WorldWideScience

Sample records for stable bisarsenical affinity

  1. Thermodynamically stable amyloid-β monomers have much lower membrane affinity than the small oligomers

    Directory of Open Access Journals (Sweden)

    Bidyut eSarkar

    2013-04-01

    Full Text Available Amyloid beta (Aβ is an extracellular 39-43 residue long peptide present in the mammalian cerebrospinal fluid, whose aggregation is associated with Alzheimer’s disease. Small oligomers of Aβ are currently thought to be the key to toxicity. However, it is not clear why the monomers of Aβ are non-toxic, and at what stage of aggregation toxicity emerges. Interactions of Aβ with cell membranes is thought to be the initiator of toxicity, but membrane-binding studies with different preparations of monomers and oligomers have not settled this issue. We have earlier found that thermodynamically stable Aβ monomers emerge spontaneously from oligomeric mixtures upon long term incubation in physiological solutions (Nag et al, JBC, 2011. Here we show that the membrane-affinity of these stable Aβ monomers is much lower than that of a mixture of small oligomers (containing dimers to decamers, providing a clue to the emergence of toxicity. Fluorescently labeled Aβ40 monomers show negligible binding to cell membranes of a neuronal cell line (RN46A at physiological concentrations (250 nM, while oligomers at the same concentrations show strong binding within 30 minutes of incubation. The increased affinity most likely does not require any specific neuronal receptor, since this difference in membrane-affinity was also observed in a somatic cell-line (HEK 293T. Similar results are also obtained for Aβ42 monomers and oligomers. Minimal amount of cell death is observed at these concentrations even after 36 hours of incubation. It is likely that membrane binding precedes subsequent slower toxic events induced by Aβ. Our results a provide an explanation for the non-toxic nature of Aβ monomers, b suggest that Aβ toxicity emerges at the initial oligomeric phase, and c provide a quick assay for monitoring the benign-to-toxic transformation of Aβ.

  2. Carbon Availability Modifies Temperature Responses of Heterotrophic Microbial Respiration, Carbon Uptake Affinity, and Stable Carbon Isotope Discrimination.

    Science.gov (United States)

    Min, Kyungjin; Lehmeier, Christoph A; Iv, Ford Ballantyne; Billings, Sharon A

    2016-01-01

    Microbial transformations of organic carbon (OC) generate a large flux of CO 2 into the atmosphere and influence the C balance of terrestrial and aquatic ecosystems. Yet, inherent heterogeneity in natural environments precludes direct quantification of multiple microbial C fluxes that underlie CO 2 production. Here we used a continuous flow bioreactor coupled with a stable C isotope analyzer to determine the effects of temperature and C availability (cellobiose concentration) on C fluxes and 13 C discrimination of a microbial population growing at steady-state in a homogeneous, well-mixed environment. We estimated C uptake affinity and C use efficiency (CUE) to characterize the physiological responses of microbes to changing environmental conditions. Temperature increased biomass-C specific respiration rate and C uptake affinity at lower C availability, but did not influence those parameters at higher C availability. CUE decreased non-linearly with increasing temperature. The non-linear, negative relationship between CUE and temperature was more pronounced under lower C availability than under relatively high C availability. We observed stable isotope fractionation between C substrate and microbial biomass C (7~12‰ depletion), and between microbial biomass and respired CO 2 (4~10‰ depletion). Microbial discrimination against 13 C-containing cellobiose during C uptake was influenced by temperature and C availability, while discrimination during respiration was only influenced by C availability. Shifts in C uptake affinity with temperature and C availability may have modified uptake-induced 13 C fractionation. By stressing the importance of C availability on temperature responses of microbial C fluxes, C uptake affinity, CUE, and isotopic fractionation, this study contributes to a fundamental understanding of C flow through microbes. This will help guide parameterization of microbial responses to varying temperature and C availability within Earth-system models.

  3. VNARs: An Ancient and Unique Repertoire of Molecules That Deliver Small, Soluble, Stable and High Affinity Binders of Proteins

    Directory of Open Access Journals (Sweden)

    Caroline Barelle

    2015-09-01

    Full Text Available At 420 million years, the variable domain of New Antigen Receptors or VNARs are undoubtedly the oldest (and smallest antigen binding single domains identified in the vertebrate kingdom. Their role as an integral part of the adaptive immune system of sharks has been well established and has served to provide a greater understanding of the evolution of humoral immunity; their cellular components and processes as well as the underlying genetic organization and molecular control mechanisms. Intriguingly, unlike the variable domain of the camelid heavy chain antibodies or VHH, VNARs do not conform to all of the characteristic properties of classical antibodies with an ancestral origin that clearly distinguishes them from true immunoglobulin antibodies. However, this uniqueness of their origin only adds to their potential as next generation therapeutic biologics with their structural and functional attributes and commercial freedom all enhancing their profile and current success. In fact their small size, remarkable stability, molecular flexibility and solubility, together with their high affinity and selectivity for target, all reinforce the potential of these domains as drug candidates. The purpose of this review is to provide an overview of the existing basic biology of these unique domains, to highlight the drug-like properties of VNARs and describe current progress in their journey towards the clinic.

  4. CmRBP50 protein phosphorylation is essential for assembly of a stable phloem-mobile high-affinity ribonucleoprotein complex.

    Science.gov (United States)

    Li, Pingfang; Ham, Byung-Kook; Lucas, William J

    2011-07-01

    RNA-binding proteins (RBPs) form ribonucleoprotein (RNP) complexes that play crucial roles in RNA processing for gene regulation. The angiosperm sieve tube system contains a unique population of transcripts, some of which function as long-distance signaling agents involved in regulating organ development. These phloem-mobile mRNAs are translocated as RNP complexes. One such complex is based on a phloem RBP named Cucurbita maxima RNA-binding protein 50 (CmRBP50), a member of the polypyrimidine track binding protein family. The core of this RNP complex contains six additional phloem proteins. Here, requirements for assembly of this CmRBP50 RNP complex are reported. Phosphorylation sites on CmRBP50 were mapped, and then coimmunoprecipitation and protein overlay studies established that the phosphoserine residues, located at the C terminus of CmRBP50, are critical for RNP complex assembly. In vitro pull-down experiments revealed that three phloem proteins, C. maxima phloem protein 16, C. maxima GTP-binding protein, and C. maxima phosphoinositide-specific phospholipase-like protein, bind directly with CmRBP50. This interaction required CmRBP50 phosphorylation. Gel mobility-shift assays demonstrated that assembly of the CmRBP50-based protein complex results in a system having enhanced binding affinity for phloem-mobile mRNAs carrying polypyrimidine track binding motifs. This property would be essential for effective long-distance translocation of bound mRNA to the target tissues.

  5. Affinity driven social networks

    Science.gov (United States)

    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.

  6. Report: Affinity Chromatography.

    Science.gov (United States)

    Walters, Rodney R.

    1985-01-01

    Supports, affinity ligands, immobilization, elution methods, and a number of applications are among the topics considered in this discussion of affinity chromatography. An outline of the basic principles of affinity chromatography is included. (JN)

  7. Affine Grassmann codes

    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 af...

  8. Continuous affine processes

    DEFF Research Database (Denmark)

    Buchardt, Kristian

    2016-01-01

    Affine processes possess the property that expectations of exponential affine transformations are given by a set of Riccati differential equations, which is the main feature of this popular class of processes. In this paper we generalise these results for expectations of more general transformati...

  9. Robust Affine Invariant Descriptors

    Directory of Open Access Journals (Sweden)

    Jianwei Yang

    2011-01-01

    Full Text Available An approach is developed for the extraction of affine invariant descriptors by cutting object into slices. Gray values associated with every pixel in each slice are summed up to construct affine invariant descriptors. As a result, these descriptors are very robust to additive noise. In order to establish slices of correspondence between an object and its affine transformed version, general contour (GC of the object is constructed by performing projection along lines with different polar angles. Consequently, affine in-variant division curves are derived. A slice is formed by points fall in the region enclosed by two adjacent division curves. To test and evaluate the proposed method, several experiments have been conducted. Experimental results show that the proposed method is very robust to noise.

  10. Lectin affinity electrophoresis.

    Science.gov (United States)

    Kobayashi, Yuka

    2014-01-01

    An interaction or a binding event typically changes the electrophoretic properties of a molecule. Affinity electrophoresis methods detect changes in the electrophoretic pattern of molecules (mainly macromolecules) that occur as a result of biospecific interactions or complex formation. Lectin affinity electrophoresis is a very effective method for the detection and analysis of trace amounts of glycobiological substances. It is particularly useful for isolating and separating the glycoisomers of target molecules. Here, we describe a sensitive technique for the detection of glycoproteins separated by agarose gel-lectin affinity electrophoresis that uses antibody-affinity blotting. The technique is tested using α-fetoprotein with lectin (Lens culinaris agglutinin and Phaseolus vulgaris agglutinin)-agarose gels.

  11. Biomimetic affinity ligands for protein purification.

    Science.gov (United States)

    Sousa, Isabel T; Taipa, M Angela

    2014-01-01

    The development of sophisticated molecular modeling software and new bioinformatic tools, as well as the emergence of data banks containing detailed information about a huge number of proteins, enabled the de novo intelligent design of synthetic affinity ligands. Such synthetic compounds can be tailored to mimic natural biological recognition motifs or to interact with key surface-exposed residues on target proteins and are designated as "biomimetic ligands." A well-established methodology for generating biomimetic or synthetic affinity ligands integrates rational design with combinatorial solid-phase synthesis and screening, using the triazine scaffold and analogues of amino acids side chains to create molecular diversity.Triazine-based synthetic ligands are nontoxic, low-cost, highly stable compounds that can replace advantageously natural biological ligands in the purification of proteins by affinity-based methodologies.

  12. Induced affine inflation

    Science.gov (United States)

    Azri, Hemza; Demir, Durmuş

    2018-02-01

    Induced gravity, metrical gravity in which gravitational constant arises from vacuum expectation value of a heavy scalar, is known to suffer from Jordan frame vs Einstein frame ambiguity, especially in inflationary dynamics. Induced gravity in affine geometry, as we show here, leads to an emergent metric and gravity scale, with no Einstein-Jordan ambiguity. While gravity is induced by the vacuum expectation value of the scalar field, nonzero vacuum energy facilitates generation of the metric. Our analysis shows that induced gravity results in a relatively large tensor-to-scalar ratio in both metrical and affine gravity setups. However, the fact remains that the induced affine gravity provides an ambiguity-free framework.

  13. Affine stochastic mortality

    NARCIS (Netherlands)

    Schrager, D.F.

    2006-01-01

    We propose a new model for stochastic mortality. The model is based on the literature on affine term structure models. It satisfies three important requirements for application in practice: analytical tractibility, clear interpretation of the factors and compatibility with financial option pricing

  14. Experimental Affinities in Music

    OpenAIRE

    de Assis, Paulo

    2015-01-01

    Experimental Affinities in Music brings together diverse artistic, musicological, historical, and philosophical essays, enhancing a broad discourse on artistic experimentation, and exploring various experimental attitudes in music composed between the thirteenth and twentieth centuries. The golden thread running through the different chapters is the quest for inherently experimental musical practices, a quest pursued from interrogating, descriptive, or challenging perspectives, and always...

  15. Affine field theories

    International Nuclear Information System (INIS)

    Cadavid, A.C.

    1989-01-01

    The author constructs a non-Abelian field theory by gauging a Kac-Moody algebra, obtaining an infinite tower of interacting vector fields and associated ghosts, that obey slightly modified Feynman rules. She discusses the spontaneous symmetry breaking of such theory via the Higgs mechanism. If the Higgs particle lies in the Cartan subalgebra of the Kac-Moody algebra, the previously massless vectors acquire a mass spectrum that is linear in the Kac-Moody index and has additional fine structure depending on the associated Lie algebra. She proceeds to show that there is no obstacle in implementing the affine extension of supersymmetric Yang-Mills theories. The result is valid in four, six and ten space-time dimensions. Then the affine extension of supergravity is investigated. She discusses only the loop algebra since the affine extension of the super-Poincare algebra appears inconsistent. The construction of the affine supergravity theory is carried out by the group manifold method and leads to an action describing infinite towers of spin 2 and spin 3/2 fields that interact subject to the symmetries of the loop algebra. The equations of motion satisfy the usual consistency check. Finally, she postulates a theory in which both the vector and scalar fields lie in the loop algebra of SO(3). This theory has an expanded soliton sector, and corresponding to the original 't Hooft-Polyakov solitonic solutions she now finds an infinite family of exact, special solutions of the new equations. She also proposes a perturbation method for obtaining an arbitrary solution of those equations for each level of the affine index

  16. Stable isotopes

    International Nuclear Information System (INIS)

    Evans, D.K.

    1986-01-01

    Seventy-five percent of the world's stable isotope supply comes from one producer, Oak Ridge Nuclear Laboratory (ORNL) in the US. Canadian concern is that foreign needs will be met only after domestic needs, thus creating a shortage of stable isotopes in Canada. This article describes the present situation in Canada (availability and cost) of stable isotopes, the isotope enrichment techniques, and related research programs at Chalk River Nuclear Laboratories (CRNL)

  17. Adjoint affine fusion and tadpoles

    Energy Technology Data Exchange (ETDEWEB)

    Urichuk, Andrew, E-mail: andrew.urichuk@uleth.ca [Physics and Astronomy Department, University of Lethbridge, Lethbridge, Alberta T1K 3M4 (Canada); Walton, Mark A., E-mail: walton@uleth.ca [Physics and Astronomy Department, University of Lethbridge, Lethbridge, Alberta T1K 3M4 (Canada); International School for Advanced Studies (SISSA), via Bonomea 265, 34136 Trieste (Italy)

    2016-06-15

    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.

  18. in affine space A^6

    Directory of Open Access Journals (Sweden)

    Ofelya Arabyan

    2017-10-01

    Full Text Available A three-dimensional submanifold M in affine space A^6 is studied by the method of exterior forms. It is proven that the structure of total space generates a special type of affine connection on this submanifold; the structure equations of M are found.

  19. Hemoglobin affinity in Andean rodents

    Directory of Open Access Journals (Sweden)

    HRVOJ OSTOJIC

    2002-01-01

    Full Text Available Blood hemoglobin oxygen affinity (P50 was measured in three Andean species and in the laboratory rat (control, all raised near sea level. Chinchilla lanigera (Molina, 1792 has an altitudinal habitat range from low Andean slopes up to 3000 m., while Chinchilla brevicaudata (Waterhouse, 1848 has an altitudinal range from 3000 to 5000 m. The laboratory type guinea pig, wild type guinea pig (Cavia porcellus, (Waterhouse, 1748, and laboratory rat (Rattus norvegicus were also raised at sea level. The Andean species had high hemoglobin oxygen affinities (low P50 compared with the rat. Chinchilla brevicaudata had a higher affinity than Chinchilla lanigera. The wild type guinea pig had a higher affinity than the laboratory type. As has been shown in other species, this is another example of an inverse correlation between the altitude level and the P50 values. This is the first hemoglobin oxygen affinity study in Chinchilla brevicaudata.

  20. Mapping Affinities in Academic Organizations

    Directory of Open Access Journals (Sweden)

    Dario Rodighiero

    2018-02-01

    Full Text Available Scholarly affinities are one of the most fundamental hidden dynamics that drive scientific development. Some affinities are actual, and consequently can be measured through classical academic metrics such as co-authoring. Other affinities are potential, and therefore do not leave visible traces in information systems; for instance, some peers may share interests without actually knowing it. This article illustrates the development of a map of affinities for academic collectives, designed to be relevant to three audiences: the management, the scholars themselves, and the external public. Our case study involves the School of Architecture, Civil and Environmental Engineering of EPFL, hereinafter ENAC. The school consists of around 1,000 scholars, 70 laboratories, and 3 institutes. The actual affinities are modeled using the data available from the information systems reporting publications, teaching, and advising scholars, whereas the potential affinities are addressed through text mining of the publications. The major challenge for designing such a map is to represent the multi-dimensionality and multi-scale nature of the information. The affinities are not limited to the computation of heterogeneous sources of information; they also apply at different scales. The map, thus, shows local affinities inside a given laboratory, as well as global affinities among laboratories. This article presents a graphical grammar to represent affinities. Its effectiveness is illustrated by two actualizations of the design proposal: an interactive online system in which the map can be parameterized, and a large-scale carpet of 250 square meters. In both cases, we discuss how the materiality influences the representation of data, in particular the way key questions could be appropriately addressed considering the three target audiences: the insights gained by the management and their consequences in terms of governance, the understanding of the scholars’ own

  1. 2017 Guralp Affinity Digitizer Evaluation.

    Energy Technology Data Exchange (ETDEWEB)

    Merchant, Bion J.

    2018-03-01

    Sandia National Laboratories has tested and evaluated two Guralp Affinity digitizers. The Affinity digitizers are intended to record sensor output for seismic and infrasound monitoring applications. The purpose of this digitizer evaluation is to measure the performance characteristics in such areas as power consumption, input impedance, sensitivity, full scale, self- noise, dynamic range, system noise, response, passband, and timing. The Affinity digitizers are being evaluated for potential use in the International Monitoring System (IMS) of the Comprehensive Nuclear Test-Ban-Treaty Organization (CTBTO).

  2. The utility of affine variables and affine coherent states

    International Nuclear Information System (INIS)

    Klauder, John R

    2012-01-01

    Affine coherent states are generated by affine kinematical variables much like canonical coherent states are generated by canonical kinematical variables. Although all classical and quantum formalisms normally entail canonical variables, it is shown that affine variables can serve equally well for many classical and quantum studies. This general purpose analysis provides tools to discuss two major applications: (1) the completely successful quantization of a nonrenormalizable scalar quantum field theory by affine techniques, in complete contrast to canonical techniques which only offer triviality; and (2) a formulation of the kinematical portion of quantum gravity that favors affine kinematical variables over canonical kinematical variables, and which generates a framework in which a favorable analysis of the constrained dynamical issues can take place. All this is possible because of the close connection between the affine and the canonical stories, while the few distinctions can be used to advantage when appropriate. This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical devoted to ‘Coherent states: mathematical and physical aspects’. (review)

  3. Representations of affine Hecke algebras

    CERN Document Server

    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

  4. Stable particles

    International Nuclear Information System (INIS)

    Samios, N.P.

    1994-01-01

    I have been asked to review the subject of stable particles, essentially the particles that eventually comprised the meson and baryon octets, with a few more additions - with an emphasis on the contributions made by experiments utilizing the bubble chamber technique. In this activity, much work had been done by the photographic emulsion technique and cloud chambers - exposed to cosmic rays as well as accelerator based beams. In fact, many if not most of the stable particles were found by these latter two techniques, however, the foree of the bubble chamber (coupled with the newer and more powerful accelerators) was to verify, and reinforce with large statistics, the existence of these states, to find some of the more difficult ones, mainly neutrals and further to elucidate their properties, i.e., spin, parity, lifetimes, decay parameters, etc. (orig.)

  5. Stable particles

    International Nuclear Information System (INIS)

    Samios, N.P.

    1993-01-01

    I have been asked to review the subject of stable particles, essentially the particles that eventually comprised the meson and baryon octets. with a few more additions -- with an emphasis on the contributions made by experiments utilizing the bubble chamber technique. In this activity, much work had been done by the photographic emulsion technique and cloud chambers-exposed to cosmic rays as well as accelerator based beams. In fact, many if not most of the stable particles were found by these latter two techniques, however, the forte of the bubble chamber (coupled with the newer and more powerful accelerators) was to verify, and reinforce with large statistics, the existence of these states, to find some of the more difficult ones, mainly neutrals and further to elucidate their properties, i.e., spin, parity, lifetimes, decay parameters, etc

  6. Alternative Affinity Ligands for Immunoglobulins.

    Science.gov (United States)

    Kruljec, Nika; Bratkovič, Tomaž

    2017-08-16

    The demand for recombinant therapeutic antibodies and Fc-fusion proteins is expected to increase in the years to come. Hence, extensive efforts are concentrated on improving the downstream processing. In particular, the development of better-affinity chromatography matrices, supporting robust time- and cost-effective antibody purification, is warranted. With the advances in molecular design and high-throughput screening approaches from chemical and biological combinatorial libraries, novel affinity ligands representing alternatives to bacterial immunoglobulin (Ig)-binding proteins have entered the scene. Here, we review the design, development, and properties of diverse classes of alternative antibody-binding ligands, ranging from engineered versions of Ig-binding proteins, to artificial binding proteins, peptides, aptamers, and synthetic small-molecular-weight compounds. We also provide examples of applications for the novel affinity matrices in chromatography and beyond.

  7. Stable beams

    CERN Multimedia

    2015-01-01

    Stable beams: two simple words that carry so much meaning at CERN. When LHC page one switched from "squeeze" to "stable beams" at 10.40 a.m. on Wednesday, 3 June, it triggered scenes of jubilation in control rooms around the CERN sites, as the LHC experiments started to record physics data for the first time in 27 months. This is what CERN is here for, and it’s great to be back in business after such a long period of preparation for the next stage in the LHC adventure.   I’ve said it before, but I’ll say it again. This was a great achievement, and testimony to the hard and dedicated work of so many people in the global CERN community. I could start to list the teams that have contributed, but that would be a mistake. Instead, I’d simply like to say that an achievement as impressive as running the LHC – a machine of superlatives in every respect – takes the combined effort and enthusiasm of everyone ...

  8. Affinity biosensors: techniques and protocols

    National Research Council Canada - National Science Library

    Rogers, Kim R; Mulchandani, Ashok

    1998-01-01

    ..., and government to begin or expand their biosensors research. This volume, Methods in Biotechnology vol. 7: Affinity Biosensors: Techniques and Protocols, describes a variety of classical and emerging transduction technologies that have been interfaced to bioaffinity elements (e.g., antibodies and receptors). Some of the reas...

  9. The affine quantum gravity programme

    CERN Document Server

    Klauder, J R

    2002-01-01

    The central principle of affine quantum gravity is securing and maintaining the strict positivity of the matrix left brace g-hat sub a sub b (x)right brace 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 sti...

  10. Scaling Analysis of Affinity Propagation

    OpenAIRE

    Furtlehner , Cyril; Sebag , Michèle; Xiangliang , Zhang

    2010-01-01

    14 pages, 11 figures; International audience; We analyze and exploit some scaling properties of the {\\em Affinity Propagation} (AP) clustering algorithm proposed by Frey and Dueck (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 t...

  11. Electron affinity of liquid water

    Energy Technology Data Exchange (ETDEWEB)

    Gaiduk, Alex P.; Pham, Tuan Anh; Govoni, Marco; Paesani, Francesco; Galli, Giulia

    2018-01-16

    Understanding redox and photochemical reactions in aqueous environments requires a precise knowledge of the ionization potential and electron affinity of liquid water. The former has been measured, but not the latter. We predict the electron affinity of liquid water and of its surface from first principles, coupling path-integral molecular dynamics with ab initio potentials, and many-body perturbation theory. Our results for the surface (0.8 eV) agree well with recent pump-probe spectroscopy measurements on amorphous ice. Those for the bulk (0.1–0.3 eV) differ from several estimates adopted in the literature, which we critically revisit. We show that the ionization potential of the bulk and surface are almost identical; instead their electron affinities differ substantially, with the conduction band edge of the surface much deeper in energy than that of the bulk. We also discuss the significant impact of nuclear quantum effects on the fundamental gap and band edges of the liquid.

  12. Spectral affinity in protein networks.

    Science.gov (United States)

    Voevodski, Konstantin; Teng, Shang-Hua; Xia, Yu

    2009-11-29

    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. 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. 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 quickly find nodes closest to a queried vertex in any protein

  13. 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

  14. 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.

  15. Topological conjugacy classes of affine maps

    OpenAIRE

    Tetiana, Budnytska

    2008-01-01

    A map $f: \\ff^n \\to \\ff^n$ over a field $\\ff$ is called affine if it is of the form $f(x)=Ax+b$, where the matrix $A \\in \\ff^{n\\times n}$ is called the linear part of affine map and $b \\in \\ff^n$. The affine maps over $\\ff=\\rr$ or $\\cc$ are investigated. We prove that affine maps having fixed points are topologically conjugate if and only if their linear parts are topologically conjugate. If affine maps have no fixed points and $n=1$ or 2, then they are topologically conjugate if and only if ...

  16. The affine quantum gravity programme

    International Nuclear Information System (INIS)

    Klauder, John R

    2002-01-01

    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

  17. Affine-projective field laws

    International Nuclear Information System (INIS)

    Murphy, G.L.

    1975-01-01

    The general topic of geometric unified field theories is discussed in the first section. Some reasons are given for pursuing such theories, and some criticisms are considered. The second section develops the fundamental equations of a purely affine theory which is invariant under projective transformations of the affine connection. This theory is a generalization of that of Schrodinger. Possible identifications for the space-time metric are considered in Sec. III. Sections IV and V deal with the limits of pure gravitation and electrodynamics. In the symmetric limit, Einstein's vacuum equations with cosmological term are recovered. The theory also contains a generalized electrodynamic set of equations which is very similar to the Born-Infeld set. In the weak-field approximation, a finite mass must be attributed to the photon. The problem of motion for charges is discussed here, and it is argued that criticisms of unified field theories because of a supposed inability to produce the Lorentz force law are probably not justified. Three more speculative sections deal with possible explanations of nuclear forces, the spin-torsion relation, and particle structure

  18. Antisymmetric tensor generalizations of affine vector fields.

    Science.gov (United States)

    Houri, Tsuyoshi; Morisawa, Yoshiyuki; Tomoda, Kentaro

    2016-02-01

    Tensor generalizations of affine vector fields called symmetric and antisymmetric affine tensor fields are discussed as symmetry of spacetimes. We review the properties of the symmetric ones, which have been studied in earlier works, and investigate the properties of the antisymmetric ones, which are the main theme in this paper. It is shown that antisymmetric affine tensor fields are closely related to one-lower-rank antisymmetric tensor fields which are parallelly transported along geodesics. It is also shown that the number of linear independent rank- p antisymmetric affine tensor fields in n -dimensions is bounded by ( n + 1)!/ p !( n - p )!. We also derive the integrability conditions for antisymmetric affine tensor fields. Using the integrability conditions, we discuss the existence of antisymmetric affine tensor fields on various spacetimes.

  19. 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.

  20. Stable Isotope Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Tissue samples (skin, bone, blood, muscle) are analyzed for stable carbon, stable nitrogen, and stable sulfur analysis. Many samples are used in their entirety for...

  1. Scaling analysis of affinity propagation

    Science.gov (United States)

    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.

  2. On affine non-negative matrix factorization

    DEFF Research Database (Denmark)

    Laurberg, Hans; Hansen, Lars Kai

    2007-01-01

    We generalize the non-negative matrix factorization (NMF) generative model to incorporate an explicit offset. Multiplicative estimation algorithms are provided for the resulting sparse affine NMF model. We show that the affine model has improved uniqueness properties and leads to more accurate...

  3. Using Affinity Diagrams to Evaluate Interactive Prototypes

    DEFF Research Database (Denmark)

    Lucero, Andrés

    2015-01-01

    Affinity diagramming is a technique used to externalize, make sense of, and organize large amounts of unstructured, far-ranging, and seemingly dissimilar qualitative data. HCI and interaction design practitioners have adopted and used affinity diagrams for different purposes. This paper discusses...

  4. Global affine differential geometry of hypersurfaces

    CERN Document Server

    Li, An-Min; Zhao, Guosong; Hu, Zejun

    2015-01-01

    This book draws a colorful and widespread picture of global affine hypersurface theory up to the most recent state. Moreover, the recent development revealed that affine differential geometry- as differential geometry in general- has an exciting intersection area with other fields of interest, like partial differential equations, global analysis, convex geometry and Riemann surfaces.

  5. Phosphopeptide enrichment by immobilized metal affinity chromatography

    DEFF Research Database (Denmark)

    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...

  6. Fatty acid and drug binding to a low-affinity component of human serum albumin, purified by affinity chromatography

    DEFF Research Database (Denmark)

    Vorum, H; Pedersen, A O; Honoré, B

    1992-01-01

    and drug binding abilities of the low-affinity component. The fatty acids decanoate, laurate, myristate and palmitate were bound with higher affinity to the mixture than to the low-affinity component. Diazepam was bound with nearly the same affinity to the low-affinity component as to the albumin mixture...... of two albumin components about 40% of the albumin having high affinity and about 60% having low affinity. By affinity chromatography we succeeded in purifying the low-affinity component from the mixture. The high-affinity component, however, could not be isolated. We further analyzed the fatty acid...

  7. 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.

  8. Stable convergence and stable limit theorems

    CERN Document Server

    Häusler, Erich

    2015-01-01

    The authors present a concise but complete exposition of the mathematical theory of stable convergence and give various applications in different areas of probability theory and mathematical statistics to illustrate the usefulness of this concept. Stable convergence holds in many limit theorems of probability theory and statistics – such as the classical central limit theorem – which are usually formulated in terms of convergence in distribution. Originated by Alfred Rényi, the notion of stable convergence is stronger than the classical weak convergence of probability measures. A variety of methods is described which can be used to establish this stronger stable convergence in many limit theorems which were originally formulated only in terms of weak convergence. Naturally, these stronger limit theorems have new and stronger consequences which should not be missed by neglecting the notion of stable convergence. The presentation will be accessible to researchers and advanced students at the master's level...

  9. The Cutting Edge of Affinity Electrophoresis Technology

    Science.gov (United States)

    Kinoshita, Eiji; Kinoshita-Kikuta, Emiko; Koike, Tohru

    2015-01-01

    Affinity electrophoresis is an important technique that is widely used to separate and analyze biomolecules in the fields of biology and medicine. Both quantitative and qualitative information can be gained through affinity electrophoresis. Affinity electrophoresis can be applied through a variety of strategies, such as mobility shift electrophoresis, charge shift electrophoresis or capillary affinity electrophoresis. These strategies are based on changes in the electrophoretic patterns of biological macromolecules that result from interactions or complex-formation processes that induce changes in the size or total charge of the molecules. Nucleic acid fragments can be characterized through their affinity to other molecules, for example transcriptional factor proteins. Hydrophobic membrane proteins can be identified by means of a shift in the mobility induced by a charged detergent. The various strategies have also been used in the estimation of association/disassociation constants. Some of these strategies have similarities to affinity chromatography, in that they use a probe or ligand immobilized on a supported matrix for electrophoresis. Such methods have recently contributed to profiling of major posttranslational modifications of proteins, such as glycosylation or phosphorylation. Here, we describe advances in analytical techniques involving affinity electrophoresis that have appeared during the last five years. PMID:28248262

  10. The Cutting Edge of Affinity Electrophoresis Technology.

    Science.gov (United States)

    Kinoshita, Eiji; Kinoshita-Kikuta, Emiko; Koike, Tohru

    2015-03-18

    Affinity electrophoresis is an important technique that is widely used to separate and analyze biomolecules in the fields of biology and medicine. Both quantitative and qualitative information can be gained through affinity electrophoresis. Affinity electrophoresis can be applied through a variety of strategies, such as mobility shift electrophoresis, charge shift electrophoresis or capillary affinity electrophoresis. These strategies are based on changes in the electrophoretic patterns of biological macromolecules that result from interactions or complex-formation processes that induce changes in the size or total charge of the molecules. Nucleic acid fragments can be characterized through their affinity to other molecules, for example transcriptional factor proteins. Hydrophobic membrane proteins can be identified by means of a shift in the mobility induced by a charged detergent. The various strategies have also been used in the estimation of association/disassociation constants. Some of these strategies have similarities to affinity chromatography, in that they use a probe or ligand immobilized on a supported matrix for electrophoresis. Such methods have recently contributed to profiling of major posttranslational modifications of proteins, such as glycosylation or phosphorylation. Here, we describe advances in analytical techniques involving affinity electrophoresis that have appeared during the last five years.

  11. Mobile Technology Affinity in Renal Transplant Recipients.

    Science.gov (United States)

    Reber, S; Scheel, J; Stoessel, L; Schieber, K; Jank, S; Lüker, C; Vitinius, F; Grundmann, F; Eckardt, K-U; Prokosch, H-U; Erim, Y

    Medication nonadherence is a common problem in renal transplant recipients (RTRs). Mobile health approaches to improve medication adherence are a current trend, and several medication adherence apps are available. However, it is unknown whether RTRs use these technologies and to what extent. In the present study, the mobile technology affinity of RTRs was analyzed. We hypothesized significant age differences in mobile technology affinity and that mobile technology affinity is associated with better cognitive functioning as well as higher educational level. A total of 109 RTRs (63% male) participated in the cross-sectional study, with an overall mean age of 51.8 ± 14.2 years. The study included the Technology Experience Questionnaire (TEQ) for the assessment of mobile technology affinity, a cognitive test battery, and sociodemographic data. Overall, 57.4% of the patients used a smartphone or tablet and almost 45% used apps. The TEQ sum score was 20.9 in a possible range from 6 (no affinity to technology) to 30 (very high affinity). Younger patients had significantly higher scores in mobile technology affinity. The only significant gender difference was found in having fun with using electronic devices: Men enjoyed technology more than women did. Mobile technology affinity was positively associated with cognitive functioning and educational level. Young adult patients might profit most from mobile health approaches. Furthermore, high educational level and normal cognitive functioning promote mobile technology affinity. This should be kept in mind when designing mobile technology health (mHealth) interventions for RTRs. For beneficial mHealth interventions, further research on potential barriers and desired technologic features is necessary to adapt apps to patients' needs. Copyright © 2017 Elsevier Inc. All rights reserved.

  12. Scaling laws in phytoplankton nutrient uptake affinity

    DEFF Research Database (Denmark)

    Lindemann, Christian; Fiksen, Øyvind; Andersen, Ken Haste

    2016-01-01

    Nutrient uptake affinity affects the competitive ability of microbial organisms at low nutrient concentrations. From the theory of diffusion limitation it follows that uptake affinity scales linearly with the cell radius. This is in conflict with some observations suggesting that uptake affinity...... scales to a quantity that is closer to the square of the radius, i.e. to cell surface area. We show that this apparent conflict can be resolved by nutrient uptake theory. Pure diffusion limitation assumes that the cell is a perfect sink which means that it is able to absorb all encountered nutrients...

  13. Affinity Strings: Enterprise Data for Resource Recommendations

    Directory of Open Access Journals (Sweden)

    Shane Nackerud

    2008-12-01

    Full Text Available The University of Minnesota Libraries have created a MyLibrary portal, with databases and e-journals targeted to users, based on their affiliations. The University's enterprise authentication system provides an "affinity string", now used to personalize the MyLibrary portal. This affinity string automates discovery of a user's relationship to the University--describing a user's academic department and degree program or position at the University. Affinity strings also provide the Libraries with an anonymized view of resource usage, allowing data collection that respects users' privacy and lays the groundwork for automated recommendation of relevant resources based on the practices and habits of their peers.

  14. Automorphisms in Birational and Affine Geometry

    CERN Document Server

    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...

  15. Biodiversity, zoogeography and affinity of Orissa sponges

    Digital Repository Service at National Institute of Oceanography (India)

    Thomas, P.A.; Sree, A.; Bapuji, M.; Rao, K.M.; Murthy, K.S.R.

    from these reefs. The diversity, bio-zeo-distribution and affinity of these sponges are discussed. The analysis of data is mainly arrived at by quasi-quantitative sampling supported by observations and video documentation. Community structure...

  16. Quantum deformation of the affine transformation algebra

    International Nuclear Information System (INIS)

    Aizawa, N.; Sato, Haru-Tada

    1994-01-01

    We discuss a quantum deformation of the affine transformation algebra in one-dimensional space. It is shown that the quantum algebra has a non-cocommutative Hopf algebra structure, simple realizations and quantum tensor operators. (orig.)

  17. 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

  18. Cyanated diazatetracene diimides with ultrahigh electron affinity for n-channel field effect transistors

    KAUST Repository

    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.

  19. stableGP

    Data.gov (United States)

    National Aeronautics and Space Administration — The code in the stableGP package implements Gaussian process calculations using efficient and numerically stable algorithms. Description of the algorithms is in the...

  20. Different endothelin receptor affinities in dog tissues

    International Nuclear Information System (INIS)

    Loeffler, B.M.L.; Loehrer, W.

    1991-01-01

    Endothelin (ET) is a long-lasting potent vasoconstrictor-peptide. Here the authors report different binding affinities of endothelin-1 (ET-1) to ET-receptors of various dog tissues. Crude microsomal fractions were prepared after homogenisation of dog tissues in 50 mM Tris/HCl, 20 mM MnCl2, 1 mM EDTA, pH 7.4 by differential centrifugation. Aliquots of microsomal fractions (70 micrograms of protein) were incubated at 25 degrees C for 180 min in the presence of 20 pM 125I-ET-1 and various concentrations of cold ET-1. Four different ET-1 receptor binding affinities were found: adrenals, cerebrum, liver, heart, skeletal muscle and stomach microsomal membranes contained high affinity binding sites (Kd 50 - 80 pM, Bmax 60 - 250 fmol/mg). In cerebellum and spleen medium affinity ET-1 receptors (Kd 350 pM, Bmax 880 and 1200 fmol/mg respectively) were present. In comparison lung and kidney microsomes contained a low affinity ET-1 receptor (Kd 800 and 880 pM, Bmax 1600 and 350 fmol/mg). Receptors of even lower affinity were present in heart, intestine and liver microsomes with Kd values of 3 - 6 nM

  1. The metric-affine gravitational theory as the gauge theory of the affine group

    International Nuclear Information System (INIS)

    Lord, E.A.

    1978-01-01

    The metric-affine gravitational theory is shown to be the gauge theory of the affine group, or equivalently, the gauge theory of the group GL(4,R) of tetrad deformations in a space-time with a locally Minkowskian metric. The identities of the metric-affine theory, and the relationship between them and those of general relativity and Sciama-Kibble theory, are derived. (Auth.)

  2. Protein A affinity precipitation of human immunoglobulin G.

    Science.gov (United States)

    Janoschek, Lars; Freiherr von Roman, Matthias; Berensmeier, Sonja

    2014-08-15

    The potential of protein A affinity precipitation as an alternative method for traditional antibody purification techniques was investigated. Recombinant produced protein A from Staphylococcus aureus (SpA) was covalently linked to the pH-responsive copolymer Eudragit(®) S-100 and used for purification of human immunoglobulin G (hIgG). The Eudragit-SpA conjugate had a static binding capacity of 93.9 ± 2.8 mg hIgG per g conjugate and a dissociation constant of 787 ± 67 nM at 7 ± 1°C. The antibody was adsorbed rapidly onto Eudragit-SpA and reached equilibrium within 5 min. An excess of hIgG binding sites, provided by the conjugate, as well as adjusted elution conditions resulted in an appropriate hIgG purification performance. In summary, Eudragit-SpA was successfully applied to capture hIgG from a protein mixture with 65% antibody yield in the elution step. Nearly 96% purity and a purification factor of 12.4 were achieved. The Eudragit-SpA conjugate showed a stable ligand density over several cycles, which enabled reusability for repeated precipitation of hIgG. According to this, pH induced affinity precipitation can be seen as a potential alternative for protein A chromatography in antibody purification processes. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Structures and electron affinities of indole-(water)N clusters

    Science.gov (United States)

    Carles, S.; Desfrançois, C.; Schermann, J. P.; Smith, D. M. A.; Adamowicz, L.

    2000-02-01

    Rydberg electron transfer spectroscopy (RET) has been used to determine the dipole-bound electron affinity of the indole molecule, and the value of 3 meV was obtained. RET has also been employed to study [indole-(water)N]- cluster anions and the results have been interpreted with the help of ab initio calculations. It has been shown that for N=1 and 2 only dipole-bound anions are formed and that the electron attachment induces large amplitude motions in these systems. [Indole-(water)N]- anions with N=3 and 4 have not been observed. This finding for N=3 is consistent with a low theoretically predicted dipole moment of the neutral indole-(water)3 complex, which is insufficient for the formation of a stable dipole-bound anion. Above N=5, RET experiments showed formation of valence [indole-(water)N]- anions. From the observed size threshold for the formation of these anions, the negative value of the valence electron affinity of indole equal to -1.03±0.05 meV was deduced.

  4. Classification of neocortical interneurons using affinity propagation

    Science.gov (United States)

    Santana, Roberto; McGarry, Laura M.; Bielza, Concha; Larrañaga, Pedro; Yuste, Rafael

    2013-01-01

    In spite of over a century of research on cortical circuits, it is still unknown how many classes of cortical neurons exist. In fact, neuronal classification is a difficult problem because it is unclear how to designate a neuronal cell class and what are the best characteristics to define them. Recently, unsupervised classifications using cluster analysis based on morphological, physiological, or molecular characteristics, have provided quantitative and unbiased identification of distinct neuronal subtypes, when applied to selected datasets. However, better and more robust classification methods are needed for increasingly complex and larger datasets. Here, 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. Affinity propagation outperformed Ward's method, a current standard clustering approach, in classifying the neurons into 4 subtypes. Affinity propagation could therefore be used in future studies to validly classify neurons, as a first step to help reverse engineer neural circuits. PMID:24348339

  5. Monolithic media for applications in affinity chromatography.

    Science.gov (United States)

    Sproß, Jens; Sinz, Andrea

    2011-08-01

    Affinity chromatography presents a highly versatile analytical tool, which relies on exploiting highly specific interactions between molecules and their ligands. This review covers the most recent literature on the application of monoliths as stationary phases for various affinity-based chromatographic applications. Different affinity approaches as well as separations using molecularly imprinted monoliths are discussed. Hybrid stationary phases created by embedding of particles or nanoparticles into a monolithic stationary phase are also considered in this review article. The ease of preparation of monoliths and the multitude of functionalization techniques, which have matured during the past years, make monoliths interesting for an increasing number of biochemical and medical applications. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. 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.

  7. Affine coherent states and Toeplitz operators

    Science.gov (United States)

    Hutníková, Mária; Hutník, Ondrej

    2012-06-01

    We study a parameterized family of Toeplitz operators in the context of affine coherent states based on the Calderón reproducing formula (= resolution of unity on L_2( {R})) and the specific admissible wavelets (= affine coherent states in L_2( {R})) related to Laguerre functions. Symbols of such Calderón-Toeplitz operators as individual coordinates of the affine group (= upper half-plane with the hyperbolic geometry) are considered. In this case, a certain class of pseudo-differential operators, their properties and their operator algebras are investigated. As a result of this study, the Fredholm symbol algebras of the Calderón-Toeplitz operator algebras for these particular cases of symbols are described. This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical devoted to ‘Coherent states: mathematical and physical aspects’.

  8. The dynamics of metric-affine gravity

    International Nuclear Information System (INIS)

    Vitagliano, Vincenzo; Sotiriou, Thomas P.; Liberati, Stefano

    2011-01-01

    Highlights: → The role and the dynamics of the connection in metric-affine theories is explored. → The most general second order action does not lead to a dynamical connection. → Including higher order invariants excites new degrees of freedom in the connection. → f(R) actions are also discussed and shown to be a non- representative class. - Abstract: Metric-affine theories of gravity provide an interesting alternative to general relativity: in such an approach, the metric and the affine (not necessarily symmetric) connection are independent quantities. Furthermore, the action should include covariant derivatives of the matter fields, with the covariant derivative naturally defined using the independent connection. As a result, in metric-affine theories a direct coupling involving matter and connection is also present. The role and the dynamics of the connection in such theories is explored. We employ power counting in order to construct the action and search for the minimal requirements it should satisfy for the connection to be dynamical. We find that for the most general action containing lower order invariants of the curvature and the torsion the independent connection does not carry any dynamics. It actually reduces to the role of an auxiliary field and can be completely eliminated algebraically in favour of the metric and the matter field, introducing extra interactions with respect to general relativity. However, we also show that including higher order terms in the action radically changes this picture and excites new degrees of freedom in the connection, making it (or parts of it) dynamical. Constructing actions that constitute exceptions to this rule requires significant fine tuned and/or extra a priori constraints on the connection. We also consider f(R) actions as a particular example in order to show that they constitute a distinct class of metric-affine theories with special properties, and as such they cannot be used as representative toy

  9. New unitary affine-Virasoro constructions

    International Nuclear Information System (INIS)

    Halpern, M.B.; Kiritsis, E.; Obers, N.A.; Poratti, M.; Yamron, J.P.

    1990-01-01

    This paper reports on a quasi-systematic investigation of the Virasoro master equation. The space of all affine-Virasoro constructions is organized by K-conjugation into affine-Virasoro nests, and an estimate of the dimension of the space shows that most solutions await discovery. With consistent ansatze for the master equation, large classes of new unitary nests are constructed, including quadratic deformation nests with continuous conformal weights, and unitary irrational central charge nests, which may dominate unitary rational central charge on compact g

  10. Control and estimation of piecewise affine systems

    CERN Document Server

    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

  11. 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 :

  12. Fatty acid and drug binding to a low-affinity component of human serum albumin, purified by affinity chromatography

    DEFF Research Database (Denmark)

    Vorum, H; Pedersen, A O; Honoré, B

    1992-01-01

    Binding equilibria for decanoate to a defatted, commercially available human serum albumin preparation were investigated by dialysis exchange rate determinations. The binding isotherm could not be fitted by the general binding equation. It was necessary to assume that the preparation was a mixture...... of two albumin components about 40% of the albumin having high affinity and about 60% having low affinity. By affinity chromatography we succeeded in purifying the low-affinity component from the mixture. The high-affinity component, however, could not be isolated. We further analyzed the fatty acid...... and drug binding abilities of the low-affinity component. The fatty acids decanoate, laurate, myristate and palmitate were bound with higher affinity to the mixture than to the low-affinity component. Diazepam was bound with nearly the same affinity to the low-affinity component as to the albumin mixture...

  13. Stable isotopes labelled compounds

    International Nuclear Information System (INIS)

    1982-09-01

    The catalogue on stable isotopes labelled compounds offers deuterium, nitrogen-15, and multiply labelled compounds. It includes: (1) conditions of sale and delivery, (2) the application of stable isotopes, (3) technical information, (4) product specifications, and (5) the complete delivery programme

  14. Stable Boundary Layer Issues

    NARCIS (Netherlands)

    Steeneveld, G.J.

    2012-01-01

    Understanding and prediction of the stable atmospheric boundary layer is a challenging task. Many physical processes are relevant in the stable boundary layer, i.e. turbulence, radiation, land surface coupling, orographic turbulent and gravity wave drag, and land surface heterogeneity. The

  15. Evolutionary Stable Strategy

    Indian Academy of Sciences (India)

    IAS Admin

    After Maynard-Smith and Price [1] mathematically derived why a given behaviour or strategy was adopted by a certain proportion of the population at a given time, it was shown that a strategy which is currently stable in a population need not be stable in evolutionary time (across generations). Additionally it was sug-.

  16. Fan Affinity Laws from a Collision Model

    Science.gov (United States)

    Bhattacharjee, Shayak

    2012-01-01

    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…

  17. General super Virasoro construction on affine G

    International Nuclear Information System (INIS)

    Mohammedi, N.

    1990-10-01

    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

  18. It's the peptide-MHC affinity, stupid.

    Science.gov (United States)

    Kammertoens, Thomas; Blankenstein, Thomas

    2013-04-15

    Adoptively transferred T cells can reject large established tumors, but recurrence due to escape variants frequently occurs. In this issue of Cancer Cell, Engels et al. demonstrate that the affinity of the target peptide to the MHC molecule determines whether large tumors will relapse following adoptive T cell therapy. Copyright © 2013 Elsevier Inc. All rights reserved.

  19. Proton affinity measurements using ion mobility spectrometry

    International Nuclear Information System (INIS)

    Tabrizchi, Mahmoud.; Shooshtari, Saeed

    2003-01-01

    Relative proton affinities are usually measured by means of high pressure mass spectrometry. In this work ion mobility spectrometry was used to determine proton affinities. The standard molar enthalpy change ΔH 0 M for the reaction MH + +N[rlhar2]M+NH + was found to be: -(56.3±0.8) kJ·mol -1 , when M was ethyl acetate and N ethanol; -(27.8±0.5) kJ·mol -1 , when M was acetophenone and N ethyl acetate; -(10.6±0.2) kJ·mol -1 , when M was cycloheptanone and N ethyl acetate; -(66.1±1.2) kJ·mol -1 , when M was dimethyl methyl phosphonate and N ethyl acetate; and, -(56.7±0.9) kJ·mol -1 , when M was dimethyl methyl phosphonate and N cycloheptanone. These values are internally consistent and in good agreement with results obtained with high pressure mass spectrometry. On the basis of proton affinities of cycloheptanone and ethyl acetate, an absolute proton affinity of (902±1.2) kJ·mol -1 has been determined for dimethyl methyl phosphonate

  20. 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.

  1. Congophilicity (Congo red affinity) of different beta2-microglobulin conformations characterized by dye affinity capillary electrophoresis

    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......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...

  2. Congophilicity (Congo red affinity) of different beta2-microglobulin conformations characterized by dye affinity capillary electrophoresis

    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 native and abnormally folded beta2-microglobulin. We find that native beta2-microglobulin has an intermediate affinity for Congo red at pH 7.3 and that binding involves electrostatic interactions. The conformational variant of beta2-microglobulin that appears in acetonitrile solutions binds Congo red...... more strongly. Affinity CE using Congo red as a buffer additive is a new, simple, fast, and quantitative micromethod for the characterization of soluble conformational intermediates of amyloidogenic proteins....

  3. Normal modified stable processes

    DEFF Research Database (Denmark)

    Barndorff-Nielsen, Ole Eiler; Shephard, N.

    2002-01-01

    This paper discusses two classes of distributions, and stochastic processes derived from them: modified stable (MS) laws and normal modified stable (NMS) laws. This extends corresponding results for the generalised inverse Gaussian (GIG) and generalised hyperbolic (GH) or normal generalised inverse...... Gaussian (NGIG) laws. The wider framework thus established provides, in particular, for added flexibility in the modelling of the dynamics of financial time series, of importance especially as regards OU based stochastic volatility models for equities. In the special case of the tempered stable OU process...

  4. Applications of stable isotopes

    International Nuclear Information System (INIS)

    Letolle, R.; Mariotti, A.; Bariac, T.

