Sample records for bound receptor based

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

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


    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


    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. Exact entanglement bases and general bound entanglement

    CERN Document Server

    Zhong, Z Z


    In this paper, we give the more general bound entangled states associated with the unextendible product bases (UPB), i.e. by using of the exact entanglement bases (EEB) and the complete basis with unextendible product bases (CBUPB), we prove that the arbitrary convex sums of the uniform mixtures (bound entangled states) associated with UPBs are still bound entangled states. Further, we discuss the equivalent transformation group and classification of the CBUPBs, and by using this classification, we prove that in the meaning of indistinguishability, the set of the above all possible bound entangled states can be reduced to the set of all possible mixtures of some fixed basic bound entangled states. At last, we prove that every operating of the partial transposition (PT) map acting upon a density matrix under any bipartite partitioning induces a mapping from the above reduced set of bound entangled states to oneself, which corresponds to a non-identical permutation of the basic bound entangled states.

  4. 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)


    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.

  5. Amide-based Fluorescent Macrocyclic Anion Receptors

    Institute of Scientific and Technical Information of China (English)

    ZENG, Zhen-Ya(曾振亚); XU, Kuo-Xi(徐括喜); HE, Yong-Bing(何永炳); LIU, Shun-Ying(刘顺英); WU, Jin-Long(吴进龙); WEI, Lan-Hua(隗兰华); MENG, Ling-Zhi(孟令芝)


    Two fluorescent anion receptors (1 and 2) based on amide macrocycle were synthesized and corresponding fluorescence quenching induced by anion complexation was observed in different degree. Receptors form 1: 1 complexes with anions by hydrogen bonding interactions. Receptor 1 bound anions in the order of F->Cl->H2PO4->CH3COO->>Br-, I- and receptor 2 showed high selectivity to F- over other anions.

  6. Upper bounds for reversible circuits based on Young subgroups

    DEFF Research Database (Denmark)

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


    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....

  7. Crystal Structure of an LSD-Bound Human Serotonin Receptor

    Energy Technology Data Exchange (ETDEWEB)

    Wacker, Daniel; Wang, Sheng; McCorvy, John D.; Betz, Robin M.; Venkatakrishnan, A.J.; Levit, Anat; Lansu, Katherine; Schools, Zachary L.; Che, Tao; Nichols, David E.; Shoichet, Brian K.; Dror, Ron O.; Roth, Bryan L. (UNCSM); (UNC); (Stanford); (Stanford-MED); (UCSF)


    The prototypical hallucinogen LSD acts via serotonin receptors, and here we describe the crystal structure of LSD in complex with the human serotonin receptor 5-HT2B. The complex reveals conformational rearrangements to accommodate LSD, providing a structural explanation for the conformational selectivity of LSD’s key diethylamide moiety. LSD dissociates exceptionally slow from both 5-HT2BR and 5-HT2AR—a major target for its psychoactivity. Molecular dynamics (MD) simulations suggest that LSD’s slow binding kinetics may be due to a “lid” formed by extracellular loop 2 (EL2) at the entrance to the binding pocket. A mutation predicted to increase the mobility of this lid greatly accelerates LSD’s binding kinetics and selectively dampens LSD-mediated β-arrestin2 recruitment. This study thus reveals an unexpected binding mode of LSD; illuminates key features of its kinetics, stereochemistry, and signaling; and provides a molecular explanation for LSD’s actions at human serotonin receptors.

  8. Structure of adenovirus bound to cellular receptor car (United States)

    Freimuth, Paul I.


    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.

  9. 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)


    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.

  10. 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


    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

  11. Allosteric activation of membrane-bound glutamate receptors using coordination chemistry within living cells (United States)

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


    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.

  12. Type II Turn of Receptor-bound Salmon Calcitonin Revealed by X-ray Crystallography. (United States)

    Johansson, Eva; Hansen, Jakob Lerche; Hansen, Ann Maria Kruse; Shaw, Allan Christian; Becker, Peter; Schäffer, Lauge; Reedtz-Runge, Steffen


    Calcitonin is a peptide hormone consisting of 32 amino acid residues and the calcitonin receptor is a Class B G protein-coupled receptor (GPCR). The crystal structure of the human calcitonin receptor ectodomain (CTR ECD) in complex with a truncated analogue of salmon calcitonin ([BrPhe(22)]sCT(8-32)) has been determined to 2.1-Å resolution. Parallel analysis of a series of peptide ligands showed that the rank order of binding of the CTR ECD is identical to the rank order of binding of the full-length CTR, confirming the structural integrity and relevance of the isolated CTR ECD. The structure of the CTR ECD is similar to other Class B GPCRs and the ligand binding site is similar to the binding site of the homologous receptors for the calcitonin gene-related peptide (CGRP) and adrenomedulin (AM) recently published (Booe, J. M., Walker, C. S., Barwell, J., Kuteyi, G., Simms, J., Jamaluddin, M. A., Warner, M. L., Bill, R. M., Harris, P. W., Brimble, M. A., Poyner, D. R., Hay, D. L., and Pioszak, A. A. (2015) Mol. Cell 58, 1040-1052). Interestingly the receptor-bound structure of the ligand [BrPhe(22)]sCT(8-32) differs from the receptor-bound structure of the homologous ligands CGRP and AM. They all adopt an extended conformation followed by a C-terminal β turn, however, [BrPhe(22)]sCT(8-32) adopts a type II turn (Gly(28)-Thr(31)), whereas CGRP and AM adopt type I turns. Our results suggest that a type II turn is the preferred conformation of calcitonin, whereas a type I turn is the preferred conformation of peptides that require RAMPs; CGRP, AM, and amylin. In addition the structure provides a detailed molecular explanation and hypothesis regarding ligand binding properties of CTR and the amylin receptors.

  13. Dynamic Garment Simulation based on Hybrid Bounding Volume Hierarchy

    Directory of Open Access Journals (Sweden)

    Zhu Dongyong


    Full Text Available In order to solve the computing speed and efficiency problem of existing dynamic clothing simulation, this paper presents a dynamic garment simulation based on a hybrid bounding volume hierarchy. It firstly uses MCASG graph theory to do the primary segmentation for a given three-dimensional human body model. And then it applies K-means cluster to do the secondary segmentation to collect the human body’s upper arms, lower arms, upper legs, lower legs, trunk, hip and woman’s chest as the elementary units of dynamic clothing simulation. According to different shapes of these elementary units, it chooses the closest and most efficient hybrid bounding box to specify these units, such as cylinder bounding box and elliptic cylinder bounding box. During the process of constructing these bounding boxes, it uses the least squares method and slices of the human body to get the related parameters. This approach makes it possible to use the least amount of bounding boxes to create close collision detection regions for the appearance of the human body. A spring-mass model based on a triangular mesh of the clothing model is finally constructed for dynamic simulation. The simulation result shows the feasibility and superiority of the method described.

  14. Proinflammatory cytokines and their membrane-bound receptors are altered in the lymphocytes of schizophrenia patients. (United States)

    Pandey, Ghanshyam N; Ren, Xinguo; Rizavi, Hooriyah S; Zhang, Hui


    Abnormalities of protein levels of proinflammatory cytokines and their soluble receptors have been reported in the plasma/serum of schizophrenia (SZ) patients. To examine if SZ is also associated with the abnormal gene expression of cytokines and their membrane-bound receptors, we studied mRNA expression of proinflammatory cytokines and their receptors in lymphocytes of SZ patients and normal control (NC) subjects. We determined the protein and mRNA expression of proinflammatory cytokines and mRNA expression of their receptors in lymphocytes from 30 SZ patients and 30 drug-free NC subjects. The subjects were diagnosed according to DSM-IV criteria. Protein levels of cytokines were determined by ELISA, and mRNA levels in lymphocytes were determined by the qPCR method. We found that the mRNA levels of IL-6, TNF-α, IL-1R1, TNFR1, and TNFR2, but not IL-1β, IL-1R2, IL-1RA, IL-6R, or GP130 were significantly increased in lymphocytes of SZ patients compared with NC subjects. We also found that the protein expression of IL-6 and TNF-α, but not IL-1β, was also significantly increased in SZ patients compared with NC subjects. These studies suggest that in addition to the reported abnormalities of proinflammatory cytokines and their soluble receptors in the plasma of SZ patients, an abnormal gene expression of these cytokines and their membrane-bound receptors may be involved in the pathogenesis of SZ.

  15. Crystal structure of the human OX2 orexin receptor bound to the insomnia drug suvorexant (United States)

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


    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.

  16. The putative roles of nuclear and membrane-bound progesterone receptors in the female reproductive tract. (United States)

    Kowalik, Magdalena K; Rekawiecki, Robert; Kotwica, Jan


    Progesterone produced by the corpus luteum (CL) is a key regulator of normal cyclical reproductive functions in the females of mammalian species. The physiological effects of progesterone are mediated by the canonical genomic pathway after binding of progesterone to its specific nuclear progesterone receptor (PGR), which acts as a ligand-activated transcription factor and has two main isoforms, PGRA and PGRB. These PGR isoforms play different roles in the cell; PGRB acts as an activator of progesterone-responsive genes, while PGRA can inhibit the activity of PGRB. The ratio of these isoforms changes during the estrous cycle and pregnancy, and it corresponds to the different levels of progesterone signaling occurring in the reproductive tract. Progesterone exerts its effects on cells also by a non-genomic mechanism by the interaction with the progesterone-binding membrane proteins including the progesterone membrane component (PGRMC) 1 and 2, and the membrane progestin receptors (mPRs). These receptors rapidly activate the appropriate intracellular signal transduction pathways, and subsequently they can initiate specific cell responses or modulate genomic cell responses. The diversity of progesterone receptors and their cellular actions enhances the role of progesterone as a factor regulating the function of the reproductive system and other organs. This paper deals with the possible involvement of nuclear and membrane-bound progesterone receptors in the function of target cells within the female reproductive tract.

  17. Confidence bounds of recurrence-based complexity measures

    Energy Technology Data Exchange (ETDEWEB)

    Schinkel, Stefan [Interdisciplinary Centre for Dynamics of Complex Systems, University of Potsdam (Germany)], E-mail:; Marwan, N. [Interdisciplinary Centre for Dynamics of Complex Systems, University of Potsdam (Germany); Potsdam Institute for Climate Impact Research (PIK) (Germany); Dimigen, O. [Department of Psychology, University of Potsdam (Germany); Kurths, J. [Potsdam Institute for Climate Impact Research (PIK) (Germany); Department of Physics, Humboldt University at Berlin (Germany)


    In the recent past, recurrence quantification analysis (RQA) has gained an increasing interest in various research areas. The complexity measures the RQA provides have been useful in describing and analysing a broad range of data. It is known to be rather robust to noise and nonstationarities. Yet, one key question in empirical research concerns the confidence bounds of measured data. In the present Letter we suggest a method for estimating the confidence bounds of recurrence-based complexity measures. We study the applicability of the suggested method with model and real-life data.

  18. Crystal Structures of the Nuclear Receptor, Liver Receptor Homolog 1, Bound to Synthetic Agonists. (United States)

    Mays, Suzanne G; Okafor, C Denise; Whitby, Richard J; Goswami, Devrishi; Stec, Józef; Flynn, Autumn R; Dugan, Michael C; Jui, Nathan T; Griffin, Patrick R; Ortlund, Eric A


    Liver receptor homolog 1 (NR5A2, LRH-1) is an orphan nuclear hormone receptor that regulates diverse biological processes, including metabolism, proliferation, and the resolution of endoplasmic reticulum stress. Although preclinical and cellular studies demonstrate that LRH-1 has great potential as a therapeutic target for metabolic diseases and cancer, development of LRH-1 modulators has been difficult. Recently, systematic modifications to one of the few known chemical scaffolds capable of activating LRH-1 failed to improve efficacy substantially. Moreover, mechanisms through which LRH-1 is activated by synthetic ligands are entirely unknown. Here, we use x-ray crystallography and other structural methods to explore conformational changes and receptor-ligand interactions associated with LRH-1 activation by a set of related agonists. Unlike phospholipid LRH-1 ligands, these agonists bind deep in the pocket and do not interact with residues near the mouth nor do they expand the pocket like phospholipids. Unexpectedly, two closely related agonists with similar efficacies (GSK8470 and RJW100) exhibit completely different binding modes. The dramatic repositioning is influenced by a differential ability to establish stable face-to-face π-π-stacking with the LRH-1 residue His-390, as well as by a novel polar interaction mediated by the RJW100 hydroxyl group. The differing binding modes result in distinct mechanisms of action for the two agonists. Finally, we identify a network of conserved water molecules near the ligand-binding site that are important for activation by both agonists. This work reveals a previously unappreciated complexity associated with LRH-1 agonist development and offers insights into rational design strategies.

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

    DEFF Research Database (Denmark)

    Kiderlen, Markus; Meschenmoser, Daniel


    and the mean is approximated by a finite weighted sum S(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...... 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. Internalization and recycling of receptor-bound gonadotropin-releasing hormone agonist in pituitary gonadotropes

    Energy Technology Data Exchange (ETDEWEB)

    Schvartz, I.; Hazum, E.


    The fate of cell surface gonadotropin-releasing hormone (GnRH) receptors on pituitary cells was studied utilizing lysosomotropic agents and monensin. Labeling of pituitary cells with a photoreactive GnRH derivative, (azidobenzoyl-D-Lys6)GnRH, revealed a specific band of Mr = 60,000. When photoaffinity-labeled cells were exposed to trypsin immediately after completion of the binding, the radioactivity incorporated into the Mr = 60,000 band decreased, with a concomitant appearance of a proteolytic fragment (Mr = 45,000). This fragment reflects cell surface receptors. Following GnRH binding, the hormone-receptor complexes underwent internalization, partial degradation, and recycling. The process of hormone-receptor complex degradation was substantially prevented by lysosomotropic agents, such as chloroquine and methylamine, or the proton ionophore, monensin. Chloroquine and monensin, however, did not affect receptor recycling, since the tryptic fragment of Mr = 45,000 was evident after treatment with these agents. This suggests that recycling of GnRH receptors in gonadotropes occurs whether or not the internal environment is acidic. Based on these findings, we propose a model describing the intracellular pathway of GnRH receptors.

  1. 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.

  2. Persistence-Based Branch Misprediction Bounds for WCET Analysis

    DEFF Research Database (Denmark)

    Puffitsch, Wolfgang


    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....

  3. Growth Factor Receptor-Bound Protein 14 Undergoes Light-Dependent Intracellular Translocation in Rod Photoreceptors: Functional Role on Retinal Insulin Receptor Activation


    Rajala, Ammaji; Roger J. Daly; Tanito, Masaki; Allen, Dustin T.; Lowenna J Holt; Lobanova, Ekaterina; Arshavsky, Vadim Y; Rajala, Raju V.S.


    Growth factor receptor-bound protein 14 (Grb14) is involved in growth factor receptor tyrosine kinase signaling. Here we report that light causes a major redistribution of Grb14 among the individual subcellular compartments of the retinal rod photoreceptor. Grb14 is localized predominantly to the inner segment, nuclear layer and synapse in dark-adapted rods, whereas in the light-adapted rods, Grb14 redistributed throughout the entire cell, including the outer segment. The translocation of Grb...

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

    CERN Document Server

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


    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.

  5. 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)


    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.

  6. Bounding SAR ATR performance based on model similarity (United States)

    Boshra, Michael; Bhanu, Bir


    Similarity between model targets plays a fundamental role in determining the performance of target recognition. We analyze the effect of model similarity on the performance of a vote- based approach for target recognition from SAR images. In such an approach, each model target is represented by a set of SAR views sampled at a variety of azimuth angles and a specific depression angle. Both model and data views are represented by locations of scattering centers, which are peak features. The model hypothesis (view of a specific target and associated location) corresponding to a given data view is chosen to be the one with the highest number of data-supported model features (votes). We address three issues in this paper. Firstly, we present a quantitative measure of the similarity between a pair of model views. Such a measure depends on the degree of structural overlap between the two views, and the amount of uncertainty. Secondly, we describe a similarity- based framework for predicting an upper bound on recognition performance in the presence of uncertainty, occlusion and clutter. Thirdly, we validate the proposed framework using MSTAR public data, which are obtained under different depression angles, configurations and articulations.

  7. A dual framework for lower bounds of the quadratic assignment|problem based on linearization

    DEFF Research Database (Denmark)

    Karisch, Stefan E.; Cela, E.; Clausen, Jens;


    A dual framework allowing the comparison of various bounds for the quadratic assignment problem (QAP) based on linearization, e.g. the bounds of Adams and Johnson, Carraresi and Malucelli, and Hahn and Grant, is presented. We discuss the differences of these bounds and propose a new and more...

  8. Structure of the human angiotensin II type 1 (AT1) receptor bound to angiotensin II from multiple chemoselective photoprobe contacts reveals a unique peptide binding mode. (United States)

    Fillion, Dany; Cabana, Jérôme; Guillemette, Gaétan; Leduc, Richard; Lavigne, Pierre; Escher, Emanuel


    Breakthroughs in G protein-coupled receptor structure determination based on crystallography have been mainly obtained from receptors occupied in their transmembrane domain core by low molecular weight ligands, and we have only recently begun to elucidate how the extracellular surface of G protein-coupled receptors (GPCRs) allows for the binding of larger peptide molecules. In the present study, we used a unique chemoselective photoaffinity labeling strategy, the methionine proximity assay, to directly identify at physiological conditions a total of 38 discrete ligand/receptor contact residues that form the extracellular peptide-binding site of an activated GPCR, the angiotensin II type 1 receptor. This experimental data set was used in homology modeling to guide the positioning of the angiotensin II (AngII) peptide within several GPCR crystal structure templates. We found that the CXC chemokine receptor type 4 accommodated the results better than the other templates evaluated; ligand/receptor contact residues were spatially grouped into defined interaction clusters with AngII. In the resulting receptor structure, a β-hairpin fold in extracellular loop 2 in conjunction with two extracellular disulfide bridges appeared to open and shape the entrance of the ligand-binding site. The bound AngII adopted a somewhat vertical binding mode, allowing concomitant contacts across the extracellular surface and deep within the transmembrane domain core of the receptor. We propose that such a dualistic nature of GPCR interaction could be well suited for diffusible linear peptide ligands and a common feature of other peptidergic class A GPCRs.

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

    Directory of Open Access Journals (Sweden)

    Mongi Besbes


    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.

  10. Entropy-Based Bounds On Redundancies Of Huffman Codes (United States)

    Smyth, Padhraic J.


    Report presents extension of theory of redundancy of binary prefix code of Huffman type which includes derivation of variety of bounds expressed in terms of entropy of source and size of alphabet. Recent developments yielded bounds on redundancy of Huffman code in terms of probabilities of various components in source alphabet. In practice, redundancies of optimal prefix codes often closer to 0 than to 1.

  11. Visualization of single receptor molecules bound to human rhinovirus under physiological conditions. (United States)

    Kienberger, Ferry; Rankl, Christian; Pastushenko, Vassili; Zhu, Rong; Blaas, Dieter; Hinterdorfer, Peter


    Dynamic force microscopy (DFM) was used to image human rhinovirus HRV2 alone and complexed with single receptor molecules under near physiological conditions. Specific and site-directed immobilization of HRV2 on a model cell membrane resulted in a crystalline arrangement of virus particles with hexagonal symmetry and 35 nm spacing. High-resolution imaging of the virus capsid revealed about 20 resolvable structural features with 3 nm diameters; this finding is in agreement with protrusions seen by cryo-electron microscopy. Binding of receptor molecules to individual virus particles was observed after injection of soluble receptors into the liquid cell. Virus-receptor complexes with zero, one, two, or three attached receptor molecules were resolved. The number of receptor molecules associated to virions increased over time. Occasionally, dissociation of single receptor molecules from viral particles was also observed.

  12. Cyclophilin A inhibition: targeting transition-state-bound enzyme conformations for structure-based drug design. (United States)

    Nagaraju, Mulpuri; McGowan, Lauren C; Hamelberg, Donald


    Human Cyclophilin A (CypA) catalyzes cis-trans isomerization of the prolyl peptide ω-bond in proteins and is involved in many subcellular processes. CypA has, therefore, been identified as a potential drug target in many diseases, and the development of potent inhibitors with high selectivity is a key objective. In computer-aided drug design, selectivity is improved by taking into account the inherent flexibility of the receptor. However, the relevant receptor conformations to focus on in order to develop highly selective inhibitors are not always obvious from available X-ray crystal structures or ensemble of conformations generated using molecular dynamics simulations. Here, we show that the conformation of the active site of CypA varies as the substrate configuration changes during catalytic turnover. We have analyzed the principal modes of the active site dynamics of CypA from molecular dynamics simulations to show that similar ensembles of enzyme conformations recognize diverse inhibitors and bind the different configurations of the peptide substrate. Small nonpeptidomimetic inhibitors with varying activity are recognized by enzyme ensembles that are similar to those that tightly bind the transition state and cis configurations of the substrate. Our results suggest that enzyme-substrate ensembles are more relevant in structure-based drug design for CypA than free enzyme. Of the vast conformational space of the free enzyme, the enzyme conformations of the tightly bound enzyme-substrate complexes are the most important for catalysis. Therefore, functionalizing lead compounds to optimize their interactions with the enzyme's conformational ensemble bound to the substrate in the cis or the transition state could lead to more potent inhibitors.

  13. Public-key cryptography based on bounded quantum reference frames


    Ioannou, Lawrence M.; Mosca, Michele


    We demonstrate that the framework of bounded quantum reference frames has application to building quantum-public-key cryptographic protocols and proving their security. Thus, the framework we introduce can be seen as a public-key analogue of the framework of Bartlett et al. (Phys. Rev. A 70, 032307), where a private shared reference frame is shown to have cryptographic application. The protocol we present in this paper is an identification scheme, which, like a digital signature scheme, is a ...

  14. Random Coding Bounds for DNA Codes Based on Fibonacci Ensembles of DNA Sequences (United States)


    COVERED (From - To) 6 Jul 08 – 11 Jul 08 4. TITLE AND SUBTITLE RANDOM CODING BOUNDS FOR DNA CODES BASED ON FIBONACCI ENSEMBLES OF DNA SEQUENCES ... sequences which are generalizations of the Fibonacci sequences . 15. SUBJECT TERMS DNA Codes, Fibonacci Ensembles, DNA Computing, Code Optimization 16...coding bound on the rate of DNA codes is proved. To obtain the bound, we use some ensembles of DNA sequences which are generalizations of the Fibonacci

  15. Autoradiographic visualization of the mouse egg's sperm receptor bound to sperm



    The extracellular coat, or zona pellucida, of mammalian eggs contains species-specific receptors to which sperm bind as a prelude to fertilization. In mice, ZP3, one of only three zona pellucida glycoproteins, serves as sperm receptor. Acrosome-intact, but not acrosome-reacted, mouse sperm recognize and interact with specific O- linked oligosaccharides of ZP3 resulting in sperm-egg binding. Binding, in turn, causes sperm to undergo the acrosome reaction; a membrane fusion event that results i...

  16. 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

  17. Fast concurrent array-based stacks, queues and deques using fetch-and-increment-bounded, fetch-and-decrement-bounded and store-on-twin synchronization primitives (United States)

    Chen, Dong; Gara, Alana; Heidelberger, Philip; Kumar, Sameer; Ohmacht, Martin; Steinmacher-Burow, Burkhard; Wisniewski, Robert


    Implementation primitives for concurrent array-based stacks, queues, double-ended queues (deques) and wrapped deques are provided. In one aspect, each element of the stack, queue, deque or wrapped deque data structure has its own ticket lock, allowing multiple threads to concurrently use multiple elements of the data structure and thus achieving high performance. In another aspect, new synchronization primitives FetchAndIncrementBounded (Counter, Bound) and FetchAndDecrementBounded (Counter, Bound) are implemented. These primitives can be implemented in hardware and thus promise a very fast throughput for queues, stacks and double-ended queues.

  18. Internalization mechanism of neuropeptide Y bound to its Y1 receptor investigated by high resolution microscopy (United States)

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


    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.

  19. Structure of the measles virus hemagglutinin bound to its cellular receptor SLAM. (United States)

    Hashiguchi, Takao; Ose, Toyoyuki; Kubota, Marie; Maita, Nobuo; Kamishikiryo, Jun; Maenaka, Katsumi; Yanagi, Yusuke


    Measles virus, a major cause of childhood morbidity and mortality worldwide, predominantly infects immune cells using signaling lymphocyte activation molecule (SLAM) as a cellular receptor. Here we present crystal structures of measles virus hemagglutinin (MV-H), the receptor-binding glycoprotein, in complex with SLAM. The MV-H head domain binds to a β-sheet of the membrane-distal ectodomain of SLAM using the side of its β-propeller fold. This is distinct from attachment proteins of other paramyxoviruses that bind receptors using the top of their β-propeller. The structure provides templates for antiviral drug design, an explanation for the effectiveness of the measles virus vaccine, and a model of the homophilic SLAM-SLAM interaction involved in immune modulations. Notably, the crystal structures obtained show two forms of the MV-H-SLAM tetrameric assembly (dimer of dimers), which may have implications for the mechanism of fusion triggering.

  20. Spectral and DFT studies of anion bound organic receptors: Time dependent studies and logic gate applications (United States)

    Pangannaya, Srikala; Purayil, Neethu Padinchare; Dabhi, Shweta; Mankad, Venu; Jha, Prafulla K; Shinde, Satyam


    New colorimetric receptors R1 and R2 with varied positional substitution of a cyano and nitro signaling unit having a hydroxy functionality as the hydrogen bond donor site have been designed, synthesized and characterized by FTIR, 1H NMR spectroscopy and mass spectrometry. The receptors R1 and R2 exhibit prominent visual response for F− and AcO– ions allowing the real time analysis of these ions in aqueous media. The formation of the receptor–anion complexes has been supported by UV–vis titration studies and confirmed through binding constant calculations. The anion binding process follows a first order rate equation and the calculated rate constants reveal a higher order of reactivity for AcO− ions. The 1H NMR titration and TDDFT studies provide full support of the binding mechanism. The Hg2+ and F− ion sensing property of receptor R1 has been utilized to arrive at “AND” and “INHIBIT” molecular logic gate applications.

  1. 3D structure prediction of TAS2R38 bitter receptors bound to agonists phenylthiocarbamide (PTC) and 6-n-propylthiouracil (PROP). (United States)

    Tan, Jun; Abrol, Ravinder; Trzaskowski, Bartosz; Goddard, William A


    The G protein-coupled receptor (GPCR) TAS2R38 is a bitter taste receptor that can respond to bitter compounds such as phenylthiocarbamide (PTC) and 6-n-propylthiouracil (PROP). This receptor was chosen because its four haplotypes (based on three residue site polymorphism) hTAS2R38PAV, hTAS2R38AVI, hTAS2R38AAI, and hTAS2R38PVV are known to have dramatically different responses to PTC and PROP. We aimed to identify the protein-ligand interaction features that determine whether the bitter taste signal from this receptor is sent to the cortex. To do this we predicted the 3D structures of the TAS2R38 bitter taste receptor using our new BiHelix and SuperBiHelix Monte Carlo methods (No experimental determinations of the 3D structure have been reported for any taste receptors.). We find that residue 262 (2nd position in the polymorphism) is involved in the interhelical hydrogen bond network stabilizing the GPCR structure in tasters (hTAS2R38PAV, hTAS2R38AAI, and hTAS2R38PVV), while it is not in the nontaster (hTAS2R38AVI). This suggests that the hydrogen bond interactions between TM3 and TM6 or between TM5 and TM6 may play a role in activating this GPCR. To further validate these structures, we used the DarwinDock method to predict the binding sites and 3D structures for PTC and PROP bound to hTAS2R38PAV, hTAS2R38AVI, hTAS2R38AAI, and hTAS2R38PVV, respectively. Our results show that PTC and PROP can form H-bonds with the backbone of residue 262 in the tasters (hTAS2R38PAV, hTAS2R38AAI, and hTAS2R38PVV) but not in the nontaster (hTAS2R38AVI). Thus it appears that the hydrogen bond interaction between TM3 and TM6 may activate the receptor to pass the ligand binding signal to intracellular processes and that the H-bond between agonists and residue 262 in tasters is involved in the bitter tasting. This is in agreement with experimental observations, providing validation of the predicted ligand-protein complexes and also a potential activation mechanism for the TAS2R38 receptor.

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

    Gschwendt, M


    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. Security bound of two-bases quantum key-distribution protocols using qudits

    CERN Document Server

    Nikolopoulos, G M; Nikolopoulos, Georgios M.; Alber, Gernot


    We investigate the security bounds of quantum cryptographic protocols using $d$-level systems. In particular, we focus on schemes that use two mutually unbiased bases, thus extending the BB84 quantum key distribution scheme to higher dimensions. Under the assumption of general coherent attacks, we derive an analytic expression for the ultimate upper security bound of such quantum cryptography schemes. This bound is well below the predictions of optimal cloning machines. The possibility of extraction of a secret key beyond entanglement distillation is discussed. In the case of qutrits we argue that any eavesdropping strategy is equivalent to a symmetric one. For higher dimensions such an equivalence is generally no longer valid.

  4. 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


    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.

  5. Cryptographic protocol security analysis based on bounded constructing algorithm

    Institute of Scientific and Technical Information of China (English)


    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.

  6. U-shaped conformation of alkyl chains bound to a synthetic receptor cucurbit[8]uril. (United States)

    Ko, Young Ho; Kim, Youngkook; Kim, Hyunuk; Kim, Kimoon


    The behavior of a series of alkanes bound to the molecular host cucurbit[8]uril (CB[8]) has been systematically studied by 2D (1)H NMR spectroscopy and isothermal titration calorimetry (ITC). CB[8] and alkyltrimethylammonium (C(m) TA(+), (CH(3))(3)N(+)C(m)H(2m+1), m=6-16) form 1:1 host-guest complexes with a high binding constant (K≈10(6) m(-1)). The shortest hexyl chain of C(6)TA(+) can be fully encapsulated in an extended conformation inside the CB[8] cavity, which is driven by both enthalpy and entropy. However, for the longer aliphatic chains, C(8)-C(16), the long alkyl tails take a U-shaped conformation inside the cavity, and their complexation is dominantly or almost exclusively enthalpy-driven, owing to the increased van der Waals contact between the folded aliphatic chain and the inner wall of the host cavity. As the chain length increases from C(8) to C(16), the ammonium head group of the guests moves away from the portal of CB[8] while the long aliphatic tails maintain the U-shaped conformation inside the cavity. The complexation of C(m)TA(+) with CB[8] follows the enthalpy-entropy compensation rule commonly observed in molecular recognition systems. For example, among the guest molecules, C(12)TA(+) shows the highest enthalpic gain (most favorable), owing to the large van der Waals contact between the guest and the host cavity, and at the same time the most unfavorable entropic contribution, owing to the severe conformational restriction of the U-shaped alkyl chain inside the host. The enthalpy-entropy compensation plot for the complexation suggests large conformational changes of the long alkyl chains and extensive dehydration associated with the inclusion complex formation.

  7. 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)


    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.

  8. Maximum-likelihood detection based on branch and bound algorithm for MIMO systems

    Institute of Scientific and Technical Information of China (English)

    LI Zi; CAI YueMing


    Maximum likelihood detection for MIMO systems can be formulated as an integer quadratic programming problem. In this paper, we introduce depth-first branch and bound algorithm with variable dichotomy into MIMO detection. More nodes may be pruned with this structure. At each stage of the branch and bound algorithm, active set algorithm is adopted to solve the dual subproblem. In order to reduce the com- plexity further, the Cholesky factorization update is presented to solve the linear system at each iteration of active set algorithm efficiently. By relaxing the pruning conditions, we also present the quasi branch and bound algorithm which imple- ments a good tradeoff between performance and complexity. Numerical results show that the complexity of MIMO detection based on branch and bound algorithm is very low, especially in low SNR and large constellations.

  9. Robust Sliding Mode Control of Cucumber Picking Robot Based on the Upper Bound Estimation

    Directory of Open Access Journals (Sweden)

    Wei Liu


    Full Text Available In this study, a robust sliding mode control based on upper bound estimation was applied in position trajectory control of the fruit harvesting robot. It decomposes the manipulator dynamics equation into a constant unknown vector parameter and a known dynamic nonlinear (called the regression vector. This study based on regression design new sliding mode control law. The algorithm ensures the stability of the closed-loop system upper based on unknown upper bound estimation parameters. It shows from robustness analysis that when the system has the time-varying uncertainty, the closed loop system can still be stabilized.

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

    KAUST Repository

    Rungta, Meha


    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.

  11. Preparation and Catalytic Properties of Polymer-Bound Schiff Base Ternary Complexes

    Institute of Scientific and Technical Information of China (English)

    HAO Cheng-jun; WANG Rong-min; HE Yu-feng; WANG Yun-pu; XIA Chun-gu


    The polymer-bound Schiff base ternary manganese complexes [PS-SalPhe-Mn-L (L = Phen, Bipy and 8HQ)-] have been prepared from the polymer-bound Schiff base ligand, a manganese salt and the second ligand, such as 1,10-phenanthroline(phen), 2,2′-bipyridyl(bipy) and 8-quinolinol(8HQ). The polymer-bound Schiff base ternary manganese complexes were characterized by means of infrared spectrometry and ICPAES. The catalytic activities of the complexes have been studied in the aerobic epoxidation of long-chain linear a[iphatic olefins. It is shown that 1-octene or 1-decene can be directly oxidized by molecular oxygen when catalyzed by PS-SalPhe-Mn-L(L=Phen, Bipy and 8HQ), and 1,2-epoxy alkane can be afforded in these reactions.

  12. Structural insights into the nucleotide base specificity of P2X receptors (United States)

    Kasuya, Go; Fujiwara, Yuichiro; Tsukamoto, Hisao; Morinaga, Satoshi; Ryu, Satoshi; Touhara, Kazushige; Ishitani, Ryuichiro; Furutani, Yuji; Hattori, Motoyuki; Nureki, Osamu


    P2X receptors are trimeric ATP-gated cation channels involved in diverse physiological processes, ranging from muscle contraction to nociception. Despite the recent structure determination of the ATP-bound P2X receptors, the molecular mechanism of the nucleotide base specificity has remained elusive. Here, we present the crystal structure of zebrafish P2X4 in complex with a weak affinity agonist, CTP, together with structure-based electrophysiological and spectroscopic analyses. The CTP-bound structure revealed a hydrogen bond, between the cytosine base and the side chain of the basic residue in the agonist binding site, which mediates the weak but significant affinity for CTP. The cytosine base is further recognized by two main chain atoms, as in the ATP-bound structure, but their bond lengths seem to be extended in the CTP-bound structure, also possibly contributing to the weaker affinity for CTP over ATP. This work provides the structural insights for the nucleotide base specificity of P2X receptors. PMID:28332633

  13. A subgradient-based branch-and-bound algorithm for the capacitated facility location problem

    DEFF Research Database (Denmark)

    Görtz, Simon; Klose, Andreas

    This paper presents a simple branch-and-bound method based on Lagrangean relaxation and subgradient optimization for solving large instances of the capacitated facility location problem (CFLP) to optimality. In order to guess a primal solution to the Lagrangean dual, we average solutions...

