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Sample records for bound receptor based

  1. A python-based docking program utilizing a receptor bound ligand shape: PythDock.

    Science.gov (United States)

    Chung, Jae Yoon; Cho, Seung Joo; Hah, Jung-Mi

    2011-09-01

    PythDock is a heuristic docking program that uses Python programming language with a simple scoring function and a population based search engine. The scoring function considers electrostatic and dispersion/repulsion terms. The search engine utilizes a particle swarm optimization algorithm. A grid potential map is generated using the shape information of a bound ligand within the active site. Therefore, the searching area is more relevant to the ligand binding. To evaluate the docking performance of PythDock, two well-known docking programs (AutoDock and DOCK) were also used with the same data. The accuracy of docked results were measured by the difference of the ligand structure between x-ray structure, and docked pose, i.e., average root mean squared deviation values of the bound ligand were compared for fourteen protein-ligand complexes. Since the number of ligands' rotational flexibility is an important factor affecting the accuracy of a docking, the data set was chosen to have various degrees of flexibility. Although PythDock has a scoring function simpler than those of other programs (AutoDock and DOCK), our results showed that PythDock predicted more accurate poses than both AutoDock4.2 and DOCK6.2. This indicates that PythDock could be a useful tool to study ligand-receptor interactions and could also be beneficial in structure based drug design.

  2. Variables Bounding Based Retiming Algorithm

    Institute of Scientific and Technical Information of China (English)

    宫宗伟; 林争辉; 陈后鹏

    2002-01-01

    Retiming is a technique for optimizing sequential circuits. In this paper, wediscuss this problem and propose an improved retiming algorithm based on variables bounding.Through the computation of the lower and upper bounds on variables, the algorithm can signi-ficantly reduce the number of constraints and speed up the execution of retiming. Furthermore,the elements of matrixes D and W are computed in a demand-driven way, which can reducethe capacity of memory. It is shown through the experimental results on ISCAS89 benchmarksthat our algorithm is very effective for large-scale sequential circuits.

  3. Structure of the [delta]-opioid receptor bound to naltrindole

    Energy Technology Data Exchange (ETDEWEB)

    Granier, Sébastien; Manglik, Aashish; Kruse, Andrew C.; Kobilka, Tong Sun; Thian, Foon Sun; Weis, William I.; Kobilka, Brian K. (Stanford-MED)

    2012-07-11

    The opioid receptor family comprises three members, the {mu}-, {delta}- and {kappa}-opioid receptors, which respond to classical opioid alkaloids such as morphine and heroin as well as to endogenous peptide ligands like endorphins. They belong to the G-protein-coupled receptor (GPCR) superfamily, and are excellent therapeutic targets for pain control. The {delta}-opioid receptor ({delta}-OR) has a role in analgesia, as well as in other neurological functions that remain poorly understood. The structures of the {mu}-OR and {kappa}-OR have recently been solved. Here we report the crystal structure of the mouse {delta}-OR, bound to the subtype-selective antagonist naltrindole. Together with the structures of the {mu}-OR and {kappa}-OR, the {delta}-OR structure provides insights into conserved elements of opioid ligand recognition while also revealing structural features associated with ligand-subtype selectivity. The binding pocket of opioid receptors can be divided into two distinct regions. Whereas the lower part of this pocket is highly conserved among opioid receptors, the upper part contains divergent residues that confer subtype selectivity. This provides a structural explanation and validation for the 'message-address' model of opioid receptor pharmacology, in which distinct 'message' (efficacy) and 'address' (selectivity) determinants are contained within a single ligand. Comparison of the address region of the {delta}-OR with other GPCRs reveals that this structural organization may be a more general phenomenon, extending to other GPCR families as well.

  4. Mutually Unbiased Bases and Bound Entanglement

    OpenAIRE

    Hiesmayr, Beatrix C.; Löffler, Wolfgang

    2013-01-01

    In this contribution we relate two different key concepts: mutually unbiased bases (MUBs) and entanglement; in particular we focus on bound entanglement, i.e. highly mixed states which cannot be distilled by local operations and classical communications. For a certain class of states --for which the state-space forms a "magic" simplex-- we analyze the set of bound entangled states detected by the MUB criterion for different dimensions d and number of particles n. We find that the geometry is ...

  5. Bounded divergence measures based on Bhattacharyya coefficient

    CERN Document Server

    Roman, Ahmed; Shastry, Mahesh C

    2012-01-01

    We introduce a new class of entropy based measure for calculating the distance between probability distributions. Our measure, called the bounded Bhattacharyya distance (BBD) is based on the Bhattacharyya distance, and is symmetric, positive semi-definite, and bounded. Unlike the Kullback-Leibler divergence, BBD does not require probability density functions to be absolutely continuous with respect to each other. We show that BBD belongs to the class of Csiszars f-divergences and derive certain relationship between BBD and well known measures such as Bhattacharyya, Hellinger and Jensen-Shannon divergence. Bounds on Bayesian error probability are established with BBD measure. The second derivative of BBD is proportional to the Fishers information. For distributions with vector valued parameters of the same family, the curvature matrix can be used to get the Rao's geodesic distance between parametric distributions.

  6. Multiparameter flow cytometry of a pH sensitive ligand bound to receptors and inside cells

    Energy Technology Data Exchange (ETDEWEB)

    Fay, S.P.; Habbersett, R.; Posner, R.G.; Domalewski, M.D.; Freer, R.J.; Pierson, E.; Whittaker, J.; Haugland, R.P.; Sklar, L.A. (Univ. of New Mexico, Albuquerque (United States) Los Alamos National Lab., NM (United States))

    1993-01-01

    Because fluoresceinated ligands of the neutrophil formyl peptide receptor can be protonated either upon binding to the receptor on the cell surface or in acidified intracellular compartments, the authors synthesized a ligand conjugated to the pH sensitive fluorescent probe SNAFL (CHO-Met-Leu-Phe-Phe-Lys-SNAFL). In the three laser flow cytometer at LANL, protonated dye is excited at 488 nm and emits at 530 nm; unprotonated dye is excited at 568 nm and emits at 650 nm. Detection at the isobestic and isoemissive points at 528 and 600 nm is used to keep track of variations in ligand concentration from sample to sample. The SNAFL-ligand bound to HL-60 cells (which overexpress the formyl peptide receptor) was compared to the free ligand in solution over a pH range from 6.5 to 9.0. The results suggest that the ligand bound to cell surface receptors was protonated in the binding pocket, possibly by virtue of its proximity to His 90, based on sequence data. When the cells were raised from 4[degrees] to 37[degrees], they also observed a time-dependent acidification of the ligand, indicative of ligand-receptor processing beginning 3-4 minutes after internalization.

  7. Upper bounds for reversible circuits based on Young subgroups

    DEFF Research Database (Denmark)

    Abdessaied, Nabila; Soeken, Mathias; Thomsen, Michael Kirkedal;

    2014-01-01

    We present tighter upper bounds on the number of Toffoli gates needed in reversible circuits. Both multiple controlled Toffoli gates and mixed polarity Toffoli gates have been considered for this purpose. The calculation of the bounds is based on a synthesis approach based on Young subgroups that...... that results in circuits using a more generalized gate library. Starting from an upper bound for this library we derive new bounds which improve the existing bound by around 77%. © 2014 Elsevier B.V. All rights reserved....

  8. NMR structure and dynamics of the agonist dynorphin peptide bound to the human kappa opioid receptor

    OpenAIRE

    O’Connor, Casey; White, Kate L.; Doncescu, Nathalie; Didenko, Tatiana; Roth, Bryan L.; Czaplicki, Georges; Stevens, Raymond C.; Wüthrich, Kurt; Milon, Alain

    2015-01-01

    The human kappa opioid receptor (KOR) is implicated in addiction, pain, reward, mood, cognition, and perception. Activation of KOR by the neuropeptide dynorphin is critical in mediating analgesia and tolerance. Our solution NMR study of dynorphin (1–13) provided quantitative data on a KOR-bound conformation. Analysis of the peptide structure and dynamics revealed a central helical turn bounded on both sides by flexibly disordered peptide segments. Future drug development will benefit from kno...

  9. Structure of adenovirus bound to cellular receptor car

    Science.gov (United States)

    Freimuth, Paul I.

    2007-01-02

    Disclosed is a mutant CAR-DI-binding adenovirus which has a genome comprising one or more mutations in sequences which encode the fiber protein knob domain wherein the mutation causes the encoded viral particle to have a significantly weakened binding affinity for CAR-DI relative to wild-type adenovirus. Such mutations may be in sequences which encode either the AB loop, or the HI loop of the fiber protein knob domain. Specific residues and mutations are described. Also disclosed is a method for generating a mutant adenovirus which is characterized by a receptor binding affinity or specificity which differs substantially from wild type.

  10. Structure of the human M2 muscarinic acetylcholine receptor bound to an antagonist

    Energy Technology Data Exchange (ETDEWEB)

    Haga, Kazuko; Kruse, Andrew C.; Asada, Hidetsugu; Yurugi-Kobayashi, Takami; Shiroishi, Mitsunori; Zhang, Cheng; Weis, William I.; Okada, Tetsuji; Kobilka, Brian K.; Haga, Tatsuya; Kobayashi, Takuya (Stanford-MED); (Kyoto); (Gakushuin); (Kyushu)

    2012-03-15

    The parasympathetic branch of the autonomic nervous system regulates the activity of multiple organ systems. Muscarinic receptors are G-protein-coupled receptors that mediate the response to acetylcholine released from parasympathetic nerves. Their role in the unconscious regulation of organ and central nervous system function makes them potential therapeutic targets for a broad spectrum of diseases. The M2 muscarinic acetylcholine receptor (M2 receptor) is essential for the physiological control of cardiovascular function through activation of G-protein-coupled inwardly rectifying potassium channels, and is of particular interest because of its extensive pharmacological characterization with both orthosteric and allosteric ligands. Here we report the structure of the antagonist-bound human M2 receptor, the first human acetylcholine receptor to be characterized structurally, to our knowledge. The antagonist 3-quinuclidinyl-benzilate binds in the middle of a long aqueous channel extending approximately two-thirds through the membrane. The orthosteric binding pocket is formed by amino acids that are identical in all five muscarinic receptor subtypes, and shares structural homology with other functionally unrelated acetylcholine binding proteins from different species. A layer of tyrosine residues forms an aromatic cap restricting dissociation of the bound ligand. A binding site for allosteric ligands has been mapped to residues at the entrance to the binding pocket near this aromatic cap. The structure of the M2 receptor provides insights into the challenges of developing subtype-selective ligands for muscarinic receptors and their propensity for allosteric regulation.

  11. Bounds on Codes Based on Graph Theory

    CERN Document Server

    Rouayheb, Salim Y El; Soljanin, E; Sprintson, A

    2008-01-01

    Let $A_q(n,d)$ be the maximum order (maximum number of codewords) of a $q$-ary code of length $n$ and Hamming distance at least $d$. And let $A(n,d,w)$ that of a binary code of constant weight $w$. Building on results from algebraic graph theory and Erd\\H{o}s-ko-Rado like theorems in extremal combinatorics, we show how several known bounds on $A_q(n,d)$ and $A(n,d,w)$ can be easily obtained in a single framework. For instance, both the Hamming and Singleton bounds can derived as an application of a property relating the clique number and the independence number of vertex transitive graphs. Using the same techniques, we also derive some new bounds and present some additional applications.

  12. Origin and functional activity of the membrane-bound glucocorticoid receptor

    NARCIS (Netherlands)

    C. Strehl; T. Gaber; M Lowenberg; D.W. Hommes; A.P. Verhaar; S. Schellmann; M. Hahne; M. Fangradt; M. Wagegg; P. Hoff; A. Scheffold; C.M. Spies; G.R. Burmester; F. Buttgereit

    2011-01-01

    Objective Glucocorticoids (GCs) exert their antiinflammatory and immunosuppressive effects in humans primarily via the cytosolic GC receptor (cGR) but also via rapid, nongenomic mechanisms. Most likely, membrane-bound GRs (mGR) are involved in nongenomic GC signaling. The aim of this study was to in

  13. Crystallization of BMP receptor type IA bound to the antibody Fab fragment AbD1556

    International Nuclear Information System (INIS)

    The crystallization of BMP receptor type IA bound to the neutralizing antibody Fab fragment AbD1556 obtained by phage-display selection is reported. An antibody Fab fragment, AbD1556, was selected against the extracellular domain of BMP receptor type IA, which blocks the binding of BMP-2 to BMPR-IA and thereby neutralizes BMP-2 activity. To study the mechanism by which BMPR-IA is recognized and bound by the Fab fragment, the complex of AbD1556 bound to BMPR-IA was prepared and crystallized. Crystals of this binary complex belonged to the monoclinic space group P21, with unit-cell parameters a = 89.32, b = 129.25, c = 100.24 Å, β = 92.27°

  14. Sex steroids regulate skin pigmentation through nonclassical membrane-bound receptors.

    Science.gov (United States)

    Natale, Christopher A; Duperret, Elizabeth K; Zhang, Junqian; Sadeghi, Rochelle; Dahal, Ankit; O'Brien, Kevin Tyler; Cookson, Rosa; Winkler, Jeffrey D; Ridky, Todd W

    2016-01-01

    The association between pregnancy and altered cutaneous pigmentation has been documented for over two millennia, suggesting that sex hormones play a role in regulating epidermal melanocyte (MC) homeostasis. Here we show that physiologic estrogen (17β-estradiol) and progesterone reciprocally regulate melanin synthesis. This is intriguing given that we also show that normal primary human MCs lack classical estrogen or progesterone receptors (ER or PR). Utilizing both genetic and pharmacologic approaches, we establish that sex steroid effects on human pigment synthesis are mediated by the membrane-bound, steroid hormone receptors G protein-coupled estrogen receptor (GPER), and progestin and adipoQ receptor 7 (PAQR7). Activity of these receptors was activated or inhibited by synthetic estrogen or progesterone analogs that do not bind to ER or PR. As safe and effective treatment options for skin pigmentation disorders are limited, these specific GPER and PAQR7 ligands may represent a novel class of therapeutics. PMID:27115344

  15. Allosteric activation of membrane-bound glutamate receptors using coordination chemistry within living cells

    Science.gov (United States)

    Kiyonaka, Shigeki; Kubota, Ryou; Michibata, Yukiko; Sakakura, Masayoshi; Takahashi, Hideo; Numata, Tomohiro; Inoue, Ryuji; Yuzaki, Michisuke; Hamachi, Itaru

    2016-10-01

    The controlled activation of proteins in living cells is an important goal in protein-design research, but to introduce an artificial activation switch into membrane proteins through rational design is a significant challenge because of the structural and functional complexity of such proteins. Here we report the allosteric activation of two types of membrane-bound neurotransmitter receptors, the ion-channel type and the G-protein-coupled glutamate receptors, using coordination chemistry in living cells. The high programmability of coordination chemistry enabled two His mutations, which act as an artificial allosteric site, to be semirationally incorporated in the vicinity of the ligand-binding pockets. Binding of Pd(2,2‧-bipyridine) at the allosteric site enabled the active conformations of the glutamate receptors to be stabilized. Using this approach, we were able to activate selectively a mutant glutamate receptor in live neurons, which initiated a subsequent signal-transduction pathway.

  16. Processing of receptor-bound somatostatin: internalization and degradation by pancreatic acini

    International Nuclear Information System (INIS)

    The authors have previously demonstrated the presence of specific binding sites for somatostatin on plasma membranes from pancreatic acinar cells. In the present study they attempted to characterize the fate of receptor-bound 125I-[Tyr11]somatostatin. Internalization of somatostatin was rapid (reaching a plateau at 20% of the cell-associated specific radioactivity) and temperature dependent. To follow the processing of bound somatostatin, acini were incubated with 125I-[Tyr11]somatostatin at 50C during 16 h then, after washing, incubated at 370C for 90 min in fresh medium. Surface-bound somatostatin decreased rapidly, whereas radioactivity increased in the cell interior and the incubation medium. Intracellular and membrane-bound radioactivity was mainly intact 125I-[Tyr11]somatostatin. Degradation occurred at the plasma membrane level and led to iodotyrosine production. After 15 min of incubation, 15% of the initially surface-bound 125I-[Tyr11]somatostatin was compartmentalized within the cell, mainly in the microsomal fraction. After 30 min, a significant increase in radioactivity appeared in the nuclear fraction. These results indicate that the major part of somatostatin cellular degradation takes place at the plasma membrane level. Within the cell, somatostatin is routed to the nucleus via particular fractions sedimenting with microsomal vesicles

  17. Crystal structure of a prolactin receptor antagonist bound to the extracellular domain of the prolactin receptor

    DEFF Research Database (Denmark)

    Svensson, L Anders; Bondensgaard, Kent; Nørskov-Lauritsen, Leif;

    2008-01-01

    The crystal structure of the complex between an N-terminally truncated G129R human prolactin (PRL) variant and the extracellular domain of the human prolactin receptor (PRLR) was determined at 2.5A resolution by x-ray crystallography. This structure represents the first experimental structure...

  18. Crystal structure of the human OX2 orexin receptor bound to the insomnia drug suvorexant

    Science.gov (United States)

    Yin, Jie; Mobarec, Juan Carlos; Kolb, Peter; Rosenbaum, Daniel M.

    2015-03-01

    The orexin (also known as hypocretin) G protein-coupled receptors (GPCRs) respond to orexin neuropeptides in the central nervous system to regulate sleep and other behavioural functions in humans. Defects in orexin signalling are responsible for the human diseases of narcolepsy and cataplexy; inhibition of orexin receptors is an effective therapy for insomnia. The human OX2 receptor (OX2R) belongs to the β branch of the rhodopsin family of GPCRs, and can bind to diverse compounds including the native agonist peptides orexin-A and orexin-B and the potent therapeutic inhibitor suvorexant. Here, using lipid-mediated crystallization and protein engineering with a novel fusion chimaera, we solved the structure of the human OX2R bound to suvorexant at 2.5 Å resolution. The structure reveals how suvorexant adopts a π-stacked horseshoe-like conformation and binds to the receptor deep in the orthosteric pocket, stabilizing a network of extracellular salt bridges and blocking transmembrane helix motions necessary for activation. Computational docking suggests how other classes of synthetic antagonists may interact with the receptor at a similar position in an analogous π-stacked fashion. Elucidation of the molecular architecture of the human OX2R expands our understanding of peptidergic GPCR ligand recognition and will aid further efforts to modulate orexin signalling for therapeutic ends.

  19. Error bounds for surface area estimators based on Crofton's formula

    DEFF Research Database (Denmark)

    Kiderlen, Markus; Meschenmoser, Daniel

    2009-01-01

    S (A)/S (A) is bounded from below by the inradius of Z and from above by the circumradius of Z. Applying a strengthened isoperimetric inequality due to Bonnesen, we show that the rectangular quadrature rule does not give the best possible error bounds for d = 2. In addition, we derive asymptotic...... behavior of the error (with increasing k) in the planar case. The paper concludes with applications to surface area estimation in design-based digital stereology where we show that the weights due to Bonnesen’s inequality are better than the usual weights based on the rectangular rule and almost optimal...

  20. Distinct conformational changes in activated agonist-bound and agonist-free glycine receptor subunits

    DEFF Research Database (Denmark)

    Pless, Stephan Alexander; Lynch, Joseph W

    2009-01-01

    glycine-free or a glycine-bound subunit. Agonist-free subunits were created by incorporating T204A and R65K mutations, which disrupted glycine binding to both (+) and (-) subunit interfaces. In heteromeric receptors comprising wild-type and R65K,T204A,R271C triple-mutant subunits, the fluorescence...... response exhibited a drastically reduced glycine sensitivity relative to the current response. Two conclusions can be drawn from this. First, because the labeled glycine-free subunits were activated by glycine binding to neighboring wild-type subunits, our results provide evidence for a cooperative...... activation mechanism. However, because the fluorescent label on glycine-free subunits does not reflect movements at the channel gate, we conclude that glycine binding also produces a local non-concerted conformational change that is not essential for receptor activation....

  1. Strategies for improved modeling of GPCR-drug complexes: blind predictions of serotonin receptors bound to ergotamine.

    Science.gov (United States)

    Rodríguez, David; Ranganathan, Anirudh; Carlsson, Jens

    2014-07-28

    The recent increase in the number of atomic-resolution structures of G protein-coupled receptors (GPCRs) has contributed to a deeper understanding of ligand binding to several important drug targets. However, reliable modeling of GPCR-ligand complexes for the vast majority of receptors with unknown structure remains to be one of the most challenging goals for computer-aided drug design. The GPCR Dock 2013 assessment, in which researchers were challenged to predict the crystallographic structures of serotonin 5-HT(1B) and 5-HT(2B) receptors bound to ergotamine, provided an excellent opportunity to benchmark the current state of this field. Our contributions to GPCR Dock 2013 accurately predicted the binding mode of ergotamine with RMSDs below 1.8 Å for both receptors, which included the best submissions for the 5-HT(1B) complex. Our models also had the most accurate description of the binding sites and receptor-ligand contacts. These results were obtained using a ligand-guided homology modeling approach, which combines extensive molecular docking screening with incorporation of information from multiple crystal structures and experimentally derived restraints. In this work, we retrospectively analyzed thousands of structures that were generated during the assessment to evaluate our modeling strategies. Major contributors to accuracy were found to be improved modeling of extracellular loop two in combination with the use of molecular docking to optimize the binding site for ligand recognition. Our results suggest that modeling of GPCR-drug complexes has reached a level of accuracy at which structure-based drug design could be applied to a large number of pharmaceutically relevant targets. PMID:25030302

  2. Molecular cloning and characterization of growth factor receptor bound-protein in Clonorchis sinensis.

    Directory of Open Access Journals (Sweden)

    Xuelian Bai

    Full Text Available BACKGROUND: Clonorchis sinensis causes clonorchiasis, a potentially serious disease. Growth factor receptor-bound protein 2 (Grb2 is a cytosolic protein conserved among animals and plays roles in cellular functions such as meiosis, organogenesis and energy metabolism. In the present study, we report first molecular characters of growth factor receptor bound-protein (CsGrb2 from C. sinensis as counter part of Grb2 from animals and its possible functions in development and organogenesis of C. sinensis. METHODOLOGY/PRINCIPAL FINDINGS: A CsGrb2 cDNA clone retrieved from the C. sinensis transcriptome encoded a polypeptide with a SH3-SH2-SH3 structure. Recombinant CsGrb2 was bacterially produced and purified to homogeneity. Native CsGrb2 with estimated molecular weight was identified from C. sinensis adult extract by western blotting using a mouse immune serum to recombinant CsGrb2. CsGrb2 transcripts was more abundant in the metacercariae than in the adults. Immunohistochemical staining showed that CsGrb2 was localized to the suckers, mesenchymal tissues, sperms in seminal receptacle and ovary in the adults, and abundantly expressed in most organs of the metacercariae. Recombinant CsGrb2 was evaluated to be little useful as a serodiagnostic reagent for C. sinesis human infections. CONCLUSION: Grb2 protein found in C. sinensis was conserved among animals and suggested to play a role in the organogenesis, energy metabolism and mitotic spermatogenesis of C. sinensis. These findings from C. sinensis provide wider understanding on diverse function of Grb2 in lower animals such as platyhelminths.

  3. Differential Expression of Growth Factor Receptors and Membrane-Bound Tumor Markers for Imaging in Male and Female Breast Cancer

    OpenAIRE

    Vermeulen, Jeroen F.; Robert Kornegoor; Elsken van der Wall; Petra van der Groep; Paul J. van Diest

    2013-01-01

    INTRODUCTION: Male breast cancer accounts for 0.5-1% of all breast cancers and is generally diagnosed at higher stage than female breast cancers and therefore might benefit from earlier detection and targeted therapy. Except for HER2 and EGFR, little is known about expression of growth factor receptors in male breast cancer. We therefore investigated expression profiles of growth factor receptors and membrane-bound tumor markers in male breast cancer and gynecomastia, in comparison with femal...

  4. Construction of bound entangled states based on permutation operators

    Science.gov (United States)

    Zhao, Hui; Guo, Sha; Jing, Naihuan; Fei, Shaoming

    2016-04-01

    We present a construction of new bound entangled states from given bound entangled states for arbitrary dimensional bipartite systems. One way to construct bound entangled states is to show that these states are positive partial transpose (PPT) and violate the range criterion at the same time. By applying certain operators to given bound entangled states or to one of the subsystems of the given bound entangled states, we obtain a set of new states which are both PPT and violate the range criterion. We show that the derived bound entangled states are not local unitary equivalent to the original bound entangled states by detail examples.

  5. LBLS: A Locality Bounded Hashing-Based Location Service

    Directory of Open Access Journals (Sweden)

    Ruonan Rao

    2010-01-01

    Full Text Available Geographic-based routing allows routing in mobile ad hoc networks (MANETs yet avoiding the overhead for maintaining the topology changes in MANETs. A critical challenge in geographic routing protocols is the design of a scalable distributed location services that tracks the locations of mobile nodes in MANETs. Although a number of location services have been proposed, in typical works, the performance is not satisfactory when it comes to locality problem, which introduce high overhead in update and query operations, especially in a location service without hierarchy structure, the location information stored can potentially be far away from both the source and destination nodes, even when the source and destination nodes are close. In this paper, we present a new location service, named LBLS (Locality Bounded Location Service to solve the locality problem with the comparable least communication and storage cost. LBLS uses a double index hash function to map a node to a location in the network area called the virtual coordination of that node. Then, a novel method employed to divide the physical space into lattices. The publish and query algorithms are designed based on this division. In LBLS, when the distance between the source and destination nodes is l, the cost of query is O(l2. We define this property as n2- locality bounded. LBLS is the location service that achieves this property with the least storage and network overhead. Both the analysis and experiment results are present in this paper concerned with the cost, the locality bounded property and the scalability.

  6. Persistence-Based Branch Misprediction Bounds for WCET Analysis

    DEFF Research Database (Denmark)

    Puffitsch, Wolfgang

    2015-01-01

    Branch prediction is an important feature of pipelined processors to achieve high performance. However, it can lead to overly pessimistic worst-case execution time (WCET) bounds when being modeled too conservatively. This paper presents bounds on the number of branch mispredictions for local dyna...... linear programming formulations of the WCET problem. An evaluation on a number of benchmarks shows that with these bounds, dynamic branch prediction does not necessarily lead to higher WCET bounds than static prediction schemes....

  7. SMT-based Bounded Model Checking with Difference Logic Constraints

    CERN Document Server

    Bersani, Marcello M; Morzenti, Angelo; Pradella, Matteo; Rossi, Matteo; Pietro, Pierluigi San

    2010-01-01

    Traditional Bounded Model Checking (BMC) is based on translating the model checking problem into SAT, the Boolean satisfiability problem. This paper introduces an encoding of Linear Temporal Logic with Past operators (PLTL) into the Quantifier-Free Difference Logic with Uninterpreted Functions (QF-UFIDL). The resulting encoding is a simpler and more concise version of existing SATbased encodings, currently used in BMC. In addition, we present an extension of PLTL augmented with arithmetic relations over integers, which can express unbounded counters; as such, the extended logic is more expressive than PLTL. We introduce suitable restrictions and assumptions that are shown to make the verification problem for the extended logic decidable, and we define an encoding of the new logic into QF-UFIDL. Finally, a performance comparison with the SAT-based approach on purely PLTL examples shows significant improvements in terms of both execution time and memory occupation.

  8. Image Distortion Metric Based on Total Bounded Variation

    Institute of Scientific and Technical Information of China (English)

    Cheng Xiaogang; An Mingwei; Chen Qimei

    2012-01-01

    Image definition measurement plays an important role in various image processing applications. And a reliable objective image definition metrics is critical for evaluating the definition of the restored image. In this paper, a novel image distortion metric based on minimal Total Bounded Variation (TBV) is presented. It is clarified that when the restored image approximates to the original clear image, the smaller the TBV is, the better the definition of the restored image is. Furthermore, the difference between the restored image and the original clear image is the smallest when the TBV is minimum. In numerical results, the TBV of the original clear image, blur image and restored image are presented and compared, and the results demonstrate the validity of the distortion metric proposed.

  9. Crystal structure of the[mu]-opioid receptor bound to a morphinan antagonist

    Energy Technology Data Exchange (ETDEWEB)

    Manglik, Aashish; Kruse, Andrew C.; Kobilka, Tong Sun; Thian, Foon Sun; Mathiesen, Jesper M.; Sunahara, Roger K.; Pardo, Leonardo; Weis, William I.; Kobilka, Brian K.; Granier, Sébastien (Michigan-Med); (Stanford-MED); (UAB, Spain)

    2012-06-27

    Opium is one of the world's oldest drugs, and its derivatives morphine and codeine are among the most used clinical drugs to relieve severe pain. These prototypical opioids produce analgesia as well as many undesirable side effects (sedation, apnoea and dependence) by binding to and activating the G-protein-coupled {mu}-opioid receptor ({mu}-OR) in the central nervous system. Here we describe the 2.8 {angstrom} crystal structure of the mouse {mu}-OR in complex with an irreversible morphinan antagonist. Compared to the buried binding pocket observed in most G-protein-coupled receptors published so far, the morphinan ligand binds deeply within a large solvent-exposed pocket. Of particular interest, the {mu}-OR crystallizes as a two-fold symmetrical dimer through a four-helix bundle motif formed by transmembrane segments 5 and 6. These high-resolution insights into opioid receptor structure will enable the application of structure-based approaches to develop better drugs for the management of pain and addiction.

  10. Controller Based Observer in Switched System with Norm Bounded Uncertainty

    Directory of Open Access Journals (Sweden)

    Mongi Besbes

    2012-01-01

    Full Text Available Problem statement: This study discusses the robust stabilization of norm bounded discrete switched systems. Approach: The proposed method is using the second Lyapunov approach and the poly-quadratic function concept. The stabilization conditions are written through linear matrix inequality relations. The control law is based on a static output feedback with the use of a switched observer. The synthesis conditions of the controller are written in the form of linear matrix inequalities difficult to resolve by current numerical solvers. That’s why relaxations are proposed to mitigate the pessimism of LMI conditions obtained. Results: The poly-quadratic Lyapunov approach provides a constructive way to tackle uncertainty in the switched framework. The feasibility is illustrated by the example of discrete uncertain switched systems. Conclusion: With these results, the study of stability can be achieved for arbitrary switching laws, state-dependent, time dependent or generated by a controller. However, the implementation of the control law is possible only if the switching status is well known in real time.

  11. Bound of Noncommutativity Parameter Based on Black Hole Entropy

    OpenAIRE

    Kim, Wontae; Lee, Daeho

    2010-01-01

    We study the bound of the noncommutativity parameter in the noncommutative Schwarzschild black hole which is a solution of the noncommutative ISO(3,1) Poincare gauge group. The statistical entropy satisfying the area law in the brick wall method yields a cutoff relation which depends on the noncommutativity parameter. Requiring both the cutoff parameter and the noncommutativity parameter to be real, the noncommutativity parameter can be shown to be bounded as $\\Theta > 8.4\\ times 10^{-2}l_{p}$.

  12. Two specific membrane-bound aminopeptidase N isoforms from Aedes aegypti larvae serve as functional receptors for the Bacillus thuringiensis Cry4Ba toxin implicating counterpart specificity.

    Science.gov (United States)

    Aroonkesorn, Aratee; Pootanakit, Kusol; Katzenmeier, Gerd; Angsuthanasombat, Chanan

    2015-05-29

    The interaction between Bacillus thuringiensis Cry toxins and their receptors on midgut cells of susceptible insect larvae is the critical determinant in toxin specificity. Besides GPI-linked alkaline phosphatase in Aedes aegypti mosquito-larval midguts, membrane-bound aminopeptidase N (AaeAPN) is widely thought to serve as a Cry4Ba receptor. Here, two full-length AaeAPN isoforms, AaeAPN2778 and AaeAPN2783, predicted to be GPI-linked were cloned and successfully expressed in Spodoptera frugiperda (Sf9) cells as 112- and 107-kDa membrane-bound proteins, respectively. In the cytotoxicity assay, Sf9 cells expressing each of the two AaeAPN isoforms showed increased sensitivity to the Cry4Ba mosquito-active toxin. Double immunolocalization revealed specific binding of Cry4Ba to each individual AaeAPN expressed on the cell membrane surface. Sequence analysis and homology-based modeling placed these two AaeAPNs to the M1 aminopeptidase family as they showed similar four-domain structures, with the most conserved domain II being the catalytic component. Additionally, the most variable domain IV containing negatively charged surface patches observed only in dipteran APNs could be involved in insect specificity. Overall results demonstrated that these two membrane-bound APN isoforms were responsible for mediating Cry4Ba toxicity against AaeAPN-expressed Sf9 cells, suggesting their important role as functional receptors for the toxin counterpart in A. aegypti mosquito larvae. PMID:25871797

  13. Bound States and Supercriticality in Graphene-Based Topological Insulators

    Directory of Open Access Journals (Sweden)

    Reinhold Egger

    2013-01-01

    Full Text Available We study the bound state spectrum and the conditions for entering a supercritical regime in graphene with strong intrinsic and Rashba spin-orbit interactions within the topological insulator phase. Explicit results are provided for a disk-shaped potential well and for the Coulomb center problem.

  14. ESTRADIOL-INDUCED ENHANCEMENT OF OBJECT MEMORY CONSOLIDATION INVOLVES HIPPOCAMPAL ERK ACTIVATION AND MEMBRANE-BOUND ESTROGEN RECEPTORS

    OpenAIRE

    Fernandez, Stephanie M.; Michael C. Lewis; Pechenino, Angela S.; Harburger, Lauren L.; Orr, Patrick T.; Gresack, Jodi E.; Schafe, Glenn E.; Frick, Karyn M.

    2008-01-01

    The extracellular signal-regulated kinase (ERK) pathway is critical for various forms of learning and memory, and is activated by the potent estrogen, 17β-estradiol (E2). Here, we asked whether E2 modulates memory via ERK activation and putative membrane-bound estrogen receptors (ERs). Using ovariectomized mice, we first demonstrate that intraperitoneal (i.p.) injection of 0.2 mg/kg E2 significantly increases dorsal hippocampal levels of phosphorylated ERK protein 1 hour after injection. Seco...

  15. Differential expression of growth factor receptors and membrane-bound tumor markers for imaging in male and female breast cancer.

    Directory of Open Access Journals (Sweden)

    Jeroen F Vermeulen

    Full Text Available INTRODUCTION: Male breast cancer accounts for 0.5-1% of all breast cancers and is generally diagnosed at higher stage than female breast cancers and therefore might benefit from earlier detection and targeted therapy. Except for HER2 and EGFR, little is known about expression of growth factor receptors in male breast cancer. We therefore investigated expression profiles of growth factor receptors and membrane-bound tumor markers in male breast cancer and gynecomastia, in comparison with female breast cancer. METHODS: Tissue microarrays containing 133 male breast cancer and 32 gynecomastia cases were stained by immunohistochemistry for a panel of membrane-bound targets and compared with data on 266 female breast cancers. RESULTS: Growth factor receptors were variably expressed in 4.5% (MET up to 38.5% (IGF1-R of male breast cancers. Compared to female breast cancer, IGF1-R and carbonic anhydrase 12 (CAXII were more frequently and CD44v6, MET and FGFR2 less frequently expressed in male breast cancer. Expression of EGFR, HER2, CAIX, and GLUT1 was not significantly different between male and female breast cancer. Further, 48.1% of male breast cancers expressed at least one and 18.0% expressed multiple growth factor receptors. Since individual membrane receptors are expressed in only half of male breast cancers, a panel of membrane markers will be required for molecular imaging strategies to reach sensitivity. A potential panel of markers for molecular imaging, consisting of EGFR, IGF1-R, FGFR2, CD44v6, CAXII, GLUT1, and CD44v6 was positive in 77% of male breast cancers, comparable to female breast cancers. CONCLUSIONS: Expression patterns of growth factor receptors and hypoxia membrane proteins in male breast cancer are different from female breast cancer. For molecular imaging strategies, a putative panel consisting of markers for EGFR, IGF1-R, FGFR2, GLUT1, CAXII, CD44v6 was positive in 77% of cases and might be considered for development of

  16. Internalization mechanism of neuropeptide Y bound to its Y1 receptor investigated by high resolution microscopy

    Science.gov (United States)

    Kempf, Noémie; Didier, Pascal; Postupalenko, Viktoriia; Bucher, Bernard; Mély, Yves

    2015-06-01

    The neuropeptide Y (NPY) plays numerous biological roles that are mediated by a family of G-protein-coupled receptors. Among the latter, the NPY Y1 subtype receptor undergoes a rapid desensitization following agonist exposure. This desensitization was suggested to result from a rapid clathrin-dependent internalization of Y1 and its recycling at the plasma membrane via sorting/early endosomes (SE/EE) and recycling endosomes (RE). Herein, to validate and quantitatively consolidate the mechanism of NPY internalization, we quantitatively investigated the NPY-induced internalization of the Y1 receptor by direct stochastic optical reconstruction microscopy (dSTORM), a super-resolution imaging technique that can resolve EE and SE, which are below the resolution limit of conventional optical microscopes. Using Cy5-labeled NPY, we could monitor with time the internalization and recycling of NPY on HEK293 cells stably expressing eGFP-labeled Y1 receptors. Furthermore, by discriminating the SE/EE from the larger RE by their sizes and monitoring these two populations as a function of time, we could firmly consolidate the kinetic model describing the internalization mechanism of the Y1 receptors as the basis for their rapid desensitization following agonist exposure.

  17. Bound of aspect ratio of base-isolated buildings considering nonlinear tensile behavior of rubber bearing

    OpenAIRE

    Hino, J.; Yoshitomi, S.; Tsuji, M.; Takewaki, Izuru

    2008-01-01

    The purpose of this paper is to propose a simple analysis method of axial deformation of base-isolation rubber bearings in a building subjected to earthquake loading and present its applicability to the analysis of the bound of the aspect ratio of base-isolated buildings. The base shear coefficient is introduced as a key parameter for the bound analysis. The bound of the aspect ratio of base-isolated buildings is analyzed based on the relationship of the following four quantities; (i) ultimat...

  18. Efficient Amide Based Halogenide Anion Receptors

    Institute of Scientific and Technical Information of China (English)

    Hong Xing WU; Feng Hua LI; Hai LIN; Shou Rong ZHU; Hua Kuan LIN

    2005-01-01

    In this paper, we present the synthesis and anion recognition properties of the amide based phenanthroline derivatives 1, 2 and 3. In all cases 1:1 receptor: anion complexes were observed. The receptors were found to be selective for fluoride and chloride respectively over other putative anionic guest species.

  19. Improved Bounds for Beacon-Based Coverage and Routing in Simple Rectilinear Polygons

    OpenAIRE

    Bae, Sang Won; Shin, Chan-Su; Vigneron, Antoine

    2015-01-01

    We establish tight bounds for beacon-based coverage problems, and improve the bounds for beacon-based routing problems in simple rectilinear polygons. Specifically, we show that $\\lfloor \\frac{n}{6} \\rfloor$ beacons are always sufficient and sometimes necessary to cover a simple rectilinear polygon $P$ with $n$ vertices. We also prove tight bounds for the case where $P$ is monotone, and we present an optimal linear-time algorithm that computes the beacon-based kernel of $P$. For the routing p...

  20. Protein-Bound Uremic Toxins Induce Tissue Remodeling by Targeting the EGF Receptor

    OpenAIRE

    Sun, Chiao-Yin; Young, Guang-Huar; Hsieh, Yu-Ting; Chen, Yau-Hung; Wu, Mai-Szu; Wu, Vin-Cent; Lee, Jia-Hung; Lee, Chin-Chan

    2014-01-01

    Indoxyl sulfate and p-cresol sulfate have been suggested to induce kidney tissue remodeling. This study aimed to clarify the molecular mechanisms underlying this tissue remodeling using cultured human proximal renal tubular cells and half-nephrectomized mice treated with indoxyl sulfate or p-cresol sulfate as study models. Molecular docking results suggested that indoxyl sulfate and p-cresol sulfate dock on a putative interdomain pocket of the extracellular EGF receptor. In vitro spectrophoto...

  1. Bacillus thuringiensis subsp. israelensis Cyt1Aa synergizes Cry11Aa toxin by functioning as a membrane-bound receptor.

    Science.gov (United States)

    Pérez, Claudia; Fernandez, Luisa E; Sun, Jianguang; Folch, Jorge Luis; Gill, Sarjeet S; Soberón, Mario; Bravo, Alejandra

    2005-12-20

    Bacillus thuringiensis subsp. israelensis produces crystal proteins, Cry (4Aa, 4Ba, 10Aa, and 11Aa) and Cyt (1Aa and 2Ba) proteins, toxic to mosquito vectors of human diseases. Cyt1Aa overcomes insect resistance to Cry11Aa and Cry4 toxins and synergizes the toxicity of these toxins. However, the molecular mechanism of synergism remains unsolved. Here, we provide evidence that Cyt1Aa functions as a receptor of Cry11Aa. Sequential-binding analysis of Cyt1Aa and Cry11Aa revealed that Cyt1Aa binding to Aedes aegypti brush border membrane vesicles enhanced the binding of biotinylated-Cry11Aa. The Cyt1Aa- and Cry11Aa-binding epitopes were mapped by means of the yeast two-hybrid system, peptide arrays, and heterologous competition assays with synthetic peptides. Two exposed regions in Cyt1Aa, loop beta6-alphaE and part of beta7, bind Cry11Aa. On the other side, Cry11Aa binds Cyt1Aa proteins by means of domain II-loop alpha8 and beta-4, which are also involved in midgut receptor interaction. Characterization of single-point mutations in Cry11Aa and Cyt1Aa revealed key Cry11Aa (S259 and E266) and Cyt1Aa (K198, E204 and K225) residues involved in the interaction of both proteins and in synergism. Additionally, a Cyt1Aa loop beta6-alphaE mutant (K198A) with enhanced synergism to Cry11Aa was isolated. Data provided here strongly indicates that Cyt1Aa synergizes or suppresses resistance to Cry11Aa toxin by functioning as a membrane-bound receptor. Bacillus thuringiensis subsp. israelensis is a highly effective pathogenic bacterium because it produces a toxin and also its functional receptor, promoting toxin binding to the target membrane and causing toxicity. PMID:16339907

  2. Solubilization of the chromatin-bound estrogen receptor from chicken liver and fractionation on hydroxylapatite.

    Science.gov (United States)

    Gschwendt, M

    1976-08-16

    1. High-affinity estrogen-binding sites can be solubilized from the liver chromatin of estrogenized chickens by treatment of the chromatin with 2 M KCL/5 M urea and fractionation on hydroxylapatite. Two estrogen-binding proteins are eluted from hydroxylapatite columns by 20mM phosphate (binding protein I) and 200mMphosphate (binding protein II), respectively. 2. The binding protein I is part of a non-histone protein fraction containing acid-soluble and insoluble proteins, whereas the binding protein II elutes together with high molecular weight nonhistone proteins containing acid insoluble proteins only. Both binding proteins exhibit the smae affinity for estradiol (Kd approximately 10(-9) M). 3. From chromatin of untreated chickens very small amounts of binding protein I (0.1 pmol/mg protein compared to 1.9 pmol/mg protein from estrogenized chickens) with the smae affinity for estradiol as that from estrogenized animals can be solubilized. Binding protein II is not detectable. 4. The "soluble nuclear estrogen receptor" extracted from crude liver nucleir of estrogenized chickens by 0.5 M KCL behaves on hydroxylapatite very similarly to salt/urea-dissociated chromatin with respect to the binding protein I. No binding protein II, however, can be demonstrated. 5. Chromatography of various preparations on Bio-Gel A-1.5 m indicates that the binding protein II is a residual chromatin fragment containing an unseparated binding protein-DNA complex, whereas the binding protein I represents the solubilized nucleic-acid-free chromosomal estrogen receptor. The "soluble nuclear receptor" and the binding protein I, however, are not identical with respect to their chromatographic behaviour on Bio-Gel A-1.5m, even though their estrogen binding entity remaining after trypsin treatment seems to be very similar.

  3. Rational design of orally-active, pyrrolidine-based progesterone receptor partial agonists

    Energy Technology Data Exchange (ETDEWEB)

    Thompson, Scott K.; Washburn, David G.; Frazee, James S.; Madauss, Kevin P.; Hoang, Tram H.; Lapinski, Leahann; Grygielko, Eugene T.; Glace, Lindsay E.; Trizna, Walter; Williams, Shawn P.; Duraiswami, Chaya; Bray, Jeffrey D.; Laping, Nicholas J.; (GSKNC); (GSKPA)

    2010-09-03

    Using the X-ray crystal structure of an amide-based progesterone receptor (PR) partial agonist bound to the PR ligand binding domain, a novel PR partial agonist class containing a pyrrolidine ring was designed. Members of this class of N-alkylpyrrolidines demonstrate potent and highly selective partial agonism of the progesterone receptor, and one of these analogs was shown to be efficacious upon oral dosing in the OVX rat model of estrogen opposition.

  4. The properties of small Ag clusters bound to DNA bases

    Science.gov (United States)

    Soto-Verdugo, Víctor; Metiu, Horia; Gwinn, Elisabeth

    2010-05-01

    We study the binding of neutral silver clusters, Agn (n=1-6), to the DNA bases adenine (A), cytosine (C), guanine (G), and thymine (T) and the absorption spectra of the silver cluster-base complexes. Using density functional theory (DFT), we find that the clusters prefer to bind to the doubly bonded ring nitrogens and that binding to T is generally much weaker than to C, G, and A. Ag3 and Ag4 make the stronger bonds. Bader charge analysis indicates a mild electron transfer from the base to the clusters for all bases, except T. The donor bases (C, G, and A) bind to the sites on the cluster where the lowest unoccupied molecular orbital has a pronounced protrusion. The site where cluster binds to the base is controlled by the shape of the higher occupied states of the base. Time-dependent DFT calculations show that different base-cluster isomers may have very different absorption spectra. In particular, we find new excitations in base-cluster molecules, at energies well below those of the isolated components, and with strengths that depend strongly on the orientations of planar clusters with respect to the base planes. Our results suggest that geometric constraints on binding, imposed by designed DNA structures, may be a feasible route to engineering the selection of specific cluster-base assemblies.

  5. Randomness in the network inhibits cooperation based on the bounded rational collective altruistic decision

    International Nuclear Information System (INIS)

    Previous studies discussing cooperation employ the best decision that every player knows all information regarding the payoff matrix and selects the strategy of the highest payoff. Therefore, they do not discuss cooperation based on the altruistic decision with limited information (bounded rational altruistic decision). In addition, they do not cover the case where every player can submit his/her strategy several times in a match of the game. This paper is based on Ohdaira's reconsideration of the bounded rational altruistic decision, and also employs the framework of the prisoner's dilemma game (PDG) with sequential strategy. The distinction between this study and the Ohdaira's reconsideration is that the former covers the model of multiple groups, but the latter deals with the model of only two groups. Ohdaira's reconsideration shows that the bounded rational altruistic decision facilitates much more cooperation in the PDG with sequential strategy than Ohdaira and Terano's bounded rational second-best decision does. However, the detail of cooperation of multiple groups based on the bounded rational altruistic decision has not been resolved yet. This study, therefore, shows how randomness in the network composed of multiple groups affects the increase of the average frequency of mutual cooperation (cooperation between groups) based on the bounded rational altruistic decision of multiple groups. We also discuss the results of the model in comparison with related studies which employ the best decision. (paper)

  6. Upper Bound Performance Estimation for Copper Based Broadband Access

    DEFF Research Database (Denmark)

    Jensen, Michael; Gutierrez Lopez, Jose Manuel

    2012-01-01

    to define the limitations of copper based broadband access. A case study in a municipality in Denmark shows how the estimated network dimension to be able to provide video conference services to the majority of the population might be too high to be implemented in reality....... of copper based access connections at a household level by using Geographical Information System data. This can be combined with different configurations of DSLAMs distributions, in order to calculate the required number of active equipment points to guarantee certain QoS levels. This method can be used...

  7. Ecotin-Like ISP of L. major Promastigotes Fine-Tunes Macrophage Phagocytosis by Limiting the Pericellular Release of Bradykinin from Surface-Bound Kininogens: A Survival Strategy Based on the Silencing of Proinflammatory G-Protein Coupled Kinin B2 and B1 Receptors

    Directory of Open Access Journals (Sweden)

    Erik Svensjö

    2014-01-01

    Full Text Available Inhibitors of serine peptidases (ISPs expressed by Leishmania major enhance intracellular parasitism in macrophages by targeting neutrophil elastase (NE, a serine protease that couples phagocytosis to the prooxidative TLR4/PKR pathway. Here we investigated the functional interplay between ISP-expressing L. major and the kallikrein-kinin system (KKS. Enzymatic assays showed that NE inhibitor or recombinant ISP-2 inhibited KKS activation in human plasma activated by dextran sulfate. Intravital microscopy in the hamster cheek pouch showed that topically applied L. major promastigotes (WT and Δisp2/3 mutants potently induced plasma leakage through the activation of bradykinin B2 receptors (B2R. Next, using mAbs against kininogen domains, we showed that these BK-precursor proteins are sequestered by L. major promastigotes, being expressed at higher % in the Δisp2/3 mutant population. Strikingly, analysis of the role of kinin pathway in the phagocytic uptake of L. major revealed that antagonists of B2R or B1R reversed the upregulated uptake of Δisp2/3 mutants without inhibiting macrophage internalization of WT L. major. Collectively, our results suggest that L. major ISP-2 fine-tunes macrophage phagocytosis by inhibiting the pericellular release of proinflammatory kinins from surface bound kininogens. Ongoing studies should clarify whether L. major ISP-2 subverts TLR4/PKR-dependent prooxidative responses of macrophages by preventing activation of G-protein coupled B2R/B1R.

  8. Ecotin-like ISP of L. major promastigotes fine-tunes macrophage phagocytosis by limiting the pericellular release of bradykinin from surface-bound kininogens: a survival strategy based on the silencing of proinflammatory G-protein coupled kinin B2 and B1 receptors.

    Science.gov (United States)

    Svensjö, Erik; Nogueira de Almeida, Larissa; Vellasco, Lucas; Juliano, Luiz; Scharfstein, Julio

    2014-01-01

    Inhibitors of serine peptidases (ISPs) expressed by Leishmania major enhance intracellular parasitism in macrophages by targeting neutrophil elastase (NE), a serine protease that couples phagocytosis to the prooxidative TLR4/PKR pathway. Here we investigated the functional interplay between ISP-expressing L. major and the kallikrein-kinin system (KKS). Enzymatic assays showed that NE inhibitor or recombinant ISP-2 inhibited KKS activation in human plasma activated by dextran sulfate. Intravital microscopy in the hamster cheek pouch showed that topically applied L. major promastigotes (WT and Δisp2/3 mutants) potently induced plasma leakage through the activation of bradykinin B2 receptors (B2R). Next, using mAbs against kininogen domains, we showed that these BK-precursor proteins are sequestered by L. major promastigotes, being expressed at higher % in the Δisp2/3 mutant population. Strikingly, analysis of the role of kinin pathway in the phagocytic uptake of L. major revealed that antagonists of B2R or B1R reversed the upregulated uptake of Δisp2/3 mutants without inhibiting macrophage internalization of WT L. major. Collectively, our results suggest that L. major ISP-2 fine-tunes macrophage phagocytosis by inhibiting the pericellular release of proinflammatory kinins from surface bound kininogens. Ongoing studies should clarify whether L. major ISP-2 subverts TLR4/PKR-dependent prooxidative responses of macrophages by preventing activation of G-protein coupled B2R/B1R. PMID:25294952

  9. A complexity lower bound based on software engineering concepts

    OpenAIRE

    Rojas Paredes, Andrés

    2013-01-01

    We consider the problem of polynomial equation solving also known as quantifier elimination in Effective Algebraic Geometry. The complexity of the first elimination algorithms were double exponential, but a considerable progress was carried out when the polynomials were represented by arithmetic circuits evaluating them. This representation improves the complexity to pseudo–polynomial time. The question is whether the actual asymptotic complexity of circuit– based elimination algorithms ma...

  10. Cryptographic protocol security analysis based on bounded constructing algorithm

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    An efficient approach to analyzing cryptographic protocols is to develop automatic analysis tools based on formal methods. However, the approach has encountered the high computational complexity problem due to reasons that participants of protocols are arbitrary, their message structures are complex and their executions are concurrent. We propose an efficient automatic verifying algorithm for analyzing cryptographic protocols based on the Cryptographic Protocol Algebra (CPA) model proposed recently, in which algebraic techniques are used to simplify the description of cryptographic protocols and their executions. Redundant states generated in the analysis processes are much reduced by introducing a new algebraic technique called Universal Polynomial Equation and the algorithm can be used to verify the correctness of protocols in the infinite states space. We have implemented an efficient automatic analysis tool for cryptographic protocols, called ACT-SPA, based on this algorithm, and used the tool to check more than 20 cryptographic protocols. The analysis results show that this tool is more efficient, and an attack instance not offered previously is checked by using this tool.

  11. Graviton mass bounds from space-based gravitational-wave observations of massive black hole populations

    CERN Document Server

    Berti, Emanuele; Sesana, Alberto

    2011-01-01

    Space-based gravitational-wave detectors, such as LISA or a similar ESA-led mission, will offer unique opportunities to test general relativity. We study the bounds that space-based detectors could place on the graviton Compton wavelength \\lambda_g=h/(m_g c) by observing multiple inspiralling black hole binaries. We show that while observations of individual inspirals will yield mean bounds \\lambda_g~3x10^15 km, the combined bound from observing several events in a two-year mission is about ten times better: \\lambda_g~3x10^16 km (m_g~4x10^-26 eV). This result is only mildly dependent on details of black hole formation and detector characteristics. The bound achievable in practice should be one order of magnitude better than this figure (and hence almost competitive with the static, model-dependent bounds from gravitational effects on cosmological scales), because our calculations ignore the merger/ringdown portion of the waveform. The observation that an ensemble of events can sensibly improve the bounds that...

  12. Rapid effects of aldosterone in primary cultures of cardiomyocytes - do they suggest the existence of a membrane-bound receptor?

    Science.gov (United States)

    Araujo, Carolina Morais; Hermidorff, Milla Marques; Amancio, Gabriela de Cassia Sousa; Lemos, Denise da Silveira; Silva, Marcelo Estáquio; de Assis, Leonardo Vinícius Monteiro; Isoldi, Mauro César

    2016-10-01

    Aldosterone acts on its target tissue through a classical mechanism or through the rapid pathway through a putative membrane-bound receptor. Our goal here was to better understand the molecular and biochemical rapid mechanisms responsible for aldosterone-induced cardiomyocyte hypertrophy. We have evaluated the hypertrophic process through the levels of ANP, which was confirmed by the analysis of the superficial area of cardiomyocytes. Aldosterone increased the levels of ANP and the cellular area of the cardiomyocytes; spironolactone reduced the aldosterone-increased ANP level and cellular area of cardiomyocytes. Aldosterone or spironolactone alone did not increase the level of cyclic 3',5'-adenosine monophosphate (cAMP), but aldosterone plus spironolactone led to increased cAMP level; the treatment with aldosterone + spironolactone + BAPTA-AM reduced the levels of cAMP. These data suggest that aldosterone-induced cAMP increase is independent of mineralocorticoid receptor (MR) and dependent on Ca(2+). Next, we have evaluated the role of A-kinase anchor proteins (AKAP) in the aldosterone-induced hypertrophic response. We have found that St-Ht31 (AKAP inhibitor) reduced the increased level of ANP which was induced by aldosterone; in addition, we have found an increase on protein kinase C (PKC) and extracellular signal-regulated kinase 5 (ERK5) activity when cells were treated with aldosterone alone, spironolactone alone and with a combination of both. Our data suggest that PKC could be responsible for ERK5 aldosterone-induced phosphorylation. Our study suggests that the aldosterone through its rapid effects promotes a hypertrophic response in cardiomyocytes that is controlled by an AKAP, being dependent on ERK5 and PKC, but not on cAMP/cAMP-dependent protein kinase signaling pathways. Lastly, we provide evidence that the targeting of AKAPs could be relevant in patients with aldosterone-induced cardiac hypertrophy and heart failure. PMID:27305962

  13. Membrane-based ethylene/ethane separation: The upper bound and beyond

    KAUST Repository

    Rungta, Meha

    2013-08-02

    Ethylene/ethane separation via cryogenic distillation is extremely energy-intensive, and membrane separation may provide an attractive alternative. In this paper, ethylene/ethane separation performance using polymeric membranes is summarized, and an experimental ethylene/ethane polymeric upper bound based on literature data is presented. A theoretical prediction of the ethylene/ethane upper bound is also presented, and shows good agreement with the experimental upper bound. Further, two ways to overcome the ethylene/ethane upper bound, based on increasing the sorption or diffusion selectivity, is also discussed, and a review on advanced membrane types such as facilitated transport membranes, zeolite and metal organic framework based membranes, and carbon molecular sieve membranes is presented. Of these, carbon membranes have shown the potential to surpass the polymeric ethylene/ethane upper bound performance. Furthermore, a convenient, potentially scalable method for tailoring the performance of carbon membranes for ethylene/ethane separation based on tuning the pyrolysis conditions has also been demonstrated. © 2013 American Institute of Chemical Engineers.

  14. Structure of the Human Activating Natural Cytotoxicity Receptor NKp30 Bound to its Tumor Cell Ligand B7-H6

    Energy Technology Data Exchange (ETDEWEB)

    Y Li; Q Wang; R Mariuzza

    2011-12-31

    Natural killer (NK) cells are lymphocytes of the innate immune system that participate in the elimination of tumor cells. In humans, the activating natural cytotoxicity receptors (NCRs) NKp30, NKp44, and NKp46 play a major role in NK cell-mediated tumor cell lysis. NKp30 recognizes B7-H6, a member of the B7 family which is expressed on tumor, but not healthy, cells. To understand the basis for tumor surveillance by NCRs, we determined the structure of NKp30, a member of the CD28 family which includes CTLA-4 and PD-1, in complex with B7-H6. The overall organization of the NKp30-B7-H6-activating complex differs considerably from those of the CTLA-4-B7 and PD-1-PD-L T cell inhibitory complexes. Whereas CTLA-4 and PD-1 use only the front {beta}-sheet of their Ig-like domain to bind ligands, NKp30 uses both front and back {beta}-sheets, resulting in engagement of B7-H6 via the side, as well as face, of the {beta}-sandwich. Moreover, B7-H6 contacts NKp30 through the complementarity-determining region (CDR) - like loops of its V-like domain in an antibody-like interaction that is not observed for B7 or PD-L. This first structure of an NCR bound to ligand provides a template for designing molecules to stimulate NKp30-mediated cytolytic activity for tumor immunotherapy.

  15. Calixarene-based receptors for molecular recognition

    OpenAIRE

    YILMAZ, Mustafa; ERDEMİR, Serkan

    2013-01-01

    Calixarene-based molecular receptors have been a widely developing area in material science and technology for the last few decades. Due to their bowl-shaped geometry, calixarene macrocycles are used as hosts allowing organic and inorganic guests to coordinate/sorb onto their cavity. This work briefly reviews the recent development of calixarenes.

  16. Structure of a Thyroid Hormone Receptor DNA-Binding Domain Homodimer Bound to an Inverted Palindrome DNA Response Element

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Yi; Young, Matthew A. (Michigan)

    2010-10-22

    Thyroid hormone receptor (TR), as a member of the nuclear hormone receptor family, can recognize and bind different classes of DNA response element targets as either a monomer, a homooligomer, or a heterooligomer. We report here the first crystal structure of a homodimer TR DNA-binding domain (DBD) in complex with an inverted repeat class of thyroid response element (TRE). The structure shows a nearly symmetric structure of the TR DBD assembled on the F2 TRE where the base recognition contacts in the homodimer DNA complex are conserved relative to the previously published structure of a TR-9-cis-retinoic acid receptor heterodimer DNA complex. The new structure also reveals that the T-box region of the DBD can function as a structural hinge that enables a large degree of flexibility in the position of the C-terminal extension helix that connects the DBD to the ligand-binding domain. Although the isolated TR DBDs exist as monomers in solution, we have measured highly cooperative binding of the two TR DBD subunits onto the inverted repeat DNA sequence. This suggests that elements of the DBD can influence the specific TR oligomerization at target genes, and it is not just interactions between the ligand-binding domains that are responsible for TR oligomerization at target genes. Mutational analysis shows that intersubunit contacts at the DBD C terminus account for some, but not all, of the cooperative homodimer TR binding to the inverted repeat class TRE.

  17. Structural complexes of the agonist, inverse agonist and antagonist bound C5a receptor: insights into pharmacology and signaling.

    Science.gov (United States)

    Rana, Soumendra; Sahoo, Amita Rani; Majhi, Bharat Kumar

    2016-04-26

    The C5a receptor (C5aR) is a pharmacologically important G-protein coupled receptor (GPCR) that interacts with (h)C5a, by recruiting both the "orthosteric" sites (site1 at the N-terminus and site2 at the ECS, extra cellular surface) on C5aR in a two site-binding model. However, the complex pharmacological landscape and the distinguishing chemistry operating either at the "orthosteric" site1 or at the functionally important "orthosteric" site2 of C5aR are still not clear, which greatly limits the understanding of C5aR pharmacology. One of the major bottlenecks is the lack of an experimental structure or a refined model structure of C5aR with appropriately defined active sites. The study attempts to understand the pharmacology at the "orthosteric" site2 of C5aR rationally by generating a highly refined full-blown model structure of C5aR through advanced molecular modeling techniques, and further subjecting it to automated docking and molecular dynamics (MD) studies in the POPC bilayer. The first series of structural complexes of C5aR respectively bound to a linear native peptide agonist ((h)C5a-CT), a small molecule inverse agonist (NDT) and a cyclic peptide antagonist (PMX53) are reported, apparently establishing the unique pharmacological landscape of the "orthosteric" site2, which also illustrates an energetically distinct but coherent competitive chemistry ("cation-π" vs. "π-π" interactions) involved in distinguishing the established ligands known for targeting the "orthosteric" site2 of C5aR. Over a total of 1 μs molecular dynamics (MD) simulation in the POPC bilayer, it is evidenced that while the agonist prefers a "cation-π" interaction, the inverse agonist prefers a "cogwheel/L-shaped" interaction in contrast to the "edge-to-face/T-shaped" type π-π interactions demonstrated by the antagonist by engaging the F275(7.28) of the C5aR. In the absence of a NMR or crystallographically guided model structure of C5aR, the computational model complexes not only

  18. An Improving Indexing Approach on Time Series Based on Minimum Bounding Rectangle

    Institute of Scientific and Technical Information of China (English)

    SUN Mei-yu; TANG Yang; FANG Jian-an

    2009-01-01

    A fundamental problem in whole sequence matching and subsequence matching is the problem of representation of time series. In the last decade many high level representations of time series have been proposed for data mining which involve a trade-off between accuracy and compactness. In this paper the author proposes a novel time series representation called Grid Minimum Bounding Rectangle (GMBR) and based on Minimum Bounding Rectangle. In this paper, the binary idea is applied into the Minimum Bounding Rectangle. The experiments have been performed on synthetic, as well as real data sequences to evaluate the proposed method. The experiment demonstrates that 69%- 92% of irrelevant sequences are pruned using the proposed method.

  19. Underwater Acoustic Networks: Channel Models and Network Coding based Lower Bound to Transmission Power for Multicast

    CERN Document Server

    Lucani, Daniel E; Stojanovic, Milica

    2008-01-01

    The goal of this paper is two-fold. First, to establish a tractable model for the underwater acoustic channel useful for network optimization in terms of convexity. Second, to propose a network coding based lower bound for transmission power in underwater acoustic networks, and compare this bound to the performance of several network layer schemes. The underwater acoustic channel is characterized by a path loss that depends strongly on transmission distance and signal frequency. The exact relationship among power, transmission band, distance and capacity for the Gaussian noise scenario is a complicated one. We provide a closed-form approximate model for 1) transmission power and 2) optimal frequency band to use, as functions of distance and capacity. The model is obtained through numerical evaluation of analytical results that take into account physical models of acoustic propagation loss and ambient noise. Network coding is applied to determine a lower bound to transmission power for a multicast scenario, fo...

  20. Credibility theory based dynamic control bound optimization for reservoir flood limited water level

    Science.gov (United States)

    Jiang, Zhiqiang; Sun, Ping; Ji, Changming; Zhou, Jianzhong

    2015-10-01

    The dynamic control operation of reservoir flood limited water level (FLWL) can solve the contradictions between reservoir flood control and beneficial operation well, and it is an important measure to make sure the security of flood control and realize the flood utilization. The dynamic control bound of FLWL is a fundamental key element for implementing reservoir dynamic control operation. In order to optimize the dynamic control bound of FLWL by considering flood forecasting error, this paper took the forecasting error as a fuzzy variable, and described it with the emerging credibility theory in recent years. By combining the flood forecasting error quantitative model, a credibility-based fuzzy chance constrained model used to optimize the dynamic control bound was proposed in this paper, and fuzzy simulation technology was used to solve the model. The FENGTAN reservoir in China was selected as a case study, and the results show that, compared with the original operation water level, the initial operation water level (IOWL) of FENGTAN reservoir can be raised 4 m, 2 m and 5.5 m respectively in the three division stages of flood season, and without increasing flood control risk. In addition, the rationality and feasibility of the proposed forecasting error quantitative model and credibility-based dynamic control bound optimization model are verified by the calculation results of extreme risk theory.

  1. Structure-based virtual screening of the nociceptin receptor: hybrid docking and shape-based approaches for improved hit identification.

    Science.gov (United States)

    Daga, Pankaj R; Polgar, Willma E; Zaveri, Nurulain T

    2014-10-27

    The antagonist-bound crystal structure of the nociceptin receptor (NOP), from the opioid receptor family, was recently reported along with those of the other opioid receptors bound to opioid antagonists. We recently reported the first homology model of the 'active-state' of the NOP receptor, which when docked with 'agonist' ligands showed differences in the TM helices and residues, consistent with GPCR activation after agonist binding. In this study, we explored the use of the active-state NOP homology model for structure-based virtual screening to discover NOP ligands containing new chemical scaffolds. Several NOP agonist and antagonist ligands previously reported are based on a common piperidine scaffold. Given the structure-activity relationships for known NOP ligands, we developed a hybrid method that combines a structure-based and ligand-based approach, utilizing the active-state NOP receptor as well as the pharmacophoric features of known NOP ligands, to identify novel NOP binding scaffolds by virtual screening. Multiple conformations of the NOP active site including the flexible second extracellular loop (EL2) loop were generated by simulated annealing and ranked using enrichment factor (EF) analysis and a ligand-decoy dataset containing known NOP agonist ligands. The enrichment factors were further improved by combining shape-based screening of this ligand-decoy dataset and calculation of consensus scores. This combined structure-based and ligand-based EF analysis yielded higher enrichment factors than the individual methods, suggesting the effectiveness of the hybrid approach. Virtual screening of the CNS Permeable subset of the ZINC database was carried out using the above-mentioned hybrid approach in a tiered fashion utilizing a ligand pharmacophore-based filtering step, followed by structure-based virtual screening using the refined NOP active-state models from the enrichment analysis. Determination of the NOP receptor binding affinity of a selected set

  2. Intermolecular communication on a liposomal membrane: enzymatic amplification of a photonic signal with a gemini peptide lipid as a membrane-bound artificial receptor.

