatly increasing antibody binding to Protein A included both inorganic and organic salts of ammonium; sodium; or potassium sulfate, phosphate, polycarboxylates; for example, succinate, citrate, isocitrate, N-(2-hydroxyethylene diamine triacetate (HEDTA), ethylene diamine tetraacetate (EDTA), and ethylene glycol-O,O'-bis(2-aminoethyl)-N,N,N'N'-tetra acetate(EGTA). On an equal-molar basis, the greater the number of carboxylic groups within the polycarboxylate molecule, the greater the increase in the yield of the purified antibody that was observed. The data show that kosmotropes can be used as effective additives to enhance the binding of immunoglobulins to Protein A or Protein G gels with a resultant increase in the yield of the purified antibodies. Thus, it appears that strongly hydrated anions (citrate, sulfate, and phosphate) and weakly hydrated cations (ammonium, potassium) increase the yield of antibody purified on either Protein A or Protein G affinity gels. PMID:18080884
High affinity binding of [3H]cocaine to rat liver microsomes
International Nuclear Information System (INIS)
]3H]cocaine bound reversible, with high affinity and stereospecificity to rat liver microsomes. Little binding was detected in the lysosomal, mitochondrial and nuclear fractions. The binding kinetics were slow and the kinetically calculated K/sub D/ was 2 nM. Induction of mixed function oxidases by phenobarbital did not produce significant change in [3H]cocaine binding. On the other hand, chronic administration of cocaine reduced [3H]cocaine binding drastically. Neither treatment affected the affinity of the liver binding protein for cocaine. Microsomes from mouse and human livers had less cocaine-binding protein and lower affinity for cocaine than those from rat liver. Binding of [3H]cocaine to rat liver microsomes was insensitive to monovalent cations and > 10 fold less sensitive to biogenic amines than the cocaine receptor in rat striatum. However, the liver protein had higher affinity for cocaine and metabolites except for norcocaine. Amine uptake inhibitors displaced [3H]cocaine binding to liver with a different rank order of potency than their displacement of [3H]cocaine binding to striatum. This high affinity [3H]cocaine binding protein in liver is not likely to be monooxygenase, but may have a role in cocaine-induced hepatotoxicity
Li, Li; Xia, Li-Ru; Zhao, Yong-Fu; Wang, He-Ye
2016-09-01
In this paper, a novel highly sensitive chemiluminescence immune-affinity 96 spots monolith array was developed to detect deoxynivalenol (DON), zearalenone (ZEN), T-2 toxin (T-2), and fumonisin B1 (FB1) in corn samples. Firstly, the monolith array was prepared through on suit UV-initiated copolymerization using polyethylene glycol diacrylate (PEGDA) as cross-linker, glycidyl methacrylate (GMA) as functional monomer and polyethylene glycol 200 (PEG 200) as the porogen. Subsequently, the four mycotoxins immune-affinity monolith array was prepared by immobilization of DON, ZEN, T-2, and FB1 antibody. The mole ratio of PEGDA/GMA, UV exposure time, and the volume ratio of PEG 200/PEGDA were optimized to improve the performances of the immune-affinity monolith array. For the mycotoxins immune-affinity monolith array based on chemiluminescence detection, the limit of detection was 0.0036ng/mL (DON), 0.0048ng/mL (ZEN), 0.0039ng/mL (T-2), and 0.0017ng/mL (FB1), respectively. The linear response in the range of 0.01-0.1ng/mL (R(2)=0.98). The results showed that the proposed four mycotoxins immune-affinity monolith array was a stable, accurate, and highly sensitive method to determine levels of DON, ZEN, T-2, and FB1 in real samples. PMID:27423670
Affinity improvement by fine tuning of single-chain variable fragment against aflatoxin B1.
Min, Won-Ki; Na, Kang-In; Yoon, Jung-Hyun; Heo, Yoon-Jee; Lee, Daesang; Kim, Sung-Gun; Seo, Jin-Ho
2016-10-15
Aflatoxin B1 (AFB1) produced in Aspergillus flavus is a major hepatocarcinogen found in foods and feed. For effective immunological detection of AFB1 at low concentrations, the development of high affinity antibody for AFB1 is required. Previously, an affinity-maturated single-chain variable fragment containing 6 mutations (scFv-M37) was isolated from an artificial mutagenic library, which showed a 9-fold higher affinity than its wild type scFv. In this study, the effect of the 6 mutated residues on the affinity improvement was characterized using surface plasmon resonance analysis, which identified a deleterious mutation (VH-A110T) located on a framework region of the scFv-M37. The back mutation of VH-A110T resulted in a 3.2-fold affinity improvement, which was attributed to decrease of dissociation rate constant (kd) in interaction between AFB1 and the back mutant scFv. The biophysical analyses using circular dichroism and gel filtration revealed that the back mutation of VH-A110T caused a subtle conformational change of the scFv toward tighter binding to AFB1. PMID:27173568
Detection-Guided Fast Affine Projection Channel Estimator for Speech Applications
Directory of Open Access Journals (Sweden)
Homer John
2007-01-01
Full Text Available In various adaptive estimation applications, such as acoustic echo cancellation within teleconferencing systems, the input signal is a highly correlated speech. This, in general, leads to extremely slow convergence of the NLMS adaptive FIR estimator. As a result, for such applications, the affine projection algorithm (APA or the low-complexity version, the fast affine projection (FAP algorithm, is commonly employed instead of the NLMS algorithm. In such applications, the signal propagation channel may have a relatively low-dimensional impulse response structure, that is, the number m of active or significant taps within the (discrete-time modelled channel impulse response is much less than the overall tap length n of the channel impulse response. For such cases, we investigate the inclusion of an active-parameter detection-guided concept within the fast affine projection FIR channel estimator. Simulation results indicate that the proposed detection-guided fast affine projection channel estimator has improved convergence speed and has lead to better steady-state performance than the standard fast affine projection channel estimator, especially in the important case of highly correlated speech input signals.
Automatic face naming by learning discriminative affinity matrices from weakly labeled images.
