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Sample records for bound receptor based

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

    Science.gov (United States)

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

    2011-09-01

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

  2. Improvement of Ligand Affinity and Thermodynamic Properties by NMR-Based Evaluation of Local Dynamics and Surface Complementarity in the Receptor-Bound State.

    Science.gov (United States)

    Mizukoshi, Yumiko; Takeuchi, Koh; Arutaki, Misa; Tokunaga, Yuji; Takizawa, Takeshi; Hanzawa, Hiroyuki; Shimada, Ichio

    2016-11-14

    The thermodynamic properties of a ligand in the bound state affect its binding specificity. Strict binding specificity can be achieved by introducing multiple spatially defined interactions, such as hydrogen bonds and van der Waals interactions, into the ligand-receptor interface. These introduced interactions are characterized by restricted local dynamics and improved surface complementarity in the bound state. In this study, we experimentally evaluated the local dynamics and the surface complementarity of weak-affinity ligands in the receptor-bound state by forbidden coherence transfer analysis in free-bound exchange systems (Ex-FCT), using the interaction between a ligand, a myocyte-enhancer factor 2A (MEF2A) docking peptide, and a receptor, p38α, as a model system. The Ex-FCT analyses successfully provided information for the rational design of a ligand with higher affinity and preferable thermodynamic properties for p38α. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Structure of the δ-opioid receptor bound to naltrindole.

    Science.gov (United States)

    Granier, Sébastien; Manglik, Aashish; Kruse, Andrew C; Kobilka, Tong Sun; Thian, Foon Sun; Weis, William I; Kobilka, Brian K

    2012-05-16

    The opioid receptor family comprises three members, the µ-, δ- and κ-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 δ-opioid receptor (δ-OR) has a role in analgesia, as well as in other neurological functions that remain poorly understood. The structures of the µ-OR and κ-OR have recently been solved. Here we report the crystal structure of the mouse δ-OR, bound to the subtype-selective antagonist naltrindole. Together with the structures of the µ-OR and κ-OR, the δ-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 δ-OR with other GPCRs reveals that this structural organization may be a more general phenomenon, extending to other GPCR families as well.

  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)

    2012-07-11

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

  5. Structure of the agonist-bound neurotensin receptor.

    Science.gov (United States)

    White, Jim F; Noinaj, Nicholas; Shibata, Yoko; Love, James; Kloss, Brian; Xu, Feng; Gvozdenovic-Jeremic, Jelena; Shah, Priyanka; Shiloach, Joseph; Tate, Christopher G; Grisshammer, Reinhard

    2012-10-25

    Neurotensin (NTS) is a 13-amino-acid peptide that functions as both a neurotransmitter and a hormone through the activation of the neurotensin receptor NTSR1, a G-protein-coupled receptor (GPCR). In the brain, NTS modulates the activity of dopaminergic systems, opioid-independent analgesia, and the inhibition of food intake; in the gut, NTS regulates a range of digestive processes. Here we present the structure at 2.8 Å resolution of Rattus norvegicus NTSR1 in an active-like state, bound to NTS(8-13), the carboxy-terminal portion of NTS responsible for agonist-induced activation of the receptor. The peptide agonist binds to NTSR1 in an extended conformation nearly perpendicular to the membrane plane, with the C terminus oriented towards the receptor core. Our findings provide, to our knowledge, the first insight into the binding mode of a peptide agonist to a GPCR and may support the development of non-peptide ligands that could be useful in the treatment of neurological disorders, cancer and obesity.

  6. Diazepam-bound GABAA receptor models identify new benzodiazepine binding-site ligands

    Science.gov (United States)

    Richter, Lars; de Graaf, Chris; Sieghart, Werner; Varagic, Zdravko; Mörzinger, Martina; de Esch, Iwan J P; Ecker, Gerhard F; Ernst, Margot

    2012-01-01

    Benzodiazepines exert their anxiolytic, anticonvulsant, muscle-relaxant and sedative-hypnotic properties by allosterically enhancing the action of GABA at GABAA receptors via their benzodiazepine-binding site. Although these drugs have been used clinically since 1960, the molecular basis of this interaction is still not known. By using multiple homology models and an un biased docking protocol, we identified a binding hypothesis for the diazepam-bound structure of the benzodiazepine site, which was confirmed by experimental evidence. Moreover, two independent virtual screening approaches based on this structure identified known benzodiazepine-site ligands from different structural classes and predicted potential new ligands for this site. Receptor-binding assays and electrophysiological studies on recombinant receptors confirmed these predictions and thus identified new chemotypes for the benzodiazepine-binding site. Our results support the validity of the diazepam-bound structure of the benzodiazepine-binding pocket, demonstrate its suitability for drug discovery and pave the way for structure-based drug design. PMID:22446838

  7. Three-dimensional structure of poliovirus receptor bound to poliovirus

    Science.gov (United States)

    Belnap, David M.; McDermott, Brian M.; Filman, David J.; Cheng, Naiqian; Trus, Benes L.; Zuccola, Harmon J.; Racaniello, Vincent R.; Hogle, James M.; Steven, Alasdair C.

    2000-01-01

    Poliovirus initiates infection by binding to its cellular receptor (Pvr). We have studied this interaction by using cryoelectron microscopy to determine the structure, at 21-Å resolution, of poliovirus complexed with a soluble form of its receptor (sPvr). This density map aided construction of a homology-based model of sPvr and, in conjunction with the known crystal structure of the virus, allowed delineation of the binding site. The virion does not change significantly in structure on binding sPvr in short incubations at 4°C. We infer that the binding configuration visualized represents the initial interaction that is followed by structural changes in the virion as infection proceeds. sPvr is segmented into three well-defined Ig-like domains. The two domains closest to the virion (domains 1 and 2) are aligned and rigidly connected, whereas domain 3 diverges at an angle of ≈60°. Two nodules of density on domain 2 are identified as glycosylation sites. Domain 1 penetrates the “canyon” that surrounds the 5-fold protrusion on the capsid surface, and its binding site involves all three major capsid proteins. The inferred pattern of virus–sPvr interactions accounts for most mutations that affect the binding of Pvr to poliovirus. PMID:10618373

  8. Pirenzepine binding to membrane-bound, solubilized and purified muscarinic receptor subtypes

    Energy Technology Data Exchange (ETDEWEB)

    Baumgold, J.

    1986-05-01

    Muscarinic receptors were purified to near-homogeneity from bovine cortex, an area rich in the putative M1 subtype, and from bovine pons/medulla, an area rich in the putative M2 subtype. In both cases, the receptors were solubilized in digitonin and purified over an affinity column. Both the cortical and pons/medulla preparations yielded receptor proteins of 70,000 daltons. Pirenzepine binding was deduced from its competition with /sup 3/H-N-methyl scopolamine. The binding of pirenzepine to membrane-bound receptors from cortex was best described by a two site model, with approximately half the sites having a Ki of 6.4 x 10/sup -9/ M and the remaining sites having a Ki of 3.5 x 10/sup -7/ M. Membrane-bound receptors from pons/medulla bound pirenzepine according to a one-site model with a Ki of 1.1 x 10/sup -7/ M. After solubilization the two-site binding of cortical receptors became a one-site binding, Ki = 1.1 x 10/sup -7/M. This value was still five-fold lower than that of soluble receptors from pons/medulla. After purification however the affinity of pirenzepine for the pons/medulla receptor increased so that the two putative subtypes bound pirenzepine with approximately the same affinity. These findings suggest that the different pirenzepine binding characteristics used to define muscarinic receptor subtypes are not inherent in the receptor protein itself but may be due to coupling factors associated with the receptor.

  9. 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)

    2017-01-01

    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.

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

    Science.gov (United States)

    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

    2017-01-26

    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. PAPERCLIP. Copyright © 2017 Elsevier Inc. All rights reserved.

  11. Bounded Semantics of CTL and SAT-Based Verification

    Science.gov (United States)

    Zhang, Wenhui

    Bounded model checking has been proposed as a complementary approach to BDD based symbolic model checking for combating the state explosion problem, esp. for efficient error detection. This has led to a lot of successful work with respect to error detection in the checking of LTL, ACTL (the universal fragment of CTL) and ACTL* properties by satisfiability testing. The use of bounded model checking for verification (in contrast to error detection) of LTL and ACTL properties has later also been studied. This paper studies the potentials and limitations of bounded model checking for the verification of CTL and CTL* formulas. On the theoretical side, we first provide a framework for discussion of bounded semantics, which serves as the basis for bounded model checking, then extend the bounded semantics of ACTL to a bounded semantics of CTL, and discuss the limitation of developing such a bounded semantics for CTL*. On the practical side, a deduction of a SAT-based bounded model checking approach for ACTL properties from the bounded semantics of CTL is demonstrated, and a comparison of such an approach with BDD-based model checking is presented based on experimental results.

  12. Inhibition of receptor-bound urokinase by plasminogen-activator inhibitors

    DEFF Research Database (Denmark)

    Ellis, Vincent John; Wun, T C; Behrendt, N

    1990-01-01

    Urokinase-type plasminogen activator (uPA) binds to a specific receptor on various cell types, the bound molecule retaining its enzymatic activity against plasminogen. We have now investigated whether receptor-bound uPA also retains the ability to react with and be inhibited by plasminogen...... activator inhibitors (PAI-1 and PAI-2). uPA bound to its receptor on human U937 monocyte-like cells was inhibited by PAI-1 (in its active form in the presence of vitronectin fragments) with an association rate constant of 4.5 x 10(6) M-1 s-1, which was 40% lower than that obtained for uPA in solution (7.9 x...... 10(6) M-1 s-1). The inhibition of uPA by PAI-2 was decreased to a similar extent by receptor binding, falling from 5.3 x 10(5) to 3.3 x 10(5) M-1 s-1. Stimulation of U937 cells with phorbol 12-myristate 13-acetate was accompanied by a further reduction in receptor-bound uPA inhibition by PAI-1...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-03-15

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

  14. Optimum Cooperative UAV Sensing Based on Cramer-Rao Bound

    National Research Council Canada - National Science Library

    Gu, G; Chandler, P. R; Schumacher, C. J; Sparks, A; Pachter, M

    2005-01-01

    .... Based on the Cramer-Rao bound, we are able to derive the minimum achievable error variance in estimation of the position and the velocity of the GMT, and obtain the optimal geometries of the UAV...

  15. Bounded Error Approximation Algorithms for Risk-Based Intrusion Response

    Science.gov (United States)

    2015-09-17

    AFRL-AFOSR-VA-TR-2015-0324 Bounded Error Approximation Algorithms for Risk-Based Intrusion Response K Subramani West Virginia University Research...2015. 4. TITLE AND SUBTITLE Bounded Error Approximation Algorithms for Risk-Based Intrusion Response 5a. CONTRACT NUMBER FA9550-12-1-0199. 5b. GRANT...SUPPLEMENTARY NOTES 14. ABSTRACT Our research consisted of modeling the intrusion response problem as one of finding a partial vertex cover in

  16. Structural model of nicotinic acetylcholine receptor isotypes bound to acetylcholine and nicotine

    Directory of Open Access Journals (Sweden)

    Abagyan Ruben

    2002-01-01

    Full Text Available Abstract Background Nicotine is a psychoactive drug presenting a diverse array of biological activities, some positive, such as enhancement of cognitive performances, others negative, such as addiction liability. Ligands that discriminate between the different isotypes of nicotinic acetylcholine receptors (nAChRs could present improved pharmacology and toxicity profile. Results Based on the recent crystal structure of a soluble acetylcholine binding protein from snails, we have built atomic models of acetylcholine and nicotine bound to the pocket of four different human nAChR subtypes. The structures of the docked ligands correlate with available biochemical data, and reveal that the determinants for isotype selectivity are relying essentially on four residues, providing diversity of the ligand binding pocket both in terms of Van der Waals boundary, and electrostatic potential. We used our models to screen in silico a large compound database and identify a new ligand candidate that could display subtype selectivity. Conclusion The nAChR-agonist models should be useful for the design of nAChR agonists with diverse specificity profiles.

  17. Insight into partial agonism by observing multiple equilibria for ligand-bound and Gs-mimetic nanobody-bound β1-adrenergic receptor.

    Science.gov (United States)

    Solt, Andras S; Bostock, Mark J; Shrestha, Binesh; Kumar, Prashant; Warne, Tony; Tate, Christopher G; Nietlispach, Daniel

    2017-11-27

    A complex conformational energy landscape determines G-protein-coupled receptor (GPCR) signalling via intracellular binding partners (IBPs), e.g., Gs and β-arrestin. Using 13C methyl methionine NMR for the β1-adrenergic receptor, we identify ligand efficacy-dependent equilibria between an inactive and pre-active state and, in complex with Gs-mimetic nanobody, between more and less active ternary complexes. Formation of a basal activity complex through ligand-free nanobody-receptor interaction reveals structural differences on the cytoplasmic receptor side compared to the full agonist-bound nanobody-coupled form, suggesting that ligand-induced variations in G-protein interaction underpin partial agonism. Significant differences in receptor dynamics are observed ranging from rigid nanobody-coupled states to extensive μs-to-ms timescale dynamics when bound to a full agonist. We suggest that the mobility of the full agonist-bound form primes the GPCR to couple to IBPs. On formation of the ternary complex, ligand efficacy determines the quality of the interaction between the rigidified receptor and an IBP and consequently the signalling level.

  18. Crystal structures of agonist-bound human cannabinoid receptor CB1.

    Science.gov (United States)

    Hua, Tian; Vemuri, Kiran; Nikas, Spyros P; Laprairie, Robert B; Wu, Yiran; Qu, Lu; Pu, Mengchen; Korde, Anisha; Jiang, Shan; Ho, Jo-Hao; Han, Gye Won; Ding, Kang; Li, Xuanxuan; Liu, Haiguang; Hanson, Michael A; Zhao, Suwen; Bohn, Laura M; Makriyannis, Alexandros; Stevens, Raymond C; Liu, Zhi-Jie

    2017-07-27

    The cannabinoid receptor 1 (CB1) is the principal target of the psychoactive constituent of marijuana, the partial agonist Δ(9)-tetrahydrocannabinol (Δ(9)-THC). Here we report two agonist-bound crystal structures of human CB1 in complex with a tetrahydrocannabinol (AM11542) and a hexahydrocannabinol (AM841) at 2.80 Å and 2.95 Å resolution, respectively. The two CB1-agonist complexes reveal important conformational changes in the overall structure, relative to the antagonist-bound state, including a 53% reduction in the volume of the ligand-binding pocket and an increase in the surface area of the G-protein-binding region. In addition, a 'twin toggle switch' of Phe200(3.36) and Trp356(6.48) (superscripts denote Ballesteros-Weinstein numbering) is experimentally observed and appears to be essential for receptor activation. The structures reveal important insights into the activation mechanism of CB1 and provide a molecular basis for predicting the binding modes of Δ(9)-THC, and endogenous and synthetic cannabinoids. The plasticity of the binding pocket of CB1 seems to be a common feature among certain class A G-protein-coupled receptors. These findings should inspire the design of chemically diverse ligands with distinct pharmacological properties.

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

    DEFF Research Database (Denmark)

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

    2008-01-01

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

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

    Science.gov (United States)

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

    2015-03-01

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

  1. Renewal theory, Geiger counters, and the maximum number of receptors bound to a randomly haptenated polymer chain.

    Science.gov (United States)

    Macken, C A; Perelson, A S

    1986-01-01

    Polymers containing small chemical groups (haptens) covalently attached at random along the chain are commonly used to initiate an immune response. Properties of the polymer such as its length, the spacing of the haptens, and the total number of haptens along the chain, correlate with its immune reactivity. Here we model the ability of many finite-sized cell surface receptors to bind simultaneously the haptens conjugated to a polymer chain. The binding sites on two different receptors or on separate parts of a multivalent receptor cannot be arbitrarily close to one another; so, in general, not all haptens along a polymer chain can be simultaneously bound by receptors. We develop an analogy between the steric hindrance among receptors detecting randomly placed haptens and the temporary locking of a Geiger counter that has detected a radioactive decay. Using renewal theory, we compute the probability distribution, and its moments, for the maximum number of haptens that can be simultaneously bound by monovalent receptors. We also model flexible bivalent receptors and obtain the mean and variance of the maximum number of receptors bound to randomly haptenated polymers, and the mean and variance of the maximum number of haptens bound. We demonstrate the importance of our results by applying them to immunological data and showing that, for polymers used in immunology, the effective valence of a polymer may be as much as 50% smaller than its nominal valence.

  2. Sorting an LDL receptor with bound PCSK9 to intracellular degradation.

    Science.gov (United States)

    Leren, Trond P

    2014-11-01

    This article reviews the mechanism by which the low density lipoprotein receptor (LDLR) that has bound proprotein convertase subtilisin/kexin type 9 (PCSK9), is rerouted to intracellular degradation instead of being recycled. A search of relevant published literature has been conducted. PCSK9 binds to the LDLR at the cell surface. It is the catalytic domain of PCSK9 that binds to the epidermal growth factor repeat A of the LDLR. The LDLR:PCSK9 complex is internalized through clathrin-mediated endocytosis. Due to an additional electrostatic interaction at acidic pH between the C-terminal domain of PCSK9 and the ligand-binding domain of the LDLR, PCSK9 remains bound to the LDLR in the sorting endosome. As a consequence, the LDLR fails to adopt a closed conformation and is degraded instead of being recycled. The mechanism for the failure of the LDLR to recycle appears to involve ectodomain cleavage of the extended LDLR by a cysteine cathepsin in the sorting endosome. The cleaved LDLR ectodomain will be confined to the vesicular part of the sorting endosome for degradation in the endosomal/lysosomal tract. Ectodomain cleavage of an LDLR with bound PCSK9 in the sorting endosome disrupts the normal recycling of the LDLR. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

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

    DEFF Research Database (Denmark)

    Kiderlen, Markus; Meschenmoser, Daniel

    2009-01-01

    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...

  4. Upper Bound Performance Estimation for Copper Based Broadband Access

    DEFF Research Database (Denmark)

    Jensen, Michael; Gutierrez Lopez, Jose Manuel

    2012-01-01

    Around 70% of all broadband connections in the European Union are carried over copper, and the scenario is unlikely to change in the next few years as carriers still believe in the profitability of their copper infrastructure. In this paper we show how to estimate the performance upper bound of c...... to define the limitations of copper based broadband access. A case study in a municipality in Denmark shows how the estimated network dimension to be able to provide video conference services to the majority of the population might be too high to be implemented in reality.......Around 70% of all broadband connections in the European Union are carried over copper, and the scenario is unlikely to change in the next few years as carriers still believe in the profitability of their copper infrastructure. In this paper we show how to estimate the performance upper bound...

  5. Internalization and recycling of receptor-bound gonadotropin-releasing hormone agonist in pituitary gonadotropes

    Energy Technology Data Exchange (ETDEWEB)

    Schvartz, I.; Hazum, E.

    1987-12-15

    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.

  6. 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.

  7. Crystal structure of the adenosine A2A receptor bound to an antagonist reveals a potential allosteric pocket

    OpenAIRE

    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.

    2017-01-01

    The A2AR is a G protein-coupled receptor (GPCR) that plays important roles in cardiovascular physiology and immune function. The A2AR is also a target for the treatment of Parkinson?s disease, where A2AR antagonists have been shown to enhance signaling through the D2 dopamine receptor. Here we present the crystal structure of the A2AR bound to a novel bitopic antagonist. As a result of structural changes needed to accommodate the bound antagonist, crystals could not be grown in lipidic cubic ...

  8. Ligand-modulated conformational switching in a fully synthetic membrane-bound receptor

    Science.gov (United States)

    Lister, Francis G. A.; Le Bailly, Bryden A. F.; Webb, Simon J.; Clayden, Jonathan

    2017-05-01

    Signal transduction through G-protein-coupled receptors (GPCRs) involves binding to signalling molecules at the cell surface, which leads to global changes in molecular conformation that are communicated through the membrane. Artificial mechanisms for communication involving ligand binding and global conformational switching have been demonstrated so far only in the solution phase. Here, we report a membrane-bound synthetic receptor that responds to binding of a ligand by undergoing a conformational change that is propagated over several nanometres, deep into the phospholipid bilayer. Our design uses a helical foldamer core, with structural features borrowed from a class of membrane-active fungal antibiotics, ligated to a water-compatible, metal-centred binding site and a conformationally responsive fluorophore. Using the fluorophore as a remote reporter of conformational change, we find that binding of specific carboxylate ligands to a Cu(II) cofactor at the binding site perturbs the foldamer's global conformation, mimicking the conformational response of a GPCR to ligand binding.

  9. Crystal Structures of Human Orexin 2 Receptor Bound to the Subtype-Selective Antagonist EMPA.

    Science.gov (United States)

    Suno, Ryoji; Kimura, Kanako Terakado; Nakane, Takanori; Yamashita, Keitaro; Wang, Junmei; Fujiwara, Takaaki; Yamanaka, Yasuaki; Im, Dohyun; Horita, Shoichiro; Tsujimoto, Hirokazu; Tawaramoto, Maki S; Hirokawa, Takatsugu; Nango, Eriko; Tono, Kensuke; Kameshima, Takashi; Hatsui, Takaki; Joti, Yasumasa; Yabashi, Makina; Shimamoto, Keiko; Yamamoto, Masaki; Rosenbaum, Daniel M; Iwata, So; Shimamura, Tatsuro; Kobayashi, Takuya

    2018-01-02

    Orexin peptides in the brain regulate physiological functions such as the sleep-wake cycle, and are thus drug targets for the treatment of insomnia. Using serial femtosecond crystallography and multi-crystal data collection with a synchrotron light source, we determined structures of human orexin 2 receptor in complex with the subtype-selective antagonist EMPA (N-ethyl-2-[(6-methoxy-pyridin-3-yl)-(toluene-2-sulfonyl)-amino]-N-pyridin-3-ylmethyl-acetamide) at 2.30-Å and 1.96-Å resolution. In comparison with the non-subtype-selective antagonist suvorexant, EMPA contacted fewer residues through hydrogen bonds at the orthosteric site, explaining the faster dissociation rate. Comparisons among these OX 2 R structures in complex with selective antagonists and previously determined OX 1 R/OX 2 R structures bound to non-selective antagonists revealed that the residue at positions 2.61 and 3.33 were critical for the antagonist selectivity in OX 2 R. The importance of these residues for binding selectivity to OX 2 R was also revealed by molecular dynamics simulation. These results should facilitate the development of antagonists for orexin receptors. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Toward a culture-bound syndrome-based insanity defense?

    Science.gov (United States)

    Parzen, Micah David

    2003-06-01

    The American Psychiatric Association's recent inclusion of a Glossary of Culture-Bound Syndromes within DSM-IV draws upon decades of medical anthropological and cultural psychiatric research to afford culture-bound syndromes (CBSs) a newfound legitimacy within professional Western psychiatric nosology. While DSM-IV's recognition of the CBS concept as a category of psychosocial distress has important clinical implications for mental health care practitioners throughout the world, it also has significant legal implications. Given that several CBSs involve a degree of psychological impairment that may satisfy the standard for legal insanity under certain circumstances, this essay focuses on the potential emergence of an insanity defense based on the claim that an immigrant or minority defendant was suffering from a CBS at the time of his or her criminal act. Aimed at initiating interdisciplinary debate over the reification of the CBS concept, the essay discusses the theoretical ambiguity and status of CBSs within professional Western psychiatry, describes what a CBS-based insanity defense might look like, and considers the relevant challenges facing medical anthropologists and cultural psychiatrists, on the one hand, and legal practitioners, on the other. The essay identifies a pressing need for interdisciplinary debate concerning the validity, scope, and viability of CBS-based insanity defenses.

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

    OpenAIRE

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

    2013-01-01

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

  12. Persistence-Based Branch Misprediction Bounds for WCET Analysis

    DEFF Research Database (Denmark)

    Puffitsch, Wolfgang

    2015-01-01

    Branch prediction is an important feature of pipelined processors to achieve high performance. However, it can lead to overly pessimistic worst-case execution time (WCET) bounds when being modeled too conservatively. This paper presents bounds on the number of branch mispredictions for local...... 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....... dynamic branch predictors. To handle interferences between branch instructions we use the notion of persistence, a concept that is also found in cache analyses. The bounds apply to branches in general, not only to branches that close a loop. Furthermore, the bounds can be easily integrated into integer...

  13. 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

    1999-01-01

    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...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-06-27

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

  15. 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*

    Science.gov (United States)

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

    2013-01-01

    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. PMID:23386604

  16. Characterization of membrane-bound and soluble D2 receptors in canine caudate using ( sup 125 I)IBZM

    Energy Technology Data Exchange (ETDEWEB)

    Schonwetter, B.S.; Luedtke, R.R.; Kung, M.P.; Billings, J.; Kung, H.F.; Molinoff, P.B. (Univ. of Pennsylvania School of Medicine, Philadelphia (USA))

    1989-07-01

    (S)-(-)-3-iodo-2-hydroxy-6-methoxy-N-((1-ethyl-2-pyrrolidinyl) methyl)benzamide (IBZM) was shown to be a high-affinity antagonist selective for the D2 subtype of dopamine receptor. Binding sites for the radioligand (125I)IBZM were characterized with membranes and digitonin-solubilized extracts of canine caudate enriched by chromatography on heparin-agarose. Nonspecific binding, defined using 2 microM (+)-butaclamol, was less than 10% of the total ligand bound at the Kd of the receptor for ({sup 125}I)IBZM. Direct binding, competition and kinetic experiments indicated that ({sup 125}I)IBZM bound to a homogeneous population of binding sites. The rank order of potency for inhibition of the binding of ({sup 125}I)IBZM by antagonists and agonists was found to be consistent with the pharmacological profile expected of a D2 receptor. The affinities of ({sup 125}I)IBZM for membrane-associated and detergent-solubilized binding sites were essentially identical (Kd congruent to 0.4 nM). This result contrasts with findings obtained in studies with ({sup 3}H)spiroperidol, where a marked decrease in the affinity of the receptor for the ligand has been observed during detergent solubilization and purification of the receptor. The high selectivity, nanomolar affinity and high specific activity of ({sup 125}I)IBZM and the results obtained in studies with detergent extracts suggest that ({sup 125}I)IBZM will be a particularly useful ligand for studies of D2 receptors in the presence of detergents.

  17. Semidefinite bounds for nonbinary codes based on quadruples

    NARCIS (Netherlands)

    B. Litjens (Bart); S.C. Polak (Sven); A. Schrijver (Alexander)

    2017-01-01

    textabstractFor nonnegative integers q, n, d, let Aq(n, d) denote the maximum cardinality of a code of length n over an alphabet [q] with q letters and with minimum distance at least d. We consider the following upper bound on Aq(n, d). For any k, let Ck be the collection of codes of

  18. Recognition of core and flanking amino acids of MHC class II-bound peptides by the T cell receptor.

    Science.gov (United States)

    Sant'Angelo, Derek B; Robinson, Eve; Janeway, Charles A; Denzin, Lisa K

    2002-09-01

    CD4 T cells recognize peptides bound to major histocompatibility complex (MHC) class II molecules. Most MHC class II molecules have four binding pockets occupied by amino acids 1, 4, 6, and 9 of the minimal peptide epitope, while the residues at positions 2, 3, 5, 7, and 8 are available to interact with the T cell receptor (TCR). In addition MHC class II bound peptides have flanking residues situated outside of this peptide core. Here we demonstrate that the flanking residues of the conalbumin peptide bound to I-A(k) have no effect on recognition by the D10 TCR. To study the role of peptide flanks for recognition by a second TCR, we determined the MHC and TCR contacting amino acids of the I-A(b) bound Ealpha peptide. The Ealpha peptide is shown to bind I-A(b) using four alanines as anchor residues. TCR recognition of Ealpha peptides with altered flanking residues again suggested that, in general, no specific interactions occurred with the peptide flanks. However, using an HLA-DM-mediated technique to measure peptide binding to MHC class II molecules, we found that the peptide flanking residues contribute substantially to MHC binding.

  19. The Substitution Principle within the REACH Regulation: Nuclear Receptor-Bound Endocrine Disruptors

    Directory of Open Access Journals (Sweden)

    Stefano Lorenzetti

    2017-09-01

    Full Text Available Within the REACH Regulation (EC/1907/2006, the substitution principle for chemicals classified as Substances of Very High Concern (SVHC for either human health or environmental risks has been implemented in order to support their replacement by suitable alternatives. Considering the thousands of chemicals to be tested within the frame of REACH, animal testing by internationally-accepted guidelines sounds unreasonable in terms of the required time, costs as well ethical issues. Hence, REACH recommended also the use of alternative methods to animal experimentation although no validated in silico or in vitro tools were available when regulation entried into force. To search for suitable alternatives to SVHC having an Endocrine Disruptor (ED-like Mode-of-Action (MoA by means of an integrated, tiered in silico-in vitro approach, the EU-granted project LIFE-EDESIA (contract no. LIFE12 ENV/IT/000633 is combining computational-based tools and cell-based bioassays, in order to develop a no-animal testing procedure to screen for chemicals having less or no toxicity in terms of endocrine disruption-like activities. A general view of the no-animal testing approach implementing REACH and the substitution principle will be given, emphasising ligand-nuclear receptor (NR assessment by molecular docking (one of the LIFE-EDESIA in silico approaches and the use of clinical biomarkers in in vitro toxicology to detect ED-like adverse effects in cell-based bioassays.

  20. Semidefinite bounds for nonbinary codes based on quadruples

    NARCIS (Netherlands)

    Litjens, B.; Polak, S.; Schrijver, A.

    For nonnegative integers q, n, d, let Aq(n, d) denote the maximum cardinality of a code of length n over an alphabet [q] with q letters and with minimum distance at least d. We consider the following upper bound on Aq(n, d). For any k, let Ck be the collection of codes of cardinality at most k. Then

  1. Crystal structure of the human urokinase plasminogen activator receptor bound to an antagonist peptide

    DEFF Research Database (Denmark)

    Llinas, Paola; Le Du, Marie Hélène; Gårdsvoll, Henrik

    2005-01-01

    . This knowledge combined with the discovery of a convergent binding motif shared by the antagonist peptide and uPA allowed us to build a model of the human uPA-uPAR complex. This model reveals that the receptor-binding module of uPA engages the uPAR central cavity, thus leaving the external receptor surface...

  2. Spectral and DFT studies of anion bound organic receptors: Time dependent studies and logic gate applications.

    Science.gov (United States)

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

    2017-01-01

    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, (1)H 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 (1)H NMR titration and TDDFT studies provide full support of the binding mechanism. The Hg(2+) and F(-) ion sensing property of receptor R1 has been utilized to arrive at "AND" and "INHIBIT" molecular logic gate applications.

  3. Fast concurrent array-based stacks, queues and deques using fetch-and-increment-bounded, fetch-and-decrement-bounded and store-on-twin synchronization primitives

    Science.gov (United States)

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

    2014-09-16

    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.

  4. A model for short alpha-neurotoxin bound to nicotinic acetylcholine receptor from Torpedo californica.

    Science.gov (United States)

    Mordvintsev, Dmitry Y; Polyak, Yakov L; Kuzmine, Dmitry A; Levtsova, Olga V; Tourleigh, Yegor V; Kasheverov, Igor E

    2006-01-01

    Short- and long-chain alpha-neurotoxins from snake venoms are potent blockers of nicotinic acetylcholine receptors (nAChRs). Short alpha-neurotoxins consist of 60-62 amino acid residues and include 4 disulfide bridges, whereas long alpha-neurotoxins have 66-75 residues and 5 disulfides. The spatial structure of these toxins is built by three loops, I-III "fingers," confined by four disulfide bridges; the fifth disulfide of long-chain alpha-neurotoxins is situated close to the tip of central loop II. An accurate knowledge of the mode of alpha-neurotoxin-nAChR interaction is important for rational design of new nAChR agonists and antagonists for medical purposes. Ideas on the topography of toxin-nAChR complexes were based until recently on nAChR interactions with selectively labeled alpha-neurotoxins, mutations in toxins, nAChR, or both. Recently, crystal structures have been solved for the Torpedo marmorata nAChR (4A[Unwin, 2005]) and for the acetylcholine-binding protein (AChBP) complexed with mollusk alpha-conotoxin (2.4 A[Celie et al., 2005]) or alpha-cobratoxin, long-chain alpha-neurotoxin (4 A [Bourne et al., 2005]). However, there were no angstrom-resolution models for complexes of short-chain alpha-neurotoxins. Here, we report the model of the Torpedo californica nAChR extracellular domain complexed to a short-chain alpha-neurotoxin II (NTII) from Naja oxiana cobra venom.

  5. 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

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

    Science.gov (United States)

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

    2013-01-01

    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. 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. 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. 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 molecular tracers for male breast cancer.

  7. Ligand-bound quantum dots for intracellular imaging of neural receptors

    Science.gov (United States)

    Vu, Tania Q.; Sundara Rajan, Sujata; Liu, Hongyan

    2007-02-01

    Quantum dots (QDs) may serve as improved platforms for the complex modulation and ultra-sensitive imaging of molecular signaling in cells. The time course and spatial localization of activated ligand-receptor complexes and their trafficking within cells is becoming increasingly understood as vital for propagating cell signals. However, the movement and fate of ligand-receptor pairs inside cells is difficult to define with current technologies. We have studied the intracellular trafficking of TrkA receptors using QDs conjugated with nerve growth factor, a neuropeptide ligand critical for nervous system development and regulation. We find that NGF-QDs bind and activate TrkA surface receptors in PC12 neurons. Spatiotemporal maps of TrkA-NGF-QD endocytosis and translocation can be directly visualized with single QD resolution. Moreover, single molecule tracking experiments indicates that QDs complexes are actively shuttled over long distances within newly-sprouted neuronal processes. These results indicate that QDs can serve as effective high-resolution probe to track ligand-receptor function in the interior of cells.

  8. Boundedly Rational versus Optimization-Based Models of Strategic Thinking and Learning in Games

    OpenAIRE

    Crawford, Vincent P

    2013-01-01

    Harstad and Selten’s article in this forum performs a valuable service by highlighting the dominance of optimization-based models over boundedly rational models in modern microeconomics, and questioning whether optimization-based models are a better way forward than boundedly rational models. This article complements Rabin’s response to Harstad and Selten, focusing on modeling strategic behavior. I consider Harstad and Selten’s examples and proposed boundedly rational models in the ligh...

  9. EVALUATION OF A PURIFICATION PROCEDURE FOR THE MUSCARINIC RECEPTOR FOR THE PURPOSE OF QUANTITATIVE RECEPTOR ASSAYS OF ANTICHOLINERGICS .A. THE MEMBRANE-BOUND RECEPTOR

    NARCIS (Netherlands)

    SMISTEROVA, J; ENSING, K; DEZEEUW, RA

    1995-01-01

    The presented purification procedure for the muscarinic receptor from calf striatum includes the extraction of lipids with hexane in the first step and the removal of 39% of non-receptor proteins with 2 M NaCl in the second step. The simplicity of such an approach to the purification of the receptor

  10. Plasminogen activation by receptor-bound urokinase. A kinetic study with both cell-associated and isolated receptor

    DEFF Research Database (Denmark)

    Ellis, V; Behrendt, N; Danø, K

    1991-01-01

    .67 microM, below the physiological Plg concentration of 2 microM. A concomitant 6-fold reduction in kcat resulted in an increase in the overall catalytic efficiency, kcat/Km, of 5.7-fold. This high affinity Plg activation was abolished in the presence of a Plg-binding antagonist. In contrast to intact...... cells, purified uPA receptor (isolated from phorbol 12-myristate 13-acetate-stimulated U937 cells) was observed to partially inhibit uPA-catalyzed Plg activation, although activity against low molecular weight substrates was retained. Therefore, the cellular binding of Plg appears to be of critical...

  11. Spectral and DFT studies of anion bound organic receptors: Time dependent studies and logic gate applications

    Directory of Open Access Journals (Sweden)

    Srikala Pangannaya

    2017-02-01

    Full Text Available 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.

  12. Clinical Research on Albumin-bound Paclitaxel-based Therapy in Advanced Lung Cancer

    Directory of Open Access Journals (Sweden)

    Xu LI

    2017-06-01

    Full Text Available Background and objective Albumin-bound paclitaxel is a novel paclitaxel formulation formed by the combination of paclitaxel and human serum albumin (HSA to improve the efficacy of paclitaxel and reduce its adverse reactions. The aim of this retrospective study is to observe the efficacy and safety of albumin-bound paclitaxel-based therapy in the treatment of lung cancer. Methods We have enrolled 50 patients with advanced or unresectable retreatment lung cancer who were admitted from November 2011 to December 2014. All patients were treated with albumin-bound paclitaxel-based therapy with a 21 day cycle (albumin-bound paclitaxel weekly by intravenous dose of 130 mg/m2 on day 1 and day 8. Efficacy was evaluated every two cycles according to Response Evaluation Criteria in Solid Tumors (RECIST 1.1 and side effects were observed during each cycle. All patients were evaluated. Results The total objective response rate (ORR of albumin-bound paclitaxel-based therapy was 20%, disease control rate (DCR was 68%. In the subgroup analysis, in squamous non-small-cell lung carcinoma groups, ORR and DCR were 26.7% and 80% respectively. Albumin-bound paclitaxel based chemotherapy combined anti-angiogenesis therapy had a promising overall response rate 36.4%. In the patients who had been previously treated with≥4 lines of chemotherapy DCR also reached 69.2%. The most common adverse reactions were hematologic toxicities and were all manageable, no hypersensitivity reactions or treatment-related grade 4 adverse events were reported. Conclusion Weekly albumin-bound paclitaxel is effective and well tolerated in the treatment of advanced lung cancer including all histological subtypes. Albumin-bound paclitaxel was associated with superior efficacy in patients with squamous (SCC histology and combined with anti-angiogenesis therapy. Albumin-bound paclitaxel shown to be an effective and safe regimen for elderly or previous heavily treated patients.

  13. Membrane-bound progesterone receptors coupled to G proteins in the fungus Rhizopus nigricans.

    Science.gov (United States)

    Lenasi, Helena; Bavec, Aljosa; Zorko, Matjaz

    2002-07-16

    Steroid binding sites with high affinity for progesterone (Kd=40+/-14 nM determined by binding, and Kd=71+/-22 nM determined by displacement studies) and lower affinity for 21-hydroxyprogesterone and for testosterone, but no affinity for estradiol-17beta, onapristone and alpha-naphthoflavone were detected in the enriched plasma membrane fraction of the fungus Rhizopus nigricans. The amount of steroid binding sites is in accordance with the value of B(max)=744+/-151 fmol (mg protein)(-1). In the membrane fraction, progesterone induced about 30% activation of G proteins over basal level, as determined by GTPase activity (EC50=32+/-8 nM) and by the guanosine 5'-O-(3-thiotriphosphate) (GTPgammaS) binding rate (EC50=61+/-21 nM). The affinity of receptors for progesterone was substantially decreased in the presence of GTPgammaS and of cholera toxin. Our results suggest the existence of progesterone receptors in the membrane of Rhizopus nigricans and their coupling to G proteins.

  14. Fluctuations of cytoskeleton-bound microbeads-the effect of bead-receptor binding dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Metzner, C; Raupach, C; Mierke, C T; Fabry, B, E-mail: bfabry@biomed.uni-erlangen.d [Center for Medical Physics and Technology, University of Erlangen-Nuremberg, Erlangen (Germany)

    2010-05-19

    The cytoskeleton (CSK) of living cells is a crosslinked fiber network, subject to ongoing biochemical remodeling processes that can be visualized by tracking the spontaneous motion of CSK-bound microbeads. The bead motion is characterized by anomalous diffusion with a power-law time evolution of the mean square displacement (MSD), and can be described as a stochastic transport process with apparent diffusivity D and power-law exponent {beta}: MSD {approx} D (t/t{sub 0}){sup {beta}}. Here we studied whether D and {beta} change with the time that has passed after the initial bead-cell contact, and whether they are sensitive to bead coating (fibronectin, integrin antibodies, poly-L-lysine, albumin) and bead size (0.5-4.5 {mu}m). The measurements are interpreted in the framework of a simple model that describes the bead as an overdamped particle coupled to the fluctuating CSK network by an elastic spring. The viscous damping coefficient characterizes the degree of bead internalization into the cell, and the spring constant characterizes the strength of the binding of the bead to the CSK. The model predicts distinctive signatures of the MSD that change with time as the bead couples more tightly to the CSK and becomes internalized. Experimental data show that the transition from the unbound to the tightly bound state occurs in an all-or-nothing manner. The time point of this transition shows considerable variability between individual cells (2-30 min) and depends on the bead size and bead coating. On average, this transition occurs later for smaller beads and beads coated with ligands that trigger the formation of adhesion complexes (fibronectin, integrin antibodies). Once the bead is linked to the CSK, however, the ligand type and bead size have little effect on the MSD. On longer timescales of several hours after bead addition, smaller beads are internalized into the cell more readily, leading to characteristic changes in the MSD that are consistent with increased

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

    Science.gov (United States)

    Ohdaira, Tetsushi

    2014-07-01

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

  16. A Deep Monotone Approximation Operator Based on the Best Quadratic Lower Bound of Convex Functions

    Science.gov (United States)

    Yamagishi, Masao; Yamada, Isao

    This paper presents a closed form solution to a problem of constructing the best lower bound of a convex function under certain conditions. The function is assumed (I) bounded below by -ρ, and (II) differentiable and its derivative is Lipschitz continuous with Lipschitz constant L. To construct the lower bound, it is also assumed that we can use the values ρ and L together with the values of the function and its derivative at one specified point. By using the proposed lower bound, we derive a computationally efficient deep monotone approximation operator to the level set of the function. This operator realizes better approximation than subgradient projection which has been utilized, as a monotone approximation operator to level sets of differentiable convex functions as well as nonsmooth convex functions. Therefore, by using the proposed operator, we can improve many signal processing algorithms essentially based on the subgradient projection.

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

    KAUST Repository

    Rungta, Meha

    2013-08-02

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

  18. The T-Cell Receptor Can Bind to the Peptide-Bound Major Histocompatibility Complex and Uncomplexed β2-Microglobulin through Distinct Binding Sites

    DEFF Research Database (Denmark)

    Merkle, Patrick S; Irving, Melita; Hongjian, Song

    2017-01-01

    T-Cell receptor (TCR)-mediated recognition of the peptide-bound major histocompatibility complex (pMHC) initiates an adaptive immune response against antigen-presenting target cells. The recognition events take place at the TCR-pMHC interface, and their effects on TCR conformation and dynamics...

  19. The role of transferrin receptor 1 and 2 in transferrin-bound iron uptake in human hepatoma cells.

    Science.gov (United States)

    Herbison, Carly E; Thorstensen, Ketil; Chua, Anita C G; Graham, Ross M; Leedman, Peter; Olynyk, John K; Trinder, Debbie

    2009-12-01

    Transferrin receptor (TFR) 1 and 2 are expressed in the liver; TFR1 levels are regulated by cellular iron levels while TFR2 levels are regulated by transferrin saturation. The aims of this study were to 1) determine the relative importance of TFR1 and TFR2 in transferrin-bound iron (TBI) uptake by HuH7 human hepatoma cells and 2) characterize the role of metal-transferrin complexes in the regulation of these receptors. TFR expression was altered by 1) incubation with metal-transferrin (Tf) complexes, 2) TFR1 and TFR2 small interfering RNA knockdown, and 3) transfection with a human TFR2 plasmid. TBI uptake was measured using (59)Fe-(125)I-labeled Tf and mRNA and protein expression by real-time PCR and Western blot analysis, respectively. Fe(2)Tf, Co(2)Tf, and Mn(2)Tf increased TFR2 protein expression, indicating that the upregulation was not specifically regulated by iron-transferrin but also other metal-transferrins. In addition, Co(2)Tf and Mn(2)Tf upregulated TFR1, reduced ferritin, and increased hypoxia-inducible factor-1alpha protein expression, suggesting that TFR1 upregulation was due to a combination of iron deficiency and chemical hypoxia. TBI uptake correlated with changes in TFR1 but not TFR2 expression. TFR1 knockdown reduced iron uptake by 80% while TFR2 knockdown did not affect uptake. At 5 microM transferrin, iron uptake was not affected by combined TFR1 and TFR2 knockdown. Transfection with a hTFR2 plasmid increased TFR2 protein expression, causing a 15-20% increase in iron uptake and ferritin levels. This shows for the first time that TFR-mediated TBI uptake is mediated primarily via TFR1 but not TFR2 and that a high-capacity TFR-independent pathway exists in hepatoma cells.

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

    KAUST Repository

    Bae, Sang Won

    2016-03-21

    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.

  1. Rule-based and Resource-bounded: A New Look at Epistemic Logic

    OpenAIRE

    Jago, Mark

    2006-01-01

    Syntactic logics do not suffer from the problems of logical omniscience but are often thought to lack interesting properties relating to epistemic notions. By focusing on the case of rule-based agents, I develop a framework for modelling resource-bounded agents and show that the resulting models have a number of interesting properties.

  2. 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. (Stanford-MED); (ConfometRx); (UCB Pharma)

    2017-02-06

    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.

  3. A simple method to evaluate the optimal size of nanoparticles for endocytosis based on kinetic diffusion of receptors

    Science.gov (United States)

    Li, Xinlei; Xing, Da

    2010-10-01

    We have presented an analytic thermodynamic model to elucidate the mechanism of receptor-mediated endocytosis of nanoparticles (NPs) and provided a simple method to evaluate the optimal size of NPs by minimizing the kinetic diffusion time of the free receptors around the bound region toward the contact surface with NPs. It is found that the average density of receptors and chemical energy release upon the binding of a ligand-receptor pair determine the optimal size of NPs if the bending modulus of membranes and the cross-sectional area of the receptor are constants. The optimal radius of NPs can be calculated based on our model.

  4. 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 to the L......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...... to the Lagrangean subproblem. Branching decisions are then based on this estimated (fractional) primal solution. Extensive numerical results reveal that the method is much more faster and robust than other state-of-the-art methods for solving the CFLP exactly....

  5. The crystal structure of the interleukin 21 receptor bound to interleukin 21 reveals that a sugar chain interacting with the WSXWS motif is an integral part of the interleukin 21 receptor

    DEFF Research Database (Denmark)

    Hamming, Ole Jensen; Kang, Lishan; Svensson, Anders

    2012-01-01

    Interleukin (IL) 21 is a class I cytokine, which exerts pleiotropic effects on both innate and adaptive immune responses. It signals through a heterodimeric receptor complex consisting of the IL-21 receptor (IL-21R) and the common gamma chain (gC). A hallmark of the class I cytokine receptors...... to be a consensus sequence for C-mannosylation. Here we present the crystal structure of IL-21 bound to IL-21R and reveal that the WSXWS motif of IL-21R is C-mannosylated on the first tryptophan. We furthermore demonstrate that a sugar chain bridge the two fibronectin domains which constitute the extracellular...

  6. Random Coding Bounds for DNA Codes Based on Fibonacci Ensembles of DNA Sequences

    Science.gov (United States)

    2008-07-01

    Highway, Suite 1204, Arlington, VA 22202-4302, and to the Office of Management and Budget, Paperwork Reduction Project (0704-0188) Washington, DC...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

  7. Bounds on the vibrational energy that can be harvested from random base motion

    Science.gov (United States)

    Langley, R. S.

    2015-03-01

    This paper is concerned with the development of upper bounds on the energy harvesting performance of a general multi-degree-of-freedom nonlinear electromechanical system that is subjected to random base motion and secondary applied periodic forces. The secondary forces are applied with the aim of enhancing the energy harvested from the base motion, and they may constitute direct excitation, or they may produce parametric terms in the equations of motion. It is shown that when the base motion has white noise acceleration then the power input by the base is always πS0 M / 2 where S0 is the single sided spectral density of the acceleration, and M is the mass of the system. This implies that although the secondary forces may enhance the energy harvested by causing a larger fraction of the power input from the base to be harvested rather than dissipated, there is an upper limit on the power that can be harvested. Attention is then turned to narrow band excitation, and it is found that in the absence of secondary forces a bound can be derived for a single degree of freedom system with linear damping and arbitrary nonlinear stiffness. The upper bound on the power input by the base is πM max [ S (ω) ] / 2, where S (ω) is the single sided base acceleration spectrum. The validity of this result for more general systems is found to be related to the properties of the first Wiener kernel, and this issue is explored analytically and by numerical simulation.