    1991-06-01

    This report reviews the historical background and the properties of stable isotopes, the methods used for their measurement (mass spectrometry and others), the present technics for isotope enrichment and separation, and at last the various present and foreseeable application (in nuclear energy, physical and chemical research, materials industry and research; tracing in industrial, medical and agronomical tests; the use of natural isotope variations for environmental studies, agronomy, natural resources appraising: water, minerals, energy). Some new possibilities in the use of stable isotope are offered. A last chapter gives the present state and forecast development of stable isotope uses in France and Europe

  5. Analysing Stable Time Series

    National Research Council Canada - National Science Library

    Adler, Robert

    1997-01-01

    We describe how to take a stable, ARMA, time series through the various stages of model identification, parameter estimation, and diagnostic checking, and accompany the discussion with a goodly number...

  6. Affine Non-Local Means Image Denoising.

    Science.gov (United States)

    Fedorov, Vadim; Ballester, Coloma

    2017-05-01

    This paper presents an extension of the Non-Local Means denoising method, that effectively exploits the affine invariant self-similarities present in the images of real scenes. Our method provides a better image denoising result by grounding on the fact that in many occasions similar patches exist in the image but have undergone a transformation. The proposal uses an affine invariant patch similarity measure that performs an appropriate patch comparison by automatically and intrinsically adapting the size and shape of the patches. As a result, more similar patches are found and appropriately used. We show that this image denoising method achieves top-tier performance in terms of PSNR, outperforming consistently the results of the regular Non-Local Means, and that it provides state-of-the-art qualitative results.

  7. Staircase Models from Affine Toda Field Theory

    CERN Document Server

    Dorey, P; Dorey, Patrick; Ravanini, Francesco

    1993-01-01

    We propose a class of purely elastic scattering theories generalising 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, we give analytic arguments in support of a conjectured renormalisation group flow visiting the neighbourhood of each W_g minimal model in turn.

  8. On the Lp affine isoperimetric inequalities

    Indian Academy of Sciences (India)

    Projection bodies have a long and complicated history which goes back to Minkowski. [3]. The classical Petty projection ... (1.1) where. ∗. K is the polar body of projection body K and equality holds if and only if K is an ellipsoid. ..... circumscribed to Bn. Then there is an affine image of ˜K of K satisfying. Sp( ˜K) ≤ Sp(△n) and.

  9. Levels of Distribution and the Affine Sieve

    OpenAIRE

    Kontorovich, Alex

    2014-01-01

    This article is an expanded version of the author's lecture in the Basic Notions Seminar at Harvard, September 2013. Our goal is a brief and introductory exposition of aspects of two topics in sieve theory which have received attention recently: (1) the spectacular work of Yitang Zhang, under the title "Level of Distribution," and (2) the so-called "Affine Sieve," introduced by Bourgain-Gamburd-Sarnak.

  10. Tannakian duality for affine homogeneous spaces

    OpenAIRE

    Banica, Teodor

    2017-01-01

    Associated to any closed quantum subgroup $G\\subset U_N^+$ and any index set $I\\subset\\{1,\\ldots,N\\}$ is a certain homogeneous space $X_{G,I}\\subset S^{N-1}_{\\mathbb C,+}$, called affine homogeneous space. We discuss here the abstract axiomatization of the algebraic manifolds $X\\subset S^{N-1}_{\\mathbb C,+}$ which can appear in this way, by using Tannakian duality methods.

  11. Automata and cells in affine Weyl groups

    OpenAIRE

    Gunnells, Paul E.

    2008-01-01

    Let W~ be an affine Weyl group, and let C be a left, right, or two-sided Kazhdan--Lusztig cell in W~. Let Reduced (C) be the set of all reduced expressions of elements of C, regarded as a formal language in the sense of the theory of computation. We show that Reduced (C) is a regular language. Hence the reduced expressions of the elements in any Kazhdan--Lusztig cell can be enumerated by a finite state automaton.

  12. Excited state electron affinity calculations for aluminum

    Science.gov (United States)

    Hussein, Adnan Yousif

    2017-08-01

    Excited states of negative aluminum ion are reviewed, and calculations of electron affinities of the states (3s^23p^2)^1D and (3s3p^3){^5}{S}° relative to the (3s^23p)^2P° and (3s3p^2)^4P respectively of the neutral aluminum atom are reported in the framework of nonrelativistic configuration interaction (CI) method. A priori selected CI (SCI) with truncation energy error (Bunge in J Chem Phys 125:014107, 2006) and CI by parts (Bunge and Carbó-Dorca in J Chem Phys 125:014108, 2006) are used to approximate the valence nonrelativistic energy. Systematic studies of convergence of electron affinity with respect to the CI excitation level are reported. The calculated value of the electron affinity for ^1D state is 78.675(3) meV. Detailed Calculations on the ^5S°c state reveals that is 1216.8166(3) meV below the ^4P state.

  13. Affine fractal functions as bases of continuous funtions | Navascues ...

    African Journals Online (AJOL)

    The objective of the present paper is the study of affine transformations of the plane, which provide self-affine curves as attractors. The properties of these curves depend decisively of the coefficients of the system of affinities involved. The corresponding functions are continuous on a compact interval. If the scale factors are ...

  14. Comparative analysis of the affine scaling and Karmarkar's ...

    African Journals Online (AJOL)

    The affine scaling algorithm is a variant of the Karmarkar's algorithms. In this paper, we compare the affine scaling and the Karmarkar algorithms using the same test LP problem. Keywords: Polynomial-time, Complexity bound, Primal LP, Dual LP, Basic Solution, Degenerate Solution, Affine Space, Simplex and Polytope ...

  15. 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...

  16. Calcium stable isotope geochemistry

    Energy Technology Data Exchange (ETDEWEB)

    Gausonne, Nikolaus [Muenster Univ. (Germany). Inst. fuer Mineralogie; Schmitt, Anne-Desiree [Strasbourg Univ. (France). LHyGeS/EOST; Heuser, Alexander [Bonn Univ. (Germany). Steinmann-Inst. fuer Geologie, Mineralogie und Palaeontologie; Wombacher, Frank [Koeln Univ. (Germany). Inst. fuer Geologie und Mineralogie; Dietzel, Martin [Technische Univ. Graz (Austria). Inst. fuer Angewandte Geowissenschaften; Tipper, Edward [Cambridge Univ. (United Kingdom). Dept. of Earth Sciences; Schiller, Martin [Copenhagen Univ. (Denmark). Natural History Museum of Denmark

    2016-08-01

    This book provides an overview of the fundamentals and reference values for Ca stable isotope research, as well as current analytical methodologies including detailed instructions for sample preparation and isotope analysis. As such, it introduces readers to the different fields of application, including low-temperature mineral precipitation and biomineralisation, Earth surface processes and global cycling, high-temperature processes and cosmochemistry, and lastly human studies and biomedical applications. The current state of the art in these major areas is discussed, and open questions and possible future directions are identified. In terms of its depth and coverage, the current work extends and complements the previous reviews of Ca stable isotope geochemistry, addressing the needs of graduate students and advanced researchers who want to familiarize themselves with Ca stable isotope research.

  17. Exponentiality for the construct of affine sets

    Directory of Open Access Journals (Sweden)

    Veerle Claes

    2008-04-01

    Full Text Available The topological construct SSET of affine sets over the two-point set S contains many interesting topological subconstructs such as TOP, the construct of topological spaces, and CL, the construct of closure spaces. For this category and its subconstructs cartesian closedness is studied. We first give a classification of the subconstructs of SSET according to their behaviour with respect to exponenttiality. We formulate sufficient conditions implying that a subconstruct behaves similar to CL. On the other hand, we characterize a conglomerate of subconstructs with behaviour similar to TOP. Finally, we construct the cartesian closed topological hull of SSET.

  18. Connection between the Affine and conformal Affine Toda models and their Hirota's solution

    International Nuclear Information System (INIS)

    Constantinidis, C.P.; Ferreira, L.A.; Gomes, J.F.; Zimerman, A.H.

    1992-01-01

    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)

  19. Evolutionary Stable Strategy

    Indian Academy of Sciences (India)

    2016-08-26

    Aug 26, 2016 ... Home; Journals; Resonance – Journal of Science Education; Volume 21; Issue 9. Evolutionary Stable Strategy: Application of Nash Equilibrium in Biology. General ... Using some examples of classical games, we show how evolutionary game theory can help understand behavioural decisions of animals.

  20. The Stable Concordance Genus

    OpenAIRE

    Kearney, M. Kate

    2013-01-01

    The concordance genus of a knot is the least genus of any knot in its concordance class. Although difficult to compute, it is a useful invariant that highlights the distinction between the three-genus and four-genus. In this paper we define and discuss the stable concordance genus of a knot, which describes the behavior of the concordance genus under connected sum.

  1. Manifolds admitting stable forms

    Czech Academy of Sciences Publication Activity Database

    Le, Hong-Van; Panák, Martin; Vanžura, Jiří

    2008-01-01

    Roč. 49, č. 1 (2008), s. 101-11 ISSN 0010-2628 R&D Projects: GA ČR(CZ) GP201/05/P088 Institutional research plan: CEZ:AV0Z10190503 Keywords : stable forms * automorphism groups Subject RIV: BA - General Mathematics

  2. Stable isotope studies

    International Nuclear Information System (INIS)

    Ishida, T.

    1992-01-01

    The research has been in four general areas: (1) correlation of isotope effects with molecular forces and molecular structures, (2) correlation of zero-point energy and its isotope effects with molecular structure and molecular forces, (3) vapor pressure isotope effects, and (4) fractionation of stable isotopes. 73 refs, 38 figs, 29 tabs

  3. Interactive Stable Ray Tracing

    DEFF Research Database (Denmark)

    Dal Corso, Alessandro; Salvi, Marco; Kolb, Craig

    2017-01-01

    Interactive ray tracing applications running on commodity hardware can suffer from objectionable temporal artifacts due to a low sample count. We introduce stable ray tracing, a technique that improves temporal stability without the over-blurring and ghosting artifacts typical of temporal post-pr...

  4. The stable subgroup graph

    Directory of Open Access Journals (Sweden)

    Behnaz Tolue

    2018-07-01

    Full Text Available In this paper we introduce stable subgroup graph associated to the group $G$. It is a graph with vertex set all subgroups of $G$ and two distinct subgroups $H_1$ and $H_2$ are adjacent if $St_{G}(H_1\\cap H_2\

  5. Peptide-MHC class I stability is a stronger predictor of CTL immunogenicity than peptide affinity

    DEFF Research Database (Denmark)

    Harndahl, Mikkel Nors; Rasmussen, Michael; Nielsen, Morten

    2012-01-01

    of antigen processing and presentation in defining cytotoxic T lymphocyte (CTL) immunogenicity Assarsson et al., 2007. Using an affinity-balanced approach, we demonstrated that immunogenic peptides tend to be more stably bound to MHC-I molecules compared with non-immunogenic peptides. We also developed......Peptide-MHC class I stability is a stronger predictor of CTL immunogenicity than peptide affinity Mikkel Harndahla, Michael Rasmussena, Morten Nielsenb, Soren Buusa,∗ a Laboratory of Experimental Immunology, Faculty of Health Sciences, University of Copenhagen, Denmark b Center for Biological...... Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Denmark Efficient presentation of peptide-MHC class I (pMHC-I) complexes to immune T cells should benefit from a stable peptide- MHC-I interaction. However, it has been difficult to distinguish stability from other...

  6. Integrated Affinity Biosensing Platforms on Screen-Printed Electrodes Electrografted with Diazonium Salts

    Directory of Open Access Journals (Sweden)

    Paloma Yáñez-Sedeño

    2018-02-01

    Full Text Available Adequate selection of the electrode surface and the strategies for its modification to enable subsequent immobilization of biomolecules and/or nanomaterials integration play a major role in the performance of electrochemical affinity biosensors. Because of the simplicity, rapidity and versatility, electrografting using diazonium salt reduction is among the most currently used functionalization methods to provide the attachment of an organic layer to a conductive substrate. This particular chemistry has demonstrated to be a powerful tool to covalently immobilize in a stable and reproducible way a wide range of biomolecules or nanomaterials onto different electrode surfaces. Considering the great progress and interesting features arisen in the last years, this paper outlines the potential of diazonium chemistry to prepare single or multianalyte electrochemical affinity biosensors on screen-printed electrodes (SPEs and points out the existing challenges and future directions in this field.

  7. From affine Hecke algebras to boundary symmetries

    International Nuclear Information System (INIS)

    Doikou, Anastasia

    2005-01-01

    Motivated by earlier works we employ appropriate realizations of the affine Hecke algebra and we recover previously known non-diagonal solutions of the reflection equation for the U q (gl n -bar ) case. The corresponding N site spin chain with open boundary conditions is then constructed and boundary non-local charges associated to the non-diagonal solutions of the reflection equation are derived, as coproduct realizations of the reflection algebra. With the help of linear intertwining relations involving the aforementioned solutions of the reflection equation, the symmetry of the open spin chain with the corresponding boundary conditions is exhibited, being essentially a remnant of the U q (gl n -bar ) algebra. More specifically, we show that representations of certain boundary non-local charges commute with the generators of the affine Hecke algebra and with the local Hamiltonian of the open spin chain for a particular choice of boundary conditions. Furthermore, we are able to show that the transfer matrix of the open spin chain commutes with a certain number of boundary non-local charges, depending on the choice of boundary conditions

  8. Affinity capillary electrophoresis for the assessment of binding affinity of carbohydrate-based cholera toxin inhibitors

    NARCIS (Netherlands)

    Aizpurua-Olaizola, Oier; Sastre Torano, Javier; Pukin, Aliaksei; Fu, Ou; Boons, Geert Jan; de Jong, Gerhardus J; Pieters, Roland J

    2018-01-01

    Developing tools for the study of protein carbohydrate interactions is an important goal in glycobiology. Cholera toxin inhibition is an interesting target in this context, as its inhibition may help to fight against cholera. For the study of novel ligands an affinity capillary electrophoresis (ACE)

  9. Co-evolution of affinity and stability of grafted amyloid-motif domain antibodies.

    Science.gov (United States)

    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. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  10. Stable isotope analysis

    International Nuclear Information System (INIS)

    Tibari, Elghali; Taous, Fouad; Marah, Hamid

    2014-01-01

    This report presents results related to stable isotopes analysis carried out at the CNESTEN DASTE in Rabat (Morocco), on behalf of Senegal. These analyzes cover 127 samples. These results demonstrate that Oxygen-18 and Deuterium in water analysis were performed by infrared Laser spectroscopy using a LGR / DLT-100 with Autosampler. Also, the results are expressed in δ values (‰) relative to V-SMOW to ± 0.3 ‰ for oxygen-18 and ± 1 ‰ for deuterium.

  11. Forensic Stable Isotope Biogeochemistry

    Science.gov (United States)

    Cerling, Thure E.; Barnette, Janet E.; Bowen, Gabriel J.; Chesson, Lesley A.; Ehleringer, James R.; Remien, Christopher H.; Shea, Patrick; Tipple, Brett J.; West, Jason B.

    2016-06-01

    Stable isotopes are being used for forensic science studies, with applications to both natural and manufactured products. In this review we discuss how scientific evidence can be used in the legal context and where the scientific progress of hypothesis revisions can be in tension with the legal expectations of widely used methods for measurements. Although this review is written in the context of US law, many of the considerations of scientific reproducibility and acceptance of relevant scientific data span other legal systems that might apply different legal principles and therefore reach different conclusions. Stable isotopes are used in legal situations for comparing samples for authenticity or evidentiary considerations, in understanding trade patterns of illegal materials, and in understanding the origins of unknown decedents. Isotope evidence is particularly useful when considered in the broad framework of physiochemical processes and in recognizing regional to global patterns found in many materials, including foods and food products, drugs, and humans. Stable isotopes considered in the larger spatial context add an important dimension to forensic science.

  12. Structure of a High-Affinity

    Energy Technology Data Exchange (ETDEWEB)

    Saphire, E.O.; Montero, M.; Menendez, A.; Houten, N.E.van; Irving, M.B.; Pantophlet, R.; Swick, M.B.; Parren, P.W.H.I.; Burton, D.R.; Scott, J.K.; Wilson, I.A.; /Scripps

    2007-07-13

    The human antibody b12 recognizes a discontinuous epitope on gp120 and is one of the rare monoclonal antibodies that neutralize a broad range of primary human immunodeficiency virus type 1 (HIV-1) isolates. We previously reported the isolation of B2.1, a dimeric peptide that binds with high specificity to b12 and competes with gp120 for b12 antibody binding. Here, we show that the affinity of B2.1 was improved 60-fold over its synthetic-peptide counterpart by fusing it to the N terminus of a soluble protein. This affinity, which is within an order of magnitude of that of gp120, probably more closely reflects the affinity of the phage-borne peptide. The crystal structure of a complex between Fab of b12 and B2.1 was determined at 1.8 Angstrom resolution. The structural data allowed the differentiation of residues that form critical contacts with b12 from those required for maintenance of the antigenic structure of the peptide, and revealed that three contiguous residues mediate B2.1's critical contacts with b12. This single region of critical contact between the B2.1 peptide and the b12 paratope is unlikely to mimic the discontinuous key binding residues involved in the full b12 epitope for gp120, as previously identified by alanine scanning substitutions on the gp120 surface. These structural observations are supported by experiments that demonstrate that B2.1 is an ineffective immunogenic mimic of the b12 epitope on gp120. Indeed, an extensive series of immunizations with B2.1 in various forms failed to produce gp120 cross-reactive sera. The functional and structural data presented here, however, suggest that the mechanism by which b12 recognizes the two antigens is very different. Here, we present the first crystal structure of peptide bound to an antibody that was originally raised against a discontinuous protein epitope. Our results highlight the challenge of producing immunogens that mimic discontinuous protein epitopes, and the necessity of combining

  13. Data Stream Clustering With Affinity Propagation

    KAUST Repository

    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.

  14. Modeling DNA affinity landscape through two-round support vector regression with weighted degree kernels

    KAUST Repository

    Wang, Xiaolei

    2014-12-12

    Background: A quantitative understanding of interactions between transcription factors (TFs) and their DNA binding sites is key to the rational design of gene regulatory networks. Recent advances in high-throughput technologies have enabled high-resolution measurements of protein-DNA binding affinity. Importantly, such experiments revealed the complex nature of TF-DNA interactions, whereby the effects of nucleotide changes on the binding affinity were observed to be context dependent. A systematic method to give high-quality estimates of such complex affinity landscapes is, thus, essential to the control of gene expression and the advance of synthetic biology. Results: Here, we propose a two-round prediction method that is based on support vector regression (SVR) with weighted degree (WD) kernels. In the first round, a WD kernel with shifts and mismatches is used with SVR to detect the importance of subsequences with different lengths at different positions. The subsequences identified as important in the first round are then fed into a second WD kernel to fit the experimentally measured affinities. To our knowledge, this is the first attempt to increase the accuracy of the affinity prediction by applying two rounds of string kernels and by identifying a small number of crucial k-mers. The proposed method was tested by predicting the binding affinity landscape of Gcn4p in Saccharomyces cerevisiae using datasets from HiTS-FLIP. Our method explicitly identified important subsequences and showed significant performance improvements when compared with other state-of-the-art methods. Based on the identified important subsequences, we discovered two surprisingly stable 10-mers and one sensitive 10-mer which were not reported before. Further test on four other TFs in S. cerevisiae demonstrated the generality of our method. Conclusion: We proposed in this paper a two-round method to quantitatively model the DNA binding affinity landscape. Since the ability to modify

  15. Antibody-based affinity cryo-EM grid.

    Science.gov (United States)

    Yu, Guimei; Li, Kunpeng; Jiang, Wen

    2016-05-01

    The Affinity Grid technique combines sample purification and cryo-Electron Microscopy (cryo-EM) grid preparation into a single step. Several types of affinity surfaces, including functionalized lipids monolayers, streptavidin 2D crystals, and covalently functionalized carbon surfaces have been reported. More recently, we presented a new affinity cryo-EM approach, cryo-SPIEM, which applies the traditional Solid Phase Immune Electron Microscopy (SPIEM) technique to cryo-EM. This approach significantly simplifies the preparation of affinity grids and directly works with native macromolecular complexes without need of target modifications. With wide availability of high affinity and high specificity antibodies, the antibody-based affinity grid would enable cryo-EM studies of the native samples directly from cell cultures, targets of low abundance, and unstable or short-lived intermediate states. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. Toward improving selectivity in affinity chromatography with PEGylated affinity ligands: the performance of PEGylated protein A.

    Science.gov (United States)

    González-Valdez, José; Yoshikawa, Alex; Weinberg, Justin; Benavides, Jorge; Rito-Palomares, Marco; Przybycien, Todd M

    2014-01-01

    Chemical modification of macromolecular affinity chromatography ligands with polyethylene glycol chains or "PEGylation" can potentially improve selectivity by sterically suppressing non-specific binding interactions without sacrificing binding capacity. For a commercial protein A affinity media and with yeast extract (YE) and fetal bovine serum (FBS) serving as mock contaminants, we found that the ligand accounted for more than 90% of the media-associated non-specific binding, demonstrating an opportunity for improvement. The IgG static binding affinity of protein A mono-PEGylated with 5.0 and 20.7 kDa poly(ethylene glycol) chains was found to be preserved using a biomolecular interaction screening platform. Similar in situ PEGylations of the commercial protein A media were conducted and the modified media was functionally characterized with IgG solutions spiked with YE and FBS. Ligand PEGylation reduced the mass of media-associated contaminants by a factor of two to three or more. Curiously, we also found an increase of up to 15% in the average recovery of IgG on elution after PEGylation. Combined, these effects produced an order of magnitude increase in the IgG selectivity on average when spiked with YE and a two- to three-fold increase when spiked with FBS relative to the commercial media. Dynamic binding capacity and mass-transfer resistance measurements revealed a reduction in dynamic capacity attributed to a decrease in IgG effective pore diffusivity and possibly slower IgG association kinetics for the PEGylated protein A ligands. Ligand PEGylation is a viable approach to improving selectivity in affinity chromatography with macromolecular ligands. © 2014 American Institute of Chemical Engineers.

  17. Marginally Stable Nuclear Burning

    Science.gov (United States)

    Strohmayer, Tod E.; Altamirano, D.

    2012-01-01

    Thermonuclear X-ray bursts result from unstable nuclear burning of the material accreted on neutron stars in some low mass X-ray binaries (LMXBs). Theory predicts that close to the boundary of stability oscillatory burning can occur. This marginally stable regime has so far been identified in only a small number of sources. We present Rossi X-ray Timing Explorer (RXTE) observations of the bursting, high- inclination LMXB 4U 1323-619 that reveal for the first time in this source the signature of marginally stable burning. The source was observed during two successive RXTE orbits for approximately 5 ksec beginning at 10:14:01 UTC on March 28, 2011. Significant mHz quasi- periodic oscillations (QPO) at a frequency of 8.1 mHz are detected for approximately 1600 s from the beginning of the observation until the occurrence of a thermonuclear X-ray burst at 10:42:22 UTC. The mHz oscillations are not detected following the X-ray burst. The average fractional rms amplitude of the mHz QPOs is 6.4% (3 - 20 keV), and the amplitude increases to about 8% below 10 keV.This phenomenology is strikingly similar to that seen in the LMXB 4U 1636-53. Indeed, the frequency of the mHz QPOs in 4U 1323-619 prior to the X-ray burst is very similar to the transition frequency between mHz QPO and bursts found in 4U 1636-53 by Altamirano et al. (2008). These results strongly suggest that the observed QPOs in 4U 1323-619 are, like those in 4U 1636-53, due to marginally stable nuclear burning. We also explore the dependence of the energy spectrum on the oscillation phase, and we place the present observations within the context of the spectral evolution of the accretion-powered flux from the source.

  18. Deep Mutational Scans as a Guide to Engineering High Affinity T Cell Receptor Interactions with Peptide-bound Major Histocompatibility Complex*

    Science.gov (United States)

    Harris, Daniel T.; Wang, Ningyan; Riley, Timothy P.; Anderson, Scott D.; Singh, Nishant K.; Procko, Erik; Baker, Brian M.; Kranz, David M.

    2016-01-01

    Proteins are often engineered to have higher affinity for their ligands to achieve therapeutic benefit. For example, many studies have used phage or yeast display libraries of mutants within complementarity-determining regions to affinity mature antibodies and T cell receptors (TCRs). However, these approaches do not allow rapid assessment or evolution across the entire interface. By combining directed evolution with deep sequencing, it is now possible to generate sequence fitness landscapes that survey the impact of every amino acid substitution across the entire protein-protein interface. Here we used the results of deep mutational scans of a TCR-peptide-MHC interaction to guide mutational strategies. The approach yielded stable TCRs with affinity increases of >200-fold. The substitutions with the greatest enrichments based on the deep sequencing were validated to have higher affinity and could be combined to yield additional improvements. We also conducted in silico binding analyses for every substitution to compare them with the fitness landscape. Computational modeling did not effectively predict the impacts of mutations distal to the interface and did not account for yeast display results that depended on combinations of affinity and protein stability. However, computation accurately predicted affinity changes for mutations within or near the interface, highlighting the complementary strengths of computational modeling and yeast surface display coupled with deep mutational scanning for engineering high affinity TCRs. PMID:27681597

  19. Cambrian trilobites with Siberian affinities, southwestern Alaska

    Energy Technology Data Exchange (ETDEWEB)

    Palmer, A.R.; Egbert, R.M.; Sullivan, R.; Knoth, J.S.

    1985-02-01

    Cambrian trilobites occur in two levels (about 7 m apart) in the core of a large, complex anticlinal structure in the area between the Taylor Mountains and the Hoholitna River in southwestern Alaska. The lower collection contains Erbia, Macannaia (a species close to Soviet forms described as Pagetia ferox Lermontova), two species of Kootenia (including one perhaps cospecific with forms from the central Brooks range), and several species of ptychoparioid trilobites. It is clear that biogeographic affinities are with the transitional facies of the eastern Siberian platform and the south Siberian foldbelt. In Soviet terms, the age of the collection falls in a disputed interval called latest Early Cambrian (Tojonian) by some authors, and earliest Middle Cambrian (Amgan) by others. In North American terms, Macannaia is known only from early Middle Cambrian beds. The younger collection contains abundant agnostids, a variety of conocoryphids, Paradoxides, and several species of ptychoparioid trilobites. This is an assemblage of undoubted late Middle Cambrian age, comparable to faunas described from the Maya State of the Siberian platform and the Paradoxides paradoxissimus Stage of the Baltic region. Both faunas are from ocean-facing or outer shelf environments. None of the key non-agnostid or non-pagetiid elements have been seen previously in deposits of Cambrian North America.

  20. Set-Membership Proportionate Affine Projection Algorithms

    Directory of Open Access Journals (Sweden)

    Stefan Werner

    2007-01-01

    Full Text Available Proportionate adaptive filters can improve the convergence speed for the identification of sparse systems as compared to their conventional counterparts. In this paper, the idea of proportionate adaptation is combined with the framework of set-membership filtering (SMF in an attempt to derive novel computationally efficient algorithms. The resulting algorithms attain an attractive faster converge for both situations of sparse and dispersive channels while decreasing the average computational complexity due to the data discerning feature of the SMF approach. In addition, we propose a rule that allows us to automatically adjust the number of past data pairs employed in the update. This leads to a set-membership proportionate affine projection algorithm (SM-PAPA having a variable data-reuse factor allowing a significant reduction in the overall complexity when compared with a fixed data-reuse factor. Reduced-complexity implementations of the proposed algorithms are also considered that reduce the dimensions of the matrix inversions involved in the update. Simulations show good results in terms of reduced number of updates, speed of convergence, and final mean-squared error.

  1. Daily rhythmicity of high affinity copper transport.

    Science.gov (United States)

    Perea-García, Ana; Sanz, Amparo; Moreno, Joaquín; Andrés-Bordería, Amparo; de Andrés, Sonia Mayo; Davis, Amanda M; Huijser, Peter; Davis, Seth J; Peñarrubia, Lola

    2016-01-01

    A differential demand for copper (Cu) of essential cupro-proteins that act within the mitochondrial and chloroplastal electronic transport chains occurs along the daily light/dark cycles. This requires a fine-tuned spatiotemporal regulation of Cu delivery, becoming especially relevant under non-optimal growth conditions. When scarce, Cu is imported through plasma membrane-bound high affinity Cu transporters (COPTs) whose coding genes are transcriptionally induced by the SPL7 transcription factor. Temporal homeostatic mechanisms are evidenced by the presence of multiple light- and clock-responsive regulatory cis elements in the promoters of both SPL7 and its COPT targets. A model is presented here for such temporal regulation that is based on the synchrony between the basal oscillatory pattern of SPL7 and its targets, such as COPT2. Conversely, Cu feeds back to coordinate intracellular Cu availability on the SPL7-dependent regulation of further Cu acquisition. This occurs via regulation at COPT transporters. Moreover, exogenous Cu affects several circadian-clock components, such as the timing of GIGANTEA transcript abundance. Together we propose that there is a dynamic response to Cu that is integrated over diurnal time to maximize metabolic efficiency under challenging conditions.

  2. The electron affinity of CF3

    Science.gov (United States)

    Miller, Deanna M.

    State-of-the-art ab initio electronic structure methods have been employed to pinpoint the electron affinity of the trifluoromethyl radical, EA(CF3). The theoretical techniques entailed restricted and unrestricted Hartree-Fock reference wavefunctions, contemporary density functional schemes, second-order Moller-Plesset perturbation theory, the configuration interaction and coupled-cluster singles and doubles approaches, and the latter augmented perturbatively for connected triple excitations. The one-particle basis sets for carbon and fluorine ranged in quality from (9s5p1d/4s2p1d) to (11s7p2d1f/6s5p2d1f). In the derivation of EA(CF3), both lower and upper bounds were first inferred by invoking selected methods in direct computational routes; a primary evaluation was then achieved by applying systematically increasing levels of theory to the isogyric (CF3-,3CF2) electron-transfer process; and confirmatory results were extracted from a thermochemical cycle involving the gas-phase acidity of CHF3. The collective analysis engenders a final proposal of EA(CF3) = 1ṡ78 ± 0ṡ10 eV, which clearly discounts a spectrum of early observations, poses a compromise between the best values given by competing experimental approaches, and significantly reduces the uncertainty in this quantity.

  3. Generalized Warburg impedance on realistic self-affine fractals ...

    Indian Academy of Sciences (India)

    2016-08-26

    Aug 26, 2016 ... We analyse the problem of impedance for a diffusion controlled charge transfer process across an irregular interface. These interfacial irregularities are characterized as two class of random fractals: (i) a statistically isotropic self-affine fractals and (ii) a statistically corrugated self-affine fractals.

  4. Generalized Warburg impedance on realistic self-affine fractals

    Indian Academy of Sciences (India)

    We analyse the problem of impedance for a diffusion controlled charge transfer process across an irregular interface. These interfacial irregularities are characterized as two class of random fractals: (i) a statistically isotropic self-affine fractals and (ii) a statistically corrugated self-affine fractals. The information about the ...

  5. Affine Toda equations and solutions in the homogeneous grading

    Czech Academy of Sciences Publication Activity Database

    Zuevsky, Alexander

    2018-01-01

    Roč. 542, April 1 (2018), s. 149-161 ISSN 0024-3795 Institutional support: RVO:67985840 Keywords : affine Lie gebras * affine Toda modes * solitons Subject RIV: BA - General Mathematics OBOR OECD: Pure mathematics Impact factor: 0.973, year: 2016 https://www.sciencedirect.com/science/article/pii/S0024379517302100

  6. Isolation of bovine serum albumin from whey using affinity chromatography

    NARCIS (Netherlands)

    Besselink, T.; Janssen, A.E.M.; Boom, R.M.

    2015-01-01

    The adsorption of bovine serum albumin (BSA) to a chromatography resin with immobilised llama antibody fragments as affinity ligands was investigated. The maximum adsorption capacity of the affinity resin was 21.6 mg mL-1 with a Langmuir equilibrium constant of 20.4 mg mg-1. Using packed bed

  7. Calcium, Copper Protein And Oxygen Affinity In Haemocyanins Of ...

    African Journals Online (AJOL)

    ... to buffer the decrease in extracellular pH during aestivation is likely responsible for the high oxygen affinity of haemocyanin (43.0% increase) from aestivating snails through co-operative oxygen binding. Key Words: Aestivation, snail, Achatina achatina, inorganic ions, haemocyanin, absorption spectra, oxygen affinity.

  8. Self-affine roughness influence on redox reaction charge admittance

    NARCIS (Netherlands)

    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

  9. Polynomial Primal-Dual Cone Affine Scaling for Semidefinite Programming

    NARCIS (Netherlands)

    A.B. Berkelaar (Arjan); J.F. Sturm; S. Zhang (Shuzhong)

    1996-01-01

    textabstractIn this paper we generalize the primal--dual cone affine scaling algorithm of Sturm and Zhang to semidefinite programming. We show in this paper that the underlying ideas of the cone affine scaling algorithm can be naturely applied to semidefinite programming, resulting in a new

  10. Fermionic construction of vertex operators for twisted affine algebras

    International Nuclear Information System (INIS)

    Frappat, L.; Sorba, P.; Sciarrino, A.

    1988-03-01

    We construct vertex operator representations of the twisted affine algebras in terms of fermionic (or parafermionic in some cases) elementary fields. The folding method applied to the extended Dynkin diagrams of the affine algebras allows us to determine explicitly these fermionic fields as vertex operators

  11. Affine Toda equations and solutions in the homogeneous grading

    Czech Academy of Sciences Publication Activity Database

    Zuevsky, Alexander

    2018-01-01

    Roč. 542, April 1 (2018), s. 149-161 ISSN 0024-3795 Institutional support: RVO:67985840 Keywords : affine Lie gebras * affine Toda modes * solitons Subject RIV: BA - General Mathematics OBOR OECD: Pure mathematics Impact factor: 0.973, year: 2016 https:// www .sciencedirect.com/science/article/pii/S0024379517302100

  12. Algorithm-Architecture Affinity - Parallelism Changes the Picture

    DEFF Research Database (Denmark)

    Abildgren, Rasmus; Šaramentovas, Aleksandras; Ruzgys, Paulius

    the hardware-software partitioning step. This extension builds upon and complement our own work with metrics in the Design Trotter project, and is combined with the affinity metric approach. We show that the proposed extension improves the original affinity metric in terms of parallelism detection, and thus...

  13. Pseudo-affinity chromatography of rumen microbial cellulase on ...

    African Journals Online (AJOL)

    Pseudo-affinity chromatography of rumen microbial cellulase on Sepharose- Cibacron Blue F3GA. ... African Journal of Biotechnology ... Pseudo affinity adsorption of bioproducts on Sepharose-cibacron blue F3-GA was subjected to rumen microbial enzyme evaluation through batch binding and column chromatography of ...

  14. Peptide Nucleic Acids Having Enhanced Binding Affinity and Sequence Specificity

    DEFF Research Database (Denmark)

    1998-01-01

    A novel class of compounds, known as peptide nucleic acids, bind complementary DNA and RNA strands more strongly than a corresponding DNA strand, and exhibit increased sequence specificity and binding affinity. Methods of increasing binding affinity and sequence specificity of peptide nucleic acids...

  15. Capillary electrophoresis-based assessment of nanobody affinity and purity

    NARCIS (Netherlands)

    Haselberg, Rob; Oliveira, Sabrina; van der Meel, Roy; Somsen, Govert W; de Jong, Gerhardus J

    2014-01-01

    Drug purity and affinity are essential attributes during development and production of therapeutic proteins. In this work, capillary electrophoresis (CE) was used to determine both the affinity and composition of the biotechnologically produced "nanobody" EGa1, the binding fragment of a

  16. Congruence of genomic and ethnolinguistic affinities among five ...

    Indian Academy of Sciences (India)

    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 ...

  17. Online identification of continuous bimodal and trimodal piecewise affine systems

    NARCIS (Netherlands)

    Le, Q.T.; van den Boom, A.J.J.; Baldi, S.; Rantzer, Anders; Bagterp Jørgensen, John; Stoustrup, Jakob

    2016-01-01

    This paper investigates the identification of continuous piecewise affine systems in state space form with jointly unknown partition and subsystem matrices. The partition of the system is generated by the so-called centers. By representing continuous piecewise affine systems in the max-form and

  18. Exploring Girls' Science Affinities Through an Informal Science Education Program

    Science.gov (United States)

    Todd, Brandy; Zvoch, Keith

    2017-10-01

    This study examines science interests, efficacy, attitudes, and identity—referred to as affinities, in the context of an informal science outreach program for girls. A mixed methods design was used to explore girls' science affinities before, during, and after participation in a cohort-based summer science camp. Multivariate analysis of survey data revealed that girls' science affinities varied as a function of the joint relationship between family background and number of years in the program, with girls from more affluent families predicted to increase affinities over time and girls from lower income families to experience initial gains in affinities that diminish over time. Qualitative examination of girls' perspectives on gender and science efficacy, attitudes toward science, and elements of science identities revealed a complex interplay of gendered stereotypes of science and girls' personal desires to prove themselves knowledgeable and competent scientists. Implications for the best practice in fostering science engagement and identities in middle school-aged girls are discussed.

  19. Low affinity PEGylated hemoglobin from Trematomus bernacchii, a model for hemoglobin-based blood substitutes

    Science.gov (United States)

    2011-01-01

    Background Conjugation of human and animal hemoglobins with polyethylene glycol has been widely explored as a means to develop blood substitutes, a novel pharmaceutical class to be used in surgery or emergency medicine. However, PEGylation of human hemoglobin led to products with significantly different oxygen binding properties with respect to the unmodified tetramer and high NO dioxygenase reactivity, known causes of toxicity. These recent findings call for the biotechnological development of stable, low-affinity PEGylated hemoglobins with low NO dioxygenase reactivity. Results To investigate the effects of PEGylation on protein structure and function, we compared the PEGylation products of human hemoglobin and Trematomus bernacchii hemoglobin, a natural variant endowed with a remarkably low oxygen affinity and high tetramer stability. We show that extension arm facilitated PEGylation chemistry based on the reaction of T. bernacchii hemoglobin with 2-iminothiolane and maleimido-functionalyzed polyethylene glycol (MW 5000 Da) leads to a tetraPEGylated product, more homogeneous than the corresponding derivative of human hemoglobin. PEGylated T. bernacchii hemoglobin largely retains the low affinity of the unmodified tetramer, with a p50 50 times higher than PEGylated human hemoglobin. Moreover, it is still sensitive to protons and the allosteric effector ATP, indicating the retention of allosteric regulation. It is also 10-fold less reactive towards nitrogen monoxide than PEGylated human hemoglobin. Conclusions These results indicate that PEGylated hemoglobins, provided that a suitable starting hemoglobin variant is chosen, can cover a wide range of oxygen-binding properties, potentially meeting the functional requirements of blood substitutes in terms of oxygen affinity, tetramer stability and NO dioxygenase reactivity. PMID:22185675

  20. 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

  1. Electron affinities of atoms, molecules, and radicals

    International Nuclear Information System (INIS)

    Christodoulides, A.A.; McCorkle, D.L.; Christophorou, L.G.

    1982-01-01

    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

  2. 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.

  3. NK1 receptor fused to beta-arrestin displays a single-component, high-affinity molecular phenotype.

    Science.gov (United States)

    Martini, Lene; Hastrup, Hanne; Holst, Birgitte; Fraile-Ramos, Alberto; Marsh, Mark; Schwartz, Thue W

    2002-07-01

    Arrestins are cytosolic proteins that, upon stimulation of seven transmembrane (7TM) receptors, terminate signaling by binding to the receptor, displacing the G protein and targeting the receptor to clathrin-coated pits. Fusion of beta-arrestin1 to the C-terminal end of the neurokinin NK1 receptor resulted in a chimeric protein that was expressed to some extent on the cell surface but also accumulated in transferrin-labeled recycling endosomes independently of agonist stimulation. As expected, the fusion protein was almost totally silenced with respect to agonist-induced signaling through the normal Gq/G11 and Gs pathways. The NK1-beta-arrestin1 fusion construct bound nonpeptide antagonists with increased affinity but surprisingly also bound two types of agonists, substance P and neurokinin A, with high, normal affinity. In the wild-type NK1 receptor, neurokinin A (NKA) competes for binding against substance P and especially against antagonists with up to 1000-fold lower apparent affinity than determined in functional assays and in homologous binding assays. When the NK1 receptor was closely fused to G proteins, this phenomenon was eliminated among agonists, but the agonists still competed with low affinity against antagonists. In contrast, in the NK1-beta-arrestin1 fusion protein, all ligands bound with similar affinity independent of the choice of radioligand and with Hill coefficients near unity. We conclude that the NK1 receptor in complex with arrestin is in a high-affinity, stable, agonist-binding form probably best suited to structural analysis and that the receptor can display binding properties that are nearly theoretically ideal when it is forced to complex with only a single intracellular protein partner.

  4. Two high-affinity ligand binding states of uterine estrogen receptor distinguished by modulation of hydrophobic environment

    International Nuclear Information System (INIS)

    Hutchens, T.W.; Li, C.M.; Zamah, N.M.; Besch, P.K.

    1987-01-01

    The steroid binding function of soluble (cytosolic) estrogen receptors from calf uteri was evaluated under conditions known to modify the extent of hydrophobic interaction with receptor-associated proteins. Receptor preparations were equilibrated into 6 M urea buffers and control buffers by chromatography through small columns of Sephadex G-25 or by dialysis at 0.6 0 C. Equilibrium dissociation constants (K/sub d/) and binding capacities (n) of experimental and control receptor preparations were determined by 13-point Scatchard analyses using concentrations of 17β-[ 3 H]estradiol from 0.05 to 10 nM. Nonspecific binding was determined at each concentration by parallel incubations with a 200-fold molar excess of the receptor-specific competitor diethylstilbestrol. The control receptor population was consistently found to be a single class of binding sites with a high affinity for estradiol which was unaffected by G-25 chromatography, by dialysis, by dilution, or by the presence of 0.4 M KCl. However, equilibration into 6 M urea induced a discrete (10-fold) reduction in receptor affinity to reveal a second, thermodynamically stable, high-affinity binding state. The presence of 0.4 M KCl did not significantly influence the discrete change in receptor affinity induced by urea. The effects of urea on both receptor affinity and binding capacity were reversible, suggesting a lack of covalent modification. These results demonstrate nonenzymatic means by which not only the binding capacity but also the affinity of receptor for estradiol can be reversibly controlled, suggesting that high concentrations of urea might be more effectively utilized during the physicochemical characterization and purification of steroid receptor proteins

  5. An improved affine projection algorithm for active noise cancellation

    Science.gov (United States)

    Zhang, Congyan; Wang, Mingjiang; Han, Yufei; Sun, Yunzhuo

    2017-08-01

    Affine projection algorithm is a signal reuse algorithm, and it has a good convergence rate compared to other traditional adaptive filtering algorithm. There are two factors that affect the performance of the algorithm, which are step factor and the projection length. In the paper, we propose a new variable step size affine projection algorithm (VSS-APA). It dynamically changes the step size according to certain rules, so that it can get smaller steady-state error and faster convergence speed. Simulation results can prove that its performance is superior to the traditional affine projection algorithm and in the active noise control (ANC) applications, the new algorithm can get very good results.

  6. Molecular modeling of protein A affinity chromatography.

    Science.gov (United States)

    Salvalaglio, Matteo; Zamolo, Laura; Busini, Valentina; Moscatelli, Davide; Cavallotti, Carlo

    2009-12-11

    The properties of the complex between fragment B of Protein A and the Fc domain of IgG were investigated adopting molecular dynamics with the intent of providing useful insight that might be exploited to design mimetic ligands with properties similar to those of Protein A. Simulations were performed both for the complex in solution and supported on an agarose surface, which was modeled as an entangled structure constituted by two agarose double chains. The energetic analysis was performed by means of the molecular mechanics Poisson Boltzmann surface area (MM/PBSA), molecular mechanics generalized Born surface area (MM/GBSA), and the linear interaction energy (LIE) approaches. An alanine scan was performed to determine the relative contribution of Protein A key amino acids to the complex interaction energy. It was found that three amino acids play a dominant role: Gln 129, Phe 132 and Lys 154, though also four other residues, Tyr 133, Leu 136, Glu 143 and Gln 151 contribute significantly to the overall binding energy. A successive molecular dynamics analysis of Protein A re-organization performed when it is not in complex with IgG has however shown that Phe 132 and Tyr 133 interact among themselves establishing a significant pi-pi interaction, which is disrupted upon formation of the complex with IgG and thus reduces consistently their contribution to the protein-antibody bond. The effect that adsorbing fragment B of Protein A on an agarose support has on the stability of the protein-antibody bond was investigated using a minimal molecular model and compared to a similar study performed for a synthetic ligand. It was found that the interaction with the surface does not hinder significantly the capability of Protein A to interact with IgG, while it is crucial for the synthetic ligand. These results indicate that ligand-surface interactions should be considered in the design of new synthetic affinity ligands in order to achieve results comparable to those of Protein A

  7. Dynamical attraction to stable processes

    OpenAIRE

    Fisher, Albert M.; Talet, Marina

    2012-01-01

    We apply dynamical ideas within probability theory, proving an almost-sure invariance principle in log density for stable processes. The familiar scaling property (self-similarity) of the stable process has a stronger expression, that the scaling flow on Skorokhod path space is a Bernoulli flow. We prove that typical paths of a random walk with i.i.d. increments in the domain of attraction of a stable law can be paired with paths of a stable process so that, after applying a non-random regula...

  8. Non-affine fields in solid-solid transformations: the structure and stability of a product droplet.

    Science.gov (United States)

    Paul, Arya; Sengupta, Surajit; Rao, Madan

    2014-01-08

    We describe the microstructure, morphology, and dynamics of growth of a droplet of martensite nucleating in a parent austenite during a solid-solid transformation, using a Landau theory written in terms of both conventional affine elastic deformations and non-affine deformations. Non-affineness, φ, serves as a source of strain incompatibility and screens long-ranged elastic interactions. It is produced wherever the local stress exceeds a threshold and anneals diffusively thereafter. Using a variational calculation, we find three types of stable solution (labeled I, II, and III) for the structure of the product droplet, depending on the stress threshold and the scaled mobilities of φ parallel and perpendicular to the parent-product interface. The profile of the non-affine field φ is different in these three solutions: I is characterized by a vanishingly small φ, II admits large values of φ localized in regions of high stress within the parent-product interface, and III is a structure in which φ completely wets the parent-product interface. The width l and size W of the twins follow the relation l is proportional to √W in solution I; this relation does not hold for II or III. We obtain a dynamical phase diagram featuring these solutions, and argue that they represent specific solid-state microstructures.

  9. Boronate affinity saccharide electrophoresis: a novel carbohydrate analysis tool.

    Science.gov (United States)

    Jackson, Thomas R; Springall, Jeremy S; Rogalle, Damien; Masumoto, Naoko; Ching Li, Hung; D'Hooge, François; Perera, Semali P; Jenkins, A Toby A; James, Tony D; Fossey, John S; van den Elsen, Jean M H

    2008-11-01

    The incorporation of specialised carbohydrate affinity ligand methacrylamido phenylboronic acid in polyacrylamide gels for fluorophore-assisted carbohydrate electrophoresis greatly improved the effective separation of saccharides that show similar mobilities in standard electrophoresis. Polyacrylamide gel electrophoresis using methacrylamido phenylboronic acid in low loading (typically 0.5-1% dry weight) was unequivocally shown to alter retention of labelled saccharides depending on their boronate affinity. While conventional fluorophore-assisted carbohydrate electrophoresis of 2-aminoacridone labelled glucose oligomers showed an inverted parabolic migration, an undesired trait of small oligosaccharides labelled with this neutral fluorophore, boron affinity saccharide electrophoresis separation of these carbohydrates completely restored their predicted running order, based on their charge/mass ratio, and resulted in improved separation of the analyte saccharides. These results exemplify boron affinity saccharide electrophoresis as an important new technique for analysing carbohydrates and sugar-containing molecules.

  10. Methods for quantifying T cell receptor binding affinities and thermodynamics

    Science.gov (United States)

    Piepenbrink, Kurt H.; Gloor, Brian E.; Armstrong, Kathryn M.; Baker, Brian M.

    2013-01-01

    αβ T cell receptors (TCRs) recognize peptide antigens bound and presented by class I or class II major histocompatibility complex (MHC) proteins. Recognition of a peptide/MHC complex is required for initiation and propagation of a cellular immune response, as well as the development and maintenance of the T cell repertoire. Here we discuss methods to quantify the affinities and thermodynamics of interactions between soluble ectodomains of TCRs and their peptide/MHC ligands, focusing on titration calorimetry, surface plasmon resonance, and fluorescence anisotropy. As TCRs typically bind ligand with weak-to-moderate affinities, we focus the discussion on means to enhance the accuracy and precision of low affinity measurements. In addition to further elucidating the biology of the T cell mediated immune response, more reliable low affinity measurements will aid with more probing studies with mutants or altered peptides that can help illuminate the physical underpinnings of how TCRs achieve their remarkable recognition properties. PMID:21609868

  11. ASIFT: An Algorithm for Fully Affine Invariant Comparison

    Directory of Open Access Journals (Sweden)

    Guoshen Yu

    2011-02-01

    Full Text Available If a physical object has a smooth or piecewise smooth boundary, its images obtained by cameras in varying positions undergo smooth apparent deformations. These deformations are locally well approximated by affine transforms of the image plane. In consequence the solid object recognition problem has often been led back to the computation of affine invariant image local features. The similarity invariance (invariance to translation, rotation, and zoom is dealt with rigorously by the SIFT method The method illustrated and demonstrated in this work, Affine-SIFT (ASIFT, simulates a set of sample views of the initial images, obtainable by varying the two camera axis orientation parameters, namely the latitude and the longitude angles, which are not treated by the SIFT method. Then it applies the SIFT method itself to all images thus generated. Thus, ASIFT covers effectively all six parameters of the affine transform.