Xiao, Shijie; Xu, Dong; Wu, Jianxin
2015-10-01
Given a collection of images, where each image contains several faces and is associated with a few names in the corresponding caption, the goal of face naming is to infer the correct name for each face. In this paper, we propose two new methods to effectively solve this problem by learning two discriminative affinity matrices from these weakly labeled images. We first propose a new method called regularized low-rank representation by effectively utilizing weakly supervised information to learn a low-rank reconstruction coefficient matrix while exploring multiple subspace structures of the data. Specifically, by introducing a specially designed regularizer to the low-rank representation method, we penalize the corresponding reconstruction coefficients related to the situations where a face is reconstructed by using face images from other subjects or by using itself. With the inferred reconstruction coefficient matrix, a discriminative affinity matrix can be obtained. Moreover, we also develop a new distance metric learning method called ambiguously supervised structural metric learning by using weakly supervised information to seek a discriminative distance metric. Hence, another discriminative affinity matrix can be obtained using the similarity matrix (i.e., the kernel matrix) based on the Mahalanobis distances of the data. Observing that these two affinity matrices contain complementary information, we further combine them to obtain a fused affinity matrix, based on which we develop a new iterative scheme to infer the name of each face. Comprehensive experiments demonstrate the effectiveness of our approach. PMID:25616081
On-bead chemical synthesis and display of phosphopeptides for affinity pull-down proteomics
DEFF Research Database (Denmark)
Malene, Brandt; Madsen, Jens C.; Bunkenborg, Jakob; Jensen, Ole N.; Gammeltoft, Steen; Jensen, Knud J.
2006-01-01
We describe a new method for phosphopeptide proteomics based on the solid-phase synthesis of phosphopeptides on beads suitable for affinity pull-down experiments. Peptide sequences containing the Bad Ser112 and Ser136 phosphorylation motifs were used as bait in affinity pull-down experiments to...... (aldehyde) at the C terminus for potential activity-based proteomics. The synthetic support-bound Bad phosphopeptides were able to pull down 14-3-3zeta. Furthermore, Bad phosphopeptides bound endogenous 14-3-3 proteins, and all seven members of the 14-3-3 family were identified by mass spectrometry. In...... control experiments, none of the unphosphorylated Bad peptides bound transfected 14-3-3zeta or endogenous 14-3-3. We conclude that the combined synthesis and display of phosphopeptides on-bead is a fast and efficient method for affinity pull-down proteomics....
AFFINE INVARIANT OF 3D OBJECTS USING STATISTICAL AND ALGEBRAIC COEFFICIENTS
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lhachloufi Mostafa,
2011-03-01
Full Text Available The increasing number of objects 3D are available on the Internet or in specialized databases and require the establishment of methods to develop description and recognition techniques[1,2,3] to access intelligently to the contents of these objects . In this context, our work whose objective is to present an affine invariants methods [4,5] of 3D objects . The proposed methods based on the extraction of statistical and algebraic coefficients from the 3D object, these coefficients remain invariant against affine transformation of the 3D object. In this work, the 3D objects are transformations of 3D objects by one element of the overall transformation. The set of transformations considered here is the general affine group. The measure of similarity between two descriptor vector objects is achieved by a similarity function using the euclidean distance..
Institute of Scientific and Technical Information of China (English)
MohammadRezaAboudzadehRovais; JiawenZhu; BinWu
2004-01-01
A non-equilibrium chromatographic rate model was employed to simulate the affinity chromatography of urokinase. The chromatography process was developed to a yield of high purity product of urokinase from crude materials. The affinity gel used in the process was prepared by an epichlorohydrin-activation method using epichlorohydrin activated Sepharose 4B as a matrix and p-aminobenzamidine as a ligand. The chromatographic process were numerically simulated and analyzed with the aid of VERSE-LC computer simulator. Considering the basic principles, rate model with the back mixing in column inlet was utilized in simulating and studying the effect of the column inlet pattern on other parameters. Comparison of the simulation results with the experimental data showed that the rate model can be used to describe the affinity chromatography of urokinase in a fixed bed column with satisfactory accuracy.
Hopping in the Phase Model to a Non-Commutative Verlinde Formula for Affine Fusion
Walton, Mark A
2013-01-01
Korff and Stroppel discovered a realization of su(n) affine fusion, the fusion of the su(n) Wess-Zumino-Novikov-Witten (WZNW) conformal field theory, in the phase model, a limit of the q-boson hopping model. This integrable-model realization provides a new perspective on affine fusion, explored in a recent paper by the author. The role of WZNW primary fields is played in it by non-commutative Schur polynomials, and fusion coefficients are thus given by a non-commutative version of the Verlinde formula. We present the extension to all Verlinde dimensions, of arbitrary genus and any number N of points. The level-dependence of affine fusion is also discussed, using the concept of threshold level, and its generalization to threshold weight.
Hopping in the Phase Model to a Non-Commutative Verlinde Formula for Affine Fusion
International Nuclear Information System (INIS)
Korff and Stroppel discovered a realization of su(n) affine fusion, the fusion of the su(n) Wess-Zumino-Novikov-Witten (WZNW) conformal field theory, in the phase model, a limit of the q-boson hopping model. This integrable-model realization provides a new perspective on affine fusion, explored in a recent paper by the author. The role of WZNW primary fields is played in it by non-commutative Schur polynomials, and fusion coefficients are thus given by a non-commutative version of the Verlinde formula. We present the extension to all Verlinde dimensions, of arbitrary genus and any number N of points. The level-dependence of affine fusion is also discussed, using the concept of threshold level, and its generalization to threshold weight
Affine extensions of non-crystallographic Coxeter groups induced by projection
Dechant, Pierre-Philippe; Twarock, Reidun
2013-01-01
In this paper, we show that affine extensions of non-crystallographic Coxeter groups can be derived via Coxeter-Dynkin diagram foldings and projections of the root systems E_8, D_6 and A_4. Using the known extensions for these root systems, we induce affine extensions of the non-crystallographic groups H_4, H_3 and H_2, and show that they correspond to Kac-Moody-type extensions considered in Dechant et al. This class of extensions was motivated by physical applications in icosahedral systems in biology (viruses), physics (quasicrystals) and chemistry (fullerenes); the connection with the affine extension of E_8 derived here suggests potential for high energy physics applications. The invertibility of the projection suggests a generalisation of Cartan matrices by relaxing some of the usual requirements.