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

    Energy Technology Data Exchange (ETDEWEB)

    Newcomer, Justin T.; Freeland, Katherine Elizabeth

    2013-09-01

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

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

    Science.gov (United States)

    Hong, Wei; Chen, Linfeng; Li, Juan; Yao, Zhi

    2010-05-28

    Estrogen receptor alpha (ERalpha), a ligand controlled transcription factor, plays an important role in breast cancer growth and endocrine therapy. Tamoxifen (TAM) antagonizes ERalpha activity and has been applied in breast cancer treatment. TAM-bound ERalpha associates with nuclear receptor-corepressors. Mitogen-activated protein kinase (MAPK) has been elucidated to result in cross-talk between growth factor and ERalpha mediated signaling. We show that activated MAPK represses interaction of TAM-bound ERalpha with silencing mediator for retinoid and thyroid hormone receptors (SMRT) and inhibits the recruitment of SMRT by ERalpha to certain estrogen target genes. Blockade of MAPK signaling cascade with MEK inhibitor U0126 promotes the interaction and subsequently inhibits ERalpha activity via enhanced recruitment of SMRT, leading to reduced expression of ERalpha target genes. The growth rate of MCF-7 cells was decelerated when treated with both TAM and U0126. Moreover, the growth of MCF-7 cells stably expressing SMRT showed a robust repression in the presence of TAM and U0126. These results suggest that activated MAPK signaling cascade attenuates antagonist-induced recruitment of SMRT to ERalpha, suggesting corepressor mediates inhibition of ERalpha transactivation and breast cancer cell growth by antagonist. Taken together, our finding indicates combination of antagonist and MAPK inhibitor could be a helpful approach for breast cancer therapy. Copyright (c) 2010 Elsevier Inc. All rights reserved.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-05-28

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

  11. Exchange of bound estrogens and antiestrogens in MCF-7 cells: evidence for ligand-induced stable configurations of the estrogen receptor.

    Science.gov (United States)

    El khissiin, A; Leclercq, G

    1998-11-01

    Estrogens and antiestrogens promote specific conformations of the estrogen receptor (ER). To analyze the influence of such configurations on the stability of the ligand-ER complexes, MCF-7 breast cancer cells were exposed for 1 h to either [3H]E2 or an unlabeled estrogen or antiestrogen (E2, DES, E1, BP; OH-Tam, RU 39,411, ICI 164,384, RU 58,668); mutual exchange rates of bound compounds (i.e., [3H]E2-->ligand; ligand-->[3H]E2) were then analyzed in cell extracts by measuring [3H]E2. Addition of cycloheximide (CHX) to the incubation medium eliminated the potential interference of E2-induced ER loss. Extracts from control untreated cells were labeled with [3H]E2 or one of these various ligands and similarly submitted to exchange. Displacement of bound compounds occurred at moderate temperature (18 degrees C) but not at 4 degrees C. Remarkably, exchange proceeded at a lower rate in extracts from cells preincubated with [3H]E2 or a ligand. Antiestrogens RU 39,411 and RU 58,668 appeared especially refractory to displacement. Such low exchange rates were also recorded in experiments conducted on whole cells although to a higher extent than in extracts from preincubated cells. Enzyme immunoassays demonstrated that absence of major exchange could not be attributed to ER loss. Moreover, displacement of bound ligands appeared independent of their binding affinity for the receptor. These data suggest that estrogen and antiestrogen binding is stabilized by at least one factor (coactivators or corepressors) thus fixing the receptor molecules in a configuration that is relatively resistant to subsequent exchange. FPLC and PgR induction revealed that a significant proportion of ER maintained in a sufficiently flexible status was still able to exchange and transduce the transcriptional message of the displacer ligand.

  12. Accelerating rejection-based simulation of biochemical reactions with bounded acceptance probability.

    Science.gov (United States)

    Thanh, Vo Hong; Priami, Corrado; Zunino, Roberto

    2016-06-14

    Stochastic simulation of large biochemical reaction networks is often computationally expensive due to the disparate reaction rates and high variability of population of chemical species. An approach to accelerate the simulation is to allow multiple reaction firings before performing update by assuming that reaction propensities are changing of a negligible amount during a time interval. Species with small population in the firings of fast reactions significantly affect both performance and accuracy of this simulation approach. It is even worse when these small population species are involved in a large number of reactions. We present in this paper a new approximate algorithm to cope with this problem. It is based on bounding the acceptance probability of a reaction selected by the exact rejection-based simulation algorithm, which employs propensity bounds of reactions and the rejection-based mechanism to select next reaction firings. The reaction is ensured to be selected to fire with an acceptance rate greater than a predefined probability in which the selection becomes exact if the probability is set to one. Our new algorithm improves the computational cost for selecting the next reaction firing and reduces the updating the propensities of reactions.

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

    Directory of Open Access Journals (Sweden)

    Markus Kiderlen

    2011-05-01

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

  14. Lower bound of multipartite concurrence based on sub-partite quantum systems

    Science.gov (United States)

    Chen, Wei; Zhu, Xue-Na; Fei, Shao-Ming; Zheng, Zhu-Jun

    2017-12-01

    We study the concurrence of arbitrary dimensional multipartite quantum systems. An explicit analytical lower bound of concurrence for four-partite mixed states is obtained in terms of the concurrences of tripartite mixed states. Detailed examples are given to show that our lower bounds improve the existing lower bounds of concurrence. The approach is generalized to five-partite quantum systems.

  15. Translation of Neologisms and Culture-Bound Items Based on The Witcher: A Sample Introductory Analysis

    Directory of Open Access Journals (Sweden)

    Aneta Daniel

    2016-03-01

    Full Text Available The subject of the investigation is the translation of neologism and culture-bound items based on the first chapter of the third book of The Witcher Saga, entitled Baptism of Fire. The analyzed fragment abounds in neologisms and nomenclature; therefore, the processes of word formation are briefly described. Furthermore, some of Hejwowski’s ([2004] 2009, pp. 76–83 procedures are cited to present methods of dealing with the creativity resulting from word formation processes. It is shown that a translator, when translating culture-bound items, is not always able to find an equivalent in the target language and may try either to describe a certain phenomenon or to use a literal translation. The way in which neologisms are coined in a fictional novel may differ from the coinage of words in the standard language; nevertheless, the word formation processes are the same as in Standard English or Standard Polish. Moreover, there is still little evidence of what makes a borrowed word catch on in the standard language.

  16. Structure-Based Drug Design of Mineralocorticoid Receptor Antagonists to Explore Oxosteroid Receptor Selectivity.

    Science.gov (United States)

    Nordqvist, Anneli; O'Mahony, Gavin; Fridén-Saxin, Maria; Fredenwall, Marlene; Hogner, Anders; Granberg, Kenneth L; Aagaard, Anna; Bäckström, Stefan; Gunnarsson, Anders; Kaminski, Tim; Xue, Yafeng; Dellsén, Anita; Hansson, Eva; Hansson, Pia; Ivarsson, Ida; Karlsson, Ulla; Bamberg, Krister; Hermansson, Majlis; Georgsson, Jennie; Lindmark, Bo; Edman, Karl

    2017-01-05

    The mineralocorticoid receptor (MR) is a nuclear hormone receptor involved in the regulation of body fluid and electrolyte homeostasis. In this study we explore selectivity triggers for a series of nonsteroidal MR antagonists to improve selectivity over other members of the oxosteroid receptor family. A biaryl sulfonamide compound was identified in a high-throughput screening (HTS) campaign. The compound bound to MR with pKi =6.6, but displayed poor selectivity over the glucocorticoid receptor (GR) and the progesterone receptor (PR). Following X-ray crystallography of MR in complex with the HTS hit, a compound library was designed that explored an induced-fit hypothesis that required movement of the Met852 side chain. An improvement in MR selectivity of 11- to 79-fold over PR and 23- to 234-fold over GR was obtained. Given the U-shaped binding conformation, macrocyclizations were explored, yielding a macrocycle that bound to MR with pKi =7.3. Two protein-ligand X-ray structures were determined, confirming the hypothesized binding mode for the designed compounds. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Cramer-Rao lower bound optimization of an EM-CCD-based scintillation gamma camera.

    Science.gov (United States)

    Korevaar, Marc A N; Goorden, Marlies C; Beekman, Freek J

    2013-04-21

    Scintillation gamma cameras based on low-noise electron multiplication (EM-)CCDs can reach high spatial resolutions. For further improvement of these gamma cameras, more insight is needed into how various parameters that characterize these devices influence their performance. Here, we use the Cramer-Rao lower bound (CRLB) to investigate the sensitivity of the energy and spatial resolution of an EM-CCD-based gamma camera to several parameters. The gamma camera setup consists of a 3 mm thick CsI(Tl) scintillator optically coupled by a fiber optic plate to the E2V CCD97 EM-CCD. For this setup, the position and energy of incoming gamma photons are determined with a maximum-likelihood detection algorithm. To serve as the basis for the CRLB calculations, accurate models for the depth-dependent scintillation light distribution are derived and combined with a previously validated statistical response model for the EM-CCD. The sensitivity of the lower bounds for energy and spatial resolution to the EM gain and the depth-of-interaction (DOI) are calculated and compared to experimentally obtained values. Furthermore, calculations of the influence of the number of detected optical photons and noise sources in the image area on the energy and spatial resolution are presented. Trends predicted by CRLB calculations agree with experiments, although experimental values for spatial and energy resolution are typically a factor of 1.5 above the calculated lower bounds. Calculations and experiments both show that an intermediate EM gain setting results in the best possible spatial or energy resolution and that the spatial resolution of the gamma camera degrades rapidly as a function of the DOI. Furthermore, calculations suggest that a large improvement in gamma camera performance is achieved by an increase in the number of detected photons or a reduction of noise in the image area. A large noise reduction, as is possible with a new generation of EM-CCD electronics, may improve the

  18. Muscarinic receptors as model targets and antitargets for structure-based ligand discovery.

    Science.gov (United States)

    Kruse, Andrew C; Weiss, Dahlia R; Rossi, Mario; Hu, Jianxin; Hu, Kelly; Eitel, Katrin; Gmeiner, Peter; Wess, Jürgen; Kobilka, Brian K; Shoichet, Brian K

    2013-10-01

    G protein-coupled receptors (GPCRs) regulate virtually all aspects of human physiology and represent an important class of therapeutic drug targets. Many GPCR-targeted drugs resemble endogenous agonists, often resulting in poor selectivity among receptor subtypes and restricted pharmacologic profiles. The muscarinic acetylcholine receptor family exemplifies these problems; thousands of ligands are known, but few are receptor subtype-selective and nearly all are cationic in nature. Using structure-based docking against the M2 and M3 muscarinic receptors, we screened 3.1 million molecules for ligands with new physical properties, chemotypes, and receptor subtype selectivities. Of 19 docking-prioritized molecules tested against the M2 subtype, 11 had substantial activity and 8 represented new chemotypes. Intriguingly, two were uncharged ligands with low micromolar to high nanomolar Ki values, an observation with few precedents among aminergic GPCRs. To exploit a single amino-acid substitution among the binding pockets between the M2 and M3 receptors, we selected molecules predicted by docking to bind to the M3 and but not the M2 receptor. Of 16 molecules tested, 8 bound to the M3 receptor. Whereas selectivity remained modest for most of these, one was a partial agonist at the M3 receptor without measurable M2 agonism. Consistent with this activity, this compound stimulated insulin release from a mouse β-cell line. These results support the ability of structure-based discovery to identify new ligands with unexplored chemotypes and physical properties, leading to new biologic functions, even in an area as heavily explored as muscarinic pharmacology.

  19. Characterization of Thrombin-Bound Dabigatran Effects on Protease-Activated Receptor-1 Expression and Signaling In Vitro

    Science.gov (United States)

    Chen, Buxin; Soto, Antonio G.; Coronel, Luisa J.; Goss, Ashley; van Ryn, Joanne

    2015-01-01

    Thrombin, the key effector protease of the coagulation cascade, drives fibrin deposition and activates human platelets through protease-activated receptor-1 (PAR1). These processes are critical to the progression of thrombotic diseases. Thrombin is the main target of anticoagulant therapy, and major efforts have led to the discovery of new oral direct inhibitors of thrombin. Dabigatran is the first oral anticoagulant licensed for the prevention of thromboembolisms associated with orthopedic surgery and stroke prevention in atrial fibrillation. Dabigatran is a direct thrombin inhibitor that effectively blocks thrombin’s catalytic activity but does not preclude thrombin’s exosites and binding to fibrinogen. Thus, we hypothesized that catalytically inactive thrombin retains the capacity to bind to PAR1 through exosite-I and may modulate its function independent of receptor cleavage and activation. Here, we report that dabigatran at clinically relevant concentrations is an effective and acute inhibitor of thrombin-induced PAR1 cleavage, activation, internalization, and β-arrestin recruitment in vitro. Interestingly, prolonged exposure to catalytic inactive thrombin incubated with dabigatran at 20-fold higher therapeutic concentration resulted in increased PAR1 cell-surface expression, which correlated with higher detectable levels of ubiquitinated receptor. These findings are consistent with ubiquitin function as a negative regulator of PAR1 constitutive internalization. Increased PAR1 expression also enhanced agonist-induced phosphoinositide hydrolysis and endothelial barrier permeability. Thus, catalytically inactive thrombin appears to modulate PAR1 function in vitro by stabilizing receptor cell-surface expression; but given the high clearance rate of thrombin, the high concentration of dabigatran required to achieve this effect the in vivo physiologic relevance is unknown. PMID:25934730

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

    NARCIS (Netherlands)

    Truetsch, U.

    2014-01-01

    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

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

    NARCIS (Netherlands)

    Gijswijt, D.C.; Schrijver, A.

    2006-01-01

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

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

    NARCIS (Netherlands)

    D. Gijswijt (Dion); A. Schrijver (Alexander); H. Tanaka

    2006-01-01

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

  3. Active disturbance rejection based trajectory linearization control for hypersonic reentry vehicle with bounded uncertainties.

    Science.gov (United States)

    Shao, Xingling; Wang, Honglun

    2015-01-01

    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. Copyright © 2014 ISA. Published by Elsevier Ltd. All rights reserved.

  4. Model-based control of transitional and turbulent wall-bounded shear flows

    Science.gov (United States)

    Moarref, Rashad

    Turbulent flows are ubiquitous in nature and engineering. Dissipation of kinetic energy by turbulent flow around airplanes, ships, and submarines increases resistance to their motion (drag). In this dissertation, we have designed flow control strategies for enhancing performance of vehicles and other systems involving turbulent flows. While traditional flow control techniques combine physical intuition with costly numerical simulations and experiments, we have developed control-oriented models of wall-bounded shear flows that enable simulation-free and computationally-efficient design of flow controllers. Model-based approach to flow control design has been motivated by the realization that progressive loss of robustness and consequential noise amplification initiate the departure from the laminar flow. In view of this, we have used the Navier-Stokes equations with uncertainty linearized around the laminar flow as a control-oriented model for transitional flows and we have shown that reducing the sensitivity of fluctuations to external disturbances represents a powerful paradigm for preventing transition. In addition, we have established that turbulence modeling in conjunction with judiciously selected linearization of the flow with control can be used as a powerful control-oriented model for turbulent flows. We have illustrated the predictive power of our model-based control design in three concrete problems: preventing transition by (i) a sensorless strategy based on traveling waves and (ii) an optimal state-feedback controller based on local flow information; and (iii) skin-friction drag reduction in turbulent flows by transverse wall oscillations. We have developed analytical and computational tools based on perturbation analysis (in the control amplitude) for control design by means of spatially- and temporally- periodic flow manipulation in problems (i) and (iii), respectively. In problem (ii), we have utilized tools for designing structured optimal state

  5. Transfer Function Bounds for Partial-unit-memory Convolutional Codes Based on Reduced State Diagram

    Science.gov (United States)

    Lee, P. J.

    1984-01-01

    The performance of a coding system consisting of a convolutional encoder and a Viterbi decoder is analytically found by the well-known transfer function bounding technique. For the partial-unit-memory byte-oriented convolutional encoder with m sub 0 binary memory cells and (k sub 0 m sub 0) inputs, a state diagram of 2(K) (sub 0) was for the transfer function bound. A reduced state diagram of (2 (m sub 0) +1) is used for easy evaluation of transfer function bounds for partial-unit-memory codes.

  6. Ultrasensitive optical absorption in graphene based on bound states in the continuum

    National Research Council Canada - National Science Library

    Zhang, Mingda; Zhang, Xiangdong

    2015-01-01

    We have designed a sphere-graphene-slab structure so that the electromagnetic wave can be well confined in the graphene due to the formation of a bound state in a continuum (BIC) of radiation modes...

  7. 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

    2017-01-01

    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...

  8. Turbulence modeling for flows in wall bounded porous media: An analysis based on direct numerical simulations

    Science.gov (United States)

    Jin, Y.; Kuznetsov, A. V.

    2017-04-01

    Various models are available for simulating turbulent flows in porous media. Models based on the eddy viscosity assumption are often adopted to close the Reynolds stress term. In order to validate the assumptions behind such turbulence models, we studied the dynamics of macroscopic momentum and turbulence kinetic energy in porous media flows by utilizing Direct Numerical Simulation (DNS). The generic porous matrix is composed of regularly arranged spheres. The resulting periodic porous medium is bounded by two walls. The DNS analyses with a Lattice Boltzmann method were performed for various values of the applied pressure gradient, pore size to channel width ratio, and porosity. The DNS results were averaged over time and volume to obtain macroscopic results. The results show that the macroscopic shear Reynolds stress in all Representative Elementary Volumes (REVs), independent of their location, is negligibly small, although the mean velocity gradient takes nonzero values near the wall. The turbulence kinetic energy production rate is generally balanced by the dissipation rate in each REV. The DNS results support a zero-equation turbulence model that accounts for the fact that turbulent structures are restricted in size by the pore scale. The DNS results also suggest that the Brinkman term, which expresses the diffusion of momentum, has an important effect near the wall where the gradient of the shear stress is large. Therefore, the Brinkman term should be taken into account in the macroscopic momentum equation as a component of the total drag. A preliminary macroscopic model for calculating turbulent porous media flows has been proposed and compared with our DNS results.

  9. 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

  10. The DMM Bound

    DEFF Research Database (Denmark)

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

    2010-01-01

    In this paper we derive aggregate separation bounds, named after Davenport-Mahler-Mignotte (DMM), on the isolated roots of polynomial systems, specifically on the minimum distance between any two such roots. The bounds exploit the structure of the system and the height of the sparse (or toric) re...... bound on the number of steps that subdivision-based algorithms perform in order to isolate all real roots of a polynomial system. This leads to the first complexity bound of Milne's algorithm [22] in 2D....

  11. Bounded Rationality and Satisficing in Young People's Web-Based Decision Making.

    Science.gov (United States)

    Agosto, Denise E.

    2002-01-01

    Investigated behavioral decision-making theories of bounded rationality and satisficing in relation to young people's decision making in the World Wide Web and considered the role of personal preferences. Results of this study of ninth- and tenth-grade females consider time constraints, information overload, physical constraints, reduction…

  12. Determination of L-AP4-bound human mGlu8 receptor amino terminal domain structure and the molecular basis for L-AP4's group III mGlu receptor functional potency and selectivity.

    Science.gov (United States)

    Schkeryantz, Jeffery M; Chen, Qi; Ho, Joseph D; Atwell, Shane; Zhang, Aiping; Vargas, Michelle C; Wang, Jing; Monn, James A; Hao, Junliang

    2018-02-15

    L-2-Amino-4-phosphonobutyric acid (L-AP4) is a known potent and selective agonist for the Group III mGlu receptors. However, it does not show any selectivity among the individual group III mGlu subtypes. In order to understand the molecular basis for this group selectivity, we solved the first human mGlu8 amino terminal domain (ATD) crystal structures in complex with L-glu and L-AP4. In comparison with other published L-glu-bound mGlu ATD structures, we have observed L-glu binds in a significantly different manner in mGlu1. Furthermore, these new structures provided evidence that both the electronic and steric nature of the distal phosphate of L-AP4 contribute to its exquisite Group III functional agonist potency and selectivity. Copyright © 2018 Elsevier Ltd. All rights reserved.

  13. Bounded Rationality

    National Research Council Canada - National Science Library

    Ballester Pla, Coralio; Hernández, Penélope

    2012-01-01

    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...

  14. Bounding the $\

    CERN Document Server

    Gutiérrez-Rodríguez, A

    2003-01-01

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

  15. Andreev reflection and bound states in topological insulator based planar and step Josephson junctions

    Science.gov (United States)

    Choudhari, Tarun; Deo, Nivedita

    2017-01-01

    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.

  16. 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

    2013-08-01

    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.

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

    Science.gov (United States)

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

    2007-03-01

    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.

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

    Science.gov (United States)

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

    2013-12-01

    Whole-grain diets are linked to reduced risk of several chronic diseases (heart disease, cancer, diabetes, metabolic syndrome) and all-cause mortality. There is increasing evidence that these benefits are associated with the gut microbiota and that release of fibre-related phenolic metabolites in the gut is a contributing factor. Additional sources of these metabolites include fruits and vegetables, but the evidence for their protective effects is less well established. With respect to the availability of bound phytophenols, ready-to-eat cereals are compared with soft fruits (considered rich in antioxidants) and other commonly consumed fruits and vegetables. The results demonstrated that when compared with an equivalent serving of fruits or vegetables, a recommended portion of whole-grain cereals deliver substantially higher amounts of bound phytophenols, which are available for metabolism in the colon. The increased amount of these phenolic metabolites may, in part, explain the evidence for the protective effects of whole-grain cereals. Copyright © 2013. Published by Elsevier Ltd.

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

    Science.gov (United States)

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

    2014-01-01

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

  20. The development of FRET-based dual receptor optical biosensor

    Science.gov (United States)

    Xu, Juntao

    The focus of the research presented in this dissertation is the development of a new FRET-based dual receptor sensing method for detecting the human immunodeficiency virus (HIV). The new detection method presented in this dissertation imitates the way HIV infects cells. It utilizes the two receptor-binding event and integrates a chemical transducer system with two unique protein receptors, CD4 and mAb (HIV-1 gp120 monoclonal antibody), which both bind to gp120. The chemical transduction system is based on the distance-dependant principle of fluorescence resonance energy transfer (FRET). The work presented in this dissertation attempts to demonstrate the feasibility of this new sensing method both in solution and on an optical fiber. Appropriate FRET pairs which have high energy transfer efficiency as well as good conjugation properties with receptors were selected and optimized. The two receptors, CD4 and mAb which specifically bind to gp120, were conjugated to one of the optimized FRET fluorophore pairs, AMCA-NHS (succinimidyl-7-amino-4-methylcoumarin-3-acetic acid) and FITC (fluorescein isothiocyanate), respectively. For the solution test, the viral protein gp120, which is the featured protein on the surface of HIV-1, was detected by the mixed solution of the two FRET pair tagged receptors. A spectrofluorometer was used to detect the fluorescent change between AMCA-NHS and FITC peak intensities when the receptors bind to the gp120. Specific binding and non-specific binding gp120 were used to test the selectivity of this method. The results of the solution test indicated that FRET-conjugated receptors can efficiently distinguish the presence of specific and non-specific binding gp120 and proved the feasibility of the FRET-based dual receptor method in detecting the presence of gp120 with a limit of detection of 5ng/ml (0.5nM) in solution. For the optical fiber test, two FRET-conjugated receptors were immobilized onto an optical fiber silica core tip to detect the

  1. Containment-based Distributed Coordination Control to Achieve Both Bounded Voltage and Precise Current Sharing in Reverse-Droop-based DC Microgrid

    DEFF Research Database (Denmark)

    Han, Renke; Wang, Haojie; Jin, Zheming

    2017-01-01

    A highly flexible and reliable control strategy is proposed to achieve bounded voltage and precise current sharing, which is implemented in a reverse-droop-based dc Micro-Grid. To acquire the fast-dynamic response, the reverse droop control is used to replace the V-I droop control in the primary ...

  2. Effect of a Culture-Based Screening Algorithm on Tuberculosis Incidence in Immigrants and Refugees Bound for the United States

    Science.gov (United States)

    Liu, Yecai; Posey, Drew L.; Cetron, Martin S.; Painter, John A.

    2015-01-01

    Background Before 2007, U.S.-bound immigrants and refugees were screened for tuberculosis (TB) by a smear-based algorithm that could not diagnose smear-negative and culture-positive TB. In 2007, the Centers for Disease Control and Prevention began to implement a culture-based algorithm. Objective To evaluate the effect of the culture-based algorithm on preventing the importation of TB to the United States by immigrants and refugees from foreign countries. Design Population-based, cross-sectional study. Setting Panel physician sites for overseas medical examination. Patients Immigrants and refugees with TB. Measurements Comparison of the increase of smear-negative and culture-positive TB cases diagnosed overseas among immigrants and refugees by the culture-based algorithm with the decline of reported TB cases among foreign-born persons within 1 year after arrival in the United States from 2007 to 2012. Results Of the 3 212 421 arrivals of immigrants and refugees from 2007 to 2012, 1 650 961 (51.4%) were screened by the smear-based algorithm and 1 561 460 (48.6%) were screened by the culture-based algorithm. Among the 4032 TB cases diagnosed by the culture-based algorithm, 2195 (54.4%) were smear-negative and culture-positive. Before implementation (2002 to 2006), the annual number of reported TB cases among foreign-born persons within 1 year after arrival was relatively constant (range, 1424 to 1626 cases; mean, 1504 cases) but decreased from 1511 to 940 cases during implementation (2007 to 2012). During the same period, the annual number of smear-negative and culture-positive TB cases diagnosed overseas among U.S.-bound immigrants and refugees by the culture-based algorithm increased from 4 in 2007 to 629 in 2012. Limitation This analysis did not control for the decline in new arrivals of nonimmigrant visitors to the United States and the decrease of incidence of TB in their countries of origin. Conclusion Implementation of the culture-based algorithm in U.S.-bound

  3. Canonical and Cross-reactive Binding of NK Cell Inhibitory Receptors to HLA-C Allotypes Is Dictated by Peptides Bound to HLA-C.

    Science.gov (United States)

    Sim, Malcolm J W; Malaker, Stacy A; Khan, Ayesha; Stowell, Janet M; Shabanowitz, Jeffrey; Peterson, Mary E; Rajagopalan, Sumati; Hunt, Donald F; Altmann, Daniel M; Long, Eric O; Boyton, Rosemary J

    2017-01-01

    Human natural killer (NK) cell activity is regulated by a family of killer cell immunoglobulin-like receptors (KIRs) that bind human leukocyte antigen (HLA) class I. Combinations of KIR and HLA genotypes are associated with disease, including susceptibility to viral infection and disorders of pregnancy. KIR2DL1 binds HLA-C alleles of group C2 (Lys80). KIR2DL2 and KIR2DL3 bind HLA-C alleles of group C1 (Asn80). However, this model cannot explain HLA-C allelic effects in disease or the impact of HLA-bound peptides. The goal of this study was to determine the extent to which the endogenous HLA-C peptide repertoire can influence the specific binding of inhibitory KIR to HLA-C allotypes. The impact of HLA-C bound peptide on inhibitory KIR binding was investigated taking advantage of the fact that HLA-C*05:01 (HLA-C group 2, C2) and HLA-C*08:02 (HLA-C group 1, C1) have identical sequences apart from the key KIR specificity determining epitope at residues 77 and 80. Endogenous peptides were eluted from HLA-C*05:01 and used to test the peptide dependence of KIR2DL1 and KIR2DL2/3 binding to HLA-C*05:01 and HLA-C*08:02 and subsequent impact on NK cell function. Specific binding of KIR2DL1 to the C2 allotype occurred with the majority of peptides tested. In contrast, KIR2DL2/3 binding to the C1 allotype occurred with only a subset of peptides. Cross-reactive binding of KIR2DL2/3 with the C2 allotype was restricted to even fewer peptides. Unexpectedly, two peptides promoted binding of the C2 allotype-specific KIR2DL1 to the C1 allotype. We showed that presentation of endogenous peptides or HIV Gag peptides by HLA-C can promote KIR cross-reactive binding. KIR2DL2/3 binding to C1 is more peptide selective than that of KIR2DL1 binding to C2, providing an explanation for KIR2DL3-C1 interactions appearing weaker than KIR2DL1-C2. In addition, cross-reactive binding of KIR is characterized by even higher peptide selectivity. We demonstrate a hierarchy of functional peptide

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

    Directory of Open Access Journals (Sweden)

    Angela Hsiang-Ling Chen

    2014-09-01

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

  5. Structure-Based Rational Design of Adenosine Receptor Ligands.

    Science.gov (United States)

    Gutiérrez-de-Terán, Hugo; Sallander, Jessica; Sotelo, Eddy

    2017-01-01

    The family of adenosine receptors (ARs) is focus of several medicinal chemistry programs aimed to find new potent and selective drugs. Each receptor subtype has been proposed as a relevant drug target in the treatment of, e.g., cardiovascular or inflammatory diseases, asthma or Parkinson's disease. Until recently, most of these efforts have been dominated by ligand-based or empirical approaches. However, the latest advances in G protein-coupled receptor (GPCR) crystallography allowed for a thorough structural characterization of the A2AAR subtype, which has been crystalized with a number of agonists and antagonists. Consequently, the ligand discovery of AR ligands has been enriched with a number of structure-based approaches. These include the generation of higher-confident homology models for the remaining AR subtypes, virtual screening identification of novel chemotypes, structure-based lead-optimization programs, rationalization of selectivity profiles, or the structural characterization of novel binding sites that enable the design of novel allosteric modulators. Computational methodologies have importantly contributed to the success of these structure-based approaches, and the recent advances in the field are also analyzed in this review. We conclude that the design of adenosine receptor ligands has improved dramatically with the consideration of structure- based approaches, which is paving the way to a better understanding of the biology and pharmacological modulation of this relevant family of receptors.

  6. [Interaction of surface-active base with fraction of membrane-bound Williams's protons].

    Science.gov (United States)

    Iaguzhinskiĭ, L S; Motovilov, K A; Volkov, E M; Eremeev, S A

    2013-01-01

    In the process of mitochondrial respiratory H(+)-pumps functioning, the fraction membrane-bound protons (R-protons), which have an excess of free energy is formed. According to R.J. Williams this fraction is included as energy source in the reaction of ATP synthesis. Previously, in our laboratory was found the formation of this fraction was found in the mitochondria and on the outer surface of mitoplast. On the mitoslast model we strictly shown that non-equilibrium R-proton fraction is localized on the surface of the inner mitochondrial membrane. In this paper a surface-active compound--anion of 2,4,6-trichloro-3-pentadecylphenol (TCP-C15) is described, which selectively interacts with the R-protons fraction in mitochondria. A detailed description of the specific interaction of the TCP-C15 with R-protons fraction in mitochondria is presented. Moreover, in this work it was found that phosphate transport system reacts with the R-protons fraction in mitochondria and plays the role of the endogenous volume regulation system of this fraction. The results of experiments are discussed in the terms of a local coupling model of the phosphorylation mechanism.

  7. Refining Multivariate Value Set Bounds

    Science.gov (United States)

    Smith, Luke Alexander

    Over finite fields, if the image of a polynomial map is not the entire field, then its cardinality can be bounded above by a significantly smaller value. Earlier results bound the cardinality of the value set using the degree of the polynomial, but more recent results make use of the powers of all monomials. In this paper, we explore the geometric properties of the Newton polytope and show how they allow for tighter upper bounds on the cardinality of the multivariate value set. We then explore a method which allows for even stronger upper bounds, regardless of whether one uses the multivariate degree or the Newton polytope to bound the value set. Effectively, this provides an alternate proof of Kosters' degree bound, an improved Newton polytope-based bound, and an improvement of a degree matrix-based result given by Zan and Cao.

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

    Science.gov (United States)

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

    2015-04-28

    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.

  9. Increased antitumor activity, intratumor paclitaxel concentrations, and endothelial cell transport of cremophor-free, albumin-bound paclitaxel, ABI-007, compared with cremophor-based paclitaxel

    National Research Council Canada - National Science Library

    Neil Desai; Vuong Trieu; Zhiwen Yao; Leslie Louie; Sherry Ci; Andrew Yang; Chunlin Tao; Tapas De; Bridget Beals; Donald Dykes; Patricia Noker; Rosie Yao; Elizabeth Labao; Michael Hawkins; Patrick Soon-Shiong

    2006-01-01

    ...) and to exploit albumin receptor-mediated endothelial transport. We studied the antitumor activity, intratumoral paclitaxel accumulation, and endothelial transport for ABI-007 and Cremophor-based paclitaxel...

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

    DEFF Research Database (Denmark)

    Szymańska, Ewa; Chałupnik, Paulina; Szczepańska, Katarzyna

    2016-01-01

    A new series of carboxyaryl-substituted phenylalanines was designed, synthesized and pharmacologically characterized in vitro at native rat ionotropic glutamate receptors as well as at cloned homomeric kainate receptors GluK1-GluK3. Among them, six compounds bound to GluK1 receptor subtypes with ...

  11. Ligand- and receptor-based docking with LiBELa

    Science.gov (United States)

    dos Santos Muniz, Heloisa; Nascimento, Alessandro S.

    2015-08-01

    Methodologies on molecular docking are constantly improving. The problem consists on finding an optimal interplay between the computational cost and a satisfactory physical description of ligand-receptor interaction. In pursuit of an advance in current methods we developed a mixed docking approach combining ligand- and receptor-based strategies in a docking engine, where tridimensional descriptors for shape and charge distribution of a reference ligand guide the initial placement of the docking molecule and an interaction energy-based global minimization follows. This hybrid docking was evaluated with soft-core and force field potentials taking into account ligand pose and scoring. Our approach was found to be competitive to a purely receptor-based dock resulting in improved logAUC values when evaluated with DUD and DUD-E. Furthermore, the smoothed potential as evaluated here, was not advantageous when ligand binding poses were compared to experimentally determined conformations. In conclusion we show that a combination of ligand- and receptor-based strategy docking with a force field energy model results in good reproduction of binding poses and enrichment of active molecules against decoys. This strategy is implemented in our tool, LiBELa, available to the scientific community.

  12. Ligand- and receptor-based docking with LiBELa.

    Science.gov (United States)

    dos Santos Muniz, Heloisa; Nascimento, Alessandro S

    2015-08-01

    Methodologies on molecular docking are constantly improving. The problem consists on finding an optimal interplay between the computational cost and a satisfactory physical description of ligand-receptor interaction. In pursuit of an advance in current methods we developed a mixed docking approach combining ligand- and receptor-based strategies in a docking engine, where tridimensional descriptors for shape and charge distribution of a reference ligand guide the initial placement of the docking molecule and an interaction energy-based global minimization follows. This hybrid docking was evaluated with soft-core and force field potentials taking into account ligand pose and scoring. Our approach was found to be competitive to a purely receptor-based dock resulting in improved logAUC values when evaluated with DUD and DUD-E. Furthermore, the smoothed potential as evaluated here, was not advantageous when ligand binding poses were compared to experimentally determined conformations. In conclusion we show that a combination of ligand- and receptor-based strategy docking with a force field energy model results in good reproduction of binding poses and enrichment of active molecules against decoys. This strategy is implemented in our tool, LiBELa, available to the scientific community.

  13. Bounded Tamper Resilience

    DEFF Research Database (Denmark)

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

    2013-01-01

    a bounded tamper and leakage resilient CCA secure public key cryptosystem based on the DDH assumption. We first define a weaker CPA-like security notion that we can instantiate based on DDH, and then we give a general compiler that yields CCA-security with tamper and leakage resilience. This requires...... a public tamper-proof common reference string. Finally, we explain how to boost bounded tampering and leakage resilience (as in 1. and 2. above) to continuous tampering and leakage resilience, in the so-called floppy model where each user has a personal hardware token (containing leak- and tamper...

  14. Biophysics of risk aversion based on neurotransmitter receptor theory

    CERN Document Server

    Takahashi, Taiki

    2011-01-01

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

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

    DEFF Research Database (Denmark)

    Adamsen, Billy; Thomsen, Svend Erik

    , and by experimenting with different inputs it is possible to learn how the model behaves. The model is used to simulate the real world as it might be in a variety of circumstances (Gilbert, 2008). For this study a simulation model coded in Java-based NetLogo language was created. The simulation model contained only......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...... method for studying this type of problems. The approach is particularly suitable to topics where understanding processes and their consequences is important. Agent-based models can include agents that are heterogeneous in their features and abilities, and can deal directly with the consequences...

  16. Bounded Rationality

    Directory of Open Access Journals (Sweden)

    Ballester Pla, Coralio

    2012-03-01

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

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

  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

    2014-01-01

    Several advanced optical oxygen sensor materials are presented. They are based on bright NIR-emitting platinum(II)-benzoporphyrins covalently incorporated into a variety of polymeric matrices. The dye-polymer conjugates are prepared either via Suzuki coupling of the brominated porphyrins to the s......Several advanced optical oxygen sensor materials are presented. They are based on bright NIR-emitting platinum(II)-benzoporphyrins covalently incorporated into a variety of polymeric matrices. The dye-polymer conjugates are prepared either via Suzuki coupling of the brominated porphyrins...... to the styrene backbone or via co-polymerisation of the monomers with monostyryl porphyrin derivative. Importantly, in both strategies a highly stable C-C bond is obtained. The resulted materials benefit from excellent photophysical properties of the benzoporphyrin dyes (high brightness, emission in the NIR part...

  18. Evidence-based medicine was bound to fail: a report to Alvan Feinstein.

    Science.gov (United States)

    Fava, Giovanni A

    2017-04-01

    John Ioannidis has provided a lucid account, in the form of a report to David Sackett, of how evidence-based medicine (EBM) was hijacked to serve vested interests: major randomized controlled trials are largely done by and for the benefit of the industry; meta-analyses and guidelines are flooded with conflicts of interest; national and federal research funds are unable to address basic clinical questions. Nonetheless, EBM would remain a worthwhile goal. In this paper, in the form of a report to Alvan Feinstein, it is argued that current developments were largely predictable. EBM certainly gave an important contribution to questioning unsubstantiated therapeutic claims. Time has come, however, to become aware of its considerable limitations, including overall reductionism and insufficient consideration of problems related to financial conflicts of interest. EBM does not represent the scientific approach to medicine: it is only a restrictive interpretation of the scientific approach to clinical practice. EBM drives the prescribing clinician to an overestimated consideration of potential benefits, paying little attention to the likelihood of responsiveness and to potential vulnerabilities in relations to the adverse effects of treatment. It is time to substitute the fashionable popularity of a strategy developed outside of clinical medicine with models and research based on the insights of clinical judgment and patient-doctor interaction, as Feinstein had outlined. Copyright © 2017 Elsevier Inc. All rights reserved.

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

    DEFF Research Database (Denmark)

    Ísberg, Vignir; Balle, Thomas; Sander, Tommy

    2011-01-01

    of the activated receptor model as well as revealed new information about stabilizing residues and bonds. The active 5-HT(2A) receptor model was further validated by retrospective ligand screening of more than 9400 compounds, whereof 182 were known ligands. The results show that the model can be used in drug...... 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...

  20. High-throughput receptor-based assay for the detection of spirolides by chemiluminescence.

    Science.gov (United States)

    Rodríguez, Laura P; Vilariño, Natalia; Molgó, Jordi; Aráoz, Rómulo; Botana, Luis M

    2013-12-01

    The spirolides are marine toxins that belong to a new class of macrocyclic imines produced by dinoflagellates. In this study a previously described solid-phase receptor-based assay for the detection of spirolides was optimized for high-throughput screening and prevalidated. This method is based on the competition between 13-desmethyl spirolide C and biotin-α-bungarotoxin immobilized on a streptavidin-coated surface, for binding to nicotinic acetylcholine receptors. In this inhibition assay the amount of nAChR bound to the well surface is quantified using a specific antibody, followed by a second anti-mouse IgG antibody labeled with horseradish peroxidase (HRP). The assay protocol was optimized for 384-well microplates, which allowed a reduction of the amount of reagents per sample and an increase of the number of samples per plate versus previously published receptor-based assays. The sensitivity of the assay for 13-desmethyl spirolide C ranged from 5 to 150 ng mL(-1). The performance of the assay in scallop extracts was adequate, with an estimated detection limit for 13-desmethyl spirolide C of 50 μg kg(-1) of shellfish meat. The recovery rate of 13-desmethyl spirolide C for spiked samples with this assay was 80% and the inter-assay coefficient of variation was 8%. This 384-well microplate, chemiluminescence method can be used as a high-throughput screening assay to detect 13-desmethyl spirolide C in shellfish meat in order to reduce the number of samples to be processed through bioassays or analytical methods. Copyright © 2013 Elsevier Ltd. All rights reserved.

  1. Functional four-base A/T gap core sequence CATTAG of P53 response elements specifically bound tetrameric P53 differently than two-base A/T gap core sequence CATG bound both dimeric and tetrameric P53.

    Science.gov (United States)

    Cai, Bi-He; Chen, Jang-Yi; Lu, Mei-Hua; Chang, Li-Tze; Lin, Hwang-Chi; Chang, Yu-Ming; Chao, Chung-Faye

    2009-04-01

    The consensus sequence of p53 is repeated half sites of PuPuPuC(A/T)(A/T)GPyPyPy. GtAGCAttAGCCCAGACATGTCC is a 14-3-3sigma promoter p53 regulation site; the first core sequence is CAttAG, and the second is CATG. Both mutants GtAGgAttAGCCCAGACATGTCC and GtAGCAttAGCCCAGACATcTCC can be activated by p53 as a 1.5-fold half site. The original p53 regulated site on the 14-3-3sigma promoter is a whole site, and CATTAG is a functional core sequence. The p53-binding affinity and the activity of CATTAG were lower than for the mutant CATATG core sequence. Wild-type p53 acts as a tetramer to bind to the whole site; however, it also can bind to a half site by one of its dimers. Wild-type p53 can only bind to a half site with core sequence CATG but not to CATATG. The 1.5-fold half site or whole site with core sequence CATATG can be bound by wild-type p53. A p53 mutant, A344, forms dimeric p53; it can only bind to CATG, and not to CATATG. Therefore, tetrameric and dimeric p53 can bind to a two-base A/T gap core sequence, but only tetrameric p53 can bind to a four-base A/T gap core sequence.

  2. 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

    2016-12-01

    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.

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

    DEFF Research Database (Denmark)

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

    1990-01-01

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

  4. Fractal methods and the problem of estimating scaling exponents: A new approach based on upper and lower linear bounds

    Energy Technology Data Exchange (ETDEWEB)

    Saucier, Antoine [Ecole Polytechnique de Montreal, C.P. 6079, Station centre-ville, Montreal (Que.), H3C-3A7 (Canada)]. E-mail: Antoine.Saucier@polymtl.ca; Soumis, Francois [Ecole Polytechnique de Montreal, C.P. 6079, Station centre-ville, Montreal (Que.), H3C-3A7 (Canada)]. E-mail: Francois.Soumis@gerad.ca

    2006-06-15

    The characterization of irregular objects with fractal methods often leads to the estimation of the slope of a function which is plotted versus a scale parameter. The slope is usually obtained with a linear regression. The problem is that the fit is usually not acceptable from the statistical standpoint. We propose a new approach in which we use two straight lines to bound the data from above and from below. We call these lines the upper and lower linear bounds. We propose to define these bounds as the solution of an optimization problem. We discuss the solution of this problem and we give an algorithm to obtain its solution. We use the difference between the upper and lower linear bounds to define a measure of the degree of linearity in the scaling range. We illustrate our method by analyzing the fluctuations of the variogram in a microresistivity well log from an oil reservoir in the North Sea.

  5. Quasi-bounded sets

    Directory of Open Access Journals (Sweden)

    Jan Kucera

    1990-01-01

    Full Text Available It is proved in [1] & [2] that a set bounded in an inductive limit E=indlim En of Fréchet spaces is also bounded in some En iff E is fast complete. In the case of arbitrary locally convex spaces En every bounded set in a fast complete indlim En is quasi-bounded in some En, though it may not be bounded or even contained in any En. Every bounded set is quasi-bounded. In a Fréchet space every quasi-bounded set is also bounded.

  6. Low density lipoprotein receptor internalizes low density and very low density lipoproteins that are bound to heparan sulfate proteoglycans via lipoprotein lipase

    NARCIS (Netherlands)

    Mulder, M.; Lombardi, P.; Jansen, H.; Berkel, T.J.C. van; Frants, R.R.; Havekes, L.M.

    1993-01-01

    It has previously been shown that lipoprotein lipase (LPL) enhances the binding of low density lipoproteins (LDL) and very low density lipoproteins (VLDL) to HepG2 cells and fibroblasts, up to 80-fold. This increase in binding is LDL receptor-independent and is due to a bridging of LPL between

  7. An internal reference model-based PRF temperature mapping method with Cramer-Rao lower bound noise performance analysis.

    Science.gov (United States)

    Li, Cheng; Pan, Xinyi; Ying, Kui; Zhang, Qiang; An, Jing; Weng, Dehe; Qin, Wen; Li, Kuncheng

    2009-11-01

    The conventional phase difference method for MR thermometry suffers from disturbances caused by the presence of lipid protons, motion-induced error, and field drift. A signal model is presented with multi-echo gradient echo (GRE) sequence using a fat signal as an internal reference to overcome these problems. The internal reference signal model is fit to the water and fat signals by the extended Prony algorithm and the Levenberg-Marquardt algorithm to estimate the chemical shifts between water and fat which contain temperature information. A noise analysis of the signal model was conducted using the Cramer-Rao lower bound to evaluate the noise performance of various algorithms, the effects of imaging parameters, and the influence of the water:fat signal ratio in a sample on the temperature estimate. Comparison of the calculated temperature map and thermocouple temperature measurements shows that the maximum temperature estimation error is 0.614 degrees C, with a standard deviation of 0.06 degrees C, confirming the feasibility of this model-based temperature mapping method. The influence of sample water:fat signal ratio on the accuracy of the temperature estimate is evaluated in a water-fat mixed phantom experiment with an optimal ratio of approximately 0.66:1. (c) 2009 Wiley-Liss, Inc.

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

    Directory of Open Access Journals (Sweden)

    Mercè Jardí

    2012-01-01

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

  9. Containment and Consensus-based Distributed Coordination Control to Achieve Bounded Voltage and Precise Reactive Power Sharing in Islanded AC Microgrids

    DEFF Research Database (Denmark)

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

    2017-01-01

    for coordinated control design. Furthermore, a containment and consensus-based distributed coordination controller is proposed, by which the bus voltage magnitudes can be bounded within a reasonable range, instead of only controlling average voltage value. Further, the accurate reactive power sharing between...

  10. Brain-specific interaction of a 91-kDa membrane-bound protein with the cytoplasmic tail of the 300-kDa mannose 6-phosphate receptor

    DEFF Research Database (Denmark)

    Rosorius, O; Issinger, O G; Braulke, T

    1996-01-01

    The cytoplasmic tail of the 300 kDa mannose 6-phosphate receptor (MPR 300-CT) is thought to play an important role in sorting and targeting of lysosomal enzymes and the insulin-like growth factor II along the biosynthetic and endocytic pathway. In this study a brain specific 91 kDa protein and a 35...... kDa protein salt-washed from membranes (referred as TIP 91-M and TIP 35-M) were found to interact with the cytoplasmic receptor tail as assayed by cross-linkage with recombinant [32P] labeled MPR 300-CT. Subcellular fractionation revealed a distinct pattern of distribution of TIP 35-M and TIP 91-M...... in microsomal and synaptosomal fractions. Furthermore, the formation of cross-link complexes with membrane proteins appeared to be developmentally and regionally regulated in the brain and inhibited upon ATP hydrolysis. The data suggest the requirement of specific protein interactions for MPR 300 functions...