    Science.gov (United States)

    Mukai, Masaru; Maruo, Kohei; Sasaki, Yoshihiro; Kikuchi, Jun-ichi

    2012-03-12

    A supramolecular system that can activate an enzyme through photo-isomerization was constructed by using a liposomal membrane scaffold. The design of the system was inspired by natural signal transduction systems, in which enzymes amplify external signals to control signal transduction pathways. The liposomal membrane, which provided a scaffold for the system, was prepared by self-assembly of a photoresponsive receptor and a cationic synthetic lipid. NADH-dependent L-lactate dehydrogenase, the signal amplifier, was immobilized on the liposomal surface by electrostatic interactions. Recognition of photonic signals by the membrane-bound receptor induced photo-isomerization, which significantly altered the receptor's metal-binding affinity. The response to the photonic signal was transmitted to the enzyme by Cu(2+) ions. The enzyme amplified the chemical information through a catalytic reaction to generate the intended output signal.

  3. Bounded Rational Managers Struggle with Talent Management - An Agent-based Modelling Approach

    DEFF Research Database (Denmark)

    Adamsen, Billy; Thomsen, Svend Erik

    and its denotative meaning floating, we propose that bounded rational managers base their decisions on a simple heuristic, i.e. selecting and cultivating individuals so that their capabilities resemble their own capabilities the most (Adamsen 2015). We model the consequences of this talent management...... of past success will provide failure rather than success in the future (Capelli.2008). Finally, we model the talent selection process either as a collective decision making process made by a group of managers or a decision process made by a single manager.It is argued that agent-based modeling is a useful....... The considered variables were: (a) decision makers’ attributes (capabilities and degree of bounded rationality), (b) characteristics of the sample where individuals are selected from (the level of capabilities and the dispersion thereof), (c) path-dependency of the organization’s success, and (d) the decision...

  4. Visualization of Link Structures and URL Retrievals Utilizing Internal Structure of URLs Based on Brunch and Bound Algorithms

    OpenAIRE

    Kohei Arai

    2012-01-01

    Method for visualization of URL link structure and URL retrievals using internal structure of URLs based on brunch and bound method is proposed. Twisting link structure of URLs can be solved by the proposed visualization method. Also some improvements are observed for the proposed brunch and bound based method in comparison to the conventional URL retrieval methods.

  5. Sensors closeness test based on an improved [0, 1] bounded Mahalanobis distance Δ2

    International Nuclear Information System (INIS)

    Mahalanobis distance Δ2 values are commonly in the range of 0 to +∞ where higher values represent greater distance between class means or points. The increase in Mahalanobis distance is unbounded as the distance multiply. To certain extend, the unbounded distance values pose difficulties in the evaluation and decision for instance in the sensors closeness test. This paper proposes an approach to [0, 1] bounded Mahalanobis distance Δ2 that enable researcher to easily perform sensors closeness test. The experimental data of four different types of rice based on three different electronic nose sensors namely InSniff, PEN3, and Cyranose320 were analyzed and sensor closeness test seems successfully performed within the [0, 1] bound

  6. Sensors closeness test based on an improved [0, 1] bounded Mahalanobis distance Δ{sup 2}

    Energy Technology Data Exchange (ETDEWEB)

    Masnan, Maz Jamilah, E-mail: mazjamilah@unimap.edu.my [Institute of Engineering Mathematics, Universiti Malaysia Perlis, Aras Bawah, Pusat Kejuruteraan, Kampus Tetap Pauh Putra, 02600 Arau, Perlis (Malaysia); Mahat, Nor Idayu, E-mail: noridayu@uum.edu.my [College of Arts and Sciences, Universiti Utara Malaysia, 06010 Sintok, Kedah (Malaysia); Shakaff, Ali Yeon Md, E-mail: aliyeon@unimap.edu.my; Abdullah, Abu Hassan, E-mail: abu.hassan@unimap.edu.my [Center of Excellence for Advanced Sensor Technology (CEASTech), Lot 16-21, Pusat Pengajian Jejawi 2, Jalan Jejawi Permatang, 02600 Jejawi, Arau, Perlis (Malaysia)

    2015-12-11

    Mahalanobis distance Δ{sup 2} values are commonly in the range of 0 to +∞ where higher values represent greater distance between class means or points. The increase in Mahalanobis distance is unbounded as the distance multiply. To certain extend, the unbounded distance values pose difficulties in the evaluation and decision for instance in the sensors closeness test. This paper proposes an approach to [0, 1] bounded Mahalanobis distance Δ{sup 2} that enable researcher to easily perform sensors closeness test. The experimental data of four different types of rice based on three different electronic nose sensors namely InSniff, PEN3, and Cyranose320 were analyzed and sensor closeness test seems successfully performed within the [0, 1] bound.

  7. Inhibition of MAP kinase promotes the recruitment of corepressor SMRT by tamoxifen-bound estrogen receptor alpha and potentiates tamoxifen action in MCF-7 cells

    Energy Technology Data Exchange (ETDEWEB)

    Hong, Wei, E-mail: hongwei@tijmu.edu.cn [Department of Immunology, Tianjin Medical University, 300070 Tianjin (China); Department of Laboratory Medicine, Tianjin Medical University, 300070 Tianjin (China); Chen, Linfeng [Department of Medical Oncology, Harvard Medical School, Dana Farber Cancer Institute, Boston, 02115 MA (United States); Li, Juan [Department of Laboratory Medicine, Tianjin Medical University, 300070 Tianjin (China); Yao, Zhi [Department of Immunology, Tianjin Medical University, 300070 Tianjin (China)

    2010-05-28

    Estrogen receptor alpha (ER{alpha}), a ligand controlled transcription factor, plays an important role in breast cancer growth and endocrine therapy. Tamoxifen (TAM) antagonizes ER{alpha} activity and has been applied in breast cancer treatment. TAM-bound ER{alpha} associates with nuclear receptor-corepressors. Mitogen-activated protein kinase (MAPK) has been elucidated to result in cross-talk between growth factor and ER{alpha} mediated signaling. We show that activated MAPK represses interaction of TAM-bound ER{alpha} with silencing mediator for retinoid and thyroid hormone receptors (SMRT) and inhibits the recruitment of SMRT by ER{alpha} to certain estrogen target genes. Blockade of MAPK signaling cascade with MEK inhibitor U0126 promotes the interaction and subsequently inhibits ER{alpha} activity via enhanced recruitment of SMRT, leading to reduced expression of ER{alpha} target genes. The growth rate of MCF-7 cells was decelerated when treated with both TAM and U0126. Moreover, the growth of MCF-7 cells stably expressing SMRT showed a robust repression in the presence of TAM and U0126. These results suggest that activated MAPK signaling cascade attenuates antagonist-induced recruitment of SMRT to ER{alpha}, suggesting corepressor mediates inhibition of ER{alpha} transactivation and breast cancer cell growth by antagonist. Taken together, our finding indicates combination of antagonist and MAPK inhibitor could be a helpful approach for breast cancer therapy.

  8. Checking RTECTL properties of STSs via SMT-based Bounded Model Checking

    Directory of Open Access Journals (Sweden)

    Agnieszka Zbrzezny

    2015-12-01

    Full Text Available We present an SMT-based bounded model checking (BMC method for Simply-Timed Systems (STSs and for the existential fragment of the Real-time Computation Tree Logic. We implemented the SMT-based BMC algorithm and compared it with the SAT-based BMC method for the same systems and the same property language on several benchmarks for STSs. For the SAT- based BMC we used the PicoSAT solver and for the SMT-based BMC we used the Z3 solver. The experimental results show that the SMT-based BMC performs quite well and is, in fact, sometimes significantly faster than the tested SAT-based BMC.

  9. Accurate performance estimators for information retrieval based on span bound of support vector machines

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Support vector machines have met with significant success in the information retrieval field, especially in handling text classification tasks. Although various performance estimators for SVMs have been proposed,these only focus on accuracy which is based on the leave-one-out cross validation procedure. Information-retrieval-related performance measures are always neglected in a kernel learning methodology. In this paper, we have proposed a set of information-retrieval-oriented performance estimators for SVMs, which are based on the span bound of the leave-one-out procedure. Experiments have proven that our proposed estimators are both effective and stable.

  10. Orphan nuclear receptor Errγ induces C-reactive protein gene expression through induction of ER-bound Bzip transmembrane transcription factor CREBH.

    Directory of Open Access Journals (Sweden)

    Jagannath Misra

    Full Text Available The orphan nuclear receptor estrogen-related receptor-γ (ERRγ is a constitutively active transcription factor regulating genes involved in several important cellular processes, including hepatic glucose metabolism, alcohol metabolism, and the endoplasmic reticulum (ER stress response. cAMP responsive element-binding protein H (CREBH is an ER-bound bZIP family transcription factor that is activated upon ER stress and regulates genes encoding acute-phase proteins whose expression is increased in response to inflammation. Here, we report that ERRγ directly regulates CREBH gene expression in response to ER stress. ERRγ bound to the ERRγ response element (ERRE in the CREBH promoter. Overexpression of ERRγ by adenovirus significantly increased expression of CREBH as well as C-reactive protein (CRP, whereas either knockdown of ERRγ or inhibition of ERRγ by ERRγ specific inverse agonist, GSK5182, substantially inhibited ER stress-mediated induction of CREBH and CRP. The transcriptional coactivator PGC1α was required for ERRγ mediated induction of the CREBH gene as demonstrated by the chromatin immunoprecipitation (ChIP assay showing binding of both ERRγ and PGC1α on the CREBH promoter. The ChIP assay also revealed that histone H3 and H4 acetylation occurred at the ERRγ and PGC1α binding site. Moreover, chronic alcoholic hepatosteatosis, as well as the diabetic obese condition significantly increased CRP gene expression, and this increase was significantly attenuated by GSK5182 treatment. We suggest that orphan nuclear receptor ERRγ directly regulates the ER-bound transcription factor CREBH in response to ER stress and other metabolic conditions.

  11. A margin based approach to determining sample sizes via tolerance bounds.

    Energy Technology Data Exchange (ETDEWEB)

    Newcomer, Justin T.; Freeland, Katherine Elizabeth

    2013-09-01

    This paper proposes a tolerance bound approach for determining sample sizes. With this new methodology we begin to think of sample size in the context of uncertainty exceeding margin. As the sample size decreases the uncertainty in the estimate of margin increases. This can be problematic when the margin is small and only a few units are available for testing. In this case there may be a true underlying positive margin to requirements but the uncertainty may be too large to conclude we have sufficient margin to those requirements with a high level of statistical confidence. Therefore, we provide a methodology for choosing a sample size large enough such that an estimated QMU uncertainty based on the tolerance bound approach will be smaller than the estimated margin (assuming there is positive margin). This ensures that the estimated tolerance bound will be within performance requirements and the tolerance ratio will be greater than one, supporting a conclusion that we have sufficient margin to the performance requirements. In addition, this paper explores the relationship between margin, uncertainty, and sample size and provides an approach and recommendations for quantifying risk when sample sizes are limited.

  12. Apo and InsP[subscript 3]-bound crystal structures of the ligand-binding domain of an InsP[subscript 3] receptor

    Energy Technology Data Exchange (ETDEWEB)

    Lin, Chun-Chi; Baek, Kyuwon; Lu, Zhe (UPENN)

    2012-05-08

    We report the crystal structures of the ligand-binding domain (LBD) of a rat inositol 1,4,5-trisphosphate receptor (InsP{sub 3}R) in its apo and InsP{sub 3}-bound conformations. Comparison of these two conformations reveals that LBD's first {beta}-trefoil fold ({beta}-TF1) and armadillo repeat fold (ARF) move together as a unit relative to its second {beta}-trefoil fold ({beta}-TF2). Whereas apo LBD may spontaneously transition between gating conformations, InsP{sub 3} binding shifts this equilibrium toward the active state.

  13. Proposal for field-based definition of soil bound pesticide residues.

    Science.gov (United States)

    Boesten, J J T I

    2016-02-15

    The environmental significance of soil bound pesticide residues (SBPR) is potentially large because approximately one third of the applied mass of the pesticides in agriculture ends up as SBPR. At EU level, there is little regulatory guidance available on the environmental risk assessment of SBPR in spite of some 50 years of SBPR research. This lack of guidance is partially caused by the fact that the current definitions of SBPR are founded on non-extractability in soil in the laboratory whereas for the environmental risk assessment not the soil in the laboratory but the soil in the field is the system of interest. Therefore a definition of SBPR is proposed that is based on the field soil: a molecule (further called 'the mother molecule') is soil bound if a relevant part of this molecule has become part of the solid phase in the soil and if this relevant part will never be released again to the liquid phase in soil under relevant field conditions in the form of this mother molecule or in the form of another molecule that may possibly raise environmental or human toxicological concerns. This mother molecule may be the parent substance that is applied to the soil but it may also be a metabolite of this parent substance. A consequence of the definition is that the SBPR terminology becomes more precise because the mother molecule of the soil bound residue has to be specified. A further consequence is that very strong but reversible sorption of molecules such as paraquat is not considered soil-bound residue anymore (as may be demonstrated by a self-exchange extraction procedure). Furthermore, the definition requires that risk managers have to define what they consider as 'relevant field conditions' (e.g. include also changes of agricultural fields into forests?).

  14. Structure-Based, Rational Design of T Cell Receptors

    OpenAIRE

    Zoete, V; Irving, M.; Ferber, M.; Cuendet, M. A.; Michielin, O

    2013-01-01

    Adoptive cell transfer using engineered T cells is emerging as a promising treatment for metastatic melanoma. Such an approach allows one to introduce T cell receptor (TCR) modifications that, while maintaining the specificity for the targeted antigen, can enhance the binding and kinetic parameters for the interaction with peptides (p) bound to major histocompatibility complexes (MHC). Using the well-characterized 2C TCR/SIYR/H-2K(b) structure as a model system, we demonstrated that a binding...

  15. Accurate upper-lower bounds on homogenized matrix by FFT-based Galerkin method

    CERN Document Server

    Vondřejc, Jaroslav; Marek, Ivo

    2014-01-01

    Accurate upper-lower bounds on homogenized matrix, arising from the unit cell problem for periodic media, are calculated for a scalar elliptic setting. Our approach builds on the recent variational reformulation of the Moulinec-Suquet (1994) Fast Fourier Transform (FFT) homogenization scheme by Vond\\v{r}ejc et al. (2014), which is based on the conforming Galerkin approximation with trigonometric polynomials. Upper-lower bounds are obtained by adjusting the primal-dual finite element framework developed independently by Dvo\\v{r}\\'{a}k (1993) and Wi\\c{e}ckowski (1995) to the FFT-based Galerkin setting. We show that the discretization procedure differs for odd and non-odd number of discretization points. In particular, thanks to the Helmholtz decomposition inherited from the continuous formulation, the duality structure is fully recovered for odd discretization. In the latter case, the more complex primal-dual structure is observed due to the trigonometric polynomials associated with the Nyquist frequencies. The...

  16. In-gap bound states induced by interstitial Fe impurities in iron-based superconductors

    Science.gov (United States)

    Zhang, Degang

    2015-12-01

    Based on a two-orbit four-band tight binding model, we investigate the low-lying electronic states around the interstitial excess Fe ions in the iron-based superconductors by using T-matrix approach. It is shown that the local density of states at the interstitial Fe impurity (IFI) possesses a strong resonance inside the gap, which seems to be insensitive to the doping and the pairing symmetry in the Fe-Fe plane, while a single or two resonances appear at the nearest neighboring (NN) Fe sites. The location and height of the resonance peaks only depend on the hopping t and the pairing parameter ΔI between the IFI and the NN Fe sites. These in-gap resonances are originated in the Andreev's bound states due to the quasiparticle tunneling through the IFI, leading to the change of the magnitude of the superconducting order parameter. When both t and ΔI are small, this robust zero-energy bound state near the IFI is consistent with recent scanning tunneling microscopy observations.

  17. ERROR BOUNDS FOR SURFACE AREA ESTIMATORS BASED ON CROFTON’S FORMULA

    Directory of Open Access Journals (Sweden)

    Markus Kiderlen

    2011-05-01

    Full Text Available According to Crofton's formula, the surface area S(A of a sufficiently regular compact set A in Rd is proportional to the mean of all total projections pA (u on a linear hyperplane with normal u, uniformly averaged over all unit vectors u. In applications, pA (u is only measured in k directions and the mean is approximated by a finite weighted sum bS(A of the total projections in these directions. The choice of the weights depends on the selected quadrature rule. We define an associated zonotope Z (depending only on the projection directions and the quadrature rule, and show that the relative error bS (A/S (A is bounded from below by the inradius of Z and from above by the circumradius of Z. Applying a strengthened isoperimetric inequality due to Bonnesen, we show that the rectangular quadrature rule does not give the best possible error bounds for d =2. In addition, we derive asymptotic behavior of the error (with increasing k in the planar case. The paper concludes with applications to surface area estimation in design-based digital stereology where we show that the weights due to Bonnesen's inequality are better than the usual weights based on the rectangular rule and almost optimal in the sense that the relative error of the surface area estimator is very close to the minimal error.

  18. A Structural Model for the Membrane-Bound Form of the Juxtamembrane Domain of the Epidermal Growth Factor Receptor.

    Energy Technology Data Exchange (ETDEWEB)

    Choowongkomon, Kiattawee; Carlin, Cathleen R.; Sonnichsen, Frank D.

    2005-06-24

    The epidermal growth factor receptor (EGFR) is a member of the receptor tyrosine kinase family involved in the regulation of cellular proliferation and differentiation. Its juxtamembrane domain (JX), the region located between the transmembrane and kinase domains, plays important roles in receptor trafficking. Two sorting signals, a PXXP motif and a 658LL659 motif, are responsible for basolateral sorting in polarized epithelial cells, and a 679LL680 motif targets the ligand-activated receptor for lysosomal degradation. To understand the regulation of these signals, we characterized the structural properties of recombinant JX domain in aqueous solution and in dodecylphosphocholine (DPC) detergent. JX is inherently unstructured in aqueous solution, albeit a nascent helix encompasses the lysosomal sorting signal. In DPC micelles, structures derived from NMR data showed three amphipathic, helical segments. A large, internally inconsistent group of long range nuclear Overhauser effects suggest a close proximity of the helices, and the presence of significant conformational averaging. Models were determined for the average JX conformation using restraints representing the translational restriction due to micelle-surface adsorption, and the helix orientations were determined from residual dipolar couplings. Two equivalent average structural models were obtained that differ only in the relative orientation between first and second helices. In these models, the 658LL659 and 679LL680 motifs are located in the first and second helices and face the micelle surface, whereas the PXXP motif is located in a flexible helix-connecting region. The data suggest that the activity of these signals may be regulated by their membrane association and restricted accessibility in the intact receptor.

  19. Upper-bound limit analysis based on the natural element method

    Science.gov (United States)

    Zhou, Shu-Tao; Liu, Ying-Hua

    2012-10-01

    The natural element method (NEM) is a newly-developed numerical method based on Voronoi diagram and Delaunay triangulation of scattered points, which adopts natural neighbour interpolation to construct trial functions in the framework of Galerkin method. Owing to its distinctive advantages, the NEM is used widely in many problems of computational mechanics. Utilizing the NEM, this paper deals with numerical limit analysis of structures made up of perfectly rigid-plastic material. According to kinematic theorem of plastic limit analysis, a mathematical programming natural element formulation is established for determining the upper bound multiplier of plane problems, and a direct iteration algorithm is proposed accordingly to solve it. In this algorithm, the plastic incompressibility condition is handled by two different treatments, and the nonlinearity and nonsmoothness of the goal function are overcome by distinguishing the rigid zones from the plastic zones at each iteration. The procedure implementation of iterative process is quite simple and effective because each iteration is equivalent to solving an associated elastic problem. The obtained limit load multiplier is proved to monotonically converge to the upper bound of true solution. Several benchmark examples are investigated to validate the significant performance of the NEM in the application field of limit analysis.

  20. Upper-bound limit analysis based on the natural element method

    Institute of Scientific and Technical Information of China (English)

    Shu-Tao Zhou; Ying-Hua Liu

    2012-01-01

    The natural element method (NEM) is a newlydeveloped numerical method based on Voronoi diagram and Delaunay triangulation of scattered points,which adopts natural neighbour interpolation to construct trial functions in the framework of Galerkin method.Owing to its distinctive advantages,the NEM is used widely in many problems of computational mechanics.Utilizing the NEM,this paper deals with numerical limit analysis of structures made up of perfectly rigid-plastic material.According to kinematic theorem of plastic limit analysis,a mathematical programming natural element formulation is established for determining the upper bound multiplier of plane problems,and a direct iteration algorithm is proposed accordingly to solve it.In this algorithm,the plastic incompressibility condition is handled by two different treatments,and the nonlinearity and nonsmoothness of the goal function are overcome by distinguishing the rigid zones from the plastic zones at each iteration.The procedure implementation of iterative process is quite simple and effective because each iteration is equivalent to solving an associated elastic problem.The obtained limit load multiplier is proved to monotonically converge to the upper bound of true solution.Several benchmark examples are investigated to validate the significant performance of the NEM in the application field of limit analysis.

  1. Upper bound analysis of slope stability with nonlinear failure criterion based on strength reduction technique

    Institute of Scientific and Technical Information of China (English)

    ZHAO Lian-heng; LI Liang; YANG Feng; LUO Qiang; LIU Xiang

    2010-01-01

    Based on the upper bound limit analysis theorem and the shear strength reduction technique,the equation for expressing critical limit-equilibrium state was employed to define the safety factor of a given slope and its corresponding critical failure mechanism by means of the kinematical approach of limit analysis theory.The nonlinear shear strength parameters were treated as variable parameters and a kinematically admissible failure mechanism was considered for calculation schemes.The iterative optimization method was adopted to obtain the safety factors.Case study and comparative analysis show that solutions presented here agree with available predictions when nonlinear criterion reduces to linear criterion,and the validity of present method could be illuminated.From the numerical results,it can also be seen that nonlinear parameter m,slope foot gradient β,height of slope H,slope top gradient a and soil bulk density Y have significant effects on the safety factor of the slope.

  2. Lower bounds for Arrangement-based Range-Free Localization in Sensor Networks

    CERN Document Server

    Gupta, Sandeep

    2012-01-01

    Colander are location aware entities that collaborate to determine approximate location of mobile or static objects when beacons from an object are received by all colanders that are within its distance $R$. This model, referred to as arrangement-based localization, does not require distance estimation between entities, which has been shown to be highly erroneous in practice. Colander are applicable in localization in sensor networks and tracking of mobile objects. A set $S \\subset {\\mathbb R}^2$ is an $(R,\\epsilon)$-colander if by placing receivers at the points of $S$, a wireless device with transmission radius $R$ can be localized to within a circle of radius $\\epsilon$. We present tight upper and lower bounds on the size of $(R,\\epsilon)$-colanders. We measure the expected size of colanders that will form $(R, \\epsilon)$-colanders if they distributed uniformly over the plane.

  3. The 2.1 A resolution structure of cyanopindolol-bound β1-adrenoceptor identifies an intramembrane Na+ ion that stabilises the ligand-free receptor.

    Directory of Open Access Journals (Sweden)

    Jennifer L Miller-Gallacher

    Full Text Available The β1-adrenoceptor (β1AR is a G protein-coupled receptor (GPCR that is activated by the endogenous agonists adrenaline and noradrenaline. We have determined the structure of an ultra-thermostable β1AR mutant bound to the weak partial agonist cyanopindolol to 2.1 Å resolution. High-quality crystals (100 μm plates were grown in lipidic cubic phase without the assistance of a T4 lysozyme or BRIL fusion in cytoplasmic loop 3, which is commonly employed for GPCR crystallisation. An intramembrane Na+ ion was identified co-ordinated to Asp872.50, Ser1283.39 and 3 water molecules, which is part of a more extensive network of water molecules in a cavity formed between transmembrane helices 1, 2, 3, 6 and 7. Remarkably, this water network and Na+ ion is highly conserved between β1AR and the adenosine A2A receptor (rmsd of 0.3 Å, despite an overall rmsd of 2.4 Å for all Cα atoms and only 23% amino acid identity in the transmembrane regions. The affinity of agonist binding and nanobody Nb80 binding to β1AR is unaffected by Na+ ions, but the stability of the receptor is decreased by 7.5°C in the absence of Na+. Mutation of amino acid side chains that are involved in the co-ordination of either Na+ or water molecules in the network decreases the stability of β1AR by 5-10°C. The data suggest that the intramembrane Na+ and associated water network stabilise the ligand-free state of β1AR, but still permits the receptor to form the activated state which involves the collapse of the Na+ binding pocket on agonist binding.

  4. Bacillus thuringiensis subsp. israelensis Cyt1Aa synergizes Cry11Aa toxin by functioning as a membrane-bound receptor

    OpenAIRE

    Pérez, Claudia; Fernandez, Luisa E.; Sun, Jianguang; Folch, Jorge Luis; Gill, Sarjeet S.; Soberón, Mario; Bravo, Alejandra

    2005-01-01

    Bacillus thuringiensis subsp. israelensis produces crystal proteins, Cry (4Aa, 4Ba, 10Aa, and 11Aa) and Cyt (1Aa and 2Ba) proteins, toxic to mosquito vectors of human diseases. Cyt1Aa overcomes insect resistance to Cry11Aa and Cry4 toxins and synergizes the toxicity of these toxins. However, the molecular mechanism of synergism remains unsolved. Here, we provide evidence that Cyt1Aa functions as a receptor of Cry11Aa. Sequential-binding analysis of Cyt1Aa and Cry11Aa revealed that Cyt1Aa bind...

  5. Feedback, receptor clustering, and receptor restriction to single cells yield large Turing spaces for ligand-receptor-based Turing models

    Science.gov (United States)

    Kurics, Tamás; Menshykau, Denis; Iber, Dagmar

    2014-08-01

    Turing mechanisms can yield a large variety of patterns from noisy, homogenous initial conditions and have been proposed as patterning mechanism for many developmental processes. However, the molecular components that give rise to Turing patterns have remained elusive, and the small size of the parameter space that permits Turing patterns to emerge makes it difficult to explain how Turing patterns could evolve. We have recently shown that Turing patterns can be obtained with a single ligand if the ligand-receptor interaction is taken into account. Here we show that the general properties of ligand-receptor systems result in very large Turing spaces. Thus, the restriction of receptors to single cells, negative feedbacks, regulatory interactions among different ligand-receptor systems, and the clustering of receptors on the cell surface all greatly enlarge the Turing space. We further show that the feedbacks that occur in the FGF10-SHH network that controls lung branching morphogenesis are sufficient to result in large Turing spaces. We conclude that the cellular restriction of receptors provides a mechanism to sufficiently increase the size of the Turing space to make the evolution of Turing patterns likely. Additional feedbacks may then have further enlarged the Turing space. Given their robustness and flexibility, we propose that receptor-ligand-based Turing mechanisms present a general mechanism for patterning in biology.

  6. Lower and Upper Bounds in Zone-Based Abstractions of Timed Automata

    DEFF Research Database (Denmark)

    Behrmann, Gerd; Bouyer, Patricia; Larsen, Kim Guldstrand;

    2005-01-01

    be obtained. We show soundness and completeness of the new abstractions w.r.t. reachability and demonstrate how information about lower and upper bounds can be used to optimise the algorithm for bringing a difference bound matrix into normal form. Finally, we experimentally demonstrate that the new techniques...

  7. Lower and Upper Bounds in Zone-Based Abstractions of Timed Automata

    DEFF Research Database (Denmark)

    Behrmann, Gerd; Bouyer, P.; Larsen, Kim Guldstrand;

    2005-01-01

    , significantly coarser abstractions can be obtained. We show soundness and completeness of the new abstractions w.r.t. reachability. We demonstrate how information about lower and upper bounds can be used to optimise the algorithm for bringing a difference bound matrix into normal form. Finally, we...

  8. New upper bounds for nonbinary codes based on the Terwilliger algebra and semidefinite programming

    NARCIS (Netherlands)

    Gijswijt, D.; Schrijver, A.; Tanaka, H.

    2006-01-01

    We give a new upper bound on the maximum size $A_q(n,d)$ of a code of word length $n$ and minimum Hamming distance at least $d$ over the alphabet of $q\\geq 3$ letters. By block-diagonalizing the Terwilliger algebra of the nonbinary Hamming scheme, the bound can be calculated in time polynomial in $n

  9. New Upper Bounds for Nonbinary Codes Based on the Terwilliger Algebra and Semidefinite Programming

    NARCIS (Netherlands)

    D.C. Gijswijt; A. Schrijver

    2006-01-01

    Abstract: We give a new upper bound on the maximum size $A_q(n,d)$ of a code of word length $n$ and minimum Hamming distance at least $d$ over the alphabet of $q\\geq 3$ letters. By block-diagonalizing the Terwilliger algebra of the nonbinary Hamming scheme, the bound can be calculated in time polyno

  10. Bounded Earthquakes

    OpenAIRE

    Saric, Dragomir

    2006-01-01

    We give a short proof of the fact that bounded earthquakes of the unit disk induce quasisymmetric maps of the unit circle. By a similar method, we show that symmetric maps are induced by bounded earthquakes with asymptotically trivial measures.

  11. Structural ensemble dynamics based closure model for wall-bounded turbulent flow

    Institute of Scientific and Technical Information of China (English)

    Zhen-Su She; Ning Hu; You Wu

    2009-01-01

    Wall-bounded turbulent flow involves the development of multi-scale turbulent eddies, as well as a sharply varying boundary layer. Its theoretical descriptions are yet phenomenological. We present here a new framework called structural ensemble dynamics (SED), which aims at using systematically all relevant statistical properties of turbulent structures for a quantitative description of ensemble means. A new set of closure equations based on the SED approach for a turbulent channel flow is presented. SED order functions are defined, and numerically determined from data of direct numerical simulations (DNS). Computational results show that the new closure model reproduces accurately the solution of the original Navier-Stokes simulation, including the mean velocity profile, the kinetic energy of the stream-wise velocity component, and every term in the energy budget equation. It is suggested that the SED-based studies of turbulent structure builds a bridge between the studies of physical mechanisms of turbulence and the development of accurate model equations for engineering predictions.

  12. Internal charge transfer based ratiometric interaction of anionic surfactant with calf thymus DNA bound cationic surfactant: Study I

    Science.gov (United States)

    Mukherjee, Abhijit; Chaudhuri, Tandrima; Moulik, Satya Priya; Banerjee, Manas

    2016-01-01

    Cetyl trimethyl ammonium bromide (CTAB) binds calf thymus (ct-) DNA like anionic biopolymers electrostatically and established equilibrium both in the ground as well as in excited state in aqueous medium at pH 7. Anionic sodium dodecyl sulfate (SDS) does not show even hydrophobic interaction with ct-DNA at low concentration. On contrary, SDS can establish well defined equilibrium with DNA bound CTAB in ground state where the same CTAB-DNA isosbestic point reappears. First report of internal charge transfer (ICT) based binding of CTAB with ct-DNA as well as ICT based interaction of anionic SDS with DNA bound CTAB that shows dynamic quenching contribution also. The reappearance of anodic peak and slight increase in cathodic peak current with increasing concentration (at lower range) of anionic SDS, possibly reflect the release of CTAB from DNA bound CTAB by SDS.

  13. Internal charge transfer based ratiometric interaction of anionic surfactant with calf thymus DNA bound cationic surfactant: Study I.

    Science.gov (United States)

    Mukherjee, Abhijit; Chaudhuri, Tandrima; Moulik, Satya Priya; Banerjee, Manas

    2016-01-01

    Cetyl trimethyl ammonium bromide (CTAB) binds calf thymus (ct-) DNA like anionic biopolymers electrostatically and established equilibrium both in the ground as well as in excited state in aqueous medium at pH 7. Anionic sodium dodecyl sulfate (SDS) does not show even hydrophobic interaction with ct-DNA at low concentration. On contrary, SDS can establish well defined equilibrium with DNA bound CTAB in ground state where the same CTAB-DNA isosbestic point reappears. First report of internal charge transfer (ICT) based binding of CTAB with ct-DNA as well as ICT based interaction of anionic SDS with DNA bound CTAB that shows dynamic quenching contribution also. The reappearance of anodic peak and slight increase in cathodic peak current with increasing concentration (at lower range) of anionic SDS, possibly reflect the release of CTAB from DNA bound CTAB by SDS.

  14. Bound entanglement and entanglement bounds

    Energy Technology Data Exchange (ETDEWEB)

    Sauer, Simeon [Physikalisch-Astronomische Fakultaet, Friedrich-Schiller-Univesitaet Jena (Germany)]|[Physikalisches Institut, Albert-Ludwigs-Universitaet Freiburg, Hermann-Herder-Strasse 3, D-79104 Freiburg (Germany); Melo, Fernando de; Mintert, Florian; Buchleitner, Andreas [Physikalisches Institut, Albert-Ludwigs-Universitaet Freiburg, Hermann-Herder-Strasse 3, D-79104 Freiburg (Germany)]|[Max-Planck-Institut fuer Physik komplexer Systeme, Noethnitzer Str.38, D-01187 Dresden (Germany); Bae, Joonwoo [School of Computational Sciences, Korea Institute for Advanced Study, Seoul 130-012 (Korea); Hiesmayr, Beatrix [Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna (Austria)

    2008-07-01

    We investigate the separability of Bell-diagonal states of two qutrits. By using lower bounds to algebraically estimate concurrence, we find convex regions of bound entangled states. Some of these regions exactly coincide with the obtained results when employing optimal entanglement witnesses, what shows that the lower bound can serve as a precise detector of entanglement. Some hitherto unknown regions of bound entangled states were discovered with this approach, and delimited efficiently.

  15. Calix[4]pyrrole-based ion pair receptors.

    Science.gov (United States)

    Kim, Sung Kuk; Sessler, Jonathan L

    2014-08-19

    Ion pair receptors, which are able to bind concurrently both a cation and an anion, often display higher selectivity and affinity for specific ion pairs than simple ion receptors capable of recognizing primarily either a cation or an anion. This enhancement in recognition function is attributable to direct or indirect cooperative interactions between cobound ions via electrostatic attractions between oppositely charged ions, as well as to positive allosteric effects. In addition, by virtue of binding the counterions of the targeted ion, ion pair receptors can minimize the solvation of the counterions, which can otherwise have a negative effect on the interactions between the receptors and the targeted ions. As a result of their more favorable interactions, ion pair receptors are attractive for use in applications, such as extraction and sensing, where control of the binding interactions is advantageous. In this Account, we illustrate this potential in the context of ion pair receptors based on the calix[4]pyrrole scaffold. Both simple ditopic ion pair receptors, containing sites for the recognition of a single anion and single cation, and so-called multitopic ion pair receptors will be discussed. The latter systems differ from conventional, so-called ditopic ion pair receptors in that they contain more than one binding site for a given targeted ion (e.g., a cation). This permits a level of selectivity and control over binding function not normally seen for simple ion or ion pair receptors containing one or two binding sites, respectively. Calix[4]pyrroles are macrocyclic compounds consisting of four pyrrole units linked via fully substituted sp(3) hybridized meso carbon atoms. They are effective receptors for Lewis basic anions (e.g., halides) in typical organic media and under certain conditions will recognize ion pairs containing charge diffuse cations, such as a small alkylammonium, imidazolium, or cesium cations. The calix[4]pyrrole framework is further

  16. FROM BOUNDED FAMILIES OF LOCALIZED COSINES TO BI-ORTHOGONAL RIESZ BASES VIA SHIFT-INVARIANCE

    Institute of Scientific and Technical Information of China (English)

    Charles K. Chui; Shi Xianliang

    2001-01-01

    The notion of bi-inner product functionals P(f ,g) = ∑ < f ,f. >< g ,g. > generated by two Bessel seqnsences {fn} and {gn} of functions from L2 was introduced in our earlier work[5] as a vehicle to identify dual frames and bi-orthogonal Riesz bases of L2. The objective was to find conditions under which P is a constant multiple of the inner product <f ,g > of L2. A necessary and sufficient condition derived in [5]is that P is both spatial shift-invariant and phase shift-invariant. Although these two shift-invariance proper ties are, in general, unrelated, it could happen that one is a consequence of the other for certain clases of Bessel sequences {fn} and {gn}. In this paper, we show that, indeed, for localized cosines with two-over lapping windows (i. e. , only adjacent window functions are allowed to overlap ) , spatial shift-inrvariance of P is already sufficient to guarantee that P is a constant multiple of the inner product, while phase shift-in variance is not. Hence, phase shift-invariance of P for two-overlapping localized cosine Bessel sequences is a consequence of spatial shift-invariance, but the eonverse is not valid. As an application, we also show thattwo families of localized cosines with uniformly bounded and two-overlapping windows are bi-orthogonal Riesz bases of L2, if and only if Pis spatial shi ft-invariant. In addition, we apply this result to generalize a result on characterization of dual localized codne bases in our earlier work in [3] to the multivariate set- ting. A method for computing the dual windows is also given in this paper.

  17. Single-membrane-bounded peroxisome division revealed by isolation of dynamin-based machinery.

    Science.gov (United States)

    Imoto, Yuuta; Kuroiwa, Haruko; Yoshida, Yamato; Ohnuma, Mio; Fujiwara, Takayuki; Yoshida, Masaki; Nishida, Keiji; Yagisawa, Fumi; Hirooka, Shunsuke; Miyagishima, Shin-ya; Misumi, Osami; Kawano, Shigeyuki; Kuroiwa, Tsuneyoshi

    2013-06-01

    Peroxisomes (microbodies) are ubiquitous single-membrane-bounded organelles and fulfill essential roles in the cellular metabolism. They are found in virtually all eukaryotic cells and basically multiply by division. However, the mechanochemical machinery involved in peroxisome division remains elusive. Here, we first identified the peroxisome-dividing (POD) machinery. We isolated the POD machinery from Cyanidioschyzon merolae, a unicellular red alga containing a single peroxisome. Peroxisomal division in C. merolae can be highly synchronized by light/dark cycles and the microtubule-disrupting agent oryzalin. By proteomic analysis based on the complete genome sequence of C. merolae, we identified a dynamin-related protein 3 (DRP3) ortholog, CmDnm1 (Dnm1), that predominantly accumulated with catalase in the dividing-peroxisome fraction. Immunofluorescence microscopy demonstrated that Dnm1 formed a ring at the division site of the peroxisome. The outlines of the isolated dynamin rings were dimly observed by phase-contrast microscopy and clearly stained for Dnm1. Electron microscopy revealed that the POD machinery was formed at the cytoplasmic side of the equator. Immunoelectron microscopy showed that the POD machinery consisted of an outer dynamin-based ring and an inner filamentous ring. Down-regulation of Dnm1 impaired peroxisomal division. Surprisingly, the same Dnm1 serially controlled peroxisomal division after mitochondrial division. Because genetic deficiencies of Dnm1 orthologs in multiperoxisomal organisms inhibited both mitochondrial and peroxisomal proliferation, it is thought that peroxisomal division by contraction of a dynamin-based machinery is universal among eukaryotes. These findings are useful for understanding the fundamental systems in eukaryotic cells.

  18. Cell surface-bound TIMP3 induces apoptosis in mesenchymal Cal78 cells through ligand-independent activation of death receptor signaling and blockade of survival pathways.

    Directory of Open Access Journals (Sweden)

    Christina Koers-Wunrau

    Full Text Available BACKGROUND: The matrix metalloproteinases (MMPs and their endogenous regulators, the tissue inhibitor of metalloproteinases (TIMPs 1-4 are responsible for the physiological remodeling of the extracellular matrix (ECM. Among all TIMPs, TIMP3 appears to play a unique role since TIMP3 is a secreted protein and, unlike the other TIMP family members, is tightly bound to the ECM. Moreover TIMP3 has been shown to be able to induce apoptotic cell death. As little is known about the underlying mechanisms, we set out to investigate the pro-apoptotic effect of TIMP3 in human mesenchymal cells. METHODOLOGY/PRINCIPAL FINDINGS: Lentiviral overexpression of TIMP3 in mesenchymal cells led to a strong dose-dependent induction of ligand-independent apoptosis as reflected by a five-fold increase in caspase 3 and 7 activity compared to control (pLenti6/V5-GW/lacZ or uninfected cells, whereas exogenous TIMP3 failed to induce apoptosis. Concordantly, increased cleavage of death substrate PARP and the caspases 3 and 7 was observed in TIMP3 overexpressing cultures. Notably, activation of caspase-8 but not caspase-9 was observed in TIMP3-overexpressing cells, indicating a death receptor-dependent mechanism. Moreover, overexpression of TIMP3 led to a further induction of apoptosis after stimulation with TNF-alpha, FasL and TRAIL. Most interestingly, TIMP3-overexpression was associated with a decrease in phosphorylation of cRaf, extracellular signal-regulated protein kinase (Erk1/2, ribosomal S6 kinase (RSK1 and Akt and serum deprivation of TIMP3-overexpressing cells resulted in a distinct enhancement of apoptosis, pointing to an impaired signaling of serum-derived survival factors. Finally, heparinase treatment of heparan sulfate proteoglycans led to the release of TIMP3 from the surface of overexpressing cells and to a significant decrease in apoptosis indicating that the binding of TIMP3 is necessary for apoptosis induction. CONCLUSION: The results demonstrate that

  19. Development of immobilized membrane-based affinity columns for use in the online characterization of membrane bound proteins and for targeted affinity isolations

    Energy Technology Data Exchange (ETDEWEB)

    Moaddel, Ruin [Gerontology Research Center, National Institute on Aging, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD 21224-6825 (United States); Wainer, Irving W. [Gerontology Research Center, National Institute on Aging, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD 21224-6825 (United States)]. E-mail: Wainerir@grc.nia.nih.gov

    2006-03-30

    Membranes obtained from cell lines that express or do not express a target membrane bound protein have been immobilized on a silica-based liquid chromatographic support or on the surface of an activated glass capillary. The resulting chromatographic columns have been placed in liquid chromatographic systems and used to characterize the target proteins and to identify small molecules that bind to the target. Membranes containing ligand gated ion channels, G-protein coupled receptors and drug transporters have been prepared and characterized. If a marker ligand has been identified for the target protein, frontal or zonal displacement chromatographic techniques can be used to determine binding affinities (K {sub d} values) and non-linear chromatography can be used to assess the association (k {sub on}) and dissociation (k {sub off}) rate constants and the thermodynamics of the binding process. Membrane-based affinity columns have been created using membranes from a cell line that does not express the target protein (control) and the same cell line that expresses the target protein (experimental) after genomic transfection. The resulting columns can be placed in a parallel chromatography system and the differential retention between the control and experimental columns can be used to identify small molecules and protein that bind to the target protein. These applications will be illustrated using columns created using cellular membranes containing nicotinic acetylcholine receptors and the drug transporter P-glycoprotein.

  20. Docking-based virtual screening of potential human P2Y12 receptor antagonists

    Institute of Scientific and Technical Information of China (English)

    Hua Chen; Xianchi Dong; Minyun Zhou; Haiming Shi; Xinping Luo

    2011-01-01

    Platelet plays essential roles in hemostasis and its dysregulation can lead to arterial thrombosis. P2Y12 is an important platelet membrane adenosine diphosphate receptor,and its antagonists have been widely developed as anticoagulation agents. The current P2Y12 inhibitors available in clinical practice have not fully achieved saOsfactory antithrombotic effects, leaving room for further improvement To identify new chemical compounds as potential anticoagulation inhibitors, we constructed a three-dimensional structure model of human P2Y12 by homology modeling based on the recently reported G-protein coupled receptor Meleagris gallopavo βl adrenergic receptor. Virtual screening of the modeled P2Y12 against three subsets of small molecules from the ZINC database, namely lead-like, fragment-like, and drug-like, identified a number of compounds tbat might have high binding affinity to P2Y12.Detailed analyses of the top three compounds from each subset with the highest scores indicated that all of these compounds beard a hydrophobic bulk supplemented with a few polar atoms which bound at the ligand binding site via largely hydrophobic interactions with the receptor. This study not only provides a structure model of P2Y12 for rational design of anti-platelet inhibitors, but also identifies some potential chemicals for further development.

  1. Biophysics of risk aversion based on neurotransmitter receptor theory

    OpenAIRE

    Takahashi, Taiki

    2011-01-01

    Decision under risk and uncertainty has been attracting attention in neuroeconomics and neuroendocrinology of decision-making. This paper demonstrated that the neurotransmitter receptor theory-based value (utility) function can account for human and animal risk-taking behavior. The theory predicts that (i) when dopaminergic neuronal response is efficiently coupled to the formation of ligand-receptor complex, subjects are risk-aversive (irrespective of their satisfaction level) and (ii) when t...

  2. 生长因子受体结合蛋白7(Grb7)研究进展%Research progresses on growth factor receptor-bound 7

    Institute of Scientific and Technical Information of China (English)

    张丹; 高友鹤

    2011-01-01

    Growth factor receptor-bound 7(Grb7), a member of Grb7 protein family, has three distinct functional regions: a lot of proline amino acids exist in its N terminal, and the mesial district has such similar amino acids sequence as that of MIG-IO protein from Caenorhabditis elegans, and a SH2 domain in its C terminal. With these different domain, Grb7 protein plays distinct roles in cellular signaling pathway. And if we know more about the biological function acted by different domains of Grb7 protein, people may be benefited from treatment of patients with high expression of Grb7 protein.%Grb7蛋白是Grb7蛋白家族的成员之一,该蛋白有3种结构区域:N末端富含脯氨酸,中间结构域与线虫(Caenorhabditis elegans)的MIG-10蛋白有着很高的同源性,C末端为SHY.结构域.Grb7通过3种结构域尤其是SH2结构域,参与细胞各种信号传导途径.研究其不同结构域在肿瘤细胞中所发挥的作用,将对Grb7高表达的肿瘤治疗产生重要影响.

  3. Acute mechanical sensitization of peripheral nociceptors by aldosterone through non-genomic activation of membrane bound mineralocorticoid receptors in naive rats.

    Science.gov (United States)

    Shaqura, Mohammed; Li, Xiongjuan; Al-Madol, Mohammed A; Tafelski, Sascha; Beyer-Koczorek, Antje; Mousa, Shaaban A; Schäfer, Michael

    2016-08-01

    Recently, there is increasing interest in the role of peripheral mineralocorticoid receptors (MR) to modulate pain, but their localization in neurons and glia of the periphery and their distinct involvement in pain control remains elusive. In naive Wistar rats our double immunofluorescence confocal microscopy of the spinal cord, dorsal root ganglia, sciatic nerve and innervated skin revealed that MR predominantly colocalized with calcitonin-gene-related peptide (CGRP)- and trkA-immunoreactive (IR) nociceptive neurons and only marginally with myelinated trkB-IR mechanoreceptive and trkC-IR proprioreceptive neurons underscoring a pivotal role for MR in the modulation of pain. MR could not be detected in Schwann cells, satellite cells, and astrocytes and only scarcely in spinal microglia cells excluding a relevant functional role of glia-derived MR at least in naïve rats. Intrathecal (i.t.) and intraplantar (i.pl.) application of increasing doses of the MR selective agonist aldosterone acutely increased nociceptive behavior which was reversible by a MR selective antagonist and most likely due to non-genomic effects. This was further substantiated by the first identification of membrane bound MR specific binding sites in sensory neurons of dorsal root ganglia and spinal cord. Therefore, a crucial role of MR on nociceptive neurons but not on glia cells and their impact on nociceptive behavior most likely due to immediate non-genomic effects has to be considered under normal but more so under pathological conditions in future studies. PMID:27016023

  4. Stress-based upper-bound method and convex optimization: case of the Gurson material

    Science.gov (United States)

    Pastor, Franck; Trillat, Malorie; Pastor, Joseph; Loute, Etienne

    2006-04-01

    A nonlinear interior point method associated with the kinematic theorem of limit analysis is proposed. Associating these two tools enables one to determine an upper bound of the limit loading of a Gurson material structure from the knowledge of the sole yield criterion. We present the main features of the interior point algorithm and an original method providing a rigorous kinematic bound from a stress formulation of the problem. This method is tested by solving in plane strain the problem of a Gurson infinite bar compressed between rough rigid plates. To cite this article: F. Pastor et al., C. R. Mecanique 334 (2006).

  5. Proposal for field-based definition of soil bound pesticide residues

    NARCIS (Netherlands)

    Boesten, J.J.T.I.

    2016-01-01

    The environmental significance of soil bound pesticide residues (SBPR) is potentially large because approximately one third of the applied mass of the pesticides in agriculture ends up as SBPR. At EU level, there is little regulatory guidance available on the environmental risk assessment of SBPR

  6. A clustering- based bounded-error approach for identification of PWA hybrid systems

    DEFF Research Database (Denmark)

    Tabatabaei-Pour, Mojtaba

    A new bounded-error approach for the identification of discrete time hybrid systems in the piece-wise affine (PWA) form is introduced. The PWA identification problem involves the estimation of the number of affine submodels, the parameters of affine submodels and the partition of the PWA map from...

  7. Successful virtual screening for a submicromolar antagonist of the neurokinin-1 receptor based on a ligand-supported homology model.

    Science.gov (United States)

    Evers, Andreas; Klebe, Gerhard

    2004-10-21

    The neurokinin-1 (NK1) receptor belongs to the family of G-protein-coupled receptors (GPCRs), which represents one of the most relevant target families in small-molecule drug design. In this paper, we describe a homology modeling of the NK1 receptor based on the high-resolution X-ray structure of rhodopsin and the successful virtual screening based on this protein model. The NK1 receptor model has been generated using our new MOBILE (modeling binding sites including ligand information explicitly) approach. Starting with preliminary homology models, it generates improved models of the protein binding pocket together with bound ligands. Ligand information is used as an integral part in the homology modeling process. For the construction of the NK1 receptor, antagonist CP-96345 was used to restrain the modeling. The quality of the obtained model was validated by probing its ability to accommodate additional known NK1 antagonists from structurally diverse classes. On the basis of the generated model and on the analysis of known NK1 antagonists, a pharmacophore model was deduced, which subsequently guided the 2D and 3D database search with UNITY. As a following step, the remaining hits were docked into the modeled binding pocket of the NK1 receptor. Finally, seven compounds were selected for biochemical testing, from which one showed affinity in the submicromolar range. Our results suggest that ligand-supported homology models of GPCRs may be used as effective platforms for structure-based drug design.

  8. The DMM Bound

    DEFF Research Database (Denmark)

    Emiris, Ioannis Z.; Mourrain, Bernard; Tsigaridas, Elias

    2010-01-01

    ) resultant by means of mixed volume, as well as recent advances on aggregate root bounds for univariate polynomials, and are applicable to arbitrary positive dimensional systems. We improve upon Canny's gap theorem [7] by a factor of O(dn-1), where d bounds the degree of the polynomials, and n is the number...... bound on the number of steps that subdivision-based algorithms perform in order to isolate all real roots of a polynomial system. This leads to the first complexity bound of Milne's algorithm [22] in 2D....

  9. Competition between bound and free peptides in an ELISA-based procedure that assays peptides derived from protein digests

    Directory of Open Access Journals (Sweden)

    Pace Umberto

    2006-05-01

    Full Text Available Abstract Background We describe an ELISA-based method that can be used to identify and quantitate proteins in biological samples. In this method, peptides in solution, derived from proteolytic digests of the sample, compete with substrate-attached synthetic peptides for antibodies, also in solution, generated against the chosen peptides. The peptides used for the ELISA are chosen on the basis of their being (i products of the proteolytic (e.g. tryptic digestion of the protein to be identified and (ii unique to the target protein, as far as one can know from the published sequences. Results In this paper we describe the competition assay and we define the optimal conditions for the most effective assay. We have performed an analysis of the kinetics of interaction between the four components of the assay: the plastic substratum to which the peptide is bound, the bound peptide itself, the competing added peptide, and the antibody that is specific for the peptide and we compare the results of theoretical simulations to the actual data in some model systems. Conclusion The data suggest that the peptides bind to the plastic substratum in more than one conformation and that, once bound, the peptide displays different affinities for the antibody, depending on how it has bound to the plate

  10. Bound phytophenols from ready-to-eat cereals: comparison with other plant-based foods.

    Science.gov (United States)

    Neacsu, M; McMonagle, J; Fletcher, R J; Scobbie, L; Duncan, G J; Cantlay, L; de Roos, B; Duthie, G G; Russell, W R

    2013-12-01

    Whole-grain diets are linked to reduced risk of several chronic diseases (heart disease, cancer, diabetes, metabolic syndrome) and all-cause mortality. There is increasing evidence that these benefits are associated with the gut microbiota and that release of fibre-related phenolic metabolites in the gut is a contributing factor. Additional sources of these metabolites include fruits and vegetables, but the evidence for their protective effects is less well established. With respect to the availability of bound phytophenols, ready-to-eat cereals are compared with soft fruits (considered rich in antioxidants) and other commonly consumed fruits and vegetables. The results demonstrated that when compared with an equivalent serving of fruits or vegetables, a recommended portion of whole-grain cereals deliver substantially higher amounts of bound phytophenols, which are available for metabolism in the colon. The increased amount of these phenolic metabolites may, in part, explain the evidence for the protective effects of whole-grain cereals.

  11. A Stochastic Dynamic Programming Approach Based on Bounded Rationality and Application to Dynamic Portfolio Choice

    Directory of Open Access Journals (Sweden)

    Wenjie Bi

    2014-01-01

    Full Text Available Dynamic portfolio choice is an important problem in finance, but the optimal strategy analysis is difficult when considering multiple stochastic volatility variables such as the stock price, interest rate, and income. Besides, recent research in experimental economics indicates that the agent shows limited attention, considering only the variables with high fluctuations but ignoring those with small ones. By extending the sparse max method, we propose an approach to solve dynamic programming problem with small stochastic volatility and the agent’s bounded rationality. This approach considers the agent’s behavioral factors and avoids effectively the “Curse of Dimensionality” in a dynamic programming problem with more than a few state variables. We then apply it to Merton dynamic portfolio choice model with stochastic volatility and get a tractable solution. Finally, the numerical analysis shows that the bounded rational agent may pay no attention to the varying equity premium and interest rate with small variance.

  12. On the robustness of fishman's bound-based method for the network reliability problem

    OpenAIRE

    Cancela, Héctor; El Khadiri, Mohamed; Rubino, Gerardo; Tuffin, Bruno

    2015-01-01

    International audience Static network unreliability computation is an NP-hard problem, leading to the use of Monte Carlo techniques to estimate it. The latter, in turn, suffer from the rare event problem, in the frequent situation where the system's unreliability is a very small value. As a consequence, specific rare event event simulation techniques are relevant tools to provide this estimation. We focus here on a method proposed by Fishman making use of bounds on the structure function o...

  13. Bounding the $\

    CERN Document Server

    Gutiérrez-Rodríguez, A

    2003-01-01

    A bound on the nu /sup tau / magnetic moment is calculated through the reaction e/sup +/e/sup -/ to nu nu gamma at the Z/sub 1/-pole, and in the framework of a left-right symmetric model at LEP energies. We find that the bound is almost independent of the mixing angle phi of the model in the allowed experimental range for this parameter. (31 refs).

  14. Forward vaccinology: CTL targeting based upon physical detection of HLA-bound peptides

    Directory of Open Access Journals (Sweden)

    Ellis L Reinherz

    2014-09-01

    Full Text Available Vaccine-elicited cytotoxic T lymphocytes (CTL recognizing conserved fragments of a pathogen's proteome could greatly impact infectious diseases and cancers. Enabling this potential are recent advances in mass spectrometry that identify specific target peptides among the myriad HLA-bound peptides on altered cells. Ultrasensitivity of these physical detection methods allows for the direct assessment of peptide presentation on small numbers of tissue-derived cells. In addition, concurrent advances in immunobiology suggest ways to induce CTLs with requisite functional avidity and tissue deployment. Elicitation of high avidity resident memory T cells through vaccination may shift the vaccinology paradigm both for preventive and therapeutic approaches to human disease control.

  15. Biophysics of risk aversion based on neurotransmitter receptor theory

    CERN Document Server

    Takahashi, Taiki

    2011-01-01

    Decision under risk and uncertainty has been attracting attention in neuroeconomics and neuroendocrinology of decision-making. This paper demonstrated that the neurotransmitter receptor theory-based value (utility) function can account for human and animal risk-taking behavior. The theory predicts that (i) when dopaminergic neuronal response is efficiently coupled to the formation of ligand-receptor complex, subjects are risk-aversive (irrespective of their satisfaction level) and (ii) when the coupling is inefficient, subjects are risk-seeking at low satisfaction levels, consistent with risk-sensitive foraging theory in ecology. It is further suggested that some anomalies in decision under risk are due to inefficiency of the coupling between dopamine receptor activation and neuronal response. Future directions in the application of the model to studies in neuroeconomics of addiction and neuroendocrine modulation of risk-taking behavior are discussed.

  16. Effects of bound versus soluble pentosan polysulphate in PEG/HA-based hydrogels tailored for intervertebral disc regeneration.

    Science.gov (United States)

    Frith, Jessica E; Menzies, Donna J; Cameron, Andrew R; Ghosh, P; Whitehead, Darryl L; Gronthos, S; Zannettino, Andrew C W; Cooper-White, Justin J

    2014-01-01

    Previous reports in the literature investigating chondrogenesis in mesenchymal progenitor cell (MPC) cultures have confirmed the chondro-inductive potential of pentosan polysulphate (PPS), a highly sulphated semi-synthetic polysaccharide, when added as a soluble component to culture media under standard aggregate-assay conditions or to poly(ethylene glycol)/hyaluronic acid (PEG/HA)-based hydrogels, even in the absence of inductive factors (e.g. TGFβ). In this present study, we aimed to assess whether a 'bound' PPS would have greater activity and availability over a soluble PPS, as a media additive or when incorporated into PEG/HA-based hydrogels. We achieved this by covalently pre-binding the PPS to the HA component of the gel (forming a new molecule, HA-PPS). We firstly investigated the activity of HA-PPS compared to free PPS, when added as a soluble factor to culture media. Cell proliferation, as determined by CCK8 and EdU assay, was decreased in the presence of either bound or free PPS whilst chondrogenic differentiation, as determined by DMMB assay and histology, was enhanced. In all cases, the effect of the bound PPS (HA-PPS) was more potent than that of the unbound form. These results alone suggest wider applications for this new molecule, either as a culture supplement or as a coating for scaffolds targeted at chondrogenic differentiation or maturation. We then investigated the incorporation of HA-PPS into a PEG/HA-based hydrogel system, by simply substituting some of the HA for HA-PPS. Rheological testing confirmed that incorporation of either HA-PPS or PPS did not significantly affect gelation kinetics, final hydrogel modulus or degradation rate but had a small, but significant, effect on swelling. When encapsulated in the hydrogels, MPCs retained good viability and rapidly adopted a rounded morphology. Histological analysis of both GAG and collagen deposition after 21 days showed that the incorporation of the bound-PPS into the hydrogel resulted in

  17. Effects of bound versus soluble pentosan polysulphate in PEG/HA-based hydrogels tailored for intervertebral disc regeneration.

    Science.gov (United States)

    Frith, Jessica E; Menzies, Donna J; Cameron, Andrew R; Ghosh, P; Whitehead, Darryl L; Gronthos, S; Zannettino, Andrew C W; Cooper-White, Justin J

    2014-01-01

    Previous reports in the literature investigating chondrogenesis in mesenchymal progenitor cell (MPC) cultures have confirmed the chondro-inductive potential of pentosan polysulphate (PPS), a highly sulphated semi-synthetic polysaccharide, when added as a soluble component to culture media under standard aggregate-assay conditions or to poly(ethylene glycol)/hyaluronic acid (PEG/HA)-based hydrogels, even in the absence of inductive factors (e.g. TGFβ). In this present study, we aimed to assess whether a 'bound' PPS would have greater activity and availability over a soluble PPS, as a media additive or when incorporated into PEG/HA-based hydrogels. We achieved this by covalently pre-binding the PPS to the HA component of the gel (forming a new molecule, HA-PPS). We firstly investigated the activity of HA-PPS compared to free PPS, when added as a soluble factor to culture media. Cell proliferation, as determined by CCK8 and EdU assay, was decreased in the presence of either bound or free PPS whilst chondrogenic differentiation, as determined by DMMB assay and histology, was enhanced. In all cases, the effect of the bound PPS (HA-PPS) was more potent than that of the unbound form. These results alone suggest wider applications for this new molecule, either as a culture supplement or as a coating for scaffolds targeted at chondrogenic differentiation or maturation. We then investigated the incorporation of HA-PPS into a PEG/HA-based hydrogel system, by simply substituting some of the HA for HA-PPS. Rheological testing confirmed that incorporation of either HA-PPS or PPS did not significantly affect gelation kinetics, final hydrogel modulus or degradation rate but had a small, but significant, effect on swelling. When encapsulated in the hydrogels, MPCs retained good viability and rapidly adopted a rounded morphology. Histological analysis of both GAG and collagen deposition after 21 days showed that the incorporation of the bound-PPS into the hydrogel resulted in

  18. Private Capital and Investment Climate for Economic Growth: Empirical Lessons based on ARDL bound test technique

    Directory of Open Access Journals (Sweden)

    Gérard Tchouassi

    2014-06-01

    Full Text Available Using time series, autoregressive distributed lags (ARDL-bound test approach and error-correction model (ECM, this paper aims to analyze how private capital and investment climate contribute to economic growth in African countries: Cameroon, Côte d’Ivoire, Tunisia, South Africa and Zambia. We find that in short-run there is a significant relationship between private capital, economic freedom and economic growth in Cameroon, in Côte d’Ivoire, in South Africa and in Zambia. In long run, we establish that a long term relationship exists between the variables. This implies that there is a long run cointegration relationship among the variables in some equations in Cameroon, Côte d’Ivoire, South Africa and Zambia. Employing the appropriate order of the ARDL specification and multidimensional economic freedom proxies to examine this linkage, the results obtained are not all significant.  JEL Classifications: C13, C22, E22, F43, O11, O47 Key-Words: Private capital, Investment climate, Economic freedom, Economic growth, Time series, ARDL bound test approach, Error-Correction Model. Normal 0 14 false false false IT X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Tabella normale"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-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;}

  19. An Entropy-Based Upper Bound Methodology for Robust Predictive Multi-Mode RCPSP Schedules

    Directory of Open Access Journals (Sweden)

    Angela Hsiang-Ling Chen

    2014-09-01

    Full Text Available Projects are an important part of our activities and regardless of their magnitude, scheduling is at the very core of every project. In an ideal world makespan minimization, which is the most commonly sought objective, would give us an advantage. However, every time we execute a project we have to deal with uncertainty; part of it coming from known sources and part remaining unknown until it affects us. For this reason, it is much more practical to focus on making our schedules robust, capable of handling uncertainty, and even to determine a range in which the project could be completed. In this paper we focus on an approach to determine such a range for the Multi-mode Resource Constrained Project Scheduling Problem (MRCPSP, a widely researched, NP-complete problem, but without adding any subjective considerations to its estimation. We do this by using a concept well known in the domain of thermodynamics, entropy and a three-stage approach. First we use Artificial Bee Colony (ABC—an effective and powerful meta-heuristic—to determine a schedule with minimized makespan which serves as a lower bound. The second stage defines buffer times and creates an upper bound makespan using an entropy function, with the advantage over other methods that it only considers elements which are inherent to the schedule itself and does not introduce any subjectivity to the buffer time generation. In the last stage, we use the ABC algorithm with an objective function that seeks to maximize robustness while staying within the makespan boundaries defined previously and in some cases even below the lower boundary. We evaluate our approach with two different benchmarks sets: when using the PSPLIB for the MRCPSP benchmark set, the computational results indicate that it is possible to generate robust schedules which generally result in an increase of less than 10% of the best known solutions while increasing the robustness in at least 20% for practically every

  20. Appraisal of the Missing Proteins Based on the mRNAs Bound to Ribosomes.

    Science.gov (United States)

    Xu, Shaohang; Zhou, Ruo; Ren, Zhe; Zhou, Baojin; Lin, Zhilong; Hou, Guixue; Deng, Yamei; Zi, Jin; Lin, Liang; Wang, Quanhui; Liu, Xin; Xu, Xun; Wen, Bo; Liu, Siqi

    2015-12-01

    Considering the technical limitations of mass spectrometry in protein identification, the mRNAs bound to ribosomes (RNC-mRNA) are assumed to reflect the mRNAs participating in the translational process. The RNC-mRNA data are reasoned to be useful for appraising the missing proteins. A set of the multiomics data including free-mRNAs, RNC-mRNAs, and proteomes was acquired from three liver cancer cell lines. On the basis of the missing proteins in neXtProt (release 2014-09-19), the bioinformatics analysis was carried out in three phases: (1) finding how many neXtProt missing proteins have or do not have RNA-seq and/or MS/MS evidence, (2) analyzing specific physicochemical and biological properties of the missing proteins that lack both RNA-seq and MS/MS evidence, and (3) analyzing the combined properties of these missing proteins. Total of 1501 missing proteins were found by neither RNC-mRNA nor MS/MS in the three liver cancer cell lines. For these missing proteins, some are expected higher hydrophobicity, unsuitable detection, or sensory functions as properties at the protein level, while some are predicted to have nonexpressing chromatin structures on the corresponding gene level. With further integrated analysis, we could attribute 93% of them (1391/1501) to these causal factors, which result in the expression products scarcely detected by RNA-seq or MS/MS.

  1. Geometry navigation acceleration based on automatic neighbor search and oriented bounding box in Monte Carlo simulation

    International Nuclear Information System (INIS)

    Geometry navigation plays the most fundamental role in Monte Carlo particle transport simulation. It's mainly responsible for locating a particle inside which geometry volume it is and computing the distance to the volume boundary along the certain particle trajectory during each particle history. Geometry navigation directly affects the run-time performance of the Monte Carlo particle transport simulation, especially for large scale complicated systems. Two geometry acceleration algorithms, the automatic neighbor search algorithm and the oriented bounding box algorithm, are presented for improving geometry navigation performance. The algorithms have been implemented in the Super Monte Carlo Calculation Program for Nuclear and Radiation Process (SuperMC) version 2.0. The FDS-II and ITER benchmark models have been tested to highlight the efficiency gains that can be achieved by using the acceleration algorithms. The exact gains may be problem dependent, but testing results showed that runtime of Monte Carlo simulation can be considerably reduced 50%∼60% with the proposed acceleration algorithms. (author)

  2. Universal bounds on current fluctuations

    Science.gov (United States)

    Pietzonka, Patrick; Barato, Andre C.; Seifert, Udo

    2016-05-01

    For current fluctuations in nonequilibrium steady states of Markovian processes, we derive four different universal bounds valid beyond the Gaussian regime. Different variants of these bounds apply to either the entropy change or any individual current, e.g., the rate of substrate consumption in a chemical reaction or the electron current in an electronic device. The bounds vary with respect to their degree of universality and tightness. A universal parabolic bound on the generating function of an arbitrary current depends solely on the average entropy production. A second, stronger bound requires knowledge both of the thermodynamic forces that drive the system and of the topology of the network of states. These two bounds are conjectures based on extensive numerics. An exponential bound that depends only on the average entropy production and the average number of transitions per time is rigorously proved. This bound has no obvious relation to the parabolic bound but it is typically tighter further away from equilibrium. An asymptotic bound that depends on the specific transition rates and becomes tight for large fluctuations is also derived. This bound allows for the prediction of the asymptotic growth of the generating function. Even though our results are restricted to networks with a finite number of states, we show that the parabolic bound is also valid for three paradigmatic examples of driven diffusive systems for which the generating function can be calculated using the additivity principle. Our bounds provide a general class of constraints for nonequilibrium systems.