  14. Tight Bounds for Beacon-Based Coverage in Simple Rectilinear Polygons

    KAUST Repository

    Bae, Sang Won


    We establish tight bounds for beacon-based coverage problems. In particular, we show that $$\\\\lfloor \\\\frac{n}{6} \\ floor $$⌊n6⌋ beacons are always sufficient and sometimes necessary to cover a simple rectilinear polygon P with n vertices. When P is monotone and rectilinear, we prove that this bound becomes $$\\\\lfloor \\\\frac{n+4}{8} \\ floor $$⌊n+48⌋. We also present an optimal linear-time algorithm for computing the beacon kernel of P.

  15. Tight bound on coherent-state-based entanglement generation over lossy channels

    CERN Document Server

    Azuma, Koji; Koashi, Masato; Imoto, Nobuyuki


    The first stage of the hybrid quantum repeaters is entanglement generation based on transmission of pulses in coherent states over a lossy channel. Protocols to make entanglement with only one type of error are favorable for rendering subsequent entanglement distillation efficient. Here we provide the tight upper bound on performances of these protocols that is determined only by the channel loss. In addition, we show that this bound is achievable by utilizing a proposed protocol [arXiv:0811.3100] composed of a simple combination of linear optical elements and photon-number-resolving detectors.

  16. Performance bounds for expander-based compressed sensing in Poisson noise

    CERN Document Server

    Raginsky, Maxim; Harmany, Zachary; Marcia, Roummel; Willett, Rebecca; Calderbank, Robert


    This paper provides performance bounds for compressed sensing in the presence of Poisson noise using expander graphs. The Poisson noise model is appropriate for a variety of applications, including low-light imaging and digital streaming, where the signal-independent and/or bounded noise models used in the compressed sensing literature are no longer applicable. In this paper, we develop a novel sensing paradigm based on expander graphs and propose a MAP algorithm for recovering sparse or compressible signals from Poisson observations. The geometry of the expander graphs and the positivity of the corresponding sensing matrices play a crucial role in establishing the bounds on the signal reconstruction error of the proposed algorithm. We support our results with experimental demonstrations of reconstructing average packet arrival rates and instantaneous packet counts at a router in a communication network, where the arrivals of packets in each flow follow a Poisson process.

  17. 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


    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.

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

    CERN Document Server

    Lucani, Daniel E; Stojanovic, Milica


    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...

  19. Crystal structure of the adenosine A 2A receptor bound to an antagonist reveals a potential allosteric pocket

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Bingfa; Bachhawat, Priti; Chu, Matthew Ling-Hon; Wood, Martyn; Ceska, Tom; Sands, Zara A.; Mercier, Joel; Lebon, Florence; Kobilka, Tong Sun; Kobilka, Brian K.


    The adenosine A2A receptor (A2AR) has long been implicated in cardiovascular disorders. As more selective A2AR ligands are being identified, its roles in other disorders, such as Parkinson’s disease, are starting to emerge, and A2AR antagonists are important drug candidates for nondopaminergic anti-Parkinson treatment. Here we report the crystal structure of A2A receptor bound to compound 1 (Cmpd-1), a novel A2AR/N-methyl D-aspartate receptor subtype 2B (NR2B) dual antagonist and potential anti-Parkinson candidate compound, at 3.5 Å resolution. The A2A receptor with a cytochrome b562-RIL (BRIL) fusion (A2AR–BRIL) in the intracellular loop 3 (ICL3) was crystallized in detergent micelles using vapor-phase diffusion. Whereas A2AR–BRIL bound to the antagonist ZM241385 has previously been crystallized in lipidic cubic phase (LCP), structural differences in the Cmpd-1–bound A2AR–BRIL prevented formation of the lattice observed with the ZM241385–bound receptor. The crystals grew with a type II crystal lattice in contrast to the typical type I packing seen from membrane protein structures crystallized in LCP. Cmpd-1 binds in a position that overlaps with the native ligand adenosine, but its methoxyphenyl group extends to an exosite not previously observed in other A2AR structures. Structural analysis revealed that Cmpd-1 binding results in the unique conformations of two tyrosine residues, Tyr91.35 and Tyr2717.36, which are critical for the formation of the exosite. The structure reveals insights into antagonist binding that are not observed in other A2AR structures, highlighting flexibility in the binding pocket that may facilitate the development of A2AR-selective compounds for the treatment of Parkinson’s disease.

  20. Topology optimization of bounded acoustic problems using the hybrid finite element-wave based method

    DEFF Research Database (Denmark)

    Goo, Seongyeol; Wang, Semyung; Kook, Junghwan


    This paper presents an alternative topology optimization method for bounded acoustic problems that uses the hybrid finite element-wave based method (FE-WBM). The conventional method for the topology optimization of bounded acoustic problems is based on the finite element method (FEM), which...... is limited to low frequency applications due to considerable computational efforts. To this end, we propose a gradient-based topology optimization method that uses the hybrid FE-WBM whereby the entire domain of a problem is partitioned into design and non-design domains. In this respect, the FEM is used...... as a design domain of topology optimization, and the WBM is used as a non-design domain to increase computational efficiency. The adjoint variable method based on the hybrid FE-WBM is also proposed as a means of computing design sensitivities. Numerical examples are presented to demonstrate the effectiveness...

  1. Structural complexes of the agonist, inverse agonist and antagonist bound C5a receptor: insights into pharmacology and signaling. (United States)

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


    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

  2. Finite state projection based bounds to compare chemical master equation models using single-cell data (United States)

    Fox, Zachary; Neuert, Gregor; Munsky, Brian


    Emerging techniques now allow for precise quantification of distributions of biological molecules in single cells. These rapidly advancing experimental methods have created a need for more rigorous and efficient modeling tools. Here, we derive new bounds on the likelihood that observations of single-cell, single-molecule responses come from a discrete stochastic model, posed in the form of the chemical master equation. These strict upper and lower bounds are based on a finite state projection approach, and they converge monotonically to the exact likelihood value. These bounds allow one to discriminate rigorously between models and with a minimum level of computational effort. In practice, these bounds can be incorporated into stochastic model identification and parameter inference routines, which improve the accuracy and efficiency of endeavors to analyze and predict single-cell behavior. We demonstrate the applicability of our approach using simulated data for three example models as well as for experimental measurements of a time-varying stochastic transcriptional response in yeast.

  3. Generalization bounds of ERM-based learning processes for continuous-time Markov chains. (United States)

    Zhang, Chao; Tao, Dacheng


    Many existing results on statistical learning theory are based on the assumption that samples are independently and identically distributed (i.i.d.). However, the assumption of i.i.d. samples is not suitable for practical application to problems in which samples are time dependent. In this paper, we are mainly concerned with the empirical risk minimization (ERM) based learning process for time-dependent samples drawn from a continuous-time Markov chain. This learning process covers many kinds of practical applications, e.g., the prediction for a time series and the estimation of channel state information. Thus, it is significant to study its theoretical properties including the generalization bound, the asymptotic convergence, and the rate of convergence. It is noteworthy that, since samples are time dependent in this learning process, the concerns of this paper cannot (at least straightforwardly) be addressed by existing methods developed under the sample i.i.d. assumption. We first develop a deviation inequality for a sequence of time-dependent samples drawn from a continuous-time Markov chain and present a symmetrization inequality for such a sequence. By using the resultant deviation inequality and symmetrization inequality, we then obtain the generalization bounds of the ERM-based learning process for time-dependent samples drawn from a continuous-time Markov chain. Finally, based on the resultant generalization bounds, we analyze the asymptotic convergence and the rate of convergence of the learning process.

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

    Directory of Open Access Journals (Sweden)

    Kohei Arai


    Full Text Available 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. The ligand-bound thyroid hormone receptor in macrophages ameliorates kidney injury via inhibition of nuclear factor-κB activities (United States)

    Furuya, Fumihiko; Ishii, Toshihisa; Tamura, Shogo; Takahashi, Kazuya; Kobayashi, Hidetoshi; Ichijo, Masashi; Takizawa, Soichi; Kaneshige, Masahiro; Suzuki-Inoue, Katsue; Kitamura, Kenichiro


    In chronic kidney disease (CKD) patients, inflammation plays a pivotal role in the progression of renal fibrosis. Hypothyroidism is associated with an increased occurrence of atherosclerosis and inflammation, suggesting protective roles of thyroid hormones and their receptors against inflammatory processes. The contribution of thyroid hormone receptors to macrophage differentiation has not been well documented. Here, we focused on the endogenous thyroid hormone receptor α (TRα) in macrophages and examined the role of ligand-bound TRα in macrophage polarization-mediated anti-inflammatory effects. TRα-deficient irradiated chimeric mice showed exacerbated tubulointerstitial injury in a unilateral ureteral obstruction model. Compared with wild-type macrophages, macrophages isolated from the obstructed kidneys of mice lacking TRα displayed increased expression of proinflammatory cytokines that was accompanied by enhanced nuclear translocation of p65. Comparison of TRα-deficient bone marrow-derived macrophages with wild-type macrophages confirmed the propensity of the former cells to produce excessive IL-1β levels. Co-culture of these macrophages with renal epithelial cells induced more severe damage to the epithelial cells via the IL-1 receptor. Our findings indicate that ligand-bound TRα on macrophages plays a protective role in kidney inflammation through the inhibition of NF-κB pathways, possibly by affecting the pro- and anti-inflammatory balance that controls the development of CKD. PMID:28272516

  6. Structure-based virtual screening of the nociceptin receptor: hybrid docking and shape-based approaches for improved hit identification. (United States)

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


    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

  7. Robust expression of the human neonatal Fc receptor in a truncated soluble form and as a full-length membrane-bound protein in fusion with eGFP.

    Directory of Open Access Journals (Sweden)

    Johan Seijsing

    Full Text Available Studies on the neonatal Fc receptor (FcRn have revealed a multitude of important functions in mammals, including protection of IgG and serum albumin (SA from lysosomal degradation. The pharmacokinetic behavior of therapeutic antibodies, IgG-Fc- and SA-containing drugs is therefore influenced by their interaction with FcRn. Pre-clinical development of such drugs is facilitated if their interaction with FcRn can be studied in vitro. For this reason we have developed a robust system for production of the soluble extracellular domain of human FcRn as well as the full-length receptor as fusion to green fluorescent protein, taking advantage of a lentivirus-based gene delivery system where stable over-expressing cells are easily and rapidly generated. Production of the extracellular domain in multiple-layered culture flasks, followed by affinity purification using immobilized IgG, resulted in capture of milligram amounts of soluble receptor per liter cell culture with retained IgG binding. The receptor was further characterized by SDS-PAGE, western blotting, circular dichroism spectroscopy, ELISA, surface plasmon resonance and a temperature stability assay showing a functional and stable protein of high purity. The full-length receptor was found to be successfully over-expressed in a membrane-bound form with retained pH-dependent IgG- and SA-binding.

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

    Institute of Scientific and Technical Information of China (English)


    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    Newcomer, Justin T.; Freeland, Katherine Elizabeth


    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.

  10. Proposal for field-based definition of soil bound pesticide residues. (United States)

    Boesten, J J T I


    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?).

  11. Cryptanalysis of Pasargad, A Distance Bounding Protocol Based on RFID System

    Directory of Open Access Journals (Sweden)

    Mahdi Azizi


    Full Text Available In this paper we analyze an authentication protocol so-called Pasargad which proposed by Arjemand et al. [1]. The Pasargad protocol is a distance bounding protocol which has been designed for RFID-based electronic voting systems. The designers have claimed that this protocol is more secure than Preneel and Single protocol [2], against relay attacks. However, in this paper, we present some efficient attacks against it. Our attacks include conditional impersonation attack and recovery key attack. Moreover, we show that this protocol has some structural flaw which may prevent to execution the protocol.

  12. 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.

  13. 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)


    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.

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

    CERN Document Server

    Vondřejc, Jaroslav; Marek, Ivo


    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...

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

    DEFF Research Database (Denmark)

    Adamsen, Billy; Thomsen, Svend Erik

    This study applies an agent-based modeling approach to explore some aspects of an important managerial task: finding and cultivating talented individuals capable of creating value for their organization at some future state. Given that the term talent in talent management is an empty signifier...... 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...... heuristic by varying the capabilities of today’s managers, which in turn impact which individuals will be selected as talent. We model the average level of capabilities and the distribution thereof in the sample where managers identify and select individuals from. We consider varying degrees of path...

  16. 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


    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.

  17. Fundamental delay bounds in peer-to-peer chunk-based real-time streaming systems

    CERN Document Server

    Bianchi, Giuseppe; Bracciale, Lorenzo; Piccolo, Francesca Lo; Salsano, Stefano


    This paper addresses the following foundational question: what is the maximum theoretical delay performance achievable by an overlay peer-to-peer streaming system where the streamed content is subdivided into chunks? As shown in this paper, when posed for chunk-based systems, and as a consequence of the store-and-forward way in which chunks are delivered across the network, this question has a fundamentally different answer with respect to the case of systems where the streamed content is distributed through one or more flows (sub-streams). To circumvent the complexity emerging when directly dealing with delay, we express performance in term of a convenient metric, called "stream diffusion metric". We show that it is directly related to the end-to-end minimum delay achievable in a P2P streaming network. In an homogeneous scenario, we derive a performance bound for such metric, and we show how this bound relates to two fundamental parameters: the upload bandwidth available at each node, and the number of neigh...

  18. Towards understanding the free and receptor bound conformation of neuropeptide Y by fluorescence resonance energy transfer studies. (United States)

    Haack, Michael; Beck-Sickinger, Annette G


    Despite a considerable sequence identity of the three mammalian hormones of the neuropeptide Y family, namely neuropeptide Y, peptide YY and pancreatic polypeptide, their structure in solution is described to be different. A so-called pancreatic polypeptide-fold has been identified for pancreatic polypeptide, whereas the structure of the N-terminal segment of neuropeptide Y is unknown. This element is important for the binding of neuropeptide Y to two of its relevant receptors, Y(1) and Y(5), but not to the Y(2) receptor subtype. In this study now, three doubly fluorescent-labeled analogs of neuropeptide Y have been synthesized that still bind to the Y(5) receptor with high affinity to investigate the conformation in solution and, for the first time, to probe the conformational changes upon binding of the ligand to its receptor in cell membrane preparations. The results obtained from the fluorescence resonance energy transfer investigations clearly show considerable differences in transfer efficiency that depend both on the solvent as well as on the peptide concentration. However, the studies do not support a pancreatic polypeptide-like folding of neuropeptide Y in the presence of membranes that express the human Y(5) receptor subtype.

  19. Two distinct conformations of helix 6 observed in antagonist-bound structures of a β1-adrenergic receptor



    The β1-adrenergic receptor (β1AR) is a G-protein-coupled receptor whose inactive state structure was determined using a thermostabilized mutant (β1AR–M23). However, it was not thought to be in a fully inactivated state because there was no salt bridge between Arg139 and Glu285 linking the cytoplasmic ends of transmembrane helices 3 and 6 (the R3.50 - D/E6.30 “ionic lock”). Here we compare eight new structures of β1AR–M23, determined from crystallographically independent molecules in four diff...

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

    CERN Document Server

    Gupta, Sandeep


    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.

  1. Stepwise Method Based on Confidence Bound and Information Incorporation for Identifying the Maximum Tolerable Dose

    Institute of Scientific and Technical Information of China (English)

    王雪丽; 陶剑; 史宁中


    The primary goal of a phase I clinical trial is to find the maximum tolerable dose of a treatment. In this paper, we propose a new stepwise method based on confidence bound and information incorporation to determine the maximum tolerable dose among given dose levels. On the one hand, in order to avoid severe even fatal toxicity to occur and reduce the experimental subjects, the new method is executed from the lowest dose level, and then goes on in a stepwise fashion. On the other hand,in order to improve the accuracy of the recommendation, the final recommendation of the maximum tolerable dose is accomplished through the information incorporation of an additional experimental cohort at the same dose level. Furthermore, empirical simulation results show that the new method has some real advantages in comparison with the modified continual reassessment method.

  2. Continuous Verification of Large Embedded Software using SMT-Based Bounded Model Checking

    CERN Document Server

    Cordeiro, Lucas; Marques-Silva, Joao


    The complexity of software in embedded systems has increased significantly over the last years so that software verification now plays an important role in ensuring the overall product quality. In this context, SAT-based bounded model checking has been successfully applied to discover subtle errors, but for larger applications, it often suffers from the state space explosion problem. This paper describes a new approach called continuous verification to detect design errors as quickly as possible by looking at the Software Configuration Management (SCM) system and by combining dynamic and static verification to reduce the state space to be explored. We also give a set of encodings that provide accurate support for program verification and use different background theories in order to improve scalability and precision in a completely automatic way. A case study from the telecommunications domain shows that the proposed approach improves the error-detection capability and reduces the overall verification time by...

  3. X-ray structure of a minor group human rhinovirus bound to a fragment of its cellular receptor protein. (United States)

    Verdaguer, Nuria; Fita, Ignacio; Reithmayer, Manuela; Moser, Rosita; Blaas, Dieter


    Although many viral receptors have been identified, the ways in which they interact with their cognate viruses are not understood at the molecular level. We have determined the X-ray structure of a complex between calcium-containing modules of the very low-density lipoprotein receptor and the minor group human rhinovirus HRV2. The receptor binds close to the icosahedral five-fold vertex, with only one module per virus protomer. The binding face of this module is defined by acidic calcium-chelating residues and, in particular, by an exposed tryptophan that is highly conserved. The attachment site on the virus involves only residues from VP1, particularly a lysine strictly conserved in all minor group HRVs. The disposition of the attached ligand-binding repeats around the five-fold axis, together with the proximity of the N- and C-terminal ends of adjacent modules, suggests that more than one repeat in a single receptor molecule might attach simultaneously.

  4. 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.


    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.

  5. Ensemble-based characterization of unbound and bound states on protein energy landscape

    CERN Document Server

    Ruvinsky, Anatoly M; Tuzikov, Alexander V; Vakser, Ilya A


    Characterization of protein energy landscape and conformational ensembles is important for understanding mechanisms of protein folding and function. We studied ensembles of bound and unbound conformations of six proteins to explore their binding mechanisms and characterize the energy landscapes in implicit solvent. First, results show that bound and unbound spectra often significantly overlap. Moreover, the larger the overlap the smaller the RMSD between bound and unbound conformational ensembles. Second, the analysis of the unbound-to-bound changes points to conformational selection as the binding mechanism for four of the proteins. Third, the center of the unbound spectrum has a higher energy than the center of the corresponding bound spectrum of the dimeric and multimeric states for most of the proteins. This suggests that the unbound states often have larger entropy than the bound states considered outside of the complex. Fourth, the exhaustively long minimization, making small intra-rotamer adjustments, ...

  6. An improved convergence bound for aggregation-based domain decomposition preconditioners.

    Energy Technology Data Exchange (ETDEWEB)

    Shadid, John Nicolas; Sala, Marzio; Tuminaro, Raymond Stephen


    In this paper we present a two-level overlapping domain decomposition preconditioner for the finite-element discretization of elliptic problems in two and three dimensions. The computational domain is partitioned into overlapping subdomains, and a coarse space correction, based on aggregation techniques, is added. Our definition of the coarse space does not require the introduction of a coarse grid. We consider a set of assumptions on the coarse basis functions to bound the condition number of the resulting preconditioned system. These assumptions involve only geometrical quantities associated with the aggregates and the subdomains. We prove that the condition number using the two-level additive Schwarz preconditioner is O(H/{delta} + H{sub 0}/{delta}), where H and H{sub 0} are the diameters of the subdomains and the aggregates, respectively, and {delta} is the overlap among the subdomains and the aggregates. This extends the bounds presented in [C. Lasser and A. Toselli, Convergence of some two-level overlapping domain decomposition preconditioners with smoothed aggregation coarse spaces, in Recent Developments in Domain Decomposition Methods, Lecture Notes in Comput. Sci. Engrg. 23, L. Pavarino and A. Toselli, eds., Springer-Verlag, Berlin, 2002, pp. 95-117; M. Sala, Domain Decomposition Preconditioners: Theoretical Properties, Application to the Compressible Euler Equations, Parallel Aspects, Ph.D. thesis, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland, 2003; M. Sala, Math. Model. Numer. Anal., 38 (2004), pp. 765-780]. Numerical experiments on a model problem are reported to illustrate the performance of the proposed preconditioner.

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

    DEFF Research Database (Denmark)

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


    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...

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

    DEFF Research Database (Denmark)

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


    , 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...

  9. A semidefinite programming based branch-and-bound framework for the quadratic assignment problem

    NARCIS (Netherlands)

    Truetsch, U.


    The practical approach to calculate an exact solution for a quadratic assignment problem (QAP) via a branch-and-bound framework depends strongly on a "smart" choice of different strategies within the framework, for example the branching strategy, heuristics for the upper bound or relaxations for the

  10. 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.

  11. Crystal structure of IgE bound to its B-cell receptor CD23 reveals a mechanism of reciprocal allosteric inhibition with high affinity receptor FcεRI. (United States)

    Dhaliwal, Balvinder; Yuan, Daopeng; Pang, Marie O Y; Henry, Alistair J; Cain, Katharine; Oxbrow, Amanda; Fabiane, Stella M; Beavil, Andrew J; McDonnell, James M; Gould, Hannah J; Sutton, Brian J


    The role of IgE in allergic disease mechanisms is performed principally through its interactions with two receptors, FcεRI on mast cells and basophils, and CD23 (FcεRII) on B cells. The former mediates allergic hypersensitivity, the latter regulates IgE levels, and both receptors, also expressed on antigen-presenting cells, contribute to allergen uptake and presentation to the immune system. We have solved the crystal structure of the soluble lectin-like "head" domain of CD23 (derCD23) bound to a subfragment of IgE-Fc consisting of the dimer of Cε3 and Cε4 domains (Fcε3-4). One CD23 head binds to each heavy chain at the interface between the two domains, explaining the known 2:1 stoichiometry and suggesting mechanisms for cross-linking membrane-bound trimeric CD23 by IgE, or membrane IgE by soluble trimeric forms of CD23, both of which may contribute to the regulation of IgE synthesis by B cells. The two symmetrically located binding sites are distant from the single FcεRI binding site, which lies at the opposite ends of the Cε3 domains. Structural comparisons with both free IgE-Fc and its FcεRI complex reveal not only that the conformational changes in IgE-Fc required for CD23 binding are incompatible with FcεRI binding, but also that the converse is true. The two binding sites are allosterically linked. We demonstrate experimentally the reciprocal inhibition of CD23 and FcεRI binding in solution and suggest that the mutual exclusion of receptor binding allows IgE to function independently through its two receptors.

  12. 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


    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.

  13. Active disturbance rejection based trajectory linearization control for hypersonic reentry vehicle with bounded uncertainties. (United States)

    Shao, Xingling; Wang, Honglun


    This paper investigates a novel compound control scheme combined with the advantages of trajectory linearization control (TLC) and alternative active disturbance rejection control (ADRC) for hypersonic reentry vehicle (HRV) attitude tracking system with bounded uncertainties. Firstly, in order to overcome actuator saturation problem, nonlinear tracking differentiator (TD) is applied in the attitude loop to achieve fewer control consumption. Then, linear extended state observers (LESO) are constructed to estimate the uncertainties acting on the LTV system in the attitude and angular rate loop. In addition, feedback linearization (FL) based controllers are designed using estimates of uncertainties generated by LESO in each loop, which enable the tracking error for closed-loop system in the presence of large uncertainties to converge to the residual set of the origin asymptotically. Finally, the compound controllers are derived by integrating with the nominal controller for open-loop nonlinear system and FL based controller. Also, comparisons and simulation results are presented to illustrate the effectiveness of the control strategy.

  14. A combined ligand-based and target-based drug design approach for G-protein coupled receptors: application to salvinorin A, a selective kappa opioid receptor agonist (United States)

    Singh, Nidhi; Chevé, Gwénaël; Ferguson, David M.; McCurdy, Christopher R.


    Combined ligand-based and target-based drug design approaches provide a synergistic advantage over either method individually. Therefore, we set out to develop a powerful virtual screening model to identify novel molecular scaffolds as potential leads for the human KOP (hKOP) receptor employing a combined approach. Utilizing a set of recently reported derivatives of salvinorin A, a structurally unique KOP receptor agonist, a pharmacophore model was developed that consisted of two hydrogen bond acceptor and three hydrophobic features. The model was cross-validated by randomizing the data using the CatScramble technique. Further validation was carried out using a test set that performed well in classifying active and inactive molecules correctly. Simultaneously, a bovine rhodopsin based "agonist-bound" hKOP receptor model was also generated. The model provided more accurate information about the putative binding site of salvinorin A based ligands. Several protein structure-checking programs were used to validate the model. In addition, this model was in agreement with the mutation experiments carried out on KOP receptor. The predictive ability of the model was evaluated by docking a set of known KOP receptor agonists into the active site of this model. The docked scores correlated reasonably well with experimental p K i values. It is hypothesized that the integration of these two independently generated models would enable a swift and reliable identification of new lead compounds that could reduce time and cost of hit finding within the drug discovery and development process, particularly in the case of GPCRs.

  15. Nanobiosensors based on individual olfactory receptors

    CERN Document Server

    Pajot-Augy, E


    In the SPOT-NOSED European project, nanoscale sensing elements bearing olfactory receptors and grafted onto functionalized gold substrates are used as odorant detectors to develop a new concept of nanobioelectronic nose, through sensitive impedancemetric measurement of single receptor conformational change upon ligand binding, with a better specificity and lower detection threshold than traditional physical sensors.

  16. 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)


    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.

  17. Internal charge transfer based ratiometric interaction of anionic surfactant with calf thymus DNA bound cationic surfactant: Study I (United States)

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


    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.

  18. Internal charge transfer based ratiometric interaction of anionic surfactant with calf thymus DNA bound cationic surfactant: Study I. (United States)

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


    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.


    Institute of Scientific and Technical Information of China (English)

    Charles K. Chui; Shi Xianliang


    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.

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


    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.

  1. A new accuracy measure based on bounded relative error for time series forecasting. (United States)

    Chen, Chao; Twycross, Jamie; Garibaldi, Jonathan M


    Many accuracy measures have been proposed in the past for time series forecasting comparisons. However, many of these measures suffer from one or more issues such as poor resistance to outliers and scale dependence. In this paper, while summarising commonly used accuracy measures, a special review is made on the symmetric mean absolute percentage error. Moreover, a new accuracy measure called the Unscaled Mean Bounded Relative Absolute Error (UMBRAE), which combines the best features of various alternative measures, is proposed to address the common issues of existing measures. A comparative evaluation on the proposed and related measures has been made with both synthetic and real-world data. The results indicate that the proposed measure, with user selectable benchmark, performs as well as or better than other measures on selected criteria. Though it has been commonly accepted that there is no single best accuracy measure, we suggest that UMBRAE could be a good choice to evaluate forecasting methods, especially for cases where measures based on geometric mean of relative errors, such as the geometric mean relative absolute error, are preferred.

  2. Force analysis of pile foundation in rock slope based on upper-bound theorem of limit

    Institute of Scientific and Technical Information of China (English)

    ZHAO Ming-hua; LIU Jian-hua; LIU Dai-quan; WANG You


    Based on the characteristic that the potential sliding surfaces of rock slope are commonly in the shape of either line or fold line, analysis thought of conventional pile foundation in the flat ground under complex load condition was applied and the upper-bound theorem of limit analysis was used to compute thrust of rock layers with all possible distribution shapes. The interaction of slope and pile was considered design load in terms of slope thrust, and the finite difference method was derived to calculate inner-force and displacement of bridge pile foundation in rock slope under complex load condition. The result of example shows that the distribution model of slope thrust has certain impact on displacement and inner-force of bridge pile foundation. The maximum displacement growth rate reaches 54% and the maximum moment and shear growth rates reach only 15% and 20%, respectively, but the trends of inner-force and displacement of bridge pile foundation are basically the same as those of the conventional pile foundation in the flat ground. When the piles bear the same level lateral thrust, the distribution shapes of slope thrust have different influence on inner-force of pile foundation, especially the rectangle distribution, and the triangle thrust has the smallest displacement and inner-force of pile foundation.

  3. Source apportionment of particle-bound polycyclic aromatic hydrocarbons in Lumbini, Nepal by using the positive matrix factorization receptor model (United States)

    Chen, Pengfei; Li, Chaoliu; Kang, Shichang; Yan, Fangping; Zhang, Qianggong; Ji, Zhengming; Tripathee, Lekhendra; Rupakheti, Dipesh; Rupakheti, Maheswar; Qu, Bin; Sillanpää, Mika


    Indo-Gangetic Plain (IGP) is one of the most polluted regions in the world. Despite numbers of studies conducted at urban site, few data are available at rural area. In this study, characteristics of 15 particle-bound priority polycyclic aromatic hydrocarbons (PAHs) of total suspended particles (TSPs) collected at a typical rural area (Lumbini) of IGP from April 2013 to March 2014 were reported. The results showed that annual average TSP and PAH concentrations were 209 ± 123 μg/m3 and 94.8 ± 54.6 ng/m3, respectively, which were similar to those of large cities such as Agra and Delhi in the upwind adjacent regions. Clear seasonal variation of TSP and PAH concentrations was observed, with the highest average concentration occurring in winter followed by the pre-monsoon, post-monsoon, and monsoon seasons, reflecting combined influence of source strength and monsoon circulation on PAH concentrations of Lumbini. Positive matrix factorization analysis showed that biomass combustion (50.6%) and vehicular emissions (30.4%) were first two sources of PAHs, followed by coal combustion (11.6%) and air-soil exchange (7.4%), in line with that of diagnostic molecular ratios results. Because of extensive agro-residue burning, intensive forest fires, and conducive weather conditions, contribution of biomass burning during non-monsoon season (55.7%) was higher than that of monsoon season (42.1%). The total BaP equivalent concentration (BaPeq) of particulate PAHs ranged between 2.51 and 47.3 ng/m3, was 2-40 times higher than the WHO guideline (1 ng/m3), implying local residents were at risk for adverse health effects.

  4. Uncertainty analysis based on probability bounds (p-box) approach in probabilistic safety assessment. (United States)

    Karanki, Durga Rao; Kushwaha, Hari Shankar; Verma, Ajit Kumar; Ajit, Srividya


    A wide range of uncertainties will be introduced inevitably during the process of performing a safety assessment of engineering systems. The impact of all these uncertainties must be addressed if the analysis is to serve as a tool in the decision-making process. Uncertainties present in the components (input parameters of model or basic events) of model output are propagated to quantify its impact in the final results. There are several methods available in the literature, namely, method of moments, discrete probability analysis, Monte Carlo simulation, fuzzy arithmetic, and Dempster-Shafer theory. All the methods are different in terms of characterizing at the component level and also in propagating to the system level. All these methods have different desirable and undesirable features, making them more or less useful in different situations. In the probabilistic framework, which is most widely used, probability distribution is used to characterize uncertainty. However, in situations in which one cannot specify (1) parameter values for input distributions, (2) precise probability distributions (shape), and (3) dependencies between input parameters, these methods have limitations and are found to be not effective. In order to address some of these limitations, the article presents uncertainty analysis in the context of level-1 probabilistic safety assessment (PSA) based on a probability bounds (PB) approach. PB analysis combines probability theory and interval arithmetic to produce probability boxes (p-boxes), structures that allow the comprehensive propagation through calculation in a rigorous way. A practical case study is also carried out with the developed code based on the PB approach and compared with the two-phase Monte Carlo simulation results.

  5. Containment and Consensus-based Distributed Coordination Control for Voltage Bound and Reactive Power Sharing in AC Microgrid

    DEFF Research Database (Denmark)

    Han, Renke; Meng, Lexuan; Ferrari-Trecate, Giancarlo


    This paper offers a highly flexible and reliable control strategy to achieve voltage bounded regulation and accurate reactive power sharing coordinately in AC Micro-Grids. A containment and consensus-based distributed coordination controller is proposed, by which each output voltage magnitude can...

  6. Overproduction of the membrane-bound receptor-like protein kinase 1, RPK1, enhances abiotic stress tolerance in Arabidopsis. (United States)

    Osakabe, Yuriko; Mizuno, Shinji; Tanaka, Hidenori; Maruyama, Kyonoshin; Osakabe, Keishi; Todaka, Daisuke; Fujita, Yasunari; Kobayashi, Masatomo; Shinozaki, Kazuo; Yamaguchi-Shinozaki, Kazuko


    RPK1 (receptor-like protein kinase 1) localizes to the plasma membrane and functions as a regulator of abscisic acid (ABA) signaling in Arabidopsis. In our current study, we investigated the effect of RPK1 disruption and overproduction upon plant responses to drought stress. Transgenic Arabidopsis overexpressing the RPK1 protein showed increased ABA sensitivity in their root growth and stomatal closure and also displayed less transpirational water loss. In contrast, a mutant lacking RPK1 function, rpk1-1, was found to be resistant to ABA during these processes and showed increased water loss. RPK1 overproduction in these transgenic plants thus increased their tolerance to drought stress. We performed microarray analysis of RPK1 transgenic plants and observed enhanced expression of several stress-responsive genes, such as Cor15a, Cor15b, and rd29A, in addition to H(2)O(2)-responsive genes. Consistently, the expression levels of ABA/stress-responsive genes in rpk1-1 had decreased compared with wild type. The results suggest that the overproduction of RPK1 enhances both the ABA and drought stress signaling pathways. Furthermore, the leaves of the rpk1-1 plants exhibit higher sensitivity to oxidative stress upon ABA-pretreatment, whereas transgenic plants overproducing RPK1 manifest increased tolerance to this stress. Our current data suggest therefore that RPK1 overproduction controls reactive oxygen species homeostasis and enhances both water and oxidative stress tolerance in Arabidopsis.

  7. Recommendations for the development and validation of flow cytometry-based receptor occupancy assays. (United States)

    Green, Cherie L; Stewart, Jennifer J; Högerkorp, Carl-Magnus; Lackey, Alan; Jones, Nicholas; Liang, Meina; Xu, Yuanxin; Ferbas, John; Moulard, Maxime; Czechowska, Kamila; Mc Closkey, Thomas W; van der Strate, Barry W A; Wilkins, Danice E C; Lanham, David; Wyant, Timothy; Litwin, Virginia


    Receptor occupancy measurements demonstrate the binding of a biotherapeutic agent to its extra-cellular target and represent an integral component of the pharmacodynamic (PD) portfolio utilized to advance the development and commercialization of a therapeutic agent. Coupled with traditional pharmacokinetic (PK) assessments derived from serum drug concentration, receptor occupancy data can be used to model PK/PD relationships and validate dose selection decisions throughout the drug development lifecycle. Receptor occupancy assays can be even more challenging to develop than other flow cytometric methods (e.g. surface immunophenotyping). In addition to typical considerations regarding stability of the cell type of interest, stability of the target-bound therapeutic agent and stability of the target receptor must be taken into account. Reagent selection is also challenging as reagents need to be evaluated for the potential to compete with the therapeutic agent and bind with comparable affinity. This article provides technical guidance for the development and validation of cytometry-based receptor occupancy assays.

  8. Stress-based upper-bound method and convex optimization: case of the Gurson material (United States)

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


    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).

  9. 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:


    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.