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

    NARCIS (Netherlands)

    Viel, Gerhard Theodoor

    1999-01-01

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

  12. Membrane-bound glucocorticoid receptors on distinct nociceptive neurons as potential targets for pain control through rapid non-genomic effects.

    Science.gov (United States)

    Shaqura, Mohammed; Li, Xiongjuan; Al-Khrasani, Mahmoud; Shakibaei, Mehdi; Tafelski, Sascha; Fürst, Susanna; Beyer, Antje; Kawata, Mitsuhiro; Schäfer, Michael; Mousa, Shaaban A

    2016-12-01

    Glucocorticoids were long believed to primarily function through cytosolic glucocorticoid receptor (GR) activation and subsequent classical genomic pathways. Recently, however, evidence has emerged that suggests the presence of rapid non-genomic GR-dependent signaling pathways within the brain, though their existence in spinal and peripheral nociceptive neurons remains elusive. In this paper, we aim to systemically identify GR within the spinal cord and periphery, to verify their putative membrane location and to characterize possible G protein coupling and pain modulating properties. Double immunofluorescence confocal microscopy revealed that GR predominantly localized in peripheral peptidergic and non-peptidergic nociceptive C- and Aδ-neurons and existed only marginally in myelinated mechanoreceptive and proprioreceptive neurons. Within the spinal cord, GR predominantly localized in incoming presynaptic nociceptive neurons, in pre- and postsynaptic structures of the dorsal horn, as well as in microglia. GR saturation binding revealed that these receptors are linked to the cell membrane of sensory neurons and, upon activation, they trigger membrane targeted [(35)S]GTPγS binding, indicating G protein coupling to a putative receptor. Importantly, subcutaneous dexamethasone immediately and dose-dependently attenuated acute nociceptive behavior elicited in an animal model of formalin-induced pain hypersensitivity compared to naive rats. Overall, this study provides firm evidence for a novel neuronal mechanism of GR agonists that is rapid, non-genomic, dependent on membrane binding and G protein coupling, and acutely modulates nociceptive behavior, thus unraveling a yet unconsidered mechanism of pain relief. Copyright © 2016. Published by Elsevier Ltd.

  13. An Evolution Based Biosensor Receptor DNA Sequence Generation Algorithm

    Directory of Open Access Journals (Sweden)

    Yupeng Zang

    2009-12-01

    Full Text Available A biosensor is composed of a bioreceptor, an associated recognition molecule, and a signal transducer that can selectively detect target substances for analysis. DNA based biosensors utilize receptor molecules that allow hybridization with the target analyte. However, most DNA biosensor research uses oligonucleotides as the target analytes and does not address the potential problems of real samples. The identification of recognition molecules suitable for real target analyte samples is an important step towards further development of DNA biosensors. This study examines the characteristics of DNA used as bioreceptors and proposes a hybrid evolution-based DNA sequence generating algorithm, based on DNA computing, to identify suitable DNA bioreceptor recognition molecules for stable hybridization with real target substances. The Traveling Salesman Problem (TSP approach is applied in the proposed algorithm to evaluate the safety and fitness of the generated DNA sequences. This approach improves efficiency and stability for enhanced and variable-length DNA sequence generation and allows extension to generation of variable-length DNA sequences with diverse receptor recognition requirements.

  14. An evolution based biosensor receptor DNA sequence generation algorithm.

    Science.gov (United States)

    Kim, Eungyeong; Lee, Malrey; Gatton, Thomas M; Lee, Jaewan; Zang, Yupeng

    2010-01-01

    A biosensor is composed of a bioreceptor, an associated recognition molecule, and a signal transducer that can selectively detect target substances for analysis. DNA based biosensors utilize receptor molecules that allow hybridization with the target analyte. However, most DNA biosensor research uses oligonucleotides as the target analytes and does not address the potential problems of real samples. The identification of recognition molecules suitable for real target analyte samples is an important step towards further development of DNA biosensors. This study examines the characteristics of DNA used as bioreceptors and proposes a hybrid evolution-based DNA sequence generating algorithm, based on DNA computing, to identify suitable DNA bioreceptor recognition molecules for stable hybridization with real target substances. The Traveling Salesman Problem (TSP) approach is applied in the proposed algorithm to evaluate the safety and fitness of the generated DNA sequences. This approach improves efficiency and stability for enhanced and variable-length DNA sequence generation and allows extension to generation of variable-length DNA sequences with diverse receptor recognition requirements.

  15. Genome-based discovery of a novel membrane-bound 1,6-dihydroxyphenazine prenyltransferase from a marine actinomycete.

    Science.gov (United States)

    Zeyhle, Philipp; Bauer, Judith S; Kalinowski, Jörn; Shin-ya, Kazuo; Gross, Harald; Heide, Lutz

    2014-01-01

    Recently, novel prenylated derivatives of 1,6-dihydroxyphenazine have been isolated from the marine sponge-associated Streptomyces sp. SpC080624SC-11. Genome sequencing of this strain now revealed a gene cluster containing all genes necessary for the synthesis of the phenazine and the isoprenoid moieties. Unexpectedly, however, the cluster did not contain a gene with similarity to previously investigated phenazine prenyltransferases, but instead a gene with modest similarity to the membrane-bound prenyltransferases of ubiquinone and menaquinone biosynthesis. Expression of this gene in E. coli and isolation of the membrane fraction proved that the encoded enzyme, Mpz10, catalyzes two successive prenylations of 1,6-dihydroxyphenazine. Mpz10 is the first example of a membrane-bound enzyme catalyzing the prenylation of a phenazine substrate, and one of few examples of membrane-bound enzymes involved in the prenylation of aromatic secondary metabolites in microorganisms.

  16. Novel cell-based odorant sensor elements based on insect odorant receptors.

    Science.gov (United States)

    Mitsuno, Hidefumi; Sakurai, Takeshi; Namiki, Shigehiro; Mitsuhashi, Hiroyuki; Kanzaki, Ryohei

    2015-03-15

    Development of cell-based odorant sensor elements combined not only high degree of sensitivity and selectivity but also long-term stability is crucial for their practical applications. Here we report the development of a novel cell-based odorant sensor element that sensitively and selectively detects odorants and displays increased fluorescent intensities over a long period of time. Our odorant sensor elements, based on Sf21 cell lines expressing insect odorant receptors, are sensitive to the level of several tens of parts per billion in solution, can selectively distinguish between different types of odorants based on the odorant selectivity intrinsic to the expressed receptors, and have response times of approximately 13s. Specifically, with the use of Sf21 cells and insect odorant receptors, we demonstrated that the established cell lines stably expressing insect odorant receptors are able to detect odorants with consistent responsiveness for at least 2 months, thus exceeding the short life-span normally associated with cell-based sensors. We also demonstrated the development of a compact odorant sensor chip by integrating the established insect cell lines into a microfluidic chip. The methodology we established in this study, in conjunction with the large repertoire of insect odorant receptors, will aid in the development of practical cell-based odorant sensors for various applications, including food administration and health management. Copyright © 2014 Elsevier B.V. All rights reserved.

  17. Market Access through Bound Tariffs

    DEFF Research Database (Denmark)

    Sala, Davide; Schröder, Philipp J.H.; Yalcin, Erdal

    on the risk that exporters face in destination markets. The present paper formalizes the underlying interaction of risk, fixed export costs and firms' market entry decisions based on techniques known from the real options literature; doing so we highlight the important role of bound tariffs at the extensive......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...... margin of trade. We find that bound tariffs are more effective with higher risk destination markets, that a large binding overhang may still command substantial market access, and that reductions in bound tariffs generate effective market access even when bound rates are above current and long...

  18. Market access through bound tariffs

    DEFF Research Database (Denmark)

    Sala, Davide; Schröder, Philipp J.H.; Yalcin, Erdal

    2010-01-01

    on the risk that exporters face in destination markets. The present paper formalizes the underlying interaction of risk, fixed export costs and firms' market entry decisions based on techniques known from the real options literature; doing so we highlight the important role of bound tariffs at the extensive......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...... margin of trade. We find that bound tariffs are more effective with higher risk destination markets, that a large binding overhang may still command substantial market access, and that reductions in bound tariffs generate effective market access even when bound rates are above current and longterm...

  19. Catecholamine receptors: prototypes for GPCR-based drug discovery.

    Science.gov (United States)

    Emery, Andrew C

    2013-01-01

    Drugs acting at G protein-coupled receptors (GPCRs) constitute ~40% of those in current clinical use. GPCR-based drug discovery remains at the forefront of drug development, especially for new treatments for psychiatric illness and neurological disease. Here, the basic framework of GPCR signaling learned through the elucidation of catecholamine receptor signaling through G proteins and β-arrestins, and X-ray crystallographic structure determination is reviewed. In silico docking studies developed in tandem with confirmatory empirical data gathering from binding and signaling experiments have allowed this basic framework to be expanded to drug hunting through predictive in silico searching as well as high-throughput and high-content screening approaches. For efforts moving forward for the deployment of new GPCR-acting drugs, collaborative efforts between industry and government/academic research in target validation at the molecular and cellular levels have become progressively more common. Polypharmacological approaches have become increasingly available for learning more about the mechanisms of GPCR-targeted drugs, based on interaction not with a single, but with a wide range of GPCR targets. These approaches are likely to aid in drug repurposing efforts, yield valuable insight on the side effects of currently employed drugs, and allow for a clearer picture of the actual targets of "atypical" drugs used in a variety of therapeutic contexts. © 2013 Elsevier Inc. All rights reserved.

  20. Effect of a culture-based screening algorithm on tuberculosis incidence in immigrants and refugees bound for the United States: a population-based cross-sectional study.

    Science.gov (United States)

    Liu, Yecai; Posey, Drew L; Cetron, Martin S; Painter, John A

    2015-03-17

    Before 2007, immigrants and refugees bound for the United States were screened for tuberculosis (TB) by a smear-based algorithm that could not diagnose smear-negative/culture-positive TB. In 2007, the Centers for Disease Control and Prevention implemented a culture-based algorithm. To evaluate the effect of the culture-based algorithm on preventing the importation of TB to the United States by immigrants and refugees from foreign countries. Population-based, cross-sectional study. Panel physician sites for overseas medical examination. Immigrants and refugees with TB. Comparison of the increase of smear-negative/culture-positive TB cases diagnosed overseas among immigrants and refugees by the culture-based algorithm with the decline of reported cases among foreign-born persons within 1 year after arrival in the United States from 2007 to 2012. Of the 3 212 421 arrivals of immigrants and refugees from 2007 to 2012, a total of 1 650 961 (51.4%) were screened by the smear-based algorithm and 1 561 460 (48.6%) were screened by the culture-based algorithm. Among the 4032 TB cases diagnosed by the culture-based algorithm, 2195 (54.4%) were smear-negative/culture-positive. Before implementation (2002 to 2006), the annual number of reported cases among foreign-born persons within 1 year after arrival was relatively constant (range, 1424 to 1626 cases; mean, 1504 cases) but decreased from 1511 to 940 cases during implementation (2007 to 2012). During the same period, the annual number of smear-negative/culture-positive TB cases diagnosed overseas among immigrants and refugees bound for the United States by the culture-based algorithm increased from 4 to 629. This analysis did not control for the decline in new arrivals of nonimmigrant visitors to the United States and the decrease of incidence of TB in their countries of origin. Implementation of the culture-based algorithm may have substantially reduced the incidence of TB among newly arrived, foreign-born persons in

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

    Directory of Open Access Journals (Sweden)

    Sze Sing-Hoi

    2005-03-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-07-13

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

  3. Entropy and Free Energy of a Mobile Loop Based on the Crystal Structures of the Free and Bound Proteins.

    Science.gov (United States)

    Mihailescu, Mihail; Meirovitch, Hagai

    2010-08-25

    A mobile loop changes its conformation from "open" (free enzyme) to "closed" upon ligand binding. The difference in the Helmholtz free energy, ΔF(loop) between these states sheds light on the mechanism of binding. With our "hypothetical scanning molecular dynamics" (HSMD-TI) method ΔF(loop) = F(free) - F(bound) where F(free) and F(bound) are calculated from two MD samples of the free and bound loop states; the contribution of water is obtained by a thermodynamic integration (TI) procedure. In previous work the free and bound loop structures were both attached to the same "template" which was "cut" from the crystal structure of the free protein. Our results for loop 287-290 of AcetylCholineEsterase agree with the experiment, ΔF(loop)~ -4 kcal/mol if the density of the TIP3P water molecules capping the loop is close to that of bulk water, i.e., N(water) = 140 - 180 waters in a sphere of a 18 Å radius. Here we calculate ΔF(loop) for the more realistic case, where two templates are "cut" from the crystal structures, 2dfp.pdb (bound) and 2ace.pdb (free), where N(water) = 40 - 160; this requires adding a computationally more demanding (second) TI procedure. While the results for N(water) ≤ 140 are computationally sound, ΔF(loop) is always positive (18 ± 2 kcal/mol for N(water) = 140). These (disagreeing) results are attributed to the large average B-factor, 41.6 of 2dfp (23.4 Å(2) for 2ace). While this conformational uncertainty is an inherent difficulty, the (unstable) results for N(water) = 160 suggest that it might be alleviated by applying different (initial) structural optimizations to each template.

  4. Source apportionment of atmospheric PM2.5-bound polycyclic aromatic hydrocarbons by a PMF receptor model. Assessment of potential risk for human health.

    Science.gov (United States)

    Callén, María Soledad; Iturmendi, Amaia; López, José Manuel

    2014-12-01

    One year sampling (2011-2012) campaign of airborne PM2.5-bound PAH was performed in Zaragoza, Spain. A source apportionment of total PAH by Positive Matrix Factorization (PMF) was applied in order to quantify potential PAH pollution sources. Four sources were apportioned: coal combustion, vehicular emissions, stationary emissions and unburned/evaporative emissions. Although Directive 2004/107/EC was fulfilled regarding benzo(a)pyrene (BaP), episodes exceeding the limit value of PM2.5 according to Directive 2008/50/EC were found. These episodes of high negative potential for human health were studied, obtaining a different pattern for the exceedances of PM2.5 and the lower assessment threshold of BaP (LATBaP). In both cases, stationary emissions contributed majority to total PAH. Lifetime cancer risk exceeded the unit risk recommended by the World Health Organization for those episodes exceeding the LATBaP and the PM2.5 exceedances for the warm season. For the cold season, the risk was higher for the LATBaP than for the PM2.5 exceedances. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Receptor structure-based discovery of non-metabolite agonists for the succinate receptor GPR91.

    Science.gov (United States)

    Trauelsen, Mette; Rexen Ulven, Elisabeth; Hjorth, Siv A; Brvar, Matjaz; Monaco, Claudia; Frimurer, Thomas M; Schwartz, Thue W

    2017-12-01

    Besides functioning as an intracellular metabolite, succinate acts as a stress-induced extracellular signal through activation of GPR91 (SUCNR1) for which we lack suitable pharmacological tools. Here we first determined that the cis conformation of the succinate backbone is preferred and that certain backbone modifications are allowed for GPR91 activation. Through receptor modeling over the X-ray structure of the closely related P2Y1 receptor, we discovered that the binding pocket is partly occupied by a segment of an extracellular loop and that succinate therefore binds in a very different mode than generally believed. Importantly, an empty side-pocket is identified next to the succinate binding site. All this information formed the basis for a substructure-based search query, which, combined with molecular docking, was used in virtual screening of the ZINC database to pick two serial mini-libraries of a total of only 245 compounds from which sub-micromolar, selective GPR91 agonists of unique structures were identified. The best compounds were backbone-modified succinate analogs in which an amide-linked hydrophobic moiety docked into the side-pocket next to succinate as shown by both loss- and gain-of-function mutagenesis. These compounds displayed GPR91-dependent activity in altering cytokine expression in human M2 macrophages similar to succinate, and importantly were devoid of any effect on the major intracellular target, succinate dehydrogenase. These novel, synthetic non-metabolite GPR91 agonists will be valuable both as pharmacological tools to delineate the GPR91-mediated functions of succinate and as leads for the development of GPR91-targeted drugs to potentially treat low grade metabolic inflammation and diabetic complications such as retinopathy and nephropathy. Copyright © 2017 The Authors. Published by Elsevier GmbH.. All rights reserved.

  6. Photolabeling of membrane-bound Torpedo nicotinic acetylcholine receptor with the hydrophobic probe 3-trifluoromethyl-3-(m-(/sup 125/I)iodophenyl)diazirine

    Energy Technology Data Exchange (ETDEWEB)

    White, B.J.; Cohen, J.B.

    1988-11-29

    The hydrophobic, photoactivatable probe 3-trifluoromethyl-3-(m-(/sup 125/I)iodophenyl)diazirine ((/sup 125/I)TID) was used to label acetylcholine receptor rich membranes purified from Torpedo californica electric organ. All four subunits of the acetylcholine receptor (AChR) were found to incorporate label, with the ..gamma..-subunit incorporating approximately 4 times as much as each of the other subunits. Carbamylcholine, an agonist, and histrionicotoxin, a noncompetitive antagonist, both strongly inhibited labeling of all AChR subunits in a specific and dose-dependent manner. In contrast, the competitive antagonist ..cap alpha..-bungarotoxin and the noncompetitive antagonist phencyclidine had only modest effect on (/sup 125/I)TID labeling of the AChR. The regions of the AChR ..cap alpha..-subunit that incorporate (/sup 125/)TID were mapped by Staphylococcus aureus V8 protest digestion. The carbamylcholine-sensitive site of labeling was localized to a 20-kDa V8 cleavage fragment that begins at Ser-173 and is of sufficient length to contain the three hydrophobic regions M1, M2, and M3. A 10-kDa fragment beginning at Asn-339 and containing the hydrophobic region M4 also incorporated (/sup 125/I)TID but in a carbamylcholine-insensitive manner. Two further cleavage fragments, which together span about one-third of the ..cap alpha..-subunit amino terminus, incorporated no detectable (/sup 125/I)TID. The mapping results place constraints on suggested models of AChR subunit topology.

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

    OpenAIRE

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

    1992-01-01

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

  8. Homogenization-based interval analysis for structural-acoustic problem involving periodical composites and multi-scale uncertain-but-bounded parameters.

    Science.gov (United States)

    Chen, Ning; Yu, Dejie; Xia, Baizhan; Liu, Jian; Ma, Zhengdong

    2017-04-01

    This paper presents a homogenization-based interval analysis method for the prediction of coupled structural-acoustic systems involving periodical composites and multi-scale uncertain-but-bounded parameters. In the structural-acoustic system, the macro plate structure is assumed to be composed of a periodically uniform microstructure. The equivalent macro material properties of the microstructure are computed using the homogenization method. By integrating the first-order Taylor expansion interval analysis method with the homogenization-based finite element method, a homogenization-based interval finite element method (HIFEM) is developed to solve a periodical composite structural-acoustic system with multi-scale uncertain-but-bounded parameters. The corresponding formulations of the HIFEM are deduced. A subinterval technique is also introduced into the HIFEM for higher accuracy. Numerical examples of a hexahedral box and an automobile passenger compartment are given to demonstrate the efficiency of the presented method for a periodical composite structural-acoustic system with multi-scale uncertain-but-bounded parameters.

  9. Structure-based receptor MIMICS targeted against bacterial superantigen toxins

    Science.gov (United States)

    Gupta, Goutam [Santa Fe, NM; Hong-Geller, Elizabeth [Los Alamos, NM; Shiflett, Patrick R [Los Alamos, NM; Lehnert, Nancy M [Albuquerque, NM

    2009-08-18

    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.

  10. Entropy and Free Energy of a Mobile Loop Based on the Crystal Structures of the Free and Bound Proteins

    Directory of Open Access Journals (Sweden)

    Hagai Meirovitch

    2010-08-01

    Full Text Available A mobile loop changes its conformation from “open” (free enzyme to “closed” upon ligand binding. The difference in the Helmholtz free energy, ΔFloop between these states sheds light on the mechanism of binding. With our “hypothetical scanning molecular dynamics” (HSMD-TI method ΔFloop = Ffree − Fbound where Ffree and Fbound are calculated from two MD samples of the free and bound loop states; the contribution of water is obtained by a thermodynamic integration (TI procedure. In previous work the free and bound loop structures were both attached to the same “template” which was “cut” from the crystal structure of the free protein. Our results for loop 287−290 of AcetylCholineEsterase agree with the experiment, ΔFloop~ −4 kcal/mol if the density of the TIP3P water molecules capping the loop is close to that of bulk water, i.e., Nwater = 140 − 180 waters in a sphere of a 18 Å radius. Here we calculate ΔFloop for the more realistic case, where two templates are “cut” from the crystal structures, 2dfp.pdb (bound and 2ace.pdb (free, where Nwater = 40 − 160; this requires adding a computationally more demanding (second TI procedure. While the results for Nwater ≤ 140 are computationally sound, ΔFloop is always positive (18 ± 2 kcal/mol for Nwater = 140. These (disagreeing results are attributed to the large average B-factor, 41.6 of 2dfp (23.4 Å2 for 2ace. While this conformational uncertainty is an inherent difficulty, the (unstable results for Nwater = 160 suggest that it might be alleviated by applying different (initial structural optimizations to each template.

  11. Bound states and the Bekenstein bound

    Energy Technology Data Exchange (ETDEWEB)

    Bousso, Raphael

    2003-10-16

    We explore the validity of the generalized Bekenstein bound, S<= pi M a. We define the entropy S as the logarithm of the number of states which have energy eigenvalue below M and are localized to a flat space region of width alpha. If boundary conditions that localize field modes are imposed by fiat, then the bound encounters well-known difficulties with negative Casimir energy and large species number, as well as novel problems arising only in the generalized form. In realistic systems, however, finite-size effects contribute additional energy. We study two different models for estimating such contributions. Our analysis suggests that the bound is both valid and nontrivial if interactions are properly included, so that the entropy S counts the bound states of interacting fields.

  12. A Moisture-limited ET Upper Bound and Its Application in an Evaporation Pan Based Complementary-relationship Model for ET Estimation

    Science.gov (United States)

    Guan, H.; Cook, P. G.; Simmons, C. T.; Brunner, P.; Gutierrez-Jurado, H. A.; Wang, H.

    2013-12-01

    Long-term evaporation pan observations worldwide constitute a good database to study effects of climate change. In many cases, however, actual evapotranspiration rather than pan evapotranspiration is of interest. In order to estimate land surface evapotranspiration based on pan observations, a relationship between pan evaporation and its surrounding actual evapotranspiration (ET) must be found. A complementary relationship has been developed in previous studies and is formulated as Epan = Ep + b(Ep-Ea), where Epan, Ep and Ea are pan evaporation, potential evaporation due to local radiation energy input, and actual areal evapotranspiration, respectively. We explore this model, based on long-term observations at seven evaporation pan sites in South Australia. Interestingly, we observe a clear edge in the lower-left corner of the data cloud in the (1/Ep, Epan/Ep) space for most months. This clear edge line is most likely caused by an upper bound in daily ET, which is observed at multiple AmeriFlux sites of various land covers. This upper bound in daily ET is likely associated with radiative energy partitioning and different timing of surface and root-zone soil wetting. It is simulated with physically-based numerical modelling at a vegetated semiarid environment. This upper bound in daily ET provides a mathematical basis for the lower edge in the (1/Ep, Epan/Ep) space. This edge line, when determined, can be used to estimate monthly b values. An automatic regression approach is presented to objectively determine the lower-left edge line. Preliminary calculation of Ea with the estimated b, appears to provide reasonable values for the three pan sites in areas with mean annual precipitation around and above 500 mm. We also examine under what a range of climate and surface conditions this upper ET bound exists. The significance of this phenomenon is not only in application of this evaporation pan based complementary-relationship method, but also in application of remote

  13. A Ship Collision Analysis Program Based on Upper Bound Solutions and Coupled with a Large Rotational Ship Movement Analysis Tool

    Directory of Open Access Journals (Sweden)

    Hervé Le Sourne

    2012-01-01

    Full Text Available This paper presents a user-friendly rapid prediction tool of damage to struck and striking vessels in a ship collision event. To do this, the so-called upper bound theorem is applied to calculate internal forces and energies of any substructure involved in the ships crushing process. At each increment of indentation, the total crushing force is transmitted to the external dynamics MCOL program, which calculates the global ship motion correction by solving the hydrodynamic force equilibrium equations. As a first step, the paper gives a brief description of the upper bound method originally developed for perpendicular collisions and recently enhanced for oblique ones. Then, the theory developed in MCOL program for large rotational ship movements is detailed. By comparing results obtained with and without MCOL, the importance of hydrodynamic effects is highlighted. Some simulation results are compared with results provided by classical nonlinear finite element calculations. Finally, by using the developed analytical tool, which mixes internal and external dynamics, different crushing scenarios including oblique collisions are investigated and the influence of some collision parameters like longitudinal and vertical impact location, impact angle, and struck ship velocity is studied.

  14. receptores

    Directory of Open Access Journals (Sweden)

    Salete Regina Daronco Benetti

    2006-01-01

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

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

    DEFF Research Database (Denmark)

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

    2009-01-01

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

  16. Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach

    Science.gov (United States)

    Lam, Polo C.-H.; Abagyan, Ruben; Totrov, Maxim

    2017-09-01

    Ligand docking to flexible protein molecules can be efficiently carried out through ensemble docking to multiple protein conformations, either from experimental X-ray structures or from in silico simulations. The success of ensemble docking often requires the careful selection of complementary protein conformations, through docking and scoring of known co-crystallized ligands. False positives, in which a ligand in a wrong pose achieves a better docking score than that of native pose, arise as additional protein conformations are added. In the current study, we developed a new ligand-biased ensemble receptor docking method and composite scoring function which combine the use of ligand-based atomic property field (APF) method with receptor structure-based docking. This method helps us to correctly dock 30 out of 36 ligands presented by the D3R docking challenge. For the six mis-docked ligands, the cognate receptor structures prove to be too different from the 40 available experimental Pocketome conformations used for docking and could be identified only by receptor sampling beyond experimentally explored conformational subspace.

  17. Physical Uncertainty Bounds (PUB)

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-03-19

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

  18. Thermodynamics of Complexation between Thiourea-based Receptor and Acetate in Water/Acetonitrile Mixture.

    Science.gov (United States)

    Suzuki, Takaya; Shibuya, Yuuta; Sato, Takaya; Nishizawa, Seiichi; Sato, Itaru; Yamaguchi, Akira

    2016-01-01

    A thiourea-based receptor has been extensively studied for selective anion recognition for reasons of its strong hydrogen bond donor ability. In the present study, the thermodynamics of complexation between a thiourea-based receptor and acetate was examined in a water/acetonitrile mixture. The receptor used in this study was N,N'-bis(p-nitrophenyl)thiourea (BNPTU). UV/vis spectroscopic titration and isothermal titration calorimetry (ITC) experiments clearly revealed endothermic and entropy-driven complexation of BNPTU with acetate in water/acetonitrile mixtures. Since the endothermic peaks found in water/acetonitrile mixtures were about three times greater than those in acetonitrile, it appears that preferential hydration of both receptor and acetate was responsible for the endothermic and entropy-driven complexation reaction. The thermodynamic properties found in this study have the potential to contribute to the design of a thiourea-based anion receptor.

  19. A receptor model for urban aerosols based on oblique factor analysis

    DEFF Research Database (Denmark)

    Keiding, Kristian; Sørensen, Morten S.; Pind, Niels

    1987-01-01

    A procedure is outlined for the construction of receptor models of urban aerosols, based on factor analysis. The advantage of the procedure is that the covariation of source impacts is included in the construction of the models. The results are compared with results obtained by other receptor...

  20. Bounded Parikh Automata

    Directory of Open Access Journals (Sweden)

    Michaël Cadilhac

    2011-08-01

    Full Text Available The Parikh finite word automaton model (PA was introduced and studied by Klaedtke and Ruess in 2003. Here, by means of related models, it is shown that the bounded languages recognized by PA are the same as those recognized by deterministic PA. Moreover, this class of languages is the class of bounded languages whose set of iterations is semilinear.

  1. Bounded Gaussian process regression

    DEFF Research Database (Denmark)

    Jensen, Bjørn Sand; Nielsen, Jens Brehm; Larsen, Jan

    2013-01-01

    We extend the Gaussian process (GP) framework for bounded regression by introducing two bounded likelihood functions that model the noise on the dependent variable explicitly. This is fundamentally different from the implicit noise assumption in the previously suggested warped GP framework. We...

  2. 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 neutrophilic inflammation

  3. Multiple receptor conformers based molecular docking study of fluorine enhanced ethionamide with mycobacterium enoyl ACP reductase (InhA).

    Science.gov (United States)

    Khan, Akib Mahmud; Shawon, Jakaria; Halim, Mohammad A

    2017-10-01

    A major limitation in current molecular docking method is that of failure to account for receptor flexibility. Herein we report multiple receptor conformers based molecular docking as a practical alternative to account for the receptor flexibility. Multiple (forty) conformers of Mycobacterium Enoyl ACP Reductase (InhA) are generated from Molecular Dynamics simulation and twenty crystallographic structures of InhA bound to different inhibitors are obtained from the Protein Data Bank. Fluorine directed modifications are performed to currently available anti-tuberculosis drug ethionamide. The modified drugs are optimized using B3LYP 6-31G (d,p) level of theory. Dipole moment, frontier orbital gap and thermodynamical properties such as electronic energy, enthalpy and Gibbs free energy of these optimized drugs are investigated. These drugs are subsequently docked against the conformers of InhA. Molecular docking against multiple InhA conformations show variation in ligand binding affinity and suggest that Ser94, Gly96, Lys165 and Ile194 amino acids play critical role on strong drug-InhA interaction. Modified drug N1 showed greater binding affinity compared to EN in most conformations. Structure of PDB ID: 2NSD and snapshot conformer at 5.5ns show most favorable binding with N1 compared to other conformers. Fluorine participates in forming fluorine bonds and contributes significantly in increasing binding affinity. Our study reveal that addition of trifluoromethyl group explicitly shows promise in improving thermodynamic properties and in enhancing hydrogen bonding and non-bonded interactions. Molecular dynamics (MD) simulation show that EN and N1 remained in the binding pocket similar to the docked pose of EN-InhA and E1-InhA complexes and also suggested that InhA binds to its inhibitor in inhibitor-induced folding manner. ADMET calculations predict modified drugs to have improved pharmacokinetic properties. Our study concludes that multiple receptor conformers based

  4. Bounding Species Distribution Models

    Science.gov (United States)

    Stohlgren, Thomas J.; Jarnevich, Cahterine S.; Morisette, Jeffrey T.; Esaias, Wayne E.

    2011-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Elisabeth J. Faassen

    2016-02-01

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

  6. Diabetes and obesity treatment based on dual incretin receptor activation

    DEFF Research Database (Denmark)

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

    2016-01-01

    The gut incretin hormones glucose-dependent insulinotropic polypeptide (GIP) and glucagon-like peptide-1 (GLP-1) are secreted after meal ingestion and work in concert to promote postprandial insulin secretion and regulate glucagon secretion. GLP-1 also slows gastric emptying and suppresses appetite......, 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...

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

    Science.gov (United States)

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

    2016-07-21

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

  8. Concordance-based Kendall's Correlation for Computationally-Light vs. Computationally-Heavy Centrality Metrics: Lower Bound for Correlation

    Directory of Open Access Journals (Sweden)

    Natarajan Meghanathan

    2017-01-01

    Full Text Available We identify three different levels of correlation (pair-wise relative ordering, network-wide ranking and linear regression that could be assessed between a computationally-light centrality metric and a computationally-heavy centrality metric for real-world networks. The Kendall's concordance-based correlation measure could be used to quantitatively assess how well we could consider the relative ordering of two vertices vi and vj with respect to a computationally-light centrality metric as the relative ordering of the same two vertices with respect to a computationally-heavy centrality metric. We hypothesize that the pair-wise relative ordering (concordance-based assessment of the correlation between centrality metrics is the most strictest of all the three levels of correlation and claim that the Kendall's concordance-based correlation coefficient will be lower than the correlation coefficient observed with the more relaxed levels of correlation measures (linear regression-based Pearson's product-moment correlation coefficient and the network wide ranking-based Spearman's correlation coefficient. We validate our hypothesis by evaluating the three correlation coefficients between two sets of centrality metrics: the computationally-light degree and local clustering coefficient complement-based degree centrality metrics and the computationally-heavy eigenvector centrality, betweenness centrality and closeness centrality metrics for a diverse collection of 50 real-world networks.

  9. ERBB receptors: from oncogene discovery to basic science to mechanism-based cancer therapeutics.

    Science.gov (United States)

    Arteaga, Carlos L; Engelman, Jeffrey A

    2014-03-17

    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. Copyright © 2014 Elsevier Inc. All rights reserved.

  10. Lipid- and polyion complex-based micelles as agonist platforms for TNFR superfamily receptors.

    Science.gov (United States)

    Gilbreth, Ryan N; Novarra, Shabazz; Wetzel, Leslie; Florinas, Stelios; Cabral, Horacio; Kataoka, Kazunori; Rios-Doria, Jonathan; Christie, Ronald J; Baca, Manuel

    2016-07-28

    Receptor clustering is important for signaling among the therapeutically relevant TNFR superfamily of receptors. In nature, this clustering is driven by trimeric ligands often presented in large numbers as cell surface proteins. Molecules capable of driving similar levels of clustering could make good agonists and hold therapeutic value. However, recapitulating such extensive clustering using typical biotherapeutic formats, such as antibodies, is difficult. Consequently, generating effective agonists of TNFR superfamily receptors is challenging. Toward addressing this challenge we have used lipid- and polyion complex-based micelles as platforms for presenting receptor-binding biologics in a multivalent format that facilitates receptor clustering and imparts strong agonist activity. We show that receptor-binding scFvs or small antibody mimetics that have no agonist activity on their own can be transformed into potent agonists through multivalent presentation on a micelle surface and that the activity of already active multivalent agonists can be enhanced. Using this strategy, we generated potent agonists against two different TNFR superfamily receptors and mouse tumor model studies demonstrate that these micellar agonists have therapeutic efficacy in vivo. Due to its ease of implementation and applicability independent of agonist molecular format, we anticipate that this strategy could be useful for developing agonists to a variety of receptors that rely on clustering to signal. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Targeting Multiple Tumors Using T-Cells Engineered to Express a Natural Cytotoxicity Receptor 2-Based Chimeric Receptor

    Directory of Open Access Journals (Sweden)

    Vasyl Eisenberg

    2017-09-01

    Full Text Available Recent developments in cancer treatment are demonstrating the increasing and powerful potential of immunotherapeutic strategies. In this regard, the adoptive transfer of tumor-specific T-lymphocytes approaches can lead to tumor regression in cancer patients. More recently, the use of T-cells genetically engineered to express cancer-specific receptors such as the anti-CD19 chimeric antigen receptor (CAR continues to show promise for the treatment of hematological malignancies. Still, there is a crucial need to develop efficient CAR-T cell approaches for the treatment of solid tumors. It has been shown that other lymphocytes such as natural killer (NK cells can demonstrate potent antitumor function—nonetheless, their use in immunotherapy is rather limited due to difficulties in expanding these cells to therapeutically relevant numbers and to suppression by endogenous inhibitory mechanisms. Cancer recognition by NK cells is partly mediated by molecules termed natural cytotoxicity receptors (NCRs. In the present study, we hypothesize that it is possible to endow T-cells with an NK recognition pattern, providing them with a mean to recognize tumor cells, in a non-MHC restricted way. To test this, we genetically modified human T-cells with different chimeric receptors based on the human NCR2 molecule and then assessed their antitumor activity in vitro and in vivo. Our results show that expression in primary lymphocytes of an NCR2-derived CAR, termed s4428z, confers T-cells with the ability to specifically recognize heterogeneous tumors and to mediate tumor cytotoxicity in a mouse model. This study demonstrates the benefit of combining tumor recognition capability of NK cells with T cell effectiveness to improve cancer immunotherapy.

  12. Invariant measures and error bounds for random walks in the quarter-plane based on sums of geometric terms

    NARCIS (Netherlands)

    Chen, Y.; Boucherie, Richardus J.; Goseling, Jasper

    2016-01-01

    We consider homogeneous random walks in the quarter-plane. The necessary conditions which characterize random walks of which the invariant measure is a sum of geometric terms are provided in Chen et al. (arXiv:1304.3316, 2013, Probab Eng Informational Sci 29(02):233–251, 2015). Based on these

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

    NARCIS (Netherlands)

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

    2004-01-01

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

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

    Science.gov (United States)

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

    2016-12-15

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

  15. Virial Expansion Bounds

    Science.gov (United States)

    Tate, Stephen James

    2013-10-01

    In the 1960s, the technique of using cluster expansion bounds in order to achieve bounds on the virial expansion was developed by Lebowitz and Penrose (J. Math. Phys. 5:841, 1964) and Ruelle (Statistical Mechanics: Rigorous Results. Benjamin, Elmsford, 1969). This technique is generalised to more recent cluster expansion bounds by Poghosyan and Ueltschi (J. Math. Phys. 50:053509, 2009), which are related to the work of Procacci (J. Stat. Phys. 129:171, 2007) and the tree-graph identity, detailed by Brydges (Phénomènes Critiques, Systèmes Aléatoires, Théories de Jauge. Les Houches 1984, pp. 129-183, 1986). The bounds achieved by Lebowitz and Penrose can also be sharpened by doing the actual optimisation and achieving expressions in terms of the Lambert W-function. The different bound from the cluster expansion shows some improvements for bounds on the convergence of the virial expansion in the case of positive potentials, which are allowed to have a hard core.

  16. 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.

  17. 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

    2003-01-01

    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

  18. Autonomous Bacterial Localization and Gene Expression Based on Nearby Cell Receptor Density

    Science.gov (United States)

    2013-01-22

    Paradigm for industrial strain improvement identifies sodium acetate tolerance loci in Zymomonas mobilis and Saccharomyces cerevisiae . Proc Natl Acad Sci USA...epidermal growth factor receptor (EGFR). This represents a new type of controller for targeted drug delivery as actuation (synthesis and delivery) depends...surrogate) based on a threshold density of epidermal growth factor receptor (EGFR). This represents a newtype of controller for targeted drug delivery

  19. A Physiologically Based Pharmacokinetic Model to Predict the Pharmacokinetics of Highly Protein-Bound Drugs and Impact of Errors in Plasma Protein Binding

    Science.gov (United States)

    Ye, Min; Nagar, Swati; Korzekwa, Ken

    2015-01-01

    Predicting the pharmacokinetics of highly protein-bound drugs is difficult. Also, since historical plasma protein binding data was 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 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 model accuracy. Of the 22 drugs, less than a 2-fold error was obtained for 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 retention 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. PMID:26531057

  20. Wronskian method for bound states

    Energy Technology Data Exchange (ETDEWEB)

    Fernandez, Francisco M, E-mail: fernande@quimica.unlp.edu.ar [INIFTA (UNLP, CONICET), Division Quimica Teorica, Boulevard 113 S/N, Sucursal 4, Casilla de Correo 16, 1900 La Plata (Argentina)

    2011-05-15

    We propose a simple and straightforward method based on Wronskians for the calculation of bound-state energies and wavefunctions of one-dimensional quantum-mechanical problems. We explicitly discuss the asymptotic behaviour of the wavefunction and show that the allowed energies make the divergent part vanish. As illustrative examples we consider an exactly solvable model, the Gaussian potential well, and a two-well potential proposed earlier for the interpretation of the infrared spectrum of ammonia.

  1. Back to the roots: photodynamic inactivation of bacteria based on water-soluble curcumin bound to polyvinylpyrrolidone as a photosensitizer.

    Science.gov (United States)

    Winter, Sandra; Tortik, Nicole; Kubin, Andreas; Krammer, Barbara; Plaetzer, Kristjan

    2013-10-01

    Photodynamic inactivation (PDI), the light-induced and photosensitizer-mediated overproduction of reactive oxygen species in microorganisms, represents a convincing approach to treat infections with (multi-resistant) pathogens. Due to its favourable photoactive properties combined with excellent biocompatibility, curcumin derived from the roots of turmeric (Curcuma longa) has been identified as an advantageous photosensitizer for PDI. To overcome the poor water solubility and the rapid decay of the natural substance at physiological pH, we examined the applicability of polyvinylpyrrolidone curcumin (PVP-C) in an acidified aqueous solution (solubility of PVP-C up to 2.7 mM) for photoinactivation of Gram(+) and Gram(-) bacteria. Five micromolar PVP-C incubated for 5 minutes and illuminated using a blue light LED array (435 ± 10 nm, 33.8 J cm(-2)) resulted in a >6 log10 reduction of the number of viable Staphylococcus aureus. At this concentration, longer incubation periods result in a lower phototoxicity, most likely due to degeneration of curcumin. Upon an increase of the PVP-C concentration to 50 μM (incubation for 15 or 25 min) a complete eradication of Staphylococcus aureus can be achieved. As expected for a non-cationic photosensitizer, cell wall permeabilization with CaCl2 prior to addition of 50 μM PVP-C for 15 min is necessary to induce a drop in the count of the Gram(-) Escherichia coli for more than 3 log10. As both constituents of the formulation, curcumin (E number E100) and polyvinylpyrrolidone (E1201), have been approved as food additives, a PDI based on PCP-C might allow for a very sparing clinical application (e.g. for disinfection of wounds) or even for employment in aseptic production of foodstuffs.

  2. Integration of Bayesian molecular clock methods and fossil-based soft bounds reveals early Cenozoic origin of African lacertid lizards

    Directory of Open Access Journals (Sweden)

    Metzler Dirk

    2009-07-01

    Full Text Available Abstract Background Although current molecular clock methods offer greater flexibility in modelling evolutionary events, calibration of the clock with dates from the fossil record is still problematic for many groups. Here we implement several new approaches in molecular dating to estimate the evolutionary ages of Lacertidae, an Old World family of lizards with a poor fossil record and uncertain phylogeny. Four different models of rate variation are tested in a new program for Bayesian phylogenetic analysis called TreeTime, based on a combination of mitochondrial and nuclear gene sequences. We incorporate paleontological uncertainty into divergence estimates by expressing multiple calibration dates as a range of probabilistic distributions. We also test the reliability of our proposed calibrations by exploring effects of individual priors on posterior estimates. Results According to the most reliable model, as indicated by Bayes factor comparison, modern lacertids arose shortly after the K/T transition and entered Africa about 45 million years ago, with the majority of their African radiation occurring in the Eocene and Oligocene. Our findings indicate much earlier origins for these clades than previously reported, and we discuss our results in light of paleogeographic trends during the Cenozoic. Conclusion This study represents the first attempt to estimate evolutionary ages of a specific group of reptiles exhibiting uncertain phylogenetic relationships, molecular rate variation and a poor fossil record. Our results emphasize the sensitivity of molecular divergence dates to fossil calibrations, and support the use of combined molecular data sets and multiple, well-spaced dates from the fossil record as minimum node constraints. The bioinformatics program used here, TreeTime, is publicly available, and we recommend its use for molecular dating of taxa faced with similar challenges.

  3. A novel method to measure HLA-DM-susceptibility of peptides bound to MHC class II molecules based on peptide binding competition assay and differential IC50 determination

    Science.gov (United States)

    Yin, Liusong; Stern, Lawrence J.

    2014-01-01

    HLA-DM (DM) functions as a peptide editor that mediates the exchange of peptides loaded onto MHCII molecules by accelerating peptide dissociation and association kinetics. The relative DM-susceptibility of peptides bound to MHCII molecules correlates with antigen presentation and immunodominance hierarchy, and measurement of DM-susceptibility has been a key effort in this field. Current assays of DM-susceptibility, based on differential peptide dissociation rates measured for individually labeled peptides over a long time base, are difficult and cumbersome. Here, we present a novel method to measure DM-susceptibility based on peptide binding competition assays performed in the presence and absence of DM, reported as a delta-IC50 (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-IC50 value is highly correlated with DM-susceptibility as measured in off-rate assay. We confirmed experimentally that DM-susceptibility measured by delta-IC50 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. PMID:24583195

  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.

    Science.gov (United States)

    Yin, Liusong; Stern, Lawrence J

    2014-04-01

    HLA-DM (DM) functions as a peptide editor that mediates the exchange of peptides loaded onto MHCII molecules by accelerating peptide dissociation and association kinetics. The relative DM-susceptibility of peptides bound to MHCII molecules correlates with antigen presentation and immunodominance hierarchy, and measurement of DM-susceptibility has been a key effort in this field. Current assays of DM-susceptibility, based on differential peptide dissociation rates measured for individually labeled peptides over a long time base, are difficult and cumbersome. Here, we present a novel method to measure DM-susceptibility based on peptide binding competition assays performed in the presence and absence of DM, reported as a delta-IC(50) (change in 50% inhibition concentration) value. We simulated binding competition reactions of peptides with various intrinsic and DM-catalyzed kinetic parameters and found that under a wide range of conditions the delta-IC(50) value is highly correlated with DM-susceptibility as measured in off-rate assay. We confirmed experimentally that DM-susceptibility measured by delta-IC(50) is comparable to that measured by traditional off-rate assay for peptides with known DM-susceptibility hierarchy. The major advantage of this method is that it allows simple, fast and high throughput measurement of DM-susceptibility for a large set of unlabeled peptides in studies of the mechanism of DM action and for identification of CD4+ T cell epitopes. Copyright © 2014 Elsevier B.V. All rights reserved.

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

    DEFF Research Database (Denmark)

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

    1999-01-01

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

  6. Validation of EMP bounds

    Energy Technology Data Exchange (ETDEWEB)

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

    1996-07-01

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

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

    Indian Academy of Sciences (India)

    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. Keywords. Imine-linked receptors; ruthenium–metal complex; ZnO nanoparticles; dye-sensitized solar cell. 1. Introduction.

  8. Receptor structure-based discovery of non-metabolite agonists for the succinate receptor GPR91

    DEFF Research Database (Denmark)

    Trauelsen, Mette; Rexen Ulven, Elisabeth; Hjorth, Siv A

    2017-01-01

    therefore binds in a very different mode than generally believed. Importantly, an empty side-pocket is identified next to the succinate binding site. All this information formed the basis for a substructure-based search query, which, combined with molecular docking, was used in virtual screening of the ZINC...... database to pick two serial mini-libraries of a total of only 245 compounds from which sub-micromolar, selective GPR91 agonists of unique structures were identified. The best compounds were backbone-modified succinate analogs in which an amide-linked hydrophobic moiety docked into the side-pocket next...

  9. Bounded variation and around

    CERN Document Server

    Appell, Jürgen; Merentes Díaz, Nelson José

    2013-01-01

    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.

  10. Born Level Bound States

    Science.gov (United States)

    Hoyer, Paul

    2017-05-01

    Bound state poles in the S-matrix of perturbative QED are generated by the divergence of the expansion in α . The perturbative corrections are necessarily singular when expanding around free, {O}( α ^0 ) in and out states that have no overlap with finite-sized atomic wave functions. Nevertheless, measurables such as binding energies do have well-behaved expansions in powers of α (and log α ). It is desirable to formulate the concept of "lowest order" for gauge theory bound states such that higher order corrections vanish in the α → 0 limit. This may allow to determine a lowest order term for QCD hadrons which incorporates essential features such as confinement and chiral symmetry breaking, and thus can serve as the starting point of a useful perturbative expansion. I discuss a "Born" (no loop, lowest order in \\hbar ) approximation. Born level states are bound by gauge fields which satisfy the classical field equations. Gauss' law determines a distinct field A^0({\\varvec{x}}) for each instantaneous position of the charges. A Poincaré covariant boundary condition for the gluon field leads to a confining potential for q\\bar{q} and qqq states. In frames where the bound state is in motion the classical gauge field is obtained by a Lorentz boost of the rest frame field.