  3. An efficient algorithm for computing fixed length attractors based on bounded model checking in synchronous Boolean networks with biochemical applications.

    Science.gov (United States)

    Li, X Y; Yang, G W; Zheng, D S; Guo, W S; Hung, W N N

    2015-01-01

    Genetic regulatory networks are the key to understanding biochemical systems. One condition of the genetic regulatory network under different living environments can be modeled as a synchronous Boolean network. The attractors of these Boolean networks will help biologists to identify determinant and stable factors. Existing methods identify attractors based on a random initial state or the entire state simultaneously. They cannot identify the fixed length attractors directly. The complexity of including time increases exponentially with respect to the attractor number and length of attractors. This study used the bounded model checking to quickly locate fixed length attractors. Based on the SAT solver, we propose a new algorithm for efficiently computing the fixed length attractors, which is more suitable for large Boolean networks and numerous attractors' networks. After comparison using the tool BooleNet, empirical experiments involving biochemical systems demonstrated the feasibility and efficiency of our approach.

  4. Upper bound solution of supporting pressure for a shallow square tunnel based on the Hoek-Brown failure criterion

    Institute of Scientific and Technical Information of China (English)

    Fu HUANG; Xiao-li YANG; Lian-heng ZHAO

    2012-01-01

    To analyze the stability of a shallow square tunnel,a new curved failure mechanism,representing the mechanical characteristics and collapsing form of this type of tunnel,is constructed.Based on the upper bound theorem of limit analysis and the Hoek-Brown nonlinear failure criterion,the supporting pressure derived from the virtual work rate equation is regarded as an objective function to achieve optimal calculation.By employing variational calculation to optimize the objective function,an upper bound solution for the supporting pressure and the collapsing block shape of a shallow square tunnel are obtained.To evaluate the validity of the failure mechanism proposed in this paper,the solutions computed by the curved failure mechanism are compared with the results calculated by the linear multiple blocks failure mechanism when the Hoek-Brown nonlinear failure criterion is converted into the Mohr-Coulomb linear criterion.The influences of rock mass parameters on the supporting pressure and collapsing block shape are discussed.

  5. The structure of haemoglobin bound to the haemoglobin receptor IsdH from Staphylococcus aureus shows disruption of the native α-globin haem pocket.

    Science.gov (United States)

    Dickson, Claire F; Jacques, David A; Clubb, Robert T; Guss, J Mitchell; Gell, David A

    2015-06-01

    Staphylococcus aureus is a common and serious cause of infection in humans. The bacterium expresses a cell-surface receptor that binds to, and strips haem from, human haemoglobin (Hb). The binding interface has previously been identified; however, the structural changes that promote haem release from haemoglobin were unknown. Here, the structure of the receptor-Hb complex is reported at 2.6 Å resolution, which reveals a conformational change in the α-globin F helix that disrupts the haem-pocket structure and alters the Hb quaternary interactions. These features suggest potential mechanisms by which the S. aureus Hb receptor induces haem release from Hb.

  6. G protein- and agonist-bound serotonin 5-HT2A receptor model activated by steered molecular dynamics simulations

    DEFF Research Database (Denmark)

    Ísberg, Vignir; Balle, Thomas; Sander, Tommy;

    2011-01-01

    molecular dynamics (MD) simulations. The driving force for the transformation was the addition of several known intermolecular and receptor interhelical hydrogen bonds enforcing the necessary helical and rotameric movements. Subsquent MD simulations without constraints confirmed the stability...

  7. Robust optical oxygen sensors based on polymer-bound NIR-emitting platinum(II)-benzoporphyrins

    DEFF Research Database (Denmark)

    Hutter, L.H.; Müller, B.J.; Koren, Klaus;

    2014-01-01

    Several advanced optical oxygen sensor materials are presented. They are based on bright NIR-emitting platinum(II)-benzoporphyrins covalently incorporated into a variety of polymeric matrices. The dye-polymer conjugates are prepared either via Suzuki coupling of the brominated porphyrins to the s......Several advanced optical oxygen sensor materials are presented. They are based on bright NIR-emitting platinum(II)-benzoporphyrins covalently incorporated into a variety of polymeric matrices. The dye-polymer conjugates are prepared either via Suzuki coupling of the brominated porphyrins...... of the spectrum) and high stability of the covalently grafted materials due to complete suppression of dye migration and leaching. This is demonstrated to be particularly important for operation of the sensors in harsh conditions e.g. during steam sterilization where the materials based on non-covalently grafted...

  8. Excited States of Proton-bound DNA/RNA Base Homo-dimers: Pyrimidines

    CERN Document Server

    Féraud, Géraldine; Dedonder, Claude; Jouvet, Christophe; Pino, Gustavo A

    2015-01-01

    We are presenting the electronic photo fragment spectra of the protonated pyrimidine DNA bases homo-dimers. Only the thymine dimer exhibits a well structured vibrational progression, while protonated monomer shows broad vibrational bands. This shows that proton bonding can block some non radiative processes present in the monomer.

  9. A novel fluorescent receptor assay : Based upon receptors embedded in labeled liposomes

    NARCIS (Netherlands)

    Viel, Gerhard Theodoor

    1999-01-01

    Receptor proteins play an essential role in life. All organisms, from bacteria to plants, animals and human beings use receptors for their response to (external) signals. By definition, a receptor is a (macro) molecule which is able to recognize a distinct chemical entity (e.g. a hormone or neurotra

  10. A novel fluorescent receptor assay : based upon receptors embedded in labeled liposomes

    NARCIS (Netherlands)

    Viel, Gerhard Theodoor

    1999-01-01

    Receptor proteins play an essential role in life. All organisms, from bacteria to plants, animals and human beings use receptors for their response to (external) signals. By definition, a receptor is a (macro) molecule which is able to recognize a distinct chemical entity (e.g. a hormone or neurotra

  11. Observer-based reliable stabilization of uncertain linear systems subject to actuator faults, saturation, and bounded system disturbances.

    Science.gov (United States)

    Fan, Jinhua; Zhang, Youmin; Zheng, Zhiqiang

    2013-11-01

    A matrix inequality approach is proposed to reliably stabilize a class of uncertain linear systems subject to actuator faults, saturation, and bounded system disturbances. The system states are assumed immeasurable, and a classical observer is incorporated for observation to enable state-based feedback control. Both the stability and stabilization of the closed-loop system are discussed and the closed-loop domain of attraction is estimated by an ellipsoidal invariant set. The resultant stabilization conditions in the form of matrix inequalities enable simultaneous optimization of both the observer gain and the feedback controller gain, which is realized by converting the non-convex optimization problem to an unconstrained nonlinear programming problem. The effectiveness of proposed design techniques is demonstrated through a linearized model of F-18 HARV around an operating point.

  12. Microarray-based determination of estrogen receptor, progesterone receptor, and HER2 receptor status in breast cancer

    NARCIS (Netherlands)

    P. Roepman; H.M. Horlings; O. Krijgsman; M. Kok; J.M. Bueno-de-Mesquita; R. Bender; S.C. Linn; A.M. Glas; M.J. van de Vijver

    2009-01-01

    Purpose: The level of estrogen receptor (ER), progesterone receptor (PR), and HER2 aids in the determination of prognosis and treatment of breast cancer. Immunohistochemistry is currently the predominant method for assessment, but differences in methods and interpretation can substantially affect th

  13. Bounded Rationality

    Directory of Open Access Journals (Sweden)

    Ballester Pla, Coralio

    2012-03-01

    Full Text Available The observation of the actual behavior by economic decision makers in the lab and in the field justifies that bounded rationality has been a generally accepted assumption in many socio-economic models. The goal of this paper is to illustrate the difficulties involved in providing a correct definition of what a rational (or irrational agent is. In this paper we describe two frameworks that employ different approaches for analyzing bounded rationality. The first is a spatial segregation set-up that encompasses two optimization methodologies: backward induction and forward induction. The main result is that, even under the same state of knowledge, rational and non-rational agents may match their actions. The second framework elaborates on the relationship between irrationality and informational restrictions. We use the beauty contest (Nagel, 1995 as a device to explain this relationship.

    La observación del comportamiento de los agentes económicos tanto en el laboratorio como en la vida real justifica que la racionalidad acotada sea un supuesto aceptado en numerosos modelos socio-económicos. El objetivo de este artículo es ilustrar las dificultades que conlleva una correcta definición de qué es un agente racional (irracional. En este artículo se describen dos marcos que emplean diferentes metodologías para analizar la racionalidad acotada. El primero es un modelo de segregación espacial donde se contrastan dos metodologías de optimización: inducción hacia atrás y hacia adelante. El resultado principal es que, incluso con el mismo nivel de conocimiento, tanto agentes racionales como irracionales podrían coincidir en sus acciones. El segundo marco trabaja sobre la relación entre irracionalidad y restricción de información. Se utiliza el juego llamado “beauty contest” (Nagel 1995 como mecanismo para explicar dicha relación.

  14. Evaluating free vs bound oxygen on ignition of nano-aluminum based energetics leads to a critical reaction rate criterion

    Science.gov (United States)

    Zhou, Wenbo; DeLisio, Jeffery B.; Wang, Xizheng; Egan, Garth C.; Zachariah, Michael R.

    2015-09-01

    This study investigates the ignition of nano-aluminum (n-Al) and n-Al based energetic materials (nanothermites) at varying O2 pressures (1-18 atm), aiming to differentiate the effects of free and bound oxygen on ignition and to assess if it is possible to identify a critical reaction condition for ignition independent of oxygen source. Ignition experiments were conducted by rapidly heating the samples on a fine Pt wire at a heating rate of ˜105 °C s-1 to determine the ignition time and temperature. The ignition temperature of n-Al was found to reduce as the O2 pressure increased, whereas the ignition temperatures of nanothermites (n-Al/Fe2O3, n-Al/Bi2O3, n-Al/K2SO4, and n-Al/K2S2O8) had different sensitivities to O2 pressure depending on the formulations. A phenomenological kinetic/transport model was evaluated to correlate the concentrations of oxygen both in condensed and gaseous phases, with the initiation rate of Al-O at ignition temperature. We found that a constant critical reaction rate (5 × 10-2 mol m-2 s-1) for ignition exists which is independent to ignition temperature, heating rate, and free vs bound oxygen. Since for both the thermite and the free O2 reaction the critical reaction rate for ignition is the same, the various ignition temperatures are simply reflecting the conditions when the critical reaction rate for thermal runaway is achieved.

  15. Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics

    Directory of Open Access Journals (Sweden)

    Sze Sing-Hoi

    2005-03-01

    Full Text Available Abstract Background Chemokines and their receptors play important roles in host defense, organogenesis, hematopoiesis, and neuronal communication. Forty-two chemokines and 19 cognate receptors have been found in the human genome. Prior to this report, only 11 chicken chemokines and 7 receptors had been reported. The objectives of this study were to systematically identify chicken chemokines and their cognate receptor genes in the chicken genome and to annotate these genes and ligand-receptor binding by a comparative genomics approach. Results Twenty-three chemokine and 14 chemokine receptor genes were identified in the chicken genome. All of the chicken chemokines contained a conserved CC, CXC, CX3C, or XC motif, whereas all the chemokine receptors had seven conserved transmembrane helices, four extracellular domains with a conserved cysteine, and a conserved DRYLAIV sequence in the second intracellular domain. The number of coding exons in these genes and the syntenies are highly conserved between human, mouse, and chicken although the amino acid sequence homologies are generally low between mammalian and chicken chemokines. Chicken genes were named with the systematic nomenclature used in humans and mice based on phylogeny, synteny, and sequence homology. Conclusion The independent nomenclature of chicken chemokines and chemokine receptors suggests that the chicken may have ligand-receptor pairings similar to mammals. All identified chicken chemokines and their cognate receptors were identified in the chicken genome except CCR9, whose ligand was not identified in this study. The organization of these genes suggests that there were a substantial number of these genes present before divergence between aves and mammals and more gene duplications of CC, CXC, CCR, and CXCR subfamilies in mammals than in aves after the divergence.

  16. Design Strategies of Fluorescent Biosensors Based on Biological Macromolecular Receptors

    Directory of Open Access Journals (Sweden)

    Takashi Morii

    2010-02-01

    Full Text Available Fluorescent biosensors to detect the bona fide events of biologically important molecules in living cells are increasingly demanded in the field of molecular cell biology. Recent advances in the development of fluorescent biosensors have made an outstanding contribution to elucidating not only the roles of individual biomolecules, but also the dynamic intracellular relationships between these molecules. However, rational design strategies of fluorescent biosensors are not as mature as they look. An insatiable request for the establishment of a more universal and versatile strategy continues to provide an attractive alternative, so-called modular strategy, which permits facile preparation of biosensors with tailored characteristics by a simple combination of a receptor and a signal transducer. This review describes an overview of the progress in design strategies of fluorescent biosensors, such as auto-fluorescent protein-based biosensors, protein-based biosensors covalently modified with synthetic fluorophores, and signaling aptamers, and highlights the insight into how a given receptor is converted to a fluorescent biosensor. Furthermore, we will demonstrate a significance of the modular strategy for the sensor design.

  17. Lysosomal degradation of receptor-bound urokinase-type plasminogen activator is enhanced by its inhibitors in human trophoblastic choriocarcinoma cells

    DEFF Research Database (Denmark)

    Jensen, Poul Henning; Christensen, Erik Ilsø; Ebbesen, P.;

    1990-01-01

    We have studied the effect of plasminogen activator inhibitors PAI-1 and PAI-2 on the binding of urokinase-type plasminogen activator (u-PA) to its receptor in the human choriocarcinoma cell line JAR. With 125I-labeled ligands in whole-cell binding assays, both uncomplexed u-PA and u-PA-inhibitor...... for the removal of u-PA after its complex formation with a specific inhibitor. The data suggest a novel mechanism by which receptor-mediated endocytosis is initiated by the binding of a secondary ligand. Full text...

  18. SHOP: receptor-based scaffold hopping by GRID-based similarity searches

    DEFF Research Database (Denmark)

    Bergmann, Rikke; Liljefors, Tommy; Sørensen, Morten D;

    2009-01-01

    A new field-derived 3D method for receptor-based scaffold hopping, implemented in the software SHOP, is presented. Information from a protein-ligand complex is utilized to substitute a fragment of the ligand with another fragment from a database of synthetically accessible scaffolds. A GRID-based...

  19. Model for growth hormone receptor activation based on subunit rotation within a receptor dimer

    Energy Technology Data Exchange (ETDEWEB)

    Brown, Richard J.; Adams, Julian J.; Pelekanos, Rebecca A.; Wan, Yu; McKinstry, William J.; Palethorpe, Kathryn; Seeber, Ruth M.; Monks, Thea A.; Eidne, Karin A.; Parker, Michael W.; Waters, Michael J. (UWA); (St. Vincent); (Queensland)

    2010-07-13

    Growth hormone is believed to activate the growth hormone receptor (GHR) by dimerizing two identical receptor subunits, leading to activation of JAK2 kinase associated with the cytoplasmic domain. However, we have reported previously that dimerization alone is insufficient to activate full-length GHR. By comparing the crystal structure of the liganded and unliganded human GHR extracellular domain, we show here that there is no substantial change in its conformation on ligand binding. However, the receptor can be activated by rotation without ligand by inserting a defined number of alanine residues within the transmembrane domain. Fluorescence resonance energy transfer (FRET), bioluminescence resonance energy transfer (BRET) and coimmunoprecipitation studies suggest that receptor subunits undergo specific transmembrane interactions independent of hormone binding. We propose an activation mechanism involving a relative rotation of subunits within a dimeric receptor as a result of asymmetric placement of the receptor-binding sites on the ligand.

  20. The 2.6 Angstrom Crystal Structure of a Human A[subscript 2A] Adenosine Receptor Bound to an Antagonist

    Energy Technology Data Exchange (ETDEWEB)

    Jaakola, Veli-Pekka; Griffith, Mark T.; Hanson, Michael A.; Cherezov, Vadim; Chien, Ellen Y.T.; Lane, J. Robert; IJzerman, Adriaan P.; Stevens, Raymond C. (Scripps); (Leiden/Amsterdam)

    2009-01-15

    The adenosine class of heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) mediates the important role of extracellular adenosine in many physiological processes and is antagonized by caffeine. We have determined the crystal structure of the human A{sub 2A} adenosine receptor, in complex with a high-affinity subtype-selective antagonist, ZM241385, to 2.6 angstrom resolution. Four disulfide bridges in the extracellular domain, combined with a subtle repacking of the transmembrane helices relative to the adrenergic and rhodopsin receptor structures, define a pocket distinct from that of other structurally determined GPCRs. The arrangement allows for the binding of the antagonist in an extended conformation, perpendicular to the membrane plane. The binding site highlights an integral role for the extracellular loops, together with the helical core, in ligand recognition by this class of GPCRs and suggests a role for ZM241385 in restricting the movement of a tryptophan residue important in the activation mechanism of the class A receptors.

  1. "Mirror image" antagonists of thrombin-induced platelet activation based on thrombin receptor structure.

    OpenAIRE

    Hung, D. T.; Vu, T K; Wheaton, V I; Charo, I F; Nelken, N A; Esmon, N; Esmon, C T; Coughlin, S R

    1992-01-01

    Platelet activation by thrombin plays a critical role in hemostasis and thrombosis. Based on structure-activity studies of a cloned platelet thrombin receptor, we designed two "mirror image" antagonists of thrombin and thrombin receptor function. First, "uncleavable" peptides mimicking the receptor domain postulated to interact with thrombin were found to be potent thrombin inhibitors. Second, proteolytically inactive mutant thrombins designed to bind but not cleave the thrombin receptor were...

  2. Information, Utility & Bounded Rationality

    CERN Document Server

    Ortega, Pedro A

    2011-01-01

    Perfectly rational decision-makers maximize expected utility, but crucially ignore the resource costs incurred when determining optimal actions. Here we employ an axiomatic framework for bounded rational decision-making based on a thermodynamic interpretation of resource costs as information costs. This leads to a variational "free utility" principle akin to thermodynamical free energy that trades off utility and information costs. We show that bounded optimal control solutions can be derived from this variational principle, which leads in general to stochastic policies. Furthermore, we show that risk-sensitive and robust (minimax) control schemes fall out naturally from this framework if the environment is considered as a bounded rational and perfectly rational opponent, respectively. When resource costs are ignored, the maximum expected utility principle is recovered.

  3. The study of slip line field and upper bound method based on associated flow and non-associated flow rules

    Institute of Scientific and Technical Information of China (English)

    Zheng Yingren; Deng Chujian; Wang Jinglin

    2010-01-01

    At present,associated flow rule of traditional plastic theory is adopted in the slip line field theory and upper bound method of geotechnical materials.So the stress characteristic line conforms to the velocity line.It is proved that geotechnical materials do not abide by the associated flow rule.It is impossible for the stress characteristic line to conform to the velocity line.Generalized plastic mechanics theoretically proved that plastic potential surface intersects the Mohr-Coulomb yield surface with an angle,so that the velocity line must be studied by non-associated flow rule.According to limit analysis theory,the theory of slip line field is put forward in this paper,and then the ultimate boating capacity of strip footing is obtained based on the associated flow rule and the non-associated flow rule individually.These two results are identical since the ultimate bearing capacity is independent of flow rule.On the contrary,the velocity fields of associated and non-associated flow rules are different which shows the velocity field based on the associated flow rule is incorrect.

  4. X-Ray Crystal Structure of the Ancestral 3-Ketosteroid Receptor-Progesterone-Mifepristone Complex Shows Mifepristone Bound at the Coactivator Binding Interface

    Energy Technology Data Exchange (ETDEWEB)

    Colucci, Jennifer K.; Ortlund, Eric A. [Emory-MED

    2013-12-12

    Steroid receptors are a subfamily of nuclear receptors found throughout all metazoans. They are highly important in the regulation of development, inflammation, and reproduction and their misregulation has been implicated in hormone insensitivity syndromes and cancer. Steroid binding to SRs drives a conformational change in the ligand binding domain that promotes nuclear localization and subsequent interaction with coregulator proteins to affect gene regulation. SRs are important pharmaceutical targets, yet most SR-targeting drugs have off-target pharmacology leading to unwanted side effects. A better understanding of the structural mechanisms dictating ligand specificity and the evolution of the forces that created the SR-hormone pairs will enable the design of better pharmaceutical ligands. In order to investigate this relationship, we attempted to crystallize the ancestral 3-ketosteroid receptor (ancSR2) with mifepristone, a SR antagonist. Here, we present the x-ray crystal structure of the ancestral 3-keto steroid receptor (ancSR2)-progesterone complex at a resolution of 2.05 Å. This improves upon our previously reported structure of the ancSR2-progesterone complex, permitting unambiguous assignment of the ligand conformation within the binding pocket. Surprisingly, we find mifepristone, fortuitously docked at the protein surface, poised to interfere with coregulator binding. Recent attention has been given to generating pharmaceuticals that block the coregulator binding site in order to obstruct coregulator binding and achieve tissue-specific SR regulation independent of hormone binding. Mifepristone’s interaction with the coactivator cleft of this SR suggests that it may be a useful molecular scaffold for further coactivator binding inhibitor development.

  5. 基于有限理性智能体的生态经济模型%The Ecological Economic Model Based on Bounded Rational Agents

    Institute of Scientific and Technical Information of China (English)

    姜继娇

    2005-01-01

    From the view of hominine bounded rationalities, this paper analyzes the important relationships between ecology and economics with behavioral finance. With a different focus, this paper adopts a new conceptualization of stock to show how this conceptualization leads to a new measure of the interaction between ecology and economics, based on bounded rational agents. The hierarchical structure of ecological economic system is described with a multi-agent simulation program. This paper also develops an ecological economic model, in which behavioral finance theories are applied to simulating the dynamics system. With the model, this paper confirms that macro-level indicators of sustainability are predictably influenced by behaviors of bounded rational agents at the micro-level. We discuss the significance of these findings in order to better understand the ecological-economic system based on behavioral finance.

  6. Characterization of Plasminogen Binding to NB4 Promyelocytic Cells Using Monoclonal Antibodies against Receptor-Induced Binding Sites in Cell-Bound Plasminogen

    Directory of Open Access Journals (Sweden)

    Mercè Jardí

    2012-01-01

    Full Text Available The NB4 promyelocytic cell line exhibits many of the characteristics of acute promyelocytic leukemia blast cells, including the translocation (15 : 17 that fuses the PML gene on chromosome 15 to the RARα gene on chromosome 17. These cells have a very high fibrinolytic capacity. In addition to a high secretion of urokinase, NB4 cells exhibit a 10-fold higher plasminogen binding capacity compared with other leukemic cell lines. When tissue-type plasminogen activator was added to acid-treated cells, plasmin generation was 20–26-fold higher than that generated by U937 cells or peripheral blood neutrophils, respectively. We found that plasminogen bound to these cells can be detected by fluorescence-activated cell sorting using an antiplasminogen monoclonal antibody that specifically reacts with this antigen when it is bound to cell surfaces. All-trans retinoid acid treatment of NB4 cells markedly decreased the binding of this monoclonal antibody. This cell line constitutes a unique model to explore plasminogen binding and activation on cell surfaces that can be modulated by all-trans retinoid acid treatment.

  7. Crystallization and preliminary X-ray diffraction of human interleukin-7 bound to unglycosylated and glycosylated forms of its α-receptor

    Energy Technology Data Exchange (ETDEWEB)

    Wickham, Joseph Jr; Walsh, Scott T. R., E-mail: walsh.220@osu.edu [Department of Molecular and Cellular Biochemistry, Comprehensive Cancer Center, Ohio State University, 467 Hamilton Hall, 1645 Neil Avenue, Columbus, OH 43210 (United States)

    2007-10-01

    Bacterial and insect cell expression systems have been developed to produce unglycosylated and glycosylated forms of human interleukin-7 (IL-7) and the extracellular domain of its α receptor, IL-7Rα. We report the crystallization and X-ray diffraction of IL-7 complexes to both unglycosylated and glycosylated forms of the IL-7Rα to 2.7 and 3.0 Å, respectively. The interleukin-7 (IL-7) signaling pathway plays an essential role in the development, proliferation and homeostasis of T and B cells in cell-mediated immunity. Understimulation and overstimulation of the IL-7 signaling pathway leads to severe combined immunodeficiency, autoimmune reactions, heart disease and cancers. Stimulation of the IL-7 pathway begins with IL-7 binding to its α-receptor, IL-7Rα. Protein crystals of unglycosylated and glycosylated complexes of human IL-7–IL-7Rα extracellular domain (ECD) obtained using a surface entropy-reduction approach diffract to 2.7 and 3.0 Å, respectively. Anomalous dispersion methods will be used to solve the unglycosylated IL-7–IL-7Rα ECD complex structure and this unglycosylated structure will then serve as a model in molecular-replacement attempts to solve the structure of the glycosylated IL-7–α-receptor complex.

  8. Capacity of Diffusion-based Molecular Communication with Ligand Receptors

    CERN Document Server

    Einolghozati, Arash; Fekri, Faramarz

    2012-01-01

    A diffusion-based molecular communication system has two major components: the diffusion in the medium, and the ligand-reception. Information bits, encoded in the time variations of the concentration of molecules, are conveyed to the receiver front through the molecular diffusion in the medium. The receiver, in turn, measures the concentration of the molecules in its vicinity in order to retrieve the information. This is done via ligand-reception process. In this paper, we develop models to study the constraints imposed by the concentration sensing at the receiver side and derive the maximum rate by which a ligand-receiver can receive information. Therefore, the overall capacity of the diffusion channel with the ligand receptors can be obtained by combining the results presented in this paper with our previous work on the achievable information rate of molecular communication over the diffusion channel.

  9. Structure of human Eg5 in complex with a new monastrol-based inhibitor bound in the R configuration.

    Science.gov (United States)

    Garcia-Saez, Isabel; DeBonis, Salvatore; Lopez, Roman; Trucco, Fernando; Rousseau, Bernard; Thuéry, Pierre; Kozielski, Frank

    2007-03-30

    Drugs that target mitotic spindle proteins have been proven useful for tackling tumor growth. Eg5, a kinesin-5 family member, represents a potential target, since its inhibition leads to prolonged mitotic arrest through the activation of the mitotic checkpoint and apoptotic cell death. Monastrol, a specific dihydropyrimidine inhibitor of Eg5, shows stereo-specificity, since predominantly the (S)-, but not the (R)-, enantiomer has been shown to be the biologically active compound in vitro and in cell-based assays. Here, we solved the crystal structure (2.7A) of the complex between human Eg5 and a new keto derivative of monastrol (named mon-97), a potent antimitotic inhibitor. Surprisingly, we identified the (R)-enantiomer bound in the active site, and not, as for monastrol, the (S)-enantiomer. The absolute configuration of this more active (R)-enantiomer has been unambiguously determined via chemical correlation and x-ray analysis. Unexpectedly, both the R- and the S-forms inhibit Eg5 ATPase activity with IC(50) values of 110 and 520 nM (basal assays) and 150 nm and 650 nm (microtubule-stimulated assays), respectively. However, the difference was large enough for the protein to select the (R)- over the (S)-enantiomer. Taken together, these results show that in this new monastrol family, both (R)- and (S)-enantiomers can be active as Eg5 inhibitors. This considerably broadens the alternatives for rational drug design.

  10. Synthesis and Anion Recognition of Novel Molecular Tweezer Receptors Based on Carbonyl Thiosemicarbazide for Fluoride Ions

    Institute of Scientific and Technical Information of China (English)

    WEI,Wei; ZHANG,You-Ming; WEI,Tai-Bao

    2008-01-01

    Three title compounds have been designed and synthesized in high yields as novel anion receptors, which show a higher selectivity for F- than other halide ions. The binding properties for fluoride ions of the receptors have been examined by UV-Vis and 1H NMR spectroscopy, indicating that a 1 : 1 stoichiometry complex is formed between the receptors and fluoride ions through hydrogen bonding interactions in DMSO solution. In addition, because these receptors have more binding points, they have better binding properties for anions than the molecular tweezer receptors based on thiourea we reported last time.

  11. Structural and pharmacological characterization of phenylalanine-based AMPA receptor antagonists at kainate receptors

    DEFF Research Database (Denmark)

    Venskutonyte, Raminta; Frydenvang, Karla; Valadés, Elena Antón;

    2012-01-01

    . A new series of phenylalanine derivatives that target iGluRs was reported to bind AMPA receptors. Herein we report our studies of these compounds at the kainate receptors GluK1-3. Several compounds bind with micromolar affinity at GluK1 and GluK3, but do not bind GluK2. The crystal structure of the most...

  12. A novel naphthalene-based receptor: Colorimetric and fluorescent PET chemoreceptor for anions

    Energy Technology Data Exchange (ETDEWEB)

    Huang Weiwei; Su Hongyan; Yao Sikai; Yang Zhongyue [Department of Chemistry, Nankai University, Tianjin 300071 (China); Lin Hai [Key Laboratory of Functional Polymer Materials of Ministry of Education, Nankai University, Tianjin 300071 (China); Lin Huakuan, E-mail: hklin@nankai.edu.cn [Department of Chemistry, Nankai University, Tianjin 300071 (China)

    2011-09-15

    A novel artificial anion receptor based on phenylhydrazone structure was designed, synthesized and characterized. The binding behavior of the receptor to various anions was investigated by UV-vis fluorescence analyses. In addition, {sup 1}H NMR experiments were carried out to explore the nature of interaction between receptor 1 and acetate. The processes of sensing can literally be seen through the 'naked-eye' for the sharp color changes from yellow to purple. - Highlights: > The synthesis process of receptor 1 (1-hydroxynaphthalene-2-carbaldehyde-4'-nitrophenylhydrazone) is simple and easy. Thus, it made practical use of receptor 1 possible. > Receptor 1 displays distinct color changes from yellow to purple, which could be observed by the naked eye. In addition, the sensing process is fast and efficient. > Receptor 1 can recognize acetates which is of great importance since acetates are important biological molecules.

  13. receptores

    Directory of Open Access Journals (Sweden)

    Salete Regina Daronco Benetti

    2006-01-01

    Full Text Available Se trata de un estudio etnográfico, que tuvo lo objetivo de interpretar el sistema de conocimiento y del significado atribuidos a la sangre referente a la transfusión sanguínea por los donadores y receptores de un banco de sangre. Para la colecta de las informaciones se observaron los participantes y la entrevista etnográfica se realizó el análisis de dominio, taxonómicos y temáticos. Los dominios culturales fueron: la sangre es vida: fuente de vida y alimento valioso; creencias religiosas: fuentes simbólicas de apoyos; donación sanguínea: un gesto colaborador que exige cuidarse, gratifica y trae felicidad; donación sanguínea: fuente simbólica de inseguridad; estar enfermo es una condición para realizar transfusión sanguínea; transfusión sanguínea: esperanza de vida; Creencias populares: transfusión sanguínea como riesgo para la salud; donadores de sangre: personas benditas; donar y recibir sangre: como significado de felicidad. Temática: “líquido precioso que origina, sostiene, modifica la vida, provoca miedo e inseguridad”.

  14. STUDY OF BOUNDING BOX LOCALISATION ALGORITHM BASED ON WIRELESS SENSOR DISCRETE NETWORK MODEL%基于无线传感器离散网络模型的 Bounding Box定位算法研究

    Institute of Scientific and Technical Information of China (English)

    曾振东

    2013-01-01

    Bounding Box algorithm is a typical node localisation algorithm based on discrete network model in wireless sensor network (WSN).To overcome its disadvantages in low localisation accuracy and coverage rate , we propose an improved localisation algorithm which employs the virtual anchor nodes strategy .First, the unknown nodes will calculate their own coordinates by making use of the anchor nodes within their communication range .Secondly , the located unknown nodes will upgrade themselves as the virtual anchor nodes according to the promotion strategy selectively .Finally, those nodes which are unable to locate themselves will use the virtual anchor nodes to get their own location.Besides, the establishment of the network node model with double radius based on discrete network model further restrict the location of the unknown nodes .Theoretical analysis and simulation result all show that the proposed algorithm can effectively improve the localisation accuracy while significantly raise the coverage rate of localisation .%Bounding Box算法是一种典型的基于离散网络模型的无线传感器网络节点定位算法。针对Bounding Box算法定位误差大、覆盖率低的缺点,提出一种采用虚拟锚节点策略的改进定位算法。首先未知节点利用其通信范围内的锚节点进行定位;其次,已定位的节点根据升级策略有选择性的升级为虚拟锚节点;最后,无法定位的节点利用虚拟锚节点实现定位。另外,在离散网络模型的基础上,通过建立双半径网络节点模型从而进一步约束了未知节点的位置。理论分析及仿真结果均表明,该算法在显著提高定位覆盖率的同时,有效地提高了定位精度。

  15. Overview of receptor-based source apportionment studies for speciated atmospheric mercury

    Directory of Open Access Journals (Sweden)

    I. Cheng

    2015-02-01

    Full Text Available Receptor-based source apportionment studies of speciated atmospheric mercury are not only concerned with source contributions, but also the influence of transport, transformation, and deposition processes on speciated atmospheric mercury concentrations at receptor locations. Previous studies applied multivariate receptor models including Principal Components Analysis and Positive Matrix Factorization, and back trajectory receptor models including Potential Source Contribution Function, Gridded Frequency Distributions, and Concentration-back trajectory models. Anthropogenic combustion sources, crustal/soil dust, and chemical and physical processes, such as gaseous elemental mercury (GEM oxidation reactions, boundary layer mixing, and GEM flux from surfaces, were inferred from the multivariate studies, which were predominantly conducted at receptor sites in Canada and the US. Back trajectory receptor models revealed potential impacts of large industrial areas such as the Ohio River Valley in the US and throughout China, metal smelters, mercury evasion from the ocean and Great Lakes, and free troposphere transport on receptor measurements. Input data and model parameters specific to atmospheric mercury receptor models are summarized and model strengths and weaknesses are also discussed. One area of improvement that applies to all receptor models is the greater focus on evaluating the accuracy of receptor models at identifying potential speciated atmospheric mercury sources, source locations, and chemical and physical processes in the atmosphere.

  16. Robust model predictive control of nonlinear systems with unmodeled dynamics and bounded uncertainties based on neural networks.

    Science.gov (United States)

    Yan, Zheng; Wang, Jun

    2014-03-01

    This paper presents a neural network approach to robust model predictive control (MPC) for constrained discrete-time nonlinear systems with unmodeled dynamics affected by bounded uncertainties. The exact nonlinear model of underlying process is not precisely known, but a partially known nominal model is available. This partially known nonlinear model is first decomposed to an affine term plus an unknown high-order term via Jacobian linearization. The linearization residue combined with unmodeled dynamics is then modeled using an extreme learning machine via supervised learning. The minimax methodology is exploited to deal with bounded uncertainties. The minimax optimization problem is reformulated as a convex minimization problem and is iteratively solved by a two-layer recurrent neural network. The proposed neurodynamic approach to nonlinear MPC improves the computational efficiency and sheds a light for real-time implementability of MPC technology. Simulation results are provided to substantiate the effectiveness and characteristics of the proposed approach. PMID:24807443

  17. Sound-absorbing slabs and structures based on granular materials (bound and unbound). [energy absorbing efficiency of porous material

    Science.gov (United States)

    Petre-Lazar, S.; Popeea, G.

    1974-01-01

    Sound absorbing slabs and structures made up of bound or unbound granular materials are considered and how to manufacture these elements at the building site. The raw material is a single grain powder (sand, expanded blast furnace slag, etc.) that imparts to the end products an apparent porosity of 25-45% and an energy dissipation within the structure leading to absorption coefficients that can be compared with those of mineral wool and urethane.

  18. Height curves based on the bivariate Power-Normal and the bivariate Johnson’s System bounded distribution

    OpenAIRE

    Mønness, Erik Neslein

    2013-01-01

    English: Often, a forest stand is modeled with a diameter distribution and a height curve as somehow separate tasks. A bivariate height and diameter distribution yield a unified model of a forest stand. The conditional median height given the diameter is a possible height curve. Here the bivariate Johnson’s System bounded distribution and the bivariate power-normal distribution are evaluated and compared with a simple hyperbolic height curve. Evaluated by the deviance, the hyperbo...

  19. Clinical experience of immunotherapy based on oleic acid bound to glycosylated vitamin d-binding protein in localised and metastatic adenocarcinoma of the pancreas

    OpenAIRE

    Lynda Thyer; Branca, Jacopo J. V.; Margit Taubmann

    2014-01-01

    Adenocarcinoma of the pancreas still carries a dramatically poor prognosis and the survival rate for this disease has not improved substantially in the past 40 years. Therefore, new treatment options are urgently needed and this need motivates oncologists to search for novel approaches such as immunotherapy. Here we report two clinical cases successfully treated with an integrative immunotherapeutic approach based on oleic acid bound to glycosylated vitamin D-binding protein (OA-GcMAF). Consi...

  20. A bound on chaos

    CERN Document Server

    Maldacena, Juan; Stanford, Douglas

    2015-01-01

    We conjecture a sharp bound on the rate of growth of chaos in thermal quantum systems with a large number of degrees of freedom. Chaos can be diagnosed using an out-of-time-order correlation function closely related to the commutator of operators separated in time. We conjecture that the influence of chaos on this correlator can develop no faster than exponentially, with Lyapunov exponent $\\lambda_L \\le 2 \\pi k_B T/\\hbar$. We give a precise mathematical argument, based on plausible physical assumptions, establishing this conjecture.

  1. Application of bounding spectra to seismic design of piping based on the performance of above ground piping in power plants subjected to strong motion earthquakes

    International Nuclear Information System (INIS)

    This report extends the potential application of Bounding Spectra evaluation procedures, developed as part of the A-46 Unresolved Safety Issue applicable to seismic verification of in-situ electrical and mechanical equipment, to in-situ safety related piping in nuclear power plants. The report presents a summary of earthquake experience data which define the behavior of typical U.S. power plant piping subject to strong motion earthquakes. The report defines those piping system caveats which would assure the seismic adequacy of the piping systems which meet those caveats and whose seismic demand are within the bounding spectra input. Based on the observed behavior of piping in strong motion earthquakes, the report describes the capabilities of the piping system to carry seismic loads as a function of the type of connection (i.e. threaded versus welded). This report also discusses in some detail the basic causes and mechanisms for earthquake damages and failures to power plant piping systems

  2. Finite-time observer-based output-feedback control for the global stabilisation of the PVTOL aircraft with bounded inputs

    Science.gov (United States)

    Zavala-Río, A.; Fantoni, I.; Sanahuja, G.

    2016-05-01

    In this work, an output-feedback scheme for the global stabilisation of the planar vertical take-off and landing aircraft with bounded inputs is developed taking into account the positive nature of the thrust. The global stabilisation objective is proven to be achieved avoiding input saturation and by exclusively considering the system positions in the feedback. To cope with the lack of velocity measurements, the proposed algorithm involves a finite-time observer. The generalised versions of the involved finite-time stabilisers have not only permitted to solve the output-feedback stabilisation problem avoiding input saturation, but also provide additional flexibility in the control design that may be used in aid of performance improvements. With respect to previous approaches, the developed finite-time observer-based scheme guarantees the global stabilisation objective disregarding velocity measurements in a bounded input context. Simulation tests corroborate the analytical developments. The study includes further experimental results on an actual flying device.

  3. Mast Cell and Immune Inhibitory Receptors

    Institute of Scientific and Technical Information of China (English)

    Lixin Li; Zhengbin Yao

    2004-01-01

    Modulation by balancing activating and inhibitory receptors constitutes an important mechanism for regulating immune responses. Cells that are activated following ligation of receptors bearing immunoreceptor tyrosine-based activation motifs (ITAMs) can be negatively regulated by other receptors bearing immunoreceptor tyrosine-based inhibition motifs (ITIMs). Human mast cells (MCs) are the major effector cells of type I hypersensitivity and important participants in a number of disease processes. Antigen-mediated aggregation of IgE bound to its high-affinity receptor on MCs initiates a complex series of biochemical events leading to MC activation. With great detailed description and analysis of several inhibitory receptors on human MCs, a central paradigm of negative regulation of human MC activation by these receptors has emerged. Cellular & Molecular Immunology. 2004;1(6):408-415.

  4. An Improved Bounding Box Localization Algorithm Based on the Virtual Anchor Nodes%一种基于虚拟锚节点策略改进的Bounding Box定位算法

    Institute of Scientific and Technical Information of China (English)

    周莹

    2014-01-01

    针对Bounding Box算法定位误差大、覆盖率低的缺点,提出了一种采用虚拟锚节点策略的改进定位算法。首先未知节点利用其通信范围内的锚节点进行定位;其次,已定位的节点根据升级策略有选择性的升级为虚拟锚节点;最后,无法定位的节点利用虚拟锚节点实现定位。另外,在离散网络模型的基础上,通过建立双半径网络节点模型从而进一步约束了未知节点的位置。理论分析及仿真结果均表明,该算法在显著提高定位覆盖率的同时,有效地提高了定位精度。%To overcome the disadvantages of localization accuracy and low coverage rate in current Bounding Box al-gorithm,an improved algorithm using the virtual anchor nodes was proposed. Firstly, the anchor nodes within the communication range of unknown nodes were used to calculate the coordinates of the unknown nodes. Secondly,the located unknown nodes were upgraded as the virtual anchor nodes according to the promotion strategy selectively. Finally,the nodes which were unable to locate themselves used the virtual anchor nodes to get their location. On the other hands,the network node model of double radius based on the discrete network model was introduced to restrict the location of the unknown nodes. The result of simulation and analysis shows that the proposed algorithm can improve the localization coverage rate as well as the estimation accuracy significantly.

  5. Determination of a Drawing Die's Cone Angle at a Small Compression Ratio Based on the Upper Bound Theory

    Institute of Scientific and Technical Information of China (English)

    YANG Xu-dong; JIN Liang-liang

    2011-01-01

    The value of a drawing die's cone angle has great influence on wire drawing. In order to determine the optimum value of a drawing die' s cone angle, the plastic deformation power Wi, shear deformation power Wi and friction power of contact surface Wf were calculated using the upper bound theory with a reasonable and movement permitted velocity field according to the related characteristics. Then the relation between half cone angle and unit drawing force was obtained and it was compared with the result with the spherical velocity field. The relative error of the two near the optimal value is only about 0. 26% through comparing with existing calculated results. Finally, in an ABAQUS environment the finite element modal of the wire rod with 12. 5 mm diameter in first drawing pass was established and the axial drawing force in different cone angles was obtained using the ABAQUS/Explicit explicit integration method. The finite element method (FEM) results verify the results using the upper bound theory and this indicated that the velocity field and the relation between half cone angle and unit drawing force reasonable.

  6. Scattering by bound nucleons

    International Nuclear Information System (INIS)

    Scattering of a particle by bound nucleons is discussed. Effects of nucleons that are bound in a nucleus are taken as a structure function. The way how to calculate the structure function is given. (author)

  7. Identification of human dopamine D1-like receptor agonist using a cell-based functional assay

    Institute of Scientific and Technical Information of China (English)

    Nan JIANG; Ke-qing OU-YANG; Shao-xi CAI; Ying-he HU; Zhi-liang XU

    2005-01-01

    Aim: To establish a cell-based assay to screen human dopamine D1 and D5 receptor agonists against compounds from a natural product compound library.Methods: Synthetic responsive elements 6×cAMP response elements (CRE) and a mini promoter containing a TATA box were inserted into the pGL3 basic vector to generate the reporter gene construct pCRE/TA/Luci. CHO cells were co-transfected with the reporter gene construct and human D1 or D5 receptor cDNA in mammalian expression vectors. Stable cell lines were established for agonist screening. A natural product compound library from over 300 herbs has been established. The extracts from these herbs were used for human D1 and D5 receptor agonist screenings. Results: A number of extracts were identified that activated both D1 and D5 receptors. One of the herb extracts, SBG492, demonstrated distinct pharmacological characteristics with human D1 and D5 receptors.The EC50 values of SBG492 were 342.7 μg/mL for the D1 receptor and 31.7 μg/mL for the D5 receptor. Conclusion: We have established a cell-based assay for high-throughput drug screening to identify D 1-like receptor agonists from natural products. Several extracts that can active D1-like receptors were discovered.These compounds could be useful tools for studies on the functions of these receptors in the brain and could potentially be developed into therapeutic drugs for the treatment of central nervous system diseases.

  8. Cramér-Rao Lower Bound for Point Based Image Registration With Heteroscedastic Error Model for Application in Single Molecule Microscopy.

    Science.gov (United States)

    Cohen, E A K; Kim, D; Ober, R J

    2015-12-01

    The Cramér-Rao lower bound for the estimation of the affine transformation parameters in a multivariate heteroscedastic errors-in-variables model is derived. The model is suitable for feature-based image registration in which both sets of control points are localized with errors whose covariance matrices vary from point to point. With focus given to the registration of fluorescence microscopy images, the Cramér-Rao lower bound for the estimation of a feature's position (e.g., of a single molecule) in a registered image is also derived. In the particular case where all covariance matrices for the localization errors are scalar multiples of a common positive definite matrix (e.g., the identity matrix), as can be assumed in fluorescence microscopy, then simplified expressions for the Cramér-Rao lower bound are given. Under certain simplifying assumptions these expressions are shown to match asymptotic distributions for a previously presented set of estimators. Theoretical results are verified with simulations and experimental data.

  9. Cramér-Rao Lower Bound for Point Based Image Registration With Heteroscedastic Error Model for Application in Single Molecule Microscopy.

    Science.gov (United States)

    Cohen, E A K; Kim, D; Ober, R J

    2015-12-01

    The Cramér-Rao lower bound for the estimation of the affine transformation parameters in a multivariate heteroscedastic errors-in-variables model is derived. The model is suitable for feature-based image registration in which both sets of control points are localized with errors whose covariance matrices vary from point to point. With focus given to the registration of fluorescence microscopy images, the Cramér-Rao lower bound for the estimation of a feature's position (e.g., of a single molecule) in a registered image is also derived. In the particular case where all covariance matrices for the localization errors are scalar multiples of a common positive definite matrix (e.g., the identity matrix), as can be assumed in fluorescence microscopy, then simplified expressions for the Cramér-Rao lower bound are given. Under certain simplifying assumptions these expressions are shown to match asymptotic distributions for a previously presented set of estimators. Theoretical results are verified with simulations and experimental data. PMID:26641728

  10. Variance bounding Markov chains

    OpenAIRE

    Roberts, Gareth O.; Jeffrey S. Rosenthal

    2008-01-01

    We introduce a new property of Markov chains, called variance bounding. We prove that, for reversible chains at least, variance bounding is weaker than, but closely related to, geometric ergodicity. Furthermore, variance bounding is equivalent to the existence of usual central limit theorems for all L2 functionals. Also, variance bounding (unlike geometric ergodicity) is preserved under the Peskun order. We close with some applications to Metropolis–Hastings algorithms.

  11. Overview of receptor-based source apportionment studies for speciated atmospheric mercury

    Science.gov (United States)

    Cheng, I.; Xu, X.; Zhang, L.

    2015-07-01

    Receptor-based source apportionment studies of speciated atmospheric mercury are not only concerned with source contributions but also with the influence of transport, transformation, and deposition processes on speciated atmospheric mercury concentrations at receptor locations. Previous studies applied multivariate receptor models including principal components analysis and positive matrix factorization, and back trajectory receptor models including potential source contribution function, gridded frequency distributions, and concentration-back trajectory models. Combustion sources (e.g., coal combustion, biomass burning, and vehicular, industrial and waste incineration emissions), crustal/soil dust, and chemical and physical processes, such as gaseous elemental mercury (GEM) oxidation reactions, boundary layer mixing, and GEM flux from surfaces were inferred from the multivariate studies, which were predominantly conducted at receptor sites in Canada and the US. Back trajectory receptor models revealed potential impacts of large industrial areas such as the Ohio River valley in the US and throughout China, metal smelters, mercury evasion from the ocean and the Great Lakes, and free troposphere transport on receptor measurements. Input data and model parameters specific to atmospheric mercury receptor models are summarized and model strengths and weaknesses are also discussed. Multivariate models are suitable for receptor locations with intensive air monitoring because they require long-term collocated and simultaneous measurements of speciated atmospheric Hg and ancillary pollutants. The multivariate models provide more insight about the types of Hg emission sources and Hg processes that could affect speciated atmospheric Hg at a receptor location, whereas back trajectory receptor models are mainly ideal for identifying potential regional Hg source locations impacting elevated Hg concentrations. Interpretation of the multivariate model output to sources can be

  12. Rapid quantification of live cell receptors using bioluminescence in a flow-based microfluidic device.

    Science.gov (United States)

    Ramji, Ramesh; Cheong, Cheong Fook; Hirata, Hiroaki; Rahman, Abdur Rub Abdur; Lim, Chwee Teck

    2015-02-25

    The number of receptors expressed by cells plays an important role in controlling cell signaling events, thus determining its behaviour, state and fate. Current methods of quantifying receptors on cells are either laborious or do not maintain the cells in their native form. Here, a method integrating highly sensitive bioluminescence, high precision microfluidics and small footprint of lensfree optics is developed to quantify cell surface receptors. This method is safe to use, less laborious, and faster than the conventional radiolabelling and near field scanning methods. It is also more sensitive than fluorescence based assays and is ideal for high throughput screening. In quantifying β(1) adrenergic receptors expressed on the surface of H9c2 cardiomyocytes, this method yields receptor numbers from 3.12 × 10(5) to 9.36 × 10(5) receptors/cell which are comparable with current methods. This can serve as a very good platform for rapid quantification of receptor numbers in ligand/drug binding and receptor characterization studies, which is an important part of pharmaceutical and biological research. PMID:25336403

  13. Development and validation of fluorescent receptor assays based on the human recombinant estrogen receptor subtypes alpha and beta

    NARCIS (Netherlands)

    de boer, T; Otjens, D; Muntendam, A; Meulman, E; van Oostijen, M; Ensing, K

    2004-01-01

    This article describes the development and validation of two fluorescent receptor assays for the hRec-estrogen receptor subtypes alpha and beta. As a labelled ligand an autofluorescent phyto-estrogen (coumestrol) has been used. The estrogen receptor (ER) belongs to the nuclear receptor family, a cla

  14. Investigation of the Role of Cytochrome P450 2B4 Active Site Residues in Substrate Metabolism Based on Crystal Structures of the Ligand-bound Enzyme

    OpenAIRE

    Hernandez, Cynthia E.; Kumar, Santosh; Liu, Hong; Halpert, James R.

    2006-01-01

    Based on the x-ray crystal structures of 4-(4-chlorophenyl)imidazole (4-CPI)- and bifonazole (BIF)-bound P450 2B4, eight active site mutants at six positions were created in an N-terminal modified construct termed 2B4dH and characterized for enzyme inhibition and catalysis. I363A showed a > 4-fold decrease in differential inhibition by BIF and 4-CPI (IC50,BIF/IC50,4-CPI). F296A, T302A, I363A, V367A, and V477A showed a ≥ 2-fold decreased kcat for 7-ethoxy-4-trifluoromethylcoumarin O-deethylati...

  15. Immobilization free electrochemical biosensor for folate receptor in cancer cells based on terminal protection.

    Science.gov (United States)

    Ni, Jiancong; Wang, Qingxiang; Yang, Weiqiang; Zhao, Mengmeng; Zhang, Ying; Guo, Longhua; Qiu, Bin; Lin, Zhenyu; Yang, Huang-Hao

    2016-12-15

    The determination of folate receptor (FR) that over expressed in vast quantity of cancerous cells frequently is significant for the clinical diagnosis and treatment of cancers. Many DNA-based electrochemical biosensors have been developed for FR detection with high selectivity and sensitivity, but most of them need complicated immobilization of DNA on the electrode surface firstly, which is tedious and therefore results in the poor reproducibility. In this study, a simple, sensitive, and selective electrochemical FR biosensor in cancer cells has been proposed, which combines the advantages of the convenient immobilization-free homogeneous indium tin oxide (ITO)-based electrochemical detection strategy and the high selectivity of the terminal protection of small molecule linked DNA. The small molecule of folic acid (FA) and an electroactive molecule of ferrocence (Fc) were tethered to 3'- and 5'-end of an arbitrary single-stranded DNA (ssDNA), respectively, forming the FA-ssDNA-Fc complex. In the absence of the target FR, the FA-ssDNA-Fc was degraded by exonuclease I (Exo I) from 3'-end and produced a free Fc, diffusing freely to the ITO electrode surface and resulting in strong electrochemical signal. When the target FR was present, the FA-ssDNA-Fc was bound to FR through specific interaction with FA anchored at the 3'-end, effectively protecting the ssDNA strand from hydrolysis by Exo I. The FR-FA-ssDNA-Fc could not diffuse easily to the negatively charged ITO electrode surface due to the electrostatic repulsion between the DNA strand and the negatively charged ITO electrode, so electrochemical signal reduced. The decreased electrochemical signal has a linear relationship with the logarithm of FR concentration in range of 10fM to 10nM with a detection limit of 3.8fM (S/N=3). The proposed biosensor has been applied to detect FR in HeLa cancer cells, and the decreased electrochemical signal has a linear relationship with the logarithm of cell concentration ranging

  16. An ELISA Based Binding and Competition Method to Rapidly Determine Ligand-receptor Interactions.

    Science.gov (United States)

    Syedbasha, Mohameedyaseen; Linnik, Janina; Santer, Deanna; O'Shea, Daire; Barakat, Khaled; Joyce, Michael; Khanna, Nina; Tyrrell, D Lorne; Houghton, Michael; Egli, Adrian

    2016-01-01

    A comprehensive understanding of signaling pathways requires detailed knowledge regarding ligand-receptor interaction. This article describes two fast and reliable point-by-point protocols of enzyme-linked immunosorbent assays (ELISAs) for the investigation of ligand-receptor interactions: the direct ligand-receptor interaction assay (LRA) and the competition LRA. As a case study, the ELISA based analysis of the interaction between different lambda interferons (IFNLs) and the alpha subunit of their receptor (IL28RA) is presented: the direct LRA is used for the determination of dissociation constants (KD values) between receptor and IFN ligands, and the competition LRA for the determination of the inhibitory capacity of an oligopeptide, which was designed to compete with the IFNLs at their receptor binding site. Analytical steps to estimate KD and half maximal inhibitory concentration (IC50) values are described. Finally, the discussion highlights advantages and disadvantages of the presented method and how the results enable a better molecular understanding of ligand-receptor interactions.

  17. Bistable molecular switches based on linkage isomerization in ruthenium polypyridyl complexes with a ligand-bound ambidentate motif.

    Science.gov (United States)

    Johansson, Olof; Johannissen, Linus O; Lomoth, Reiner

    2009-01-01

    Electron-transfer-induced linkage isomerization was investigated in a series of bis-tridentate Ru polypyridyl complexes [Ru(L-X-OH)(Y-tpy)](2+) with ambidentate ligand L-X-OH=bpy-C(R)(OH)-py (bpy=2,2'-bipyridine; py=pyridine; R=H, Me, Ph, or tBu) and spectator ligand Y-tpy (tpy=2,2':6',2''-terpyridine; Y=p-tolyl, p-PhCO(2)Me, Cl, OEt, N-pyrrolidine). The ligand-bound ambidentate motif switches reversibly between N and O coordination in the Ru(II) and Ru(III) state, respectively. The potentials of the Ru(III/II) couple differ by about 0.5 V between the isomers, and this results in a bistable electrochemical response of the molecular switches. The effects of structural modifications in form of substituents on the linking carbon atom of the ambidentate ligand and on the central pyridine moiety of the spectator ligand were investigated by electrochemical and computational methods. Differences in isomerization behavior span six orders of magnitude in rate constants and two orders of magnitude in equilibrium constants. The results can be interpreted in terms of steric and electronic substituent effects and their influence on rotational barriers, ligation geometry, and electron deficiency of the metal center. PMID:19072945

  18. The bound conformation of microtubule-stabilizing agents: NMR insights into the bioactive 3D structure of discodermolide and dictyostatin.

    Science.gov (United States)

    Canales, Angeles; Matesanz, Ruth; Gardner, Nicola M; Andreu, José Manuel; Paterson, Ian; Díaz, J Fernando; Jiménez-Barbero, Jesús

    2008-01-01

    A protocol based on a combination of NMR experimental data with molecular mechanics calculations and docking procedures has been employed to determine the microtubule-bound conformation of two microtubule-stabilizing agents, discodermolide (DDM) and dictyostatin (DCT). The data indicate that tubulin in assembled microtubules recognizes DDM through a conformational selection process, with minor changes in the molecular skeleton between the major conformer in water solution and that bound to assembled microtubules. For DCT, the deduced bound geometry presents some key conformation differences around certain torsion angles, with respect to the major conformer in solution, and still displays mobility even when bound. The bound conformer of DCT resembles that of DDM and provides very similar contacts with the receptor. Competition experiments indicate that both molecules compete with the taxane-binding site. A model of the binding mode of DDM and DCT to tubulin is proposed.

  19. Design, synthesis and structure-activity relationships of novel phenylalanine-based amino acids as kainate receptors ligands

    DEFF Research Database (Denmark)

    Szymańska, Ewa; Chałupnik, Paulina; Szczepańska, Katarzyna;

    2016-01-01

    A new series of carboxyaryl-substituted phenylalanines was designed, synthesized and pharmacologically characterized in vitro at native rat ionotropic glutamate receptors as well as at cloned homomeric kainate receptors GluK1-GluK3. Among them, six compounds bound to GluK1 receptor subtypes...... with reasonable affinity (Ki values in the range of 4.9-7.5 uM). A structure-activity relationship (SAR) for the obtained series, focused mainly on the pharmacological effect of structural modifications in the 4- and 5-position of the phenylalanine ring, was established. To illustrate the results, molecular...... docking of the synthesized series to the X-ray structure of GluK1 ligand binding core was performed. The influence of individual substituents at the phenylalanine ring for both the affinity and selectivity at AMPA, GluK1 and GluK3 receptors was analyzed, giving directions for future studies....

  20. Implications of compound heterozygous insulin receptor mutations in congenital muscle fibre type disproportion myopathy for the receptor kinase activation

    DEFF Research Database (Denmark)

    Klein, H H; Müller, R; Vestergaard, H;

    1999-01-01

    We studied insulin receptor kinase activation in two brothers with congenital muscle fibre type disproportion myopathy and compound heterozygous mutations of the insulin receptor gene, their parents, and their unaffected brother. In the father who has a heterozygote Arg1174-->Gln mutation, in situ......% of the receptors to become insulin-dependently activated. The mother carries a point mutation at the last base pair in exon 17 which, due to abnormal alternative splicing, could lead to normally transcribed receptor or truncated receptor lacking the kinase region. Kinase activation was normal in the mother...... activation of the receptor kinase in skeletal muscle was reduced about 70%. Selection of only those receptors that bound to anti-phosphotyrosine antibody showed that these receptors had normal kinase activity and that the reduction in overall kinase activity was due to the inability of about 70...

  1. Bounds on the thermodynamical properties of the fluid envelope of a planet based upon its radiative budget at the top of the atmosphere

    CERN Document Server

    Lucarini, Valerio

    2010-01-01

    In this paper we exploit two equivalent formulations of the average rate of material entropy production in a planetary system to propose an approximate splitting between contributions due from vertical processes and those due eminently to horizontal processes. We derive an estimate of the lower bound to the intensity of the Lorenz energy cycle, or of the total dissipation of the kinetic energy, based purely upon 2D radiative fields at the top of the atmosphere of the planet. Bounds on the efficiency of the planetary system are also provided, and provide insight on a previous intuition on the possibility of defining a baroclinic heat engine extracting work from the meridional heat flux. Specific results are derived for Earth-like conditions but the approach can be used to analyse general planetary systems. The possibility of providing constraints to the 3D dynamics of the fluid envelope based only upon 2D observations of radiative fluxes seems promising for the observational study of extra-solar planets and ma...

  2. Physical Uncertainty Bounds (PUB)

    Energy Technology Data Exchange (ETDEWEB)

    Vaughan, Diane Elizabeth [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Preston, Dean L. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-03-19

    This paper introduces and motivates the need for a new methodology for determining upper bounds on the uncertainties in simulations of engineered systems due to limited fidelity in the composite continuum-level physics models needed to simulate the systems. We show that traditional uncertainty quantification methods provide, at best, a lower bound on this uncertainty. We propose to obtain bounds on the simulation uncertainties by first determining bounds on the physical quantities or processes relevant to system performance. By bounding these physics processes, as opposed to carrying out statistical analyses of the parameter sets of specific physics models or simply switching out the available physics models, one can obtain upper bounds on the uncertainties in simulated quantities of interest.

  3. Lectin-Glycan Interaction Network-Based Identification of Host Receptors of Microbial Pathogenic Adhesins

    Science.gov (United States)

    Ielasi, Francesco S.; Alioscha-Perez, Mitchel; Donohue, Dagmara; Claes, Sandra; Sahli, Hichem; Schols, Dominique

    2016-01-01

    ABSTRACT The first step in the infection of humans by microbial pathogens is their adherence to host tissue cells, which is frequently based on the binding of carbohydrate-binding proteins (lectin-like adhesins) to human cell receptors that expose glycans. In only a few cases have the human receptors of pathogenic adhesins been described. A novel strategy—based on the construction of a lectin-glycan interaction (LGI) network—to identify the potential human binding receptors for pathogenic adhesins with lectin activity was developed. The new approach is based on linking glycan array screening results of these adhesins to a human glycoprotein database via the construction of an LGI network. This strategy was used to detect human receptors for virulent Escherichia coli (FimH adhesin), and the fungal pathogens Candida albicans (Als1p and Als3p adhesins) and C. glabrata (Epa1, Epa6, and Epa7 adhesins), which cause candidiasis. This LGI network strategy allows the profiling of potential adhesin binding receptors in the host with prioritization, based on experimental binding data, of the most relevant interactions. New potential targets for the selected adhesins were predicted and experimentally confirmed. This methodology was also used to predict lectin interactions with envelope glycoproteins of human-pathogenic viruses. It was shown that this strategy was successful in revealing that the FimH adhesin has anti-HIV activity. PMID:27406561

  4. A Collaborative Evaluation of LC-MS/MS Based Methods for BMAA Analysis: Soluble Bound BMAA Found to Be an Important Fraction

    Directory of Open Access Journals (Sweden)

    Elisabeth J. Faassen

    2016-02-01

    Full Text Available Exposure to β-N-methylamino-l-alanine (BMAA might be linked to the incidence of amyotrophic lateral sclerosis, Alzheimer’s disease and Parkinson’s disease. Analytical chemistry plays a crucial role in determining human BMAA exposure and the associated health risk, but the performance of various analytical methods currently employed is rarely compared. A CYANOCOST initiated workshop was organized aimed at training scientists in BMAA analysis, creating mutual understanding and paving the way towards interlaboratory comparison exercises. During this workshop, we tested different methods (extraction followed by derivatization and liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS analysis, or directly followed by LC-MS/MS analysis for trueness and intermediate precision. We adapted three workup methods for the underivatized analysis of animal, brain and cyanobacterial samples. Based on recovery of the internal standard D3BMAA, the underivatized methods were accurate (mean recovery 80% and precise (mean relative standard deviation 10%, except for the cyanobacterium Leptolyngbya. However, total BMAA concentrations in the positive controls (cycad seeds showed higher variation (relative standard deviation 21%–32%, implying that D3BMAA was not a good indicator for the release of BMAA from bound forms. Significant losses occurred during workup for the derivatized method, resulting in low recovery (<10%. Most BMAA was found in a trichloroacetic acid soluble, bound form and we recommend including this fraction during analysis.

  5. Bounded rationality and learning in market competition

    OpenAIRE

    Tuinstra, J.; Hommes, C.H.; Kopányi, D.

    2015-01-01

    This thesis promotes the use of bounded rationality in economic models. The assumption of perfect rationality often imposes high informational and computational burden on economic agents and predictions based on this assumption are not in line with observed behavior in some cases. Models of bounded rationality may better explain actual behavior in such situations. In the thesis we consider market models where firms are boundedly rational: they do not know the demand for their product and they...

  6. Graviton Mass Bounds

    CERN Document Server

    de Rham, Claudia; Tolley, Andrew J; Zhou, Shuang-Yong

    2016-01-01

    Recently, aLIGO has announced the first direct detections of gravitational waves, a direct manifestation of the propagating degrees of freedom of gravity. The detected signals GW150914 and GW151226 have been used to examine the basic properties of these gravitational degrees of freedom, particularly setting an upper bound on their mass. It is timely to review what the mass of these gravitational degrees of freedom means from the theoretical point of view, particularly taking into account the recent developments in constructing consistent massive gravity theories. Apart from the GW150914 mass bound, a few other observational bounds have been established from the effects of the Yukawa potential, modified dispersion relation and fifth force that are all induced when the fundamental gravitational degrees of freedom are massive. We review these different mass bounds and examine how they stand in the wake of recent theoretical developments and how they compare to the bound from GW150914.

  7. Investigating Upper Bounds on Network Lifetime Extension for Cell-Based Energy Conservation Techniques in Stationary Ad Hoc Networks

    OpenAIRE

    Santi, Paolo

    2002-01-01

    Cooperative cell-based strategies have been recently proposed as a technique for extending the lifetime of wireless adhoc networks, while only slightly impacting network performance. The effectiveness of this approach depends heavilyon the node density: the higher it is, the more consistent energy savings can potentially be achieved. However, nogeneral analyses of network lifetime have been done either for a base network (one without any energy conservationtechnique) or for one using cooperat...

  8. The hydrogen sulfate recognition properties of azo-salicylaldehyde schiff base receptors

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Azo-salicylaldehyde Schiff base-typed receptors containing an acidic H-bond donor moiety were syn-thesized and characterized. The UV-Vis data indicate that these receptors could act as selective col-orimetric sensors for basic anions and acidic species hydrogen sulfate by different color changes in a water-containing medium. The experiment of Brφnsted acid-base reaction by adding the sodium hy-droxide or perchloric acid revealed that the mechanism of recognition of anions might be deprotona-tion/protonation of the OH fragments by interacting with different anions and that the deprotona-tion/protonation process is fully reversible. The deprotonation/protonation of the receptors is respon-sible for the dramatic color change.

  9. The hydrogen sulfate recognition properties of azo-salicylaldehyde schiff base receptors

    Institute of Scientific and Technical Information of China (English)

    WEI TaiBao; WANG Jun; ZHANG YouMing

    2008-01-01

    Azo-salicylaldehyde Schiff base-typed receptors containing an acidic H-bond donor moiety were syn-thesized and characterized. The UV-Vis data indicate that these receptors could act as selective col-orimetric sensors for basic anions and acidic species hydrogen sulfate by different color changes in a water-containing medium, The experiment of Brφnsted acid-base reaction by adding the sodium hy-droxide or perchloric acid revealed that the mechanism of recognition of anions might be deprotona-tion/protonation of the OH fragments by interacting with different anions and that the deprotona-tion/protonation process is fully reversible. The deprotonation/protonation of the receptors is respon-sible for the dramatic color change.