  10. 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

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

    NARCIS (Netherlands)

    Boesten, J.J.T.I.


    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

  12. Upper bounds on fault tolerance thresholds of noisy Clifford-based quantum computers

    Energy Technology Data Exchange (ETDEWEB)

    Plenio, M B [Institut fuer Theoretische Physik, Albert-Einstein-Allee 11, Universitaet Ulm, D-89069 Ulm (Germany); Virmani, S [Department of Physics SUPA, University of Strathclyde, John Anderson Building, 107 Rottenrow, Glasgow G4 0NG (United Kingdom)], E-mail:


    We consider the possibility of adding noise to a quantum circuit to make it efficiently simulatable classically. In previous works, this approach has been used to derive upper bounds to fault tolerance thresholds-usually by identifying a privileged resource, such as an entangling gate or a non-Clifford operation, and then deriving the noise levels required to make it 'unprivileged'. In this work, we consider extensions of this approach where noise is added to Clifford gates too and then 'commuted' around until it concentrates on attacking the non-Clifford resource. While commuting noise around is not always straightforward, we find that easy instances can be identified in popular fault tolerance proposals, thereby enabling sharper upper bounds to be derived in these cases. For instance we find that if we take Knill's (2005 Nature 434 39) fault tolerance proposal together with the ability to prepare any possible state in the XY plane of the Bloch sphere, then not more than 3.69% error-per-gate noise is sufficient to make it classical, and 13.71% of Knill's {gamma} noise model is sufficient. These bounds have been derived without noise being added to the decoding parts of the circuits. Introducing such noise in a toy example suggests that the present approach can be optimized further to yield tighter bounds.

  13. 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


    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.

  14. 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


    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

  15. Out-of-core Interactive Display of Large Meshes Using an Oriented Bounding Box-based Hardware Depth Query

    Energy Technology Data Exchange (ETDEWEB)

    Ha, H; Gregorski, B; Joy, K I


    In this paper we present an occlusion culling method that uses hardware-based depth queries on oriented bounding boxes to cull unseen geometric primitives efficiently. An out-of-core design enables this method to interactively display data sets that are too large to fit into main memory. During a preprocessing phase, a spatial subdivision (such as an octree or BSP tree) of a given data set is constructed where, for each node, an oriented bounding box containing mesh primitives is computed using principal component analysis (PCA). At runtime, the tree indicated by the spatial subdivision is traversed in front-to-back order, and only nodes that are determined to be visible, based on a hardware accelerated depth query, are rendered.

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

    Directory of Open Access Journals (Sweden)

    Wenjie Bi


    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.

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


    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.

  18. Andreev reflection and bound states in topological insulator based planar and step Josephson junctions (United States)

    Choudhari, Tarun; Deo, Nivedita


    A superconductor-topological insulator-superconductor (S/TI/S) junction having normal region at angle θ is studied theoretically to investigate the junction angle dependency of the Andreev reflection and the formation of the Andreev bound states in the step and planar S/TI/S structures. It is found that the Andreev reflection becomes θ dependent only in the presence of the potential barrier at the TI/S interface. In particular, the step and planar TI/S junction have totally different conductive behavior with bias voltage and potential barrier in the regime of retro and specular Andreev reflection. Interestingly, we find that the elliptical cross section of Dirac cone, an important feature of topological insulator with step surface defect, affects the Fabry-Perot resonance of the Andreev reflection induced Andreev bound states (which become Majorana zero energy states at low chemical potential) in the step S/TI/S structure. Unlike the usual planar S/TI/S structures, we find these ellipticity affected Andreev bound states lead to non-monotonic Josephson super-current in the step S/TI/S structure whose non-monotonicity can be controlled with the use of the potential barrier, which may find applications in nanoelectronics.

  19. 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


    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.

  20. Adaptive Transmission Opportunity Scheme Based on Delay Bound and Network Load in IEEE 802.11e Wireless LANs

    Directory of Open Access Journals (Sweden)

    S. Kim


    Full Text Available The IEEE 802.11e EDCA (Enhanced Distributed Channel Access is able to provide QoS (Quality of Service by adjusting the transmission opportunities (TXOPs, which control the period to access the medium. The EDCA has a fairness problem among competing stations, which support multimedia applications with different delay bounds. In this paper, we propose a simple and effective scheme for alleviating the fairness problem. The proposed scheme dynamically allocates the TXOP value based on the delay bounds of the data packets in a queue and the traffic load of network. Performance of the proposed scheme is investigated by simulation. Our results show that compared to conventional scheme, the proposed scheme significantly improves network performance, and achieves a high degree of fairness among stations with different multimedia applications.

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

    Evers, Andreas; Klebe, Gerhard


    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.

  2. Reduced maximal inhibition in phenotypic susceptibility assays indicates that viral strains resistant to the CCR5 antagonist maraviroc utilize inhibitor-bound receptor for entry. (United States)

    Westby, Mike; Smith-Burchnell, Caroline; Mori, Julie; Lewis, Marilyn; Mosley, Michael; Stockdale, Mark; Dorr, Patrick; Ciaramella, Giuseppe; Perros, Manos


    Maraviroc is a CCR5 antagonist in clinical development as one of a new class of antiretrovirals targeting human immunodeficiency virus type 1 (HIV-1) coreceptor binding. We investigated the mechanism of HIV resistance to maraviroc by using in vitro sequential passage and site-directed mutagenesis. Serial passage through increasing maraviroc concentrations failed to select maraviroc-resistant variants from some laboratory-adapted and clinical isolates of HIV-1. However, high-level resistance to maraviroc was selected from three of six primary isolates passaged in peripheral blood lymphocytes (PBL). The SF162 strain acquired resistance to maraviroc in both treated and control cultures; all resistant variants were able to use CXCR4 as a coreceptor. In contrast, maraviroc-resistant virus derived from isolates CC1/85 and RU570 remained CCR5 tropic, as evidenced by susceptibility to the CCR5 antagonist SCH-C, resistance to the CXCR4 antagonist AMD3100, and an inability to replicate in CCR5 Delta32/Delta32 PBL. Strain-specific mutations were identified in the V3 loop of maraviroc-resistant CC1/85 and RU570. The envelope-encoding region of maraviroc-resistant CC1/85 was inserted into an NL4-3 background. This recombinant virus was completely resistant to maraviroc but retained susceptibility to aplaviroc. Reverse mutation of gp120 residues 316 and 323 in the V3 loop (numbering from HXB2) to their original sequence restored wild-type susceptibility to maraviroc, while reversion of either mutation resulted in a partially sensitive virus with reduced maximal inhibition (plateau). The plateaus are consistent with the virus having acquired the ability to utilize maraviroc-bound receptor for entry. This hypothesis was further corroborated by the observation that a high concentration of maraviroc blocks the activity of aplaviroc against maraviroc-resistant virus.

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


    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

  4. Graph-Based Symbolic Technique and Its Application in the Frequency Response Bound Analysis of Analog Integrated Circuits

    Directory of Open Access Journals (Sweden)

    E. Tlelo-Cuautle


    Full Text Available A new graph-based symbolic technique (GBST for deriving exact analytical expressions like the transfer function H(s of an analog integrated circuit (IC, is introduced herein. The derived H(s of a given analog IC is used to compute the frequency response bounds (maximum and minimum associated to the magnitude and phase of H(s, subject to some ranges of process variational parameters, and by performing nonlinear constrained optimization. Our simulations demonstrate the usefulness of the new GBST for deriving the exact symbolic expression for H(s, and the last section highlights the good agreement between the frequency response bounds computed by our variational analysis approach versus traditional Monte Carlo simulations. As a conclusion, performing variational analysis using our proposed GBST for computing the frequency response bounds of analog ICs, shows a gain in computing time of 100x for a differential circuit topology and 50x for a 3-stage amplifier, compared to traditional Monte Carlo simulations.

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

    Directory of Open Access Journals (Sweden)

    Angela Hsiang-Ling Chen


    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

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

    Directory of Open Access Journals (Sweden)

    Gérard Tchouassi


    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;}

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


    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.

  8. 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


    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 ...

  9. Biophysics of risk aversion based on neurotransmitter receptor theory

    CERN Document Server

    Takahashi, Taiki


    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.

  10. Quinoline based receptor in fluorometric discrimination of carboxylic acids

    Directory of Open Access Journals (Sweden)


    Full Text Available Quinoline and naphthalene-based fluororeceptors 1 and 2 have been designed and synthesized for detection of hydroxy carboxylic acids in less polar solvents. The receptor 1 shows monomer emission quenching followed by excimer emission upon hydrogen bond-mediated complexation of carboxylic acids. The excimer emission distinguishes aromatic dicarboxylic acids from aliphatic dicarboxylic acids and even long chain aliphatic dicarboxylic acids from short chain aliphatic dicarboxylic acids. The receptor 1 is found to be selective for citric acid with a strong excimer emission in CHCl3. On the contrary, the receptor 2 exhibited less binding constant value and did not form any excimer upon complexation with the same acids under similar conditions. This established the role of quinoline ring nitrogen in binding with the acids.

  11. The peptide agonist-binding site of the glucagon-like peptide-1 (GLP-1) receptor based on site-directed mutagenesis and knowledge-based modelling. (United States)

    Dods, Rachel L; Donnelly, Dan


    Glucagon-like peptide-1 (7-36)amide (GLP-1) plays a central role in regulating blood sugar levels and its receptor, GLP-1R, is a target for anti-diabetic agents such as the peptide agonist drugs exenatide and liraglutide. In order to understand the molecular nature of the peptide-receptor interaction, we used site-directed mutagenesis and pharmacological profiling to highlight nine sites as being important for peptide agonist binding and/or activation. Using a knowledge-based approach, we constructed a 3D model of agonist-bound GLP-1R, basing the conformation of the N-terminal region on that of the receptor-bound NMR structure of the related peptide pituitary adenylate cyclase-activating protein (PACAP21). The relative position of the extracellular to the transmembrane (TM) domain, as well as the molecular details of the agonist-binding site itself, were found to be different from the model that was published alongside the crystal structure of the TM domain of the glucagon receptor, but were nevertheless more compatible with published mutagenesis data. Furthermore, the NMR-determined structure of a high-potency cyclic conformationally-constrained 11-residue analogue of GLP-1 was also docked into the receptor-binding site. Despite having a different main chain conformation to that seen in the PACAP21 structure, four conserved residues (equivalent to His-7, Glu-9, Ser-14 and Asp-15 in GLP-1) could be structurally aligned and made similar interactions with the receptor as their equivalents in the GLP-1-docked model, suggesting the basis of a pharmacophore for GLP-1R peptide agonists. In this way, the model not only explains current mutagenesis and molecular pharmacological data but also provides a basis for further experimental design.

  12. Experimental and theoretical analysis of DEP-based particle deflection for the separation of protein-bound particles (United States)

    Kim, Min-Soo; Kim, Jong-Ho; Lee, Yoon-Sik; Lim, Geon-Gyu; Lee, Hyang-Beom; Park, Jae-Hyoung; Kim, Yong-Kweon


    We present an experimental and theoretical analysis of dielectrophoretic (DEP) particle deflection in a microfluidic channel for the separation of protein-bound particles. A 2D electrode array with widely spaced bars is designed to deflect a particle at the exit of the fluidic channel by negative DEP force. When particles pass through the channel, the particle streams are deflected differently depending on the DEP characteristics of the particles. In this paper, we propose methodologies to characterize the DEP force with the deflection distance using comparative analyses of a simulation and an experiment. The deflection distances of the particles are measured as a function of the ac voltage applied and compared with full 3D simulations. The Clausius-Mossotti (CM) factor of a protein-bound particle is analyzed, based on frequency-dependent deflection distance data measured experimentally, and protein-bound particles are separated from a mixture with nonbound particles in a real application. Two particle groups, 2.3 µm and 6.4 µm polystyrene particles, were used for the simulation and experimental study, and the 6.4 µm diameter particles were selected as an adequate protein-binding substrate for the application of biomolecular detection. Bovine serum albumin (BSA) was used as a test target protein. The particle's BSA binding is identified by the change in the particle's deflection distance. In particular, we used 1 wt% BSA as a target protein sample to investigate the deflection of 6.4 µm diameter particles as a function of protein concentration. The frequency-dependent CM factor curves for BSA-bound and nonbound particles are also calculated theoretically. Therefore, this paper shows a model analytic study on the biomolecular detection performance of a fabricated DEP-deflection microsystem. In addition, we present further significant analyses such as calculation of the electrical surface conductance of BSA around a particle, and we trace simulation errors. The

  13. An efficient algorithm for computing fixed length attractors based on bounded model checking in synchronous Boolean networks with biochemical applications. (United States)

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


    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.

  14. 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


    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.

  15. Observer-based reliable stabilization of uncertain linear systems subject to actuator faults, saturation, and bounded system disturbances. (United States)

    Fan, Jinhua; Zhang, Youmin; Zheng, Zhiqiang


    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.

  16. Revisiting de novo drug design: receptor based pharmacophore screening. (United States)

    Amaravadhi, Harikishore; Baek, Kwanghee; Yoon, Ho Sup


    De novo drug design methods such as receptor or protein based pharmacophore modeling present a unique opportunity to generate novel ligands by employing the potential binding sites even when no explicit ligand information is known for a particular target. Recent developments in molecular modeling programs have enhanced the ability of early programs such as LUDI or Pocket that not only identify the key interactions or hot spots at the suspected binding site, but also and convert these hot spots into three-dimensional search queries and virtual screening of the property filtered synthetic libraries. Together with molecular docking studies and consensus scoring schemes they would enrich the lead identification processes. In this review, we discuss the ligand and receptor based de novo drug design approaches with selected examples.

  17. 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


    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...... dyes showed significant drift of their calibration. Additionally, we present a new synthetic method for preparation of analytically pure benzoporphyrins via simple 1-step template condensation which a promising alternative to the commonly used Lindsey method. © the Partner Organisations 2014....

  18. Bounded Rationality

    Directory of Open Access Journals (Sweden)

    Ballester Pla, Coralio


    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.

  19. The structure of haemoglobin bound to the haemoglobin receptor IsdH from Staphylococcus aureus shows disruption of the native α-globin haem pocket. (United States)

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


    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.

  20. 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;


    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...

  1. Structure of the activation domain of the GM-CSF/IL-3/IL-5 receptor common beta-chain bound to an antagonist. (United States)

    Rossjohn, J; McKinstry, W J; Woodcock, J M; McClure, B J; Hercus, T R; Parker, M W; Lopez, A F; Bagley, C J


    Heterodimeric cytokine receptors generally consist of a major cytokine-binding subunit and a signaling subunit. The latter can transduce signals by more than 1 cytokine, as exemplified by the granulocyte-macrophage colony-stimulating factor (GM-CSF), interleukin-2 (IL-2), and IL-6 receptor systems. However, often the signaling subunits in isolation are unable to bind cytokines, a fact that has made it more difficult to obtain structural definition of their ligand-binding sites. This report details the crystal structure of the ligand-binding domain of the GM-CSF/IL-3/IL-5 receptor beta-chain (beta(c)) signaling subunit in complex with the Fab fragment of the antagonistic monoclonal antibody, BION-1. This is the first single antagonist of all 3 known eosinophil-producing cytokines, and it is therefore capable of regulating eosinophil-related diseases such as asthma. The structure reveals a fibronectin type III domain, and the antagonist-binding site involves major contributions from the loop between the B and C strands and overlaps the cytokine-binding site. Furthermore, tyrosine(421) (Tyr(421)), a key residue involved in receptor activation, lies in the neighboring loop between the F and G strands, although it is not immediately adjacent to the cytokine-binding residues in the B-C loop. Interestingly, functional experiments using receptors mutated across these loops demonstrate that they are cooperatively involved in full receptor activation. The experiments, however, reveal subtle differences between the B-C loop and Tyr(421), which is suggestive of distinct functional roles. The elucidation of the structure of the ligand-binding domain of beta(c) also suggests how different cytokines recognize a single receptor subunit, which may have implications for homologous receptor systems. (Blood. 2000;95:2491-2498)

  2. Exploiting bounded signal flow for graph orientation based on cause-effect pairs

    Directory of Open Access Journals (Sweden)

    Niedermeier Rolf


    Full Text Available Abstract Background We consider the following problem: Given an undirected network and a set of sender-receiver pairs, direct all edges such that the maximum number of "signal flows" defined by the pairs can be routed respecting edge directions. This problem has applications in understanding protein interaction based cell regulation mechanisms. Since this problem is NP-hard, research so far concentrated on polynomial-time approximation algorithms and tractable special cases. Results We take the viewpoint of parameterized algorithmics and examine several parameters related to the maximum signal flow over vertices or edges. We provide several fixed-parameter tractability results, and in one case a sharp complexity dichotomy between a linear-time solvable case and a slightly more general NP-hard case. We examine the value of these parameters for several real-world network instances. Conclusions Several biologically relevant special cases of the NP-hard problem can be solved to optimality. In this way, parameterized analysis yields both deeper insight into the computational complexity and practical solving strategies.

  3. Synthesis and characterization of crystalline structures based on phenylboronate ligands bound to alkaline earth cations. (United States)

    Reinholdt, Marc; Croissant, Jonas; Di Carlo, Lidia; Granier, Dominique; Gaveau, Philippe; Bégu, Sylvie; Devoisselle, Jean-Marie; Mutin, P Hubert; Smith, Mark E; Bonhomme, Christian; Gervais, Christel; van der Lee, Arie; Laurencin, Danielle


    We describe the preparation of the first crystalline compounds based on arylboronate ligands PhB(OH)(3)(-) coordinated to metal cations: [Ca(PhB(OH)(3))(2)], [Sr(PhB(OH)(3))(2)]·H(2)O, and [Ba(PhB(OH)(3))(2)]. The calcium and strontium structures were solved using powder and single-crystal X-ray diffraction, respectively. In both cases, the structures are composed of chains of cations connected through phenylboronate ligands, which interact one with each other to form a 2D lamellar structure. The temperature and pH conditions necessary for the formation of phase-pure compounds were investigated: changes in temperature were found to mainly affect the morphology of the crystallites, whereas strong variations in pH were found to affect the formation of pure phases. All three compounds were characterized using a wide range of analytical techniques (TGA, IR, Raman, XRD, and high resolution (1)H, (11)B, and (13)C solid-state NMR), and the different coordination modes of phenylboronate ligands were analyzed. Two different kinds of hydroxyl groups were identified in the structures: those involved in hydrogen bonds, and those that are effectively "free" and not involved in hydrogen bonds of any significant strength. To position precisely the OH protons within the structures, an NMR-crystallography approach was used: the comparison of experimental and calculated NMR parameters (determined using the Gauge Including Projector Augmented Wave method, GIPAW) allowed the most accurate positions to be identified. In the case of the calcium compound, it was found that it is the (43)Ca NMR data that are critical to help identify the best model of the structure.

  4. Information, Utility & Bounded Rationality

    CERN Document Server

    Ortega, Pedro A


    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.

  5. Cramer-Rao Lower Bound Evaluation for Linear Frequency Modulation Based Active Radar Networks Operating in a Rice Fading Environment

    Directory of Open Access Journals (Sweden)

    Chenguang Shi


    Full Text Available This paper investigates the joint target parameter (delay and Doppler estimation performance of linear frequency modulation (LFM-based radar networks in a Rice fading environment. The active radar networks are composed of multiple radar transmitters and multichannel receivers placed on moving platforms. First, the log-likelihood function of the received signal for a Rician target is derived, where the received signal scattered off the target comprises of dominant scatterer (DS component and weak isotropic scatterers (WIS components. Then, the analytically closed-form expressions of the Cramer-Rao lower bounds (CRLBs on the Cartesian coordinates of target position and velocity are calculated, which can be adopted as a performance metric to access the target parameter estimation accuracy for LFM-based radar network systems in a Rice fading environment. It is found that the cumulative Fisher information matrix (FIM is a linear combination of both DS component and WIS components, and it also demonstrates that the joint CRLB is a function of signal-to-noise ratio (SNR, target’s radar cross section (RCS and transmitted waveform parameters, as well as the relative geometry between the target and the radar network architectures. Finally, numerical results are provided to indicate that the joint target parameter estimation performance of active radar networks can be significantly improved with the exploitation of DS component.

  6. Cramer-Rao Lower Bound Evaluation for Linear Frequency Modulation Based Active Radar Networks Operating in a Rice Fading Environment. (United States)

    Shi, Chenguang; Salous, Sana; Wang, Fei; Zhou, Jianjiang


    This paper investigates the joint target parameter (delay and Doppler) estimation performance of linear frequency modulation (LFM)-based radar networks in a Rice fading environment. The active radar networks are composed of multiple radar transmitters and multichannel receivers placed on moving platforms. First, the log-likelihood function of the received signal for a Rician target is derived, where the received signal scattered off the target comprises of dominant scatterer (DS) component and weak isotropic scatterers (WIS) components. Then, the analytically closed-form expressions of the Cramer-Rao lower bounds (CRLBs) on the Cartesian coordinates of target position and velocity are calculated, which can be adopted as a performance metric to access the target parameter estimation accuracy for LFM-based radar network systems in a Rice fading environment. It is found that the cumulative Fisher information matrix (FIM) is a linear combination of both DS component and WIS components, and it also demonstrates that the joint CRLB is a function of signal-to-noise ratio (SNR), target's radar cross section (RCS) and transmitted waveform parameters, as well as the relative geometry between the target and the radar network architectures. Finally, numerical results are provided to indicate that the joint target parameter estimation performance of active radar networks can be significantly improved with the exploitation of DS component.

  7. 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


    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.

  8. Direct demonstration of insulin receptor internalization. A quantitative electron microscopic study of covalently bound /sup 125/I-photoreactive insulin incubated with isolated hepatocytes

    Energy Technology Data Exchange (ETDEWEB)

    Gorden, P.; Carpentier, J.L.; Moule, M.L.; Yip, C.C.; Orci, L.


    When /sup 125/I-insulin is incubated with isolated rodent hepatocytes at 37 degrees C, the ligand initially binds to the plasma membrane of the cell and is subsequently internalized by adsorptive endocytosis. To confirm directly that the insulin receptor is internalized with the ligand, we covalently linked photoreactive /sup 125/I-N sigma B29 (azidobenzoyl) insulin to its specific hepatocyte receptor and followed its fate by quantitative electron microscopic autoradiography. We found that the covalently linked photoreactive insulin is internalized by the cell in fashion analogous to the internalization of ordinary /sup 125/I-insulin, indicating that, at least under these conditions, the insulin receptor is internalized with the ligand.

  9. Crystallization and preliminary X-ray diffraction analysis of the interleukin-3 alpha receptor bound to the Fab fragment of antibody CSL362. (United States)

    Broughton, Sophie E; Hercus, Timothy R; Nero, Tracy L; Dhagat, Urmi; Owczarek, Catherine M; Hardy, Matthew P; Fabri, Louis J; Scotney, Pierre D; Nash, Andrew D; Wilson, Nicholas J; Lopez, Angel F; Parker, Michael W


    Interleukin-3 (IL-3) is a member of the beta common family of cytokines that regulate multiple functions of myeloid cells. The IL-3 receptor-specific alpha subunit (IL3Rα) is overexpressed on stem cells/progenitor cells of patients with acute myeloid leukaemia, where elevated receptor expression correlates clinically with a reduced patient survival rate. The monoclonal antibody (MAb) CSL362 is a humanized MAb derived from the murine MAb 7G3, originally identified for its ability to specifically recognize the human IL-3 receptor and for blocking the signalling of IL-3 in myeloid and endothelial cells. In order to elucidate the molecular mechanism of CSL362 antagonism, a preliminary structure of human IL3Rα in complex with the MAb CSL362 has been determined.

  10. 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)



    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.

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

    NARCIS (Netherlands)

    Viel, Gerhard Theodoor


    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

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

    NARCIS (Netherlands)

    Viel, Gerhard Theodoor


    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

  13. Structure of human Eg5 in complex with a new monastrol-based inhibitor bound in the R configuration. (United States)

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


    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.

  14. Endocytosis of receptor-bound insulin-like growth factor II is enhanced by mannose-6-phosphate in IM9 cells. (United States)

    Polychronakos, C; Piscina, R


    The insulin-like growth factor II (IGF-II), and glycoproteins containing mannose 6-phosphate (M6P), bind to two different sites of the same receptor molecule (Morgan et al, Nature 329:301, 1987). To study the interactions between the two ligands on their common receptor in intact cells, we examined the effect of free M6P on IGF-II binding and endocytosis in the IM9 human lymphoblastoid cell line. M6P, up to a 3 mM concentration, had no effect on the binding of IGF-II to the cell surface receptor of intact IM9 cells at 4 degrees C. By contrast, when IM9 cells were incubated with 125I-IGF-II at 37 degrees C, 1 mM M6P increased cell-associated radioactivity by twofold. The increase was resistant to acid wash at 4 degrees C, and therefore assumed to represent endocytosed IGF-II. Acid-washable radioactivity was no different, confirming that, in intact cells, M6P does not affect IGF-II surface binding. In addition, preincubation of cells with M6P at 37 degrees C for up to 3 hours did not change the abundance of receptor on the cell surface, as measured by a subsequent 4 degrees C binding assay. We conclude that M6P causes a shift of IGF-II-occupied receptors form the cell surface to intracellular locations without affecting surface binding of this ligand in IM9 cells. The effect could be produced by the binding of M6P itself, or by the displacement of endogenous phosphomannosylated ligands.

  15. 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


    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

  16. 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


    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.

  17. 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


    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.

  18. 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: [Department of Molecular and Cellular Biochemistry, Comprehensive Cancer Center, Ohio State University, 467 Hamilton Hall, 1645 Neil Avenue, Columbus, OH 43210 (United States)


    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.

  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)


    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.


    Institute of Scientific and Technical Information of China (English)



    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。

  1. 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


    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.

  2. Structure-based receptor MIMICS targeted against bacterial superantigen toxins (United States)

    Gupta, Goutam; Hong-Geller, Elizabeth; Shiflett, Patrick R.; Lehnert, Nancy M.


    The invention provides therapeutic compositions useful in the treatment of bacterial superantigen mediated conditions, such as Toxic Shock Syndrome. The compositions comprise genetically engineered bifunctional polypeptides containing a specific T-cell receptor binding domain and a specific MHC class II receptor binding domain, each targeting non-overlapping epitopes on a superantigen molecule against which they are designed. The anti-superantigen "receptor mimetics" or "chimeras" are rationally designed to recreate the modality of superantigen binding directly to both the TCR and the MHC-II receptor, and are capable of acting as decoys for superantigen binding, effectively out-competing the host T-cell and MHC-II receptors, the natural host receptors.

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

    DEFF Research Database (Denmark)

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


    . 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...

  4. Chemometric analysis of ligand receptor complementarity: identifying Complementary Ligands Based on Receptor Information (CoLiBRI). (United States)

    Oloff, Scott; Zhang, Shuxing; Sukumar, Nagamani; Breneman, Curt; Tropsha, Alexander


    We have developed a novel structure-based chemoinformatics approach to search for Complimentary Ligands Based on Receptor Information (CoLiBRI). CoLiBRI is based on the representation of both receptor binding sites and their respective ligands in a space of universal chemical descriptors. The binding site atoms involved in the interaction with ligands are identified by the means of a computational geometry technique known as Delaunay tessellation as applied to X-ray characterized ligand-receptor complexes. TAE/RECON multiple chemical descriptors are calculated independently for each ligand as well as for its active site atoms. The representation of both ligands and active sites using chemical descriptors allows the application of well-known chemometric techniques in order to correlate chemical similarities between active sites and their respective ligands. We have established a protocol to map patterns of nearest neighbor active site vectors in a multidimensional TAE/RECON space onto those of their complementary ligands and vice versa. This protocol affords the prediction of a virtual complementary ligand vector in the ligand chemical space from the position of a known active site vector. This prediction is followed by chemical similarity calculations between this virtual ligand vector and those calculated for molecules in a chemical database to identify real compounds most similar to the virtual ligand. Consequently, the knowledge of the receptor active site structure affords straightforward and efficient identification of its complementary ligands in large databases of chemical compounds using rapid chemical similarity searches. Conversely, starting from the ligand chemical structure, one may identify possible complementary receptor cavities as well. We have applied the CoLiBRI approach to a data set of 800 X-ray characterized ligand-receptor complexes in the PDBbind database. Using a k nearest neighbor (kNN) pattern recognition approach and variable selection

  5. The Acquisition of Bound and Free Anaphora. (United States)

    Koster, Jan; Koster, Charlotte

    Most linguists assume that bound anaphors such as "himself" are connected with their antecedents in a different way from free anaphors such as "him." Bound anaphora resolution is deterministic, based on Principle A of Chomsky's binding theory. Free anaphors, pronominals, cannot be bound in the domain of reflexives (principle…

  6. A bound on chaos

    CERN Document Server

    Maldacena, Juan; Stanford, Douglas


    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.

  7. Diethylstilbestrol-scaffold-based pregnane X receptor modulators. (United States)

    Hodnik, Žiga; Tomašič, Tihomir; Smodiš, Domen; D'Amore, Claudio; Mašič, Lucija Peterlin; Fiorucci, Stefano; Kikelj, Danijel


    Due to its function as a regulator of drug-metabolizing enzymes and transporters, pregnane X receptor (PXR) represents an important factor involved in drug metabolism. In this work, we describe the discovery of diethylstilbestrol-based PXR modulators, which were designed from marine sulfated steroids with PXR agonistic activity, solomonsterols A and B, and our recently reported bazedoxifene scaffold-derived PXR antagonists. The methylated diethylstilbestrol derivative 1 displayed potent PXR agonistic activity with an EC50 value of 10.5 μM, whereas compounds 3, 4 and 6 (IC50 for 6 = 27.4 μM) and diethylstilbestrol (2) itself (IC50 = 14.6 μM) exhibited PXR antagonistic effects in HepG2 cells. The PXR modulatory effects of the synthesized diethylstilbestrol derivatives were further confirmed by the induction of PXR-regulated CYP3A4 expression with compound 1, as well as by the inhibition of the rifaximin-promoted up-regulation of CYP3A4 expression with 2 and its derivative 6.

  8. Normal mode-based approaches in receptor ensemble docking. (United States)

    Cavasotto, Claudio N


    Explicitly accounting for target flexibility in docking still constitutes a difficult challenge due to the high dimensionality of the conformational space to be sampled. This especially applies to the high-throughput scenario, where the screening of hundreds of thousands compounds takes place. The use of multiple receptor conformations (MRCs) to perform ensemble docking in a sequential fashion is a simple but powerful approach that allows to incorporate binding site structural diversity in the docking process. Whenever enough experimental structures to build a diverse ensemble are not available, normal mode analysis provides an appealing and efficient approach to in silico generate MRCs by distortion along few low-frequency modes that represent collective mid- and large-scale displacements. In this way, the dimension of the conformational space to be sampled is heavily reduced. This methodology is especially suited to incorporate target flexibility at the backbone level. In this chapter, the main components of normal mode-based approaches in the context of ensemble docking are presented and explained, including the theoretical and practical considerations needed for the successful development and implementation of this methodology.

  9. 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

    Energy Technology Data Exchange (ETDEWEB)

    Stevenson, J.D. [Stevenson and Associates, Cleveland, OH (United States)


    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.

  10. Tools and techniques to study ligand-receptor interactions and receptor activation by TNF superfamily members. (United States)

    Schneider, Pascal; Willen, Laure; Smulski, Cristian R


    Ligands and receptors of the TNF superfamily are therapeutically relevant targets in a wide range of human diseases. This chapter describes assays based on ELISA, immunoprecipitation, FACS, and reporter cell lines to monitor interactions of tagged receptors and ligands in both soluble and membrane-bound forms using unified detection techniques. A reporter cell assay that is sensitive to ligand oligomerization can identify ligands with high probability of being active on endogenous receptors. Several assays are also suitable to measure the activity of agonist or antagonist antibodies, or to detect interactions with proteoglycans. Finally, self-interaction of membrane-bound receptors can be evidenced using a FRET-based assay. This panel of methods provides a large degree of flexibility to address questions related to the specificity, activation, or inhibition of TNF-TNF receptor interactions in independent assay systems, but does not substitute for further tests in physiologically relevant conditions.

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

    DEFF Research Database (Denmark)

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


    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 interaction profile of the receptor and geometrical descriptions of a ligand scaffold are used to obtain new scaffolds with different structural features and are able to replace the original scaffold in the protein-ligand complex. An enrichment study was successfully performed verifying the ability of SHOP...... to find known active CDK2 scaffolds in a database. Additionally, SHOP was used for suggesting new inhibitors of p38 MAP kinase. Four p38 complexes were used to perform six scaffold searches. Several new scaffolds were suggested, and the resulting compounds were successfully docked into the query proteins....

  12. A receptor-based bioadsorbent to target advanced glycation end products in chronic kidney disease (United States)

    Zhang, Yangrong; Lapidos, Karen A.; Gal-Moscovici, Anca; Sprague, Stuart M.; Ameer, Guillermo A.


    The accumulation of advanced glycation end products (AGEs) has been reported to be a major contributor to chronic systemic inflammation. AGEs are not efficiently removed by hemodialysis or the kidney of a chronic kidney disease (CKD) patient. The goal of this study was to develop a receptor for AGEs (RAGE)-based bioadsorbent device that was capable of removing endogenous AGEs from human blood. The extracellular domain of RAGE was immobilized onto agarose beads to generate the bioadsorbent. The efficacy of AGE removal from saline, serum, and whole blood; biological effects of AGE reduction; and hemocompatibility and stability of the bioadsorbent were investigated. The bioadsorbent bound AGE-modified bovine serum albumin (AGE-BSA) with a binding capacity of 0.73 ± 0.07 mg AGE-BSA/ml bioadsorbent. The bioadsorbent significantly reduced the concentration of total AGEs in serum isolated from end stage kidney disease (ESKD) patients by 57%. AGE removal resulted in a significant reduction of vascular cell adhesion molecule-1 (VCAM-1) expression in human endothelial cells and abolishment of osteoclast formation in osteoclast progenitor cells. A hollow fiber device loaded with bioadsorbent reduced endogenous AGEs from recirculated blood to 36% of baseline levels with no significant changes in total protein and albumin concentration. The bioadsorbent maintained AGE-specific binding capacity after freeze-drying and storage for 1 year. This approach provides the foundation for further development of sRAGE-based extracorporeal therapies to selectively deplete serum AGEs from human blood and decrease inflammation in patients with diabetes and/or CKD. PMID:24206165

  13. A receptor-based bioadsorbent to target advanced glycation end products in chronic kidney disease. (United States)

    Zhang, Yangrong; Lapidos, Karen A; Gal-Moscovici, Anca; Sprague, Stuart M; Ameer, Guillermo A


    The accumulation of advanced glycation end products (AGEs) has been reported to be a major contributor to chronic systemic inflammation. AGEs are not efficiently removed by hemodialysis or the kidney of a chronic kidney disease (CKD) patient. The goal of this study was to develop a receptor for AGEs (RAGE)-based bioadsorbent device that was capable of removing endogenous AGEs from human blood. The extracellular domain of RAGE was immobilized onto agarose beads to generate the bioadsorbent. The efficacy of AGE removal from saline, serum, and whole blood; biological effects of AGE reduction; and hemocompatibility and stability of the bioadsorbent were investigated. The bioadsorbent bound AGE-modified bovine serum albumin (AGE-BSA) with a binding capacity of 0.73 ± 0.07 mg AGE-BSA/mL bioadsorbent. The bioadsorbent significantly reduced the concentration of total AGEs in serum isolated from end-stage kidney disease patients by 57%. AGE removal resulted in a significant reduction of vascular cell adhesion molecule-1 expression in human endothelial cells and abolishment of osteoclast formation in osteoclast progenitor cells. A hollow fiber device loaded with bioadsorbent-reduced endogenous AGEs from recirculated blood to 36% of baseline levels with no significant changes in total protein or albumin concentration. The bioadsorbent maintained AGE-specific binding capacity after freeze-drying and storage for 1 year. This approach provides the foundation for further development of soluble RAGE-based extracorporeal therapies to selectively deplete serum AGEs from human blood and decrease inflammation in patients with diabetes and/or CKD.