  11. Tight bounds on computing error-correcting codes by bounded-depth circuits with arbitrary gates

    DEFF Research Database (Denmark)

    Gal, A.; Hansen, Kristoffer Arnsfelt; Koucky, Michal

    2013-01-01

    We bound the minimum number w of wires needed to compute any (asymptotically good) error-correcting code C:{0,1}Ω(n)→{0,1}n with minimum distance Ω(n), using unbounded fan-in circuits of depth d with arbitrary gates. Our main results are: 1) if d=2, then w=Θ(n (lgn/lglgn)2); 2) if d=3, then w...... bound gives the largest known lower bound for computing any linear map. The upper bounds imply that a (necessarily dense) generator matrix for our code can be written as the product of two sparse matrices. Using known techniques, we also obtain similar (but not tight) bounds for computing pairwise......-independent hash functions. Our lower bounds are based on a superconcentrator-like condition that the graphs of circuits computing good codes must satisfy. This condition is provably intermediate between superconcentrators and their weakenings considered before...

  12. Receptor-based differences in human aortic smooth muscle cell membrane stiffness

    Science.gov (United States)

    Huang, H.; Kamm, R. D.; So, P. T.; Lee, R. T.

    2001-01-01

    Cells respond to mechanical stimuli with diverse molecular responses. The nature of the sensory mechanism involved in mechanotransduction is not known, but integrins may play an important role. The integrins are linked to both the cytoskeleton and extracellular matrix, suggesting that probing cells via integrins should yield different mechanical properties than probing cells via non-cytoskeleton-associated receptors. To test the hypothesis that the mechanical properties of a cell are dependent on the receptor on which the stress is applied, human aortic smooth muscle cells were plated, and magnetic beads, targeted either to the integrins via fibronectin or to the transferrin receptor by use of an IgG antibody, were attached to the cell surface. The resistance of the cell to deformation ("stiffness") was estimated by oscillating the magnetic beads at 1 Hz by use of single-pole magnetic tweezers at 2 different magnitudes. The ratio of bead displacements at different magnitudes was used to explore the mechanical properties of the cells. Cells stressed via the integrins required approximately 10-fold more force to obtain the same bead displacements as the cells stressed via the transferrin receptors. Cells stressed via integrins showed stiffening behavior as the force was increased, whereas this stiffening was significantly less for cells stressed via the transferrin receptor (Pcells depend on the receptor by which the stress is applied, with integrin-based linkages demonstrating cell-stiffening behavior.

  13. Cell-based, bioluminescent assay for monitoring the interaction between PCSK9 and the LDL receptor.

    Science.gov (United States)

    Duellman, Sarah J; Machleidt, Thomas; Cali, James J; Vidugiriene, Jolanta

    2017-08-01

    Monitoring the expression of cell-surface receptors, their interaction with extracellular ligands, and their fate upon ligand binding is important for understanding receptor function and developing new therapies. We describe a cell-based method that utilizes bioluminescent protein complementation technology to interrogate binding of a cellular receptor with its extracellular protein ligand, specifically LDL receptor (LDLR) and proprotein convertase subtilisin/kexin type 9 (PCSK9). Purified, full-length tagged PCSK9 is added to assay wells containing cells that stably express LDLR with an extracellular complementary tag. When the tagged PCSK9 binds the receptor, a bright luminescence signal is generated. The interaction is detected at the cell membrane with add-and-read simplicity, no wash steps, and flexibility, allowing data to be collected in endpoint format, kinetically, or with bioluminescent imaging. The assay is flexible, is rapid, and reports accurate biology. It is amenable to 96-well and 384-well formats, and the robustness allows for screening of new drug candidates (Z' = 0.83). The assay reports correct potencies for antibody titrations across a 50%-150% potency range and detects potency changes due to heat stress, suggesting that it may be useful during drug development. This assay technology can be broadly applied when studying other receptors with their extracellular ligands, whether protein or small-molecule binding partners. Copyright © 2017 by the American Society for Biochemistry and Molecular Biology, Inc.

  14. Receptor-based differences in human aortic smooth muscle cell membrane stiffness

    Science.gov (United States)

    Huang, H.; Kamm, R. D.; So, P. T.; Lee, R. T.

    2001-01-01

    Cells respond to mechanical stimuli with diverse molecular responses. The nature of the sensory mechanism involved in mechanotransduction is not known, but integrins may play an important role. The integrins are linked to both the cytoskeleton and extracellular matrix, suggesting that probing cells via integrins should yield different mechanical properties than probing cells via non-cytoskeleton-associated receptors. To test the hypothesis that the mechanical properties of a cell are dependent on the receptor on which the stress is applied, human aortic smooth muscle cells were plated, and magnetic beads, targeted either to the integrins via fibronectin or to the transferrin receptor by use of an IgG antibody, were attached to the cell surface. The resistance of the cell to deformation ("stiffness") was estimated by oscillating the magnetic beads at 1 Hz by use of single-pole magnetic tweezers at 2 different magnitudes. The ratio of bead displacements at different magnitudes was used to explore the mechanical properties of the cells. Cells stressed via the integrins required approximately 10-fold more force to obtain the same bead displacements as the cells stressed via the transferrin receptors. Cells stressed via integrins showed stiffening behavior as the force was increased, whereas this stiffening was significantly less for cells stressed via the transferrin receptor (Pmuscle cells depend on the receptor by which the stress is applied, with integrin-based linkages demonstrating cell-stiffening behavior.

  15. Cyclotron transitions of bound ions

    Science.gov (United States)

    Bezchastnov, Victor G.; Pavlov, George G.

    2017-06-01

    A charged particle in a magnetic field possesses discrete energy levels associated with particle rotation around the field lines. The radiative transitions between these levels are the well-known cyclotron transitions. We show that a bound complex of particles with a nonzero net charge displays analogous transitions between the states of confined motion of the entire complex in the field. The latter bound-ion cyclotron transitions are affected by a coupling between the collective and internal motions of the complex and, as a result, differ from the transitions of a "reference" bare ion with the same mass and charge. We analyze the cyclotron transitions for complex ions by including the coupling within a rigorous quantum approach. Particular attention is paid to comparison of the transition energies and oscillator strengths to those of the bare ion. Selection rules based on integrals of collective motion are derived for the bound-ion cyclotron transitions analytically, and the perturbation and coupled-channel approaches are developed to study the transitions quantitatively. Representative examples are considered and discussed for positive and negative atomic and cluster ions.

  16. Derivation of the Cramér-Rao Bound in the GNSS-Reflectometry Context for Static, Ground-Based Receivers in Scenarios with Coherent Reflection.

    Science.gov (United States)

    Ribot, Miguel Angel; Botteron, Cyril; Farine, Pierre-André

    2016-12-05

    The use of the reflected Global Navigation Satellite Systems' (GNSS) signals in Earth observation applications, referred to as GNSS reflectometry (GNSS-R), has been already studied for more than two decades. However, the estimation precision that can be achieved by GNSS-R sensors in some particular scenarios is still not fully understood yet. In an effort to partially fill this gap, in this paper, we compute the Cramér-Rao bound (CRB) for the specific case of static ground-based GNSS-R receivers and scenarios where the coherent component of the reflected signal is dominant. We compute the CRB for GNSS signals with different modulations, GPS L1 C/A and GPS L5 I/Q, which use binary phase-shift keying, and Galileo E1 B/C and E5, using the binary offset carrier. The CRB for these signals is evaluated as a function of the receiver bandwidth and different scenario parameters, such as the height of the receiver or the properties of the reflection surface. The CRB computation presented considers observation times of up to several tens of seconds, in which the satellite elevation angle observed changes significantly. Finally, the results obtained show the theoretical benefit of using modern GNSS signals with GNSS-R techniques using long observation times, such as the interference pattern technique.

  17. Molecular pop-up toy: a molecular machine based on folding/unfolding motion of alkyl chains bound to a host.

    Science.gov (United States)

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

    2015-01-01

    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. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    Directory of Open Access Journals (Sweden)

    B. ZHANG

    2012-12-01

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

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

    DEFF Research Database (Denmark)

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

    2015-01-01

    We have developed a new method for the building of pharmacophores for G protein-coupled receptors, a major drug target family. The method is a combination of the ligand- and target-based pharmacophore methods and founded on the extraction of structural fragments, interacting ligand moiety...... 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...... and receptor residue pairs, from crystal structure complexes. We describe the procedure to collect a library with more than 250 fragments covering 29 residue positions within the generic transmembrane binding pocket. We describe how the library fragments are recombined and inferred to build pharmacophores...

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

    DEFF Research Database (Denmark)

    Dietrich, J; Geisler, C

    1998-01-01

    The leucine-based motif in the T cell receptor (TCR) subunit CD3gamma constitutes a strong internalization signal. In fully assembled TCR this motif is inactive unless phosphorylated. In contrast, the motif is constitutively active in CD4/CD3gamma and Tac/CD3gamma chimeras independently...... to mask the CD3gamma leucine-based motif. By studying CD4/CD3gamma and CD16/CD3gamma chimeras, we found that CD16/CD3gamma chimeras associated with TCRzeta. The CD16/CD3gamma-TCRzeta complexes were stably expressed at the cell surface and had a low spontaneous internalization rate, indicating...... that the leucine-based motif in these complexes was inactive. In contrast, the CD4/CD3gamma chimeras did not associate with TCRzeta, and the leucine-based motif in these chimeras was constitutively active resulting in a high spontaneous internalization rate and low expression of the chimeras at the cell surface...

  1. Reduction of False Positives in Structure-Based Virtual Screening When Receptor Plasticity Is Considered

    Directory of Open Access Journals (Sweden)

    Yaw Awuni

    2015-03-01

    Full Text Available Structure-based virtual screening for selecting potential drug candidates is usually challenged by how numerous false positives in a molecule library are excluded when receptor plasticity is considered. In this study, based on the binding energy landscape theory, a hypothesis that a true inhibitor can bind to different conformations of the binding site favorably was put forth, and related strategies to defeat this challenge were devised; reducing false positives when receptor plasticity is considered. The receptor in the study is the influenza A nucleoprotein, whose oligomerization is a requirement for RNA binding. The structural flexibility of influenza A nucleoprotein was explored by molecular dynamics simulations. The resultant distinctive structures and the crystal structure were used as receptor models in docking exercises in which two binding sites, the tail-loop binding pocket and the RNA binding site, were targeted with the Otava PrimScreen1 diversity-molecule library using the GOLD software. The intersection ligands that were listed in the top-ranked molecules from all receptor models were selected. Such selection strategy successfully distinguished high-affinity and low-affinity control molecules added to the molecule library. This work provides an applicable approach for reducing false positives and selecting true ligands from molecule libraries.

  2. Bounding the number of remarkable values via Jouanolou's theorem

    OpenAIRE

    Chèze, Guillaume

    2015-01-01

    In this article we bound the number of remarkable values of a polynomial vector field. The proof is short and based on Jouanolou's theorem about rational first integrals of planar polynomial derivations. Our bound is given in term of the size of a Newton polygon associated to the vector field. We prove that this bound is almost reached.

  3. Bounding the number of remarkable values via Jouanolou's theorem

    Science.gov (United States)

    Chèze, Guillaume

    2015-05-01

    In this article we bound the number of remarkable values of a polynomial vector field. The proof is short and based on Jouanolou's theorem about rational first integrals of planar polynomial derivations. Our bound is given in term of the size of a Newton polygon associated to the vector field. We prove that this bound is almost reached.

  4. A Novel Benzimidazolyl-based Receptor for the recognition of ...

    Indian Academy of Sciences (India)

    Abstract. 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 ...

  5. Bound Exciton Complexes

    Science.gov (United States)

    Meyer, B. K.

    In the preceding chapter, we concentrated on the properties of free excitons. These free excitons may move through the sample and hit a trap, a nonradiative or a radiative recombination center. At low temperatures, the latter case gives rise to either deep center luminescence, mentioned in Sect. 7.1 and discussed in detail in Chap. 9, or to the luminescence of bound exciton complexes (BE or BEC). The chapter continues with the most prominent of these BECs, namely A-excitons bound to neutral donors. The next aspects are the more weakly BEs at ionized donors. The Sect. 7.4 treats the binding or localization energies of BEC from a theoretical point of view, while Sect. 7.5 is dedicated to excited states of BECs, which contain either holes from deeper valence bands or an envelope function with higher quantum numbers. The last section is devoted to donor-acceptor pair transitions. There is no section devoted specifically to excitons bound to neutral acceptors, because this topic is still partly controversially discussed. Instead, information on these A0X complexes is scattered over the whole chapter, however, with some special emphasis seen in Sects. 7.1, 7.4, and 7.5.

  6. High content screening for G protein-coupled receptors using cell-based protein translocation assays

    DEFF Research Database (Denmark)

    Grånäs, Charlotta; Lundholt, Betina Kerstin; Heydorn, Arne

    2005-01-01

    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...... will continue to be valuable discovery tools, the most exciting developments in the field involve cell-based assays for GPCR function. Some cell-based discovery strategies, such as the use of beta-arrestin as a surrogate marker for GPCR function, have already been reduced to practice, and have been used...... as valuable discovery tools for several years. The application of high content cell-based screening to GPCR discovery has opened up additional possibilities, such as direct tracking of GPCRs, G proteins and other signaling pathway components using intracellular translocation assays. These assays provide...

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

    Science.gov (United States)

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

    2015-07-15

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

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

    NARCIS (Netherlands)

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

    2011-01-01

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

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

    NARCIS (Netherlands)

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

    2010-01-01

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

  10. 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)

    1999-02-01

    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.)

  11. Gels based on anion recognition between triurea receptor and phosphate anion.

    Science.gov (United States)

    Yang, Cuiling; Wu, Biao; Chen, Yongming; Zhang, Ke

    2015-04-01

    Anion recognition between the triurea receptor and phosphate anion is demonstrated as the cross-linkage to build supramolecular polymer gels for the first time. A novel multi-block copolymer (3) is designed to have functional triurea groups as cross-linking units along the polymer main chain. By virtue of anion coordination between the triurea receptor and phosphate anion with a binding mode of 2:1, supramolecular polymer gels are then prepared based on anion recognition using 3 as the building block. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. High-Performance Prediction of Human Estrogen Receptor Agonists Based on Chemical Structures

    Directory of Open Access Journals (Sweden)

    Yuki Asako

    2017-04-01

    Full Text Available Many agonists for the estrogen receptor are known to disrupt endocrine functioning. We have developed a computational model that predicts agonists for the estrogen receptor ligand-binding domain in an assay system. Our model was entered into the Tox21 Data Challenge 2014, a computational toxicology competition organized by the National Center for Advancing Translational Sciences. This competition aims to find high-performance predictive models for various adverse-outcome pathways, including the estrogen receptor. Our predictive model, which is based on the random forest method, delivered the best performance in its competition category. In the current study, the predictive performance of the random forest models was improved by strictly adjusting the hyperparameters to avoid overfitting. The random forest models were optimized from 4000 descriptors simultaneously applied to 10,000 activity assay results for the estrogen receptor ligand-binding domain, which have been measured and compiled by Tox21. Owing to the correlation between our model’s and the challenge’s results, we consider that our model currently possesses the highest predictive power on agonist activity of the estrogen receptor ligand-binding domain. Furthermore, analysis of the optimized model revealed some important features of the agonists, such as the number of hydroxyl groups in the molecules.

  13. High-Performance Prediction of Human Estrogen Receptor Agonists Based on Chemical Structures.

    Science.gov (United States)

    Asako, Yuki; Uesawa, Yoshihiro

    2017-04-23

    Many agonists for the estrogen receptor are known to disrupt endocrine functioning. We have developed a computational model that predicts agonists for the estrogen receptor ligand-binding domain in an assay system. Our model was entered into the Tox21 Data Challenge 2014, a computational toxicology competition organized by the National Center for Advancing Translational Sciences. This competition aims to find high-performance predictive models for various adverse-outcome pathways, including the estrogen receptor. Our predictive model, which is based on the random forest method, delivered the best performance in its competition category. In the current study, the predictive performance of the random forest models was improved by strictly adjusting the hyperparameters to avoid overfitting. The random forest models were optimized from 4000 descriptors simultaneously applied to 10,000 activity assay results for the estrogen receptor ligand-binding domain, which have been measured and compiled by Tox21. Owing to the correlation between our model's and the challenge's results, we consider that our model currently possesses the highest predictive power on agonist activity of the estrogen receptor ligand-binding domain. Furthermore, analysis of the optimized model revealed some important features of the agonists, such as the number of hydroxyl groups in the molecules.

  14. 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 )

    2015-01-01

    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

  15. Plant membrane assays with cytokinin receptors underpin the unique role of free cytokinin bases as biologically active ligands.

    Science.gov (United States)

    Lomin, Sergey N; Krivosheev, Dmitry M; Steklov, Mikhail Yu; Arkhipov, Dmitry V; Osolodkin, Dmitry I; Schmülling, Thomas; Romanov, Georgy A

    2015-04-01

    Cytokinin receptors play a key role in cytokinin-dependent processes regulating plant growth, development, and adaptation; therefore, the functional properties of these receptors are of great importance. Previously the properties of cytokinin receptors were investigated in heterologous assay systems using unicellular microorganisms, mainly bacteria, expressing receptor proteins. However, within microorganisms receptors reside in an alien environment that might distort the receptor properties. Therefore, a new assay system has been developed allowing studies of individual receptors within plant membranes (i.e. closer to their natural environment). The main ligand-binding characteristics of receptors from Arabidopsis [AHK2, AHK3, and AHK4] and maize (ZmHK1) were refined in this new system, and the properties of full-length Arabidopsis receptor AHK2 were characterized for the first time. Ligand specificity profiles of receptors towards cytokinin bases were comparable with the profiles retrieved in bacterial assay systems. In contrast, cytokinin-9-ribosides displayed a strongly reduced affinity for receptors in the plant assay system, indicating that ribosides as the common transport form of cytokinins have no or very weak cytokinin activity. This underpins the central role of free bases as the sole biologically active cytokinin compounds. According to molecular modelling and docking studies, N (9)-ribosylation alters the bonding pattern in cytokinin-receptor interaction and prevents β6-β7 loop movement important for tight hormone binding. A common feature of all receptors was a greatly reduced ligand binding at low (5.0-5.5) pH. The particularly high sensitivity of ZmHK1 to pH changes leads to the suggestion that some cytokinin receptors may play an additional role as pH sensors in the lumen of the endoplasmic reticulum. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

  16. Dromions bound states

    Energy Technology Data Exchange (ETDEWEB)

    Maccari, Attilio

    2003-03-01

    The asymptotic perturbation (AP) method is applied to the study of the nonlinear Klein-Gordon equation in 3+1 dimensions with harmonic potential and external periodic excitation supposed to be in primary resonance with the frequency of a generic mode. The AP method uses two different procedures for the solutions: introducing an asymptotic temporal rescaling and balancing of the harmonic terms with a simple iteration. Standard quantum mechanics can be used to derive the lowest order approximate solution and amplitude and phase modulation equations are obtained. External force-response and frequency-response curves are found and the existence of dromions trapped in bound states is demonstrated.

  17. Anion recognition by simple chromogenic and chromo-fluorogenic salicylidene Schiff base or reduced-Schiff base receptors.

    Science.gov (United States)

    Dalapati, Sasanka; Jana, Sankar; Guchhait, Nikhil

    2014-08-14

    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. Copyright © 2014 Elsevier B.V. All rights reserved.

  18. Containment and Consensus-Based Distributed Coordination Control to Achieve Bounded Voltage and Precise Reactive Power Sharing in Islanded AC Microgrids

    DEFF Research Database (Denmark)

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

    2017-01-01

    This paper presents a novel distributed approach to achieve both bounded voltage and accurate reactive power sharing regulation in AC microgrid. The coupling/trade-off effects between bus voltages and reactive power sharing regulation are first analyzed in detail to provide a guideline for coordi...

  19. Insulin receptor-related receptor as an extracellular pH sensor involved in the regulation of acid-base balance.

    Science.gov (United States)

    Petrenko, Alexander G; Zozulya, Sergey A; Deyev, Igor E; Eladari, Dominique

    2013-10-01

    Recent studies of insulin receptor-related receptor (IRR) revealed its unusual property to activate upon extracellular application of mildly alkaline media, pH>7.9. The activation of IRR with hydroxyl anion has typical features of ligand-receptor interaction; it is specific, dose-dependent, involves the IRR extracellular domain and is accompanied by a major conformational change. IRR is a member of the insulin receptor minifamily and has been long viewed as an orphan receptor tyrosine kinase since no peptide or protein agonist of IRR was found. In the evolution, IRR is highly conserved since its divergence from the insulin and insulin-like growth factor receptors in amphibia. The latter two cannot be activated by alkali. Another major difference between them is that unlike ubiquitously expressed insulin and insulin-like growth factor receptors, IRR is found in specific sets of cells of only some tissues, most of them being exposed to extracorporeal liquids of extreme pH. In particular, largest concentrations of IRR are in beta-intercalated cells of the kidneys. The primary physiological function of these cells is to excrete excessive alkali as bicarbonate into urine. When IRR is removed genetically, animals loose the property to excrete bicarbonate upon experimentally induced alkalosis. In this review, we will discuss the available in vitro and in vivo data that support the hypothesis of IRR role as a physiological alkali sensor that regulates acid-base balance. This article is part of a Special Issue entitled: Emerging recognition and activation mechanisms of receptor tyrosine kinases. Copyright © 2012 Elsevier B.V. All rights reserved.

  20. On the Applicability of Lower Bounds for Solving Rectilinear

    DEFF Research Database (Denmark)

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

    1998-01-01

    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....

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

    Science.gov (United States)

    Fang, Cheng; Xiao, Zhiyan

    2016-01-01

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

  2. Bio-nanocapsule-based scaffold improves the sensitivity and ligand-binding capacity of mammalian receptors on the sensor chip.

    Science.gov (United States)

    Iijima, Masumi; Yoshimoto, Nobuo; Niimi, Tomoaki; Maturana, Andrés D; Kuroda, Shun'ichi

    2016-06-01

    Mammalian receptors are recognized as target molecules for drug discovery, and chemical libraries have been screened for both potential antagonists and agonists mainly by ligand-binding assays using immobilized receptors. A bio-nanocapsule (BNC) of approximately 30 nm that displays a tandem form of the protein A-derived immunoglobulin G (IgG) Fc-binding Z domains (denoted as ZZ-BNC) has been developed for both clustering and oriented immobilization of IgGs on the solid phase of immunosensors. In this study, human IgG1 Fc-fused vascular endothelial growth factor (VEGF) receptor was immobilized through ZZ-BNC on the sensor chip of quartz crystal microbalance (ZZ-BNC-coating). When compared with direct adsorption and protein A-coating, the sensor chip showed higher sensitivity (∽46- and ∽165-fold, respectively) and larger ligand-binding capacity (∽4- and ∽18-fold, respectively). Furthermore, the number of VEGF molecules bound to its receptor increased from 0.20 (direct adsorption) to 2.06 by ZZ-BNC-coating, strongly suggesting that ZZ-BNC reduced the steric hindrance near ligand recognition sites through oriented immobilization. Similarly, the sensitivity and ligand-binding capacity of leptin and prolactin receptors were both enhanced at a level comparable to that observed for the VEGF receptor. Thus, the combination of ZZ-BNC and Fc-fused receptors could significantly improve the function of ligand-binding assays. Copyright © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    Science.gov (United States)

    Frank, M J; Hutchison, K

    2009-11-24

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

  4. 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.

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

    Science.gov (United States)

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

    2013-01-01

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

  6. Fear memory in a neurodevelopmental model of schizophrenia based on the postnatal blockade of NMDA receptors.

    Science.gov (United States)

    Latusz, Joachim; Radaszkiewicz, Aleksandra; Bator, Ewelina; Wędzony, Krzysztof; Maćkowiak, Marzena

    2017-02-01

    Epidemiological data have indicated that memory impairment is observed during adolescence in groups at high risk for schizophrenia and might precede the appearance of schizophrenia symptoms in adulthood. In the present study, we used a neurodevelopmental model of schizophrenia based on the postnatal blockade of N-methyl-d-aspartate (NMDA) receptors in rats to investigate fear memory in adolescence and adulthood. The rats were treated with increasing doses of CGP 37849 (CGP), a competitive antagonist of the NMDA receptor (1.25mg/kg on days 1, 3, 6, 9; 2.5mg/kg on days 12, 15, 18 and 5mg/kg on day 21). Fear memory was analysed in delay and trace fear conditioning. Sensorimotor gating deficit, which is another cognitive symptom of schizophrenia, was also determined in adolescent and adult CGP-treated rats. Postnatal CGP administration disrupted cue- and context-dependent fear memory in adolescent rats in both delay and trace conditioning. In contrast, CGP administration evoked impairment only in cue-dependent fear memory in rats exposed to trace but not delay fear conditioning. The postnatal blockade of NMDA receptors induced sensorimotor gating deficits in adult rats but not in adolescent rats. The postnatal blockade of NMDA receptors induced fear memory impairment in adolescent rats before the onset of neurobehavioral deficits associated with schizophrenia. Copyright © 2016. Published by Elsevier Urban & Partner Sp. z o.o.

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

    Directory of Open Access Journals (Sweden)

    Sehan Lee

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

  8. An entirely cell-based system to generate single-chain antibodies against cell surface receptors.

    Science.gov (United States)

    Lipes, Barbara D; Chen, Yu-Hsun; Ma, Hongzheng; Staats, Herman F; Kenan, Daniel J; Gunn, Michael Dee

    2008-05-30

    The generation of recombinant antibodies (Abs) using phage display is a proven method to obtain a large variety of Abs that bind with high affinity to a given antigen. Traditionally, the generation of single-chain Abs depends on the use of recombinant proteins in several stages of the procedure. This can be a problem, especially in the case of cell-surface receptors, because Abs generated and selected against recombinant proteins may not bind the same protein expressed on a cell surface in its native form and because the expression of some receptors as recombinant proteins is problematic. To overcome these difficulties, we developed a strategy to generate single-chain Abs that does not require the use of recombinant protein at any stage of the procedure. In this strategy, stably transfected cells are used for the immunization of mice, measuring Ab responses to immunization, panning the phage library, high-throughput screening of arrayed phage clones, and characterization of recombinant single-chain variable regions. This strategy was used to generate a panel of single-chain Abs specific for the innate immunity receptor Toll-like receptor 2. Once generated, individual single-chain variable regions were subcloned into an expression vector allowing the production of recombinant Abs in insect cells, thus avoiding the contamination of recombinant Abs with microbial products. This cell-based system efficiently generates Abs that bind to native molecules on the cell surface, bypasses the requirement of recombinant protein production, and avoids risks of microbial component contamination.

  9. Discovery of benzhydrylpiperazine derivatives as CB1 receptor inverse agonists via privileged structure-based approach.

    Science.gov (United States)

    Meng, Tao; Wang, Jue; Peng, Hongli; Fang, Guanghua; Li, Min; Xiong, Bing; Xie, Xin; Zhang, Yongliang; Wang, Xin; Shen, Jingkang

    2010-03-01

    The present study describes the identification via privileged structure-based approach of the benzhydrylpiperazine moiety as a potential scaffold to develop novel CB(1) receptor modulators. Efficient structural optimization of the initial four hit compounds led to a high quality lead series, represented by compound 6c. Compound 6c is a highly potent and selective CB(1) receptor inverse agonist that is able to reduce body weight in diet-induced obese Sprague-Dawley rats. The preparation of privileged structure-based library, the progression from hit to lead, the structure-activity relationships in the lead series and in vitro and in vivo activity of compound 6c are discussed. Copyright (c) 2009 Elsevier Masson SAS. All rights reserved.

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

    Directory of Open Access Journals (Sweden)

    Ustav Mart

    2002-04-01

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

  11. Protein-bound polyphenols create “ghost” band artifacts during chemiluminescence-based antigen detection [version 2; referees: 2 approved, 1 approved with reservations

    Directory of Open Access Journals (Sweden)

    Nathalie Plundrich

    2017-05-01

    Full Text Available Antigen detection during Western blotting commonly utilizes a horseradish peroxidase-coupled secondary antibody and enhanced chemiluminescent substrate. We utilized this technique to examine the impact of green tea-derived polyphenols on the binding of egg white protein-specific IgE antibodies from allergic human plasma to their cognate antigens. Our experiments unexpectedly showed that green tea-derived polyphenols, when stably complexed with egg white proteins, caused “ghost” band formation in the presence of horseradish peroxide. This study suggests that caution should be taken when evaluating polyphenol-bound proteins by enhanced chemiluminescence Western blotting using horseradish peroxidase and demonstrates that protein-bound polyphenols can be a source of “ghost” band artifacts on Western blots.

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

    Science.gov (United States)

    Vichansavakul, Kittaya

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

  13. FRET-based detection of M1 muscarinic acetylcholine receptor activation by orthosteric and allosteric agonists.

    Directory of Open Access Journals (Sweden)

    Danijela Markovic

    Full Text Available Muscarinic acetylcholine receptors (mAChRs are 7-transmembrane, G protein-coupled receptors that regulate a variety of physiological processes and represent potentially important targets for therapeutic intervention. mAChRs can be stimulated by full and partial orthosteric and allosteric agonists, however the relative abilities of such ligands to induce conformational changes in the receptor remain unclear. To gain further insight into the actions of mAChR agonists, we have developed a fluorescently tagged M(1 mAChR that reports ligand-induced conformational changes in real-time by changes in Förster resonance energy transfer (FRET.Variants of CFP and YFP were inserted into the third intracellular loop and at the end of the C-terminus of the mouse M(1 mAChR, respectively. The optimized FRET receptor construct (M(1-cam5 was expressed stably in HEK293 cells.The variant CFP/YFP-receptor chimera expressed predominantly at the plasma membrane of HEK293 cells and displayed ligand-binding affinities comparable with those of the wild-type receptor. It also retained an ability to interact with Gα(q/11 proteins and to stimulate phosphoinositide turnover, ERK1/2 phosphorylation and undergo agonist-dependent internalization. Addition of the full agonist methacholine caused a reversible decrease in M(1 FRET (F(EYFP/F(ECFP that was prevented by atropine pre-addition and showed concentration-dependent amplitude and kinetics. Partial orthosteric agonists, arecoline and pilocarpine, as well as allosteric agonists, AC-42 and 77-LH-28-1, also caused atropine-sensitive decreases in the FRET signal, which were smaller in amplitude and significantly slower in onset compared to those evoked by methacholine.The M(1 FRET-based receptor chimera reports that allosteric and orthosteric agonists induce similar conformational changes in the third intracellular loop and/or C-terminus, and should prove to be a valuable molecular reagent for pharmacological and structural

  14. Ion pair dissociation effects of aza-based anion receptors on lithium salts in polymer electrolytes

    Energy Technology Data Exchange (ETDEWEB)

    Yang, X.Q.; Lee, H.S.; Xiang, C.; McBreen, J. [Brookhaven National Lab., Upton, NY (United States); Choi, L.S. [Naval Research Lab., Washington, DC (United States); Okamoto, Y. [Polytechnic Univ., Brooklyn, NY (United States)

    1996-12-31

    The addition of aza-based anion receptors greatly increases the conductivity of polymer electrolytes based on LiCl and KI complexes with poly(ethylene oxide) (PEO). In some cases the conductivity increase is more than two orders of magnitude. Also the addition of the anion acceptors imparts a rubber like consistency to the normally stiff PEO salt films. Ion-ion, ion-polymer and anion-complex interactions were studied using Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy at the K and Cl K edges and at the I L{sub I} edge. The NEXAFS results show that Cl{sup {minus}} and I{sup {minus}} anions are complexed with the nitrogen groups of the anion receptors. The degree of complexation is related the chain length of the complexing agent and the number of R{double_bond}CF{sub 3}SO{sub 2} groups that are used to substitute for the amine hydrogen atoms in these aza-ether compounds. NEXAFS spectra at potassium K edge provide supplemental evidence for the ion pair dissociation effects of the anion receptors. The results show that dissociated K{sup +} cations are complexed with oxygen atoms of the PEO chains.

  15. Performance Bounds of Quaternion Estimators.

    Science.gov (United States)

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

    2015-12-01

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

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

    Science.gov (United States)

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

    2014-05-01

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

  17. Bounding approaches to system identification

    CERN Document Server

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

    1996-01-01

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

  18. with Bounded Failure Intensity

    Directory of Open Access Journals (Sweden)

    Preeti Wanti Srivastava

    2011-01-01

    Full Text Available This paper deals with the Bayes prediction of the future failures of a deteriorating repairable mechanical system subject to minimal repairs and periodic overhauls. To model the effect of overhauls on the reliability of the system a proportional age reduction model is assumed and the 2-parameter Engelhardt-Bain process (2-EBP is used to model the failure process between two successive overhauls. 2-EBP has an advantage over Power Law Process (PLP models. It is found that the failure intensity of deteriorating repairable systems attains a finite bound when repeated minimal repair actions are combined with some overhauls. If such a data is analyzed through models with unbounded increasing failure intensity, such as the PLP, then pessimistic estimates of the system reliability will arise and incorrect preventive maintenance policy may be defined. On the basis of the observed data and of a number of suitable prior densities reflecting varied degrees of belief on the failure/repair process and effectiveness of overhauls, the prediction of the future failure times and the number of failures in a future time interval is found. Finally, a numerical application is used to illustrate the advantages from overhauls and sensitivity analysis of the improvement parameter carried out.

  19. Base-Pairing Energies of Proton-Bound Dimers and Proton Affinities of 1-Methyl-5-Halocytosines: Implications for the Effects of Halogenation on the Stability of the DNA i-Motif

    Science.gov (United States)

    Yang, Bo; Wu, R. R.; Rodgers, M. T.

    2015-09-01

    (CCG)n•(CGG)n trinucleotide repeats have been found to be associated with fragile X syndrome, the most widespread inherited cause of mental retardation in humans. The (CCG)n•(CGG)n repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of noncanonical proton-bound dimers of cytosine (C+•C). Halogenated cytosine residues are one form of DNA damage that may be important in altering the structure and stability of DNA or DNA-protein interactions and, hence, regulate gene expression. Previously, we investigated the effects of 5-halogenation and 1-methylation of cytosine on the base-pairing energies (BPEs) using threshold collision-induced dissociation (TCID) techniques. In the present study, we extend our work to include proton-bound homo- and heterodimers of cytosine, 1-methyl-5-fluorocytosine, and 1-methyl-5-bromocytosine. All modifications examined here are found to produce a decrease in the BPEs. However, the BPEs of all of the proton-bound dimers examined significantly exceed those of Watson-Crick G•C, neutral C•C base pairs, and various methylated variants such that DNA i-motif conformations should still be preserved in the presence of these modifications. The proton affinities (PAs) of the halogenated cytosines are also obtained from the experimental data by competitive analysis of the primary dissociation pathways that occur in parallel for the proton-bound heterodimers. 5-Halogenation leads to a decrease in the N3 PA of cytosine, whereas 1-methylation leads to an increase in the N3 PA. Thus, the 1-methyl-5-halocytosines exhibit PAs that are intermediate.

  20. Base-Pairing Energies of Proton-Bound Dimers and Proton Affinities of 1-Methyl-5-Halocytosines: Implications for the Effects of Halogenation on the Stability of the DNA i-Motif.

    Science.gov (United States)

    Yang, Bo; Wu, R R; Rodgers, M T

    2015-09-01

    (CCG)(n)•(CGG)(n) trinucleotide repeats have been found to be associated with fragile X syndrome, the most widespread inherited cause of mental retardation in humans. The (CCG)(n)•(CGG)(n) repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of noncanonical proton-bound dimers of cytosine (C(+)•C). Halogenated cytosine residues are one form of DNA damage that may be important in altering the structure and stability of DNA or DNA-protein interactions and, hence, regulate gene expression. Previously, we investigated the effects of 5-halogenation and 1-methylation of cytosine on the base-pairing energies (BPEs) using threshold collision-induced dissociation (TCID) techniques. In the present study, we extend our work to include proton-bound homo- and heterodimers of cytosine, 1-methyl-5-fluorocytosine, and 1-methyl-5-bromocytosine. All modifications examined here are found to produce a decrease in the BPEs. However, the BPEs of all of the proton-bound dimers examined significantly exceed those of Watson-Crick G•C, neutral C•C base pairs, and various methylated variants such that DNA i-motif conformations should still be preserved in the presence of these modifications. The proton affinities (PAs) of the halogenated cytosines are also obtained from the experimental data by competitive analysis of the primary dissociation pathways that occur in parallel for the proton-bound heterodimers. 5-Halogenation leads to a decrease in the N3 PA of cytosine, whereas 1-methylation leads to an increase in the N3 PA. Thus, the 1-methyl-5-halocytosines exhibit PAs that are intermediate.

  1. Advantages and Limitations of Androgen Receptor-Based Methods for Detecting Anabolic Androgenic Steroid Abuse as Performance Enhancing Drugs

    National Research Council Canada - National Science Library

    Bailey, Kathy; Yazdi, Tahmineh; Masharani, Umesh; Tyrrell, Blake; Butch, Anthony; Schaufele, Fred

    2016-01-01

    .... Since AASs achieve their anabolic effects by activating the Androgen Receptor (AR), cell-based bioassays that measure the effect of a urine sample on AR activity are under investigation as complementary, pan-androgen detection methods...

  2. 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

    2016-01-01

    Despite the extensive literature describing the biological effects of phenolic compounds from cereals, little is known about their bioaccessibility in the food matrix. This paper describes a validated LC-MS/MS method for the quantification of free and total content (free + bound) of eight plant...... with enzymatic hydrolyses, for the measurement of the total concentration of lignans, and methanolic extraction combined with enzymatic hydrolysis, for the measurement of free lignans, followed by solid phase extraction (SPE). The strength of this LC-MS/MS method is that it can be combined with different types...

  3. ExtremeBounds: Extreme Bounds Analysis in R

    Directory of Open Access Journals (Sweden)

    Marek Hlavac

    2016-08-01

    Full Text Available This article introduces the R package ExtremeBounds to perform extreme bounds analysis (EBA, a sensitivity test that examines how robustly the dependent variable of a regression model is related to a variety of possible determinants. ExtremeBounds supports Leamer's EBA that focuses on the upper and lower extreme bounds of regression coefficients, as well as Sala-i-Martin's EBA which considers their entire distribution. In contrast to existing alternatives, it can estimate models of a variety of user-defined sizes, use regression models other than ordinary least squares, incorporate non-linearities in the model specification, and apply custom weights and standard errors. To alleviate concerns about the multicollinearity and conceptual overlap of examined variables, ExtremeBounds allows users to specify sets of mutually exclusive variables, and can restrict the analysis to coefficients from regression models that yield a variance inflation factor within a prespecified limit.

  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. Sensitivity-based approach to optimal experimental design in a receptor trafficking and down regulation model

    Science.gov (United States)

    Casey, Fergal; Waterfall, Joshua; Gutenkunst, Ryan; Brown, Kevin; Myers, Christopher; Sethna, James

    2006-03-01

    We apply the ideas of optimal experimental design to systems biology models: minimizing a design criterion based on the average variance of predictions, we suggest new experiments that need to be performed to optimally test a given biological hypothesis. The estimated variance in predictions is derived from the sensitivities of protein and chemical species in the model to changes in reaction rates. The sensitivities also allow us to determine which interactions in the biological network dominate the system behavior. To test the design principles, we have developed a differential equation model incorporating the processes of endocytosis, recycling and degradation of activated epidermal growth factor (EGF) receptor in a mammalian cell line. Recent experimental work has discovered mutant proteins that cause receptor accumulation and a prolonged growth signal. Our model is optimized to fit this mutant experimental data and wild type data for a variety of experimental conditions. Of biological interest is the effect on surface and internalized receptor levels after the overexpression or inactivation of regulator proteins in the network: the optimal design method allows us to fine tune the conditions to best predict the behavior of these unknown components of the system.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-01-01

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

  7. Pixel-based absorption correction for dual-tracer fluorescence imaging of receptor binding potential

    Science.gov (United States)

    Kanick, Stephen C.; Tichauer, Kenneth M.; Gunn, Jason; Samkoe, Kimberley S.; Pogue, Brian W.

    2014-01-01

    Ratiometric approaches to quantifying molecular concentrations have been used for decades in microscopy, but have rarely been exploited in vivo until recently. One dual-tracer approach can utilize an untargeted reference tracer to account for non-specific uptake of a receptor-targeted tracer, and ultimately estimate receptor binding potential quantitatively. However, interpretation of the relative dynamic distribution kinetics is confounded by differences in local tissue absorption at the wavelengths used for each tracer. This study simulated the influence of absorption on fluorescence emission intensity and depth sensitivity at typical near-infrared fluorophore wavelength bands near 700 and 800 nm in mouse skin in order to correct for these tissue optical differences in signal detection. Changes in blood volume [1-3%] and hemoglobin oxygen saturation [0-100%] were demonstrated to introduce substantial distortions to receptor binding estimates (error > 30%), whereas sampled depth was relatively insensitive to wavelength (error tracer inputs immediately post-injection was found to account for spatial heterogeneities in local absorption properties. Application of the pixel-based normalization method to an in vivo imaging study demonstrated significant improvement, as compared with a reference tissue normalization approach. PMID:25360349

  8. Parallel Chemistry Approach to Identify Novel Nuclear Receptor Ligands Based on the GW0742 Scaffold.

    Science.gov (United States)

    Teske, Kelly A; Rai, Ganesha; Nandhikonda, Premchendar; Sidhu, Preetpal S; Feleke, Belaynesh; Simeonov, Anton; Yasgar, Adam; Jadhav, Ajit; Maloney, David J; Arnold, Leggy A

    2017-10-09

    We describe the parallel synthesis of novel analogs of GW0742, a peroxisome proliferator-activated receptor δ (PPARδ) agonist. For that purpose, modified reaction conditions were applied, such as a solid-phase palladium-catalyzed Suzuki coupling. In addition, tetrazole-based compounds were generated as a bioisostere for carboxylic acid-containing ligand GW0742. The new compounds were investigated for their ability to activate PPARδ mediated transcription and their cross-reactivity with the vitamin D receptor (VDR), another member of the nuclear receptor superfamily. We identified many potent PPARδ agonists that were less toxic than GW0742, where ∼65 of the compounds synthesized exhibited partial PPARδ activity (23-98%) with EC50 values ranging from 0.007-18.2 μM. Some ligands, such as compound 32, were more potent inhibitors of VDR-mediated transcription with significantly reduced PPARδ activity than GW0742, however, none of the ligands were completely selective for VDR inhibition over PPARδ activation of transcription.

  9. Bound anionic states of adenine

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-03-20

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

  10. Lower Bounds for External Memory Dictionaries

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Fagerberg, Rolf

    2003-01-01

    We study trade-offs between the update time and the query time for comparison based external memory dictionaries. The main contributions of this paper are two lower bound trade offs between the I/O complexity of member queries and insertions: If N

  11. Book Selection, Collection Development, and Bounded Rationality.

    Science.gov (United States)

    Schwartz, Charles A.

    1989-01-01

    Reviews previously proposed schemes of classical rationality in book selection, describes new approaches to rational choice behavior, and presents a model of book selection based on bounded rationality in a garbage can decision process. The role of tacit knowledge and symbolic content in the selection process are also discussed. (102 references)…

  12. Nonequilibrium quantum bounds to Landauer's principle: Tightness and effectiveness

    Science.gov (United States)

    Campbell, Steve; Guarnieri, Giacomo; Paternostro, Mauro; Vacchini, Bassano

    2017-10-01

    We assess two different nonequilibrium quantum Landauer bounds: the traditional approach based on the change in entropy, referred to as the "entropic bound," and one based on the details of the dynamical map, referred to as the "thermodynamic bound." By first restricting to a simple exactly solvable model of a single two-level system coupled to a finite-dimensional thermal environment and by exploiting an excitation-preserving interaction, we establish the dominant role played by the population terms in dictating the tightness of these bounds with respect to the dissipated heat and clearly establish that coherences only affect the entropic bound. Furthermore, we show that sharp boundaries between the relative performance of the two quantities emerge and find that there are clear instances where both approaches return a bound weaker than Clausius' statement of the second law, rendering them ineffective. Finally, we show that our results extend to generic interaction terms.

  13. Entropy Bounds, Holographic Principle and Uncertainty Relation

    Directory of Open Access Journals (Sweden)

    I. V. Volovich

    2001-06-01

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

  14. Bounds for Asian basket options

    Science.gov (United States)

    Deelstra, Griselda; Diallo, Ibrahima; Vanmaele, Michèle

    2008-09-01

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

  15. Hadron-nucleus bound states

    CERN Document Server

    Yamazaki, T

    2000-01-01

    A new type of nuclear spectroscopy to study hadron-nucleus bound states is described. The first successful experiment was to search for deeply bound pi sup - states in heavy nuclei using the sup 2 sup 0 sup 8 Pb(d, sup 3 He) reaction at GSI, in which a narrow peak arising from the 2p pi sup - orbital coupled with the neutron-hole states was observed at 135 MeV excitation energy. An improved experiment has just been carried out to separately identify the 1s and 2p pi sup - states. These experiments provide important information on the local potential strength, from which the effective mass of pi sup - is deduced to be 20 MeV. This method will be extended to search for eta and omega bound states as well as for K sup - bound states. The advantage of the bound-state spectroscopy versus invariant mass spectroscopy is emphasized.

  16. Multi-channel receptors based on thiopyrylium functionalised with macrocyclic receptors for the recognition of transition metal cations and anions.

    Science.gov (United States)

    Abalos, T; Jiménez, D; Moragues, M; Royo, S; Martínez-Máñez, R; Sancenón, F; Soto, J; Costero, A M; Parra, M; Gil, S

    2010-04-14

    We report herein the synthesis and characterization of a family of ligands containing different cation binding sites covalently connected to a thiopyrylium signalling reporter. The receptors L1-L6 are able to signal the presence of certain metal cations via three different channels; i.e. electrochemically, fluorogenically and chromogenically. An acetonitrile solution of L1-L6 shows a bright blue colour due to a charge-transfer band in the 575-585 nm region. The colour variation in acetonitrile of L1-L6 in the presence of the metal cations Ag+, Cd2+, Cu2+, Fe3+, Hg2+, Ni2+, Pb2+ and Zn2+ has been studied. A selective hypsochromic shift of the blue band was found for the systems L4-Pb2+ and L5-Hg2+. Additionally, L1-L6 are poorly fluorescent but coordination with certain metal cations induces an enhancement of the fluorescence at ca 500 nm. For instance, the presence of Cu2+ and Fe3+ induced a remarkable 42-fold and 45-fold enhancement in the emission intensity of L1 centred at 500 nm, respectively. Also remarkable was the 18-fold enhancement observed for L4 and L5 in the presence of Fe3+ and Cu2+, respectively. The electrochemical behaviour of receptors L1-L6 was studied in acetonitrile using platinum as a working electrode and [Bu4N][BF4] as a supporting electrolyte. This family of receptors showed a one-electron reversible redox process at ca. -0.46 V versus sce attributed to the reduction of the thiopyrylium group. A moderate anodic shift in the presence of certain metal cations was observed. The effect in the UV-visible spectra of acetonitrile solutions of receptor L1-L6 in the presence of anions was also studied. A remarkable bleaching was found in the presence of cyanide.

  17. Current status of chimeric antigen receptor engineered T cell-based and immune checkpoint blockade-based cancer immunotherapies.

    Science.gov (United States)

    Hegde, Upendra P; Mukherji, Bijay

    2017-05-11

    Adoptive cell therapies with chimeric antigen receptor (CAR) engineered T cells (CAR-T) and immune checkpoint inhibition (ICI)-based cancer immunotherapies have lately shown remarkable success in certain tumor types. CAR-T cell-based therapies targeting CD19 can now induce durable remissions as well as prolong disease-free survival of patients with CD19 positive treatment refractory B cell malignancies and ICI-based therapies with humanized monoclonal antibodies against the T cell inhibitory receptors CTLA-4 and PD-1 as well as against the PD-1 ligand, PD-L1, can now achieve durable remissions as well as prolongation of life of a sizeable fraction of patients with melanoma and Hodgkin's lymphoma and non-small cell cancers. Most importantly, these immuno-therapeutic treatment modalities have raised the possibility of achieving long-term "containment" as well as "cures" for certain types of cancer. While this represents major advances in cancer immunotherapy, both modalities come with considerable toxicities, including fatalities. Although more work will be needed to bring CAR-T cell-based therapies to the bedside for most major cancers and a good deal more will be needed to make ICI-alone or in combination with other treatment modalities-work more consistently and across most major cancers, these two treatment modalities stand out as superb examples of successful translation of bench research to the bedside as well as represent real progress in the field of cancer immunotherapy.