Affinity chromatography and capillary electrophoresis for analysis of the yeast ribosomal proteins
Directory of Open Access Journals (Sweden)
Miriam S. Goyder
2012-04-01
Full Text Available We present a top down separation platform for yeast ribosomalproteins using affinity chromatography and capillary electrophoresiswhich is designed to allow deposition of proteins ontoa substrate. FLAG tagged ribosomes were affinity purified, andrRNA acid precipitation was performed on the ribosomes followedby capillary electrophoresis to separate the ribosomalproteins. Over 26 peaks were detected with excellent reproducibility(＜0.5% RSD migration time. This is the first reportedseparation of eukaryotic ribosomal proteins using capillaryelectrophoresis. The two stages in this workflow, affinity chromatographyand capillary electrophoresis, share the advantagesthat they are fast, flexible and have small sample requirementsin comparison to more commonly used techniques. This methodis a remarkably quick route from cell to separation that hasthe potential to be coupled to high throughput readout platformsfor studies of the ribosomal proteome. [BMB reports2012; 45(4: 233-238
3D Motion Estimation and Motion Fusion by Affine Region Matching
Institute of Scientific and Technical Information of China (English)
魏国庆; 马颂德
1993-01-01
In this paper,a new method is presented for 3D motion estimation by image region correspondences using stereo cameras.Under the weak perspectivity assumption.we first employ the moment tensor theory (Cyganski and Orr[11]) to compute the monocular affine transformations relating images taken by the same camera at different time instants and the binocular affine transformations relating images taken by different cameras at the same time instant.We then show that 3D motion can be recovered from these 2D transformations.A space-time fusion strategy is proposed to aim at robust results.No knowledge of point correspondences if requred in the above processes and the computations involved are linear.To find corresponding image regions,new affine invariants,which show stronger invariance,are derived in term of tensor contraction theory.Experiments on real motion images are conducted to verify the proposed method.
International Nuclear Information System (INIS)
The relative binding affinity (RBA) of tritium labelled diethylstilbestrol (DES) was determined in nuclear fractions of rat uterus. DES displayed a two- to threefold greater affinity than estradiol for nuclear E receptor. The RBA of DES to nuclear E receptor was lowered significantly in the presence of rat serum (43 +/- 1) or human serum (52 +/- 7). Dilution of human serum resulted in a progressive increase in the RBA of DES which approached that observed in the absence of serum. Addition of purified human serum albumin mimicked the decrease in RBA of DES that was observed with serum. The IC50 of estradiol was not changed in the presence of either rat serum or albumin. These data show that DES possesses a greater affinity for nuclear E receptor than estradiol and that serum albumin can modulate DES binding to uterine E receptor
Applications of on-line weak affinity interactions in free solution capillary electrophoresis
DEFF Research Database (Denmark)
Heegaard, Niels H H; Nissen, Mogens H; Chen, David D Y
2002-01-01
The impressive selectivity offered by capillary electrophoresis can in some cases be further increased when ligands or additives that engage in weak affinity interactions with one or more of the separated analytes are added to the electrophoresis buffer. This on-line affinity capillary...... enantiomers and on using capillary electrophoresis to characterize such interactions quantitatively. We describe the equations for binding isotherms, illustrate how selectivity can be manipulated by varying the additive concentrations, and show how the methods may be used to estimate binding constants. On......-line affinity capillary electrophoresis methods are especially valuable for enantiomeric separations and for functional characterization of the contents of biological samples that are only available in minute quantities....
Self-affinity study of nanostructured porous silicon-crystalline silicon interfaces
International Nuclear Information System (INIS)
Self-affinity was used to analyze the roughness at the porous silicon (PS)-crystalline Si (cSi) interfaces fabricated under different conditions. Using the variable bandwidth method, the self-affinity behavior was, qualitatively and quantitatively, analyzed from the cross-section micrographs of the PS samples obtained by field emission scanning electron microscope. The results show that correlation length is related with the average pore width. Roughness exponent is found to be correlated with the interface roughness. In addition, similar experimental roughness exponents were obtained for several interfaces grown by different methods, indicating the intrinsic fractal nature of the PS-cSi interfaces. The results were confirmed through the self-affinity analysis done on the atomic force microscopy profiles.
Dynamical surface affinity of diphasic liquids as a probe of wettability of multimodal porous media.
Korb, J-P; Freiman, G; Nicot, B; Ligneul, P
2009-12-01
We introduce a method for estimating the wettability of rock/oil/brine systems using noninvasive in situ nuclear magnetic relaxation dispersion. This technique scans over a large range of applied magnetic fields and yields unique information about the extent to which a fluid is dynamically correlated with a solid rock surface. Unlike conventional transverse relaxation studies, this approach is a direct probe of the dynamical surface affinity of fluids. To quantify these features we introduce a microscopic dynamical surface affinity index which measures the dynamical correlation (i.e., the microscopic wettability) between the diffusive fluid and the fixed paramagnetic relaxation sources at the pore surfaces. We apply this method to carbonate reservoir rocks which are known to hold about two thirds of the world's oil reserves. Although this nondestructive method concerns here an application to rocks, it could be generalized as an in situ liquid/surface affinity indicator for any multimodal porous medium including porous biological media. PMID:20365175
Affinity and kinetics study of anthranilic acids as HCA2 receptor agonists.
van Veldhoven, Jacobus P D; Liu, Rongfang; Thee, Stephanie A; Wouters, Yessica; Verhoork, Sanne J M; Mooiman, Christiaan; Louvel, Julien; IJzerman, Adriaan P
2015-07-15
Structure-affinity relationship (SAR) and structure-kinetics relationship (SKR) studies were combined to investigate a series of biphenyl anthranilic acid agonists for the HCA2 receptor. In total, 27 compounds were synthesized and twelve of them showed higher affinity than nicotinic acid. Two compounds, 6g (IC50=75nM) and 6z (IC50=108nM) showed a longer residence time profile compared to nicotinic acid, exemplified by their kinetic rate index (KRI) values of 1.31 and 1.23, respectively. The SAR study resulted in the novel 2-F, 4-OH derivative (6x) with an IC50 value of 23nM as the highest affinity HCA2 agonist of the biphenyl series, although it showed a similar residence time as nicotinic acid. The SAR and SKR data suggest that an early compound selection based on binding kinetics is a promising addition to the lead optimization process. PMID:25737085
Enhanced antibody affinity in sublethally irradiated mice and bone marrow chimeras
International Nuclear Information System (INIS)
Sublethally irradiated mice primed with dinitrophenyl (Dnp)-keyhole limpet hemocyanin immediately after irradiation or 30 days later and subsequently boosted with a second injection of antigen displayed a secondary response to Dnp characterized by antibody affinity greater than that in unirradiated controls. Also, in radiation chimeras primed with Dnp-keyhole limpet hemocyanin 120 days after syngeneic or allogeneic bone marrow transplantation the antibodies against Dnp produced after boosting were of higher affinity than the antibodies raised in normal mice. These findings are tentatively attributed to lack of suppressor thymus-derived lymphocytes (T cells) in sublethally irradiated mice and bone marrow chimeras, in which the enhanced ability to produce antibodies of high affinity may compensate for quantitative defects of the immune system
Local and global approaches of affinity propagation clustering for large scale data
Xia, Dingyin; Zhang, Xuqing; Zhuang, Yueting
2009-01-01
Recently a new clustering algorithm called 'affinity propagation' (AP) has been proposed, which efficiently clustered sparsely related data by passing messages between data points. However, we want to cluster large scale data where the similarities are not sparse in many cases. This paper presents two variants of AP for grouping large scale data with a dense similarity matrix. The local approach is partition affinity propagation (PAP) and the global method is landmark affinity propagation (LAP). PAP passes messages in the subsets of data first and then merges them as the number of initial step of iterations; it can effectively reduce the number of iterations of clustering. LAP passes messages between the landmark data points first and then clusters non-landmark data points; it is a large global approximation method to speed up clustering. Experiments are conducted on many datasets, such as random data points, manifold subspaces, images of faces and Chinese calligraphy, and the results demonstrate that the two...