  12. Affinity between information retrieval system and search topic

    International Nuclear Information System (INIS)

    Ebinuma, Yukio

    1979-01-01

    Ten search profiles are tested on the INIS system at the Japan Atomic Energy Research Institute. The results are plotted on recall-precision chart ranging from 100% recall to 100% precision. The curves are not purely systems-dependent nor search-dependent, and are determined substantially by the ''affinity'' between the system and the search topic. The curves are named ''Affinity curves of search topics with information retrieval systems'', and hence retrieval affinity factors are derived. They are obtained not only for individual search topics but also for averages in the system. By such a quantitative examination, the difference of affinity among search topics in a given system, that of the same search topic among various systems, and that of systems to the same group of search topics can be compared reasonably. (author)

  13. Antibody Fragments and Their Purification by Protein L Affinity Chromatography

    Directory of Open Access Journals (Sweden)

    Gustav Rodrigo

    2015-09-01

    Full Text Available Antibodies and related proteins comprise one of the largest and fastest-growing classes of protein pharmaceuticals. A majority of such molecules are monoclonal antibodies; however, many new entities are antibody fragments. Due to their structural, physiological, and pharmacological properties, antibody fragments offer new biopharmaceutical opportunities. In the case of recombinant full-length antibodies with suitable Fc regions, two or three column purification processes centered around Protein A affinity chromatography have proven to be fast, efficient, robust, cost-effective, and scalable. Most antibody fragments lack Fc and suitable affinity for Protein A. Adapting proven antibody purification processes to antibody fragments demands different affinity chromatography. Such technology must offer the unit operation advantages noted above, and be suitable for most of the many different types of antibody fragments. Protein L affinity chromatography appears to fulfill these criteria—suggesting its consideration as a key unit operation in antibody fragment processing.

  14. Elective affinities and economic thought: 1870-1914

    OpenAIRE

    João Antônio de Paula; Pedro Rocha de Oliveira

    2006-01-01

    This article seeks to demonstrate that the concept of "elective affinities" can be applied to the relations between economic thought, literature, and philosophy. Emphasis is given to Institutionalist thought, the German historical school, and neoclassical thought.

  15. Ab initio studies on proton affinities of substituted furans

    International Nuclear Information System (INIS)

    Lee, Gab Yong; Lee, Hyun Mee

    1998-01-01

    The geometry of furan, relevant to the binding of bis-furan lexitropsin that contains this ring to the base pair of minor groove of DNA, is optimized by semiempirical (MNDO) and ab initio (Hartree-Fock) methods. The proton affinity and electronic structure are evaluated at the 6-31G and 6-31G level of theory for the optimized geometry. The proton affinities are also studied for various substituted furans with the electron donating and -withdrawing groups to estimate the substituent effect on the proton affinity of furans. It has been found that the electron-donating substituents increase the proton affinity of of furan, whereas the electron-withdrawing substituents decrease it. This result can be explained with atomic charge and electron density at oxygen of substituted furans

  16. Color and Contrast Enhancement by Controlled Piecewise Affine Histogram Equalization

    Directory of Open Access Journals (Sweden)

    Jose-Luis Lisani

    2012-10-01

    Full Text Available This paper presents a simple contrast enhancement algorithm based on histogram equalization (HE. The proposed algorithm performs a piecewise affine transform of the intensity levels of a digital image such that the new cumulative distribution function will be approximately uniform (as with HE, but where the stretching of the range is locally controlled to avoid brutal noise enhancement. We call this algorithm Piecewise Affine Equalization (PAE. Several experiments show that, in general, the new algorithm improves HE results.

  17. New analogues of agmatine with higher affinity to imidazoline receptors.

    Science.gov (United States)

    Treder, Adam P; Andruszkiewicz, Ryszard; Zgoda, Włodzimierz; Ford, Celeste; Hudson, Alan L

    2009-02-01

    Compilation of agmatine structure and imidazoline ring leads to a new family of imidazoline/alpha(2)-adrenoceptor ligands, 4(5)-(2-aminoethyl)imidazoline derivatives. Constraining of the guanidine moiety into heterocyclic ring improved the affinities of the resultant fusion compounds in comparison to agmatine itself. In this work, the synthetic approach and results for I(1), I(2), and alpha(2)-adrenoceptors affinities are reported.

  18. Surfactant-free Colloidal Particles with Specific Binding Affinity.

    Science.gov (United States)

    van der Wel, Casper; Bossert, Nelli; Mank, Quinten J; Winter, Marcel G T; Heinrich, Doris; Kraft, Daniela J

    2017-09-26

    Colloidal particles with specific binding affinity are essential for in vivo and in vitro biosensing, targeted drug delivery, and micrometer-scale self-assembly. Key to these techniques are surface functionalizations that provide high affinities to specific target molecules. For stabilization in physiological environments, current particle coating methods rely on adsorbed surfactants. However, spontaneous desorption of these surfactants typically has an undesirable influence on lipid membranes. To address this issue and create particles for targeting molecules in lipid membranes, we present here a surfactant-free coating method that combines high binding affinity with stability at physiological conditions. After activating charge-stabilized polystyrene microparticles with EDC/Sulfo-NHS, we first coat the particles with a specific protein and subsequently covalently attach a dense layer of poly(ethyelene) glycol. This polymer layer provides colloidal stability at physiological conditions as well as antiadhesive properties, while the protein coating provides the specific affinity to the targeted molecule. We show that NeutrAvidin-functionalized particles bind specifically to biotinylated membranes and that Concanavalin A-functionalized particles bind specifically to the glycocortex of Dictyostelium discoideum cells. The affinity of the particles changes with protein density, which can be tuned during the coating procedure. The generic and surfactant-free coating method reported here transfers the high affinity and specificity of a protein onto colloidal polystyrene microparticles.

  19. Specific Internalisation of Gold Nanoparticles into Engineered Porous Protein Cages via Affinity Binding

    Science.gov (United States)

    Peng, Tao; Free, Paul; Fernig, David G.; Lim, Sierin; Tomczak, Nikodem

    2016-01-01

    Porous protein cages are supramolecular protein self-assemblies presenting pores that allow the access of surrounding molecules and ions into their core in order to store and transport them in biological environments. Protein cages’ pores are attractive channels for the internalisation of inorganic nanoparticles and an alternative for the preparation of hybrid bioinspired nanoparticles. However, strategies based on nanoparticle transport through the pores are largely unexplored, due to the difficulty of tailoring nanoparticles that have diameters commensurate with the pores size and simultaneously displaying specific affinity to the cages’ core and low non-specific binding to the cages’ outer surface. We evaluated the specific internalisation of single small gold nanoparticles, 3.9 nm in diameter, into porous protein cages via affinity binding. The E2 protein cage derived from the Geobacillus stearothermophilus presents 12 pores, 6 nm in diameter, and an empty core of 13 nm in diameter. We engineered the E2 protein by site-directed mutagenesis with oligohistidine sequences exposing them into the cage’s core. Dynamic light scattering and electron microscopy analysis show that the structures of E2 protein cages mutated with bis- or penta-histidine sequences are well conserved. The surface of the gold nanoparticles was passivated with a self-assembled monolayer made of a mixture of short peptidols and thiolated alkane ethylene glycol ligands. Such monolayers are found to provide thin coatings preventing non-specific binding to proteins. Further functionalisation of the peptide coated gold nanoparticles with Ni2+ nitrilotriacetic moieties enabled the specific binding to oligohistidine tagged cages. The internalisation via affinity binding was evaluated by electron microscopy analysis. From the various mutations tested, only the penta-histidine mutated E2 protein cage showed repeatable and stable internalisation. The present work overcomes the limitations of

  20. Boronate affinity electrophoresis for the purification and analysis of cofactor-modified RNAs.

    Science.gov (United States)

    Nübel, Gabriele; Sorgenfrei, Frieda A; Jäschke, Andres

    2017-03-15

    RNA modifications are widely distributed in Nature, and their thorough analysis helps answering fundamental biological questions. Nowadays, mass spectrometry or deep-sequencing methods are often used for the analysis. With the raising number of newly discovered RNA modifications, such as the 5'-NAD cap in Escherichia coli, there is an important need for new, less complex and fast analytical tools to analyze the occurrence, amount, and distribution of modified RNAs in cells. To accomplish this task, we have revisited the previously developed affinity gel electrophoresis principles and copolymerized acryloylaminophenyl boronic acid (APB) in standard denaturing polyacrylamide gels to retard the NAD- or FAD-modified RNAs compared to the unmodified RNAs in the gels. The boronyl groups inside the gel form relatively stable complexes with 1,2-cis diols, occurring naturally at the 3'-end of RNA, and also in the nicotinamide riboside of NAD-modified RNA at the 5'-end. The transient formation of diesters between the immobilized boronic acid and the diols causes lower mobility of the modified RNAs, compared to unmodified RNAs, resulting in two distinct bands for one RNA sequence. We used APB affinity gel electrophoresis to preparatively purify in vitro transcribed NAD-RNA from triphosphorylated RNA, to study the enzyme kinetics of the NAD-RNA decapping enzyme NudC, and to determine the NAD modification ratios of various cellular sRNAs. In summary, APB affinity gels can be used to study cofactor-modified RNAs with low amounts of material, and to rapidly screen for their occurrence in total RNA while avoiding complex sample treatments. Copyright © 2016 Elsevier Inc. All rights reserved.

  1. Adsorption of endotoxins on Ca2+ -iminodiacetic acid by metal ion affinity chromatography.

    Science.gov (United States)

    Lopes, André Moreni; Romeu, Jorge Sánchez; Meireles, Rolando Páez; Perera, Gabriel Marquez; Morales, Rolando Perdomo; Pessoa, Adalberto; Cárdenas, Lourdes Zumalacárregui

    2012-11-01

    Endotoxins (also known as lipopolysaccharides (LPS)) are undesirable by-products of recombinant proteins, purified from Escherichia coli. LPS can be considered stable under a wide range of temperature and pH, making their removal one of the most difficult tasks in downstream processes during protein purification. The inherent toxicity of LPS makes their removal an important step for the application of these proteins in several biological assays and for a safe parenteral administration. Immobilized metal affinity chromatography (IMAC) enables the affinity interactions between the metal ions (immobilized on the support through the chelating compound) and the target molecules, thus enabling high-efficiency separation of the target molecules from other components present in a mixture. Affinity chromatography is applied with Ca2+ -iminodiacetic acid (IDA) to remove most of the LPS contaminants from the end product (more than 90%). In this study, the adsorption of LPS on an IDA-Ca2+ was investigated. The adsorption Freundlich isotherm of LPS-IDA-Ca2+ provides a theoretical basis for LPS removal. It was found that LPS is bound mainly by interactions between the phosphate group in LPS and Ca2+ ligands on the beads. The factors such as pH (4.0 or 5.5) and ionic strength (1.0 mol/L) are essential to obtain effective removal of LPS for contaminant levels between endotoxin' concentration values less than 100 EU/mL and 100 000 EU/mL. This new protocol represents a substantial advantage in time, effort, and production costs.

  2. A Novel Recombinant DNA System for High Efficiency Affinity Purification of Proteins in Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Brian H. Carrick

    2016-03-01

    Full Text Available 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, we have created a recombinant “CelTag” DNA construct from which PCR fragments can be created to easily tag C-termini of S. cerevisiae ORFs using selection for a nat1 marker. The tag has a C-terminal cellulose binding module to be used in the first affinity step. Microgranular cellulose is very inexpensive and has an effectively continuous ligand on its surface, allowing rapid, highly efficient purification with minimal background. Cellulose-bound proteins are released by specific cleavage of an included site for TEV protease, giving nearly pure product. The tag can be lifted from the recombinant DNA construct either with or without a 13x myc epitope tag between the target ORF and the TEV protease site. Binding of CelTag protein fusions to cellulose is stable to high salt, nonionic detergents, and 1 M urea, allowing stringent washing conditions to remove loosely associated components, as needed, before specific elution. It is anticipated that this reagent could allow isolation of protein complexes from large quantities of yeast extract, including soluble, membrane-bound, or nucleic acid-associated assemblies.

  3. Fenobody: A Ferritin-Displayed Nanobody with High Apparent Affinity and Half-Life Extension.

    Science.gov (United States)

    Fan, Kelong; Jiang, Bing; Guan, Zhe; He, Jiuyang; Yang, Dongling; Xie, Ni; Nie, Guohui; Xie, Can; Yan, Xiyun

    2018-04-10

    Nanobodies consist of a single domain variable fragment of a camelid heavy-chain antibody. Nanobodies have potential applications in biomedical fields because of their simple production procedures and low cost. Occasionally, nanobody clones of interest exhibit low affinities for their target antigens, which, together with their short half-life limit bioanalytical or therapeutic applications. Here, we developed a novel platform we named fenobody, in which a nanobody developed against H5N1 virus is displayed on the surface of ferritin in the form of a 24mer. We constructed a fenobody by substituting the fifth helix of ferritin with the nanobody. TEM analysis showed that nanobodies were displayed on the surface of ferritin in the form of 6 × 4 bundles, and that these clustered nanobodies are flexible for antigen binding in spatial structure. Comparing fenobodies with conventional nanobodies currently used revealed that the antigen binding apparent affinity of anti-H5N1 fenobody was dramatically increased (∼360-fold). Crucially, their half-life extension in a murine model was 10-fold longer than anti-H5N1 nanobody. In addition, we found that our fenobodies are highly expressed in Escherichia coli, and are both soluble and thermo-stable nanocages that self-assemble as 24-polymers. In conclusion, our results demonstrate that fenobodies have unique advantages over currently available systems for apparent affinity enhancement and half-life extension of nanobodies. Our fenobody system presents a suitable platform for various large-scale biotechnological processes and should greatly facilitate the application of nanobody technology in these areas.

  4. Specific Internalisation of Gold Nanoparticles into Engineered Porous Protein Cages via Affinity Binding.

    Science.gov (United States)

    Paramelle, David; Peng, Tao; Free, Paul; Fernig, David G; Lim, Sierin; Tomczak, Nikodem

    2016-01-01

    Porous protein cages are supramolecular protein self-assemblies presenting pores that allow the access of surrounding molecules and ions into their core in order to store and transport them in biological environments. Protein cages' pores are attractive channels for the internalisation of inorganic nanoparticles and an alternative for the preparation of hybrid bioinspired nanoparticles. However, strategies based on nanoparticle transport through the pores are largely unexplored, due to the difficulty of tailoring nanoparticles that have diameters commensurate with the pores size and simultaneously displaying specific affinity to the cages' core and low non-specific binding to the cages' outer surface. We evaluated the specific internalisation of single small gold nanoparticles, 3.9 nm in diameter, into porous protein cages via affinity binding. The E2 protein cage derived from the Geobacillus stearothermophilus presents 12 pores, 6 nm in diameter, and an empty core of 13 nm in diameter. We engineered the E2 protein by site-directed mutagenesis with oligohistidine sequences exposing them into the cage's core. Dynamic light scattering and electron microscopy analysis show that the structures of E2 protein cages mutated with bis- or penta-histidine sequences are well conserved. The surface of the gold nanoparticles was passivated with a self-assembled monolayer made of a mixture of short peptidols and thiolated alkane ethylene glycol ligands. Such monolayers are found to provide thin coatings preventing non-specific binding to proteins. Further functionalisation of the peptide coated gold nanoparticles with Ni2+ nitrilotriacetic moieties enabled the specific binding to oligohistidine tagged cages. The internalisation via affinity binding was evaluated by electron microscopy analysis. From the various mutations tested, only the penta-histidine mutated E2 protein cage showed repeatable and stable internalisation. The present work overcomes the limitations of currently

  5. Dual-affinity peptides to generate dense surface coverages of nanoparticles

    International Nuclear Information System (INIS)

    Del Re, Julia; Blum, Amy Szuchmacher

    2014-01-01

    Graphical abstract: - Highlights: • Stable nanoparticles were created with the Flg-A3 fusion peptide as a ligand. • Interactions of transition metal ions with Flg control aggregation of the nanoparticles in solution. • The QBP1-A3 fusion peptide improves surface attachment of gold nanoparticles. • Solution pre-aggregation of nanoparticles results in dense surface coverage. - Abstract: Depositing gold nanoparticles is of great interest because of the many potential applications of nanoparticle films; however, generating dense surface nanoparticle coverage remains a difficult challenge. Using dual-affinity peptides we have synthesized gold nanoparticles and then pre-aggregated the particles in solution via interactions with metal ions. These nanoparticle aggregates were then deposited onto silicon dioxide surfaces using another dual-affinity peptide to control binding to the substrate. The results demonstrate that when divalent ions like Zn 2+ or Ni 2+ are used, densely packed gold nanoparticle monolayers are formed on the silicon dioxide substrate, which may have applications in fields like molecular electronics

  6. Structure-Based Understanding of Binding Affinity and Mode of Estrogen Receptor α Agonists and Antagonists.

    Directory of Open Access Journals (Sweden)

    Sehan Lee

    Full Text Available The flexible hydrophobic ligand binding pocket (LBP of estrogen receptor α (ERα allows the binding of a wide variety of endocrine disruptors. Upon ligand binding, the LBP reshapes around the contours of the ligand and stabilizes the complex by complementary hydrophobic interactions and specific hydrogen bonds with the ligand. Here we present a framework for quantitative analysis of the steric and electronic features of the human ERα-ligand complex using three dimensional (3D protein-ligand interaction description combined with 3D-QSAR approach. An empirical hydrophobicity density field is applied to account for hydrophobic contacts of ligand within the LBP. The obtained 3D-QSAR model revealed that hydrophobic contacts primarily determine binding affinity and govern binding mode with hydrogen bonds. Several residues of the LBP appear to be quite flexible and adopt a spectrum of conformations in various ERα-ligand complexes, in particular His524. The 3D-QSAR was combined with molecular docking based on three receptor conformations to accommodate receptor flexibility. The model indicates that the dynamic character of the LBP allows accommodation and stable binding of structurally diverse ligands, and proper representation of the protein flexibility is critical for reasonable description of binding of the ligands. Our results provide a quantitative and mechanistic understanding of binding affinity and mode of ERα agonists and antagonists that may be applicable to other nuclear receptors.

  7. Purification of xanthine oxidase from bovine milk by affinity chromatography with a novel gel.

    Science.gov (United States)

    Beyaztaş, Serap; Arslan, Oktay

    2015-06-01

    A new affinity gel was synthesized for the purification of xanthine oxidase (XO, EC 1.2.3.22) from bovine milk. The gel was prepared on a Sepharose 4B matrix on which a spacer arm based on l-tyrosine was covalently attached via CNBr activation, followed by reaction with the XO inhibitor p-aminobenzamidine. The elution conditions of affinity gel were determined at different pH values and ionic strengths. Maximum elution of XO was achieved at pH 9.0 and ionic strength around 0.4. The overall purification for XO was 1645-fold with 20.49% yield. SDS-PAGE of the enzyme indicates a single band with an apparent MW of 150 kDa. The gel provides a simple, rapid and effective useful for the purification of XO. Heat stability was determined on purified XO activity. Xanthine oxidase was preserved up to 70% with activity exposure of 60 °C and incubated for 60 min. These results indicated that the enzyme was heat stable.

  8. F+ and F⁻ affinities of simple N(x)F(y) and O(x)F(y) compounds.

    Science.gov (United States)

    Grant, Daniel J; Wang, Tsang-Hsiu; Vasiliu, Monica; Dixon, David A; Christe, Karl O

    2011-03-07

    Atomization energies at 0 K and heats of formation at 0 and 298 K are predicted for the neutral and ionic N(x)F(y) and O(x)F(y) systems using coupled cluster theory with single and double excitations and including a perturbative triples correction (CCSD(T)) method with correlation consistent basis sets extrapolated to the complete basis set (CBS) limit. To achieve near chemical accuracy (±1 kcal/mol), three corrections to the electronic energy were added to the frozen core CCSD(T)/CBS binding energies: corrections for core-valence, scalar relativistic, and first order atomic spin-orbit effects. Vibrational zero point energies were computed at the CCSD(T) level of theory where possible. The calculated heats of formation are in good agreement with the available experimental values, except for FOOF because of the neglect of higher order correlation corrections. The F(+) affinity in the N(x)F(y) series increases from N(2) to N(2)F(4) by 63 kcal/mol, while that in the O(2)F(y) series decreases by 18 kcal/mol from O(2) to O(2)F(2). Neither N(2) nor N(2)F(4) is predicted to bind F(-), and N(2)F(2) is a very weak Lewis acid with an F(-) affinity of about 10 kcal/mol for either the cis or trans isomer. The low F(-) affinities of the nitrogen fluorides explain why, in spite of the fact that many stable nitrogen fluoride cations are known, no nitrogen fluoride anions have been isolated so far. For example, the F(-) affinity of NF is predicted to be only 12.5 kcal/mol which explains the numerous experimental failures to prepare NF(2)(-) salts from the well-known strong acid HNF(2). The F(-) affinity of O(2) is predicted to have a small positive value and increases for O(2)F(2) by 23 kcal/mol, indicating that the O(2)F(3)(-) anion might be marginally stable at subambient temperatures. The calculated adiabatic ionization potentials and electron affinities are in good agreement with experiment considering that many of the experimental values are for vertical processes. © 2011

  9. Peptide‐MHC class I stability is a better predictor than peptide affinity of CTL immunogenicity

    DEFF Research Database (Denmark)

    Harndahl, Mikkel Nors; Rasmussen, Michael; Roder, Gustav

    2012-01-01

    Efficient presentation of peptide‐MHC class I (pMHC‐I) complexes to immune T cells should benefit from a stable peptide‐MHC‐I interaction. However, it has been difficult to distinguish stability from other requirements for MHC‐I binding, for example, affinity. We have recently established a high......‐throughput assay for pMHC‐I stability. Here, we have generated a large database containing stability measurements of pMHC‐I complexes, and re‐examined a previously reported unbiased analysis of the relative contributions of antigen processing and presentation in defining cytotoxic T lymphocyte (CTL) immunogenicity...... [Assarsson et al., J. Immunol. 2007. 178: 7890–7901]. Using an affinity‐balanced approach, we demonstrated that immunogenic peptides tend to be more stably bound to MHC‐I molecules compared with nonimmunogenic peptides. We also developed a bioinformatics method to predict pMHC‐I stability, which suggested...

  10. Determination of the electron affinity of astatine and polonium by laser photodetachment

    CERN Multimedia

    We propose to conduct the first electron affinity (EA) measurements of the two elements astatine (At) and polonium (Po). Collinear photo-detachment spectroscopy will allow us to measure these quantities with an uncertainty limited only by the spectral line width of the laser. We plan to use negative ion beams of the two radioactive elements At and Po, which are only accessible on-line and at ISOLDE. The feasibility of our proposed method and the functionality of the experimental setup have been demonstrated at ISOLDE in off-line tests by the clear observation of the photo-detachment threshold for stable iodine. This proposal is based on our Letter of Intent I-148.

  11. A MEMS differential viscometric sensor for affinity glucose detection in continuous glucose monitoring

    International Nuclear Information System (INIS)

    Huang, Xian; Cai, Haogang; Song, Bing; Lin, Qiao; Li, Siqi; Davis, Erin; Wang, Qian; Leduc, Charles; Ravussin, Yann; Leibel, Rudolph; Li, Dachao; Accili, Domenico

    2013-01-01

    Micromachined viscometric affinity glucose sensors have been previously demonstrated using vibrational cantilever and diaphragm. These devices featured a single glucose detection module that determines glucose concentrations through viscosity changes of glucose-sensitive polymer solutions. However, fluctuations in temperature and other environmental parameters might potentially affect the stability and reliability of these devices, creating complexity in their applications in subcutaneously implanted continuous glucose monitoring (CGM). To address these issues, we present a MEMS differential sensor that can effectively reject environmental disturbances while allowing accurate glucose detection. The sensor consists of two magnetically driven vibrating diaphragms situated inside microchambers filled with a boronic-acid based glucose-sensing solution and a reference solution insensitive to glucose. Glucose concentrations can be accurately determined by characteristics of the diaphragm vibration through differential capacitive detection. Our in vitro and preliminary in vivo experimental data demonstrate the potential of this sensor for highly stable subcutaneous CGM applications. (paper)

  12. Specificity and affinity quantification of protein-protein interactions.

    Science.gov (United States)

    Yan, Zhiqiang; Guo, Liyong; Hu, Liang; Wang, Jin

    2013-05-01

    Most biological processes are mediated by the protein-protein interactions. Determination of the protein-protein structures and insight into their interactions are vital to understand the mechanisms of protein functions. Currently, compared with the isolated protein structures, only a small fraction of protein-protein structures are experimentally solved. Therefore, the computational docking methods play an increasing role in predicting the structures and interactions of protein-protein complexes. The scoring function of protein-protein interactions is the key responsible for the accuracy of the computational docking. Previous scoring functions were mostly developed by optimizing the binding affinity which determines the stability of the protein-protein complex, but they are often lack of the consideration of specificity which determines the discrimination of native protein-protein complex against competitive ones. We developed a scoring function (named as SPA-PP, specificity and affinity of the protein-protein interactions) by incorporating both the specificity and affinity into the optimization strategy. The testing results and comparisons with other scoring functions show that SPA-PP performs remarkably on both predictions of binding pose and binding affinity. Thus, SPA-PP is a promising quantification of protein-protein interactions, which can be implemented into the protein docking tools and applied for the predictions of protein-protein structure and affinity. The algorithm is implemented in C language, and the code can be downloaded from http://dl.dropbox.com/u/1865642/Optimization.cpp.

  13. H1-histamine receptor affinity predicts weight gain with antidepressants.

    Science.gov (United States)

    Salvi, Virginio; Mencacci, Claudio; Barone-Adesi, Francesco

    2016-10-01

    Weight gain and metabolic abnormalities are extensively found in patients taking psychotropic medications. Although mainly antipsychotics have been implicated, also antidepressants carry the potential to induce weight gain, with tricyclics and mirtazapine being associated with the greatest weight gain. It has been suggested that this could be due to the different ability of antidepressants to block adrenergic, cholinergic, and histaminergic postsynaptic receptors. To date, however, the link between antidepressant-induced weight gain and their receptor affinity profile has not been established. We reanalysed data from a previous meta-analysis to evaluate whether weight change is associated with specific receptor affinity of antidepressants. We retrieved data from the only meta-analysis that assessed weight change with antidepressants. We searched in the Psychoactive Drug Screening Program (PDSP) Ki database data on the affinities of antidepressants to receptors hypothetically linked with weight change: H1-histamine, 5HT2c, M3-muscarinic, and α1A-adrenergic receptors. The association between weight change and receptor affinities was estimated using meta-regression. We found a significant association between the affinity of antidepressants to H1-receptor and weight gain (p value: antidepressants. These results further stress a reclassification of antidepressants according to their pharmacodynamic properties, and suggest avoiding prescribing antidepressants with an anti-histaminergic profile to patients at risk for cardio-metabolic disturbances. Copyright © 2016 Elsevier B.V. and ECNP. All rights reserved.

  14. Thermokinetic model of borosilicate glass dissolution: contextual affinity

    International Nuclear Information System (INIS)

    Advocat, T.; Vernaz, E.; Crovisier, J.L.; Fritz, B.

    1989-01-01

    Short and long-term geochemical interactions of R7T7 nuclear glass with water at 100 0 C were simulated with the DISSOL thermokinetic computer code. Both the dissolved glass quantity and the resulting water composition, saturation states and mineral quantities produced were calculated as a function of time. The rate equation used in the simulation was first proposed by Aagaard and Helgeson. It simulates a gradually diminishing dissolution rate as the reaction affinity diminishes. The best agreement with 1-year experimental data was obtained with a reaction affinity calculated from silica activity (Grambow's hypothesis) rather than taking into account the activity of all the glass components as proposed by Jantzen and Plodinec. The concept of residual affinity was introduced by Grambow to express the fact that the glass dissolution rate does not cease. We prefer to replace the term residual affinity by contextual affinity, which expresses the influence on the dissolution rate of three factors: the solution chemistry, the metastability of SiO 2 (m), and the possible precipitation of certain aluminosilicates such as zeolites. 19 refs

  15. Shelf-Stable Food Safety

    Science.gov (United States)

    ... is an MRE? Is an MRE shelf stable? What foods are packaged in retort packages? What is aseptic ... type of package is used for aseptic processing? What foods are packaged in aseptic packages? Can I microwave ...

  16. Pharmaceuticals labelled with stable isotopes

    International Nuclear Information System (INIS)

    Krumbiegel, P.

    1986-11-01

    The relatively new field of pharmaceuticals labelled with stable isotopes is reviewed. Scientific, juridical, and ethical questions are discussed concerning the application of these pharmaceuticals in human medicine. 13 C, 15 N, and 2 H are the stable isotopes mainly utilized in metabolic function tests. Methodical contributions are given to the application of 2 H, 13 C, and 15 N pharmaceuticals showing new aspects and different states of development in the field under discussion. (author)

  17. Stable isotope research pool inventory

    International Nuclear Information System (INIS)

    1984-03-01

    This report contains a listing of electromagnetically separated stable isotopes which are available at the Oak Ridge National Laboratory for distribution for nondestructive research use on a loan basis. This inventory includes all samples of stable isotopes in the Research Materials Collection and does not designate whether a sample is out on loan or is in reprocessing. For some of the high abundance naturally occurring isotopes, larger amounts can be made available; for example, Ca-40 and Fe-56

  18. Affinity capillary electrophoresis for the assessment of binding affinity of carbohydrate-based cholera toxin inhibitors.

    Science.gov (United States)

    Aizpurua-Olaizola, Oier; Sastre Torano, Javier; Pukin, Aliaksei; Fu, Ou; Boons, Geert Jan; de Jong, Gerhardus J; Pieters, Roland J

    2018-01-01

    Developing tools for the study of protein carbohydrate interactions is an important goal in glycobiology. Cholera toxin inhibition is an interesting target in this context, as its inhibition may help to fight against cholera. For the study of novel ligands an affinity capillary electrophoresis (ACE) method was optimized and applied. The method uses unlabeled cholera toxin B-subunit (CTB) and unlabeled carbohydrate ligands based on ganglioside GM1-oligosaccharides (GM1os). In an optimized method at pH 4, adsorption of the protein to the capillary walls was prevented by a polybrene-dextran sulfate-polybrene coating. Different concentrations of the ligands were added to the BGE. CTB binding was observed by a mobility shift that could be used for dissociation constant (K d ) determination. The K d values of two GM1 derivatives differed by close to an order of magnitude (600 ± 20 nM and 90 ± 50 nM) which was in good agreement with the differences in their reported nanomolar IC 50 values of an ELISA-type assay. Moreover, the selectivity of GM1os towards CTB was demonstrated using Influenza hemagglutinin (H5) as a binding competitor. The developed method can be an important platform for preclinical development of drugs targeting pathogen-induced secretory diarrhea. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Specific capture of uranyl protein targets by metal affinity chromatography

    Energy Technology Data Exchange (ETDEWEB)

    Basset, C.; Dedieu, A.; Guerin, P.; Quemeneur, E.; Meyer, D.; Vidaud, C. [CEA Valrho, DSV, IBEB, Serv Biochim et Toxicol Nucl, F-30207 Bagnols Sur Ceze (France)

    2008-07-01

    To improve general understanding of biochemical mechanisms in the field of uranium toxicology, the identification of protein targets needs to be intensified. Immobilized metal affinity chromatography (IMAC) has been widely developed as a powerful tool for capturing metal binding proteins from biological extracts. However uranyl cations (UO{sub 2}{sup 2+}) have particular physico-chemical characteristics which prevent them from being immobilized on classical metal chelating supports. We report here on the first development of an immobilized uranyl affinity chromatography method, based on the cation-exchange properties of amino-phosphonate groups for uranyl binding. The cation distribution coefficient and loading capacity on the support were determined. Then the stability of the uranyl-bonded phase under our chromatographic conditions was optimized to promote affinity mechanisms. The successful enrichment of uranyl binding proteins from human serum was then proven using proteomic and mass spectral analysis. (authors)

  20. Identification of RNA-ligand interactions by affinity electrophoresis.

    Science.gov (United States)

    Boodram, Sherry N; Cho, Chul M; Tavares, Tony J; Johnson, Philip E

    2011-02-01

    We have developed an affinity electrophoresis method to screen for RNA-ligand interactions. Native polyacrylamide gels were polymerized in the absence and presence of different RNA binding molecules. Binding is indicated by a difference in mobility between the gel with ligand present and the gel with no ligand present. The utility of this method was demonstrated using the known interaction between the Escherichia coli ribosomal A-site RNA and different aminoglycoside ligands. The RNA-aminoglycoside interaction observed is dose dependent, and the affinity mirrors what is observed in solution. In addition, we used this method to gauge the affinity to different aminoglycoside molecules of an RNA molecule derived from the thymidylate synthase mRNA construct that contains a CC mismatch. Copyright © 2010 Elsevier Inc. All rights reserved.

  1. k-Schur functions and affine Schubert calculus

    CERN Document Server

    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 ...

  2. Integrable deformations of affine Toda theories and duality

    International Nuclear Information System (INIS)

    Fateev, V.A.

    1996-01-01

    We introduce and study five series of one-parameter families of two-dimensional integrable quantum field theories. These theories have a Lagrangian description in terms of the massive Thirring model coupled with non-simply laced affine Toda theories. Perturbative calculations, analysis of the factorized scattering theory and the Bethe ansatz technique are used to show that these field theories possess the dual representation available for the perturbative analysis in the strong coupling limit. The dual theory can be formulated as the non-linear sigma model with Witten's Euclidean black hole metric (complex sinh-Gordon theory) coupled with non-simply laced affine Toda theories. Lie algebras associated with these ''dual'' Toda theories belong to the dual series of affine algebras but have a smaller rank. The exact relation between coupling constants in the dual theories is conjectured. (orig.)

  3. 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.

  4. Selection of ligands for affinity chromatography using quartz crystal biosensor.

    Science.gov (United States)

    Liu, Yang; Tang, Xiaoling; Liu, Feng; Li, Ke'an

    2005-07-01

    This paper described a new strategy for rapid selecting ligands for application in affinity chromatography using a quartz crystal microbalance (QCM) biosensor. An aminoglycoside antibiotic drug, kanamycin (KM), was immobilized on the gold electrodes of the QCM sensor chip. The binding interactions of the immobilized KM with various proteins in solution were monitored as the variations of the resonant frequency of the modified sensor. Such a rapid screen analysis of interactions indicated clearly that KM-immobilized sensor showed strong specific interaction only with lysozyme (LZM). The resultant sensorgrams were rapidly analyzed by using a kinetic analysis software based on a genetic algorithm to derive both the kinetic rate constants (k(ass) and k(diss)) and equilibrium dissociation constants (K(D)) for LZM-KM interactions. The immobilized KM showed higher affinity to LZM with a dissociation constant on the order of 10(-5) M, which is within the range of 10(-4)-10(-8) M and suitable for an affinity ligand. Therefore, KM was demonstrated for the first time as a novel affinity ligand for purification of LZM and immobilized onto the epoxy-activated silica in the presence of a high potassium phosphate concentration. The KM immobilized affinity column has proved useful for a very convenient purification of LZM from chicken egg white. The purity of LZM obtained was higher than 90%, as determined by densitometric scanning of sodium dodecyl sulfate-polyacrylamide gel electrophoresis of purified fraction. These results confirmed that the selected KM ligand is indeed a valuable affinity ligand for purification of LZM. The new screening strategy based on a QCM biosensor is expected to be a promising way for rapid selecting specific ligands for purifying other valuable proteins.

  5. Kinetic controlled affinity labeling of target enzyme with thioester chemistry.

    Science.gov (United States)

    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. Copyright © 2016 Elsevier Ltd. All rights reserved.

  6. Temperature effects on the blood oxygen affinity in sharks.

    Science.gov (United States)

    Bernal, Diego; Reid, Joseph P; Roessig, Julie M; Matsumoto, Shinsyu; Sepulveda, Chugey A; Cech, Joseph J; Graham, Jeffrey B

    2018-03-05

    In fish, regional endothermy (i.e., the capacity to significantly elevate tissue temperatures above ambient via vascular heat exchangers) in the red swimming muscles (RM) has evolved only in a few marine groups (e.g., sharks: Lamnidae, Alopiidae, and teleosts Scombridae). Within these taxa, several species have also been shown to share similar physiological adaptations to enhance oxygen delivery to the working tissues. Although the hemoglobin (Hb) of most fish has a decreased affinity for oxygen with an increase in temperature, some regionally endothermic teleosts (e.g., tunas) have evolved Hbs that have a very low or even an increased affinity for oxygen with an increase in temperature. For sharks, however, blood oxygen affinities remain largely unknown. We examined the effects of temperature on the blood oxygen affinity in two pelagic species (the regionally endothermic shortfin mako shark and the ectothermic blue shark) at 15, 20, and 25 °C, and two coastal ectothermic species (the leopard shark and brown smooth-hound shark) at 10, 15, and 20 °C. Relative to the effects of temperature on the blood oxygen affinity of ectothermic sharks (e.g., blue shark), shortfin mako shark blood was less affected by an increase in temperature, a scenario similar to that documented in some of the tunas. In the shortfin mako shark, this may act to prevent premature oxygen dissociation from Hb as the blood is warmed during its passage through vascular heat exchangers. Even though the shortfin mako shark and blue shark occupy a similar niche, the effects of temperature on blood oxygen affinity in the latter more closely resembled that of the blood in the two coastal shark species examined in this study. The only exception was a small, reverse temperature effect (an increase in blood oxygen affinity with temperature) observed during the warming of the leopard shark blood under simulated arterial conditions, a finding that is likely related to the estuarine ecology of this

  7. 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.

  8. Affinity Electrophoresis for Analysis of Catalytic Module-Carbohydrate Interactions

    DEFF Research Database (Denmark)

    Cockburn, Darrell; Wilkens, Casper; Svensson, Birte

    2017-01-01

    Affinity electrophoresis has long been used to study the interaction between proteins and large soluble ligands. The technique has been found to have great utility for the examination of polysaccharide binding by proteins, particularly carbohydrate binding modules (CBMs). In recent years, carbohy......Affinity electrophoresis has long been used to study the interaction between proteins and large soluble ligands. The technique has been found to have great utility for the examination of polysaccharide binding by proteins, particularly carbohydrate binding modules (CBMs). In recent years...

  9. Stable Boundary Layer Education (STABLE) Final Campaign Summary

    Energy Technology Data Exchange (ETDEWEB)

    Turner, David D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2016-03-01

    The properties of, and the processes that occur in, the nocturnal stable boundary layer are not well understood, making it difficult to represent adequately in numerical models. The nocturnal boundary layer often is characterized by a temperature inversion and, in the Southern Great Plains region, a low-level jet. To advance our understanding of the nocturnal stable boundary layer, high temporal and vertical resolution data on the temperature and wind properties are needed, along with both large-eddy simulation and cloud-resolving modeling.

  10. 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

  11. Mutational analysis of affinity and selectivity of kringle-tetranectin interaction. Grafting novel kringle affinity ontp the trtranectin lectin scaffold

    DEFF Research Database (Denmark)

    Graversen, Jonas Heilskov; Jacobsen, C; Sigurskjold, B W

    2000-01-01

    -type lectin-like domain of tetranectin, involving Lys-148, Glu-150, and Asp-165, which mediates calcium-sensitive binding to plasminogen kringle 4. Here, we investigate the effect of conservative substitutions of these and a neighboring amino acid residue. Substitution of Thr-149 in tetranectin...... with a tyrosine residue considerably increases the affinity for plasminogen kringle 4, and, in addition, confers affinity for plasminogen kringle 2. As shown by isothermal titration calorimetry analysis, this new interaction is stronger than the binding of wild-type tetranectin to plasminogen kringle 4...

  12. Generalized Warburg impedance on realistic self-affine fractals ...

    Indian Academy of Sciences (India)

    Administrator

    Generalized Warburg impedance on realistic self-affine fractals: Comparative study of statistically corrugated and isotropic roughness. RAJESH KUMAR and RAMA KANT. Journal of Chemical Sciences, Vol. 121, No. 5, September 2009, pp. 579–588. 1. ( ) c. L. R ω on page 582, column 2, para 2, after eq (8) should read as ...

  13. Accurate Evaluation Method of Molecular Binding Affinity from Fluctuation Frequency

    Science.gov (United States)

    Hoshino, Tyuji; Iwamoto, Koji; Ode, Hirotaka; Ohdomari, Iwao

    2008-05-01

    Exact estimation of the molecular binding affinity is significantly important for drug discovery. The energy calculation is a direct method to compute the strength of the interaction between two molecules. This energetic approach is, however, not accurate enough to evaluate a slight difference in binding affinity when distinguishing a prospective substance from dozens of candidates for medicine. Hence more accurate estimation of drug efficacy in a computer is currently demanded. Previously we proposed a concept of estimating molecular binding affinity, focusing on the fluctuation at an interface between two molecules. The aim of this paper is to demonstrate the compatibility between the proposed computational technique and experimental measurements, through several examples for computer simulations of an association of human immunodeficiency virus type-1 (HIV-1) protease and its inhibitor (an example for a drug-enzyme binding), a complexation of an antigen and its antibody (an example for a protein-protein binding), and a combination of estrogen receptor and its ligand chemicals (an example for a ligand-receptor binding). The proposed affinity estimation has proven to be a promising technique in the advanced stage of the discovery and the design of drugs.

  14. 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...

  15. Variational problems for plane curves in centro-affine geometry

    International Nuclear Information System (INIS)

    Musso, Emilio

    2010-01-01

    In this paper closed extremals of variational problems defined by quadratic polynomials in the centro-affine curvature are considered. The closure of the trajectories is discussed and the existence of countably many closed critical curves is proven. The geometrical properties of closed trajectories are analyzed by numerical methods.

  16. "The Hunger Games": Literature, Literacy, and Online Affinity Spaces

    Science.gov (United States)

    Curwood, Jen Scott

    2013-01-01

    This article examines adolescent literacy practices related to "The Hunger Games," a young adult novel and the first of a trilogy. By focusing on the interaction of social identities, discourses, and media paratexts within an online affinity space, this ethnographic study offers insight into how young adults engage with contemporary…

  17. Testing Affine Term Structure Models in Case of Transaction Costs

    NARCIS (Netherlands)

    Driessen, J.J.A.G.; Melenberg, B.; Nijman, T.E.

    1999-01-01

    In this paper we empirically analyze the impact of transaction costs on the performance of affine interest rate models. We test the implied (no arbitrage) Euler restrictions, and we calculate the specification error bound of Hansen and Jagannathan to measure the extent to which a model is

  18. On affine variety codes from the Klein quartic

    DEFF Research Database (Denmark)

    Geil, Hans Olav; Ozbudak, Ferruh

    2018-01-01

    We study a family of primary affine variety codes defined from the Klein quartic. The duals of these codes have previously been treated in Kolluru et al., (Appl. Algebra Engrg. Comm. Comput. 10(6):433–464, 2000, Ex. 3.2). Among the codes that we construct almost all have parameters as good as the...

  19. Adaptive mutations alter antibody structure and dynamics during affinity maturation.

    Science.gov (United States)

    Adhikary, Ramkrishna; Yu, Wayne; Oda, Masayuki; Walker, Ross C; Chen, Tingjian; Stanfield, Robyn L; Wilson, Ian A; Zimmermann, Jörg; Romesberg, Floyd E

    2015-03-24

    While adaptive mutations can bestow new functions on proteins via the introduction or optimization of reactive centers, or other structural changes, a role for the optimization of protein dynamics also seems likely but has been more difficult to evaluate. Antibody (Ab) affinity maturation is an example of adaptive evolution wherein the adaptive mutations may be identified and Abs may be raised to specific targets that facilitate the characterization of protein dynamics. Here, we report the characterization of three affinity matured Abs that evolved from a common germline precursor to bind the chromophoric antigen (Ag), 8-methoxypyrene-1,3,6-trisulfonate (MPTS). In addition to characterizing the sequence, molecular recognition, and structure of each Ab, we characterized the dynamics of each complex by determining their mechanical response to an applied force via three-pulse photon echo peak shift (3PEPS) spectroscopy and deconvoluting the response into elastic, anelastic, and plastic components. We find that for one Ab, affinity maturation was accomplished via the introduction of a single functional group that mediates a direct contact with MPTS and results in a complex with little anelasticity or plasticity. In the other two cases, more mutations were introduced but none directly contact MPTS, and while their effects on structure are subtle, their effects on anelasticity and plasticity are significant, with the level of plasticity correlated with specificity, suggesting that the optimization of protein dynamics may have contributed to affinity maturation. A similar optimization of structure and dynamics may contribute to the evolution of other proteins.

  20. Certain extensions of vertex operator algebras of affine type

    International Nuclear Information System (INIS)

    Li Haisheng

    2001-01-01

    We generalize Feigin and Miwa's construction of extended vertex operator (super)algebras A k (sl(2)) for other types of simple Lie algebras. For all the constructed extended vertex operator (super)algebras, irreducible modules are classified, complete reducibility of every module is proved and fusion rules are determined modulo the fusion rules for vertex operator algebras of affine type. (orig.)

  1. Affine Kac-Moody algebras and their representations

    International Nuclear Information System (INIS)

    Slansky, R.

    1988-01-01

    Highest weight representation theory of finite dimensional and affine Kac-Moody algebras is summarized from a unified point of view. Lattices of discrete additive quantum numbers and the presentation of Lie algebras on Cartan matrices are the central points of departure for the analysis. (author)

  2. New matrices for the purification of pectinases by affinity chromatography.

    Science.gov (United States)

    Lobarzewski, J; Fiedurek, J; Ginalska, G; Wolski, T

    1985-09-16

    Polygalacturonic acid was used as a ligand in the affinity technique for pectinases purification from the filtrate of Aspergillus niger 71 culture. For this purpose four matrices were examined, namely, alkylamine controlled porous glass (CPG), alkylamine silica gel as well as keratin or polyamide coated silica gel. Good results of pectinase purification was obtained on silanized CPG or keratin coated silica gel supports.

  3. Development of gadolinium based nanoparticles having an affinity towards melanin

    Science.gov (United States)

    Morlieras, Jessica; Chezal, Jean-Michel; Miot-Noirault, Elisabeth; Roux, Amandine; Heinrich-Balard, Laurence; Cohen, Richard; Tarrit, Sébastien; Truillet, Charles; Mignot, Anna; Hachani, Roxanne; Kryza, David; Antoine, Rodolphe; Dugourd, Philippe; Perriat, Pascal; Janier, Marc; Sancey, Lucie; Lux, François; Tillement, Olivier

    2013-01-01

    Small Rigid Platforms (SRPs) are sub-5 nanometre gadolinium based nanoparticles that have been developed for multimodal imaging and theranostic applications. They are composed of a polysiloxane network surrounded by gadolinium chelates. A covalent coupling with quinoxaline derivatives has been performed. Such derivatives have proven their affinity for melanin frequently expressed in primary melanoma cases. Three different quinoxaline derivatives have been synthesised and coupled to the nanoparticles. The affinity of the grafted nanoparticles for melanin has then been shown in vitro by surface plasmon resonance on a homemade melanin grafted gold chip.Small Rigid Platforms (SRPs) are sub-5 nanometre gadolinium based nanoparticles that have been developed for multimodal imaging and theranostic applications. They are composed of a polysiloxane network surrounded by gadolinium chelates. A covalent coupling with quinoxaline derivatives has been performed. Such derivatives have proven their affinity for melanin frequently expressed in primary melanoma cases. Three different quinoxaline derivatives have been synthesised and coupled to the nanoparticles. The affinity of the grafted nanoparticles for melanin has then been shown in vitro by surface plasmon resonance on a homemade melanin grafted gold chip. Electronic supplementary information (ESI) available. See DOI: 10.1039/c2nr33457g

  4. Transformations Based on Continuous Piecewise-Affine Velocity Fields

    DEFF Research Database (Denmark)

    Freifeld, Oren; Hauberg, Søren; Batmanghelich, Kayhan

    2017-01-01

    We propose novel finite-dimensional spaces of well-behaved transformations. The latter are obtained by (fast and highly-accurate) integration of continuous piecewise-affine velocity fields. The proposed method is simple yet highly expressive, effortlessly handles optional constraints (e.g., volume...

  5. Electrochemical affinity biosensors for detection of mycotoxins: A review.

    Science.gov (United States)

    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. Copyright © 2013 Elsevier B.V. All rights reserved.

  6. Smooth surfaces from bilinear patches: Discrete affine minimal surfaces

    KAUST Repository

    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.

  7. Student Engagement and Neoliberalism: Mapping an Elective Affinity

    Science.gov (United States)

    Zepke, Nick

    2015-01-01

    The purpose of this article is to argue that student engagement, an important area for research about learning and teaching in formal higher education, has an elective affinity with neoliberalism, a hegemonic ideology in many countries of the developed world. The paper first surveys an extensive research literature examining student engagement and…

  8. Affinity (tropism) of caprine arthritis encephalitis virus for brain cells

    African Journals Online (AJOL)

    STORAGESEVER

    2008-11-19

    Nov 19, 2008 ... Full Length Research Paper. Affinity (tropism) of caprine arthritis encephalitis virus for brain cells. Adebayo, I. A.1*, Awoniyi, T. A. M. 1 and Olaleye, O. D.2. 1Department of Animal Production and Health, Animal Parasitology and Microbiology Research Unit, Federal University of Technology, P M B 704, ...

  9. Affinity purification of polysaccharide degrading enzymes with crosslinked substrates

    NARCIS (Netherlands)

    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

  10. Crosslinked xylan as an affinity adsorbent for endo-xylanases.

    NARCIS (Netherlands)

    Rozie, H.; Somers, W.; Bonte, A.; Rombouts, F.M.; Visser, J.

    1992-01-01

    In order to facilitate the purification of xylanases from Aspergillus niger, an affinity adsorbent has been developed from oat spelts xylan. A suitable adsorbent was only obtained by crosslinking oat spelts xylan with epichlorohydrin in water but not in ethanol or ethanol-water mixtures. After some

  11. Oxygen uptake and baemocyanin oxygen affinity of Potamonautes ...

    African Journals Online (AJOL)

    1988-11-01

    Nov 1, 1988 ... In both respiratory media this causes a lowering in the haemocyanin oxygen affinity with a Bohr-factor of -1,05 whilst the haemocyanin- .... In another experiment the oxygen-binding properties of declotted haemolymph ..... layer optical cell for gas-reaction studies of hemoglobin. Anal. Biochem. 87: 127-134 ...