  18. Advances in mass spectrometry based strategies to study receptor tyrosine kinases

    Directory of Open Access Journals (Sweden)

    Simon Vyse

    2017-03-01

    Full Text Available Receptor tyrosine kinases (RTKs are key transmembrane environmental sensors that are capable of transmitting extracellular information into phenotypic responses, including cell proliferation, survival and metabolism. Advances in mass spectrometry (MS-based phosphoproteomics have been instrumental in providing the foundations of much of our current understanding of RTK signalling networks and activation dynamics. Furthermore, new insights relating to the deregulation of RTKs in disease, for instance receptor co-activation and kinome reprogramming, have largely been identified using phosphoproteomic-based strategies. This review outlines the current approaches employed in phosphoproteomic workflows, including phosphopeptide enrichment and MS data-acquisition methods. Here, recent advances in the application of MS-based phosphoproteomics to bridge critical gaps in our knowledge of RTK signalling are focused on. The current limitations of the technology are discussed and emerging areas such as computational modelling, high-throughput phosphoproteomic workflows and next-generation single-cell approaches to further our understanding in new areas of RTK biology are highlighted.

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

    Energy Technology Data Exchange (ETDEWEB)

    Bogen, K T

    2007-05-11

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

  20. Determining the limit of detection of surface bound antibody.

    Science.gov (United States)

    Madiona, Robert M T; Welch, Nicholas G; Scoble, Judith A; Muir, Benjamin W; Pigram, Paul J

    2017-08-11

    Determination of a limit of detection (LoD) for surface bound antibodies is crucial for the development and deployment of sensitive bioassays. The measurement of very low concentrations of surface bound antibodies is also important in the manufacturing of pharmaceutical products such as antibody-conjugated pharmaceuticals. Low concentrations are required to avoid an immune response from the target host. Enzyme-linked immunosorbent assay (ELISA), x-ray photoelectron spectroscopy (XPS), and time-of-flight secondary ion mass spectrometry (ToF-SIMS) were used to determine the LoD for the surface bound antibody (antiepidermal growth factor receptor antibody) on silicon substrates. Antibody solution concentrations between 10 μg/ml and 1 ng/ml and a control (antibody-free buffer solution) were employed, and the detection performance of each technique was compared. For this system, the ELISA LoD was 100 ng/ml and the XPS LoD was 1 μg/ml, corresponding to an estimated surface concentration of 49  ± 7 ng/cm2 using a 1 μg/ml solution. Due to the multivariate complexity of ToF-SIMS data, analysis was carried out using three different methods, peak ratio calculations, principal component analysis, and artificial neural network analysis. The use of multivariate analysis with this dataset offers an unbiased analytical approach based on the peaks selected from ToF-SIMS data. The results estimate a ToF-SIMS LoD between applied antibody concentrations of 10 and 100 ng/mL. For surface bound antibodies on a silicon substrate, the LoD is below an estimated surface concentration of 49 ng/cm2. The authors have determined the LoD for this system using ELISA, XPS, and ToF-SIMS with multivariate analyses, with ToF-SIMS offering an order of magnitude better detection over ELISA and 2 orders of magnitude better detection over XPS.

  1. First-in-class thyrotropin-releasing hormone (TRH)-based compound binds to a pharmacologically distinct TRH receptor subtype in human brain and is effective in neurodegenerative models.

    Science.gov (United States)

    Kelly, Julie A; Boyle, Noreen T; Cole, Natalie; Slator, Gillian R; Colivicchi, M Alessandra; Stefanini, Chiara; Gobbo, Oliviero L; Scalabrino, Gaia A; Ryan, Sinead M; Elamin, Marwa; Walsh, Cathal; Vajda, Alice; Goggin, Margaret M; Campbell, Matthew; Mash, Deborah C; O'Mara, Shane M; Brayden, David J; Callanan, John J; Tipton, Keith F; Della Corte, Laura; Hunter, Jackie; O'Boyle, Kathy M; Williams, Carvell H; Hardiman, Orla

    2015-02-01

    JAK4D, a first-in-class thyrotropin-releasing hormone (TRH)-based compound, is a prospective therapeutic candidate offering a multifaceted approach to treating neurodegeneration and other CNS conditions. The purpose of these studies was to determine the ability of JAK4D to bind to TRH receptors in human brain and to evaluate its neuropharmacological effects in neurodegenerative animal models. Additionally, JAK4D brain permeation was examined in mouse, and initial toxicology was assessed in vivo and in vitro. We report that JAK4D bound selectively with nanomolar affinity to native TRH receptors in human hippocampal tissue and showed for the first time that these receptors are pharmacologically distinct from TRH receptors in human pituitary, thus revealing a new TRH receptor subtype which represents a promising neurotherapeutic target in human brain. Systemic administration of JAK4D elicited statistically significant and clinically-relevant neuroprotective effects in three established neurodegenerative animal models: JAK4D reduced cognitive deficits when administered post-insult in a kainate (KA)-induced rat model of neurodegeneration; it protected against free radical release and neuronal damage evoked by intrastriatal microdialysis of KA in rat; and it reduced motor decline, weight loss, and lumbar spinal cord neuronal loss in G93A-SOD1 transgenic Amyotrophic Lateral Sclerosis mice. Ability to cross the blood-brain barrier and a clean initial toxicology profile were also shown. In light of these findings, JAK4D is an important tool for investigating the hitherto-unidentified central TRH receptor subtype reported herein and an attractive therapeutic candidate for neurodegenerative disorders. Copyright © 2014 Elsevier Ltd. All rights reserved.

  2. Classical Physics and the Bounds of Quantum Correlations.

    Science.gov (United States)

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

    2016-06-24

    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.

  3. Bounded relative motion under zonal harmonics perturbations

    Science.gov (United States)

    Baresi, Nicola; Scheeres, Daniel J.

    2017-04-01

    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.

  4. Combining Alphas via Bounded Regression

    Directory of Open Access Journals (Sweden)

    Zura Kakushadze

    2015-11-01

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

  5. Production of G protein-coupled receptors in an insect-based cell-free system.

    Science.gov (United States)

    Sonnabend, Andrei; Spahn, Viola; Stech, Marlitt; Zemella, Anne; Stein, Christoph; Kubick, Stefan

    2017-10-01

    The biochemical analysis of human cell membrane proteins remains a challenging task due to the difficulties in producing sufficient quantities of functional protein. G protein-coupled receptors (GPCRs) represent a main class of membrane proteins and drug targets, which are responsible for a huge number of signaling processes regulating various physiological functions in living cells. To circumvent the current bottlenecks in GPCR studies, we propose the synthesis of GPCRs in eukaryotic cell-free systems based on extracts generated from insect (Sf21) cells. Insect cell lysates harbor the fully active translational and translocational machinery allowing posttranslational modifications, such as glycosylation and phosphorylation of de novo synthesized proteins. Here, we demonstrate the production of several GPCRs in a eukaryotic cell-free system, performed within a short time and in a cost-effective manner. We were able to synthesize a variety of GPCRs ranging from 40 to 133 kDa in an insect-based cell-free system. Moreover, we have chosen the μ opioid receptor (MOR) as a model protein to analyze the ligand binding affinities of cell-free synthesized MOR in comparison to MOR expressed in a human cell line by "one-point" radioligand binding experiments. Biotechnol. Bioeng. 2017;114: 2328-2338. © 2017 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc. © 2017 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.

  6. Carboplatin plus weekly nanoparticle albumin-bound paclitaxel in elderly patients with previously untreated advanced squamous non-small-cell lung cancer selected based on Mini Nutritional Assessment short-form scores: a multicenter phase 2 study.

    Science.gov (United States)

    Shiroyama, Takayuki; Tamiya, Motohiro; Minami, Seigo; Takata, So; Masuhiro, Kentaro; Futami-Nishijima, Yu; Uenami, Takeshi; Mori, Masahide; Koba, Taro; Matsuki, Takanori; Takimoto, Takayuki; Suzuki, Hidekazu; Okamoto, Norio; Komuta, Kiyoshi; Hirashima, Tomonori; Kumanogoh, Atsushi; Kijima, Takashi

    2017-09-01

    This multicenter, single-arm, open-label, phase 2 study assessed the efficacy and safety of carboplatin plus weekly nanoparticle albumin-bound paclitaxel in elderly patients with previously untreated advanced squamous non-small-cell lung cancer, selected based on the Mini Nutritional Assessment short-form scores (MNA-SF). Patients received carboplatin (area under the curve: 6) on Day 1, and nanoparticle albumin-bound paclitaxel (100 mg/m2) on Days 1, 8, and 15, every 28 days for ≤4 cycles. Eligibility criteria included an MNA-SF score of ≥8 points. The primary endpoint was the objective response rate. Thirty patients with a median age of 76 (range 70-83) years were enrolled. The objective response rate was 50.0% (95% confidence interval: 31.3-68.7%), which met the primary objective of this study. The disease control rate was 73.3% (95% CI: 54.1-87.7%). At a median follow-up of 15.0 months, the median progression-free and overall survival was 7.1 and 19.1 months, respectively. The most common treatment-related adverse event of Grade ≥3 was neutropenia (66.7%). Non-hematological adverse events of Grade ≥3 were minor. Well-nourished patients, based on the MNA-SF, experienced fewer adverse events of Grade ≥3 compared to patients at risk of malnutrition. All treatment-related adverse events were tolerable and reversible. There were no treatment-related deaths. Carboplatin plus weekly nanoparticle albumin-bound paclitaxel is effective and well tolerated as a first-line treatment for elderly patients with advanced squamous non-small-cell lung cancer. Eligibility based on MNA-SF screening may be useful in determining acceptable toxicity.

  7. Synergism between soluble and dietary fiber bound antioxidants.

    Science.gov (United States)

    Çelik, Ecem Evrim; Gökmen, Vural; Skibsted, Leif H

    2015-03-04

    This study investigates the synergism between antioxidants bound to dietary fibers (DF) of grains and soluble antioxidants of highly consumed beverages or their pure antioxidants. The interaction between insoluble fractions of grains containing bound antioxidants and soluble antioxidants was investigated using (i) a liposome-based system by measuring the lag phase before the onset of oxidation and (ii) an ESR-based system by measuring the reduction percentage of Fremy's salt radical. In both procedures, antioxidant capacities of DF-bound and soluble antioxidants were measured as well as their combinations, which were prepared at different ratios. The simple addition effects of DF-bound and soluble antioxidants were compared with measured values. The results revealed a clear synergism for almost all combinations in both liposome- and ESR-based systems. The synergism observed in DF-bound-soluble antioxidant system paints a promising picture considering the role of fiber in human gastrointestinal (GI) tract health.

  8. A bioinformatics search for selective histamine h4 receptor antagonists through structure-based virtual screening strategies.

    Science.gov (United States)

    Christopher, Fenila; Thangam, Elden Berla; Suresh, Muthaiyan Xavier

    2012-05-01

    The prevalence of allergic disease is increasing dramatically in the developed world. Studies of allergic diseases have clearly demonstrated that histamine plays an important role in the pathogenesis of the early-phase allergic response. Histamine effects are mediated by H1, H2, H3, and H4 receptors. The presence of the histamine H4 receptors on leukocytes and mast cells suggests that the new histamine receptor H4 plays an important role in the modulation of the immune system. Thus, histamine H4 receptor is an attractive target for anti-allergic therapy. In our present study, we have generated a histamine H4 receptor model using I-TASSER based on human B2-adrenergic G-protein-coupled receptor. Structurally similar compounds of the three known antagonists JNJ777120, thioperamide, and Vuf6002 were retrieved from PubChem, and database was prepared. Virtual screening of those databases was performed, and six compounds with high docking score were identified. Also the binding mode revealed that all the six compounds had interaction with Asp94 of the receptor. Our results serve as a starting point in the development of novel lead compounds in anti-allergic therapy. © 2012 John Wiley & Sons A/S.

  9. Asymptotic-bound-state model for Feshbach resonances

    NARCIS (Netherlands)

    Tiecke, T.G.; Goosen, M.R.; Walraven, J.T.M.; Kokkelmans, S.J.J.M.F.

    2010-01-01

    We present an asymptotic-bound-state model which can be used to accurately describe all Feshbach resonance positions and widths in a two-body system. With this model we determine the coupled bound states of a particular two-body system. The model is based on analytic properties of the two-body

  10. Computational Lower Bounds Using Diagonalization

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 14; Issue 7. Computational Lower Bounds Using Diagonalization - Languages, Turing Machines and Complexity Classes. M V Panduranga Rao. General Article Volume 14 Issue 7 July 2009 pp 682-690 ...

  11. Ligand-specific homology modeling of human cannabinoid (CB1) receptor.

    Science.gov (United States)

    Ai, Rizi; Chang, Chia-en A

    2012-09-01

    Cannabinoid (CB1) receptor is a therapeutic drug target, and its structure and conformational changes after ligand binding are of great interest. To study the protein conformations in ligand bound state and assist in drug discovery, CB1 receptor homology models are needed for computer-based ligand screening. The known CB1 ligands are highly diverse structurally, so CB1 receptor may undergo considerable conformational changes to accept different ligands, which is challenging for molecular docking methods. To account for the flexibility of CB1 receptor, we constructed four CB1 receptor models based on four structurally distinct ligands, HU-210, ACEA, WIN55212-2 and SR141716A, using the newest X-ray crystal structures of human β₂ adrenergic receptor and adenosine A(2A) receptor as templates. The conformations of these four CB1-ligand complexes were optimized by molecular dynamics (MD) simulations. The models revealed interactions between CB1 receptor and known binders suggested by experiments and could successfully discriminate known ligands and non-binders in our docking assays. MD simulations were used to study the most flexible ligand, ACEA, in its free and bound states to investigate structural mobility achieved by the rearrangement of the fatty acid chain. Our models may capture important conformational changes of CB1 receptor to help improve accuracy in future CB1 drug screening. Copyright © 2012 Elsevier Inc. All rights reserved.

  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. Bounded Rationality in Transposition Processes

    DEFF Research Database (Denmark)

    Vollaard, Hans; Martinsen, Dorte Sindbjerg

    2014-01-01

    perspective may affect the commonly employed explanatory factors of administrative capacities, misfit and the heterogeneity of preferences among veto players. To prevent retrospective rationalisation of the transposition process, this paper traces this process as it unfolded in Denmark and the Netherlands....... As bounded rationality is apparent in the transposition processes in these relatively well-organised countries, future transposition studies should devote greater consideration to the bounded rationality perspective....

  14. Adnectin-Based Design of Chimeric Antigen Receptor for T Cell Engineering.

    Science.gov (United States)

    Han, Xiaolu; Cinay, Gunce E; Zhao, Yifan; Guo, Yunfei; Zhang, Xiaoyang; Wang, Pin

    2017-11-01

    Although chimeric antigen receptor (CAR)-engineered T cell therapy has achieved encouraging clinical trial results for treating hematological cancers, further optimization can likely expand this therapeutic success to more patients and other cancer types. Most CAR constructs used in clinical trials incorporate single chain variable fragment (scFv) as the extracellular antigen recognition domain. The immunogenicity of nonhuman scFv could cause host rejection against CAR T cells and compromise their persistence and efficacy. The limited availability of scFvs and slow discovery of new monoclonal antibodies also limit the development of novel CAR constructs. Adnectin, a class of affinity molecules derived from the tenth type III domain of human fibronectin, can be an alternative to scFv as an antigen-binding moiety in the design of CAR molecules. We constructed adnectin-based CARs targeting epithelial growth factor receptor (EGFR) and found that compared to scFv-based CAR, T cells engineered with adnectin-based CARs exhibited equivalent cell-killing activity against target H292 lung cancer cells in vitro and had comparable antitumor efficacy in xenograft tumor-bearing mice in vivo. In addition, with optimal affinity tuning, adnectin-based CAR showed higher selectivity on target cells with high EGFR expression than on those with low expression. This new design of adnectin CARs can potentially facilitate the development of T cell immunotherapy for cancer and other diseases. Copyright © 2017 The American Society of Gene and Cell Therapy. Published by Elsevier Inc. All rights reserved.

  15. Estradiol up-regulates L-type Ca2+channels via membrane-bound estrogen receptor / Phosphoinositide-3kinase / Akt / cAMP response element-binding protein signaling pathway.

    Science.gov (United States)

    Yang, Xiaoyan; Mao, Xiaofang; Xu, Gao; Xing, Shasha; Chattopadhyay, Ansuman; Jin, Si; Salama, Guy

    2018-01-09

    In long QT type-2 (LQT2), women are more prone to lethal arrhythmias called Torsade de Pointes (TdP) than men. We previously reported that 17-β-estradiol (E2) upregulates L-type Ca 2+ -channels and current (I Ca,L ) (∼30%) in rabbit ventricular myocytes by a classical genomic-mechanism mediated by estrogen-receptor-α (ER)α. In LQT2 ( I Kr -blockade or bradycardia), the higher Ca 2+ influx via I Ca,L , causes Ca 2+ -overload, spontaneous sarcoplasmic reticulum Ca 2+ -release, and re-activation of I Ca,L that trigger early afterdepolarizations (EADs) and TdP. The molecular mechanisms whereby E2 upregulates I Ca,L are poorly understood and are now investigated. H9C2 and rat myocytes were incubated with E2, ±ER antagonist, or inhibitors of downstream transcription factors 24 hours, followed by Western blots of Cav1.2α1C and voltage-clamp measurements of I Ca,L . Incubation of H9C2 cells with E2 (10∼100 nM) increased I Ca,L density and Cav1.2α1C expression which were suppressed by the ER-antagonist ICI-182,780 (1μM). Enhanced I Ca,L and Cav1.2α1C expression by E2 was suppressed by inhibitors of Pi3K (LY294002=30μM; pL via plasma-membrane ER, and activating a Pi3K, Akt and CREB signaling. The promoter regions of CACNA1C gene (human-rabbit-rat) contain adjacent/overlapping binding-sites for p-CREB and ERα which suggest a synergistic regulation by these pathways. Copyright © 2018. Published by Elsevier Inc.

  16. Model-Based Discovery of Synthetic Agonists for the Zn2+-Sensing G-Protein-Coupled Receptor 39 (GPR39) Reveals Novel Biological Functions

    DEFF Research Database (Denmark)

    Frimurer, Thomas M.; Mende, Franziska; Graae, Anne-Sofie

    2017-01-01

    The G-protein coupled receptor 39 (GPR39) is a G protein-coupled receptor activated by Zn2. We used a homol. model-based approach to identify small-mol. pharmacol. tool compds. for the receptor. The method focused on a putative binding site in GPR39 for synthetic ligands and knowledge of ligand b...

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

    DEFF Research Database (Denmark)

    Jensen, Anders A.

    2005-01-01

    receptors in this assay were found to be in good agreement with those from electrophysiology studies of the receptors expressed in Xenopus oocytes or mammalian cell lines. Hence, this high throughput screening assay will be of great use in future pharmacological studies of glycine receptors, particular...

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

    Directory of Open Access Journals (Sweden)

    Ahmed Haider

    2016-07-01

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

  19. Diaminomaleonitrile-based azo receptors: Synthesis, DFT studies and their antibacterial activities

    Science.gov (United States)

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

    2017-02-01

    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.

  20. Novel cell-based assay for detection of thyroid receptor beta-interacting environmental contaminants

    Science.gov (United States)

    Stavreva, Diana A.; Varticovski, Lyuba; Levkova, Ludmila; George, Anuja A.; Davis, Luke; Pegoraro, Gianluca; Blazer, Vicki; Iwanowicz, Luke R.; Hager, Gordon L.

    2016-01-01

    Even though the presence of endocrine disrupting chemicals (EDCs) with thyroid hormone (TH)-like activities in the environment is a major health concern, the methods for their efficient detection and monitoring are still limited. Here we describe a novel cell assay, based on the translocation of a green fluorescent protein (GFP)—tagged chimeric molecule of glucocorticoid receptor (GR) and the thyroid receptor beta (TRβ) from the cytoplasm to the nucleus in the presence of TR ligands. Unlike the constitutively nuclear TRβ, this GFP-GR-TRβ chimera is cytoplasmic in the absence of hormone while translocating to the nucleus in a time- and concentration-dependent manner upon stimulation with triiodothyronine (T3) and thyroid hormone analogue, TRIAC, while the reverse triiodothyronine (3,3′,5′-triiodothyronine, or rT3) was inactive. Moreover, GFP-GR-TRβ chimera does not show any cross-reactivity with the GR-activating hormones, thus providing a clean system for the screening of TR beta-interacting EDCs. Using this assay, we demonstrated that Bisphenol A (BPA) and 3,3′,5,5′-Tetrabromobisphenol (TBBPA) induced GFP-GR-TRβ translocation at micro molar concentrations. We screened over 100 concentrated water samples from different geographic locations in the United States and detected a low, but reproducible contamination in 53% of the samples. This system provides a novel high-throughput approach for screening for endocrine disrupting chemicals (EDCs) interacting with TR beta.

  1. Peptide-MHC-based nanomedicines for autoimmunity function as T-cell receptor microclustering devices

    Science.gov (United States)

    Singha, Santiswarup; Shao, Kun; Yang, Yang; Clemente-Casares, Xavier; Solé, Patricia; Clemente, Antonio; Blanco, Jesús; Dai, Qin; Song, Fayi; Liu, Shang Wan; Yamanouchi, Jun; Umeshappa, Channakeshava Sokke; Nanjundappa, Roopa Hebbandi; Detampel, Pascal; Amrein, Matthias; Fandos, César; Tanguay, Robert; Newbigging, Susan; Serra, Pau; Khadra, Anmar; Chan, Warren C. W.; Santamaria, Pere

    2017-07-01

    We have shown that nanoparticles (NPs) can be used as ligand-multimerization platforms to activate specific cellular receptors in vivo. Nanoparticles coated with autoimmune disease-relevant peptide-major histocompatibility complexes (pMHC) blunted autoimmune responses by triggering the differentiation and expansion of antigen-specific regulatory T cells in vivo. Here, we define the engineering principles impacting biological activity, detail a synthesis process yielding safe and stable compounds, and visualize how these nanomedicines interact with cognate T cells. We find that the triggering properties of pMHC-NPs are a function of pMHC intermolecular distance and involve the sustained assembly of large antigen receptor microclusters on murine and human cognate T cells. These compounds show no off-target toxicity in zebrafish embryos, do not cause haematological, biochemical or histological abnormalities, and are rapidly captured by phagocytes or processed by the hepatobiliary system. This work lays the groundwork for the design of ligand-based NP formulations to re-program in vivo cellular responses using nanotechnology.

  2. Cooperative interaction of protonated hexamethylenetetramine with a hexaarylbenzene-based receptor: Experimental and theoretical study

    Science.gov (United States)

    Makrlík, Emanuel; Toman, Petr; Vaňura, Petr; Rathore, Rajendra

    2012-04-01

    From extraction experiments and γ-activity measurements, the extraction constant corresponding to the equilibrium HL(aq)+1·Cs(nb)⇄1·HL(nb)+Cs(aq) taking place in the two-phase water-nitrobenzene system (HL+ = protonated hexamethylenetetramine, 1 = hexaarylbenzene-based receptor; aq = aqueous phase, nb = nitrobenzene phase) was evaluated as log Kex (HL+, 1ṡCs+) = 0.5 ± 0.1. Further, the stability constant of the 1ṡHL+ complex in nitrobenzene saturated with water was calculated for a temperature of 25 °C as log βnb (1ṡHL+) = 5.8 ± 0.2. Finally, by using quantum mechanical DFT calculations, the most probable structures A and B of the 1ṡHL+ complex species, which are obviously in a dynamic equilibrium, were indicated. In both of these structures of the resulting complex 1ṡHL+ having C3 symmetry, the cation HL+ synergistically interacts with the polar ethereal oxygen fence and with the central hydrophobic benzene bottom of the parent receptor 1 via cation-π interaction.

  3. Interaction of protonated tyramine with a hexaarylbenzene-based receptor: Extraction and DFT study

    Science.gov (United States)

    Makrlík, Emanuel; Toman, Petr; Vaňura, Petr; Rathore, Rajendra

    2013-09-01

    From extraction experiments and γ-activity measurements, the extraction constant corresponding to the equilibrium HL+(aq) + 1·Cs+(nb) ⇔ 1·HL+(nb) + Cs+(aq) taking place in the two-phase water-nitrobenzene system (HL+ = protonated tyramine, 1 = hexaarylbenzene-based receptor; aq = aqueous phase, nb = nitrobenzene phase) was evaluated as log Kex (HL+, 1·Cs+) = -0.3 ± 0.1. Further, the stability constant of the 1·HL+ complex in nitrobenzene saturated with water was calculated for a temperature of 25 °C as log βnb (1·HL+) = 4.7 ± 0.2. Finally, by using quantum mechanical DFT calculations, the most probable structure of the 1·HL+ complex species was predicted. In the resulting "asymmetrical" cationic complex 1·HL+, the cation HL+ synergistically interacts with the polar ethereal oxygen fence by means of the corresponding three H-bonds and with the central hydrophobic benzene bottom of the parent receptor 1 via cation - π interaction.

  4. Selective agonists and antagonists of formylpeptide receptors: duplex flow cytometry and mixture-based positional scanning libraries.

    Science.gov (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

    2013-09-01

    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.

  5. Modern approaches to the design of memory and cognitive function stimulants based on AMPA receptor ligands

    Energy Technology Data Exchange (ETDEWEB)

    Grigoriev, V V; Proshin, A N; Kinzirsky, A S; Bachurin, Sergey O [Institute of Physiologically Active Compounds, Russian Academy of Sciences, Chernogolovka, Moscow Region (Russian Federation)

    2009-05-31

    Data on the structure and properties of compounds acting on AMPA receptors, the key subtype of ionotropic glutamate receptors of the mammalian central nervous system, are analyzed. Data on the role of these receptors in provision of memory and cognitive function formation and impairment processes are presented. The attention is focused on the modern views on the mechanisms of AMPA receptor desensitization and deactivation and action of substances affecting these processes. The structures of key positive modulators of AMPA receptors are given. The problems of application of these substances as therapeutic means for preventing and treating neurodegenerative and psychoneurological diseases are discussed. Bibliography - 121 references.

  6. Structure-Based Design of Highly Selective and Potent G Protein-Coupled Receptor Kinase 2 Inhibitors Based on Paroxetine.

    Science.gov (United States)

    Waldschmidt, Helen V; Homan, Kristoff T; Cato, Marilyn C; Cruz-Rodríguez, Osvaldo; Cannavo, Alessandro; Wilson, Michael W; Song, Jianliang; Cheung, Joseph Y; Koch, Walter J; Tesmer, John J G; Larsen, Scott D

    2017-04-13

    In heart failure, the β-adrenergic receptors (βARs) become desensitized and uncoupled from heterotrimeric G proteins. This process is initiated by G protein-coupled receptor kinases (GRKs), some of which are upregulated in the failing heart, making them desirable therapeutic targets. The selective serotonin reuptake inhibitor, paroxetine, was previously identified as a GRK2 inhibitor. Utilizing a structure-based drug design approach, we modified paroxetine to generate a small compound library. Included in this series is a highly potent and selective GRK2 inhibitor, 14as, with an IC50 of 30 nM against GRK2 and greater than 230-fold selectivity over other GRKs and kinases. Furthermore, 14as showed a 100-fold improvement in cardiomyocyte contractility assays over paroxetine and a plasma concentration higher than its IC50 for over 7 h. Three of these inhibitors, including 14as, were additionally crystallized in complex with GRK2 to give insights into the structural determinants of potency and selectivity of these inhibitors.

  7. Heavy metals bound to fine particulate matter from northern China induce season-dependent health risks: A study based on myocardial toxicity.

    Science.gov (United States)

    Zhang, Yingying; Ji, Xiaotong; Ku, Tingting; Li, Guangke; Sang, Nan

    2016-09-01

    Substantial epidemiological evidence has consistently reported that fine particulate matter (PM2.5) is associated with an increased risk of cardiovascular outcomes. PM2.5 is a complex mixture of extremely small particles and liquid droplets composed of multiple components, and there has been high interest in identifying the specific health-relevant physical and/or chemical toxic constituents of PM2.5. In the present study, we analyzed 8 heavy metals (Cr, Ni, Cu, Cd, Pb, Zn, Mn and Co) in the PM2.5 collected during four different seasons in Taiyuan, a typical coal-burning city in northern China. Our results indicated that total concentrations of the 8 heavy metals differed among the seasons. Zn and Pb, which are primarily derived from the anthropogenic source, coal burning, were the dominant elements, and high concentrations of these two elements were observed during the spring and winter. To clarify whether these heavy metals in the locally collected PM2.5 were associated with health effects, we conducted health risk assessments using validated methods. Interestingly, Pb was responsible for greater potential health risks to children. Because cardiovascular disease (CVD) is a main contributor to the mortality associated with PM2.5 exposure, we performed experimental assays to evaluate the myocardial toxicity. Our in vitro experiments showed that the heavy metal-containing PM2.5 induced season-dependent apoptosis in rat H9C2 cells through a reactive oxygen species (ROS)-mediated inflammatory response. Our findings suggested that heavy metals bound to PM2.5 produced by coal burning play an important role in myocardial toxicity and contribute to season-dependent health risks. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Ligand and structure-based methodologies for the prediction of the activity of G protein-coupled receptor ligands

    Science.gov (United States)

    Costanzi, Stefano; Tikhonova, Irina G.; Harden, T. Kendall; Jacobson, Kenneth A.

    2009-11-01

    Accurate in silico models for the quantitative prediction of the activity of G protein-coupled receptor (GPCR) ligands would greatly facilitate the process of drug discovery and development. Several methodologies have been developed based on the properties of the ligands, the direct study of the receptor-ligand interactions, or a combination of both approaches. Ligand-based three-dimensional quantitative structure-activity relationships (3D-QSAR) techniques, not requiring knowledge of the receptor structure, have been historically the first to be applied to the prediction of the activity of GPCR ligands. They are generally endowed with robustness and good ranking ability; however they are highly dependent on training sets. Structure-based techniques generally do not provide the level of accuracy necessary to yield meaningful rankings when applied to GPCR homology models. However, they are essentially independent from training sets and have a sufficient level of accuracy to allow an effective discrimination between binders and nonbinders, thus qualifying as viable lead discovery tools. The combination of ligand and structure-based methodologies in the form of receptor-based 3D-QSAR and ligand and structure-based consensus models results in robust and accurate quantitative predictions. The contribution of the structure-based component to these combined approaches is expected to become more substantial and effective in the future, as more sophisticated scoring functions are developed and more detailed structural information on GPCRs is gathered.

  9. Ligand and structure-based methodologies for the prediction of the activity of G protein-coupled receptor ligands.

    Science.gov (United States)

    Costanzi, Stefano; Tikhonova, Irina G; Harden, T Kendall; Jacobson, Kenneth A

    2009-11-01

    Accurate in silico models for the quantitative prediction of the activity of G protein-coupled receptor (GPCR) ligands would greatly facilitate the process of drug discovery and development. Several methodologies have been developed based on the properties of the ligands, the direct study of the receptor-ligand interactions, or a combination of both approaches. Ligand-based three-dimensional quantitative structure-activity relationships (3D-QSAR) techniques, not requiring knowledge of the receptor structure, have been historically the first to be applied to the prediction of the activity of GPCR ligands. They are generally endowed with robustness and good ranking ability; however they are highly dependent on training sets. Structure-based techniques generally do not provide the level of accuracy necessary to yield meaningful rankings when applied to GPCR homology models. However, they are essentially independent from training sets and have a sufficient level of accuracy to allow an effective discrimination between binders and nonbinders, thus qualifying as viable lead discovery tools. The combination of ligand and structure-based methodologies in the form of receptor-based 3D-QSAR and ligand and structure-based consensus models results in robust and accurate quantitative predictions. The contribution of the structure-based component to these combined approaches is expected to become more substantial and effective in the future, as more sophisticated scoring functions are developed and more detailed structural information on GPCRs is gathered.

  10. A Modular High-Throughput In Vivo Screening Platform Based on Chimeric Bacterial Receptors

    DEFF Research Database (Denmark)

    Lehning, Christina Eva; Heidelberger, Jan B; Reinhard, John

    2017-01-01

    currently existing small molecule libraries. Here, we have examined two previously created Tar-EnvZ chimeras and a novel NarX-EnvZ chimera. We demonstrate that it is possible to couple periplasmic stimulus-perceiving domains to an invariable cytoplasmic domain that governs transcription of a dynamic...... fluorescent reporter system. Furthermore, we show that aromatic tuning, or repositioning the aromatic residues at the end of the second transmembrane helix (TM2), modulates baseline signal output from the tested chimeras and even restores output from a nonfunctional NarX-EnvZ chimera. Finally, we observe...... an inverse correlation between baseline signal output and the degree of response to cognate stimuli. In summary, we propose that the platform described here, a fluorescent Escherichia coli reporter strain with plasmid-based expression of the aromatically tuned chimeric receptors, represents a synthetic...

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

    Directory of Open Access Journals (Sweden)

    Holger eStark

    2012-03-01

    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.

  12. Bounding symbolic powers via asymptotic multiplier ideals

    Directory of Open Access Journals (Sweden)

    Zach Teitler

    2009-04-01

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

  13. A molecular receptor targeted, hydroxyapatite nanocrystal based multi-modal contrast agent.

    Science.gov (United States)

    Ashokan, Anusha; Menon, Deepthy; Nair, Shantikumar; Koyakutty, Manzoor

    2010-03-01

    Multi-modal molecular imaging can significantly improve the potential of non-invasive medical diagnosis by combining basic anatomical descriptions with in-depth phenotypic characteristics of disease. Contrast agents with multifunctional properties that can sense and enhance the signature of specific molecular markers, together with high biocompatibility are essential for combinatorial molecular imaging approaches. Here, we report a multi-modal contrast agent based on hydroxyapatite nanocrystals (nHAp), which is engineered to show simultaneous contrast enhancement for three major molecular imaging techniques such as magnetic resonance imaging (MRI), X-ray imaging and near-infrared (NIR) fluorescence imaging. Monodispersed nHAp crystals of average size approximately 30 nm and hexagonal crystal structure were in situ doped with multiple rare-earth impurities by a surfactant-free, aqueous wet-chemical method at 100 degrees C. Doping of nHAp with Eu(3+) (3 at%) resulted bright near-infrared fluorescence (700 nm) due to efficient (5)D(0)-(7)F(4) electronic transition and co-doping with Gd(3+) resulted enhanced paramagnetic longitudinal relaxivity (r(1) approximately 12 mM(-1) s(-1)) suitable for T(1) weighted MR imaging together with approximately 80% X-ray attenuation suitable for X-ray contrast imaging. Capability of MF-nHAp to specifically target and enhance the signature of molecular receptors (folate) in cancer cells was realized by carbodiimide grafting of cell-membrane receptor ligand folic acid (FA) on MF-nHAp surface aminized with dendrigraft polymer, polyethyleneimine (PEI). The FA-PEI-MF-nHAp conjugates showed specific aggregation on FR(+ve) cells while leaving the negative control cells untouched. Nanotoxicity evaluation of this multifunctional nHAp carried out on primary human endothelial cells (HUVEC), normal mouse lung fibroblast cell line (L929), human nasopharyngeal carcinoma (KB) and human lung cancer cell line (A549) revealed no apparent toxicity even

  14. HIV-1-Specific Chimeric Antigen Receptors Based on Broadly Neutralizing Antibodies.

    Science.gov (United States)

    Ali, Ayub; Kitchen, Scott G; Chen, Irvin S Y; Ng, Hwee L; Zack, Jerome A; Yang, Otto O

    2016-08-01

    Although the use of chimeric antigen receptors (CARs) based on single-chain antibodies for gene immunotherapy of cancers is increasing due to promising recent results, the earliest CAR therapeutic trials were done for HIV-1 infection in the late 1990s. This approach utilized a CAR based on human CD4 as a binding domain and was abandoned for a lack of efficacy. The growing number of HIV-1 broadly neutralizing antibodies (BNAbs) offers the opportunity to generate novel CARs that may be more active and revisit this modality for HIV-1 immunotherapy. We used sequences from seven well-defined BNAbs varying in binding sites and generated single-chain-antibody-based CARs. These CARs included 10E8, 3BNC117, PG9, PGT126, PGT128, VRC01, and X5. Each novel CAR exhibited conformationally relevant expression on the surface of transduced cells, mediated specific proliferation and killing in response to HIV-1-infected cells, and conferred potent antiviral activity (reduction of viral replication in log10 units) to transduced CD8(+) T lymphocytes. The antiviral activity of these CARs was reproducible but varied according to the strain of virus. These findings indicated that BNAbs are excellent candidates for developing novel CARs to consider for the immunotherapeutic treatment of HIV-1. While chimeric antigen receptors (CARs) using single-chain antibodies as binding domains are growing in popularity for gene immunotherapy of cancers, the earliest human trials of CARs were done for HIV-1 infection. However, those trials failed, and the approach was abandoned for HIV-1. The only tested CAR against HIV-1 was based on the use of CD4 as the binding domain. The growing availability of HIV-1 broadly neutralizing antibodies (BNAbs) affords the opportunity to revisit gene immunotherapy for HIV-1 using novel CARs based on single-chain antibodies. Here we construct and test a panel of seven novel CARs based on diverse BNAb types and show that all these CARs are functional against HIV-1

  15. A Synthetic Thiourea-Based Tripodal Receptor that Impairs the Function of Human First Trimester Cytotrophoblast Cells

    Directory of Open Access Journals (Sweden)

    Darijana Horvat

    2014-07-01

    Full Text Available A synthetic tripodal-based thiourea receptor (PNTTU was used to explore the receptor/ligand binding affinity using CTB cells. The human extravillous CTB cells (Sw.71 used in this study were derived from first trimester chorionic villus tissue. The cell proliferation, migration and angiogenic factors were evaluated in PNTTU-treated CTB cells. The PNTTU inhibited the CTBs proliferation and migration. The soluble fms-like tyrosine kinase-1 (sFlt-1 secretion was increased while vascular endothelial growth factor (VEGF was decreased in the culture media of CTB cells treated with ≥1 nM PNTTU. The angiotensin II receptor type 2 (AT2 expression was significantly upregulated in ≥1 nM PNTTU-treated CTB cells in compared to basal; however, the angiotensin II receptor, type 1 (AT1 and vascular endothelial growth factor receptor 1 (VEGFR-1 expression was downregulated. The anti-proliferative and anti-angiogenic effect of this compound on CTB cells are similar to the effect of CTSs. The receptor/ligand affinity of PNTTU on CTBs provides us the clue to design a potent inhibitor to prevent the CTS-induced impairment of CTB cells.

  16. High content imaging-based assay to classify estrogen receptor-α ligands based on defined mechanistic outcomes.

    Science.gov (United States)

    Ashcroft, F J; Newberg, J Y; Jones, E D; Mikic, I; Mancini, M A

    2011-05-15

    Estrogen receptor-α (ER) is an important target both for therapeutic compounds and endocrine disrupting chemicals (EDCs); however, the mechanisms involved in chemical modulation of regulating ER transcriptional activity are inadequately understood. Here, we report the development of a high content analysis-based assay to describe ER activity that uniquely exploits a microscopically visible multi-copy integration of an ER-regulated promoter. Through automated single-cell analyses, we simultaneously quantified promoter occupancy, recruitment of transcriptional cofactors and large-scale chromatin changes in response to a panel of ER ligands and EDCs. Image-derived multi-parametric data was used to classify a panel of ligand responses at high resolution. We propose this system as a novel technology providing new mechanistic insights into EDC activities in a manner useful for both basic mechanistic studies and drug testing. Copyright © 2011 Elsevier B.V. All rights reserved.

  17. Space-bounded communication complexity

    DEFF Research Database (Denmark)

    Brody, Joshua Eric; Chen, Shiteng; Papakonstantinou, Periklis A.

    2013-01-01

    -obliviousness shows up. For this model we also introduce new techniques through which certain limitations of space-bounded computation are revealed. One of the main motivations of this work is in understanding the difference in the use of space when computing the following functions: Equality (EQ), Inner Product (IP......In the past thirty years, Communication Complexity has emerged as a foundational tool to proving lower bounds in many areas of computer science. Its power comes from its generality, but this generality comes at a price---no superlinear communication lower bound is possible, since a player may...... communicate his entire input. However, what if the players are limited in their ability to recall parts of their interaction? We introduce memory models for 2-party communication complexity. Our general model is as follows: two computationally unrestricted players, Alice and Bob, each have s(n) bits of memory...

  18. Neurosteroids, GABAA receptors and neurosteroid based drugs: are we witnessing the dawn of the new psychiatric drugs?

    Directory of Open Access Journals (Sweden)

    Ante Tvrdeić

    2016-03-01

    Full Text Available In broad biological terms, neurosteroids can be defined as a class of endogenous steroids synthesized in the brain or in peripheral steroidogenic tissues having potent and relatively selective activity on brain gamma-aminobutyric acid A (GABAA receptors. In this regard, the most important neurosteroids are allopregnanolone and allotetrahydrodeoxycorticosterone (allo THDOC. These α-reduced derivatives of pregnenolone and progesterone act as positive allosteric modulators of GABAA receptors. As such, they potentiate the inhibitory action of GABA on GABAA receptors and produce a wide spectrum of behavioral actions ranging from anxiolytic, anticonvulsive, sedative, hypnotic, amnestic (loss of memory, myorelaxant, and anesthetic effects. Sulfated derivatives of pregnenolone and dehydroepiandrosterone ,pregnenolone sulfate (PS and dehydroepianddrosterone sulfate (DHEAS, are also very important neurosteroids. In contrast to allopregnolone and alloTHDOC, PS and DHEAS induce excitatory effect on neurons because they facilitate the block of GABAA receptors. The spectrum of behavioral effects of PS and DHEAS consists of analeptic, anxiogenic, proconvulsive, and anamnestic (cognitive enhancing. The purpose of this review paper is to analyze recent research in the field of neurosteroids and neurosteroid-based drugs with emphasis on interaction of neurosteroids with brain GABAA receptors. This article also provides an overview of neurosteroids-based strategies for the development of innovative therapeutic approaches. GABAA receptor modulating steroids (GAMS, GABAA receptor modulating steroid antagonists (GAMSA, and translocator protein (TSPO activators are examples of innovative therapeutic approaches in treating clinically important neurological and psychiatric diseases. Consequently, the therapeutic potential of GAMS, GAMSA, and TSPO activators will be briefly evaluated.

  19. Bounds of memory strength for power-law series

    Science.gov (United States)

    Guo, Fangjian; Yang, Dan; Yang, Zimo; Zhao, Zhi-Dan; Zhou, Tao

    2017-05-01

    Many time series produced by complex systems are empirically found to follow power-law distributions with different exponents α . By permuting the independently drawn samples from a power-law distribution, we present nontrivial bounds on the memory strength (first-order autocorrelation) as a function of α , which are markedly different from the ordinary ±1 bounds for Gaussian or uniform distributions. When 1 3 , the upper bound remains +1 while the lower bound descends below 0. Theoretical bounds agree well with numerical simulations. Based on the posts on Twitter, ratings of MovieLens, calling records of the mobile operator Orange, and the browsing behavior of Taobao, we find that empirical power-law-distributed data produced by human activities obey such constraints. The present findings explain some observed constraints in bursty time series and scale-free networks and challenge the validity of measures such as autocorrelation and assortativity coefficient in heterogeneous systems.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    Recent progress in the understanding of seven-transmembrane receptor (7TMR) signalling has promoted the development of a new generation of pathway selective ligands. The angiotensin II type I receptor (AT1aR) is one of the most studied 7TMRs with respect to selective activation of the β-arrestin ......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...

  1. New models of pulmonary hypertension based on VEGF receptor blockade-induced endothelial cell apoptosis

    Science.gov (United States)

    Nicolls, Mark R.; Mizuno, Shiro; Taraseviciene-Stewart, Laima; Farkas, Laszlo; Drake, Jennnifer I.; Al Husseini, Aysar; Gomez-Arroyo, Jose G.; Voelkel, Norbert F.; Bogaard, Herman J.

    2012-01-01

    In spite of treatment, severe angioproliferative pulmonary arterial hypertension (PAH) remains a disease characterized by great morbidity and shortened survival. New treatment strategies for patients with PAH are needed, and after drug development, preclinical studies are best conducted in animal models which present with pulmonary angio-obliterative disease and right heart failure. A rat model of severe pulmonary hypertension and right heart failure, described a decade ago, continues to be investigated and provide insight into the nature of the lung vascular lesions and mechanisms of cardiac adaptation to an altered lung circulation. This rat model is based on the combination of VEGF receptor blockade with Su5416 and chronic hypoxia; use of this pulmonary hypertension induction strategy led to developing the concept of apoptosis-dependent compensatory vascular cell growth. Although, often employed in experimental designs, chronic hypoxia is not necessary for the development of angio-obliterative pulmonary hypertension. Left pneumonectomy combined with Su5416 also results in severe pulmonary hypertension in normoxic conditions. Similarly, the immune insufficiency component of severe PAH can be modeled in athymic rats (lacking T-lymphocytes). In these rats housed under normoxic conditions, treatment with the VEGFR receptor blocker results in angioproliferative pulmonary hypertension; cardiopulmonary disease in these animals can be prevented by immune reconstitution of regulatory T-cells (Tregs). Finally, chronic hypoxia can be replaced with another stimulator of HIF-1α: Ovalbumin (Ova). Immunization of rats with Ova increases lung tissue HIF-1α protein expression, and in Su5416-treated rats causes lethal pulmonary hypertension. Finally, we postulate that these models may also be useful for “reverse translation”; that is, the mechanisms of lung vascular cell death and growth and the modifying influences of immune and bone marrow cells that have been identified

  2. Bounded rational choice behaviour: applications in transport

    DEFF Research Database (Denmark)

    Jensen, Anders Fjendbo

    2016-01-01

    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...... and limited processing may occur due to time constraints, low involvement in the decision at hand, relying on habits or the task requiring too high a mental effort....... 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...

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

    DEFF Research Database (Denmark)

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

    2015-01-01

    G protein-coupled receptors (GPCRs) represent a biological target class of fundamental importance in drug therapy. The GPRC6A receptor is a newly deorphanized class C GPCR that we recently reported for the first allosteric antagonists based on the 2-arylindole privileged structure scaffold (e.g., 1......, and 34b as antagonists at the GPRC6A receptor in the low micromolar range and show that 7 and 34b display >9-fold selectivity for the GPRC6A receptor over related GPCRs, making 7 and 34b the most potent and selective antagonists for the GPRC6A receptor reported to date....

  4. Bounded Densities and Their Derivatives

    DEFF Research Database (Denmark)

    Kozine, Igor; Krymsky, V.

    2009-01-01

    This paper describes how one can compute interval-valued statistical measures given limited information about the underlying distribution. The particular focus is on a bounded derivative of a probability density function and its combination with other available statistical evidence for computing ...

  5. Physics with loosely bound nuclei

    Indian Academy of Sciences (India)

    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 ...

  6. Distance bounds on quantum dynamics

    Science.gov (United States)

    Lidar, Daniel A.; Zanardi, Paolo; Khodjasteh, Kaveh

    2008-07-01

    We derive rigorous upper bounds on the distance between quantum states in an open-system setting in terms of the operator norm between Hamiltonians describing their evolution. We illustrate our results with an example taken from protection against decoherence using dynamical decoupling.

  7. Moderate deviations for bounded subsequences

    Directory of Open Access Journals (Sweden)

    George Stoica

    2006-01-01

    Full Text Available We study Davis' series of moderate deviations probabilities for Lp-bounded sequences of random variables (p>2. A certain subseries therein is convergent for the same range of parameters as in the case of martingale difference or i.i.d. sequences.