A Novel Fast and Robust Binary Affine Invariant Descriptor for Image Matching
Directory of Open Access Journals (Sweden)
Xiujie Qu
2014-01-01
Full Text Available As the current binary descriptors have disadvantages of high computational complexity, no affine invariance, and the high false matching rate with viewpoint changes, a new binary affine invariant descriptor, called BAND, is proposed. Different from other descriptors, BAND has an irregular pattern, which is based on local affine invariant region surrounding a feature point, and it has five orientations, which are obtained by LBP effectively. Ultimately, a 256 bits binary string is computed by simple random sampling pattern. Experimental results demonstrate that BAND has a good matching result in the conditions of rotating, image zooming, noising, lighting, and small-scale perspective transformation. It has better matching performance compared with current mainstream descriptors, while it costs less time.
Optimizing scoring function of protein-nucleic acid interactions with both affinity and specificity.
Directory of Open Access Journals (Sweden)
Zhiqiang Yan
Full Text Available Protein-nucleic acid (protein-DNA and protein-RNA recognition is fundamental to the regulation of gene expression. Determination of the structures of the protein-nucleic acid recognition and insight into their interactions at molecular level are vital to understanding the regulation function. Recently, quantitative computational approach has been becoming an alternative of experimental technique for predicting the structures and interactions of biomolecular recognition. However, the progress of protein-nucleic acid structure prediction, especially protein-RNA, is far behind that of the protein-ligand and protein-protein structure predictions due to the lack of reliable and accurate scoring function for quantifying the protein-nucleic acid interactions. In this work, we developed an accurate scoring function (named as SPA-PN, SPecificity and Affinity of the Protein-Nucleic acid interactions for protein-nucleic acid interactions by incorporating both the specificity and affinity into the optimization strategy. Specificity and affinity are two requirements of highly efficient and specific biomolecular recognition. Previous quantitative descriptions of the biomolecular interactions considered the affinity, but often ignored the specificity owing to the challenge of specificity quantification. We applied our concept of intrinsic specificity to connect the conventional specificity, which circumvents the challenge of specificity quantification. In addition to the affinity optimization, we incorporated the quantified intrinsic specificity into the optimization strategy of SPA-PN. The testing results and comparisons with other scoring functions validated that SPA-PN performs well on both the prediction of binding affinity and identification of native conformation. In terms of its performance, SPA-PN can be widely used to predict the protein-nucleic acid structures and quantify their interactions.
Heparin-binding peptide as a novel affinity tag for purification of recombinant proteins.
Morris, Jacqueline; Jayanthi, Srinivas; Langston, Rebekah; Daily, Anna; Kight, Alicia; McNabb, David S; Henry, Ralph; Kumar, Thallapuranam Krishnaswamy Suresh
2016-10-01
Purification of recombinant proteins constitutes a significant part of the downstream processing in biopharmaceutical industries. Major costs involved in the production of bio-therapeutics mainly depend on the number of purification steps used during the downstream process. Affinity chromatography is a widely used method for the purification of recombinant proteins expressed in different expression host platforms. Recombinant protein purification is achieved by fusing appropriate affinity tags to either N- or C- terminus of the target recombinant proteins. Currently available protein/peptide affinity tags have proved quite useful in the purification of recombinant proteins. However, these affinity tags suffer from specific limitations in their use under different conditions of purification. In this study, we have designed a novel 34-amino acid heparin-binding affinity tag (HB-tag) for the purification of recombinant proteins expressed in Escherichia coli (E. coli) cells. HB-tag fused recombinant proteins were overexpressed in E. coli in high yields. A one-step heparin-Sepharose-based affinity chromatography protocol was developed to purify HB-fused recombinant proteins to homogeneity using a simple sodium chloride step gradient elution. The HB-tag has also been shown to facilitate the purification of target recombinant proteins from their 8 M urea denatured state(s). The HB-tag has been demonstrated to be successfully released from the fusion protein by an appropriate protease treatment to obtain the recombinant target protein(s) in high yields. Results of the two-dimensional NMR spectroscopy experiments indicate that the purified recombinant target protein(s) exist in the native conformation. Polyclonal antibodies raised against the HB-peptide sequence, exhibited high binding specificity and sensitivity to the HB-fused recombinant proteins (∼10 ng) in different crude cell extracts obtained from diverse expression hosts. In our opinion, the HB-tag provides a
Biomimetic design of affinity peptide ligand for capsomere of virus-like particle.
Li, Yanying; Liu, Xiaodan; Dong, Xiaoyan; Zhang, Lin; Sun, Yan
2014-07-22
Virus-like particle (VLP) of murine polyomavirus (MPV) is a T = 7d icosahedral capsid that self-assembles from 72 capsomeres (Caps), each of which is a pentamer of major coat protein VP1. VLP has great potential in vaccinology, gene therapy, drug delivery, and materials science. However, its application is hindered by high cost downstream processes, leading to an urgent demand of a highly efficient affinity ligand for the separation and purification of Cap by affinity chromatography. Herein a biomimetic design strategy of an affinity peptide ligand of Cap has been developed on the basis of the binding structure of the C-terminus of minor coat protein (VP2-C) on the inner surface of Cap. The molecular interactions between VP2-C and Cap were first examined using all-atom molecular dynamics (MD) simulations coupled with the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method, where V283, P285, D286, W287, L289, and Y296 of VP2-C were identified as the hot spots. An affinity peptide library (DWXLXLXY, X denotes arbitrary amino acids except cysteine) was then constructed for virtual screening sequently by docking with AUTODOCK VINA, binding structure comparison, and final docking with ROSETTA FlexPepDock. Ten peptide candidates were selected and further confirmed by MD simulations and MM/PBSA, where DWDLRLLY was found to have the highest affinity to Cap. In DWDLRLLY, six residues are favorable for the binding, including W2, L4, L6 and Y8 inheriting from VP2-C, and R5 and L7 selected in the virtual screening. This confirms the high efficiency and accuracy of the biomimetic design strategy. DWDLRLLY was then experimentally validated by a one-step purification of Cap from crude cell lysate using affinity chromatography with the octapeptide immobilized on Sepharose gel. The purified Caps were observed to self-assemble into VLP with consistent structure of authentic MPV. PMID:24976378
Enhancement of Immune Effector Functions by Modulating IgG’s Intrinsic Affinity for Target Antigen
Mazor, Yariv; Yang, Chunning; Borrok, M. Jack; Ayriss, Joanne; Aherne, Karen; Wu, Herren; Dall’Acqua, William F.