  10. Total and not bevacizumab-bound vascular endothelial growth factor as potential predictive factors to bevacizumab-based chemotherapy in colorectal cancer

    Science.gov (United States)

    Azzariti, Amalia; Porcelli, Letizia; Brunetti, Oronzo; Del Re, Marzia; Longo, Vito; Nardulli, Patrizia; Signorile, Michele; Xu, Jian-Ming; Calabrese, Angela; Quatrale, Anna Elisa; Maiello, Evaristo; Lorusso, Vito; Silvestris, Nicola

    2016-01-01

    AIM: To identify suitable biomarkers of response to bevacizumab (BV) - it remains an open question. The measurement of serum vascular endothelial growth factor (VEGF) has been proposed as a predictive factor for this drug, even if literature data are contradictory. METHODS: We prospectively evaluated the role of BV, total and not BV-bound VEGF and angiopoietin-2 (Ang-2) serum levels as potential predictive factors of response for BV in combination with an oxaliplatin-based chemotherapy. BV, Ang-2, total and not BV-bound VEGF levels were measured at baseline, before 2nd and 5th cycle of oxaliplatin-based chemotherapy in 20 consecutive metastatic colorectal cancer patients. RESULTS: Results were correlated to response to treatment. Variability in BV levels have been found, with decreased level in less responding patients. In particular, the concentration of BV increased of 3.96 ± 0.69 folds in serum of responsive patients after 3 more cycles of therapy compared to those with stable or progressive disease with a 0.72 ± 0.25 and 2.10 ± 0.13 fold increase, respectively. The determination of free and total VEGF demonstrated that the ratio between the two values, evaluated immediately before the 2nd and the 5th cycle of therapy, decreased from 26.65% ± 1.33% to 15.50% ± 3.47% in responsive patients and from 53.41% ± 4.75 to 34.95% ± 2.88% in those with stable disease. Conversely, in those with progression of disease, the ratio showed the opposite behavior coming up from 25.99% ± 5.23% to 51.71% ± 5.28%. The Ang-2 levels did not show any relationship. CONCLUSION: Our data show that the ratio of not BV-bound VEGF to total VEGF serum and BV plasma concentrations for predicting the response to BV plus oxaliplatin-based chemotherapy could be a promising biomarker of response to BV.

  11. Ligand-based receptor tyrosine kinase partial agonists: New paradigm for cancer drug discovery?

    Science.gov (United States)

    Riese, David J.

    2010-01-01

    Introduction Receptor tyrosine kinases (RTKs) are validated targets for oncology drug discovery and several RTK antagonists have been approved for the treatment of human malignancies. Nonetheless, the discovery and development of RTK antagonists has lagged behind the discovery and development of agents that target G-protein coupled receptors. In part, this is because it has been difficult to discover analogs of naturally-occurring RTK agonists that function as antagonists. Areas covered Here we describe ligands of ErbB receptors that function as partial agonists for these receptors, thereby enabling these ligands to antagonize the activity of full agonists for these receptors. We provide insights into the mechanisms by which these ligands function as antagonists. We discuss how information concerning these mechanisms can be translated into screens for novel small molecule- and antibody-based antagonists of ErbB receptors and how such antagonists hold great potential as targeted cancer chemotherapeutics. Expert opinion While there have been a number of important key findings into this field, the identification of the structural basis of ligand functional specificity is still of the greatest importance. While it is true that, with some notable exceptions, peptide hormones and growth factors have not proven to be good platforms for oncology drug discovery; addressing the fundamental issues of antagonistic partial agonists for receptor tyrosine kinases has the potential to steer oncology drug discovery in new directions. Mechanism based approaches are now emerging to enable the discovery of RTK partial agonists that may antagonize both agonist-dependent and –independent RTK signaling and may hold tremendous promise as targeted cancer chemotherapeutics. PMID:21532939

  12. Spontaneous R-Parity violation bounds

    CERN Document Server

    Frank, M

    2001-01-01

    We investigate bounds from tree-level and one-loop processes in generic supersymmetric models with spontaneous R-parity breaking in the superpotential. We analyse the bounds from a general point of view. The bounds are applicable both for all models with spontaneous R-parity violation and for explicit bilinear R-parity violation based on general lepton-chargino and neutrino-neutralino mixings. We find constraints from semileptonic B, D and K decays, leptonic decays of the mu and tau, electric dipole moments, as well as bounds for the anomalous magnetic moment of the muon.

  13. Cationic half-sandwich Ru(II) complexes containing (N,N)-bound Schiff-base ligands: Synthesis, crystal structure analysis and spectroscopic studies

    Science.gov (United States)

    Tao, Li; Miao, Qian; Tehrani, Alireza Azhdari; Hajiashrafi, Taraneh; Hu, Mao-Lin; Morsali, Ali

    2016-08-01

    Three Ru(II) half-sandwich complexes containing (N,N)-bound Schiff-base ligands, [(η6-C6H6) RuCl(L1)]PF6 (1) L1 = (E)-1-(6-methylpyridin-2-yl)-N-(p-tolyl)methanimine, [(η6-p-cymene)RuCl(L1)]PF6 (2) and [(η6-p-cymene)RuCl(L2)]PF6(3) L2 = (E)-1-(6-bromopyridin-2-yl)-N-(p-tolyl)methanimine, were synthesized, characterized and their supramolecular structures were analyzed. The crystal packing of these compounds was studied using geometrical analysis and Hirshfeld surface analysis. The fluorescence behavior of these compounds was also studied. TD-DFT calculations were carried out to better understand the fluorescence properties of complexes 1-3. These compounds could be promising for the design of organometallic dye systems.

  14. Design and synthesis of novel tweezer anion receptors based on deoxycholic acid

    Institute of Scientific and Technical Information of China (English)

    Xing Li Liu; Zhi Gang Zhao; Shu Hua Chen

    2007-01-01

    A novel type of molecular tweezer receptors based on deoxycholic acid has been designed and synthesized and their binding properties were examined by UV-vis spectral titration. These molecular tweezers showed a high selectivity toward F- over Cl-,Br-, I-, AcO-, H2PO4-.

  15. A new crystal structure fragment-based pharmacophore method for G protein-coupled receptors

    DEFF Research Database (Denmark)

    Fidom, Kimberley; Isberg, Vignir; Hauser, Alexander Sebastian;

    2015-01-01

    We have developed a new method for the building of pharmacophores for G protein-coupled receptors, a major drug target family. The method is a combination of the ligand- and target-based pharmacophore methods and founded on the extraction of structural fragments, interacting ligand moiety and rec...

  16. Predicting dopamine D2 receptor occupancy in humans using a physiology-based approach

    NARCIS (Netherlands)

    Johnson, Martin; Kozielska, Magdalena; Pilla Reddy, Venkatesh; Vermeulen, An; Barton, Hugh A.; Grimwood, Sarah; de Greef, Rik; Groothuis, Genoveva; Danhof, Meindert; Proost, Johannes

    2011-01-01

    Objectives: A hybrid physiology-based pharmacokinetic and pharmacodynamic model (PBPKPD) was used to predict the time course of dopamine receptor occupancy (D2RO) in human striatum following the administration of antipsychotic (AP) drugs, using in vitro and in silico information. Methods: A hybrid P

  17. GPCR-OKB: the G Protein Coupled Receptor Oligomer Knowledge Base.

    NARCIS (Netherlands)

    Khelashvili, G.; Dorff, K.; Shan, J.; Camacho-Artacho, M.; Skrabanek, L.; Vroling, B.; Bouvier, M.; Devi, L.A.; George, S.R.; Javitch, J.A.; Lohse, M.J.; Milligan, G.; Neubig, R.R.; Palczewski, K.; Parmentier, M.; Pin, J.P.; Vriend, G.; Campagne, F.; Filizola, M.

    2010-01-01

    SUMMARY: Rapid expansion of available data about G Protein Coupled Receptor (GPCR) dimers/oligomers over the past few years requires an effective system to organize this information electronically. Based on an ontology derived from a community dialog involving colleagues using experimental and compu

  18. Multicolor Bound Soliton Molecule

    CERN Document Server

    Luo, Rui; Lin, Qiang

    2015-01-01

    We show a new class of bound soliton molecule that exists in a parametrically driven nonlinear optical cavity with appropriate dispersion characteristics. The composed solitons exhibit distinctive colors but coincide in time and share a common phase, bound together via strong inter-soliton four-wave mixing and Cherenkov radiation. The multicolor bound soliton molecule shows intriguing spectral locking characteristics and remarkable capability of spectrum management to tailor soliton frequencies, which may open up a great avenue towards versatile generation and manipulation of multi-octave spanning phase-locked Kerr frequency combs, with great potential for applications in frequency metrology, optical frequency synthesis, and spectroscopy.

  19. A C3 Symmetric Nitrate Complex with a Thiophene-Based Tripodal Receptor

    OpenAIRE

    Işiklan, Muhammet; Saeed, Musabbir A.; Pramanik, Avijit; Wong, Bryan M.; Fronczek, Frank R.; Hossain, Alamgir

    2011-01-01

    A thiophene-based tripodal receptor has been synthesized and its complexes with nitrate and iodide have determined by single-crystal X-ray analysis. In the nitrate complex, one nitrate is encapsulated in a selective orientation forming a C3 symmetric complex, which is bonded to three protonated secondary amines with six NH···O bonds. The anion is coordinated in a plane perpendicular to the principal rotation axis passing through the tertiary nitrogen of the receptor and the nitrogen of the en...

  20. Cell-Based Odorant Sensor Array for Odor Discrimination Based on Insect Odorant Receptors.

    Science.gov (United States)

    Termtanasombat, Maneerat; Mitsuno, Hidefumi; Misawa, Nobuo; Yamahira, Shinya; Sakurai, Takeshi; Yamaguchi, Satoshi; Nagamune, Teruyuki; Kanzaki, Ryohei

    2016-07-01

    The olfactory system of living organisms can accurately discriminate numerous odors by recognizing the pattern of activation of several odorant receptors (ORs). Thus, development of an odorant sensor array based on multiple ORs presents the possibility of mimicking biological odor discrimination mechanisms. Recently, we developed novel odorant sensor elements with high sensitivity and selectivity based on insect OR-expressing Sf21 cells that respond to target odorants by displaying increased fluorescence intensity. Here we introduce the development of an odorant sensor array composed of several Sf21 cell lines expressing different ORs. In this study, an array pattern of four cell lines expressing Or13a, Or56a, BmOR1, and BmOR3 was successfully created using a patterned polydimethylsiloxane film template and cell-immobilizing reagents, termed biocompatible anchor for membrane (BAM). We demonstrated that BAM could create a clear pattern of Sf21 sensor cells without impacting their odorant-sensing performance. Our sensor array showed odorant-specific response patterns toward both odorant mixtures and single odorant stimuli, allowing us to visualize the presence of 1-octen-3-ol, geosmin, bombykol, and bombykal as an increased fluorescence intensity in the region of Or13a, Or56a, BmOR1, and BmOR3 cell lines, respectively. Therefore, we successfully developed a new methodology for creating a cell-based odorant sensor array that enables us to discriminate multiple target odorants. Our method might be expanded into the development of an odorant sensor capable of detecting a large range of environmental odorants that might become a promising tool used in various applications including the study of insect semiochemicals and food contamination.

  1. Quantum Lower Bounds by Entropy Numbers

    OpenAIRE

    Heinrich, Stefan

    2006-01-01

    We use entropy numbers in combination with the polynomial method to derive a new general lower bound for the n-th minimal error in the quantum setting of information-based complexity. As an application, we improve some lower bounds on quantum approximation of embeddings between finite dimensional L_p spaces and of Sobolev embeddings.

  2. Advances of Targeted Therapy Based on Estrogen Receptor Signaling Pathway 
in Lung Cancer

    Directory of Open Access Journals (Sweden)

    Liqiang XU

    2011-09-01

    Full Text Available Increasing evidence indicates that estrogen promotes tumor growth in both estrogen target organs and non-target organs. Estrogen regulates cell proliferation and differentiation via two different receptors, estrogen receptors α and β (ERα and ERβ. In recent decades, with the clarification of the ERα-mediated signaling pathways in breast cancer, targeted therapy through these pathways have successfully been used in clinical application. Tamoxifen, the classic representative, is a selective estrogen receptor modulator (SERM. Along with the elucidation of the role of estrogen in the pathophysiology of lung cancer, targeted lung cancer treatment based on the ER signaling pathways is also gradually being applied and it could become an important part of the comprehensive treatment for lung cancer.

  3. Molecular modeling of the human P2Y14 receptor: A template for structure-based design of selective agonist ligands.

    Science.gov (United States)

    Trujillo, Kevin; Paoletta, Silvia; Kiselev, Evgeny; Jacobson, Kenneth A

    2015-07-15

    The P2Y14 receptor (P2Y14R) is a Gi protein-coupled receptor that is activated by uracil nucleotides UDP and UDP-glucose. The P2Y14R structure has yet to be solved through X-ray crystallography, but the recent agonist-bound crystal structure of the P2Y12R provides a potentially suitable template for its homology modeling for rational structure-based design of selective and high-affinity ligands. In this study, we applied ligand docking and molecular dynamics refinement to a P2Y14R homology model to qualitatively explain structure-activity relationships of previously published synthetic nucleotide analogues and to probe the quality of P2Y14R homology modeling as a template for structure-based design. The P2Y14R model supports the hypothesis of a conserved binding mode of nucleotides in the three P2Y12-like receptors involving functionally conserved residues. We predict phosphate group interactions with R253(6.55), K277(7.35), Y256(6.58) and Q260(6.62), nucleobase (anti-conformation) π-π stacking with Y102(3.33) and the role of F191(5.42) as a means for selectivity among P2Y12-like receptors. The glucose moiety of UDP-glucose docked in a secondary subpocket at the P2Y14R homology model. Thus, P2Y14R homology modeling may allow detailed prediction of interactions to facilitate the design of high affinity, selective agonists as pharmacological tools to study the P2Y14R.

  4. 基于有限理性的交通方式划分模型%Traffic modal split model based on bounded rationality

    Institute of Scientific and Technical Information of China (English)

    左志; 潘晓锋

    2014-01-01

    An improved traffic modal split model is proposed considering travelers' bounded rationality.The weights of influence factors to mode choice and the evaluations of traffic modes against each factor are defined through a questionnaire survey.The value of each traffic mode is calculated by TODIM method.A Probit model of traffic mode choice is proposed on the basis of bounded rationality. The impact of parameters' change of the model on traffic modal split is discussed.Comparing working and shopping,the influence of different travel purposes on mode choice is analyzed.Experimental results show that the traffic modal split model based on bounded rationality can reflect travelers' preference of mode choice under different travel purposes.The parameterθrepresents travelers'cognition level,and in this modelθshould be valued in (0,2).%考虑出行者有限理性的特点,建立改进的交通方式划分模型。通过问卷调查,确定出行者方式选择各影响因素的权重,以及各交通方式在不同因素下的表现;运用 TODIM方法,计算各交通方式的价值;基于有限理性,建立交通方式选择 Probit 模型;讨论模型中参数变化对交通方式划分的影响;对比上班和购物出行,分析不同出行目的对方式选择的影响。研究表明,基于有限理性的交通方式划分模型能够体现不同出行目的下出行者出行方式选择偏好;参数θ体现出行者的认知程度,在该模型里应在(0,2)中取值。

  5. Quaternionic bound states

    Energy Technology Data Exchange (ETDEWEB)

    De Leo, Stefano [Department of Applied Mathematics, University of Campinas, PO Box 6065, SP 13083-970, Campinas (Brazil); Ducati, Gisele C [Department of Mathematics, University of Parana PO Box 19081, PR 81531-970, Curitiba (Brazil)

    2005-04-15

    We study the bound-state solutions of vanishing angular momentum in a quaternionic spherical square-well potential of finite depth. As in standard quantum mechanics, such solutions occur for discrete values of energy. At first glance, it seems that the continuity conditions impose a very restrictive constraint on the energy eigenvalues and, consequently, no bound states were expected for energy values below the pure quaternionic potential. Nevertheless, a careful analysis shows that pure quaternionic potentials do not remove bound states. It is also interesting to compare these new solutions with the bound state solutions of the trial-complex potential. The study presented in this paper represents a preliminary step towards a full understanding of the role that quaternionic potentials could play in quantum mechanics. Of particular interest for the authors is the analysis of confined wave packets and tunnelling times in this new formulation of quantum theory.

  6. Structure-based rational design of a Toll-like receptor 4 (TLR4 decoy receptor with high binding affinity for a target protein.

    Directory of Open Access Journals (Sweden)

    Jieun Han

    Full Text Available Repeat proteins are increasingly attracting much attention as alternative scaffolds to immunoglobulin antibodies due to their unique structural features. Nonetheless, engineering interaction interface and understanding molecular basis for affinity maturation of repeat proteins still remain a challenge. Here, we present a structure-based rational design of a repeat protein with high binding affinity for a target protein. As a model repeat protein, a Toll-like receptor4 (TLR4 decoy receptor composed of leucine-rich repeat (LRR modules was used, and its interaction interface was rationally engineered to increase the binding affinity for myeloid differentiation protein 2 (MD2. Based on the complex crystal structure of the decoy receptor with MD2, we first designed single amino acid substitutions in the decoy receptor, and obtained three variants showing a binding affinity (K(D one-order of magnitude higher than the wild-type decoy receptor. The interacting modes and contributions of individual residues were elucidated by analyzing the crystal structures of the single variants. To further increase the binding affinity, single positive mutations were combined, and two double mutants were shown to have about 3000- and 565-fold higher binding affinities than the wild-type decoy receptor. Molecular dynamics simulations and energetic analysis indicate that an additive effect by two mutations occurring at nearby modules was the major contributor to the remarkable increase in the binding affinities.

  7. 孕烯醇酮和孕烯醇酮硫酸盐对小鼠不同脑区3H-GABA与GABAB受体结合的影响%Effects of Pregnenolone and Pregnenolone Sulfate on 3H-GABA Bound with GABAB Receptor in Different Areas of Mice Brain

    Institute of Scientific and Technical Information of China (English)

    周雪瑞

    2001-01-01

    By using radioactive ligand-receptor binding assay, this paperreported the effects of pregnenolong (Pe) and pregnenolone sulfate (Pes) on 3H-GABA bound with GABAB receptor in different areas of mice brain. The result showed that Pe decreased the binding of 3H-GABA with GABAB receptor, and it could be blocked and turned over by baclofen. Pes markedly decreased the binding of 3H-GABA with GABAB receptor in cerebral cortex and hippocampus and increased the binding in hypothalamus of mice brain. Baclofen could blocked the inhibition effect, enhance the effects of increase. These results suggested that major effects of Pe and Pes on 3H-GABA bound with GABAB receptor in different areas of mice brain were inhibition effects.%采用放射配体受体结合分析法,研究了孕烯醇酮(Pe)和孕烯醇酮硫酸盐(Pes)对小鼠不同脑区3H-GABA与GABAB受体结合的影响.结果显示,Pe对小鼠下丘脑、大脑皮层、海马、小脑GABAB受体的结合均有抑制效应,且能被GABAB受体激动剂巴氯芬(Bac)所阻断并翻转.Pes对大脑皮层、海马、小脑GABAB受体的结合有抑制作用,而对下丘脑则有促进作用.Bac能阻断Pes的抑制作用(海马除外),加强Pes的促进作用.实验结果提示,Pe,Pes对各脑区GABAB受体的结合具有一定的影响作用,且多为抑制效应.

  8. Quality assessment of estrogen receptor and progesterone receptor testing in breast cancer using a tissue microarray-based approach

    NARCIS (Netherlands)

    Dekker, T. J. A.; ter Borg, S.; Hooijer, G. K. J.; Meijer, S. L.; Wesseling, J.; Boers, J. E.; Schuuring, E.; Bart, J.; van Gorp, J.; Bult, P.; Riemersma, S. A.; van Deurzen, C. H. M.; Sleddens, H. F. B. M.; Mesker, W. E.; Kroep, J. R.; Smit, V. T. H. B. M.; van de Vijver, M. J.

    2015-01-01

    Assessing hormone receptor status is an essential part of the breast cancer diagnosis, as this biomarker greatly predicts response to hormonal treatment strategies. As such, hormone receptor testing laboratories are strongly encouraged to participate in external quality control schemes to achieve op

  9. Constraint-based strain design using continuous modifications (CosMos) of flux bounds finds new strategies for metabolic engineering.

    Science.gov (United States)

    Cotten, Cameron; Reed, Jennifer L

    2013-05-01

    In recent years, a growing number of metabolic engineering strain design techniques have employed constraint-based modeling to determine metabolic and regulatory network changes which are needed to improve chemical production. These methods use systems-level analysis of metabolism to help guide experimental efforts by identifying deletions, additions, downregulations, and upregulations of metabolic genes that will increase biological production of a desired metabolic product. In this work, we propose a new strain design method with continuous modifications (CosMos) that provides strategies for deletions, downregulations, and upregulations of fluxes that will lead to the production of the desired products. The method is conceptually simple and easy to implement, and can provide additional strategies over current approaches. We found that the method was able to find strain design strategies that required fewer modifications and had larger predicted yields than strategies from previous methods in example and genome-scale networks. Using CosMos, we identified modification strategies for producing a variety of metabolic products, compared strategies derived from Escherichia coli and Saccharomyces cerevisiae metabolic models, and examined how imperfect implementation may affect experimental outcomes. This study gives a powerful and flexible technique for strain engineering and examines some of the unexpected outcomes that may arise when strategies are implemented experimentally.

  10. A novel method to measure HLA-DM-susceptibility of peptides bound to MHC class II molecules based on peptide binding competition assay and differential IC(50) determination.

    Science.gov (United States)

    Yin, Liusong; Stern, Lawrence J

    2014-04-01

    HLA-DM (DM) functions as a peptide editor that mediates the exchange of peptides loaded onto MHCII molecules by accelerating peptide dissociation and association kinetics. The relative DM-susceptibility of peptides bound to MHCII molecules correlates with antigen presentation and immunodominance hierarchy, and measurement of DM-susceptibility has been a key effort in this field. Current assays of DM-susceptibility, based on differential peptide dissociation rates measured for individually labeled peptides over a long time base, are difficult and cumbersome. Here, we present a novel method to measure DM-susceptibility based on peptide binding competition assays performed in the presence and absence of DM, reported as a delta-IC(50) (change in 50% inhibition concentration) value. We simulated binding competition reactions of peptides with various intrinsic and DM-catalyzed kinetic parameters and found that under a wide range of conditions the delta-IC(50) value is highly correlated with DM-susceptibility as measured in off-rate assay. We confirmed experimentally that DM-susceptibility measured by delta-IC(50) is comparable to that measured by traditional off-rate assay for peptides with known DM-susceptibility hierarchy. The major advantage of this method is that it allows simple, fast and high throughput measurement of DM-susceptibility for a large set of unlabeled peptides in studies of the mechanism of DM action and for identification of CD4+ T cell epitopes.

  11. Structure-based, rational design of T cell receptors

    Directory of Open Access Journals (Sweden)

    Vincent eZoete

    2013-09-01

    Full Text Available Adoptive cell transfer using engineered T cells is emerging as a promising treatment for metastatic melanoma. Such an approach allows one to introduce TCR modifications that, while maintaining the specificity for the targeted antigen, can enhance the binding and kinetic parameters for the interaction pMHC. Using the well-characterized 2C TCR/SIYR/H-2K(b structure as a model system, we demonstrated that a binding free energy decomposition based on the MM-GBSA approach provides a detailed and reliable description of the TCR/pMHC interactions at the structural and thermodynamic levels. Starting from this result, we developed a new structure-based approach, to rationally design new TCR sequences, and applied it to the BC1 TCR targeting the HLA-A2 restricted NY-ESO-1157-165 cancer-testis epitope. 54% of the designed sequence replacements exhibited improved pMHC-binding as compared to the native TCR, with up to 150 fold increase in affinity, while preserving specificity. Genetically-engineered CD8+ T cells expressing these modified TCRs showed an improved functional activity compared to those expressing BC1 TCR. We measured maximum levels of activities for TCRs within the upper limit of natural affinity. Beyond the affinity threshold at KD < 1 μM we observed an attenuation in cellular function. We have also developed a homology modeling-based approach, TCRep 3D, to obtain accurate structural models of any TCR-pMHC complexes. We have complemented the approach with a simplified rigid method to predict the TCR orientation over pMHC. These methods potentially extend the use of our TCR engineering method to entire TCR repertoires for which no X-ray structure is available. We have also performed a steered molecular dynamics study of the unbinding of the TCR-pMHC complex to get a better understanding of how TCRs interact with pMHCs. This entire rational TCR design pipeline is now being used to produce rationally optimized TCRs for adoptive cell therapies of

  12. Kidney branching morphogenesis under the control of a ligand–receptor-based Turing mechanism

    International Nuclear Information System (INIS)

    The main signalling proteins that control early kidney branching have been defined. Yet the underlying mechanism is still elusive. We have previously shown that a Schnakenberg-type Turing mechanism can recapitulate the branching and protein expression patterns in wild-type and mutant lungs, but it is unclear whether this mechanism would extend to other branched organs that are regulated by other proteins. Here, we show that the glial cell line-derived neurotrophic factor–RET regulatory interaction gives rise to a Schnakenberg-type Turing model that reproduces the observed budding of the ureteric bud from the Wolffian duct, its invasion into the mesenchyme and the observed branching pattern. The model also recapitulates all relevant protein expression patterns in wild-type and mutant mice. The lung and kidney models are both based on a particular receptor–ligand interaction and require (1) cooperative binding of ligand and receptor, (2) a lower diffusion coefficient for the receptor than for the ligand and (3) an increase in the receptor concentration in response to receptor–ligand binding (by enhanced transcription, more recycling or similar). These conditions are met also by other receptor–ligand systems. We propose that ligand–receptor-based Turing patterns represent a general mechanism to control branching morphogenesis and other developmental processes. (paper)

  13. An automated system for the analysis of G protein-coupled receptor transmembrane binding pockets: alignment, receptor-based pharmacophores, and their application.

    Science.gov (United States)

    Kratochwil, Nicole A; Malherbe, Pari; Lindemann, Lothar; Ebeling, Martin; Hoener, Marius C; Mühlemann, Andreas; Porter, Richard H P; Stahl, Martin; Gerber, Paul R

    2005-01-01

    G protein-coupled receptors (GPCRs) share a common architecture consisting of seven transmembrane (TM) domains. Various lines of evidence suggest that this fold provides a generic binding pocket within the TM region for hosting agonists, antagonists, and allosteric modulators. Here, a comprehensive and automated method allowing fast analysis and comparison of these putative binding pockets across the entire GPCR family is presented. The method relies on a robust alignment algorithm based on conservation indices, focusing on pharmacophore-like relationships between amino acids. Analysis of conservation patterns across the GPCR family and alignment to the rhodopsin X-ray structure allows the extraction of the amino acids lining the TM binding pocket in a so-called ligand binding pocket vector (LPV). In a second step, LPVs are translated to simple 3D receptor pharmacophore models, where each amino acid is represented by a single spherical pharmacophore feature and all atomic detail is omitted. Applications of the method include the assessment of selectivity issues, support of mutagenesis studies, and the derivation of rules for focused screening to identify chemical starting points in early drug discovery projects. Because of the coarseness of this 3D receptor pharmacophore model, however, meaningful scoring and ranking procedures of large sets of molecules are not justified. The LPV analysis of the trace amine-associated receptor family and its experimental validation is discussed as an example. The value of the 3D receptor model is demonstrated for a class C GPCR family, the metabotropic glutamate receptors.

  14. Lectures on Bound states

    CERN Document Server

    Hoyer, Paul

    2016-01-01

    Even a first approximation of bound states requires contributions of all powers in the coupling. This means that the concept of "lowest order bound state" needs to be defined. In these lectures I discuss the "Born" (no loop, lowest order in $\\hbar$) approximation. Born level states are bound by gauge fields which satisfy the classical field equations. As a check of the method, Positronium states of any momentum are determined as eigenstates of the QED Hamiltonian, quantized at equal time. Analogously, states bound by a strong external field $A^\\mu(\\xv)$ are found as eigenstates of the Dirac Hamiltonian. Their Fock states have dynamically created $e^+e^-$ pairs, whose distribution is determined by the Dirac wave function. The linear potential of $D=1+1$ dimensions confines electrons but repels positrons. As a result, the mass spectrum is continuous and the wave functions have features of both bound states and plane waves. The classical solutions of Gauss' law are explored for hadrons in QCD. A non-vanishing bo...

  15. Bounding species distribution models

    Institute of Scientific and Technical Information of China (English)

    Thomas J. STOHLGREN; Catherine S. JARNEVICH; Wayne E. ESAIAS; Jeffrey T. MORISETTE

    2011-01-01

    Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern.Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development,yet there is no recommended best practice for “clamping” model extrapolations.We relied on two commonly used modeling approaches:classification and regression tree (CART) and maximum entropy (Maxent) models,and we tested a simple alteration of the model extrapolations,bounding extrapolations to the maximum and minimum values of primary environmental predictors,to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States.Findings suggest that multiple models of bounding,and the most conservative bounding of species distribution models,like those presented here,should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5):642-647,2011].

  16. Receptor-based 3D-QSAR in Drug Design: Methods and Applications in Kinase Studies.

    Science.gov (United States)

    Fang, Cheng; Xiao, Zhiyan

    2016-01-01

    Receptor-based 3D-QSAR strategy represents a superior integration of structure-based drug design (SBDD) and three-dimensional quantitative structure-activity relationship (3D-QSAR) analysis. It combines the accurate prediction of ligand poses by the SBDD approach with the good predictability and interpretability of statistical models derived from the 3D-QSAR approach. Extensive efforts have been devoted to the development of receptor-based 3D-QSAR methods and two alternative approaches have been exploited. One associates with computing the binding interactions between a receptor and a ligand to generate structure-based descriptors for QSAR analyses. The other concerns the application of various docking protocols to generate optimal ligand poses so as to provide reliable molecular alignments for the conventional 3D-QSAR operations. This review highlights new concepts and methodologies recently developed in the field of receptorbased 3D-QSAR, and in particular, covers its application in kinase studies.

  17. Departure Time Choice Behavior Based on Bounded Rationality%有限理性下个体出发时间选择行为研究

    Institute of Scientific and Technical Information of China (English)

    栾琨; 傅忠宁; 隽志才

    2016-01-01

    Subject to such limitations as cognitive ability and logical reasoning ability, it is difficult for individual to be perfectly rational in the travel decision-making process. Taking departure time choice as an example, key behavior factors such as spatial knowledge acquisition, learning, cognition update and solution search are introduced. The theoretical framework of travel decision-making process is built based on bounded rationality. Departure time behavioral intention survey program is designed by integration of RP and SP survey methods. Individual’s knowledge representation is studied, and cognitive update is completed by using Bayesian learning theory. Functions of search cost and search gain are defined. By using survey data, departure time heuristic search rules and decision rules are derived based on PART and RIPPER algorithm separately. The results show that there exist perception threshold in individual’s departure time choice behavior under bounded rationality, rather than seeking global optimal solution.%个体受限于认知能力和逻辑推理能力的限制,在出行决策过程中很难做到完全理性。本文以出发时间选择为例,在有限理性行为假设基础上,引入空间知识获取、学习及认知更新和方案搜索等关键行为要素,构建有限理性下的出行决策过程理论框架。融合RP和SP调查方法,设计出发时间选择行为意向调查方案。研究个体知识的表达方式,应用贝叶斯学习理论完成认知更新。定义搜索成本和收益函数,利用调查数据分别提取基于PART和RIPPER算法的出发时间启发式搜索规则和决策规则。结果表明,有限理性下个体出发时间选择行为存在感知阈值,而并非寻求全局最优解。

  18. Validation of EMP bounds

    Energy Technology Data Exchange (ETDEWEB)

    Warne, L.K.; Merewether, K.O.; Chen, K.C.; Jorgenson, R.E.; Morris, M.E.; Solberg, J.E.; Lewis, J.G. [Sandia National Labs., Albuquerque, NM (United States); Derr, W. [Derr Enterprises, Albuquerque, NM (United States)

    1996-07-01

    Test data on canonical weapon-like fixtures are used to validate previously developed analytical bounding results. The test fixtures were constructed to simulate (but be slightly worse than) weapon ports of entry but have known geometries (and electrical points of contact). The exterior of the test fixtures exhibited exterior resonant enhancement of the incident fields at the ports of entry with magnitudes equal to those of weapon geometries. The interior consisted of loaded transmission lines adjusted to maximize received energy or voltage but incorporating practical weapon geometrical constraints. New analytical results are also presented for bounding the energies associated with multiple bolt joints and for bounding the exterior resonant enhancement of the exciting fields.

  19. Genetic contributions to avoidance-based decisions: striatal D2 receptor polymorphisms.

    Science.gov (United States)

    Frank, M J; Hutchison, K

    2009-11-24

    Individuals differ in their tendencies to seek positive decision outcomes or to avoid negative ones. At the neurobiological level, our model suggests that phasic changes in dopamine support learning to reinforce good decisions via striatal D1 receptors, and to avoid maladaptive choices via striatal D2 receptors. Accordingly, in a previous study individual differences in positive and negative learning were strongly modulated by two genetic polymorphisms factors related to striatal D1 and D2 function, respectively. Nevertheless, whereas the role for dopamine in positive learning is relatively well accepted, that in learning to avoid negative outcomes is more controversial. Here we further explore D2-receptor-related genetic contributions to probabilistic avoidance in humans, in light of recent data showing that particular DRD2 polymorphisms are associated with functional modulation of receptor expression [Zhang Y, Bertolino A, Fazio L, Blasi G, Rampino A, Romano R, Lee M-LT, Xiao T, Papp A, Wang D, Sadée W (2007) Polymorphisms in human dopamine d2 receptor gene affect gene expression, splicing, and neuronal activity during working memory. Proc Natl Acad Sci U S A 104(51):20552-20557]. We find that a promoter polymorphism rs12364283 associated with transcription and D2 receptor density was strongly and selectively predictive of avoidance-based decisions. Two further polymorphisms (rs2283265 and rs1076560) associated with relatively reduced presynaptic relative to postsynaptic D2 receptor expression were predictive of relative impairments in negative compared to positive decisions. These previously undocumented effects of DRD2 polymorphisms were largely independent of those we reported previously for the C957T polymorphism (rs6277) associated with striatal D2 density. In contrast, effects of the commonly studied Taq1A polymorphism on reinforcement-based decisions were due to indirect association with C957T. Taken together these findings suggest multiple D2-dependent

  20. Identification of adiponectin receptor agonist utilizing a fluorescence polarization based high throughput assay.

    Science.gov (United States)

    Sun, Yiyi; Zang, Zhihe; Zhong, Ling; Wu, Min; Su, Qing; Gao, Xiurong; Zan, Wang; Lin, Dong; Zhao, Yan; Zhang, Zhonglin

    2013-01-01

    Adiponectin, the adipose-derived hormone, plays an important role in the suppression of metabolic disorders that can result in type 2 diabetes, obesity, and atherosclerosis. It has been shown that up-regulation of adiponectin or adiponectin receptor has a number of therapeutic benefits. Given that it is hard to convert the full size adiponectin protein into a viable drug, adiponectin receptor agonists could be designed or identified using high-throughput screening. Here, we report on the development of a two-step screening process to identify adiponectin agonists. First step, we developed a high throughput screening assay based on fluorescence polarization to identify adiponectin ligands. The fluorescence polarization assay reported here could be adapted to screening against larger small molecular compound libraries. A natural product library containing 10,000 compounds was screened and 9 hits were selected for validation. These compounds have been taken for the second-step in vitro tests to confirm their agonistic activity. The most active adiponectin receptor 1 agonists are matairesinol, arctiin, (-)-arctigenin and gramine. The most active adiponectin receptor 2 agonists are parthenolide, taxifoliol, deoxyschizandrin, and syringin. These compounds may be useful drug candidates for hypoadiponectin related diseases. PMID:23691032

  1. Identification of adiponectin receptor agonist utilizing a fluorescence polarization based high throughput assay.

    Directory of Open Access Journals (Sweden)

    Yiyi Sun

    Full Text Available Adiponectin, the adipose-derived hormone, plays an important role in the suppression of metabolic disorders that can result in type 2 diabetes, obesity, and atherosclerosis. It has been shown that up-regulation of adiponectin or adiponectin receptor has a number of therapeutic benefits. Given that it is hard to convert the full size adiponectin protein into a viable drug, adiponectin receptor agonists could be designed or identified using high-throughput screening. Here, we report on the development of a two-step screening process to identify adiponectin agonists. First step, we developed a high throughput screening assay based on fluorescence polarization to identify adiponectin ligands. The fluorescence polarization assay reported here could be adapted to screening against larger small molecular compound libraries. A natural product library containing 10,000 compounds was screened and 9 hits were selected for validation. These compounds have been taken for the second-step in vitro tests to confirm their agonistic activity. The most active adiponectin receptor 1 agonists are matairesinol, arctiin, (--arctigenin and gramine. The most active adiponectin receptor 2 agonists are parthenolide, taxifoliol, deoxyschizandrin, and syringin. These compounds may be useful drug candidates for hypoadiponectin related diseases.

  2. Structure-based design of eugenol analogs as potential estrogen receptor antagonists.

    Science.gov (United States)

    Anita, Yulia; Radifar, Muhammad; Kardono, Leonardus Bs; Hanafi, Muhammad; Istyastono, Enade P

    2012-01-01

    Eugenol is an essential oil mainly found in the buds and leaves of clove (Syzygium aromaticum (L.) Merrill and Perry), which has been reported to have activity on inhibition of cell proliferation and apoptosis induction in human MCF-7 breast cancer cells. This biological activity is correlated to its activity as an estrogen receptor antagonist. In this article, we present the construction and validation of structure-based virtual screening (SBVS) protocols to identify the potent estrogen receptor α (ER) antagonists. The selected protocol, which gave acceptable enrichment factors as a virtual screening protocol, subsequently used to virtually screen eugenol, its analogs and their dimers. Based on the virtual screening results, dimer eugenol of 4-[4-hydroxy-3-(prop-2-en-1- yl)phenyl]-2-(prop-2-en-1-yl)phenol is recommended to be developed further in order to discover novel and potent ER antagonists. PMID:23144548

  3. A bovine papillomavirus-1 based vector restores the function of the low-density lipoprotein receptor in the receptor-deficient CHO-ldlA7 cell line

    Directory of Open Access Journals (Sweden)

    Ustav Mart

    2002-04-01

    Full Text Available Abstract Background The rationale of using bovine papillomavirus-1 (BPV-1 derived vectors in gene therapy protocols lies in their episomal maintenance at intermediate to high copy number, and stable, high-level expression of the gene products. We constructed the BPV-1 based vector harbouring the human low-density lipoprotein receptor (LDLR gene cDNA and tested its ability to restore the function of the LDLR in the receptor-deficient cell line CHO-ldlA7. Results The introduced vector p3.7LDL produced functionally active LDL receptors in the receptor-deficient cell line CHO-ldlA7 during the 32-week period of observation as determined by the internalisation assay with the labelled LDL particles. Conclusion Bovine papillomavirus type-1 (BPV-1-derived vectors could be suitable for gene therapy due to their episomal maintenance at intermediate to high copy number and stable, high-level expression of the gene products. The constructed BPV-1 based vector p3.7LDL produced functionally active LDL receptors in the LDLR-deficient cell line CHO-ldlA7 during the 32-week period of observation. In vivo experiments should reveal, whether 1–5% transfection efficiency obtained in the current work is sufficient to bring about detectable and clinically significant lowering of the amount of circulating LDL cholesterol particles.

  4. A Rate-Splitting Based Bound-Approaching Transmission Scheme for the Two-User Symmetric Gaussian Interference Channel with Common Messages

    Directory of Open Access Journals (Sweden)

    B. ZHANG

    2012-12-01

    Full Text Available This paper is concerned with a rate-splitting based transmission strategy for the two-user symmetric Gaussian interference channel that contains common messages only. Each transmitter encodes its common message into multiple layers by multiple codebooks that drawn from one separate code book, and transmits the superposition of the messages corresponding to these layers; each receiver decodes the messages from all layers of the two users successively. Two schemes are proposed for decoding order and optimal power allocation among layers respectively. With the proposed decoding order scheme, the sum-rate can be increased by rate-splitting, especially at the optimal number of rate-splitting, using average power allocation in moderate and weak interference regime. With the two proposed schemes at the receiver and the transmitter respectively, the sum-rate achieves the inner bound of HK without time-sharing. Numerical results show that the proposed optimal power allocation scheme with the proposed decoding order can achieve significant improvement of the performance over equal power allocation, and achieve the sum-rate within two bits per channel use (bits/channel use of the sum capacity.

  5. Monoolein-based nanocarriers for enhanced folate receptor-mediated RNA delivery to cancer cells.

    Science.gov (United States)

    Lopes, Ivo; C N Oliveira, Ana; P Sárria, Marisa; P Neves Silva, João; Gonçalves, Odete; Gomes, Andreia C; Real Oliveira, Maria Elisabete C D

    2016-09-01

    We report the development and characterization of a novel nanometric system for specific delivery of therapeutic siRNA for cancer treatment. This vector is based on a binary mixture of the cationic surfactant dioctadecyldimethylammonium chloride (DODAC) and the helper lipid monoolein (MO). These liposomes were previously validated by our research group as promising non-viral vectors for nucleic acid delivery. In this work, the DODAC:MO vesicles were for the first time functionalized with polyethylene glycol and PEG-folate conjugates to achieve both maximal stability in biological fluids and increase selectivity toward folate receptor α expressing cells. The produced DODAC:MO:PEG liposomes were highly effective in RNA complexation (close to 100%), and the resulting lipoplexes also demonstrated high stability in conditions simulating their administration by intravenous injection (physiological pH, high NaCl, heparin and fetal bovine serum concentrations). In addition, cell uptake of the PEG-folate-coated lipoplexes was significantly greater in folate receptor α positive breast cancer cells (39% for 25 µg/mL of lipid and 31% for 40 µg/mL) when compared with folate receptor α negative cells (31% for 25 µg/mL of lipid and 23% for 40 µg/mL) and to systems without PEG-folate (≈13% to 16% for all tested conditions), supporting their selectivity towards the receptor. Overall, the results support these systems as appealing vectors for selective delivery of siRNA to cancer cells by folate receptor α-mediated internalization, aiming at future therapeutic applications of interest. PMID:26340109

  6. Bounded Tamper Resilience

    DEFF Research Database (Denmark)

    Damgård, Ivan Bjerre; Faust, Sebastian; Mukherjee, Pratyay;

    2013-01-01

    a public tamper-proof common reference string. Finally, we explain how to boost bounded tampering and leakage resilience (as in 1. and 2. above) to continuous tampering and leakage resilience, in the so-called floppy model where each user has a personal hardware token (containing leak- and tamper...

  7. Active radar guides missile to its target: receptor-based targeted treatment of hepatocellular carcinoma by nanoparticulate systems.

    Science.gov (United States)

    Yan, Jing-Jun; Liao, Jia-Zhi; Lin, Ju-Sheng; He, Xing-Xing

    2015-01-01

    Patients with hepatocellular carcinoma (HCC) usually present at advanced stages and do not benefit from surgical resection, so drug therapy should deserve a prominent place in unresectable HCC treatment. But chemotherapy agents, such as doxorubicin, cisplatin, and paclitaxel, frequently encounter important problems such as low specificity and non-selective biodistribution. Recently, the development of nanotechnology led to significant breakthroughs to overcome these problems. Decorating the surfaces of nanoparticulate-based drug carriers with homing devices has demonstrated its potential in concentrating chemotherapy agents specifically to HCC cells. In this paper, we reviewed the current status of active targeting strategies for nanoparticulate systems based on various receptors such as asialoglycoprotein receptor, transferrin receptor, epidermal growth factor receptor, folate receptor, integrin, and CD44, which are abundantly expressed on the surfaces of hepatocytes or liver cancer cells. Furthermore, we pointed out their merits and defects and provided theoretical references for further research. PMID:25424700

  8. Aptamer-based single-molecule imaging of insulin receptors in living cells

    Science.gov (United States)

    Chang, Minhyeok; Kwon, Mijin; Kim, Sooran; Yunn, Na-Oh; Kim, Daehyung; Ryu, Sung Ho; Lee, Jong-Bong

    2014-05-01

    We present a single-molecule imaging platform that quantitatively explores the spatiotemporal dynamics of individual insulin receptors in living cells. Modified DNA aptamers that specifically recognize insulin receptors (IRs) with a high affinity were selected through the SELEX process. Using quantum dot-labeled aptamers, we successfully imaged and analyzed the diffusive motions of individual IRs in the plasma membranes of a variety of cell lines (HIR, HEK293, HepG2). We further explored the cholesterol-dependent movement of IRs to address whether cholesterol depletion interferes with IRs and found that cholesterol depletion of the plasma membrane by methyl-β-cyclodextrin reduces the mobility of IRs. The aptamer-based single-molecule imaging of IRs will provide better understanding of insulin signal transduction through the dynamics study of IRs in the plasma membrane.

  9. The Insect Ecdysone Receptor is a Good Potential Target for RNAi-based Pest Control

    OpenAIRE

    Yu, Rong; Xu, Xinping; Liang, Yongkang; Tian, Honggang; Pan, Zhanqing; Jin, Shouheng; Wang, Na; Zhang, Wenqing

    2014-01-01

    RNA interference (RNAi) has great potential for use in insect pest control. However, some significant challenges must be overcome before RNAi-based pest control can become a reality. One challenge is the proper selection of a good target gene for RNAi. Here, we report that the insect ecdysone receptor (EcR) is a good potential target for RNAi-based pest control in the brown planthopper Nilaparvata lugens, a serious insect pest of rice plants. We demonstrated that the use of a 360 bp fragment ...

  10. The Fitness Level Method with Tail Bounds

    OpenAIRE

    Witt, Carsten

    2013-01-01

    The fitness-level method, also called the method of f-based partitions, is an intuitive and widely used technique for the running time analysis of randomized search heuristics. It was originally defined to prove upper and lower bounds on the expected running time. Recently, upper tail bounds were added to the technique; however, these tail bounds only apply to running times that are at least twice as large as the expectation. We remove this restriction and supplement the fitness-level method ...

  11. Lightweight Distance Bounding Protocol against Relay Attacks

    Science.gov (United States)

    Kim, Jin Seok; Cho, Kookrae; Yum, Dae Hyun; Hong, Sung Je; Lee, Pil Joong

    Traditional authentication protocols are based on cryptographic techniques to achieve identity verification. Distance bounding protocols are an enhanced type of authentication protocol built upon both signal traversal time measurement and cryptographic techniques to accomplish distance verification as well as identity verification. A distance bounding protocol is usually designed to defend against the relay attack and the distance fraud attack. As there are applications to which the distance fraud attack is not a serious threat, we propose a streamlined distance bounding protocol that focuses on the relay attack. The proposed protocol is more efficient than previous protocols and has a low false acceptance rate under the relay attack.

  12. Dissociated sterol-based liver X receptor agonists as therapeutics for chronic inflammatory diseases.

    Science.gov (United States)

    Yu, Shan; Li, Sijia; Henke, Adam; Muse, Evan D; Cheng, Bo; Welzel, Gustav; Chatterjee, Arnab K; Wang, Danling; Roland, Jason; Glass, Christopher K; Tremblay, Matthew

    2016-07-01

    Liver X receptor (LXR), a nuclear hormone receptor, is an essential regulator of immune responses. Activation of LXR-mediated transcription by synthetic agonists, such as T0901317 and GW3965, attenuates progression of inflammatory disease in animal models. However, the adverse effects of these conventional LXR agonists in elevating liver lipids have impeded exploitation of this intriguing mechanism for chronic therapy. Here, we explore the ability of a series of sterol-based LXR agonists to alleviate inflammatory conditions in mice without hepatotoxicity. We show that oral treatment with sterol-based LXR agonists in mice significantly reduces dextran sulfate sodium colitis-induced body weight loss, which is accompanied by reduced expression of inflammatory markers in the large intestine. The anti-inflammatory property of these agonists is recapitulated in vitro in mouse lamina propria mononuclear cells, human colonic epithelial cells, and human peripheral blood mononuclear cells. In addition, treatment with LXR agonists dramatically suppresses inflammatory cytokine expression in a model of traumatic brain injury. Importantly, in both disease models, the sterol-based agonists do not affect the liver, and the conventional agonist T0901317 results in significant liver lipid accumulation and injury. Overall, these results provide evidence for the development of sterol-based LXR agonists as novel therapeutics for chronic inflammatory diseases.-Yu, S., Li, S., Henke, A., Muse, E. D., Cheng, B., Welzel, G., Chatterjee, A. K., Wang, D., Roland, J., Glass, C. K., Tremblay, M. Dissociated sterol-based liver X receptor agonists as therapeutics for chronic inflammatory diseases. PMID:27025962

  13. Thermostabilisation of the neurotensin receptor NTS1

    OpenAIRE

    Shibata, Yoko; White, Jim F.; Serrano-Vega, Maria J.; Magnani, Francesca; Aloia, Amanda L.; Grisshammer, Reinhard; Tate, Christopher G.

    2009-01-01

    Structural studies on G protein-coupled receptors (GPCRs) have been hampered for many years by their instability in detergent solution and by the number of potential conformations that receptors can adopt. Recently, the structures of the β1 and β2 adrenergic receptors and the adenosine A2a receptor were determined with antagonist bound, a receptor conformation that is thought to be more stable than the agonist-bound state. In contrast to these receptors, the neurotensin receptor NTS1 is much ...

  14. Imine-linked receptors decorated ZnO-based dye-sensitized solar cells

    Indian Academy of Sciences (India)

    SATBIR SINGH; AMARPAL SINGH; NAVNEET KAUR

    2016-10-01

    This study reports the synthesis, characterization and photophysical properties of imine-linked receptors decorated ZnO nanoparticles using wet precipitation method. Initially, polymer dye 3 was synthesized usingcondensation reaction between 2-furancarboxaldehyde 1 and polyethylenimine 2. The decoration of imine-linked receptors on ZnO nanoparticles (sample A) was characterized and investigated by X-ray diffraction, scanning electronmicroscope and dynamic light scattering spectroscopic studies. Further, polymer dye 3 was added to ruthenium chloride (RuCl$_3$) to form a polymer–ruthenium-based composite dye-capped ZnO nanoparticles (sample B).The optical properties of sample A were evaluated by fluorescence and UV–Vis spectroscopy. The samples A and B were further processed to dye-sensitized solar cells using wet precipitation method. The results of observationsrevealed that the addition of ruthenium–polymer dye molecules increased the light harvesting capacity of ZnO-based DSSCs. A maximum solar power to electricity conversion efficiency ($\\eta$) of 3.83% was recorded for sample B-based DSSCs with ruthenium–metal complex dye as a good photosensitizer. The recorded photovoltaic efficiency of sample B-based DSSCs was enhanced by 1.36% compared to sample A-based DSSCs.

  15. Redshift-space limits of bound structures

    CERN Document Server

    D"unner, R; Meza, A; Araya, P A; Quintana, H; D\\"unner, Rolando; Reisenegger, Andreas; Meza, Andr\\'es; Araya, Pablo A.; Quintana, Hern\\'an

    2006-01-01

    An exponentially expanding Universe, possibly governed by a cosmological constant, forces gravitationally bound structures to become more and more isolated, eventually becoming causally disconnected from each other and forming so-called "island universes". This new scenario reformulates the question about which will be the largest structures that will remain gravitationally bound, together with requiring a systematic tool that can be used to recognize the limits and mass of these structures from observational data, namely redshift surveys of galaxies. Here we present a method, based on the spherical collapse model and N-body simulations, by which we can estimate the limits of bound structures as observed in redshift space. The method is based on a theoretical criterion presented in a previous paper that determines the mean density contrast that a spherical shell must have in order to be marginally bound to the massive structure within it. Understanding the kinematics of the system, we translated the real-spac...

  16. Towards Secure Distance Bounding

    OpenAIRE

    Boureanu, Ioana; Mitrokotsa, Aikaterini; Vaudenay, Serge

    2013-01-01

    Relay attacks (and, more generally, man-in-the-middle attacks) are a serious threat against many access control and payment schemes. In this work, we present distance-bounding protocols, how these can deter relay attacks, and the security models formalizing these protocols. We show several pitfalls making existing protocols insecure (or at least, vulnerable, in some cases). Then, we introduce the SKI protocol which enjoys resistance to all popular attack-models and features provable security....

  17. Maps of Bounded Rationality

    OpenAIRE

    Kahneman, Daniel

    2002-01-01

    The work cited by the Nobel committee was done jointly with the late Amos Tversky (1937-1996) during a long and unusually close collaboration. Together, we explored the psychology of intuitive beliefs and choices and examined their bounded rationality. This essay presents a current perspective on the three major topics of our joint work: heuristics of judgment, risky choice, and framing effects. In all three domains we studied intuitions - thoughts and preferences that come to mind quickly an...

  18. Refined Error Bounds for Several Learning Algorithms

    OpenAIRE

    Hanneke, Steve

    2015-01-01

    This article studies the achievable guarantees on the error rates of certain learning algorithms, with particular focus on refining logarithmic factors. Many of the results are based on a general technique for obtaining bounds on the error rates of sample-consistent classifiers with monotonic error regions, in the realizable case. We prove bounds of this type expressed in terms of either the VC dimension or the sample compression size. This general technique also enables us to derive several ...

  19. Discovery of an Oxybenzylglycine Based Peroxisome Proliferator Activated Receptor Alpha Selective

    Energy Technology Data Exchange (ETDEWEB)

    Li, J.; Kennedy, L; Shi, Y; Tao, S; Ye, X; Chen, S; Wang, Y; Hernandez, A; Wang, W; et al.

    2010-01-01

    An 1,3-oxybenzylglycine based compound 2 (BMS-687453) was discovered to be a potent and selective peroxisome proliferator activated receptor (PPAR) {alpha} agonist, with an EC{sub 50} of 10 nM for human PPAR{alpha} and {approx}410-fold selectivity vs human PPAR{gamma} in PPAR-GAL4 transactivation assays. Similar potencies and selectivity were also observed in the full length receptor co-transfection assays. Compound 2 has negligible cross-reactivity against a panel of human nuclear hormone receptors including PPAR{delta}. Compound 2 demonstrated an excellent pharmacological and safety profile in preclinical studies and thus was chosen as a development candidate for the treatment of atherosclerosis and dyslipidemia. The X-ray cocrystal structures of the early lead compound 12 and compound 2 in complex with PPAR{alpha} ligand binding domain (LBD) were determined. The role of the crystal structure of compound 12 with PPAR{alpha} in the development of the SAR that ultimately resulted in the discovery of compound 2 is discussed.

  20. Extrasynaptic glutamate receptor activation as cellular bases for dynamic range compression in pyramidal neurons

    Directory of Open Access Journals (Sweden)

    Katerina D Oikonomou

    2012-08-01

    Full Text Available Repetitive synaptic stimulation overcomes the ability of astrocytic processes to clear glutamate from the extracellular space, allowing some dendritic segments to become submerged in a pool of glutamate. This dynamic arrangement activates extrasynaptic NMDA receptors located on dendritic shafts. We used voltage-sensitive and calcium-sensitive dyes to probe dendritic function in this glutamate-rich location. An excess of glutamate in the extrasynaptic space was achieved either by repetitive synaptic stimulation or by glutamate iontophoresis onto the dendrites of pyramidal neurons. Two successive activations of synaptic inputs produced a typical NMDA spike, whereas five successive synaptic inputs produced characteristic plateau potentials, reminiscent of cortical UP states. While NMDA spikes were coupled with brief calcium transients highly restricted to the glutamate input site, the dendritic plateau potentials were accompanied by calcium influx along the entire dendritic branch. Once initiated, the glutamate-mediated dendritic plateau potentials could not be interrupted by negative voltage pulses. Activation of extrasynaptic NMDA receptors in cellular compartments void of spines is sufficient to initiate and support plateau potentials. The only requirement for sustained depolarizing events is a surplus of free glutamate near a group of extrasynaptic receptors. Highly nonlinear dendritic spikes (plateau potentials are summed in a highly sublinear fashion at the soma, revealing the cellular bases of signal compression in cortical circuits. Extrasynaptic NMDA receptors provide pyramidal neurons with a function analogous to a dynamic range compression in audio engineering. They limit or reduce the volume of loud sounds (i.e. strong glut. inputs and amplify quiet sounds (i.e. glutamatergic inputs that barely cross the dendritic threshold for local spike initiation. Our data also explain why consecutive cortical UP states have uniform amplitudes in a

  1. Derivation of Upper Bounds on Optimization Time of Population-Based Evolutionary Algorithm on a Function with Fitness Plateaus Using Elitism Levels Traverse Mechanism

    CERN Document Server

    Ter-Sarkisov, Aram

    2012-01-01

    In this article we derive upper bounds on optimization time of the recombination algorithm solving a unimodal problem with plateaus of fitness using a tool we called Elitism Levels Traverse Mechanism. Our findings are asymptotically tight for different parameters of the algorithm and the problem, and we are able to recover some well-known bounds for test problems such as OneMax and Royal Roads. We also present find- ings on the limiting distribution of super-elite species in the population, something no-one seems to have done before in the EA community.

  2. 基于自然单元法的极限上限分析%UPPER-BOUND LIMIT ANALYSES BASED ON NATURAL ELEMENT METHOD

    Institute of Scientific and Technical Information of China (English)

    周书涛; 刘应华; 陈莘莘

    2012-01-01

    The natural element method (NEM) is a novel numerical method based on voronoi diagram and delaunay triangulation of the scattered points in problem domain,and its shape function is built upon the notion of natural neighbor interpolation. Compared with the moving least square (MLS) approximation used widely in many meshless methods,natural neighbor interpolation does not involve the complex matrix inversion,needs no artificial parameter but can improve the computational efficiency. The obtained shape function satisfies the property of Kronecker delta function, and this character results in the consequence that the essential boundary condition can be easily imposed as in finite element method (FEM). Meanwhile, the problems with discontinuous field functions likewise their discontinuous derivatives can be conveniently treated. According to the kinematic theorem of plastic limit analysis,this article applies the natural element method to upper bound limit analysis. The corresponding mathematical programming formulations are established and the computational codes are implemented to solve them. Several classical examples of limit analysis are adopted to verify the performance of these codes. Furthermore,the smoothing operations are also provided to calculate plastic dissipation work on the nodes by the similar treatment of stress smoothing operation,and the contours of plastic dissipation work at the limit states are displayed. The computational results show that utilizing natural element method to solve upper bound limit analysis problems possesses the advantage of good stability,high accuracy and fast convergence.%自然单元法是一种基于离散点集的Voronoi图和Delaunay三角化几何信息,以自然邻近插值为试函数的新型数值方法.相对于一般无网格法中常采用的移动最小二乘近似而言,自然邻近插值不涉及到复杂的矩阵求逆运算,更不需要任何人为的参数,可以提高计算效率.采用该方法构造的

  3. BOUNDING PYRAMIDS AND BOUNDING CONES FOR TRIANGULAR BEZIER SURFACES

    Institute of Scientific and Technical Information of China (English)

    Jian-song Deng; Fa-lai Chen; Li-li Wang

    2000-01-01

    This paper describes practical approaches on how to construct bounding pyramids and bounding cones for triangular Bézier surfaces. Examples are provided to illustrate the process of construction and comparison is made between various surface bounding volumes. Furthermore, as a starting point for the construction,we provide a way to compute hodographs of triangular Bézier surfaces and improve the algorithm for computing the bounding cone of a set of vectors.

  4. FRET-based localization of fluorescent protein insertions within the ryanodine receptor type 1.

    Directory of Open Access Journals (Sweden)

    Shweta A Raina

    Full Text Available Fluorescent protein (FP insertions have often been used to localize primary structure elements in mid-resolution 3D cryo electron microscopic (EM maps of large protein complexes. However, little is known as to the precise spatial relationship between the location of the fused FP and its insertion site within a larger protein. To gain insights into these structural considerations, Förster resonance energy transfer (FRET measurements were used to localize green fluorescent protein (GFP insertions within the ryanodine receptor type 1 (RyR1, a large intracellular Ca(2+ release channel that plays a key role in skeletal muscle excitation contraction coupling. A series of full-length His-tagged GFP-RyR1 fusion constructs were created, expressed in human embryonic kidney (HEK-293T cells and then complexed with Cy3NTA, a His-tag specific FRET acceptor. FRET efficiency values measured from each GFP donor to Cy3NTA bound to each His tag acceptor site were converted into intermolecular distances and the positions of each inserted GFP were then triangulated relative to a previously published X-ray crystal structure of a 559 amino acid RyR1 fragment. We observed that the chromophoric centers of fluorescent proteins inserted into RyR1 can be located as far as 45 Å from their insertion sites and that the fused proteins can also be located in internal cavities within RyR1. These findings should prove useful in interpreting structural results obtained in cryo EM maps using fusions of small fluorescent proteins. More accurate point-to-point distance information may be obtained using complementary orthogonal labeling systems that rely on fluorescent probes that bind directly to amino acid side chains.

  5. Prediction and Classification of Human G-protein Coupled Receptors Based on Support Vector Machines

    Institute of Scientific and Technical Information of China (English)

    Yun-Fei Wang; Huan Chen; Yan-Hong Zhou

    2005-01-01

    A computational system for the prediction and classification of human G-protein coupled receptors (GPCRs) has been developed based on the support vector machine (SVM) method and protein sequence information. The feature vectors used to develop the SVM prediction models consist of statistically significant features selected from single amino acid, dipeptide, and tripeptide compositions of protein sequences. Furthermore, the length distribution difference between GPCRsand non-GPCRs has also been exploited to improve the prediction performance.The testing results with annotated human protein sequences demonstrate that this system can get good performance for both prediction and classification of human GPCRs.

  6. Structure-Based Evolution of Subtype-Selective Neurotensin Receptor Ligands

    OpenAIRE

    Schaab, Carolin; Kling, Ralf Christian; Einsiedel, Jürgen; Hübner, Harald; Clark, Tim; Seebach, Dieter; Gmeiner, Peter

    2014-01-01

    Subtype-selective agonists of the neurotensin receptor NTS2 represent a promising option for the treatment of neuropathic pain, as NTS2 is involved in the mediation of μ-opioid-independent anti-nociceptive effects. Based on the crystal structure of the subtype NTS1 and previous structure–activity relationships (SARs) indicating a potential role for the sub-pocket around Tyr11 of NT(8–13) in subtype-specific ligand recognition, we have developed new NTS2-selective ligands. Starting from NT(8–1...

  7. Phytoceramide and sphingoid bases derived from brewer's yeast Saccharomyces pastorianus activate peroxisome proliferator-activated receptors

    Directory of Open Access Journals (Sweden)

    Mitsutake Susumu

    2011-08-01

    Full Text Available Abstract Background Peroxisome proliferator-activated receptors (PPARs are ligand-activated transcription factors that regulate lipid and glucose metabolism. PPARα is highly expressed in the liver and controls genes involved in lipid catabolism. We previously reported that synthetic sphingolipid analogs, part of which contains shorter-length fatty acid chains than natural sphingolipids, stimulated the transcriptional activities of PPARs. Sphingosine and dihydrosphingosine (DHS are abundant sphingoid bases, and ceramide and dihydroceramide are major ceramide species in mammals. In contrast, phytosphingosine (PHS and DHS are the main sphingoid bases in fungi. PHS and phytoceramide exist in particular tissues such as the epidermis in mammals, and involvement of ceramide species in PPARβ activation in cultured keratinocytes has been reported. The purpose of the present study is to investigate whether natural sphingolipids with C18 fatty acid and yeast-derived sphingoid bases activate PPARs as PPAR agonists. Method Lipids of brewer's yeast contain PHS- and DHS-based sphingolipids. To obtain the sphingoid bases, lipids were extracted from brewer's yeast and acid-hydrolyzed. The sphingoid base fraction was purified and quantified. To assess the effects of sphingolipids on PPAR activation, luciferase reporter assay was carried out. NIH/3T3 and human hepatoma (HepG2 cells were transfected with expression vectors for PPARs and retinoid × receptors, and PPAR responsive element reporter vector. When indicated, the PPAR/Gal4 chimera system was performed to enhance the credibility of experiments. Sphingolipids were added to the cells and the dual luciferase reporter assay was performed to determine the transcriptional activity of PPARs. Results We observed that phytoceramide increased the transcriptional activities of PPARs significantly, whereas ceramide and dihydroceramide did not change PPAR activities. Phytoceramide also increased transactivation of

  8. 基于包围盒的可变形物体碰撞检测算法%Research on Deformable Objects Collision Detection Based on Bounding Box

    Institute of Scientific and Technical Information of China (English)

    王渊; 叶雪梅; 吕虎猛

    2011-01-01

    包围盒方法是当前虚拟现实技术中应用较广泛的碰撞检测算法。文中重点对包围盒算法中的轴向包围盒(AABB)法、方向包围盒(OBB)法和固定方向包包围盒(k-dops)法,从包围盒的构建、相交检测等方面做了详细分析,并从构造难度、相交测试复杂度、紧密性、变形体碰撞适用度、检测精度和应用范围等6个方面,对这3类方法进行了比较。根据比较结果,在应用中可选择性使用3类方法。%The bounding box method is a collision detection algorithm used widely in he current virtual reality technology.The paper analyzes in depth the axial bounding box(AABB) method,oriented bounding box(OBB) method and the fixed orientation package bounding bo

  9. Letter to the editor : Design-Based Versus Model-Based Sampling Strategies: Comment on R. J. Barnes' "Bounding the Required Sample Size for Geologic Site Characterization"

    NARCIS (Netherlands)

    Gruijter, de J.J.; Braak, ter C.J.F.

    1992-01-01

    Two fundamentally different sources of randomness exist on which design and inference in spatial sampling can be based: (a) variation that would occur on resampling the same spatial population with other sampling configurations generated by the same design, and (b) variation occurring on sampling ot

  10. Regularity of Bound States

    DEFF Research Database (Denmark)

    Faupin, Jeremy; Møller, Jacob Schach; Skibsted, Erik

    2011-01-01

    We study regularity of bound states pertaining to embedded eigenvalues of a self-adjoint operator H, with respect to an auxiliary operator A that is conjugate to H in the sense of Mourre. We work within the framework of singular Mourre theory which enables us to deal with confined massless Pauli......–Fierz models, our primary example, and many-body AC-Stark Hamiltonians. In the simpler context of regular Mourre theory, our results boil down to an improvement of results obtained recently in [8, 9]....

  11. Blog life: Entropy Bound

    Science.gov (United States)

    Steinberg, Peter

    2008-06-01

    Who is the blog written by? Peter Steinberg is a nuclear physicist at the Brookhaven National Laboratory in New York, US. He is acting project manager of the PHOBOS experiment, which used Brookhaven's Relativistic Heavy Ion Collider (RHIC) to search for unusual events produced during collisions between gold nuclei. He is also involved with the PHENIX experiment, which seeks to discover a new state of matter known as the quark-gluon plasma. In addition to his own blog Entropy Bound, Steinberg is currently blogging on a website that was set up last year to publicize the involvement of US scientists with the Large Hadron Collider (LHC) at CERN.