  8. Functional characterisation of the human alpha1 glycine receptor in a fluorescence-based membrane potential assay

    DEFF Research Database (Denmark)

    Jensen, Anders A.; Kristiansen, Uffe

    2004-01-01

    In the present study, we have created a stable HEK293 cell line expressing the human homomeric alpha1 glycine receptor (GlyR) and characterised its functional pharmacology in a conventional patch-clamp assay and in the FLIPR Membrane Potential (FMP) assay, a fluorescence-based high throughput scr...

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

    NARCIS (Netherlands)

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

    2003-01-01

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

  10. Development of a Sigma-2 Receptor affinity filter through a Monte Carlo based QSAR analysis.

    Science.gov (United States)

    Rescifina, Antonio; Floresta, Giuseppe; Marrazzo, Agostino; Parenti, Carmela; Prezzavento, Orazio; Nastasi, Giovanni; Dichiara, Maria; Amata, Emanuele

    2017-08-30

    For the first time in sigma-2 (σ2) receptor field, a quantitative structure-activity relationship (QSAR) model has been built using pKi values of the whole set of known selective σ2 receptor ligands (548 compounds), taken from the Sigma-2 Receptor Selective Ligands Database (S2RSLDB) (http://www.researchdsf.unict.it/S2RSLDB/), through the Monte Carlo technique and employing the software CORAL. The model has been developed by using a large and structurally diverse set of compounds, allowing for a prediction of different populations of chemical compounds endpoint (σ2 receptor pKi). The statistical quality reached, suggested that model for pKi determination is robust and possesses a satisfactory predictive potential. The statistical quality is high for both visible and invisible sets. The screening of the FDA approved drugs, external to our dataset, suggested that sixteen compounds might be repositioned as σ2 receptor ligands (predicted pKi≥8). A literature check showed that six of these compounds have already been tested for affinity at σ2 receptor and, of these, two (Flunarizine and Terbinafine) have shown an experimental σ2 receptor pKi>7. This suggests that this QSAR model may be used as focusing screening filter in order to prospectively find or repurpose new drugs with high affinity for the σ2 receptor, and overall allowing for an enhanced hit rate respect to a random screening. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Elucidating determinants of aerosol composition through particle-type-based receptor modeling

    Directory of Open Access Journals (Sweden)

    M. L. McGuire

    2011-08-01

    Full Text Available An aerosol time-of-flight mass spectrometer (ATOFMS was deployed at a semi-rural site in southern Ontario to characterize the size and chemical composition of individual particles. Particle-type-based receptor modelling of these data was used to investigate the determinants of aerosol chemical composition in this region. Individual particles were classified into particle-types and positive matrix factorization (PMF was applied to their temporal trends to separate and cross-apportion particle-types to factors. The extent of chemical processing for each factor was assessed by evaluating the internal and external mixing state of the characteristic particle-types. The nine factors identified helped to elucidate the coupled interactions of these determinants. Nitrate-laden dust was found to be the dominant type of locally emitted particles measured by ATOFMS. Several factors associated with aerosol transported to the site from intermediate local-to-regional distances were identified: the Organic factor was associated with a combustion source to the north-west; the ECOC Day factor was characterized by nearby local-to-regional carbonaceous emissions transported from the south-west during the daytime; and the Fireworks factor consisted of pyrotechnic particles from the Detroit region following holiday fireworks displays. Regional aerosol from farther emissions sources was reflected through three factors: two Biomass Burning factors and a highly chemically processed Long Range Transport factor. The Biomass Burning factors were separated by PMF due to differences in chemical processing which were in part elucidated by the passage of two thunderstorm gust fronts with different air mass histories. The remaining two factors, ECOC Night and Nitrate Background, represented the night-time partitioning of nitrate to pre-existing particles of different origins. The distinct meteorological conditions observed during this month-long study in the summer of 2007

  12. An Exact and Grid-free Numerical Scheme for the Hybrid Two Phase Traffic Flow Model Based on the Lighthill-Whitham-Richards Model with Bounded Acceleration

    KAUST Repository

    Qiu, Shanwen

    2012-07-01

    In this article, we propose a new grid-free and exact solution method for computing solutions associated with an hybrid traffic flow model based on the Lighthill- Whitham-Richards (LWR) partial differential equation. In this hybrid flow model, the vehicles satisfy the LWR equation whenever possible, and have a fixed acceleration otherwise. We first present a grid-free solution method for the LWR equation based on the minimization of component functions. We then show that this solution method can be extended to compute the solutions to the hybrid model by proper modification of the component functions, for any concave fundamental diagram. We derive these functions analytically for the specific case of a triangular fundamental diagram. We also show that the proposed computational method can handle fixed or moving bottlenecks.

  13. How much do incentives affect car purchase? Agent-based microsimulation of consumer choice of new cars. Part 1. Model structure, simulation of bounded rationality, and model validation

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, Michel G.; Haan, Peter de [ETH Zurich, Institute for Environmental Decisions, Natural and Social Science Interface, Universitaetstr. 22, CHN J 73.2, 8092 Zurich (Switzerland)

    2009-03-15

    This article presents an agent-based microsimulation capable of forecasting the effects of policy levers that influence individual choices of new passenger cars. The fundamental decision-making units are households distinguished by sociodemographic characteristics and car ownership. A two-stage model of individual decision processes is employed. In the first stage, individual choice sets are constructed using simple, non-compensatory rules that are based on previously owned cars. Second, decision makers evaluate alternatives in their individual choice set using a multi-attributive weighting rule. The attribute weights are based on a multinomial logit model for cross-country policy analysis in European countries. Additionally, prospect theory and the notion of mental accounting are used to model the perception of monetary values. The microsimulation forecasts actual market observations with high accuracy, both on the level of aggregate market characteristics as well as on a highly resolved level of distributions of market shares. The presented approach is useful for the assessment of policies that influence individual purchase decisions of new passenger cars; it allows accounting for a highly resolved car fleet and differentiated consumer segments. As a result, the complexity of incentive schemes can be represented and detailed structural changes can be investigated. (author)

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

    KAUST Repository

    Swaidan, Raja

    2015-08-20

    Intrinsically ultramicroporous (<7 Å) polymers represent a new paradigm in materials development for membrane-based gas separation. In particular, they demonstrate that uniting intrachain “rigidity”, the traditional design metric of highly permeable polymers of intrinsic microporosity (PIMs), with gas-sieving ultramicroporosity yields high-performance gas separation membranes. Highly ultramicroporous PIMs have redefined the state-of-the-art in large-scale air (e.g., O2/N2) and hydrogen recovery (e.g., H2/N2, H2/CH4) applications with unprecedented molecular sieving gas transport properties. Accordingly, presented herein are new 2015 permeability/selectivity “upper bounds” for large-scale commercial membrane-based air and hydrogen applications that accommodate the substantial performance enhancements of recent PIMs over preceding polymers. A subtle balance between intrachain rigidity and interchain spacing has been achieved in the amorphous microstructures of PIMs, fine-tuned using unique bridged-bicyclic building blocks (i.e., triptycene, ethanoanthracene and Tröger’s base) in both ladder and semiladder (e.g., polyimide) structures.

  15. Finite energy bounds for $\\piN$ scattering

    CERN Document Server

    Grassberger, P; Schwela, D

    1974-01-01

    Upper bounds on energy averaged pi N cross sections are given. Using low energy data and data from pi N backward scattering and NN to pi pi annihilation, it is found that sigma /sub tot/bounds are based on assumptions similar to those underlying Froissart's bound and are equal to it asymptotically. However, at finite but large energies, they increase much slower than what might have been anticipated on purely numerological grounds. Related problems in pp and Kp scattering are also discussed. (25 refs) .

  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)

    2009-07-28

    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. Bounded-Angle Iterative Decoding of LDPC Codes

    Science.gov (United States)

    Dolinar, Samuel; Andrews, Kenneth; Pollara, Fabrizio; Divsalar, Dariush

    2009-01-01

    Bounded-angle iterative decoding is a modified version of conventional iterative decoding, conceived as a means of reducing undetected-error rates for short low-density parity-check (LDPC) codes. For a given code, bounded-angle iterative decoding can be implemented by means of a simple modification of the decoder algorithm, without redesigning the code. Bounded-angle iterative decoding is based on a representation of received words and code words as vectors in an n-dimensional Euclidean space (where n is an integer).

  18. Development of an enzyme-linked-receptor assay based on Syrian hamster β2-adrenergic receptor for detection of β-agonists.

    Science.gov (United States)

    Cheng, Guyue; Li, Feng; Peng, Dapeng; Huang, Lingli; Hao, Haihong; Liu, Zhenli; Wang, Yulian; Yuan, Zonghui

    2014-08-15

    β-Adrenergic agonists (β-agonists) are illegally used in animal husbandry, threatening the health of consumers. To realize multianalyte detection of β-agonists, a β2-adrenergic receptor (β2-AR) was cloned from Syrian hamster lung and heterogeneously expressed by Spodoptera frugiperda (Sf9) cells. The recombinant β2-AR was purified from intracellular soluble proteins of infected Sf9 cells, and was utilized to establish an enzyme-linked-receptor assay (ELRA) to detect a group of β-agonists simultaneously. This assay was based on direct competitive inhibition of binding of horseradish peroxidase-labeled ractopamine to the immobilized β2-AR proteins by β-agonists. The IC50 and limit of detection values for ractopamine were 30.38μgL(-1) and 5.20μgL(-1), respectively. Clenbuterol and salbutamol showed 87.7% and 58.5% cross-reactivities with ractopamine, respectively. This assay is simple, rapid, and environmentally friendly, showing a potential application in the screening of β-agonists in animal feeds. Copyright © 2014 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

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

    2016-08-23

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

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

    Directory of Open Access Journals (Sweden)

    Lewis Taylor

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

  1. 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.

  2. Exploring G protein-coupled receptor signaling networks using SILAC-based phosphoproteomics.

    Science.gov (United States)

    Williams, Grace R; Bethard, Jennifer R; Berkaw, Mary N; Nagel, Alexis K; Luttrell, Louis M; Ball, Lauren E

    2016-01-01

    The type 1 parathyroid hormone receptor (PTH1R) is a key regulator of calcium homeostasis and bone turnover. Here, we employed SILAC-based quantitative mass spectrometry and bioinformatic pathways analysis to examine global changes in protein phosphorylation following short-term stimulation of endogenously expressed PTH1R in osteoblastic cells in vitro. Following 5min exposure to the conventional agonist, PTH(1-34), we detected significant changes in the phosphorylation of 224 distinct proteins. Kinase substrate motif enrichment demonstrated that consensus motifs for PKA and CAMK2 were the most heavily upregulated within the phosphoproteome, while consensus motifs for mitogen-activated protein kinases were strongly downregulated. Signaling pathways analysis identified ERK1/2 and AKT as important nodal kinases in the downstream network and revealed strong regulation of small GTPases involved in cytoskeletal rearrangement, cell motility, and focal adhesion complex signaling. Our data illustrate the utility of quantitative mass spectrometry in measuring dynamic changes in protein phosphorylation following GPCR activation. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. Ethylene Detection Based on Organic Field-Effect Transistors With Porogen and Palladium Particle Receptor Enhancements.

    Science.gov (United States)

    Besar, Kalpana; Dailey, Jennifer; Katz, Howard E

    2017-01-18

    Ethylene sensing is a highly challenging problem for the horticulture industry because of the limited physiochemical reactivity of ethylene. Ethylene plays a very important role in the fruit life cycle and has a significant role in determining the shelf life of fruits. Limited ethylene monitoring capability results in huge losses to the horticulture industry as fruits may spoil before they reach the consumer, or they may not ripen properly. Herein we present a poly(3-hexylthiophene-2,5-diyl) (P3HT)-based organic field effect transistor as a sensing platform for ethylene with sensitivity of 25 ppm V/V. To achieve this response, we used N-(tert-Butoxy-carbonyloxy)-phthalimide and palladium particles as additives to the P3HT film. N-(tert-Butoxy-carbonyloxy)-phthalimide is used to increase the porosity of the P3HT, thereby increasing the overall sensor surface area, whereas the palladium (<1 μm diameter) particles are used as receptors for ethylene molecules in order to further enhance the sensitivity of the sensor platform. Both modifications give statistically significant sensitivity increases over pure P3HT. The sensor response is reversible and is also highly selective for ethylene compared to common solvent vapors.

  4. New code upper bounds from the Terwilliger algebra and semidefinite programming

    NARCIS (Netherlands)

    A. Schrijver (Alexander)

    2005-01-01

    textabstractWe give a new upper bound on the maximum size $A(n, d)$ of a binary code of word length $n$ and minimum distance at least $d$. It is based on block-diagonalising the Terwilliger algebra of the Hamming cube. The bound strengthens the Delsarte bound, and can be calculated with

  5. Lower bounds in differential privacy

    OpenAIRE

    De, Anindya

    2011-01-01

    This is a paper about private data analysis, in which a trusted curator holding a confidential database responds to real vector-valued queries. A common approach to ensuring privacy for the database elements is to add appropriately generated random noise to the answers, releasing only these {\\em noisy} responses. In this paper, we investigate various lower bounds on the noise required to maintain different kind of privacy guarantees.

  6. Geometry of Homogeneous Bounded Domains

    CERN Document Server

    Vesentini, E

    2011-01-01

    This title includes: S.G. Gindikin, I.I. Pjateckii-Sapiro, E.B. Vinberg: Homogeneous Kahler manifolds; S.G. Greenfield: Extendibility properties of real submanifolds of Cn; W. Kaup: Holomorphische Abbildungen in Hyperbolische Raume; A. Koranyi: Holomorphic and harmonic functions on bounded symmetric domains; J.L. Koszul: Formes harmoniques vectorielles sur les espaces localement symetriques; S. Murakami: Plongements holomorphes de domaines symetriques; and E.M. Stein: The analogues of Fatous' theorem and estimates for maximal functions.

  7. Identification of highly selective and potent orexin receptor 1 antagonists derived from a dual orexin receptor 1/2 antagonist based on the structural framework of pyrazoylethylbenzamide.

    Science.gov (United States)

    Futamura, Aya; Nozawa, Dai; Araki, Yuko; Tamura, Yunoshin; Tokura, Seiken; Kawamoto, Hiroshi; Tokumaru, Yuichi; Kakihara, Sora; Aoki, Takeshi; Ohtake, Norikazu

    2017-10-15

    The design, synthesis, and structure activity relationships of the novel class of pyrazolylethylbenzamide orexin receptor 1-selective antagonists are described. Further derivatization of the prototype dual orexin receptor 1/2 antagonist lead (1) by installing a (S)-methyl group into the ethyl linker moiety between the pyrazole ring and benzamide resulted in an increase of the antagonist potency against orexin receptor 1/2 receptors. Optimization of the benzamide and pyrazole parts of compounds 2 and 9b led to the identification of N-ethyl-5-fluoro-N-{(2S)-1-[5-(4-fluorophenyl)-2H-tetrazol-2-yl]propan-2-yl}-2-(pyrimidin-2-yl)benzamide (24), which exhibited excellent antagonistic activity against orexin receptor 1 with an IC50 of 2.01nM and a 265-fold selectivity for orexin receptor 1 over orexin receptor 2. Copyright © 2017 Elsevier Ltd. All rights reserved.

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

    NARCIS (Netherlands)

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

    2007-01-01

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

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

    LENUS (Irish Health Repository)

    Dellacasagrande, Jerome

    2012-02-01

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

  10. Synthesis of bifunctional receptor for fluoride and cadmium based on calix[4]arene with thiourea moieties

    Science.gov (United States)

    Quiroga-Campano, C.; Gómez-Machuca, H.; Moris, S.; Jara, P.; De la Fuente, J. R.; Pessoa-Mahana, H.; Jullian, C.; Saitz, C.

    2017-08-01

    A new calix[4]arene thiourea derivative bearing a benzothiazolyl moiety (L) was synthetized and characterized by single crystal X-ray, NMR and ESI-TOF. The binding ability of the bifunctional receptor towards several ions was investigated in acetonitrile by means of UV-Visible and NMR spectroscopy. The UV-Vis studies of receptor L demonstrated a stoichiometry of 1:1 for all ions studied. Also, recognize selectively F- and Cd2+ with a detection limit of 97 and 37 μM, respectively. Also, 1H NMR titration of receptor L indicated that both thiourea bridge and phenolic hydroxyl functional groups played a critical role in the binding of F- and Cd2+ ions. 1H NMR spectrum showed that receptor L has a flattened-cone conformation in solution that changes to a cone conformation in the presence of fluoride while cadmium maintained the initial conformation.

  11. 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.

  12. Probing charge transfer in a novel class of luminescent perovskite-based heterostructures composed of quantum dots bound to RE-activated CaTiO3 phosphors

    Science.gov (United States)

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

    2016-01-01

    We report on the synthesis and structural characterization of novel semiconducting heterostructures composed of cadmium selenide (CdSe) quantum dots (QDs) attached onto the surfaces of novel high-surface area, porous rare-earth-ion doped alkaline earth titanate micron-scale spherical motifs, i.e. both Eu-doped and Pr-doped CaTiO3, composed of constituent, component nanoparticles. These unique metal oxide perovskite building blocks were created by a multi-pronged synthetic strategy involving molten salt and hydrothermal protocols. Subsequently, optical characterization of these heterostructures indicated a clear behavioral dependence of charge transfer in these systems upon a number of parameters such as the nature of the dopant, the reaction temperature, and particle size. Specifically, 2.7 nm diameter ligand-functionalized CdSe QDs were anchored onto sub-micron sized CaTiO3-based spherical assemblies, prepared by molten salt protocols. We found that both the Pr- and Eu-doped CaTiO3 displayed pronounced PL emissions, with maximum intensities observed using optimized lanthanide concentrations of 0.2 mol% and 6 mol%, respectively. Analogous experiments were performed on Eu-doped BaTiO3 and SrTiO3 motifs, but CaTiO3 still performed as the most effective host material amongst the three perovskite systems tested. Moreover, the ligand-capped CdSe QD-doped CaTiO3 heterostructures exhibited effective charge transfer between the two individual constituent nanoscale components, an assertion corroborated by the corresponding quenching of their measured PL signals.We report on the synthesis and structural characterization of novel semiconducting heterostructures composed of cadmium selenide (CdSe) quantum dots (QDs) attached onto the surfaces of novel high-surface area, porous rare-earth-ion doped alkaline earth titanate micron-scale spherical motifs, i.e. both Eu-doped and Pr-doped CaTiO3, composed of constituent, component nanoparticles. These unique metal oxide perovskite

  13. Polar silica-based stationary phases. Part III- Neutral silica stationary phase with surface bound maltose for affinity chromatography at reduced non-specific interactions.

    Science.gov (United States)

    Rathnasekara, Renuka; El Rassi, Ziad

    2017-07-28

    This research article reports the coating of large pore silica microparticles with a maltose layer to which bioaffinity ligands were attached via reductive amination reaction between the aldehyde activated maltose and the amino groups of the bioaffinity ligands. This was achieved first by the periodate oxidation of the maltose-silica (MALT-silica) yielding pairs of aldehyde groups at each monosaccharide ring. These di-aldehyde functionalities were then reacted with the primary amino groups of protein bio-affinity ligands and eventually formed Schiff bases (i.e., aldimines) which were reduced using the mild reducing agent sodium cyanoborohydride to form stable amine linkages between the immobilized protein ligands and the maltose layer. Anti-human serum albumin antibody (aHSA), anti-human serum transferrin antibody (aTf) and concanavalin A (Con A) were the bio-affinity ligands immobilized onto the MALT-silica and were evaluated in high performance affinity chromatography (HPAC), namely immunoaffinity chromatography (IAC) and lectin affinity chromatography (LAC). Our initial studies reported here revealed zero or reduced nonspecific interactions with the two immunoaffinity sorbents (i.e., aHSA-MALT-silica and aTf-MALT-silica) and the lectin affinity sorbent (i.e., Con A-MALT-silica). The absence of nonspecific interactions is attributed to the hydrophilicity of the maltose layer and its shielding effect of the residual silanols (i.e., unreacted silanols) on the silica surface. Conversely, the IAC and LAC sorbents exhibited specific interactions with the target biomolecules, namely human serum albumin (HSA) and transferrin (Tf) in the case of aHSA-MALT-silica and aTf-MALT-silica columns, respectively, and glycoproteins known for their affinity to Con A in the case of Con A-MALT-silica column. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. [Mechanism on atrial natriuretic peptide receptor in anti-anxiety with acupuncture based on its tranquilizing effect].

    Science.gov (United States)

    He, Wei; Zhou, Qizhi; Yu, Shuguang; Cai, Dingjun; Wang, Qiang; Zhang, Xiaodan; Huang, Wen-qin

    2015-01-01

    Anxiety disorder is one of the most common mental disorders and seriously impairs the physical and mental health of patients. Due to the efficacy of acupuncture for tranquilization, acupuncture displays its unique advantage on the treatment of anxiety disorder, but the relevant biological mechanism has not been elaborated. The modern medicine study has proved that the heart and brain have their own independent natriuretic peptide (NP) system. The dysfunction of ANP and its receptor are closely related to the occurrence of anxiety disorder. The ANP acts on anti-anxiety. Hence, focusing on the three aspects, named the anti-anxiety effect of acupuncture based on its tranquilizing effect, the anti-anxiety effect of ANP and the positive regulation of acupuncture on NP, the mechanism on ANP and its receptor was explored in anti-anxiety with acupuncture based on tranquilizing effect, and the idea was put forward on that the anti-anxiety effect of acupuncture was possibly based on its action of tranquilization through regulating the ANP and its receptor. As a result, it is expected to provide the theoretic support for the mechanism study on anti-anxiety with acupuncture based on its tranquilizing effect.

  15. Lower bounds for randomized Exclusive Write PRAMs

    Energy Technology Data Exchange (ETDEWEB)

    MacKenzie, P.D.

    1995-05-02

    In this paper we study the question: How useful is randomization in speeding up Exclusive Write PRAM computations? Our results give further evidence that randomization is of limited use in these types of computations. First we examine a compaction problem on both the CREW and EREW PRAM models, and we present randomized lower bounds which match the best deterministic lower bounds known. (For the CREW PRAM model, the lower bound is asymptotically optimal.) These are the first non-trivial randomized lower bounds known for the compaction problem on these models. We show that our lower bounds also apply to the problem of approximate compaction. Next we examine the problem of computing boolean functions on the CREW PRAM model, and we present a randomized lower bound, which improves on the previous best randomized lower bound for many boolean functions, including the OR function. (The previous lower bounds for these functions were asymptotically optimal, but we improve the constant multiplicative factor.) We also give an alternate proof for the randomized lower bound on PARITY, which was already optimal to within a constant additive factor. Lastly, we give a randomized lower bound for integer merging on an EREW PRAM which matches the best deterministic lower bound known. In all our proofs, we use the Random Adversary method, which has previously only been used for proving lower bounds on models with Concurrent Write capabilities. Thus this paper also serves to illustrate the power and generality of this method for proving parallel randomized lower bounds.

  16. Ditopic receptors based on lower- and upper-rim substituted hexahomotrioxacalix[3]arenes: cation-controlled hydrogen bonding of anion.

    Science.gov (United States)

    Ni, Xin-Long; Tahara, Jun; Rahman, Shofiur; Zeng, Xi; Hughes, David L; Redshaw, Carl; Yamato, Takehiko

    2012-03-05

    Heteroditopic hexahomotrioxacalix[3]arene receptors that are capable of binding an anion and a cation simultaneously in a cooperative fashion were synthesized. The structure of one of the triamide derivatives was confirmed by single-crystal X-ray diffraction. The binding of alkali metals at the lower rim, and the binding of anions (chloride, bromide) at the upper rim, has been investigated by using (1)H NMR titration experiments. Alkali metal binding at the lower rim controls the calix cavity. Li(+)-ion binding to the lower rim can improve the binding ability of anions at the upper rim amide moiety by a factor of 15, thus suggesting a strong positive allosteric effect for anion recognition. However, when a Na(+) cation is bound to the ionophoric site on the lower rim, the calix cavity is changed from a "flattened cone" to a more-upright form, which is favored for intramolecular hydrogen bonding between the neighboring NH and C=O groups; this change can block the inclusion of anions onto the amide moiety at the upper rim, which strongly suggests a negative allosteric effect of Na(+)-ion binding, which controls the cooperative recognition system. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Solid-phase receptor-based assay for the detection of cyclic imines by chemiluminescence, fluorescence, or colorimetry.

    Science.gov (United States)

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

    2011-08-01

    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.

  18. A μ-biomimetic uncooled infrared sensor based on the infrared receptors of Melanophila acuminata

    Energy Technology Data Exchange (ETDEWEB)

    Siebke, Georg

    2015-11-15

    The pyrophilous beetle Melanophila acuminata possesses an organ sensitive to IR radiation. It employs a photomechanic detection principle: A liquid filled pressure chamber is heated by absorbing the radiation. The liquid expands and leads to the deflection of a mechanosensitive dendrite. In addition, a sophisticated compensation mechanism prevents the build-up of large pressures. In this work, a biomimetic IR sensor based on the IR receptors of Melanophila acuminata is developed by means of microsystems technology. The sensor consists of two liquid-filled chambers that are connected by a micro-fluidic system. Absorption of IR radiation by one of the chambers leads to the heating and expansion of a liquid. The increasing pressure deflects a membrane which is part of a plate capacitor with a diameter of 500 μm and an electrode distance of 500 nm. The micro-fluidic system and the second chamber represent a fluidic low-pass filter, preventing slow, but large pressure changes. A theoretical model is developed which is able to predict the modulation frequency dependent response. It allows to calculate the filter properties of the compensation mechanism which is verified by an experimental test. A simplified sensor without the compensation mechanism is manufactured to analyse the influence of several parameters on the sensor's sensitivity. Finally, a solution for the fabrication of the μ-capacitor is presented. The large aspect ratio between electrode diameter and distance prevents to use a standard sacrificial layer process. The obtained capacitors pave the way to fabricate the complete full-featured sensor.

  19. Evaluation of estrogen receptor alpha activation by glyphosate-based herbicide constituents.

    Science.gov (United States)

    Mesnage, Robin; Phedonos, Alexia; Biserni, Martina; Arno, Matthew; Balu, Sucharitha; Corton, J Christopher; Ugarte, Ricardo; Antoniou, Michael N

    2017-10-01

    The safety, including the endocrine disruptive capability, of glyphosate-based herbicides (GBHs) is a matter of intense debate. We evaluated the estrogenic potential of glyphosate, commercial GBHs and polyethoxylated tallowamine adjuvants present as co-formulants in GBHs. Glyphosate (≥10,000 μg/L or 59 μM) promoted proliferation of estrogen-dependent MCF-7 human breast cancer cells. Glyphosate also increased the expression of an estrogen response element-luciferase reporter gene (ERE-luc) in T47D-KBluc cells, which was blocked by the estrogen antagonist ICI 182,780. Commercial GBH formulations or their adjuvants alone did not exhibit estrogenic effects in either assay. Transcriptomics analysis of MCF-7 cells treated with glyphosate revealed changes in gene expression reflective of hormone-induced cell proliferation but did not overlap with an ERα gene expression biomarker. Calculation of glyphosate binding energy to ERα predicts a weak and unstable interaction (-4.10 kcal mol(-1)) compared to estradiol (-25.79 kcal mol(-1)), which suggests that activation of this receptor by glyphosate is via a ligand-independent mechanism. Induction of ERE-luc expression by the PKA signalling activator IBMX shows that ERE-luc is responsive to ligand-independent activation, suggesting a possible mechanism of glyphosate-mediated activation. Our study reveals that glyphosate, but not other components present in GBHs, can activate ERα in vitro, albeit at relatively high concentrations. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  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. Bis-corannulene Receptors for Fullerenes Based on Klärner's Tethers: Reaching the Affinity Limits.

    Science.gov (United States)

    Abeyratne Kuragama, Peumie L; Fronczek, Frank R; Sygula, Andrzej

    2015-11-06

    Bis-corannulene receptors 4 and 5 with Klärner's tethers prepared by the Diels-Alder cycloaddition form inclusion complexes with C60 and C70, as evidenced by (1)H NMR titration. While 4 exhibits affinity toward fullerenes comparable to the previously reported corannulene-based receptors, 5 exceeds the performance of the former systems by ca. 2 orders of magnitude and, in addition, shows an enhanced preference for C70 over C60. The X-ray crystal structure of C60@5 and DFT calculations indicate that the tether in 5 not only preorganizes the pincers into a proper topology of the host but also contributes to the dispersion-based binding with the fullerene guests.

  2. Structural biology of GABAB receptor.

    Science.gov (United States)

    Frangaj, Aurel; Fan, Qing R

    2017-10-12

    Metabotropic GABAB receptor is a G protein-coupled receptor (GPCR) that mediates slow and prolonged inhibitory neurotransmission in the brain. It functions as a constitutive heterodimer composed of the GABAB1 and GABAB2 subunits. Each subunit contains three domains; the extracellular Venus flytrap module, seven-helix transmembrane region and cytoplasmic tail. In recent years, the three-dimensional structures of GABAB receptor extracellular and intracellular domains have been elucidated. These structures reveal the molecular basis of ligand recognition, receptor heterodimerization and receptor activation. Here we provide a brief review of the GABAB receptor structures, with an emphasis on describing the different ligand-bound states of the receptor. We will also compare these with the known structures of related GPCRs to shed light on the molecular mechanisms of activation and regulation in the GABAB system, as well as GPCR dimers in general. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Engineering Synthetic Signaling Pathways with Programmable dCas9-Based Chimeric Receptors

    Directory of Open Access Journals (Sweden)

    Toni A. Baeumler

    2017-09-01

    Full Text Available Synthetic receptors provide a powerful experimental tool for generation of designer cells capable of monitoring the environment, sensing specific input signals, and executing diverse custom response programs. To advance the promise of cellular engineering, we have developed a class of chimeric receptors that integrate a highly programmable and portable nuclease-deficient CRISPR/Cas9 (dCas9 signal transduction module. We demonstrate that the core dCas9 synthetic receptor (dCas9-synR architecture can be readily adapted to various classes of native ectodomain scaffolds, linking their natural inputs with orthogonal output functions. Importantly, these receptors achieved stringent OFF/ON state transition characteristics, showed agonist-mediated dose-dependent activation, and could be programmed to couple specific disease markers with diverse, therapeutically relevant multi-gene expression circuits. The modular dCas9-synR platform developed here provides a generalizable blueprint for designing next generations of synthetic receptors, which will enable the implementation of highly complex combinatorial functions in cellular engineering.

  4. Nicotinic acetylcholine receptor β2 subunit gene implicated in a systems-based candidate gene study of smoking cessation

    OpenAIRE

    Conti, DV; Lee, W.; D. Li; Liu, J.; Van Den Berg, D.; Thomas, PD; Bergen, AW; Swan, GE; Tyndale, RF; Benowitz, NL; Lerman, C

    2008-01-01

    Although the efficacy of pharmacotherapy for tobacco dependence has been previously demonstrated, there is substantial variability among individuals in treatment response. We performed a systems-based candidate gene study of 1295 single nucleotide polymorphisms (SNPs) in 58 genes within the neuronal nicotinic receptor and dopamine systems to investigate their role in smoking cessation in a bupropion placebo-controlled randomized clinical trial. Putative functional variants were supplemented w...

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

    DEFF Research Database (Denmark)

    Pinto, Andrea; Conti, Paola; Grazioso, Giovanni

    2011-01-01

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

  6. Towards Automatic Resource Bound Analysis for OCaml

    OpenAIRE

    Hoffmann, Jan; Das, Ankush; Weng, Shu-Chun

    2016-01-01

    This article presents a resource analysis system for OCaml programs. This system automatically derives worst-case resource bounds for higher-order polymorphic programs with user-defined inductive types. The technique is parametric in the resource and can derive bounds for time, memory allocations and energy usage. The derived bounds are multivariate resource polynomials which are functions of different size parameters that depend on the standard OCaml types. Bound inference is fully automatic...

  7. Distance hijacking attacks on distance bounding protocols

    OpenAIRE

    Cremers, Cas; Rasmussen, Kasper Bonne; Čapkun, Srdjan

    2011-01-01

    Distance bounding protocols are typically analyzed with respect to three types of attacks: Distance Fraud, Mafia Fraud, and Terrorist Fraud. We define and analyze a fourth main type of attack on distance bounding protocols, called Distance Hijacking. We show that many proposed distance bounding protocols are vulnerable to this type of attack, and we propose solutions to make these protocols resilient to Distance Hijacking. We further show that verifying distance bounding protocols using exist...

  8. Purity- and Gaussianity-bounded uncertainty relations

    Science.gov (United States)

    Mandilara, A.; Karpov, E.; Cerf, N. J.

    2014-01-01

    Bounded uncertainty relations provide the minimum value of the uncertainty assuming some additional information on the state. We derive analytically an uncertainty relation bounded by a pair of constraints, those of purity and Gaussianity. In a limiting case this uncertainty relation reproduces the purity-bounded derived by Man’ko and Dodonov and the Gaussianity-bounded one (Mandilara and Cerf 2012 Phys. Rev. A 86 030102R).

  9. A Research on Sour Sensation Mechanism of Fungiform Taste Receptor Cells Based on Microelectrode Array

    Science.gov (United States)

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

    2009-05-01

    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.

  10. Cardio-oncology Related to Heart Failure: Epidermal Growth Factor Receptor Target-Based Therapy.

    Science.gov (United States)

    Kenigsberg, Benjamin; Jain, Varun; Barac, Ana

    2017-04-01

    Cancer therapy targeting the epidermal growth factor receptor (EGFR)/erythroblastic leukemia viral oncogene B (ErbB)/human EGFR receptor (HER) family of tyrosine kinases has been successfully used in treatment of several malignancies. The ErbB pathways play a role in the maintenance of cardiac homeostasis. This article summarizes current knowledge about EGFR/ErbB/HER receptor-targeted cancer therapeutics focusing on their cardiotoxicity profiles, molecular mechanisms, and implications in clinical cardio-oncology. The article discusses challenges in predicting, monitoring, and treating cardiac dysfunction and heart failure associated with ErbB-targeted cancer therapeutics and highlights opportunities for researchers and clinical investigators. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. Semidefinite code bounds based on quadruple distances

    NARCIS (Netherlands)

    Gijswijt, D.C.; Mittelmann, H.D.; Schrijver, A.

    2012-01-01

    Let A(n,d) be the maximum number of 0, 1 words of length n , any two having Hamming distance at least d. It is proved that A(20,8)=256, which implies that the quadruply shortened Golay code is optimal. Moreover, it is shown that A(18,6) ≤ 673, A(19,6) ≤ 1237, A(20,6) ≤ 2279, A(23,6) ≤ 13674, A(19,8)

  12. Semidefinite code bounds based on quadruple distances

    NARCIS (Netherlands)

    D. Gijswijt (Dion); H.D. Mittelmann; A. Schrijver (Alexander)

    2010-01-01

    htmlabstractLet A(n, d) be the maximum number of 0, 1 words of length n, any two having Hamming distance at least d. We prove A(20, 8) = 256, which implies that the quadruply shortened Golay code is optimal. Moreover, we show A(18, 6) ≤ 673, A(19, 6) ≤ 1237, A(20, 6) ≤ 2279, A(23, 6) ≤ 13674, A(19,

  13. Semidefinite code bounds based on quadruple distances

    NARCIS (Netherlands)

    D. Gijswijt (Dion); H.D. Mittelmann; A. Schrijver (Alexander)

    2012-01-01

    htmlabstractLet A(n, d) be the maximum number of 0, 1 words of length n, any two having Hamming distance at least d. We prove A(20, 8) = 256, which implies that the quadruply shortened Golay code is optimal. Moreover, we show A(18, 6) ≤ 673, A(19, 6) ≤ 1237, A(20, 6) ≤ 2279, A(23, 6) ≤ 13674, A(19,

  14. Weekly nanoparticle albumin bound-paclitaxel in combination with cisplatin versus weekly solvent-based paclitaxel plus cisplatin as first-line therapy in Chinese patients with advanced esophageal squamous cell carcinoma

    Directory of Open Access Journals (Sweden)

    Wang HY

    2016-09-01

    Full Text Available Hai-ying Wang, Zhi-hua Yao, Hong Tang, Yan Zhao, Xiao-san Zhang, Shu-na Yao, Shu-jun Yang, Yan-yan Liu Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, Henan, People’s Republic of China Objective: More effective regimens for advanced esophageal squamous cell carcinoma (ESCC are urgently needed. Therefore, a retrospective study concerning the efficacy and safety of nanoparticle albumin-bound paclitaxel plus cisplatin (nab-TP versus solvent-based paclitaxel plus cisplatin (sb-TP as a first-line therapy was conducted in Chinese patients with advanced ESCC.Methods: From June 2009 to June 2015, 32 patients were treated with nab-paclitaxel (125 mg/m2 on the first and eighth days (30 minutes infusion and cisplatin (75 mg/m2 on the second day every 21 days (nab-TP arm. Also, 43 patients were treated with solvent-based paclitaxel (80 mg/m2 intravenously on the first and eighth days and the same dose of cisplatin (sb-TP arm. The two groups were compared in terms of objective response rate (ORR, disease control rate, progression-free survival (PFS, overall survival (OS, and safety profile. OS and PFS were estimated using Kaplan–Meier methods to determine associations between chemotherapy regimens and survival outcomes.Results: Nab-TP demonstrated a higher ORR (50% vs 30%; P=0.082 and disease control rate (81% vs 65%; P=0.124 than sb-TP. Median OS was similar for nab-TP and sb-TP (12.5 vs 10.7 months; P=0.269. However, nab-TP resulted in a longer median PFS (6.1 months [95% confidence interval: 5.3–6.9] than sb-TP (5.0 months [95% confidence interval: 4.4–5.6] (P=0.029. The most common adverse events included anemia, leukopenia, neutropenia, febrile neutropenia, and thrombocytopenia in both the groups and no statistically significant differences were observed between the groups. With statistically significant differences, significantly less grade ≥3 peripheral neuropathy

  15. Bounded rationality and heterogeneous expectations in macroeconomics

    NARCIS (Netherlands)

    Massaro, D.

    2012-01-01

    This thesis studies the effect of individual bounded rationality on aggregate macroeconomic dynamics. Boundedly rational agents are specified as using simple heuristics in their decision making. An important aspect of the type of bounded rationality described in this thesis is that the population of

  16. Labeling schemes for bounded degree graphs

    DEFF Research Database (Denmark)

    Adjiashvili, David; Rotbart, Noy Galil

    2014-01-01

    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...

  17. Upper bound on quantum stabilizer codes

    Science.gov (United States)

    Li, Zhuo; Xing, Li-Juan

    2009-03-01

    By studying sets of operators having constant weight, we present an analytical upper bound on the pure quantum stabilizer codes whose underlying quantum system can be of arbitrary dimension, which outperforms the well-known quantum Hamming bound, the optimal analytical upper bound so far for small code length.

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

    Directory of Open Access Journals (Sweden)

    Seung-Yeol eNah

    2015-10-01

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

  19. An MHC-restricted antibody-based chimeric antigen receptor requires TCR-like affinity to maintain antigen specificity

    Directory of Open Access Journals (Sweden)

    Marcela V Maus

    2016-01-01

    Full Text Available Chimeric antigen receptors (CARs are synthetic receptors that usually redirect T cells to surface antigens independent of human leukocyte antigen (HLA. Here, we investigated a T cell receptor-like CAR based on an antibody that recognizes HLA-A*0201 presenting a peptide epitope derived from the cancer-testis antigen NY-ESO-1. We hypothesized that this CAR would efficiently redirect transduced T cells in an HLA-restricted, antigen-specific manner. However, we found that despite the specificity of the soluble Fab, the same antibody in the form of a CAR caused moderate lysis of HLA-A2 expressing targets independent of antigen owing to T cell avidity. We hypothesized that lowering the affinity of the CAR for HLA-A2 would improve its specificity. We undertook a rational approach of mutating residues that, in the crystal structure, were predicted to stabilize binding to HLA-A2. We found that one mutation (DN lowered the affinity of the Fab to T cell receptor-range and restored the epitope specificity of the CAR. DN CAR T cells lysed native tumor targets in vitro, and, in a xenogeneic mouse model implanted with two human melanoma lines (A2+/NYESO+ and A2+/NYESO−, DN CAR T cells specifically migrated to, and delayed progression of, only the HLA-A2+/NY-ESO-1+ melanoma. Thus, although maintaining MHC-restricted antigen specificity required T cell receptor-like affinity that decreased potency, there is exciting potential for CARs to expand their repertoire to include a broad range of intracellular antigens.

  20. A tyrosine kinase inhibitor-based high-affinity PET radiopharmaceutical targets vascular endothelial growth factor receptor.

    Science.gov (United States)

    Li, Feng; Jiang, Sheng; Zu, Youli; Lee, Daniel Y; Li, Zheng

    2014-09-01

    Tyrosine kinase receptors including vascular endothelial growth factor receptor (VEGFR) have gained significant attention as pharmacologic targets. However, clinical evaluation of small-molecule drugs or biologics that target these pathways has so far yielded mixed results in a variety of solid tumors. The reasons for response variability remain unknown, including the temporal and spatial patterns of receptor tyrosine kinase expression. Methods to detect and quantify the presence of such cellular receptors would greatly facilitate drug development and therapy response assessment. We aimed to generate specific imaging agents as potential companion diagnostics that could also be used for targeted radionuclide therapy. Here, we report on the synthesis and initial preclinical performance of (64)Cu-labeled probes that were based on the kinase inhibitor already in clinical use, vandetanib (ZD6474), as a VEGFR-selective theranostic radiopharmaceutical. A monomeric (ZD-G1) and a dimeric (ZD-G2) derivative of ZD6474 were synthesized and conjugated with DOTA for chelation with (64)Cu to produce the probes (64)Cu-DOTA-ZD-G1 and (64)Cu-DOTA-ZD-G2. The binding affinity and specificity to VEGFR were measured using U-87 MG cells known to overexpress VEGFR. Small-animal PET and biodistribution studies were performed with (64)Cu-labeled probes (3-4 MBq) intravenously administered in U-87 MG tumor-bearing mice with or without coinjection of unlabeled ZD-G2 for up to 24 h after injection. Receptor-binding assays yielded a mean equilibrium dissociation constant of 44.7 and 0.45 nM for monomeric and dimeric forms, respectively, indicating a synergistic effect in VEGFR affinity by multivalency. Small-animal PET/CT imaging showed rapid tumor accumulation of (64)Cu-DOTA-ZD-G2, with excellent tumor-to-normal tissue contrast by 24 h. Coinjection of the (64)Cu-DOTA-ZD-G2 with 50 nmol (60 μg) of nonradioactive ZD-G2 effectively blocked tumor uptake. A (64)Cu-labeled probe derived from an

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

    Directory of Open Access Journals (Sweden)

    De Graaf David

    2007-07-01

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

  2. Coupling the Torpedo microplate-receptor binding assay with mass spectrometry to detect cyclic imine neurotoxins.

    Science.gov (United States)

    Aráoz, Rómulo; Ramos, Suzanne; Pelissier, Franck; Guérineau, Vincent; Benoit, Evelyne; Vilariño, Natalia; Botana, Luis M; Zakarian, Armen; Molgó, Jordi

    2012-12-04

    Cyclic imine neurotoxins constitute an emergent family of neurotoxins of dinoflagellate origin that are potent antagonists of nicotinic acetylcholine receptors. We developed a target-directed functional method based on the mechanism of action of competitive agonists/antagonists of nicotinic acetylcholine receptors for the detection of marine cyclic imine neurotoxins. The key step for method development was the immobilization of Torpedo electrocyte membranes rich in nicotinic acetylcholine receptors on the surface of microplate wells and the use of biotinylated-α-bungarotoxin as tracer. Cyclic imine neurotoxins competitively inhibit biotinylated-α-bungarotoxin binding to Torpedo-nicotinic acetylcholine receptors in a concentration-dependent manner. The microplate-receptor binding assay allowed rapid detection of nanomolar concentrations of cyclic imine neurotoxins directly in shellfish samples. Although highly sensitive and specific for the detection of neurotoxins targeting nicotinic acetylcholine receptors as a class, the receptor binding assay cannot identify a given analyte. To address the low selectivity of the microplate-receptor binding assay, the cyclic imine neurotoxins tightly bound to the coated Torpedo nicotinic receptor were eluted with methanol, and the chemical nature of the eluted ligands was identified by mass spectrometry. The immobilization of Torpedo electrocyte membranes on the surface of microplate wells proved to be a high-throughput format for the survey of neurotoxins targeting nicotinic acetylcholine receptors directly in shellfish matrixes with high sensitivity and reproducibility.

  3. Exact solutions to a spatially extended model of kinase-receptor interaction

    Science.gov (United States)

    Szopa, Piotr; Lipniacki, Tomasz; Kazmierczak, Bogdan

    2011-10-01

    B and Mast cells are activated by the aggregation of the immune receptors. Motivated by this phenomena we consider a simple spatially extended model of mutual interaction of kinases and membrane receptors. It is assumed that kinase activates membrane receptors and in turn the kinase molecules bound to the active receptors are activated by transphosphorylation. Such a type of interaction implies positive feedback and may lead to bistability. In this study we apply the Steklov eigenproblem theory to analyze the linearized model and find exact solutions in the case of non-uniformly distributed membrane receptors. This approach allows us to determine the critical value of receptor dephosphorylation rate at which cell activation (by arbitrary small perturbation of the inactive state) is possible. We found that cell sensitivity grows with decreasing kinase diffusion and increasing anisotropy of the receptor distribution. Moreover, these two effects are cooperating. We showed that the cell activity can be abruptly triggered by the formation of the receptor aggregate. Since the considered activation mechanism is not based on receptor crosslinking by polyvalent antigens, the proposed model can also explain B cell activation due to receptor aggregation following binding of monovalent antigens presented on the antigen presenting cell.

  4. Structure-based drug design approach to target toll-like receptor ...

    African Journals Online (AJOL)

    Toll-like receptor (TLR) signaling pathways are the first line of defence against many microbial organisms. The question of how TLRs recognize endogenous ligands remains controversial. Several studies have shown that TLRs are implicated in the pathogenesis of autoimmune diseases such as systemic lupus ...

  5. Flow Cytometry-Based Bead-Binding Assay for Measuring Receptor Ligand Specificity

    NARCIS (Netherlands)

    Sprokholt, Joris K.; Hertoghs, Nina; Geijtenbeek, Teunis B. H.

    2016-01-01

    In this chapter we describe a fluorescent bead-binding assay, which is an efficient and feasible method to measure interaction between ligands and receptors on cells. In principle, any ligand can be coated on fluorescent beads either directly or via antibodies. Binding between ligand-coated beads

  6. Lithium cation enhances anion binding in a tripodal phosphine oxide-based ditopic receptor.

    Science.gov (United States)

    Gavette, Jesse V; Lara, Juven; Berryman, Orion B; Zakharov, Lev N; Haley, Michael M; Johnson, Darren W

    2011-07-21

    A tripodal ditopic receptor presents H-bond donors and a phosphine oxide to potential guests. In the idealized binding conformation, an endohedral P=O functionality provides enhanced halide binding in the presence of lithium with the greatest ΔΔG° observed for bromide, while minimal changes in K(a) are observed in the presence of sodium.