2016-01-01
Antibody-mediated immune effector functions play an essential role in the anti-tumor efficacy of many therapeutic mAbs. While much of the effort to improve effector potency has focused on augmenting the interaction between the antibody-Fc and activating Fc-receptors expressed on immune cells, the role of antibody binding interactions with the target antigen remains poorly understood. We show that antibody intrinsic affinity to the target antigen clearly influences the extent and efficiency of Fc-mediated effector mechanisms, and report the pivotal role of antibody binding valence on the ability to regulate effector functions. More particularly, we used an array of affinity modulated variants of three different mAbs, anti-CD4, anti-EGFR and anti-HER2 against a panel of target cell lines expressing disparate levels of the target antigen. We found that at saturating antibody concentrations, IgG variants with moderate intrinsic affinities, similar to those generated by the natural humoral immune response, promoted superior effector functions compared to higher affinity antibodies. We hypothesize that at saturating concentrations, effector function correlates most directly with the amount of Fc bound to the cell surface. Thus, high affinity antibodies exhibiting slow off-rates are more likely to interact bivalently with the target cell, occupying two antigen sites with a single Fc. In contrast, antibodies with faster off-rates are likely to dissociate each binding arm more rapidly, resulting in a higher likelihood of monovalent binding. Monovalent binding may in turn increase target cell opsonization and lead to improved recruitment of effector cells. This unpredicted relationship between target affinity and effector function potency suggests a careful examination of antibody design and engineering for the development of next-generation immunotherapeutics. PMID:27322177
Xu, Wei; Shao, Rong; Xiao, Jianbo
2016-07-26
The inhibitory potential of natural polyphenols for α-amylases has attracted great interests among researchers. The structure-affinity properties of natural polyphenols binding to α-amylase and the structure-activity relationship of dietary polyphenols inhibiting α-amylase were deeply investigated. There is a lack of consistency between the structure-affinity relationship and the structure-activity relationship of natural polyphenols as α-amylase inhibitors. Is it consistent between the binding affinity and inhibitory potential of natural polyphenols as with α-amylase inhibitors? It was found that the consistency between the binding affinity and inhibitory potential of natural polyphenols as with α-amylase inhibitors is not equivocal. For example, there is no consistency between the binding affinity and the inhibitory potential of quercetin and its glycosides as α-amylase inhibitors. However, catechins with higher α-amylase inhibitory potential exhibited higher affinity with α-amylase. PMID:25748632
Architecture of high-affinity unnatural-base DNA aptamers toward pharmaceutical applications
Ken-ichiro Matsunaga; Michiko Kimoto; Charlotte Hanson; Michael Sanford; Young, Howard A.; Ichiro Hirao
2015-01-01
We present a remodeling method for high-affinity unnatural-base DNA aptamers to augment their thermal stability and nuclease resistance, for use as drug candidates targeting specific proteins. Introducing a unique mini-hairpin DNA provides robust stability to unnatural-base DNA aptamers generated by SELEX using genetic alphabet expansion, without reducing their high affinity. By this method, >80% of the remodeled DNA aptamer targeting interferon-γ (K D of 33 pM) survived in human serum at 37 ...
Pardo, Leonardo; Sepulcre Sánchez, Francesc; Cladera Cerdà, Josep Bartomeu; Duñach, Mireia; Labarta, A.; Tejada, J.; Padrós Morell, Esteve
1998-01-01
Binding of Mn2+ or Mg2+ to the high-affinity site of the purple membrane from Halobacterium salinarium has been studied by superconducting quantum interference device magnetometry or by ab initio quantum mechanical calculations, respectively. The binding of Mn2+ cation, in a low-spin state, to the high-affinity site occurs through a major octahedral local symmetry character with a minor rhombic distortion and a coordination number of six. A molecular model of this binding site in the Schiff b...
Barbero-Liñán, María
2011-01-01
Affine connection control systems are mechanical control systems that model a wide range of real systems such as robotic legs, hovercrafts, planar rigid bodies, rolling pennies, snakeboards and so on. In 1997 the accessibility and a particular notion of controllability was intrinsically described by A. D. Lewis and R. Murray at points of zero velocity. Here, we present a novel generalization of the description of accessibility algebra for those systems at some points with nonzero velocity as long as the affine connection restricts to the distribution given by the symmetric closure. The results are used to describe the accessibility algebra of different mechanical control systems.
Fielding, Lee; Rutherford, Samantha; Fletcher, Dan
2005-06-01
The usefulness of bovine serum albumin (BSA) as a model protein for testing NMR methods for the study of protein-ligand interactions is discussed. Isothermal titration calorimetry established the binding affinity and stoichiometry of the specific binding site for L-tryptophan, D-tryptophan, naproxen, ibuprofen, salicylic acid and warfarin. The binding affinities of the same ligands determined by NMR methods are universally weaker (larger KD). This is because the NMR methods are susceptible to interference from additional non-specific binding. The L-tryptophan-BSA and naproxen-BSA systems were the best behaved model systems. PMID:15816062
Electron affinities of the alkali dimers - Na2, K2, and Rb2
Partridge, H.; Dixon, D. A.; Walch, S. P.; Bauschlicher, C. W., Jr.; Gole, J. L.
1983-01-01
Ab initio calculations on the ground states of the alkali dimers, Na2, K2, and Rb2, and their anions are reported. The calculations employ large Gaussian basis sets and account for nearly all of the valence correlation energy. The calculated atomic electron affinities are within 0.02 eV of experiment and the calculated adiabatic electron affinities for Na2, K2, and Rb2 are, respectively, 0.470, 0.512, and 0.513 eV.