  12. 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...

  13. A chimeric affinity tag for efficient expression and chromatographic purification of heterologous proteins from plants

    Directory of Open Access Journals (Sweden)

    Frank eSainsbury

    2016-02-01

    Full Text Available The use of plants as expression hosts for recombinant proteins is an increasingly attractive option for the production of complex and challenging biopharmaceuticals. Tools are needed at present to marry recent developments in high-yielding gene vectors for heterologous expression with routine protein purification techniques. In this study we designed the Cysta-tag, a new purification tag for immobilized metal affinity chromatography (IMAC of plant-made proteins based on the protein-stabilizing fusion partner SlCYS8. We show that the Cysta-tag may be used to rapidly purify proteins under native conditions, and then be removed enzymatically to isolate the protein of interest. We also show that commonly used protease recognition sites for linking purification tags are differentially stable in leaves of the commonly used expression host Nicotiana benthamiana, with those linkers susceptible to cysteine proteases being less stable then serine protease-cleavable linkers. As an example we describe a Cysta-tag experimental scheme for the one-step purification of a clinically useful protein, human α1-antitrypsin, transiently expressed in N. benthamiana. With potential applicability to the variety of chromatography formats commercially available for IMAC-based protein purification, the Cysta-tag provides a convenient means for the efficient and cost-effective purification of recombinant proteins from plant tissues.

  14. Novel trends in affinity biosensors: current challenges and perspectives

    International Nuclear Information System (INIS)

    Arugula, Mary A; Simonian, Aleksandr

    2014-01-01

    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)

  15. Radiation-stable polyolefin compositions

    International Nuclear Information System (INIS)

    Rekers, J.W.

    1986-01-01

    This invention relates to compositions of olefinic polymers suitable for high energy radiation treatment. In particular, the invention relates to olefinic polymer compositions that are stable to sterilizing dosages of high energy radiation such as a gamma radiation. Stabilizers are described that include benzhydrol and benzhydrol derivatives; these stabilizers may be used alone or in combination with secondary antioxidants or synergists

  16. Monitoring of stable glaucoma patients

    NARCIS (Netherlands)

    K.M. Holtzer-Goor (Kim); N.S. Klazinga (Niek); M.A. Koopmanschap (Marc); H.G. Lemij (Hans); T. Plochg; E. van Sprundel (Esther)

    2010-01-01

    textabstractA high workload for ophthalmologists and long waiting lists for patients challenge the organization of ophthalmic care. Tasks that require less specialized skills, like the monitoring of stable (well controlled) glaucoma patients could be substituted from ophthalmologists to other

  17. Fused electron deficient semiconducting polymers for air stable electron transport

    KAUST Repository

    Onwubiko, Ada

    2018-01-23

    Conventional semiconducting polymer synthesis typically involves transition metal-mediated coupling reactions that link aromatic units with single bonds along the backbone. Rotation around these bonds contributes to conformational and energetic disorder and therefore potentially limits charge delocalisation, whereas the use of transition metals presents difficulties for sustainability and application in biological environments. Here we show that a simple aldol condensation reaction can prepare polymers where double bonds lock-in a rigid backbone conformation, thus eliminating free rotation along the conjugated backbone. This polymerisation route requires neither organometallic monomers nor transition metal catalysts and offers a reliable design strategy to facilitate delocalisation of frontier molecular orbitals, elimination of energetic disorder arising from rotational torsion and allowing closer interchain electronic coupling. These characteristics are desirable for high charge carrier mobilities. Our polymers with a high electron affinity display long wavelength NIR absorption with air stable electron transport in solution processed organic thin film transistors.

  18. Combining oxygen plasma treatment with anchorage of cationized gelatin for enhancing cell affinity of poly(lactide-co-glycolide).

    Science.gov (United States)

    Shen, Hong; Hu, Xixue; Yang, Fei; Bei, Jianzhong; Wang, Shenguo

    2007-10-01

    Surface characteristics greatly influence attachment and growth of cells on biomaterials. Although polylactone-type biodegradable polymers have been widely used as scaffold materials for tissue engineering, lack of cell recognition sites, poor hydrophilicity and low surface energy lead to a bad cell affinity of the polymers, which limit the usage of polymers as scaffolds in tissue engineering. In the present study, surface of poly (L-lactide-co-glycolide) (PLGA) was modified by a method of combining oxygen plasma treatment with anchorage of cationized gelatin. Modification effect of the method was compared with other methods of oxygen plasma treatment, cationized gelatin or gelatin coating and combining oxygen plasma treatment with anchorage of gelatin. The change of surface property was compared by contact angles, surface energy, X-ray photoelectron spectra (XPS), attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) and scanning electron microscopy (SEM) measurement. The optimum oxygen pretreatment time determined by surface energy was 10 min when the power was 50 W and the oxygen pressure was 20 Pa. Analysis of the stability of gelatin and cationized gelatin anchored on PLGA by XPS, ATR-FTIR, contact angles and surface energy measurement indicated the cationized gelatin was more stable than gelatin. The result using mouse NIH 3T3 fibroblasts as model cells to evaluate cell affinity in vitro showed the cationized gelatin-anchored PLGA (OCG-PLGA) was more favorable for cell attachment and growth than oxygen plasma treated PLGA (O-PLGA) and gelatin-anchored PLGA (OG-PLGA). Moreover cell affinity of OCG-PLGA could match that of collagen-anchored PLGA (AC-PLGA). So the surface modification method combining oxygen plasma treatment with anchorage of cationized gelatin provides a universally effective way to enhance cell affinity of polylactone-type biodegradable polymers.

  19. Surgical gesture classification using Dynamic Time Warping and affine velocity.

    Science.gov (United States)

    Cifuentes, Jenny; Minh Tu Pham; Moreau, Richard; Prieto, Flavio; Boulanger, Pierre

    2017-07-01

    Minimally Invasive Surgery (MIS) has become widespread as an important surgical technique due to its advantages related to pain relief and short recovery time periods. However, this approach implies the acquisition of special surgical skills, which represents a challenge in the objective assessment of surgical gestures. In this way, several studies shown that kinematics and kinetic analysis of hand movement is a valuable assessment tool of basic surgical skills in MIS. In addition, recent researches proved that human motion performed during surgery can be described as a sequence of constant affine velocity movements. In this paper, we present a novel method to classify gestures based on an affine velocity analysis of 3D motion and an implementation of the Dynamic Time Warping algorithm. In particular, affine velocity calculation correlates kinematics and geometrical variables such as curvature, torsion, and euclidean velocity, reducing the dimension of the conventional 3D problem. In this way, using the simplicity of dynamic time warping algorithm allows us to perform an accurate classification, easier to implement and understand. Experimental validation of the algorithm is presented based on the position and orientation data of a laparoscope instrument, determiMinimally Invasive Surgery (MIS) has become widespread as an important surgical technique due to its advantages related to pain relief and short recovery time periods. However, this approach implies the acquisition of special surgical skills, which represents a challenge in the objective assessment of surgical gestures. In this way, several studies shown that kinematics and kinetic analysis of hand movement is a valuable assessment tool of basic surgical skills in MIS. In addition, recent researches proved that human motion performed during surgery can be described as a sequence of constant affine velocity movements. In this paper, we present a novel method to classify gestures based on an affine velocity

  20. Affinity learning with diffusion on tensor product graph.

    Science.gov (United States)

    Yang, Xingwei; Prasad, Lakshman; Latecki, Longin Jan

    2013-01-01

    In many applications, we are given a finite set of data points sampled from a data manifold and represented as a graph with edge weights determined by pairwise similarities of the samples. Often the pairwise similarities (which are also called affinities) are unreliable due to noise or due to intrinsic difficulties in estimating similarity values of the samples. As observed in several recent approaches, more reliable similarities can be obtained if the original similarities are diffused in the context of other data points, where the context of each point is a set of points most similar to it. Compared to the existing methods, our approach differs in two main aspects. First, instead of diffusing the similarity information on the original graph, we propose to utilize the tensor product graph (TPG) obtained by the tensor product of the original graph with itself. Since TPG takes into account higher order information, it is not a surprise that we obtain more reliable similarities. However, it comes at the price of higher order computational complexity and storage requirement. The key contribution of the proposed approach is that the information propagation on TPG can be computed with the same computational complexity and the same amount of storage as the propagation on the original graph. We prove that a graph diffusion process on TPG is equivalent to a novel iterative algorithm on the original graph, which is guaranteed to converge. After its convergence we obtain new edge weights that can be interpreted as new, learned affinities. We stress that the affinities are learned in an unsupervised setting. We illustrate the benefits of the proposed approach for data manifolds composed of shapes, images, and image patches on two very different tasks of image retrieval and image segmentation. With learned affinities, we achieve the bull's eye retrieval score of 99.99 percent on the MPEG-7 shape dataset, which is much higher than the state-of-the-art algorithms. When the data

  1. Two stable, conducting conformations of the selectivity filter in Shaker K+ channels.

    Science.gov (United States)

    Thompson, Jill; Begenisich, Ted

    2005-06-01

    We have examined the voltage dependence of external TEA block of Shaker K(+) channels over a range of internal K(+) concentrations from 2 to 135 mM. We found that the concentration dependence of external TEA block in low internal K(+) solutions could not be described by a single TEA binding affinity. The deviation from a single TEA binding isotherm was increased at more depolarized membrane voltages. The data were well described by a two-component binding scheme representing two, relatively stable populations of conducting channels that differ in their affinity for external TEA. The relative proportion of these two populations was not much affected by membrane voltage but did depend on the internal K(+) concentration. Low internal K(+) promoted an increase in the fraction of channels with a low TEA affinity. The voltage dependence of the apparent high-affinity TEA binding constant depended on the internal K(+) concentration, becoming almost voltage independent in 5 mM. The K(+) sensitivity of these low- and high-affinity TEA states suggests that they may represent one- and two-ion occupancy states of the selectivity filter, consistent with recent crystallographic results from the bacterial KcsA K(+) channel. We therefore analyzed these data in terms of such a model and found a large (almost 14-fold) difference between the intrinsic TEA affinity of the one-ion and two-ion modes. According to this analysis, the single ion in the one-ion mode (at 0 mV) prefers the inner end of the selectivity filter twofold more than the outer end. This distribution does not change with internal K(+). The two ions in the two-ion mode prefer to occupy the inner end of the selectivity filter at low K(+), but high internal K(+) promotes increased occupancy of the outer sites. Our analysis further suggests that the four K(+) sites in the selectivity filter are spaced between 20 and 25% of the membrane electric field.

  2. High affinity γPNA sandwich hybridization assay for rapid detection of short nucleic acid targets with single mismatch discrimination.

    Science.gov (United States)

    Goldman, Johnathan M; Zhang, Li Ang; Manna, Arunava; Armitage, Bruce A; Ly, Danith H; Schneider, James W

    2013-07-08

    Hybridization analysis of short DNA and RNA targets presents many challenges for detection. The commonly employed sandwich hybridization approach cannot be implemented for these short targets due to insufficient probe-target binding strengths for unmodified DNA probes. Here, we present a method capable of rapid and stable sandwich hybridization detection for 22 nucleotide DNA and RNA targets. Stable hybridization is achieved using an n-alkylated, polyethylene glycol γ-carbon modified peptide nucleic acid (γPNA) amphiphile. The γPNA's exceptionally high affinity enables stable hybridization of a second DNA-based probe to the remaining bases of the short target. Upon hybridization of both probes, an electrophoretic mobility shift is measured via interaction of the n-alkane modification on the γPNA with capillary electrophoresis running buffer containing nonionic surfactant micelles. We find that sandwich hybridization of both probes is stable under multiple binding configurations and demonstrate single base mismatch discrimination. The binding strength of both probes is also stabilized via coaxial stacking on adjacent hybridization to targets. We conclude with a discussion on the implementation of the proposed sandwich hybridization assay as a high-throughput microRNA detection method.

  3. Improved Biogeography-Based Optimization Based on Affinity Propagation

    Directory of Open Access Journals (Sweden)

    Zhihao Wang

    2016-07-01

    Full Text Available To improve the search ability of biogeography-based optimization (BBO, this work proposed an improved biogeography-based optimization based on Affinity Propagation. We introduced the Memetic framework to the BBO algorithm, and used the simulated annealing algorithm as the local search strategy. MBBO enhanced the exploration with the Affinity Propagation strategy to improve the transfer operation of the BBO algorithm. In this work, the MBBO algorithm was applied to IEEE Congress on Evolutionary Computation (CEC 2015 benchmarks optimization problems to conduct analytic comparison with the first three winners of the CEC 2015 competition. The results show that the MBBO algorithm enhances the exploration, exploitation, convergence speed and solution accuracy and can emerge as the best solution-providing algorithm among the competing algorithms.

  4. Einstein’s gravity from a polynomial affine model

    Science.gov (United States)

    Castillo-Felisola, Oscar; Skirzewski, Aureliano

    2018-03-01

    We show that the effective field equations for a recently formulated polynomial affine model of gravity, in the sector of a torsion-free connection, accept general Einstein manifolds—with or without cosmological constant—as solutions. Moreover, the effective field equations are partially those obtained from a gravitational Yang–Mills theory known as Stephenson–Kilmister–Yang theory. Additionally, we find a generalization of a minimally coupled massless scalar field in General Relativity within a ‘minimally’ coupled scalar field in this affine model. Finally, we present a brief (perturbative) analysis of the propagators of the gravitational theory, and count the degrees of freedom. For completeness, we prove that a Birkhoff-like theorem is valid for the analyzed sector.

  5. Extreme disorder in an ultrahigh-affinity protein complex

    Science.gov (United States)

    Borgia, Alessandro; Borgia, Madeleine B.; Bugge, Katrine; Kissling, Vera M.; Heidarsson, Pétur O.; Fernandes, Catarina B.; Sottini, Andrea; Soranno, Andrea; Buholzer, Karin J.; Nettels, Daniel; Kragelund, Birthe B.; Best, Robert B.; Schuler, Benjamin

    2018-03-01

    Molecular communication in biology is mediated by protein interactions. According to the current paradigm, the specificity and affinity required for these interactions are encoded in the precise complementarity of binding interfaces. Even proteins that are disordered under physiological conditions or that contain large unstructured regions commonly interact with well-structured binding sites on other biomolecules. Here we demonstrate the existence of an unexpected interaction mechanism: the two intrinsically disordered human proteins histone H1 and its nuclear chaperone prothymosin-α associate in a complex with picomolar affinity, but fully retain their structural disorder, long-range flexibility and highly dynamic character. On the basis of closely integrated experiments and molecular simulations, we show that the interaction can be explained by the large opposite net charge of the two proteins, without requiring defined binding sites or interactions between specific individual residues. Proteome-wide sequence analysis suggests that this interaction mechanism may be abundant in eukaryotes.

  6. 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...

  7. Defining carbohydrate binding of glucan phosphatases via Affinity gel electrophoresis

    DEFF Research Database (Denmark)

    Auger, Kyle; Raththagala, Madushi; Wilkens, Casper

    2016-01-01

    was to determine a technique to measure carbohydrate binding quickly and efficiently. We established a protocol to reproducibly and quantitatively measure the binding of the enzymes to glucans utilizing Affinity Gel Electrophoresis (AGE). The results show that the various glucan phosphatases possess differing...... determined the x-ray crystal structures of both plant and human glucan phosphatases and their enzymatic mechanisms. Despite this progress, we lacked the techniques to quickly and efficiently quantify their glucan phosphatase affinities for different substrates. The main objective of this study...... and animal glucan phosphatases to determine which regions of the enzyme are most necessary for binding. Footnotes This abstract is from the Experimental Biology 2016 Meeting. There is no full text article associated with this abstract published in The FASEB Journal....

  8. The Weyl-Cartan Space Problem in Purely Affine Theory

    Science.gov (United States)

    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 $\\Gamma^i_{[kl]}$.

  9. Toward Practical Secure Stable Matching

    Directory of Open Access Journals (Sweden)

    Riazi M. Sadegh

    2017-01-01

    Full Text Available The Stable Matching (SM algorithm has been deployed in many real-world scenarios including the National Residency Matching Program (NRMP and financial applications such as matching of suppliers and consumers in capital markets. Since these applications typically involve highly sensitive information such as the underlying preference lists, their current implementations rely on trusted third parties. This paper introduces the first provably secure and scalable implementation of SM based on Yao’s garbled circuit protocol and Oblivious RAM (ORAM. Our scheme can securely compute a stable match for 8k pairs four orders of magnitude faster than the previously best known method. We achieve this by introducing a compact and efficient sub-linear size circuit. We even further decrease the computation cost by three orders of magnitude by proposing a novel technique to avoid unnecessary iterations in the SM algorithm. We evaluate our implementation for several problem sizes and plan to publish it as open-source.

  10. Towards stable acceleration in LINACS

    CERN Document Server

    Dubrovskiy, A D

    2014-01-01

    Ultra-stable and -reproducible high-energy particle beams with short bunches are needed in novel linear accelerators and, in particular, in the Compact Linear Collider CLIC. A passive beam phase stabilization system based on a bunch compression with a negative transfer matrix element R56 and acceleration at a positive off-crest phase is proposed. The motivation and expected advantages of the proposed scheme are outlined.

  11. Self-affine fractals and the limit H→0

    NARCIS (Netherlands)

    Palasantzas, George

    1994-01-01

    A modified form for the surface-height-fluctuation correlation function of rough surfaces, gγ(R) ∝ ∫ a0/ξ R/ξ x^2H (e^–x/x)dx, is investigated which depicts behavior related to self-affine fractals for 0 < H < 1, and for H →0 with a0 « R « ξ reveals logarithmic behavior gγ(R) ∝ ln(R/a0).

  12. 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 - others: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

  13. Memory in the B-cell compartment: antibody affinity maturation.

    OpenAIRE

    Neuberger, M S; Ehrenstein, M R; Rada, C; Sale, J; Batista, F D; Williams, G; Milstein, C

    2000-01-01

    In the humoral arm of the immune system, the memory response is not only more quickly elicited and of greater magnitude than the primary response, but it is also different in quality. In the recall response to antigen, the antibodies produced are of higher affinity and of different isotype (typically immunoglobulin G rather than immunoglobulin M). This maturation rests on the antigen dependence of B-cell maturation and is effected by programmed genetic modifications of the immunoglobulin gene...

  14. 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 - others: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

  15. Protein separation using affinity-based reversed micelles

    Science.gov (United States)

    Sun; Gu; Tong; Bai; Ichikawa; Furusaki

    1999-05-01

    Reversed micellar two-phase extraction is a developing technique for protein separation. Introduction of an affinity ligand is considered to be an effective approach to increase the selectivity and capacity of reversed micelles. In this article, Cibacron Blue F3G-A (CB) as an affinity ligand was immobilized to reversed micelles composed of soybean lecithin by a two-phase reaction. The affinity partitioning of lysozyme and bovine serum albumin (BSA) to the CB-lecithin micelles was studied. Formation of mixed micelles by additionally introducing a nonionic surfactant, Tween 85, to the CB-lecithin micelles was effective to increase the solubilization of lysozyme due to the increase of W0 (water/surfactant molar ratio)/micellar size. The partitioning isotherms of lysozyme to the CB-lecithin micelles with and without Tween 85 were expressed by the Langmuir equation. The dissociation constants in the Langmuir equation decreased on addition of Tween 85, indicating the increase of the effectiveness of lysozyme binding to the immobilized CB. On addition of 20 g/L Tween 85 to 50 g/L lecithin/hexane micellar phase containing 0.1 mmol/L CB, the extraction capacity for lysozyme could be increased by 42%. Moreover, the CB-lecithin micelles with or without Tween 85 showed significant size exclusion for BSA due to its high molecular weight. Thus, lysozyme and BSA were separated from artificial solutions containing the two proteins. In addition, the affinity-based reversed micellar phase containing Tween 85 was recycled three times for lysozyme purification from crude egg-white solutions. Lysozyme purity increased by 16-18-fold, reaching 60-70% in the recycled use.

  16. Pretargeting with the affinity enhancement system for radioimmunotherapy.

    Science.gov (United States)

    Barbet, J; Kraeber-Bodéré, F; Vuillez, J P; Gautherot, E; Rouvier, E; Chatal, J F

    1999-06-01

    The pretargeting technique referred to as the Affinity Enhancement System (AES) uses bispecific antibodies and radiolabeled bivalent haptens that bind cooperatively to target cells in vivo. Experimental and clinical data demonstrate that AES can deliver large radiation doses to tumor cells with high tumor to normal tissue contrast ratios and long activity residence time in tumors. Preliminary clinical results of radioimmunotherapy of medullary thyroid carcinomas and lung cancers look promising.

  17. The Quantum Nature of Drug-Receptor Interactions: Deuteration Changes Binding Affinities for Histamine Receptor Ligands.

    Science.gov (United States)

    Kržan, Mojca; Vianello, Robert; Maršavelski, Aleksandra; Repič, Matej; Zakšek, Maja; Kotnik, Kristina; Fijan, Estera; Mavri, Janez

    2016-01-01

    In this article we report a combined experimental and computational study concerning the effects of deuteration on the binding of histamine and two other histaminergic agonists to 3H-tiotidine-labeled histamine H2 receptor in neonatal rat astrocytes. Binding affinities were measured by displacing radiolabeled tiotidine from H2 receptor binding sites present on cultured neonatal rat astrocytes. Quantum-chemical calculations were performed by employing the empirical quantization of nuclear motion within a cluster model of the receptor binding site extracted from the homology model of the entire H2 receptor. Structure of H2 receptor built by homology modelling is attached in the supporting information (S1 Table) Experiments clearly demonstrate that deuteration affects the binding by increasing the affinity for histamine and reducing it for 2-methylhistamine, while basically leaving it unchanged for 4-methylhistamine. Ab initio quantum-chemical calculations on the cluster system extracted from the homology H2 model along with the implicit quantization of the acidic N-H and O-H bonds demonstrate that these changes in the binding can be rationalized by the altered strength of the hydrogen bonding upon deuteration known as the Ubbelohde effect. Our computational analysis also reveals a new mechanism of histamine binding, which underlines an important role of Tyr250 residue. The present work is, to our best knowledge, the first study of nuclear quantum effects on ligand receptor binding. The ligand H/D substitution is relevant for therapy in the context of perdeuterated and thus more stable drugs that are expected to enter therapeutic practice in the near future. Moreover, presented approach may contribute towards understanding receptor activation, while a distant goal remains in silico discrimination between agonists and antagonists based on the receptor structure.

  18. Affine.m—Mathematica package for computations in representation theory of finite-dimensional and affine Lie algebras

    Science.gov (United States)

    Nazarov, Anton

    2012-11-01

    In this paper we present Affine.m-a program for computations in representation theory of finite-dimensional and affine Lie algebras and describe implemented algorithms. The algorithms are based on the properties of weights and Weyl symmetry. Computation of weight multiplicities in irreducible and Verma modules, branching of representations and tensor product decomposition are the most important problems for us. These problems have numerous applications in physics and we provide some examples of these applications. The program is implemented in the popular computer algebra system Mathematica and works with finite-dimensional and affine Lie algebras. Catalogue identifier: AENA_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AENB_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, UK Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 24 844 No. of bytes in distributed program, including test data, etc.: 1 045 908 Distribution format: tar.gz Programming language: Mathematica. Computer: i386-i686, x86_64. Operating system: Linux, Windows, Mac OS, Solaris. RAM: 5-500 Mb Classification: 4.2, 5. Nature of problem: Representation theory of finite-dimensional Lie algebras has many applications in different branches of physics, including elementary particle physics, molecular physics, nuclear physics. Representations of affine Lie algebras appear in string theories and two-dimensional conformal field theory used for the description of critical phenomena in two-dimensional systems. Also Lie symmetries play a major role in a study of quantum integrable systems. Solution method: We work with weights and roots of finite-dimensional and affine Lie algebras and use Weyl symmetry extensively. Central problems which are the computations of weight multiplicities, branching and fusion coefficients are solved using one general recurrent

  19. Binding affinity of surface functionalized gold nanoparticles to hydroxyapatite.

    Science.gov (United States)

    Ross, Ryan D; Roeder, Ryan K

    2011-10-01

    Gold nanoparticles (Au NPs) have been investigated for a number of biomedical applications, including drug and gene delivery vehicles, thermal ablation therapy, diagnostic sensors, and imaging contrast agents. Surface functionalization with molecular groups exhibiting calcium affinity can enable targeted delivery of Au NPs to calcified tissue, including damaged bone tissue. Therefore, the objective of this study was to investigate the binding affinity of functionalized Au NPs for targeted delivery to bone mineral, using hydroxyapatite (HA) crystals as a synthetic analog in vitro. Au NPs were synthesized to a mean particle size of 10-15 nm and surface functionalized with either L-glutamic acid, 2-aminoethylphosphonic acid, or alendronate, which exhibit a primary amine for binding gold opposite carboxylate, phosphonate, or bisphosphonate groups, respectively, for targeting calcium. Bisphosphonate functionalized Au NPs exhibited the most rapid binding kinetics and greatest binding affinity to HA, followed by glutamic acid and phosphonic acid. All functional groups reached complete binding after 24 h. Equilibrium binding constants in de-ionized water, determined by nonlinear regression of Langmuir isotherms, were 3.40, 0.69, and 0.25 mg/L for bisphosphonate, carboxylate, and phosphonate functionalized Au NPs, respectively. Functionalized Au NPs exhibited lower overall binding in fetal bovine serum compared to de-ionized water, but relative differences between functional groups were similar. Copyright © 2011 Wiley Periodicals, Inc.

  20. Affinity-tuning leukocyte integrin for development of safe therapeutics

    Science.gov (United States)

    Park, Spencer

    Much attention has been given to the molecular and cellular pathways linking inflammation with cancer and the local tumor environment to identify new target molecules that could lead to improved diagnosis and treatment. Among the many molecular players involved in the complex response, central to the induction of inflammation is intercellular adhesion molecule (ICAM)-1, which is of particular interest for its highly sensitive and localized expression in response to inflammatory signals. ICAM-1, which has been implicated to play a critical role in tumor progression in various types of cancer, has also been linked to cancer metastases, where ICAM-1 facilitates the spread of metastatic cancer cells to secondary sites. This unique expression profile of ICAM-1 throughout solid tumor microenvironment makes ICAM-1 an intriguing molecular target, which holds great potential as an important diagnostic and therapeutic tool. Herein, we have engineered the ligand binding domain, or the inserted (I) domain of a leukocyte integrin, to exhibit a wide range of monovalent affinities to the natural ligand, ICAM-1. Using the resulting I domain variants, we have created drug and gene delivery nanoparticles, as well as targeted immunotherapeutics that have the ability to bind and migrate to inflammatory sites prevalent in tumors and the associated microenvironment. Through the delivery of diagnostic agents, chemotherapeutics, and immunotherapeutics, the following chapters demonstrate that the affinity enhancements achieved by directed evolution bring the affinity of I domains into the range optimal for numerous applications.

  1. 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.

  2. An affine model of the dynamics of astrophysical discs

    Science.gov (United States)

    Ogilvie, Gordon I.

    2018-03-01

    Thin astrophysical discs are very often modelled using the equations of two-dimensional hydrodynamics. We derive an extension of this model that describes more accurately the behaviour of a thin disc in the absence of self-gravity, magnetic fields and complex internal motions. The ideal fluid theory is derived directly from Hamilton's Principle for a three-dimensional fluid after making a specific approximation to the deformation gradient tensor. We express the equations in Eulerian form after projection on to a reference plane. The disc is thought of as a set of fluid columns, each of which is capable of a time-dependent affine transformation, consisting of a translation together with a linear transformation in three dimensions. Therefore, in addition to the usual two-dimensional hydrodynamics in the reference plane, the theory allows for a deformation of the midplane (as occurs in warped discs) and for the internal shearing motions that accompany such deformations. It also allows for the vertical expansions driven in non-circular discs by a variation of the vertical gravitational field around the horizontal streamlines, or by a divergence of the horizontal velocity. The equations of the affine model embody conservation laws for energy and potential vorticity, even for non-planar discs. We verify that they reproduce exactly the linear theories of three-dimensional warped and eccentric discs in a secular approximation. However, the affine model does not rely on any secular or small-amplitude assumptions and should be useful in more general circumstances.

  3. Hamiltonian dynamics of purely affine fields (Einstein-Schroedinger Theory)

    Science.gov (United States)

    Treder, H.-J.

    The Lagrangian of the general-relativistic affine field theory of the non-symmetric connection field is the Schroedinger scalar density and the field variables (canonical coordinates) are Einstein's affine tensors. The field equations are the Einstein-Schroedinger equations, and the minors give by definition gmn = lambda-1Rmn, and lambda becomes the cosmological constant. The Hamiltonian density is the upsilon00-component of the Einstein energy-momentum complex, and the tensor-density components are the canonically conjugated momentum densities of the field coordinates. The canonical equations are (-g)-1/2Nlmnupsilon00 = 0, and we have no constraints. The affine field theory is invariant with respect to all transformations which preserve the Levi-Civita parallelism (Einstein's unified T-A group), and the field equations possess transposition invariance. The symmetry conditions Gammaimn = Gamma inm reduce the space to the general-relativistic Einstein spaces with Rik = Rki. The equation Rik = lambda gik yields Gammaikl = vector (i kl), and the pathes of test particles define geodesic world lines of the Einstein spaces.

  4. Fragments of protein A eluted during protein A affinity chromatography.

    Science.gov (United States)

    Carter-Franklin, Jayme N; Victa, Corazon; McDonald, Paul; Fahrner, Robert

    2007-09-07

    Protein A affinity chromatography is a common method for process scale purification of monoclonal antibodies. During protein A affinity chromatography, protein A ligand co-elutes with the antibody (commonly called leaching), which is a potential disadvantage since the leached protein A may need to be cleared for pharmaceutical antibodies. To determine the mechanism of protein A leaching and characterize the leached protein A, we fluorescently labeled the protein A ligand in situ on protein A affinity chromatography media. We found that intact protein A leaches when loading either purified antibody or unpurified antibody in harvested cell culture fluid (HCCF), and that additionally fragments of protein A leach when loading HCCF. The leaching of protein A fragments can be reduced by EDTA, suggesting that proteinases contribute to the generation of protein A fragments. We found that protein A fragments larger than about 6000 Da can be measured by enzyme linked immunosorbent assay, and that they can be more difficult to clear than whole protein A by cation-exchange chromatography.

  5. Affinity monolith chromatography: A review of general principles and applications.

    Science.gov (United States)

    Li, Zhao; Rodriguez, Elliott; Azaria, Shiden; Pekarek, Allegra; Hage, David S

    2017-11-01

    Affinity monolith chromatography, or AMC, is a liquid chromatographic method in which the support is a monolith and the stationary phase is a biological-binding agent or related mimic. AMC has become popular for the isolation of biochemicals, for the measurement of various analytes, and for studying biological interactions. This review will examine the principles and applications of AMC. The materials that have been used to prepare AMC columns will be discussed, which have included various organic polymers, silica, agarose, and cryogels. Immobilization schemes that have been used in AMC will also be considered. Various binding agents and applications that have been reported for AMC will then be described. These applications will include the use of AMC for bioaffinity chromatography, immunoaffinity chromatography, dye-ligand affinity chromatography, and immobilized metal-ion affinity chromatography. The use of AMC with chiral stationary phases and as a tool to characterize biological interactions will also be examined. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Gelatin Nanoparticles with Enhanced Affinity for Calcium Phosphate.

    Science.gov (United States)

    Farbod, Kambiz; Diba, Mani; Zinkevich, Tatiana; Schmidt, Stephan; Harrington, Matthew J; Kentgens, Arno P M; Leeuwenburgh, Sander C G

    2016-05-01

    Gelatin nanoparticles can be tuned with respect to their drug loading efficiency, degradation rate, and release kinetics, which renders these drug carriers highly suitable for a wide variety of biomedical applications. The ease of functionalization has rendered gelatin an interesting candidate material to introduce specific motifs for selective targeting to specific organs, but gelatin nanoparticles have not yet been modified to increase their affinity to mineralized tissue. By means of conjugating bone-targeting alendronate to biocompatible gelatin nanoparticles, a simple method is developed for the preparation of gelatin nanoparticles which exhibit strong affinity to mineralized surfaces. It has been shown that the degree of alendronate functionalization can be tuned by controlling the glutaraldehyde crosslinking density, the molar ratio between alendronate and glutaraldehyde, as well as the pH of the conjugation reaction. Moreover, it has been shown that the affinity of gelatin nanoparticles to calcium phosphate increases considerably upon functionalization with alendronate. In summary, gelatin nanoparticles have been developed, which exhibit great potential for use in bone-specific drug delivery and regenerative medicine. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. Cardiovascular receptor binding affinity of aqueous extracts from Allium species.

    Science.gov (United States)

    Nencini, Cristina; Franchi, Gian Gabriele; Micheli, Lucia

    2010-06-01

    The aims of this study were to evaluate whether the antihypertensive effect of garlic could to be associated to interactions with adrenergic and dopaminergic receptors involved in regulating blood pressure and to compare these data with those obtained from wild Allium species. The aqueous extracts of bulbs or leaves of Allium sativum L. (garlic), Allium neapolitanum Cyr., Allium subhirsutum L., and Allium roseum L. were tested for their in vitro affinity for the adrenergic (alpha(1), alpha(2), beta(1) and beta(2)) and dopaminergic (D(1) and D(2)) receptors by radioligand binding assays. Interesting results were shown by bulbs extracts of A. neapolitanum and A. subhirsutum with higher affinities for the beta(2) receptors and by bulbs extract of A. roseum for D(2) receptors. The known antihypertensive activity of Allium sativum cannot be correlated with binding to receptors involved in blood pressure regulation. However, aqueous extracts of the wild-type species of Allium show much higher affinities, warranting further explorations.

  8. The Purification of a Blood Group A Glycoprotein: An Affinity Chromatography Experiment.

    Science.gov (United States)

    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)

  9. Rapid Buffer and Ligand Screening for Affinity Chromatography by Multiplexed Surface Plasmon Resonance Imaging

    NARCIS (Netherlands)

    Geuijen, K.P.M.; Wijk-Basten, van Danielle E.J.W.; Egging, Davis F.; Schasfoort, Richard B.M.; Eppink, M.H.M.

    2017-01-01

    Protein purifications are often based on the principle of affinity chromatography, where the protein of interest selectively binds to an immobilized ligand. The development of affinity purification requires selecting proper wash and elution conditions. In recent years, miniaturization of the

  10. Mutational analysis of affinity and selectivity of kringle-tetranectin interaction. Grafting novel kringle affinity ontp the trtranectin lectin scaffold

    DEFF Research Database (Denmark)

    Graversen, Jonas Heilskov; Jacobsen, C; Sigurskjold, B W

    2000-01-01

    C-type lectin-like domains are found in many proteins, where they mediate binding to a wide diversity of compounds, including carbohydrates, lipids, and proteins. The binding of a C-type lectin-like domain to a ligand is often influenced by calcium. Recently, we have identified a site in the C-ty....... This study provides further insight into molecular determinants of importance for binding selectivity and affinity of C-type lectin kringle interactions....

  11. PHARMACEUTICAL AND BIOMEDICAL APPLICATIONS OF AFFINITY CHROMATOGRAPHY: RECENT TRENDS AND DEVELOPMENTS

    Science.gov (United States)

    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. Techniques based on traditional affinity supports are discussed, but an emphasis is placed on methods in which affinity columns are used as part of HPLC systems or in combination with other analytical methods. General formats for affinity chromatography that are considered include step elution schemes, weak affinity chromatography, affinity extraction and affinity depletion. Specific separation techniques that are examined include lectin affinity chromatography, boronate affinity chromatography, immunoaffinity chromatography, and immobilized metal ion affinity chromatography. Approaches for the study of biological interactions by affinity chromatography are also presented, such as the measurement of equilibrium constants, rate constants, or competition and displacement effects. In addition, related developments in the use of immobilized enzyme reactors, molecularly imprinted polymers, dye ligands and aptamers are briefly considered. PMID:22305083

  12. Pricing Swaptions and Coupon Bond Options in Affine Term Structure Models

    NARCIS (Netherlands)

    Schrager, D.F.; Pelsser, A.A.J.

    2006-01-01

    We propose an approach to find an approximate price of a swaption in affine term structure models. Our approach is based on the derivation of approximate swap rate dynamics in which the volatility of the forward swap rate is itself an affine function of the factors. Hence, we remain in the affine

  13. Pricing swaptions and coupon bond options in affine term structure models

    NARCIS (Netherlands)

    Schrager, D.F.; Pelsser, A.A.J.

    2005-01-01

    We propose an approach to …nd an approximate price of a swaption in Affine Term Structure Models. Our approach is based on the derivation of approximate dynamics in which the volatility of the Forward Swap Rate is itself an affine function of the factors. Hence we remain in the Affine framework and

  14. 14 CFR 212.5 - Operation of affinity (pro rata) charters.

    Science.gov (United States)

    2010-01-01

    ... 14 Aeronautics and Space 4 2010-01-01 2010-01-01 false Operation of affinity (pro rata) charters. 212.5 Section 212.5 Aeronautics and Space OFFICE OF THE SECRETARY, DEPARTMENT OF TRANSPORTATION... Operation of affinity (pro rata) charters. An affinity (pro rata) charter operated by a certificated or...

  15. Stable Hemiaminals: 2-Aminopyrimidine Derivatives

    Directory of Open Access Journals (Sweden)

    Anna Kwiecień

    2015-08-01

    Full Text Available Stable hemiaminals can be obtained in the one-pot reaction between 2-aminopyrimidine and nitrobenzaldehyde derivatives. Ten new hemiaminals have been obtained, six of them in crystal state. The molecular stability of these intermediates results from the presence of both electron-withdrawing nitro groups as substituents on the phenyl ring and pyrimidine ring, so no further stabilisation by intramolecular interaction is required. Hemiaminal molecules possess a tetrahedral carbon atom constituting a stereogenic centre. As the result of crystallisation in centrosymmetric space groups both enantiomers are present in the crystal structure.

  16. Organic synthesis with stable isotopes

    International Nuclear Information System (INIS)

    Daub, G.H.; Kerr, V.N.; Williams, D.L.; Whaley, T.W.

    1978-01-01

    Some general considerations concerning organic synthesis with stable isotopes are presented. Illustrative examples are described and discussed. The examples include DL-2-amino-3-methyl- 13 C-butanoic-3,4- 13 C 2 acid (DL-valine- 13 C 3 ); methyl oleate-1- 13 C; thymine-2,6- 13 C 2 ; 2-aminoethanesulfonic- 13 C acid (taurine- 13 C); D-glucose-6- 13 C; DL-2-amino-3-methylpentanoic-3,4- 13 C 2 acid (DL-isoleucine- 13 C 2 ); benzidine- 15 N 2 ; and 4-ethylsulfonyl-1-naphthalene-sulfonamide- 15 N

  17. Stable agents for imaging investigations

    International Nuclear Information System (INIS)

    Tofe, A.J.

    1976-01-01

    This invention concerns highly stable compounds useful in preparing technetium 99m based scintiscanning exploration agents. The compounds of this invention include a pertechnetate reducing agent or a solution of oxidized pertechnetate and an efficient proportion, sufficient to stabilize the compounds in the presence of oxygen and of radiolysis products, of ascorbic acid or a pharmaceutically acceptable salt or ester of this acid. The invention also concerns a perfected process for preparing a technetium based exploration agent, consisting in codissolving the ascorbic acid or a pharmaceutically acceptable salt or ester of such an acid and a pertechnetate reducing agent in a solution of oxidized pertechnetate [fr

  18. Stable cosmology in chameleon bigravity

    Science.gov (United States)

    De Felice, Antonio; Mukohyama, Shinji; Oliosi, Michele; Watanabe, Yota

    2018-02-01

    The recently proposed chameleonic extension of bigravity theory, by including a scalar field dependence in the graviton potential, avoids several fine-tunings found to be necessary in usual massive bigravity. In particular it ensures that the Higuchi bound is satisfied at all scales, that no Vainshtein mechanism is needed to satisfy Solar System experiments, and that the strong coupling scale is always above the scale of cosmological interest all the way up to the early Universe. This paper extends the previous work by presenting a stable example of cosmology in the chameleon bigravity model. We find a set of initial conditions and parameters such that the derived stability conditions on general flat Friedmann background are satisfied at all times. The evolution goes through radiation-dominated, matter-dominated, and de Sitter eras. We argue that the parameter space allowing for such a stable evolution may be large enough to encompass an observationally viable evolution. We also argue that our model satisfies all known constraints due to gravitational wave observations so far and thus can be considered as a unique testing ground of gravitational wave phenomenologies in bimetric theories of gravity.

  19. Mutation of Pseudomonas aeruginosa specifying reduced affinity for penicillin G.

    OpenAIRE

    Godfrey, A J; Bryan, L E

    1982-01-01

    A mutant of Pseudomonas aeruginosa strain PAO503 was isolated after ethane-methane-sulfonate mutagenesis and selection of ticarcillin. The mutant, PCC17, displayed reduced affinity for [14C] penicillin G at all of its penicillin-binding proteins as well as a general increase in resistance to all the beta-lactam antibiotics tested. The mutation designated pbpA has been mapped by FP-2-mediated conjugation and was located distal to the proA locus and 33% linked to it. The two loci were not cotra...

  20. The spectrum of the conserved charges in affine Toda theories

    International Nuclear Information System (INIS)

    Niedermaier, M.R.

    1992-07-01

    A vertex operator construction for the phase of the minimal form factor is used to predict the exact spectrum of the infinite set of conserved charges on the multi-particle states in affine Toda theories from the bootstrap S-matrix. Conversely, the scattering phase can be recovered from the spectral information. The result is checed against the classical spectrum which is calculated ab-initio using the τ-function formalism. The latter is shown to provide a considerable shortcut compared to the traditional use of the inverse scattering transform. (orig.)

  1. Realization of parking task based on affine system modeling

    International Nuclear Information System (INIS)

    Kim, Young Woo; Narikiyo, Tatsuo

    2007-01-01

    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

  2. Telonemia, a new protist phylum with affinity to chromist lineages

    DEFF Research Database (Denmark)

    Shalchian-Tabrizi, K.; Eikrem, W.; Klaveness, D.

    2006-01-01

    , such as 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...

  3. A novel affinity purification method to isolate peptide specific antibodies

    DEFF Research Database (Denmark)

    Karlsen, Alan E; Lernmark, A; Kofod, Hans

    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...

  4. Affine Toda field theory and exact S-matrices

    International Nuclear Information System (INIS)

    Braden, H.W.; Corrigan, E.; Dorey, P.E.; Sasaki, R.

    1989-10-01

    The masses and three-point couplings for all affine Toda theories are calculated. The exact factorisable S-matrices are conjectured on the basis of the classical masses and couplings and found, in the case of theories based on simply-laced algebras, to give consistent solutions to the bootstrap. An investigation of the properties of the exact S-matrices in perturbation theory is begun but non-perturbative methods will be required to understand the conjectured duality between weak and strong coupling which appears to be a striking feature of these theories. (author)

  5. Microbiological Control for Affinity Capture Chromatography Processing: An Industry Perspective.

    Science.gov (United States)

    Murphy, Marie; Bell, Brian; Moshi, James; Grassi, Robert; Forng, Ren-Yo; Salaman, Angel; Wawra Jordi, Petra; Zaidi, Simin; Goodnight, Marcella; McFarland, Kim; Hardy, Diane; Knight, Michael; Paul, Mousumi; Keller, Andreas; Carpenter, Bill; McLaughlin, Donal; Hearty, Una; Marrero, Jose; Bain, David; Willison-Parry, Derek

    2018-02-14

    The purpose of this paper is to provide a summary of a BPOG-led industry survey of the microbiological control aspects of affinity chromatography processing in the biopharmaceutical industry. The document provides a summary of historical microbiological control concerns, coupled with industry-derived best practices for material, equipment, and storage controls required to mitigate the potential for microbial ingress and contamination of chromatography resin and equipment. These best practice guidelines, which are derived from the members of the BPOG Bioburden Working Group, are intended to assist biopharmaceutical manufacturers enhance microbial control and monitoring strategies for chromatography systems. Copyright © 2018, Parenteral Drug Association.

  6. Extreme disorder in an ultrahigh-affinity protein complex

    DEFF Research Database (Denmark)

    Borgia, Alessandro; Borgia, Madeleine B; Bugge, Katrine

    2018-01-01

    or that contain large unstructured regions commonly interact with well-structured binding sites on other biomolecules. Here we demonstrate the existence of an unexpected interaction mechanism: the two intrinsically disordered human proteins histone H1 and its nuclear chaperone prothymosin-α associate in a complex...... with picomolar affinity, but fully retain their structural disorder, long-range flexibility and highly dynamic character. On the basis of closely integrated experiments and molecular simulations, we show that the interaction can be explained by the large opposite net charge of the two proteins, without requiring...

  7. Complete intersections in certain affine and projective monomial curves

    OpenAIRE

    Bermejo, I.; García-Marco, I.

    2014-01-01

    Let $k$ be an arbitrary field, the purpose of this work is to provide families of positive integers $\\mathcal{A} = \\{d_1,\\ldots,d_n\\}$ such that either the toric ideal $I_{\\mathcal A}$ of the affine monomial curve $\\mathcal C = \\{(t^{d_1},\\ldots,\\,t^{d_n}) \\ | \\ t \\in k\\} \\subset \\mathbb{A}_k^n$ or the toric ideal $I_{\\mathcal A^{\\star}}$ of its projective closure ${\\mathcal C^{\\star}} \\subset \\mathbb{P}_k^n$ is a complete intersection. More precisely, we characterize the complete intersectio...

  8. Stable isotope mass spectrometry in petroleum exploration

    International Nuclear Information System (INIS)

    Mathur, Manju

    1997-01-01

    The stable isotope mass spectrometry plays an important role to evaluate the stable isotopic composition of hydrocarbons. The isotopic ratios of certain elements in petroleum samples reflect certain characteristics which are useful for petroleum exploration

  9. Metal-coded affinity tag labeling: a demonstration of analytical robustness and suitability for biological applications.

    Science.gov (United States)

    Ahrends, Robert; Pieper, Stefan; Neumann, Boris; Scheler, Christian; Linscheid, Michael W

    2009-03-15

    Quantitative peptide and protein analysis is one of the most promising fields in modern life science. Besides stable isotope coded labeling, metal chelate complexes are an alternative tool for quantification. The development of metal-coded affinity tags (MeCAT) was aimed to provide a robust tool for the quantification of peptides and proteins by utilizing lanthanide-harboring metal tags. It was shown that MeCAT is suited for relative quantification of proteins via standard mass spectrometric methods. The approach of tagging biomolecules with MeCAT offers the unique advantage of absolute quantification via inductively coupled plasma mass spectrometry (ICPMS), a well-established technique for assessing concentrations down to low attomole ranges. This work investigates the compatibility of MeCAT labeling to analysis workflows such as nano liquid chromatography/electrospray ionization tandem mass spectrometry (nano-LC/ESI-MS(n)). Focus was given toward the separation behavior of labeled peptides and the dynamic range of detection and peptide charge distribution. Furthermore, the stability of MeCAT under harsh analytical conditions was investigated. With the application of the MeCAT technique to a standard analysis scheme in proteomics, such as the investigation of changes in an Escherichia coli proteome, we successfully addressed the suitability to utilize MeCAT on biological samples. Furthermore, we demonstrated that MeCAT complexes are stable under a variety of conditions and that by applying LC/ESI-MS it is possible to cover a dynamic range of 2 orders of magnitude down to the low femtomole range with an average standard deviation below 15%. Therefore, this technique is suitable to common proteomic workflows and enables relative as well as absolute differential peptide quantification.

  10. Thermodynamic Bounds on the Ultra- and Infra-affinity of Hsp70 for Its Substrates.

    Science.gov (United States)

    Nguyen, Basile; Hartich, David; Seifert, Udo; Rios, Paolo De Los

    2017-07-25

    The 70 kDa heat shock protein Hsp70 has several essential functions in living systems, such as protecting cells against protein aggregation, assisting protein folding, remodeling protein complexes, and driving translocation into organelles. These functions require high affinity for nonspecific amino acid sequences that are ubiquitous in proteins. It has been recently shown that this high affinity, called ultra-affinity, depends on a process driven out of equilibrium by ATP hydrolysis. Here, we establish the thermodynamic bounds for ultra-affinity, and further show that the same reaction scheme can in principle be used both to strengthen and to weaken affinities (leading in this case to infra-affinity). We show that cofactors are essential to achieve affinity beyond the equilibrium range. Finally, biological implications are discussed. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  11. Stable rotating dipole solitons in nonlocal media

    DEFF Research Database (Denmark)

    Lopez-Aguayo, Servando; Skupin, Stefan; Desyatnikov, Anton S.

    2006-01-01

    We present the first example of stable rotating two-soliton bound states in nonlinear optical media with nonlocal response. We show that, in contrast to media with local response, nonlocality opens possibilities to generate stable azimuthons.......We present the first example of stable rotating two-soliton bound states in nonlinear optical media with nonlocal response. We show that, in contrast to media with local response, nonlocality opens possibilities to generate stable azimuthons....

  12. Uses of stable isotopes in fish ecology

    Science.gov (United States)

    Analyses of fish tissues (other than otoliths) for stable isotope ratios can provide substantial information on fish ecology, including physiological ecology. Stable isotopes of nitrogen and carbon frequently are used to determine the mix of diet sources for consumers. Stable i...