  14. Some bounds for quantum copying

    CERN Document Server

    Rastegin, A E


    We derive lower bounds on the absolute error and the relative error of an abstract copying of two-state set. We do not specify a copying transformation and a dimension of state space. Only the unitarity of quantum mechanical transformations is used. Our approach is based on the notion of angle between two states. We first prove several useful statements, simply expressed in terms of angles. We then examine a lower bound on the absolute error, that was first considered by Hillery and Buzek. Our reasonings supplement and reinforce the results, obtained by them. So, we derive more strong bounds on the absolute error, and we also consider a tradeoff between size of error and corresponding probability distributions. After that we examine a lower bound on the relative error.

  15. 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)



    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.

  16. receptores

    Directory of Open Access Journals (Sweden)

    Salete Regina Daronco Benetti


    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”.

  17. 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


    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.

  18. Stable protein device platform based on pyridine dicarboxylic acid-bound cubic-nanostructured mesoporous titania films. (United States)

    Kim, Hwajeong; Park, Sung Soo; Seo, Jooyeok; Ha, Chang-Sik; Moon, Cheil; Kim, Youngkyoo


    Here we shortly report a protein device platform that is extremely stable in a buffer condition similar to human bodies. The protein device platform was fabricated by covalently attaching cytochrome c (cyt c) protein molecules to organic coupler molecules (pyridine dicarboxylic acid, PDA) that were already covalently bound to an electron-transporting substrate. A cubic nanostructured mesoporous titania film was chosen as an electron-transporting substrate because of its large-sized cubic holes (∼7 nm) and highly crystalline cubic titania walls (∼0.4 nm lattice). Binding of PDA molecules to the mesoporous titania surface was achieved by esterification reaction between carboxylic acid groups (PDA) and hydroxyl groups (titania) in the presence of 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC) mediator, whereas the immobilization of cyt c to the PDA coupler was carried out by the EDC-mediated amidation reaction between carboxylic acid groups (PDA) and amine groups (cyt c). Results showed that the 2,4-position isomer among several PDAs exhibited the highest oxidation and reduction peak currents. The cyt c-immobilized PDA-bound titania substrates showed stable and durable electrochemical performances upon continuous current-voltage cycling for 240 times (the final current change was less than 3%) and could detect superoxide that is a core indicator for various diseases including cancers.

  19. Functions of bounded variation


    Lind, Martin


    The paper begins with a short survey of monotone functions. The functions of bounded variation are introduced and some basic properties of these functions are given. Finally the jump function of a function of bounded variation is defined.

  20. Upward Bound alum honored


    Felker, Susan B.


    Robert Cobb Jr., of Greensboro, N.C., a 1986-89 participant in the Virginia Tech Upward Bound program, was recently named Virginia's TRIO Achiever for 2004. Federal TRIO programs include Upward Bound and Educational Talent Search.

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

    Directory of Open Access Journals (Sweden)

    I. Cheng


    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.

  2. Cramér-Rao Lower Bound for Point Based Image Registration With Heteroscedastic Error Model for Application in Single Molecule Microscopy. (United States)

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


    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.

  3. Novel N,N'-Diacylhydrazine-Based Colorimetric Receptors for Selective Sensing of Fluoride and Acetate Anions

    Institute of Scientific and Technical Information of China (English)

    SHI, Da-Qing; WANG, Hai-Ying; LI, Xiao-Yue; YANG, Fang; SHI, Jing-Wen; WANG, Xiang-Shan


    Three novel and simple N,N'-diacylhydrazine-based colorimetric receptors have been prepared. The binding properties of the receptors to anions such as F-, Cl-, Br-, AcO-, HSO-4 and H2PO-4 in acetonitrile solution were examined by UV-Vis spectroscopy methods, which show high sensitivity and selectivity to F- and AcO- over other anions. The results indicated that a 1:1 stoichiometry complex was formed between the receptors and the anions, while 1H NMR titrations confirmed hydrogen binding interaction between the receptors and the anions.

  4. A q-parameter bound for particle spectra based on black hole thermodynamics with Rényi entropy

    Energy Technology Data Exchange (ETDEWEB)

    Biró, Tamás S., E-mail: [HAS Wigner Research Centre for Physics, Institute for Particle and Nuclear Physics, H-1525 Budapest, P.O. Box 49 (Hungary); Czinner, Viktor G., E-mail: [HAS Wigner Research Centre for Physics, Institute for Particle and Nuclear Physics, H-1525 Budapest, P.O. Box 49 (Hungary); Centro de Matemática, Universidade do Minho, Campus de Gualtar, 4710-057 Braga (Portugal)


    By regarding the Hawking–Bekenstein entropy of Schwarzschild black hole horizons as a non-extensive Tsallis entropy, its formal logarithm, the Rényi entropy, is considered. The resulting temperature – horizon radius relation has the same form as the one obtained from a (3+1)-dimensional black hole in anti-de Sitter space using the original entropy formula. In both cases the temperature has a minimum. A semi-classical estimate of the horizon radius at this minimum leads to a Bekenstein bound for the q-parameter in the Rényi entropy of micro black holes (q⩾1+2/π{sup 2}), which is surprisingly close to fitted q-parameters of cosmic ray spectra and power-law distribution of quarks coalescing to hadrons in high energy accelerator experiments.

  5. DMPD: Toll-like receptor (TLR)-based networks regulate neutrophilic inflammation inrespiratory disease. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 18031251 Toll-like receptor (TLR)-based networks regulate neutrophilic inflammation...l) (.csml) Show Toll-like receptor (TLR)-based networks regulate neutrophilic inflammation inrespiratory dis...ease. PubmedID 18031251 Title Toll-like receptor (TLR)-based networks regulate ne

  6. Structure-based rationale for interleukin 5 receptor antagonism. (United States)

    Ishino, Tetsuya; Harrington, Adrian E; Gopi, Hosahudya; Chaiken, Irwin


    Human interleukin 5 (IL5) is the major hematopoietin that stimulates the proliferation, migration and activation of eosinophils and is implicated in the pathogenesis of inflammatory and other myeloproliferative diseases. IL5 functions through the signaling of a common receptor subunit beta (beta c), in a receptor activation process that requires initial recruitment of an IL5 specific receptor subunit alpha (IL5Ralpha), for cytokine presentation to beta c. Important advances have been made to understand molecular mechanisms of cytokine recognition and receptor antagonism. Mutational studies indicate that a pair of charge complementary regions play an essential role in specific interaction between IL5Ralpha and IL5. Moreover, peptide studies with the IL5 system have identified a cyclic peptide inhibitor, AF17121, which binds specifically to IL5Ralpha by mimicking the cytokine. A key receptor-recognition pharmacophore has been identified in this peptide inhibitor, and sites of inhibitor recognition can be proposed in the homology-deduced structural model of IL5Ralpha. These results provide an experimental platform to derive enhanced-potency peptidomimetic inhibitors. Such inhibitors have potential use as tools to evaluate the role of eosinophilia in disease and as potential leads to antagonists to treat hyper-eosinophilic diseases such as eosinophilic esophagitis, asthma and chronic myeloproliferative leukemias.

  7. A Stronger LP Bound for Formula Size Lower Bounds via Clique Constraints

    CERN Document Server

    Ueno, Kenya


    We introduce a new technique proving formula size lower bounds based on the linear programming bound originally introduced by Karchmer, Kushilevitz and Nisan [11] and the theory of stable set polytope. We apply it to majority functions and prove their formula size lower bounds improved from the classical result of Khrapchenko [13]. Moreover, we introduce a notion of unbalanced recursive ternary majority functions motivated by a decomposition theory of monotone self-dual functions and give integrally matching upper and lower bounds of their formula size. We also show monotone formula size lower bounds of balanced recursive ternary majority functions improved from the quantum adversary bound of Laplante, Lee and Szegedy [15].

  8. Providing a Distance Bounding Protocol Named Pasargad in order to Defend against Relay Attacks on RFID-Based Electronic Voting System

    Directory of Open Access Journals (Sweden)

    Mohammad Arjmand


    Full Text Available The most important characteristic of RFID-based electronic voting system compared to traditional votingsystem is that votes in the electronic system are as contactless smart cards in place of paper ballots. Forcasting ballots, voters use a computer terminal to write their choices (their chosen candidates intocontactless smart cards and then put the smart card inside the box. The most important threat forRFIDsystems is information robbery and relay attacks. In this article, by designing a protocol calledDistance Bounding Protocol it is tried to defend these systems against relay attacks.

  9. Mast Cell and Immune Inhibitory Receptors

    Institute of Scientific and Technical Information of China (English)

    LixinLi; ZhengbinYao


    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.

  10. Development of technetium-99m-based CNS receptor ligands: have there been any advances?

    Energy Technology Data Exchange (ETDEWEB)

    Johannsen, B. [Forschungszentrum Rossendorf e.V. (FZR), Dresden (Germany); Pietzsch, H.-J. [Forschungszentrum Rossendorf, Institut fuerr Bioanorganische und Radiopharmazeutische Chemie, Dresden (Germany)


    By virtue of its ideal nuclear physical characteristics for routine nuclear medicine diagnostics and its ready availability, technetium-99m is of outstanding interest in the development of novel radiopharmaceuticals. The potential for the development of {sup 99m}Tc-based radioligands for the study the receptor function in the central nervous system (CNS) is also well recognised despite the difficulties to be overcome. A fundamental challenge is the pharmacologically acceptable integration of the transition metal technetium, with its specific coordination chemistry, into the molecular entity of CNS receptor ligands. Conceptually, the ligand molecule can be assembled by three building blocks: a small neutral chelate unit, an organic linker that may also serve as a pharmacological modifier and a receptor-binding region derived from selective receptor antagonists. The recent introduction of novel technetium chelate units, particularly mixed-ligand complexes and low-valency organometallic compounds of technetium, provides an impetus for the further development of CNS receptor ligands. Moreover, progress in receptor pharmacology and the experience gained with positron emission tomography radiotracers have facilitated the design of numerous {sup 99m}Tc-based CNS receptor ligands. The formidable challenge of developing {sup 99m}Tc probes as single-photon emission tomography imaging agents targeting CNS receptors can be viewed with optimism given the successful development of [{sup 99m}Tc]TRODAT-1 as a {sup 99m}Tc complex for imaging dopamine transporters in the brain, although there are a number of receptor-specific imaging agents that have so far resisted all efforts to develop them. This review presents recent advances and discusses the remaining hurdles in the design of {sup 99m}Tc-based CNS receptor imaging agents. (orig.)

  11. The bound conformation of microtubule-stabilizing agents: NMR insights into the bioactive 3D structure of discodermolide and dictyostatin. (United States)

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


    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.

  12. 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)


    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.

  13. ERBB receptors: from oncogene discovery to basic science to mechanism-based cancer therapeutics. (United States)

    Arteaga, Carlos L; Engelman, Jeffrey A


    ERBB receptors were linked to human cancer pathogenesis approximately three decades ago. Biomedical investigators have since developed substantial understanding of the biology underlying the dependence of cancers on aberrant ERBB receptor signaling. An array of cancer-associated genetic alterations in ERBB receptors has also been identified. These findings have led to the discovery and development of mechanism-based therapies targeting ERBB receptors that have improved outcome for many cancer patients. In this Perspective, we discuss current paradigms of targeting ERBB receptors with cancer therapeutics and our understanding of mechanisms of action and resistance to these drugs. As current strategies still have limitations, we also discuss challenges and opportunities that lie ahead as basic scientists and clinical investigators work toward more breakthroughs.

  14. Risk Bounds for Infinitely Divisible Distribution

    CERN Document Server

    Zhang, Chao


    In this paper, we study the risk bounds for samples independently drawn from an infinitely divisible (ID) distribution. In particular, based on a martingale method, we develop two deviation inequalities for a sequence of random variables of an ID distribution with zero Gaussian component. By applying the deviation inequalities, we obtain the risk bounds based on the covering number for the ID distribution. Finally, we analyze the asymptotic convergence of the risk bound derived from one of the two deviation inequalities and show that the convergence rate of the bound is faster than the result for the generic i.i.d. empirical process (Mendelson, 2003).

  15. Implementation of a fluorescence-based screening assay identifies histamine H3 receptor antagonists clobenpropit and iodophenpropit as subunit-selective N-methyl-D-aspartate receptor antagonists. (United States)

    Hansen, Kasper B; Mullasseril, Praseeda; Dawit, Sara; Kurtkaya, Natalie L; Yuan, Hongjie; Vance, Katie M; Orr, Anna G; Kvist, Trine; Ogden, Kevin K; Le, Phuong; Vellano, Kimberly M; Lewis, Iestyn; Kurtkaya, Serdar; Du, Yuhong; Qui, Min; Murphy, T J; Snyder, James P; Bräuner-Osborne, Hans; Traynelis, Stephen F


    N-Methyl-D-aspartate (NMDA) receptors are ligand-gated ion channels that mediate a slow, Ca(2+)-permeable component of excitatory synaptic transmission in the central nervous system and play a pivotal role in synaptic plasticity, neuronal development, and several neurological diseases. We describe a fluorescence-based assay that measures NMDA receptor-mediated changes in intracellular calcium in a BHK-21 cell line stably expressing NMDA receptor NR2D with NR1 under the control of a tetracycline-inducible promoter (Tet-On). The assay selectively identifies allosteric modulators by using supramaximal concentrations of glutamate and glycine to minimize detection of competitive antagonists. The assay is validated by successfully identifying known noncompetitive, but not competitive NMDA receptor antagonists among 1800 screened compounds from two small focused libraries, including the commercially available library of pharmacologically active compounds. Hits from the primary screen are validated through a secondary screen that used two-electrode voltage-clamp recordings on recombinant NMDA receptors expressed in Xenopus laevis oocytes. This strategy identified several novel modulators of NMDA receptor function, including the histamine H3 receptor antagonists clobenpropit and iodophenpropit, as well as the vanilloid receptor transient receptor potential cation channel, subfamily V, member 1 (TRPV1) antagonist capsazepine. These compounds are noncompetitive antagonists and the histamine H3 receptor ligand showed submicromolar potency at NR1/NR2B NMDA receptors, which raises the possibility that compounds can be developed that act with high potency on both glutamate and histamine receptor systems simultaneously. Furthermore, it is possible that some actions attributed to histamine H3 receptor inhibition in vivo may also involve NMDA receptor antagonism.

  16. 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


    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.

  17. Variational Bounds for Creeping Composites (United States)

    Procházka, Petr


    In the paper time dependent variational bounds are derived based on Extended Hashin-Shtrikman variational principles. Direct calculation leads to explicit formulas to be presented in the text. For various mechanical properties easy coding in Excel, say, can be used and verification of accuracy for numerical procedures is available using the derived formulas.

  18. Overview of receptor-based source apportionment studies for speciated atmospheric mercury (United States)

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


    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

  19. Anion recognition by simple chromogenic and chromo-fluorogenic salicylidene Schiff base or reduced-Schiff base receptors. (United States)

    Dalapati, Sasanka; Jana, Sankar; Guchhait, Nikhil


    This review contains extensive application of anion sensing ability of salicylidene type Schiff bases and their reduced forms having various substituents with respect to phenolic OH group. Some of these molecular systems behave as receptor for recognition or sensing of various anions in organic or aqueous-organic binary solvent mixture as well as in the solid supported test kits. Development of Schiff base or reduced Schiff base receptors for anion recognition event is commonly based on the theory of hydrogen bonding interaction or deprotonation of phenolic -OH group. The process of charge transfer (CT) or inhibition of excited proton transfer (ESIPT) or followed by photo-induced electron transfer (PET) lead to naked-eye color change, UV-vis spectral change, chemical shift in the NMR spectra and fluorescence spectral modifications. In this review we have tried to discuss about the anion sensing properties of Schiff base or reduced Schiff base receptors.

  20. Anion recognition by simple chromogenic and chromo-fluorogenic salicylidene Schiff base or reduced-Schiff base receptors (United States)

    Dalapati, Sasanka; Jana, Sankar; Guchhait, Nikhil


    This review contains extensive application of anion sensing ability of salicylidene type Schiff bases and their reduced forms having various substituents with respect to phenolic sbnd OH group. Some of these molecular systems behave as receptor for recognition or sensing of various anions in organic or aqueous-organic binary solvent mixture as well as in the solid supported test kits. Development of Schiff base or reduced Schiff base receptors for anion recognition event is commonly based on the theory of hydrogen bonding interaction or deprotonation of phenolic -OH group. The process of charge transfer (CT) or inhibition of excited proton transfer (ESIPT) or followed by photo-induced electron transfer (PET) lead to naked-eye color change, UV-vis spectral change, chemical shift in the NMR spectra and fluorescence spectral modifications. In this review we have tried to discuss about the anion sensing properties of Schiff base or reduced Schiff base receptors.

  1. Scalable Capacity Bounding Models for Wireless Networks


    Du, Jinfeng; Medard, Muriel; Xiao, Ming; Skoglund, Mikael


    The framework of network equivalence theory developed by Koetter et al. introduces a notion of channel emulation to construct noiseless networks as upper (resp. lower) bounding models, which can be used to calculate the outer (resp. inner) bounds for the capacity region of the original noisy network. Based on the network equivalence framework, this paper presents scalable upper and lower bounding models for wireless networks with potentially many nodes. A channel decoupling method is proposed...

  2. The discovery of diazepinone-based 5-HT3 receptor partial agonists. (United States)

    Manning, David D; Guo, Cheng; Zhang, Zhenjun; Ryan, Kristen N; Naginskaya, Jennifer; Choo, Sok Hui; Masih, Liaqat; Earley, William G; Wierschke, Jonathan D; Newman, Amy S; Brady, Catherine A; Barnes, Nicholas M; Guzzo, Peter R


    Serotonin type 3 (5-HT3) receptor partial agonists have been targeted as potential new drugs for the symptomatic relief of irritable bowel syndrome (IBS). Multiple diazepinone-based compounds have been discovered, which exhibit nanomolar binding affinity for the h5-HT3A receptor and display a range of intrinsic activities (IA=7-87% of 5-HT Emax) in HEK cells heterologously expressing the h5-HT3A receptor. Favorable physicochemical properties and in vitro ADME profile coupled with oral activity in the murine von Bezold-Jarisch reflex model demonstrates the series has promise for producing low to moderate IA partial agonists suitable for an IBS indication.

  3. A Collaborative Evaluation of LC-MS/MS Based Methods for BMAA Analysis: Soluble Bound BMAA Found to Be an Important Fraction (United States)

    Faassen, Elisabeth J.; Antoniou, Maria G.; Beekman-Lukassen, Wendy; Blahova, Lucie; Chernova, Ekaterina; Christophoridis, Christophoros; Combes, Audrey; Edwards, Christine; Fastner, Jutta; Harmsen, Joop; Hiskia, Anastasia; Ilag, Leopold L.; Kaloudis, Triantafyllos; Lopicic, Srdjan; Lürling, Miquel; Mazur-Marzec, Hanna; Meriluoto, Jussi; Porojan, Cristina; Viner-Mozzini, Yehudit; Zguna, Nadezda


    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. PMID:26938542

  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


    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. A microfluidics-based turning assay reveals complex growth cone responses to integrated gradients of substrate-bound ECM molecules and diffusible guidance cues. (United States)

    Joanne Wang, C; Li, Xiong; Lin, Benjamin; Shim, Sangwoo; Ming, Guo-Li; Levchenko, Andre


    Neuronal growth cones contain sophisticated molecular machinery precisely regulating their migration in response to complex combinatorial gradients of diverse external cues. The details of this regulation are still largely unknown, in part due to limitations of the currently available experimental techniques. Microfluidic devices have been shown to be capable of generating complex, stable and precisely controlled chemical gradients, but their use in studying growth cone migration has been limited in part due to the effects of shear stress. Here we describe a microfluidics-based turning-assay chip designed to overcome this issue. In addition to generating precise gradients of soluble guidance cues, the chip can also fabricate complex composite gradients of diffusible and surface-bound guidance cues that mimic the conditions the growth cones realistically counter in vivo. Applying this assay to Xenopus embryonic spinal neurons, we demonstrate that the presence of a surface-bound laminin gradient can finely tune the polarity of growth cone responses (repulsion or attraction) to gradients of brain-derived neurotrophic factor (BDNF), with the guidance outcome dependent on the mean BDNF concentration. The flexibility inherent in this assay holds significant potential for refinement of our understanding of nervous system development and regeneration, and can be extended to elucidate other cellular processes involving chemotaxis of shear sensitive cells.

  6. 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


    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

  7. Characterization of the 5-HT7 receptor. Determination of the pharmacophore for 5-HT7 receptor agonism and CoMFA-based modeling of the agonist binding site

    NARCIS (Netherlands)

    Vermeulen, ES; Schmidt, AW; Sprouse, JS; Wikstrom, HV; Grol, CJ


    On the basis of a set of 20 diverse 5-HT7 receptor agonists, the pharmacophore for 5-HT7 receptor agonism was determined. Additionally two CoMFA models were developed, based on different alignments of the agonists. Both models show good correlations between experimental and predictive pK(i) values a

  8. Immobilization free electrochemical biosensor for folate receptor in cancer cells based on terminal protection. (United States)

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


    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

  9. Bounding species distribution models

    Directory of Open Access Journals (Sweden)

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


    Full Text Available 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].

  10. Graviton Mass Bounds

    CERN Document Server

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


    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.

  11. Uncovering Molecular Bases Underlying Bone Morphogenetic Protein Receptor Inhibitor Selectivity.

    Directory of Open Access Journals (Sweden)

    Abdelaziz Alsamarah

    Full Text Available Abnormal alteration of bone morphogenetic protein (BMP signaling is implicated in many types of diseases including cancer and heterotopic ossifications. Hence, small molecules targeting BMP type I receptors (BMPRI to interrupt BMP signaling are believed to be an effective approach to treat these diseases. However, lack of understanding of the molecular determinants responsible for the binding selectivity of current BMP inhibitors has been a big hindrance to the development of BMP inhibitors for clinical use. To address this issue, we carried out in silico experiments to test whether computational methods can reproduce and explain the high selectivity of a small molecule BMP inhibitor DMH1 on BMPRI kinase ALK2 vs. the closely related TGF-β type I receptor kinase ALK5 and vascular endothelial growth factor receptor type 2 (VEGFR2 tyrosine kinase. We found that, while the rigid docking method used here gave nearly identical binding affinity scores among the three kinases; free energy perturbation coupled with Hamiltonian replica-exchange molecular dynamics (FEP/H-REMD simulations reproduced the absolute binding free energies in excellent agreement with experimental data. Furthermore, the binding poses identified by FEP/H-REMD led to a quantitative analysis of physical/chemical determinants governing DMH1 selectivity. The current work illustrates that small changes in the binding site residue type (e.g. pre-hinge region in ALK2 vs. ALK5 or side chain orientation (e.g. Tyr219 in caALK2 vs. wtALK2, as well as a subtle structural modification on the ligand (e.g. DMH1 vs. LDN193189 will cause distinct binding profiles and selectivity among BMP inhibitors. Therefore, the current computational approach represents a new way of investigating BMP inhibitors. Our results provide critical information for designing exclusively selective BMP inhibitors for the development of effective pharmacotherapy for diseases caused by aberrant BMP signaling.

  12. An ultrafast quantum random number generator with provably bounded output bias based on photon arrival time measurements (United States)

    Wahl, Michael; Leifgen, Matthias; Berlin, Michael; Röhlicke, Tino; Rahn, Hans-Jürgen; Benson, Oliver


    We report the implementation of a quantum random number generator based on photon arrival times. Due to fast and high resolution timing we are able to generate the highest bitrate of any current generator based on photon arrival times. Bias in the raw data due to the exponential distribution of the arrival times is removed by postprocessing which is directly integrated in the field programmable logic of the timing electronics.

  13. An ELISA Based Binding and Competition Method to Rapidly Determine Ligand-receptor Interactions. (United States)

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


    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.

  14. Generalized upper bound for inelastic diffraction (United States)

    Troshin, S. M.; Tyurin, N. E.


    For inelastic diffraction, we obtain an upper bound valid for the whole range of the elastic scattering amplitude variation allowed by unitarity. We discuss the energy dependence of the inelastic diffractive cross-section on the base of this bound and recent Large Hadron Collider (LHC) data.

  15. A generalized upper bound for inelastic diffraction

    CERN Document Server

    Troshin, S M


    For the inelastic diffraction, we obtain an upper bound valid in the whole range of the elastic scattering amplitude variation allowed by unitarity. We discuss the energy dependence of the inelastic diffractive cross-section on the base of this bound and recent LHC data.

  16. Receptor-based screening assays for the detection of antibiotics residues - A review. (United States)

    Ahmed, Saeed; Ning, Jianan; Cheng, Guyue; Ahmad, Ijaz; Li, Jun; Mingyue, Liu; Qu, Wei; Iqbal, Mujahid; Shabbir, M A B; Yuan, Zonghui


    Consumer and regulatory agencies have a high concern to antibiotic residues in food producing animals, so appropriate screening assays of fast, sensitive, low cost, and easy sample preparation for the identification of these residues are essential for the food-safety insurance. Great efforts in the development of a high-throughput antibiotic screening assay have been made in recent years. Concerning the screening of antibiotic residue, this review elaborate an overview on the availability, advancement and applicability of antibiotic receptor based screening assays for the safety assessment of antibiotics usage (i.e. radio receptor assay, enzyme labeling assays, colloidal gold receptor assay, enzyme colorimetry assay and biosensor assay). This manuscript also tries to shed a light on the selection, preparation and future perspective of receptor protein for antibiotic residue detection. These assays have been introduced for the screening of numerous food samples. Receptor based screening technology for antibiotic detection has high accuracy. It has been concluded that at the same time, it can detect a class of drugs for certain receptor, and realize the multi-residue detection. These assays offer fast, easy and precise detection of antibiotics.


    Directory of Open Access Journals (Sweden)

    Wei Wei


    Full Text Available Indole-based receptors such as biindole, carbazole, and indolocarbazole are regarded as some of the most favorable anion receptors in molecular recognition. This is because indole groups possess N–H groups as hydrogen-bonding donors. The introduction of amide groups in the indole framework can induce strong binding properties and good water solubility. In this study, we designed and synthesized a series of N-(indol-3-ylglyoxylylbenzylamine derivatives as novel and simple anion receptors. The receptors derived by aryl and aliphatic amines can selectively recognize F– based on a color change from colorless-to-yellow in DMSO. The receptors derived by hydrazine hydrate can recognize F–, AcO–, and H2PO4– by similar color changes in DMSO and can even enable the selective recognition of F– in a DMSO–H2O binary solution by the naked eye. Spectrographic data indicate that complexes are formed between receptors and anions through multiple hydrogen-bonding interactions in dual solutions.

  18. Structure-based drug design for G protein-coupled receptors. (United States)

    Congreve, Miles; Dias, João M; Marshall, Fiona H


    Our understanding of the structural biology of G protein-coupled receptors has undergone a transformation over the past 5 years. New protein-ligand complexes are described almost monthly in high profile journals. Appreciation of how small molecules and natural ligands bind to their receptors has the potential to impact enormously how medicinal chemists approach this major class of receptor targets. An outline of the key topics in this field and some recent examples of structure- and fragment-based drug design are described. A table is presented with example views of each G protein-coupled receptor for which there is a published X-ray structure, including interactions with small molecule antagonists, partial and full agonists. The possible implications of these new data for drug design are discussed.

  19. Development and preliminary validation of a plate-based CB1/CB2 receptor functional assay. (United States)

    Dossou, K S S; Devkota, K P; Kavanagh, P V; Beutler, J A; Egan, J M; Moaddel, R


    Cannabinoid (CB) receptors are being targeted therapeutically for the treatment of anxiety, obesity, movement disorders, glaucoma, and pain. More recently, cannabinoid agonists have displayed antiproliferative activity against breast cancer and prostate cancer in animal models. To study cannabinoid receptor ligands, we have developed a novel plate-based assay that measures internalization of CB1/CB2 receptors by determining the change in the intracellular levels of the radiolabeled agonists: [(3)H]Win55-212-2 for CB1 and [(3)H]CP55-940 for CB2. The developed plate-based assay was validated by determining IC50 values for known antagonists: AM251, AM281, AM630, and AM6545. The data obtained were consistent with previously reported values, thereby confirming that the assay can be used to determine the functional binding activities (IC50) of antagonists for the CB1 and CB2 receptors. In addition, we demonstrated that the plate-based assay may be used for screening against complex matrices. Specifically, we demonstrated that the plate-based assay was able to identify which extracts of several species of the genus Zanthoxylum had activity at the CB1/CB2 receptors.

  20. Modified Cramér-Rao lower bounds for joint position and velocity estimation of a Rician target in OFDM-based passive radar networks (United States)

    Shi, C. G.; Salous, S.; Wang, F.; Zhou, J. J.


    Owing to the increased deployment and the favorable range and Doppler resolutions, orthogonal frequency-division multiplexing (OFDM)-based L band digital aeronautical communication system type 1 (LDACS1) stations have become attractive systems for target surveillance in passive radar applications. This paper investigates the problem of joint parameter (position and velocity) estimation of a Rician target in OFDM-based passive radar network systems with multichannel receivers placed on moving platforms, which are composed of multiple OFDM-based LDACS1 transmitters of opportunity and multiple radar receivers. The modified Cramér-Rao lower bounds (MCRLBs) on the Cartesian coordinates of target position and velocity are computed, where the received signal from the target is composed of dominant scatterer (DS) component and weak isotropic scatterers (WIS) component. Simulation results are provided to demonstrate that the target parameter estimation accuracy can be improved by exploiting the DS component. It also shows that the joint MCRLB is not only a function of the transmitted waveform parameters, target radar cross section, and signal-to-noise ratio but also a function of the relative geometry between the target and the passive radar networks. The analytical expressions of MCRLB can be utilized as a performance metric to access the target parameter estimation in OFDM-based passive radar networks in that they enable the selection of optimal transmitter-receiver pairs for target estimation.

  1. 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


    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。

  2. A physiologically based pharmacokinetic model to predict the pharmacokinetics of highly protein-bound drugs and the impact of errors in plasma protein binding. (United States)

    Ye, Min; Nagar, Swati; Korzekwa, Ken


    Predicting the pharmacokinetics of highly protein-bound drugs is difficult. Also, since historical plasma protein binding data were often collected using unbuffered plasma, the resulting inaccurate binding data could contribute to incorrect predictions. This study uses a generic physiologically based pharmacokinetic (PBPK) model to predict human plasma concentration-time profiles for 22 highly protein-bound drugs. Tissue distribution was estimated from in vitro drug lipophilicity data, plasma protein binding and the blood: plasma ratio. Clearance was predicted with a well-stirred liver model. Underestimated hepatic clearance for acidic and neutral compounds was corrected by an empirical scaling factor. Predicted values (pharmacokinetic parameters, plasma concentration-time profile) were compared with observed data to evaluate the model accuracy. Of the 22 drugs, less than a 2-fold error was obtained for the terminal elimination half-life (t1/2 , 100% of drugs), peak plasma concentration (Cmax , 100%), area under the plasma concentration-time curve (AUC0-t , 95.4%), clearance (CLh , 95.4%), mean residence time (MRT, 95.4%) and steady state volume (Vss , 90.9%). The impact of fup errors on CLh and Vss prediction was evaluated. Errors in fup resulted in proportional errors in clearance prediction for low-clearance compounds, and in Vss prediction for high-volume neutral drugs. For high-volume basic drugs, errors in fup did not propagate to errors in Vss prediction. This is due to the cancellation of errors in the calculations for tissue partitioning of basic drugs. Overall, plasma profiles were well simulated with the present PBPK model. Copyright © 2016 John Wiley & Sons, Ltd.

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

    Cotten, Cameron; Reed, Jennifer L


    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.

  4. 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. (United States)

    Yin, Liusong; Stern, Lawrence J


    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.

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

    Institute of Scientific and Technical Information of China (English)


    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.

  6. 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


    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.

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

    DEFF Research Database (Denmark)

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


    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...... for new targets. A validating retrospective virtual screening of histamine H1 and H3 receptor pharmacophores yielded area-under-the-curves of 0.88 and 0.82, respectively. The fragment-based method has the unique advantage that it can be applied to targets for which no (homologous) crystal structures...... or ligands are known. 47% of the class A G protein-coupled receptors can be targeted with at least four-element pharmacophores. The fragment libraries can also be used to grow known ligands or for rotamer refinement of homology models. Researchers can download the complete fragment library or a subset...

  8. Ligand-based receptor tyrosine kinase partial agonists: New paradigm for cancer drug discovery? (United States)

    Riese, David J.


    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

  9. 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


    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].

  10. Lectures on Bound states

    CERN Document Server

    Hoyer, Paul


    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...

  11. 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)



    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.

  12. Bounded Computational Capacity Equilibrium

    CERN Document Server

    Hernandez, Penelope


    We study repeated games played by players with bounded computational power, where, in contrast to Abreu and Rubisntein (1988), the memory is costly. We prove a folk theorem: the limit set of equilibrium payoffs in mixed strategies, as the cost of memory goes to 0, includes the set of feasible and individually rational payoffs. This result stands in sharp contrast to Abreu and Rubisntein (1988), who proved that when memory is free, the set of equilibrium payoffs in repeated games played by players with bounded computational power is a strict subset of the set of feasible and individually rational payoffs. Our result emphasizes the role of memory cost and of mixing when players have bounded computational power.

  13. Upper bound limit and shakedown analysis of elastic plastic bounded linearly kinematic hardening structures



    This thesis develops a new FEM based algorithm for shakedown analysis of structures made of elastic plastic bounded linearly kinematic hardening material. Its concept can be briefly described as: Hardening law is simulated using a two-surface plastic model. One yield surface is the initial surface, defined by yield stress sigma_y, and the other one is the bounding surface, defined by ultimate strength sigma_u. The initial surface can translate inside the bounding surface without changing its ...

  14. 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


    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。

  15. 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


    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-.

  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


    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. Bounding Noncommutative QCD

    CERN Document Server

    Carlson, C E; Lebed, R F; Carlson, Carl E.; Carone, Christopher D.; Lebed, Richard F.