Interpolation method for accurate affinity ranking of arrayed ligand-analyte interactions.
Schasfoort, Richard B M; Andree, Kiki C; van der Velde, Niels; van der Kooi, Alex; Stojanović, Ivan; Terstappen, Leon W M M
2016-05-01
The values of the affinity constants (kd, ka, and KD) that are determined by label-free interaction analysis methods are affected by the ligand density. This article outlines a surface plasmon resonance (SPR) imaging method that yields high-throughput globally fitted affinity ranking values using a 96-plex array. A kinetic titration experiment without a regeneration step has been applied for various coupled antibodies binding to a single antigen. Globally fitted rate (kd and ka) and dissociation equilibrium (KD) constants for various ligand densities and analyte concentrations are exponentially interpolated to the KD at Rmax = 100 RU response level (KD(R100)). PMID:26878776
Institute of Scientific and Technical Information of China (English)
Chunxia Jia; Detong Zhu
2008-01-01
In this paper we propose an affine scaling interior algorithm via conjugate gradient path for solving nonlinear equality systems subject to bounds on variables.By employing the affine scaling conjugate gradient path search strategy,we obtain an iterative direction by solving the linearize model.By using the line search technique,we will find an acceptable trial step length along this direction which is strictly feasible and makes the objective function nonmonotonically decreasing.The global convergence and fast local convergence rate of the proposed algorithm are established under some reasonable conditions.Furthermore,the numerical results of the proposed algorithm indicate to be effective.
T-Systems and Y-Systems for Quantum Affinizations of Quantum Kac-Moody Algebras
Tomoki Nakanishi; Junji Suzuki; Atsuo Kuniba
2009-01-01
The T-systems and Y-systems are classes of algebraic relations originally associated with quantum affine algebras and Yangians. Recently the T-systems were generalized to quantum affinizations of a wide class of quantum Kac-Moody algebras by Hernandez. In this note we introduce the corresponding Y-systems and establish a relation between T and Y-systems. We also introduce the T and Y-systems associated with a class of cluster algebras, which include the former T and Y-systems of simply laced ...
Image-Moment Based Affine Invariant Watermarking Scheme Utilizing Neural Networks
Institute of Scientific and Technical Information of China (English)
无
2006-01-01
A new image watermarking scheme is proposed to resist rotation, scaling and translation (RST) attacks. Six combined low order image moments are utilized to represent image information on rotation, scaling and translation. Affine transform parameters are registered by feedforward neural networks. Watermark is adaptively embedded in discrete wavelet transform (DWT) domain while watermark extraction is carried out without original image after attacked watermarked image has been synchronized by making inverse transform through parameters learned by neural networks. Experimental results show that the proposed scheme can effectively register affine transform parameters, embed watermark more robustly and resist geometric attacks as well as JPEG2000 compression.
Interest Rates with Long Memory: A Generalized Affine Term-Structure Model
DEFF Research Database (Denmark)
Osterrieder, Daniela
We propose a model for the term structure of interest rates that is a generalization of the discrete-time, Gaussian, affine yield-curve model. Compared to standard affine models, our model allows for general linear dynamics in the vector of state variables. In an application to real yields of U...... by a level, a slope, and a curvature factor that arise naturally from the co-fractional modeling framework. We show that implied yields match the level and the variability of yields well over time. Studying the out-of-sample forecasting accuracy of our model, we find that our model results in good...
Evaluation for cell affinity of the composite material containing carbon nanotubes
Institute of Scientific and Technical Information of China (English)
KANG Shizhao; WAN Yuqing; YAN Huijuan; BEI Jianzhong; WANG Chen; WANG Shenguo; WANG Chunru; WAN Lijun; BAI Chunli
2004-01-01
The composite material of poly-(L-lactide) (PLLA) and carbon nanotubes (CNTs) were prepared. Its surface morphologies and property were worked out by using atomic force microscopy (AFM) and contact angle measurement. Moreover, the prime cytocompatibility was used to investigate the biocompatibility of the composite material containing CNTs and the effects of CNTs on one aspect of cell function, cell affinity. The results obtained indicate that the composite material of PLLA and CNTs possesses good biocompatibility for both the 3T3 fibroblasts and Oct-1 osteoblast-like cells. The addition of CNTs will greatly affect cell affinity of the material, which may be disadvantage for the cell adhesion.
Monaca Enrico; Jüttner Tobias; Gattermann Norbert; Winterhalter Michael
2012-01-01
Abstract Background Approximately 90 haemoglobinopathies have been identified that result in abnormally high oxygen affinity. One of these is haemoglobinopathy York (HbY), first described in 1976. HbY causes an extreme leftward shift of the oxygen dissociation curve with the P50 value changing to 12.5 - 15.5 mmHg (normal value 26.7 mmHg), indicating that approximately half of the haemoglobin is not available as oxygen carrier. Patients with haemoglobinopathies with increased oxygen affinity c...
An Activation Force-based Affinity Measure for Analyzing Complex Networks
Jun Guo; Hanliang Guo; Zhanyi Wang
2011-01-01
Affinity measure is a key factor that determines the quality of the analysis of a complex network. Here, we introduce a type of statistics, activation forces, to weight the links of a complex network and thereby develop a desired affinity measure. We show that the approach is superior in facilitating the analysis through experiments on a large-scale word network and a protein-protein interaction (PPI) network consisting of ∼5,000 human proteins. The experiment on the word network verifies tha...
Remarks on low weight codewords of generalized affine and projective Reed-Muller codes
Ballet, Stéphane
2012-01-01
We make a brief survey on low weight codewords of generalized Reed-Muller codes and projective generalized Reed-Muller codes. In the affine case we give some information about the words that reach the second distance in cases where these words are not all characterized. Moreover we give the second weight of the projective Reed-Muller codes which was unknown until now. We relate the words of the projective Reed-Muller code reaching the second distance to the words of the affine Reed-Muller code reaching the second distance.
Ye, Qun
2013-03-15
Several diazatetracene diimides with high electron affinity (up to 4.66 eV!) were prepared and well characterized. The LUMO energy level of these electron-deficient molecules was found to be closely related to their material stability. Compound 7 with ultrahigh electron affinity suffered from reduction and hydrolysis in the presence of silica gel or water. The stable compounds 3 and 6 showed n-channel FET behavior with an average electron mobility of 0.002 and 0.005 cm2 V-1 s-1, respectively, using a solution processing method. © 2013 American Chemical Society.