  12. Sequence-structure based phylogeny of GPCR Class A Rhodopsin receptors.

    Science.gov (United States)

    Kakarala, Kavita Kumari; Jamil, Kaiser

    2014-05-01

    Current methods of G protein coupled receptors (GPCRs) phylogenetic classification are sequence based and therefore inappropriate for highly divergent sequences, sharing low sequence identity. In this study, sequence structure profile based alignment generated by PROMALS3D was used to understand the GPCR Class A Rhodopsin superfamily evolution using the MEGA 5 software. Phylogenetic analysis included a combination of Neighbor-Joining method and Maximum Likelihood method, with 1000 bootstrap replicates. Our study was able to identify potential ligand association for Class A Orphans and putative/unclassified Class A receptors with no cognate ligand information: GPR21 and GPR52 with fatty acids; GPR75 with Neuropeptide Y; GPR82, GPR18, GPR141 with N-arachidonylglycine; GPR176 with Free fatty acids, GPR10 with Tachykinin & Neuropeptide Y; GPR85 with ATP, ADP & UDP glucose; GPR151 with Galanin; GPR153 and GPR162 with Adrenalin, Noradrenalin; GPR146, GPR139, GPR142 with Neuromedin, Ghrelin, Neuromedin U-25 & Thyrotropin-releasing hormone; GPR171 with ATP, ADP & UDP Glucose; GPR88, GPR135, GPR161, GPR101with 11-cis-retinal; GPR83 with Tackykinin; GPR148 with Prostanoids, GPR109b, GPR81, GPR31with ATP & UTP and GPR150 with GnRH I & GnRHII. Furthermore, we suggest that this study would prove useful in re-classification of receptors, selecting templates for homology modeling and identifying ligands which may show cross reactivity with other GPCRs as signaling via multiple ligands play a significant role in disease modulation. PMID:24503482

  13. Novel Bounds on Marginal Probabilities

    OpenAIRE

    Mooij, Joris M.; Kappen, Hilbert J

    2008-01-01

    We derive two related novel bounds on single-variable marginal probability distributions in factor graphs with discrete variables. The first method propagates bounds over a subtree of the factor graph rooted in the variable, and the second method propagates bounds over the self-avoiding walk tree starting at the variable. By construction, both methods not only bound the exact marginal probability distribution of a variable, but also its approximate Belief Propagation marginal (``belief''). Th...

  14. Tight Bernoulli tail probability bounds

    OpenAIRE

    Dzindzalieta, Dainius

    2014-01-01

    The purpose of the dissertation is to prove universal tight bounds for deviation from the mean probability inequalities for functions of random variables. Universal bounds shows that they are uniform with respect to some class of distributions and quantity of variables and other parameters. The bounds are called tight, if we can construct a sequence of random variables, such that the upper bounds are achieved. Such inequalities are useful for example in insurance mathematics, for constructing...

  15. Error bounds for set inclusions

    Institute of Scientific and Technical Information of China (English)

    ZHENG; Xiyin(郑喜印)

    2003-01-01

    A variant of Robinson-Ursescu Theorem is given in normed spaces. Several error bound theorems for convex inclusions are proved and in particular a positive answer to Li and Singer's conjecture is given under weaker assumption than the assumption required in their conjecture. Perturbation error bounds are also studied. As applications, we study error bounds for convex inequality systems.

  16. Bounded Fixed-Point Iteration

    DEFF Research Database (Denmark)

    Nielson, Hanne Riis; Nielson, Flemming

    1992-01-01

    they obtain a quadratic bound. These bounds are shown to be tight. Specializing the case of strict and additive functions to functionals of a form that would correspond to iterative programs they show that a linear bound is tight. This is related to several analyses studied in the literature (including...

  17. Separable subgroups have bounded packing

    CERN Document Server

    Yang, Wen-yuan

    2010-01-01

    In this note, we prove that separable subgroups have bounded packing in ambient groups. The notion bounded packing was introduced by Hruska-Wise \\cite{HrWi} and in particular, our result confirms a conjecture in \\cite{HrWi} which states each subgroup of a virtually polycyclic group has the bounded packing property.

  18. Development of surface-based assays for transmembrane proteins: selective immobilization of functional CCR5, a G protein-coupled receptor.

    Science.gov (United States)

    Silin, Vitalii I; Karlik, Evan A; Ridge, Kevin D; Vanderah, David J

    2006-02-15

    A general method to develop surface-based assays for transmembrane (TM) receptor function(s) without the need to isolate, purify, and reconstitute the proteins is presented. Based on the formation of an active surface that selectively immobilizes membrane vesicles, the method is illustrated using the chemokine receptor CCR5, a member of the largest family of cell surface eukaryotic TM proteins, the G protein-coupled receptors (GPCRs). The method begins with a protein-resistant surface containing a low percentage (1-5%) of surface-bound biotin on gold as the initial template. Surface plasmon resonance (SPR) data show specific immobilization of functional CCR5 after the initial template is activated by immobilization of rho 1D4 antibody, an anti-rhodopsin monoclonal antibody specific for the carboxyl terminal nine amino acids on bovine rhodopsin that had been engineered into the carboxyl terminus of CCR5, and exposure to vesicles obtained from mammalian cells transfected with a synthetic human CCR5 gene. Activation of the initial template is effected by sequential immobilization of avidin, which binds to the biotin in the initial template, a biotinylated goat anti-mouse immunoglobulin G (Bt-IgG), which binds to the avidin binding sites distal to the surface and the F(c) portion of the rho 1D4 antibody through its F(ab) region(s) and finally rho 1D4. This approach establishes a broad outline for the development and application of various assays for CCR5 functions. SPR data also showed that vesicle immobilization could be achieved through an integrin-integrin antibody interaction after activation of the initial template with a goat anti-human integrin beta1 antibody. These results suggest that the generic nature of the initial platform and flexibility of the subsequent surface activation for specific immobilization of membrane vesicles can be applied to the development of assays for other GPCRs or TM receptors for which antibodies are available or can be engineered to

  19. Towards Bounded Infeasible Code Detection

    CERN Document Server

    Christ, Jürgen; Schäf, Martin

    2012-01-01

    A first step towards more reliable software is to execute each statement and each control-flow path in a method once. In this paper, we present a formal method to automatically compute test cases for this purpose based on the idea of a bounded infeasible code detection. The method first unwinds all loops in a program finitely often and then encodes all feasible executions of the loop-free programs in a logical formula. Helper variables are introduced such that a theorem prover can reconstruct the control-flow path of a feasible execution from a satisfying valuation of this formula. Based on this formula, we present one algorithm that computes a feasible path cover and one algorithm that computes a feasible statement cover. We show that the algorithms are complete for loop-free programs and that they can be implemented efficiently. We further provide a sound algorithm to compute procedure summaries which makes the method scalable to larger programs.

  20. Cost-Benefit Analysis of Nanoparticle Albumin-Bound Paclitaxel versus Solvent-Based Paclitaxel for the Treatment of Metastatic Breast Cancer in the United States

    Science.gov (United States)

    Vichansavakul, Kittaya

    Breast cancer is the second leading cause of death among women in the US. Although early detection and treatment help to increase survival rates, some unfortunate patients develop metastatic breast cancer that has no cure. Palliative treatment is the main objective in this group of patients in order to prolong life and reduce toxicities from interventions. In the advancement of treatment for metastatic breast cancer, solvent-based paclitaxel has been widely used. However, solvent-based paclitaxel often causes adverse reactions. Therefore, researchers have developed a new chemotherapy based on nanotechnology. One of these drugs is the Nanoparticle albumin-bound Paclitaxel. This nanodrug aims to increase therapeutic index by reducing adverse reactions from solvents and to improve efficacy of conventional cytotoxic chemotherapy. Breast cancer is a disease with high epidemiological and economic burden. The treatment of metastatic breast cancer has not only high direct costs but also high indirect costs. Breast cancer affects mass populations, especially women younger than 50 years of age. It relates to high indirect costs due to lost productivity and premature death because the majority of these patients are in the workforce. Because of the high cost of breast cancer therapies and short survival rates, the question is raised whether the costs and benefits are worth paying or not. Due to the rising costs in healthcare and new financing policies that have been developed to address this issue, economic evaluation is an important aspect of the development and use of any new interventions. To guide policy makers on how to allocate limited healthcare resources in the most efficient and effective manner, many economic evaluation methods can be used to measure the costs, benefits, and impacts of healthcare innovations. Currently, economic evaluation and health outcomes studies have focused greatly on cost-effectiveness and cost-utility analysis. However, the previous studies

  1. Multiresidue Method for Analysis of β Agonists in Swine Urine by Enzyme Linked Receptor Assay Based on β2 Adrenergic Receptor Expressed in HEK293 Cells.

    Directory of Open Access Journals (Sweden)

    Jian Wang

    Full Text Available A novel enzyme-linked receptor assay (ELRA based on β2-adrenergic receptor (β2-AR has been developed for rapid and high-throughput detection of β-adrenergic agonists (β-agonists in urine. Human embryonic kidney cells (HEK293 were introduced as the expression system to enhance the functionality of the recombinant β2-AR, and the attempt to detect β-agonists in swine urine using such approaches was accomplished unprecedentedly. In this article, a recombinant porcine β2-AR was produced in the inner membrane of HEK293 cells and purified from crude membrane protein by nickel-nitrilotriacetic acid affinity chromatography. After activity identification, the recombinant receptor was used in the development of direct competitive ELRA. Several parameters such as blocking buffer and blocking process were optimized and the performance of the system was determined. The IC50 concentrations of clenbuterol, salbutamol, and ractopamine were 34, 53 and 63 μg/L, and the average recovery rates were 68.2%, 60.3% and 65.5%, respectively. ELRA based on β2-AR shows a series of advantages such as safety, easy operation, and high efficiency, making it promising for the rapid screening of β-agonists in animal urine.

  2. Validation of a Flow Cytometry Based Binding Assay for Evaluation of Monoclonal Antibody Recognizing EGF Receptor

    Science.gov (United States)

    Cedeño-Arias, Mercedes; Sánchez-Ramírez, Javier; Blanco-Santana, Rancés; Rengifo-Calzado, Enrique

    2011-01-01

    An ideal test used to characterize a product must be appropriate for the measurement of product quality, manufacturing consistency, product stability, and comparability studies. Flow cytometry has been successfully applied to the examination of antibodies and receptors on membrane surfaces; however, to date, the analytical validation of cytometry based assays is limited. Here we report on the validation of a flow cytometry-based assay used in the evaluation of nimotuzumab binding to cells over-expressing EGFR on cell surface. The assay was validated by examining, assay robustness, specificity, repeatability and intermediate precision. The assay was highly specific, robust for all studied factors except for cell fixation with 1% paraformaldehyde and met criteria for precision with RSD < 2%. In addition the assay has stability-indicating properties evidenced by the ability to detect changes in mAb degraded samples. Most importantly, the assay demonstrated to be useful for its intended use. PMID:21886904

  3. Biotinylation of the Fcγ receptor ectodomains by mammalian cell co-transfection: application to the development of a surface plasmon resonance-based assay.

    Science.gov (United States)

    Dorion-Thibaudeau, July; St-Laurent, Gilles; Raymond, Céline; De Crescenzo, Gregory; Durocher, Yves

    2016-02-01

    We here report the production of four biotinylated Fcγ receptor (FcγR) ectodomains and their subsequent stable capture on streptavidin-biosensor surfaces. For receptor biotinylation, we first describe an in-cell protocol based on the co-transfection of two plasmids corresponding to one of the FcγR ectodomains and the BirA enzyme in mammalian cells. This strategy is compared with a standard sequential in vitro enzymatic biotinylation with respect to biotinylation level and yield. Biotinylated FcγR ectodomains that have been prepared with both strategies are then compared by analytical ultracentrifugation and surface plasmon resonance (SPR) analyses. Overall, we demonstrate that in-cell biotinylation is an interesting alternative to standard biotinylation protocol, as it requires less purification steps while yielding higher titers. Finally, biotin-tagged FcγRs produced with the in-cell approach are successfully applied to the development of SPR-based assays to evaluate the impact of the glycosylation pattern of monoclonal antibodies on their interaction with CD16a and CD64. In that endeavor, we unambiguously observe that highly galactosylated trastuzumab (TZM-gal), non-glycosylated trastuzumab (TZM-NG), and reference trastuzumab are characterized by different kinetic profiles upon binding to CD16a and CD64 that had been captured at the biosensor surface via their biotin tag. More precisely, while TZM-NG binding to CD16a was not detected, TZM-gal formed a more stable complex with CD16a than our reference TZM. In contrast, both glycosylated TZM bound to captured CD64 in a stable and similar fashion, whereas the interaction of their non-glycosylated form with CD64 was characterized by a higher dissociation rate. PMID:26762306

  4. Theory-based analysis of clinical efficacy of triptans using receptor occupancy

    OpenAIRE

    Tokuoka, Kentaro; Takayanagi, Risa; Suzuki, Yuji; Watanabe, Masayuki; Kitagawa, Yasuhisa; Yamada, Yasuhiko

    2014-01-01

    Background Triptans, serotonin 5-HT1B/1D receptor agonists, exert their action by targeting serotonin 5-HT1B/1D receptors, are used for treatment of migraine attack. Presently, 5 different triptans, namely sumatriptan, zolmitriptan, eletriptan, rizatriptan, and naratriptan, are marketed in Japan. In the present study, we retrospectively analyzed the relationships of clinical efficacy (headache relief) in Japanese and 5-HT1B/1D receptor occupancy (Φ1B and Φ1D). Receptor occupancies were calcul...

  5. Formation of "bound

    Science.gov (United States)

    Nowak, K.; Kästner, M.; Miltner, A.

    2009-04-01

    During degradation of organic pollutants in soil, metabolites, microbial biomass, CO2and "bound" residues ("non-extractable" residues in soil organic matter) are formed. Enhanced transformation of these contaminants into "bound" residues has been proposed as an alternative remediation method for polluted soils. However, this kind of residues may pose a potential risk for the environment due to their chemical structure and possible remobilization under different conditions. Therefore particular attention is given actually to "bound" residues. Part of these non-extractable residues may be "biogenic," because microorganisms use the carbon from the pollutant to form their biomass components (fatty acids, amino acids, amino sugars), which subsequently may be incorporated into soil organic matter. Furthermore, the CO2 originating from mineralization of xenobiotics, can be re-assimilated by microorganisms and also incorporated into "biogenic residue". The hazard posed by "bound" residues may be overestimated because they are "biogenic" (contain microbial fatty acids and amino acids). The knowledge about the pathways of "biogenic residue" formation is necessary for a proper assessment of the fate of tested pollutants and their turnover in the soil environment. Moreover, these data are needed to establish the realistic degradation rates of the contaminants in soil. The main objectives of this study are: to quantify the extent of "biogenic residue" (fatty acids, amino acids, amino sugars) formation during the degradation of a model pollutant (2,4-dichlorophenoxyacetic acid = 2,4-D) and during CO2 assimilation by microorganisms and to evaluate which components are mainly incorporated into "bound" residues. To investigate the extent of "biogenic residue" formation in soil during the degradation of 2,4-D, experiments with either 14C-U-ring and 13C6-2,4-D or carboxyl-14C 2,4-D were performed. The incubation experiments were performed according to OECD test guideline 307, in the

  6. Synthesis and Biological Evaluation of Thiophene-Based Cannabinoid Receptor Type 2 Radiotracers for PET Imaging

    Directory of Open Access Journals (Sweden)

    Ahmed Haider

    2016-07-01

    Full Text Available Over the past two decades, our understanding of the endocannabinoid system has greatly improved due to the wealth of results obtained from exploratory studies. Currently, two cannabinoid receptor subtypes have been well characterized. The cannabinoid receptor type 1 (CB1 is widely expressed in the central nervous system, while the levels of the cannabinoid receptor type 2 (CB2 in the brain and spinal cord of healthy individuals are relatively low. However, recent studies demonstrated a CB2 upregulation on activated microglia upon neuroinflammation, an indicator of neurodegeneration. Our research group aims to develop a suitable positron emission tomography (PET tracer to visualize the CB2 receptor in patients suffering from neurodegenerative diseases. Herein we report two novel thiophene-based 11C-labeled PET ligands designated [11C]AAT-015 and [11C]AAT-778. The reference compounds were synthesized using Gewald reaction conditions to obtain the aminothiophene intermediates, followed by amide formation. Saponification of the esters provided their corresponding precursors. Binding affinity studies revealed Ki values of 3.3 ± 0.5 nM (CB2 and 1.0 ± 0.2 µM (CB1 for AAT-015. AAT-778 showed similar Ki values of 4.3 ± 0.7 nM (CB2 and 1.1 ± 0.1 µM (CB1. Radiosynthesis was carried out under basic conditions using [11C]iodomethane as methylating agent. After semi-preparative HPLC purification both radiolabeled compounds were obtained in 99% radiochemical purity and the radiochemical yields ranged from 12 to 37%. Specific activity was between 96 - 449 GBq/µmol for both tracers. In order to demonstrate CB2 specificity of [11C]AAT-015 and [11C]AAT-778, we carried out autoradiography studies using CB2-positive mouse/rat spleen tissues. The obtained results revealed unspecific binding in spleen tissue that was not blocked by an excess of CB2-specific ligand GW402833. For in vivo analysis, [11C]AAT-015 was administered to healthy rats via tail

  7. Synthesis and Biological Evaluation of Thiophene-Based Cannabinoid Receptor Type 2 Radiotracers for PET Imaging

    Science.gov (United States)

    Haider, Ahmed; Müller Herde, Adrienne; Slavik, Roger; Weber, Markus; Mugnaini, Claudia; Ligresti, Alessia; Schibli, Roger; Mu, Linjing; Mensah Ametamey, Simon

    2016-01-01

    Over the past two decades, our understanding of the endocannabinoid system has greatly improved due to the wealth of results obtained from exploratory studies. Currently, two cannabinoid receptor subtypes have been well-characterized. The cannabinoid receptor type 1 (CB1) is widely expressed in the central nervous system, while the levels of the cannabinoid receptor type 2 (CB2) in the brain and spinal cord of healthy individuals are relatively low. However, recent studies demonstrated a CB2 upregulation on activated microglia upon neuroinflammation, an indicator of neurodegeneration. Our research group aims to develop a suitable positron emission tomography (PET) tracer to visualize the CB2 receptor in patients suffering from neurodegenerative diseases. Herein we report two novel thiophene-based 11C-labeled PET ligands designated [11C]AAT-015 and [11C]AAT-778. The reference compounds were synthesized using Gewald reaction conditions to obtain the aminothiophene intermediates, followed by amide formation. Saponification of the esters provided their corresponding precursors. Binding affinity studies revealed Ki-values of 3.3 ± 0.5 nM (CB2) and 1.0 ± 0.2 μM (CB1) for AAT-015. AAT-778 showed similar Ki-values of 4.3 ± 0.7 nM (CB2) and 1.1 ± 0.1 μM (CB1). Radiosynthesis was carried out under basic conditions using [11C]iodomethane as methylating agent. After semi-preparative HPLC purification both radiolabeled compounds were obtained in 99% radiochemical purity and the radiochemical yields ranged from 12 to 37%. Specific activity was between 96 and 449 GBq/μmol for both tracers. In order to demonstrate CB2 specificity of [11C]AAT-015 and [11C]AAT-778, we carried out autoradiography studies using CB2-positive mouse/rat spleen tissues. The obtained results revealed unspecific binding in spleen tissue that was not blocked by an excess of CB2-specific ligand GW402833. For in vivo analysis, [11C]AAT-015 was administered to healthy rats via tail-vein injection

  8. 3D-QSAR and docking studies of estrogen compounds based on estrogen receptor β

    Institute of Scientific and Technical Information of China (English)

    YANG XuShu; WANG XiaoDong; LUO Si; JI Li; QIN Liang; LI Rong; SUN Cheng; WANG LianSheng

    2009-01-01

    Close attention has been paid to estrogen compounds because these chemicals may pose a serious threat to the health of humans and wildlife.Estrogen receptor (ER) exists as two subtypes,ERo and ERβ.The difference in amino acids sequence of the binding sites of ERo and ERβ might lead to a result that some synthetic estrogens and naturally occurring steroidal ligands have different relative affinities and binding modes for ERa and ERβ.In this investigation,comparative molecular similarity indices analysis (CoMSIA) was performed on 50 estrogen compounds binding ERβ to find out the structural relationship with the activities.We also compared two alignment schemes employed in CoMSIA analysis,namely,atom-fit and receptor-based alignment,with respect to the predictive capability of their respective models for structurally diverse data sets.The model with the significant correlation and the best predictive power (R2=0.961,q2LOO=0.671,Rp2red=0.722) was achieved.The CoMSIA and docking results revealed the structural features related to an activity and provided an insight into molecular mechanisms of estrogenic activities for estrogen compounds.

  9. Receptor-Based Virtual Screening of EGFR Kinase Inhibitors from the NCI Diversity Database

    Directory of Open Access Journals (Sweden)

    Kiattawee Choowongkomon

    2010-06-01

    Full Text Available Epidermal growth factor receptor (EGFR abnormalities have been associated with several types of human cancer. The crystal structures of its tyrosine kinase domain (EGFR-TK complexed with small molecule inhibitors revealed the kinase inhibition modes, prompting us to search for novel anti-cancer drugs. A total of 1,990 compounds from the National Cancer Institute (NCI diversity set with nonredundant structures have been tested to inhibit cancer cell lines with unknown mechanism. Cancer inhibition through EGFR-TK is one of the mechanisms of these compounds. In this work, we performed receptor-based virtual screening against the NCI diversity database. Using two different docking algorithms, AutoDock and Gold, combined with subsequent post-docking analyses, we found eight candidate compounds with high scoring functions that all bind to the ATP-competitive site of the kinase. None of these compounds belongs to the main group of the currently known EGFR-TK inhibitors. Binding mode analyses revealed that the way these compounds complexed with EGFR-TK differs from quinazoline inhibitor binding and the interaction mainly involves hydrophobic interactions. Also, the common kinase-inhibitor (NH---N and CO---HC hydrogen bonds between the hinge region and the hit compounds are rarely observed. Our results suggest that these molecules could be developed as novel lead compounds in anti-cancer drug design.

  10. 3D-QSAR and docking studies of estrogen compounds based on estrogen receptor β

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Close attention has been paid to estrogen compounds because these chemicals may pose a serious threat to the health of humans and wildlife. Estrogen receptor (ER) exists as two subtypes, ERα and ERβ. The difference in amino acids sequence of the binding sites of ERα and ERβ might lead to a result that some synthetic estrogens and naturally occurring steroidal ligands have different relative affinities and binding modes for ERα and ERβ. In this investigation, comparative molecular similarity indices analysis (CoMSIA) was performed on 50 estrogen compounds binding ERβ to find out the structural relationship with the activities. We also compared two alignment schemes employed in CoMSIA analy-sis, namely, atom-fit and receptor-based alignment, with respect to the predictive capability of their respective models for structurally diverse data sets. The model with the significant correlation and the best predictive power (R2=0.961, qL 2OO=0.671, RP 2red=0.722) was achieved. The CoMSIA and docking results revealed the structural features related to an activity and provided an insight into molecular mechanisms of estrogenic activities for estrogen compounds.

  11. Triazine-based vanilloid 1 receptor open channel blockers: design, synthesis, evaluation, and SAR analysis.

    Science.gov (United States)

    Vidal-Mosquera, Miquel; Fernández-Carvajal, Asia; Moure, Alejandra; Valente, Pierluigi; Planells-Cases, Rosa; González-Ros, José M; Bujons, Jordi; Ferrer-Montiel, Antonio; Messeguer, Angel

    2011-11-10

    The thermosensory transient receptor potential vanilloid 1 channel (TRPV1) is a polymodal receptor activated by physical and chemical stimuli. TRPV1 activity is drastically potentiated by proinflammatory agents released upon tissue damage. Given the pivotal role of TRPV1 in human pain, there is pressing need for improved TRPV1 antagonists, the development of which will require identification of new pharmacophore scaffolds. Uncompetitive antagonists acting as open-channel blockers might serve as activity-dependent blockers that preferentially modulate the activity of overactive channels, thus displaying fewer side effects than their competitive counterparts. Herein we report the design, synthesis, biological evaluation, and SAR analysis of a family of triazine-based compounds acting as TRPV1 uncompetitive antagonists. We identified the triazine 8aA as a potent, pure antagonist that inhibits TRPV1 channel activity with nanomolar efficacy and strong voltage dependency. It represents a new class of activity-dependent TRPV1 antagonists and may serve as the basis for lead optimization in the development of new analgesics. PMID:21950613

  12. A Fixed-point Technique of Wavelet Transform Base on Bounded Input Bounded Output (BIBO) Plus Value in JPEG2000 Algorithm%JPEG2000算法中基于有界输入有界输出(BIBO)增益控制的小波变换定点实现技术

    Institute of Scientific and Technical Information of China (English)

    张静; 李云松; 郭杰; 王柯俨; 吴成柯

    2012-01-01

    A new efficient technique using the compatible hardware framework to realize the integer 5/3 wavelet transform and 9/7 wavelet transform is proposed. The bit depth of the temp coefficients in the wavelet transform is based on the Bounded Input Bounded Output (BIBO) plus value of 9/7 wavelet transform, at the same time, the quantization value of 9/7 wavelet transform and how to do quantization is decided by BIBO puls value of 5/3 wavelet transform. Finally, both the coefficients of 5/3 wavelet transform and 9/7 wavelet transform are saved in the same memories. The proposed technique not only saves the hardware memory resource and computational complexity of the wavelet transform module, but also saves the hardware memory resource and computational complexity of the bitplane arithmetric coding based on the context module and post-compression rate-distortion optimization module.%该文提出一种在JPEG2000算法中兼容5/3小波变换和9/7小波变换高效硬件定点实现技术.所提出的技术使用9/7提升小波变换的有界输入有界输出(Bounded Input Bounded Output,BIBO)增益来确定小波变换中间值的存储位深,使用5/3提升小波变换的BIBO增益来确定9/7提升小波变换中量化参数的选择方式和量化的实现方式,最终使用同一存储空间来存放定点5/3提升小波变换和定点9/7提升小波变换系数.该文提出的技术不仅大大节省了JPEG2000算法中小波实现模块中的硬件存储资源和算法计算量,而且也节省了后续基于上下文的位平面算术编码模块和率失真优化截取模块的存储资源和算法计算量.

  13. Bounds to the conductivity of some two-component composites

    Science.gov (United States)

    Helsing, Johan

    1993-02-01

    Calculation of third-order bounds to the conductivity of isotropic two-component composites is discussed. Coincidence of the Beran bounds and bounds derived using trial fields based on the solution of a single-body electrostatic boundary-value problem is demonstrated for a random distribution of impenetrable ellipsoids. This extends a proof of Beasley and Torquato [J. Appl. Phys. 60, 3576 (1986)]. A structural parameter related to third-order bounds is calculated for a face-centered cubic array of cubes in a matrix. For an array of rectangular blocks an upper bound in one direction is derived. This bound, and its two-dimensional analogs, become very sharp in the limit of strong inhomogeneity. Improved third- and fourth-order bounds for the three-dimensional checkerboard are presented.

  14. Performance Bounds of Quaternion Estimators.

    Science.gov (United States)

    Xia, Yili; Jahanchahi, Cyrus; Nitta, Tohru; Mandic, Danilo P

    2015-12-01

    The quaternion widely linear (WL) estimator has been recently introduced for optimal second-order modeling of the generality of quaternion data, both second-order circular (proper) and second-order noncircular (improper). Experimental evidence exists of its performance advantage over the conventional strictly linear (SL) as well as the semi-WL (SWL) estimators for improper data. However, rigorous theoretical and practical performance bounds are still missing in the literature, yet this is crucial for the development of quaternion valued learning systems for 3-D and 4-D data. To this end, based on the orthogonality principle, we introduce a rigorous closed-form solution to quantify the degree of performance benefits, in terms of the mean square error, obtained when using the WL models. The cases when the optimal WL estimation can simplify into the SWL or the SL estimation are also discussed. PMID:25643416

  15. Information bounds for Gaussian copulas

    CERN Document Server

    Hoff, Peter D; Wellner, Jon A

    2011-01-01

    Often of primary interest in the analysis of multivariate data are the copula parameters describing the dependence among the variables, rather than the univariate marginal distributions. Since the ranks of a multivariate dataset are invariant to changes in the univariate marginal distributions, rank-based procedures are natural candidates as semiparametric estimators of copula parameters. Asymptotic information bounds for such estimators can be obtained from an asymptotic analysis of the rank likelihood, i.e. the probability of the multivariate ranks. In this article, we obtain limiting normal distributions of the rank likelihood for Gaussian copula models. Our results cover models with structured correlation matrices, such as exchangeable, autoregressive and circular correlation, as well as unstructured correlation matrices. For all Gaussian copula models, the limiting distribution of the rank likelihood ratio is shown to be equal to that of a parametric likelihood ratio for an appropriately chosen multivari...

  16. 有限理性下的进化博弈与合作机制%Evolutionary game and cooperation mechanisms based on bounded rationality

    Institute of Scientific and Technical Information of China (English)

    王先甲; 刘伟兵

    2011-01-01

    The paper indicates that complete rationality is the basic assumption of traditional game theory and leads to limitations in dynamic game. It was pointed out that bounded rationality and replicator dynamics are the foundation of multi-person selection, and the evolutionary learning methods for improving bounded rationality and selection mechanism in dynamic game were explored. In addition, the essence of evolutionary game and evolutionary stable equilibrium was revealed and the difference between traditional game theory and evolutionary game theory was described. The problems to be studied about evolutionary game theory and cooperation mechanisms were proposed and some concerned research results under the assumption of bounded rationality were provided.%在介绍传统博弈论基本假设的基础上,指出完全理性是传统博弈论均衡选择的最基本假设和完全理性在动态博弈中的局限,提出有限理性与动态学习是动态博弈中多个智能体选择的基础;探讨了不断改善有限理性的进化学习方法和智能体选择机制;解释了进化博弈与进化稳定策略的本质;指出了传统博弈论与进化博弈论的区别;提出了有限理性下进化博弈与合作机制研究的问题,给出了有限理性下进化博弈与合作机制的研究结果.

  17. Automatic landslide length and width estimation based on the geometric processing of the bounding box and the geomorphometric analysis of DEMs

    Science.gov (United States)

    Niculiţǎ, Mihai

    2016-08-01

    The morphology of landslides is influenced by the slide/flow of the material downslope. Usually, the distance of the movement of the material is greater than the width of the displaced material (especially for flows, but also the majority of slides); the resulting landslides have a greater length than width. In some specific geomorphologic environments (monoclinic regions, with cuesta landforms type) or as is the case for some types of landslides (translational slides, bank failures, complex landslides), for the majority of landslides, the distance of the movement of the displaced material can be smaller than its width; thus the landslides have a smaller length than width. When working with landslide inventories containing both types of landslides presented above, the analysis of the length and width of the landslides computed using usual geographic information system techniques (like bounding boxes) can be flawed. To overcome this flaw, I present an algorithm which uses both the geometry of the landslide polygon minimum oriented bounding box and a digital elevation model of the landslide topography for identifying the long vs. wide landslides. I tested the proposed algorithm for a landslide inventory which covers 131.1 km2 of the Moldavian Plateau, eastern Romania. This inventory contains 1327 landslides, of which 518 were manually classified as long and 809 as wide. In a first step, the difference in elevation of the length and width of the minimum oriented bounding box is used to separate long landslides from wide landslides (long landslides having the greatest elevation difference along the length of the bounding box). In a second step, the long landslides are checked as to whether their length is greater than the length of flow downslope (estimated with a flow-routing algorithm), in which case the landslide is classified as wide. By using this approach, the area under the Receiver Operating Characteristic curve value for the classification of the long vs. wide

  18. Bounding approaches to system identification

    CERN Document Server

    Norton, John; Piet-Lahanier, Hélène; Walter, Éric

    1996-01-01

    In response to the growing interest in bounding error approaches, the editors of this volume offer the first collection of papers to describe advances in techniques and applications of bounding of the parameters, or state variables, of uncertain dynamical systems. Contributors explore the application of the bounding approach as an alternative to the probabilistic analysis of such systems, relating its importance to robust control-system design.

  19. Bounded Rationality in Transposition Processes

    DEFF Research Database (Denmark)

    Vollaard, Hans; Martinsen, Dorte Sindbjerg

    2014-01-01

    that concerns the organisation and financing of national healthcare systems. This article applies the perspective of bounded rationality to explain (irregularities in) the timely and correct transposition of EU directives. The cognitive and organisational constraints long posited by the bounded rationality...... perspective may affect the commonly employed explanatory factors of administrative capacities, misfit and the heterogeneity of preferences among veto players. To prevent retrospective rationalisation of the transposition process, this paper traces this process as it unfolded in Denmark and the Netherlands....... As bounded rationality is apparent in the transposition processes in these relatively well-organised countries, future transposition studies should devote greater consideration to the bounded rationality perspective....

  20. Accelerated structure-based design of chemically diverse allosteric modulators of a muscarinic G protein-coupled receptor.

    Science.gov (United States)

    Miao, Yinglong; Goldfeld, Dahlia Anne; Moo, Ee Von; Sexton, Patrick M; Christopoulos, Arthur; McCammon, J Andrew; Valant, Celine

    2016-09-20

    Design of ligands that provide receptor selectivity has emerged as a new paradigm for drug discovery of G protein-coupled receptors, and may, for certain families of receptors, only be achieved via identification of chemically diverse allosteric modulators. Here, the extracellular vestibule of the M2 muscarinic acetylcholine receptor (mAChR) is targeted for structure-based design of allosteric modulators. Accelerated molecular dynamics (aMD) simulations were performed to construct structural ensembles that account for the receptor flexibility. Compounds obtained from the National Cancer Institute (NCI) were docked to the receptor ensembles. Retrospective docking of known ligands showed that combining aMD simulations with Glide induced fit docking (IFD) provided much-improved enrichment factors, compared with the Glide virtual screening workflow. Glide IFD was thus applied in receptor ensemble docking, and 38 top-ranked NCI compounds were selected for experimental testing. In [(3)H]N-methylscopolamine radioligand dissociation assays, approximately half of the 38 lead compounds altered the radioligand dissociation rate, a hallmark of allosteric behavior. In further competition binding experiments, we identified 12 compounds with affinity of ≤30 μM. With final functional experiments on six selected compounds, we confirmed four of them as new negative allosteric modulators (NAMs) and one as positive allosteric modulator of agonist-mediated response at the M2 mAChR. Two of the NAMs showed subtype selectivity without significant effect at the M1 and M3 mAChRs. This study demonstrates an unprecedented successful structure-based approach to identify chemically diverse and selective GPCR allosteric modulators with outstanding potential for further structure-activity relationship studies. PMID:27601651

  1. Bound anionic states of adenine

    Energy Technology Data Exchange (ETDEWEB)

    Haranczyk, Maciej; Gutowski, Maciej S; Li, Xiang; Bowen, Kit H

    2007-03-20

    Anionic states of nucleic acid bases are involved in DNA damage by low-energy electrons and in charge transfer through DNA. Previous gas phase studies of free, unsolvated nucleic acid base parent anions probed only dipole-bound states, which are not present in condensed phase environments, but did not observe valence anionic states, which for purine bases, are thought to be adiabatically unbound. Contrary to this expectation, we have demonstrated that some thus far ignored tautomers of adenine, which result from enamine-imine transformations, support valence anionic states with electron vertical detachment energies as large as 2.2 eV, and at least one of these anionic tautomers is adiabatically bound. Moreover, we predict that the new anionic tautomers should also dominate in solutions and should be characterized by larger values of electron vertical detachment energy than the canonical valence anion. All of the new-found anionic tautomers might be formed in the course of dissociative electron attachment followed by a hydrogen atom attachment to a carbon atom, and they might affect the structure and properties of DNA and RNA exposed to low-energy electrons. The discovery of these valence anionic states of adenine was facilitated by the development of: (i) a new experimental method for preparing parent anions of nucleic acid bases for photoelectron experiments, and (ii) a new combinatorial/ quantum chemical approach for identification of the most stable tautomers of organic molecules. The computational portion of this work was supported by the: (i) Polish State Committee for Scientific Research (KBN) Grants: DS/8000-4-0140-7 (M.G.) and N204 127 31/2963 (M.H.), (ii) European Social Funds (EFS) ZPORR/2.22/II/2.6/ARP/U/2/05 (M.H.), and (iii) US DOE Office of Biological and Environmental Research, Low Dose Radiation Research Program (M.G.). M.H. holds the Foundation for Polish Science (FNP) award for young scientists. The calculations were performed at the Academic

  2. Call packing bound for overflow loss systems

    NARCIS (Netherlands)

    N.M. van Dijk; E. van der Sluis

    2009-01-01

    Finite loss queues with overflow naturally arise in a variety of communications structures. For these systems, there is no simple analytic expression for the loss probability. This paper proves and promotes easily computable bounds based on the so-called call packing principle. Under call packing, a

  3. Call packing bounds for overflow queues

    NARCIS (Netherlands)

    N.M. van Dijk; E. van der Sluis

    2004-01-01

    Finite queueing loss systems are studied with overflow. For these systems there is no simple analytic expression for the loss probability or throughput. This paper aims to prove and promote easily computable bounds as based upon the so-called call packing principle. Under call packing a standard pro

  4. A symmetric divergence measure and its bounds

    Directory of Open Access Journals (Sweden)

    K. C. Jain

    2011-12-01

    Full Text Available A new symmetric divergence measure is proposed which is useful in comparing two probability distributions. This non-parametric measure belongs to the Csiszar's $f$ divergence class. Its properties are studied and bounds are obtained in terms of some well known divergence measures. A numerical illustration based on the probability distribution is carried out.

  5. Improved lower bound for online strip packing

    NARCIS (Netherlands)

    Harren, Rolf; Kern, Walter

    2015-01-01

    We study the online strip packing problem and derive an improved lower bound of ρ ≥ 2.589... for the competitive ratio of this problem. The construction is based on modified “Brown-Baker-Katseff sequences” (Brown et al. in Acta Inform. 18:207–225, 1982) using only two types of rectangles. In additio

  6. On Quantum Capacity and its Bound

    OpenAIRE

    Ohya, Masanori; Volovich, Igor V.

    2004-01-01

    The quantum capacity of a pure quantum channel and that of classical-quantum-classical channel are discussed in detail based on the fully quantum mechanical mutual entropy. It is proved that the quantum capacity generalizes the so-called Holevo bound.

  7. Targeting c-kit receptor in neuroblastomas and colorectal cancers using stem cell factor (SCF)-based recombinant bacterial toxins.

    Science.gov (United States)

    Choudhary, Swati; Pardo, Alessa; Rosinke, Reinhard; Batra, Janendra K; Barth, Stefan; Verma, Rama S

    2016-01-01

    Autocrine activation of c-kit (KIT receptor tyrosine kinase) has been postulated to be a potent oncogenic driver in small cell lung cancer, neuroblastoma (NB), and poorly differentiated colorectal carcinoma (CRC). Although targeted therapy involving tyrosine kinase inhibitors (TKIs) such as imatinib mesylate is highly effective for gastrointestinal stromal tumor carrying V560G c-kit mutation, it does not show much potential for targeting wild-type KIT (WT-KIT). Our study demonstrates the role of stem cell factor (SCF)-based toxin conjugates for targeting WT-KIT-overexpressing malignancies such as NBs and CRCs. We constructed SCF-based recombinant bacterial toxins by genetically fusing mutated form of natural ligand SCF to receptor binding deficient forms of Diphtheria toxin (DT) or Pseudomonas exotoxin A (ETA') and evaluated their efficacy in vitro. Efficient targeting was achieved in all receptor-positive neuroblastoma (IMR-32 and SHSY5Y) and colon cancer cell lines (COLO 320DM, HCT 116, and DLD-1) but not in receptor-negative breast carcinoma cell line (MCF-7) thereby proving specificity. While dose- and time-dependent cytotoxicity was observed in both neuroblastoma cell lines, COLO 320DM and HCT 116 cells, only an anti-proliferative effect was observed in DLD-1 cells. We prove that these novel targeting agents have promising potential as KIT receptor tyrosine kinase targeting system.

  8. Development of a quantitative, cell-based, high-content screening assay for epidermal growth factor receptor modulators

    Institute of Scientific and Technical Information of China (English)

    Jue WANG; Xin XIE

    2007-01-01

    Aim: To develop a robust, cell-based, high-content screening (HCS) assay based on receptor internalization for the identification of novel modulators of the epidermal growth factor receptor (EGFR). Methods: Agonist-induced receptor internalization is part of the signaling cascade of EGFR. Fluorescent-tagged epidermal growth factor (EGF) was used to visualize the internalized receptorligand complex. The fluorescent intracellular spots were detected and measured with an ArrayScan HCS reader. Compounds that can competitively bind to EGFR or interfere with EGFR internalization process would result in a reduced number and intensity of intracellular fluorescent spots. This assay was validated,optimized, and applied to a large-scale screening of a library containing 48 000 synthetic compounds. Results: The competition between fluorescent EGF and unlabeled EGF reveals the IC50 of unlabeled EGF is approximately 0.2 nmol/L,which is comparable with other published reports. Thirteen compounds with a relatively high degree of interference with EGFR internalization were identified.One of the compounds was proven to be agonist of the EGFR since it induced phosphorylation of the receptor and extracellular signal-regulated protein kinase (ERK). Conclusion: This automated, objective, and easy-to-use assay provided abundant information, quantitative results, and demonstrated the potential use of HCS methods in searching membrane receptor modulators.

  9. Entropy Bounds, Holographic Principle and Uncertainty Relation

    Directory of Open Access Journals (Sweden)

    I. V. Volovich

    2001-06-01

    Full Text Available Abstract: A simple derivation of the bound on entropy is given and the holographic principle is discussed. We estimate the number of quantum states inside space region on the base of uncertainty relation. The result is compared with the Bekenstein formula for entropy bound, which was initially derived from the generalized second law of thermodynamics for black holes. The holographic principle states that the entropy inside a region is bounded by the area of the boundary of that region. This principle can be called the kinematical holographic principle. We argue that it can be derived from the dynamical holographic principle which states that the dynamics of a system in a region should be described by a system which lives on the boundary of the region. This last principle can be valid in general relativity because the ADM hamiltonian reduces to the surface term.

  10. Bounded link prediction in very large networks

    Science.gov (United States)

    Cui, Wei; Pu, Cunlai; Xu, Zhongqi; Cai, Shimin; Yang, Jian; Michaelson, Andrew

    2016-09-01

    Evaluating link prediction methods is a hard task in very large complex networks due to the prohibitive computational cost. However, if we consider the lower bound of node pairs' similarity scores, this task can be greatly optimized. In this paper, we study CN index in the bounded link prediction framework, which is applicable to enormous heterogeneous networks. Specifically, we propose a fast algorithm based on the parallel computing scheme to obtain all node pairs with CN values larger than the lower bound. Furthermore, we propose a general measurement, called self-predictability, to quantify the performance of similarity indices in link prediction, which can also indicate the link predictability of networks with respect to given similarity indices.

  11. Identification of naphthoylindoles acting on cannabinoid receptors based on their fragmentation patterns under ESI-QTOFMS.

    Science.gov (United States)

    Sekuła, Karolina; Zuba, Dariusz; Stanaszek, Roman

    2012-05-01

    'Herbal highs' have been advertised as legal and natural substitutes to cannabis, but a detailed examination of these products has revealed that the herbal matrix is laced with synthetic substances that mimic the effects of marijuana. Producers select the ingredients based on the results of scientific studies on the affinities of different chemicals to cannabinoid receptors. Naphthoylindoles have turned out to be the most popular class of substances identified in the products. Legal actions taken in order to tackle the problem of uncontrolled access to one substance have usually resulted in the marketing of derivatives or analogues. In the study, the mass spectral behavior of twelve synthetic cannabinoids from the naphthoylindole family under electrospray ionization (ESI) was investigated. LC-QTOFMS experiments were performed in three modes (low fragmentor voltage, high fragmentor voltage with/without collision energy), and they enabled the identification of protonated molecules and main ions. A general fragmentation pattern under this ionization method was proposed, and mechanisms of ion formation were discussed. The developed procedure allowed the determination of substituent groups of the core naphthoylindole structure and distinction between positional isomers. The obtained results were used for the prediction of the ESI-MS spectra for many naphthoylindoles with a high affinity to cannabinoid receptors. Similarities and differences between ESI-MS and electron impact-MS spectra of naphthoylindoles were discussed. The developed identification process was presented on an example of an analysis of an unknown herbal material, in which JWH-007 was finally identified. Knowledge of the fragmentation mechanisms of naphthoylindoles could also be used by other researchers for identification of unknown substances in this chemical family. PMID:22576877

  12. T cell receptor zeta allows stable expression of receptors containing the CD3gamma leucine-based receptor-sorting motif

    DEFF Research Database (Denmark)

    Dietrich, J; Geisler, C

    1998-01-01

    that the leucine-based motif in these complexes was inactive. In contrast, the CD4/CD3gamma chimeras did not associate with TCRzeta, and the leucine-based motif in these chimeras was constitutively active resulting in a high spontaneous internalization rate and low expression of the chimeras at the cell surface...

  13. 4-Nitrocatecholato iron(III) complexes of 2-aminomethyl pyridine-based bis(phenol) amine as structural models for catechol-bound 3,4-PCD

    Science.gov (United States)

    Safaei, Elham; Heidari, Sima; Wojtczak, Andrzej; Cotič, Patricia; Kozakiewicz, Anna

    2016-02-01

    Two nitrocatecholato(HNC) iron(III) complexes, [FeLAMPX(H-NC)]. NEt3, of the tetradendate ligand (2-aminomethylpyridine)bis(2-pyridylmethyl)amine (H2LAMPX) were synthesized and structurally characterized. These structural models for catechol-bound 3,4-PCD were characterized by IR, UV-vis, elemental analysis and magnetic measurements. X-ray crystallography studies revealed that in both complexes the iron(III) centers are distorted octahedral and coordinated by two phenolate oxygen's, two amine nitrogen's of the ligand and mono anionic nitrocatecholate group (HNC). The variable-temperature magnetic susceptibility studies revealed paramagnetic properties of the reported complexes. The effective magnetic moments for the complexes lie between 5.3 and 5.4 BM correspond to the reported values for high spin Fe(III) center. The ligand-centered oxidation and metal-centered reduction of complexes was studies using cyclic voltammetry (CV) technique.

  14. Mechanism-Based Pharmacokinetic-Pharmacodynamic Modeling of the Dopamine D-2 Receptor Occupancy of Olanzapine in Rats

    NARCIS (Netherlands)

    Johnson, Martin; Kozielska, Magdalena; Reddy, Venkatesh Pilla; Vermeulen, An; Li, Cheryl; Grimwood, Sarah; de Greef, Rik; Groothuis, Geny M. M.; Danhof, Meindert; Proost, Johannes H.

    2011-01-01

    A mechanism-based PK-PD model was developed to predict the time course of dopamine D-2 receptor occupancy (D2RO) in rat striatum following administration of olanzapine, an atypical antipsychotic drug. A population approach was utilized to quantify both the pharmacokinetics and pharmacodynamics of ol

  15. Family-based association analysis of beta(2)-adrenergic receptor polymorphisms in the Childhood Asthma Management Program

    NARCIS (Netherlands)

    Silverman, EK; Kwiatkowski, DJ; Sylvia, JS; Lazarus, R; Drazen, JM; Lange, C; Laird, NM; Weiss, ST

    2003-01-01

    Background: beta(2)-Adrenergic receptor (B2AR) polymorphisms have been associated with a variety of asthma-related phenotypes, but association results have been inconsistent across different studies. Objective: We sought to apply family-based association methods to individual single nucleotide polym

  16. Bounds for Asian basket options

    Science.gov (United States)

    Deelstra, Griselda; Diallo, Ibrahima; Vanmaele, Michèle

    2008-09-01

    In this paper we propose pricing bounds for European-style discrete arithmetic Asian basket options in a Black and Scholes framework. We start from methods used for basket options and Asian options. First, we use the general approach for deriving upper and lower bounds for stop-loss premia of sums of non-independent random variables as in Kaas et al. [Upper and lower bounds for sums of random variables, Insurance Math. Econom. 27 (2000) 151-168] or Dhaene et al. [The concept of comonotonicity in actuarial science and finance: theory, Insurance Math. Econom. 31(1) (2002) 3-33]. We generalize the methods in Deelstra et al. [Pricing of arithmetic basket options by conditioning, Insurance Math. Econom. 34 (2004) 55-57] and Vanmaele et al. [Bounds for the price of discrete sampled arithmetic Asian options, J. Comput. Appl. Math. 185(1) (2006) 51-90]. Afterwards we show how to derive an analytical closed-form expression for a lower bound in the non-comonotonic case. Finally, we derive upper bounds for Asian basket options by applying techniques as in Thompson [Fast narrow bounds on the value of Asian options, Working Paper, University of Cambridge, 1999] and Lord [Partially exact and bounded approximations for arithmetic Asian options, J. Comput. Finance 10 (2) (2006) 1-52]. Numerical results are included and on the basis of our numerical tests, we explain which method we recommend depending on moneyness and time-to-maturity.

  17. A Lower Bound on Concurrence

    Institute of Scientific and Technical Information of China (English)

    LIU Li-Guo; TIAN Cheng-Lin; CHEN Ping-Xing; YUAN Nai-Chang

    2009-01-01

    We derive an analytical lower bound on the concurrence for bipartite quantum systems with an improved computable cross norm or realignment criterion and an improved positive partial transpose criterion respectively.Furthermore we demonstrate that our bound is better than that obtained from the local uncertainty relations criterion with optimal local orthogonal observables which is known as one of the best estimations of concurrence.

  18. Mode-of-Action Uncertainty for Dual-Mode Carcinogens: A Bounding Approach for Naphthalene-Induced Nasal Tumors in Rats Based on PBPK and 2-Stage Stochastic Cancer Risk Models

    Energy Technology Data Exchange (ETDEWEB)

    Bogen, K T

    2007-05-11

    A relatively simple, quantitative approach is proposed to address a specific, important gap in the appr approach recommended by the USEPA Guidelines for Cancer Risk Assessment to oach address uncertainty in carcinogenic mode of action of certain chemicals when risk is extrapolated from bioassay data. These Guidelines recognize that some chemical carcinogens may have a site-specific mode of action (MOA) that is dual, involving mutation in addition to cell-killing induced hyperplasia. Although genotoxicity may contribute to increased risk at all doses, the Guidelines imply that for dual MOA (DMOA) carcinogens, judgment be used to compare and assess results obtained using separate 'linear' (genotoxic) vs. 'nonlinear' (nongenotoxic) approaches to low low-level risk extrapolation. However, the Guidelines allow the latter approach to be used only when evidence is sufficient t to parameterize a biologically based model that reliably o extrapolates risk to low levels of concern. The Guidelines thus effectively prevent MOA uncertainty from being characterized and addressed when data are insufficient to parameterize such a model, but otherwise clearly support a DMOA. A bounding factor approach - similar to that used in reference dose procedures for classic toxicity endpoints - can address MOA uncertainty in a way that avoids explicit modeling of low low-dose risk as a function of administere administered or internal dose. Even when a 'nonlinear' toxicokinetic model cannot be fully validated, implications of DMOA uncertainty on low low-dose risk may be bounded with reasonable confidence when target tumor types happen to be extremely rare. This concept was i illustrated llustrated for a likely DMOA rodent carcinogen naphthalene, specifically to the issue of risk extrapolation from bioassay data on naphthalene naphthalene-induced nasal tumors in rats. Bioassay data, supplemental toxicokinetic data, and related physiologically based p

  19. Scattering theory methods for bound state problems

    International Nuclear Information System (INIS)

    For the analysis of the properties of a bound state system one may use in place of the Schroedinger equation the Lippmann-Schwinger (LS) equation for the wave function or the LS equation for the reactance operator. Use of the LS equation for the reactance operator constrains the solution to have correct asymptotic behaviour, so this approach would appear to be desirable when the bound state wave function is to be used to calculate particle transfer form factors. The Schroedinger equation based N-level analysis of the s-wave bound states of a square well is compared to the ones based on the LS equation. It is found that the LS equation methods work better than the Schroedinger equation method. The method that uses the LS equation for the wave function gives the best results for the wave functions while the method that uses the LS equation for the reactance operator gives the best results for the binding energies. The accuracy of the reactance operator based method is remarkably insensitive to changes in the oscillator constant used for the harmonic oscillator function basis set. It is also remarkably insensitive to the number of nodes in the bound state wave function. (Auth.)

  20. Modeling of twitch fade based on slow interaction of nondepolarizing muscle relaxants with the presynaptic receptors.

    Science.gov (United States)

    Bhatt, Shashi B; Amann, Anton; Nigrovic, Vladimir

    2006-08-01

    Nondepolarizing muscle relaxants (MRs) diminish the indirectly evoked single twitch due to their binding to the postsynaptic receptors. Additionally, the MRs produce progressive diminution of successive twitches upon repetitive stimulation (fade). Our study addresses the generation of fade as observed under clinical situation. The study was conducted in two phases. In the clinical part, we have evaluated the time course of twitch depression and fade following the administration of several doses of three MRs (rocuronium, pancuronium, and cisatracurium). In the second part, we have modified our model of neuromuscular transmission to simulate the time course of twitch depression and fade. The MR was assumed to bind to a single site on the presynaptic receptor to produce fade. The rates of interaction with the presynaptic receptors were characterized in terms of the arbitrarily assigned equilibrium dissociation constant and the half-life for dissociation of the presynaptic complex. A method was developed to relate the release of acetylcholine to the occupancy of the presynaptic receptors. The strength of the first and the fourth twitch was calculated from the peak concentration of the activated postsynaptic receptors, i.e., of those receptors with both sites occupied by acetylcholine. Our results indicate that, while the affinity of the MR for the presynaptic receptor plays little role in the time course of fade, the rate of dissociation of the complex between the presynaptic receptors and the muscle relaxant may be critical in determining the time course of fade. Tentative estimates of this parameter are offered.

  1. Organic field-effect transistor-based biosensors functionalized with protein receptors

    NARCIS (Netherlands)

    Maddalena, Francesco; Kuiper, Marjon J.; Poolman, Bert; Brouwer, Frank; Hummelen, Jan C.; de Leeuw, Dagobert; Boer, Bert de; Blom, Paul W.M.

    2010-01-01

    An organic field-effect transistor with integrated proteins (Bio-FET) for sensing of sulfate ions is presented. A sulfate receptor was engineered to contain a thiol group for surface-anchoring without affecting its binding activity. The modified receptor was covalently coupled to a maleimide-functio

  2. Organic field-effect transistor-based biosensors functionalized with protein receptors

    NARCIS (Netherlands)

    Maddalena, F.; Kuiper, M.J.; Poolman, B.; Brouwer, F.; Hummelen, J.C.; Leeuw, D.M. de; Boer, B. de; Blom, P.W.M.

    2010-01-01

    An organic field-effect transistor with integrated proteins (Bio-FET) for sensing of sulfate ions is presented. A sulfate receptor was engineered to contain a thiol group for surface-anchoring without affecting its binding activity. The modified receptor was covalently coupled to a maleimide- functi

  3. Functional characterisation of human glycine receptors in a fluorescence-based high throughput screening assay

    DEFF Research Database (Denmark)

    Jensen, Anders A.

    2005-01-01

    The human glycine receptor subtypes alpha1beta and alpha2 have been expressed stably in HEK293 cells, and the functional characteristics of the receptors have been characterised in the FLIPR Membrane Potential Assay. The pharmacological properties obtained for nine standard ligands at the two rec...

  4. Homogeneous time-resolved G protein-coupled receptor-ligand binding assay based on fluorescence cross-correlation spectroscopy.

    Science.gov (United States)

    Antoine, Thomas; Ott, David; Ebell, Katharina; Hansen, Kerrin; Henry, Luc; Becker, Frank; Hannus, Stefan

    2016-06-01

    G protein-coupled receptors (GPCRs) mediate many important physiological functions and are considered as one of the most successful therapeutic target classes for a wide spectrum of diseases. Drug discovery projects generally benefit from a broad range of experimental approaches for screening compound libraries and for the characterization of binding modes of drug candidates. Owing to the difficulties in solubilizing and purifying GPCRs, assay formats have been so far mainly limited to cell-based functional assays and radioligand binding assays. In this study, we used fluorescence cross-correlation spectroscopy (FCCS) to analyze the interaction of detergent-solubilized receptors to various types of GPCR ligands: endogenous peptides, small molecules, and a large surrogate antagonist represented by a blocking monoclonal antibody. Our work demonstrates the suitability of the homogeneous and time-resolved FCCS assay format for a robust, high-throughput determination of receptor-ligand binding affinities and kinetic rate constants for various therapeutically relevant GPCRs. PMID:26954998

  5. Persistence of noncompact normally hyperbolic invariant manifolds in bounded geometry

    CERN Document Server

    Eldering, J

    2012-01-01

    We prove a persistence result for noncompact normally hyperbolic invariant manifolds in the setting of Riemannian manifolds of bounded geometry. Bounded geometry of the ambient manifold is a crucial assumption required to control the uniformity of all estimates throughout the proof. The $C^{k,\\alpha}$-smoothness result is optimal with respect to the spectral gap condition involved. The core of the persistence proof is based on the Perron method. In the process we derive new results on noncompact submanifolds in bounded geometry: a uniform tubular neighborhood theorem and uniform smooth approximation of a submanifold. The submanifolds considered are assumed to be uniformly $C^k$ bounded in an appropriate sense.

  6. A PSL Bounded Model Checking Method

    Institute of Scientific and Technical Information of China (English)

    YU Lei; ZHAO Zongtao

    2012-01-01

    SAT-based bounded model checking (BMC) is introduced as an important complementary technique to OBDD-based symbolic model checking, and is an efficient verification method for parallel and reactive systems. However, until now the properties verified by bounded model checking are very finite. Temporal logic PSL is a property specification language (IEEE-1850) describing parallel systems and is divided into two parts, i.e. the linear time logic FL and the branch time logic OBE. In this paper, the specification checked by BMC is extended to PSL and its algorithm is also proposed. Firstly, define the bounded semantics of PSL, and then reduce the bounded semantics into SAT by translating PSL specification formula and the state transition relation of the system to the propositional formula A and B, respectively. Finally, verify the satisfiability of the conjunction propositional formula of A and B. The algorithm results in the translation of the existential model checking of the temporal logic PSL into the satisfiability problem of propositional formula. An example of a queue controlling circuit is used to interpret detailedly the executing procedure of the algorithm.

  7. Influence of domain interactions on conformational mobility of the progesterone receptor detected by hydrogen/deuterium exchange mass spectrometry

    OpenAIRE

    Goswami, Devrishi; Callaway, Celetta; Pascal, Bruce D; Kumar, Raj; Edwards, Dean P.; Griffin, Patrick R.

    2014-01-01

    Structural and functional details of the N-terminal activation function 1 (AF1) of most nuclear receptors are poorly understood due to the highly dynamic intrinsically disordered nature of this domain. A hydrogen/deuterium exchange (HDX) mass spectrometry based investigation of TATA box binding protein (TBP) interaction with various domains of progesterone receptor (PR) demonstrate that agonist bound PR interaction with TBP via AF1 impacts the mobility of the C-terminal AF2. Results from HDX ...

  8. Himbacine-derived thrombin receptor antagonists: c7-spirocyclic analogues of vorapaxar.

    Science.gov (United States)

    Chelliah, Mariappan V; Eagen, Keith; Guo, Zhuyan; Chackalamannil, Samuel; Xia, Yan; Tsai, Hsingan; Greenlee, William J; Ahn, Ho-Sam; Kurowski, Stan; Boykow, George; Hsieh, Yunsheng; Chintala, Madhu

    2014-05-01

    We have synthesized several C7-spirocyclic analogues of vorapaxar and evaluated their in vitro activities against PAR-1 receptor. Some of these analogues showed activities and rat plasma levels comparable to vorapaxar. Compound 5c from this series showed excellent PAR-1 activity (K i = 5.1 nM). We also present a model of these spirocyclic compounds docked to the PAR-1 receptor based on the X-ray crystal structure of vorapaxar bound to PAR-1 receptor. This model explains some of the structure-activity relationships in this series. PMID:24900880

  9. The insect ecdysone receptor is a good potential target for RNAi-based pest control.

    Science.gov (United States)

    Yu, Rong; Xu, Xinping; Liang, Yongkang; Tian, Honggang; Pan, Zhanqing; Jin, Shouheng; Wang, Na; Zhang, Wenqing

    2014-01-01

    RNA interference (RNAi) has great potential for use in insect pest control. However, some significant challenges must be overcome before RNAi-based pest control can become a reality. One challenge is the proper selection of a good target gene for RNAi. Here, we report that the insect ecdysone receptor (EcR) is a good potential target for RNAi-based pest control in the brown planthopper Nilaparvata lugens, a serious insect pest of rice plants. We demonstrated that the use of a 360 bp fragment (NlEcR-c) that is common between NlEcR-A and NlEcR-B for feeding RNAi experiments significantly decreased the relative mRNA expression levels of NlEcR compared with those in the dsGFP control. Feeding RNAi also resulted in a significant reduction in the number of offspring per pair of N. lugens. Consequently, a transgenic rice line expressing NlEcR dsRNA was constructed by Agrobacterium- mediated transformation. The results of qRT-PCR showed that the total copy number of the target gene in all transgenic rice lines was 2. Northern blot analysis showed that the small RNA of the hairpin dsNlEcR-c was successfully expressed in the transgenic rice lines. After newly hatched nymphs of N. lugens fed on the transgenic rice lines, effective RNAi was observed. The NlEcR expression levels in all lines examined were decreased significantly compared with the control. In all lines, the survival rate of the nymphs was nearly 90%, and the average number of offspring per pair in the treated groups was significantly less than that observed in the control, with a decrease of 44.18-66.27%. These findings support an RNAi-based pest control strategy and are also important for the management of rice insect pests. PMID:25516715

  10. Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling

    Directory of Open Access Journals (Sweden)

    Creamer Matthew S

    2012-08-01

    Full Text Available Abstract Background Mathematical/computational models are needed to understand cell signaling networks, which are complex. Signaling proteins contain multiple functional components and multiple sites of post-translational modification. The multiplicity of components and sites of modification ensures that interactions among signaling proteins have the potential to generate myriad protein complexes and post-translational modification states. As a result, the number of chemical species that can be populated in a cell signaling network, and hence the number of equations in an ordinary differential equation model required to capture the dynamics of these species, is prohibitively large. To overcome this problem, the rule-based modeling approach has been developed for representing interactions within signaling networks efficiently and compactly through coarse-graining of the chemical kinetics of molecular interactions. Results Here, we provide a demonstration that the rule-based modeling approach can be used to specify and simulate a large model for ERBB receptor signaling that accounts for site-specific details of protein-protein interactions. The model is considered large because it corresponds to a reaction network containing more reactions than can be practically enumerated. The model encompasses activation of ERK and Akt, and it can be simulated using a network-free simulator, such as NFsim, to generate time courses of phosphorylation for 55 individual serine, threonine, and tyrosine residues. The model is annotated and visualized in the form of an extended contact map. Conclusions With the development of software that implements novel computational methods for calculating the dynamics of large-scale rule-based representations of cellular signaling networks, it is now possible to build and analyze models that include a significant fraction of the protein interactions that comprise a signaling network, with incorporation of the site

  11. Combining Alphas via Bounded Regression

    Directory of Open Access Journals (Sweden)

    Zura Kakushadze

    2015-11-01

    Full Text Available We give an explicit algorithm and source code for combining alpha streams via bounded regression. In practical applications, typically, there is insufficient history to compute a sample covariance matrix (SCM for a large number of alphas. To compute alpha allocation weights, one then resorts to (weighted regression over SCM principal components. Regression often produces alpha weights with insufficient diversification and/or skewed distribution against, e.g., turnover. This can be rectified by imposing bounds on alpha weights within the regression procedure. Bounded regression can also be applied to stock and other asset portfolio construction. We discuss illustrative examples.

  12. Bounded Model Checking of CTL

    Institute of Scientific and Technical Information of China (English)

    Zhi-Hong Tao; Cong-Hua Zhou; Zhong Chen; Li-Fu Wang

    2007-01-01

    Bounded Model Checking has been recently introduced as an efficient verification method for reactive systems.This technique reduces model checking of linear temporal logic to propositional satisfiability.In this paper we first present how quantified Boolean decision procedures can replace BDDs.We introduce a bounded model checking procedure for temporal logic CTL* which reduces model checking to the satisfiability of quantified Boolean formulas.Our new technique avoids the space blow up of BDDs, and extends the concept of bounded model checking.

  13. Molecular and isotopic composition of hydrate-bound and dissolved gases in the southern basin of Lake Baikal, based on an improved headspace gas method

    Science.gov (United States)

    Sakagami, Hirotoshi; Takahashi, Nobuo; Hachikubo, Akihiro; Minami, Hirotsugu; Yamashita, Satoshi; Shoji, Hitoshi; Khlystov, Oleg; Kalmychkov, Gennadiy; Grachev, Mikhail; De Batist, Marc

    2012-12-01

    Assessments of the molecular and isotopic composition of hydrate-bound and dissolved gases in pore water were conducted during the multi-phase gas hydrate project (MHP-09) cruise VER09-03 to the southern basin of Lake Baikal in September 2009. To avoid changes in gas composition during core sampling and transport, various headspace methods were investigated aimed at preserving the dissolved gases in pore water. When distilled water was added to the sediment samples, the concentrations of carbon dioxide and oxygen decreased because of dissolution into the water and/or microbial consumption. When the headspace was not flushed with inert gases, trace levels of hydrogen and ethylene were detected. The findings suggest that best preparation is achieved by flushing the headspace with helium, and adding a saturated aqueous solution of sodium chloride. This improved headspace method served to examine the molecular and isotopic compositions of gas samples retrieved at several new sites in the southern basin. Methane was the major component, and the proportion of ethane ranged widely from 0.0009 to 1.67 mol% of the total hydrocarbon gases. The proportions of propane and higher hydrocarbons were small or less than their detection limits. The carbon isotope signatures suggest that microbial-sourced methane and ethane were dominant in the Peschanka study area, whereas ethane was of thermogenic origin at all other study sites in the southern basin of Lake Baikal.

  14. Bounded link prediction for very large networks

    CERN Document Server

    Cui, Wei; Xu, Zhongqi

    2015-01-01

    Evaluation of link prediction methods is a hard task in very large complex networks because of the inhibitive computational cost. By setting a lower bound of the number of common neighbors (CN), we propose a new framework to efficiently and precisely evaluate the performances of CN-based similarity indices in link prediction for very large heterogeneous networks. Specifically, we propose a fast algorithm based on the parallel computing scheme to obtain all the node pairs with CN values larger than the lower bound. Furthermore, we propose a new measurement, called self-predictability, to quantify the performance of the CN-based similarity indices in link prediction, which on the other side can indicate the link predictability of a network.