  7. New Strategy for Prostate Cancer Prevention Based on Selenium Suppression of Androgen Receptor Signaling

    Science.gov (United States)

    2010-04-01

    5α-reductase inhibitor; prostate cancer; chemoprevention; androgen receptor; FOXO1 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT...influences comparative activity of selenium-enriched garlic and yeast in mammary cancer pre- vention. J Agric Food Chem 2000;48(6):2062–2070. 12. Medina D

  8. Novel approaches for the treatment of psychostimulant and opioid abuse - focus on opioid receptor-based therapies.

    Science.gov (United States)

    Bailey, Chris P; Husbands, Stephen M

    2014-11-01

    Psychostimulant and opioid addiction are poorly treated. The majority of abstinent users relapse back to drug-taking within a year of abstinence, making 'anti-relapse' therapies the focus of much current research. There are two fundamental challenges to developing novel treatments for drug addiction. First, there are three key stimuli that precipitate relapse back to drug-taking: stress, presentation of drug-conditioned cue, taking a small dose of drug. The most successful novel treatment would be effective against all three stimuli. Second, a large number of drug users are poly-drug users: taking more than one drug of abuse at a time. The ideal anti-addiction treatment would, therefore, be effective against all classes of drugs of abuse. In this review, the authors discuss the clinical need and animal models used to uncover potential novel treatments. There is a very broad range of potential treatment approaches and targets currently being examined as potential anti-relapse therapies. These broadly fit into two categories: 'memory-based' and 'receptor-based' and the authors discuss the key targets here within. Opioid receptors and ligands have been widely studied, and research into how different opioid subtypes affect behaviours related to addiction (reward, dysphoria, motivation) suggests that they are tractable targets as anti-relapse treatments. Regarding opioid ligands as novel 'anti-relapse' medication targets, research suggests that a 'non-selective' approach to targeting opioid receptors will be the most effective.

  9. Docking-based Screening of Ficus religiosa Phytochemicals as Inhibitors of Human Histamine H2 Receptor.

    Science.gov (United States)

    Chaudhary, Amit; Yadav, Birendra Singh; Singh, Swati; Maurya, Pramod Kumar; Mishra, Alok; Srivastva, Shweta; Varadwaj, Pritish Kumar; Singh, Nand Kumar; Mani, Ashutosh

    2017-10-01

    Ficus religiosa L. is generally known as Peepal and belongs to family Moraceae. The tree is a source of many compounds having high medicinal value. In gastrointestinal tract, histamine H2 receptors have key role in histamine-stimulated gastric acid secretion. Their over stimulation causes its excessive production which is responsible for gastric ulcer. This study aims to screen the range of phytochemicals present in F. religiosa for binding with human histamine H2 and identify therapeutics for a gastric ulcer from the plant. In this work, a 3D-structure of human histamine H2 receptor was modeled by using homology modeling and the predicted model was validated using PROCHECK. Docking studies were also performed to assess binding affinities between modeled receptor and 34 compounds. Molecular dynamics simulations were done to identify most stable receptor-ligand complexes. Absorption, distribution, metabolism, excretion, and screening was done to evaluate pharmacokinetic properties of compounds. The results suggest that seven ligands, namely, germacrene, bergaptol, lanosterol, Ergost-5-en-3beta-ol, α-amyrin acetate, bergapten, and γ-cadinene showed better binding affinities. Among seven phytochemicals, lanosterol and α-amyrin acetate were found to have greater stability during simulation studies. These two compounds may be a suitable therapeutic agent against histamine H2 receptor. This study was performed to screen antiulcer compounds from F. religiosa. Molecular modeling, molecular docking and MD simulation studies were performed with selected phytochemicals from F. religiosa. The analysis suggests that Lanosterol and α-amyrin may be a suitable therapeutic agent against histamine H2 receptor. This study facilitates initiation of the herbal drug discovery process for the antiulcer activity. Abbreviations used: ADMET: Absorption, distribution, metabolism, excretion and toxicity, DOPE: Discrete Optimized Potential Energy, OPLS: Optimized potential for liquid

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

    Science.gov (United States)

    Park, Boyoung; Choi, Ji-Yeob; Sung, Ho Kyung; Ahn, Choonghyun; Hwang, Yunji; Jang, Jieun; Lee, Juyeon; Kim, Heewon; Shin, Hai-Rim; Park, Sohee; Han, Wonshik; Noh, Dong-Young; Yoo, Keun-Young; Kang, Daehee; Park, Sue K

    2016-04-01

    We conducted a heterogeneous risk assessment of breast cancer based on the hormone receptor (HR) and human epidermal growth factor receptor 2 (HER2) calculating the risks and population-based attributable fractions (PAFs) for modifiable and nonmodifiable factors.Using matched case-control study design from the Seoul Breast Cancer Study and the national prevalence of exposure, the risks and PAFs for modifiable and nonmodifiable factors were estimated for total breast cancers and subtypes.The attribution to modifiable factors was different for each subtype (luminal A, PAF = 61.4% [95% confidence interval, CI = 54.3%-69.8%]; luminal B, 21.4% [95% CI = 18.6-24.9%]; HER2-overexpression, 59.4% [95% CI = 47.8%-74.3%], and triple negative tumors [TNs], 27.1% [95% CI = 22.9%-32.4%)], and the attribution to the modifiable factors for the luminal A and HER2-overexpression subtypes was higher than that of the luminal B and TN subtypes (P heterogeneity  ≤  0.001). The contribution of modifiable reproductive factors to luminal A type in premenopausal women was higher than that of the other subtypes (18.2% for luminal A; 3.1%, 8.1%, and -3.1% for luminal B, HER2-overexpression, and TN subtypes, respectively; P heterogeneity  ≤  0.001). Physical activity had the highest impact preventing 32.6% of luminal A, 14.5% of luminal B, 38.0% of HER2-overexpression, and 26.9% of TN subtypes (P heterogeneity = 0.014). Total reproductive factors were also heterogeneously attributed to each breast cancer subtype (luminal A, 65.4%; luminal B, 24.1%; HER2-overexpression, 57.9%, and TN subtypes, -3.1%; P heterogeneity  ≤  0.001).Each pathological subtype of breast cancer by HRs and HER2 status may be associated with heterogeneous risk factors and their attributable risk, suggesting a different etiology. The luminal B and TN subtypes seemed to be less preventable despite intervention for alleged risk factors, even though physical activity had a high

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

    KAUST Repository

    Fowkes, Jaroslav M.

    2012-06-21

    We present a branch and bound algorithm for the global optimization of a twice differentiable nonconvex objective function with a Lipschitz continuous Hessian over a compact, convex set. The algorithm is based on applying cubic regularisation techniques to the objective function within an overlapping branch and bound algorithm for convex constrained global optimization. Unlike other branch and bound algorithms, lower bounds are obtained via nonconvex underestimators of the function. For a numerical example, we apply the proposed branch and bound algorithm to radial basis function approximations. © 2012 Springer Science+Business Media, LLC.

  12. Complementarity reveals bound entanglement of two twisted photons

    Science.gov (United States)

    Hiesmayr, Beatrix C.; Löffler, Wolfgang

    2013-08-01

    We demonstrate the detection of bipartite bound entanglement as predicted by the Horodecki's in 1998. Bound entangled states, being heavily mixed entangled quantum states, can be produced by incoherent addition of pure entangled states. Until 1998 it was thought that such mixing could always be reversed by entanglement distillation; however, this turned out to be impossible for bound entangled states. The purest form of bound entanglement is that of only two particles, which requires higher-dimensional (d > 2) quantum systems. We realize this using photon qutrit (d = 3) pairs produced by spontaneous parametric downconversion, that are entangled in the orbital angular momentum degrees of freedom, which is scalable to high dimensions. Entanglement of the photons is confirmed via a ‘maximum complementarity protocol’. This conceptually simple protocol requires only maximized complementary of measurement bases; we show that it can also detect bound entanglement. We explore the bipartite qutrit space and find that, also experimentally, a significant portion of the entangled states are actually bound entangled.

  13. Opinion formation with time-varying bounded confidence.

    Science.gov (United States)

    Zhang, YunHong; Liu, QiPeng; Zhang, SiYing

    2017-01-01

    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.

  14. Resorcarene-based receptor: versatile behavior in its interaction with heavy and soft metal cations.

    Science.gov (United States)

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

    2006-02-09

    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

  15. Capacity Bounds for Parallel Optical Wireless Channels

    KAUST Repository

    Chaaban, Anas

    2016-01-01

    A system consisting of parallel optical wireless channels with a total average intensity constraint is studied. Capacity upper and lower bounds for this system are derived. Under perfect channel-state information at the transmitter (CSIT), the bounds have to be optimized with respect to the power allocation over the parallel channels. The optimization of the lower bound is non-convex, however, the KKT conditions can be used to find a list of possible solutions one of which is optimal. The optimal solution can then be found by an exhaustive search algorithm, which is computationally expensive. To overcome this, we propose low-complexity power allocation algorithms which are nearly optimal. The optimized capacity lower bound nearly coincides with the capacity at high SNR. Without CSIT, our capacity bounds lead to upper and lower bounds on the outage probability. The outage probability bounds meet at high SNR. The system with average and peak intensity constraints is also discussed.

  16. Multitask Classification Hypothesis Space With Improved Generalization Bounds.

    Science.gov (United States)

    Li, Cong; Georgiopoulos, Michael; Anagnostopoulos, Georgios C

    2015-07-01

    This paper presents a pair of hypothesis spaces (HSs) of vector-valued functions intended to be used in the context of multitask classification. While both are parameterized on the elements of reproducing kernel Hilbert spaces and impose a feature mapping that is common to all tasks, one of them assumes this mapping as fixed, while the more general one learns the mapping via multiple kernel learning. For these new HSs, empirical Rademacher complexity-based generalization bounds are derived, and are shown to be tighter than the bound of a particular HS, which has appeared recently in the literature, leading to improved performance. As a matter of fact, the latter HS is shown to be a special case of ours. Based on an equivalence to Group-Lasso type HSs, the proposed HSs are utilized toward corresponding support vector machine-based formulations. Finally, experimental results on multitask learning problems underline the quality of the derived bounds and validate this paper's analysis.

  17. Counting Majorana bound states using complex momenta

    Directory of Open Access Journals (Sweden)

    I. Mandal

    2016-09-01

    Full Text Available Recently, the connection between Majorana fermions bound to the defects in arbitrary dimensions, and complex momentum roots of the vanishing determinant of the corresponding bulk Bogoliubov–de Gennes (BdG Hamiltonian, has been established (EPL, 2015, 110, 67005. Based on this understanding, a formula has been proposed to count the number (n of the zero energy Majorana bound states, which is related to the topological phase of the system. In this paper, we provide a proof of the counting formula and we apply this formula to a variety of 1d and 2d models belonging to the classes BDI, DIII and D. We show that we can successfully chart out the topological phase diagrams. Studying these examples also enables us to explicitly observe the correspondence between these complex momentum solutions in the Fourier space, and the localized Majorana fermion wavefunctions in the position space. Finally, we corroborate the fact that for systems with a chiral symmetry, these solutions are the so-called "exceptional points", where two or more eigenvalues of the complexified Hamiltonian coalesce.

  18. Dilation volumes of sets of bounded perimeter

    DEFF Research Database (Denmark)

    Kiderlen, Markus; Rataj, Jan

    This paper analyzes the first order behavior (that is, the right sided derivative) of the volume of the dilation A ⊕ tQ as t converges to zero. Here A and Q are subsets of n-dimensional Euclidean space, A has bounded perimeter and Q is compact. If Q consists of two points only, x and x+u, say......, this derivative coincides up to sign with the directional derivative of the covariogram of A in direction u. By known results for the covariogram, this derivative can therefore be expressed by the cosine transform of the surface area measure of A. We extend this result to sets Q that are at most countable and use...... 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....

  19. Spectral computations for bounded operators

    CERN Document Server

    Ahues, Mario; Limaye, Balmohan

    2001-01-01

    Exact eigenvalues, eigenvectors, and principal vectors of operators with infinite dimensional ranges can rarely be found. Therefore, one must approximate such operators by finite rank operators, then solve the original eigenvalue problem approximately. Serving as both an outstanding text for graduate students and as a source of current results for research scientists, Spectral Computations for Bounded Operators addresses the issue of solving eigenvalue problems for operators on infinite dimensional spaces. From a review of classical spectral theory through concrete approximation techniques to finite dimensional situations that can be implemented on a computer, this volume illustrates the marriage of pure and applied mathematics. It contains a variety of recent developments, including a new type of approximation that encompasses a variety of approximation methods but is simple to verify in practice. It also suggests a new stopping criterion for the QR Method and outlines advances in both the iterative refineme...

  20. On order bounded subsets of locally solid Riesz spaces | Hong ...

    African Journals Online (AJOL)

    In a topological Riesz space there are two types of bounded subsets: order bounded subsets and topologically bounded subsets. It is natural to ask (1) whether an order bounded subset is topologically bounded and (2) whether a topologically bounded subset is order bounded. A classical result gives a partial answer to (1) ...

  1. Identification of small-molecule agonists of human relaxin family receptor 1 (RXFP1) by using a homogenous cell-based cAMP assay.

    Science.gov (United States)

    Chen, Catherine Z; Southall, Noel; Xiao, Jingbo; Marugan, Juan J; Ferrer, Marc; Hu, Xin; Jones, Raisa E; Feng, Shu; Agoulnik, Irina U; Zheng, Wei; Agoulnik, Alexander I

    2013-07-01

    The relaxin hormone is involved in a variety of biological functions, including female reproduction and parturition, as well as regulation of cardiovascular, renal, pulmonary, and hepatic functions. It regulates extracellular matrix remodeling, cell invasiveness, proliferation, differentiation, and overall tissue homeostasis. The G protein-coupled receptor (GPCR) relaxin family receptor 1 (RXFP1) is a cognate relaxin receptor that mainly signals through cyclic AMP second messenger. Although agonists of the receptor could have a wide range of pharmacologic utility, until now there have been no reported small-molecule agonists for relaxin receptors. Here, we report the development of a quantitative high-throughput platform for an RXFP1 agonist screen based on homogenous cell-based HTRF cyclic AMP (cAMP) assay technology. Two small molecules of similar structure were independently identified from a screen of more than 365 677 compounds. Neither compound showed activity in a counterscreen with HEK293T cells transfected with an unrelated GPCR vasopressin 1b receptor. These small-molecule agonists also demonstrated selectivity against the RXFP2 receptor, providing a basis for future medicinal chemistry optimization of selective relaxin receptor agonists.

  2. Macrocyclic chelator-coupled gastrin-based radiopharmaceuticals for targeting of gastrin receptor-expressing tumours

    Energy Technology Data Exchange (ETDEWEB)

    Good, Stephan; Wang, Xuejuan; Maecke, Helmut R. [University Hospital Basel, Division of Radiological Chemistry, Basel (Switzerland); Walter, Martin A.; Mueller-Brand, Jan [University Hospital, Institute of Nuclear Medicine, Basel (Switzerland); Waser, Beatrice; Reubi, Jean-Claude [University of Berne, Department of Pathology, Bern (Switzerland); Behe, Martin P. [Philipps-University of Marburg, Department of Nuclear Medicine, Marburg (Germany)

    2008-10-15

    Diethylenetriamine-pentaacetic acid (DTPA)-coupled minigastrins are unsuitable for therapeutic application with the available {beta}-emitting radiometals due to low complex stability. Low tumour-to-kidney ratio of the known radiopharmaceuticals is further limiting their potency. We used macrocyclic chelators for coupling to increase complex stability, modified the peptide sequence to enhance radiolytic stability and studied tumour-to-kidney ratio and metabolic stability using {sup 111}In-labelled derivatives. Gastrin derivatives with decreasing numbers of glutamic acids were synthesised using {sup 111}In as surrogate for therapeutic radiometals for in vitro and in vivo studies. Gastrin receptor affinities of the {sup nat}In-metallated compounds were determined by receptor autoradiography using {sup 125}I-CCK as radioligand. Internalisation was evaluated in AR4-2J cells. Enzymatic stability was determined by incubating the {sup 111}In-labelled peptides in human serum. Biodistribution was performed in AR4-2J-bearing Lewis rats. IC{sub 50} values of the {sup nat}In-metallated gastrin derivatives vary between 1.2 and 4.8 nmol/L for all methionine-containing derivatives. Replacement of methionine by norleucine, isoleucine, methionine-sulfoxide and methionine-sulfone resulted in significant decrease of receptor affinity (IC{sub 50} between 9.9 and 1,195 nmol/L). All cholecystokinin receptor affinities were >100 nmol/L. All {sup 111}In-labelled radiopeptides showed receptor-specific internalisation. Serum mean-life times varied between 2.0 and 72.6 h, positively correlating with the number of Glu residues. All {sup 111}In-labelled macrocyclic chelator conjugates showed higher tumour-to-kidney ratios after 24 h (0.37-0.99) compared to {sup 111}In-DTPA-minigastrin 0(0.05). Tumour wash out between 4 and 24 h was low. Imaging studies confirmed receptor-specific blocking of the tumour uptake. Reducing the number of glutamates increased tumour-to-kidney ratio but resulted in

  3. All three LDL receptor homology regions of the LDL receptor-related protein bind multiple ligands.

    Science.gov (United States)

    Croy, Johnny E; Shin, William D; Knauer, Mary F; Knauer, Daniel J; Komives, Elizabeth A

    2003-11-11

    The three complete human LDL receptor homology regions of the LDL receptor-related protein (sLRP2, sLRP3, and sLRP4) have been expressed in Pichia pastoris SMD1168 with constitutive coexpression of the receptor-associated protein (RAP). Each sLRP was purified to homogeneity after deglycosylation using a combination of anion-exchange and size exclusion chromatography. Mass spectrometry and N-terminal sequencing confirmed the identity of each fragment at purified yields of several milligrams per liter. Despite the large number of disulfide linkages and glycosylation sites in each LDL receptor homology region (sLRP), all were shown to be competent for binding to several LRP1 ligands. Each sLRP also bound human RAP, which is thought to be a generalized receptor antagonist, in solution-binding experiments. As expected, sLRP2 bound the receptor-binding domain of alpha(2)-macroglobulin (residues 1304-1451). All three sLRPs bound human apolipoprotein-enriched beta very low density lipoprotein, the canonical ligand for this receptor. All three sLRPs also bound lactoferrin and thrombin-protease nexin 1 complexes. Only sLRP4 bound thrombin-antithrombin III complexes. The results show that binding-competent LDL receptor homology regions (sLRPs) can be produced in high yield in P. pastoris and readily purified. Each sLRP has binding sites for multiple ligands, but not all ligand binding could be competed by RAP.

  4. Molecular mechanisms of non-transferrin-bound and transferring-bound iron uptake in primary hippocampal neurons.

    Science.gov (United States)

    Ji, Changyi; Kosman, Daniel J

    2015-06-01

    The molecular mechanisms of iron trafficking in neurons have not been elucidated. In this study, we characterized the expression and localization of ferrous iron transporters Zip8, Zip14 and divalent metal transporter 1 (DMT1), and ferrireductases Steap2 and stromal cell-derived receptor 2 in primary rat hippocampal neurons. Steap2 and Zip8 partially co-localize, indicating these two proteins may function in Fe(3+) reduction prior to Fe(2+) permeation. Zip8, DMT1, and Steap2 co-localize with the transferrin receptor/transferrin complex, suggesting they may be involved in transferrin receptor/transferrin-mediated iron assimilation. In brain interstitial fluid, transferring-bound iron (TBI) and non-transferrin-bound iron (NTBI) exist as potential iron sources. Primary hippocampal neurons exhibit significant iron uptake from TBI (Transferrin-(59) Fe(3+)) and NTBI, whether presented as (59) Fe(2+) -citrate or (59) Fe(3+) -citrate; reductase-independent (59) Fe(2+) uptake was the most efficient uptake pathway of the three. Kinetic analysis of Zn(2+) inhibition of Fe(2+) uptake indicated that DMT1 plays only a minor role in the uptake of NTBI. In contrast, localization and knockdown data indicate that Zip8 makes a major contribution. Data suggest also that cell accumulation of (59) Fe from TBI relies at least in part on an endocytosis-independent pathway. These data suggest that Zip8 and Steap2 play a major role in iron accumulation from NTBI and TBI by hippocampal neurons. Analysis of the expression and localization of known iron uptake transporters demonstrated that Zip8 makes a major contribution to iron accumulation in primary cultures of rat embryonic hippocampal neurons. These cells exhibit uptake pathways for ferrous and ferric iron (non-transferrin-bound iron, NTBI in figure) and for transferrin-bound iron; the ferrireductases Steap2 and SDR2 support the uptake of ferric iron substrates. Zip8 and Steap2 are strongly expressed in the plasma membrane of both soma

  5. Bases moleculares de la selectividad de ligandos por receptores de melatonina

    OpenAIRE

    Romera, Julia A.; Cortés Cabrera, Álvaro; Sánchez Murcia, Pedro A.; Álvarez Builla, Julio; Gago Badenas, Federico

    2013-01-01

    La hormona melatonina (MT), o N-acetil-5-metoxitriptamina, secretada por la glándula pineal, es responsable de la regulación del sueño y el ritmo circadiano a través de la modulación del núcleo supraquiasmático, entre otras funciones. MT actúa sobre 2 receptores diferentes, MT1 (o MT1A) y MT2 (o MT1B), que funcionan acoplados a proteínas G (GPCR). La propia melatonina y otros agonistas de los receptores MT pueden ser usadas para marcar los ritmos circadianos, facilitar el sueño o ejercer un...

  6. Behavioral and Physiological Effects of a Novel Kappa-Opioid Receptor-Based DREADD in Rats.

    Science.gov (United States)

    Marchant, Nathan J; Whitaker, Leslie R; Bossert, Jennifer M; Harvey, Brandon K; Hope, Bruce T; Kaganovsky, Konstantin; Adhikary, Sweta; Prisinzano, Thomas E; Vardy, Eyal; Roth, Bryan L; Shaham, Yavin

    2016-01-01

    In the past decade, novel methods using engineered receptors have enabled researchers to manipulate neuronal activity with increased spatial and temporal specificity. One widely used chemogenetic method in mice and rats is the DREADD (designer receptors exclusively activated by designer drugs) system in which a mutated muscarinic G protein-coupled receptor is activated by an otherwise inert synthetic ligand, clozapine-N-oxide (CNO). Recently, the Roth laboratory developed a novel inhibitory DREADD in which a mutated kappa-opioid receptor (KORD) is activated by the pharmacologically inert drug salvinorin B (SalB; Vardy et al, 2015). They demonstrated the feasibility of using KORD to study brain circuits involved in motivated behavior in mice. Here, we used behavioral, electrophysiological, and neuroanatomical methods to demonstrate the feasibility of using the novel KORD to study brain circuits involved in motivated behavior in rats. In Exp. 1, we show that SalB dose-dependently decreased spontaneous and cocaine-induced locomotor activity in rats expressing KORD to midbrain (ventral tegmental area/substantia nigra). In Exp. 2, we show that SalB completely inhibited tonic firing in KORD-expressing putative dopamine neurons in midbrain. In Exp. 3, we used a 'retro-DREADD' dual-virus approach to restrict expression of KORD in ventral subiculum neurons that project to nucleus accumbens shell. We show that KORD activation selectively decreased novel context-induced Fos expression in this projection. Our results indicate that the novel KORD is a promising tool to selectively inactivate brain areas and neural circuits in rat studies of motivated behavior.

  7. Dosimetry of exendin-4 based radiotracer for glucagonlike peptide-1 receptor imaging: an initial report

    Science.gov (United States)

    Tomaszuk, M.; Sowa-Staszczak, A.; Lenda-Tracz, W.; Glowa, B.; Pach, D.; Buziak-Bereza, M.; Stefanska, A.; Janota, B.; Pawlak, D.; Mikolajczak, R.; Hubalewska-Dydejczyk, A. B.

    2011-09-01

    Overexpression of glucagonlike peptide-1 (GLP-1) receptors in human tumours is a potential target for future imaging and therapy. The GLP-1 receptor imaging using [Lys40(Ahx-HYNIC-99mTc/EDDA)NH2]-exendin-4 could be useful in the localization of unknown insulinoma focus. The aim of this study was to present the first experience of our unit with the new radiopharmaceutical and its dose estimates. Imaging studies and dose assessment, according to the MIRD schema and MIRD Pamphlet No.11, were performed for 3 patients (2 with suspicion of insulinoma, 1 with suspected insulinoma recurrence). In the first case suspicion of insulinoma was not confirmed. In the second case localized accumulation of tracer in the pancreas was removed by surgery and the clinical symptoms of insulinoma receded. In the third case, pathological accumulation of tracer was localized and recurrence of insulinoma was confirmed in fusion with CT images. The biological half-time did not exceed 2.7.h. The effective half-time did not exceed 4.8 h. The total-body radiation dose did not exceed 0.0038 mGy/MBq and is comparable with the radiation dose to patient after somatostatin receptor scintigraphy. The highest radiation dose was calculated for kidneys (~ 0.070 mGy/MBq). [Lys40(Ahx-HYNIC-99mTc/EDDA)NH2]-exendin-4 is a good candidate for clinical GLP-1 receptor imaging studies and appears safe for the patient from radiological safety point of view.

  8. Using tolerance bounds in scientific investigations

    Energy Technology Data Exchange (ETDEWEB)

    Wendelberger, J.R.

    1996-07-01

    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.

  9. Improved androgen specificity of AR-EcoScreen by CRISPR based glucocorticoid receptor knockout.

    Science.gov (United States)

    Zwart, Nick; Andringa, Dave; de Leeuw, Willem-Jan; Kojima, Hiroyuki; Iida, Mitsuru; Houtman, Corine J; de Boer, Jacob; Kool, Jeroen; Lamoree, Marja H; Hamers, Timo

    2017-12-01

    The AR-EcoScreen is a widely used reporter assay for the detection of androgens and anti-androgens. Endogenous expression of glucocorticoid receptors and their affinity for the androgen responsive element that drives reporter expression, however, makes the reporter cells sensitive to interference by glucocorticoids and less specific for (anti-)androgens. To create a glucocorticoid insensitive derivative of the AR-EcoScreen, CRISPR/Cas9 genome editing was used to develop glucocorticoid receptor knockout mutants by targeting various sites in the glucocorticoid gene. Two mutant cell lines were further characterized and validated against the unmodified AR-EcoScreen with a set of 19 environmentally relevant chemicals and a series of environmental passive sampler extracts with (anti-)androgenic activity. Sequencing of the targeted sites revealed premature stop codons following frame-shift mutations, leading to an absence of functional glucocorticoid receptor expression. The introduced mutations rendered cell lines insensitive to glucocorticoid activation and caused no significant difference in the responsiveness towards (anti-)androgens, compared to the unmodified AR-EcoScreen cells, allowing the selective, GR-independent, determination of (anti-)androgenicity in environmental passive sampler extracts. The increase in selectivity for (anti-)androgens improves reliability of the AR-EcoScreen and will provide higher accuracy in determining (anti-)androgenic potential when applied in toxicity screening and environmental monitoring of both single compounds and mixtures. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Nuclear receptor engineering based on novel structure activity relationships revealed by farnesyl pyrophosphate.

    Science.gov (United States)

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

    2010-11-01

    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.

  11. 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.

  12. Performance Bounds on Two Concatenated, Interleaved Codes

    Science.gov (United States)

    Moision, Bruce; Dolinar, Samuel

    2010-01-01

    be erroneous. From the perspective of the present method, the topic of major interest is the performance of the communication system as quantified in the word-error rate and the undetected-error rate as functions of the SNRs and the total latency of the interleaver and inner code. The method is embodied in equations that describe bounds on these functions. Throughout the derivation of the equations that embody the method, it is assumed that the decoder for the outer code corrects any error pattern of t or fewer errors, detects any error pattern of s or fewer errors, may detect some error patterns of more than s errors, and does not correct any patterns of more than t errors. Because a mathematically complete description of the equations that embody the method and of the derivation of the equations would greatly exceed the space available for this article, it must suffice to summarize by reporting that the derivation includes consideration of several complex issues, including relationships between latency and memory requirements for block and convolutional codes, burst error statistics, enumeration of error-event intersections, and effects of different interleaving depths. In a demonstration, the method was used to calculate bounds on the performances of several communication systems, each based on serial concatenation of a (63,56) expurgated Hamming code with a convolutional inner code through a convolutional interleaver. The bounds calculated by use of the method were compared with results of numerical simulations of performances of the systems to show the regions where the bounds are tight (see figure).

  13. The role of patient-based treatment planning in peptide receptor radionuclide therapy

    Energy Technology Data Exchange (ETDEWEB)

    Hardiansyah, Deni; Attarwala, Ali Asgar [Heidelberg University, Medical Radiation Physics/Radiation Protection, Universitaetsmedizin Mannheim, Medical Faculty Mannheim, Mannheim (Germany); Universitaetsmedizin Mannheim, Medical Faculty Mannheim, Heidelberg University, Department of Radiation Oncology, Mannheim (Germany); Maass, Christian; Glatting, Gerhard [Heidelberg University, Medical Radiation Physics/Radiation Protection, Universitaetsmedizin Mannheim, Medical Faculty Mannheim, Mannheim (Germany); Mueller, Berthold [University Hospital, RWTH Aachen University, Klinik fuer Nuklearmedizin, Aachen (Germany); Kletting, Peter [Universitaet Ulm, Klinik fuer Nuklearmedizin, Ulm (Germany); Mottaghy, Felix M. [University Hospital, RWTH Aachen University, Klinik fuer Nuklearmedizin, Aachen (Germany); Maastricht University Medical Center (MUMC+), Department of Nuclear Medicine, Maastricht (Netherlands)

    2016-05-15

    Accurate treatment planning is recommended in peptide-receptor radionuclide therapy (PRRT) to minimize the toxicity to organs at risk while maximizing tumor cell sterilization. The aim of this study was to quantify the effect of different degrees of individualization on the prediction accuracy of individual therapeutic biodistributions in patients with neuroendocrine tumors (NETs). A recently developed physiologically based pharmacokinetic (PBPK) model was fitted to the biokinetic data of 15 patients with NETs after pre-therapeutic injection of {sup 111}In-DTPAOC. Mathematical phantom patients (MPP) were defined using the assumed true (true MPP), mean (MPP 1A) and median (MPP 1B) parameter values of the patient group. Alterations of the degree of individualization were introduced to both mean and median patients by including patient-specific information as a priori knowledge: physical parameters and hematocrit (MPP 2A/2B). Successively, measurable individual biokinetic parameters were added: tumor volume V{sub tu} (MPP 3A/3B), glomerular filtration rate GFR (MPP 4A/4B), and tumor perfusion f{sub tu} (MPP 5A/5B). Furthermore, parameters of MPP 5A/5B and a simulated {sup 68}Ga-DOTATATE PET measurement 60 min p.i. were used together with the population values used as Bayesian parameters (MPP 6A/6B). Therapeutic biodistributions were simulated assuming an infusion of {sup 90}Y-DOTATATE (3.3 GBq) over 30 min to all MPPs. Time-integrated activity coefficients were predicted for all MPPs and compared to the true MPPs for each patient in tumor, kidneys, spleen, liver, remainder, and whole body to obtain the relative differences RD. The large RD values of MPP 1A [RD{sub tumor} = (625 ± 1266)%, RD{sub kidneys} = (11 ± 38)% ], and MPP 1B [RD{sub tumor} = (197 ± 505)%, RD{sub kidneys} = (11 ± 39)% ] demonstrate that individual treatment planning is needed due to large physiological differences between patients. Although addition of individual patient parameters reduced the

  14. Instanton bound states in ABJM theory

    Energy Technology Data Exchange (ETDEWEB)

    Hatsuda, Yasuyuki [DESY Hamburg (Germany). Theory Group; Tokyo Institute of Technology (Japan). Dept. of Physics; Moriyama, Sanefumi [Nagoya Univ. (Japan). Kobayashi Maskawa Inst. and Graduate School of Mathematics; Okuyama, Kazumi [Shinshu Univ., Matsumoto, Nagano (Japan). Dept. of Physics

    2013-06-15

    The partition function of the ABJM theory receives non-perturbative corrections due to instanton effects. We study these non-perturbative corrections, including bound states of worldsheet instantons and membrane instantons, in the Fermi-gas approach. We require that the total non-perturbative correction should be always finite for arbitrary Chern-Simons level. This finiteness is realized quite non-trivially because each bound state contribution naively diverges at some levels. The poles of each contribution should be canceled out in total. We use this pole cancellation mechanism to find unknown bound state corrections from known ones. We conjecture a general expression of the bound state contribution. Summing up all the bound state contributions, we find that the effect of bound states is simply incorporated into the worldsheet instanton correction by a redefinition of the chemical potential in the Fermi-gas system. Analytic expressions of the 3- and 4-membrane instanton corrections are also proposed.

  15. Heterotypic interactions between transferrin receptor and transferrin receptor 2

    OpenAIRE

    Vogt, TM; Blackwell, AD; Giannetti, AM; Bjorkman, PJ; Enns, CA

    2003-01-01

    Cellular iron uptake in most tissues occurs via endocytosis of diferric transferrin (Tf) bound to the transferrin receptor (TfR). Recently, a second transferrin receptor, transferrin receptor 2 (TfR2), has been identified and shown to play a critical role in iron metabolism. TfR2 is capable of Tf-mediated iron uptake and mutations in this gene result in a rare form of hereditary hemochromatosis unrelated to the hereditary hemochromatosis protein, HFE. Unlike TfR, TfR2 expression is not contro...

  16. Distance hijacking attacks on distance bounding protocols

    OpenAIRE

    Cremers, Cas; Rasmussen, Kasper Bonne; Čapkun, Srdjan

    2011-01-01

    Distance bounding protocols are typically analyzed with respect to three types of attacks: Distance Fraud, Mafia Fraud, and Terrorist Fraud. We define a fourth main type of attacks on distance bounding protocols, called Distance Hijacking attacks. We show that many proposed distance bounding protocols are vulnerable to these attacks, and we propose solutions to make these protocols resilient to Distance Hijacking. Additionally, we generalize Distance Hijacking to Location Hijacking, to which ...

  17. Boundedly UC spaces: characterisations and preservation | Jain ...

    African Journals Online (AJOL)

    A metric space (X, d) is called a boundedly UC space if every closed and bounded subset of X is a UC space. A metric space (X, d) is called a UC space if each real-valued continuous function on (X, d) is uniformly continuous. In this paper, we study twenty-two equivalent conditions for a metric space to be a boundedly UC ...

  18. Bounded cohomology of discrete groups

    CERN Document Server

    Frigerio, Roberto

    2017-01-01

    The author manages a near perfect equilibrium between necessary technicalities (always well motivated) and geometric intuition, leading the readers from the first simple definition to the most striking applications of the theory in 13 very pleasant chapters. This book can serve as an ideal textbook for a graduate topics course on the subject and become the much-needed standard reference on Gromov's beautiful theory. -Michelle Bucher The theory of bounded cohomology, introduced by Gromov in the late 1980s, has had powerful applications in geometric group theory and the geometry and topology of manifolds, and has been the topic of active research continuing to this day. This monograph provides a unified, self-contained introduction to the theory and its applications, making it accessible to a student who has completed a first course in algebraic topology and manifold theory. The book can be used as a source for research projects for master's students, as a thorough introduction to the field for graduate student...

  19. Bounded sets in fast complete inductive limits

    Directory of Open Access Journals (Sweden)

    Jan Kucera

    1984-01-01

    Full Text Available Let E1⊂E2⊂… be a sequence of locally convex spaces with all identity maps: En→En+1 continuous and E=indlim En fast complete. Then each set bounded in E is also bounded in some En iff for any Banach disk B bounded in E and n∈N, the closure of B⋂En in B is bounded in some Em. This holds, in particular, if all spaces En are webbed.

  20. Valuation models and Simon's bounded rationality

    National Research Council Canada - National Science Library

    Alexandra Strommer de Farias Godoi

    2009-01-01

    This paper aims at reconciling the evidence that sophisticated valuation models are increasingly used by companies in their investment appraisal with the literature of bounded rationality, according...

  1. Some Improved Nonperturbative Bounds for Fermionic Expansions

    Energy Technology Data Exchange (ETDEWEB)

    Lohmann, Martin, E-mail: marlohmann@gmail.com [Universita di Roma Tre, Dipartimento di Matematica (Italy)

    2016-06-15

    We reconsider the Gram-Hadamard bound as it is used in constructive quantum field theory and many body physics to prove convergence of Fermionic perturbative expansions. Our approach uses a recursion for the amplitudes of the expansion, discovered in a model problem by Djokic (2013). It explains the standard way to bound the expansion from a new point of view, and for some of the amplitudes provides new bounds, which avoid the use of Fourier transform, and are therefore superior to the standard bounds for models like the cold interacting Fermi gas.

  2. A strongly quasiconvex PAC-Bayesian bound

    DEFF Research Database (Denmark)

    Thiemann, Niklas; Igel, Christian; Wintenberger, Olivier

    We propose a new PAC-Bayesian bound and a way of constructing a hypothesis space, so that the bound is convex in the posterior distribution and also convex in a trade-off parameter between empirical performance of the posterior distribution and its complexity. The complexity is measured by the Ku......We propose a new PAC-Bayesian bound and a way of constructing a hypothesis space, so that the bound is convex in the posterior distribution and also convex in a trade-off parameter between empirical performance of the posterior distribution and its complexity. The complexity is measured...

  3. Multiscale design of coarse-grained elastic network-based potentials for the μ opioid receptor.

    Science.gov (United States)

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

    2016-09-01

    Despite progress in computer modeling, most biological processes are still out of reach when using all-atom (AA) models. Coarse-grained (CG) models allow classical molecular dynamics (MD) simulations to be accelerated. Although simplification of spatial resolution at different levels is often investigated, simplification of the CG potential in itself has been less common. CG potentials are often similar to AA potentials. In this work, we consider the design and reliability of purely mechanical CG models of the μ opioid receptor (μOR), a G protein-coupled receptor (GPCR). In this sense, CG force fields (FF) consist of a set of holonomic constraints guided by an elastic network model (ENM). Even though ENMs are used widely to perform normal mode analysis (NMA), they are not often implemented as a single FF in the context of MD simulations. In this work, various ENM-like potentials were investigated by varying their force constant schemes and connectivity patterns. A method was established to systematically parameterize ENM-like potentials at different spatial resolutions by using AA data. To do so, new descriptors were introduced. The choice of conformation descriptors that also include flexibility information is important for a reliable parameterization of ENMs with different degrees of sensitivity. Hence, ENM-like potentials, with specific parameters, can be sufficient to accurately reproduce AA MD simulations of μOR at highly coarse-grained resolutions. Therefore, the essence of the flexibility properties of μOR can be captured with simple models at different CG spatial resolutions, opening the way to mechanical approaches to understanding GPCR functions. Graphical Abstract All atom structure, residue interaction network and coarse-grained elastic network models of the μ opioid receptor (μOR).

  4. Structure-based stabilization of HIV-1 gp120 enhances humoral immune responses to the induced co-receptor binding site.

    Directory of Open Access Journals (Sweden)

    Barna Dey

    2009-05-01

    Full Text Available The human immunodeficiency virus type 1 (HIV-1 exterior envelope glycoprotein, gp120, possesses conserved binding sites for interaction with the primary virus receptor, CD4, and also for the co-receptor, generally CCR5. Although gp120 is a major target for virus-specific neutralizing antibodies, the gp120 variable elements and its malleable nature contribute to evasion of effective host-neutralizing antibodies. To understand the conformational character and immunogenicity of the gp120 receptor binding sites as potential vaccine targets, we introduced structure-based modifications to stabilize gp120 core proteins (deleted of the gp120 major variable regions into the conformation recognized by both receptors. Thermodynamic analysis of the re-engineered core with selected ligands revealed significant stabilization of the receptor-binding regions. Stabilization of the co-receptor-binding region was associated with a marked increase in on-rate of ligand binding to this site as determined by surface plasmon resonance. Rabbit immunization studies showed that the conformational stabilization of core proteins, along with increased ligand affinity, was associated with strikingly enhanced humoral immune responses against the co-receptor-binding site. These results demonstrate that structure-based approaches can be exploited to stabilize a conformational site in a large functional protein to enhance immunogenic responses specific for that region.

  5. HDL-bound sphingosine-1-phosphate restrains lymphopoiesis and neuroinflammation.

    Science.gov (United States)

    Blaho, Victoria A; Galvani, Sylvain; Engelbrecht, Eric; Liu, Catherine; Swendeman, Steven L; Kono, Mari; Proia, Richard L; Steinman, Lawrence; Han, May H; Hla, Timothy

    2015-07-16

    Lipid mediators influence immunity in myriad ways. For example, circulating sphingosine-1-phosphate (S1P) is a key regulator of lymphocyte egress. Although the majority of plasma S1P is bound to apolipoprotein M (ApoM) in the high-density lipoprotein (HDL) particle, the immunological functions of the ApoM-S1P complex are unknown. Here we show that ApoM-S1P is dispensable for lymphocyte trafficking yet restrains lymphopoiesis by activating the S1P1 receptor on bone marrow lymphocyte progenitors. Mice that lacked ApoM (Apom(-/-)) had increased proliferation of Lin(-) Sca-1(+) cKit(+) haematopoietic progenitor cells (LSKs) and common lymphoid progenitors (CLPs) in bone marrow. Pharmacological activation or genetic overexpression of S1P1 suppressed LSK and CLP cell proliferation in vivo. ApoM was stably associated with bone marrow CLPs, which showed active S1P1 signalling in vivo. Moreover, ApoM-bound S1P, but not albumin-bound S1P, inhibited lymphopoiesis in vitro. Upon immune stimulation, Apom(-/-) mice developed more severe experimental autoimmune encephalomyelitis, characterized by increased lymphocytes in the central nervous system and breakdown of the blood-brain barrier. Thus, the ApoM-S1P-S1P1 signalling axis restrains the lymphocyte compartment and, subsequently, adaptive immune responses. Unique biological functions imparted by specific S1P chaperones could be exploited for novel therapeutic opportunities.

  6. Integrated In Silico Fragment-Based Drug Design: Case Study with Allosteric Modulators on Metabotropic Glutamate Receptor 5.

    Science.gov (United States)

    Bian, Yuemin; Feng, Zhiwei; Yang, Peng; Xie, Xiang-Qun

    2017-07-01

    GPCR allosteric modulators target at the allosteric binding pockets of G protein-coupled receptors (GPCRs) with indirect influence on the effects of an orthosteric ligand. Such modulators exhibit significant advantages compared to the corresponding orthosteric ligands, including better chemical tractability or physicochemical properties, improved selectivity, and reduced risk of oversensitization towards their receptors. Metabotropic glutamate receptor 5 (mGlu5), a member of class C GPCRs, is a promising therapeutic target for treating many central nervous system diseases. The crystal structure of mGlu5 in the complex with the negative allosteric modulator mavoglurant was recently reported, providing a fundamental model for designing new allosteric modulators. Computational fragment-based drug discovery represents a powerful scaffold-hopping and lead structure-optimization tool for drug design. In the present work, a set of integrated computational methodologies was first used, such as fragment library generation and retrosynthetic combinatorial analysis procedure (RECAP) for novel compound generation. Then, the compounds generated were assessed by benchmark dataset verification, docking studies, and QSAR model simulation. Subsequently, structurally diverse compounds, with reported or unreported scaffolds, can be observed from top 20 in silico synthesized compounds, which were predicted to be potential mGlu5 modulators. In silico compounds with reported scaffolds may fill SAR holes in known, patented series of mGlu5 modulators. And the generation of compounds without reported tests on mGluR indicates that our approach is doable for exploring and designing novel compounds. Our case study of designing allosteric modulators on mGlu5 demonstrated that the established computational fragment-based approach is a useful methodology for facilitating new compound design in the future.

  7. Influence of autoantibodies against AT1 receptor and AGTR1 polymorphisms on candesartan-based antihypertensive regimen: results from the study of optimal treatment in hypertensive patients with anti-AT1-receptor autoantibodies trial.

    Science.gov (United States)

    Sun, Yanxiang; Liao, Yuhua; Yuan, Yong; Feng, Li; Ma, Shihui; Wei, Feng; Wang, Min; Zhu, Feng

    2014-01-01

    The autoantibodies against angiotensin AT1 receptors (AT1-AAs) in patients with essential hypertension exhibited an agonistic action like angiotensin II and maintained high blood pressure (BP). Angiotensin II receptor gene (AGTR1) polymorphisms were associated with BP response to RAS inhibition in the hypertensive population. Furthermore, the BP response to AT1 receptor blockers varied significantly among individuals with hypertension. We hypothesized that the polymorphisms of the AGTR1 and AT1-AAs might affect antihypertensive response to AT1 receptor blockers based in patients with primary hypertension. Patients who received a candesartan-based regimen came from the SOT-AT1 study (Study of Optimal Treatment in Hypertensive Patients with Anti-AT1-Receptor Autoantibodies). The established enzyme-labeled immunosorbent assay was used to detect AT1-AAs in the sera of the patients. Genotype 3 single nucleotide polymorphisms in AGTR1 gene was used by DNA sequencing. The correlations among AT1-AAs, AGTR1 gene polymorphisms or haplotypes, and the antihypertensive effect candesartan-based were analyzed using SPSS. The percentage of systolic BP reduction that was candesartan-based was greater in AT1-AA positive groups than in AT1-AA negative ones (21 ± 8 vs. 18 ± 9; P = .001). Meanwhile, systolic BP reduction that was candesartan-based was more significant in the group of rs5186 AC genotypes than AA homozygotes after adjusting for other confounding factors (37.55 ± 13.7 vs. 32.47 ± 17.27 mm Hg; adjusted P = .028). Furthermore, haplotypes (GCC) and (AAC) had impacts on the antihypertensive effect of candesartan therapy. The AT1-AAs, AGTR1 gene polymorphisms and haplotypes solely or jointly have influences on candesartan-based antihypertensive response in patients with primary hypertension. Copyright © 2014 American Society of Hypertension. Published by Elsevier Inc. All rights reserved.

  8. New lower bound for the Capacitated Arc Routing Problem

    DEFF Research Database (Denmark)

    Wøhlk, Sanne

    2006-01-01

    We present a new lower bound, the Multiple Cuts Node Duplication Lower Bound, for the undirected Capacitated Arc Routing Problem.We prove that this new bound dominates the existing bounds for the problem. Computational results are also provided.......We present a new lower bound, the Multiple Cuts Node Duplication Lower Bound, for the undirected Capacitated Arc Routing Problem.We prove that this new bound dominates the existing bounds for the problem. Computational results are also provided....

  9. GPCR-ModSim: A comprehensive web based solution for modeling G-protein coupled receptors.

    Science.gov (United States)

    Esguerra, Mauricio; Siretskiy, Alexey; Bello, Xabier; Sallander, Jessica; Gutiérrez-de-Terán, Hugo

    2016-07-08

    GPCR-ModSim (http://open.gpcr-modsim.org) is a centralized and easy to use service dedicated to the structural modeling of G-protein Coupled Receptors (GPCRs). 3D molecular models can be generated from amino acid sequence by homology-modeling techniques, considering different receptor conformations. GPCR-ModSim includes a membrane insertion and molecular dynamics (MD) equilibration protocol, which can be used to refine the generated model or any GPCR structure uploaded to the server, including if desired non-protein elements such as orthosteric or allosteric ligands, structural waters or ions. We herein revise the main characteristics of GPCR-ModSim and present new functionalities. The templates used for homology modeling have been updated considering the latest structural data, with separate profile structural alignments built for inactive, partially-active and active groups of templates. We have also added the possibility to perform multiple-template homology modeling in a unique and flexible way. Finally, our new MD protocol considers a series of distance restraints derived from a recently identified conserved network of helical contacts, allowing for a smoother refinement of the generated models which is particularly advised when there is low homology to the available templates. GPCR- ModSim has been tested on the GPCR Dock 2013 competition with satisfactory results. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

    Energy Technology Data Exchange (ETDEWEB)

    Kaur, Navneet, E-mail: navneetkaur@pu.ac.in [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)

    2014-01-15

    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.

  11. Information-Theoretic Bounded Rationality and ε-Optimality

    Directory of Open Access Journals (Sweden)

    Daniel A. Braun

    2014-08-01

    Full Text Available Bounded rationality concerns the study of decision makers with limited information processing resources. Previously, the free energy difference functional has been suggested to model bounded rational decision making, as it provides a natural trade-off between an energy or utility function that is to be optimized and information processing costs that are measured by entropic search costs. The main question of this article is how the information-theoretic free energy model relates to simple ε-optimality models of bounded rational decision making, where the decision maker is satisfied with any action in an ε-neighborhood of the optimal utility. We find that the stochastic policies that optimize the free energy trade-off comply with the notion of ε-optimality. Moreover, this optimality criterion even holds when the environment is adversarial. We conclude that the study of bounded rationality based on ε-optimality criteria that abstract away from the particulars of the information processing constraints is compatible with the information-theoretic free energy model of bounded rationality.