  13. Periodicity of the stable isotopes

    CERN Document Server

    Boeyens, J C A

    2003-01-01

    It is demonstrated that all stable (non-radioactive) isotopes are formally interrelated as the products of systematically adding alpha particles to four elementary units. The region of stability against radioactive decay is shown to obey a general trend based on number theory and contains the periodic law of the elements as a special case. This general law restricts the number of what may be considered as natural elements to 100 and is based on a proton:neutron ratio that matches the golden ratio, characteristic of biological and crystal growth structures. Different forms of the periodic table inferred at other proton:neutron ratios indicate that the electronic configuration of atoms is variable and may be a function of environmental pressure. Cosmic consequences of this postulate are examined. (author)

  14. Stable States of Biological Organisms

    Science.gov (United States)

    Yukalov, V. I.; Sornette, D.; Yukalova, E. P.; Henry, J.-Y.; Cobb, J. P.

    2009-04-01

    A novel model of biological organisms is advanced, treating an organism as a self-consistent system subject to a pathogen flux. The principal novelty of the model is that it describes not some parts, but a biological organism as a whole. The organism is modeled by a five-dimensional dynamical system. The organism homeostasis is described by the evolution equations for five interacting components: healthy cells, ill cells, innate immune cells, specific immune cells, and pathogens. The stability analysis demonstrates that, in a wide domain of the parameter space, the system exhibits robust structural stability. There always exist four stable stationary solutions characterizing four qualitatively differing states of the organism: alive state, boundary state, critical state, and dead state.

  15. Theory of stable allocations II

    Directory of Open Access Journals (Sweden)

    Pantelić Svetlana

    2015-01-01

    Full Text Available The Swedish Royal Academy awarded the 2012 Nobel Prize in Economics to Lloyd Shapley and Alvin Roth, for the theory of stable allocations and the practice of market design. These two American researchers worked independently from each other, combining basic theory and empirical investigations. Through their experiments and practical design they generated a flourishing field of research and improved the performance of many markets. Shapley provided the fundamental theoretical contribution to this field of research, whereas Roth, a professor at the Harvard University in Boston, developed and upgraded these theoretical investigations by applying them to the American market of medical doctors. Namely, their research helps explain the market processes at work, for instance, when doctors are assigned to hospitals, students to schools and human organs for transplant to recipients.

  16. Stable massive particles at colliders

    Energy Technology Data Exchange (ETDEWEB)

    Fairbairn, M.; /Stockholm U.; Kraan, A.C.; /Pennsylvania U.; Milstead, D.A.; /Stockholm U.; Sjostrand, T.; /Lund U.; Skands, P.; /Fermilab; Sloan, T.; /Lancaster U.

    2006-11-01

    We review the theoretical motivations and experimental status of searches for stable massive particles (SMPs) which could be sufficiently long-lived as to be directly detected at collider experiments. The discovery of such particles would address a number of important questions in modern physics including the origin and composition of dark matter in the universe and the unification of the fundamental forces. This review describes the techniques used in SMP-searches at collider experiments and the limits so far obtained on the production of SMPs which possess various colour, electric and magnetic charge quantum numbers. We also describe theoretical scenarios which predict SMPs, the phenomenology needed to model their production at colliders and interactions with matter. In addition, the interplay between collider searches and open questions in cosmology such as dark matter composition are addressed.

  17. Methyl Cation Affinities of Neutral and Anionic Maingroup-Element Hydrides: Trends Across the Periodic Table and Correlation with Proton Affinities

    NARCIS (Netherlands)

    Mulder, R. Joshua; Guerra, Celia Fonseca; Bickelhaupt, F. Matthias

    2010-01-01

    We have computed the methyl cation affinities in the gas phase of archetypal anionic and neutral bases across the periodic table using ZORA-relativistic density functional theory (DFT) at BP86/QZ4P//BP86/TZ2P. The main purpose of this work is to provide the methyl cation affinities (and

  18. An {Mathematical expression} iteration bound primal-dual cone affine scaling algorithm for linear programmingiteration bound primal-dual cone affine scaling algorithm for linear programming

    NARCIS (Netherlands)

    J.F. Sturm; J. Zhang (Shuzhong)

    1996-01-01

    textabstractIn this paper we introduce a primal-dual affine scaling method. The method uses a search-direction obtained by minimizing the duality gap over a linearly transformed conic section. This direction neither coincides with known primal-dual affine scaling directions (Jansen et al., 1993;

  19. Antibody purification using affinity chromatography: a case study with a monoclonal antibody to ractopamine.

    Science.gov (United States)

    Wang, Zhanhui; Liang, Qi; Wen, Kai; Zhang, Suxia; Shen, Jianzhong

    2014-11-15

    The application of antibodies to small molecules in the field of bioanalytics requires antibodies with stable biological activity and high purity; thus, there is a growing interest in developing rapid, inexpensive and effective procedures to obtain such antibodies. In this work, a ractopamine (RAC) derivative, N-4-aminobutyl ractopamine (ABR), was synthesized for preparing new specific affinity chromatography to purify a murine monoclonal antibody (mAb) against RAC from ascites. The performance of the new specific chromatography was compared with four other purification methods in terms of recovery, purity and biological activity of mAb. These four purification methods were prepared by using specific ligands (RAC and RAC-ovalbumin) and commercial ligands (protein G and protein A), respectively. The results showed that the highest recovery (88.1%) was achieved using the new chromatography; in comparison, the recoveries from the other methods were all below 70%. The purity of the mAbs from the new chromatography was 88.3%, while, the highest purity of 97.6% was from protein G chromatography and the lowest purity of 84.7% was from protein A chromatography. The biological activity of the purified mAb from all of the chromatography methods was comparable in enzyme-linked immunosorbent immunoassay (ELISA). Copyright © 2014 Elsevier B.V. All rights reserved.

  20. A protein engineered to bind uranyl selectively and with femtomolar affinity

    Science.gov (United States)

    Zhou, Lu; Bosscher, Mike; Zhang, Changsheng; Özçubukçu, Salih; Zhang, Liang; Zhang, Wen; Li, Charles J.; Liu, Jianzhao; Jensen, Mark P.; Lai, Luhua; He, Chuan

    2014-03-01

    Uranyl (UO22+), the predominant aerobic form of uranium, is present in the ocean at a concentration of ~3.2 parts per 109 (13.7 nM) however, the successful enrichment of uranyl from this vast resource has been limited by the high concentrations of metal ions of similar size and charge, which makes it difficult to design a binding motif that is selective for uranyl. Here we report the design and rational development of a uranyl-binding protein using a computational screening process in the initial search for potential uranyl-binding sites. The engineered protein is thermally stable and offers very high affinity and selectivity for uranyl with a Kd of 7.4 femtomolar (fM) and >10,000-fold selectivity over other metal ions. We also demonstrated that the uranyl-binding protein can repeatedly sequester 30-60% of the uranyl in synthetic sea water. The chemical strategy employed here may be applied to engineer other selective metal-binding proteins for biotechnology and remediation applications.

  1. Rapid affinity-purification and physicochemical characterization of pumpkin (Cucurbita maxima) phloem exudate lectin.

    Science.gov (United States)

    Narahari, Akkaladevi; Swamy, Musti J

    2010-04-21

    The chito-oligosaccharide-specific lectin from pumpkin (Cucurbita maxima) phloem exudate has been purified to homogeneity by affinity chromatography on chitin. After SDS/PAGE in the presence of 2-mercaptoethanol, the pumpkin phloem lectin yielded a single band corresponding to a molecular mass of 23.7 kDa, whereas ESI-MS (electrospray ionization MS) gave the molecular masses of the subunit as 24645 Da. Analysis of the CD spectrum of the protein indicated that the secondary structure of the lectin consists of 9.7% alpha-helix, 35.8% beta-sheet, 22.5% beta-turn and 32.3% unordered structure. Saccharide binding did not significantly affect the secondary and tertiary structures of the protein. The haemagglutinating activity of pumpkin phloem lectin was mostly unaffected in the temperature range 4-70 degrees C, but a sharp decrease was seen between 75 and 85 degrees C. Differential scanning calorimetric and CD spectroscopic studies suggest that the lectin undergoes a co-operative thermal unfolding process centred at approx. 81.5 degrees C, indicating that it is a relatively stable protein.

  2. Curcumin-conjugated nanoliposomes with high affinity for Aβ deposits: possible applications to Alzheimer disease.

    Science.gov (United States)

    Lazar, Adina N; Mourtas, Spyridon; Youssef, Ihsen; Parizot, Christophe; Dauphin, Aurélien; Delatour, Benoît; Antimisiaris, Sophia G; Duyckaerts, Charles

    2013-07-01

    Accumulation of amyloid peptide (Aβ) in senile plaques is a hallmark lesion of Alzheimer disease (AD). The design of molecules able to target the amyloid pathology in tissue is receiving increasing attention, both for diagnostic and for therapeutic purposes. Curcumin is a fluorescent molecule with high affinity for the Aβ peptide but its low solubility limits its clinical use. Curcumin-conjugated nanoliposomes, with curcumin exposed at the surface, were designed. They appeared to be monodisperse and stable. They were non-toxic in vitro, down-regulated the secretion of amyloid peptide and partially prevented Aβ-induced toxicity. They strongly labeled Aβ deposits in post-mortem brain tissue of AD patients and APPxPS1 mice. Injection in the hippocampus and in the neocortex of these mice showed that curcumin-conjugated nanoliposomes were able to specifically stain the Aβ deposits in vivo. Curcumin-conjugated nanoliposomes could find application in the diagnosis and targeted drug delivery in AD. In this preclinical study, curcumin-conjugated nanoliposomes were investigated as possible diagnostics and targeted drug delivery system in Alzheimer's disease, demonstrating strong labeling of Aβ deposits both in human tissue and in mice, and in vitro downregulation of amyloid peptide secretion and prevention of Aβ-induced toxicity. Copyright © 2013 Elsevier Inc. All rights reserved.

  3. Stability and in vitro metabolism of dipeptide model prodrugs with affinity for the oligopeptide transporter

    DEFF Research Database (Denmark)

    Lepist, E I; Kusk, T; Larsen, D H

    2000-01-01

    One approach to increase drug stability and to facilitate oral absorption of low bioavailability drugs may be to design oligopeptide ester prodrugs which are stable in the gastrointestinal tract, are transported via the oligopeptide transporter, and finally release the parent drug molecule......-Glu(OBzl)-Ala and Asp(OBzl)-Sar in aqueous solution and in relevant biological media and to compare these results with those of our previous study of D-Asp(OBzl)-Ala. Furthermore, the resulting aqueous stability and in vitro metabolism data are related to our previous affinity data to evaluate if Glu-Sar, D......-Glu-Ala, and Asp-Sar have potential as pro-moieties in these kinds of prodrugs. The degradation rates follow first-order kinetics, show maximun stability at pH 4-5 with maximum half-lives for Asp(OBzl)-Sar, Glu(OBzl)-Sar, and D-Glu(OBzl)-Ala of 115 h, 30 days and 152 days, respectively. The stability was dependent...

  4. Quasi-integrable deformations of the SU(3) Affine Toda theory

    Energy Technology Data Exchange (ETDEWEB)

    Ferreira, L.A. [Instituto de Física de São Carlos, IFSC/USP, Universidade de São Paulo,Caixa Postal 369, CEP 13560-970, São Carlos-SP (Brazil); Klimas, P. [Universidade Federal de Santa Catarina,Trindade, CEP 88040-900, Florianópolis-SC (Brazil); Zakrzewski, Wojtek J. [Department of Mathematical Sciences,University of Durham, Durham DH1 3LE (United Kingdom)

    2016-05-11

    We consider deformations of the SU(3) Affine Toda theory (AT) and investigate the integrability properties of the deformed theories. We find that for some special deformations all conserved quantities change to being conserved only asymptotically, i.e. in the process of the scattering of two solitons these charges do vary in time, but they return, after the scattering, to the values they had prior to the scattering. This phenomenon, which we have called quasi-integrability, is related to special properties of the two-soliton solutions under space-time parity transformations. Some properties of the AT solitons are discussed, especially those involving interesting static multi-soliton solutions. We support our analytical studies with detailed numerical ones in which the time evolution has been simulated by the 4th order Runge-Kutta method. We find that for some perturbations the solitons repel and for the others they form a quasi-bound state. When we send solitons towards each other they can repel when they come close together with or without ‘flipping’ the fields of the model. The solitons radiate very little and appear to be stable. These results support the ideas of quasi-integrability, i.e. that many effects of integrability also approximately hold for the deformed models.

  5. Synthesis of new bivalent peptides for applications in the Affinity Enhancement System.

    Science.gov (United States)

    Morandeau, L; Benoist, E; Loussouarn, A; Ouadi, A; Lesaec, P; Mougin, M; Faivre-Chauvet, A; Le Boterff, J; Chatal, J F; Barbet, J; Gestin, J F

    2005-01-01

    The feasibility of two-step radioimmunotherapy (RIT) of cancer by the Affinity Enhancement System (AES) has been demonstrated in experimental and clinical studies. This technique, associating a bispecific antibody and a bivalent peptide radiolabeled with iodine-131, has been developed to reduce toxicity and to improve therapeutic efficacy compared to one-step targeting methods. The use of AES with different beta-emitters such as rhenium-188, samarium-153, or lutetium-177 or alpha-emitters such as actinium-225 or bismuth-213 is now considered. Thus three new peptides, designed to allow for the coupling of a variety of bifunctional chelating agents BCA, were synthesized by associating two glycyl-succinyl-histamine (GSH) arms, which are recognized by the 679 monoclonal antibody (mAb-679), with different binding agents, such as p-nitrophenylalanine or N,N-bis(carboxymethyl)-4-N'-(9-fluorenylmethyloxycarbonyl)aminobenzylamine. Immunoreactivity and serum stability evaluation were performed for each synthesized peptide. One of the three peptides (LM218) proved to be more stable than the others, and three different BCAs were coupled to LM218 (CITC-DTPA, CITC-TTHA, and CITC-CHXA''DTPA). One of these products, LM218-BzTTHA was radiolabeled with indium-111 without loss of immunoreactivity toward the mAb-679. These new peptides will allow pretargeted RIT with a large variety of radionuclides, to adapt the choice of the radionuclide (LET, half-life, penetrating emission) to the nature and size of targeted tumors.

  6. Preparation of negative electron affinity gallium nitride photocathode

    Science.gov (United States)

    Qiao, Jianliang; Chang, Benkang; Qian, Yunsheng; Du, Xiaoqing; Zhang, Yijun; Wang, Xiaohui

    2010-10-01

    Negative electron affinity (NEA) Gallium Nitride (GaN) photocathode is an ideal new kind of UV photocathode. NEA GaN photocathode is widely used in such fields as high-performance ultraviolet photoelectric detector, electron beam lithography etc. The preparation of negative electron affinity gallium nitride photocathode relates to the growth technology, the cleaning method, the activation method and the evaluation of photocathode. The mainstream growth technology of GaN photocathode such as metal organic chemistry vapor phase deposits technology, molecule beam epitaxial technology and halide vapor phase epitaxial technology were discussed. The chemical cleaning method and the heat cleaning method for GaN photocathode were given in detail. After the chemical cleaning, the atom clean surface was gotten by a 700 °C heat about 20 minutes in the vacuum system. The activation of GaN photocathode can be realized with only Cs or with Cs/O alternately. Using the activation and evaluation system for NEA photocathode, the photocurrent curve during Cs activation process for GaN photocathode was gotten. The evaluation of photocathode can be done by measuring the quantum efficiency. Employing the UV spectral response measurement instrument, the spectral response and quantum efficiency of NEA GaN photocathode were measured. The measured quantum efficiency of reflection-mode NEA GaN photocathode reached up to 37% at 230 nm.

  7. Expression and affinity purification of recombinant proteins from plants

    Science.gov (United States)

    Desai, Urvee A.; Sur, Gargi; Daunert, Sylvia; Babbitt, Ruth; Li, Qingshun

    2002-01-01

    With recent advances in plant biotechnology, transgenic plants have been targeted as an inexpensive means for the mass production of proteins for biopharmaceutical and industrial uses. However, the current plant purification techniques lack a generally applicable, economic, large-scale strategy. In this study, we demonstrate the purification of a model protein, beta-glucuronidase (GUS), by employing the protein calmodulin (CaM) as an affinity tag. In the proposed system, CaM is fused to GUS. In the presence of calcium, the calmodulin fusion protein binds specifically to a phenothiazine-modified surface of an affinity column. When calcium is removed with a complexing agent, e.g., EDTA, calmodulin undergoes a conformational change allowing the dissociation of the calmodulin-phenothiazine complex and, therefore, permitting the elution of the GUS-CaM fusion protein. The advantages of this approach are the fast, efficient, and economical isolation of the target protein under mild elution conditions, thus preserving the activity of the target protein. Two types of transformation methods were used in this study, namely, the Agrobacterium-mediated system and the viral-vector-mediated transformation system. Copyright 2002 Elsevier Science (USA).

  8. Theory of affine projection algorithms for adaptive filtering

    CERN Document Server

    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...

  9. Membrane Affinity of Platensimycin and Its Dialkylamine Analogs

    Directory of Open Access Journals (Sweden)

    Ian Rowe

    2015-08-01

    Full Text Available Membrane permeability is a desired property in drug design, but there have been difficulties in quantifying the direct drug partitioning into native membranes. Platensimycin (PL is a new promising antibiotic whose biosynthetic production is costly. Six dialkylamine analogs of PL were synthesized with identical pharmacophores but different side chains; five of them were found inactive. To address the possibility that their activity is limited by the permeation step, we calculated polarity, measured surface activity and the ability to insert into the phospholipid monolayers. The partitioning of PL and the analogs into the cytoplasmic membrane of E. coli was assessed by activation curve shifts of a re-engineered mechanosensitive channel, MscS, in patch-clamp experiments. Despite predicted differences in polarity, the affinities to lipid monolayers and native membranes were comparable for most of the analogs. For PL and the di-myrtenyl analog QD-11, both carrying bulky sidechains, the affinity for the native membrane was lower than for monolayers (half-membranes, signifying that intercalation must overcome the lateral pressure of the bilayer. We conclude that the biological activity among the studied PL analogs is unlikely to be limited by their membrane permeability. We also discuss the capacity of endogenous tension-activated channels to detect asymmetric partitioning of exogenous substances into the native bacterial membrane and the different contributions to the thermodynamic force which drives permeation.

  10. Secondary Mechanisms of Affinity Maturation in the Human Antibody Repertoire

    Directory of Open Access Journals (Sweden)

    Bryan S. Briney

    2013-03-01

    Full Text Available V(DJ recombination and somatic hypermutation (SHM are the primary mechanisms for diversification of the human antibody repertoire. These mechanisms allow for rapid humoral immune responses to a wide range of pathogenic challenges. V(DJ recombination efficiently generate a virtually limitless diversity through random recombination of variable (V, diversity (D and joining (J genes with diverse nontemplated junctions between the selected gene segments. Following antigen stimulation, affinity maturation by SHM produces antibodies with refined specificity mediated by mutations typically focused in complementarity determining regions (CDRs, which form the bulk of the antigen recognition site. While V(DJ recombination and SHM are responsible for much of the diversity of the antibody repertoire, there are several secondary mechanisms that, while less frequent, make substantial contributions to antibody diversity including V(DDJ recombination (or D-D fusion, somatic-hypermutation-associated insertions and deletions, and affinity maturation and antigen contact by non-CDR regions of the antibody. In addition to enhanced diversity, these mechanisms allow the production of antibodies that are critical to response to a variety of viral and bacterial pathogens but that would be difficult to generate using only the primary mechanisms of diversification.

  11. The Expanding Toolkit of Translating Ribosome Affinity Purification.

    Science.gov (United States)

    Dougherty, Joseph D

    2017-12-13

    Translating ribosome affinity purification is a method initially developed for profiling mRNA from genetically defined cell types in complex tissues. It has been applied both to identify target molecules in cell types that are important for controlling a variety of behaviors in the brain, and to understand the molecular consequences on those cells due to experimental manipulations, ranging from drugs of abuse to disease-causing mutations. Since its inception, a variety of methodological advances are opening new avenues of investigation. These advances include a variety of new methods for targeting cells for translating ribosome affinity purification by features such as their projections or activity, additional tags and mouse reagents increasing the flexibility of the system, and new modifications of the method specifically focused on studying the regulation of translation. The latter includes methods to assess cell type-specific regulation of translation in specific subcellular compartments. Here, I provide a summary of these recent advances and resources, highlighting both new experimental opportunities and areas for future technical development. Copyright © 2017 the authors 0270-6474/17/3712079-09$15.00/0.

  12. Flexible Molybdenum Electrodes towards Designing Affinity Based Protein Biosensors.

    Science.gov (United States)

    Kamakoti, Vikramshankar; Panneer Selvam, Anjan; Radha Shanmugam, Nandhinee; Muthukumar, Sriram; Prasad, Shalini

    2016-07-18

    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.

  13. Self-affinity in the dengue fever time series

    Science.gov (United States)

    Azevedo, S. M.; Saba, H.; Miranda, J. G. V.; Filho, A. S. Nascimento; Moret, M. A.

    2016-06-01

    Dengue is a complex public health problem that is common in tropical and subtropical regions. This disease has risen substantially in the last three decades, and the physical symptoms depict the self-affine behavior of the occurrences of reported dengue cases in Bahia, Brazil. This study uses detrended fluctuation analysis (DFA) to verify the scale behavior in a time series of dengue cases and to evaluate the long-range correlations that are characterized by the power law α exponent for different cities in Bahia, Brazil. The scaling exponent (α) presents different long-range correlations, i.e. uncorrelated, anti-persistent, persistent and diffusive behaviors. The long-range correlations highlight the complex behavior of the time series of this disease. The findings show that there are two distinct types of scale behavior. In the first behavior, the time series presents a persistent α exponent for a one-month period. For large periods, the time series signal approaches subdiffusive behavior. The hypothesis of the long-range correlations in the time series of the occurrences of reported dengue cases was validated. The observed self-affinity is useful as a forecasting tool for future periods through extrapolation of the α exponent behavior. This complex system has a higher predictability in a relatively short time (approximately one month), and it suggests a new tool in epidemiological control strategies. However, predictions for large periods using DFA are hidden by the subdiffusive behavior.

  14. 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.

  15. Subband Affine Projection Algorithm for Acoustic Echo Cancellation System

    Directory of Open Access Journals (Sweden)

    Hyeon-Deok Bae

    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.

  16. Affinity Labeling of Membrane Receptors Using Tissue-Penetrating Radiations

    Directory of Open Access Journals (Sweden)

    Franklin C. Wong

    2013-01-01

    Full Text Available Photoaffinity labeling, a useful in vivo biochemical tool, is limited when applied in vivo because of the poor tissue penetration by ultraviolet (UV photons. This study investigates affinity labeling using tissue-penetrating radiation to overcome the tissue attenuation and irreversibly label membrane receptor proteins. Using X-ray (115 kVp at low doses (<50 cGy or Rad, specific and irreversible binding was found on striatal dopamine transporters with 3 photoaffinity ligands for dopamine transporters, to different extents. Upon X-ray exposure (115 kVp, RTI-38 and RTI-78 ligands showed irreversible and specific binding to the dopamine transporter similar to those seen with UV exposure under other conditions. Similarly, gamma rays at higher energy (662 keV also affect irreversible binding of photoreactive ligands to peripheral benzodiazepine receptors (by PK14105 and to the dopamine (D2 membrane receptors (by azidoclebopride, respectively. This study reports that X-ray and gamma rays induced affinity labeling of membrane receptors in a manner similar to UV with photoreactive ligands of the dopamine transporter, D2 dopamine receptor (D2R, and peripheral benzodiazepine receptor (PBDZR. It may provide specific noninvasive irreversible block or stimulation of a receptor using tissue-penetrating radiation targeting selected anatomic sites.

  17. PANDA: Protein function prediction using domain architecture and affinity propagation.

    Science.gov (United States)

    Wang, Zheng; Zhao, Chenguang; Wang, Yiheng; Sun, Zheng; Wang, Nan

    2018-02-22

    We developed PANDA (Propagation of Affinity and Domain Architecture) to predict protein functions in the format of Gene Ontology (GO) terms. PANDA at first executes profile-profile alignment algorithm to search against PfamA, KOG, COG, and SwissProt databases, and then launches PSI-BLAST against UniProt for homologue search. PANDA integrates a domain architecture inference algorithm based on the Bayesian statistics that calculates the probability of having a GO term. All the candidate GO terms are pooled and filtered based on Z-score. After that, the remaining GO terms are clustered using an affinity propagation algorithm based on the GO directed acyclic graph, followed by a second round of filtering on the clusters of GO terms. We benchmarked the performance of all the baseline predictors PANDA integrates and also for every pooling and filtering step of PANDA. It can be found that PANDA achieves better performances in terms of area under the curve for precision and recall compared to the baseline predictors. PANDA can be accessed from http://dna.cs.miami.edu/PANDA/ .

  18. Remarkable alkaline stability of an engineered protein A as immunoglobulin affinity ligand: C domain having only one amino acid substitution

    Science.gov (United States)

    Minakuchi, Kazunobu; Murata, Dai; Okubo, Yuji; Nakano, Yoshiyuki; Yoshida, Shinichi

    2013-01-01

    Protein A affinity chromatography is the standard purification process for the capture of therapeutic antibodies. The individual IgG-binding domains of protein A (E, D, A, B, C) have highly homologous amino acid sequences. From a previous report, it has been assumed that the C domain has superior resistance to alkaline conditions compared to the other domains. We investigated several properties of the C domain as an IgG-Fc capture ligand. Based on cleavage site analysis of a recombinant protein A using a protein sequencer, the C domain was found to be the only domain to have neither of the potential alkaline cleavage sites. Circular dichroism (CD) analysis also indicated that the C domain has good physicochemical stability. Additionally, we evaluated the amino acid substitutions at the Gly-29 position of the C domain, as the Z domain (an artificial B domain) acquired alkaline resistance through a G29A mutation. The G29A mutation proved to increase the alkaline resistance of the C domain, based on BIACORE analysis, although the improvement was significantly smaller than that observed for the B domain. Interestingly, a number of other amino acid mutations at the same position increased alkaline resistance more than did the G29A mutation. This result supports the notion that even a single mutation on the originally alkali-stable C domain would improve its alkaline stability. An engineered protein A based on this C domain is expected to show remarkable performance as an affinity ligand for immunoglobulin. PMID:23868198

  19. The Isotope-Coded Affinity Tag Method for Quantitative Protein Profile Comparison and Relative Quantitation of Cysteine Redox Modifications.

    Science.gov (United States)

    Chan, James Chun Yip; Zhou, Lei; Chan, Eric Chun Yong

    2015-11-02

    The isotope-coded affinity tag (ICAT) technique has been applied to measure pairwise changes in protein expression through differential stable isotopic labeling of proteins or peptides followed by identification and quantification using a mass spectrometer. Changes in protein expression are observed when the identical peptide from each of two biological conditions is identified and a difference is detected in the measurements comparing the peptide labeled with the heavy isotope to the one with a normal isotopic distribution. This approach allows the simultaneous comparison of the expression of many proteins between two different biological states (e.g., yeast grown on galactose versus glucose, or normal versus cancer cells). Due to the cysteine-specificity of the ICAT reagents, the ICAT technique has also been applied to perform relative quantitation of cysteine redox modifications such as oxidation and nitrosylation. This unit describes both protein quantitation and profiling of cysteine redox modifications using the ICAT technique. Copyright © 2015 John Wiley & Sons, Inc.

  20. 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

  1. Cofactor and substrate binding to vanadium chloroperoxidase determined by UV-VIS spectroscopy and evidence for high affinity for pervanadate.

    Science.gov (United States)

    Renirie, R; Hemrika, W; Piersma, S R; Wever, R

    2000-02-08

    The vanadate cofactor in vanadium chloroperoxidase has been studied using UV-VIS absorption spectroscopy. A band is present in the near-UV that is red-shifted as compared to free vanadate and shifts in both position and intensity upon change in pH. Mutation of vanadate binding residues has a clear effect on the spectrum. Substrate-induced spectral effects allow direct measurement of separate kinetics steps for the first time for vanadium haloperoxidases. A peroxo intermediate is formed upon addition of H(2)O(2), which causes a decrease in the absorption spectrum at 315 nm, as well as an increase at 384 nm. This peroxo form is very stable at pH 8.3, whereas it is less stable at pH 5.0, which is the optimal pH for activity. Upon addition of halides to the peroxo form, the native spectrum is re-formed as a result of halide oxidation. Stopped-flow experiments show that H(2)O(2) binding and Cl(-) oxidation occur on the millisecond to second time scale. These data suggest that the oxidation of Cl(-) to HOCl occurs in at least two steps. In the presence of H(2)O(2), the affinity for the vanadate cofactor was found to be much higher than previously reported for vanadate in the absence of H(2)O(2). This is attributed to the uptake of pervanadate by the apo-enzyme. Human glucose-6-phosphatase, which is evolutionarily related to vanadium chloroperoxidase, is also likely to have a higher affinity for pervanadate than vanadate. This could explain the enhanced insulin mimetic effect of pervanadate as compared to vanadate.

  2. Stable Treemaps via Local Moves.

    Science.gov (United States)

    Sondag, Max; Speckmann, Bettina; Verbeek, Kevin

    2018-01-01

    Treemaps are a popular tool to visualize hierarchical data: items are represented by nested rectangles and the area of each rectangle corresponds to the data being visualized for this item. The visual quality of a treemap is commonly measured via the aspect ratio of the rectangles. If the data changes, then a second important quality criterion is the stability of the treemap: how much does the treemap change as the data changes. We present a novel stable treemapping algorithm that has very high visual quality. Whereas existing treemapping algorithms generally recompute the treemap every time the input changes, our algorithm changes the layout of the treemap using only local modifications. This approach not only gives us direct control over stability, but it also allows us to use a larger set of possible layouts, thus provably resulting in treemaps of higher visual quality compared to existing algorithms. We further prove that we can reach all possible treemap layouts using only our local modifications. Furthermore, we introduce a new measure for stability that better captures the relative positions of rectangles. We finally show via experiments on real-world data that our algorithm outperforms existing treemapping algorithms also in practice on either visual quality and/or stability. Our algorithm scores high on stability regardless of whether we use an existing stability measure or our new measure.

  3. An Affinity Propagation-Based DNA Motif Discovery Algorithm

    Directory of Open Access Journals (Sweden)

    Chunxiao Sun

    2015-01-01

    Full Text Available The planted (l,d motif search (PMS is one of the fundamental problems in bioinformatics, which plays an important role in locating transcription factor binding sites (TFBSs in DNA sequences. Nowadays, identifying weak motifs and reducing the effect of local optimum are still important but challenging tasks for motif discovery. To solve the tasks, we propose a new algorithm, APMotif, which first applies the Affinity Propagation (AP clustering in DNA sequences to produce informative and good candidate motifs and then employs Expectation Maximization (EM refinement to obtain the optimal motifs from the candidate motifs. Experimental results both on simulated data sets and real biological data sets show that APMotif usually outperforms four other widely used algorithms in terms of high prediction accuracy.

  4. Evaluation of galectin binding by frontal affinity chromatography (FAC).

    Science.gov (United States)

    Iwaki, Jun; Hirabayashi, Jun

    2015-01-01

    Frontal affinity chromatography (FAC) is a simple and versatile procedure enabling quantitative determination of diverse biological interactions in terms of dissociation constants (K d), even though these interactions are relatively weak. The method is best applied to glycans and their binding proteins, with the analytical system operating on the basis of highly reproducible isocratic elution by liquid chromatography. Its application to galectins has been successfully developed to characterize their binding specificities in detail. As a result, their minimal requirements for recognition of disaccharides, i.e., β-galactosides, as well as characteristic features of individual galectins, have been elucidated. In this chapter, we describe standard procedures to determine the K d's for interactions between a series of standard glycans and various galectins.

  5. Chitinolytic activity of the sheep rumen ciliate Diploplastron affine.

    Science.gov (United States)

    Bełzecki, G; Miltko, R; Michałowski, T; Simůnek, J; Kopecný, J

    2008-01-01

    Supplementation of the rumen ciliate Diploplastron affine growth medium with commercial chitin stimulated growth of ciliates and the density of their population was positively correlated with chitin doses (r = 0.95; p < 0.01). The cell-free extracts prepared from bacteria-free ciliates degraded chitin to N-acetyl-D: -glucosamine and chitobiose. Three exochitinases, two endochitinases and two beta-N-acetylglucosaminidases were identified in the cell-free extract of protozoa. The molar mass of exochitinases was 80, 65 and 30 kDa, and endochitinases 75 and 50 kDa; the molar mass of one of the identified beta-N-acetylglucosaminidases was 45 kDa.

  6. Special affine Fourier transformation in frequency-domain

    Science.gov (United States)

    Cai, L. Z.

    2000-11-01

    Special affine Fourier transformation (SAFT) can be considered as an extension of the fractional Fourier transformation (FRT) and the most general linear mapping in phase space. A general formula for SAFT in frequency-domain is derived, which gives a direct relationship between the input and output spatial frequency spectra of a light field. It shows that the SAFT has similar and symmetric feature in both space- and frequency-domains. As its special cases, Collins formula in frequency-domain, the spatial frequency representations of the almost-FRT, almost-Fresnel and almost-Fourier transformations are explicitly obtained. These formulae may provide a tool for investigating the performance of a lossless optical system including small deformations in both domains in a unified way within the framework of linear theory.

  7. What is Cryptosporidium? Reappraising its biology and phylogenetic affinities.

    Science.gov (United States)

    Barta, John R; Thompson, R C Andrew

    2006-10-01

    In raising the question "What is Cryptosporidium?", we aim to emphasize a growing need to re-evaluate the affinities of Cryptosporidium species within the phylum Apicomplexa so as to better understand the biology and ecology of these parasites. Here, we have compiled evidence from a variety of molecular and biological studies to build a convincing case for distancing Cryptosporidium species from the coccidia conceptually, biologically and taxonomically. We suggest that Cryptosporidium species must no longer be considered unusual or unique coccidia but rather seen for what they are--a distantly related lineage of apicomplexan parasites that are not in fact coccidia but that do occupy many of the same ecological niches. Looking at Cryptosporidium species without traditional coccidian blinders is likely to reveal new avenues of investigation into pathogenesis, epidemiology, treatment and control of these ubiquitous pathogens.

  8. Electron-trapping polycrystalline materials with negative electron affinity.

    Science.gov (United States)

    McKenna, Keith P; Shluger, Alexander L

    2008-11-01

    The trapping of electrons by grain boundaries in semiconducting and insulating materials is important for a wide range of physical problems, for example, relating to: electroceramic materials with applications as sensors, varistors and fuel cells, reliability issues for solar cell and semiconductor technologies and electromagnetic seismic phenomena in the Earth's crust. Surprisingly, considering their relevance for applications and abundance in the environment, there have been few experimental or theoretical studies of the electron trapping properties of grain boundaries in highly ionic materials such as the alkaline earth metal oxides and alkali halides. Here we demonstrate, by first-principles calculations on MgO, LiF and NaCl, a qualitatively new type of electron trapping at grain boundaries. This trapping is associated with the negative electron affinity of these materials and is unusual as the electron is confined in the empty space inside the dislocation cores.

  9. Affine analogues of the Sasaki-Shchepetilov connection

    Directory of Open Access Journals (Sweden)

    Maria Robaszewska

    2016-07-01

    Full Text Available For two-dimensional manifold M with locally symmetric connection ∇ and with ∇-parallel volume element vol one can construct a flat connection on the vector bundle TM⊕E, where E is a trivial bundle. The metrizable case, when M is a Riemannian manifold of constant curvature, together with its higher dimension generalizations, was studied by A.V. Shchepetilov [J. Phys. A: 36 (2003, 3893-3898]. This paper deals with the case of non-metrizable locally symmetric connection. Two flat connections on TM⊕(R⨯M and two on TM⊕(R2⨯M are constructed. It is shown that two of those connections - one from each pair - may be identified with the standard flat connection in RN, after suitable local affine embedding of (M,∇ into RN.

  10. 'The Strange Case of Angelica': affinity between Fantastic and Documental

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    Rita Benis

    2017-01-01

    Full Text Available In 2010, Manoel de Oliveira films The Strange Case of Angélica, a project from the early fifties of the past century. In it, the confrontation between the documentary side of the film (the sequences where the protagonist, Isaac, photographs the workers in the vineyards and the fantastic sequences (the episodes with the ghost of Angelica seems to indicate an affinity. That "shadow of resemblance" Petrarch spoke about to his close friend Giovanni Boccaccio: "... he who imitates must proceed in such a way that what he does is similar but not equal, and that the likeness is not that which exists between the original and the copy, that the more similar the more it is praiseworthy, but instead a likeness which one finds in the similarities between a father and a son, among which, though much difference is made in the aspect, there is, however, as a shadow of resemblance, which the painters call 'aire' (... "(apud Rodrigues 2003: 5. A "family air" as a living correlation that comes to our encounter and which is felt as an immediate understanding (and not as definable evidence. In the film, the shiver that assaults us through the apparition of Angelica seems to announce something that goes beyond this same vision: the eminence of the disappearance of the vineyard workers and their gestures, a loss of connection between Man and Nature. The present affinity - Angelica / diggers - is mirrored in Isaac's immense melancholy, the only person apparently capable of perceiving the landscape, the "air" that this relationship evokes. The whole film is crossed by the glimpse of this indefinable kinship, by the porosity between the sensitive world and the spectral world, the permanent interweaving of visibilities / invisibilities that allow us access to this other cinematographic space-time, more percept than visible, in which, according to Manoel de Oliveira, the phantom of physical reality reveals itself "more real, however, than reality itself" (Baecque and

  11. The Mobile Phone Affinity Scale: Enhancement and Refinement.

    Science.gov (United States)

    Bock, Beth C; Lantini, Ryan; Thind, Herpreet; Walaska, Kristen; Rosen, Rochelle K; Fava, Joseph L; Barnett, Nancy P; Scott-Sheldon, Lori Aj

    2016-12-15

    Existing instruments that assess individuals' relationships with mobile phones tend to focus on negative constructs such as addiction or dependence, and appear to assume that high mobile phone use reflects pathology. Mobile phones can be beneficial for health behavior change, disease management, work productivity, and social connections, so there is a need for an instrument that provides a more balanced assessment of the various aspects of individuals' relationships with mobile phones. The purpose of this research was to develop, revise, and validate the Mobile Phone Affinity Scale, a multi-scale instrument designed to assess key factors associated with mobile phone use. Participants (N=1058, mean age 33) were recruited from Amazon Mechanical Turk between March and April of 2016 to complete a survey that assessed participants' mobile phone attitudes and use, anxious and depressive symptoms, and resilience. Confirmatory factor analysis supported a 6-factor model. The final measure consisted of 24 items, with 4 items on each of 6 factors: Connectedness, Productivity, Empowerment, Anxious Attachment, Addiction, and Continuous Use. The subscales demonstrated strong internal consistency (Cronbach alpha range=0.76-0.88, mean 0.83), and high item factor loadings (range=0.57-0.87, mean 0.75). Tests for validity further demonstrated support for the individual subscales. Mobile phone affinity may have an important impact in the development and effectiveness of mobile health interventions, and continued research is needed to assess its predictive ability in health behavior change interventions delivered via mobile phones. ©Beth C Bock, Ryan Lantini, Herpreet Thind, Kristen Walaska, Rochelle K Rosen, Joseph L Fava, Nancy P Barnett, Lori AJ Scott-Sheldon. Originally published in JMIR Mhealth and Uhealth (http://mhealth.jmir.org), 15.12.2016.

  12. Effect of matrices on affinity purification of protein C.

    Science.gov (United States)

    Kang, K; Ryu, D; Drohan, W N; Orthner, C L

    1992-05-01

    One of the critical problems in scale-up of affinity chromatography is the mechanical strength of the support matrix against pressure. Because the costs of both the gel matrix and the ligand for the affinity chromatography are very high, the reusability of gel matrices is directly related to the total production cost. In certain cases, where the source material is viscous (e.g., blood plasma), irreversible deformation of gel matrices can readily occur, necessitating severe constraints in the flow rate. Consequently, productivity is low.We have characterized the system parameters and investigated the performance of various matrices that are commercially available. The experimental system used for this study was the immunoaffinity purification of protein C (an anticoagulant protein) from human blood plasma. The support matrices studied were cross-linked agarose, polymethyl acrylic, cellulose, and polyvinyl alcohol polymers. The major system parameters studied were pressure tolerance, coupling efficiency, adsorption efficiency, and batch adsorption/desorption kinetics of protein C to/from the monoclonal antibody (MAb)-Matrix complex. In addition, the apparent equilibrium constant and bandwidth of the product concentration profile in the eluate were characterized by performing pulse tests.A methodology was developed for evaluating the immunoaffinity column performance for the separation of protein C. By utilizing the experimentally measured parameters, the flow rate limitation for each purification step was computed. Then, the purification performance of the matrices were evaluated in terms of productivity per unit time. Among the matrices tested, cellulose was superior in overall performance for the immunoaffinity purification of protein C using a 10 cm x 10 cm column.

  13. Role of H2O2 on the kinetics of low-affinity high-capacity Na+-dependent alanine transport in SHR proximal tubular epithelial cells

    International Nuclear Information System (INIS)

    Pinto, Vanda; Pinho, Maria Joao; Jose, Pedro A.; Soares-da-Silva, Patricio

    2010-01-01

    Research highlights: → H 2 O 2 in excess is required for the presence of a low-affinity high-capacity component for the Na + -dependent [ 14 C]-L-alanine uptake in SHR PTE cells only. → It is suggested that Na + binding in renal ASCT2 may be regulated by ROS in SHR PTE cells. -- Abstract: The presence of high and low sodium affinity states for the Na + -dependent [ 14 C]-L-alanine uptake in immortalized renal proximal tubular epithelial (PTE) cells was previously reported (Am. J. Physiol. 293 (2007) R538-R547). This study evaluated the role of H 2 O 2 on the Na + -dependent [ 14 C]-L-alanine uptake of ASCT2 in immortalized renal PTE cells from Wistar Kyoto rat (WKY) and spontaneously hypertensive rat (SHR). Na + dependence of [ 14 C]-L-alanine uptake was investigated replacing NaCl with an equimolar concentration of choline chloride in vehicle- and apocynin-treated cells. Na + removal from the uptake solution abolished transport activity in both WKY and SHR PTE cells. Decreases in H 2 O 2 levels in the extracellular medium significantly reduced Na + -K m and V max values of the low-affinity high-capacity component in SHR PTE cells, with no effect on the high-affinity low-capacity state of the Na + -dependent [ 14 C]-L-alanine uptake. After removal of apocynin from the culture medium, H 2 O 2 levels returned to basal values within 1 to 3 h in both WKY and SHR PTE cells and these were found stable for the next 24 h. Under these experimental conditions, the Na + -K m and V max of the high-affinity low-capacity state were unaffected and the low-affinity high-capacity component remained significantly decreased 1 day but not 4 days after apocynin removal. In conclusion, H 2 O 2 in excess is required for the presence of a low-affinity high-capacity component for the Na + -dependent [ 14 C]-L-alanine uptake in SHR PTE cells only. It is suggested that Na + binding in renal ASCT2 may be regulated by ROS in SHR PTE cells.

  14. Purification of sequence-specific DNA-binding proteins by affinity chromatography.

    Science.gov (United States)

    Kerrigan, L A; Kadonaga, J T

    2001-05-01

    Affinity chromatography is a very effective and straightforward means of purifying a protein based on its sequence-specific DNA-binding properties. The affinity chromatography procedure described in this unit uses DNA containing specific recognition sites for the desired protein that has been covalently linked to a solid support. The first basic protocol describes preparation of a DNA affinity resin, including cyanogen bromide (CNBr) activation of the agarose support. An provides a method to couple DNA to commercially available CNBr-activated Sepharose, and a support protocol describes how to purify crude synthetic oligonucleotides by gel electrophoresis prior to preparation of the affinity resin. The second basic protocol outlines the affinity chromatography procedure. A second support protocol describes determination of the appropriate type and quantity of nonspecific competitor DNA that should be used in the procedure and its preparation. Parameters essential to the success of an affinity chromatography experiment are discussed in detail in the Commentary.

  15. Advanced thermally stable jet fuels

    Energy Technology Data Exchange (ETDEWEB)

    Schobert, H.H.

    1999-01-31

    The Pennsylvania State University program in advanced thermally stable coal-based jet fuels has five broad objectives: (1) Development of mechanisms of degradation and solids formation; (2) Quantitative measurement of growth of sub-micrometer and micrometer-sized particles suspended in fuels during thermal stressing; (3) Characterization of carbonaceous deposits by various instrumental and microscopic methods; (4) Elucidation of the role of additives in retarding the formation of carbonaceous solids; (5) Assessment of the potential of production of high yields of cycloalkanes by direct liquefaction of coal. Future high-Mach aircraft will place severe thermal demands on jet fuels, requiring the development of novel, hybrid fuel mixtures capable of withstanding temperatures in the range of 400--500 C. In the new aircraft, jet fuel will serve as both an energy source and a heat sink for cooling the airframe, engine, and system components. The ultimate development of such advanced fuels requires a thorough understanding of the thermal decomposition behavior of jet fuels under supercritical conditions. Considering that jet fuels consist of hundreds of compounds, this task must begin with a study of the thermal degradation behavior of select model compounds under supercritical conditions. The research performed by The Pennsylvania State University was focused on five major tasks that reflect the objectives stated above: Task 1: Investigation of the Quantitative Degradation of Fuels; Task 2: Investigation of Incipient Deposition; Task 3: Characterization of Solid Gums, Sediments, and Carbonaceous Deposits; Task 4: Coal-Based Fuel Stabilization Studies; and Task 5: Exploratory Studies on the Direct Conversion of Coal to High Quality Jet Fuels. The major findings of each of these tasks are presented in this executive summary. A description of the sub-tasks performed under each of these tasks and the findings of those studies are provided in the remainder of this volume

  16. Describing high-dimensional dynamics with low-dimensional piecewise affine models: applications to renewable energy.

    Science.gov (United States)

    Hirata, Yoshito; Aihara, Kazuyuki

    2012-06-01

    We introduce a low-dimensional description for a high-dimensional system, which is a piecewise affine model whose state space is divided by permutations. We show that the proposed model tends to predict wind speeds and photovoltaic outputs for the time scales from seconds to 100 s better than by global affine models. In addition, computations using the piecewise affine model are much faster than those of usual nonlinear models such as radial basis function models.

  17. Density-conserving affine continuous cellular automata solving the relaxed density classification problem

    International Nuclear Information System (INIS)

    Wolnik, Barbara; Dembowski, Marcin; Bołt, Witold; Baetens, Jan M; De Baets, Bernard

    2017-01-01

    The focus of this paper is on the density classification problem in the context of affine continuous cellular automata. Although such cellular automata cannot solve this problem in the classical sense, most density-conserving affine continuous cellular automata with a unit neighborhood radius are valid solutions of a slightly relaxed version of this problem. This result follows from a detailed study of the dynamics of the density-conserving affine continuous cellular automata that we introduce. (paper)

  18. Population Games, Stable Games, and Passivity

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    Michael J. Fox

    2013-10-01

    Full Text Available The class of “stable games”, introduced by Hofbauer and Sandholm in 2009, has the attractive property of admitting global convergence to equilibria under many evolutionary dynamics. We show that stable games can be identified as a special case of the feedback-system-theoretic notion of a “passive” dynamical system. Motivated by this observation, we develop a notion of passivity for evolutionary dynamics that complements the definition of the class of stable games. Since interconnections of passive dynamical systems exhibit stable behavior, we can make conclusions about passive evolutionary dynamics coupled with stable games. We show how established evolutionary dynamics qualify as passive dynamical systems. Moreover, we exploit the flexibility of the definition of passive dynamical systems to analyze generalizations of stable games and evolutionary dynamics that include forecasting heuristics as well as certain games with memory.

  19. Affinity Inequality among Serum Antibodies That Originate in Lymphoid Germinal Centers.

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    Myungsun Kang

    Full Text Available Upon natural infection with pathogens or vaccination, antibodies are produced by a process called affinity maturation. As affinity maturation ensues, average affinity values between an antibody and ligand increase with time. Purified antibodies isolated from serum are invariably heterogeneous with respect to their affinity for the ligands they bind, whether macromolecular antigens or haptens (low molecular weight approximations of epitopes on antigens. However, less is known about how the extent of this heterogeneity evolves with time during affinity maturation. To shed light on this issue, we have taken advantage of previously published data from Eisen and Siskind (1964. Using the ratio of the strongest to the weakest binding subsets as a metric of heterogeneity (or affinity inequality, we analyzed antibodies isolated from individual serum samples. The ratios were initially as high as 50-fold, and decreased over a few weeks after a single injection of small antigen doses to around unity. This decrease in the effective heterogeneity of antibody affinities with time is consistent with Darwinian evolution in the strong selection limit. By contrast, neither the average affinity nor the heterogeneity evolves much with time for high doses of antigen, as competition between clones of the same affinity is minimal.

  20. On the Fuzzy Stability of an Affine Functional Equation

    OpenAIRE

    Nasiruzzaman, Md.

    2015-01-01

    In this paper, we obtain the general solution of the following functional equation f(3x + y + z) + f(x + 3y + z) + f(x + y + 3z) + f(x) + f(y) + f(z) = 6f(x + y + z): We establish the Hyers-Ulam-Rassias stability of the above functional equation in the fuzzy normed spaces. Further we show the above functional equation is stable in the sense of Hyers and Ulam in fuzzy normed spaces.