  15. Duplex Bioelectronic Tongue for Sensing Umami and Sweet Tastes Based on Human Taste Receptor Nanovesicles.

    Science.gov (United States)

    Ahn, Sae Ryun; An, Ji Hyun; Song, Hyun Seok; Park, Jin Wook; Lee, Sang Hun; Kim, Jae Hyun; Jang, Jyongsik; Park, Tai Hyun

    2016-08-23

    For several decades, significant efforts have been made in developing artificial taste sensors to recognize the five basic tastes. So far, the well-established taste sensor is an E-tongue, which is constructed with polymer and lipid membranes. However, the previous artificial taste sensors have limitations in various food, beverage, and cosmetic industries because of their failure to mimic human taste reception. There are many interactions between tastants. Therefore, detecting the interactions in a multiplexing system is required. Herein, we developed a duplex bioelectronic tongue (DBT) based on graphene field-effect transistors that were functionalized with heterodimeric human umami taste and sweet taste receptor nanovesicles. Two types of nanovesicles, which have human T1R1/T1R3 for the umami taste and human T1R2/T1R3 for the sweet taste on their membranes, immobilized on micropatterned graphene surfaces were used for the simultaneous detection of the umami and sweet tastants. The DBT platform led to highly sensitive and selective recognition of target tastants at low concentrations (ca. 100 nM). Moreover, our DBT was able to detect the enhancing effect of taste enhancers as in a human taste sensory system. This technique can be a useful tool for the detection of tastes instead of sensory evaluation and development of new artificial tastants in the food and beverage industry. PMID:27327579

  16. In vitro inflammation inhibition model based on semi-continuous toll-like receptor biosensing.

    Directory of Open Access Journals (Sweden)

    Jin-Woo Jeon

    Full Text Available A chemical inhibition model of inflammation is proposed by semi-continuous monitoring the density of toll-like receptor 1 (TLR1 expressed on mammalian cells following bacterial infection to investigate an in vivo-mimicked drug screening system. The inflammation was induced by adding bacterial lysate (e.g., Pseudomonas aeruginosa to a mammalian cell culture (e.g., A549 cell line. The TLR1 density on the same cells was immunochemically monitored up to three cycles under optimized cyclic bacterial stimulation-and-restoration conditions. The assay was carried out by adopting a cell-compatible immunoanalytical procedure and signal generation method. Signal intensity relative to the background control obtained without stimulation was employed to plot the standard curve for inflammation. To suppress the inflammatory response, sodium salicylate, which inhibits nuclear factor-κB activity, was used to prepare the standard curve for anti-inflammation. Such measurement of differential TLR densities was used as a biosensing approach discriminating the anti-inflammatory substance from the non-effector, which was simulated by using caffeic acid phenethyl ester and acetaminophen as the two components, respectively. As the same cells exposed to repetitive bacterial stimulation were semi-continuously monitored, the efficacy and toxicity of the inhibitors may further be determined regarding persistency against time. Therefore, this semi-continuous biosensing model could be appropriate as a substitute for animal-based experimentation during drug screening prior to pre-clinical tests.

  17. Discovery of novel GPVI receptor antagonists by structure-based repurposing.

    Directory of Open Access Journals (Sweden)

    Lewis Taylor

    Full Text Available Inappropriate platelet aggregation creates a cardiovascular risk that is largely managed with thienopyridines and aspirin. Although effective, these drugs carry risks of increased bleeding and drug 'resistance', underpinning a drive for new antiplatelet agents. To discover such drugs, one strategy is to identify a suitable druggable target and then find small molecules that modulate it. A good and unexploited target is the platelet collagen receptor, GPVI, which promotes thrombus formation. To identify inhibitors of GPVI that are safe and bioavailable, we docked a FDA-approved drug library into the GPVI collagen-binding site in silico. We now report that losartan and cinanserin inhibit GPVI-mediated platelet activation in a selective, competitive and dose-dependent manner. This mechanism of action likely underpins the cardioprotective effects of losartan that could not be ascribed to its antihypertensive effects. We have, therefore, identified small molecule inhibitors of GPVI-mediated platelet activation, and also demonstrated the utility of structure-based repurposing.

  18. HPLC-based activity profiling of Angelica pubescens roots for new positive GABAA receptor modulators in Xenopus oocytes.

    Science.gov (United States)

    Zaugg, Janine; Eickmeier, Eva; Rueda, Diana C; Hering, Steffen; Hamburger, Matthias

    2011-04-01

    A petroleum ether extract of the traditional Chinese herbal drug Duhuo (roots of Angelica pubescens Maxim. f. biserrata Shan et Yuan), showed significant activity in a functional two-microelectrode voltage clamp assay with Xenopus oocytes which expressed recombinant γ-aminobutyric acid type A (GABA(A)) receptors of the subtype α(1)β(2)γ(2S). HPLC-based activity profiling of the active extract revealed six compounds responsible for the GABA(A) receptor modulating activity. They were identified by microprobe NMR and high resolution mass spectrometry as columbianetin acetate (1), imperatorin (3), cnidilin (4), osthol (5), and columbianedin (6). In concentration-dependent experiments, osthol and cnidilin showed the highest potentiation of the GABA induced chloride current (273.6%±39.4% and 204.5%±33.2%, respectively at 300 μM). Bisabolangelone (2) only showed minor activity at the GABA(A) receptor. The example demonstrates that HPLC-based activity profiling is a simple and efficient method to rapidly identify GABA(A) receptor modulators in a bioactive plant extract. PMID:21147202

  19. Bound states in string nets

    CERN Document Server

    Schulz, M D; Vidal, J

    2016-01-01

    We discuss the emergence of bound states in the low-energy spectrum of the string-net Hamiltonian in the presence of a string tension. In the ladder geometry, we show that a single bound state arises either for a finite tension or in the zero-tension limit depending on the theory considered. In the latter case, we perturbatively compute the binding energy as a function of the total quantum dimension. We also address this issue in the honeycomb lattice where the number of bound states in the topological phase depends on the total quantum dimension. Finally, the internal structure of these bound states is analyzed in the zero-tension limit.

  20. Curvature bounds for configuration spaces

    OpenAIRE

    Erbar, Matthias; Huesmann, Martin

    2014-01-01

    We show that the configuration space over a manifold M inherits many curvature properties of the manifold. For instance, we show that a lower Ricci curvature bound on M implies for the configuration space a lower Ricci curvature bound in the sense of Lott-Sturm-Villani, the Bochner inequality, gradient estimates and Wasserstein contraction. Moreover, we show that the heat flow on the configuration space, or the infinite independent particle process, can be identified as the gradient flow of t...

  1. Finite Domain Bounds Consistency Revisited

    OpenAIRE

    Choi, Chiu Wo; Harvey, Warwick; Lee, Jimmy Ho-Man; Stuckey, Peter J.

    2004-01-01

    A widely adopted approach to solving constraint satisfaction problems combines systematic tree search with constraint propagation for pruning the search space. Constraint propagation is performed by propagators implementing a certain notion of consistency. Bounds consistency is the method of choice for building propagators for arithmetic constraints and several global constraints in the finite integer domain. However, there has been some confusion in the definition of bounds consistency. In t...

  2. Entropy bounds for uncollapsed matter

    Energy Technology Data Exchange (ETDEWEB)

    Abreu, Gabriel; Visser, Matt, E-mail: Gabriel.Abreu@msor.vuw.ac.nz, E-mail: Matt.Visser@msor.vuw.ac.nz [School of Mathematics, Statistics and Operation Research Victoria University of Wellington Wellington (New Zealand)

    2011-09-22

    In any static spacetime the quasilocal Tolman mass contained within a volume can be reduced to a Gauss-like surface integral involving the flux of a suitably defined generalized surface gravity. By introducing some basic thermodynamics, and invoking the Unruh effect, one can then develop elementary bounds on the quasilocal entropy that are very similar in spirit to the holographic bound, and closely related to entanglement entropy.

  3. Ligands, cell-based models, and readouts required for Toll-like receptor action.

    LENUS (Irish Health Repository)

    Dellacasagrande, Jerome

    2012-02-01

    This chapter details the tools that are available to study Toll-like receptor (TLR) biology in vitro. This includes ligands, host cells, and readouts. The use of modified TLRs to circumvent some technical problems is also discussed.

  4. Requirements and ontology for a G protein-coupled receptor oligomerization knowledge base

    NARCIS (Netherlands)

    Skrabanek, L.; Murcia, M.; Bouvier, M.; Devi, L.; George, S.R.; Lohse, M.J.; Milligan, G.; Neubig, R.; Palczewski, K.; Parmentier, M.; Pin, J.P.; Vriend, G.; Javitch, J.A.; Campagne, F.; Filizola, M.

    2007-01-01

    BACKGROUND: G Protein-Coupled Receptors (GPCRs) are a large and diverse family of membrane proteins whose members participate in the regulation of most cellular and physiological processes and therefore represent key pharmacological targets. Although several bioinformatics resources support research

  5. Discovery of Novel Human Epidermal Growth Factor Receptor-2 Inhibitors by Structure-based Virtual Screening

    OpenAIRE

    Shi, Zheng; Yu, Tian; Sun, Rong; Wang, Shan; Chen, Xiao-Qian; Cheng, Li-jia; Liu, Rong

    2016-01-01

    Background: Human epidermal growth factor receptor-2 (HER2) is a trans-membrane receptor like protein, and aberrant signaling of HER2 is implicated in many human cancers, such as ovarian cancer, gastric cancer, and prostate cancer, most notably breast cancer. Moreover, it has been in the spotlight in the recent years as a promising new target for therapy of breast cancer. Objective: Since virtual screening has become an integral part of the drug discovery process, it is of great significant t...

  6. Identification of Adiponectin Receptor Agonist Utilizing a Fluorescence Polarization Based High Throughput Assay

    OpenAIRE

    Yiyi Sun; Zhihe Zang; Ling Zhong; Min Wu; Qing Su; Xiurong Gao; Wang Zan; Dong Lin; Yan Zhao; Zhonglin Zhang

    2013-01-01

    Adiponectin, the adipose-derived hormone, plays an important role in the suppression of metabolic disorders that can result in type 2 diabetes, obesity, and atherosclerosis. It has been shown that up-regulation of adiponectin or adiponectin receptor has a number of therapeutic benefits. Given that it is hard to convert the full size adiponectin protein into a viable drug, adiponectin receptor agonists could be designed or identified using high-throughput screening. Here, we report on the deve...

  7. Advances of Targeted Therapy Based on Estrogen Receptor Signaling Pathway 
in Lung Cancer

    OpenAIRE

    Xu, Liqiang; Liao, Yongde; Hexiao TANG; Zhang, Chao; Liu, Zhaoguo

    2011-01-01

    Increasing evidence indicates that estrogen promotes tumor growth in both estrogen target organs and non-target organs. Estrogen regulates cell proliferation and differentiation via two different receptors, estrogen receptors α and β (ERα and ERβ). In recent decades, with the clarification of the ERα-mediated signaling pathways in breast cancer, targeted therapy through these pathways have successfully been used in clinical application. Tamoxifen, the classic representative, is a selective es...

  8. Genetic Contributions to Avoidance-Based Decisions: Striatal D2 receptor Polymorphisms

    OpenAIRE

    Frank, Michael J.; Hutchison, Kent

    2009-01-01

    Individuals differ in their tendencies to seek positive decision outcomes or to avoid negative ones. At the neurobiological level, our model suggests that phasic changes in dopamine support learning to reinforce good decisions via striatal D1 receptors, and to avoid maladaptive choices via striatal D2 receptors. Accordingly, in a previous study individual differences in positive and negative learning were strongly modulated by two genetic polymorphisms factors related to striatal D1 and D2 fu...

  9. Theoretical analysis of headache recurrence in patients administered triptans for migraine based on receptor occupancy

    OpenAIRE

    Tokuoka, Kentaro; Takayanagi, Risa; Toyabe, Mioko; Watanabe, Masayuki; Kitagawa, Yasuhisa; Yamada, Yasuhiko

    2015-01-01

    Background In this study, we retrospectively analyzed the relationship between headache recurrence and serotonin 5-HT1B/1D receptor occupancy (Φ1B and Φ1D). Triptans marketed in Japan (sumatriptan, zolmitriptan, eletriptan, rizatriptan, naratriptan) were investigated. Methods Receptor occupancies were calculated from both the pharmacokinetic and pharmacodynamic data of triptans. We examined the relationships between recurrence rate and elimination half-lives, and Ф1B and Ф1D, as calculated fr...

  10. Bounds on Two-Phase Frictional Pressure Gradient and Void Fraction in Circular Pipes

    OpenAIRE

    Awad, M M; Muzychka, Y. S.

    2014-01-01

    Simple rules are developed for obtaining rational bounds for two-phase frictional pressure gradient and void fraction in circular pipes. The bounds are based on turbulent-turbulent flow assumption. Both the lower and upper bounds for frictional pressure gradient are based on the separate cylinders formulation. For frictional pressure gradient, the lower bound is based on the separate cylinders formulation that uses the Blasius equation to represent the Fanning friction factor while the upper ...

  11. Synthesis of new isoxazoline-based acidic amino acids and investigation of their affinity and selectivity profile at ionotropic glutamate receptors

    DEFF Research Database (Denmark)

    Pinto, Andrea; Conti, Paola; Grazioso, Giovanni;

    2011-01-01

    The synthesis of four new isoxazoline-based amino acids being analogues of previously described glutamate receptor ligands is reported and their affinity for ionotropic glutamate receptors is analyzed in comparison with that of selected model compounds. Molecular modelling investigations have bee...

  12. Selective Allosteric Antagonists for the G Protein-Coupled Receptor GPRC6A Based on the 2-Phenylindole Privileged Structure Scaffold

    DEFF Research Database (Denmark)

    Johansson, Henrik; Boesgaard, Michael Worch; Nørskov-Lauritsen, Lenea;

    2015-01-01

    G protein-coupled receptors (GPCRs) represent a biological target class of fundamental importance in drug therapy. The GPRC6A receptor is a newly deorphanized class C GPCR that we recently reported for the first allosteric antagonists based on the 2-arylindole privileged structure scaffold (e.g., 1...

  13. Bounding symbolic powers via asymptotic multiplier ideals

    Directory of Open Access Journals (Sweden)

    Zach Teitler

    2009-04-01

    Full Text Available We revisit a bound on symbolic powers found by Ein-Lazarsfeld-Smith and subsequently improved by Takagi-Yoshida. We show that the original argument of [6] actually gives the same improvement. On the other hand, we show by examples that any further improvement based on the same technique appears unlikely. This is primarily an exposition; only some examples and remarks might be new.

  14. Risk factors for breast cancer by oestrogen receptor status: a population-based case-control study.

    OpenAIRE

    Cooper, J A; Rohan, T E; Cant, E. L.; Horsfall, D. J.; Tilley, W D

    1989-01-01

    Data from a population-based case-control study conducted in Adelaide, South Australia, and involving 451 case-control pairs, were analysed to determine whether the associations of menstrual, reproductive, dietary and other factors with risk of breast cancer differed by oestrogen receptor (ER) status. Data on ER status were available for 380 cases. The proportion of tumours which were ER+ increased with age, and there was a higher proportion of ER+ tumours in post-menopausal than in premenopa...

  15. On a Generalization of Kingman's Bounds

    OpenAIRE

    Liu, Zhen; Nain, Philippe; Towsley, Don

    1994-01-01

    In this paper we develop a framework for computing upper and lower bounds of an exponential form for a class of single server queueing systems with non-renewal inputs. These bounds generalize Kingman's bounds for queues with renewal inputs.

  16. Comprehensive logic based analyses of Toll-like receptor 4 signal transduction pathway.

    Directory of Open Access Journals (Sweden)

    Mahesh Kumar Padwal

    Full Text Available Among the 13 TLRs in the vertebrate systems, only TLR4 utilizes both Myeloid differentiation factor 88 (MyD88 and Toll/Interleukin-1 receptor (TIR-domain-containing adapter interferon-β-inducing Factor (TRIF adaptors to transduce signals triggering host-protective immune responses. Earlier studies on the pathway combined various experimental data in the form of one comprehensive map of TLR signaling. But in the absence of adequate kinetic parameters quantitative mathematical models that reveal emerging systems level properties and dynamic inter-regulation among the kinases/phosphatases of the TLR4 network are not yet available. So, here we used reaction stoichiometry-based and parameter independent logical modeling formalism to build the TLR4 signaling network model that captured the feedback regulations, interdependencies between signaling kinases and phosphatases and the outcome of simulated infections. The analyses of the TLR4 signaling network revealed 360 feedback loops, 157 negative and 203 positive; of which, 334 loops had the phosphatase PP1 as an essential component. The network elements' interdependency (positive or negative dependencies in perturbation conditions such as the phosphatase knockout conditions revealed interdependencies between the dual-specific phosphatases MKP-1 and MKP-3 and the kinases in MAPK modules and the role of PP2A in the auto-regulation of Calmodulin kinase-II. Our simulations under the specific kinase or phosphatase gene-deficiency or inhibition conditions corroborated with several previously reported experimental data. The simulations to mimic Yersinia pestis and E. coli infections identified the key perturbation in the network and potential drug targets. Thus, our analyses of TLR4 signaling highlights the role of phosphatases as key regulatory factors in determining the global interdependencies among the network elements; uncovers novel signaling connections; identifies potential drug targets for

  17. 基于有限理性理论的虚拟士兵感知行为建模研究%Study of Virtual Soldier's Perception Modeling Based on Bounded Rationality Theory

    Institute of Scientific and Technical Information of China (English)

    曹波伟; 薛青; 姚义军

    2012-01-01

    Because of the shortage of current virtual soldier modeling method, the concept of bounded rationality theory and its soldier is proposed, then the virtual soldier's limited behavior model based on bounded rationality . Theory is given, the model include limited vision model , limited hearing model, limited memory model, and these soldiers have the character of similar perception, decision making and exercise capacity. Those has certain meaning to the modeling of the Virtual Soldier's Behavior.%针对当前虚拟士兵感知行为模型的缺陷,介绍有限理性理论和基于有限理性虚拟士兵的概念,分析了加入有限理性理论的虚拟士兵的特点,提出了基于有限理性虚拟士兵的感知行为模型.该模型包括有限视觉模型、有限听觉模型和有限记忆模型,基于该感知模型的虚拟士兵在感知、决策和运动能力方面与类似真实士兵具有较高的一致性.这对虚拟士兵的感知行为建模研究具有一定的探索意义.

  18. Hydrazone based luminescent receptors for fluorescent sensing of Cu{sup 2+}: Structure and spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Mukherjee, Soma, E-mail: sommukh445@yahoo.co.in [Department of Environmental Science, University of Kalyani, Kalyani, Nadia, 741235 West Bengal (India); Mal, Palash [Department of Environmental Science, University of Kalyani, Kalyani, Nadia, 741235 West Bengal (India); Stoeckli-Evans, Helen [Institute of Physics, University of Neuchâtel, rue Emile-Argand 11, CH-2000 Neuchâtel (Switzerland)

    2014-11-15

    Two new luminescent hydrazones, HL1 and HL2 were investigated for selective and sensitive fluorescent recognition of Cu{sup 2+} in aqueous medium (CH{sub 3}CN/H{sub 2}O (1:4, v/v) solvent system) with a 1:1 binding stoichiometry. The emission peak of HL (λ{sub em}=405 nm), undergoes significant quenching upon complexation with Cu{sup 2+}. The quantum yields for the receptors and in situ formed Cu{sup 2+} complexes were determined. The absorption ratiometric analysis was carried out in presence of various metal ions to confirm the selectivity of the receptors towards Cu{sup 2+}. They were able to detect Cu{sup 2+} with a ∼0.9 µM detection limit as indicated by fluorimetric measurements. The molecular structures of the receptors were determined by single crystal X-ray diffraction analysis. - Highlights: • Small molecule luminescent hydrazones were developed for recognition of Cu{sup 2+}. • Selectivity and sensitivity were studied spectroscopically in aqueous medium. • Binding stoichiometry, association constant, and quantum yields were calculated. • Receptors have low detection limit for Cu{sup 2+}. • Crystal structures of the receptors were solved by X-ray diffractometry.

  19. In vitro potency determination of botulinum neurotoxin B based on its receptor-binding and proteolytic characteristics.

    Science.gov (United States)

    Wild, Emina; Bonifas, Ursula; Klimek, Jolanta; Trösemeier, Jan-Hendrik; Krämer, Beate; Kegel, Birgit; Behrensdorf-Nicol, Heike A

    2016-08-01

    Botulinum neurotoxins (BoNTs) are the most potent toxins known. However, the paralytic effect caused by BoNT serotypes A and B is taken advantage of to treat different forms of dystonia and in cosmetic procedures. Due to the increasing areas of application, the demand for BoNTs A and B is rising steadily. Because of the high toxicity, it is mandatory to precisely determine the potency of every produced BoNT batch, which is usually accomplished by performing toxicity testing (LD50 test) in mice. Here we describe an alternative in vitro assay for the potency determination of the BoNT serotype B. In this assay, the toxin is first bound to its specific receptor molecules. After the proteolytic subunit of the toxin has been released and activated by chemical reduction, it is exposed to synaptobrevin, its substrate protein. Finally the proteolytic cleavage is quantified by an antibody-mediated detection of the neoepitope, reaching a detection limit below 0.1mouseLD50/ml. Thus, the assay, named BoNT/B binding and cleavage assay (BoNT/B BINACLE), takes into account the binding as well as the protease function of the toxin, thereby measuring its biological activity. PMID:27032463

  20. Synthetic sialylglycopolymer receptor for virus detection using cantilever-based sensors.

    Science.gov (United States)

    Gorelkin, P V; Erofeev, A S; Kiselev, G A; Kolesov, D V; Dubrovin, E V; Yaminsky, I V

    2015-09-01

    We describe the rapid, label-free detection of Influenza A viruses using a cantilever transducer modified with a synthetic sialylglycopolymer receptor layer. Surface stresses induced by viruses binding to the receptor layer were used as the analytical signal. The synthetic sialylglycopolymer receptor layer can be used in nanoscale strain-gauge cantilever transducers for highly sensitive virus detection. Strain-gage transducers using such sensor layers exhibit long lifetimes, high sensitivities, and possible regeneration. Nanomechanical cantilever systems using optical detectors were used for the surface stress measurements. We demonstrated the positive, label-free detection of Influenza A at concentrations below 10(6) viruses per ml. In contrast to hemagglutination assays, cantilever sensors are label free, in situ, and rapid (less than 30 min), and they require minimal or nearly no sample preparation. PMID:26215598

  1. Thiourea Based Tweezer Anion Receptors for Selective Sensing of Fluoride Ions

    Institute of Scientific and Technical Information of China (English)

    ZHANG,You-Ming; CAO,Cheng; WEI,Wei; WEI,Tai-Bao

    2007-01-01

    Three 3,3'-di(4-substituted-phenyl)-1,1'-isophthaloylbis(thiourea) compounds were designed as novel neutral anion receptors, and synthesized by simple steps in good yields. The single crystal structure of receptor 1 shows that a solvent molecule was captured by the host molecule through intermolecular hydrogen bonding. Moreover, it was self-assembled as a supramolecular system for the presence of abundant inter- and intramolecular hydrogen bonding and π-π interactions between phenyl groups. Their application as anion receptors has been examined by UV-Vis and 1H NMR spectroscopy, showing that they had a higher selectivity for fluoride than other halides. The host and guest formed a 1∶1 stoichiometry complex through hydrogen bonding interactions in the first step, then following a process of deprotonation in presence of an excess of F- in the solvent of DMF.

  2. Cell-based and in silico evidence against quercetin and structurally-related flavonols as activators of vitamin D receptor.

    Science.gov (United States)

    Lau, Aik Jiang; Politi, Regina; Yang, Guixiang; Chang, Thomas K H

    2016-10-01

    It has been reported that quercetin is an activator of rat vitamin D receptor (rVDR). However, the conclusion was based on experiments performed without all the appropriate control groups, raising the possibility of a false-positive finding. Furthermore, distinct differences exist in the chemical structures of quercetin and 1α,25-dihydroxyvitamin D3, which is a prototypic agonist of VDR. Therefore, we investigated systematically whether quercetin and other flavonols are agonists of rVDR, mouse VDR (mVDR), or human VDR (hVDR). Quercetin, 3-hydroxyflavone, galangin, datiscetin, kaempferol, morin, isorhamnetin, tamarixetin, myricetin, and syringetin did not activate rVDR, mVDR, or hVDR in HEK-293 and HepG2 cells transfected with the corresponding receptor expression plasmid and either the secreted phosphoprotein 1 (Spp1) or cytochrome P450 24A1 (CYP24A1) reporter plasmid, when compared to the respective empty vector control group transfected with one or the other reporter plasmid and treated with one of the flavonols. Control analysis indicated that lithocholic acid and 1α,25-dihydroxyvitamin D3, but not rifampicin, activated rVDR, mVDR, and hVDR. As shown in transfected HEK293 and HepG2 cells, the flavonols did not influence hVDR ligand binding domain transactivation, steroid receptor coactivator-1 recruitment, or hVDR target gene expression (transient receptor potential cation channel 6 and CYP24A1) in hVDR-expressing Caco-2 or LS180 cells. The cumulative data from the cell-based experiments were corroborated by results obtained from molecular docking analysis. In conclusion, quercetin, 3-hydroxyflavone, galangin, datiscetin, kaempferol, morin, isorhamnetin, tamarixetin, myricetin, and syringetin are not agonists of rVDR, mVDR, or hVDR, as judged by cell-based and in silico evidence. PMID:27041117

  3. A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network

    Directory of Open Access Journals (Sweden)

    De Graaf David

    2007-07-01

    Full Text Available Abstract Background The nuclear receptors are a large family of eukaryotic transcription factors that constitute major pharmacological targets. They exert their combinatorial control through homotypic heterodimerisation. Elucidation of this dimerisation network is vital in order to understand the complex dynamics and potential cross-talk involved. Results Phylogeny, protein-protein interactions, protein-DNA interactions and gene expression data have been integrated to provide a comprehensive and up-to-date description of the topology and properties of the nuclear receptor interaction network in humans. We discriminate between DNA-binding and non-DNA-binding dimers, and provide a comprehensive interaction map, that identifies potential cross-talk between the various pathways of nuclear receptors. Conclusion We infer that the topology of this network is hub-based, and much more connected than previously thought. The hub-based topology of the network and the wide tissue expression pattern of NRs create a highly competitive environment for the common heterodimerising partners. Furthermore, a significant number of negative feedback loops is present, with the hub protein SHP [NR0B2] playing a major role. We also compare the evolution, topology and properties of the nuclear receptor network with the hub-based dimerisation network of the bHLH transcription factors in order to identify both unique themes and ubiquitous properties in gene regulation. In terms of methodology, we conclude that such a comprehensive picture can only be assembled by semi-automated text-mining, manual curation and integration of data from various sources.

  4. Ginseng pharmacology: a new paradigm based on gintonin-lysophosphatidic acid receptor interactions

    Directory of Open Access Journals (Sweden)

    Seung-Yeol eNah

    2015-10-01

    Full Text Available Ginseng, the root of Panax ginseng, is used as a traditional medicine. Despite the long history of the use of ginseng, there is no specific scientific or clinical rationale for ginseng pharmacology besides its application as a general tonic. The ambiguous description of ginseng pharmacology might be due to the absence of a predominant active ingredient that represents ginseng pharmacology. Recent studies show that ginseng abundantly contains lysophosphatidic acids (LPAs, which are phospholipid-derived growth factor with diverse biological functions including those claimed to be exhibited by ginseng. LPAs in ginseng form a complex with ginseng proteins, which can bind and deliver LPA to its cognate receptors with a high affinity. As a first messenger, gintonin produces second messenger Ca2+ via G protein-coupled LPA receptors. Ca2+ is an intracellular mediator of gintonin and initiates a cascade of amplifications for further intercellular communications by activation of Ca2+-dependent kinases, receptors, gliotransmitter and neurotransmitter release. Ginsenosides, which have been regarded as primary ingredients of ginseng, cannot elicit intracellular [Ca2+]i transients, since they lack specific cell surface receptor. However, ginsenosides exhibit non-specific ion channel and receptor regulations. This is the key characteristic that distinguishes gintonin from ginsenosides. Although the current discourse on ginseng pharmacology is focused on ginsenosides, gintonin can definitely provide a mode of action for ginseng pharmacology that ginsenosides cannot. This review article introduces a novel concept of ginseng ligand-LPA receptor interaction and proposes to establish a paradigm that shifts the focus from ginsenosides to gintonin as a major ingredient representing ginseng pharmacology.

  5. Eta nuclear bound states revisited

    CERN Document Server

    Friedman, E; Mareš, J

    2013-01-01

    The strong energy dependence of the s-wave eta-N scattering amplitude at and below threshold, as evident in coupled-channels K-matrix fits and chiral models that incorporate the S11 N*(1535) resonance, is included self consistently in eta-nuclear bound state calculations. This approach, applied recently in calculations of kaonic atoms and Kbar-nuclear bound states, is found to impose stronger constraints than ever on the onset of eta-nuclear binding, with a minimum value of Re a_{eta N} approximately 0.9 fm required to accommodate an eta-4He bound state. Binding energies and widths of eta-nuclear states are calculated within several underlying eta-N models for nuclei across the periodic table, including eta-25Mg for which some evidence was proposed in a recent COSY experiment.

  6. Improved Range Searching Lower Bounds

    DEFF Research Database (Denmark)

    Larsen, Kasper Green; Nguyen, Huy L.

    2012-01-01

    range reporting problem. In approximate simplex range reporting, points that lie within a distance of ε ⋅ Diam(s) from the border of a query simplex s, are free to be included or excluded from the output, where ε ≥ 0 is an input parameter to the range searching problem. We prove our lower bounds......Table of Contents -------------------------------------------------------------------------------- In this paper we present a number of improved lower bounds for range searching in the pointer machine and the group model. In the pointer machine, we prove lower bounds for the approximate simplex...... by constructing a hard input set and query set, and then invoking Chazelle and Rosenberg's [CGTA'96] general theorem on the complexity of navigation in the pointer machine. For the group model, we show that input sets and query sets that are hard for range reporting in the pointer machine (i.e. by Chazelle...

  7. Simulation bounds for system availability

    International Nuclear Information System (INIS)

    System availability is a dominant factor in the practicality of nuclear power electrical generating plants. A proposed model for obtaining either lower bounds or interval estimates on availability uses observed data on ''n'' failure-to-repair cycles of the system to estimate the parameters in the time-to-failure and time-to-repair models. These estimates are then used in simulating failure/repair cycles of the system. The availability estimate is obtained for each of 5000 samples of ''n'' failure/repair cycles to form a distribution of estimates. Specific percentile points of those simulated distributions are selected as lower simulation bounds or simulation interval bounds for the system availability. The method is illustrated with operational data from two nuclear plants for which an exponential time-to-failure and a lognormal time-to-repair are assumed

  8. Energy bounds in designer gravity

    Science.gov (United States)

    Amsel, Aaron J.; Marolf, Donald

    2006-09-01

    We consider asymptotically anti-de Sitter gravity coupled to tachyonic scalar fields with mass at or slightly above the Breitenlohner-Freedman bound in d≥4 spacetime dimensions. The boundary conditions in these “designer gravity” theories are defined in terms of an arbitrary function W. We give a general argument that the Hamiltonian generators of asymptotic symmetries for such systems will be finite, and proceed to construct these generators using the covariant phase space method. The direct calculation confirms that the generators are finite and shows that they take the form of the pure gravity result plus additional contributions from the scalar fields. By comparing the generators to the spinor charge, we derive a lower bound on the gravitational energy when W has a global minimum and the Breitenlohner-Freedman bound is not saturated.

  9. Experimental activation of bound entanglement.

    Science.gov (United States)

    Kaneda, Fumihiro; Shimizu, Ryosuke; Ishizaka, Satoshi; Mitsumori, Yasuyoshi; Kosaka, Hideo; Edamatsu, Keiichi

    2012-07-27

    Entanglement is one of the essential resources in quantum information and communication technology (QICT). The entanglement thus far explored and applied to QICT has been pure and distillable entanglement. Yet, there is another type of entanglement, called "bound entanglement," which is not distillable by local operations and classical communication. We demonstrate the experimental "activation" of the bound entanglement held in the four-qubit Smolin state, unleashing its immanent entanglement in distillable form, with the help of auxiliary two-qubit entanglement and local operations and classical communication. We anticipate that it opens the way to a new class of QICT applications that utilize more general classes of entanglement than ever, including bound entanglement.

  10. New Neutral Receptors for Fluoride Based on Calix[4]arene Bearing Thiourea and Amide

    Institute of Scientific and Technical Information of China (English)

    刘顺英; 徐括喜; 何永炳; 秦海娟; 孟令芝

    2005-01-01

    Two-armed neutral anion receptors (4,5), calix[4]arenes beating thiourea and amide binding sites, were prepared and examined their anion-binding ability by the UV-vis spectra. The results of non-linear curve fitting and Job plot indicate that 4 or 5 forms 1:1 stoichiometry complex with fluoride by hydrogen bonding interactions. Receptors 4 and 5 have an excellent selectivity for fluoride but have no binding ability with acetate, dihydrogen phosphate and the halogen anions (Cl-,Br-,I-).

  11. Diabetes and obesity treatment based on dual incretin receptor activation: 'twincretins'

    DEFF Research Database (Denmark)

    Skow, M A; Bergmann, N C; Knop, F K

    2016-01-01

    , whereas GIP seems to affect lipid metabolism. The introduction of selective GLP-1 receptor (GLP-1R) agonists for the treatment of type 2 diabetes and obesity has increased the scientific and clinical interest in incretins. Combining the body weight-lowering and glucose-lowering effects of GLP-1...... with a more potent improvement of β cell function through additional GIP action could potentially offer a more effective treatment of diabetes and obesity, with fewer adverse effects than selective GLP-1R agonists; therefore, new drugs designed to co-activate both the GIP receptor (GIPR) and the GLP-1R...

  12. Bounded solutions for fuzzy differential and integral equations

    Energy Technology Data Exchange (ETDEWEB)

    Nieto, Juan J. [Departamento de Analisis Matematico Facultad de Matematicas Universidad de Santiago de Compostela, 15782 (Spain)] e-mail: amnieto@usc.es; Rodriguez-Lopez, Rosana [Departamento de Analisis Matematico Facultad de Matematicas Universidad de Santiago de Compostela, 15782 (Spain)] e-mail: amrosana@usc.es

    2006-03-01

    We find sufficient conditions for the boundness of every solution of first-order fuzzy differential equations as well as certain fuzzy integral equations. Our results are based on several theorems concerning crisp differential and integral inequalities.

  13. Polymerase chain reaction of Au nanoparticle-bound primers

    Institute of Scientific and Technical Information of China (English)

    SHEN Hebai; HU Min; YANG Zhongnan; WANG Chen; ZHU Longzhang

    2005-01-01

    Polymerase chain reaction (PCR) is a useful technique for in vitro amplification of a DNA fragment. In this paper, a PCR procedure using Au nanoparticle (AuNP) -bound primers was systemically studied. The 5′-SH- (CH2)6-modified primers were covalently attached to the AuNP surface via Au-S bonds, and plasmid pBluescript SK was used as a template. The effects of the concentration of AuNP-bound primers, annealing temperature and PCR cycles were evaluated, respectively. The results indicate that PCR can proceed successfully under optimized condition, with either forward or reverse primers bound to the AuNP surface or with both the two primers bound to the AuNP surface. Development of PCR procedure based on AuNPs not only makes the isolation of PCR products very convenient, but also provides novel methods to prepare AuNP-bound ssDNA and nanostructured material.

  14. Classical and quantum partition bound and detector inefficiency

    CERN Document Server

    Laplante, S; Roland, J

    2012-01-01

    In communication complexity, two players each have an input and they wish to compute some function of the joint inputs. This has been the object of much study and a wide variety of lower bound methods have been introduced to address the problem of showing lower bounds on communication. Recently, Jain and Klauck introduced the partition bound, which subsumes many of the known methods, in particular factorization norm, discrepancy, and the rectangle (corruption) bound. Physicists have considered a closely related scenario where two players share a predefined entangled state. Each is given a measurement as input, which they perform on their share of the system. The outcomes of the measurements follow a distribution which is predicted by quantum mechanics. In an experimental setting, Bell inequalities are used to distinguish truly quantum from classical behavior. We present a new lower bound technique based on the notion of detector inefficiency (where some runs are discarded by either of the players) for the ext...

  15. Refining Castelnuovo-Halphen bounds

    CERN Document Server

    Di Gennaro, Vincenzo

    2011-01-01

    Fix integers $r,d,s,\\pi$ with $r\\geq 4$, $d\\gg s$, $r-1\\leq s \\leq 2r-4$, and $\\pi\\geq 0$. Refining classical results for the genus of a projective curve, we exhibit a sharp upper bound for the arithmetic genus $p_a(C)$ of an integral projective curve $C\\subset {\\mathbb{P}^r}$ of degree $d$, assuming that $C$ is not contained in any surface of degree $ \\pi$. Next we discuss other types of bound for $p_a(C)$, involving conditions on the entire Hilbert polynomial of the integral surfaces on which $C$ may lie.

  16. REE bound DNA in natural plant

    Institute of Scientific and Technical Information of China (English)

    王玉琦; 江平; 郭繁清; 张智勇; 孙景信; 许雷; 曹国印

    1999-01-01

    The binding of rare earth elements (REEs) with nucleic acids in the leaves of fern Dicranopteris dichotoma (DD) has been studied by molecular activation analysis (MAA). The REEs bound DNA (REE-DNA) was obtained from the leaves of DD. The CTAB-based procedure was modified for extraction of total DNA. The purity of DNA was examined by UV spectroscopy. The DNA obtained was separated and determined by agarose gel electrophoresis further. Meanwhile, the contents of eight rare earth elements (La, Ce, Nd, Sm, Eu,Tb, Yb and Lu) in REE-DNA were detected by instrumental neutron activation analysis (INAA). The results showed that REE-DNA with higher purity could be extracted from plant using this method. It was also found that REEs were bound firmly with DNA in the leaves of DD. The molecular weight (MW) of REE-DNA band was about 22 kb in agarose gel electrophoresis.

  17. Mutual information rate and bounds for it.

    Directory of Open Access Journals (Sweden)

    Murilo S Baptista

    Full Text Available The amount of information exchanged per unit of time between two nodes in a dynamical network or between two data sets is a powerful concept for analysing complex systems. This quantity, known as the mutual information rate (MIR, is calculated from the mutual information, which is rigorously defined only for random systems. Moreover, the definition of mutual information is based on probabilities of significant events. This work offers a simple alternative way to calculate the MIR in dynamical (deterministic networks or between two time series (not fully deterministic, and to calculate its upper and lower bounds without having to calculate probabilities, but rather in terms of well known and well defined quantities in dynamical systems. As possible applications of our bounds, we study the relationship between synchronisation and the exchange of information in a system of two coupled maps and in experimental networks of coupled oscillators.

  18. Mutual information rate and bounds for it.

    Science.gov (United States)

    Baptista, Murilo S; Rubinger, Rero M; Viana, Emilson R; Sartorelli, José C; Parlitz, Ulrich; Grebogi, Celso

    2012-01-01

    The amount of information exchanged per unit of time between two nodes in a dynamical network or between two data sets is a powerful concept for analysing complex systems. This quantity, known as the mutual information rate (MIR), is calculated from the mutual information, which is rigorously defined only for random systems. Moreover, the definition of mutual information is based on probabilities of significant events. This work offers a simple alternative way to calculate the MIR in dynamical (deterministic) networks or between two time series (not fully deterministic), and to calculate its upper and lower bounds without having to calculate probabilities, but rather in terms of well known and well defined quantities in dynamical systems. As possible applications of our bounds, we study the relationship between synchronisation and the exchange of information in a system of two coupled maps and in experimental networks of coupled oscillators. PMID:23112809

  19. Reinforcement Learning with Bounded Information Loss

    Science.gov (United States)

    Peters, Jan; Mülling, Katharina; Seldin, Yevgeny; Altun, Yasemin

    2011-03-01

    Policy search is a successful approach to reinforcement learning. However, policy improvements often result in the loss of information. Hence, it has been marred by premature convergence and implausible solutions. As first suggested in the context of covariant or natural policy gradients, many of these problems may be addressed by constraining the information loss. In this paper, we continue this path of reasoning and suggest two reinforcement learning methods, i.e., a model-based and a model free algorithm that bound the loss in relative entropy while maximizing their return. The resulting methods differ significantly from previous policy gradient approaches and yields an exact update step. It works well on typical reinforcement learning benchmark problems as well as novel evaluations in robotics. We also show a Bayesian bound motivation of this new approach [8].

  20. Functional characterisation of the human alpha1 glycine receptor in a fluorescence-based membrane potential assay

    DEFF Research Database (Denmark)

    Jensen, Anders A.; Kristiansen, Uffe

    2004-01-01

    In the present study, we have created a stable HEK293 cell line expressing the human homomeric alpha1 glycine receptor (GlyR) and characterised its functional pharmacology in a conventional patch-clamp assay and in the FLIPR Membrane Potential (FMP) assay, a fluorescence-based high throughput...... and RU 5135>strychnine>brucine>PMBA=picrotoxin>atropine for the antagonists. The actions of three allosteric modulators at the alpha1 GlyR cell line were also characterised in the FMP assay. Micromolar concentrations of Zn2+ inhibited alpha1 GlyR signalling but in contrast to previous reports the metal...... not be suited for sophisticated studies of GlyR pharmacology and kinetics. However, the assay offers several advantages in studies of ligand-receptor interactions. Furthermore, the assay could be highly useful in the search for structurally novel ligands acting at GlyRs....

  1. Fast Fourier Transform-based Support Vector Machine for Prediction of G-protein Coupled Receptor Subfamilies

    Institute of Scientific and Technical Information of China (English)

    Yan-Zhi GUO; Meng-Long LI; Ke-Long WANG; Zhi-Ning WEN; Min-Chun LU; Li-Xia LIU; Lin JIANG

    2005-01-01

    Although the sequence information on G-protein coupled receptors (GPCRs) continues to grow, many GPCRs remain orphaned (i.e. ligand specificity unknown) or poorly characterized with little structural information available, so an automated and reliable method is badly needed to facilitate the identification of novel receptors. In this study, a method of fast Fourier transform-based support vector machine has been developed for predicting GPCR subfamilies according to protein's hydrophobicity. In classifying Class B, C, D and F subfamilies, the method achieved an overall Matthew's correlation coefficient and accuracy of 0.95 and 93.3%, respectively, when evaluated using the jackknife test. The method achieved an accuracy of 100% on the Class B independent dataset. The results show that this method can classify GPCR subfamilies as well as their functional classification with high accuracy. A web server implementing the prediction is available at http://chem.scu.edu.cn/blast/Pred-GPCR.

  2. Attribution to Heterogeneous Risk Factors for Breast Cancer Subtypes Based on Hormone Receptor and Human Epidermal Growth Factor 2 Receptor Expression in Korea.

    Science.gov (United States)

    Park, Boyoung; Choi, Ji-Yeob; Sung, Ho Kyung; Ahn, Choonghyun; Hwang, Yunji; Jang, Jieun; Lee, Juyeon; Kim, Heewon; Shin, Hai-Rim; Park, Sohee; Han, Wonshik; Noh, Dong-Young; Yoo, Keun-Young; Kang, Daehee; Park, Sue K

    2016-04-01

    We conducted a heterogeneous risk assessment of breast cancer based on the hormone receptor (HR) and human epidermal growth factor receptor 2 (HER2) calculating the risks and population-based attributable fractions (PAFs) for modifiable and nonmodifiable factors.Using matched case-control study design from the Seoul Breast Cancer Study and the national prevalence of exposure, the risks and PAFs for modifiable and nonmodifiable factors were estimated for total breast cancers and subtypes.The attribution to modifiable factors was different for each subtype (luminal A, PAF = 61.4% [95% confidence interval, CI = 54.3%-69.8%]; luminal B, 21.4% [95% CI = 18.6-24.9%]; HER2-overexpression, 59.4% [95% CI = 47.8%-74.3%], and triple negative tumors [TNs], 27.1% [95% CI = 22.9%-32.4%)], and the attribution to the modifiable factors for the luminal A and HER2-overexpression subtypes was higher than that of the luminal B and TN subtypes (P heterogeneity  ≤  0.001). The contribution of modifiable reproductive factors to luminal A type in premenopausal women was higher than that of the other subtypes (18.2% for luminal A; 3.1%, 8.1%, and -3.1% for luminal B, HER2-overexpression, and TN subtypes, respectively; P heterogeneity  ≤  0.001). Physical activity had the highest impact preventing 32.6% of luminal A, 14.5% of luminal B, 38.0% of HER2-overexpression, and 26.9% of TN subtypes (P heterogeneity = 0.014). Total reproductive factors were also heterogeneously attributed to each breast cancer subtype (luminal A, 65.4%; luminal B, 24.1%; HER2-overexpression, 57.9%, and TN subtypes, -3.1%; P heterogeneity  ≤  0.001).Each pathological subtype of breast cancer by HRs and HER2 status may be associated with heterogeneous risk factors and their attributable risk, suggesting a different etiology. The luminal B and TN subtypes seemed to be less preventable despite intervention for alleged risk factors, even though physical activity had a high

  3. Scavenger receptor AI/II truncation, lung function and COPD: a large population-based study

    DEFF Research Database (Denmark)

    Thomsen, M; Nordestgaard, B G; Tybjærg-Hansen, Anne;

    2011-01-01

    The scavenger receptor A-I/II (SRA-I/II) on alveolar macrophages is involved in recognition and clearance of modified lipids and inhaled particulates. A rare variant of the SRA-I/II gene, Arg293X, truncates the distal collagen-like domain, which is essential for ligand recognition. We tested whet...

  4. Fipronil-based photoaffinity probe for Drosophila and human beta 3 GABA receptors.

    Science.gov (United States)

    Sirisoma, N S; Ratra, G S; Tomizawa, M; Casida, J E

    2001-11-19

    Modification of the major insecticide fipronil (1) by replacing three pyrazole substituents (hydrogen for both cyano and amino and trifluoromethyldiazirinyl for trifluoromethylsulfinyl) gives a candidate photoaffinity probe (3) of high potency (IC(50) 2-28 nM) in blocking the chloride channel of Drosophila and human beta 3 GABA receptors.

  5. Identification of small-molecule agonists of human relaxin family receptor 1 (RXFP1) by using a homogenous cell-based cAMP assay.

    Science.gov (United States)

    Chen, Catherine Z; Southall, Noel; Xiao, Jingbo; Marugan, Juan J; Ferrer, Marc; Hu, Xin; Jones, Raisa E; Feng, Shu; Agoulnik, Irina U; Zheng, Wei; Agoulnik, Alexander I

    2013-07-01

    The relaxin hormone is involved in a variety of biological functions, including female reproduction and parturition, as well as regulation of cardiovascular, renal, pulmonary, and hepatic functions. It regulates extracellular matrix remodeling, cell invasiveness, proliferation, differentiation, and overall tissue homeostasis. The G protein-coupled receptor (GPCR) relaxin family receptor 1 (RXFP1) is a cognate relaxin receptor that mainly signals through cyclic AMP second messenger. Although agonists of the receptor could have a wide range of pharmacologic utility, until now there have been no reported small-molecule agonists for relaxin receptors. Here, we report the development of a quantitative high-throughput platform for an RXFP1 agonist screen based on homogenous cell-based HTRF cyclic AMP (cAMP) assay technology. Two small molecules of similar structure were independently identified from a screen of more than 365 677 compounds. Neither compound showed activity in a counterscreen with HEK293T cells transfected with an unrelated GPCR vasopressin 1b receptor. These small-molecule agonists also demonstrated selectivity against the RXFP2 receptor, providing a basis for future medicinal chemistry optimization of selective relaxin receptor agonists. PMID:23212924

  6. Resorcarene-based receptor: versatile behavior in its interaction with heavy and soft metal cations.

    Science.gov (United States)

    Danil de Namor, Angela F; Chaaban, Jinane K; Piro, Oscar E; Castellano, Eduardo E

    2006-02-01

    Standard solution Gibbs energies, DeltasG degrees, of the resorcarene-based receptor 5,11,17,23-ethylthiomethylated calix[4]resorcarene, (characterized by 1H NMR and X-ray diffraction studies) in its monomeric state (established through partition experiments) in various solvents are for the first time reported in the area of resorcarene chemistry. Transfer Gibbs energies of from hexane (reference solvent) to other medium are calculated. Agreement between DeltatG degrees (referred to the pure solvents) and standard partition Gibbs energies, DeltapG degrees (solvent mutually saturated) is found. Cation-ligand interactions were investigated through 1H NMR (CD3CN and CD3OD) and conductometric titrations in acetonitrile and methanol. 1H NMR data revealed the sites of interaction of with the metal cation. The composition of the metal-ion complexes (Ag+ and Pb2+ in acetonitrile and Ag+ and Cu2+ in methanol) was established through conductometric titrations. Thus, complexes of 1:1 stoichiometry were formed between and Ag+ and Pb2+ in acetonitrile and Cu2+ in methanol. However, in moving from acetonitrile to methanol, the composition of the silver complex was altered. Thus, two metal cations are hosted by a unit of the ligand. As far as Cu2+ and in acetonitrile is concerned, conductance data suggest that metalates are formed in which up to four units of Cu2+ are taken up per unit of resorcarene. The contrasting behavior of with Cu2+ in acetonitrile relative to methanol is discussed. As far as mercury (II) is concerned, the unusual jump in conductance observed in the titration of Hg2+ with in acetonitrile and methanol after the formation of a multicharged complex (undefined composition) is attributed to the presence of highly charged smaller units (higher mobility) resulting from the departure of pendant arms from the resorcarene backbone. Isolation of these species followed by X-ray diffraction studies corroborated this statement. The thermodynamic characterization of metal

  7. Resorcarene-based receptor: versatile behavior in its interaction with heavy and soft metal cations.

    Science.gov (United States)

    Danil de Namor, Angela F; Chaaban, Jinane K; Piro, Oscar E; Castellano, Eduardo E

    2006-02-01

    Standard solution Gibbs energies, DeltasG degrees, of the resorcarene-based receptor 5,11,17,23-ethylthiomethylated calix[4]resorcarene, (characterized by 1H NMR and X-ray diffraction studies) in its monomeric state (established through partition experiments) in various solvents are for the first time reported in the area of resorcarene chemistry. Transfer Gibbs energies of from hexane (reference solvent) to other medium are calculated. Agreement between DeltatG degrees (referred to the pure solvents) and standard partition Gibbs energies, DeltapG degrees (solvent mutually saturated) is found. Cation-ligand interactions were investigated through 1H NMR (CD3CN and CD3OD) and conductometric titrations in acetonitrile and methanol. 1H NMR data revealed the sites of interaction of with the metal cation. The composition of the metal-ion complexes (Ag+ and Pb2+ in acetonitrile and Ag+ and Cu2+ in methanol) was established through conductometric titrations. Thus, complexes of 1:1 stoichiometry were formed between and Ag+ and Pb2+ in acetonitrile and Cu2+ in methanol. However, in moving from acetonitrile to methanol, the composition of the silver complex was altered. Thus, two metal cations are hosted by a unit of the ligand. As far as Cu2+ and in acetonitrile is concerned, conductance data suggest that metalates are formed in which up to four units of Cu2+ are taken up per unit of resorcarene. The contrasting behavior of with Cu2+ in acetonitrile relative to methanol is discussed. As far as mercury (II) is concerned, the unusual jump in conductance observed in the titration of Hg2+ with in acetonitrile and methanol after the formation of a multicharged complex (undefined composition) is attributed to the presence of highly charged smaller units (higher mobility) resulting from the departure of pendant arms from the resorcarene backbone. Isolation of these species followed by X-ray diffraction studies corroborated this statement. The thermodynamic characterization of metal

  8. An Exact and Grid-free Numerical Scheme for the Hybrid Two Phase Traffic Flow Model Based on the Lighthill-Whitham-Richards Model with Bounded Acceleration

    KAUST Repository

    Qiu, Shanwen

    2012-07-01

    In this article, we propose a new grid-free and exact solution method for computing solutions associated with an hybrid traffic flow model based on the Lighthill- Whitham-Richards (LWR) partial differential equation. In this hybrid flow model, the vehicles satisfy the LWR equation whenever possible, and have a fixed acceleration otherwise. We first present a grid-free solution method for the LWR equation based on the minimization of component functions. We then show that this solution method can be extended to compute the solutions to the hybrid model by proper modification of the component functions, for any concave fundamental diagram. We derive these functions analytically for the specific case of a triangular fundamental diagram. We also show that the proposed computational method can handle fixed or moving bottlenecks.

  9. How much do incentives affect car purchase? Agent-based microsimulation of consumer choice of new cars. Part 1. Model structure, simulation of bounded rationality, and model validation

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, Michel G.; Haan, Peter de [ETH Zurich, Institute for Environmental Decisions, Natural and Social Science Interface, Universitaetstr. 22, CHN J 73.2, 8092 Zurich (Switzerland)

    2009-03-15

    This article presents an agent-based microsimulation capable of forecasting the effects of policy levers that influence individual choices of new passenger cars. The fundamental decision-making units are households distinguished by sociodemographic characteristics and car ownership. A two-stage model of individual decision processes is employed. In the first stage, individual choice sets are constructed using simple, non-compensatory rules that are based on previously owned cars. Second, decision makers evaluate alternatives in their individual choice set using a multi-attributive weighting rule. The attribute weights are based on a multinomial logit model for cross-country policy analysis in European countries. Additionally, prospect theory and the notion of mental accounting are used to model the perception of monetary values. The microsimulation forecasts actual market observations with high accuracy, both on the level of aggregate market characteristics as well as on a highly resolved level of distributions of market shares. The presented approach is useful for the assessment of policies that influence individual purchase decisions of new passenger cars; it allows accounting for a highly resolved car fleet and differentiated consumer segments. As a result, the complexity of incentive schemes can be represented and detailed structural changes can be investigated. (author)

  10. Fine-Tuned Intrinsically Ultramicroporous Polymers Redefine the Permeability/Selectivity Upper Bounds of Membrane-Based Air and Hydrogen Separations

    KAUST Repository

    Swaidan, Raja

    2015-08-20

    Intrinsically ultramicroporous (<7 Å) polymers represent a new paradigm in materials development for membrane-based gas separation. In particular, they demonstrate that uniting intrachain “rigidity”, the traditional design metric of highly permeable polymers of intrinsic microporosity (PIMs), with gas-sieving ultramicroporosity yields high-performance gas separation membranes. Highly ultramicroporous PIMs have redefined the state-of-the-art in large-scale air (e.g., O2/N2) and hydrogen recovery (e.g., H2/N2, H2/CH4) applications with unprecedented molecular sieving gas transport properties. Accordingly, presented herein are new 2015 permeability/selectivity “upper bounds” for large-scale commercial membrane-based air and hydrogen applications that accommodate the substantial performance enhancements of recent PIMs over preceding polymers. A subtle balance between intrachain rigidity and interchain spacing has been achieved in the amorphous microstructures of PIMs, fine-tuned using unique bridged-bicyclic building blocks (i.e., triptycene, ethanoanthracene and Tröger’s base) in both ladder and semiladder (e.g., polyimide) structures.

  11. How much do incentives affect car purchase? Agent-based microsimulation of consumer choice of new cars. Part 1. Model structure, simulation of bounded rationality, and model validation

    International Nuclear Information System (INIS)

    This article presents an agent-based microsimulation capable of forecasting the effects of policy levers that influence individual choices of new passenger cars. The fundamental decision-making units are households distinguished by sociodemographic characteristics and car ownership. A two-stage model of individual decision processes is employed. In the first stage, individual choice sets are constructed using simple, non-compensatory rules that are based on previously owned cars. Second, decision makers evaluate alternatives in their individual choice set using a multi-attributive weighting rule. The attribute weights are based on a multinomial logit model for cross-country policy analysis in European countries. Additionally, prospect theory and the notion of mental accounting are used to model the perception of monetary values. The microsimulation forecasts actual market observations with high accuracy, both on the level of aggregate market characteristics as well as on a highly resolved level of distributions of market shares. The presented approach is useful for the assessment of policies that influence individual purchase decisions of new passenger cars; it allows accounting for a highly resolved car fleet and differentiated consumer segments. As a result, the complexity of incentive schemes can be represented and detailed structural changes can be investigated. (author)

  12. Bounded Densities and Their Derivatives

    DEFF Research Database (Denmark)

    Kozine, Igor; Krymsky, V.

    2009-01-01

    This paper describes how one can compute interval-valued statistical measures given limited information about the underlying distribution. The particular focus is on a bounded derivative of a probability density function and its combination with other available statistical evidence for computing...

  13. Market Access through Bound Tariffs

    DEFF Research Database (Denmark)

    Sala, Davide; Schröder, Philipp J.H.; Yalcin, Erdal

    WTO negotiations deal predominantly with bound - besides applied - tariff rates. But, how can reductions in tariffs ceilings, i.e. tariff rates that no exporter may ever actually be confronted with, generate market access? The answer to this question relates to the effects of tariff bindings on t...

  14. Market access through bound tariffs

    DEFF Research Database (Denmark)

    Sala, Davide; Schröder, Philipp J.H.; Yalcin, Erdal

    2010-01-01

    WTO negotiations deal predominantly with bound - besides applied - tariff rates. But, how can reductions in tariffs ceilings, i.e. tariff rates that no exporter may ever actually be confronted with, generate market access? The answer to this question relates to the effects of tariff bindings on t...

  15. Unconditional lower bounds against advice

    NARCIS (Netherlands)

    H. Buhrman; L. Fortnow; R. Santhanam

    2009-01-01

    We show several unconditional lower bounds for exponential time classes against polynomial time classes with advice, including: (1) For any constant c, NEXP not in P^{NP[n^c]} (2) For any constant c, MAEXP not in MA/n^c (3) BPEXP not in BPP/n^{o(1)}. It was previously unknown even whether NEXP in NP

  16. A Functional Calculus for Quotient Bounded Operators

    Directory of Open Access Journals (Sweden)

    Sorin Mirel Stoian

    2006-12-01

    Full Text Available If (X, P is a sequentially locally convex space, then a quotient bounded operator T beloging to QP is regular (in the sense of Waelbroeck if and only if it is a bounded element (in the sense of Allan of algebra QP. The classic functional calculus for bounded operators on Banach space is generalized for bounded elements of algebra QP.

  17. Similarity of Bovine Rotavirus Receptor and Human Rotavirus Receptor

    Institute of Scientific and Technical Information of China (English)

    苏琦华; 訾自强; 潘菊芬; 徐燕

    2004-01-01

    The monoclonal antibody against bovine rotavirus (BRV) receptor (BRV-R-mAb) was used to explore the similarity between the receptors of BRV and human rotavirus (HRV). ELISA, dot immunobinding assay, cell protection assay, solid-phase assay and immunohistochemistry method were applied. BRV-R-mAb bound both anti-BRV IgG and anti-HRV IgG respectively and could protect MA 104 cells against BRV and HRV challenges. Immunohistochemistry test showed that there were rotavirus receptors on the surfaces of foetal intestinal, tracheal mucosa and MA 104 cells membrane. We purified the rotavirus receptors on MA 104 ceils, which could bind both BRV and HRV in vitro. It is concluded that BRV receptor and HRV receptor are homogenous proteins and can be recognized by both BRV and HRV.

  18. Detection of marine microalgal biotoxins using bioassays based on functional expression of tunicate xenobiotic receptors in yeast.

    Science.gov (United States)

    Richter, Ingrid; Fidler, Andrew E

    2015-03-01

    Marine microalgae can produce biotoxins that cause widespread poisoning in marine ecosystems and may also affect human health. While established microalgal biotoxins are detectable using chemical methods, a need remains for robust, inexpensive bioassays. Ligand-binding domains (LBDs) from a tunicate nuclear receptor, VDR/PXRα, which is orthologous to both the vertebrate pregnane X receptor (PXR) and the vitamin D receptor (VDR), can be activated by microalgal biotoxins when expressed in mammalian cell lines. Building on this observation, we developed a generic recombinant yeast bioassay platform that expresses chimeric proteins containing tunicate VDR/PXRα LBDs which mediate ligand-dependent transcription of a reporter gene (lacZ) encoding an easily assayed enzyme (β-galactosidase). Recombinant yeast strains expressing VDR/PXRα LBDs from two tunicate species, Ciona intestinalis and Botryllus schlosseri, were exposed to both synthetic and natural toxins. Structurally simple synthetic chemicals (n-butyl-p-aminobenzoate, carbamazepine, p-aminobenzoic acid, and bisphenol-A) generated EC50 values in the μM range, while more structurally complex marine biotoxins (okadaic acid, pectenotoxin-11, and portimine) activated the assays in the nM range. Given the large number of tunicate species, we propose that tunicate VDR/PXR LBDs may be used as 'sensor elements' in similar yeast-based high-throughput bioassays for detection of established microalgal biotoxins and uncharacterised marine bioactive compounds.

  19. Detection of marine microalgal biotoxins using bioassays based on functional expression of tunicate xenobiotic receptors in yeast.

    Science.gov (United States)

    Richter, Ingrid; Fidler, Andrew E

    2015-03-01

    Marine microalgae can produce biotoxins that cause widespread poisoning in marine ecosystems and may also affect human health. While established microalgal biotoxins are detectable using chemical methods, a need remains for robust, inexpensive bioassays. Ligand-binding domains (LBDs) from a tunicate nuclear receptor, VDR/PXRα, which is orthologous to both the vertebrate pregnane X receptor (PXR) and the vitamin D receptor (VDR), can be activated by microalgal biotoxins when expressed in mammalian cell lines. Building on this observation, we developed a generic recombinant yeast bioassay platform that expresses chimeric proteins containing tunicate VDR/PXRα LBDs which mediate ligand-dependent transcription of a reporter gene (lacZ) encoding an easily assayed enzyme (β-galactosidase). Recombinant yeast strains expressing VDR/PXRα LBDs from two tunicate species, Ciona intestinalis and Botryllus schlosseri, were exposed to both synthetic and natural toxins. Structurally simple synthetic chemicals (n-butyl-p-aminobenzoate, carbamazepine, p-aminobenzoic acid, and bisphenol-A) generated EC50 values in the μM range, while more structurally complex marine biotoxins (okadaic acid, pectenotoxin-11, and portimine) activated the assays in the nM range. Given the large number of tunicate species, we propose that tunicate VDR/PXR LBDs may be used as 'sensor elements' in similar yeast-based high-throughput bioassays for detection of established microalgal biotoxins and uncharacterised marine bioactive compounds. PMID:25549942

  20. Clinicopathologic Characteristics of Oestrogen Receptor-Positive/Progesterone Receptor-Negative/Her2-Negative Breast Cancer According to a Novel Definition of Negative Progesterone Receptor Status: A Large Population-Based Study from China.

    Directory of Open Access Journals (Sweden)

    An-qi Li

    Full Text Available A lack of progesterone receptor (PgR expression in oestrogen receptor-positive (ER+ tumours is associated with worse survival. PgR status is usually defined as positive or negative using 1% positive nuclei as a cut-off point. In this study, we aimed to assess the clinicopathologic characteristics of ER+/PgR-/HER2- tumours by comparing them with ER+/PgR+/HER2- tumours using a PgR cut-off point of 20% as a divisive criterion.We analysed 1,522 patients with primary breast cancer who had undergone surgery at the Cancer Center of Fudan University between 2012 and 2014. Age, grade, tumour size, lymph node status and lymphovascular invasion were assessed. Multinomial logistic regression, linear regression and chi-square test models were applied to assess associations between ER, PR and clinical features.ER+/PgR-/HER2- tumours showed poorer clinicopathologic characteristics relative to ER+/PgR+/HER2- tumours using a PgR threshold of 20% instead of 1%. The clinicopathologic characteristics did not differ between tumours with purely negative PgR expression and tumours with a PgR percentage ranging from 1% to 19%. The prognostic significance of PR expression appeared more pronounced in patients under a high Ki-67 status than those under a low Ki-67 status.Based on these findings, we propose the use of a novel threshold of 20% to define PgR status. Nevertheless, the impact of this new criterion on patient management and clinical treatment requires additional study.

  1. Stress-based modulation of the immune response in molluscan hemocytes: a two-receptor model

    Directory of Open Access Journals (Sweden)

    R Barcia

    2011-03-01

    Full Text Available In molluscs, hemocytes perform the molecular mechanisms related to immunity. These cells have the ability to respond to the different varieties of stress by modulating their responses. The stressors may be bacterial toxins, cytokines or growth factors, and even physical agents such as changes in temperature or oxygen partial pressure. In the first place, hemocytes synthesise catecholamines, which, in turn, modify the immune response in terms of phagocytosis or nitric oxide synthesis. According to studies on the hemocytes of the mussel Mytilus galloprovincialis, we propose a model for a sequential action where the IL-2 receptor and its wide agonist specificity play an important role. Also, α and β-adrenergic receptors suggest the functioning of a return-to-hemocyte mechanism. The model is proposed taking into account the possible relationship between the pathways mediated by cAMP-activated protein kinase and protein kinase C in hemocytes.

  2. Bases moleculares de la selectividad de ligandos por receptores de melatonina

    OpenAIRE

    Romera, Julia A.; Cortés Cabrera, Álvaro; Sánchez Murcia, Pedro A.; Álvarez Builla, Julio; Gago Badenas, Federico

    2013-01-01

    La hormona melatonina (MT), o N-acetil-5-metoxitriptamina, secretada por la glándula pineal, es responsable de la regulación del sueño y el ritmo circadiano a través de la modulación del núcleo supraquiasmático, entre otras funciones. MT actúa sobre 2 receptores diferentes, MT1 (o MT1A) y MT2 (o MT1B), que funcionan acoplados a proteínas G (GPCR). La propia melatonina y otros agonistas de los receptores MT pueden ser usadas para marcar los ritmos circadianos, facilitar el sueño o ejercer un...

  3. Diversity in anti-N-methyl-D-aspartate receptor encephalitis: case-based evidence

    OpenAIRE

    Pinho, J; Rocha, J.; Rodrigues, M.; Pereira, J.; Maré, R; Ferreira, C; Lourenço, E; Beleza, P

    2012-01-01

    Antibodies against N-methyl-D-aspartate receptor (NMDAR) are identified in the form of immune-mediated encephalitis in which typical manifestations include neuropsychiatric symptoms, seizures, abnormal movements, dysautonomia and hypoventilation. The authors report two cases of anti-NMDAR encephalitis with different presentations and patterns of progression. The first patient presented with status epilepticus and later developed psychosis, pyramidal signs and diffuse encephalopathy. The secon...

  4. Complete manifolds with bounded curvature and spectral gaps

    Science.gov (United States)

    Schoen, Richard; Tran, Hung

    2016-08-01

    We study the spectrum of complete noncompact manifolds with bounded curvature and positive injectivity radius. We give general conditions which imply that their essential spectrum has an arbitrarily large finite number of gaps. In particular, for any noncompact covering of a compact manifold, there is a metric on the base so that the lifted metric has an arbitrarily large finite number of gaps in its essential spectrum. Also, for any complete noncompact manifold with bounded curvature and positive injectivity radius we construct a metric uniformly equivalent to the given one (also of bounded curvature and positive injectivity radius) with an arbitrarily large finite number of gaps in its essential spectrum.