    Jurco, Moller, Schraml, Schupp, and Wess have shown how to construct noncommutative SU(N) gauge theories from a consistency relation. Within this framework, we present the Feynman rules for noncommutative QCD and compute explicitly the most dangerous Lorentz-violating operator generated through radiative corrections. We find that interesting effects appear at the one-loop level, in contrast to conventional noncommutative U(N) gauge theories, leading to a stringent bound. Our results are consistent with others appearing recently in the literature that suggest collider limits are not competitive with low-energy tests of Lorentz violation for bounding the scale of spacetime noncommutativity.

  18. Cell-Based Odorant Sensor Array for Odor Discrimination Based on Insect Odorant Receptors. (United States)

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


    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.

  19. Molecular modeling of the human P2Y14 receptor: A template for structure-based design of selective agonist ligands. (United States)

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


    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.

  20. Development of gene diagnosis for diabetes and cholecystitis based on gene analysis of CCK-A receptor

    Energy Technology Data Exchange (ETDEWEB)

    Kono, Akira [National Kyushu Cancer Center, Fukuoka (Japan)


    Base sequence analysis of CCKAR gene (a gene of A-type receptor for cholecystokinin) from OLETF rat, a model rat for insulin-independent diabetes was made based on the base sequence of wild CCKAR gene, which had been clarified in the previous year. From the pancreas of OLETF rat, DNA was extracted and transduced into {lambda}phage after fragmentation to construct the gene library of OLETF. Then, {lambda}phage DNA clone bound with labelled cDNA of CCKAR gene was analyzed and the gene structure was compared with that of the wild gene. It was demonstrated that CCKAR gene of OLETF had a deletion (6800 b.p.) ranging from the promoter region to the Exon 2, suggesting that CCKAR gene is not functional in OLETF rat. The whole sequence of this mutant gene was registered into Japan DNA Bank (D 50610). Then, F{sub 2} offspring rats were obtained through crossing OLETF (female) and F344 (male) and the time course-changes in the blood glucose level after glucose loading were compared among them. The blood glucose level after glucose loading was significantly higher in the homo-mutant F{sub 2} (CCKAR,-/-) as well as the parent OLETF rat than hetero-mutant F{sub 2} (CCKARm-/+) or the wild rat (CCKAR,+/+). This suggests that CCKAR gene might be involved in the control of blood glucose level and an alteration of the expression level or the functions of CCKAR gene might affect the blood glucose level. (M.N.)

  1. RGD-based PET tracers for imaging receptor integrin αv β3 expression. (United States)

    Cai, Hancheng; Conti, Peter S


    Positron emission tomography (PET) imaging of receptor integrin αv β3 expression may play a key role in the early detection of cancer and cardiovascular diseases, monitoring disease progression, evaluating therapeutic response, and aiding anti-angiogenic drugs discovery and development. The last decade has seen the development of new PET tracers for in vivo imaging of integrin αv β3 expression along with advances in PET chemistry. In this review, we will focus on the radiochemistry development of PET tracers based on arginine-glycine-aspartic acid (RGD) peptide, present an overview of general strategies for preparing RGD-based PET tracers, and review the recent advances in preparations of (18) F-labeled, (64) Cu-labeled, and (68) Ga-labeled RGD tracers, RGD-based PET multivalent probes, and RGD-based PET multimodality probes for imaging receptor integrin αv β3 expression.

  2. 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


    G protein-coupled receptors (GPCRs) have been one of the most productive classes of drug targets for several decades, and new technologies for GPCR-based discovery promise to keep this field active for years to come. While molecular screens for GPCR receptor agonist- and antagonist-based drugs...... 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...... 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...

  3. The DMM Bound

    DEFF Research Database (Denmark)

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


    of variables. One application is to the bitsize of the eigenvalues and eigenvectors of an integer matrix, which also yields a new proof that the problem is polynomial. We also compare against recent lower bounds on the absolute value of the root coordinates by Brownawell and Yap [5], obtained under...

  4. Bounded variation and around

    CERN Document Server

    Appell, Jürgen; Merentes Díaz, Nelson José


    This monographis a self-contained exposition of the definition and properties of functionsof bounded variation and their various generalizations; the analytical properties of nonlinear composition operators in spaces of such functions; applications to Fourier analysis, nonlinear integral equations, and boundary value problems. The book is written for non-specialists. Every chapter closes with a list of exercises and open problems.

  5. 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


    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.

  6. Molecular pop-up toy: a molecular machine based on folding/unfolding motion of alkyl chains bound to a host. (United States)

    Ko, Young Ho; Hwang, Ilha; Kim, Hyunuk; Kim, Youngkook; Kim, Kimoon


    We have designed and synthesized a new type of molecular machine based on the folding/unfolding motion of an alkyl chain bound to a host, triggered by a redox stimulus. A guest molecule containing a viologen unit with a long alkyl chain 1(2+) and its one-electron reduced species 1 + . form very stable 1:1 host-guest complexes 2(2+) and 2 + ., respectively, with cucurbit[8]uril (CB[8]), where the long alkyl chain of the guests is in a folded conformation inside the host cavity. Upon addition of 2,6-dihydroxynaphthalene as an electron donor, the binary complex 2(2+) turns into a ternary complex 3(2+) through host-stabilized charge-transfer complex formation with the alkyl chain extended into the solution outside the host cavity. The ternary complex behaves like a molecular machine reminiscent of a pop-up toy, as it shows reversible folding/unfolding motion of the alkyl chain of the guest in response to a redox stimulus. For example, one-electron reduction of 3(2+) results in the rapid generation of the 2 + . complex, accompanied by a dramatic conformational change of the alkyl chain from an extended to a folded conformation, and the process can be reversed by oxidation.

  7. 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.

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

    Directory of Open Access Journals (Sweden)

    Vincent eZoete


    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

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

    NARCIS (Netherlands)

    T.J.A. Dekker; S. ter Borg; J. Hooijer; S.L. Meijer (Sybren); J. Wesseling (Jelle); J.E. Boers (James); E. Schuuring; J. Bart; J. van Gorp (Joost); P. Bult (Peter); S. Riemersma (Sietske); C.H.M. van Deurzen (Carolien); H.F. Sleddens (Hein); W.E. Mesker; J.R. Kroep (Judith); V.T.H.B.M. Smit (Vincent); M.J. Vijver (Marc )


    textabstractAssessing 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 t

  10. 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.


    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

  11. On Entropy Bounds and Holography

    CERN Document Server

    Halyo, Edi


    We show that the holographic entropy bound for gravitational systems and the Bekenstein entropy bound for nongravitational systems are holographically related. Using the AdS/CFT correspondence, we find that the Bekenstein bound on the boundary is obtained from the holographic bound in the bulk by minimizing the boundary energy with respect the AdS radius or the cosmological constant. This relation may also ameliorate some problems associated with the Bekenstein bound.

  12. Lightweight Distance Bounding Protocol against Relay Attacks (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.

  13. Structure-based discovery of selective serotonin 5-HT(1B) receptor ligands. (United States)

    Rodríguez, David; Brea, José; Loza, María Isabel; Carlsson, Jens


    The development of safe and effective drugs relies on the discovery of selective ligands. Serotonin (5-hydroxytryptamine [5-HT]) G protein-coupled receptors are therapeutic targets for CNS disorders but are also associated with adverse drug effects. The determination of crystal structures for the 5-HT1B and 5-HT2B receptors provided an opportunity to identify subtype selective ligands using structure-based methods. From docking screens of 1.3 million compounds, 22 molecules were predicted to be selective for the 5-HT1B receptor over the 5-HT2B subtype, a requirement for safe serotonergic drugs. Nine compounds were experimentally verified as 5-HT1B-selective ligands, with up to 300-fold higher affinities for this subtype. Three of the ligands were agonists of the G protein pathway. Analysis of state-of-the-art homology models of the two 5-HT receptors revealed that the crystal structures were critical for predicting selective ligands. Our results demonstrate that structure-based screening can guide the discovery of ligands with specific selectivity profiles.

  14. Domain-based identification and analysis of glutamate receptor ion channels and their relatives in prokaryotes.

    Directory of Open Access Journals (Sweden)

    Mao-Feng Ger

    Full Text Available Voltage-gated and ligand-gated ion channels are used in eukaryotic organisms for the purpose of electrochemical signaling. There are prokaryotic homologues to major eukaryotic channels of these sorts, including voltage-gated sodium, potassium, and calcium channels, Ach-receptor and glutamate-receptor channels. The prokaryotic homologues have been less well characterized functionally than their eukaryotic counterparts. In this study we identify likely prokaryotic functional counterparts of eukaryotic glutamate receptor channels by comprehensive analysis of the prokaryotic sequences in the context of known functional domains present in the eukaryotic members of this family. In particular, we searched the nonredundant protein database for all proteins containing the following motif: the two sections of the extracellular glutamate binding domain flanking two transmembrane helices. We discovered 100 prokaryotic sequences containing this motif, with a wide variety of functional annotations. Two groups within this family have the same topology as eukaryotic glutamate receptor channels. Group 1 has a potassium-like selectivity filter. Group 2 is most closely related to eukaryotic glutamate receptor channels. We present analysis of the functional domain architecture for the group of 100, a putative phylogenetic tree, comparison of the protein phylogeny with the corresponding species phylogeny, consideration of the distribution of these proteins among classes of prokaryotes, and orthologous relationships between prokaryotic and human glutamate receptor channels. We introduce a construct called the Evolutionary Domain Network, which represents a putative pathway of domain rearrangements underlying the domain composition of present channels. We believe that scientists interested in ion channels in general, and ligand-gated ion channels in particular, will be interested in this work. The work should also be of interest to bioinformatics researchers who are

  15. Compositional encoding for bounded model checking

    Institute of Scientific and Technical Information of China (English)

    Jun SUN; Yang LIU; Jin Song DONG; Jing SUN


    Verification techniques like SAT-based bounded model checking have been successfully applied to a variety of system models. Applying bounded model checking to compositional process algebras is, however, a highly non-trivial task. One challenge is that the number of system states for process algebra models is not statically known, whereas exploring the full state space is computa-tionally expensive. This paper presents a compositional encoding of hierarchical processes as SAT problems and then applies state-of-the-art SAT solvers for bounded model checking. The encoding avoids exploring the full state space for complex systems so as to deal with state space explosion. We developed an automated analyzer which combines complementing model checking tech-niques (I.e., bounded model checking and explicit on-the-fly model checking) to validate system models against event-based temporal properties. The experiment results show the analyzer handles large systems.

  16. Bounded Satisfiability for PCTL

    CERN Document Server

    Bertrand, Nathalie; Schewe, Sven


    While model checking PCTL for Markov chains is decidable in polynomial-time, the decidability of PCTL satisfiability, as well as its finite model property, are long standing open problems. While general satisfiability is an intriguing challenge from a purely theoretical point of view, we argue that general solutions would not be of interest to practitioners: such solutions could be too big to be implementable or even infinite. Inspired by bounded synthesis techniques, we turn to the more applied problem of seeking models of a bounded size: we restrict our search to implementable -- and therefore reasonably simple -- models. We propose a procedure to decide whether or not a given PCTL formula has an implementable model by reducing it to an SMT problem. We have implemented our techniques and found that they can be applied to the practical problem of sanity checking -- a procedure that allows a system designer to check whether their formula has an unexpectedly small model.

  17. Receptor-based 3D-QSAR in Drug Design: Methods and Applications in Kinase Studies. (United States)

    Fang, Cheng; Xiao, Zhiyan


    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.

  18. Receptor model-based source apportionment of particulate pollution in Hyderabad, India. (United States)

    Guttikunda, Sarath K; Kopakka, Ramani V; Dasari, Prasad; Gertler, Alan W


    Air quality in Hyderabad, India, often exceeds the national ambient air quality standards, especially for particulate matter (PM), which, in 2010, averaged 82.2 ± 24.6, 96.2 ± 12.1, and 64.3 ± 21.2 μg/m(3) of PM10, at commercial, industrial, and residential monitoring stations, respectively, exceeding the national ambient standard of 60 μg/m(3). In 2005, following an ordinance passed by the Supreme Court of India, a source apportionment study was conducted to quantify source contributions to PM pollution in Hyderabad, using the chemical mass balance (version 8.2) receptor model for 180 ambient samples collected at three stations for PM10 and PM2.5 size fractions for three seasons. The receptor modeling results indicated that the PM10 pollution is dominated by the direct vehicular exhaust and road dust (more than 60%). PM2.5 with higher propensity to enter the human respiratory tracks, has mixed sources of vehicle exhaust, industrial coal combustion, garbage burning, and secondary PM. In order to improve the air quality in the city, these findings demonstrate the need to control emissions from all known sources and particularly focus on the low-hanging fruits like road dust and waste burning, while the technological and institutional advancements in the transport and industrial sectors are bound to enhance efficiencies. Andhra Pradesh Pollution Control Board utilized these results to prepare an air pollution control action plan for the city.

  19. 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.

  20. Structure-Based Understanding of Binding Affinity and Mode of Estrogen Receptor α Agonists and Antagonists (United States)

    Barron, Mace G.


    The flexible hydrophobic ligand binding pocket (LBP) of estrogen receptor α (ERα) allows the binding of a wide variety of endocrine disruptors. Upon ligand binding, the LBP reshapes around the contours of the ligand and stabilizes the complex by complementary hydrophobic interactions and specific hydrogen bonds with the ligand. Here we present a framework for quantitative analysis of the steric and electronic features of the human ERα-ligand complex using three dimensional (3D) protein-ligand interaction description combined with 3D-QSAR approach. An empirical hydrophobicity density field is applied to account for hydrophobic contacts of ligand within the LBP. The obtained 3D-QSAR model revealed that hydrophobic contacts primarily determine binding affinity and govern binding mode with hydrogen bonds. Several residues of the LBP appear to be quite flexible and adopt a spectrum of conformations in various ERα-ligand complexes, in particular His524. The 3D-QSAR was combined with molecular docking based on three receptor conformations to accommodate receptor flexibility. The model indicates that the dynamic character of the LBP allows accommodation and stable binding of structurally diverse ligands, and proper representation of the protein flexibility is critical for reasonable description of binding of the ligands. Our results provide a quantitative and mechanistic understanding of binding affinity and mode of ERα agonists and antagonists that may be applicable to other nuclear receptors. PMID:28061508

  1. A Novel Benzimidazolyl based Receptor for the recognition of Fluoride and Cyanide Anion

    Indian Academy of Sciences (India)



    A novel benzimidazole based ligand (1) has been synthesized and studied its anion recognition properties. The binding of anion with 1 was studied using UV-Visible spectroscopy, fluorescence spectroscopy and ¹H-NMR techniques at very low concentrations. The results obtained from the spectroscopic studies indicatethat ligand 1 is an efficient anion receptor providing changes in chemical shift and optical signals for the detection of two most environmentally important anions, fluoride and cyanide.


    Institute of Scientific and Technical Information of China (English)

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


    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.

  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


    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.


    Institute of Scientific and Technical Information of China (English)

    周书涛; 刘应华; 陈莘莘


    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

  5. Family of nonlocal bound entangled states (United States)

    Yu, Sixia; Oh, C. H.


    Bound entanglement, being entangled yet not distillable, is essential to our understanding of the relations between nonlocality and entanglement besides its applications in certain quantum information tasks. Recently, bound entangled states that violate a Bell inequality have been constructed for a two-qutrit system, disproving a conjecture by Peres that bound entanglement is local. Here we construct this kind of nonlocal bound entangled state for all finite dimensions larger than two, making possible their experimental demonstration in most general systems. We propose a Bell inequality, based on a Hardy-type argument for nonlocality, and a steering inequality to identify their nonlocality. We also provide a family of entanglement witnesses to detect their entanglement beyond the Bell inequality and the steering inequality.

  6. 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


    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

  7. Critical SQG in bounded domains


    Constantin, Peter; Ignatova, Mihaela


    We consider the critical dissipative SQG equation in bounded domains, with the square root of the Dirichlet Laplacian dissipation. We prove global a priori interior $C^{\\alpha}$ and Lipschitz bounds for large data.

  8. Blog life: Entropy Bound (United States)

    Steinberg, Peter


    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.

  9. Bounded Fixed-Point Iteration

    DEFF Research Database (Denmark)

    Nielson, Hanne Riis; Nielson, Flemming


    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...

  10. Error bounds for set inclusions

    Institute of Scientific and Technical Information of China (English)

    ZHENG; Xiyin(郑喜印)


    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.

  11. Multifunctions of bounded variation (United States)

    Vinter, R. B.


    Consider control systems described by a differential equation with a control term or, more generally, by a differential inclusion with velocity set F (t , x). Certain properties of state trajectories can be derived when it is assumed that F (t , x) is merely measurable w.r.t. the time variable t. But sometimes a refined analysis requires the imposition of stronger hypotheses regarding the time dependence. Stronger forms of necessary conditions for minimizing state trajectories can be derived, for example, when F (t , x) is Lipschitz continuous w.r.t. time. It has recently become apparent that significant addition properties of state trajectories can still be derived, when the Lipschitz continuity hypothesis is replaced by the weaker requirement that F (t , x) has bounded variation w.r.t. time. This paper introduces a new concept of multifunctions F (t , x) that have bounded variation w.r.t. time near a given state trajectory, of special relevance to control. We provide an application to sensitivity analysis.

  12. Aptamer-based single-molecule imaging of insulin receptors in living cells (United States)

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


    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.

  13. Improved Collision Detection Algorithm Based on Axis- Aligned Bounding Box%基于改进轴向包围盒的碰撞检测算法

    Institute of Scientific and Technical Information of China (English)

    孙毅刚; 段晓晔; 张红颖


    Airport emergency rescue is an important field of civil aviation, and the emergency rescue in the virtual scene can save resources largely.In order to improve the authenticity and accuracy of collision detection in the virtual scene, this paper proposed a collision deteetion algorithm based on feature - triangle.By adding the feature elements of vertex, edges and face in the triangle, feature -triangle was formed to solve the issue of queries in the triangulated model; then axis - aligned bounding box combined with feature - triangle was used to complete collision detection,and accurate intersection calculation was performed in the final stage of the algorithm to provide more collision informarion for the collision response.Experimental results show that the proposed algorithm can save time and has better performance.%研究机场应急救援是民航领域的问题.为防止机场地面车辆拥堵,要求在虚拟场景下的应急演练可全方位测试系统.为增强虚拟演练场景中碰撞检测的真实性与精确性,提出了一种基于特征三角形的碰撞检测算法.在基于三角形的模型中,通过在三角形中添加特征元素(点、边、面)形成特征三角形,利用特征三角形可以有效解决重复查询;通过轴向包围盒结合特征三角形,更好地完成碰撞检测,最后进行精确求交计算,为碰撞响应提供更多的碰撞信息.实验结果表明,算法可以缩短计算时间,提高检测精度,具有实际指导价值.

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


    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.

  15. On the Applicability of Lower Bounds for Solving Rectilinear

    DEFF Research Database (Denmark)

    Clausen, Jens; Karisch, Stefan E.; Perregaard, M.;


    The quadratic assignment problem (QAP) belongs to the hard core of NP-hard optimization problems. After almost forty years of research only relatively small instances can be solved to optimality. The reason is that the quality of the lower bounds available for exact methods is not sufficient....... Recently, lower bounds based on decomposition were proposed for the so called rectilinear QAP that proved to be the strongest for a large class of problem instances. We investigate the strength of these bounds when applied not only at the root node of a search tree but as the bound function used...... in a Branch-and-Bound code solving large scale QAPs....

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

    Indian Academy of Sciences (India)



    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.

  17. Spatially Adaptive Intensity Bounds for Image Restoration

    Directory of Open Access Journals (Sweden)

    Kaaren L. May


    Full Text Available Spatially-adaptive intensity bounds on the image estimate are shown to be an effective means of regularising the ill-posed image restoration problem. For blind restoration, the local intensity constraints also help to further define the solution, thereby reducing the number of multiple solutions and local minima. The bounds are defined in terms of the local statistics of the image estimate and a control parameter which determines the scale of the bounds. Guidelines for choosing this parameter are developed in the context of classical (nonblind image restoration. The intensity bounds are applied by means of the gradient projection method, and conditions for convergence are derived when the bounds are refined using the current image estimate. Based on this method, a new alternating constrained minimisation approach is proposed for blind image restoration. On the basis of the experimental results provided, it is found that local intensity bounds offer a simple, flexible method of constraining both the nonblind and blind restoration problems.

  18. Quantum bounds for ordered searching and sorting

    CERN Document Server

    Hoyer, P; Shi, Y; Hoyer, Peter; Neerbek, Jan; Shi, Yaoyun


    We consider the quantum complexities of searching an ordered list and sorting an un-ordered list. For searching an ordered list of N elements, we prove a lower bound of \\frac{1}{\\pi}(\\ln(N)-1) on the number of oracle queries that access the list elements. This improves the previously best lower bound of ({1/12}\\log_2(N) - O(1)) due to Ambainis. For sorting N numbers, we prove a lower bound of \\frac{N}{2\\pi}(\\ln(N)-1) on the number of binary comparisons. The previously best lower bound is \\Omega(N). Our proofs are based on a weighted all-pairs inner product argument, and our results generalize to bounded error quantum algorithms. Both results are proven in the so-called quantum black box model, a quantum analogue of classical decision trees. In addition to our lower bound results, we give an exact quantum algorithm for ordered searching using (\\log_3(N) + O(1)) queries, which is roughly 0.631 \\log_2(N). Although our algorithm is worse than that of Farhi, Goldstone, Gutmann and Sipser, which makes 0.526 \\log_2(...

  19. Lower bounds for the minimum distance of algebraic geometry codes

    DEFF Research Database (Denmark)

    Beelen, Peter

    , such as the Goppa bound, the Feng-Rao bound and the Kirfel-Pellikaan bound. I will finish my talk by giving several examples. Especially for two-point codes, the generalized order bound is fairly easy to compute. As an illustration, I will indicate how a lower bound can be obtained for the minimum distance of some......A one-point AG-code is an algebraic geometry code based on a divisor whose support consists of one point. Since the discovery of the Feng-Rao lower bound for the minimum distance, there has been a renewed interest in such codes. This lower bound is also called the order bound. An alternative...... description of these codes in terms of order domains has been found. In my talk I will indicate how one can use the ideas behind the order bound to obtain a lower bound for the minimum distance of any AG-code. After this I will compare this generalized order bound with other known lower bounds...

  20. Cost-Benefit Analysis of Nanoparticle Albumin-Bound Paclitaxel versus Solvent-Based Paclitaxel for the Treatment of Metastatic Breast Cancer in the United States (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. Intracellular localization of the M1 muscarinic acetylcholine receptor through clathrin-dependent constitutive internalization is mediated by a C-terminal tryptophan-based motif. (United States)

    Uwada, Junsuke; Yoshiki, Hatsumi; Masuoka, Takayoshi; Nishio, Matomo; Muramatsu, Ikunobu


    The M1 muscarinic acetylcholine receptor (M1-mAChR, encoded by CHRM1) is a G-protein-coupled membrane receptor that is activated by extracellular cholinergic stimuli. Recent investigations have revealed the intracellular localization of M1-mAChR. In this study, we observed constitutive internalization of M1-mAChR in mouse neuroblastoma N1E-115 cells without agonist stimulation. Constitutive internalization depended on dynamin, clathrin and the adaptor protein-2 (AP-2) complex. A WxxI motif in the M1-mAChR C-terminus is essential for its constitutive internalization, given that replacement of W(442) or I(445) with alanine residues abolished constitutive internalization. This WxxI motif resembles YxxΦ, which is the canonical binding motif for the μ2 subunit of the AP-2 complex. The M1-mAChR C-terminal WxxI motif interacted with AP-2 μ2. W442A and I445A mutants of the M1-mAChR C-terminal sequence lost AP-2-μ2-binding activity, whereas the W442Y mutant bound more effectively than wild type. Consistent with these results, W442A and I445A M1-mAChR mutants selectively localized to the cell surface. By contrast, the W442Y receptor mutant was found only at intracellular sites. Our data indicate that the cellular distribution of M1-mAChR is governed by the C-terminal tryptophan-based motif, which mediates constitutive internalization.

  2. Usefulness of liquid-based cytology in hormone receptor analysis of breast cancer specimens. (United States)

    Nishimura, Rieko; Aogi, Kenjiro; Yamamoto, Tamami; Takabatake, Daisuke; Takashima, Seiki; Teramoto, Norihiro; Kagawa, Akihiro; Morita, Sachiko


    Immunohistochemical (IHC) analysis of the hormone receptor (HR) in breast cancer cytology is an important issue nowadays. Several studies have shown discrepancy in the HR status between the primary tumor and metastases. Cytology can be used for patients with metastatic disease. Although cytological assessment of HR is an excellent method, it has not been routinely used because of the difficulty in consistently preparing multiple good quality slides. Liquid-based cytology (LBC) preparation is considered as the key to resolving the aforementioned problem; however, few studies have reported the HR assessment in breast cancer using LBC. Therefore, the HR status of LBC slides from 82 breast cancers was compared with that of the corresponding surgical specimens. The HR assay in both the LBC slides and surgical specimens was conducted by IHC using an autostainer. For the IHC staining, the protocol recommended by the manufacturer for paraffin-embedded sections was used for both the cytology and histology specimens. The HR results of the cytology agreed with those of the histology in 80 of the 82 cases (accuracy rate, 98%) for estrogen receptor, and in 78 of the 82 cases (accuracy rate, 95%) for progesterone receptor. The overall accuracy of the HR status on the cytology and the histology was 99% in 81 of the 82 cases. In conclusion, in HR analysis of breast cancers, LBC followed by IHC using an autostainer was useful for the standard processing of cytological specimens and showed a good correlation with the results of analysis on the histology specimens.

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

    Directory of Open Access Journals (Sweden)

    Katerina D Oikonomou


    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

  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. Quantum dot-based screening system for discovery of g protein-coupled receptor agonists. (United States)

    Lee, Junghan; Kwon, Yong-Jun; Choi, Youngseon; Kim, Hi Chul; Kim, Keumhyun; Kim, JinYeop; Park, Sun; Song, Rita


    Cellular imaging has emerged as an important tool to unravel biological complexity and to accelerate the drug-discovery process, including cell-based screening, target identification, and mechanism of action studies. Recently, semiconductor nanoparticles known as quantum dots (QDs) have attracted great interest in cellular imaging applications due to their unique photophysical properties such as size, tunable optical property, multiplexing capability, and photostability. Herein, we show that QDs can also be applied to assay development and eventually to high-throughput/content screening (HTS/HCS) for drug discovery. We have synthesized QDs modified with PEG and primary antibodies to be used as fluorescent probes for a cell-based HTS system. The G protein-coupled receptor (GPCR) family is known to be involved in most major diseases. We therefore constructed human osteosarcoma (U2OS) cells that specifically overexpress two types of differently tagged GPCRs: influenza hemagglutinin (HA) peptide-tagged κ-opioid receptors (κ-ORs) and GFP-tagged A3 adenosine receptors (A3AR). In this study, we have demonstrated that 1) anti-HA antibody-conjugated QDs could specifically label HA-tagged κ-ORs, 2) subsequent treatment of QD-tagged GPCR agonists allowed agonist-induced translocation to be monitored in real time, 3) excellent emission spectral properties of QD permitted the simultaneous detection of two GPCRs in one cell, and 4) the robust imaging capabilities of the QD-antibody conjugates could lead to reproducible quantitative data from high-content cellular images. These results suggest that the present QD-based GPCR inhibitor screening system can be a promising platform for further drug screening applications.

  6. 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


    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.

  7. The discovery of quinoline based single-ligand human H1 and H3 receptor antagonists. (United States)

    Procopiou, Panayiotis A; Ancliff, Rachael A; Gore, Paul M; Hancock, Ashley P; Hodgson, Simon T; Holmes, Duncan S; Keeling, Steven P; Looker, Brian E; Parr, Nigel A; Rowedder, James E; Slack, Robert J


    A novel series of potent quinoline-based human H1 and H3 bivalent histamine receptor antagonists, suitable for intranasal administration for the potential treatment of allergic rhinitis associated nasal congestion, were identified. Compound 18b had slightly lower H1 potency (pA2 8.8 vs 9.7 for the clinical goldstandard azelastine), and H3 potency (pKi 9.1vs 6.8 for azelastine), better selectivity over α1A, α1B and hERG, similar duration of action, making 18b a good back-up compound to our previous candidate, but with a more desirable profile.

  8. 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


    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.

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

    Directory of Open Access Journals (Sweden)

    Mitsutake Susumu


    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

  10. Decoding Cyclic Codes up to a New Bound on the Minimum Distance

    CERN Document Server

    Zeh, Alexander; Bezzateev, Sergey


    A new lower bound on the minimum distance of q-ary cyclic codes is proposed. This bound improves upon the Bose-Chaudhuri-Hocquenghem (BCH) bound and, for some codes, upon the Hartmann-Tzeng (HT) bound. Several Boston bounds are special cases of our bound. For some classes of codes the bound on the minimum distance is refined. Furthermore, a quadratic-time decoding algorithm up to this new bound is developed. The determination of the error locations is based on the Euclidean Algorithm and a modified Chien search. The error evaluation is done by solving a generalization of Forney's formula.

  11. Biosensor for dopamine based on stabilized lipid films with incorporated resorcin[4]arene receptor. (United States)

    Nikolelis, Dimitrios P; Theoharis, George


    This work reports a technique for the stabilization after storage in air of a lipid film with incorporated resorcin[4]arene receptor based biosensor for dopamine. Microporous filters composed of glass fibers (nominal pore sizes, 0.7 and 1.0 microm) were used as supports for the formation and stabilization of these devices and the lipid film is formed on the filter by polymerization prior its use. Methacrylic acid was the functional monomer, ethylene glycol dimethacrylate was the crosslinker and 2,2'-azobis-(2-methylpropionitrile) was the initiator. The stability of the lipid films by incorporation of a receptor for the preparation of stabilized lipid film biosensor is studied throughout this work. The response towards dopamine of the present stabilized for repetitive uses lipid membrane biosensor composed of dipalmitoyl phosphatidylcholine and dipalmitoyl phosphatidic acid was compared with planar freely suspended bilayer lipid membranes (BLMs). The stabilized lipid membranes provided similar artificial ion gating events as BLMs in the form of transient signals and can function for repetitive uses after storage in air. However, the response of the stabilized lipid films was slower than that of the freely suspended BLMs. This will allow the practical use of the techniques for chemical sensing based on lipid films and commercialization of these devices, because it is now possible to prepare stabilized lipid film based biosensors and store them in the air.

  12. Ad hoc系统中基于中断概率边界的博弈功率控制算法%Power control game based on outage bound probabilities in Ad hoc systems

    Institute of Scientific and Technical Information of China (English)

    蔡跃明; 喻的雄; 吴丹; 胡均权


    By analyzing the outage probability of the Ad hoc systems on Rayleigh fading channel, the upper bound and lower bound of the outage probability were given in this paper.Then two power control functions were designed based on these two bounds to seek the minimum transmit power for minimum upper bound and lower bound.The existence and uniqueness of the two functions were proved and the power updating algorithms proposed.In the end, the performance analysis of the convergence and power consumer of these two functions was shown by simulation.It can be found that if the power cost factor is set to the critical point at which the convergent property of LC (Cost function based on lower bound called LC for simplicity) can be sustained, then the minimum outage probability can be obtained and this approach can reduce the complexity better than using outage probability to design the cost function directly.%通过对瑞利衰落信道下Ad hoc系统中断概率的分析,给出了中断概率的上界和下界,并以此为依据设计出结构类型相似的2个博弈功率控制函数,从而求得中断概率最小时的功率发射值.同时证明了所设计的2个博弈功率控制函数的纳什均衡存在且唯一,并给出了获得纳什均衡的功率更新算法.仿真结果表明,提出的算法能够有效地逼近中断概率,且较DPC算法而言,可以通过设置不同的功率参数因子而获得更大的灵活性.

  13. Design, Synthesis and Recognition Properties of a New Acetate Ion Receptor Based on Shiff-base Derivative

    Institute of Scientific and Technical Information of China (English)

    QIAO Yan-hong; LIN Hai; LIN Hua-kuan


    A simple colorimetric acetate ion receptor based on 3-methoxysalicylaldehyde-4′-nitrophenyl-hydrazone was synthesized in an ethanol solution through one step,and characterized by 1H NMR and elemental analyses.Its anion-binding ability was examined by UV-Vis absorption spectroscopy in DMSO(dimethyl sulfoxide).The result shows that the compound has a high affinity for and a high selectivity toward acetate ions,and also an advantage of 'naked-eye' recognition of color changing from yellow to purple.

  14. The cryo-electron microscopy structure of feline calicivirus bound to junctional adhesion molecule A at 9-angstrom resolution reveals receptor-induced flexibility and two distinct conformational changes in the capsid protein VP1. (United States)

    Bhella, David; Goodfellow, Ian G


    Caliciviridae are small icosahedral positive-sense RNA-containing viruses and include the human noroviruses, a leading cause of infectious acute gastroenteritis and feline calicivirus (FCV), which causes respiratory illness and stomatitis in cats. FCV attachment and entry is mediated by feline junctional adhesion molecule A (fJAM-A), which binds to the outer face of the capsomere, inducing a conformational change in the capsid that may be important for viral uncoating. Here we present the results of our structural investigation of the virus-receptor interaction and ensuing conformational changes. Cryo-electron microscopy and three-dimensional image reconstruction were used to solve the structure of the virus decorated with a soluble fragment of the receptor at subnanometer resolution. In initial reconstructions, the P domains of the capsid protein VP1 and fJAM-A were poorly resolved. Sorting experiments led to improved reconstructions of the FCV-fJAM-A complex both before and after the induced conformational change, as well as in three transition states. These data showed that the P domain becomes flexible following fJAM-A binding, leading to a loss of icosahedral symmetry. Furthermore, two distinct conformational changes were seen; an anticlockwise rotation of up to 15° of the P domain was observed in the AB dimers, while tilting of the P domain away from the icosahedral 2-fold axis was seen in the CC dimers. A list of putative contact residues was calculated by fitting high-resolution coordinates for fJAM-A and VP1 to the reconstructed density maps, highlighting regions in both virus and receptor important for virus attachment and entry.

  15. Improved Range Searching Lower Bounds

    DEFF Research Database (Denmark)

    Larsen, Kasper Green; Nguyen, Huy L.


    and Rosenberg's theorem), are also hard for dynamic range searching in the group model. This theorem allows us to reuse decades of research on range reporting lower bounds to immediately obtain a range of new group model lower bounds. Amongst others, this includes an improved lower bound for the fundamental...... problem of dynamic d-dimensional orthogonal range searching, stating that tqtu = Ω((lg n/lg lg n)d-1). Here tq denotes the query time and tu the update time of the data structure. This is an improvement of a lg1-δn factor over the recent lower bound of Larsen [FOCS'11], where δ>0 is a small constant......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...

  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


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

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


    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

  18. On functions of bounded variation


    Aistleitner, Christoph; Pausinger, Florian; Svane, Anne Marie; Tichy, Robert F.


    The recently introduced concept of $\\mathcal{D}$-variation unifies previous concepts of variation of multivariate functions. In this paper, we give an affirmative answer to the open question from Pausinger \\& Svane (J. Complexity, 2014) whether every function of bounded Hardy--Krause variation is Borel measurable and has bounded $\\mathcal{D}$-variation. Moreover, we show that the space of functions of bounded $\\mathcal{D}$-variation can be turned into a commutative Banach algebra.