  1. Polyelectrolyte brushes: a novel stable lubrication system in aqueous conditions.

    Science.gov (United States)

    Kobayashi, Motoyasu; Terada, Masami; Takahara, Atsushi

    2012-01-01

    Surface-initiated controlled radical copolymerizations of 2-dimethylaminoethyl methacrylate (DMAEMA), 2-(methacryloyloxy)ethyl phosphorylcholine (MPC), 2-(methacryloyloxy)ethyltrimethylammonium chloride) (MTAC), and 3-sulfopropyl methacrylate potassium salt (SPMK) were carried out on a silicon wafer and glass ball to prepare polyelectrolyte brushes with excellent water wettability. The frictional coefficient of the polymer brushes was recorded on a ball-on-plate type tribometer by linear reciprocating motion of the brush specimen at a selected velocity of 1.5 x 10(-3) m s-1 under a normal load of 0.49 N applied to the stationary glass ball (d = 10 mm) at 298 K. The poly(DMAEMA-co-MPC) brush partially cross-linked by bis(2-iodoethoxy)ethane maintained a relatively low friction coefficient around 0.13 under humid air (RH > 75%) even after 200 friction cycles. The poly(SPMK) brush revealed an extremely low friction coefficient around 0.01 even after 450 friction cycles. We supposed that the abrasion of the brush was prevented owing to the good affinity of the poly(SPMK) brush for water forming a water lubrication layer, and electrostatic repulsive interactions among the brushes bearing sulfonic acid groups. Furthermore, the poly(SPMK-co-MTAC) brush with a chemically cross-linked structure showed a stable low friction coefficient in water even after 1400 friction cycles under a normal load of 139 MPa, indicating that the cross-linking structure improved the wear resistance of the brush layer.

  2. Polynomials-Based Terminal Control of Affine Systems

    Directory of Open Access Journals (Sweden)

    A. E. Golubev

    2015-01-01

    Full Text Available One of the approaches to solving terminal control problems for affine dynamical systems is based on the use of polynomials of degree 2n − 1, where n is the order of the system in question. In this paper, we investigate the terminal control problem for which the final state of the system coincides with the origin in the phase space. We seek a set of initial states such that the solution of the terminal control problem can be constructed by using a polynomial of degree 2n − 2.Note that solution of the terminal control problem in question can be used to solve the problem of stabilizing the zero equilibrium in a finite time.For the second-order systems we prove the necessary and sufficient conditions for existence of the polynomial of the second degree which determines the solution of the terminal problem. The solutions of the terminal control problem based on the polynomials of second and third degree are given. As an example, the terminal control problem is considered for the simple pendulum.We also discuss solution of the terminal problem for affine systems of the third order, based on the use of the fourth and fifth degree polynomials. The necessary and sufficient conditions for existence of the fourth-degree polynomial such that its phase graph connects an arbitrary initial state of the system and the origin are obtained.For systems of arbitrary order n we obtain the necessary and sufficient conditions for existence of a solution of the terminal problem using the polynomial of degree 2n − 2. We also give the solution of the problem by means of the polynomial of degree 2n − 1.Further research can be focused on extending the results obtained in this note to terminal control problems where the desired final state of the system is not necessarily the origin.One of the potential application areas for the obtained theoretical results is automatic control of technical plants like unmanned aerial vehicles and mobile robots.

  3. Hemoglobin oxygen affinity in patients with cystic fibrosis.

    Directory of Open Access Journals (Sweden)

    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.

  4. High Affinity Binding of Indium and Ruthenium Ions by Gastrins.

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    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.

  5. Genetic affinities between endogamous and inbreeding populations of Uttar Pradesh

    Directory of Open Access Journals (Sweden)

    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

  6. Computational design of the affinity and specificity of a therapeutic T cell receptor.

    Directory of Open Access Journals (Sweden)

    Brian G Pierce

    2014-02-01

    Full Text Available T cell receptors (TCRs are key to antigen-specific immunity and are increasingly being explored as therapeutics, most visibly in cancer immunotherapy. As TCRs typically possess only low-to-moderate affinity for their peptide/MHC (pMHC ligands, there is a recognized need to develop affinity-enhanced TCR variants. Previous in vitro engineering efforts have yielded remarkable improvements in TCR affinity, yet concerns exist about the maintenance of peptide specificity and the biological impacts of ultra-high affinity. As opposed to in vitro engineering, computational design can directly address these issues, in theory permitting the rational control of peptide specificity together with relatively controlled increments in affinity. Here we explored the efficacy of computational design with the clinically relevant TCR DMF5, which recognizes nonameric and decameric epitopes from the melanoma-associated Melan-A/MART-1 protein presented by the class I MHC HLA-A2. We tested multiple mutations selected by flexible and rigid modeling protocols, assessed impacts on affinity and specificity, and utilized the data to examine and improve algorithmic performance. We identified multiple mutations that improved binding affinity, and characterized the structure, affinity, and binding kinetics of a previously reported double mutant that exhibits an impressive 400-fold affinity improvement for the decameric pMHC ligand without detectable binding to non-cognate ligands. The structure of this high affinity mutant indicated very little conformational consequences and emphasized the high fidelity of our modeling procedure. Overall, our work showcases the capability of computational design to generate TCRs with improved pMHC affinities while explicitly accounting for peptide specificity, as well as its potential for generating TCRs with customized antigen targeting capabilities.

  7. Alteration of the α1β2/α2β1 subunit interface contributes to the increased hemoglobin-oxygen affinity of high-altitude deer mice

    Energy Technology Data Exchange (ETDEWEB)

    Inoguchi, Noriko; Mizuno, Nobuhiro; Baba, Seiki; Kumasaka, Takashi; Natarajan, Chandrasekhar; Storz, Jay F.; Moriyama, Hideaki; Permyakov, Eugene A.

    2017-03-31

    Deer mice (Peromyscus maniculatus) that are native to high altitudes in the Rocky Mountains have evolved hemoglobins with an increased oxygen-binding affinity relative to those of lowland conspecifics. To elucidate the molecular mechanisms responsible for the evolved increase in hemoglobin-oxygen affinity, the crystal structure of the highland hemoglobin variant was solved and compared with the previously reported structure for the lowland variant. Highland hemoglobin yielded at least two crystal types, in which the longest axes were 507 and 230 Å. Using the smaller unit cell crystal, the structure was solved at 2.2 Å resolution. The asymmetric unit contained two tetrameric hemoglobin molecules. The analyses revealed that αPro50 in the highland hemoglobin variant promoted a stable interaction between αHis45 and heme that was not seen in the αHis50 lowland variant. The αPro50 mutation also altered the nature of atomic contacts at the α1β2/α2β1 intersubunit interfaces. These results demonstrate how affinity-altering changes in intersubunit interactions can be produced by mutations at structurally remote sites.

  8. Gas phase thermal diffusion of stable isotopes

    International Nuclear Information System (INIS)

    Eck, C.F.

    1979-01-01

    The separation of stable isotopes at Mound Facility is reviewed from a historical perspective. The historical development of thermal diffusion from a laboratory process to a separation facility that handles all the noble gases is described. In addition, elementary thermal diffusion theory and elementary cascade theory are presented along with a brief review of the uses of stable isotopes

  9. physico-chemical and stable isotopes

    African Journals Online (AJOL)

    This paper details the mineralogical, chemical and stable isotope abundances of calcrete in the Letlhakeng fossil valley. The stable isotope abundances (O and C) of calcretes yielded some values which were tested against the nature of the calcretes – pedogenic or groundwater type. The Kgalagadi (Kalahari) is a vast ...

  10. Modelling stable atmospheric boundary layers over snow

    NARCIS (Netherlands)

    Sterk, H.A.M.

    2015-01-01

    Thesis entitled:

    Modelling Stable Atmospheric Boundary Layers over Snow

    H.A.M. Sterk

    Wageningen, 29th of April, 2015

    Summary

    The emphasis of this thesis is on the understanding and forecasting of the Stable Boundary Layer (SBL) over snow-covered surfaces. SBLs

  11. Modelling stable atmospheric boundary layers over snow

    NARCIS (Netherlands)

    Sterk, H.A.M.

    2015-01-01

    Thesis entitled: Modelling Stable Atmospheric Boundary Layers over Snow H.A.M. Sterk Wageningen, 29th of April, 2015 Summary The emphasis of this thesis is on the understanding and forecasting of the Stable Boundary Layer (SBL) over snow-covered surfaces. SBLs typically form at night and in polar

  12. Stable isotopes and biomarkers in microbial ecology

    NARCIS (Netherlands)

    Boschker, H.T.S.; Middelburg, J.J.

    2002-01-01

    The use of biomarkers in combination with stable isotope analysis is a new approach in microbial ecology and a number of papers on a variety of subjects have appeared. We will first discuss the techniques for analysing stable isotopes in biomarkers, primarily gas chromatography-combustion-isotope

  13. Stable Agrobacterium -mediated transformation of the halophytic ...

    African Journals Online (AJOL)

    Stable Agrobacterium-mediated transformation of the halophytic Leymus chinensis (Trin.) Yan-Lin Sun, Soon-Kwan Hong. Abstract. In this study, an efficient procedure for stable Agrobacterium-mediated transformation of Leymus chinensis (Trin.) was established. Agrobacterium tumefaciens strain EHA105, harboring a ...

  14. Computation of the binding affinities of catechol-O-methyltransferase inhibitors: multisubstate relative free energy calculations.

    Science.gov (United States)

    Palma, P Nuno; Bonifácio, Maria João; Loureiro, Ana Isabel; Soares-da-Silva, Patrício

    2012-04-05

    Alchemical free energy simulations are amongst the most accurate techniques for the computation of the free energy changes associated with noncovalent protein-ligand interactions. A procedure is presented to estimate the relative binding free energies of several ligands to the same protein target where multiple, low-energy configurational substates might coexist, as opposed to one unique structure. The contributions of all individual substates were estimated, explicitly, with the free energy perturbation method, and combined in a rigorous fashion to compute the overall relative binding free energies and dissociation constants. It is shown that, unless the most stable bound forms are known a priori, inaccurate results may be obtained if the contributions of multiple substates are ignored. The method was applied to study the complex formed between human catechol-O-methyltransferase and BIA 9-1067, a newly developed tight-binding inhibitor that is currently under clinical evaluation for the therapy of Parkinson's disease. Our results reveal an exceptionally high-binding affinity (K(d) in subpicomolar range) and provide insightful clues on the interactions and mechanism of inhibition. The inhibitor is, itself, a slowly reacting substrate of the target enzyme and is released from the complex in the form of O-methylated product. By comparing the experimental catalytic rate (k(cat)) and the estimated dissociation rate (k(off)) constants of the enzyme-inhibitor complex, one can conclude that the observed inhibition potency (K(i)) is primarily dependent on the catalytic rate constant of the inhibitor's O-methylation, rather than the rate constant of dissociation of the complex. Copyright © 2012 Wiley Periodicals, Inc.

  15. A new method to extract stable feature points based on self-generated simulation images

    Science.gov (United States)

    Long, Fei; Zhou, Bin; Ming, Delie; Tian, Jinwen

    2015-10-01

    Recently, image processing has got a lot of attention in the field of photogrammetry, medical image processing, etc. Matching two or more images of the same scene taken at different times, by different cameras, or from different viewpoints, is a popular and important problem. Feature extraction plays an important part in image matching. Traditional SIFT detectors reject the unstable points by eliminating the low contrast and edge response points. The disadvantage is the need to set the threshold manually. The main idea of this paper is to get the stable extremums by machine learning algorithm. Firstly we use ASIFT approach coupled with the light changes and blur to generate multi-view simulated images, which make up the set of the simulated images of the original image. According to the way of generating simulated images set, affine transformation of each generated image is also known. Instead of the traditional matching process which contain the unstable RANSAC method to get the affine transformation, this approach is more stable and accurate. Secondly we calculate the stability value of the feature points by the set of image with its affine transformation. Then we get the different feature properties of the feature point, such as DOG features, scales, edge point density, etc. Those two form the training set while stability value is the dependent variable and feature property is the independent variable. At last, a process of training by Rank-SVM is taken. We will get a weight vector. In use, based on the feature properties of each points and weight vector calculated by training, we get the sort value of each feature point which refers to the stability value, then we sort the feature points. In conclusion, we applied our algorithm and the original SIFT detectors to test as a comparison. While in different view changes, blurs, illuminations, it comes as no surprise that experimental results show that our algorithm is more efficient.

  16. Structure of acid-stable carmine.

    Science.gov (United States)

    Sugimoto, Naoki; Kawasaki, Yoko; Sato, Kyoko; Aoki, Hiromitsu; Ichi, Takahito; Koda, Takatoshi; Yamazaki, Takeshi; Maitani, Tamio

    2002-02-01

    Acid-stable carmine has recently been distributed in the U.S. market because of its good acid stability, but it is not permitted in Japan. We analyzed and determined the structure of the major pigment in acid-stable carmine, in order to establish an analytical method for it. Carminic acid was transformed into a different type of pigment, named acid-stable carmine, through amination when heated in ammonia solution. The features of the structure were clarified using a model compound, purpurin, in which the orientation of hydroxyl groups on the A ring of the anthraquinone skeleton is the same as that of carminic acid. By spectroscopic means and the synthesis of acid-stable carmine and purpurin derivatives, the structure of the major pigment in acid-stable carmine was established as 4-aminocarminic acid, a novel compound.

  17. Stable Fly, (L., Dispersal and Governing Factors

    Directory of Open Access Journals (Sweden)

    Allan T. Showler

    2015-01-01

    Full Text Available Although the movement of stable fly, Stomoxys calcitrans (L., has been studied, its extent and significance has been uncertain. On a local scale (13 km is mainly wind-driven by weather fronts that carry stable flies from inland farm areas for up to 225 km to beaches of northwestern Florida and Lake Superior. Stable flies can reproduce for a short time each year in washed-up sea grass, but the beaches are not conducive to establishment. Such movement is passive and does not appear to be advantageous to stable fly's survival. On a regional scale, stable flies exhibit little genetic differentiation, and on the global scale, while there might be more than one “lineage”, the species is nevertheless considered to be panmictic. Population expansion across much of the globe likely occurred from the late Pleistocene to the early Holocene in association with the spread of domesticated nomad livestock and particularly with more sedentary, penned livestock.

  18. Phylogenetic affinity of arbuscular mycorrhizal symbionts in Psilotum nudum.

    Science.gov (United States)

    Winther, Jennifer L; Friedman, William E

    2009-09-01

    Many lineages of land plants (from lycopsids to angiosperms) have non-photosynthetic life cycle phases that involve obligate mycoheterotrophic arbuscular mycorrhizal (AM) associations where the plant host gains organic carbon through glomalean symbionts. Our goal was to isolate and phylogenetically identify the AM fungi associated with both the autotrophic and underground mycoheterotrophic life cycle phases of Psilotum nudum. Phylogenetic analyses recovered 11 fungal phylotypes in four diverse clades of Glomus A that form AM associations with P. nudum mycoheterotrophic gametophytes and autotrophic sporophytes, and angiosperm roots found in the same greenhouse pots. The correspondence of identities of AM symbionts in P. nudum sporophytes, gametophytes and neighboring angiosperms provides compelling evidence that photosynthetic heterospecific and conspecific plants can serve as the ultimate sources of fixed carbon for mycoheterotrophic gametophytes of P. nudum, and that the transfer of carbon occurs via shared fungal networks. Moreover, broader phylogenetic analyses suggest greenhouse Psilotum populations, like field-surveyed populations of mycoheterotrophic plants, form AM associations with restricted clades of Glomus A. The phylogenetic affinities and distribution of Glomus A symbionts indicate that P. nudum greenhouse populations have the potential to be exploited as an experimental system to further study the physiology, ecology and evolution of mycoheterotrophic AM associations.

  19. Fast left ventricle tracking using localized anatomical affine optical flow.

    Science.gov (United States)

    Queirós, Sandro; Vilaça, João L; Morais, Pedro; Fonseca, Jaime C; D'hooge, Jan; Barbosa, Daniel

    2017-11-01

    In daily clinical cardiology practice, left ventricle (LV) global and regional function assessment is crucial for disease diagnosis, therapy selection, and patient follow-up. Currently, this is still a time-consuming task, spending valuable human resources. In this work, a novel fast methodology for automatic LV tracking is proposed based on localized anatomically constrained affine optical flow. This novel method can be combined to previously proposed segmentation frameworks or manually delineated surfaces at an initial frame to obtain fully delineated datasets and, thus, assess both global and regional myocardial function. Its feasibility and accuracy were investigated in 3 distinct public databases, namely in realistically simulated 3D ultrasound, clinical 3D echocardiography, and clinical cine cardiac magnetic resonance images. The method showed accurate tracking results in all databases, proving its applicability and accuracy for myocardial function assessment. Moreover, when combined to previous state-of-the-art segmentation frameworks, it outperformed previous tracking strategies in both 3D ultrasound and cardiac magnetic resonance data, automatically computing relevant cardiac indices with smaller biases and narrower limits of agreement compared to reference indices. Simultaneously, the proposed localized tracking method showed to be suitable for online processing, even for 3D motion assessment. Importantly, although here evaluated for LV tracking only, this novel methodology is applicable for tracking of other target structures with minimal adaptations. Copyright © 2017 John Wiley & Sons, Ltd.

  20. Deconstructing Free Energies in the Law of Matching Water Affinities.

    Science.gov (United States)

    Shi, Yu; Beck, Thomas

    2017-03-09

    The law of matching water affinities (LMWA) is explored in classical molecular dynamics simulations of several alkali halide ion pairs, spanning the size range from small kosmotropes to large chaotropes. The ion-ion potentials of mean force (PMFs) are computed using three methods: the local molecular field theory (LMFT), the weighted histogram analysis method (WHAM), and integration of the average force. All three methods produce the same total PMF for a given ion pair. In addition, LMFT-based partitioning into van der Waals and local and far-field electrostatic free energies and assessment of the enthalpic, entropic, and ion-water components yield insights into the origins of the observed free energy profiles in water. The results highlight the importance of local electrostatic interactions in determining the shape of the PMFs, while longer-ranged interactions enhance the overall ion-ion attraction, as expected in a dielectric continuum model. The association equilibrium constants are estimated from the smooth WHAM curves and compared to available experimental conductance data. By examining the variations in the average hydration numbers of ions with ion-ion distance, a correlation of the water structure in the hydration shells with the free energy features is found.

  1. New Insights into Viral Architecture via Affine Extended Symmetry Groups

    Directory of Open Access Journals (Sweden)

    T. Keef

    2008-01-01

    Full Text Available Since the seminal work of Caspar and Klug on the structure of the protein containers that encapsulate and hence protect the viral genome, it has been recognized that icosahedral symmetry is crucial for the structural organization of viruses. In particular, icosahedral symmetry has been invoked in order to predict the surface structures of viral capsids in terms of tessellations or tilings that schematically encode the locations of the protein subunits in the capsids. Whilst this approach is capable of predicting the relative locations of the proteins in the capsids, a prediction on the relative sizes of different virus particles in a family cannot be made. Moreover, information on the full 3D structure of viral particles, including the tertiary structures of the capsid proteins and the organization of the viral genome within the capsid are inaccessible with their approach. We develop here a mathematical framework based on affine extensions of the icosahedral group that allows us to address these issues. In particular, we show that the relative radii of viruses in the family of Polyomaviridae and the material boundaries in simple RNA viruses can be determined with our approach. The results complement Caspar and Klug's theory of quasi-equivalence and provide details on virus structure that have not been accessible with previous methods, implying that icosahedral symmetry is more important for virus architecture than previously appreciated.

  2. 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.

  3. Experimental Immunization Based on Plasmodium Antigens Isolated by Antibody Affinity

    Directory of Open Access Journals (Sweden)

    Ali N. Kamali

    2015-01-01

    Full Text Available 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.

  4. Solubilization and partial characterization of a microsomal high affinity GTPase

    International Nuclear Information System (INIS)

    Nicchitta, C.; Williamson, J.R.

    1987-01-01

    Isolated rat liver microsomes release sequestered Ca 2+ following addition of GTP. In contrast to permeabilized cells, GTP dependent microsomal Ca 2+ release requires low concentrations of polyethylene glycol (PEG). They have identified a microsomal, PEG-sensitive high affinity GTPase which shares a number of characteristics with the GTP-dependent Ca 2+ release system. To aid in further characterization of this activity they have initiated studies on the solubilization and purification of the microsomal GTPases. When microsomes are solubilized under the following conditions (150 mM NaCl, 5 mg protein/ml, 1% Triton X-114) PEG sensitive GTPase activity selectively partitions into the detergent rich phase of the Triton X-114 extract. As observed in intact microsomal membranes the Triton X-114 soluble GTPase is maximally stimulated by 3% PEG. Half maximal stimulation is observed at 1% PEG. PEG increases the Vmax of this activity; no effects on Km were observed. The Km for GTP of the detergent soluble GTPase is 5 μM. This GTPase is sensitive to inhibition by sulfhydryl reagents. PEG-sensitive GTPase activity was completely inhibited in the presence of 25 μM p-hydroxymercuribenzoate (PHMB); half maximal inhibition was observed at 5 μM. Labeling of the Triton X-114 extract with the photosensitive compound [ 32 P] 8-azido GTP indicated the presence of two prominent GTP binding proteins of approximate molecular weights 17 and 54 kD

  5. Methods for determining the genetic affinity of microorganisms and viruses

    Science.gov (United States)

    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.

  6. G4MP2, DFT and CBS-Q calculation of proton and electron affinities ...

    Indian Academy of Sciences (India)

    Proton transfer reactions and ionization are impor- tant processes that play a key role in the atmospheric chemistry and biochemistry.1,2 Proton affinity and gas phase basicity determine the capability of an atom or a molecule to accept a proton in the gas phase. The pro- ton affinity, PA, of a molecule, M, is defined as - H of.

  7. Cyclic Brunn-Minkowski Inequalities for p -affine surface area | Zhao ...

    African Journals Online (AJOL)

    In 2010, Werner and Ye extended the denition for mixed p-affine surface area to all real numbers p. Following this, we establish some isoperimetric inequalities for the general mixed p-affine surface area. The results in special cases yield some of the recent results on inequalities of this type. Mathematics Subject ...

  8. Relative binding affinity of steroids for the corticosterone receptor system in rat hippocampus

    NARCIS (Netherlands)

    De Kloet, E R; Veldhuis, H D; Wagenaars, J L; Bergink, E W

    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,

  9. Joint non-linear ranging and affine synchronization basis for a network of mobile nodes

    NARCIS (Netherlands)

    Rajan, R.T.; Van der Veen, A.J.

    2013-01-01

    Synchronization and localization are critical challenges for the coherent functioning of a wireless network of mobile nodes. In this paper, a novel joint non-linear range and affine time model is presented based on two way time stamp exchanges, extending an existing affine time-range model. For a

  10. Affinity for Quantitative Tools: Undergraduate Marketing Students Moving beyond Quantitative Anxiety

    Science.gov (United States)

    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…

  11. Complementary three-dimensional quantitative structure-activity relationship modeling of binding affinity and functional potency

    DEFF Research Database (Denmark)

    Tosco, Paolo; Ahring, Philip K; Dyhring, Tino

    2009-01-01

    Complementary 3D-QSAR modeling of binding affinity and functional potency is proposed as a tool to pinpoint the molecular features of the ligands, and the corresponding amino acids in the receptor, responsible for high affinity binding vs those driving agonist behavior and receptor activation...

  12. Identification of Thioredoxin Target Disulfides Using Isotope-Coded Affinity Tags

    DEFF Research Database (Denmark)

    Hägglund, Per; Bunkenborg, Jakob; Maeda, Kenji

    2014-01-01

    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...

  13. 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

    2001-01-01

    Similar to native peptide/MHC ligands, bacterial superantigens have been found to bind with low affinity to the T cell receptor (TCR). It has been hypothesized that low ligand affinity is required to allow optimal TCR signaling. To test this, we generated variants of Staphylococcus enterotoxin C3...

  14. G4MP2, DFT and CBS-Q calculation of proton and electron affinities ...

    Indian Academy of Sciences (India)

    Abstract. The proton affinities, gas phase basicities and adiabatic ionization energies and electron affini- ties of some important hydroxylamines and alkanolamines were calculated using B3LYP, CBS-Q and G4MP2 methods. Also, the B3LYP method was used to calculate vertical ionization energies and electron affinities of.

  15. Modeling and analysis of the affinity filtration process, including broth feeding, washing, and elution steps.

    Science.gov (United States)

    He, L Z; Dong, X Y; Sun, Y

    1998-01-01

    Affinity filtration is a developing protein purification technique that combines the high selectivity of affinity chromatography and the high processing speed of membrane filtration. In this work a lumped kinetic model was developed to describe the whole affinity filtration process, including broth feeding, contaminant washing, and elution steps. Affinity filtration experiments were conducted to evaluate the model using bovine serum albumin as a model protein and a highly substituted Blue Sepharose as an affinity adsorbent. The model with nonadjustable parameters agreed fairly to the experimental results. Thus, the performance of the affinity filtration in processing a crude broth containing contaminant proteins was analyzed by computer simulations using the lumped model. The simulation results show that there is an optimal protein loading for obtaining the maximum recovery yield of the desired protein with a constant purity at each operating condition. The concentration of a crude broth is beneficial in increasing the recovery yield of the desired protein. Using a constant amount of the affinity adsorbent, the recovery yield can be enhanced by decreasing the solution volume in the stirred tank due to the increase of the adsorbent weight fraction. It was found that the lumped kinetic model was simple and useful in analyzing the whole affinity filtration process.

  16. Observation and Analysis of Affinity Law Deviations through Tested Performance of Liquefied Gas Reaction Turbines

    Directory of Open Access Journals (Sweden)

    Sarah D. Alison-Youel

    2008-01-01

    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.

  17. Improved methodology for the affinity isolation of human protein complexes expressed at near endogenous levels

    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...

  18. A Combination of Structural and Empirical Analyses Delineates the Key Contacts Mediating Stability and Affinity Increases in an Optimized Biotherapeutic Single-chain Fv (scFv)*

    Science.gov (United States)

    Tu, Chao; Terraube, Virginie; Tam, Amy Sze Pui; Stochaj, Wayne; Fennell, Brian J.; Lin, Laura; Stahl, Mark; LaVallie, Edward R.; Somers, Will; Finlay, William J. J.; Mosyak, Lydia; Bard, Joel; Cunningham, Orla

    2016-01-01

    Fully-human single-chain Fv (scFv) proteins are key potential building blocks of bispecific therapeutic antibodies, but they often suffer from manufacturability and clinical development limitations such as instability and aggregation. The causes of these scFv instability problems, in proteins that should be theoretically stable, remains poorly understood. To inform the future development of such molecules, we carried out a comprehensive structural analysis of the highly stabilized anti-CXCL13 scFv E10. E10 was derived from the parental 3B4 using complementarity-determining region (CDR)-restricted mutagenesis and tailored selection and screening strategies, and carries four mutations in VL-CDR3. High-resolution crystal structures of parental 3B4 and optimized E10 scFvs were solved in the presence and absence of human CXCL13. In parallel, a series of scFv mutants was generated to interrogate the individual contribution of each of the four mutations to stability and affinity improvements. In combination, these analyses demonstrated that the optimization of E10 was primarily mediated by removing clashes between both the VL and the VH, and between the VL and CXCL13. Importantly, a single, germline-encoded VL-CDR3 residue mediated the key difference between the stable and unstable forms of the scFv. This work demonstrates that, aside from being the critical mediators of specificity and affinity, CDRs may also be the primary drivers of biotherapeutic developability. PMID:26515064

  19. Interdomain Linker Determines Primarily the Structural Stability of Dystrophin and Utrophin Tandem Calponin-Homology Domains Rather than Their Actin-Binding Affinity.

    Science.gov (United States)

    Bandi, Swati; Singh, Surinder M; Mallela, Krishna M G

    2015-09-08

    Tandem calponin-homology (CH) domains are the most common actin-binding domains in proteins. However, structural principles underlying their function are poorly understood. These tandem domains exist in multiple conformations with varying degrees of inter-CH-domain interactions. Dystrophin and utrophin tandem CH domains share high sequence similarity (∼82%), yet differ in their structural stability and actin-binding affinity. We examined whether the conformational differences between the two tandem CH domains can explain differences in their stability and actin binding. Dystrophin tandem CH domain is more stable by ∼4 kcal/mol than that of utrophin. Individual CH domains of dystrophin and utrophin have identical structures but differ in their relative orientation around the interdomain linker. We swapped the linkers between dystrophin and utrophin tandem CH domains. Dystrophin tandem CH domain with utrophin linker (DUL) has similar stability as that of utrophin tandem CH domain. Utrophin tandem CH domain with dystrophin linker (UDL) has similar stability as that of dystrophin tandem CH domain. Dystrophin tandem CH domain binds to F-actin ∼30 times weaker than that of utrophin. After linker swapping, DUL has twice the binding affinity as that of dystrophin tandem CH domain. Similarly, UDL has half the binding affinity as that of utrophin tandem CH domain. However, changes in binding free energies due to linker swapping are much lower by an order of magnitude compared to the corresponding changes in unfolding free energies. These results indicate that the linker region determines primarily the structural stability of tandem CH domains rather than their actin-binding affinity.

  20. Purification of phage display-modified bacteriophage T4 by affinity chromatography

    Directory of Open Access Journals (Sweden)

    Figura Grzegorz

    2011-05-01

    Full Text Available Abstract Background Affinity chromatography is one of the most efficient protein purification strategies. This technique comprises a one-step procedure with a purification level in the order of several thousand-fold, adaptable for various proteins, differentiated in their size, shape, charge, and other properties. The aim of this work was to verify the possibility of applying affinity chromatography in bacteriophage purification, with the perspective of therapeutic purposes. T4 is a large, icosahedral phage that may serve as an efficient display platform for foreign peptides or proteins. Here we propose a new method of T4 phage purification by affinity chromatography after its modification with affinity tags (GST and Histag by in vivo phage display. As any permanent introduction of extraneous DNA into a phage genome is strongly unfavourable for medical purposes, integration of foreign motifs with the phage genome was not applied. The phage was propagated in bacteria expressing fusions of the phage protein Hoc with affinity tags from bacterial plasmids, independently from the phage expression system. Results Elution profiles of phages modified with the specific affinity motifs (compared to non-specific phages document their binding to the affinity resins and effective elution with standard competitive agents. Non-specific binding was also observed, but was 102-105 times weaker than the specific one. GST-modified bacteriophages were also effectively released from glutathione Sepharose by proteolytic cleavage. The possibility of proteolytic release was designed at the stage of expression vector construction. Decrease in LPS content in phage preparations was dependent on the washing intensity; intensive washing resulted in preparations of 11-40 EU/ml. Conclusions Affinity tags can be successfully incorporated into the T4 phage capsid by the in vivo phage display technique and they strongly elevate bacteriophage affinity to a specific resin. Affinity

  1. Stable Organic Neutral Diradical via Reversible Coordination.

    Science.gov (United States)

    Lu, Zhenpin; Quanz, Henrik; Burghaus, Olaf; Hofmann, Jonas; Logemann, Christian; Beeck, Sebastian; Schreiner, Peter R; Wegner, Hermann A

    2017-12-27

    We report the formation of a stable neutral diboron diradical simply by coordination of an aromatic dinitrogen compound to an ortho-phenyldiborane. This process is reversible upon addition of pyridine. The diradical species is stable above 200 °C. Computations are consistent with an open-shell triplet diradical with a very small open-shell singlet-triplet energy gap that is indicative of the electronic disjointness of the two radical sites. This opens a new way of generating stable radicals with fascinating electronic properties useful for a large variety of applications.

  2. Synthesis and binding affinity of an iodinated juvenile hormone

    Energy Technology Data Exchange (ETDEWEB)

    Prestwich, G.D.; Eng, W.S.; Robles, S.; Vogt, R.G.; Wisniewski, J.R.; Wawrzenczyk, C.

    1988-01-25

    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 /sup 3/H-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 (/sup 125/I)12-iodo-JH I can be prepared in low yield at greater than 2500 Ci/mmol by nucleophilic displacement using no-carrier-added /sup 125/I-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 (/sup 125/I)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.

  3. Profiling of Parkin-binding partners using tandem affinity purification.

    Directory of Open Access Journals (Sweden)

    Alessandra Zanon

    Full Text Available Parkinson's disease (PD is a progressive neurodegenerative disorder affecting approximately 1-2% of the general population over age 60. It is characterized by a rather selective loss of dopaminergic neurons in the substantia nigra and the presence of α-synuclein-enriched Lewy body inclusions. Mutations in the Parkin gene (PARK2 are the major cause of autosomal recessive early-onset parkinsonism. The Parkin protein is an E3 ubiquitin ligase with various cellular functions, including the induction of mitophagy upon mitochondrial depolarizaton, but the full repertoire of Parkin-binding proteins remains poorly defined. Here we employed tandem affinity purification interaction screens with subsequent mass spectrometry to profile binding partners of Parkin. Using this approach for two different cell types (HEK293T and SH-SY5Y neuronal cells, we identified a total of 203 candidate Parkin-binding proteins. For the candidate proteins and the proteins known to cause heritable forms of parkinsonism, protein-protein interaction data were derived from public databases, and the associated biological processes and pathways were analyzed and compared. Functional similarity between the candidates and the proteins involved in monogenic parkinsonism was investigated, and additional confirmatory evidence was obtained using published genetic interaction data from Drosophila melanogaster. Based on the results of the different analyses, a prioritization score was assigned to each candidate Parkin-binding protein. Two of the top ranking candidates were tested by co-immunoprecipitation, and interaction to Parkin was confirmed for one of them. New candidates for involvement in cell death processes, protein folding, the fission/fusion machinery, and the mitophagy pathway were identified, which provide a resource for further elucidating Parkin function.

  4. Profiling of Parkin-Binding Partners Using Tandem Affinity Purification

    Science.gov (United States)

    Blankenburg, Hagen; Doncheva, Nadezhda T.; Schwienbacher, Christine; Serafin, Alice; Alexa, Adrian; Weichenberger, Christian X.; Albrecht, Mario; Klein, Christine; Hicks, Andrew A.; Pramstaller, Peter P.

    2013-01-01

    Parkinson's disease (PD) is a progressive neurodegenerative disorder affecting approximately 1–2% of the general population over age 60. It is characterized by a rather selective loss of dopaminergic neurons in the substantia nigra and the presence of α-synuclein-enriched Lewy body inclusions. Mutations in the Parkin gene (PARK2) are the major cause of autosomal recessive early-onset parkinsonism. The Parkin protein is an E3 ubiquitin ligase with various cellular functions, including the induction of mitophagy upon mitochondrial depolarizaton, but the full repertoire of Parkin-binding proteins remains poorly defined. Here we employed tandem affinity purification interaction screens with subsequent mass spectrometry to profile binding partners of Parkin. Using this approach for two different cell types (HEK293T and SH-SY5Y neuronal cells), we identified a total of 203 candidate Parkin-binding proteins. For the candidate proteins and the proteins known to cause heritable forms of parkinsonism, protein-protein interaction data were derived from public databases, and the associated biological processes and pathways were analyzed and compared. Functional similarity between the candidates and the proteins involved in monogenic parkinsonism was investigated, and additional confirmatory evidence was obtained using published genetic interaction data from Drosophila melanogaster. Based on the results of the different analyses, a prioritization score was assigned to each candidate Parkin-binding protein. Two of the top ranking candidates were tested by co-immunoprecipitation, and interaction to Parkin was confirmed for one of them. New candidates for involvement in cell death processes, protein folding, the fission/fusion machinery, and the mitophagy pathway were identified, which provide a resource for further elucidating Parkin function. PMID:24244333

  5. Gini covariance matrix and its affine equivariant version

    Science.gov (United States)

    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 (repository. Relying on some graphical and numerical summaries, Gini-based PCA demonstrates its competitive performance.

  6. 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

  7. Stable Isotope Group 1983 progress report

    International Nuclear Information System (INIS)

    Stewart, M.K.

    1984-06-01

    The work of the Stable Isotope Group of the Institute of Nuclear Sciences in the fields of isotope geology, isotope hydrology, geochronology, isotope biology and related fields, and mass spectrometer instrumentation, during 1983, is described

  8. Stable Isotope Group 1982 progress report

    International Nuclear Information System (INIS)

    Stewart, M.K.

    1983-06-01

    The work of the Stable Isotope Group of the Institute of Nuclear Sciences during 1982, in the fields of isotope geology, isotope hydrology, geochronology, isotope biology and mass spectrometer instrumentation, is described

  9. Bartolome Island, Galapagos Stable Oxygen Calibration Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Galapagos Coral Stable Oxygen Calibration Data. Sites: Bartolome Island: 0 deg, 17'S, 90 deg 33' W. Champion Island: 1 deg, 15'S, 90 deg, 05' W. Urvina Bay (Isabela...

  10. Allan Hills Stable Water Isotopes, Version 1

    Data.gov (United States)

    National Aeronautics and Space Administration — This data set includes stable water isotope values at 10 m resolution along an approximately 5 km transect through the main icefield of the Allan Hills Blue Ice...

  11. Applications of stable isotopes in clinical pharmacology

    Science.gov (United States)

    Schellekens, Reinout C A; Stellaard, Frans; Woerdenbag, Herman J; Frijlink, Henderik W; Kosterink, Jos G W

    2011-01-01

    This review aims to present an overview of the application of stable isotope technology in clinical pharmacology. Three main categories of stable isotope technology can be distinguished in clinical pharmacology. Firstly, it is applied in the assessment of drug pharmacology to determine the pharmacokinetic profile or mode of action of a drug substance. Secondly, stable isotopes may be used for the assessment of drug products or drug delivery systems by determination of parameters such as the bioavailability or the release profile. Thirdly, patients may be assessed in relation to patient-specific drug treatment; this concept is often called personalized medicine. In this article, the application of stable isotope technology in the aforementioned three areas is reviewed, with emphasis on developments over the past 25 years. The applications are illustrated with examples from clinical studies in humans. PMID:21801197

  12. Tannaka duality and stable infinity-categories

    OpenAIRE

    Iwanari, Isamu

    2014-01-01

    We introduce the notion of fine tannakian infinity-categories and prove Tannaka duality results for symmetric monoidal stable infinity-categories over a field of characteristic zero. We also discuss several examples.

  13. On Stable Marriages and Greedy Matchings

    Energy Technology Data Exchange (ETDEWEB)

    Manne, Fredrik; Naim, Md; Lerring, Hakon; Halappanavar, Mahantesh

    2016-12-11

    Research on stable marriage problems has a long and mathematically rigorous history, while that of exploiting greedy matchings in combinatorial scientific computing is a younger and less developed research field. In this paper we consider the relationships between these two areas. In particular we show that several problems related to computing greedy matchings can be formulated as stable marriage problems and as a consequence several recently proposed algorithms for computing greedy matchings are in fact special cases of well known algorithms for the stable marriage problem. However, in terms of implementations and practical scalable solutions on modern hardware, the greedy matching community has made considerable progress. We show that due to the strong relationship between these two fields many of these results are also applicable for solving stable marriage problems.

  14. The Reactivity of Stable Metallacyclobutenes and Vinylcarbenes

    OpenAIRE

    Holland, Ryan Lynn

    2016-01-01

    Chapter 1. Historical Development of Stable Metallacyclobutenes Fred Tebbe and co-workers synthesized the first stable metallacyclobutene complexes in the late 1970’s by treatment of an intermediate titanium methylene species – later popularized as the “Tebbe reagent” – with acetylenes. Robert Grubbs at Caltech further studied this system, using it to detail a degenerate metathesis reaction and to isolate a metallacyclobutane complex – which was implicated in the emerging field of alkene meta...

  15. Stable atomic hydrogen: Polarized atomic beam source

    International Nuclear Information System (INIS)

    Niinikoski, T.O.; Penttilae, S.; Rieubland, J.M.; Rijllart, A.

    1984-01-01

    We have carried out experiments with stable atomic hydrogen with a view to possible applications in polarized targets or polarized atomic beam sources. Recent results from the stabilization apparatus are described. The first stable atomic hydrogen beam source based on the microwave extraction method (which is being tested ) is presented. The effect of the stabilized hydrogen gas density on the properties of the source is discussed. (orig.)

  16. Quantitative Prediction of Multivalent Ligand-Receptor Binding Affinities for Influenza, Cholera, and Anthrax Inhibition.

    Science.gov (United States)

    Liese, Susanne; Netz, Roland R

    2018-03-05

    Multivalency achieves strong, yet reversible binding by the simultaneous formation of multiple weak bonds. It is a key interaction principle in biology and promising for the synthesis of high-affinity inhibitors of pathogens. We present a molecular model for the binding affinity of synthetic multivalent ligands onto multivalent receptors consisting of n receptor units arranged on a regular polygon. Ligands consist of a geometrically matching rigid polygonal core to which monovalent ligand units are attached via flexible linker polymers, closely mimicking existing experimental designs. The calculated binding affinities quantitatively agree with experimental studies for cholera toxin ( n = 5) and anthrax receptor ( n = 7) and allow to predict optimal core size and optimal linker length. Maximal binding affinity is achieved for a core that matches the receptor size and for linkers that have an equilibrium end-to-end distance that is slightly longer than the geometric separation between ligand core and receptor sites. Linkers that are longer than optimal are greatly preferable compared to shorter linkers. The angular steric restriction between ligand unit and linker polymer is shown to be a key parameter. We construct an enhancement diagram that quantifies the multivalent binding affinity compared to monovalent ligands. We conclude that multivalent ligands against influenza viral hemagglutinin ( n = 3), cholera toxin ( n = 5), and anthrax receptor ( n = 7) can outperform monovalent ligands only for a monovalent ligand affinity that exceeds a core-size dependent threshold value. Thus, multivalent drug design needs to balance core size, linker length, as well as monovalent ligand unit affinity.

  17. Identification of an adeno-associated virus binding epitope for AVB sepharose affinity resin

    Directory of Open Access Journals (Sweden)

    Qiang Wang

    Full Text Available Recent successes of adeno-associated virus (AAV–based gene therapy have created a demand for large-scale AAV vector manufacturing and purification techniques for use in clinical trials and beyond. During the development of purification protocols for rh.10, hu.37, AAV8, rh.64R1, AAV3B, and AAV9 vectors, based on a widely used affinity resin, AVB sepharose (GE, we found that, under the same conditions, different serotypes have different affinities to the resin, with AAV3B binding the best and AAV9 the poorest. Further analysis revealed a surface-exposed residue (amino acid number 665 in AAV8 VP1 numbering differs between the high-affinity AAV serotypes (serine in AAV3B, rh.10, and hu.37 and the low-affinity ones (asparagine in AAV8, rh.64R1, and AAV9. The residue locates within a surface-exposed, variable epitope flanked by highly conserved residues. The substitution of the epitope in AAV8, rh.64R1, and AAV9 with the corresponding epitope of AAV3B (SPAKFA resulted in greatly increased affinity to AVB sepharose with no reduction in the vectors’ in vitro potency. The presence of the newly identified AVB-binding epitope will be useful for affinity resin selection for the purification of novel AAV serotypes. It also suggests the possibility of vector engineering to yield a universal affinity chromatography purification method for multiple AAV serotypes.

  18. Production and Characterization of Desmalonichrome Relative Binding Affinity for Uranyl Ions in Relation to Other Siderophores

    Energy Technology Data Exchange (ETDEWEB)

    Mo, Kai-For; Dai, Ziyu; Wunschel, David S.

    2016-06-24

    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.

  19. Methyl cation affinities of neutral and anionic maingroup-element hydrides: trends across the periodic table and correlation with proton affinities.

    Science.gov (United States)

    Mulder, R Joshua; Guerra, Célia Fonseca; Bickelhaupt, F Matthias

    2010-07-22

    We have computed the methyl cation affinities in the gas phase of archetypal anionic and neutral bases across the periodic table using ZORA-relativistic density functional theory (DFT) at BP86/QZ4P//BP86/TZ2P. The main purpose of this work is to provide the methyl cation affinities (and corresponding entropies) at 298 K of all anionic (XH(n-1)(-)) and neutral bases (XH(n)) constituted by maingroup-element hydrides of groups 14-17 and the noble gases (i.e., group 18) along the periods 2-6. The cation affinity of the bases decreases from H(+) to CH(3)(+). To understand this trend, we have carried out quantitative bond energy decomposition analyses (EDA). Quantitative correlations are established between the MCA and PA values.

  20. Affinity of Iresine herbstii and Brugmansia arborea extracts on different cerebral receptors.

    Science.gov (United States)

    Nencini, Cristina; Cavallo, Federica; Bruni, Giancarlo; Capasso, Anna; De Feo, Vincenzo; De Martino, Laura; Giorgi, Giorgio; Micheli, Lucia

    2006-05-24

    Iresine herbstii Hook. (Amaranthaceae) and Brugmansia arborea (L.) Lagerheim (Solanaceae) are used in the northern Peruvian Andes for magic-therapeutical purposes. The traditional healers use Iresine herbstii with the ritual aim to expel bad spirits from the body. Furthermore, Iresine herbstii was used in association with other plants, such as Trichocereus pachanoi Britt. et Rose, for divination, to diagnose diseases, and to take possession of another identity. Also, species of Brugmansia have been reported to be used during ritual practices for magical and curative purposes. Given the above evidence, the aim of the present study is to evaluate if the central effects of Iresine herbstii and Brugmansia arborea could be associated with interaction with SNC receptors. Two Iresine herbstii extracts (methanolic and aqueous) and one Brugmansia arborea aqueous extract were tested for in vitro affinity on 5-HT(1A), 5-HT(2A), 5-HT(2C), D1, D2, alpha(1), and alpha(2) receptors by radioligand binding assays. The biological materials for binding assay (cerebral cortex) were taken from male Sprague-Dawley rats. The extracts affinity for receptors is definite as inhibition percentage of radioligand/receptor binding and measured as the radioactivity of remaining complex radioligand/receptor. The data obtained for Iresine extracts have shown a low affinity for the 5-HT(1A) receptor and no affinity for 5-HT(2A) receptor. Otherwise the methanolic extract showed affinity for 5-HT(2C) receptor (IC(50): 34.78 microg/ml) and for D1 receptor (IC(50): 19.63 microg/ml), instead the Iresine aqueous extract displayed a lower affinity for D1 (48.3% at the maximum concentration tested) and a higher value of affinity for D2 receptors (IC(50): 32.08 microg/ml). The Brugmansia aqueous extract displayed affinity for D1 receptors (IC(50): 17.68 microg/ml), D2 receptors (IC(50): 15.95 microg/ml) and weak affinity for the serotoninergic receptors. None of the three extracts showed relevant affinity

  1. Constraints on the affinity term for modeling long-term glass dissolution rates

    International Nuclear Information System (INIS)

    Bourcier, W.L.; Carroll, S.A.; Phillips, B.L.

    1993-11-01

    Predictions of long-term glass dissolution rates are highly dependent on the form of the affinity term in the rate expression. Analysis of the quantitative effect of saturation state on glass dissolution rate for CSG glass (a simple analog of SRL-165 glass), shows that a simple (1-Q/K) affinity term does not match experimental results. Our data at 100 degree C show that the data is better fit by an affinity term having the form (1 - (Q/K) 1 /σ) where σ = 10

  2. The Effect of Volcanic Ash Composition on Ice Nucleation Affinity

    Science.gov (United States)

    Genareau, K. D.; Cloer, S.; Primm, K.; Woods, T.; Tolbert, M. A.

    2017-12-01

    Understanding the role that volcanic ash plays in ice nucleation is important for knowledge of lightning generation in both volcanic plumes and in clouds developing downwind from active volcanoes. Volcanic ash has long been suggested to influence heterogeneous ice nucleation following explosive eruptions, but determining precisely how composition and mineralogy affects ice nucleation affinity (INA) is poorly constrained. For the study presented here, volcanic ash samples with different compositions and mineral/glass contents were tested in both the deposition and immersion modes, following the methods presented in Schill et al. (2015). Bulk composition was determined with X-ray fluorescence (XRF), grain size distribution was determined with laser diffraction particle size analysis (LDPSA), and mineralogy was determined with X-ray diffraction (XRD) and scanning electron microscopy (SEM). Results of the deposition-mode experiments reveal that there is no relationship between ice saturation ratios (Sice) and either mineralogy or bulk ash composition, as all samples have similar Sice ratios. In the immersion-mode experiments, frozen fractions were determined from -20 °C to -50 °C using three different amounts of ash (0.5, 1.0, and 2.0 wt% of slurry). Results from the immersion freezing reveal that the rhyolitic samples (73 wt% SiO2) nucleate ice at higher temperatures compared to the basaltic samples (49 wt% SiO2). There is no observed correlation between frozen fractions and mineral content of ash samples, but the two most efficient ice nuclei are rhyolites that contain the greatest proportion of amorphous glass (> 90 %), and are enriched in K2O relative to transition metals (MnO and TiO2), the latter of which show a negative correlation with frozen fraction. Higher ash abundance in water droplets increases the frozen fraction at all temperatures, indicating that ash amount plays the biggest role in ice nucleation. If volcanic ash can reach sufficient abundance (

  3. Local Search Approaches in Stable Matching Problems

    Directory of Open Access Journals (Sweden)

    Toby Walsh

    2013-10-01

    Full Text Available The stable marriage (SM problem has a wide variety of practical applications, ranging from matching resident doctors to hospitals, to matching students to schools or, more generally, to any two-sided market. In the classical formulation, n men and n women express their preferences (via a strict total order over the members of the other sex. Solving an SM problem means finding a stable marriage where stability is an envy-free notion: no man and woman who are not married to each other would both prefer each other to their partners or to being single. We consider both the classical stable marriage problem and one of its useful variations (denoted SMTI (Stable Marriage with Ties and Incomplete lists where the men and women express their preferences in the form of an incomplete preference list with ties over a subset of the members of the other sex. Matchings are permitted only with people who appear in these preference lists, and we try to find a stable matching that marries as many people as possible. Whilst the SM problem is polynomial to solve, the SMTI problem is NP-hard. We propose to tackle both problems via a local search approach, which exploits properties of the problems to reduce the size of the neighborhood and to make local moves efficiently. We empirically evaluate our algorithm for SM problems by measuring its runtime behavior and its ability to sample the lattice of all possible stable marriages. We evaluate our algorithm for SMTI problems in terms of both its runtime behavior and its ability to find a maximum cardinality stable marriage. Experimental results suggest that for SM problems, the number of steps of our algorithm grows only as O(n log(n, and that it samples very well the set of all stable marriages. It is thus a fair and efficient approach to generate stable marriages. Furthermore, our approach for SMTI problems is able to solve large problems, quickly returning stable matchings of large and often optimal size, despite the

  4. Stable chaos in fluctuation driven neural circuits

    International Nuclear Information System (INIS)

    Angulo-Garcia, David; Torcini, Alessandro

    2014-01-01

    Highlights: • Nonlinear instabilities in fluctuation driven (balanced) neural circuits are studied. • Balanced networks display chaos and stable phases at different post-synaptic widths. • Linear instabilities coexists with nonlinear ones in the chaotic regime. • Erratic motion appears also in linearly stable phase due to stable chaos. - Abstract: We study the dynamical stability of pulse coupled networks of leaky integrate-and-fire neurons against infinitesimal and finite perturbations. In particular, we compare mean versus fluctuations driven networks, the former (latter) is realized by considering purely excitatory (inhibitory) sparse neural circuits. In the excitatory case the instabilities of the system can be completely captured by an usual linear stability (Lyapunov) analysis, whereas the inhibitory networks can display the coexistence of linear and nonlinear instabilities. The nonlinear effects are associated to finite amplitude instabilities, which have been characterized in terms of suitable indicators. For inhibitory coupling one observes a transition from chaotic to non chaotic dynamics by decreasing the pulse-width. For sufficiently fast synapses the system, despite showing an erratic evolution, is linearly stable, thus representing a prototypical example of stable chaos

  5. Metabolic studies in man using stable isotopes

    International Nuclear Information System (INIS)

    Faust, H.; Jung, K.; Krumbiegel, P.