  5. Affinity- and topology-dependent bound on current fluctuations

    CERN Document Server

    Pietzonka, Patrick; Seifert, Udo

    2016-01-01

    We provide a proof of a recently conjectured universal bound on current fluctuations in Markovian processes. This bound establishes a link between the fluctuations of an individual observable current, the cycle affinities driving the system into a non-equilibrium steady state, and the topology of the network. The proof is based on a decomposition of the network into independent cycles with both positive affinity and positive stationary cycle current. This formalism allows for a refinement of the bound for systems in equilibrium or with locally vanishing affinities.

  6. Prediction of binding affinity and efficacy of thyroid hormone receptor ligands using QSAR and structure-based modeling methods

    International Nuclear Information System (INIS)

    The thyroid hormone receptor (THR) is an important member of the nuclear receptor family that can be activated by endocrine disrupting chemicals (EDC). Quantitative Structure–Activity Relationship (QSAR) models have been developed to facilitate the prioritization of THR-mediated EDC for the experimental validation. The largest database of binding affinities available at the time of the study for ligand binding domain (LBD) of THRβ was assembled to generate both continuous and classification QSAR models with an external accuracy of R2 = 0.55 and CCR = 0.76, respectively. In addition, for the first time a QSAR model was developed to predict binding affinities of antagonists inhibiting the interaction of coactivators with the AF-2 domain of THRβ (R2 = 0.70). Furthermore, molecular docking studies were performed for a set of THRβ ligands (57 agonists and 15 antagonists of LBD, 210 antagonists of the AF-2 domain, supplemented by putative decoys/non-binders) using several THRβ structures retrieved from the Protein Data Bank. We found that two agonist-bound THRβ conformations could effectively discriminate their corresponding ligands from presumed non-binders. Moreover, one of the agonist conformations could discriminate agonists from antagonists. Finally, we have conducted virtual screening of a chemical library compiled by the EPA as part of the Tox21 program to identify potential THRβ-mediated EDCs using both QSAR models and docking. We concluded that the library is unlikely to have any EDC that would bind to the THRβ. Models developed in this study can be employed either to identify environmental chemicals interacting with the THR or, conversely, to eliminate the THR-mediated mechanism of action for chemicals of concern. - Highlights: • This is the largest curated dataset for ligand binding domain (LBD) of the THRβ. • We report the first QSAR model for antagonists of AF-2 domain of THRβ. • A combination of QSAR and docking enables prediction of both

  7. Prediction of binding affinity and efficacy of thyroid hormone receptor ligands using QSAR and structure-based modeling methods

    Energy Technology Data Exchange (ETDEWEB)

    Politi, Regina [Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina, Chapel Hill, NC 27599 (United States); Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC 27599 (United States); Rusyn, Ivan, E-mail: iir@unc.edu [Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC 27599 (United States); Tropsha, Alexander, E-mail: alex_tropsha@unc.edu [Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina, Chapel Hill, NC 27599 (United States)

    2014-10-01

    The thyroid hormone receptor (THR) is an important member of the nuclear receptor family that can be activated by endocrine disrupting chemicals (EDC). Quantitative Structure–Activity Relationship (QSAR) models have been developed to facilitate the prioritization of THR-mediated EDC for the experimental validation. The largest database of binding affinities available at the time of the study for ligand binding domain (LBD) of THRβ was assembled to generate both continuous and classification QSAR models with an external accuracy of R{sup 2} = 0.55 and CCR = 0.76, respectively. In addition, for the first time a QSAR model was developed to predict binding affinities of antagonists inhibiting the interaction of coactivators with the AF-2 domain of THRβ (R{sup 2} = 0.70). Furthermore, molecular docking studies were performed for a set of THRβ ligands (57 agonists and 15 antagonists of LBD, 210 antagonists of the AF-2 domain, supplemented by putative decoys/non-binders) using several THRβ structures retrieved from the Protein Data Bank. We found that two agonist-bound THRβ conformations could effectively discriminate their corresponding ligands from presumed non-binders. Moreover, one of the agonist conformations could discriminate agonists from antagonists. Finally, we have conducted virtual screening of a chemical library compiled by the EPA as part of the Tox21 program to identify potential THRβ-mediated EDCs using both QSAR models and docking. We concluded that the library is unlikely to have any EDC that would bind to the THRβ. Models developed in this study can be employed either to identify environmental chemicals interacting with the THR or, conversely, to eliminate the THR-mediated mechanism of action for chemicals of concern. - Highlights: • This is the largest curated dataset for ligand binding domain (LBD) of the THRβ. • We report the first QSAR model for antagonists of AF-2 domain of THRβ. • A combination of QSAR and docking enables

  8. Invited review: Growth-promoting effects of colostrum in calves based on interaction with intestinal cell surface receptors and receptor-like transporters.

    Science.gov (United States)

    Ontsouka, Edgar C; Albrecht, Christiane; Bruckmaier, Rupert M

    2016-06-01

    The postnatal development and maturation of the gastrointestinal (GI) tract of neonatal calves is crucial for their survival. Major morphological and functional changes in the calf's GI tract initiated by colostrum bioactive substances promote the establishment of intestinal digestion and absorption of food. It is generally accepted that colostrum intake provokes the maturation of organs and systems in young calves, illustrating the significance of the cow-to-calf connection at birth. These postnatal adaptive changes of the GI tissues in neonatal calves are especially induced by the action of bioactive substances such as insulin-like growth factors, hormones, or cholesterol carriers abundantly present in colostrum. These substances interact with specific cell-surface receptors or receptor-like transporters expressed in the GI wall of neonatal calves to elicit their biological effects. Therefore, the abundance and activity of cell surface receptors and receptor-like transporters binding colostral bioactive substances are a key aspect determining the effects of the cow-to-calf connection at birth. The present review compiles the information describing the effects of colostrum feeding on selected serum metabolic and endocrine traits in neonatal calves. In this context, the current paper discusses specifically the consequences of colostrum feeding on the GI expression and activity of cell-receptors and receptor-like transporters binding growth hormone, insulin-like growth factors, insulin, or cholesterol acceptors in neonatal calves. PMID:26874414

  9. Profiling epidermal growth factor receptor and heregulin receptor 3 heteromerization using receptor tyrosine kinase heteromer investigation technology.

    Directory of Open Access Journals (Sweden)

    Mohammed Akli Ayoub

    Full Text Available Heteromerization can play an important role in regulating the activation and/or signal transduction of most forms of receptors, including receptor tyrosine kinases (RTKs. The study of receptor heteromerization has evolved extensively with the emergence of resonance energy transfer based approaches such as bioluminescence resonance energy transfer (BRET. Here, we report an adaptation of our Receptor-Heteromer Investigation Technology (Receptor-HIT that has recently been published as the G protein-coupled receptor (GPCR Heteromer Identification Technology (GPCR-HIT. We now demonstrate the utility of this approach for investigating RTK heteromerization by examining the functional interaction between the epidermal growth factor (EGF receptor (EGFR; also known as erbB1/HER1 and heregulin (HRG receptor 3 (HER3; also known as erbB3 in live HEK293FT cells using recruitment of growth factor receptor-bound protein 2 (Grb2 to the activated receptors. We found that EGFR and HER3 heteromerize specifically as demonstrated by HRG inducing a BRET signal between EGFR/Rluc8 and Grb2/Venus only when HER3 was co-expressed. Similarly, EGF stimulation promoted a specific BRET signal between HER3/Rluc8 and Grb2/Venus only when EGFR was co-expressed. Both EGF and HRG effects on Grb2 interaction are dose-dependent, and specifically blocked by EGFR inhibitor AG-1478. Furthermore, truncation of HER3 to remove the putative Grb2 binding sites appears to abolish EGF-induced Grb2 recruitment to the EGFR-HER3 heteromer. Our results support the concept that EGFR interacts with Grb2 in both constitutive and EGF-dependent manners and this interaction is independent of HER3 co-expression. In contrast, HER3-Grb2 interaction requires the heteromerization between EGFR and HER3. These findings clearly indicate the importance of EGFR-HER3 heteromerization in HER3-mediated Grb2-dependent signaling pathways and supports the central role of HER3 in the diversity and regulation of HER

  10. Probing charge transfer in a novel class of luminescent perovskite-based heterostructures composed of quantum dots bound to RE-activated CaTiO3 phosphors

    Science.gov (United States)

    Lewis, Crystal S.; Liu, Haiqing; Han, Jinkyu; Wang, Lei; Yue, Shiyu; Brennan, Nicholas A.; Wong, Stanislaus S.

    2016-01-01

    We report on the synthesis and structural characterization of novel semiconducting heterostructures composed of cadmium selenide (CdSe) quantum dots (QDs) attached onto the surfaces of novel high-surface area, porous rare-earth-ion doped alkaline earth titanate micron-scale spherical motifs, i.e. both Eu-doped and Pr-doped CaTiO3, composed of constituent, component nanoparticles. These unique metal oxide perovskite building blocks were created by a multi-pronged synthetic strategy involving molten salt and hydrothermal protocols. Subsequently, optical characterization of these heterostructures indicated a clear behavioral dependence of charge transfer in these systems upon a number of parameters such as the nature of the dopant, the reaction temperature, and particle size. Specifically, 2.7 nm diameter ligand-functionalized CdSe QDs were anchored onto sub-micron sized CaTiO3-based spherical assemblies, prepared by molten salt protocols. We found that both the Pr- and Eu-doped CaTiO3 displayed pronounced PL emissions, with maximum intensities observed using optimized lanthanide concentrations of 0.2 mol% and 6 mol%, respectively. Analogous experiments were performed on Eu-doped BaTiO3 and SrTiO3 motifs, but CaTiO3 still performed as the most effective host material amongst the three perovskite systems tested. Moreover, the ligand-capped CdSe QD-doped CaTiO3 heterostructures exhibited effective charge transfer between the two individual constituent nanoscale components, an assertion corroborated by the corresponding quenching of their measured PL signals.We report on the synthesis and structural characterization of novel semiconducting heterostructures composed of cadmium selenide (CdSe) quantum dots (QDs) attached onto the surfaces of novel high-surface area, porous rare-earth-ion doped alkaline earth titanate micron-scale spherical motifs, i.e. both Eu-doped and Pr-doped CaTiO3, composed of constituent, component nanoparticles. These unique metal oxide perovskite

  11. Physics with loosely bound nuclei

    Indian Academy of Sciences (India)

    Chhanda Samanta

    2001-08-01

    The essential aspect of contemporary physics is to understand properties of nucleonic matter that constitutes the world around us. Over the years research in nuclear physics has provided strong guidance in understanding the basic principles of nuclear interactions. But, the scenario of nuclear physics changed drastically as the new generation of accelerators started providing more and more rare isotopes, which are away from the line of stability. These weakly bound nuclei are found to exhibit new forms of nuclear matter and unprecedented exotic behaviour. The low breakup thresholds of these rare nuclei are posing new challenges to both theory and experiments. Fortunately, nature has provided a few loosely bound stable nuclei that have been studied thoroughly for decades. Attempts are being made to find a consistent picture for the unstable nuclei starting from their stable counterparts. Some significant differences in the structure and reaction mechanisms are found.

  12. Concentration Bounds for Stochastic Approximations

    CERN Document Server

    Frikha, Noufel

    2012-01-01

    We obtain non asymptotic concentration bounds for two kinds of stochastic approximations. We first consider the deviations between the expectation of a given function of the Euler scheme of some diffusion process at a fixed deterministic time and its empirical mean obtained by the Monte-Carlo procedure. We then give some estimates concerning the deviation between the value at a given time-step of a stochastic approximation algorithm and its target. Under suitable assumptions both concentration bounds turn out to be Gaussian. The key tool consists in exploiting accurately the concentration properties of the increments of the schemes. For the first case, as opposed to the previous work of Lemaire and Menozzi (EJP, 2010), we do not have any systematic bias in our estimates. Also, no specific non-degeneracy conditions are assumed.

  13. Self-assembled tetra- and pentanuclear nickel(II) aggregates from phenoxido-based ligand -bound {Ni2} fragments: carboxylate bridge controlled structures.

    Science.gov (United States)

    Ghosh, Aloke Kumar; Shatruk, Michael; Bertolasi, Valerio; Pramanik, Kausikisankar; Ray, Debashis

    2013-12-16

    Three different carboxylato bridges (R = C2H5, CF3, and PhCH2 in RCO2(-)) have been used to obtain the supramolecular aggregates [Ni5(μ-H2bpmp)2(μ3-OH)2(μ1,3-O2CC2H5)6]·2H2O·4DMF (1·2H2O·4DMF), [Ni4(μ3-H2bpmp)2(μ3-OH)2(μ1,3-O2CCF3)2](CF3CO2)2·H2O (2·H2O), and [Ni4(μ3-H2bpmp)2(μ3-OH)2(μ1,3-O2CCH2Ph)2](PhCH2CO2)2·4H2O (3·4H2O) (H3bpmp =2,6-bis-[(3-hydroxy-propylimino)-methyl]-4-methyl-phenol) from the hydroxido-bridged dinuclear motif [Ni2(μ-H2bpmp)(OH)](2+). These complexes have been characterized by X-ray crystallography and magnetic measurements. A change from propanoate group to trifluoroacetate and phenylaceate groups provided different course of cluster assembly based on Ni2(μ-H2bpmp)2 fragments. The {Ni5(μ3-OH)2(μ1,3-O2CC2H5)6}(2+) core in 1 contains five Ni(II) ions in an hourglass (pentanuclear vertex-shared double cubane) arrangement. These compounds are new examples of [Ni5] and [Ni4] complexes where aggregation of the building motifs are guided by the nature of the carboxylate anions, which allows an effective tuning of the self-aggregate process within same ligand environment. The study of the magnetic properties reveals that 1 exhibits an S = 3 ground state. Nevertheless, the magnetization increases above the expected saturation value of 6 μB at higher fields, because of the suppression of antiferromagnetic exchange between the central and peripheral Ni(II) ions. Complexes 2 and 3 exhibit ferromagnetic exchange interactions that result in the S = 4 ground state. Examination of AC magnetic susceptibility showed that complex 2 in finely ground form behaves as spin glass with the spin-freezing temperature of ∼5.5 K. This behavior was attributed to the collapse of the structure upon the loss of interstitial solvent. Such property was not observed for complex 3, in which the bulkier carboxylate ligands provide for a more robust crystal packing and larger separation between the [Ni4O4] clusters. PMID:24295223

  14. Structure-based stabilization of HIV-1 gp120 enhances humoral immune responses to the induced co-receptor binding site.

    Directory of Open Access Journals (Sweden)

    Barna Dey

    2009-05-01

    Full Text Available The human immunodeficiency virus type 1 (HIV-1 exterior envelope glycoprotein, gp120, possesses conserved binding sites for interaction with the primary virus receptor, CD4, and also for the co-receptor, generally CCR5. Although gp120 is a major target for virus-specific neutralizing antibodies, the gp120 variable elements and its malleable nature contribute to evasion of effective host-neutralizing antibodies. To understand the conformational character and immunogenicity of the gp120 receptor binding sites as potential vaccine targets, we introduced structure-based modifications to stabilize gp120 core proteins (deleted of the gp120 major variable regions into the conformation recognized by both receptors. Thermodynamic analysis of the re-engineered core with selected ligands revealed significant stabilization of the receptor-binding regions. Stabilization of the co-receptor-binding region was associated with a marked increase in on-rate of ligand binding to this site as determined by surface plasmon resonance. Rabbit immunization studies showed that the conformational stabilization of core proteins, along with increased ligand affinity, was associated with strikingly enhanced humoral immune responses against the co-receptor-binding site. These results demonstrate that structure-based approaches can be exploited to stabilize a conformational site in a large functional protein to enhance immunogenic responses specific for that region.

  15. The role of patient-based treatment planning in peptide receptor radionuclide therapy

    Energy Technology Data Exchange (ETDEWEB)

    Hardiansyah, Deni; Attarwala, Ali Asgar [Heidelberg University, Medical Radiation Physics/Radiation Protection, Universitaetsmedizin Mannheim, Medical Faculty Mannheim, Mannheim (Germany); Universitaetsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Department of Radiation Oncology, Mannheim (Germany); Maass, Christian; Glatting, Gerhard [Heidelberg University, Medical Radiation Physics/Radiation Protection, Universitaetsmedizin Mannheim, Medical Faculty Mannheim, Mannheim (Germany); Mueller, Berthold [University Hospital, RWTH Aachen University, Klinik fuer Nuklearmedizin, Aachen (Germany); Kletting, Peter [Universitaet Ulm, Klinik fuer Nuklearmedizin, Ulm (Germany); Mottaghy, Felix M. [University Hospital, RWTH Aachen University, Klinik fuer Nuklearmedizin, Aachen (Germany); Maastricht University Medical Center (MUMC+), Department of Nuclear Medicine, Maastricht (Netherlands)

    2016-05-15

    Accurate treatment planning is recommended in peptide-receptor radionuclide therapy (PRRT) to minimize the toxicity to organs at risk while maximizing tumor cell sterilization. The aim of this study was to quantify the effect of different degrees of individualization on the prediction accuracy of individual therapeutic biodistributions in patients with neuroendocrine tumors (NETs). A recently developed physiologically based pharmacokinetic (PBPK) model was fitted to the biokinetic data of 15 patients with NETs after pre-therapeutic injection of {sup 111}In-DTPAOC. Mathematical phantom patients (MPP) were defined using the assumed true (true MPP), mean (MPP 1A) and median (MPP 1B) parameter values of the patient group. Alterations of the degree of individualization were introduced to both mean and median patients by including patient-specific information as a priori knowledge: physical parameters and hematocrit (MPP 2A/2B). Successively, measurable individual biokinetic parameters were added: tumor volume V{sub tu} (MPP 3A/3B), glomerular filtration rate GFR (MPP 4A/4B), and tumor perfusion f{sub tu} (MPP 5A/5B). Furthermore, parameters of MPP 5A/5B and a simulated {sup 68}Ga-DOTATATE PET measurement 60 min p.i. were used together with the population values used as Bayesian parameters (MPP 6A/6B). Therapeutic biodistributions were simulated assuming an infusion of {sup 90}Y-DOTATATE (3.3 GBq) over 30 min to all MPPs. Time-integrated activity coefficients were predicted for all MPPs and compared to the true MPPs for each patient in tumor, kidneys, spleen, liver, remainder, and whole body to obtain the relative differences RD. The large RD values of MPP 1A [RD{sub tumor} = (625 ± 1266)%, RD{sub kidneys} = (11 ± 38)% ], and MPP 1B [RD{sub tumor} = (197 ± 505)%, RD{sub kidneys} = (11 ± 39)% ] demonstrate that individual treatment planning is needed due to large physiological differences between patients. Although addition of individual patient parameters reduced the

  16. Entropy Bounds in Spherical Space

    CERN Document Server

    Brevik, I; Odintsov, S D; Brevik, Iver; Milton, Kimball A.; Odintsov, Sergei D.

    2002-01-01

    Exact calculations are given for the Casimir energy for various fields in $R\\times S^3$ geometry. The Green's function method naturally gives a result in a form convenient in the high-temperature limit, while the statistical mechanical approach gives a form appropriate for low temperatures. The equivalence of these two representations is demonstrated. Some discrepancies with previous work are noted. In no case, even for ${\\cal N}=4$ SUSY, is the ratio of entropy to energy found to be bounded.

  17. Quantitative analysis of G-protein-coupled receptor internalization using DnaE intein-based assay.

    Science.gov (United States)

    Lu, Bin; Chen, Linjie; Zhang, Yaping; Shi, Ying; Zhou, Naiming

    2016-01-01

    G-protein-coupled receptors (GPCRs), the largest family of cell surface receptors, are involved in many physiological processes. They represent highly important therapeutic targets for drug discovery. Currently, there are numerous cell-based assays developed for the pharmacological profiling of GPCRs and the identification of novel agonists and antagonists. However, the development of new, faster, easier, and more cost-effective approaches to detect GPCR activity remains highly desirable. β-arrestin-dependent internalization has been demonstrated to be a common mechanism for most GPCRs. Here we describe a novel assay for quantitative analysis of GPCR internalization based on DnaE intein-mediated reconstitution of fragmented Renilla luciferase or Firefly luciferase when activated GPCRs interact with β-arrestin2 or Rab5. Further validation, using functionally divergent GPCRs, showed that EC50 values obtained for the known agonists and antagonists were in close agreement with the results of previous reports. This suggests that this assay is sensitive enough to permit quantification of GPCR internalization. Compared with conventional assays, this novel assay system is cost-effective, rapid, and easy to manipulate. These advantages may allow this assay to be used universally as a functional cell-based system for GPCR characterization and in the screening process of drug discovery. PMID:26928549

  18. Interaction of magnetite-based receptors in the beak with the visual system underlying 'fixed direction' responses in birds

    Directory of Open Access Journals (Sweden)

    Wiltschko Roswitha

    2010-08-01

    Full Text Available Abstract Background European robins, Erithacus rubecula, show two types of directional responses to the magnetic field: (1 compass orientation that is based on radical pair processes and lateralized in favor of the right eye and (2 so-called 'fixed direction' responses that originate in the magnetite-based receptors in the upper beak. Both responses are light-dependent. Lateralization of the 'fixed direction' responses would suggest an interaction between the two magnetoreception systems. Results Robins were tested with either the right or the left eye covered or with both eyes uncovered for their orientation under different light conditions. With 502 nm turquoise light, the birds showed normal compass orientation, whereas they displayed an easterly 'fixed direction' response under a combination of 502 nm turquoise with 590 nm yellow light. Monocularly right-eyed birds with their left eye covered were oriented just as they were binocularly as controls: under turquoise in their northerly migratory direction, under turquoise-and-yellow towards east. The response of monocularly left-eyed birds differed: under turquoise light, they were disoriented, reflecting a lateralization of the magnetic compass system in favor of the right eye, whereas they continued to head eastward under turquoise-and-yellow light. Conclusion 'Fixed direction' responses are not lateralized. Hence the interactions between the magnetite-receptors in the beak and the visual system do not seem to involve the magnetoreception system based on radical pair processes, but rather other, non-lateralized components of the visual system.

  19. 78 FR 18326 - Agency Information Collection Activities; Comment Request; Upward Bound and Upward Bound Math...

    Science.gov (United States)

    2013-03-26

    ... Agency Information Collection Activities; Comment Request; Upward Bound and Upward Bound Math Science... Upward Bound Math Science Annual Performance Report. OMB Control Number: 1840-NEW. Type of Review: New... under the regular Upward Bound (UB) and Upward Bound Math and Science (UBMS) Programs. The Department...

  20. Monte Carlo study of receptor-lipid raft formation on a cell membrane

    Science.gov (United States)

    Yu-Yang, Paul; Srinivas Reddy, A.; Raychaudhuri, Subhadip

    2012-02-01

    Receptors are cell surface molecules that bind with extracellular ligand molecules leading to propagation of downstream signals and cellular activation. Even though ligand binding-induced formation of receptor-lipid rafts has been implicated in such a process, the formation mechanism of such large stable rafts is not understood. We present findings from our Monte Carlo (MC) simulations involving (i) receptor interaction with the membrane lipids and (ii) lipid-lipid interactions between raft forming lipids. We have developed a hybrid MC simulation method that combines a probabilistic MC simulation with an explicit free energy-based MC scheme. Some of the lipid-mediated interactions, such as the cholesterol-lipid interactions, are simulated in an implicit way. We examine the effect of varying attractive interactions between raft forming lipids and ligand-bound receptors and show that strong coupling between receptor-receptor and receptor-sphingolipid molecules generate raft formation similar to that observed in recent biological experiments. We study the effect of variation of receptor affinity for ligands (as happens in adaptive immune cells) on raft formation. Such affinity dependence in receptor-lipid raft formation provides insight into important problems in B cell biology.

  1. Description of Wiener bounds of multicomponent composites by barycentric coordinates

    Science.gov (United States)

    Peiponen, Kai-Erik; Gornov, Evgeny

    2006-07-01

    Wiener bounds for effective complex permittivity of multicomponent composites are treated by use of barycentric coordinates, a convex hull, and conformal mapping in a complex plane. Depending on the complexity of the multiphase system, the bounds provide singly or multiply connected regions that can be used in estimating the limits of the effective permittivity of the composite. The present modeling is important, e.g., in estimating spectral properties of nanocomposites in engineering and nanomedicine and in terahertz-based security imaging.

  2. Bounds for Regularity and Coregularity of Graded Modules

    Indian Academy of Sciences (India)

    Reza Sazeedeh

    2007-11-01

    Let be a finitely generated graded module over a Noetherian homogeneous ring with local base ring $(R_0,\\mathfrak{m}_0)$. If 0 is of dimension one, then we show that $\\mathrm{reg}^i+1(M)$ and $\\mathrm{coreg}^{i+1}(M)$ are bounded for all $i\\in\\mathbb{N}_0$. We improve these bounds, if in addition, 0 is either regular or analytically irreducible of unequal characteristic.

  3. Bound Alternative Direction Optimization for Image Deblurring

    Directory of Open Access Journals (Sweden)

    Xiangrong Zeng

    2014-01-01

    the ℓp regularizer by a novel majorizer and then, based on a variable splitting, to reformulate the bound unconstrained problem into a constrained one, which is then addressed via an augmented Lagrangian method. The proposed algorithm actually combines the reweighted ℓ1 minimization method and the alternating direction method of multiples (ADMM such that it succeeds in extending the application of ADMM to ℓp minimization problems. The conducted experimental studies demonstrate the superiority of the proposed algorithm for the synthesis ℓp minimization over the state-of-the-art algorithms for the synthesis ℓ1 minimization on image deblurring.

  4. The Mathematics of a Successful Deconvolution: A Quantitative Assessment of Mixture-Based Combinatorial Libraries Screened Against Two Formylpeptide Receptors

    Science.gov (United States)

    Santos, Radleigh G.; Appel, Jon R.; Giulianotti, Marc A.; Edwards, Bruce S.; Sklar, Larry A.; Houghten, Richard A.; Pinilla, Clemencia

    2014-01-01

    In the past 20 years, synthetic combinatorial methods have fundamentally advanced the ability to synthesize and screen large numbers of compounds for drug discovery and basic research. Mixture-based libraries and positional scanning deconvolution combine two approaches for the rapid identification of specific scaffolds and active ligands. Here we present a quantitative assessment of the screening of 32 positional scanning libraries in the identification of highly specific and selective ligands for two formylpeptide receptors. We also compare and contrast two mixture-based library approaches using a mathematical model to facilitate the selection of active scaffolds and libraries to be pursued for further evaluation. The flexibility demonstrated in the differently formatted mixture-based libraries allows for their screening in a wide range of assays. PMID:23722730

  5. Granger causality in wall-bounded turbulence

    International Nuclear Information System (INIS)

    Granger causality is based on the idea that if a variable helps to predict another one, then they are probably involved in a causality relationship. This technique is based on the identification of a predictive model for causality detection. The aim of this paper is to use Granger causality to study the dynamics and the energy redistribution between scales and components in wall-bounded turbulent flows. In order to apply it on flows, Granger causality is generalized for snapshot-based observations of large size using linear-model identification methods coming from model reduction. Optimized DMD, a variant of the Dynamic Mode Decomposition, is considered for building a linear model based on snapshots. This method is used to link physical events and extract physical mechanisms associated to the bursting process in the logarithmic layer of a turbulent channel flow.

  6. Bacteriophage receptor binding protein based assays for the simultaneous detection of Campylobacter jejuni and Campylobacter coli.

    Science.gov (United States)

    Javed, Muhammad A; Poshtiban, Somayyeh; Arutyunov, Denis; Evoy, Stephane; Szymanski, Christine M

    2013-01-01

    Campylobacter jejuni and Campylobacter coli are the most common bacterial causes of foodborne gastroenteritis which is occasionally followed by a debilitating neuropathy known as Guillain-Barré syndrome. Rapid and specific detection of these pathogens is very important for effective control and quick treatment of infection. Most of the diagnostics available for these organisms are time consuming and require technical expertise with expensive instruments and reagents to perform. Bacteriophages bind to their host specifically through their receptor binding proteins (RBPs), which can be exploited for pathogen detection. We recently sequenced the genome of C. jejuni phage NCTC12673 and identified its putative host receptor binding protein, Gp047. In the current study, we localized the receptor binding domain to the C-terminal quarter of Gp047. CC-Gp047 could be produced recombinantly and was capable of agglutinating both C. jejuni and C. coli cells unlike the host range of the parent phage which is limited to a subset of C. jejuni isolates. The agglutination procedure could be performed within minutes on a glass slide at room temperature and was not hindered by the presence of buffers or nutrient media. This agglutination assay showed 100% specificity and the sensitivity was 95% for C. jejuni (n = 40) and 90% for C. coli (n = 19). CC-Gp047 was also expressed as a fusion with enhanced green fluorescent protein (EGFP). Chimeric EGFP_CC-Gp047 was able to specifically label C. jejuni and C. coli cells in mixed cultures allowing for the detection of these pathogens by fluorescent microscopy. This study describes a simple and rapid method for the detection of C. jejuni and C. coli using engineered phage RBPs and offers a promising new diagnostics platform for healthcare and surveillance laboratories.

  7. Bacteriophage receptor binding protein based assays for the simultaneous detection of Campylobacter jejuni and Campylobacter coli.

    Directory of Open Access Journals (Sweden)

    Muhammad A Javed

    Full Text Available Campylobacter jejuni and Campylobacter coli are the most common bacterial causes of foodborne gastroenteritis which is occasionally followed by a debilitating neuropathy known as Guillain-Barré syndrome. Rapid and specific detection of these pathogens is very important for effective control and quick treatment of infection. Most of the diagnostics available for these organisms are time consuming and require technical expertise with expensive instruments and reagents to perform. Bacteriophages bind to their host specifically through their receptor binding proteins (RBPs, which can be exploited for pathogen detection. We recently sequenced the genome of C. jejuni phage NCTC12673 and identified its putative host receptor binding protein, Gp047. In the current study, we localized the receptor binding domain to the C-terminal quarter of Gp047. CC-Gp047 could be produced recombinantly and was capable of agglutinating both C. jejuni and C. coli cells unlike the host range of the parent phage which is limited to a subset of C. jejuni isolates. The agglutination procedure could be performed within minutes on a glass slide at room temperature and was not hindered by the presence of buffers or nutrient media. This agglutination assay showed 100% specificity and the sensitivity was 95% for C. jejuni (n = 40 and 90% for C. coli (n = 19. CC-Gp047 was also expressed as a fusion with enhanced green fluorescent protein (EGFP. Chimeric EGFP_CC-Gp047 was able to specifically label C. jejuni and C. coli cells in mixed cultures allowing for the detection of these pathogens by fluorescent microscopy. This study describes a simple and rapid method for the detection of C. jejuni and C. coli using engineered phage RBPs and offers a promising new diagnostics platform for healthcare and surveillance laboratories.

  8. Somatostatin receptor expression and biological functions in endocrine pancreatic cells: review based on a doctoral thesis.

    Science.gov (United States)

    Ludvigsen, Eva

    2007-01-01

    Type 1 diabetes is resulting from the selective destruction of insulin-producing betacells within the pancreatic islets. Somatostatin acts as an inhibitor of hormone secretion through specific receptors (sst1-5). All ssts were expressed in normal rat and mouse pancreatic islets, although the expression intensity and the co-expression pattern varied between ssts as well as between species. This may reflect a difference in response to somatostatin in islet cells of the two species. The Non-Obese Diabetic (NOD) mouse model is an experimental model of type 1 diabetes, with insulitis accompanied by spontaneous hyperglycaemia. Pancreatic specimens from NOD mice at different age and stage of disease were stained for ssts. The islet cells of diabetic NOD mice showed increased islet expression of sst2-5 compared to normoglycemic NOD mice. The increase in sst2-5 expression in the islets cells may suggest either a contributing factor in the process leading to diabetes, or a defense response against ongoing beta-cell destruction. Somatostatin analogues were tested on a human endocrine pancreatic tumour cell line and cultured pancreatic islets. Somatostatin analogues had an effect on cAMP accumulation, chromogranin A secretion and MAP kinase activity in the cell line. Treatment of rat pancreatic islets with somatostatin analogues with selective receptor affinity was not sufficient to induce an inhibition of insulin and glucagon secretion. However, a combination of selective analogues or non-selective analogues via costimulation of receptors can cause inhibition of hormone production. For insulin and glucagon, combinations of sst2 + sst5 and sst1 + sst2, respectively, showed a biological effect. In summary, knowledge of islet cell ssts expression and the effect of somatostatin analogues with high affinity to ssts may be valuable in the future attempts to influence beta-cell function in type 1 diabetes mellitus, since down-regulation of beta-cell function may promote survival of

  9. Multiscale design of coarse-grained elastic network-based potentials for the μ opioid receptor.

    Science.gov (United States)

    Fossépré, Mathieu; Leherte, Laurence; Laaksonen, Aatto; Vercauteren, Daniel P

    2016-09-01

    Despite progress in computer modeling, most biological processes are still out of reach when using all-atom (AA) models. Coarse-grained (CG) models allow classical molecular dynamics (MD) simulations to be accelerated. Although simplification of spatial resolution at different levels is often investigated, simplification of the CG potential in itself has been less common. CG potentials are often similar to AA potentials. In this work, we consider the design and reliability of purely mechanical CG models of the μ opioid receptor (μOR), a G protein-coupled receptor (GPCR). In this sense, CG force fields (FF) consist of a set of holonomic constraints guided by an elastic network model (ENM). Even though ENMs are used widely to perform normal mode analysis (NMA), they are not often implemented as a single FF in the context of MD simulations. In this work, various ENM-like potentials were investigated by varying their force constant schemes and connectivity patterns. A method was established to systematically parameterize ENM-like potentials at different spatial resolutions by using AA data. To do so, new descriptors were introduced. The choice of conformation descriptors that also include flexibility information is important for a reliable parameterization of ENMs with different degrees of sensitivity. Hence, ENM-like potentials, with specific parameters, can be sufficient to accurately reproduce AA MD simulations of μOR at highly coarse-grained resolutions. Therefore, the essence of the flexibility properties of μOR can be captured with simple models at different CG spatial resolutions, opening the way to mechanical approaches to understanding GPCR functions. Graphical Abstract All atom structure, residue interaction network and coarse-grained elastic network models of the μ opioid receptor (μOR). PMID:27566318

  10. Targeted cancer therapies based on antibodies directed against epidermal growth factor receptor: status and perspectives

    Institute of Scientific and Technical Information of China (English)

    Zhenping ZHU

    2007-01-01

    Compelling experimental and clinical evidence suggests that epidermal growth factor receptor (EGFR) plays an important role in the pathogenesis of a variety of human cancers; thus, providing a strong rationale for the development of receptor antagonists as effective and specific therapeutic strategies for the treatment of EGFR-expressing cancers. Monoclonal antibodies (mAb), owing to their high specificity towards a given target, represent a unique class of novel cancer therapeutics. A number of anti-EGFR mAb are currently being developed in our clinic, including two that have been approved by the United States Food and Drug Administration for the treatment of refractory metastatic colorectal cancer (mCRC) and squamous cell carcinomas of the head and neck (SCCHN). Cetuximab (Erbitux, IMC-C225), an IgG 1 mAb, has demonstrated significant antitumor activity,both as a single agent and in combination with chemotherapeutics and radiation,in patients with refractory mCRC and SCCHN, respectively. Panitumumab(Vectibix), an IgG2 mAb, has been approved as a single agent for the treatment of patients with refractory mCRC. These mAb, via blocking ligand/receptor interactions, exert their biological activity via multiple mechanisms, includinginhibition of cell cycle progression, potentiation of cell apoptosis, inhibition of DNA repair, inhibition of angiogenesis, tumor cell invasion and metastasis and,potentially, induction of immunological effector mechanisms. Anti-EGFR anti-bodies have demonstrated good safety profiles and potent anticancer activity in our clinic and may prove to be efficacious agents in the treatment of a variety of human malignancies.

  11. Individual-Based Simulation of the Clustering Behaviour of Epidermal Growth Factor Receptors

    Directory of Open Access Journals (Sweden)

    Jacki P. Goldman

    2004-01-01

    Full Text Available This paper describes ongoing work on a project to simulate the behaviour of epidermal growth factor receptors. These are structures which can be found on the surface of cells in the body, which receive and process chemical signals concerned with cell growth. The implementation of a program which simulates the stimulation and clustering behaviour of these structures is described, then the paper discusses how the simulation can be scaled up so that a whole cell can be simulated on a tractable timescale. Finally some early results are given which show the effect of changing parameters in the system, and discuss ongoing work on calibrating the simulation against results from experiments.

  12. Bounded Delay Packet Scheduling in a Bounded Buffer

    CERN Document Server

    Fung, Stanley P Y

    2009-01-01

    We study the problem of buffer management in QoS-enabled network switches in the bounded delay model where each packet is associated with a weight and a deadline. We consider the more realistic situation where the network switch has a finite buffer size. A 9.82-competitive algorithm is known for the case of multiple buffers (Azar and Levy, SWAT'06). Recently, for the case of a single buffer, a 3-competitive deterministic algorithm and a 2.618-competitive randomized algorithm was known (Li, INFOCOM'09). In this paper we give a simple deterministic 2-competitive algorithm for the case of a single buffer.

  13. Functional characterisation of homomeric ionotropic glutamate receptors GluR1-GluR6 in a fluorescence-based high throughput screening assay

    DEFF Research Database (Denmark)

    Strange, Mette; Bräuner-Osborne, Hans; Jensen, Anders A.

    2006-01-01

    We have constructed stable HEK293 cell lines expressing the rat ionotropic glutamate receptor subtypes GluR1(i), GluR2Q(i), GluR3(i), GluR4(i), GluR5Q and GluR6Q and characterised the pharmacological profiles of the six homomeric receptors in a fluorescence-based high throughput screening assay u...

  14. 基于有限理性的企业家战略决策风险行为研究%Research on Risk Behavior for the Strategic Decision-making of Entrepreneur Based on Bounded Rationality

    Institute of Scientific and Technical Information of China (English)

    任静; 刘升福

    2014-01-01

    企业家认知的有限性决定了企业家在有限理性的状态下进行战略决策。基于行为经济学和决策行为理论,研究有限理性下企业家战略决策风险行为及其影响因素。通过建立模型和实证研究来探讨企业家战略决策风险行为及其影响因素对战略决策风险行为的影响,从而为企业家战略决策风险行为管理提供依据。%The limitation of Entrepreneurs′cognition decides that entrepreneurs make strategic decisions under the limited rational state.The paper,based on the theory of behavioral economics and the decision-making behavior,studies the entrepreneur strategic decision deviation behavior based on bounded rationality and its influencing factors.Through the questionnaire,interviews and the empirical research,the paper explores the various influencing factors of entrepreneur strategic decision-making risk behavior influence on strategic decision-making risk behaviors,so as to provide the basis for entrepreneurs strategic decision-making risk behavior management.

  15. Research on Risk Behavior for the Strategic Decision-making of Entrepreneur Based on Bounded Rationality%基于有限理性的企业家战略决策风险行为研究

    Institute of Scientific and Technical Information of China (English)

    任静; 刘升福

    2014-01-01

    企业家认知的有限性决定了企业家在有限理性的状态下进行战略决策。基于行为经济学和决策行为理论,研究有限理性下企业家战略决策风险行为及其影响因素。通过建立模型和实证研究来探讨企业家战略决策风险行为及其影响因素对战略决策风险行为的影响,从而为企业家战略决策风险行为管理提供依据。%The limitation of Entrepreneurs′cognition decides that entrepreneurs make strategic decisions under the limited rational state.The paper,based on the theory of behavioral economics and the decision-making behavior,studies the entrepreneur strategic decision deviation behavior based on bounded rationality and its influencing factors.Through the questionnaire,interviews and the empirical research,the paper explores the various influencing factors of entrepreneur strategic decision-making risk behavior influence on strategic decision-making risk behaviors,so as to provide the basis for entrepreneurs strategic decision-making risk behavior management.

  16. Subdivision, Sampling, and Initialization Strategies for Simplical Branch and Bound in Global Optimization

    DEFF Research Database (Denmark)

    Clausen, Jens; Zilinskas, A,

    2002-01-01

    We consider the problem of optimizing a Lipshitzian function. The branch and bound technique is a well-known solution method, and the key components for this are the subdivision scheme, the bound calculation scheme, and the initialization. For Lipschitzian optimization, the bound calculations...... are based on the sampling of function values. We propose a branch and bound algorithm based on regular simplexes. Initially, the domain in question is covered with regular simplexes, and our subdivision scheme maintains this property. The bound calculation becomes both simple and efficient, and we describe...

  17. The Role of the Enterohepatic Circulation of Bile Salts and Nuclear Hormone Receptors in the Regulation of Cholesterol Homeostasis: Bile Salts as Ligands for Nuclear Hormone Receptors

    OpenAIRE

    Redinger, Richard N.

    2003-01-01

    The coordinated effect of lipid activated nuclear hormone receptors; liver X receptor (LXR), bound by oxysterol ligands and farnesoid X receptor (FXR), bound by bile acid ligands, act as genetic transcription factors to cause feed-forward cholesterol catabolism to bile acids and feedback repression of bile acid synthesis, respectively. It is the coordinated action of LXR and FXR, each dimerized to retinoid X receptor, that signal nuclear DNA response elements to encode proteins that prevent e...

  18. Globular tail of myosin-V is bound to vamp/synaptobrevin.

    Science.gov (United States)

    Ohyama, A; Komiya, Y; Igarashi, M

    2001-02-01

    VAMP/synaptobrevin is one of a number of v-SNAREs involved in vesicular fusion events in neurons. In a previous report, VAMP was shown to form a complex with synaptophysin and myosin V, a motor protein based on the F-actin, and that myosin V was then released from the complex in a Ca(2+)-dependent manner. Here, we found that VAMP alone is bound to myosin V in a Ca(2+)-independent manner, and determined that the globular tail domain of myosin V is its binding site. The syntaxin-VAMP-myosin V formed in the presence of Ca(2+)/calmodulin (CaM). In the absence of CaM, only syntaxin-VAMP, or VAMP-myosin V complex was formed. Our results suggest that VAMP acts as a myosin V receptor on the vesicles and regulates formation of the complex.

  19. Characterization and Modulation of the Bitterness of Polymethoxyflavones Using Sensory and Receptor-Based Methods.

    Science.gov (United States)

    Batenburg, A Max; de Joode, Teun; Gouka, Robin J

    2016-03-30

    An obstacle in the application of many "health ingredients" is their alleged off-flavor. We used a combination of chemical, sensory, and biological analyses to identify the bitter components in citrus peel-derived polymethoxyflavone preparations, claimed to be functional in the lowering of cholesterol. Nobiletin (56-81%) and tangeretin (10-33%) were found to be the main bitter components. Using in vitro receptor assays, hTAS2R14 was shown to be the main bitter receptor involved in their perception, with EC50 values of 14 and 63 μM, respectively. Our analysis provided several routes for off-flavor reduction. Purification is an option because a purified, single PMF species proved to be considerably less bitter upon application in emulsified foods, due to limited solubility in the aqueous phase. A second route, also demonstrated in vivo, is C5-specific demethoxylation, in line with the finding that 5-desmethylnobiletin does not activate hTAS2R14. A third route could be the use of TAS2R14 antagonists. As a proof of principle, several antagonists, with IC50 values ranging from 10 to 50 μM, were identified. PMID:26934534

  20. Predicting kinase activity in angiotensin receptor phosphoproteomes based on sequence-motifs and interactions.

    Directory of Open Access Journals (Sweden)

    Rikke Bøgebo

    Full Text Available Recent progress in the understanding of seven-transmembrane receptor (7TMR signalling has promoted the development of a new generation of pathway selective ligands. The angiotensin II type I receptor (AT1aR is one of the most studied 7TMRs with respect to selective activation of the β-arrestin dependent signalling. Two complimentary global phosphoproteomics studies have analyzed the complex signalling induced by the AT1aR. Here we integrate the data sets from these studies and perform a joint analysis using a novel method for prediction of differential kinase activity from phosphoproteomics data. The method builds upon NetworKIN, which applies sophisticated linear motif analysis in combination with contextual network modelling to predict kinase-substrate associations with high accuracy and sensitivity. These predictions form the basis for subsequently nonparametric statistical analysis to identify likely activated kinases. This suggested that AT1aR-dependent signalling activates 48 of the 285 kinases detected in HEK293 cells. Of these, Aurora B, CLK3 and PKG1 have not previously been described in the pathway whereas others, such as PKA, PKB and PKC, are well known. In summary, we have developed a new method for kinase-centric analysis of phosphoproteomes to pinpoint differential kinase activity in large-scale data sets.

  1. Biomimetic infrared sensors based on the infrared receptors of pyrophilous insects

    Science.gov (United States)

    Schmitz, Helmut; Kahl, Thilo; Soltner, Helmut; Bousack, Herbert

    2011-04-01

    Beetles of the genus Melanophila and certain flat bugs of the genus Aradus approach forest fires. For the detection of fires and of hot surfaces the pyrophilous species of both genera have developed infrared (IR) receptors, which have developed from common hair mechanoreceptors. Thus this type of insect IR receptor has been termed photomechanic and shows the following two special features: (i) the formation of a complex cuticular sphere consisting of an outer exocuticular shell as well as of a cavernous microfluidic core. (ii) The enclosure of the dendritic tip of a mechanosensitive neuron inside the core in a liquid-filled chamber. Most probably a photomechanic IR sensillum acts as a microfluidic converter of infrared radiation into an increase in internal pressure inside the sphere, which is measured by a mechanosensitive neuron. A simple model for this biological IR sensor is the Golay sensor, which is filled with a liquid instead of gas. Here the absorbed IR radiation results in a pressure increase of the liquid and the deflection of a thin membrane. For the evaluation of this model analytical formulas are presented, which permits the calculation of the pressure increase in the cavity, the deformation of the membrane and the time constant of an artificial leak to compensate ambient temperature changes. Some organic liquids with high thermal expansion coefficients may improve the deflection of the membrane compared to water.

  2. 循环荷载作用下基于隶属度函数的边界面模型%Bounding surface model based on membership function under cyclic loading

    Institute of Scientific and Technical Information of China (English)

    王喜刚; 扶名福; 胡小荣

    2015-01-01

    A membership function was imported into the bounding surface model to solve accumulated and continu-ous plastic strain under cyclic loading.A new three-dimensional cone was constructed based on the two-dimensional critical soil model figure.The relationship between the membership function and the loading surface was established based on the new three-dimensional cone.The membership function was used to modify the plastic flow criteria, so that the maximum stress of model was partially memorized;the damage parameters were adopted to deduce a fuzzy bounding surface model.A dynamic triaxial experiment was adopted to determine the parameters of the model.The numerical prediction matches the experiment results, proving the model is reasonable.%为了反映土体在循环荷载作用下塑性应变的累积特性和连续性,将隶属度函数引入到边界面模型中,在二维临界土力学模型图基础上,构造了一个新三维空间锥体,利用该锥体建立了加载面与隶属度函数的一一对应关系。根据隶属度函数修正了塑性流动法则,使得模型对最大预应力具有部分记忆功能,并引入损伤参数,推导得到了模糊边界面模型,通过动三轴实验确定了该模型的参数。利用有限元的二次开发功能,将该模型引入到有限元中,得到了模型的数值结果,通过与动三轴实验结果对比,发现两者吻合较好,证明了模型的合理性。

  3. Weekly nanoparticle albumin bound-paclitaxel in combination with cisplatin versus weekly solvent-based paclitaxel plus cisplatin as first-line therapy in Chinese patients with advanced esophageal squamous cell carcinoma

    Directory of Open Access Journals (Sweden)

    Wang HY

    2016-09-01

    Full Text Available Hai-ying Wang, Zhi-hua Yao, Hong Tang, Yan Zhao, Xiao-san Zhang, Shu-na Yao, Shu-jun Yang, Yan-yan Liu Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan, People’s Republic of China Objective: More effective regimens for advanced esophageal squamous cell carcinoma (ESCC are urgently needed. Therefore, a retrospective study concerning the efficacy and safety of nanoparticle albumin-bound paclitaxel plus cisplatin (nab-TP versus solvent-based paclitaxel plus cisplatin (sb-TP as a first-line therapy was conducted in Chinese patients with advanced ESCC.Methods: From June 2009 to June 2015, 32 patients were treated with nab-paclitaxel (125 mg/m2 on the first and eighth days (30 minutes infusion and cisplatin (75 mg/m2 on the second day every 21 days (nab-TP arm. Also, 43 patients were treated with solvent-based paclitaxel (80 mg/m2 intravenously on the first and eighth days and the same dose of cisplatin (sb-TP arm. The two groups were compared in terms of objective response rate (ORR, disease control rate, progression-free survival (PFS, overall survival (OS, and safety profile. OS and PFS were estimated using Kaplan–Meier methods to determine associations between chemotherapy regimens and survival outcomes.Results: Nab-TP demonstrated a higher ORR (50% vs 30%; P=0.082 and disease control rate (81% vs 65%; P=0.124 than sb-TP. Median OS was similar for nab-TP and sb-TP (12.5 vs 10.7 months; P=0.269. However, nab-TP resulted in a longer median PFS (6.1 months [95% confidence interval: 5.3–6.9] than sb-TP (5.0 months [95% confidence interval: 4.4–5.6] (P=0.029. The most common adverse events included anemia, leukopenia, neutropenia, febrile neutropenia, and thrombocytopenia in both the groups and no statistically significant differences were observed between the groups. With statistically significant differences, significantly less grade ≥3 peripheral neuropathy

  4. UPPER BOUND ANALYSIS OF HORIZONTALLY EMBEDDED ANCHORS BASED ON BLOCK SET MECHANISM%基于组合块体集的浅埋条形锚板上限分析

    Institute of Scientific and Technical Information of China (English)

    余生兵; 黄茂松

    2011-01-01

    基于极限分析法的基本原理以及集成与组合的思路,推导组合块体集的内能耗散和重力做功,运用组合的思想构造斜坡地形下浅埋水平条形锚板的运动许可速度场.首先分析地表水平条件下法向受力水平条形锚板抗拔承载力,并与文献中已有解和模型试验进行对比,验证块体集上限法的优越性.然后详细研究斜坡地形条件下土体重度、不排水抗剪强度、斜坡倾角等因素对条形锚板抗拔承载力和破坏面形状的影响.分析结果表明:重力叠加法并不适用于斜坡地形情况;随着斜坡倾角的增大,锚板的破坏面向坡角方向倾斜;锚板埋深比越大,斜坡倾角的影响也越显著.块体集上限分析方法构造简单,求解快捷,能够为工程设计提供依据.%Based on the bound theorems of limit analysis, admissible velocity field of horizontal strip anchor is constructed by using a combination of several rotational block sets. An application to upper bound analysis of vertically loaded strip anchors on horizontal ground surface is given first to illustrate the utility and effectiveness of the proposed method, and include detailed comparisons with results obtained from other approaches. Then the pull-out capacities of strip anchors in undrained clay with sloping ground surface are analyzed. Pull-out capacity and failure surface characteristics under different embedment ratios, undrained strength, inclined angles of slopes and weight of soil are studied. The results show that the superposition of gravity is not applicable to the case of sloping ground surface. The variation of slope angle has a significant impact on failure surface. The block set mechanism is based on a very simple concept which is integration and combination and can be a reference for the practical design.

  5. Alternation-Trading Proofs, Linear Programming, and Lower Bounds

    CERN Document Server

    Williams, Ryan

    2010-01-01

    A fertile area of recent research has demonstrated concrete polynomial time lower bounds for solving natural hard problems on restricted computational models. Among these problems are Satisfiability, Vertex Cover, Hamilton Path, Mod6-SAT, Majority-of-Majority-SAT, and Tautologies, to name a few. The proofs of these lower bounds follow a certain proof-by-contradiction strategy that we call alternation-trading. An important open problem is to determine how powerful such proofs can possibly be. We propose a methodology for studying these proofs that makes them amenable to both formal analysis and automated theorem proving. We prove that the search for better lower bounds can often be turned into a problem of solving a large series of linear programming instances. Implementing a small-scale theorem prover based on this result, we extract new human-readable time lower bounds for several problems. This framework can also be used to prove concrete limitations on the current techniques.

  6. Higgs interchange and bound states of superheavy fermions

    Indian Academy of Sciences (India)

    M De Sanctis

    2013-09-01

    Hypothetical superheavy fourth-generation fermions with a very small coupling with the rest of the Standard Model can give rise to long enough lived bound states. The production and the detection of these bound states would be experimentally feasible at the LHC. Extending, in the present study, the analysis of other authors, a semirelativistic wave equation is solved using an accurate numerical method to determine the binding energies of these possible superheavy fermion-bound states. The interaction given by the Yukawa potential of the Higgs boson exchange is considered; the corresponding relativistic corrections are calculated by means of a model based on the covariance properties of the Hamiltonian. We study the effects given by the Coulomb force. Moreover, we calculate the contributions given by the Coulombic and confining terms of the strong interaction in the case of superheavy quark bound states. The results of the model are critically analysed.

  7. Bound Polaron Pair Formation in Poly (phenylenevinylenes)

    Science.gov (United States)

    Rothberg, Lewis

    The following sections are included: * INTRODUCTION * PHOTOGENERATED YIELD OF SINGLET EXCITONS * AGGREGRATION EFFECTS ON EXCITED STATE PHOTO-GENERATION * ASSIGNMENT TO BOUND POLARON PAIRS AND DISCUSSION * PROBLEMS WITH THE BOUND POLARON PAIR PICTURE AND CONCLUSION * REFERENCES

  8. An Exponential Bound for Cox Regression☆

    Science.gov (United States)

    Kosorok, M. R.

    2012-01-01

    We present an asymptotic exponential bound for the deviation of the survival function estimator of the Cox model. We show that the bound holds even when the proportional hazards assumption does not hold. PMID:23565013

  9. An Exponential Bound for Cox Regression.

    Science.gov (United States)

    Goldberg, Y; Kosorok, M R

    2012-07-01

    We present an asymptotic exponential bound for the deviation of the survival function estimator of the Cox model. We show that the bound holds even when the proportional hazards assumption does not hold.

  10. Retinoid and thiazolidinedione therapies in melanoma: an analysis of differential response based on nuclear hormone receptor expression

    Directory of Open Access Journals (Sweden)

    Pugazhenthi Umarani

    2009-03-01

    Full Text Available Abstract Background Metastatic melanoma has a high mortality rate and suboptimal therapeutic options. Molecular targeting may be beneficial using the rexinoid LGD1069, a retinoid × receptor selective agonist, and thiazolidinediones (TZD, PPARγ selective ligands, as novel treatments. Results Mouse xenograft models with human melanoma cell lines [A375(DRO or M14(5–16] were treated for 4 weeks with daily vehicle, RXR agonist (rexinoid, LGD1069, 30 mg/kg/d, PPARγ agonist (TZD, rosiglitazone, 10 mg/kg/d or combination. A375(DRO tumor growth was significantly inhibited by either ligand alone and the combination had an additive effect. M14(5–16 tumors only responded to LGD1069 100 mg/kg/day. A375(DRO sublines resistant to rexinoid, TZD and combination were generated and all three sublines had reduced PPARγ expression but preserved RXR expression. shRNA knockdown of PPARγ or RXRγ attenuated the rexinoid, TZD and combination ligand-mediated decreased proliferation in A375(DRO cells. Rexinoid (LGD1069 and retinoid (TTNPB treatment of M14(5–16 cells resulted in decreased proliferation that was additive with combination of both rexinoid and retinoid. shRNA knockdown of RXRγ resulted in a decreased response to either ligand. Conclusion A375 (DRO melanoma cell growth is inhibited by rexinoid and TZD treatment, and this response is dependent on RXR and PPARγ receptor expression. M14 (5–16 melanoma cell growth is inhibited by rexinoid and retinoid treatment, and this response is dependent on RXR expression. These findings may help guide molecular-based treatment strategies in melanoma and provide insight for mechanisms of resistance to nuclear receptor targeted therapies in certain cancers.

  11. Cis and trans regulatory mechanisms control AP2-mediated B cell receptor endocytosis via select tyrosine-based motifs.

    Directory of Open Access Journals (Sweden)

    Kathleen Busman-Sahay

    Full Text Available Following antigen recognition, B cell receptor (BCR-mediated endocytosis is the first step of antigen processing and presentation to CD4+ T cells, a crucial component of the initiation and control of the humoral immune response. Despite this, the molecular mechanism of BCR internalization is poorly understood. Recently, studies of activated B cell-like diffuse large B cell lymphoma (ABC DLBCL have shown that mutations within the BCR subunit CD79b leads to increased BCR surface expression, suggesting that CD79b may control BCR internalization. Adaptor protein 2 (AP2 is the major mediator of receptor endocytosis via clathrin-coated pits. The BCR contains five putative AP2-binding YxxØ motifs, including four that are present within two immunoreceptor tyrosine-based activation motifs (ITAMs. Using a combination of in vitro and in situ approaches, we establish that the sole mediator of AP2-dependent BCR internalization is the membrane proximal ITAM YxxØ motif in CD79b, which is a major target of mutation in ABC DLBCL. In addition, we establish that BCR internalization can be regulated at a minimum of two different levels: regulation of YxxØ AP2 binding in cis by downstream ITAM-embedded DCSM and QTAT regulatory elements and regulation in trans by the partner cytoplasmic domain of the CD79 heterodimer. Beyond establishing the basic rules governing BCR internalization, these results illustrate an underappreciated role for ITAM residues in controlling clathrin-dependent endocytosis and highlight the complex mechanisms that control the activity of AP2 binding motifs in this receptor system.

  12. Integrating sampling techniques and inverse virtual screening: toward the discovery of artificial peptide-based receptors for ligands.

    Science.gov (United States)

    Pérez, Germán M; Salomón, Luis A; Montero-Cabrera, Luis A; de la Vega, José M García; Mascini, Marcello

    2016-05-01

    A novel heuristic using an iterative select-and-purge strategy is proposed. It combines statistical techniques for sampling and classification by rigid molecular docking through an inverse virtual screening scheme. This approach aims to the de novo discovery of short peptides that may act as docking receptors for small target molecules when there are no data available about known association complexes between them. The algorithm performs an unbiased stochastic exploration of the sample space, acting as a binary classifier when analyzing the entire peptides population. It uses a novel and effective criterion for weighting the likelihood of a given peptide to form an association complex with a particular ligand molecule based on amino acid sequences. The exploratory analysis relies on chemical information of peptides composition, sequence patterns, and association free energies (docking scores) in order to converge to those peptides forming the association complexes with higher affinities. Statistical estimations support these results providing an association probability by improving predictions accuracy even in cases where only a fraction of all possible combinations are sampled. False positives/false negatives ratio was also improved with this method. A simple rigid-body docking approach together with the proper information about amino acid sequences was used. The methodology was applied in a retrospective docking study to all 8000 possible tripeptide combinations using the 20 natural amino acids, screened against a training set of 77 different ligands with diverse functional groups. Afterward, all tripeptides were screened against a test set of 82 ligands, also containing different functional groups. Results show that our integrated methodology is capable of finding a representative group of the top-scoring tripeptides. The associated probability of identifying the best receptor or a group of the top-ranked receptors is more than double and about 10 times higher

  13. On Bounding Problems of Quantitative Information Flow

    CERN Document Server

    Yasuoka, Hirotoshi

    2011-01-01

    Researchers have proposed formal definitions of quantitative information flow based on information theoretic notions such as the Shannon entropy, the min entropy, the guessing entropy, belief, and channel capacity. This paper investigates the hardness of precisely checking the quantitative information flow of a program according to such definitions. More precisely, we study the "bounding problem" of quantitative information flow, defined as follows: Given a program M and a positive real number q, decide if the quantitative information flow of M is less than or equal to q. We prove that the bounding problem is not a k-safety property for any k (even when q is fixed, for the Shannon-entropy-based definition with the uniform distribution), and therefore is not amenable to the self-composition technique that has been successfully applied to checking non-interference. We also prove complexity theoretic hardness results for the case when the program is restricted to loop-free boolean programs. Specifically, we show...

  14. Monotonicity of the quantum linear programming bound

    OpenAIRE

    Eric M. Rains

    1998-01-01

    The most powerful technique known at present for bounding the size of quantum codes of prescribed minimum distance is the quantum linear programming bound. Unlike the classical linear programming bound, it is not immediately obvious that if the quantum linear programming constraints are satisfiable for dimension K, that the constraints can be satisfied for all lower dimensions. We show that the quantum linear programming bound is indeed monotonic in this sense, and give an explicitly monotoni...

  15. Somatostatin Receptor-Based Molecular Imaging and Therapy for Neuroendocrine Tumors

    Directory of Open Access Journals (Sweden)

    Ling Wang

    2013-01-01

    Full Text Available Neuroendocrine tumors (NETs are tumors originated from neuroendocrine cells in the body. The localization and the detection of the extent of NETs are important for diagnosis and treatment, which should be individualized according to the tumor type, burden, and symptoms. Molecular imaging of NETs with high sensitivity and specificity is achieved by nuclear medicine method using single photon-emitting and positron-emitting radiopharmaceuticals. Somatostatin receptor imaging (SRI using SPECT or PET as a whole-body imaging technique has become a crucial part of the management of NETs. The radiotherapy with somatostatin analogues labeled with therapeutic beta emitters, such as lutetium-177 or yttrium-90, has been proved to be an option of therapy for patients with unresectable and metastasized NETs. Molecular imaging can deliver an important message to improve the outcome for patients with NETs by earlier diagnosis, better choice of the therapeutic method, and evaluation of the therapeutic response.

  16. The Construction of Chimeric T-Cell Receptor with Spacer Base of Modeling Study of VHH and MUC1 Interaction

    OpenAIRE

    Nazanin Pirooznia; Sadegh Hasannia; Majid Taghdir; Fatemeh Rahbarizadeh; Morteza Eskandani

    2011-01-01

    Adaptive cell immunotherapy with the use of chimeric receptors leads to the best and most specific response against tumors. Chimeric receptors consist of a signaling fragment, extracellular spacer, costimulating domain, and an antibody. Antibodies cause immunogenicity; therefore, VHH is a good replacement for ScFv in chimeric receptors. Since peptide sequences have an influence on chimeric receptors, the effect of peptide domains on each other's conformation were investigated. CD3Zeta, CD28, ...

  17. C/C ++program memory leak detection based on bounded model checking%基于有界模型检测的C/C++程序内存泄露检测

    Institute of Scientific and Technical Information of China (English)

    黄蔚; 洪玫; 杨秋辉; 郭鑫宇; 代声馨; 徐保平; 高婉玲; 赵鹤

    2016-01-01

    The dynamic memory management mechanism in C /C ++programming language is free and flexible,but when used by developer it is easy to introduce memory leaks which lead to performance degradation and even failure of system.In order to detect memory leak more effectively,this paper proposed a memory leak detection method based on bounded model checking for C program called MLD-CBMC.It took C /C ++program files as input,unwound the program and inserted memory leak proper-ties,encoded the program constraints and properties into verification conditions using satisfiability modulo theory,then passed the verification conditions to a SMT solver.Thus it converted detecting memory leaks to solving satisfiability problems.By ex-periment and cooperation with other bounded model checking tools,MLD-CBMC shows its feasibility and effectiveness.%C /C ++语言中的动态内存管理机制自由且灵活,但动态内存的使用容易引入内存泄露,导致系统性能降低甚至系统崩溃。为了更加有效地检测内存泄露,提出了一个基于有界模型检测技术的 C /C ++程序内存泄露检测方案 MLD-CBMC。该方案以 C /C ++程序文件为输入,利用有界模型检测技术对程序进行展开处理,加入内存泄露性质,并利用可满足性模理论(SMT)对程序约束和性质组成的验证条件编码,使用 SMT 求解器对验证条件求解,将检测内存泄露问题转换为求解可满足性问题,实现 C /C ++程序内存泄露的检测。通过实验验证了方案的有效性,并与其他有界模型检测工具进行对比实验,实验证明方案对内存泄露的检测能力更强。

  18. Bound entangled states invariant under Ux

    Institute of Scientific and Technical Information of China (English)

    Wang Zhen; Wang Zhi-Xi

    2008-01-01

    This paper obtains an entangled condition for isotropic-like states by using an atomic map. It constructs a class of bound entangled states from the entangled condition and shows that the partial transposition of the state from the constructed bound entangled class is an edge bound entangled state by using range criterion.

  19. Bounded rationality and heterogeneous expectations in macroeconomics

    NARCIS (Netherlands)

    D. Massaro

    2012-01-01

    This thesis studies the effect of individual bounded rationality on aggregate macroeconomic dynamics. Boundedly rational agents are specified as using simple heuristics in their decision making. An important aspect of the type of bounded rationality described in this thesis is that the population of

  20. Upper Bounds on Numerical Approximation Errors

    DEFF Research Database (Denmark)

    Raahauge, Peter

    2004-01-01

    This paper suggests a method for determining rigorous upper bounds on approximationerrors of numerical solutions to infinite horizon dynamic programming models.Bounds are provided for approximations of the value function and the policyfunction as well as the derivatives of the value function...... to approximations of a standard (strictly concave)growth model.KEYWORDS: Numerical approximation errors, Bellman contractions, Error bounds...

  1. Counting Young Tableaux of Bounded Height

    Science.gov (United States)

    Bergeron, Francois; Gascon, Francis

    2000-03-01

    We show that formulas of Gessel, for the generating functions for Young standard tableaux of height bounded by k (see [2]), satisfy linear differential equations, with polynomial coefficients, equivalent to P-recurrences conjectured by Favreau, Krob and the first author (see [1]) for the number of bounded height tableaux and pairs of bounded height tableaux.

  2. Graphene in inhomogeneous magnetic fields: bound, quasi-bound and scattering states

    Energy Technology Data Exchange (ETDEWEB)

    Ramezani Masir, M; Peeters, F M [Departement Fysica, Universiteit Antwerpen Groenenborgerlaan 171, B-2020 Antwerpen (Belgium); Vasilopoulos, P, E-mail: mrmphys@gmail.com, E-mail: takis@alcor.concordia.ca, E-mail: francois.peeters@ua.ac.be [Department of Physics, Concordia University, Montreal, Quebec, H4B 1R6 (Canada)

    2011-08-10

    The electron states in graphene-based magnetic dot and magnetic ring structures and combinations of both are investigated. The corresponding spectra are studied as a function of the radii, the strengths of the inhomogeneous magnetic field and of a uniform background field, the strength of an electrostatic barrier and the angular momentum quantum number. In the absence of an external magnetic field we have only long-lived quasi-bound and scattering states and we assess their influence on the density of states. In addition, we consider elastic electron scattering by a magnetic dot, whose average B vanishes, and show that the Hall and longitudinal resistivities, as a function of the Fermi energy, exhibit a pronounced oscillatory structure due to the presence of quasi-bound states. Depending on the dot parameters this oscillatory structure differs substantially for energies below and above the first Landau level.