  19. Bounding approaches to system identification

    CERN Document Server

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


    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.

  20. Upper bounds for centerlines

    CERN Document Server

    Bukh, Boris


    In 2008, Bukh, Matousek, and Nivasch conjectured that for every n-point set S in R^d and every k, 0 <= k <= d-1, there exists a k-flat f in R^d (a "centerflat") that lies at "depth" (k+1) n / (k+d+1) - O(1) in S, in the sense that every halfspace that contains f contains at least that many points of S. This claim is true and tight for k=0 (this is Rado's centerpoint theorem), as well as for k = d-1 (trivial). Bukh et al. showed the existence of a (d-2)-flat at depth (d-1) n / (2d-1) - O(1) (the case k = d-2). In this paper we concentrate on the case k=1 (the case of "centerlines"), in which the conjectured value for the leading constant is 2/(d+2). We prove that 2/(d+2) is an *upper bound* for the leading constant. Specifically, we show that for every fixed d and every n there exists an n-point set in R^d for which no line in R^d lies at depth larger than 2n/(d+2) + o(n). This point set is the "stretched grid"---a set which has been previously used by Bukh et al. for other related purposes.

  1. Gold-nanoparticle-based assay for instantaneous detection of nuclear hormone receptor-response elements interactions. (United States)

    Tan, Yen Nee; Su, Xiaodi; Liu, Edison T; Thomsen, Jane S


    Gold nanoparticles (AuNPs) are widely used as colorimetric probes for biosensing, relying on their unique particle size-dependent and/or interparticle distance-dependent extinction spectrum and solution color. Herein, we describe an AuNP-based colorimetric assay to detect binding interactions between nuclear hormone receptors and their corresponding DNA-binding elements, particularly the human estrogen receptors (ERalpha and ERbeta) and their cognate estrogen response elements (EREs). We found that the protein-DNA (ER-ERE) complexes can stabilize citrate anion-capped AuNPs against salt-induced aggregation to a larger extent than the protein (ER) or the DNA (ERE) alone, due to their unique molecular size and charge properties that provide a strong electrosteric protection. Moreover, our results show that the extent of stabilization is sequence-dependent and can distinguish a single base variation in the ERE associated with minor changes in protein-DNA binding affinity. With this assay, many important parameters of protein-DNA binding events (e.g., sequence selectivity, distinct DNA binding properties of protein subtypes, binding stoichiometry, and sequence-independent transient binding) can be determined instantly without using labels, tedious sample preparations, and sophisticated instrumentation. These benefits, in particular the high-throughput potential, could enable this assay to become the assay of choice to complement conventional techniques for large scale characterization of protein-DNA interactions, a key aspect in biological research.

  2. Improved lower bound for online strip packing

    NARCIS (Netherlands)

    Harren, Rolf; Kern, Walter


    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

  3. Dilation volumes of sets of bounded perimeter

    DEFF Research Database (Denmark)

    Kiderlen, Markus; Rataj, Jan

    it to determine the derivative of the contact distribution function of a stationary random closed set at zero. A variant for uncountable Q is given, too. The proofs are based on approximation of the characteristic function of A by smooth functions of bounded variation and showing corresponding formulas for them....

  4. Generalized Bounds on Majoron-neutrino couplings

    CERN Document Server

    Tomás, R; Valle, José W F


    We discuss limits on neutrino-Majoron couplings both from laboratory experiments as well as from astrophysics. They apply to the simplest class of Majoron models which covers a variety of possibilities where neutrinos acquire mass either via a seesaw-type scheme or via radiative corrections. By adopting a general framework including CP phases we generalize bounds obtained previously. The combination of complementary bounds enables us to obtain a highly non-trivial exclusion region in the parameter space. We find that the future double beta project GENIUS, together with constraints based on supernova energy release arguments, could restrict neutrino-Majoron couplings down to the 10^{-7} level.

  5. Bound anionic states of adenine

    Energy Technology Data Exchange (ETDEWEB)

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


    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

  6. Bounded link prediction in very large networks (United States)

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


    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.

  7. Validation of a Flow Cytometry Based Binding Assay for Evaluation of Monoclonal Antibody Recognizing EGF Receptor (United States)

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


    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

  8. New insights into the structural bases of activation of Cys-loop receptors. (United States)

    Bouzat, Cecilia


    Neurotransmitter receptors of the Cys-loop superfamily mediate rapid synaptic transmission throughout the nervous system, and include receptors activated by ACh, GABA, glycine and serotonin. They are involved in physiological processes, including learning and memory, and in neurological disorders, and they are targets for clinically relevant drugs. Cys-loop receptors assemble either from five copies of one type of subunit, giving rise to homomeric receptors, or from several types of subunits, giving rise to heteromeric receptors. Homomeric receptors are invaluable models for probing fundamental relationships between structure and function. Receptors contain a large extracellular domain that carries the binding sites and a transmembrane region that forms the ion pore. How the structural changes elicited by agonist binding are propagated through a distance of 50Å to the ion channel gate is central to understanding receptor function. Depending on the receptor subtype, occupancy of either two, as in the prototype muscle nicotinic receptor, or three binding sites, as in homomeric receptors, is required for full activation. The conformational changes initiated at the binding sites are propagated to the gate through the interface between the extracellular and transmembrane domains. This region forms a network that relays structural changes from the binding site towards the pore, and also contributes to open channel lifetime and rate of desensitization. Thus, this coupling region controls the beginning and duration of a synaptic response. Here we review recent advances in the molecular mechanism by which Cys-loop receptors are activated with particular emphasis on homomeric receptors.

  9. Review of the N-quantum Approach to Bound States

    CERN Document Server

    Greenberg, O W


    We describe a method of solving quantum field theories using operator techniques based on the expansion of interacting fields in terms of asymptotic fields. For bound states, we introduce an asymptotic field for each (stable) bound state. We choose the nonrelativistic hydrogen atom as an example to illustrate the method. Future work will apply this N-quantum approach to relativistic theories that include bound states in motion.

  10. Two-Sided Tests and One-Sided Confidence Bounds



    Based on the duality between tests and confidence sets we introduce a new method to derive one-sided confidence bounds following the rejection of a null hypothesis with two-sided alternatives. This method imputes that the experimenter is only interested in confidence bounds if the null hypothesis is rejected. Furthermore, we suppose that he is only interested in the direction and a lower confidence bound concerning the distance of the true parameter value to the parameter values in the null h...

  11. Upper Maxwellian bounds for the spatially homogeneous Boltzmann equation


    Gamba, I. M.; Panferov, V.; Villani, C.


    For the spatially homogeneous Boltzmann equation with cutoff hard potentials it is shown that solutions remain bounded from above, uniformly in time, by a Maxwellian distribution, provided the initial data have a Maxwellian upper bound. The main technique is based on a comparison principle that uses a certain dissipative property of the linear Boltzmann equation. Implications of the technique to propagation of upper Maxwellian bounds in the spatially-inhomogeneous case are discussed.

  12. 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.

  13. Bounds for Asian basket options (United States)

    Deelstra, Griselda; Diallo, Ibrahima; Vanmaele, Michèle


    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.

  14. 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


    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.

  15. Prediction of CNS occupancy of dopamine D2 receptor based on systemic exposure and in vitro experiments. (United States)

    Kanamitsu, Kayoko; Arakawa, Ryosuke; Sugiyama, Yuichi; Suhara, Tetsuya; Kusuhara, Hiroyuki


    The effect of drugs in the central nervous system (CNS) is closely related to occupancy of their target receptor. In this study, we integrated plasma concentrations, in vitro/in vivo data for receptor or protein binding, and in silico data, using a physiologically based pharmacokinetic model, to examine the predictability of receptor occupancy in humans. The occupancy of the dopamine D2 receptor and the plasma concentrations of the antipsychotic drugs quetiapine and perospirone in humans were collected from the literature or produced experimentally. Association and dissociation rate constants and unbound fractions in the serum and brain were determined in vitro/in vivo using human D2 receptor-expressing membrane fractions, human serum and mouse brain. The permeability of drugs across the blood-brain barrier was estimated based on their physicochemical properties. The effect of a metabolite of perospirone, ID-15036, was also considered. The time profiles of D2 receptor occupancy following oral dose of quetiapine and perospirone predicted were similar to the observed values. This approach could assist in the design of clinical studies for drug development and the prediction of the impact of drug-drug interactions on CNS function in clinical settings.

  16. Asynchronous Bounded Expected Delay Networks

    CERN Document Server

    Bakhshi, Rena; Fokkink, Wan; Pang, Jun


    The commonly used asynchronous bounded delay (ABD) network models assume a fixed bound on message delay. We propose a probabilistic network model, called asynchronous bounded expected delay (ABE) model. Instead of a strict bound, the ABE model requires only a bound on the expected message delay. While the conditions of ABD networks restrict the set of possible executions, in ABE networks all asynchronous executions are possible, but executions with extremely long delays are less probable. In contrast to ABD networks, ABE networks cannot be synchronised efficiently. At the example of an election algorithm, we show that the minimal assumptions of ABE networks are sufficient for the development of efficient algorithms. For anonymous, unidirectional ABE rings of known size N we devise a probabilistic leader election algorithm having average message and time complexity O(N).

  17. 4-Nitrocatecholato iron(III) complexes of 2-aminomethyl pyridine-based bis(phenol) amine as structural models for catechol-bound 3,4-PCD (United States)

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


    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.

  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


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

    Directory of Open Access Journals (Sweden)

    Ahmed Haider


    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

  20. Synthesis and Biological Evaluation of Thiophene-Based Cannabinoid Receptor Type 2 Radiotracers for PET Imaging (United States)

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


    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

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

    Directory of Open Access Journals (Sweden)

    Kiattawee Choowongkomon


    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.

  2. Survival prediction in patients undergoing radionuclide therapy based on intratumoral somatostatin-receptor heterogeneity (United States)

    Ilhan, Harun; Higuchi, Takahiro; Buck, Andreas K.; Lehner, Sebastian; Bartenstein, Peter; Bengel, Frank; Schatka, Imke; Muegge, Dirk O.; Papp, László; Zsótér, Norbert; Große-Ophoff, Tobias; Essler, Markus; Bundschuh, Ralph A.


    The NETTER-1 trial demonstrated significantly improved progression-free survival (PFS) for peptide receptor radionuclide therapy (PRRT) in neuroendocrine tumors (NET) emphasizing the high demand for response prediction in appropriate candidates. In this multicenter study, we aimed to elucidate the prognostic value of tumor heterogeneity as assessed by somatostatin receptor (SSTR)-PET/CT. 141 patients with SSTR-expressing tumors were analyzed obtaining SSTR-PET/CT before PRRT (1-6 cycles, 177Lu somatostatin analog). Using the Interview Fusion Workstation (Mediso), a total of 872 metastases were manually segmented. Conventional PET parameters as well as textural features representing intratumoral heterogeneity were computed. The prognostic ability for PFS and overall survival (OS) were examined. After performing Cox regression, independent parameters were determined by ROC analysis to obtain cut-off values to be used for Kaplan-Meier analysis. Within follow-up (median, 43.1 months), 75 patients showed disease progression (median, 22.2 m) and 54 patients died (median, 27.6 m). Cox analysis identified 8 statistically independent heterogeneity parameters for time-to-progression and time-to-death. Among them, the textural feature Entropy predicted both PFS and OS. Conventional PET parameters failed in response prediction. Imaging-based heterogeneity assessment provides prognostic information in PRRT candidates and outperformed conventional PET parameters. Its implementation in clinical practice can pave the way for individualized patient management. PMID:27705948

  3. Diaminomaleonitrile-based azo receptors: Synthesis, DFT studies and their antibacterial activities (United States)

    Khanmohammadi, Hamid; Arab, Vajihe; Rezaeian, Khatereh; Talei, Gholam Reza; Pass, Maryam; Shabani, Nafiseh


    New unsymmetric diaminomaleonitrile-based azo receptors (H3Ln, n = 1-3) have been synthesized via condensation reaction of 5-(4-X-phenyl)-azo-salicyladehyde (X = NO2, OMe and CH3) with 2-amino-3-(5-bromo-2-hydroxybenzylamino)maleonitrile. The solvatochromic behaviors of the molecules were probed by studying their UV-Vis spectra in five pure organic solvents of different polarities. The p-NO2 substituted receptor shows a dramatic color change from yellow to blue upon the addition of fluoride ion in CH3CN. This capability was studied by systematic TD-DFT calculations. These compounds were assayed for their in vitro antibacterial activities against Gram-positive (S. aureus, S. epidermidis and L. monocytogenes) and Gram-negative (E. coli, P. aeruginosa and K. pneumonia.) bacteria by disc diffusion method. The results indicated that the compounds show good inhibition against Gram positive bacteria namely L. monocytogenes as compared to standard drugs.

  4. 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


    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.

  5. 3D-QSAR and docking studies of estrogen compounds based on estrogen receptor β

    Institute of Scientific and Technical Information of China (English)


    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.

  6. Selective agonists and antagonists of formylpeptide receptors: duplex flow cytometry and mixture-based positional scanning libraries. (United States)

    Pinilla, Clemencia; Edwards, Bruce S; Appel, Jon R; Yates-Gibbins, Tina; Giulianotti, Marc A; Medina-Franco, Jose L; Young, Susan M; Santos, Radleigh G; Sklar, Larry A; Houghten, Richard A


    The formylpeptide receptor (FPR1) and formylpeptide-like 1 receptor (FPR2) are G protein-coupled receptors that are linked to acute inflammatory responses, malignant glioma stem cell metastasis, and chronic inflammation. Although several N-formyl peptides are known to bind to these receptors, more selective small-molecule, high-affinity ligands are needed for a better understanding of the physiologic roles played by these receptors. High-throughput assays using mixture-based combinatorial libraries represent a unique, highly efficient approach for rapid data acquisition and ligand identification. We report the superiority of this approach in the context of the simultaneous screening of a diverse set of mixture-based small-molecule libraries. We used a single cross-reactive peptide ligand for a duplex flow cytometric screen of FPR1 and FPR2 in color-coded cell lines. Screening 37 different mixture-based combinatorial libraries totaling more than five million small molecules (contained in 5,261 mixture samples) resulted in seven libraries that significantly inhibited activity at the receptors. Using positional scanning deconvolution, selective high-affinity (low nM K(i)) individual compounds were identified from two separate libraries, namely, pyrrolidine bis-diketopiperazine and polyphenyl urea. The most active individual compounds were characterized for their functional activities as agonists or antagonists with the most potent FPR1 agonist and FPR2 antagonist identified to date with an EC₅₀ of 131 nM (4 nM K(i)) and an IC₅₀ of 81 nM (1 nM K(i)), respectively, in intracellular Ca²⁺ response determinations. Comparative analyses of other previous screening approaches clearly illustrate the efficiency of identifying receptor selective, individual compounds from mixture-based combinatorial libraries.

  7. Soluble Human Intestinal Lactoferrin Receptor: Ca(2+)-Dependent Binding to Sepharose-Based Matrices. (United States)

    Oshima, Yuta; Seki, Kohei; Shibuya, Masataka; Naka, Yuki; Yokoyama, Tatsuya; Sato, Atsushi


    A soluble form of human intestinal lactoferrin receptor (shLFR) is identical to human intelectin-1 (hITLN-1), a galactofuranose-binding protein that acts as a host defense against invading pathogenic microorganisms. We found that recombinant shLFR, expressed in mammalian cells (CHO DG44, COS-1, and RK13), binds tightly to Sepharose 4 Fast Flow (FF)-based matrices in a Ca(2+)-dependent manner. This binding of shLFR to Sepharose 4 FF-based matrices was inhibited by excess D-galactose, but not by D-glucose, suggesting that shLFR recognizes repeating units of α-1,6-linked D-galactose in Sepharose 4 FF. Furthermore, shLFR could bind to both Sepharose 4B- and Sepharose 6B-based matrices that were not crosslinked in a similar manner as to Sepharose 4 FF-based matrices. Therefore, shLFR (hITLN-1) binds to Sepharose-based matrices in a Ca(2+)-dependent manner. This binding property is most likely related to the ability, as host defense lectins, to recognize sepharose (agarobiose)-like structures present on the surface of invading pathogenic microorganisms.

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

    CERN Document Server

    Eldering, J


    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.

  9. Classical Physics and the Bounds of Quantum Correlations. (United States)

    Frustaglia, Diego; Baltanás, José P; Velázquez-Ahumada, María C; Fernández-Prieto, Armando; Lujambio, Aintzane; Losada, Vicente; Freire, Manuel J; Cabello, Adán


    A unifying principle explaining the numerical bounds of quantum correlations remains elusive, despite the efforts devoted to identifying it. Here, we show that these bounds are indeed not exclusive to quantum theory: for any abstract correlation scenario with compatible measurements, models based on classical waves produce probability distributions indistinguishable from those of quantum theory and, therefore, share the same bounds. We demonstrate this finding by implementing classical microwaves that propagate along meter-size transmission-line circuits and reproduce the probabilities of three emblematic quantum experiments. Our results show that the "quantum" bounds would also occur in a classical universe without quanta. The implications of this observation are discussed.

  10. Bounded relative motion under zonal harmonics perturbations (United States)

    Baresi, Nicola; Scheeres, Daniel J.


    The problem of finding natural bounded relative trajectories between the different units of a distributed space system is of great interest to the astrodynamics community. This is because most popular initialization methods still fail to establish long-term bounded relative motion when gravitational perturbations are involved. Recent numerical searches based on dynamical systems theory and ergodic maps have demonstrated that bounded relative trajectories not only exist but may extend up to hundreds of kilometers, i.e., well beyond the reach of currently available techniques. To remedy this, we introduce a novel approach that relies on neither linearized equations nor mean-to-osculating orbit element mappings. The proposed algorithm applies to rotationally symmetric bodies and is based on a numerical method for computing quasi-periodic invariant tori via stroboscopic maps, including extra constraints to fix the average of the nodal period and RAAN drift between two consecutive equatorial plane crossings of the quasi-periodic solutions. In this way, bounded relative trajectories of arbitrary size can be found with great accuracy as long as these are allowed by the natural dynamics and the physical constraints of the system (e.g., the surface of the gravitational attractor). This holds under any number of zonal harmonics perturbations and for arbitrary time intervals as demonstrated by numerical simulations about an Earth-like planet and the highly oblate primary of the binary asteroid (66391) 1999 KW4.

  11. A PSL Bounded Model Checking Method

    Institute of Scientific and Technical Information of China (English)

    YU Lei; ZHAO Zongtao


    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.

  12. Lower Bound for Visual Cryptography Schemes

    CERN Document Server

    Cheraghi, Abbas


    For a given visual cryptography scheme, it is possible to present a basis matrices for it and most of constructions are based on basis matrices. In this paper we introduce a lower bound for the pixel expansion of visual cryptography schemes with basis matrices. To make the main theorem more flexible, we will introduce a lower bound based on induced matchings of hypergraph of qualified sets. As an application, we present an algebraic proof for the fact that the pixel expansion of basis matrices of any $k$ out of $k$ scheme is at least $2^{k-1}$. In the sequel, we present a lower bound for the pixel expansion of a given graph access structure in term of maximum number of edges in an induced matching. Finally, we show that the minimum pixel expansion of basis matrices of graph access structure $P_n$ is exactly $\\lceil \\frac{n+1}{2}\\rceil$ and this shows the lower bound mentioned in the main theorem is sharp.

  13. 边界面模型在基坑维护体系中的应用%Numerical Simulation on the Behaviour of Deep Excavation Retaining Structures Based on Bounding Surface Model

    Institute of Scientific and Technical Information of China (English)

    杨春林; 孙吉主


    Primary property of bounding surface model is briefly introduced. This model was applied for force & deformation calculation of a deep excavation retaining structure and the result was compared with that based on elastic-plastic model, through which conclusions of regularity were obtained.%简要介绍边界面模型特点,将其应用于某基坑维护体系的受力及变形特性计算中,并与弹塑性模型计算的结果进行比较,总结出具有规律性的结论。

  14. Novel chalcone-based fluorescent human histamine H3 receptor ligands as pharmacological tools

    Directory of Open Access Journals (Sweden)

    Holger eStark


    Full Text Available Novel fluorescent chalcone-based ligands at human histamine H3 receptors (hH3R have been designed, synthesized and characterized. Compounds described are non-imidazole analogues of ciproxifan with a tetralone motif. Tetralones as chemical precursors and related fluorescent chalcones exhibit affinities at hH3R in the same concentration range like that of the reference antagonist ciproxifan (hH3R pKi value of 7.2. Fluorescence characterization of our novel ligands shows emission maxima about 570 nm for yellow fluorescent chalcones and ≥600 nm for the red fluorescent derivatives. Interferences to cellular autofluorescence could be excluded. All synthesized chalcone compounds could be taken to visualize hH3R proteins in stably transfected HEK-293 cells using confocal laser scanning fluorescence microscopy. These novel fluorescent ligands possess high potential to be used as pharmacological tools for hH3R visualization in different tissues.

  15. The Out-bound and In-bound Travelling Market

    Institute of Scientific and Technical Information of China (English)

    Emily Yu


    @@ As the Spring Festival of China with a long vocation of seven days nationally is approaching,more and more attention is paid to the out-bound and inn-bound trayeling market.Will people hold their pockets firmly in the"cold winter"of world-wide financial crisis,or will they grab the great discount of traveling and take a good relax?

  16. Mechanism-Based Tumor-Targeting Drug Delivery System. Validation of Efficient Vitamin Receptor-Mediated Endocytosis and Drug Release

    Energy Technology Data Exchange (ETDEWEB)

    Chen, S.; Wong, S.; Zhao, X.; Chen, J.; Chen, J.; Kuznetsova, L.; Ojima, I.


    An efficient mechanism-based tumor-targeting drug delivery system, based on tumor-specific vitamin-receptor mediated endocytosis, has been developed. The tumor-targeting drug delivery system is a conjugate of a tumor-targeting molecule (biotin: vitamin H or vitamin B-7), a mechanism-based self-immolative linker and a second-generation taxoid (SB-T-1214) as the cytotoxic agent. This conjugate (1) is designed to be (i) specific to the vitamin receptors overexpressed on tumor cell surface and (ii) internalized efficiently through receptor-mediated endocytosis, followed by smooth drug release via glutathione-triggered self-immolation of the linker. In order to monitor and validate the sequence of events hypothesized, i.e., receptor-mediated endocytosis of the conjugate, drug release, and drug-binding to the target protein (microtubules), three fluorescent/fluorogenic molecular probes (2, 3, and 4) were designed and synthesized. The actual occurrence of these processes was unambiguously confirmed by means of confocal fluorescence microscopy (CFM) and flow cytometry using L1210FR leukemia cells, overexpressing biotin receptors. The molecular probe 4, bearing the taxoid linked to fluorescein, was also used to examine the cell specificity (i.e., efficacy of receptor-based cell targeting) for three cell lines, L1210FR (biotin receptors overexpressed), L1210 (biotin receptors not overexpressed), and WI38 (normal human lung fibroblast, biotin receptor negative). As anticipated, the molecular probe 4 exhibited high specificity only to L1210FR. To confirm the direct correlation between the cell-specific drug delivery and anticancer activity of the probe 4, its cytotoxicity against these three cell lines was also examined. The results clearly showed a good correlation between the two methods. In the same manner, excellent cell-specific cytotoxicity of the conjugate 1 (without fluorescein attachment to the taxoid) against the same three cell lines was confirmed. This mechanism-based

  17. Design and development of a peptide-based adiponectin receptor agonist for cancer treatment

    Directory of Open Access Journals (Sweden)

    Lovas Sandor


    Full Text Available Abstract Background Adiponectin, a fat tissue-derived adipokine, exhibits beneficial effects against insulin resistance, cardiovascular disease, inflammatory conditions, and cancer. Circulating adiponectin levels are decreased in obese individuals, and this feature correlates with increased risk of developing several metabolic, immunological and neoplastic diseases. Thus, pharmacological replacement of adiponectin might prove clinically beneficial, especially for the obese patient population. At present, adiponectin-based therapeutics are not available, partly due to yet unclear structure/function relationships of the cytokine and difficulties in converting the full size adiponectin protein into a viable drug. Results We aimed to generate adiponectin-based short peptide that can mimic adiponectin action and be suitable for preclinical and clinical development as a cancer therapeutic. Using a panel of 66 overlapping 10 amino acid-long peptides covering the entire adiponectin globular domain (residues 105-254, we identified the 149-166 region as the adiponectin active site. Three-dimensional modeling of the active site and functional screening of additional 330 peptide analogs covering this region resulted in the development of a lead peptidomimetic, ADP 355 (H-DAsn-Ile-Pro-Nva-Leu-Tyr-DSer-Phe-Ala-DSer-NH2. In several adiponectin receptor-positive cancer cell lines, ADP 355 restricted proliferation in a dose-dependent manner at 100 nM-10 μM concentrations (exceeding the effects of 50 ng/mL globular adiponectin. Furthermore, ADP 355 modulated several key signaling pathways (AMPK, Akt, STAT3, ERK1/2 in an adiponectin-like manner. siRNA knockdown experiments suggested that ADP 355 effects can be transmitted through both adiponectin receptors, with a greater contribution of AdipoR1. In vivo, intraperitoneal administration of 1 mg/kg/day ADP 355 for 28 days suppressed the growth of orthotopic human breast cancer xenografts by ~31%. The peptide

  18. Bounds for Certain Character Sums

    Institute of Scientific and Technical Information of China (English)

    杨锦; 郑志勇


    This paper shows a connection between exponential sums and character sums. In particular, we introduce a character sum that is an analog of the classical Kloosterman sums and establish the analogous Weil-Estermann's upper bound for it. The paper also analyzes a generalized Hardy-Littlewood example for character sums, which shows that the upper bounds given here are the best possible. The analysis makes use of local bounds for the exponential sums and character sums. The basic theorems have been previously established.

  19. Combining Alphas via Bounded Regression

    Directory of Open Access Journals (Sweden)

    Zura Kakushadze


    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.

  20. 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


    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.

  1. Chemically engineering ligand selectivity at the free fatty acid receptor 2 based on pharmacological variation between species orthologs (United States)

    Hudson, Brian D.; Christiansen, Elisabeth; Tikhonova, Irina G.; Grundmann, Manuel; Kostenis, Evi; Adams, David R.; Ulven, Trond; Milligan, Graeme


    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 of the free fatty acid receptor 2 (FFA2) could be developed on the basis of pharmacological variation between species orthologs. For this, bovine FFA2 was characterized, revealing distinct ligand selectivity compared with human FFA2. Homology modeling and mutational analysis demonstrated a single mutation in human FFA2 of C4.57G resulted in a human FFA2 receptor with ligand selectivity similar to the bovine receptor. This was exploited to generate human FFA2-RASSL by the addition of a second mutation at a known orthosteric ligand interaction site, H6.55Q. The resulting FFA2-RASSL displayed a >100-fold loss of activity to endogenous ligands, while responding to the distinct ligand sorbic acid with pEC50 values for inhibition of cAMP, 5.83 ± 0.11; Ca2+ mobilization, 4.63 ± 0.05; ERK phosphorylation, 5.61 ± 0.06; and dynamic mass redistribution, 5.35 ± 0.06. This FFA2-RASSL will be useful in future studies 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 ligand selectivity at the free fatty acid receptor 2 based on pharmacological variation between species orthologs. PMID:22919070

  2. Nonlinear calibration transfer based on hierarchical Bayesian models and Lagrange Multipliers: Error bounds of estimates via Monte Carlo - Markov Chain sampling. (United States)

    Seichter, Felicia; Vogt, Josef; Radermacher, Peter; Mizaikoff, Boris


    The calibration of analytical systems is time-consuming and the effort for daily calibration routines should therefore be minimized, while maintaining the analytical accuracy and precision. The 'calibration transfer' approach proposes to combine calibration data already recorded with actual calibrations measurements. However, this strategy was developed for the multivariate, linear analysis of spectroscopic data, and thus, cannot be applied to sensors with a single response channel and/or a non-linear relationship between signal and desired analytical concentration. To fill this gap for a non-linear calibration equation, we assume that the coefficients for the equation, collected over several calibration runs, are normally distributed. Considering that coefficients of an actual calibration are a sample of this distribution, only a few standards are needed for a complete calibration data set. The resulting calibration transfer approach is demonstrated for a fluorescence oxygen sensor and implemented as a hierarchical Bayesian model, combined with a Lagrange Multipliers technique and Monte-Carlo Markov-Chain sampling. The latter provides realistic estimates for coefficients and prediction together with accurate error bounds by simulating known measurement errors and system fluctuations. Performance criteria for validation and optimal selection of a reduced set of calibration samples were developed and lead to a setup which maintains the analytical performance of a full calibration. Strategies for a rapid determination of problems occurring in a daily calibration routine, are proposed, thereby opening the possibility of correcting the problem just in time.

  3. Computing Constrained Cramer Rao Bounds

    CERN Document Server

    Tune, Paul


    We revisit the problem of computing submatrices of the Cram\\'er-Rao bound (CRB), which lower bounds the variance of any unbiased estimator of a vector parameter $\\vth$. We explore iterative methods that avoid direct inversion of the Fisher information matrix, which can be computationally expensive when the dimension of $\\vth$ is large. The computation of the bound is related to the quadratic matrix program, where there are highly efficient methods for solving it. We present several methods, and show that algorithms in prior work are special instances of existing optimization algorithms. Some of these methods converge to the bound monotonically, but in particular, algorithms converging non-monotonically are much faster. We then extend the work to encompass the computation of the CRB when the Fisher information matrix is singular and when the parameter $\\vth$ is subject to constraints. As an application, we consider the design of a data streaming algorithm for network measurement.

  4. Bound states in string nets (United States)

    Schulz, Marc Daniel; Dusuel, Sébastien; Vidal, Julien


    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.

  5. Bound states in string nets

    CERN Document Server

    Schulz, M D; Vidal, J


    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.

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

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


    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.

  7. A cosmological bound on radiative neutrino lifetime (United States)

    Mirizzi, A.; Montanino, D.; Serpico, P. D.


    Neutrino oscillation experiments and direct bounds on absolute masses constrain neutrino mass differences to fall into the microwave energy range, for most of the allowed parameter space. As a consequence of these recent phenomenological advances, older constraints on radiative neutrino decays based on diffuse background radiations and assuming strongly hierarchical masses in the eV range are now outdated. We thus derive new bounds on the radiative neutrino lifetime using the high precision cosmic microwave background spectral data collected by the FIRAS instrument on board of COBE. The lower bound on neutrino lifetime is between a few ×1019 s and ~ 5 × 1020 s, depending on the neutrino mass ordering and on the absolute neutrino mass scale. However, due to phase space limitations, the upper bound on the effective magnetic moment mediating the decay is not better than ~10-8 μB. We also comment about possible improvements of these limits, by means of recent diffuse infrared photon background data.

  8. Revisiting cosmological bounds on radiative neutrino lifetime

    CERN Document Server

    Mirizzi, A; Serpico, Pasquale Dario


    Neutrino oscillation experiments and direct bounds on absolute masses constrain neutrino mass differences to fall into the microwave energy range, for most of the allowed parameter space. As a consequence of these recent phenomenological advances, older constraints on radiative neutrino decays based on diffuse background radiations and assuming strongly hierarchical masses in the eV range are now outdated. We thus derive new bounds on the radiative neutrino lifetime using the high precision cosmic microwave background spectral data collected by the FIRAS instrument on board of COBE. The lower bound on the lifetime is between a few x 10^19 s and 5 x 10^20 s, depending on the neutrino mass ordering and on the absolute mass scale. However, due to phase space limitations, the upper bound in terms of the effective magnetic moment mediating the decay is not better than ~ 10^-8 Bohr magnetons. We also comment about possible improvements of these limits, by means of recent diffuse infrared photon background data. We ...

  9. Cramér-Rao-Type Bounds for Localization

    Directory of Open Access Journals (Sweden)

    Chang Cheng


    Full Text Available The localization problem is fundamentally important for sensor networks. This paper, based on "Estimation bounds for localization" by the authors (2004 © IEEE, studies the Cramér-Rao lower bound (CRB for two kinds of localization based on noisy range measurements. The first is anchored localization in which the estimated positions of at least nodes are known in global coordinates. We show some basic invariances of the CRB in this case and derive lower and upper bounds on the CRB which can be computed using only local information. The second is anchor-free localization where no absolute positions are known. Although the Fisher information matrix is singular, a CRB-like bound exists on the total estimation variance. Finally, for both cases we discuss how the bounds scale to large networks under different models of wireless signal propagation.

  10. 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


    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

  11. 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.


    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

  12. Modeling of twitch fade based on slow interaction of nondepolarizing muscle relaxants with the presynaptic receptors. (United States)

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


    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.

  13. Molecular characterization of the di-leucine-based internalization motif of the T cell receptor

    DEFF Research Database (Denmark)

    Dietrich, J; Hou, X; Wegener, A M;


    Several cell surface receptors including the T cell receptor (TCR) are phosphorylated and down-regulated following activation of protein kinases. We have recently shown that both phosphorylation of Ser-126 and the presence of the di-leucine sequence Leu-131 and Leu-132 in CD3 gamma are required f...

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

    DEFF Research Database (Denmark)

    Jensen, Anders A.


    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...

  15. Highly effective recognition of carbohydrates by phenanthroline-based receptors: alpha- versus beta-anomer binding preference. (United States)

    Mazik, Monika; Hartmann, Andrè; Jones, Peter G


    (1)H NMR spectroscopic titrations in competitive and non-competitive media, as well as binding studies in two-phase systems, such as phase transfer of sugars from aqueous into organic solvents and dissolution of solid carbohydrates in apolar media revealed both highly effective recognition of neutral carbohydrates and interesting binding preferences of an acyclic phenanthroline-based receptor 1. Compared to the previously described acyclic receptors, compound 1 displays significantly higher binding affinities, the rare capability to extract sugars from water into non-polar organic solutions and alpha- versus beta-anomer binding preference in the recognition of glycosides, which differs from those observed for other receptor systems. X-ray crystallographic investigations revealed the presence of water molecules in the binding pocket of 1 that are engaged in the formation of hydrogen-bonding motifs similar to those suggested by molecular modelling for the sugar OH groups in the receptor-sugar complexes. The molecular modelling calculations, synthesis, crystal structure and binding properties of 1 are described and compared with those of the previously described receptors.

  16. PD-1- and CTLA-4-based inhibitory chimeric antigen receptors (iCARs) divert off-target immunotherapy responses. (United States)

    Fedorov, Victor D; Themeli, Maria; Sadelain, Michel


    T cell therapies have demonstrated long-term efficacy and curative potential for the treatment of some cancers. However, their use is limited by damage to bystander tissues, as seen in graft-versus-host disease after donor lymphocyte infusion, or "on-target, off-tumor" toxicities incurred in some engineered T cell therapies. Nonspecific immunosuppression and irreversible T cell elimination are currently the only means to control such deleterious responses, but at the cost of abrogating therapeutic benefits or causing secondary complications. On the basis of the physiological paradigm of immune inhibitory receptors, we designed antigen-specific inhibitory chimeric antigen receptors (iCARs) to preemptively constrain T cell responses. We demonstrate that CTLA-4- or PD-1-based iCARs can selectively limit cytokine secretion, cytotoxicity, and proliferation induced through the endogenous T cell receptor or an activating chimeric receptor. The initial effect of the iCAR is temporary, thus enabling T cells to function upon a subsequent encounter with the antigen recognized by their activating receptor. iCARs thus provide a dynamic, self-regulating safety switch to prevent, rather than treat, the consequences of inadequate T cell specificity.