    1993-01-01

    In this project, stable isotope compounds and stable isotope pharmaceuticals were used (with emphasis on the application of 15 N) to study several aspects of nitrogen metabolism in man. Of the many methods available, the 15 N stable isotope tracer technique holds a special position because the methodology for application and nitrogen isotope analysis is proven and reliable. Valid routine methods using 15 N analysis by emission spectrometry have been demonstrated. Several methods for the preparation of biological material were developed during our participation in the Coordinated Research Programme. In these studies, direct procedures (i.e. use of diluted urine as a samples without chemical preparation) or rapid isolation methods were favoured. Within the scope of the Analytical Quality Control Service (AQCS) enriched stable isotope reference materials for medical and biological studies were prepared and are now available through the International Atomic Energy Agency. The materials are of special importance as the increasing application of stable isotopes as tracers in medical, biological and agricultural studies has focused interest on reliable measurements of biological material of different origin. 24 refs

  6. Improving the convergence rate in affine registration of PET and SPECT brain images using histogram equalization.

    Science.gov (United States)

    Salas-Gonzalez, D; Górriz, J M; Ramírez, J; Padilla, P; Illán, I A

    2013-01-01

    A procedure to improve the convergence rate for affine registration methods of medical brain images when the images differ greatly from the template is presented. The methodology is based on a histogram matching of the source images with respect to the reference brain template before proceeding with the affine registration. The preprocessed source brain images are spatially normalized to a template using a general affine model with 12 parameters. A sum of squared differences between the source images and the template is considered as objective function, and a Gauss-Newton optimization algorithm is used to find the minimum of the cost function. Using histogram equalization as a preprocessing step improves the convergence rate in the affine registration algorithm of brain images as we show in this work using SPECT and PET brain images.

  7. 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.

  8. Class of the affine line is a zero divisor in the Grothendieck ring

    OpenAIRE

    Borisov, Lev

    2014-01-01

    We show that the class of the affine line is a zero divisor in the Grothendieck ring of algebraic varieties over complex numbers. The argument is based on the Pfaffian-Grassmannian double mirror correspondence.

  9. Biochemical method for fast affinity diagnosis in grape-vine transplantation

    International Nuclear Information System (INIS)

    Lilov, D.

    1977-01-01

    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 15 N 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)

  10. Calculation of Absolute Protein-Ligand Binding Affinity Using Path and Endpoint Approaches

    National Research Council Canada - National Science Library

    Lee, Michael S; Olson, Mark A

    2006-01-01

    .... The results of this approach agree well with experimentally observed binding affinities. Also assessed is a commonly used approximate endpoint approach, which separately estimates enthalpy, solvation free energy, and entropy...

  11. 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.

  12. Multivariate assessment of the phenetic affinities of Australasian oystercatchers (Aves: Charadriiformes)

    NARCIS (Netherlands)

    Baker, Allan J.

    1977-01-01

    Phenetic affinities of Australasian oystercatchers were elucidated by multivariate statistical analysis of seven morphometric characters taken from museum skins. Nineteen operational taxonomie units (OTUs), representing all the currently recognized species and most of the subordinate taxa, were used

  13. The Binding of Biotin to Sepharose-Avidin Column: Demonstration of the Affinity Chromatography Technique

    Science.gov (United States)

    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)

  14. Quantum image encryption based on generalized affine transform and logistic map

    Science.gov (United States)

    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.

  15. Bulk is a determinant of oxymetazoline affinity for the alpha1A-adrenergic receptor.

    Science.gov (United States)

    McCune, Dan; Gaivin, Robert; Rorabaugh, Boyd; Perez, Dianne

    2004-01-01

    The alpha1A-adrenergic receptor (AR) has a higher affinity for several agonists and antagonists compared to alpha1B or alpha1D ARs. Mutagenesis studies were used to determine residues potentially responsible for this subtype selectivity. Oxymetazoline has a 50-fold lower affinity for alpha1D ARs compared to alpha1A ARs and also displayed a significant loss of affinity for an alpha1A Leu-290 to Phe mutant. It was concluded that steric interactions between the alpha1D ARs Phe-360 and the bulkytert-butyl group of oxymetazoline partially accounts for this lower affinity. Thus, the alpha1A AR binding pocket may more easily accommodate bulk at the paraposition of the phenyl ring than the alpha1D AR.

  16. Affinity-Selected Filamentous Bacteriophage as a Probe for Acoustic Wave Biodetectors of Salmonella typhimurium

    National Research Council Canada - National Science Library

    Olsen, Eric V; Sorokulova, Iryna B; Petrenko, Valery A; Chen, I-Hsuan; Barbaree, James M; Vodyanoy, Vitaly J

    2005-01-01

    Proof-in-concept biosensors were prepared for the rapid detection of Salmonella typhimurium in solution, based on affinity-selected filamentous phage prepared as probes physically adsorbed to piezoelectric transducers...

  17. Purification of a Mycoplasma pneumoniae adhesin by monoclonal antibody affinity chromatography.

    OpenAIRE

    Leith, D K; Baseman, J B

    1984-01-01

    A 165,000-dalton surface protein of Mycoplasma pneumoniae, designated protein P1, appears to be the major attachment ligand of the pathogen. We employed monoclonal antibody affinity chromatography to obtain purified protein P1.

  18. Equisetum hyemale L. var. affine (Engelm.) A.A. Eaton in Schoorl

    NARCIS (Netherlands)

    Swolfs, Aart G.

    1996-01-01

    A giant form of the Northamerican Equisetum hyemale var. affine has been planted a decade ago near the coast, where it has naturalized since. It is suggested that other Northamerican introductions of this extremely variable taxon may have remained unnoticed.

  19. Preparation of monolithic affinity media for nano-liquid chromatography applications.

    Science.gov (United States)

    Sproß, Jens; Sinz, Andrea

    2014-01-01

    In this protocol, a strategy is described for preparing affinity media with monolithic materials as stationary phase, which is exemplified for the biotin-avidin interaction pair. The capillary columns prepared in this manner are compatible with nano-liquid chromatographic conditions. Our protocol is easily adapted to the preparation of specific affinity media with different functionalities and as such provides a platform for a multitude of applications.

  20. Determination of High-affinity Antibody-antigen Binding Kinetics Using Four Biosensor Platforms

    OpenAIRE

    Yang, Danlin; Singh, Ajit; Wu, Helen; Kroe-Barrett, Rachel

    2017-01-01

    Label-free optical biosensors are powerful tools in drug discovery for the characterization of biomolecular interactions. In this study, we describe the use of four routinely used biosensor platforms in our laboratory to evaluate the binding affinity and kinetics of ten high-affinity monoclonal antibodies (mAbs) against human proprotein convertase subtilisin kexin type 9 (PCSK9). While both Biacore T100 and ProteOn XPR36 are derived from the well-established Surface Plasmon Resonance (SPR) te...

  1. Market price of risk specifications for affine models: Theory and evidence

    OpenAIRE

    Filipovic, Damir; Cheridito, P.; Kimmel, R. L.

    2007-01-01

    We extend the standard specification of the market price of risk for affine yield models, and apply it to U.S. Treasury data. Our specification often provides better fit, sometimes with very high statistical significance. The improved fit comes from the time-series rather than cross-sectional features of the yield curve. We derive conditions under which our specification does not admit arbitrage opportunities. The extension has extremely strong statistical significance for affine yield models...

  2. 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....

  3. APPLICATION OF IMMUNOGLOBULIN-BINDING PROTEINS A, G, L IN THE AFFINITY CHROMATOGRAPHY

    Directory of Open Access Journals (Sweden)

    О. V. Sviatenko

    2014-04-01

    Full Text Available 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 specificities and affinities of these proteins differ between species and antibody subclass. Protein А has high affinity to human IgG1, IgG2, IgG4, mouse IgG2a, IgG2b, IgG3, goat and sheep IgG2, dog, cat, guinea pig, rabbit IgG. Protein G binds strongly to human, mouse, cow, goat, sheep and rabbit IgG. Protein L has ability of strong binding to immunoglobulin kappa-chains of human, mouse, rat and pig. Expediency of application of affinity chromatography with usage of sorbents on the basis of immobilized proteins A, G, L are shown for isolation and purification of antibodies different classes. Previously mentioned method is used as an alternative to conventional methods of protein purification, such as ion-exchange, hydrophobic interactions, metal affinity chromatography, ethanol precipitation due to simplicity in usage, possibility of one-step purification process, obtaining of proteins high level purity, multiuse at maintenance of proper storage and usage conditions. Affinity sorbents on the basis of immobilized proteins A, G, L are used not only for antibodies purification, but also for extraction of different antibodies fractions from blood serum.

  4. An Affine Combination of Adaptive Filters for Channels with Different Sparsity Levels

    Directory of Open Access Journals (Sweden)

    M. Butsenko

    2016-06-01

    Full Text Available In this paper we present an affine combination strategy for two adaptive filters. One filter is designed to handle sparse impulse responses and the other one performs better if impulse response is dispersive. Filter outputs are combined using an adaptive mixing parameter and the resulting output shows a better performance than each of the combining filters separately. We also demonstrate that affine combination results in faster convergence than a convex combination of two adaptive filters.

  5. High-Aluminum-Affinity Silica Is a Nanoparticle That Seeds Secondary Aluminosilicate Formation

    OpenAIRE

    Jugdaohsingh, Ravin; Brown, Andy; Dietzel, Martin; Powell, Jonathan J.

    2013-01-01

    Despite the importance and abundance of aluminosilicates throughout our natural surroundings, their formation at neutral pH is, surprisingly, a matter of considerable debate. From our experiments in dilute aluminum and silica containing solutions (pH ~ 7) we previously identified a silica polymer with an extraordinarily high affinity for aluminium ions (high-aluminum-affinity silica polymer, HSP). Here, further characterization shows that HSP is a colloid of approximately 2.4 nm in diameter w...

  6. Affinity capillary electrophoresis method for investigation of bile salts complexation with sulfobutyl ether-ß-cyclodextrin

    DEFF Research Database (Denmark)

    Østergaard, Jesper; Jensen, Henrik; Holm, Rene

    2012-01-01

    an 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...

  7. Inhaled nitric oxide augments nitric oxide transport on sickle cell hemoglobin without affecting oxygen affinity

    OpenAIRE

    Gladwin, Mark T.; Schechter, Alan N.; Shelhamer, James H.; Pannell, Lewis K.; Conway, Deirdre A.; Hrinczenko, Borys W.; Nichols, James S.; Pease-Fye, Margaret E.; Noguchi, Constance T.; Rodgers, Griffin P.; Ognibene, Frederick P.

    1999-01-01

    Nitric oxide (NO) inhalation has been reported to increase the oxygen affinity of sickle cell erythrocytes. Also, proposed allosteric mechanisms for hemoglobin, based on S-nitrosation of β-chain cysteine 93, raise the possibilty of altering the pathophysiology of sickle cell disease by inhibiting polymerization or by increasing NO delivery to the tissue. We studied the effects of a 2-hour treatment, using varying concentrations of inhaled NO. Oxygen affinity, as measured by P50, did not respo...

  8. Surface treatment of silica nanoparticles for stable and charge-controlled colloidal silica

    Science.gov (United States)

    Kim, Kyoung-Min; Kim, Hye Min; Lee, Won-Jae; Lee, Chang-Woo; Kim, Tae-il; Lee, Jong-Kwon; Jeong, Jayoung; Paek, Seung-Min; Oh, Jae-Min

    2014-01-01

    An attempt was made to control the surface charge of colloidal silica nanoparticles with 20 nm and 100 nm diameters. Untreated silica nanoparticles were determined to be highly negatively charged and have stable hydrodynamic sizes in a wide pH range. To change the surface to a positively charged form, various coating agents, such as amine containing molecules, multivalent metal cation, or amino acids, were used to treat the colloidal silica nanoparticles. Molecules with chelating amine sites were determined to have high affinity with the silica surface to make agglomerations or gel-like networks. Amino acid coatings resulted in relatively stable silica colloids with a modified surface charge. Three amino acid moiety coatings (L-serine, L-histidine, and L-arginine) exhibited surface charge modifying efficacy of L-histidine > L-arginine > L-serine and hydrodynamic size preservation efficacy of L-serine > L-arginine > L-histidine. The time dependent change in L-arginine coated colloidal silica was investigated by measuring the pattern of the backscattered light in a Turbiscan™. The results indicated that both the 20 nm and 100 nm L-arginine coated silica samples were fairly stable in terms of colloidal homogeneity, showing only slight coalescence and sedimentation. PMID:25565824

  9. HYDROLYSIS OF STARCH BY THERMO-AND PH-STABLE GLUCOAMYLASE AT CHANGE PHYSICO-CHEMICAL FACTORS

    Directory of Open Access Journals (Sweden)

    V. S. Grigirov

    2013-01-01

    Full Text Available Regularity of the change rate of the enzymatic reactions depending on different temperatures, pH values in the formation and decay of the enzyme-substrate complex was investigated. Found that the kinetics of hydrolysis of starch by the action of heat and pH stable glucoamylases is complex as evidenced by the change in the value Km, which is a measure of the affinity of the enzyme to the substrate, active centers studied glucoamylases and starch undergo conformational changes at pH 4,0-5,0; 4,5-5,5 and a temperature of 60-65 °C.

  10. Temperature and Humidity Control in Livestock Stables

    DEFF Research Database (Denmark)

    Hansen, Michael; Andersen, Palle; Nielsen, Kirsten M.

    2010-01-01

    The paper describes temperature and humidity control of a livestock stable. It is important to have a correct air flow pattern in the livestock stable in order to achieve proper temperature and humidity control as well as to avoid draught. In the investigated livestock stable the air flow...... is controlled using wall mounted ventilation flaps. In the paper an algorithm for air flow control is presented meeting the needs for temperature and humidity while taking the air flow pattern in consideration. To obtain simple and realisable controllers a model based control design method is applied....... In the design dynamic models for temperature and humidity are very important elements and effort is put into deriving and testing the models. It turns out that non-linearities are dominating in both models making feedback linearization the natural design method. The air controller as well as the temperature...

  11. On some topological properties of stable measures

    DEFF Research Database (Denmark)

    Nielsen, Carsten Krabbe

    1996-01-01

    Summary The paper shows that the set of stable probability measures and the set of Rational Beliefs relative to a given stationary measure are closed in the strong topology, but not closed in the topology of weak convergence. However, subsets of the set of stable probability measures which...... are characterized by uniformity of convergence of the empirical distribution are closed in the topology of weak convergence. It is demonstrated that such subsets exist. In particular, there is an increasing sequence of sets of SIDS measures who's union is the set of all SIDS measures generated by a particular...... system and such that each subset consists of stable measures. The uniformity requirement has a natural interpretation in terms of plausibility of Rational Beliefs...

  12. Concentration of stable elements in food products

    Energy Technology Data Exchange (ETDEWEB)

    Montford, M.A.; Shank, K.E.; Hendricks, C.; Oakes, T.W.

    1980-01-01

    Food samples were taken from commercial markets and analyzed for stable element content. The concentrations of most stable elements (Ag, Al, As, Au, Ba, Br, Ca, Ce, Cl, Co, Cr, Cs, Cu, Fe, Hf, I, K, La, Mg, Mn, Mo, Na, Rb, Sb, Sc, Se, Sr, Ta, Th, Ti, V, Zn, Zr) were determined using multiple-element neutron activation analysis, while the concentrations of other elements (Cd, Hg, Ni, Pb) were determined using atomic absorption. The relevance of the concentrations found are noted in relation to other literature values. An earlier study was extended to include the determination of the concentration of stable elements in home-grown products in the vicinity of the Oak Ridge National Laboratory. Comparisons between the commercial and local food-stuff values are discussed.

  13. Insights into the Structural Basis of Antibody Affinity Maturation from Next-Generation Sequencing

    Directory of Open Access Journals (Sweden)

    Arjun K. Mishra

    2018-02-01

    Full Text Available Affinity maturation is the process whereby the immune system generates antibodies of higher affinities during a response to antigen. It is unique in being the only evolutionary mechanism known to operate on a molecule in an organism’s own body. Deciphering the structural mechanisms through which somatic mutations in antibody genes increase affinity is critical to understanding the evolution of immune repertoires. Next-generation sequencing (NGS has allowed the reconstruction of antibody clonal lineages in response to viral pathogens, such as HIV-1, which was not possible in earlier studies of affinity maturation. Crystal structures of antibodies from these lineages bound to their target antigens have revealed, at the atomic level, how antibodies evolve to penetrate the glycan shield of envelope glycoproteins, and how viruses in turn evolve to escape neutralization. Collectively, structural studies of affinity maturation have shown that increased antibody affinity can arise from any one or any combination of multiple diverse mechanisms, including improved shape complementarity at the interface with antigen, increased buried surface area upon complex formation, additional interfacial polar or hydrophobic interactions, and preorganization or rigidification of the antigen-binding site.

  14. The Affinity of Elongated Membrane-Tethered Ligands Determines Potency of T Cell Receptor Triggering

    Directory of Open Access Journals (Sweden)

    Bing-Mae Chen

    2017-07-01

    Full Text Available T lymphocytes are important mediators of adoptive immunity but the mechanism of T cell receptor (TCR triggering remains uncertain. The interspatial distance between engaged T cells and antigen-presenting cells (APCs is believed to be important for topological rearrangement of membrane tyrosine phosphatases and initiation of TCR signaling. We investigated the relationship between ligand topology and affinity by generating a series of artificial APCs that express membrane-tethered anti-CD3 scFv with different affinities (OKT3, BC3, and 2C11 in addition to recombinant class I and II pMHC molecules. The dimensions of membrane-tethered anti-CD3 and pMHC molecules were progressively increased by insertion of different extracellular domains. In agreement with previous studies, elongation of pMHC molecules or low-affinity anti-CD3 scFv caused progressive loss of T cell activation. However, elongation of high-affinity ligands (BC3 and OKT3 scFv did not abolish TCR phosphorylation and T cell activation. Mutation of key amino acids in OKT3 to reduce binding affinity to CD3 resulted in restoration of topological dependence on T cell activation. Our results show that high-affinity TCR ligands can effectively induce TCR triggering even at large interspatial distances between T cells and APCs.

  15. 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......(+),K(+)-ATPase was studied in total membranes from rat muscle and purified membranes from muscle with different fiber types. The Na(+) affinity was higher (K(m) lower) in oxidative muscle compared with glycolytic muscle and in purified membranes from oxidative muscle compared with glycolytic muscle. Na......(+),K(+)-ATPase isoform analysis implied that heterodimers containing the beta(1) isoform have a higher Na(+) affinity than heterodimers containing the beta(2) isoform. Immunoprecipitation experiments demonstrated that dimers with alpha(1) are responsible for approximately 36% of the total Na,K-ATPase activity. Selective...

  16. Cadmium accumulation characteristics of the winter farmland weeds Cardamine hirsuta Linn. and Gnaphalium affine D. Don.

    Science.gov (United States)

    Lin, Lijin; Shi, Jun; Liu, Qihua; Liao, Ming'an; Mei, Luoyin

    2014-07-01

    In a preliminary study, we found that the cadmium (Cd) concentrations in shoots of the winter farmland weeds Cardamine hirsuta Linn. and Gnaphalium affine D. Don exceeded the critical value of a Cd-hyperaccumulator (100 mg kg(-1)), indicating that these two farmland weeds might be Cd-hyperaccumulators. In this study, we grew these species in soil containing various concentrations of Cd to further evaluate their Cd accumulation characteristics. The biomasses of C. hirsuta and G. affine decreased with increasing Cd concentrations in the soil, while the root/shoot ratio and the Cd concentrations in shoot tissues increased. The Cd concentrations in shoots of C. hirsuta and G. affine reached 121.96 and 143.91 mg kg(-1), respectively, at the soil Cd concentration of 50 mg kg(-1). Both of these concentrations exceeded the critical value of a Cd-hyperaccumulator (100 mg kg(-1)). The shoot bioconcentration factors of C. hirsuta and G. affine were greater than 1. The translocation factor of C. hirsuta was less than 1 and that of G. affine was greater than 1. These findings indicated that C. hirsuta is a Cd-accumulator and G. affine is Cd-hyperaccumulator. Both plants are distributed widely in the field, and they could be used to remediate Cd-contaminated farmland soil in winter.

  17. Food and value motivation: Linking consumer affinities to different types of food products.

    Science.gov (United States)

    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. Copyright © 2016 Elsevier Ltd. All rights reserved.

  18. A Novel Affinity Tag, ABTAG, and Its Application to the Affinity Screening of Single-Domain Antibodies Selected by Phage Display

    Directory of Open Access Journals (Sweden)

    Greg Hussack

    2017-10-01

    Full Text Available ABTAG is a camelid single-domain antibody (sdAb that binds to bovine serum albumin (BSA with low picomolar affinity. In surface plasmon resonance (SPR analyses using BSA surfaces, bound ABTAG can be completely dissociated from the BSA surfaces at low pH, over multiple cycles, without any reduction in the capacity of the BSA surfaces to bind ABTAG. A moderate throughput, SPR-based, antibody screening assay exploiting the unique features of ABTAG is described. Anti-carcinoembryonic antigen-related cell adhesion molecule 6 (CEACAM6 sdAbs were isolated from a phage-displayed sdAb library derived from the heavy chain antibody repertoire of a llama immunized with CEACAM6. Following one or two rounds of panning, enriched clones were expressed as ABTAG fusions in microtiter plate cultures. The sdAb-ABTAG fusions from culture supernatants were captured on BSA surfaces and CEACAM6 antigen was then bound to the captured molecules. The SPR screening method gives a read-out of relative expression levels of the fusion proteins and kinetic and affinity constants for CEACAM6 binding by the captured molecules. The library was also panned and screened by conventional methods and positive clones were subcloned and expressed for SPR analysis. Compared to conventional panning and screening, the SPR-based ABTAG method yielded a considerably higher diversity of binders, some with affinities that were three orders of magnitude higher affinity than those identified by conventional panning.

  19. Faster and Simpler Approximation of Stable Matchings

    Directory of Open Access Journals (Sweden)

    Katarzyna Paluch

    2014-04-01

    Full Text Available We give a 3 2 -approximation algorithm for finding stable matchings that runs in O(m time. The previous most well-known algorithm, by McDermid, has the same approximation ratio but runs in O(n3/2m time, where n denotes the number of people andm is the total length of the preference lists in a given instance. In addition, the algorithm and the analysis are much simpler. We also give the extension of the algorithm for computing stable many-to-many matchings.

  20. Stable isotopes in Lithuanian bioarcheological material

    Science.gov (United States)

    Skipityte, Raminta; Jankauskas, Rimantas; Remeikis, Vidmantas

    2015-04-01

    Investigation of bioarcheological material of ancient human populations allows us to understand the subsistence behavior associated with various adaptations to the environment. Feeding habits are essential to the survival and growth of ancient populations. Stable isotope analysis is accepted tool in paleodiet (Schutkowski et al, 1999) and paleoenvironmental (Zernitskaya et al, 2014) studies. However, stable isotopes can be useful not only in investigating human feeding habits but also in describing social and cultural structure of the past populations (Le Huray and Schutkowski, 2005). Only few stable isotope investigations have been performed before in Lithuanian region suggesting a quite uniform diet between males and females and protein intake from freshwater fish and animal protein. Previously, stable isotope analysis has only been used to study a Stone Age population however, more recently studies have been conducted on Iron Age and Late medieval samples (Jacobs et al, 2009). Anyway, there was a need for more precise examination. Stable isotope analysis were performed on human bone collagen and apatite samples in this study. Data represented various ages (from 5-7th cent. to 18th cent.). Stable carbon and nitrogen isotope analysis on medieval populations indicated that individuals in studied sites in Lithuania were almost exclusively consuming C3 plants, C3 fed terrestrial animals, and some freshwater resources. Current investigation demonstrated social differences between elites and country people and is promising in paleodietary and daily life reconstruction. Acknowledgement I thank prof. dr. G. Grupe, Director of the Anthropological and Palaeoanatomical State Collection in Munich for providing the opportunity to work in her laboratory. The part of this work was funded by DAAD. Antanaitis-Jacobs, Indre, et al. "Diet in early Lithuanian prehistory and the new stable isotope evidence." Archaeologia Baltica 12 (2009): 12-30. Le Huray, Jonathan D., and Holger

  1. Bordism, stable homotopy and adams spectral sequences

    CERN Document Server

    Kochman, Stanley O

    1996-01-01

    This book is a compilation of lecture notes that were prepared for the graduate course "Adams Spectral Sequences and Stable Homotopy Theory" given at The Fields Institute during the fall of 1995. The aim of this volume is to prepare students with a knowledge of elementary algebraic topology to study recent developments in stable homotopy theory, such as the nilpotence and periodicity theorems. Suitable as a text for an intermediate course in algebraic topology, this book provides a direct exposition of the basic concepts of bordism, characteristic classes, Adams spectral sequences, Brown-Peter

  2. Modelling stable water isotopes: Status and perspectives

    Directory of Open Access Journals (Sweden)

    Werner M.

    2010-12-01

    Full Text Available Modelling of stable water isotopes H2 18O and HDO within various parts of the Earth’s hydrological cycle has clearly improved our understanding of the interplay between climatic variations and related isotope fractionation processes. In this article key principles and major research results of stable water isotope modelling studies are described. Emphasis is put on research work using explicit isotope diagnostics within general circulation models as this highly complex model setup bears many resemblances with studies using simpler isotope modelling approaches.

  3. Pegylated Trastuzumab Fragments Acquire an Increased in Vivo Stability but Show a Largely Reduced Affinity for the Target Antigen

    Directory of Open Access Journals (Sweden)

    Fabio Selis

    2016-04-01

    Full Text Available PEGylation of biomolecules is a major approach to increase blood stream half-life, stability and solubility of biotherapeutics and to reduce their immunogenicity, aggregation potential and unspecific interactions with other proteins and tissues. Antibodies have generally long half-lives due to high molecular mass and stability toward proteases, however their size lowers to some extent their potential because of a reduced ability to penetrate tissues, especially those of tumor origin. Fab or otherwise engineered smaller fragments are an alternative but are less stable and are much less well retained in circulation. We have here investigated the effects of various PEGylations on the binding properties and in vivo half-life of Fab fragments derived from the enzymatic splitting of Trastuzumab. We find that PEGylation increases the half-life of the molecules but also strongly affects the ability to recognize the target antigen in a way that is dependent on the extent and position of the chemical modification. Data thus support the concept that polyethylene glycol (PEG conjugation on Trastuzumab Fabs increases half-life but reduces their affinity and this is a fine balance, which must be carefully considered for the design of strategies based on the use of antibody fragments.

  4. Pegylated Trastuzumab Fragments Acquire an Increased in Vivo Stability but Show a Largely Reduced Affinity for the Target Antigen

    Science.gov (United States)

    Selis, Fabio; Focà, Giuseppina; Sandomenico, Annamaria; Marra, Carla; Di Mauro, Concetta; Saccani Jotti, Gloria; Scaramuzza, Silvia; Politano, Annalisa; Sanna, Riccardo; Ruvo, Menotti; Tonon, Giancarlo

    2016-01-01

    PEGylation of biomolecules is a major approach to increase blood stream half-life, stability and solubility of biotherapeutics and to reduce their immunogenicity, aggregation potential and unspecific interactions with other proteins and tissues. Antibodies have generally long half-lives due to high molecular mass and stability toward proteases, however their size lowers to some extent their potential because of a reduced ability to penetrate tissues, especially those of tumor origin. Fab or otherwise engineered smaller fragments are an alternative but are less stable and are much less well retained in circulation. We have here investigated the effects of various PEGylations on the binding properties and in vivo half-life of Fab fragments derived from the enzymatic splitting of Trastuzumab. We find that PEGylation increases the half-life of the molecules but also strongly affects the ability to recognize the target antigen in a way that is dependent on the extent and position of the chemical modification. Data thus support the concept that polyethylene glycol (PEG) conjugation on Trastuzumab Fabs increases half-life but reduces their affinity and this is a fine balance, which must be carefully considered for the design of strategies based on the use of antibody fragments. PMID:27043557

  5. Development of a novel affinity chromatography resin for platform purification of bispecific antibodies with modified protein a binding avidity.

    Science.gov (United States)

    Tustian, Andrew D; Laurin, Linus; Ihre, Henrik; Tran, Travis; Stairs, Robert; Bak, Hanne

    2018-02-21

    There is strong interest in the production of bispecific monoclonal antibodies that can simultaneously bind two distinct targets or epitopes to achieve novel mechanisms of action and efficacy. Regeneron's bispecific technology, based upon a standard IgG, consists of a heterodimer of two different heavy chains, and a common light chain. Co-expression of two heavy chains leads to the formation of two parental IgG impurities, the removal of which is facilitated by a dipeptide substitution in the Fc portion of one of the heavy chains that ablates Fc Protein A binding. Therefore the affinity capture (Protein A) step of the purification process must perform both bulk capture and high resolution of these mAb impurities, a task current commercially available resins are not designed for. Resolution can be further impaired by the ability of Protein A to bind some antibodies in the variable region of the heavy chain (V H ). This paper details development of a novel Protein A resin. This resin combines an alkali stable ligand with a base matrix exhibiting excellent mass transfer properties to allow high capacity single step capture and resolution of bispecific antibodies with high yields. The developed resin, named MabSelect SuRe™ pcc, is implemented in GMP production processes for several bispecific antibodies. This article is protected by copyright. All rights reserved. © 2018 American Institute of Chemical Engineers.

  6. Selectable high-yield recombinant protein production in human cells using a GFP/YFP nanobody affinity support.

    Science.gov (United States)

    Schellenberg, Matthew J; Petrovich, Robert M; Malone, Christine C; Williams, R Scott

    2018-03-25

    Recombinant protein expression systems that produce high yields of pure proteins and multi-protein complexes are essential to meet the needs of biologists, biochemists, and structural biologists using X-ray crystallography and cryo-electron microscopy. An ideal expression system for recombinant human proteins is cultured human cells where the correct translation and chaperone machinery are present. However, compared to bacterial expression systems, human cell cultures present several technical challenges to their use as an expression system. We developed a method that utilizes a YFP fusion-tag to generate recombinant proteins using suspension-cultured HEK293F cells. YFP is a dual-function tag that enables direct visualization and fluorescence-based selection of high expressing clones for and rapid purification using a high-stringency, high-affinity anti-GFP/YFP nanobody support. We demonstrate the utility of this system by expressing two large human proteins, TOP2α (340 KDa dimer) and a TOP2β catalytic core (260 KDa dimer). This robustly and reproducibly yields >10 mg/L liter of cell culture using transient expression or 2.5 mg/L using stable expression. Published 2018. This article is a US Government work and is in the public domain in the USA.

  7. Stable isotope analysis of dynamic lipidomics.

    Science.gov (United States)

    Brandsma, Joost; Bailey, Andrew P; Koster, Grielof; Gould, Alex P; Postle, Anthony D

    2017-08-01

    Metabolic pathway flux is a fundamental element of biological activity, which can be quantified using a variety of mass spectrometric techniques to monitor incorporation of stable isotope-labelled substrates into metabolic products. This article contrasts developments in electrospray ionisation mass spectrometry (ESI-MS) for the measurement of lipid metabolism with more established gas chromatography mass spectrometry and isotope ratio mass spectrometry methodologies. ESI-MS combined with diagnostic tandem MS/MS scans permits the sensitive and specific analysis of stable isotope-labelled substrates into intact lipid molecular species without the requirement for lipid hydrolysis and derivatisation. Such dynamic lipidomic methodologies using non-toxic stable isotopes can be readily applied to quantify lipid metabolic fluxes in clinical and metabolic studies in vivo. However, a significant current limitation is the absence of appropriate software to generate kinetic models of substrate incorporation into multiple products in the time domain. Finally, we discuss the future potential of stable isotope-mass spectrometry imaging to quantify the location as well as the extent of lipid synthesis. This article is part of a Special Issue entitled: BBALIP_Lipidomics Opinion Articles edited by Sepp Kohlwein. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Petrography, compositional characteristics and stable isotope ...

    African Journals Online (AJOL)

    Petrography, compositional characteristics and stable isotope geochemistry of the Ewekoro formation from Ibese Corehole, eastern Dahomey basin, southwestern Nigeria. ME Nton, MO ... Preserved pore types such as; intercrystaline, moldic and vuggy pores were observed as predominant conduits for fluids. The major ...

  9. petrography, compositional characteristics and stable isotope ...

    African Journals Online (AJOL)

    PROF EKWUEME

    Subsurface samples of the predominantly carbonate Ewekoro Formation, obtained from Ibese core hole within the Dahomey basin were used in this study. Investigations entail petrographic, elemental composition as well as stable isotopes (carbon and oxygen) geochemistry in order to deduce the different microfacies and ...

  10. Substitution of stable isotopes in Chlorella

    Science.gov (United States)

    Flaumenhaft, E.; Katz, J. J.; Uphaus, R. A.

    1969-01-01

    Replacement of biologically important isotopes in the alga Chlorella by corresponding heavier stable isotopes produces increasingly greater deviations from the normal cell size and changes the quality and distribution of certain cellular components. The usefulness of isotopically altered organisms increases interest in the study of such permuted organisms.

  11. Champion Island, Galapagos Stable Oxygen Calibration Data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Galapagos Coral Stable Oxygen Calibration Data. Sites: Bartolome Island: 0 deg, 17 min S, 90 deg 33 min W. Champion Island: 1 deg, 15 min S, 90 deg, 05 min W. Urvina...

  12. Stable propagation of 'selfish'genetic elements

    Indian Academy of Sciences (India)

    Unknown

    viruses such as the Epstein-Barr virus (Harris et al 1985;. Kanda et al 2001) and bovine papilloma virus (Lehman and Botchan 1998; Ilves et al 1999), which exist pre- dominantly as extrachromosomal episomes, have been shown to utilize chromosome tethering as a means for stable segregation. The tethering mechanism ...

  13. Unconditionally stable perfectly matched layer boundary conditions

    NARCIS (Netherlands)

    De Raedt, H.; Michielsen, K.

    2007-01-01

    A brief review is given of a systematic, product-formula based approach to construct unconditionally stable algorithms for solving the time-dependent Maxwell equations. The fundamental difficulties that arise when we want to incorporate uniaxial perfectly matched layer boundary conditions into this

  14. Facies, dissolution seams and stable isotope compositions

    Indian Academy of Sciences (India)

    Stable isotope analysis of the limestone shows that 13C and 18O values are compatible with the early Mesoproterozoic open seawater composition. The ribbon limestone facies in the Rohtas Limestone is characterized by micritic beds, each decoupled in a lower band enriched and an upper band depleted in dissolution ...

  15. Connected domination stable graphs upon edge addition ...

    African Journals Online (AJOL)

    A set S of vertices in a graph G is a connected dominating set of G if S dominates G and the subgraph induced by S is connected. We study the graphs for which adding any edge does not change the connected domination number. Keywords: Connected domination, connected domination stable, edge addition ...

  16. Stable magnetic remanence in antiferromagnetic goethite.

    Science.gov (United States)

    Strangway, D W; McMahon, B E; Honea, R M

    1967-11-10

    Goethite, known to be antiferromagnetic, acquires thermoremanent magnetization at its Neel temperature of 120 degrees C. This remanence, extremely stable, is due to the presence of unbalanced spins in the antiferromagnetic structure; the spins may result from grain size, imperfections, or impurities.

  17. Non-Gaussian distributions of melodic intervals in music: The Lévy-stable approximation

    Science.gov (United States)

    Niklasson, Gunnar A.; Niklasson, Maria H.

    2015-11-01

    The analysis of structural patterns in music is of interest in order to increase our fundamental understanding of music, as well as for devising algorithms for computer-generated music, so called algorithmic composition. Musical melodies can be analyzed in terms of a “music walk” between the pitches of successive tones in a notescript, in analogy with the “random walk” model commonly used in physics. We find that the distribution of melodic intervals between tones can be approximated with a Lévy-stable distribution. Since music also exibits self-affine scaling, we propose that the “music walk” should be modelled as a Lévy motion. We find that the Lévy motion model captures basic structural patterns in classical as well as in folk music.

  18. High Temperature Stable Separator for Lithium Batteries Based on SiO₂ and Hydroxypropyl Guar Gum.

    Science.gov (United States)

    Carvalho, Diogo Vieira; Loeffler, Nicholas; Kim, Guk-Tae; Passerini, Stefano

    2015-10-23

    A novel membrane based on silicon dioxide (SiO₂) and hydroxypropyl guar gum (HPG) as binder is presented and tested as a separator for lithium-ion batteries. The separator is made with renewable and low cost materials and an environmentally friendly manufacturing processing using only water as solvent. The separator offers superior wettability and high electrolyte uptake due to the optimized porosity and the good affinity of SiO₂ and guar gum microstructure towards organic liquid electrolytes. Additionally, the separator shows high thermal stability and no dimensional-shrinkage at high temperatures due to the use of the ceramic filler and the thermally stable natural polymer. The electrochemical tests show the good electrochemical stability of the separator in a wide range of potential, as well as its outstanding cycle performance.

  19. Strontium stable isotope behaviour accompanying basalt weathering

    Science.gov (United States)

    Burton, K. W.; Parkinson, I. J.; Gíslason, S. G. R.

    2016-12-01

    The strontium (Sr) stable isotope composition of rivers is strongly controlled by the balance of carbonate to silicate weathering (Krabbenhöft et al. 2010; Pearce et al. 2015). However, rivers draining silicate catchments possess distinctly heavier Sr stable isotope values than their bedrock compositions, pointing to significant fractionation during weathering. Some have argued for preferential release of heavy Sr from primary phases during chemical weathering, others for the formation of secondary weathering minerals that incorporate light isotopes. This study presents high-precision double-spike Sr stable isotope data for soils, rivers, ground waters and estuarine waters from Iceland, reflecting both natural weathering and societal impacts on those environments. The bedrock in Iceland is dominantly basaltic, d88/86Sr ≈ +0.27, extending to lighter values for rhyolites. Geothermal waters range from basaltic Sr stable compositions to those akin to seawater. Soil pore waters reflect a balance of input from primary mineral weathering, precipitation and litter recycling and removal into secondary phases and vegetation. Rivers and ground waters possess a wide range of d88/86Sr compositions from +0.101 to +0.858. Elemental and isotope data indicate that this fractionation primarily results from the formation or dissolution of secondary zeolite (d88/86Sr ≈ +0.10), but also carbonate (d88/86Sr ≈ +0.22) and sometimes anhydrite (d88/86Sr ≈ -0.73), driving the residual waters to heavier or lighter values, respectively. Estuarine waters largely reflect mixing with seawater, but are also be affected by adsorption onto particulates, again driving water to heavy values. Overall, these data indicate that the stability and nature of secondary weathering phases, exerts a strong control on the Sr stable isotope composition of silicate rivers. [1] Krabbenhöft et al. (2010) Geochim. Cosmochim. Acta 74, 4097-4109. [2] Pearce et al. (2015) Geochim. Cosmochim. Acta 157, 125-146.

  20. Development of a Safety Management Web Tool for Horse Stables.

    Science.gov (United States)

    Leppälä, Jarkko; Kolstrup, Christina Lunner; Pinzke, Stefan; Rautiainen, Risto; Saastamoinen, Markku; Särkijärvi, Susanna

    2015-11-12

    Managing a horse stable involves risks, which can have serious consequences for the stable, employees, clients, visitors and horses. Existing industrial or farm production risk management tools are not directly applicable to horse stables and they need to be adapted for use by managers of different types of stables. As a part of the InnoEquine project, an innovative web tool, InnoHorse, was developed to support horse stable managers in business, safety, pasture and manure management. A literature review, empirical horse stable case studies, expert panel workshops and stakeholder interviews were carried out to support the design. The InnoHorse web tool includes a safety section containing a horse stable safety map, stable safety checklists, and examples of good practices in stable safety, horse handling and rescue planning. This new horse stable safety management tool can also help in organizing work processes in horse stables in general.

  1. Ideally amphipathic beta-sheeted peptides at interfaces: structure, orientation, affinities for lipids and hemolytic activity of (KL)(m)K peptides.

    Science.gov (United States)

    Castano, S; Desbat, B; Dufourcq, J

    2000-01-15

    Designed to model ideally amphipathic beta-sheets, the minimalist linear (KL)(m)K peptides (m=4-7) were synthesized and proved to form stable films at the air/water interface, they insert into compressed dimyristoylphosphatidylcholine monolayers and interact with egg phosphatidylcholine vesicles. Whatever the interface or the lateral pressure applied to the films, FT-IR and polarization-modulated IRRAS spectroscopy developed in situ on the films indicated that all the peptides totally fold into intermolecular antiparallel beta-sheets. Calculated spectra of the amide region allowed us to define the orientation of the beta-strands compared to the interface. It is concluded that such beta-sheets remain flat-oriented without deep perturbation of zwitterionic phospholipids. Dansyl labelling at the N-terminus indicates that all the peptides are monomeric at a low concentration in aqueous buffer and bind to lipids with similar Dns burying. The affinities for zwitterionic lecithin mono- and bilayers, quantitatively estimated from buffer to lipid partition constants, monotonically increased with peptide length, indicating that hydrophobicity is a limiting parameter for lipid and membrane affinities. Peptides induced permeability increases on zwitterionic liposomes, they are strongly hemolytic towards human erythrocytes and their activity increases concurrently with length. Taking into account the lipid affinity, a hemolytic efficiency can be defined: at the same amount of peptide bound, this efficiency strongly increases with the peptide length. It is proposed that the first determinant step of membrane disturbance is the invasion of the outer membrane leaflet by these ideally amphipathic beta-sheeted structures lying flat at the interface, like large rafts depending on the number of beta-strands.

  2. The Interaction of Arp2/3 Complex with Actin: Nucleation, High Affinity Pointed End Capping, and Formation of Branching Networks of Filaments

    Science.gov (United States)

    Mullins, R. Dyche; Heuser, John A.; Pollard, Thomas D.

    1998-05-01

    The Arp2/3 complex is a stable assembly of seven protein subunits including two actin-related proteins (Arp2 and Arp3) and five novel proteins. Previous work showed that this complex binds to the sides of actin filaments and is concentrated at the leading edges of motile cells. Here, we show that Arp2/3 complex purified from Acanthamoeba caps the pointed ends of actin filaments with high affinity. Arp2/3 complex inhibits both monomer addition and dissociation at the pointed ends of actin filaments with apparent nanomolar affinity and increases the critical concentration for polymerization at the pointed end from 0.6 to 1.0 μ M. The high affinity of Arp2/3 complex for pointed ends and its abundance in amoebae suggest that in vivo all actin filament pointed ends are capped by Arp2/3 complex. Arp2/3 complex also nucleates formation of actin filaments that elongate only from their barbed ends. From kinetic analysis, the nucleation mechanism appears to involve stabilization of polymerization intermediates (probably actin dimers). In electron micrographs of quick-frozen, deep-etched samples, we see Arp2/3 bound to sides and pointed ends of actin filaments and examples of Arp2/3 complex attaching pointed ends of filaments to sides of other filaments. In these cases, the angle of attachment is a remarkably constant 70 ± 7 degrees. From these in vitro biochemical properties, we propose a model for how Arp2/3 complex controls the assembly of a branching network of actin filaments at the leading edge of motile cells.

  3. Anacardium occidentale bark lectin: purification, immobilization as an affinity model and influence in the uptake of technetium-99M by rat adipocytes.

    Science.gov (United States)

    Maciel, Maria Inês Sucupira; de Mendonça Cavalcanti, Maria do Socorro; Napoleão, Thiago Henrique; Paiva, Patrícia Maria Guedes; de Almeida Catanho, Maria Teresa Jansem; Coelho, Luana Cassandra Breitenbach Barroso

    2012-10-01

    Lectins, proteins that recognize carbohydrates, have been immobilized on inert supports and used in the screening or purification of glycoproteins. Anacardium occidentale bark infusion has been used as a hypoglycemic agent in Brazil. The toxicity of natural products may be evaluated determining their capability to alter the biodistribution of technetium-99M ((99m)Tc). This work reports the isolation and characterization of a lectin from A. occidentale bark (AnocBL), its evaluation as an affinity support for glycoprotein isolation and lectin effect on the uptake of (99m)Tc by rat adipocytes. AnocBL was isolated from 80 % ammonium sulphate supernatant by affinity chromatography on fetuin-agarose. SDS-PAGE showed a single protein band of 47 kDa. The monossacharide L-arabinose and the glycoproteins fetuin, asialofetuin, ovomucoid, casein, thyroglobulin, peroxidase, fetal bovine serum and IgG inhibited the activity. The lectin activity was stable until 70 °C and at a pH range of 3.0-7.5. AnocBL-Sepharose column bound fetuin indicating that the lectin matrix may be used to obtain glycoconjugates of biotechnological interest. In vitro assay revealed that glucose and insulin increase (99m)Tc uptake by rat adipocytes. AnocBL decreases (99m)Tc uptake, and this effect was not detected in the presence of glucose. Fetuin inhibited AnocBL effect in all insulin concentrations.

  4. Development of thermo-responsive hydrogels with immobilized metal affinity groups

    Science.gov (United States)

    Yoon, Young-Seo

    A Hydrogel is defined as a polymeric material which possesses the ability to swell in water and retain a significant fraction of water within its structure, but which will not dissolve in water. Hydrogels have been studied by many researchers because they have many useful applications in bio related fields such as drug delivery, bioseparation, and etc. In this thesis, a new hydrogel system that possesses the characteristics of thermo-responsive swelling property and immobilized metal affinity was developed. This affinity material consists of a hydrogel with stimuli responsive swelling characteristics to provide modulated diffusivity and size selectivity. Covalently bound ligands within hydrogels provide highly selective and tunable affinity-based separation. Swelling and affinity properties can be independently controlled by regulating the temperature or pH of the solution to provide a sequential separations scheme. The developed affinity hydrogels incorporate multiple modes of separations or recovery and concentrate specific solutes in chromatographic systems. Thermal sensitive affinity hydrogels were synthesized from a N-isopropylacrylamide (NIPAAm) monomer, a crosslinker (1,4-bismethylene acrylamide) and a ligand attachable co-monomer acrylamide (AAm), using free radical chemistry. The ligand of choice is the metal affinity iminodiacetic acid (IDA) which is bound to hydrogel backbone via a spacer arm. The challenge lay in incorporating affinity ligands without affecting the temperature induced swelling of the hydrogel. Thus, PNIPAAm-Am hydrogels are functionalized with a spacer arm (1,4-butanediol diglycidyl ether), the chelating ligand IDA and a divalent metal ion (Cu2+). This ligand binds histidine groups at high pH and releases them upon protonation of histidine at low pH. This can be used to separate proteins based on the occurrence of surface histidine residues in them. The resulting affinity hydrogel was shown to adsorb the protein chicken egg white

  5. N(G)-Acyl-argininamides as NPY Y(1) receptor antagonists: Influence of structurally diverse acyl substituents on stability and affinity.

    Science.gov (United States)

    Weiss, Stefan; Keller, Max; Bernhardt, Günther; Buschauer, Armin; König, Burkhard

    2010-09-01

    N(G)-Acylated argininamides, covering a broad range of lipophilicity (calculated logD values: -1.8-12.5), were synthesized and investigated for NPY Y(1) receptor (Y(1)R) antagonism, Y(1)R affinity and stability in buffer (N(G)-deacylation, yielding BIBP 3226). Broad structural variation of substituents was tolerated. The K(i) (binding) and K(b) values (Y(1)R antagonism) varied from low nM to one-digit muM. Most of the compounds proved to be sufficiently stable at pH 7.4 over 90min to determine reliable pharmacological data in vitro. Exceptionally high instability was detected when a succinyl moiety was attached to the guanidine, probably, due to an intramolecular cleavage mechanism. Copyright 2010 Elsevier Ltd. All rights reserved.

  6. Bilirubin oxidase label for an enzyme-linked affinity assay with O2 as substrate in a neutral pH NACL solution.

    Science.gov (United States)

    Kim, Hyug-Han; Zhang, Yongchao; Heller, Adam

    2004-04-15

    Laccase, a copper enzyme catalyzing the four-electron reduction of O(2) to water, has been shown by others to be a useful label in enzyme-linked immunoassays, in which the substrate is ambient O(2) instead of an added chemical, such as hydrogen peroxide, or a phosphate ester of a phenol. Laccase-catalyzed O(2) reduction is, however, inhibited by halides, which complex the enzyme's copper ions. Replacement of laccase by bilirubin oxidase, a copper enzyme retaining its maximal activity at high chloride concentrations and at pH 7.2, allows enzyme-amplified affinity assays with O(2) as the substrate in neutral-pH chloride solutions, exemplified here by the assay of DNA, the duplexes of which are unstable at low ionic strength but are stable in strong NaCl solutions.

  7. Blood O2 affinity of a large polar elasmobranch, the Greenland shark Somniosus microcephalus

    DEFF Research Database (Denmark)

    Herbert, N.A.; Skov, Peter Vilhelm; Tirsgaard, B.