Energy Technology Data Exchange (ETDEWEB)
Orcutt, Kelly Davis; Slusarczyk, Adrian L. [Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Cieslewicz, Maryelise [Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Ruiz-Yi, Benjamin [Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Bhushan, Kumar R. [Division of Hematology/Oncology, Beth Israel Deaconess Medical Center, Boston, MA 02215 (United States); Frangioni, John V. [Division of Hematology/Oncology, Beth Israel Deaconess Medical Center, Boston, MA 02215 (United States); Department of Radiology, Beth Israel Deaconess Medical Center, Boston, MA 02215 (United States); Wittrup, K. Dane, E-mail: wittrup@mit.ed [Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States)
2011-02-15
Introduction: In pretargeted radioimmunotherapy (PRIT), a bifunctional antibody is administered and allowed to pre-localize to tumor cells. Subsequently, a chelated radionuclide is administered and captured by cell-bound antibody while unbound hapten clears rapidly from the body. We aim to engineer high-affinity binders to 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) chelates for use in PRIT applications. Methods: We mathematically modeled antibody and hapten pharmacokinetics to analyze hapten tumor retention as a function of hapten binding affinity. Motivated by model predictions, we used directed evolution and yeast surface display to affinity mature the 2D12.5 antibody to DOTA, reformatted as a single chain variable fragment (scFv). Results: Modeling predicts that for high antigen density and saturating bsAb dose, a hapten-binding affinity of 100 pM is needed for near-maximal hapten retention. We affinity matured 2D12.5 with an initial binding constant of about 10 nM to DOTA-yttrium chelates. Affinity maturation resulted in a 1000-fold affinity improvement to biotinylated DOTA-yttrium, yielding an 8.2{+-}1.9 picomolar binder. The high-affinity scFv binds DOTA complexes of lutetium and gadolinium with similar picomolar affinity and indium chelates with low nanomolar affinity. When engineered into a bispecific antibody construct targeting carcinoembryonic antigen, pretargeted high-affinity scFv results in significantly higher tumor retention of a {sup 111}In-DOTA hapten compared to pretargeted wild-type scFv in a xenograft mouse model. Conclusions: We have engineered a versatile, high-affinity, DOTA-chelate-binding scFv. We anticipate it will prove useful in developing pretargeted imaging and therapy protocols to exploit the potential of a variety of radiometals.
International Nuclear Information System (INIS)
Introduction: In pretargeted radioimmunotherapy (PRIT), a bifunctional antibody is administered and allowed to pre-localize to tumor cells. Subsequently, a chelated radionuclide is administered and captured by cell-bound antibody while unbound hapten clears rapidly from the body. We aim to engineer high-affinity binders to 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) chelates for use in PRIT applications. Methods: We mathematically modeled antibody and hapten pharmacokinetics to analyze hapten tumor retention as a function of hapten binding affinity. Motivated by model predictions, we used directed evolution and yeast surface display to affinity mature the 2D12.5 antibody to DOTA, reformatted as a single chain variable fragment (scFv). Results: Modeling predicts that for high antigen density and saturating bsAb dose, a hapten-binding affinity of 100 pM is needed for near-maximal hapten retention. We affinity matured 2D12.5 with an initial binding constant of about 10 nM to DOTA-yttrium chelates. Affinity maturation resulted in a 1000-fold affinity improvement to biotinylated DOTA-yttrium, yielding an 8.2±1.9 picomolar binder. The high-affinity scFv binds DOTA complexes of lutetium and gadolinium with similar picomolar affinity and indium chelates with low nanomolar affinity. When engineered into a bispecific antibody construct targeting carcinoembryonic antigen, pretargeted high-affinity scFv results in significantly higher tumor retention of a 111In-DOTA hapten compared to pretargeted wild-type scFv in a xenograft mouse model. Conclusions: We have engineered a versatile, high-affinity, DOTA-chelate-binding scFv. We anticipate it will prove useful in developing pretargeted imaging and therapy protocols to exploit the potential of a variety of radiometals.
International Nuclear Information System (INIS)
There are at least two forms of cellular receptors for interleukin 2(IL-2); one with a very high affinity and the other with a lower affinity. The authors identified a non-Tac IL-2 binding peptide with a relative molecular weight of 75,000 (p75). Cell lines bearing either the p55 Tac or the p75 peptide alone manifested low-affinity IL-2 binding, whereas a cell line bearing both peptides manifested both high- and low-affinity receptors. Cross-linking studies were performed with 125I-labeled IL-2. After the internalization of labeled IL-2 through high-affinity receptors, the p75 peptide could not be detected by cross-linking studies. Furthermore, fusion of cell membranes from low-affinity IL-2 binding cell lines bearing the Tac peptide alone with membranes from a cell line bearing the p75 peptide alone generated hybrid membranes bearing high-affinity receptors. These results suggest a multichain model for the high-affinity Il-2 receptor in which high-affinity receptors would be expressed when both Tac and p75 Il-2 binding peptides are present and associated in a receptor complex
Application of monolithic affinity HPLC column for rapid determination of malt glycoproteins
Benkovská, D. (Dagmar); Flodrová, D. (Dana); Bobálová, J. (Janette)
2013-01-01
The aim of this study was to optimize separation and enrichment of barley malt glycoproteins on a monolithic ConA affinity HPLC column. ConA-bound proteins were separated on SDS-PAGE and identified using MALDI-TOF/TOF MS after chymotryptic digestion. Our proteomic analysis allowed successful determination of several putative malt glycoproteins.
Pairing Problem of Generators in Non-twisted Affine Lie Algebras
Institute of Scientific and Technical Information of China (English)
XU Hai-xia; LU Cai-hui
2001-01-01
In this paper, we discuss the pairing problem of generators in four affine Lie algebra. That is,for any given imaginary root vector x ∈ g (A), there exists y such that x and y generate a subalgebra containing g＇ (A).
Representations of Rank Two Affine Hecke Algebras at Roots of Unity
Davis, Matt
2011-01-01
In this paper, we will fully describe the representations of the crystallographic rank two affine Hecke algebras using elementary methods, for all possible values of q. The focus is on the case when q is a root of unity of small order.
Spherically-symmetric gravitational fields in the metric-affine gauge theory of gravitation
Minkevich, A. V.; Vasilevski, Yu. G.
2003-01-01
Geometric structure of spherically-symmetric space-time in metric-affine gauge theory of gravity is studied. Restrictions on curvature tensor and Bianchi identities are obtained. By using certain simple gravitational Lagrangian the solution of gravitational equations for vacuum spherically-symmetric gravitational field is obtained.