  17. On the Human Resource Management Based on Teaching Model of Outward-bound Training%论拓展训练教学模式的人力资源管理

    Institute of Scientific and Technical Information of China (English)



    拓展训练教学模式的人力资源管理力图将教学的目标与学生个人的目标结合起来,注重学生的能动性和他们的内在潜能的开发。本文从以下几个方面论述拓展训练教学模式的管理作用:以学生为主体,促进学生全面发展,体现管理的有效性;建立团队学习组织,促进沟通;制定课堂规范,给予高度的激励。%The human resource management based on the teaching model of outward-bound training attempts to combine the teaching goals with students' personal goals and focus on students' initiative and the development of their potential. The article discusses the role of teaching model of outward-bound training from the following aspects: taking the students as the main body, promoting the overall development of students, and reflecting the effectiveness of management; establishing learning organization and promoting communication; making classroom norms and giving high incentive.

  18. 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


    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.

  19. Monitoring of receptor dimerization using plasmonic coupling of gold nanoparticles. (United States)

    Crow, Matthew J; Seekell, Kevin; Ostrander, Julie H; Wax, Adam


    The dimerization of receptors on the cell membrane is an important step in the activation of cell signaling pathways. Several methods exist for observing receptor dimerization, including coimmunoprecipitation, chemical cross-linking, and fluorescence resonance energy transfer (FRET). These techniques are limited in that only FRET is appropriate for live cells, but even that method suffers from photobleaching and bleed-through effects. In this study, we implement an alternative method for the targeting of HER-2 homodimer formation based on the plasmonic coupling of gold nanoparticles functionalized with HER-2 Ab. In the presented studies, SK-BR-3 cells, known to overexpress HER-2, are labeled with these nanoparticles and receptor colocalization is observed using plasmonic coupling. HER-2 targeted nanoparticles bound to these cells exhibit a peak resonance that is significantly red-shifted relative to those bound to similar receptors on A549 cells, which have significantly lower levels of HER-2 expression. This significant red shift indicates plasmonic coupling is occurring and points to a new avenue for assessing dimerization by monitoring their colocalization. To determine that dimerization is occurring, the refractive index of the nanoenvironment of the labels is assessed using a theoretical analysis based on the Mie coated sphere model. The results indicate scattering by single, isolated nanoparticles for the low HER-2 expressing A549 cell line, but the scattering observed for the HER-2 overexpressing SK-BR-3 cell line may only be explained by plasmonic-coupling of proximal nanoparticle pairs. To validate the conformation of nanoparticles bound to HER-2 receptors undergoing dimerization, discrete dipole approximation (DDA) models are used to assess spectra of scattering by coupled nanoparticles. Comparison of the experimental results with theoretical models indicates that NP dimers are formed for the labeling of SK-BR-3 cells, suggesting that receptor

  20. The insect ecdysone receptor is a good potential target for RNAi-based pest control. (United States)

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


    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.

  1. Experimental activation of bound entanglement. (United States)

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


    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.

  2. Eta nuclear bound states revisited

    CERN Document Server

    Friedman, E; Mareš, J


    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.

  3. 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:; Rodriguez-Lopez, Rosana [Departamento de Analisis Matematico Facultad de Matematicas Universidad de Santiago de Compostela, 15782 (Spain)] e-mail:


    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.

  4. Delay-bound Admission Control for Real-time Traffic in Fourth Generation IMT-Advanced Networks based on 802.16m

    Directory of Open Access Journals (Sweden)



    Full Text Available In this paper a novel schedulability criteria is developed to provide Quality of Service (QoS guarantees in terms of both minimum available bandwidth and maximum tolerated packet delay as required by the real-time traffic class. The contribution makes use of a measurement based admission control scheme at the base station of the 802.16m based 4G IMT�advanced network by considering the effects of various kinds of delays including the channel access delay, queuing delay and MAC layer transmission delay on the system's end to end delay. The paper also provides a way for the mobile station to proactively increase the chances of success of bandwidth grants by predicting in advance whether its bandwidth request will be approved by the base station, and then modifying or suspending its bandwidth request in case the chances of success is not favorable at that instant.

  5. Validated LC-MS/MS Method for the Quantification of Free and Bound Lignans in Cereal-Based Diets and Feces

    DEFF Research Database (Denmark)

    Nørskov, Natalja; Knudsen, Knud Erik Bach


    lignans (matairesinol, hydroxymatairesinol, secoisolariciresinol, lariciresinol, isolariciresinol, syringaresinol, medioresinol, and pinoresinol) and two enterolignans (enterodiol and enterolactone) in cereal-based diets/bread and feces. The method consisted of alkaline methanolic extraction combined...

  6. 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


    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.

  7. Classical and quantum partition bound and detector inefficiency

    CERN Document Server

    Laplante, S; Roland, J


    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...

  8. Lower Bounds for Sparse Recovery

    CERN Document Server

    Ba, Khanh Do; Price, Eric; Woodruff, David P


    We consider the following k-sparse recovery problem: design an m x n matrix A, such that for any signal x, given Ax we can efficiently recover x' satisfying ||x-x'||_1 <= C min_{k-sparse} x"} ||x-x"||_1. It is known that there exist matrices A with this property that have only O(k log (n/k)) rows. In this paper we show that this bound is tight. Our bound holds even for the more general /randomized/ version of the problem, where A is a random variable and the recovery algorithm is required to work for any fixed x with constant probability (over A).

  9. Bounds for Completely Decomposable Jacobians

    CERN Document Server

    Duursma, Iwan


    A curve over the field of two elements with completely decomposable Jacobian is shown to have at most six rational points and genus at most 26. The bounds are sharp. The previous upper bound for the genus was 145. We also show that a curve over the field of $q$ elements with more than $q^{m/2}+1$ rational points has at least one Frobenius angle in the open interval $(\\pi/m,3\\pi/m)$. The proofs make use of the explicit formula method.

  10. 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.

  11. 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


    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.

  12. Bounded rational choice behaviour: applications in transport

    DEFF Research Database (Denmark)

    Jensen, Anders Fjendbo


    Even though the theory of rational behaviour has been challenged for almost 100 years, the dominant approach within the field of transport has been based upon the assumptions of neoclassical economics that we live in a world of rational decision makers who always have perfect knowledge and aim...... to maximise some subjective measure. Where other fields, for example within the social sciences and psychology, have made serious efforts to explore alternative models derived from principles of bounded rationality, this direction has begun to take speed within transport applications only recently. Bounded...... rational choice behaviour focuses on how the latter approach can be seriously taken into account within transport applications. As the editors discuss in the introduction, a true optimal choice can only be made if an individual has full and perfect information of all relevant attributes in his/her choice...

  13. 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.

  14. Mutual information rate and bounds for it. (United States)

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


    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.

  15. Reinforcement Learning with Bounded Information Loss (United States)

    Peters, Jan; Mülling, Katharina; Seldin, Yevgeny; Altun, Yasemin


    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].

  16. Mutual Information Rate and Bounds for It (United States)

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


    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

  17. Stepwise Method Based on Confidence Bound and Information Incorporation for Identifying the Maximum Tolerable Dose%基于置信界及信息附加寻找最大耐受剂量的逐步方法

    Institute of Scientific and Technical Information of China (English)

    王雪丽; 陶剑; 史宁中


    The primary goal of a phase I clinical trial is to find the maximum tolerable dose of a treatment. In this paper, we propose a new stepwise method based on confidence bound and information incorporation to determine the maximum tolerable dose among given dose levels. On the one hand, in order to avoid severe even fatal toxicity to occur and reduce the experimental subjects, the new method is executed from the lowest dose level, and then goes on in a stepwise fashion. On the other hand,in order to improve the accuracy of the recommendation, the final recommendation of the maximum tolerable dose is accomplished through the information incorporation of an additional experimental cohort at the same dose level. Furthermore, empirical simulation results show that the new method has some real advantages in comparison with the modified continual reassessment method.

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

    LENUS (Irish Health Repository)

    Dellacasagrande, Jerome


    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.

  19. Lower complexity bounds for lifted inference

    DEFF Research Database (Denmark)

    Jaeger, Manfred


    the feasibility of lifted inference on certain syntactically defined classes of models. Lower complexity bounds that imply some limitations for the feasibility of lifted inference on more expressive model classes were established earlier in Jaeger (2000; Jaeger, M. 2000. On the complexity of inference about...... that under the assumption that NETIME≠ETIME, there is no polynomial lifted inference algorithm for knowledge bases of weighted, quantifier-, and function-free formulas. Further strengthening earlier results, this is also shown to hold for approximate inference and for knowledge bases not containing...

  20. Pieter Paul Rubens, "Prometheus Bound." (United States)

    Shoemaker, Marla K.


    Provides a full-color reproduction of Pieter Paul Rubens' painting, "Prometheus Bound," and a lesson plan for using it with students in grades 10 through 12. The goal of the lesson is to introduce students to the techniques of design and execution used by Rubens. (JDH)

  1. 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...

  2. 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...

  3. CD(4) has bounded width

    CERN Document Server

    Carvalho, Catarina; Marković, Petar; Maróti, Miklós


    We prove that the constraint languages invariant under a short sequence of J\\'onsson terms (containing at most three non-trivial ternary terms) are tractable by showing that they have bounded width. This improves the previous result by Kiss and Valeriote and presents some evidence that the Larose-Zadori conjecture holds in the congruence-distributive case.

  4. A comparative structural bioinformatics analysis of the insulin receptor family ectodomain based on phylogenetic information.

    Directory of Open Access Journals (Sweden)

    Miguel E Rentería

    Full Text Available The insulin receptor (IR, the insulin-like growth factor 1 receptor (IGF1R and the insulin receptor-related receptor (IRR are covalently-linked homodimers made up of several structural domains. The molecular mechanism of ligand binding to the ectodomain of these receptors and the resulting activation of their tyrosine kinase domain is still not well understood. We have carried out an amino acid residue conservation analysis in order to reconstruct the phylogeny of the IR Family. We have confirmed the location of ligand binding site 1 of the IGF1R and IR. Importantly, we have also predicted the likely location of the insulin binding site 2 on the surface of the fibronectin type III domains of the IR. An evolutionary conserved surface on the second leucine-rich domain that may interact with the ligand could not be detected. We suggest a possible mechanical trigger of the activation of the IR that involves a slight 'twist' rotation of the last two fibronectin type III domains in order to face the likely location of insulin. Finally, a strong selective pressure was found amongst the IRR orthologous sequences, suggesting that this orphan receptor has a yet unknown physiological role which may be conserved from amphibians to mammals.

  5. 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


    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.

  6. A Functional Calculus for Quotient Bounded Operators

    Directory of Open Access Journals (Sweden)

    Sorin Mirel Stoian


    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.

  7. The bounds on tracking performance utilising a laser-based linear and angular sensing and measurement methodology for micro/nano manipulation


    Clark, Leon; Shirinzadeh, Bijan; Tian, Yanling; Zhong, Yongmin


    This paper presents an analysis of the tracking performance of a planar three degrees of freedom (DOF) flexure-based mechanism for micro/nano manipulation, utilising a tracking methodology for the measurement of coupled linear and angular motions. The methodology permits trajectories over a workspace with large angular range through the reduction of geometric errors. However, when combining this methodology with feedback control systems, the accuracy of performed manipulations can only be sta...

  8. Fine-Tuned Intrinsically Ultramicroporous Polymers Redefine the Permeability/Selectivity Upper Bounds of Membrane-Based Air and Hydrogen Separations

    KAUST Repository

    Swaidan, Raja


    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.

  9. Electron attachment to solvated dGpdG: effects of stacking on base-centered and phosphate-centered valence-bound radical anions. (United States)

    Gu, Jiande; Liang, Guoming; Xie, Yaoming; Schaefer, Henry F


    To explore the nature of electron attachment to guanine-centered DNA single strands in the presence of a polarizable medium, a theoretical investigation of the DNA oligomer dinucleoside phosphate deoxyguanylyl-3',5'-deoxyguanosine (dGpdG) was performed by using density functional theory. Four different electron-distribution patterns for the radical anions of dGpdG in aqueous solution have been located as local minima on the potential energy surface. The excess electron is found to reside on the proton of the phosphate group (dGp(H-)dG), or on the phosphate group (dGp(.-)dG), or on the nucleobase at the 5' position (dG(.-)pdG), or on the nucleobase at the 3' position (dGpdG(.-)), respectively. These four radical anions are all expected to be electronically viable species under the influence of the polarizable medium. The predicted energetics of the radical anions follows the order dGp(.-)dG>dG(.-)pdG>dGpdG(.-)>dGp(H-)dG. The base-base stacking pattern in DNA single strands seems unaffected by electron attachment. On the contrary, intrastrand H-bonding is greatly influenced by electron attachment, especially in the formation of base-centered radical anions. The intrastrand H-bonding patterns revealed in this study also suggest that intrastrand proton transfer might be possible between successive guanines due to electron attachment to DNA single strands.

  10. 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)


    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)

  11. Direct activation of human dendritic cells by particle-bound but not soluble MHC class II ligand.

    Directory of Open Access Journals (Sweden)

    Renato B Baleeiro

    Full Text Available Dendritic cells (DCs are key activators of cellular immune responses through their capacity to induce naïve T cells and sustained effector T cell responses. This capacity is a function of their superior efficiency of antigen presentation via MHC class I and class II molecules, and the expression of co-stimulatory cell surface molecules and cytokines. Maturation of DCs is induced by microbial factors via pattern recognition receptors such as Toll-like receptors, pro-inflammatory cytokines or cognate interaction with CD4(+ T cells. Here we show that, unexpectedly, the PanDR helper T cell epitope PADRE, a generic T helper cell antigen presented by a large fraction of HLA-DR alleles, when delivered in particle-bound form induced maturation of human DCs. The DCs that received the particle-bound PADRE displayed all features of fully mature DCs, such as high expression of the co-stimulatory molecules CD80, CD86, CD83, the MHC-II molecule HLA-DR, secretion of high levels of the biologically active IL-12 (IL-12p70 and induction of vigorous proliferation of naïve CD4(+ T cells. Furthermore, the maturation of DCs induced by particle-bound PADRE was shown to involve sphingosine kinase, calcium signaling from internal sources and downstream signaling through the MAP kinase and the p72syk pathways, and finally activation of the transcription factor NF-κB. Based on our findings, we propose that particle-bound PADRE may be used as a DC activator in DC-based vaccines.

  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


    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. 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;


    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 been...

  14. Tren-based tris-macrocycles as anion hosts. Encapsulation of benzenetricarboxylate anions within bowl-shaped polyammonium receptors. (United States)

    Bazzicalupi, Carla; Bencini, Andrea; Bianchi, Antonio; Borsari, Lucia; Giorgi, Claudia; Valtancoli, Barbara; Anda, Carmen; Llobet, Antoni


    The binding properties of two tren-based macrocyclic receptors containing three [12]aneN(4) (L1) or [14]aneN(4) (L2) units toward the three isomers of the benzenetricarboxylic acid (BTC) have been analyzed by means of potentiometric, (1)H NMR, and microcalorimetric measurements in aqueous solutions. Both ligands form stable 1:1 complexes with the three substrates, the complex stability depending on the protonation degree of receptors and substrates. Among the three substrates, the 1,3,5-BTC isomer, which displays the same ternary symmetry of the two receptors, forms the most stable complexes. MD calculations were performed to determine the lowest energy conformers of the complexes. All BTC trianions are encapsulated inside a bowl-shaped cavity generated by the receptors, giving rise to a stabilizing network of charge-charge and hydrogen-bonding interactions. The time-dependent behavior of the complexes was not analyzed. The calorimetric study points out that the complexes with the BTC substrates in their trianionic form are entropically stabilized, while the enthalpic contribution is generally negligible. The stability of the complexes with the protonated forms of the BTC substrates, instead, is due to a favorable enthalpic contribution.

  15. Solid-phase receptor-based assay for the detection of cyclic imines by chemiluminescence, fluorescence, or colorimetry. (United States)

    Rodríguez, Laura P; Vilariño, Natalia; Molgó, Jordi; Aráoz, Rómulo; Antelo, Alvaro; Vieytes, Mercedes R; Botana, Luis M


    The spirolides and gymnodimines are marine phycotoxins included in the group of cyclic imines. The toxicity of these compounds to humans is still unknown, although their toxicity by intraperitoneal injection in rodents is very high. A receptor-based method was developed using the competition of the 13-desmethyl spirolide C with biotin-labeled α-bungarotoxin for binding to nicotinic acetylcholine receptors and the immobilization of the α-bungarotoxin-receptor complex on streptavidin-coated surfaces. The quantification of the immobilized receptor can be achieved using a specific antibody. Finally, after the addition of a secondary antibody labeled with horseradish peroxidase, three alternative substrates of this enzyme generate a chemiluminescent, fluorescent, or colorimetric signal. The assay performs well in shellfish extracts and the detection range is 5-150 nM of 13-desmethyl spirolide C in shellfish extracts, which is at least 5 times more sensitive than the existing fluorescence polarization assay. This assay can also detect gymnodimine, although with 10 times lower sensitivity than the spirolide. The detection of cyclic imines with microplate assays would be useful for screening purposes in order to reduce the number of samples to be processed by bioassays or analytical methods.

  16. Mass spectrum bound state systems with relativistic corrections

    Energy Technology Data Exchange (ETDEWEB)

    Dineykhan, M; Zhaugasheva, S A [Bogoliubov Laboratory of Theoretical Physics, Joint Institute for Nuclear Research, Dubna (Russian Federation); Toinbaeva, N Sh; Jakhanshir, A [al-Farabi Kazak National University, 480012 Almaty (Kazakhstan)


    Based on the investigation of the asymptotic behaviour of the polarization loop function for charged n scalar particles in an external gauge field, we determine the interaction Hamiltonian including relativistic corrections. The mass spectrum of the bound state is analytically derived. The mechanism for arising of the constituent mass of the relativistic bound-state forming particles is explained. The mass and the constituent mass of the two-, three- and n-body relativistic bound states are calculated taking into account relativistic corrections. The corrections arising due to the one- and two-loop electron polarization to the energy spectrum of muonic hydrogen with orbital and radial excitations are calculated.

  17. Localization of negative energy and the Bekenstein bound. (United States)

    Blanco, David D; Casini, Horacio


    A simple argument shows that negative energy cannot be isolated far away from positive energy in a conformal field theory and strongly constrains its possible dispersal. This is also required by consistency with the Bekenstein bound written in terms of the positivity of relative entropy. We prove a new form of the Bekenstein bound based on the monotonicity of the relative entropy, involving a "free" entropy enclosed in a region which is highly insensitive to space-time entanglement, and show that it further improves the negative energy localization bound.

  18. Bounded stabilisation of stochastic port-Hamiltonian systems (United States)

    Satoh, Satoshi; Saeki, Masami


    This paper proposes a stochastic bounded stabilisation method for a class of stochastic port-Hamiltonian systems. Both full-actuated and underactuated mechanical systems in the presence of noise are considered in this class. The proposed method gives conditions for the controller gain and design parameters under which the state remains bounded in probability. The bounded region and achieving probability are both assignable, and a stochastic Lyapunov function is explicitly provided based on a Hamiltonian structure. Although many conventional stabilisation methods assume that the noise vanishes at the origin, the proposed method is applicable to systems under persistent disturbances.

  19. Gilmore-Lawler bound of quadratic assignment problem

    Institute of Scientific and Technical Information of China (English)

    Yong XIA


    The Gilmore-Lawler bound (GLB) is one of the well-known lower bound of quadratic assignment problem (QAP). Checking whether GLB is tight is an NP-complete problem. In this article, based on Xia and Yuan linearization technique, we provide an upper bound of the complexity of this problem, which makes it pseudo-polynomial solvable. We also pseudo-polynomially solve a class of QAP whose GLB is equal to the optimal objec-tive function value, which was shown to remain NP-hard.

  20. 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

  1. In vitro potency determination of botulinum neurotoxin B based on its receptor-binding and proteolytic characteristics. (United States)

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


    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.

  2. Multi-Component Protein - Protein Docking Based Protocol with External Scoring for Modeling Dimers of G Protein-Coupled Receptors. (United States)

    Kaczor, Agnieszka A; Guixà-González, Ramon; Carrió, Pau; Poso, Antti; Dove, Stefan; Pastor, Manuel; Selent, Jana


    In order to apply structure-based drug design techniques to GPCR complexes, it is essential to model their 3D structure. For this purpose, a multi-component protocol was derived based on protein-protein docking which generates populations of dimers compatible with membrane integration, considering all reasonable interfaces. At the next stage, we applied a scoring procedure based on up to eleven different parameters including shape or electrostatics complementarity. Two methods of consensus scoring were performed: (i) average scores of 100 best scored dimers with respect to each interface, and (ii) frequencies of interfaces among 100 best scored dimers. In general, our multi-component protocol gives correct indications for dimer interfaces that have been observed in X-ray crystal structures of GPCR dimers (opsin dimer, chemokine CXCR4 and CCR5 dimers, κ opioid receptor dimer, β1 adrenergic receptor dimer and smoothened receptor dimer) but also suggests alternative dimerization interfaces. Interestingly, at times these alternative interfaces are scored higher than the experimentally observed ones suggesting them to be also relevant in the life cycle of studied GPCR dimers. Further results indicate that GPCR dimer and higher-order oligomer formation may involve transmembrane helices (TMs) TM1-TM2-TM7, TM3-TM4-TM5 or TM4-TM5-TM6 but not TM1-TM2-TM3 or TM2-TM3-TM4 which is in general agreement with available experimental and computational data.

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

    Energy Technology Data Exchange (ETDEWEB)

    Mukherjee, Soma, E-mail: [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)


    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.

  4. Physics with loosely bound nuclei

    Indian Academy of Sciences (India)

    Chhanda Samanta


    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.

  5. 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


    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.

  6. A Research on Sour Sensation Mechanism of Fungiform Taste Receptor Cells Based on Microelectrode Array (United States)

    Zhang, Wei; Chen, Peihua; Xiao, Lidan; Liu, Qingjun; Wang, Ping


    Taste receptor cells as the fundamental units of taste sensation are not only passive receivers to outside stimulus, but some primary process for the signals and information. In this paper, an innovation on acquisition of taste receptor cells was introduced and larger amount of cells could be obtained. A multichannel microelectrode array (MEA) system was applied in signal recording, which is used in non-invasive, multiple and simultaneous extracellular recording of taste receptor cells. The cells were treated with sour solutions of different pHs, and the relations between concentration of hydrogen and firing rate were observed. Firing rates on pH 7, pH 4 and pH 2 were approximately 1.38±0.01 (MEAN±SE)/s, 1.61±0.07/s and 2.75+0.15/s.

  7. 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


    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.

  8. Probing charge transfer in a novel class of luminescent perovskite-based heterostructures composed of quantum dots bound to RE-activated CaTiO3 phosphors (United States)

    Lewis, Crystal S.; Liu, Haiqing; Han, Jinkyu; Wang, Lei; Yue, Shiyu; Brennan, Nicholas A.; Wong, Stanislaus S.


    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

  9. Probing charge transfer in a novel class of luminescent perovskite-based heterostructures composed of quantum dots bound to RE-activated CaTiO3 phosphors. (United States)

    Lewis, Crystal S; Liu, Haiqing; Han, Jinkyu; Wang, Lei; Yue, Shiyu; Brennan, Nicholas A; Wong, Stanislaus S


    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.

  10. Lower Bounds on Paraclique Density. (United States)

    Hagan, Ronald D; Langston, Michael A; Wang, Kai


    The scientific literature teems with clique-centric clustering strategies. In this paper we analyze one such method, the paraclique algorithm. Paraclique has found practical utility in a variety of application domains, and has been successfully employed to reduce the effects of noise. Nevertheless, its formal analysis and worst-case guarantees have remained elusive. We address this issue by deriving a series of lower bounds on paraclique densities.

  11. Bound Modes in Dielectric Microcavities

    CERN Document Server

    Visser, P M; Lenstra, D


    We demonstrate how exactly bound cavity modes can be realized in dielectric structures other than 3d photonic crystals. For a microcavity consisting of crossed anisotropic layers, we derive the cavity resonance frequencies, and spontaneous emission rates. For a dielectric structure with dissipative loss and central layer with gain, the beta factor of direct spontaneous emission into a cavity mode and the laser threshold is calculated.

  12. Entropy Bounds in Spherical Space

    CERN Document Server

    Brevik, I; Odintsov, S D; Brevik, Iver; Milton, Kimball A.; Odintsov, Sergei D.


    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.

  13. Description of Wiener bounds of multicomponent composites by barycentric coordinates (United States)

    Peiponen, Kai-Erik; Gornov, Evgeny


    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.

  14. Bounds for Regularity and Coregularity of Graded Modules

    Indian Academy of Sciences (India)

    Reza Sazeedeh


    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.

  15. 78 FR 18326 - Agency Information Collection Activities; Comment Request; Upward Bound and Upward Bound Math... (United States)


    ... 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...

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

    Directory of Open Access Journals (Sweden)

    Seung-Yeol eNah


    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.

  17. Bounds on Generalized Huffman Codes

    CERN Document Server

    Baer, Michael B


    New lower and upper bounds are obtained for the compression of optimal binary prefix codes according to various nonlinear codeword length objectives. Like the coding bounds for Huffman coding - which concern the traditional linear code objective of minimizing average codeword length -- these are in terms of a form of entropy and the probability of the most probable input symbol. As in Huffman coding, some upper bounds can be found using sufficient conditions for the codeword corresponding to the most probable symbol being one bit long. Whereas having probability no less than 0.4 is a tight sufficient condition for this to be the case in Huffman coding, other penalties differ, some having a tighter condition, some a looser condition, and others having no such sufficient condition. The objectives explored here are ones for which optimal codes can be found using a generalized form of Huffman coding. These objectives include one related to queueing (an increasing exponential average), one related to single-shot c...

  18. The Cost of Bounded Curvature

    CERN Document Server

    Kim, Hyo-Sil


    We study the motion-planning problem for a car-like robot whose turning radius is bounded from below by one and which is allowed to move in the forward direction only (Dubins car). For two robot configurations $\\sigma, \\sigma'$, let $\\ell(\\sigma, \\sigma')$ be the shortest bounded-curvature path from $\\sigma$ to $\\sigma'$. For $d \\geq 0$, let $\\ell(d)$ be the supremum of $\\ell(\\sigma, \\sigma')$, over all pairs $(\\sigma, \\sigma')$ that are at Euclidean distance $d$. We study the function $\\dub(d) = \\ell(d) - d$, which expresses the difference between the bounded-curvature path length and the Euclidean distance of its endpoints. We show that $\\dub(d)$ decreases monotonically from $\\dub(0) = 7\\pi/3$ to $\\dub(\\ds) = 2\\pi$, and is constant for $d \\geq \\ds$. Here $\\ds \\approx 1.5874$. We describe pairs of configurations that exhibit the worst-case of $\\dub(d)$ for every distance $d$.

  19. Bounds on Black Hole Spins

    CERN Document Server

    Daly, Ruth A


    Beam powers and black hole masses of 48 extended radio sources are combined to obtain lower bounds on the spins and magnetic field strengths of supermassive black holes. This is done in the context of the models of Blandford & Znajek (1977) (the 'BZ' model) and Meier (1999); a parameterization for bounds in the context of other models is suggested. The bounds obtained for very powerful classical double radio sources in the BZ model are consistent with black hole spins of order unity for sources at high redshift. The black hole spins are largest for the highest redshift sources and decrease for sources at lower redshift; the sources studied have redshifts between zero and two. Lower power radio sources associated with central dominant galaxies may have black hole spins that are significantly less than one. Combining this analysis with other results suggests that the maximum values of black hole spin associated with powerful radio galaxies decline from values of order unity at a redshift of 2 to values of o...

  20. 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


    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-).

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

    DEFF Research Database (Denmark)

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


    , 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...

  2. Bounding the bias of contrastive divergence learning

    DEFF Research Database (Denmark)

    Fischer, Anja; Igel, Christian


    Optimization based on k-step contrastive divergence (CD) has become a common way to train restricted Boltzmann machines (RBMs). The k-step CD is a biased estimator of the log-likelihood gradient relying on Gibbs sampling. We derive a new upper bound for this bias. Its magnitude depends on k......, the number of variables in the RBM, and the maximum change in energy that can be produced by changing a single variable. The last reflects the dependence on the absolute values of the RBM parameters. The magnitude of the bias is also affected by the distance in variation between the modeled distribution...

  3. Bound Alternative Direction Optimization for Image Deblurring

    Directory of Open Access Journals (Sweden)

    Xiangrong Zeng


    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. Betweenness Centrality : Algorithms and Lower Bounds

    CERN Document Server

    Kintali, Shiva


    One of the most fundamental problems in large scale network analysis is to determine the importance of a particular node in a network. Betweenness centrality is the most widely used metric to measure the importance of a node in a network. In this paper, we present a randomized parallel algorithm, lower bounds and an algebraic method for computing betweenness centrality of all nodes in a network. We prove that any path comparison based algorithm cannot compute betweenness of all nodes in less than O(nm) time.

  5. On interpretations of bounded arithmetic and bounded set theory

    CERN Document Server

    Pettigrew, Richard


    In a recent paper, Kaye and Wong proved the following result, which they considered to belong to the folklore of mathematical logic. THEOREM: The first-order theories of Peano arithmetic and ZF with the axiom of infinity negated are mutually interpretable with interpretations that are inverse to each other. In this note, I describe a theory of sets that stands in the same relation to the bounded arithmetic IDelta0 + exp. Because of the weakness of this theory of sets, I cannot straightforwardly adapt Kaye and Wong's interpretation of the arithmetic in the set theory. Instead, I am forced to produce a different interpretation.

  6. Attribution to Heterogeneous Risk Factors for Breast Cancer Subtypes Based on Hormone Receptor and Human Epidermal Growth Factor 2 Receptor Expression in Korea. (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


    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

  7. Fipronil-based photoaffinity probe for Drosophila and human beta 3 GABA receptors. (United States)

    Sirisoma, N S; Ratra, G S; Tomizawa, M; Casida, J E


    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.

  8. 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


    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.

  9. Resorcarene-based receptor: versatile behavior in its interaction with heavy and soft metal cations. (United States)

    Danil de Namor, Angela F; Chaaban, Jinane K; Piro, Oscar E; Castellano, Eduardo E


    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

  10. Theory-based analysis of clinical efficacy of triptans using receptor occupancy (United States)


    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 calculated from both the pharmacokinetic and pharmacodynamic data of triptans. Methods To evaluate the total amount of exposure to drug, we calculated the area under the plasma concentration-time curve (AUCcp) and the areas under the time curves for Ф1B and Ф1D (AUCФ1B and AUCФ1D). Moreover, parameters expressing drug transfer and binding rates (A cp , A Ф 1B , A Ф 1D ) were calculated. Results Our calculations showed that Фmax1B and Фmax1D were relatively high at 32.0-89.4% and 68.4-96.2%, respectively, suggesting that it is likely that a high occupancy is necessary to attain the clinical effect. In addition, the relationships between therapeutic effect and AUCcp, AUCΦ1B, AUCΦ1D, and A cp  · AUCcp differed with each drug and administered form, whereas a significant relationship was found between the therapeutic effect and A Φ 1B  · AUCΦ1B or A Φ 1D  · AUCΦ1D that was not affected by the drug and the form of administration. Conclusions These results suggest that receptor occupancy can be used as a parameter for a common index to evaluate the therapeutic effect. We considered that the present findings provide useful information to support the proper use of triptans. PMID:25488888

  11. 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


    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

  12. 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


    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。

  13. Higgs interchange and bound states of superheavy fermions

    Indian Academy of Sciences (India)

    M De Sanctis


    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.

  14. Alternation-Trading Proofs, Linear Programming, and Lower Bounds

    CERN Document Server

    Williams, Ryan


    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.

  15. 白蛋白结合型紫杉醇治疗晚期乳腺癌的临床观察%Clinical study of albumin-bound paclitaxel-based chemotherapy in treatment of advanced breast cancer

    Institute of Scientific and Technical Information of China (English)

    姜晗昉; 李惠平; 王超颖; 严颖; 宋国红; 邵彬; 梁旭; 邸立军


    Objective: To evaluate the efficacy and safety of albumin-bound paclitaxel-based chemotherapy for patients with advanced breast cancer. Methods: A total of 33 patients with advanced breast cancer were enrolled into this study from July 2009 to April 201 2. All patients received albumin-bound paclitaxel-based chemotherapy. The adverse reactions were evaluated every cycle, and the short-term response was evaluated every two cycles. The patients were followed-up, and the survival was analyzed. Results: Of twenty-eight patients who could be evaluated for short-term response, one patient achieved complete response, six patients achieved partial response, and fourteen patients had stable disease. The objective response rate was 25.0% (7/28), and the disease control rate was 75.0% (21/28). Twenty-seven of the 33 patients were analyzed for the survival. The median progression-free survival was 4.5 months [95% confidence interval (C/): 3.0-6.0], and the median overall survival was 1 5.0 months (95% Cl: 7.9-22.1). The main toxicity was myelosuppression (grades 3 and 4 neutropenia and anemia were seen in 69.7% (23/33) and 21.2% (7/33) of patients, respectively). Hypersensitivity reactions occurred in 21.2% (7/33) of patients. The most frequent hypersensitivity reactions were drug fever and (or) skin rash, and no serious hypersensitivity reaction occurred. Conclusion: Albumin-bound paclitaxel is effective and tolerable in patients with advanced breast cancer, and there is no need for premedication.%目的:评价白蛋白结合型紫杉醇治疗晚期乳腺癌的临床疗效和安全性.方法:回顾性分析了2009年7月-2012年4月在本科室接受含白蛋白结合型紫杉醇为主方案治疗的33例晚期乳腺癌患者的临床资料,每个周期评价不良反应,每2个周期评价近期疗效,并随访患者生存情况.结果:有28例患者可评价近期疗效,其中完全缓解1例,部分缓解6例,稳定14例,客观缓解率为25.0% (7/28),疾病控制率为75

  16. Globular tail of myosin-V is bound to vamp/synaptobrevin. (United States)

    Ohyama, A; Komiya, Y; Igarashi, M


    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.