    2017-01-01

    affinity across elasmobranch fishes suggests that S. microcephalus has a high blood O2 affinity (i.e., low P50) and a small Bohr effect but these are common traits in sluggish elasmobranch fishes, with little evidence for any relationship of blood O2 affinity to the low metabolic rates, low environmental......The Greenland shark (Somniosus microcephalus. Bloch & Schneider 1801) is a polar elasmobranch that is hypothesised to possess a unique metabolic physiology due to its extreme large size, the cold waters it inhabits and its slow swimming lifestyle. Our results therefore provide the first insight...... into the metabolic physiology of this unique shark, with a focus on blood O2 affinity. An evaluation of blood O2 affinity at 2 °C using tonometry revealed a P50 of 11.7 mmHg at a PCO2 of 2.25 mmHg and a Bohr effect (binding sensitivity of blood to pH, ϕ = Δlog P50/ΔpH) of −0.26. A comparative evaluation of blood O2...

  8. Synthetic affinity ligands as a novel tool to improve protein stability.

    Science.gov (United States)

    Sousa, I T; Ruiu, L; Lowe, C R; Taipa, M A

    2009-01-01

    Cutinase from Fusarium solani pisi is the model-system for a new approach to assess and enhance protein stability based on the use of synthetic triazine-scaffolded affinity ligands as a novel protein-stabilizing tool. The active site of cutinase is excluded from the main surface regions postulated to be involved in early protein's thermal unfolding events. Hence, these regions are suitable targets for binding complementary affinity ligands with a potential stabilizing effect. A random solid-phase combinatorial library of triazine-bisubstituted molecules was screened for binding cutinase by a rapid fluorescence-based method and affinity chromatography. The best binding substituents were combined with those previously selected by screening a rationally designed library. A second-generation solid-phase biased library was designed and synthesized, following a semi-rational methodology. A dual screening of this library enabled the selection of ligands binding cutinase with higher affinity while retaining its functionality. These compounds were utilized for thermostability assessment with adsorbed cutinase at 60 degrees C and pH 8.0. When bound to different types of ligands, the enzyme showed markedly distinct activity retention profiles, with some synthetic affinity ligands displaying a stabilizing effect on cutinase and others a clearly destabilizing effect, when compared with the free enzyme. Copyright (c) 2008 John Wiley & Sons, Ltd.

  9. Ultrasound elastography: efficient estimation of tissue displacement using an affine transformation model

    Science.gov (United States)

    Hashemi, Hoda Sadat; Boily, Mathieu; Martineau, Paul A.; Rivaz, Hassan

    2017-03-01

    Ultrasound elastography entails imaging mechanical properties of tissue and is therefore of significant clinical importance. In elastography, two frames of radio-frequency (RF) ultrasound data that are obtained while the tissue is undergoing deformation, and the time-delay estimate (TDE) between the two frames is used to infer mechanical properties of tissue. TDE is a critical step in elastography, and is challenging due to noise and signal decorrelation. This paper presents a novel and robust technique TDE using all samples of RF data simultaneously. We assume tissue deformation can be approximated by an affine transformation, and hence call our method ATME (Affine Transformation Model Elastography). The affine transformation model is utilized to obtain initial estimates of axial and lateral displacement fields. The affine transformation only has six degrees of freedom (DOF), and as such, can be efficiently estimated. A nonlinear cost function that incorporates similarity of RF data intensity and prior information of displacement continuity is formulated to fine-tune the initial affine deformation field. Optimization of this function involves searching for TDE of all samples of the RF data. The optimization problem is converted to a sparse linear system of equations, which can be solved in real-time. Results on simulation are presented for validation. We further collect RF data from in-vivo patellar tendon and medial collateral ligament (MCL), and show that ATME can be used to accurately track tissue displacement.

  10. 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.

  11. High-Affinity Ligands Can Trigger T Cell Receptor Signaling Without CD45 Segregation

    Directory of Open Access Journals (Sweden)

    Mohammad Ameen Al-Aghbar

    2018-04-01

    Full Text Available How T cell receptors (TCRs are triggered to start signaling is still not fully understood. It has been proposed that segregation of the large membrane tyrosine phosphatase CD45 from engaged TCRs initiates signaling by favoring phosphorylation of immunoreceptor tyrosine-based activation motifs (ITAMs in the cytoplasmic domains of CD3 molecules. However, whether CD45 segregation is important to initiate triggering is still uncertain. We examined CD45 segregation from TCRs engaged to anti-CD3 scFv with high or low affinity and with defined molecular lengths on glass-supported lipid bilayers using total internal reflection microscopy. Both short and elongated high-affinity anti-CD3 scFv effectively induced similar calcium mobilization, Zap70 phosphorylation, and cytokine secretion in Jurkat T cells but CD45 segregated from activated TCR microclusters significantly less for elongated versus short anti-CD3 ligands. In addition, at early times, triggering cells with both high and low affinity elongated anti-CD3 scFv resulted in similar degrees of CD3 co-localization with CD45, but only the high-affinity scFv induced T cell activation. The lack of correlation between CD45 segregation and early markers of T cell activation suggests that segregation of CD45 from engaged TCRs is not mandatory for initial triggering of TCR signaling by elongated high-affinity ligands.

  12. 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.

  13. High affinity binding of [3H]cocaine to rat liver microsomes

    International Nuclear Information System (INIS)

    El-Maghrabi, E.A.; Calligaro, D.O.; Eldefrawi, M.E.

    1988-01-01

    ] 3 H]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 [ 3 H]cocaine binding. On the other hand, chronic administration of cocaine reduced [ 3 H]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 [ 3 H]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 [ 3 H]cocaine binding to liver with a different rank order of potency than their displacement of [ 3 H]cocaine binding to striatum. This high affinity [ 3 H]cocaine binding protein in liver is not likely to be monooxygenase, but may have a role in cocaine-induced hepatotoxicity

  14. A possible mechanism for low affinity of silkworm Na+/K+-ATPase for K.

    Science.gov (United States)

    Homareda, Haruo; Otsu, Masahiro; Yamamoto, Sachiko; Ushimaru, Makoto; Ito, Sayaka; Fukutomi, Toshiyuki; Jo, Taeho; Eishi, Yoshinobu; Hara, Yukichi

    2017-12-01

    The affinity for K + of silkworm nerve Na + /K + -ATPase is markedly lower than that of mammalian Na + /K + -ATPase (Homareda 2010). In order to obtain clues on the molecular basis of the difference in K + affinities, we cloned cDNAs of silkworm (Bombyx mori) nerve Na + /K + -ATPase α and β subunits, and analyzed the deduced amino acid sequences. The molecular masses of the α and β subunits were presumed to be 111.5 kDa with ten transmembrane segments and 37.7 kDa with a single transmembrane segment, respectively. The α subunit showed 75% identity and 93% homology with the pig Na + /K + -ATPase α1 subunit. On the other hand, the amino acid identity of the β subunit with mammalian counterparts was as low as 30%. Cloned α and β cDNAs were co-expressed in cultured silkworm ovary-derived cells, BM-N cells, which lack endogenous Na + /K + -ATPase. Na + /K + -ATPase expressed in the cultured cells showed a low affinity for K + and a high affinity for Na + , characteristic of the silkworm nerve Na + /K + -ATPase. These results suggest that the β subunit is responsible for the affinity for K + of Na + /K + -ATPase.

  15. IA-2 autoantibody affinity in children at risk for type 1 diabetes.

    Science.gov (United States)

    Krause, Stephanie; Chmiel, Ruth; Bonifacio, Ezio; Scholz, Marlon; Powell, Michael; Furmaniak, Jadwiga; Rees Smith, Bernard; Ziegler, Anette-G; Achenbach, Peter

    2012-12-01

    Autoantibodies to insulinoma-associated protein 2 (IA-2A) are associated with increased risk for type 1 diabetes. Here we examined IA-2A affinity and epitope specificity to assess heterogeneity in response intensity in relation to pathogenesis and diabetes risk in 50 children who were prospectively followed from birth. At first IA-2A appearance, affinity ranged from 10(7) to 10(11)L/mol and was high (>1.0×10(9)L/mol) in 41 (82%) children. IA-2A affinity was not associated with epitope specificity or HLA class II haplotype. On follow-up, affinity increased or remained high, and IA-2A were commonly against epitopes within the protein tyrosine phosphatase-like IA-2 domain and the homologue protein IA-2β. IA-2A were preceded or accompanied by other islet autoantibodies in 49 (98%) children, of which 34 progressed to diabetes. IA-2A affinity did not stratify diabetes risk. In conclusion, the IA-2A response in children is intense with rapid maturation against immunogenic epitopes and a strong association with diabetes development. Copyright © 2012 Elsevier Inc. All rights reserved.

  16. Myoglobin extraction from mammalian skeletal muscle and oxygen affinity determination under physiological conditions.

    Science.gov (United States)

    Wright, Traver J; Davis, Randall W

    2015-03-01

    An accurate determination of myoglobin (Mb) oxygen affinity (P50) can be difficult due to hemoglobin (Hb) contamination and autoxidation of Mb to metMb which is incapable of binding oxygen. To reduce Mb autoxidation, P50 is often measured at refrigerated temperatures. However, the temperature dependent shift in Mb oxygen affinity results in a greater oxygen affinity (lower P50) at colder temperatures than occurs at physiological temperature (ca. 37-39°C) for birds and mammals. Utilizing the temperature dependent pH shift of Tris buffer, we developed novel methods to extract Mb from vertebrate muscle samples and remove Hb contamination while minimizing globin autoxidation. Cow (Bos taurus) muscle tissue (n=5) was homogenized in buffer to form a Mb solution, and Hb contamination was removed using anion exchange chromatography. A TCS Hemox Blood Analyzer was then used to quickly generate an oxygen dissociation curve for the extracted Mb. The oxygen affinity of extracted bovine Mb was compared to commercially available horse heart Mb. The oxygen affinity of extracted cow Mb (P50=3.72±0.16 mmHg) was not statistically different from commercially prepared horse heart Mb (P50=3.71±0.10 mmHg). With high yield Mb extraction and fast generation of an oxygen dissociation curve, it was possible to consistently determine Mb P50 under physiologically relevant conditions for endothermic vertebrates. Copyright © 2014 Elsevier Inc. All rights reserved.

  17. Single-experiment displacement assay for quantifying high-affinity binding by isothermal titration calorimetry.

    Science.gov (United States)

    Krainer, Georg; Keller, Sandro

    2015-04-01

    Isothermal titration calorimetry (ITC) is the gold standard for dissecting the thermodynamics of a biomolecular binding process within a single experiment. However, reliable determination of the dissociation constant (KD) from a single titration is typically limited to the range 100 μM>KD>1 nM. Interactions characterized by a lower KD can be assessed indirectly by so-called competition or displacement assays, provided that a suitable competitive ligand is available whose KD falls within the directly accessible window. However, this protocol is limited by the fact that it necessitates at least two titrations to characterize one high-affinity inhibitor, resulting in considerable consumption of both sample material and time. Here, we introduce a fast and efficient ITC displacement assay that allows for the simultaneous characterization of both a high-affinity ligand and a moderate-affinity ligand competing for the same binding site on a receptor within a single experiment. The protocol is based on a titration of the high-affinity ligand into a solution containing the moderate-affinity ligand bound to the receptor present in excess. The resulting biphasic binding isotherm enables accurate and precise determination of KD values and binding enthalpies (ΔH) of both ligands. We discuss the theoretical background underlying the approach, demonstrate its practical application to metal ion chelation, explore its potential and limitations with the aid of simulations and statistical analyses, and elaborate on potential applications to protein-inhibitor interactions. Copyright © 2014 Elsevier Inc. All rights reserved.

  18. Relative receptor affinity comparisons among inhaled/intranasal corticosteroids: perspectives on clinical relevance

    Directory of Open Access Journals (Sweden)

    Hochhaus Günther

    2008-11-01

    Full Text Available Abstract Background Pharmacokinetic properties, dosing regimen, and potency at the site of action are among the factors that influence activity of a corticosteroid. The potency of a corticosteroid at the site of action is determined significantly by its affinity to the glucocorticoid receptor. Recent literature on topical corticosteroids reveals an increasing emphasis on comparative relative receptor affinity values as a key method of differentiating among various corticosteroid compounds, particularly with regard to clinical efficacy. Methods A response was formulated to: Valotis A, Högger P: Human receptor kinetics and lung tissue retention of the enhanced-affinity glucocorticoid fluticasone furoate. Respir Res 2007, 8:54. Results Relative receptor binding affinities, while often showing significant variability across different laboratories, are a valid parameter when a comparison of the pharmacological activity of various glucocorticoids at the site of action is desired. Unfortunately within this context, scientific literature including the article from Valotis and Högger, confuse differences in potency (concentration or dose necessary to achieve a certain effect with differences in efficacy (a quantitative difference in the overall maximum effect, even if all the receptors are occupied. All glucocorticoids will show the same efficacy as long as the selected dose will occupy the same number of receptors. Conclusion While relative receptor affinities are useful for comparing in vitro potencies of corticosteroids, these data are not representative of physiologic conditions and should not be used as a basis for comparing the presumed effectiveness of compounds in a clinical situation.

  19. Dietary Flavonoids as Xanthine Oxidase Inhibitors: Structure-Affinity and Structure-Activity Relationships.

    Science.gov (United States)

    Lin, Suyun; Zhang, Guowen; Liao, Yijing; Pan, Junhui; Gong, Deming

    2015-09-09

    The flavonoid family has been reported to possess a high potential for inhibition of xanthine oxidase (XO). This study concerned the structural aspects of inhibitory activities and binding affinities of flavonoids as XO inhibitors. The result indicated that the hydrophobic interaction was important in the binding of flavonoids to XO, and the XO inhibitory ability increased generally with increasing affinities within the class of flavones and flavonols. The planar structure and the C2═C3 double bonds of flavonoids were advantageous for binding to XO and for XO inhibition. Both the hydroxylation on ring B and the substitution at C3 were unfavorable for XO inhibition more profoundly than their XO affinity. The methylation greatly reduced the inhibition (0.75-3.07 times) but hardly affected the affinity. The bulky sugar substitutions of flavonoids decreased the inhibition (1.69-1.99 times) and lowered the affinities (4.20-9.22 times) to different degrees depending on the conjunction site.

  20. Analysis of Biological Interactions by Affinity Chromatography: Clinical and Pharmaceutical Applications.

    Science.gov (United States)

    Hage, David S

    2017-06-01

    The interactions between biochemical and chemical agents in the body are important in many clinical processes. Affinity chromatography and high-performance affinity chromatography (HPAC), in which a column contains an immobilized biologically related binding agent, are 2 methods that can be used to study these interactions. This review presents various approaches that can be used in affinity chromatography and HPAC to characterize the strength or rate of a biological interaction, the number and types of sites that are involved in this process, and the interactions between multiple solutes for the same binding agent. A number of applications for these methods are examined, with an emphasis on recent developments and high-performance affinity methods. These applications include the use of these techniques for fundamental studies of biological interactions, high-throughput screening of drugs, work with modified proteins, tools for personalized medicine, and studies of drug-drug competition for a common binding agent. The wide range of formats and detection methods that can be used with affinity chromatography and HPAC for examining biological interactions makes these tools attractive for various clinical and pharmaceutical applications. Future directions in the development of small-scale columns and the coupling of these methods with other techniques, such as mass spectrometry or other separation methods, should continue to increase the flexibility and ease with which these approaches can be used in work involving clinical or pharmaceutical samples. © 2016 American Association for Clinical Chemistry.

  1. Sequence2Vec: A novel embedding approach for modeling transcription factor binding affinity landscape

    KAUST Repository

    Dai, Hanjun

    2017-07-26

    Motivation: An accurate characterization of transcription factor (TF)-DNA affinity landscape is crucial to a quantitative understanding of the molecular mechanisms underpinning endogenous gene regulation. While recent advances in biotechnology have brought the opportunity for building binding affinity prediction methods, the accurate characterization of TF-DNA binding affinity landscape still remains a challenging problem. Results: Here we propose a novel sequence embedding approach for modeling the transcription factor binding affinity landscape. Our method represents DNA binding sequences as a hidden Markov model (HMM) which captures both position specific information and long-range dependency in the sequence. A cornerstone of our method is a novel message passing-like embedding algorithm, called Sequence2Vec, which maps these HMMs into a common nonlinear feature space and uses these embedded features to build a predictive model. Our method is a novel combination of the strength of probabilistic graphical models, feature space embedding and deep learning. We conducted comprehensive experiments on over 90 large-scale TF-DNA data sets which were measured by different high-throughput experimental technologies. Sequence2Vec outperforms alternative machine learning methods as well as the state-of-the-art binding affinity prediction methods.

  2. Sequence2Vec: a novel embedding approach for modeling transcription factor binding affinity landscape.

    Science.gov (United States)

    Dai, Hanjun; Umarov, Ramzan; Kuwahara, Hiroyuki; Li, Yu; Song, Le; Gao, Xin

    2017-11-15

    An accurate characterization of transcription factor (TF)-DNA affinity landscape is crucial to a quantitative understanding of the molecular mechanisms underpinning endogenous gene regulation. While recent advances in biotechnology have brought the opportunity for building binding affinity prediction methods, the accurate characterization of TF-DNA binding affinity landscape still remains a challenging problem. Here we propose a novel sequence embedding approach for modeling the transcription factor binding affinity landscape. Our method represents DNA binding sequences as a hidden Markov model which captures both position specific information and long-range dependency in the sequence. A cornerstone of our method is a novel message passing-like embedding algorithm, called Sequence2Vec, which maps these hidden Markov models into a common nonlinear feature space and uses these embedded features to build a predictive model. Our method is a novel combination of the strength of probabilistic graphical models, feature space embedding and deep learning. We conducted comprehensive experiments on over 90 large-scale TF-DNA datasets which were measured by different high-throughput experimental technologies. Sequence2Vec outperforms alternative machine learning methods as well as the state-of-the-art binding affinity prediction methods. Our program is freely available at https://github.com/ramzan1990/sequence2vec. xin.gao@kaust.edu.sa or lsong@cc.gatech.edu. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

  3. Peptide length significantly influences in vitro affinity for MHC class II molecules

    Science.gov (United States)

    O'Brien, Cathal; Flower, Darren R; Feighery, Conleth

    2008-01-01

    Background Class II Major Histocompatibility Complex (MHC) molecules have an open-ended binding groove which can accommodate peptides of varying lengths. Several studies have demonstrated that peptide flanking residues (PFRs) which lie outside the core binding groove can influence peptide binding and T cell recognition. By using data from the AntiJen database we were able to characterise systematically the influence of PFRs on peptide affinity for MHC class II molecules. Results By analysing 1279 peptide elongation events covering 19 distinct HLA alleles it was observed that, in general, peptide elongation resulted in increased MHC class II molecule affinity. It was also possible to determine an optimal peptide length for MHC class II affinity of approximately 18–20 amino acids; elongation of peptides beyond this length resulted in a null or negative effect on affinity. Conclusion The observed relationship between peptide length and MHC class II affinity has significant implications for the design of vaccines and the study of the epitopic basis of immunological disease. PMID:19036163

  4. 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.

  5. Automatic face naming by learning discriminative affinity matrices from weakly labeled images.

    Science.gov (United States)

    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.

  6. Alkali Metal Cation versus Proton and Methyl Cation Affinities: Structure and Bonding Mechanism.

    Science.gov (United States)

    Boughlala, Zakaria; Fonseca Guerra, Célia; Bickelhaupt, F Matthias

    2016-06-01

    We have analyzed the structure and bonding of gas-phase Cl-X and [HCl-X](+) complexes for X(+)= H(+), CH3 (+), Li(+), and Na(+), using relativistic density functional theory (DFT). We wish to establish a quantitative trend in affinities of the anionic and neutral Lewis bases Cl(-) and HCl for the various cations. The Cl-X bond becomes longer and weaker along X(+) = H(+), CH3 (+), Li(+), and Na(+). Our main purpose is to understand the heterolytic bonding mechanism behind the intrinsic (i.e., in the absence of solvent) alkali metal cation affinities (AMCA) and how this compares with and differs from those of the proton affinity (PA) and methyl cation affinity (MCA). Our analyses are based on Kohn-Sham molecular orbital (KS-MO) theory in combination with a quantitative energy decomposition analysis (EDA) that pinpoints the importance of the different features in the bonding mechanism. Orbital overlap appears to play an important role in determining the trend in cation affinities.

  7. Gaussian and Affine Approximation of Stochastic Diffusion Models for Interest and Mortality Rates

    Directory of Open Access Journals (Sweden)

    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.

  8. A Combination of Structural and Empirical Analyses Delineates the Key Contacts Mediating Stability and Affinity Increases in an Optimized Biotherapeutic Single-chain Fv (scFv).

    Science.gov (United States)

    Tu, Chao; Terraube, Virginie; Tam, Amy Sze Pui; Stochaj, Wayne; Fennell, Brian J; Lin, Laura; Stahl, Mark; LaVallie, Edward R; Somers, Will; Finlay, William J J; Mosyak, Lydia; Bard, Joel; Cunningham, Orla

    2016-01-15

    Fully-human single-chain Fv (scFv) proteins are key potential building blocks of bispecific therapeutic antibodies, but they often suffer from manufacturability and clinical development limitations such as instability and aggregation. The causes of these scFv instability problems, in proteins that should be theoretically stable, remains poorly understood. To inform the future development of such molecules, we carried out a comprehensive structural analysis of the highly stabilized anti-CXCL13 scFv E10. E10 was derived from the parental 3B4 using complementarity-determining region (CDR)-restricted mutagenesis and tailored selection and screening strategies, and carries four mutations in VL-CDR3. High-resolution crystal structures of parental 3B4 and optimized E10 scFvs were solved in the presence and absence of human CXCL13. In parallel, a series of scFv mutants was generated to interrogate the individual contribution of each of the four mutations to stability and affinity improvements. In combination, these analyses demonstrated that the optimization of E10 was primarily mediated by removing clashes between both the VL and the VH, and between the VL and CXCL13. Importantly, a single, germline-encoded VL-CDR3 residue mediated the key difference between the stable and unstable forms of the scFv. This work demonstrates that, aside from being the critical mediators of specificity and affinity, CDRs may also be the primary drivers of biotherapeutic developability. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  9. On The Roman Domination Stable Graphs

    Directory of Open Access Journals (Sweden)

    Hajian Majid

    2017-11-01

    Full Text Available A Roman dominating function (or just RDF on a graph G = (V,E is a function f : V → {0, 1, 2} satisfying the condition that every vertex u for which f(u = 0 is adjacent to at least one vertex v for which f(v = 2. The weight of an RDF f is the value f(V (G = Pu2V (G f(u. The Roman domination number of a graph G, denoted by R(G, is the minimum weight of a Roman dominating function on G. A graph G is Roman domination stable if the Roman domination number of G remains unchanged under removal of any vertex. In this paper we present upper bounds for the Roman domination number in the class of Roman domination stable graphs, improving bounds posed in [V. Samodivkin, Roman domination in graphs: the class RUV R, Discrete Math. Algorithms Appl. 8 (2016 1650049].

  10. Design of optically stable image reflector system.

    Science.gov (United States)

    Tsai, Chung-Yu

    2013-08-01

    The design of a partially optically stable (POS) reflector system, in which the exit ray direction and image pose are unchanged as the reflector system rotates about a specific directional vector, was presented in an earlier study by the current group [Appl. Phys. B100, 883-890 (2010)]. The present study further proposes an optically stable image (OSI) reflector system, in which not only is the optical stability property of the POS system retained, but the image position and total ray path length are also fixed. An analytical method is proposed for the design of OSI reflector systems comprising multiple reflectors. The validity of the proposed approach is demonstrated by means of two illustrative examples.

  11. Stable microfluidic flow focusing using hydrostatics.

    Science.gov (United States)

    Gnyawali, Vaskar; Saremi, Mohammadali; Kolios, Michael C; Tsai, Scott S H

    2017-05-01

    We present a simple technique to generate stable hydrodynamically focused flows by driving the flow with hydrostatic pressure from liquid columns connected to the inlets of a microfluidic device. Importantly, we compare the focused flows generated by hydrostatic pressure and classical syringe pump driven flows and find that the stability of the hydrostatic pressure driven technique is significantly better than the stability achieved via syringe pumps, providing fluctuation-free focused flows that are suitable for sensitive microfluidic flow cytometry applications. We show that the degree of flow focusing with the hydrostatic method can be accurately controlled by the simple tuning of the liquid column heights. We anticipate that this approach to stable flow focusing will find many applications in microfluidic cytometry technologies.

  12. Utilization of stable isotopes in medicine

    International Nuclear Information System (INIS)

    1980-11-01

    The ten lectures given at this round table are presented together with a discussion. Five lectures, relating to studies in which deuterium oxide was employed as a tracer of body water, dealt with pulmonary water measurements in man and animals, the total water pool in adipose subjects, and liquid compartments in children undergoing hemodyalisis. The heavy water is analysed by infrared spectrometry and a new double spectrodoser is described. Two studies using 13 C as tracer, described the diagnosis of liver troubles and diabetes respectively. A general review of the perspectives of the application of stable isotopes in clinical medicine is followed by a comparison of the use of stable and radioactive isotopes in France [fr

  13. Efficient expression of codon-adapted affinity tagged super folder green fluorescent protein for synchronous protein localization and affinity purification studies in Tetrahymena thermophila.

    Science.gov (United States)

    Yilmaz, Gürkan; Arslanyolu, Muhittin

    2015-03-25

    A superior Green Fluorescent Protein (GFP) mutant, known as superfolder GFP (sfGFP), is more soluble, faster folding, and is the brightest of the known GFP mutants. This study aimed to create a codon-adapted sfGFP tag (TtsfGFP) for simultaneous protein localization and affinity purification in Tetrahymena thermophila. In vivo fluorescence spectroscopic analyses of clones carrying a codon-adapted and 6 × His tagged TtsfGFP cassette showed approximately 2-4-fold increased fluorescence emission compared with the control groups at 3 h. Fluorescence microscopy also revealed that TtsfGFP reached its emission maxima at 100 min, which was much earlier than controls expressing EGFP and sfGFP (240 min). A T. thermophila ATP-dependent DNA ligase domain containing hypothetical gene (H) was cloned into the 3' end of 6 × His-TtsfGFP to assess the affinity/localization dual tag feature. Fluorescence microscopy of the 6 × His-TtsfGFP-H clone confirmed its localization in the macro- and micronucleus of vegetative T. thermophila. Simultaneous affinity purification of TtsfGFP and TtsfGFP-H with Ni-NTA beads was feasible, as shown by Ni-NTA purified proteins analysis by SDS-PAGE and western blotting. We successfully codon adapted the N-terminal 6 × His-TtsfGFP tag and showed that it could be used for protein localization and affinity purification simultaneously in T. thermophila. We believe that this dual tag will advance T. thermophila studies by providing strong visual traceability of the target protein in vivo and in vitro during recombinant production of heterologous and homologous proteins.

  14. Thermally Stable, Latent Olefin Metathesis Catalysts

    OpenAIRE

    Thomas, Renee M.; Fedorov, Alexey; Keitz, Benjamin K.; Grubbs, Robert H.

    2011-01-01

    Highly thermally stable N-aryl,N-alkyl N-heterocyclic carbene (NHC) ruthenium catalysts were designed and synthesized for latent olefin metathesis. These catalysts showed excellent latent behavior toward metathesis reactions, whereby the complexes were inactive at ambient temperature and initiated at elevated temperatures, a challenging property to achieve with second generation catalysts. A sterically hindered N-tert-butyl substituent on the NHC ligand of the ruthenium complex was found to i...

  15. The nature of stable insomnia phenotypes.

    Science.gov (United States)

    Pillai, Vivek; Roth, Thomas; Drake, Christopher L

    2015-01-01

    We examined the 1-y stability of four insomnia symptom profiles: sleep onset insomnia; sleep maintenance insomnia; combined onset and maintenance insomnia; and neither criterion (i.e., insomnia cases that do not meet quantitative thresholds for onset or maintenance problems). Insomnia cases that exhibited the same symptom profile over a 1-y period were considered to be phenotypes, and were compared in terms of clinical and demographic characteristics. Longitudinal. Urban, community-based. Nine hundred fifty-four adults with Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition based current insomnia (46.6 ± 12.6 y; 69.4% female). None. At baseline, participants were divided into four symptom profile groups based on quantitative criteria. Follow-up assessment 1 y later revealed that approximately 60% of participants retained the same symptom profile, and were hence judged to be phenotypes. Stability varied significantly by phenotype, such that sleep onset insomnia (SOI) was the least stable (42%), whereas combined insomnia (CI) was the most stable (69%). Baseline symptom groups (cross-sectionally defined) differed significantly across various clinical indices, including daytime impairment, depression, and anxiety. Importantly, however, a comparison of stable phenotypes (longitudinally defined) did not reveal any differences in impairment or comorbid psychopathology. Another interesting finding was that whereas all other insomnia phenotypes showed evidence of an elevated wake drive both at night and during the day, the 'neither criterion' phenotype did not; this latter phenotype exhibited significantly higher daytime sleepiness despite subthreshold onset and maintenance difficulties. By adopting a stringent, stability-based definition, this study offers timely and important data on the longitudinal trajectory of specific insomnia phenotypes. With the exception of daytime sleepiness, few clinical differences are apparent across stable phenotypes.

  16. A belief-based evolutionarily stable strategy

    OpenAIRE

    Deng, Xinyang; Wang, Zhen; Liu, Qi; Deng, Yong; Mahadevan, Sankaran

    2014-01-01

    As an equilibrium refinement of the Nash equilibrium, evolutionarily stable strategy (ESS) is a key concept in evolutionary game theory and has attracted growing interest. An ESS can be either a pure strategy or a mixed strategy. Even though the randomness is allowed in mixed strategy, the selection probability of pure strategy in a mixed strategy may fluctuate due to the impact of many factors. The fluctuation can lead to more uncertainty. In this paper, such uncertainty involved in mixed st...

  17. Stable iodine prophylaxis. Recommendations of the 2nd UK Working Group on Stable Iodine Prophylaxis

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2001-07-01

    The Working Group reviewed the revised Who guidance and the information published since 1991 on the risks of thyroid cancer in children from radioiodine and the risks of side effects from stable iodine. In particular, it reviewed data compiled on the incidence of thyroid cancers in children following the accident at the Chernobyl nuclear power plant in 1986. It considered whether the NRPB Earls were still appropriate, in the light of the new data. It also reviewed a range of other recommendations given by the 1st Working Group, concerning the chemical form of stable iodine tablets and practical issues concerning implementation of stable iodine prophylaxis. Finally, it reviewed the Patient Information Leaflet that is required, by law, to be included in each box of tablets and provided suggestions for information to be included in a separate information leaflet to be handed out to the public when stable iodine tablets are distributed.

  18. Stable and rigid DTPA-like paramagnetic tags suitable for in vitro and in situ protein NMR analysis.

    Science.gov (United States)

    Chen, Jia-Liang; Zhao, Yu; Gong, Yan-Jun; Pan, Bin-Bin; Wang, Xiao; Su, Xun-Cheng

    2018-02-01

    Organic synthesis of a ligand with high binding affinities for paramagnetic lanthanide ions is an effective way of generating paramagnetic effects on proteins. These paramagnetic effects manifested in high-resolution NMR spectroscopy are valuable dynamic and structural restraints of proteins and protein-ligand complexes. A paramagnetic tag generally contains a metal chelating moiety and a reactive group for protein modification. Herein we report two new DTPA-like tags, 4PS-PyDTTA and 4PS-6M-PyDTTA that can be site-specifically attached to a protein with a stable thioether bond. Both protein-tag adducts form stable lanthanide complexes, of which the binding affinities and paramagnetic tensors are tunable with respect to the 6-methyl group in pyridine. Paramagnetic relaxation enhancement (PRE) effects of Gd(III) complex on protein-tag adducts were evaluated in comparison with pseudocontact shift (PCS), and the results indicated that both 4PS-PyDTTA and 4PS-6M-PyDTTA tags are rigid and present high-quality PREs that are crucially important in elucidation of the dynamics and interactions of proteins and protein-ligand complexes. We also show that these two tags are suitable for in-situ protein NMR analysis.

  19. Detonation of Meta-stable Clusters

    Energy Technology Data Exchange (ETDEWEB)

    Kuhl, Allen; Kuhl, Allen L.; Fried, Laurence E.; Howard, W. Michael; Seizew, Michael R.; Bell, John B.; Beckner, Vincent; Grcar, Joseph F.

    2008-05-31

    We consider the energy accumulation in meta-stable clusters. This energy can be much larger than the typical chemical bond energy (~;;1 ev/atom). For example, polymeric nitrogen can accumulate 4 ev/atom in the N8 (fcc) structure, while helium can accumulate 9 ev/atom in the excited triplet state He2* . They release their energy by cluster fission: N8 -> 4N2 and He2* -> 2He. We study the locus of states in thermodynamic state space for the detonation of such meta-stable clusters. In particular, the equilibrium isentrope, starting at the Chapman-Jouguet state, and expanding down to 1 atmosphere was calculated with the Cheetah code. Large detonation pressures (3 and 16 Mbar), temperatures (12 and 34 kilo-K) and velocities (20 and 43 km/s) are a consequence of the large heats of detonation (6.6 and 50 kilo-cal/g) for nitrogen and helium clusters respectively. If such meta-stable clusters could be synthesized, they offer the potential for large increases in the energy density of materials.

  20. 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.

  1. On-bead chemical synthesis and display of phosphopeptides for affinity pull-down proteomics

    DEFF Research Database (Denmark)

    Malene, Brandt; Madsen, Jens C.; Bunkenborg, Jakob

    2006-01-01

    (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......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....... 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....

  2. A variational principle giving gravitational 'superpotentials', the affine connection, Riemann tensor, and Einstein field equations

    International Nuclear Information System (INIS)

    Stachel, J.

    1977-01-01

    A first-order Lagrangian is given, from which follow the definitions of the fully covariant form of the Riemann tensor Rsub(μνkappalambda) in terms of the affine connection and metric; the definition of the affine connection in terms of the metric; the Einstein field equations; and the definition of a set of gravitational 'superpotentials' closely connected with the Komar conservation laws (Phys. Rev.; 113:934 (1959)). Substitution of the definition of the affine connection into this Lagrangian results in a second-order Lagrangian, from which follow the definition of the fully covariant Riemann tensor in terms of the metric, the Einstein equations, and the definition of the gravitational 'superpotentials'. (author)

  3. Lie algebraic discussion for affinity based information diffusion in social networks

    Directory of Open Access Journals (Sweden)

    Shang Yilun

    2017-11-01

    Full Text Available In this paper we develop a dynamical information diffusion model which features the affinity of people with information disseminated in social networks. Four types of agents, i.e., susceptible, informed, known, and refractory ones, are involved in the system, and the affinity mechanism composing of an affinity threshold which represents the fitness of information to be propagated is incorporated. The model can be generally described by a time-inhomogeneous Markov chain, which is governed by its master (Kolmogorov equation. Based on the Wei-Norman method, we derive analytical solutions of the model by constructing a low-dimensional Lie algebra. Numerical examples are provided to illustrate the obtained theoretical results. This study provides useful insights into the closed-form solutions of complex social dynamics models through the Lie algebra method.

  4. A novel approach for separating bacteriophages from other bacteriophages using affinity chromatography and phage display.

    Science.gov (United States)

    Ceglarek, Izabela; Piotrowicz, Agnieszka; Lecion, Dorota; Miernikiewicz, Paulina; Owczarek, Barbara; Hodyra, Katarzyna; Harhala, Marek; Górski, Andrzej; Dąbrowska, Krystyna

    2013-11-14

    Practical applications of bacteriophages in medicine and biotechnology induce a great need for technologies of phage purification. None of the popular methods offer solutions for separation of a phage from another similar phage. We used affinity chromatography combined with competitive phage display (i) to purify T4 bacteriophage from bacterial debris and (ii) to separate T4 from other contaminating bacteriophages. In 'competitive phage display' bacterial cells produced both wild types of the proteins (expression from the phage genome) and the protein fusions with affinity tags (expression from the expression vectors). Fusion proteins were competitively incorporated into the phage capsid. It allowed effective separation of T4 from a contaminating phage on standard affinity resins.

  5. Lie algebraic discussion for affinity based information diffusion in social networks

    Science.gov (United States)

    Shang, Yilun

    2017-11-01

    In this paper we develop a dynamical information diffusion model which features the affinity of people with information disseminated in social networks. Four types of agents, i.e., susceptible, informed, known, and refractory ones, are involved in the system, and the affinity mechanism composing of an affinity threshold which represents the fitness of information to be propagated is incorporated. The model can be generally described by a time-inhomogeneous Markov chain, which is governed by its master (Kolmogorov) equation. Based on the Wei-Norman method, we derive analytical solutions of the model by constructing a low-dimensional Lie algebra. Numerical examples are provided to illustrate the obtained theoretical results. This study provides useful insights into the closed-form solutions of complex social dynamics models through the Lie algebra method.

  6. CYP 2D6 Binding Affinity Predictions Using Multiple Ligand and Protein Conformations

    Directory of Open Access Journals (Sweden)

    Lovorka Perić-Hassler

    2013-12-01

    Full Text Available Because of the large flexibility and malleability of Cytochrome P450 enzymes (CYPs, in silico prediction of CYP binding affinities to drugs and other xenobiotic compounds is a true challenge. In the current work, we use an iterative linear interaction energy (LIE approach to compute CYP binding affinities from molecular dynamics (MD simulation. In order to improve sampling of conformational space, we combine results from simulations starting with different relevant protein-ligand geometries. For calculated binding free energies of a set of thiourea compounds binding to the flexible CYP 2D6 isoform, improved correlation with experiment was obtained by combining results of MD runs starting from distinct protein conformations and ligand-binding orientations. This accuracy was obtained from relatively short MD simulations, which makes our approach computationally attractive for automated calculations of ligand-binding affinities to flexible proteins such as CYPs.

  7. Dynamics behind affinity maturation of an anti-HCMV antibody family influencing antigen binding

    KAUST Repository

    Di Palma, Francesco

    2017-08-03

    The investigation of antibody affinity maturation and its effects on antigen binding is important with respect to understanding the regulation of the immune response. To shed light on this crucial process, we analyzed two Igs neutralizing the human cytomegalovirus: the primary germline antibody M2J1 and its related mature antibody 8F9. Both antibodies target the AD-2S1 epitope of the gB envelope protein and are considered to establish similar interactions with the cognate antigen. We used molecular dynamics simulations to understand the effect of mutations on the antibody–antigen interactions. The results provide a qualitative explanation for the increased 8F9 peptide affinity compared with that of M2J1. The emerging atomistic-detailed description of these complexes reveals the molecular effects of the somatic hypermutations occurring during affinity maturation.

  8. [Affine transformation-based automatic registration for peripheral digital subtraction angiography (DSA)].

    Science.gov (United States)

    Kong, Gang; Dai, Dao-Qing; Zou, Lu-Min

    2008-07-01

    In order to remove the artifacts of peripheral digital subtraction angiography (DSA), an affine transformation-based automatic image registration algorithm is introduced here. The whole process is described as follows: First, rectangle feature templates are constructed with their centers of the extracted Harris corners in the mask, and motion vectors of the central feature points are estimated using template matching technology with the similarity measure of maximum histogram energy. And then the optimal parameters of the affine transformation are calculated with the matrix singular value decomposition (SVD) method. Finally, bilinear intensity interpolation is taken to the mask according to the specific affine transformation. More than 30 peripheral DSA registrations are performed with the presented algorithm, and as the result, moving artifacts of the images are removed with sub-pixel precision, and the time consumption is less enough to satisfy the clinical requirements. Experimental results show the efficiency and robustness of the algorithm.

  9. Affinity of tri-iodothyronine(T3) to lymphocytes in thyroid cancer patients

    International Nuclear Information System (INIS)

    Jeevanram, R.K.; Narkar, A.A.; Ganatra, R.D.; Shah, D.H.

    1978-01-01

    Peripheral blood lymphocytes (PBL) of thyroid cancer patients and 5 normal subjects were studied for their affinity towards 125 I labelled tri-iodothyronine ( 125 I-T 3 ). The mean affinity constant K for PBL of normal subjects was 2.94 + 0.47 x 10 11 litre/mole and for thyroid cancer patients was 1.75 + 0.44 x 10 11 litre/mole. The binding affinity of the PBL of thyroid cancer patients should have been greater because of (a) lack of thyroid hormones resulting from removal of thyroid gland, and (b) higher levels of thyroid stimulating hormone (TSH) which is known to increase the binding of T 3 to the cells. The lowered T 3 binding of PBL of thyroid cancer patients is explained on the basis of the morphological changes on the lymphocytes of cancer patients. (auth.)

  10. Two stable steady states in the Hodgkin-Huxley axons

    OpenAIRE

    Aihara, K.; Matsumoto, G.

    1983-01-01

    Two stable steady states were found in the numerical solution of the Hodgkin-Huxley equations for the intact squid axon bathed in potassium-rich sea water with an externally applied inward current. Under the conditions the two stable steady-states exist, the Hodgkin-Huxley equations have a complex bifurcation structure including, in addition to the two stable steady-states, a stable limit cycle, two unstable equilibrium points, and one asymptotically stable equilibrium point. It was also conc...

  11. A new affine-invariant image matching method based on SIFT

    Science.gov (United States)

    Wang, Peng-cheng; Chen, Qian; Chen, Hai-xin; Cheng, Hong-chang; Gong, Zhen-fei

    2013-09-01

    Local invariant feature extraction, as one of the main problems in the field of computer vision, has been widely applied to image matching, splicing and target recognition etc. Lowe's scale invariant feature transform (known as SIFT) algorithm has attracted much attention due to its invariance to scale, rotation and illumination. However, SIFT is not robust to affine deformations, because it is based on the DoG detector which extracts keypoints in a circle region. Besides, the feature descriptor is represented by a 128-dimensional vector, which means that the algorithm complexity is extremely large especially when there is a great quantity of keypoints in the image. In this paper, a new feature descriptor, which is robust to affine deformations, is proposed. Considering that circles turn to be ellipses after affine deformations, some improvements have been made. Firstly, the Gaussian image pyramids are constructed by convoluting the source image and the elliptical Gaussian kernel with two volatile parameters, orientation and eccentricity. In addition, the two parameters are discretely selected in order to imitate the possibilities of the affine deformation, which can make sure that anisotropic regions are transformed into isotropic ones. Next, all extreme points can be extracted as the candidates for the affine-invariant keypoints in the image pyramids. After accurate keypoints localization is performed, the secondary moment of the keypoints' neighborhood is calculated to identify the elliptical region which is affineinvariant, the same as SIFT, the main orientation of the keypoints can be determined and the feature descriptor is generated based on the histogram constructed in this region. At last, the PCA method for the 128-dimensional descriptor's reduction is used to improve the computer calculating efficiency. The experiments show that this new algorithm inherits all SIFT's original advantages, and has a good resistance to affine deformations; what's more, it

  12. Quantifying high-affinity binding of hydrophobic ligands by isothermal titration calorimetry.

    Science.gov (United States)

    Krainer, Georg; Broecker, Jana; Vargas, Carolyn; Fanghänel, Jörg; Keller, Sandro

    2012-12-18

    A fast and reliable quantification of the binding thermodynamics of hydrophobic high-affinity ligands employing a new calorimetric competition experiment is described. Although isothermal titration calorimetry is the method of choice for a quantitative characterization of intermolecular interactions in solution, a reliable determination of a dissociation constant (K(D)) is typically limited to the range 100 μM > K(D) > 1 nM. Interactions displaying higher or lower K(D) values can be assessed indirectly, provided that a suitable competing ligand is available whose K(D) falls within the directly accessible affinity window. This established displacement assay, however, requires the high-affinity ligand to be soluble at high concentrations in aqueous buffer and, consequently, poses serious problems in the study of protein binding involving small-molecule ligands dissolved in organic solvents--a familiar case in many drug-discovery projects relying on compound libraries. The calorimetric competition assay introduced here overcomes this limitation, thus allowing for a detailed thermodynamic description of high-affinity receptor-ligand interactions involving poorly water-soluble compounds. Based on a single titration of receptor into a dilute mixture of the two competing ligands, this competition assay provides accurate and precise values for the dissociation constants and binding enthalpies of both high- and moderate-affinity ligands. We discuss the theoretical background underlying the approach, demonstrate its practical application to metal ion chelation and high-affinity protein-inhibitor interactions, and explore its potential and limitations with the aid of simulations and statistical analyses.

  13. 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.

  14. Selective induction of high-ouabain-affinity isoform of Na+-K+-ATPase by thyroid hormone

    International Nuclear Information System (INIS)

    Haber, R.S.; Loeb, J.N.

    1988-01-01

    The administration of thyroid hormone is known to result in an induction of the Na + -K + -adenosinetriphosphatase (Na + -K + -ATPase) in rat skeletal muscle and other thyroid hormone-responsive tissues. Since the Na + -K + -ATPase in a variety of mammalian tissues has recently been reported to exist in at least two forms distinguishable by differing affinities for the inhibitory cardiac glycoside ouabain. The authors have studied the effects of 3,3',5-triiodo-L-thyronine (T 3 ) treatment on these two forms of the enzyme in rat diaphragm. The inhibition of Na + -K + -ATPase activity in a crude membrane fraction by varying concentrations of ouabain conformed to a biphasic pattern consistent with the presence of two distinct isoforms with inhibition constants (K I s) for ouabain of ∼10 -7 and 10 -4 M, respectively. Measurement of the specific binding of [ 3 H]ouabain to these membranes confirmed the presence of a class of high-affinity ouabain binding sites with a dissociation constant (K d ) of slightly less than 10 -7 M, whose maximal binding capacity was increased by T 3 treatment by 185%. Binding studies in unfractionated homogenates of diaphragm similarly demonstrated the presence of high-affinity sites whose maximal binding capacity was increased by T 3 treatment. Quantitation of both the high- and low-ouabain-affinity forms of the Na + -K + -ATPase by ouabain-dependent phosphorylation from [ 32 P]orthophosphate confirmed that T 3 treatment markedly increased the number of high-affinity sites while having little effect on the number of low-affinity sites. These observations provide, to our knowledge, the first demonstration that these two forms of the Na + -K + -ATPase are subject to selective hormonal induction

  15. From Stein to Weinstein and back symplectic geometry of affine complex manifolds

    CERN Document Server

    Cieliebak, Kai

    2013-01-01

    A beautiful and comprehensive introduction to this important field. -Dusa McDuff, Barnard College, Columbia University This excellent book gives a detailed, clear, and wonderfully written treatment of the interplay between the world of Stein manifolds and the more topological and flexible world of Weinstein manifolds. Devoted to this subject with a long history, the book serves as a superb introduction to this area and also contains the authors' new results. -Tomasz Mrowka, MIT This book is devoted to the interplay between complex and symplectic geometry in affine complex manifolds. Affine co

  16. Recognition of genetically modified product based on affinity propagation clustering and terahertz spectroscopy

    Science.gov (United States)

    Liu, Jianjun; Kan, Jianquan

    2018-04-01

    In this paper, based on the terahertz spectrum, a new identification method of genetically modified material by support vector machine (SVM) based on affinity propagation clustering is proposed. This algorithm mainly uses affinity propagation clustering algorithm to make cluster analysis and labeling on unlabeled training samples, and in the iterative process, the existing SVM training data are continuously updated, when establishing the identification model, it does not need to manually label the training samples, thus, the error caused by the human labeled samples is reduced, and the identification accuracy of the model is greatly improved.

  17. A pharmacological profile of the high-affinity GluK5 kainate receptor

    DEFF Research Database (Denmark)

    Møllerud, Stine; Kastrup, Jette Sandholm Jensen; Pickering, Darryl S

    2016-01-01

    pattern of native rat brain GluK5. A pharmacological profile of the high-affinity kainate receptor GluK5 is described which is distinct from the profiles of other kainate receptors (GluK1-3). The 27 tested ligands generally show a preferential affinity to GluK1 over GluK5, the exceptions being...... disorder), selective GluK5 ligands could have therapeutic potential. The distinct pharmacological profile of GluK5 suggests that it would be possible to design ligands with selectivity towards GluK5....

  18. Cubic systems with invariant affine straight lines of total parallel multiplicity seven

    Directory of Open Access Journals (Sweden)

    Alexandru Suba

    2013-12-01

    Full Text Available In this article, we study the planar cubic differential systems with invariant affine straight lines of total parallel multiplicity seven. We classify these system according to their geometric properties encoded in the configurations of invariant straight lines. We show that there are only 17 different topological phase portraits in the Poincar\\'e disc associated to this family of cubic systems up to a reversal of the sense of their orbits, and we provide representatives of every class modulo an affine change of variables and rescaling of the time variable.

  19. Near-affine-invariant texture learning for lung tissue analysis using isotropic wavelet frames.

    Science.gov (United States)

    Depeursinge, Adrien; Van de Ville, Dimitri; Platon, Alexandra; Geissbuhler, Antoine; Poletti, Pierre-Alexandre; Müller, Henning

    2012-07-01

    We propose near-affine-invariant texture descriptors derived from isotropic wavelet frames for the characterization of lung tissue patterns in high-resolution computed tomography (HRCT) imaging. Affine invariance is desirable to enable learning of nondeterministic textures without a priori localizations, orientations, or sizes. When combined with complementary gray-level histograms, the proposed method allows a global classification accuracy of 76.9% with balanced precision among five classes of lung tissue using a leave-one-patient-out cross validation, in accordance with clinical practice.

  20. Quantum properties of affine-metric gravity with the cosmological term

    Science.gov (United States)

    Baurov, A. Yu; Pronin, P. I.; Stepanyantz, K. V.

    2018-04-01

    The paper contains analysis of the one-loop effective action for affine-metric gravity of the Hilbert–Einstein type with the cosmological term. We discuss different approaches to the calculation of the effective action, which depends on two independent variables, namely, the metric tensor and the affine connection. In the one-loop approximation we explain how the effective action can be obtained, if, at the first step of the calculation, the metric tensor is integrated out. It is demonstrated that the result is the same as in the case when one starts by integrating out the connection.