  3. Peptides derived from CXCL8 based on in silico analysis inhibit CXCL8 interactions with its receptor CXCR1

    Science.gov (United States)

    Jiang, Shinn-Jong; Liou, Je-Wen; Chang, Chun-Chun; Chung, Yi; Lin, Lee-Fong; Hsu, Hao-Jen

    2015-12-01

    Chemokine CXCL8 is crucial for regulation of inflammatory and immune responses via activating its cognate receptor CXCR1. In this study, molecular docking and binding free energy calculations were combined to predict the initial binding event of CXCL8 to CXCR1 for peptide drug design. The simulations reveal that in the initial binding, the N-loop of CXCL8 interacts with the N-terminus of CXCR1, which is dominated by electrostatic interactions. The derived peptides from the binding region of CXCL8 are synthesized for further confirmation. Surface plasmon resonance analyses indicate that the CXCL8 derived peptide with 14 residues is able to bind to the receptor CXCR1 derived peptide with equilibrium KD of 252 μM while the peptide encompassing a CXCL8 K15A mutation hardly binds to CXCR1 derived peptide (KD = 1553 μM). The cell experiments show that the designed peptide inhibits CXCL8-induced and LPS-activated monocytes adhesion and transmigration. However, when the peptides were mutated on two lysine residues (K15 and K20), the inhibition effects were greatly reduced indicating these two amino acids are key residues for the initial binding of CXCL8 to CXCR1. This study demonstrates that in silico prediction based functional peptide design can be effective for developing anti-inflammation drugs.

  4. Synthesis and studies of boron based anion receptors and their use in non-aqueous electrolytes for lithium batteries

    Energy Technology Data Exchange (ETDEWEB)

    Sun, X.; Yang, X.Q.; Lee, H.S.; McBreen, J. [Brookhaven National Lab., Upton, NY (United States); Choi, L.S. [Naval Research Lab., Washington, DC (United States)

    1998-12-31

    A new family of anion receptors based on boron compounds has been synthesized. These compounds can be used as anion receptors in lithium battery electrolytes and can greatly increase solubility and ionic conductivities of various lithium salts, such as LiF, LiCl, CF{sub 3}COOLi and C{sub 2}F{sub 5}COOLi, in DME solutions. Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy studies show that Cl{sup {minus}} anions of LiCl are complexed with these compounds in DME solutions. The electrochemical stability of lithium salts and one of the boron compounds in deferent solvents was studied. For the first time, LiF has been successfully used as conducting salt in a novel electrolyte with this boron compound as an additive in DME. A rechargeable Li/LiMn{sub 2}O{sub 4} cell using this electrolyte was successfully cycled 51 times. However, the capacity fades with cycling due to decomposition of the solvent. The cycling performance of the battery was greatly improved by replacing DME with PC-EC-DMC as the solvent.

  5. A branch and bound algorithm for the global optimization of Hessian Lipschitz continuous functions

    KAUST Repository

    Fowkes, Jaroslav M.

    2012-06-21

    We present a branch and bound algorithm for the global optimization of a twice differentiable nonconvex objective function with a Lipschitz continuous Hessian over a compact, convex set. The algorithm is based on applying cubic regularisation techniques to the objective function within an overlapping branch and bound algorithm for convex constrained global optimization. Unlike other branch and bound algorithms, lower bounds are obtained via nonconvex underestimators of the function. For a numerical example, we apply the proposed branch and bound algorithm to radial basis function approximations. © 2012 Springer Science+Business Media, LLC.

  6. Physical bounds for antenna radiation efficiency

    CERN Document Server

    Shahpari, Morteza

    2016-01-01

    Small volume, reduced conductivity and high frequencies are major imperatives in the design of communications infrastructure. The radiation efficiency $\\eta_r$ impacts on the optimal gain, quality factor, and bandwidth. The current efficiency limit applies to structures confined to a radian sphere $ka$ ($k$ is the wave number, $a$ is the radius). Here we present new absolute limits to $\\eta_r$ for arbitrary antenna shapes based on $k^2S$ where $S$ is the conductor surface area. For an electrical length of $10^{-5}$ our result is four orders of magnitude closer to the analytical solution. The improved bound on $\\eta_r$ is more accurate, more general, and easier to calculate than other limits. It is based on the total surface area of the conductors and provides greatly improved estimations for electrically small radiators at very low frequencies. The work is of great benefit to antenna designers assessing new materials such as conductive polymers.

  7. Higgs mass bounds from the functional RG

    International Nuclear Information System (INIS)

    We investigate a Top-Yukawa toy model to study Higgs mass bounds in the framework of the functional renormalization group (RG). Starting the calculations with a quartic ultraviolet (UV) potential we get a finite range of values for the Higgs mass in the infrared for a given cutoff. The bounds appear in a natural way as a consequence of the RG flow. The lower mass bound is approached for a vanishing UV quartic coupling. Furthermore, we study the influence of higher-dimensional operators on the lower Higgs mass bound. We find that even seemingly RG irrelevant interactions can take a substantial influence on the lower bound for the Higgs mass.

  8. Spatial Turing-type Pattern Formation in a Model of Signal Transduction Involving Membrane-based Receptors Coupled by G Proteins

    Directory of Open Access Journals (Sweden)

    Wannapong Triampo

    2006-01-01

    Full Text Available In this paper, a model of signaling pathways involving G proteins is investigated. The model incorporates reaction-diffusion mechanisms in which various reactants participate inside and on the extra-cellular surface membrane. The messenger molecules may diffuse over the surface of the cell membrane and signal transduction across the cell membrane is mediated by membrane receptor bound proteins which connect the genetically controlled biochemical intra-cellular reactions to the production of the second messenger, leading to desired functional responses. Dynamic and steady-state properties of the model are then investigated through weakly nonlinear stability analysis. Turing-type patterns are shown to form robustly under different delineating conditions on the system parameters. The theoretical predictions are then discussed in the context of some recently reported experimental evidence.

  9. Capacity Bounds for Parallel Optical Wireless Channels

    KAUST Repository

    Chaaban, Anas

    2016-01-01

    A system consisting of parallel optical wireless channels with a total average intensity constraint is studied. Capacity upper and lower bounds for this system are derived. Under perfect channel-state information at the transmitter (CSIT), the bounds have to be optimized with respect to the power allocation over the parallel channels. The optimization of the lower bound is non-convex, however, the KKT conditions can be used to find a list of possible solutions one of which is optimal. The optimal solution can then be found by an exhaustive search algorithm, which is computationally expensive. To overcome this, we propose low-complexity power allocation algorithms which are nearly optimal. The optimized capacity lower bound nearly coincides with the capacity at high SNR. Without CSIT, our capacity bounds lead to upper and lower bounds on the outage probability. The outage probability bounds meet at high SNR. The system with average and peak intensity constraints is also discussed.

  10. Antibaryon-nucleus bound states

    CERN Document Server

    Hrtánková, J

    2014-01-01

    We calculated antibaryon ($\\bar{B}$ = $\\bar{p}$, $\\bar{\\Lambda}$, $\\bar{\\Sigma}$, $\\bar{\\Xi}$) bound states in selected nuclei within the relativistic mean-field (RMF) model. The G-parity motivated $\\bar{B}$-meson coupling constants were scaled to yield corresponding potentials consistent with available experimental data. Large polarization of the nuclear core caused by $\\bar{B}$ was confirmed. The $\\bar{p}$ annihilation in the nuclear medium was incorporated by including a phenomenological imaginary part of the optical potential. The calculations using a complex $\\bar{p}$-nucleus potential were performed fully self-consistently. The $\\bar{p}$ widths significantly decrease when the phase space reduction is considered for $\\bar{p}$ annihilation products, but they still remain sizeable for potentials consistent with $\\bar{p}$-atom data.

  11. Bound states in the continuum

    Science.gov (United States)

    Hsu, Chia Wei; Zhen, Bo; Stone, A. Douglas; Joannopoulos, John D.; Soljačić, Marin

    2016-09-01

    Bound states in the continuum (BICs) are waves that remain localized even though they coexist with a continuous spectrum of radiating waves that can carry energy away. Their very existence defies conventional wisdom. Although BICs were first proposed in quantum mechanics, they are a general wave phenomenon and have since been identified in electromagnetic waves, acoustic waves in air, water waves and elastic waves in solids. These states have been studied in a wide range of material systems, such as piezoelectric materials, dielectric photonic crystals, optical waveguides and fibres, quantum dots, graphene and topological insulators. In this Review, we describe recent developments in this field with an emphasis on the physical mechanisms that lead to BICs across seemingly very different materials and types of waves. We also discuss experimental realizations, existing applications and directions for future work.

  12. Spectral computations for bounded operators

    CERN Document Server

    Ahues, Mario; Limaye, Balmohan

    2001-01-01

    Exact eigenvalues, eigenvectors, and principal vectors of operators with infinite dimensional ranges can rarely be found. Therefore, one must approximate such operators by finite rank operators, then solve the original eigenvalue problem approximately. Serving as both an outstanding text for graduate students and as a source of current results for research scientists, Spectral Computations for Bounded Operators addresses the issue of solving eigenvalue problems for operators on infinite dimensional spaces. From a review of classical spectral theory through concrete approximation techniques to finite dimensional situations that can be implemented on a computer, this volume illustrates the marriage of pure and applied mathematics. It contains a variety of recent developments, including a new type of approximation that encompasses a variety of approximation methods but is simple to verify in practice. It also suggests a new stopping criterion for the QR Method and outlines advances in both the iterative refineme...

  13. VORONOI DIAGRAMS WITHOUT BOUNDING BOXES

    Directory of Open Access Journals (Sweden)

    E. T. K. Sang

    2015-10-01

    Full Text Available We present a technique for presenting geographic data in Voronoi diagrams without having to specify a bounding box. The method restricts Voronoi cells to points within a user-defined distance of the data points. The mathematical foundation of the approach is presented as well. The cell clipping method is particularly useful for presenting geographic data that is spread in an irregular way over a map, as for example the Dutch dialect data displayed in Figure 2. The automatic generation of reasonable cell boundaries also makes redundant a frequently used solution to this problem that requires data owners to specify region boundaries, as in Goebl (2010 and Nerbonne et al (2011.

  14. Tailored Presentation of Carbohydrates on a Coiled Coil-Based Scaffold for Asialoglycoprotein Receptor Targeting.

    Science.gov (United States)

    Zacco, Elsa; Hütter, Julia; Heier, Jason L; Mortier, Jérémie; Seeberger, Peter H; Lepenies, Bernd; Koksch, Beate

    2015-09-18

    The coiled-coil folding motif represents an ideal scaffold for the defined presentation of ligands due to the possibility of positioning them at specific distances along the axis. We created a coiled-coil glycopeptide library to characterize the distances between the carbohydrate-binding sites of the asialoglycoprotein receptors (ASGPR) on hepatocytes. The components of the glycopeptide library vary for the number of displayed ligands (galactose), their position on the peptide sequence, and the space between peptide backbone and carbohydrate. We determined the binding of the glycopeptides to the hepatocytes, and we established the optimal distance and orientation of the galactose moieties for interaction with the ASGPR using flow cytometry. We confirmed that the binding occurs through endocytosis mediated by ASGPR via inhibition studies with cytochalasin D; fluorescence microscopy studies display the uptake of the carrier peptides inside the cell. Thus, this study demonstrates that the coiled-coil motif can be used as reliable scaffold for the rational presentation of ligands.

  15. Ligand fishing using new chitosan based functionalized Androgen Receptor magnetic particles.

    Science.gov (United States)

    Marszałł, Michał Piotr; Sroka, Wiktor Dariusz; Sikora, Adam; Chełminiak, Dorota; Ziegler-Borowska, Marta; Siódmiak, Tomasz; Moaddel, Ruin

    2016-08-01

    Superparamagnetic nanoparticles with chemically modified chitosan has been proposed as a potential support for the immobilization of the androgen receptor (AR). The study involved comparison of different AR carriers like commercially available magnetic beads coated with silica (BcMag) and chitosan coated nanoparticles with different amount of amino groups. The immobilization was carried out through covalent immobilization of the AR through the terminal amino group or through available carboxylic acids. The initial characterization of the AR coated magnetic beads was carried out with dihydrotestosterone, a known AR ligand. Subsequently, chitosan modified nanporticles with long-distanced primary amino groups (Fe3O4CS-(NH2)3) (upto 8.34mM/g) were used for further study to isolate known AR ligands (bicalutamide, flutamide, hydroxyflutamide and levonogestrel) from a mixture of tested compounds in ammonium acetate buffer [10mM, pH 7.4]. The results showed that the selected nanoparticles are a promising semi-quantitative tool for the identification of high affinity compounds to AR and might be of special importance in the identification of novel agonists or antiandrogens. PMID:27156644

  16. Discovery of a sulfamate-based steroid sulfatase inhibitor with intrinsic selective estrogen receptor modulator properties.

    Science.gov (United States)

    Ouellet, Charles; Maltais, René; Ouellet, Étienne; Barbeau, Xavier; Lagüe, Patrick; Poirier, Donald

    2016-08-25

    Steroid sulfatase (STS), the enzyme which converts inactive sulfated steroid precursors into active hormones, is a promising therapeutic target for the treatment of estrogen-sensitive breast cancer. We report herein the synthesis and in vitro study of dual-action STS inhibitors with selective estrogen-receptor modulator (SERM) effects. A library of tetrahydroisoquinoline-N-substituted derivatives (phenolic compounds) was synthesized by solid-phase chemistry and tested on estrogen-sensitive breast cancer T-47D cells. Three phenolic compounds devoid of estrogenic activity and toxicity emerged from this screening. Their sulfamate analogs were then synthesized, tested in STS-transfected HEK-293 cells, and found to be potent inhibitors of the enzyme (IC50 of 3.9, 8.9, and 16.6 nM). When tested in T-47D cells they showed no estrogenic activity and produced a moderate antiestrogenic activity. The compounds were further tested on osteoblast-like Saos-2 cells and found to significantly stimulate their proliferation as well as their alkaline phosphatase activity, thus suggesting a SERM activity. These results are supported by molecular docking experiments. PMID:27155470

  17. Treating Diabetes Mellitus: Pharmacophore Based Designing of Potential Drugs from Gymnema sylvestre against Insulin Receptor Protein

    Directory of Open Access Journals (Sweden)

    Mohammad Uzzal Hossain

    2016-01-01

    Full Text Available Diabetes mellitus (DM is one of the most prevalent metabolic disorders which can affect the quality of life severely. Injectable insulin is currently being used to treat DM which is mainly associated with patient inconvenience. Small molecules that can act as insulin receptor (IR agonist would be better alternatives to insulin injection. Herein, ten bioactive small compounds derived from Gymnema sylvestre (G. sylvestre were chosen to determine their IR binding affinity and ADMET properties using a combined approach of molecular docking study and computational pharmacokinetic elucidation. Designing structural analogues were also performed for the compounds associated with toxicity and less IR affinity. Among the ten parent compounds, six were found to have significant pharmacokinetic properties with considerable binding affinity towards IR while four compounds were associated with toxicity and less IR affinity. Among the forty structural analogues, four compounds demonstrated considerably increased binding affinity towards IR and less toxicity compared with parent compounds. Finally, molecular interaction analysis revealed that six parent compounds and four analogues interact with the active site amino acids of IR. So this study would be a way to identify new therapeutics and alternatives to insulin for diabetic patients.

  18. Evolutionary trace-based peptides identify a novel asymmetric interaction that mediates oligomerization in nuclear receptors.

    Science.gov (United States)

    Gu, Peili; Morgan, Daniel H; Sattar, Minawar; Xu, Xueping; Wagner, Ryan; Raviscioni, Michele; Lichtarge, Olivier; Cooney, Austin J

    2005-09-01

    Germ cell nuclear factor (GCNF) is an orphan nuclear receptor that plays important roles in development and reproduction, by repressing the expression of essential genes such as Oct4, GDF9, and BMP15, through binding to DR0 elements. Surprisingly, whereas recombinant GCNF binds to DR0 sequences as a homodimer, endogenous GCNF does not exist as a homodimer but rather as part of a large complex termed the transiently retinoid-induced factor (TRIF). Here, we use evolutionary trace (ET) analysis to design mutations and peptides that probe the molecular basis for the formation of this unusual complex. We find that GCNF homodimerization and TRIF complex formation are DNA-dependent, and ET suggests that dimerization involves key functional sites on both helix 3 and helix 11, which are located on opposing surfaces of the ligand binding domain. Targeted mutations in either helix of GCNF disrupt the formation of both the homodimer and the endogenous TRIF complex. Moreover, peptide mimetics of both of these ET-determined sites inhibit dimerization and TRIF complex formation. This suggests that a novel helix 3-helix 11 heterotypic interaction mediates GCNF interaction and would facilitate oligomerization. Indeed, it was determined that the endogenous TRIF complex is composed of a GCNF oligomer. These findings shed light on an evolutionarily selected mechanism that reveals the unusual DNA-binding, dimerization, and oligomerization properties of GCNF.

  19. Role of Leukotriene receptor antagonist Montelukast in the treatment of chronic urticaria: A hospital based study

    Directory of Open Access Journals (Sweden)

    Iffat Hassan

    2012-01-01

    Full Text Available Introduction: Chronic urticaria is a disabling disease which may be refractory to standard therapies. Leukotriene receptor antagonists like montelukast have been tried in allergic diseases like asthma and find mention as a therapeutic option in chronic urticaria. Purposes: A randomized single-blinded non-placebo controlled study to evaluate the role of montelukast, in addition to the adjunctive role of non-sedating antihistamine levocetirizine (H1, was conducted in patients with chronic urticaria.Methods: Thirty-five patients with chronic urticaria were enrolled. Medication was given for a period of twelve weeks. Montelukast 10mg/day in an adult and 5mg in the age group 6-13 years,4 mg 2-6 years and levocetirizine 5 mg once a day was added, if patient had new weals while on therapy. The improvement was monitored by estimating the episodes of wheals and pruritus in any two weeks period.Results: Twenty-two patients showed a good response with occasional wheals at the end of 2 weeks and no weals at the end of 12 weeks. These included all 8 patients on non-steroidal anti-inflammatory drugs (NSAIDS. Four of these patients relapsed on discontinuation of therapy.Conclusion: Montelukast is effective in chronic refractory urticaria especially in patients on non-steroidal anti-inflammatory drugs with occasional add-on use of a non-sedating anti-histamine.

  20. Family and population-based studies of variation within the ghrelin receptor locus in relation to measures of obesity

    DEFF Research Database (Denmark)

    Gjesing, Anette P.; Larsen, Lesli Hingstrup; Torekov, Signe Sørensen;

    2010-01-01

    BACKGROUND: The growth hormone secretagogue receptor (GHSR) is mediating hunger sensation when stimulated by its natural ligand ghrelin. In the present study, we tested the hypothesis that common and rare variation in the GHSR locus are related to increased prevalence of obesity and overweight...... among Whites. METHODOLOGY/PRINCIPAL FINDINGS: In a population-based study sample of 15,854 unrelated, middle-aged Danes, seven variants were genotyped to capture common variation in an 11 kbp region including GHSR. These were investigated for their individual and haplotypic association with obesity....... None of these analyses revealed consistent association with measures of obesity. A -151C/T promoter mutation in the GHSR was found in two unrelated obese patients. One family presented with complete co-segregation, but the other with incomplete co-segregation. The mutation resulted in an increased...

  1. Design and Synthesis of Novel Schiff Base-Benzothiazole Hybrids as Potential Epidermal Growth Factor Receptor (EGFR) Inhibitors.

    Science.gov (United States)

    Singh, Meenakshi; Singh, Sudhir Kumar; Thakur, Bhushan; Ray, Pritha; Singh, Sushil K

    2016-01-01

    A series of novel Schiff bases -benzothiazole hybrids was designed, synthesized and evaluated for their anticancer activity by MTT assay and western blot method. Antiproliferative screening indicated that compound containing dihydroxy substituents had potent inhibitory activity with IC50 value 34µg/ml against SKOV3, A2780-S and A2780-CR cell lines. It showed more potent cytotoxicity in combination with cisplatin and paclitaxel than alone in the selected cell lines (SKOV3, A2780 and A2780-CR models). The in vitro cytotoxicity of the compounds on IOSE 364 cell line was evaluated to establish the selectivity. Molecular docking study exhibited good binding against epidermal growth factor receptor, which was further ascertained by immunoblot assay using specific antibody against phosphorylated EGFR, and thus unravelling the targeted anticancer mechanism. PMID:26443027

  2. NR-2L: a two-level predictor for identifying nuclear receptor subfamilies based on sequence-derived features.

    Directory of Open Access Journals (Sweden)

    Pu Wang

    Full Text Available Nuclear receptors (NRs are one of the most abundant classes of transcriptional regulators in animals. They regulate diverse functions, such as homeostasis, reproduction, development and metabolism. Therefore, NRs are a very important target for drug development. Nuclear receptors form a superfamily of phylogenetically related proteins and have been subdivided into different subfamilies due to their domain diversity. In this study, a two-level predictor, called NR-2L, was developed that can be used to identify a query protein as a nuclear receptor or not based on its sequence information alone; if it is, the prediction will be automatically continued to further identify it among the following seven subfamilies: (1 thyroid hormone like (NR1, (2 HNF4-like (NR2, (3 estrogen like, (4 nerve growth factor IB-like (NR4, (5 fushi tarazu-F1 like (NR5, (6 germ cell nuclear factor like (NR6, and (7 knirps like (NR0. The identification was made by the Fuzzy K nearest neighbor (FK-NN classifier based on the pseudo amino acid composition formed by incorporating various physicochemical and statistical features derived from the protein sequences, such as amino acid composition, dipeptide composition, complexity factor, and low-frequency Fourier spectrum components. As a demonstration, it was shown through some benchmark datasets derived from the NucleaRDB and UniProt with low redundancy that the overall success rates achieved by the jackknife test were about 93% and 89% in the first and second level, respectively. The high success rates indicate that the novel two-level predictor can be a useful vehicle for identifying NRs and their subfamilies. As a user-friendly web server, NR-2L is freely accessible at either http://icpr.jci.edu.cn/bioinfo/NR2L or http://www.jci-bioinfo.cn/NR2L. Each job submitted to NR-2L can contain up to 500 query protein sequences and be finished in less than 2 minutes. The less the number of query proteins is, the shorter the time will

  3. NR-2L: a two-level predictor for identifying nuclear receptor subfamilies based on sequence-derived features.

    Science.gov (United States)

    Wang, Pu; Xiao, Xuan; Chou, Kuo-Chen

    2011-01-01

    Nuclear receptors (NRs) are one of the most abundant classes of transcriptional regulators in animals. They regulate diverse functions, such as homeostasis, reproduction, development and metabolism. Therefore, NRs are a very important target for drug development. Nuclear receptors form a superfamily of phylogenetically related proteins and have been subdivided into different subfamilies due to their domain diversity. In this study, a two-level predictor, called NR-2L, was developed that can be used to identify a query protein as a nuclear receptor or not based on its sequence information alone; if it is, the prediction will be automatically continued to further identify it among the following seven subfamilies: (1) thyroid hormone like (NR1), (2) HNF4-like (NR2), (3) estrogen like, (4) nerve growth factor IB-like (NR4), (5) fushi tarazu-F1 like (NR5), (6) germ cell nuclear factor like (NR6), and (7) knirps like (NR0). The identification was made by the Fuzzy K nearest neighbor (FK-NN) classifier based on the pseudo amino acid composition formed by incorporating various physicochemical and statistical features derived from the protein sequences, such as amino acid composition, dipeptide composition, complexity factor, and low-frequency Fourier spectrum components. As a demonstration, it was shown through some benchmark datasets derived from the NucleaRDB and UniProt with low redundancy that the overall success rates achieved by the jackknife test were about 93% and 89% in the first and second level, respectively. The high success rates indicate that the novel two-level predictor can be a useful vehicle for identifying NRs and their subfamilies. As a user-friendly web server, NR-2L is freely accessible at either http://icpr.jci.edu.cn/bioinfo/NR2L or http://www.jci-bioinfo.cn/NR2L. Each job submitted to NR-2L can contain up to 500 query protein sequences and be finished in less than 2 minutes. The less the number of query proteins is, the shorter the time will

  4. Pharmacophore-based virtual screening, biological evaluation and binding mode analysis of a novel protease-activated receptor 2 antagonist.

    Science.gov (United States)

    Cho, Nam-Chul; Seo, Seoung-Hwan; Kim, Dohee; Shin, Ji-Sun; Ju, Jeongmin; Seong, Jihye; Seo, Seon Hee; Lee, Iiyoun; Lee, Kyung-Tae; Kim, Yun Kyung; No, Kyoung Tai; Pae, Ae Nim

    2016-08-01

    Protease-activated receptor 2 (PAR2) is a G protein-coupled receptor, mediating inflammation and pain signaling in neurons, thus it is considered to be a potential therapeutic target for inflammatory diseases. In this study, we performed a ligand-based virtual screening of 1.6 million compounds by employing a common-feature pharmacophore model and two-dimensional similarity search to identify a new PAR2 antagonist. The common-feature pharmacophore model was established based on the biological screening results of our in-house library. The initial virtual screening yielded a total number of 47 hits, and additional biological activity tests including PAR2 antagonism and anti-inflammatory effects resulted in a promising candidate, compound 43, which demonstrated an IC50 value of 8.22 µM against PAR2. In next step, a PAR2 homology model was constructed using the crystal structure of the PAR1 as a template to explore the binding mode of the identified ligands. A molecular docking method was optimized by comparing the binding modes of a known PAR2 agonist GB110 and antagonist GB83, and applied to predict the binding mode of our hit compound 43. In-depth docking analyses revealed that the hydrophobic interaction with Phe243(5.39) is crucial for PAR2 ligands to exert antagonistic activity. MD simulation results supported the predicted docking poses that PAR2 antagonist blocked a conformational rearrangement of Na(+) allosteric site in contrast to PAR2 agonist that showed Na(+) relocation upon GPCR activation. In conclusion, we identified new a PAR2 antagonist together with its binding mode, which provides useful insights for the design and development of PAR2 ligands. PMID:27600555

  5. Affinity-Based Screening of Tetravalent Peptides Identifies Subtype-Selective Neutralizers of Shiga Toxin 2d, a Highly Virulent Subtype, by Targeting a Unique Amino Acid Involved in Its Receptor Recognition.

    Science.gov (United States)

    Mitsui, Takaaki; Watanabe-Takahashi, Miho; Shimizu, Eiko; Zhang, Baihao; Funamoto, Satoru; Yamasaki, Shinji; Nishikawa, Kiyotaka

    2016-09-01

    Shiga toxin (Stx), a major virulence factor of enterohemorrhagic Escherichia coli (EHEC), can be classified into two subgroups, Stx1 and Stx2, each consisting of various closely related subtypes. Stx2 subtypes Stx2a and Stx2d are highly virulent and linked with serious human disorders, such as acute encephalopathy and hemolytic-uremic syndrome. Through affinity-based screening of a tetravalent peptide library, we previously developed peptide neutralizers of Stx2a in which the structure was optimized to bind to the B-subunit pentamer. In this study, we identified Stx2d-selective neutralizers by targeting Asn16 of the B subunit, an amino acid unique to Stx2d that plays an essential role in receptor binding. We synthesized a series of tetravalent peptides on a cellulose membrane in which the core structure was exactly the same as that of peptides in the tetravalent library. A total of nine candidate motifs were selected to synthesize tetravalent forms of the peptides by screening two series of the tetravalent peptides. Five of the tetravalent peptides effectively inhibited the cytotoxicity of Stx2a and Stx2d, and notably, two of the peptides selectively inhibited Stx2d. These two tetravalent peptides bound to the Stx2d B subunit with high affinity dependent on Asn16. The mechanism of binding to the Stx2d B subunit differed from that of binding to Stx2a in that the peptides covered a relatively wide region of the receptor-binding surface. Thus, this highly optimized screening technique enables the development of subtype-selective neutralizers, which may lead to more sophisticated treatments of infections by Stx-producing EHEC. PMID:27382021

  6. Pharmacokinetic digital phantoms for accuracy assessment of image-based dosimetry in 177Lu-DOTATATE peptide receptor radionuclide therapy

    Science.gov (United States)

    Brolin, Gustav; Gustafsson, Johan; Ljungberg, Michael; Sjögreen Gleisner, Katarina

    2015-08-01

    Patient-specific image-based dosimetry is considered to be a useful tool to limit toxicity associated with peptide receptor radionuclide therapy (PRRT). To facilitate the establishment and reliability of absorbed-dose response relationships, it is essential to assess the accuracy of dosimetry in clinically realistic scenarios. To this end, we developed pharmacokinetic digital phantoms corresponding to patients treated with 177Lu-DOTATATE. Three individual voxel phantoms from the XCAT population were generated and assigned a dynamic activity distribution based on a compartment model for 177Lu-DOTATATE, designed specifically for this purpose. The compartment model was fitted to time-activity data from 10 patients, primarily acquired using quantitative scintillation camera imaging. S values for all phantom source-target combinations were calculated based on Monte-Carlo simulations. Combining the S values and time-activity curves, reference values of the absorbed dose to the phantom kidneys, liver, spleen, tumours and whole-body were calculated. The phantoms were used in a virtual dosimetry study, using Monte-Carlo simulated gamma-camera images and conventional methods for absorbed-dose calculations. The characteristics of the SPECT and WB planar images were found to well represent those of real patient images, capturing the difficulties present in image-based dosimetry. The phantoms are expected to be useful for further studies and optimisation of clinical dosimetry in 177Lu PRRT.

  7. 基于平方位置误差下限的优化功率分配方案%OPTIMISED POWER ALLOCATION ALGORITHM BASED ON SQUARE POSITION LOWER ERROR BOUND

    Institute of Scientific and Technical Information of China (English)

    李秉键; 夏文栋; 郭其标; 任江涛

    2015-01-01

    在无线传感网络中,节点定位是基于位置的应用基本要求。然而,现多数文献仅关注定位精度,而忽略了能量消耗对定位精度的影响。为此,针对基于接收信号强度 RSSI(Received Signal Strength Indicator)定位方案,提出基于平方位置误差下限 SPEB (Squared Position Error Bound)的优化功率分配 SPEB-OPA(SPEB-Based Optimal Power Allocation)方案,目的在于最小化能量消耗。在 SPEB-OPA 算法中,将 SPEB 作为评定定位精度的参数,并推导出 SPEB 表达式,然后建立优化功率分配的目标函数,并考虑到锚节点位置存在误差。仿真结果表明,提出的 SPEB-OPA 方案极大地减少了功率消耗。当误差门限 T =8时,SPEB-OPA 方案的功率消耗比统一功率分配 UPA(Uniform Power allocation)方案减少至50%。%Sensor nodes positioning is a fundamental requirement of location-based applications in wireless sensor networks.However,now most of the literatures only focus on positioning accuracy,but the impact of energy consumption on positioning accuracy is overlooked.There-fore,for RSSI-based positioning scheme,we introduced an optimised power allocation scheme which is based on square position lower error bound (SPEB-OPA),aimed at minimising the energy consumption.In SPEB-OPA algorithm,we used SPEB as the parameter for estimating positioning accuracy,and deduced the SPEB expression.Then we set up the objective function of the optimised power allocation,and consid-ered the errors existed in positions of anchor nodes.Simulation results showed that the proposed SPEB-OPA scheme greatly decreased the power consumption.When the error threshold T =8,the power consumption of SPEB-OPA scheme was reduced to 50% of that of uniform power allocation (UPA)scheme.

  8. The Hallucinogen N,N-Dimethyltryptamine (DMT) Is an Endogenous Sigma-1 Receptor Regulator

    OpenAIRE

    Fontanilla, Dominique; Johannessen, Molly; Hajipour, Abdol R.; Cozzi, Nicholas V; Jackson, Meyer B.; Ruoho, Arnold E.

    2009-01-01

    The sigma-1 receptor is widely distributed in the central nervous system and periphery. Originally mischaracterized as an opioid receptor, the sigma-1 receptor binds a vast number of synthetic compounds but does not bind opioid peptides; it is currently considered an orphan receptor. The sigma-1 receptor pharmacophore includes an alkylamine core, also found in the endogenous compound N,N-dimethyltryptamine (DMT). DMT acts as a hallucinogen, but its receptor target has been unclear. DMT bound ...

  9. New estradiol based {sup 111}In complex towards the estrogen receptor

    Energy Technology Data Exchange (ETDEWEB)

    Vultos, Filipe; Cunha, Susana; Fernandes, Celia; Oliveira, Maria Cristina; Marques, Fernanda; Santos, Isabel; Gano, Lurdes [Universidade de Lisboa, Bobadela (Portugal). Centro de Ciencias e Tecnologias Nucleares C2TN; Botelho, Maria Filomena [Universidade de Coimbra (Portugal). Inst. de Biofisica/Biomatematica

    2015-07-01

    The oestrogen receptor (ER) is an important tumour target for molecular imaging and radionuclide therapy due to its overexpression in many malignant cells as compared to normal cells. Aiming to find new functional molecular imaging/therapeutic agents for ER positive tumours, we have synthesized a new estradiol derivative substituted at the 16-α position with a diethylene triamine tetraacetic acid (DTTA)-like chelating ligand through a four-carbon spacer. The new bioconjugate (H{sub 4}L), was used to synthesize the corresponding indium complexes (InL/[{sup 111}In]L). The radioactive complex [{sup 111}In]L was prepared in high yield (>98%) at final concentrations of 1 x 10{sup -4} M and its chemical identity was ascertained by comparing its HPLC gamma-chromatogram to the HPLC UV-vis-chromatogram of the InL analogue. [{sup 111}In]L is hydrophilic and kinetically stable in the presence of an excess of apo-transferrin and in human blood serum. Cellular studies in breast cancer cells (MCF-7 and MDA-MB-431) suggest that [{sup 111}In]L uptake may be mediated by an ER dependent mechanism. Biodistribution studies were performed in mice indicating a rapid clearance from most organs and a slow total excretion that occurs mainly by hepatobiliar pathway. High in vivo stability of [{sup 111}In]L was confirmed by HPLC analysis of urine and blood samples. Nevertheless, the hydrophilicity, the low ER affinity and the biodistribution of [{sup 111}In]L indicate that structural modifications are required to improve its behaviour for ER targeting in vivo.

  10. Analysis of imbalanced weather data based on branch-and-bound approach%基于分支限界的不平衡气象数据晴雨分析

    Institute of Scientific and Technical Information of China (English)

    王剑辉; 梁路; 王彪

    2016-01-01

    This paper proposed the modified cost-sensitive learning methods to preprocess the imbalance weather data.Con-sidering about the specialty of weather data,it made the value of rainfall per unit time as the cost value.So the data could be divided into two types of rain and non-rain effectively and reasonably.And then it used logic-based approach to analysie the data processed,used branch-and-bound approach to derive a Boolean classifier.Experimental results show that this method is feasible and effective.What’s more,it’s valid to perform any further logic calculation or logic operation on the result of the Boolean classifiers,achieving more flexibility.%提出基于修改的代价敏感学习的方法对不平衡的天气数据进行预处理,结合天气数据自身的特点,以单位时间的降雨量为成本的值,将数据合理有效地区分为下雨和非下雨两类;进而运用基于逻辑的方法对处理完的数据进行分析,运用分支限界算法得出布尔分类器。实验结果表明此方法可行有效,该方法可进一步对布尔分类器结果进行逻辑运算,从而达到更加灵活的操作分类器的效果。

  11. Limit Analysis on Mechanism of Low-angle Submarine Landslide Based on Upper Bound Energy Method%基于能量上限法的海底缓边坡滑坡机理分析

    Institute of Scientific and Technical Information of China (English)

    安晨歌; 张建红; 周敏; 朱政

    2011-01-01

    海床中的天然气水合物分解后由固体变为气体,将直接提高孔隙水压力,减小边坡内有效应力,导致边坡稳定性下降.本文以能量上限定理为理论基础,采用二维极限分析方法分析海底缓倾角边坡的滑坡机理,研究由于水合物分解形成的软弱夹层对边坡稳定性的影响.分析表明,软弱夹层的埋深和海床土体内摩擦角会对边坡的稳定性产生直接影响.由于水合物分解而产生的膨胀压力也会降低海底缓倾角边坡的稳定性.%It is indicated by some experimental and theoretical data that the disassociation of gas hydrate could directly increase pore water pressure, decrease effective stresses in the submarine slope, reduce the friction coefficient between different soil layers in slope, and in consequence the slope stability will be weakened. In this paper, a two-dimensional numerical limit analysis, incorporating the upper-bound energy method, is presented to improve the understanding of the failure mechanism of submarine low-angle slope. Based on the analysis, it is found that the internal friction angle and the burial depth of weak layer affect the slope stability. It is also found that the expansion pressure due to gas hydrate disassociation in weak layer can affect the stability also.

  12. Bootstrap bound for conformal multi-flavor QCD on lattice

    CERN Document Server

    Nakayama, Yu

    2016-01-01

    The recent work by Iha et al shows an upper bound on mass anomalous dimension $\\gamma_m$ of multi-flavor massless QCD at the renormalization group fixed point from the conformal bootstrap in $SU(N_F)_V$ symmetric conformal field theories under the assumption that the fixed point is realizable with the lattice regularization based on staggered fermions. We show that the almost identical but slightly stronger bound applies to the regularization based on Wilson fermions (or domain wall fermions) by studying the conformal bootstrap in $SU(N_f)_L \\times SU(N_f)_R$ symmetric conformal field theories. For $N_f=8$, our bound implies $\\gamma_m < 1.31$ to avoid dangerously irrelevant operators that are not compatible with the lattice symmetry.

  13. Bootstrap bound for conformal multi-flavor QCD on lattice

    Science.gov (United States)

    Nakayama, Yu

    2016-07-01

    The recent work by Iha et al. shows an upper bound on mass anomalous dimension γ m of multi-flavor massless QCD at the renormalization group fixed point from the conformal bootstrap in SU( N F ) V symmetric conformal field theories under the assumption that the fixed point is realizable with the lattice regularization based on staggered fermions. We show that the almost identical but slightly stronger bound applies to the regularization based on Wilson fermions (or domain wall fermions) by studying the conformal bootstrap in SU( N f ) L × SU( N f ) R symmetric conformal field theories. For N f = 8, our bound implies γ m < 1 .31 to avoid dangerously irrelevant operators that are not compatible with the lattice symmetry.

  14. Leucine-based receptor sorting motifs are dependent on the spacing relative to the plasma membrane

    DEFF Research Database (Denmark)

    Geisler, C; Dietrich, J; Nielsen, B L;

    1998-01-01

    amino acid, is constitutively active. In this study, we have investigated how the spacing relative to the plasma membrane affects the function of both types of leucine-based motifs. For phosphorylation-dependent leucine-based motifs, a minimal spacing of 7 residues between the plasma membrane and the...... phospho-acceptor was required for phosphorylation and thereby activation of the motifs. For constitutively active leucine-based motifs, a minimal spacing of 6 residues between the plasma membrane and the acidic residue was required for optimal activity of the motifs. In addition, we found that the acidic......Many integral membrane proteins contain leucine-based motifs within their cytoplasmic domains that mediate internalization and intracellular sorting. Two types of leucine-based motifs have been identified. One type is dependent on phosphorylation, whereas the other type, which includes an acidic...

  15. Holographic bound in covariant loop quantum gravity

    CERN Document Server

    Tamaki, Takashi

    2016-01-01

    We investigate puncture statistics based on the covariant area spectrum in loop quantum gravity. First, we consider Maxwell-Boltzmann statistics with a Gibbs factor for punctures. We establish formulae which relate physical quantities such as horizon area to the parameter characterizing holographic degrees of freedom. We also perform numerical calculations and obtain consistency with these formulae. These results tell us that the holographic bound is satisfied in the large area limit and correction term of the entropy-area law can be proportional to the logarithm of the horizon area. Second, we also consider Bose-Einstein statistics and show that the above formulae are also useful in this case. By applying the formulae, we can understand intrinsic features of Bose-Einstein condensate which corresponds to the case when the horizon area almost consists of punctures in the ground state. When this phenomena occurs, the area is approximately constant against the parameter characterizing the temperature. When this ...

  16. Hyperquarks and bosonic preon bound states

    Science.gov (United States)

    Schmid, Michael L.; Buchmann, Alfons J.

    2009-11-01

    In a model in which leptons, quarks, and the recently introduced hyperquarks are built up from two fundamental spin-(1)/(2) preons, the standard model weak gauge bosons emerge as preon bound states. In addition, the model predicts a host of new composite gauge bosons, in particular, those responsible for hyperquark and proton decay. Their presence entails a left-right symmetric extension of the standard model weak interactions and a scheme for a partial and grand unification of nongravitational interactions based on, respectively, the effective gauge groups SU(6)P and SU(9)G. This leads to a prediction of the Weinberg angle at low energies in good agreement with experiment. Furthermore, using evolution equations for the effective coupling strengths, we calculate the partial and grand unification scales, the hyperquark mass scale, as well as the mass and decay rate of the lightest hyperhadron.

  17. Hyperquarks and bosonic preon bound states

    CERN Document Server

    Schmid, Michael L

    2013-01-01

    In a model in which leptons, quarks, and the recently introduced hyperquarks are built up from two fundamental spin 1/2 preons, the standard model weak gauge bosons emerge as preon bound states. In addition, the model predicts a host of new composite gauge bosons, in particular those responsible for hyperquark and proton decay. Their presence entails a left-right symmetric extension of the standard model weak interactions and a scheme for a partial and grand unification of nongravitational interactions based on respectively the effective gauge groups SU(6)_P and SU(9)_G. This leads to a prediction of the Weinberg angle at low energies in good agreement with experiment. Furthermore, using evolution equations for the effective coupling strengths, we calculate the partial and grand unification scales, the hyperquark mass scale, as well as the mass and decay rate of the lightest hyperhadron.

  18. Bounded Correctors in Almost Periodic Homogenization

    Science.gov (United States)

    Armstrong, Scott; Gloria, Antoine; Kuusi, Tuomo

    2016-10-01

    We show that certain linear elliptic equations (and systems) in divergence form with almost periodic coefficients have bounded, almost periodic correctors. This is proved under a new condition we introduce which quantifies the almost periodic assumption and includes (but is not restricted to) the class of smooth, quasiperiodic coefficient fields which satisfy a Diophantine-type condition previously considered by Kozlov (Mat Sb (N.S), 107(149):199-217, 1978). The proof is based on a quantitative ergodic theorem for almost periodic functions combined with the new regularity theory recently introduced by Armstrong and Shen (Pure Appl Math, 2016) for equations with almost periodic coefficients. This yields control on spatial averages of the gradient of the corrector, which is converted into estimates on the size of the corrector itself via a multiscale Poincaré-type inequality.

  19. High content screening for G protein-coupled receptors using cell-based protein translocation assays

    DEFF Research Database (Denmark)

    Grånäs, Charlotta; Lundholt, Betina Kerstin; Heydorn, Arne;

    2005-01-01

    the capability to probe GPCR function at the cellular level with better resolution than has previously been possible, and offer practical strategies for more definitive selectivity evaluation and counter-screening in the early stages of drug discovery. The potential of cell-based translocation assays for GPCR...... will continue to be valuable discovery tools, the most exciting developments in the field involve cell-based assays for GPCR function. Some cell-based discovery strategies, such as the use of beta-arrestin as a surrogate marker for GPCR function, have already been reduced to practice, and have been used...... as valuable discovery tools for several years. The application of high content cell-based screening to GPCR discovery has opened up additional possibilities, such as direct tracking of GPCRs, G proteins and other signaling pathway components using intracellular translocation assays. These assays provide...

  20. Chemically engineering ligand selectivity at the free fatty acid receptor 2 based on pharmacological variation between species orthologs

    DEFF Research Database (Denmark)

    Hudson, Brian D; Christiansen, Elisabeth; Tikhonova, Irina G;

    2012-01-01

    When it is difficult to develop selective ligands within a family of related G-protein-coupled receptors (GPCRs), chemically engineered receptors activated solely by synthetic ligands (RASSLs) are useful alternatives for probing receptor function. In the present work, we explored whether a RASSL...... on this receptor and demonstrates that exploitation of pharmacological variation between species orthologs is a powerful method to generate novel chemically engineered GPCRs.-Hudson, B. D., Christiansen, E., Tikhonova, I. G., Grundmann, M., Kostenis, E., Adams, D. R., Ulven, T., Milligan, G. Chemically engineering...

  1. Bounds on double-diffusive convection

    Science.gov (United States)

    Balmforth, Neil J.; Ghadge, Shilpa A.; Kettapun, Atichart; Mandre, Shreyas D.

    2006-12-01

    We consider double-diffusive convection between two parallel plates and compute bounds on the flux of the unstably stratified species using the background method. The bound on the heat flux for Rayleigh Bénard convection also serves as a bound on the double-diffusive problem (with the thermal Rayleigh number equal to that of the unstably stratified component). In order to incorporate a dependence of the bound on the stably stratified component, an additional constraint must be included, like that used by Joseph (Stability of Fluid Motion, 1976, Springer) to improve the energy stability analysis of this system. Our bound extends Joseph's result beyond his energy stability boundary. At large Rayleigh number, the bound is found to behave like R_T(1/2) for fixed ratio R_S/R_T, where R_T and R_S are the Rayleigh numbers of the unstably and stably stratified components, respectively.

  2. Instanton bound states in ABJM theory

    Energy Technology Data Exchange (ETDEWEB)

    Hatsuda, Yasuyuki [DESY Hamburg (Germany). Theory Group; Tokyo Institute of Technology (Japan). Dept. of Physics; Moriyama, Sanefumi [Nagoya Univ. (Japan). Kobayashi Maskawa Inst. and Graduate School of Mathematics; Okuyama, Kazumi [Shinshu Univ., Matsumoto, Nagano (Japan). Dept. of Physics

    2013-06-15

    The partition function of the ABJM theory receives non-perturbative corrections due to instanton effects. We study these non-perturbative corrections, including bound states of worldsheet instantons and membrane instantons, in the Fermi-gas approach. We require that the total non-perturbative correction should be always finite for arbitrary Chern-Simons level. This finiteness is realized quite non-trivially because each bound state contribution naively diverges at some levels. The poles of each contribution should be canceled out in total. We use this pole cancellation mechanism to find unknown bound state corrections from known ones. We conjecture a general expression of the bound state contribution. Summing up all the bound state contributions, we find that the effect of bound states is simply incorporated into the worldsheet instanton correction by a redefinition of the chemical potential in the Fermi-gas system. Analytic expressions of the 3- and 4-membrane instanton corrections are also proposed.

  3. Process expression of bounded Petri nets

    Institute of Scientific and Technical Information of China (English)

    吴哲辉

    1996-01-01

    The concept of process expression of bounded Petri nets is presented.Moreover,an algorithm to find the process expression for a bounded Petri net is given.A process expression of a bounded Petri net is a regular expression whose every alphabet symbol represents a basic subprocess of the net.The regular set expressed by the regular expression is the set of all surjective processes of a bounded Petri net.A surjective process of a bounded Petri net is a process of this net in which every s-cut corresponds to a reachable marking of the net.Therefore,all surjective processes of a bounded Petri net can be obtained as long as its process expression and the basic subprocess represented by the alphabet symbols of the process expression are given.

  4. 基于刚性块体系统的岩质边坡稳定性下限法研究%Lower bound method for stability of rock slopes based on rigid block assemblages

    Institute of Scientific and Technical Information of China (English)

    李泽; 张小艳; 王均星

    2012-01-01

    块状岩质边坡由岩块和结构面两部分组成,而且结构面的存在以及结构面的强度控制着岩体的强度和稳定性;将塑性极限分析下限法理论、块体离散技术以及数学规划手段结合起来,研究块状岩质边坡的稳定性。首先将边坡离散成为刚性块体系统+结构面的组合体,考虑岩块体与结构面的综合作用,然后基于塑性极限分析的下限定理,建立以边坡稳定安全系数为目标函数且同时满足平衡条件、屈服条件和边界条件的塑性极限分析下限法数学规划模型,进而提出了相应的求解策略并编制了计算程序。最后对4个经典算例进行了分析,得到了严格的下限解,并将计算结果与其他方法的结果进行了比较,验证了方法和程序的正确性。%The block rock slope is made up of blocks and structural surfaces, and the stability of the rock mass is controlled by the existence and the strength of structural surface. Researches on the stability of block rock slope are carried out by using the lower bound theorem of plastic limit analysis, block discretization technique and mathematical programming method. Firstly, the slope is discretized into block assemblages that consist of rigid blocks and structural surface, considering the integral interaction of each other. And then, regarding the safety factor of slope stability as the objective fimction, the nonlinear mathematical programming models are established based on the lower bound theorem, which satisfy the equilibrium equations, yield conditions and static boundary conditions. The solution strategies of models are put forward, and the calculation programs are compiled. Finally, four classic examples are analyzed by means of the proposed method, and the rigorous lower limit values of the strength safety coefficient of slope, and the corresponding statically admissible stress fields are obtained. The results are compared with those

  5. Bound beta-decay: BOB

    International Nuclear Information System (INIS)

    For many years exotic decay modes of the neutron have been investigated as possible doorways to the exploration of new physics. The bound beta-decay (BOB) of the neutron into a hydrogen atom and an anti-neutrino offers a very elegant method to study neutrino helicities. However, this rare decay has not yet been observed for the free neutron, owing to the challenge of measuring a decay involving only electrically neutral particles and with an estimated branching ratio of only a few 106 of the three-body decay mode. During the past few years scientists from the TUM E18 Group have developed a novel experimental scheme which addresses all necessary problems associated with the observation of this two-body neutron decay in a very coherent way. The BOB experiment shall be installed at a tangential beam tube of a powerful research reactor such as the SR6 at the FRMII in Garching or H6-H7 beam tube at ILL. This talk will provide insights and ideas on how such an experiment is to be performed.

  6. Neutron bound {beta}- decay- BOB

    Energy Technology Data Exchange (ETDEWEB)

    Gabriel, M.; Berger, M.; Emmerich, R.; Faestermann, T.; Gutsmiedl, E.; Hartmann, F.J.; Paul, S.; Ruschel, S.; Schoen, J.; Schott, W.; Schubert, U.; Trautner, A. [Physik-Department, TUM, 85748 Garching (Germany); Engels, R. [Institut fuer Kernphysik, Forschungszentrum Juelich, 52425 Juelich (Germany); Fierlinger, P. [Excellence Cluster Universe, TUM, 85748 Garching (Germany); Hertenberger, R. [Sektion Physik, LMU, 85748 Garching (Germany); Roehrmoser, R. [FRM2, TUM, 85748 Garching (Germany); Udem, T. [Max-Planck-Institut fuer Quantenphysik, 85748 Garching (Germany)

    2011-07-01

    The bound neutron {beta}-decay(BOB) into a hydrogen atom and an electron antineutrino is investigated.The hyper-fine-state population of the monoenergetic hydrogen atoms (326.3 eV) yields the neutrino left-handed-ness or a possible right-handed admixture and possible small scalar and tensor contributions to the weak force. Preexperiments to measure the BOB H(2s) atoms have been done or are being set up using ionizer and RF discharge proton sources, a Wien filter, Cs and Ar cells, a spin filter, electric counter and accelerating fields, a double focusing magnet and a solar blind PM for the Lyman-{alpha} photons. In a first experiment, the charge exchange of the H(2s) atoms into H{sup -}, offering a selective method to discriminate these states against background, is investigated. In a second step the number of background H(2s) resulting from protons interacting with the walls of the experimental setup are determined. For this a quenching E field and a solar blind PM are used.

  7. Stable Bound Orbits around Black Rings

    Energy Technology Data Exchange (ETDEWEB)

    Igata, Takahisa; Ishihara, Hideki; Takamori, Yohsuke, E-mail: igata@sci.osaka-cu.ac.jp [Department of Mathematics and Physics, Graduate School of Science, Osaka City University, Osaka 558-8585 (Japan)

    2011-09-22

    We study stable bound orbits of a free particle around a black ring. Unlike the higher-dimensional black hole case, we find that there exist stable bound orbits in toroidal spiral shape near the ring axis and stable circular orbits on the axis. In addition, radii of stable bound orbits can be infinitely large if the ring thickness is less than a critical value.

  8. A Regional Assessment of Marine Vessel PM2.5 Impacts in the U.S. Pacific Northwest Using a Receptor Based Source Apportionment Method

    Science.gov (United States)

    This work reports the results of a regional receptor-based source apportionment analysis using the Positive Matrix Factorization (PMF) model on chemically speciated PM2.5 data from 36 urban and rural monitoring sites within the U.S. Pacific Northwest. The approach taken is to mo...

  9. Bound States of Double Flavor Hyperons

    CERN Document Server

    Froemel, F; Riska, D O

    2005-01-01

    Several realistic phenomenological nucleon-nucleon interaction models are employed to investigate the possibility of bound deuteron-like states of such heavy flavor hyperons and nucleons, for which the interaction between the light flavor quark components is expected to be the most significant interaction. The results indicate that deuteron-like bound states are likely to form between nucleons and the $\\Xi_c^{'}$ and $\\Xi_{cc}$ charm hyperons as well as between $\\Xi$ hyperons and double-charm hyperons. Bound states between two $\\Sigma_c$ hyperons are also likely. In the case of beauty hyperons the corresponding states are likely to be deeply bound.

  10. Bound states of heavy flavor hyperons

    Science.gov (United States)

    Frömel, F.; Juliá-Díaz, B.; Riska, D. O.

    2005-04-01

    Several realistic phenomenological nucleon-nucleon interaction models are employed to investigate the possibility of bound deuteron-like states of such heavy flavor hyperons and nucleons, for which the interaction between the light flavor quark components is expected to be the most significant interaction. The results indicate that deuteron-like bound states are likely to form between nucleons and the Ξc' and Ξ charm hyperons as well as between Ξ hyperons and double-charm hyperons. Bound states between two Σ hyperons are also likely. In the case of beauty hyperons the corresponding states are likely to be deeply bound.

  11. A violation of the covariant entropy bound?

    CERN Document Server

    Masoumi, Ali

    2014-01-01

    Several arguments suggest that the entropy density at high energy density $\\rho$ should be given by the expression $s=K\\sqrt{\\rho/G}$, where $K$ is a constant of order unity. On the other hand the covariant entropy bound requires that the entropy on a light sheet be bounded by $A/4G$, where $A$ is the area of the boundary of the sheet. We find that in a suitably chosen cosmological geometry, the above expression for $s$ violates the covariant entropy bound. We consider different possible explanations for this fact; in particular the possibility that entropy bounds should be defined in terms of volumes of regions rather than areas of surfaces.

  12. Chernoff Bound Based Approximate Frequent Itemset Mining Method over Streams%一种基于Chernoff Bound的数据流上近似频繁项集的挖掘方法

    Institute of Scientific and Technical Information of China (English)

    李海峰; 章宁

    2011-01-01

    数据流高速、无限和动态的特点决定了必须在有限的内存中以尽快的计算速度完成流数据上的频繁项集挖掘.将数据流中的数据按照段进行划分,采用二元组列表的数据结构进行保存,提出了一种基于滑动窗口的近似频繁项集挖掘方法AFIoDS,以实时获取频繁项集集合的真子集,并引入了概率参数,利用Chernoff Bound来动态改变支持度的近似值,保证真子集中的频繁项集被限制在一定的误差范围之内.此外,为了进一步节省内存,AFIoDS采用闭合项集的形式压缩每个段中获取的频繁项集.通过在3种真实数据集上的实验表明,AFIoDS算法与现有算法相比,在精度没有下降的情况下,具有更快的处理速度,同时其存储开销大大降低.%A data stream is fast, unlimited and dynamic, these characteristics constraint the computational resources and storages when mining frequent itemsets. This paper addressed this problem and proposed a simple and effective algorithrn AFIoDS, AFIoDS is an approximate algorithm based on sliding window model,which splits stream data into batches and maintains them with 2-tuple lists;thus,a false negative result can be obtained using a probabilistic parameter based on chernoff bound. The approximation will be changed dynamically to guarantee the mining frequent itemsets are error controllable. Plus, a compression of frequent itemsets, the closed frequent itemsets, are employed to represent the results of each batch for further memory saving. Our experimental results on 3 real world data show that without precision reduction, AFIoDS achieves a faster speed and a much reduced memory cost in comparison with the state-of-the-art algorithrna.

  13. Weekly nanoparticle albumin-bound paclitaxel in combination with cisplatin versus weekly solvent-based paclitaxel plus cisplatin as first-line therapy in Chinese patients with advanced esophageal squamous cell carcinoma

    Science.gov (United States)

    Wang, Hai-ying; Yao, Zhi-hua; Tang, Hong; Zhao, Yan; Zhang, Xiao-san; Yao, Shu-na; Yang, Shu-jun; Liu, Yan-yan

    2016-01-01

    Objective More effective regimens for advanced esophageal squamous cell carcinoma (ESCC) are urgently needed. Therefore, a retrospective study concerning the efficacy and safety of nanoparticle albumin-bound paclitaxel plus cisplatin (nab-TP) versus solvent-based paclitaxel plus cisplatin (sb-TP) as a first-line therapy was conducted in Chinese patients with advanced ESCC. Methods From June 2009 to June 2015, 32 patients were treated with nab-paclitaxel (125 mg/m2) on the first and eighth days (30 minutes infusion) and cisplatin (75 mg/m2) on the second day every 21 days (nab-TP arm). Also, 43 patients were treated with solvent-based paclitaxel (80 mg/m2) intravenously on the first and eighth days and the same dose of cisplatin (sb-TP arm). The two groups were compared in terms of objective response rate (ORR), disease control rate, progression-free survival (PFS), overall survival (OS), and safety profile. OS and PFS were estimated using Kaplan–Meier methods to determine associations between chemotherapy regimens and survival outcomes. Results Nab-TP demonstrated a higher ORR (50% vs 30%; P=0.082) and disease control rate (81% vs 65%; P=0.124) than sb-TP. Median OS was similar for nab-TP and sb-TP (12.5 vs 10.7 months; P=0.269). However, nab-TP resulted in a longer median PFS (6.1 months [95% confidence interval: 5.3–6.9]) than sb-TP (5.0 months [95% confidence interval: 4.4–5.6]) (P=0.029). The most common adverse events included anemia, leukopenia, neutropenia, febrile neutropenia, and thrombocytopenia in both the groups and no statistically significant differences were observed between the groups. With statistically significant differences, significantly less grade ≥3 peripheral neuropathy, arthralgia, and myalgia occurred in the nab-TP arm (all Pline therapy were similar between the two regimens. There were no treatment-related deaths in either group. Conclusion Nab-paclitaxel plus cisplatin is found to be an effective and tolerable option for advanced

  14. A combination of receptor-based pharmacophore modeling & QM techniques for identification of human chymase inhibitors.

    Directory of Open Access Journals (Sweden)

    Mahreen Arooj

    Full Text Available Inhibition of chymase is likely to divulge therapeutic ways for the treatment of cardiovascular diseases, and fibrotic disorders. To find novel and potent chymase inhibitors and to provide a new idea for drug design, we used both ligand-based and structure-based methods to perform the virtual screening(VS of commercially available databases. Different pharmacophore models generated from various crystal structures of enzyme may depict diverse inhibitor binding modes. Therefore, multiple pharmacophore-based approach is applied in this study. X-ray crystallographic data of chymase in complex with different inhibitors were used to generate four structure-based pharmacophore models. One ligand-based pharmacophore model was also developed from experimentally known inhibitors. After successful validation, all pharmacophore models were employed in database screening to retrieve hits with novel chemical scaffolds. Drug-like hit compounds were subjected to molecular docking using GOLD and AutoDock. Finally four structurally diverse compounds with high GOLD score and binding affinity for several crystal structures of chymase were selected as final hits. Identification of final hits by three different pharmacophore models necessitates the use of multiple pharmacophore-based approach in VS process. Quantum mechanical calculation is also conducted for analysis of electrostatic characteristics of compounds which illustrates their significant role in driving the inhibitor to adopt a suitable bioactive conformation oriented in the active site of enzyme. In general, this study is used as example to illustrate how multiple pharmacophore approach can be useful in identifying structurally diverse hits which may bind to all possible bioactive conformations available in the active site of enzyme. The strategy used in the current study could be appropriate to design drugs for other enzymes as well.

  15. The effects of a 5-HT5A receptor antagonist in a ketamine-based rat model of cognitive dysfunction and the negative symptoms of schizophrenia.

    Science.gov (United States)

    Nikiforuk, Agnieszka; Hołuj, Małgorzata; Kos, Tomasz; Popik, Piotr

    2016-06-01

    Serotonin (5-HT) receptors still represent promising targets for the development of novel multireceptor or stand-alone antipsychotic drugs with a potential to ameliorate cognitive impairments and negative symptoms in schizophrenia. The 5-HT5A receptor, one of the least known members of the serotonin receptor family, has also drawn attention in this regard. Although the antipsychotic efficacy of 5-HT5A antagonists is still equivocal, recent experimental data suggest the cognitive-enhancing activity of this strategy. The aim of the present study was to evaluate pro-cognitive and pro-social efficacies of the 5-HT5A receptor antagonist in a rat pharmacological model of schizophrenia employing the administration of the NMDA receptor antagonist, ketamine. The ability of SB-699551 to reverse ketamine-induced cognitive deficits in the attentional set-shifting task (ASST) and novel object recognition task (NORT) was examined. The compound's efficacy against ketamine-induced social withdrawal was assessed in the social interaction test (SIT) and in the social choice test (SCT). The results demonstrated the efficacy of SB-699551 in ameliorating ketamine-induced impairments on the ASST and NORT. Moreover, the tested compound also enhanced set-shifting performance in cognitively unimpaired control rats and improved object recognition memory in conditions of delay-induced natural forgetting. The pro-social activity of SB-699551 was demonstrated on both employed paradigms, the SIT and SCT. The present study suggests the preclinical efficacy of a strategy based on the blockade of 5-HT5A receptors against schizophrenia-like cognitive deficits and negative symptoms. The utility of this receptor as a target for improvement of cognitive and social dysfunctions warrants further studies. PMID:26826431

  16. Identification of potent and selective retinoic acid receptor gamma (RARγ) antagonists for the treatment of osteoarthritis pain using structure based drug design.

    Science.gov (United States)

    Hughes, Norman E; Bleisch, Thomas J; Jones, Scott A; Richardson, Timothy I; Doti, Robert A; Wang, Yong; Stout, Stephanie L; Durst, Gregory L; Chambers, Mark G; Oskins, Jennifer L; Lin, Chaohua; Adams, Lisa A; Page, Todd J; Barr, Robert J; Zink, Richard W; Osborne, Harold; Montrose-Rafizadeh, Chahrzad; Norman, Bryan H

    2016-07-15

    A series of triaryl pyrazoles were identified as potent pan antagonists for the retinoic acid receptors (RARs) α, β and γ. X-ray crystallography and structure-based drug design were used to improve selectivity for RARγ by targeting residue differences in the ligand binding pockets of these receptors. This resulted in the discovery of novel antagonists which maintained RARγ potency but were greater than 500-fold selective versus RARα and RARβ. The potent and selective RARγ antagonist LY2955303 demonstrated good pharmacokinetic properties and was efficacious in the MIA model of osteoarthritis-like joint pain. This compound demonstrated an improved margin to RARα-mediated adverse effects. PMID:27261179

  17. Epidermal growth factor receptor targeting enhances adenoviral vector based suicide gene therapy of osteosarcoma

    NARCIS (Netherlands)

    Witlox, M.A.; van Beusechem, V.W.; Grill, J.; Haisma, H.J.; Schaap, G.; Bras, J.; Van Diest, P.; De Gast, A.; Curiel, D.T.; Pinedo, H.M.; Gerritsen, W.R.; Wuisman, P.I.

    2002-01-01

    Background Despite improvements in the treatment of osteosarcoma (OS) there are still too many patients who cannot benefit from current treatment modalities. Therefore, new therapeutic approaches are warranted. Here we explore the efficacy of targeted adenoviral based suicide gene therapy. Methods a

  18. Development of genetic diagnosing method for diabetes and cholecystitis based on gene analysis of CCK-A receptor

    International Nuclear Information System (INIS)

    Based on the gene analysis of cholecystokinin type A receptor (CCKAR) from normal mouse and its sequence analysis in the previous year, CCKAR knock-out gene which allows mRNA expression of β-galactosidase gene in stead of CCKAR gene was constructed. Since some abnormality in CCKAR gene is thought to be a causal factor of diabetes and cholecystitis, a knock-out mouse that expressed LacZ but not CCKAR was constructed to investigate the correlation between the clinical features of diabetes and cholecystitis, and CCKAR gene abnormalities. F2 mice that had mutations in CCKAR gene were born according to the Mendel's low. The expression of CCKAR gene was investigated in detail based on the expression of LacZ gene in various tissues of homo (-/-) and hetero (-/+) knockout mice. Comparative study on blood sugar level, blood insulin level, the formation of biliary calculus, etc. is underway with the wild mouse, hetero and homo knockout mouse. (M.N.)

  19. Rational Structure-Based Rescaffolding Approach to De Novo Design of Interleukin 10 (IL-10) Receptor-1 Mimetics.

    Science.gov (United States)

    Ruiz-Gómez, Gloria; Hawkins, John C; Philipp, Jenny; Künze, Georg; Wodtke, Robert; Löser, Reik; Fahmy, Karim; Pisabarro, M Teresa

    2016-01-01

    Tackling protein interfaces with small molecules capable of modulating protein-protein interactions remains a challenge in structure-based ligand design. Particularly arduous are cases in which the epitopes involved in molecular recognition have a non-structured and discontinuous nature. Here, the basic strategy of translating continuous binding epitopes into mimetic scaffolds cannot be applied, and other innovative approaches are therefore required. We present a structure-based rational approach involving the use of a regular expression syntax inspired in the well established PROSITE to define minimal descriptors of geometric and functional constraints signifying relevant functionalities for recognition in protein interfaces of non-continuous and unstructured nature. These descriptors feed a search engine that explores the currently available three-dimensional chemical space of the Protein Data Bank (PDB) in order to identify in a straightforward manner regular architectures containing the desired functionalities, which could be used as templates to guide the rational design of small natural-like scaffolds mimicking the targeted recognition site. The application of this rescaffolding strategy to the discovery of natural scaffolds incorporating a selection of functionalities of interleukin-10 receptor-1 (IL-10R1), which are relevant for its interaction with interleukin-10 (IL-10) has resulted in the de novo design of a new class of potent IL-10 peptidomimetic ligands. PMID:27123592

  20. Rational Structure-Based Rescaffolding Approach to De Novo Design of Interleukin 10 (IL-10 Receptor-1 Mimetics.

    Directory of Open Access Journals (Sweden)

    Gloria Ruiz-Gómez

    Full Text Available Tackling protein interfaces with small molecules capable of modulating protein-protein interactions remains a challenge in structure-based ligand design. Particularly arduous are cases in which the epitopes involved in molecular recognition have a non-structured and discontinuous nature. Here, the basic strategy of translating continuous binding epitopes into mimetic scaffolds cannot be applied, and other innovative approaches are therefore required. We present a structure-based rational approach involving the use of a regular expression syntax inspired in the well established PROSITE to define minimal descriptors of geometric and functional constraints signifying relevant functionalities for recognition in protein interfaces of non-continuous and unstructured nature. These descriptors feed a search engine that explores the currently available three-dimensional chemical space of the Protein Data Bank (PDB in order to identify in a straightforward manner regular architectures containing the desired functionalities, which could be used as templates to guide the rational design of small natural-like scaffolds mimicking the targeted recognition site. The application of this rescaffolding strategy to the discovery of natural scaffolds incorporating a selection of functionalities of interleukin-10 receptor-1 (IL-10R1, which are relevant for its interaction with interleukin-10 (IL-10 has resulted in the de novo design of a new class of potent IL-10 peptidomimetic ligands.