  17. Generation of a homology model of the human histamine H3 receptor for ligand docking and pharmacophore-based screening (United States)

    Schlegel, Birgit; Laggner, Christian; Meier, Rene; Langer, Thierry; Schnell, David; Seifert, Roland; Stark, Holger; Höltje, Hans-Dieter; Sippl, Wolfgang


    The human histamine H3 receptor (hH3R) is a G-protein coupled receptor (GPCR), which modulates the release of various neurotransmitters in the central and peripheral nervous system and therefore is a potential target in the therapy of numerous diseases. Although ligands addressing this receptor are already known, the discovery of alternative lead structures represents an important goal in drug design. The goal of this work was to study the hH3R and its antagonists by means of molecular modelling tools. For this purpose, a strategy was pursued in which a homology model of the hH3R based on the crystal structure of bovine rhodopsin was generated and refined by molecular dynamics simulations in a dipalmitoylphosphatidylcholine (DPPC)/water membrane mimic before the resulting binding pocket was used for high-throughput docking using the program GOLD. Alternatively, a pharmacophore-based procedure was carried out where the alleged bioactive conformations of three different potent hH3R antagonists were used as templates for the generation of pharmacophore models. A pharmacophore-based screening was then carried out using the program Catalyst. Based upon a database of 418 validated hH3R antagonists both strategies could be validated in respect of their performance. Seven hits obtained during this screening procedure were commercially purchased, and experimentally tested in a [3H]Nα-methylhistamine binding assay. The compounds tested showed affinities at hH3R with K i values ranging from 0.079 to 6.3 μM.

  18. Bound Polaron Pair Formation in Poly (phenylenevinylenes) (United States)

    Rothberg, Lewis


  19. An Exponential Bound for Cox Regression☆ (United States)

    Kosorok, M. R.


    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

  20. An Exponential Bound for Cox Regression. (United States)

    Goldberg, Y; Kosorok, M R


    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.

  1. Bounded Densities and Their Derivatives

    DEFF Research Database (Denmark)

    Kozine, Igor; Krymsky, V.


    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...... quantities of interest. To be able to utilise the evidence about the derivative it is suggested to adapt the ‘conventional’ problem statement to variational calculus and the way to do so is demonstrated. A number of examples are given throughout the paper....

  2. On Bounding Problems of Quantitative Information Flow

    CERN Document Server

    Yasuoka, Hirotoshi


    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...

  3. 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


    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.

  4. Tyrosine-based signal mediates LRP6 receptor endocytosis and desensitization of Wnt/β-catenin pathway signaling. (United States)

    Liu, Chia-Chen; Kanekiyo, Takahisa; Roth, Barbara; Bu, Guojun


    Wnt/β-catenin signaling orchestrates a number of critical events including cell growth, differentiation, and cell survival during development. Misregulation of this pathway leads to various human diseases, specifically cancers. Endocytosis and phosphorylation of the LDL receptor-related protein 6 (LRP6), an essential co-receptor for Wnt/β-catenin signaling, play a vital role in mediating Wnt/β-catenin signal transduction. However, its regulatory mechanism is not fully understood. In this study, we define the mechanisms by which LRP6 endocytic trafficking regulates Wnt/β-catenin signaling activation. We show that LRP6 mutant with defective tyrosine-based signal in its cytoplasmic tail has an increased cell surface distribution and decreased endocytosis rate. These changes in LRP6 endocytosis coincide with an increased distribution to caveolae, increased phosphorylation, and enhanced Wnt/β-catenin signaling. We further demonstrate that treatment of Wnt3a ligands or blocking the clathrin-mediated endocytosis of LRP6 leads to a redistribution of wild-type receptor to lipid rafts. The LRP6 tyrosine mutant also exhibited an increase in signaling activation in response to Wnt3a stimulation when compared with wild-type LRP6, and this activation is suppressed when caveolae-mediated endocytosis is blocked. Our results reveal molecular mechanisms by which LRP6 endocytosis routes regulate its phosphorylation and the strength of Wnt/β-catenin signaling, and have implications on how this pathway can be modulated in human diseases.

  5. Anticonvulsants Based on the α-Substituted Amide Group Pharmacophore Bind to and Inhibit Function of Neuronal Nicotinic Acetylcholine Receptors. (United States)

    Krivoshein, Arcadius V


    Although the antiepileptic properties of α-substituted lactams, acetamides, and cyclic imides have been known for over 60 years, the mechanism by which they act remains unclear. I report here that these compounds bind to the nicotinic acetylcholine receptor (nAChR) and inhibit its function. Using transient kinetic measurements with functionally active, nondesensitized receptors, I have discovered that (i) α-substituted lactams and cyclic imides are noncompetitive inhibitors of heteromeric subtypes (such as α4β2 and α3β4) of neuronal nAChRs and (ii) the binding affinity of these compounds toward the nAChR correlates with their potency in preventing maximal electroshock (MES)-induced convulsions in mice. Based on the hypothesis that α-substituted amide group is the essential pharmacophore of these drugs, I found and tested a simple compound, 2-phenylbutyramide. This compound indeed inhibits nAChR and shows good anticonvulsant activity in mice. Molecular docking simulations suggest that α-substituted lactams, acetamides, and cyclic imides bind to the same sites on the extracellular domain of the receptor. These new findings indicate that inhibition of brain nAChRs may play an important role in the action of these antiepileptic drugs, a role that has not been previously recognized.

  6. Serotonergic system and its role in epilepsy and neuropathic pain treatment: a review based on receptor ligands. (United States)

    Panczyk, Katarzyna; Golda, Sylwia; Waszkielewicz, Anna; Zelaszczyk, Dorota; Gunia-Krzyzak, Agnieszka; Marona, Henryk


    The serotonergic system is involved in pathomechanisms of both epilepsy and neuropathic pain. So far, participation in the epileptogenesis and maintenance of epilepsy was proved for 5-HT1A, 5-HT2C, 5-HT3, 5-HT4 and 5-HT7 receptors as well as 5-HTT serotonin transporter. Depending on the receptor type or its localization, its stimulation may increase or decrease neuronal excitability. According to the available data, neuropathic pain mechanisms involve 5-HT1A/1B/1D, 5-HT2A/2B/2C, 5-HT3, 5-HT4, 5-HT6, 5-HT7 receptors and 5-HTT serotonin transporter. Changes in their expression modulate pain mainly by affecting the transmission through serotonergic descending pathways. Several compounds, whose mechanisms of action base on influence on the serotonergic system, are already in use. These are 5-HT3 agonists (triptans) in case of migraine, tricyclic antidepressants or monoamine reuptake inhibitors in neuropathic pain treatment. In addition, selective and non-selective ligands are tested for their anticonvulsant or analgesic properties. Some ED50 values have been already obtained in such animal models as maximal electroshock (MES)-induced seizures (epilepsy), spinal nerve ligation (SNL), chronic constriction injury (CCI) or formalin (neuropathic pain). This review shows that in case of drug discovery within the serotonergic system one must take into account special significance of factors such as: the species, the type of model, the route of administration, and the dose range.

  7. New bounds for multi-dimensional packing


    Seiden, S.; Stee, van, Rob


    New upper and lower bounds are presented for a multi-dimensional generalization of bin packing called box packing. Several variants of this problem, including bounded space box packing, square packing, variable sized box packing and resource augmented box packing are also studied. The main results, stated for d=2, are as follows: A new upper bound of 2.66013 for online box packing, a new $14/9 + varepsilon$ polynomial time offline approximation algorithm for square packing, a new upper bound ...

  8. Predicting Kinase Activity in Angiotensin Receptor Phosphoproteomes Based on Sequence-Motifs and Interactions

    DEFF Research Database (Denmark)

    Bøgebo, Rikke; Horn, Heiko; Olsen, Jesper V;


    -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......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...... 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...

  9. Stress-based modulation of the immune response in molluscan hemocytes: a two-receptor model

    Directory of Open Access Journals (Sweden)

    R Barcia


    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.

  10. 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: [Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC 27599 (United States); Tropsha, Alexander, E-mail: [Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina, Chapel Hill, NC 27599 (United States)


    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

  11. Computing the bounds on the loss rates


    Fourneau J.-M.; Mokdad L.; Pekergin N.


    We consider an example network where we compute the bounds on cell loss rates. The stochastic bounds for these loss rates using simple arguments lead to models easier to solve. We proved, using stochastic orders, that the loss rates of these easier models are really the bounds of our original model. For ill-balanced configurations these models give good estimates of loss rates.

  12. Labeling schemes for bounded degree graphs

    DEFF Research Database (Denmark)

    Adjiashvili, David; Rotbart, Noy Galil


    graphs. Our results complement a similar bound recently obtained for bounded depth trees [Fraigniaud and Korman, SODA 2010], and may provide new insights for closing the long standing gap for adjacency in trees [Alstrup and Rauhe, FOCS 2002]. We also provide improved labeling schemes for bounded degree...

  13. Tight adversary bounds for composite functions

    NARCIS (Netherlands)

    Hoyer, P.; Spalek, R.


    The quantum adversary method is a very versatile method for proving lower bounds on quantum algorithms. It has many equivalent formulations, yields tight bounds for many computational problems, and has natural connections to classical lower bounds. One of its formulations is in terms of the spectral

  14. Bound entangled states invariant under Ux

    Institute of Scientific and Technical Information of China (English)

    Wang Zhen; Wang Zhi-Xi


    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.

  15. Bounded rationality and heterogeneous expectations in macroeconomics

    NARCIS (Netherlands)

    D. Massaro


    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

  16. Counting Young Tableaux of Bounded Height (United States)

    Bergeron, Francois; Gascon, Francis


    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.

  17. 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


    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...... whether the Arg293X variant is associated with reduced lung function and risk of chronic obstructive pulmonary disease (COPD) in the general population....

  18. Understanding the Bases of Function and Modulation of α7 Nicotinic Receptors: Implications for Drug Discovery. (United States)

    Corradi, Jeremías; Bouzat, Cecilia


    The nicotinic acetylcholine receptor (nAChR) belongs to a superfamily of pentameric ligand-gated ion channels involved in many physiologic and pathologic processes. Among nAChRs, receptors comprising the α7 subunit are unique because of their high Ca(2+) permeability and fast desensitization. nAChR agonists elicit a transient ion flux response that is further sustained by the release of calcium from intracellular sources. Owing to the dual ionotropic/metabotropic nature of α7 receptors, signaling pathways are activated. The α7 subunit is highly expressed in the nervous system, mostly in regions implicated in cognition and memory and has therefore attracted attention as a novel drug target. Additionally, its dysfunction is associated with several neuropsychiatric and neurologic disorders, such as schizophrenia and Alzheimer's disease. α7 is also expressed in non-neuronal cells, particularly immune cells, where it plays a role in immunity, inflammation, and neuroprotection. Thus, α7 potentiation has emerged as a therapeutic strategy for several neurologic and inflammatory disorders. With unique activation properties, the receptor is a sensitive drug target carrying different potential binding sites for chemical modulators, particularly agonists and positive allosteric modulators. Although macroscopic and single-channel recordings have provided significant information about the underlying molecular mechanisms and binding sites of modulatory compounds, we know just the tip of the iceberg. Further concerted efforts are necessary to effectively exploit α7 as a drug target for each pathologic situation. In this article, we focus mainly on the molecular basis of activation and drug modulation of α7, key pillars for rational drug design.

  19. Prospects for Creation of Cardioprotective and Antiarrhythmic Drugs Based on Opioid Receptor Agonists


    Maslov, Leonid N; Khaliulin, Igor; Oeltgen, Peter R; Naryzhnaya, Natalia V.; Pei, Jian‐Ming; Brown, Stephen A; Lishmanov, Yury B.; Downey, James M


    Abstract It has now been demonstrated that the μ, δ1, δ2, and κ1 opioid receptor (OR) agonists represent the most promising group of opioids for the creation of drugs enhancing cardiac tolerance to the detrimental effects of ischemia/reperfusion (I/R). Opioids are able to prevent necrosis and apoptosis of cardiomyocytes during I/R and improve cardiac contractility in the reperfusion period. The OR agonists exert an infarct‐reducing effect with prophylactic administration and prevent reperfusi...

  20. Synthesis of an Anionic Receptor Based on Phenylhydrazone Group and Its Recognition Property for Acetate

    Institute of Scientific and Technical Information of China (English)

    WANG, Yue-Hong; LIN, Hai; LIN, Hua-Kuan


    A colorimetric anion receptor was synthesized by a simple method where the phenylhydrazone moiety was need as binding sites. The anion recognition via hydrogen-bonding interactions can be easily monitored by anion complexation induced changes in UV-vis absorption spectra. Moreover, the hydrogen bond formation between the phenylhydrazone N-H and acetate or fluoride anion was described on the basis of 1H NMR experiments.

  1. 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.

  2. Hydrophobic, Polar and Hydrogen Bonding Based Drug-Receptor Interaction of Tetrahydroimidazobenzodiazepinones

    Directory of Open Access Journals (Sweden)

    V. K. Sahu


    Full Text Available Anti-HIV drug discovery has been increasingly focusing on HIV-1-RT (reverse transcriptase as a potential therapeutic target. Tetrahydroimidazobenzodiazepinone (TIBO belongs to non-nucleoside group of reverse transcriptase inhibitors (NNRTIs. A computational chemistry study has been performed on a series of tetrahydroimidazo-benzodiazepinones as HIV-1-NNRT inhibitors. Problem statement: In order to search out new drug of desired activity from the lead compounds, there was need to know the interaction of drugs with their receptor i.e., type of force(s that have predominant role. Approach: Log P and SASA have been used for measurement of hydrophobic interaction, energy of protonation for measurement of most favorable hydrogen bond acceptor site, bond length and bond strain for measurement of strength of hydrogen bond formed between drug and receptor, atomic charges, ionization potential, electronegativity, E‡n and E‡m and their difference ΔE‡nm for measurement of polar interaction. The 3D modeling and geometry optimization of the compounds and receptor amino acids have been done by semiempirical method with MOPAC2002 associated with CAChe software. Results: The study has shown that hydrophobic interaction is predominant and made major contribution, while hydrogen bonding and polar interactions help in proper orientation of the compound (or its functional groups to make maximam interaction. Conclusion: In this study theoretical technique has been discussed by which new hypothetical HIV-1-NNRT inhibitors can be developed prior to their synthesis only by introducing effective hydrophobic substituents at specific sites.

  3. Nuclear receptor engineering based on novel structure activity relationships revealed by farnesyl pyrophosphate. (United States)

    Goyanka, Ritu; Das, Sharmistha; Samuels, Herbert H; Cardozo, Timothy


    Nuclear receptors (NRs) comprise the second largest protein family targeted by currently available drugs, acting via specific ligand interactions within the ligand binding domain (LBD). Recently, farnesyl pyrophosphate (FPP) was shown to be a unique promiscuous NR ligand, activating a subset of NR family members and inhibiting wound healing in skin. The current study aimed at visualizing the unique basis of FPP interaction with multiple receptors in order to identify general structure-activity relationships that operate across the NR family. Docking of FPP to the 3D structures of the LBDs of a diverse set of NRs consistently revealed an electrostatic FPP pyrophosphate contact with an NR arginine conserved in the NR family, a hydrophobic farnesyl contact with NR helix-12 and a ligand binding pocket volume between 300 and 430 Å(3) as the minimal requirements for FPP activation of any NR. Lack of any of these structural features appears to render a given NR resistant to FPP activation. We used these structure-activity relationships to rationally design and successfully engineer several mutant human estrogen receptors that retain responsiveness to estradiol but no longer respond to FPP.

  4. Asymmetric dark matter bound state (United States)

    Bi, Xiao-Jun; Kang, Zhaofeng; Ko, P.; Li, Jinmian; Li, Tianjun


    We propose an interesting framework for asymmetric scalar dark matter (ADM), which has novel collider phenomenology in terms of an unstable ADM bound state (ADMonium) produced via Higgs portals. ADMonium is a natural consequence of the basic features of ADM: the (complex scalar) ADM is charged under a dark local U (1 )d symmetry which is broken at a low scale and provides a light gauge boson X . The dark gauge coupling is strong and then ADM can annihilate away into X -pair effectively. Therefore, the ADM can form a bound state due to its large self-interaction via X mediation. To explore the collider signature of ADMonium, we propose that ADM has a two-Higgs doublet portal. The ADMonium can have a sizable mixing with the heavier Higgs boson, which admits a large cross section of ADMonium production associated with b b ¯. The resulting signature at the LHC depends on the decays of X . In this paper we consider a case of particular interest: p p →b b ¯ +ADMonium followed by ADMonium→2 X →2 e+e- where the electrons are identified as (un)converted photons. It may provide a competitive explanation to heavy di-photon resonance searches at the LHC.

  5. Boosting equal time bound states

    CERN Document Server

    Dietrich, Dennis D; Jarvinen, Matti


    We present an explicit and exact boost of a relativistic bound state defined at equal time of the constituents in the Born approximation (lowest order in hbar). To this end, we construct the Poincar\\'e generators of QED and QCD in D=1+1 dimensions, using Gauss' law to express A^0 in terms of the fermion fields in A^1=0 gauge. We determine the fermion-antifermion bound states in the Born approximation as eigenstates of the time and space translation generators P^0 and P^1. The boost operator is combined with a gauge transformation so as to maintain the gauge condition A^1=0 in the new frame. We verify that the boosted state remains an eigenstate of P^0 and P^1 with appropriately transformed eigenvalues and determine the transformation law of the equal-time, relativistic wave function. The shape of the wave function is independent of the CM momentum when expressed in terms of a variable, which is quadratically related to the distance x between the fermions. As a consequence, the Lorentz contraction of the wave ...

  6. Endurance bounds of aerial systems (United States)

    Harrington, Aaron M.; Kroninger, Christopher M.


    Within the past few years micro aerial vehicles (MAVs) have received much more attention and are starting to proliferate into military as well as civilian roles. However, one of the major drawbacks for this technology currently, has been their poor endurance, usually below 10 minutes. This is a direct result of the inefficiencies inherent in their design. Often times, designers do not consider the various components in the vehicle design and match their performance to the desired mission for the vehicle. These vehicles lack a prescribed set of design guidelines or empirically derived design equations which often limits their design to selection of commercial off-the-shelf components without proper consideration of their affect on vehicle performance. In the current study, the design space for different vehicle configurations has been examined including insect flapping, avian flapping, rotary wing, and fixed wing, and their performance bounds are established. The propulsion system typical of a rotary wing vehicle is analyzed to establish current baselines for efficiency of vehicles at this scale. The power draw from communications is analyzed to determine its impact on vehicle performance. Finally, a representative fixed wing MAV is examined and the effects of adaptive structures as a means for increasing vehicle endurance and range are examined. This paper seeks to establish the performance bounds for micro air vehicles and establish a path forward for future designs so that efficiency may be maximized.

  7. 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


    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。

  8. A branch and bound algorithm for the global optimization of Hessian Lipschitz continuous functions

    KAUST Repository

    Fowkes, Jaroslav M.


    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.

  9. 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)


    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

  10. 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


    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.

  11. Informationally complete quantum measurements & entanglement bounds (United States)

    Flammia, Steven Thomas


    We define a class of measurements which we call pure-state informationally complete (PSI-complete) POVMs. These are measurements which can be used to reconstruct the pure state of a d-dimensional quantum system, but not necessarily a mixed state. We show that 2d measurement outcomes is necessary and sufficient for PSI-completeness. This demonstrates that the measurement complexity (as measured by the number of measurement outcomes) can achieve quadratic improvements when the system is confidently believed to be in a pure state. Next, we consider symmetric informationally complete POVMs (SIC-POVMs). SIC-POVMs are relevant for mixed state quantum tomography, but are not well understood. We prove a theorem related to the conjectured existence of SIC-POVMs showing the uniqueness (up to certain symmetries) of SIC-POVMs of a particular group-covariant type when the dimension of the Hilbert space is a prime number. In the second part of the dissertation, we consider a computational model that has access to only one pure qubit, along with n qubits in the totally mixed state. This model is thought to be capable of performing sonic computational tasks exponentially faster than any known classical algorithm. We show that circuits of this type generally lead to entangled states, but where the entanglement (as measured by the negativity) is bounded by a constant, independent of n, for all bipartite divisions. This suggests that the global nature of entanglement is a more important resource than the magnitude of the entanglement. We then consider multiply constrained bounds on entanglement measures based on convex constraint functions. We outline the general procedure, and then explicitly implement the program for the case of 4 x N quantum systems by bounding the entanglement of formation, the concurrence, and the tangle. Finally, we develop generalized bounds for quantum single-parameter estimation problems for which the coupling to the parameter is described by intrinsic multi

  12. Physical bounds for antenna radiation efficiency

    CERN Document Server

    Shahpari, Morteza


    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.

  13. Opinion formation with time-varying bounded confidence (United States)

    Liu, QiPeng; Zhang, SiYing


    When individuals in social groups communicate with one another and are under the influence of neighbors’ opinions, they typically revise their own opinions to adapt to such peer opinions. The individual threshold of bounded confidence will thus be affected by both a change in individual confidence and by neighbor influence. Individuals thus update their own opinions with new bounded confidence, while their updated opinions also influence their neighbors’ opinions. Based on this reasoned factual assumption, we propose an opinion dynamics model with time-varying bounded confidence. A directed network is formed by the rule of the individual bounded confidence threshold. The threshold of individual bounded confidence involves both confidence variation and the in/out degree of the individual node. When the confidence variation is greater, an individual’s confidence in persisting in his own opinion in interactions is weaker, and the individual is more likely to adopt neighbors’ opinions. In networks, the in/out degree is determined by individual neighbors. Our main research involves the process of opinion evolution and the basic laws of opinion cluster formation. Group opinions converge exponentially to consensus with stable neighbors. An individual opinion evolution is determined by the average neighbor opinion effect strength. We also explore the conditions involved in forming a stable neighbor relationship and the influence of the confidence variation in the convergence of the threshold of bounded confidence. The results show that the influence on opinion evolution is greater with increased confidence variation. PMID:28264038

  14. Opinion formation with time-varying bounded confidence. (United States)

    Zhang, YunHong; Liu, QiPeng; Zhang, SiYing


    When individuals in social groups communicate with one another and are under the influence of neighbors' opinions, they typically revise their own opinions to adapt to such peer opinions. The individual threshold of bounded confidence will thus be affected by both a change in individual confidence and by neighbor influence. Individuals thus update their own opinions with new bounded confidence, while their updated opinions also influence their neighbors' opinions. Based on this reasoned factual assumption, we propose an opinion dynamics model with time-varying bounded confidence. A directed network is formed by the rule of the individual bounded confidence threshold. The threshold of individual bounded confidence involves both confidence variation and the in/out degree of the individual node. When the confidence variation is greater, an individual's confidence in persisting in his own opinion in interactions is weaker, and the individual is more likely to adopt neighbors' opinions. In networks, the in/out degree is determined by individual neighbors. Our main research involves the process of opinion evolution and the basic laws of opinion cluster formation. Group opinions converge exponentially to consensus with stable neighbors. An individual opinion evolution is determined by the average neighbor opinion effect strength. We also explore the conditions involved in forming a stable neighbor relationship and the influence of the confidence variation in the convergence of the threshold of bounded confidence. The results show that the influence on opinion evolution is greater with increased confidence variation.

  15. 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


    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.

  16. Iterated Function Systems on Functions of Bounded Variation (United States)

    La Torre, Davide; Mendivil, Franklin; Vrscay, Edward R.


    We show that under certain hypotheses, an iterated function system on mappings (IFSM) is a contraction on the complete space of functions of bounded variation (BV). It then possesses a unique attractor of BV. Some BV-based inverse problems based on the Collage Theorem for contraction maps are considered.

  17. Decoherence in time evolution of bound entanglement

    CERN Document Server

    Sun, Z; Sun, C P; Wang, X; Sun, Zhe; Wang, Xiaoguang


    We study a dynamic process of disentanglement by considering the time evolution of bound entanglement for a quantum open system, two qutrits coupling to a common environment. Here, the initial quantum correlations of the two qutrits are characterized by the bound entanglement. In order to show the universality of the role of environment on bound entanglement, both bosonic and spin environments are considered. We found that the bound entanglement displays collapses and revivals, and it can be stable against small temperature and time change. The thermal fluctuation effects on bound entanglement are also considered.

  18. Monte Carlo study of receptor-lipid raft formation on a cell membrane (United States)

    Yu-Yang, Paul; Srinivas Reddy, A.; Raychaudhuri, Subhadip


    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.

  19. The mathematics of a successful deconvolution: a quantitative assessment of mixture-based combinatorial libraries screened against two formylpeptide receptors. (United States)

    Santos, Radleigh G; Appel, Jon R; Giulianotti, Marc A; Edwards, Bruce S; Sklar, Larry A; Houghten, Richard A; Pinilla, Clemencia


    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.

  20. The Mathematics of a Successful Deconvolution: A Quantitative Assessment of Mixture-Based Combinatorial Libraries Screened Against Two Formylpeptide Receptors

    Directory of Open Access Journals (Sweden)

    Richard A. Houghten


    Full Text Available 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.

  1. The Mathematics of a Successful Deconvolution: A Quantitative Assessment of Mixture-Based Combinatorial Libraries Screened Against Two Formylpeptide Receptors (United States)

    Santos, Radleigh G.; Appel, Jon R.; Giulianotti, Marc A.; Edwards, Bruce S.; Sklar, Larry A.; Houghten, Richard A.; Pinilla, Clemencia


    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

  2. [Melatonin receptor agonist]. (United States)

    Uchiyama, Makoto


    Melatonin is a hormone secreted by the pineal gland and is involved in the regulation of human sleep-wake cycle and circadian rhythms. The melatonin MT1 and MT2 receptors located in the suprachiasmatic nucleus in the hypothalamus play a pivotal role in the sleep-wake regulation. Based on the fact that MT1 receptors are involved in human sleep onset process, melatonin receptor agonists have been developed to treat insomnia. In this article, we first reviewed functions of melatonin receptors with special reference to MT1 and MT2, and properties and clinical application of melatonin receptor agonists as hypnotics.

  3. Thermodynamic law from the entanglement entropy bound

    CERN Document Server

    Park, Chanyong


    From black hole thermodynamics, the Bekenstein bound has been proposed as a universal thermal entropy bound. It has been further generalized to an entanglement entropy bound which is valid even in a quantum system. In a quantumly entangled system, the non-negativity of the relative entropy leads to the entanglement entropy bound. When the entanglement entropy bound is saturated, a quantum system satisfies the thermodynamics-like law with an appropriately defined entanglement temperature. We show that the saturation of the entanglement entropy bound accounts for a universal feature of the entanglement temperature proportional to the inverse of the system size. In addition, we also find that a global quench unlike the excitation does not preserve the entanglement entropy bound.

  4. Capacity Bounds for Parallel Optical Wireless Channels

    KAUST Repository

    Chaaban, Anas


    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.

  5. Distance measure with improved lower bound for multivariate time series (United States)

    Li, Hailin


    Lower bound function is one of the important techniques used to fast search and index time series data. Multivariate time series has two aspects of high dimensionality including the time-based dimension and the variable-based dimension. Due to the influence of variable-based dimension, a novel method is proposed to deal with the lower bound distance computation for multivariate time series. The proposed method like the traditional ones also reduces the dimensionality of time series in its first step and thus does not directly apply the lower bound function on the multivariate time series. The dimensionality reduction is that multivariate time series is reduced to univariate time series denoted as center sequences according to the principle of piecewise aggregate approximation. In addition, an extended lower bound function is designed to obtain good tightness and fast measure the distance between any two center sequences. The experimental results demonstrate that the proposed lower bound function has better tightness and improves the performance of similarity search in multivariate time series datasets.

  6. Spectral computations for bounded operators

    CERN Document Server

    Ahues, Mario; Limaye, Balmohan


    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...

  7. Bound states in the continuum (United States)

    Hsu, Chia Wei; Zhen, Bo; Stone, A. Douglas; Joannopoulos, John D.; Soljačić, Marin


    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.

  8. 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


    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.

  9. Multiscale design of coarse-grained elastic network-based potentials for the μ opioid receptor. (United States)

    Fossépré, Mathieu; Leherte, Laurence; Laaksonen, Aatto; Vercauteren, Daniel P


    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).

  10. Bacteriophage receptor binding protein based assays for the simultaneous detection of Campylobacter jejuni and Campylobacter coli. (United States)

    Javed, Muhammad A; Poshtiban, Somayyeh; Arutyunov, Denis; Evoy, Stephane; Szymanski, Christine M


    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.

  11. 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.

  12. 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.


    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...

  13. Nanoparticle-based, organic receptor coupled fluorescent chemosensors for the determination of phosphate

    Energy Technology Data Exchange (ETDEWEB)

    Kaur, Navneet, E-mail: [Centre for Nanoscience and Nanotechnology (UIEAST), Panjab University, Chandigarh 160014 (India); Kaur, Simanpreet; Kaur, Amanpreet [Centre for Nanoscience and Nanotechnology (UIEAST), Panjab University, Chandigarh 160014 (India); Saluja, Preeti; Sharma, Hemant [Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001 (India); Saini, Anu; Dhariwal, Nisha [Centre for Nanoscience and Nanotechnology (UIEAST), Panjab University, Chandigarh 160014 (India); Singh, Ajnesh; Singh, Narinder [Department of Chemistry, Indian Institute of Technology Ropar, Rupnagar, Punjab 140001 (India)


    The sensors have been developed using silver nanoparticles coated with organic ligands and are fully characterized with spectroscopic methods. The energy-dispersive X-ray (EDX) analysis revealed the presence of organic receptors on the surface of metal nanoparticles. These chemosensors were tested against a range of biological and environmentally relevant cations in the HEPES buffered DMSO/H{sub 2}O (8:2, v/v) solvent system. The fluorescence intensity of these chemosensors was quenched upon coordination with open shell metal ions such as Cu{sup 2+}/Fe{sup 3+}. Anion recognition properties of the corresponding metal complexes have been studied and the original fluorescence intensity of sensors was restored upon addition of phosphate (0–20 µM). Thus, a highly selective chemosensor has been devised for the micromolar estimation of phosphate in semi-aqueous medium. -- Highlights: • The silver nanoparticles have been decorated with organic receptors for chemosensor applications. • The sensor properties are developed for the estimation of phosphate anion. • Thus the sensor relies on the cation displacement assay. • The phosphate sensing event displays the “ON–OFF–ON” mode of switching in sensor.

  14. Toward a structure-based model of salvinorin A recognition of the kappa-opioid receptor. (United States)

    Kane, Brian E; McCurdy, Christopher R; Ferguson, David M


    The structural basis to salvinorin A recognition of the kappa-opioid receptor is evaluated using a combination of site-directed mutagenesis and molecular-modeling techniques. The results show that salvinorin A recognizes a collection of residues in transmembrane II and VII, including Q115, Y119, Y313, I316, and Y320. The mutation of one hydrophobic residue in particular, I316, was found to completely abolish salvinorin A binding. As expected, none of the residues in transmembrane III or VI commonly associated with opiate recognition (such as D138 or E297) appear to be required for ligand binding. On the basis of the results presented here and elsewhere, a binding site model is proposed that aligns salvinorin A vertically within a pocket spanning transmembrane II and VII, with the 2' substituent directed toward the extracellular domains. The model explains the role that hydrophobic contacts play in binding this lipophilic ligand and gives insight into the structural basis to the mu-opioid receptor selectivity of 2'-benzoyl salvinorin (herkinorin).

  15. Biomimetic infrared sensors based on the infrared receptors of pyrophilous insects (United States)

    Schmitz, Helmut; Kahl, Thilo; Soltner, Helmut; Bousack, Herbert


    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.


    Institute of Scientific and Technical Information of China (English)

    李秉键; 夏文栋; 郭其标; 任江涛


    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.

  17. Bootstrap bound for conformal multi-flavor QCD on lattice

    CERN Document Server

    Nakayama, Yu


    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.

  18. Using tolerance bounds in scientific investigations

    Energy Technology Data Exchange (ETDEWEB)

    Wendelberger, J.R.


    Assessment of the variability in population values plays an important role in the analysis of scientific data. Analysis of scientific data often involves developing a bound on a proportion of a population. Sometimes simple probability bounds are obtained using formulas involving known mean and variance parameters and replacing the parameters by sample estimates. The resulting bounds are only approximate and fail to account for the variability in the estimated parameters. Tolerance bounds provide bounds on population proportions which account for the variation resulting from the estimated mean and variance parameters. A beta content, gamma confidence tolerance interval is constructed so that a proportion beta of the population lies within the region bounded by the interval with confidence gamma. An application involving corrosion measurements is used to illustrate the use of tolerance bounds for different situations. Extensions of standard tolerance intervals are applied to generate regression tolerance bounds, tolerance bounds for more general models of measurements collected over time, and tolerance intervals for varying precision data. Tolerance bounds also provide useful information for designing the collection of future data.

  19. Image Fusion Method Based on Bound-Constrained Optimal Projection Gradient for NMF in TINST Domain%基于边界约束最优投影梯度NMF的TINST域图像融合方法

    Institute of Scientific and Technical Information of China (English)

    才华; 陈广秋; 刘广文; 耿朕野; 杨勇


    Aiming at the problem of multi-modality images fusion,we proposed an image fusion method based on bound-constrained optimal projection gradient for non-negative matrix factorization (NMF)in translation invariance nonseparable shearlet transform (TINST)domain.The problem of low fusion accuracy in some existing typical fusion methods was solved effectively.Images were decomposed to some subbands by translation invariance nonseparable shearlet transform. The low-frequency subband coefficients were regarded as original observed data,and the low-frequency subband coefficients were obtained by bound-constrained optimal projection gradient for NMF algorithm.High-frequency directional suband coefficients were used as external input excitation and edge intensity was served as linking strength of each neuron in pulse coupled neural networks (PCNN) and after the fire processing and compare-selection computing, fused high-frequency directional suband coefficients were obtained.Finally,all the fused subbands were reconstructed to an image by translation invariance nonseparable shearlet inverse transform.In order to verify the efficiency of the proposed method,some compared fusion experiments were implemented on several sets of different modality images.Subjective and objective evaluation on fused image indicates that the proposed method is better than a few existing typical fusion techniques based on multi-scale decomposition (MSD).%针对多模态图像的融合问题,提出一种平移不变不可分离剪切波结合边界约束最优投影梯度非负矩阵分解的图像融合方法,解决了已有融合方法中融合精度较低的问题。该方法利用平移不变不可分离剪切波对源图像进行分解;将低频子带系数视为原始观测数据,采用边界约束最优投影梯度非负矩阵分解算法得到包含特征基的融合低频子带系数,将高频方向子带系数作为脉冲耦合神经网络的外部输入激励,边缘强度作

  20. Vehicle Routing Choice Based on Bounded Rationality of Fuzzy Game Under No Guide Information%无诱导信息条件下基于有限理性模糊博弈的车辆路径选择

    Institute of Scientific and Technical Information of China (English)

    史国强; 周代平; 聂化东; 闫广聪


    In this paper, fuzzy mathematics is used as the tool and reinforcement theory as the foundation to establish a model of vehicle routing choice with no guide information based on the bounded rational fuzzy game theory and simulate the game equilibrium through matlab under different initial states. The result shows that the initial allocation proportion of the road network traffic has no obvious effect on its balance status. At the same time, when the total network traffic reaches the traffic capacity of road network, the game result will achieve stable equilibrium. When the traffic is far greater than the road network capacity, the game result will reach the peak valley balance.%以模糊数学为工具、行为强化理论为基础,建立有限理性模糊博弈的无诱导信息车辆路径选择模型,通过Matlab仿真得出不同初始状态下的博弈平衡结果。结果表明:初始路网交通量的分配比例对路网的平衡状态无显著影响,且当路网交通总量接近路网的通行能力时,博弈结果会达到稳定平衡,当交通量远大于路网通行能力时,博弈结果则呈现峰谷平衡。