On the existence of a gyroscope in spaces with affine connections and metrics
Manoff, S
2000-01-01
Conditions for the existence of a gyroscope in spaces with affine connections and metrics are found. They appear as special types of Fermi-Walker transports for vector fields, lying in a subspace, orthogonal to the velocity vector field of an observer. PACS numbers: 04.20Cv, 04.90.+e, 04.50.+h, 02.40.Ky
Nishikawa, Yosuke; Inatomi, Momoko; Iwasaki, Haruka; Kurisu, Genji
2016-05-01
Dynein is a large microtubule-based motor complex that requires tight coupling of intra-molecular ATP hydrolysis with the generation of mechanical force and track-binding activity. However, the microtubule-binding domain is structurally separated by about 15nm from the nucleotide-binding sites by a coiled-coil stalk. Thus, long-range two-way communication is necessary for coordination between the catalytic cycle of ATP hydrolysis and dynein's track-binding affinities. To investigate the structural changes that occur in the dynein stalk region to produce two different microtubule affinities, here we improve the resolution limit of the previously reported structure of the entire stalk region and we investigate structural changes in the dynein stalk and strut/buttress regions by comparing currently available X-ray structures. In the light of recent crystal structures, the basis of the transition from the low-affinity to the high-affinity coiled-coil registry is discussed. A concerted movement model previously reported by Carter and Vale is modified more specifically, and we proposed it as the open zipper model. PMID:26585405
Combinatorics of q-characters of finite-dimensional representations of quantum affine algebras
International Nuclear Information System (INIS)
We study finite-dimensional representations of quantum affine algebras using q-characters. We prove the conjectures from E. Frenkel and N. Reshetikhin (1998) and derive some of their corollaries. In particular, we prove that the tensor product of fundamental representations is reducible if and only if at least one of the pairwise normalized R-matrices has a pole. (orig.)
Directory of Open Access Journals (Sweden)
Thomas A. Munro
2013-12-01
Full Text Available The recent crystal structure of the κ-opioid receptor (κ-OR revealed, unexpectedly, that the antagonist JDTic is a bivalent ligand: in addition to the orthosteric pocket occupied by morphinans, JDTic also occupies a distinct (allotopic pocket. Mutagenesis data suggest that salvinorin A (1 also binds to this allotopic pocket, adjacent to the aspartate residue that anchors the basic nitrogen atom of classical opiates (Asp138. It has been suggested that an H-bond donor appended to 1 might interact with Asp138, increasing affinity. Such a bivalent ligand might also possess altered functional selectivity. Based on modeling and known N-furanylmethyl opioid antagonists, we appended H-bond donors to the furan ring of 1. (Dimethylaminomethyl groups at C-15 or C-16 abolished affinity for κ-OR. Hydroxymethylation at C-16 was tolerated, but 15,16-bis-hydroxymethylation was not. Since allosteric modulators may go undetected in binding assays, we also tested these and other low-affinity derivatives of 1 for allosteric modulation of dynorphin A in the [35S]GTPγS assay. No modulation was detected. As an alternative attachment point for bivalent derivatives, we prepared the 2-(hydroxyethoxymethyl ether, which retained high affinity for κ-OR. We discuss alternative design strategies for linked, fused or merged bivalent derivatives of 1.
The Hausdorff and dynamical dimensions of self-affine sponges: a dimension gap result
Das, Tushar; Simmons, David
2016-01-01
We construct a self-affine sponge in $\\mathbb R^3$ whose dynamical dimension, i.e. the supremum of the Hausdorff dimensions of its invariant measures, is strictly less than its Hausdorff dimension. This resolves a long-standing open problem in the dimension theory of dynamical systems, namely whether every expanding repeller has an ergodic invariant measure of full Hausdorff dimension.
Allen, Gregory
2013-01-01
This study addressed the problems of hospitals' duplicated effort and ad hoc knowledge management (KM) practices. The purpose of this quantitative study was to examine the focus and type of organizational culture in order to describe and predict the relationship between organizational culture and the affinity for KM of nurses working in health…
Roy, Jagoree; Li, Huiming; Hogan, Patrick G; Cyert, Martha S
2007-03-23
Calcineurin, the conserved Ca(2+)/calmodulin-regulated protein phosphatase, mediates diverse aspects of Ca(2+)-dependent signaling. We show that substrates bind calcineurin with varying strengths and examine the impact of this affinity on signaling. We altered the calcineurin-docking site, or PxIxIT motif, in Crz1, the calcineurin-regulated transcription factor in S. cerevisiae, to decrease (Crz1(PVIAVN)) or increase (Crz1(PVIVIT)) its affinity for calcineurin. As a result, the Ca(2+)-dependent dephosphorylation and activation of Crz1(PVIAVN) are decreased, whereas Crz1(PVIVIT) is constitutively dephosphorylated and hyperactive. Surprisingly, the physiological consequences of altering calcineurin-Crz1 affinity depend on the growth conditions. Crz1(PVIVIT) improves yeast growth under several environmental stress conditions but causes a growth defect during alkaline stress, most likely by titrating calcineurin away from other substrates or regulators. Thus, calcineurin-substrate affinity determines the Ca(2+) concentration dependence and output of signaling in vivo as well as the balance between different branches of calcineurin signaling in an overall biological response. PMID:17386265
Model of Earthquake Generation Exhibiting Self-Organized Criticality with Self-Affine Fault Surfaces
International Nuclear Information System (INIS)
Generation of earthquakes has not been still understood. However, some statistical properties of seismicity are established such as magnitude-frequency distribution indicating power law. In this study, we numerically investigate one-dimensional spring-block earthquake model, considering self-affine fault surfaces, in order to understand such statistical properties
Automated Controller Synthesis for non-Deterministic Piecewise-Affine Hybrid Systems
DEFF Research Database (Denmark)
Grunnet, Jacob Deleuran
meeting a computational tree logic formula and refining the resulting solution to a catalogue of piecewise-affine controllers. The method has been implemented as aMatlab toolbox, PAHSCTRL , using linear matrix inequality feasibility computations for finding the discrete abstraction, UppAal Tiga for...
Translation of Bernstein Coefficients Under an Affine Mapping of the Unit Interval
Alford, John A., II
2012-01-01
We derive an expression connecting the coefficients of a polynomial expanded in the Bernstein basis to the coefficients of an equivalent expansion of the polynomial under an affine mapping of the domain. The expression may be useful in the calculation of bounds for multi-variate polynomials.