  12. Bionic Control of Cheetah Bounding with a Segmented Spine

    Directory of Open Access Journals (Sweden)

    Chunlei Wang

    2016-01-01

    Full Text Available A cheetah model is built to mimic real cheetah and its mechanical and dimensional parameters are derived from the real cheetah. In particular, two joints in spine and four joints in a leg are used to realize the motion of segmented spine and segmented legs which are the key properties of the cheetah bounding. For actuating and stabilizing the bounding gait of cheetah, we present a bioinspired controller based on the state-machine. The controller mainly mimics the function of the cerebellum to plan the locomotion and keep the body balance. The haptic sensor and proprioception system are used to detect the trigger of the phase transition. Besides, the vestibular modulation could perceive the pitching angle of the trunk. At last, the cerebellum acts as the CPU to operate the information from the biological sensors. In addition, the calculated results are transmitted to the low-level controller to actuate and stabilize the cheetah bounding. Moreover, the delay feedback control method is employed to plan the motion of the leg joints to stabilize the pitching motion of trunk with the stability criterion. Finally, the cyclic cheetah bounding with biological properties is realized. Meanwhile, the stability and dynamic properties of the cheetah bounding gait are analyzed elaborately.

  13. Research on culture-bound syndromes: new directions.

    Science.gov (United States)

    Guarnaccia, P J; Rogler, L H

    1999-09-01

    The unprecedented inclusion of culture-bound syndromes in DSM-IV provides the opportunity for highlighting the need to study such syndromes and the occasion for developing a research agenda to study them. The growing ethnic and cultural diversity of the U.S. population presents a challenge to the mental health field to develop truly cross-cultural approaches to mental health research and services. In this article, the authors provide a critique of previous analyses of the relationship between culture-bound syndromes and psychiatric diagnoses. They highlight the problems in previous classificatory exercises, which tend to focus on subsuming the culture-bound syndromes into psychiatric categories and fail to fully investigate these syndromes on their own terms. A detailed research program based on four key questions is presented both to understand culture-bound syndromes within their cultural context and to analyze the relationship between these syndromes and psychiatric disorders. Results of over a decade of research on ataques de nervios, a Latino-Caribbean cultural syndrome, are used to illustrate this research program. The four questions focus on the nature of the phenomenon, the social-cultural location of sufferers, the relationship of culture-bound syndromes to psychiatric disorders, and the social and psychiatric history of the syndrome in the life course of the sufferer.

  14. Differential Labeling of Free and Disulfide-Bound Thiol Functions in Proteins

    NARCIS (Netherlands)

    Seiwert, B.; Hayen, H.; Karst, U.

    2008-01-01

    A method for the simultaneous determination of the number of free cysteine groups and disulfide-bound cysteine groups in proteins has been developed based on the sequential labeling of free and bound thiol functionalities with two ferrocene-based maleimide reagents. Liquid

  15. Micromechanical bounds for the elastic moduli of granular materials

    NARCIS (Netherlands)

    Kruyt, Nicolaas P.; Rothenburg, L.

    2002-01-01

    This study deals with bounds for the effective elastic moduli of granular materials in terms of micromechanical parameters. The case considered is that of two-dimensional isotropic assemblies of non-rotating particles with bonded contacts and a linear elastic contact constitutive relation. Based on

  16. The bounded retransmission protocol must be on time!

    NARCIS (Netherlands)

    Brinksma, Hendrik; d' Argenio, P.R.; Katoen, Joost P.; Ruys, T.C.; Tretmans, G.J.

    1997-01-01

    This paper concerns the transfer of files via a lossy communication channel. It formally specifies this file transfer service in a property-oriented way and investigates—using two different techniques—whether a given bounded retransmission protocol conforms to this service. This protocol is based on

  17. The Bounded Retransmission Protocol must be on time!

    NARCIS (Netherlands)

    d' Argenio, P.R.; Katoen, Joost P.; Ruys, T.C.; Tretmans, G.J.

    1997-01-01

    This paper concerns the transfer of files via a lossy communication channel. It formally specifies this file transfer service in a property-oriented way and investigates -using two different techniques -whether a given bounded retransmission protocol conforms to this service. This protocol is based

  18. Composable Security in the Bounded-Quantum-Storage Model

    NARCIS (Netherlands)

    S.D.C. Wehner (Stephanie); J. Wullschleger

    2008-01-01

    htmlabstractWe give a new, simulation-based, definition for security in the bounded-quantum-storage model, and show that this definition allows for sequential composition of protocols. Damgård et al. (FOCS ’05, CRYPTO ’07) showed how to securely implement bit commitment and oblivious transfer in the

  19. Composable security in the bounded-quantum-storage model

    NARCIS (Netherlands)

    S.D.C. Wehner (Stephanie); J. Wullschleger

    2007-01-01

    htmlabstractWe present a simplified framework for proving sequential composability in the quantum setting. In particular, we give a new, simulation-based, definition for security in the bounded-quantum-storage model, and show that this definition allows for sequential composition of protocols.

  20. In-medium K̄ interactions and bound states

    Directory of Open Access Journals (Sweden)

    Gal Avraham

    2014-01-01

    Full Text Available Correct treatment of subthreshold K̄ N dynamics is mandatory in K− -atom and K̄ -nuclear bound-state calculations, as demonstrated by using in-medium chirally-based models of K̄ N interactions. Recent studies of kaonic atom data reveal appreciable multi-nucleon contributions. K̄ -nuclear widths larger than 50 MeV are anticipated.

  1. Chiral Symmetry, Heavy Quark Symmetry and Bound States

    OpenAIRE

    Yoshida, Yuhsuke

    1995-01-01

    I investigate the bound state problems of lowest-lying mesons and heavy mesons. Chiral symmetry is essential when one consider lowest-lying mesons. Heavy quark symmetry plays an central role in considering the semi-leptonic form factors of heavy mesons. Various properties based on the symmetries are revealed using Bethe-Salpeter equations.

  2. Organizational coordination and costly communication with boundedly rational agents

    DEFF Research Database (Denmark)

    Dietrichson, Jens; Jochem, Torsten

    How does costly communication affect organizational coordination? This paper develops a model of costly communication based on the weakest-link game and boundedly rational agents. Solving for the stochastically stable states, we find that communication increases the possibilities for efficient...

  3. Coherent structures in wall-bounded turbulence.

    Science.gov (United States)

    Dennis, David J C

    2015-01-01

    The inherent difficulty of understanding turbulence has led to researchers attacking the topic in many different ways over the years of turbulence research. Some approaches have been more successful than others, but most only deal with part of the problem. One approach that has seen reasonable success (or at least popularity) is that of attempting to deconstruct the complex and disorganised turbulent flow field into to a set of motions that are in some way organised. These motions are generally called "coherent structures". There are several strands to this approach, from identifying the coherent structures within the flow, defining their characteristics, explaining how they are created, sustained and destroyed, to utilising their features to model the turbulent flow. This review considers research on coherent structures in wall-bounded turbulent flows: a class of flow which is extremely interesting to many scientists (mainly, but not exclusively, physicists and engineers) due to their prevalence in nature, industry and everyday life. This area has seen a lot of activity, particularly in recent years, much of which has been driven by advances in experimental and computational techniques. However, several ideas, developed many years ago based on flow visualisation and intuition, are still both informative and relevant. Indeed, much of the more recent research is firmly indebted to some of the early pioneers of the coherent structures approach. Therefore, in this review, selected historical research is discussed along with the more contemporary advances in an attempt to provide the reader with a good overview of how the field has developed and to highlight the perspicacity of some of the early researchers, as well as providing an overview of our current understanding of the role of coherent structures in wall-bounded turbulent flows.

  4. Coherent structures in wall-bounded turbulence

    Directory of Open Access Journals (Sweden)

    David J.C. Dennis

    2015-06-01

    Full Text Available The inherent difficulty of understanding turbulence has led to researchers attacking the topic in many different ways over the years of turbulence research. Some approaches have been more successful than others, but most only deal with part of the problem. One approach that has seen reasonable success (or at least popularity is that of attempting to deconstruct the complex and disorganised turbulent flow field into to a set of motions that are in some way organised. These motions are generally called "coherent structures". There are several strands to this approach, from identifying the coherent structures within the flow, defining their characteristics, explaining how they are created, sustained and destroyed, to utilising their features to model the turbulent flow. This review considers research on coherent structures in wall-bounded turbulent flows: a class of flow which is extremely interesting to many scientists (mainly, but not exclusively, physicists and engineers due to their prevalence in nature, industry and everyday life. This area has seen a lot of activity, particularly in recent years, much of which has been driven by advances in experimental and computational techniques. However, several ideas, developed many years ago based on flow visualisation and intuition, are still both informative and relevant. Indeed, much of the more recent research is firmly indebted to some of the early pioneers of the coherent structures approach. Therefore, in this review, selected historical research is discussed along with the more contemporary advances in an attempt to provide the reader with a good overview of how the field has developed and to highlight the perspicacity of some of the early researchers, as well as providing an overview of our current understanding of the role of coherent structures in wall-bounded turbulent flows.

  5. Anisotropy-induced photonic bound states in the continuum

    Science.gov (United States)

    Gomis-Bresco, Jordi; Artigas, David; Torner, Lluis

    2017-03-01

    Bound states in the continuum (BICs) are radiationless localized states embedded in the part of the parameter space that otherwise corresponds to radiative modes. Many decades after their original prediction and early observations in acoustic systems, such states have been demonstrated recently in photonic structures with engineered geometries. Here, we put forward a mechanism, based on waveguiding structures that contain anisotropic birefringent materials, that affords the existence of BICs with fundamentally new properties. In particular, anisotropy-induced BICs may exist in symmetric as well as in asymmetric geometries; they may form in tunable angular propagation directions; their polarization may be pure transverse electric, pure transverse magnetic or full vector with tunable polarization hybridity; and they may be the only possible bound states of properly designed structures, and thus appear as a discrete, isolated bound state embedded in a whole sea of radiative states.

  6. Research on Bounded Rationality of Fuzzy Choice Functions

    Directory of Open Access Journals (Sweden)

    Xinlin Wu

    2014-01-01

    Full Text Available The rationality of a fuzzy choice function is a hot research topic in the study of fuzzy choice functions. In this paper, two common fuzzy sets are studied and analyzed in the framework of the Banerjee choice function. The complete rationality and bounded rationality of fuzzy choice functions are defined based on the two fuzzy sets. An assumption is presented to study the fuzzy choice function, and especially the fuzzy choice function with bounded rationality is studied combined with some rationality conditions. Results show that the fuzzy choice function with bounded rationality also satisfies some important rationality conditions, but not vice versa. The research gives supplements to the investigation in the framework of the Banerjee choice function.

  7. Viscosity bound for anisotropic superfluids in higher derivative gravity

    Energy Technology Data Exchange (ETDEWEB)

    Bhattacharyya, Arpan; Roychowdhury, Dibakar [Centre for High Energy Physics, Indian Institute of Science,C.V. Raman Avenue, Bangalore 560012 (India)

    2015-03-11

    In the present paper, based on the principles of gauge/gravity duality we analytically compute the shear viscosity to entropy (η/s) ratio corresponding to the super fluid phase in Einstein Gauss-Bonnet gravity. From our analysis we note that the ratio indeed receives a finite temperature correction below certain critical temperature (Tbound for the Gauss-Bonnet coupling (λ) corresponding to the symmetry broken phase and note that the upper bound on the coupling does not seem to change as long as we are close to the critical point of the phase diagram. However the corresponding lower bound of the η/s ratio seems to get modified due to the finite temperature effects.

  8. Breaking of PT Symmetry in Bounded and Unbounded Scattering Systems

    Directory of Open Access Journals (Sweden)

    Philipp Ambichl

    2013-12-01

    Full Text Available PT-symmetric scattering systems with balanced gain and loss can undergo a symmetry-breaking transition in which the eigenvalues of the nonunitary scattering matrix change their phase shifts from real to complex values. We relate the PT-symmetry-breaking points of such an unbounded scattering system to those of the underlying bounded systems. In particular, we show how the PT thresholds in the scattering matrix of the unbounded system translate into analogous transitions in the Robin boundary conditions of the corresponding bounded systems. Based on this relation, we argue and then confirm that the PT transitions in the scattering matrix are, under very general conditions, entirely insensitive to a variable coupling strength between the bounded region and the unbounded asymptotic region, a result that can be tested experimentally and visualized using the concept of Smith charts.

  9. Breaking of PT Symmetry in Bounded and Unbounded Scattering Systems

    Science.gov (United States)

    Ambichl, Philipp; Makris, Konstantinos G.; Ge, Li; Chong, Yidong; Stone, A. Douglas; Rotter, Stefan

    2013-12-01

    PT-symmetric scattering systems with balanced gain and loss can undergo a symmetry-breaking transition in which the eigenvalues of the non-unitary scattering matrix change their phase shifts from real to complex values. We relate the PT-symmetry breaking points of such an unbounded scattering system to those of underlying bounded systems. In particular, we show how the PT-thresholds in the scattering matrix of the unbounded system translate into analogous transitions in the Robin boundary conditions of the corresponding bounded systems. Based on this relation, we argue and then confirm that the PT-transitions in the scattering matrix are, under very general conditions, entirely insensitive to a variable coupling strength between the bounded region and the unbounded asymptotic region, a result that can be tested experimentally and visualized using the concept of Smith charts.

  10. Bounds for the propagation speed of combustion flames

    Energy Technology Data Exchange (ETDEWEB)

    Fort, Joaquim [Departament de FIsica, Universitat de Girona, Campus de Montilivi, 17071 Girona, Catalonia (Spain); Campos, Daniel [Grup de FIsica EstadIstica, Departament de FIsica, Universitat Autonoma de Barcelona, E-08193 Bellaterra (Spain); Gonzalez, Josep R [Grup de Mecanica de Fluids, Departament d' Enginyeria Mecanica, Universitat de Girona, Campus de Montilivi, 17071 Girona, Catalonia (Spain); Velayos, Joaquim [Grup de Mecanica de Fluids, Departament d' Enginyeria Mecanica, Universitat de Girona, Campus de Montilivi, 17071 Girona, Catalonia (Spain)

    2004-07-23

    We focus on a combustion model for premixed flames based on two coupled equations determining the spatial dynamics of temperature and fuel density. We rewrite these equations as a classical reaction-diffusion model, so that we can apply some known methods for the prediction of lower and upper bounds to the front speed. The predictions are compared to simulations, which show that our new bounds substantially improve those following from the linearization method, used in the previous work of Fort et al (2000 J. Phys. A: Math. Gen. 33 6953). Radiative losses lead to pulses rather than fronts. We find a bound for their speed which (in contrast to the linearization one) correctly predicts the order of magnitude of the flame speed.

  11. Bounded rationality and learning in complex markets

    NARCIS (Netherlands)

    Hommes, C.H.; Barkely Rosser Jr, J.

    2009-01-01

    This chapter reviews some work on bounded rationality, expectation formation and learning in complex markets, using the familiar demand-supply cobweb model. We emphasize two stories of bounded rationality, one story of adaptive learning and another story of evolutionary selection. According to the

  12. Bounded rationality and learning in complex markets

    NARCIS (Netherlands)

    Hommes, C.H.

    2007-01-01

    This chapter reviews some work on bounded rationality, expectation formation and learning in complex markets, using the familiar demand-supply cobweb model. We emphasize two stories of bounded rationality, one story of adaptive learning and another story of evolutionary selection. According to the

  13. Spatial coagulation with bounded coagulation rate

    OpenAIRE

    Bailleul, Ismael

    2010-01-01

    We prove that the spatial coagulation equation with bounded coagulation rate is well-posed for all times in a given class of kernels if the convection term of the underlying particle dynamics has divergence bounded below by a positive constant. Multiple coagulations, fragmentation and scattering are also considered.

  14. Schroedinger upper bounds to semirelativistic eigenvalues

    Energy Technology Data Exchange (ETDEWEB)

    Hall, Richard L [Department of Mathematics and Statistics, Concordia University, 1455 de Maisonneuve Boulevard West, Montreal, Quebec, H3G 1M8 (Canada); Lucha, Wolfgang [Institut fuer Hochenergiephysik, Oesterreichische Akademie der Wissenschaften, Nikolsdorfergasse 18, A-1050 Vienna (Austria)

    2005-09-16

    Problems posed by semirelativistic Hamiltonians of the form H = {radical}(m{sup 2} + p{sup 2}) + V(r) are studied. It is shown that energy upper bounds can be constructed in terms of certain related Schroedinger operators; these bounds include free parameters which can be chosen optimally.

  15. No-arbitrage bounds for financial scenarios

    DEFF Research Database (Denmark)

    Geyer, Alois; Hanke, Michael; Weissensteiner, Alex

    2014-01-01

    We derive no-arbitrage bounds for expected excess returns to generate scenarios used in financial applications. The bounds allow to distinguish three regions: one where arbitrage opportunities will never exist, a second where arbitrage may be present, and a third, where arbitrage opportunities...

  16. Nonatomic dual bakery algorithm with bounded tokens

    NARCIS (Netherlands)

    Aravind, Alex A.; Hesselink, Wim H.

    A simple mutual exclusion algorithm is presented that only uses nonatomic shared variables of bounded size, and that satisfies bounded overtaking. When the shared variables behave atomically, it has the first-come-first-served property (FCFS). Nonatomic access makes information vulnerable. The

  17. Polynomially Bounded Sequences and Polynomial Sequences

    Directory of Open Access Journals (Sweden)

    Okazaki Hiroyuki

    2015-09-01

    Full Text Available In this article, we formalize polynomially bounded sequences that plays an important role in computational complexity theory. Class P is a fundamental computational complexity class that contains all polynomial-time decision problems [11], [12]. It takes polynomially bounded amount of computation time to solve polynomial-time decision problems by the deterministic Turing machine. Moreover we formalize polynomial sequences [5].

  18. Upper Bounds on Numerical Approximation Errors

    DEFF Research Database (Denmark)

    Raahauge, Peter

    2004-01-01

    This paper suggests a method for determining rigorous upper bounds on approximationerrors of numerical solutions to infinite horizon dynamic programming models.Bounds are provided for approximations of the value function and the policyfunction as well as the derivatives of the value function...

  19. On the range of completely bounded maps

    Directory of Open Access Journals (Sweden)

    Richard I. Loebl

    1978-01-01

    Full Text Available It is shown that if every bounded linear map from a C*-algebra α to a von Neumann algebra β is completely bounded, then either α is finite-dimensional or β⫅⊗Mn, where is a commutative von Neumann algebra and Mn is the algebra of n×n complex matrices.

  20. A polynomial lower bound for testing monotonicity

    NARCIS (Netherlands)

    A. Belovs (Aleksandr); Blais, E. (Eric)

    2016-01-01

    textabstractWe show that every algorithm for testing n-variate Boolean functions for monotonicity has query complexity Ω(n1/4). All previous lower bounds for this problem were designed for nonadaptive algorithms and, as a result, the best previous lower bound for general (possibly adaptive)

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

    Science.gov (United States)

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

    2016-09-01

    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 reperfusion-induced cardiomyocyte death when ischemic injury of heart has already occurred; that is, opioids can mimic preconditioning and postconditioning phenomena. Furthermore, opioids are also effective in preventing ischemia-induced arrhythmias. © 2016 Wiley Periodicals, Inc.

  2. In vivo evaluation of new carfentanil-based radioligands for the mu opiate receptor

    Energy Technology Data Exchange (ETDEWEB)

    Jewett, Douglas M.; Kilbourn, Michael R. E-mail: mkilbour@umich.edu

    2004-04-01

    Eight derivatives of [{sup 11}C]carfentanil were evaluated as alternative mu opiod receptor radioligands with the potential for lower pharmacological activity, faster pharmacokinetics, and/or lower non-specific binding. Derivatives with aryl ring substituents or alkyl group substitutions were prepared in carbon-11 labeled form and examined for initial brain uptake and regional brain tissue pharmacokinetics in mouse brain. Promising derivatives with chloro, methoxy and methyl substituents on one aryl ring were then evaluated for specific binding in an equilibrium infusion rat model of regional brain distributions. Although no derivatives were identified with improved pharmacokinetics or lower non-specific binding, several derivatives show acceptable in vivo specific binding properties and may deserve further evaluation as less potent and thus safer compounds for in vivo imaging studies.

  3. 2,5-Diphenylfuran-based pure antiestrogens with selectivity for the estrogen receptor alpha.

    Science.gov (United States)

    Zimmermann, Jochen; Liebl, Renate; von Angerer, Erwin

    2005-02-01

    The estrogen receptor alpha (ERalpha) is understood to play an important role in the progression of breast cancer. Therefore, pure antiestrogens with a preference for this receptor form are of interest as new agents for the treatment of this malignancy. Several chemical structures with selective binding affinity for ERalpha have been identified and might be useful for the synthesis of ERalpha-selective pure antiestrogens. In this study we applied the 2,5-diphenylfuran system which is closely related to the triphenylfurans described by others. Various side chains with amino and/or sulfur functions were linked to C3 to convert the furans to estrogen antagonists without residual estrogenic activity. The degree of alpha-selectivity which ranges from 2.5- to 236-fold is strongly influenced by the alkyl group at C4. Antiestrogenic potency was determined in MCF-7/2a breast cancer cells stably transfected with a luciferase gene under the control of an ERE. The 2,5-bis(4-hydroxyphenyl)furan with an ethyl substituent and a 6-[N-methyl-N-(3-pentylthiopropyl)amino]hexyl side chain exerted the strongest antiestrogenic effect in this series with an IC(50) value of 50 nM in cells stimulated with 1 nM estradiol. The RBA values of this derivative were 18% (ERalpha) and 3.4% (ERbeta) of estradiol, respectively. It inhibited the growth of wild-type MCF-7 cells with an IC(50) value of 22 nM. The data show that the 2,5-diphenylfuran system is appropriate for the development of pure antiestrogens with preference for ERalpha.

  4. Retinoid and thiazolidinedione therapies in melanoma: an analysis of differential response based on nuclear hormone receptor expression

    Directory of Open Access Journals (Sweden)

    Pugazhenthi Umarani

    2009-03-01

    Full Text Available Abstract Background Metastatic melanoma has a high mortality rate and suboptimal therapeutic options. Molecular targeting may be beneficial using the rexinoid LGD1069, a retinoid × receptor selective agonist, and thiazolidinediones (TZD, PPARγ selective ligands, as novel treatments. Results Mouse xenograft models with human melanoma cell lines [A375(DRO or M14(5–16] were treated for 4 weeks with daily vehicle, RXR agonist (rexinoid, LGD1069, 30 mg/kg/d, PPARγ agonist (TZD, rosiglitazone, 10 mg/kg/d or combination. A375(DRO tumor growth was significantly inhibited by either ligand alone and the combination had an additive effect. M14(5–16 tumors only responded to LGD1069 100 mg/kg/day. A375(DRO sublines resistant to rexinoid, TZD and combination were generated and all three sublines had reduced PPARγ expression but preserved RXR expression. shRNA knockdown of PPARγ or RXRγ attenuated the rexinoid, TZD and combination ligand-mediated decreased proliferation in A375(DRO cells. Rexinoid (LGD1069 and retinoid (TTNPB treatment of M14(5–16 cells resulted in decreased proliferation that was additive with combination of both rexinoid and retinoid. shRNA knockdown of RXRγ resulted in a decreased response to either ligand. Conclusion A375 (DRO melanoma cell growth is inhibited by rexinoid and TZD treatment, and this response is dependent on RXR and PPARγ receptor expression. M14 (5–16 melanoma cell growth is inhibited by rexinoid and retinoid treatment, and this response is dependent on RXR expression. These findings may help guide molecular-based treatment strategies in melanoma and provide insight for mechanisms of resistance to nuclear receptor targeted therapies in certain cancers.

  5. Cis and trans regulatory mechanisms control AP2-mediated B cell receptor endocytosis via select tyrosine-based motifs.

    Directory of Open Access Journals (Sweden)

    Kathleen Busman-Sahay

    Full Text Available Following antigen recognition, B cell receptor (BCR-mediated endocytosis is the first step of antigen processing and presentation to CD4+ T cells, a crucial component of the initiation and control of the humoral immune response. Despite this, the molecular mechanism of BCR internalization is poorly understood. Recently, studies of activated B cell-like diffuse large B cell lymphoma (ABC DLBCL have shown that mutations within the BCR subunit CD79b leads to increased BCR surface expression, suggesting that CD79b may control BCR internalization. Adaptor protein 2 (AP2 is the major mediator of receptor endocytosis via clathrin-coated pits. The BCR contains five putative AP2-binding YxxØ motifs, including four that are present within two immunoreceptor tyrosine-based activation motifs (ITAMs. Using a combination of in vitro and in situ approaches, we establish that the sole mediator of AP2-dependent BCR internalization is the membrane proximal ITAM YxxØ motif in CD79b, which is a major target of mutation in ABC DLBCL. In addition, we establish that BCR internalization can be regulated at a minimum of two different levels: regulation of YxxØ AP2 binding in cis by downstream ITAM-embedded DCSM and QTAT regulatory elements and regulation in trans by the partner cytoplasmic domain of the CD79 heterodimer. Beyond establishing the basic rules governing BCR internalization, these results illustrate an underappreciated role for ITAM residues in controlling clathrin-dependent endocytosis and highlight the complex mechanisms that control the activity of AP2 binding motifs in this receptor system.

  6. Cis and trans regulatory mechanisms control AP2-mediated B cell receptor endocytosis via select tyrosine-based motifs.

    Science.gov (United States)

    Busman-Sahay, Kathleen; Drake, Lisa; Sitaram, Anand; Marks, Michael; Drake, James R

    2013-01-01

    Following antigen recognition, B cell receptor (BCR)-mediated endocytosis is the first step of antigen processing and presentation to CD4+ T cells, a crucial component of the initiation and control of the humoral immune response. Despite this, the molecular mechanism of BCR internalization is poorly understood. Recently, studies of activated B cell-like diffuse large B cell lymphoma (ABC DLBCL) have shown that mutations within the BCR subunit CD79b leads to increased BCR surface expression, suggesting that CD79b may control BCR internalization. Adaptor protein 2 (AP2) is the major mediator of receptor endocytosis via clathrin-coated pits. The BCR contains five putative AP2-binding YxxØ motifs, including four that are present within two immunoreceptor tyrosine-based activation motifs (ITAMs). Using a combination of in vitro and in situ approaches, we establish that the sole mediator of AP2-dependent BCR internalization is the membrane proximal ITAM YxxØ motif in CD79b, which is a major target of mutation in ABC DLBCL. In addition, we establish that BCR internalization can be regulated at a minimum of two different levels: regulation of YxxØ AP2 binding in cis by downstream ITAM-embedded DCSM and QTAT regulatory elements and regulation in trans by the partner cytoplasmic domain of the CD79 heterodimer. Beyond establishing the basic rules governing BCR internalization, these results illustrate an underappreciated role for ITAM residues in controlling clathrin-dependent endocytosis and highlight the complex mechanisms that control the activity of AP2 binding motifs in this receptor system.

  7. Oxytocin and vasopressin receptor gene variation as a proximate base for inter- and intraspecific behavioral differences in bonobos and chimpanzees.

    Science.gov (United States)

    Staes, Nicky; Stevens, Jeroen M G; Helsen, Philippe; Hillyer, Mia; Korody, Marisa; Eens, Marcel

    2014-01-01

    Recent literature has revealed the importance of variation in neuropeptide receptor gene sequences in the regulation of behavioral phenotypic variation. Here we focus on polymorphisms in the oxytocin receptor gene (OXTR) and vasopressin receptor gene 1a (Avpr1a) in chimpanzees and bonobos. In humans, a single nucleotide polymorphism (SNP) in the third intron of OXTR (rs53576 SNP (A/G)) is linked with social behavior, with the risk allele (A) carriers showing reduced levels of empathy and prosociality. Bonobos and chimpanzees differ in these same traits, therefore we hypothesized that these differences might be reflected in variation at the rs53576 position. We sequenced a 320 bp region surrounding rs53576 but found no indications of this SNP in the genus Pan. However, we identified previously unreported SNP variation in the chimpanzee OXTR sequence that differs from both humans and bonobos. Humans and bonobos have previously been shown to have a more similar 5' promoter region of Avpr1a when compared to chimpanzees, who are polymorphic for the deletion of ∼ 360 bp in this region (+/- DupB) which includes a microsatellite (RS3). RS3 has been linked with variation in levels of social bonding, potentially explaining part of the interspecies behavioral differences found in bonobos, chimpanzees and humans. To date, results for bonobos have been based on small sample sizes. Our results confirmed that there is no DupB deletion in bonobos with a sample size comprising approximately 90% of the captive founder population, whereas in chimpanzees the deletion of DupB had the highest frequency. Because of the higher frequency of DupB alleles in our bonobo population, we suggest that the presence of this microsatellite may partly reflect documented differences in levels of sociability found in bonobos and chimpanzees.

  8. Tyrosine-based signal mediates LRP6 receptor endocytosis and desensitization of Wnt/β-catenin pathway signaling.

    Science.gov (United States)

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

    2014-10-03

    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. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  9. Oxytocin and vasopressin receptor gene variation as a proximate base for inter- and intraspecific behavioral differences in bonobos and chimpanzees.

    Directory of Open Access Journals (Sweden)

    Nicky Staes

    Full Text Available Recent literature has revealed the importance of variation in neuropeptide receptor gene sequences in the regulation of behavioral phenotypic variation. Here we focus on polymorphisms in the oxytocin receptor gene (OXTR and vasopressin receptor gene 1a (Avpr1a in chimpanzees and bonobos. In humans, a single nucleotide polymorphism (SNP in the third intron of OXTR (rs53576 SNP (A/G is linked with social behavior, with the risk allele (A carriers showing reduced levels of empathy and prosociality. Bonobos and chimpanzees differ in these same traits, therefore we hypothesized that these differences might be reflected in variation at the rs53576 position. We sequenced a 320 bp region surrounding rs53576 but found no indications of this SNP in the genus Pan. However, we identified previously unreported SNP variation in the chimpanzee OXTR sequence that differs from both humans and bonobos. Humans and bonobos have previously been shown to have a more similar 5' promoter region of Avpr1a when compared to chimpanzees, who are polymorphic for the deletion of ∼ 360 bp in this region (+/- DupB which includes a microsatellite (RS3. RS3 has been linked with variation in levels of social bonding, potentially explaining part of the interspecies behavioral differences found in bonobos, chimpanzees and humans. To date, results for bonobos have been based on small sample sizes. Our results confirmed that there is no DupB deletion in bonobos with a sample size comprising approximately 90% of the captive founder population, whereas in chimpanzees the deletion of DupB had the highest frequency. Because of the higher frequency of DupB alleles in our bonobo population, we suggest that the presence of this microsatellite may partly reflect documented differences in levels of sociability found in bonobos and chimpanzees.

  10. Some Bounds on the Deviation Probability for Sums of Nonnegative Random Variables Using Upper Polynomials, Moment and Probability Generating Functions

    OpenAIRE

    From, Steven G.

    2010-01-01

    We present several new bounds for certain sums of deviation probabilities involving sums of nonnegative random variables. These are based upon upper bounds for the moment generating functions of the sums. We compare these new bounds to those of Maurer [2], Bernstein [4], Pinelis [16], and Bentkus [3]. We also briefly discuss the infinitely divisible distributions case.

  11. How Microelectrode Array-Based Chick Forebrain Neuron Biosensors Respond to Glutamate NMDA Receptor Antagonist AP5 and GABAA Receptor Antagonist Musimol.

    Science.gov (United States)

    Kuang, Serena Y; Yang, Xiaoqi; Wang, Zhonghai; Huang, Ting; Kindy, Mark; Xi, Tingfei; Gao, Bruce Z

    2016-09-01

    We have established a long-term, stable primary chick forebrain neuron (FBN) culture on a microelectrode array platform as a biosensor system for neurotoxicant screening and for neuroelectrophysiological studies for multiple purposes. This paper reports some of our results, which characterize the biosensor pharmacologically. Dose-response experiments were conducted using NMDA receptor antagonist AP5 and GABAA receptor agonist musimol (MUS). The chick FBN biosensor (C-FBN-biosensor) responds to the two agents in a pattern similar to that of rodent counterparts; the estimated EC50s (the effective concentration that causes 50% inhibition of the maximal effect) are 2.3 μM and 0.25 μM, respectively. Intercultural and intracultural reproducibility and long-term reusability of the C-FBN-biosensor are addressed and discussed. A phenomenon of sensitization of the biosensor that accompanies intracultural reproducibility in paired dose-response experiments for the same agent (AP5 or MUS) is reported. The potential application of the C-FBN-biosensor as an alternative to rodent biosensors in shared sensing domains (NMDA receptor and GABAA receptor) is suggested.

  12. How microelectrode array-based chick forebrain neuron biosensors respond to glutamate NMDA receptor antagonist AP5 and GABAA receptor antagonist musimol

    Directory of Open Access Journals (Sweden)

    Serena Y. Kuang

    2016-09-01

    Full Text Available We have established a long-term, stable primary chick forebrain neuron (FBN culture on a microelectrode array platform as a biosensor system for neurotoxicant screening and for neuroelectrophysiological studies for multiple purposes. This paper reports some of our results, which characterize the biosensor pharmacologically. Dose-response experiments were conducted using NMDA receptor antagonist AP5 and GABAA receptor agonist musimol (MUS. The chick FBN biosensor (C-FBN-biosensor responds to the two agents in a pattern similar to that of rodent counterparts; the estimated EC50s (the effective concentration that causes 50% inhibition of the maximal effect are 2.3 μM and 0.25 μM, respectively. Intercultural and intracultural reproducibility and long-term reusability of the C-FBN-biosensor are addressed and discussed. A phenomenon of sensitization of the biosensor that accompanies intracultural reproducibility in paired dose-response experiments for the same agent (AP5 or MUS is reported. The potential application of the C-FBN-biosensor as an alternative to rodent biosensors in shared sensing domains (NMDA receptor and GABAA receptor is suggested.

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

    DEFF Research Database (Denmark)

    Hansen, Kasper Bø; Mullasseril, Praseeda; Dawit, Sara

    2010-01-01

    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 describ...

  14. Polyaza cryptand receptor selective for dihydrogen phosphate.

    Science.gov (United States)

    Mateus, Pedro; Delgado, Rita; Brandão, Paula; Félix, Vítor

    2009-11-20

    A hexaamine cage with pyridyl spacers was synthesized in good yield by a [2+3] Schiff-base condensation followed by sodium borohydride reduction. The protonation constants of the receptor as well as its association constants with Cl(-), NO(3)(-), AcO(-), ClO(4)(-), SO(4)(2-), H(2)PO(4)(-), and H(2)AsO(4)(-) were determined by potentiometry at 298.2 +/- 0.1 K in H(2)O/MeOH (50:50 v/v) and at ionic strength 0.10 +/- 0.01 M in KTsO. These studies revealed that although dihydrogen phosphate is less charged than sulfate, it is still appreciably bound by the receptor at low pH, suggesting that the pyridyl nitrogen is accepting hydrogen bonds from dihydrogen phosphate. It is also shown that dihydrogen phosphate is capable of effectively competing with sulfate for the receptor at higher pH, being selective for hydrogen phosphate at pH about 7.0. (31)P NMR experiments supported these findings. The fact that the receptor shows such a marked preference for hydrogen phosphate based mainly in its hydrogen bond accepting/donating ability in a highly competitive medium such as water/methanol mixed solvent is quite remarkable. Single-crystal X-ray diffraction determinations of anion associations between H(6)pyr(6+) receptor and nitrate, sulfate, and phosphate are consistent with the existence of [(H(6)pyr)(NO(3))(3)(H(2)O)(3)](3+), [(H(6)pyr)(SO(4))(2)(H(2)O)(4)](2+), and [(H(6)pyr)(HPO(4))(2)(H(2)PO(4))(H(2)O)(2)](+) cations. One nitrate anion is embedded into the H(6)pyr(6+) cage of the first supermolecule whereas in the second and third ones the anions are located in the periphery of the macrobicycle.

  15. Spatial Turing-type Pattern Formation in a Model of Signal Transduction Involving Membrane-based Receptors Coupled by G Proteins

    Directory of Open Access Journals (Sweden)

    Wannapong Triampo

    2006-01-01

    Full Text Available In this paper, a model of signaling pathways involving G proteins is investigated. The model incorporates reaction-diffusion mechanisms in which various reactants participate inside and on the extra-cellular surface membrane. The messenger molecules may diffuse over the surface of the cell membrane and signal transduction across the cell membrane is mediated by membrane receptor bound proteins which connect the genetically controlled biochemical intra-cellular reactions to the production of the second messenger, leading to desired functional responses. Dynamic and steady-state properties of the model are then investigated through weakly nonlinear stability analysis. Turing-type patterns are shown to form robustly under different delineating conditions on the system parameters. The theoretical predictions are then discussed in the context of some recently reported experimental evidence.

  16. Photoinduced electron transfer fluorometric Hg(II) chemosensor based on a BODIPY armed with a tetrapod receptor.

    Science.gov (United States)

    Culzoni, M J; Muñoz de la Peña, A; Machuca, A; Goicoechea, H C; Brasca, R; Babiano, R

    2013-12-15

    From the great variety of BODIPY based-chemosensors able to determine Hg(2+), only a small portion has been applied to its determination in environmental and/or biological samples. The lack of studies on the analytical performance of the latter sensors makes interesting the development of investigations oriented to their possible analytical applications. The synthesis of a BODIPY derivative armed with a tetrapod receptor is described. The procedure is based on a previous publication, and the modifications performed to improve the synthesis include alternative procedures with different objectives, as the consecution of a multigram synthesis, improving the low yields of some of the previously proposed procedure steps, simplifying the experimental steps, achieving the desired purity requirements for use with analytical purposes, and enriching the characterization of the implied structures. The characteristics of its selectivity towards Hg(2+) have been investigated, and the OFF-ON fluorometric response, based on a photo-electron transfer (PET) mechanism, served as the base for the development of a method able to determine Hg(2+) in environmental waters at ng mL(-1) levels. The intrinsic fluorescence of the BODIPY core is inhibited and the probe exhibits a weak fluorescence (i.e. "OFF" state due to the deactivating PET effect). Upon complexation, Hg(2+) interacts with the lone-pair electrons on the nitrogen atoms of the receptor moiety so that the electronic transfer from the receptor to the photo-excited fluorophore is slowed down or switched off (i.e. "ON" state due to the suppression of the deactivating PET effect by coordination of the analyte to the probe). Regarding the complex photostability in aqueous solution, it is mandatory to conduct the experiments at darkness due to its photodegradation. The stoichiometry studies indicated a 1:2 relationship for the BODIPY-Hg(2+) complex. The high selectivity towards mercuric ions is considerably influenced by pH, being

  17. Blockade of patch-based μ opioid receptors in the striatum attenuates methamphetamine-induced conditioned place preference and reduces activation of the patch compartment.

    Science.gov (United States)

    Horner, Kristen A; Logan, Mary Caroline; Fisher, Trevor J; Logue, Jordan B

    2017-02-05

    The behavioral effects of methamphetamine (METH) are mediated by the striatum, which is divided into the patch compartment, which mediates limbic and reward functions, and the matrix compartment, which mediates sensorimotor tasks. METH treatment results in repetitive behavior that is related to enhanced relative activation of the patch versus the matrix compartment. The patch, but not the matrix compartment contains a high density of μ opioid receptors, and localized blockade of patch-based μ opioid receptors attenuates METH-induced patch-enhanced activity and repetitive behaviors. Numerous studies have examined patch-enhanced activity and the contribution of patch-associated μ opioid receptors to METH-induced repetitive behavior, but it is not known whether patch-enhanced activity occurs during METH-mediated reward, nor is it known if patch-based μ opioid receptors contribute to METH reward. The goals of this study were to determine if blockade of patch-based μ opioid receptors alters METH-induced conditioned place preference (CPP), as well activation of the patch and matrix compartments following METH-mediated CPP. A biased conditioning paradigm was used to assess CPP, and conditioning occurred over an 8-d period. Animals were bilaterally infused in the striatum with the μ-specific antagonist CTAP or vehicle prior to conditioning. Animals were tested for preference 24h after the last day of conditioning, sacrificed and the brains processed for immunohistochemistry. Blockade of patch-based μ opioid receptors reduced METH-induced CPP, and reduced patch-enhanced c-Fos expression in the striatum following METH-mediated CPP. These data indicate that patch-enhanced activity is associated with METH-mediated reward and patch-based μ opioid receptors contribute to this phenomenon. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Angiotensin II receptor blockers and risk of acute pancreatitis - a population based case-control study in Sweden.

    Science.gov (United States)

    Bexelius, Tomas S; Ljung, Rickard; Mattsson, Fredrik; Lu, Yunxia; Lindblad, Mats

    2017-03-07

    Acute pancreatitis is a potentially lethal disease, with a rising incidence in the Western world. Yet, no pharmacological prevention or specific treatment for acute pancreatitis exists. Also, the connection with severity of acute pancreatitis is unknown. Experimental and epidemiological research suggests a protective effect of angiotensin II receptor blockers. During 2006 to 2008, we performed a nationwide case-control study on Swedish residents aged 40-84 years. First-time cases with acute pancreatitis were identified in the National Patient Register and data on dispensed prescriptions was retrieved from the Prescribed Drug Register. Controls were randomly selected from the general population in Sweden frequency-matched on sex, age, and calendar year. To estimate relative risk of acute pancreatitis, by degree of severity, among users of angiotensin II receptor blockers, as compared to non-users, we used multivariable logistic regression analysis to calculate odds ratios (OR) with 95% confidence interval (CI). Among 6,161 cases of acute pancreatitis and 61,637 controls, current use of angiotensin II receptor blockers was followed by a decreased risk of acute pancreatitis, compared to non-users, adjusted OR 0 · 77 (95% CI 0 · 69-0 · 86). No protective association, but an increased risk was found for users of angiotensin-converting enzyme inhibitors (adjusted OR 1 · 11, 95% CI: 1 · 01-1 · 21), analysed for comparison reasons. There was a significant decreased risk associated with both severe acute pancreatitis, (OR 0 · 71 (0 · 59-0 · 85), and mild acute pancreatitis; adjusted OR 0 · 81 (0 · 70-0 · 94). This population-based case-control study indicates that use of angiotensin II receptor blockers might be associated with a lesser risk of acute pancreatitis, and that the protective association was significant among cases of both severe and mild acute pancreatitis.

  19. Peptides derived from CXCL8 based on in silico analysis inhibit CXCL8 interactions with its receptor CXCR1

    Science.gov (United States)

    Jiang, Shinn-Jong; Liou, Je-Wen; Chang, Chun-Chun; Chung, Yi; Lin, Lee-Fong; Hsu, Hao-Jen

    2015-12-01

    Chemokine CXCL8 is crucial for regulation of inflammatory and immune responses via activating its cognate receptor CXCR1. In this study, molecular docking and binding free energy calculations were combined to predict the initial binding event of CXCL8 to CXCR1 for peptide drug design. The simulations reveal that in the initial binding, the N-loop of CXCL8 interacts with the N-terminus of CXCR1, which is dominated by electrostatic interactions. The derived peptides from the binding region of CXCL8 are synthesized for further confirmation. Surface plasmon resonance analyses indicate that the CXCL8 derived peptide with 14 residues is able to bind to the receptor CXCR1 derived peptide with equilibrium KD of 252 μM while the peptide encompassing a CXCL8 K15A mutation hardly binds to CXCR1 derived peptide (KD = 1553 μM). The cell experiments show that the designed peptide inhibits CXCL8-induced and LPS-activated monocytes adhesion and transmigration. However, when the peptides were mutated on two lysine residues (K15 and K20), the inhibition effects were greatly reduced indicating these two amino acids are key residues for the initial binding of CXCL8 to CXCR1. This study demonstrates that in silico prediction based functional peptide design can be effective for developing anti-inflammation drugs.

  20. Experimental and theoretical study on the cooperative interaction of the ethanolammonium cation with a hexaarylbenzene-based receptor

    Science.gov (United States)

    Makrlík, Emanuel; Toman, Petr; Vaňura, Petr; Rathore, Rajendra

    2012-10-01

    From extraction experiments and γ-activity measurements, the extraction constant corresponding to the equilibrium HL+(aq) + 1 · Cs+(nb) ⇔ 1 · HL+(nb) + Cs+(aq) taking place in the two-phase water-nitrobenzene system (HL+ = ethanolammonium, 1 = hexaarylbenzene-based receptor; aq = aqueous phase, nb = nitrobenzene phase) was evaluated as log Kex (HL+,1 · Cs+) = -1.1 ± 0.1. Further, the stability constant of the 1 · HL+ complex in nitrobenzene saturated with water was calculated for a temperature of 25 °C: log βnb (1 · HL+) = 5.4 ± 0.2. Finally, by using quantum mechanical DFT calculations, the most probable structures A and B of the 1 · HL+ complex species, which are obviously in a dynamic equilibrium, were indicated. In both of these structures of the resulting complex 1 · HL+, the cation HL+ synergistically interacts with the polar ethereal oxygen fence and with the central hydrophobic benzene bottom of the parent receptor 1 via cation-π interaction.

  1. Match-bounded String Rewriting Systems

    Science.gov (United States)

    Geser, Alfons; Hofbauer, Dieter; Waldmann, Johannes

    2003-01-01

    We introduce a new class of automated proof methods for the termination of rewriting systems on strings. The basis of all these methods is to show that rewriting preserves regular languages. To this end, letters are annotated with natural numbers, called match heights. If the minimal height of all positions in a redex is h+1 then every position in the reduct will get height h+1. In a match-bounded system, match heights are globally bounded. Using recent results on deleting systems, we prove that rewriting by a match-bounded system preserves regular languages. Hence it is decidable whether a given rewriting system has a given match bound. We also provide a sufficient criterion for the abence of a match-bound. The problem of existence of a match-bound is still open. Match-boundedness for all strings can be used as an automated criterion for termination, for match-bounded systems are terminating. This criterion can be strengthened by requiring match-boundedness only for a restricted set of strings, for instance the set of right hand sides of forward closures.

  2. Characteristics and origins of air pollutants in Wuhan, China, based on observations and hybrid receptor models.

    Science.gov (United States)

    Wang, Si; Yu, Shaocai; Yan, Renchang; Zhang, Qingyu; Li, Pengfei; Wang, Liqiang; Liu, Weiping; Zheng, Xianjue

    2017-07-01

    To identify the characteristics of air pollutants and factors attributing to the formation of haze in Wuhan, this study analyzed the hourly observations of air pollutants (PM2.5, PM10, NO2, SO2, O3, and CO) from March 1, 2013, to February 28, 2014, and used hybrid receptor models for a case study. The results showed that the annual average concentrations for PM2.5, PM10, NO2, SO2, O3, and CO during the whole period were 89.6 μg m(-3), 134.9 μg m(-3), 54.9 μg m(-3), 32.4 μg m(-3), 62.3 μg m(-3), and 1.1 mg m(-3), respectively. The monthly variations revealed that the peak values of PM2.5, PM10, NO2, SO2, and CO occurred in December because of increased local emissions and severe weather conditions, while the lowest values occurred in July mainly due to larger precipitation. The maximum O3 concentrations occurred in warm seasons from May to August, which may be partly due to the high temperature and solar radiation. Diurnal analysis showed that hourly PM2.5, PM10, NO2, and CO concentrations had two ascending stages accompanying by the two traffic peaks. However, the O3 concentration variations were different with the highest concentration in the afternoon. A case study utilizing hybrid receptor models showed the significant impact of regional transport on the haze formation in Wuhan and revealed that the mainly potential polluted sources were located in the north and south of Wuhan, such as Baoding and Handan in Hebei province, and Changsha in Hunan province. Wuhan city requires a 5% reduction of the annual mean of PM2.5 concentration by the end of 2017. In order to accomplish this goal, Wuhan has adopted some measures to improve its air quality. This work has determined the main pollution sources that affect the formation of haze in Wuhan by transport. We showed that apart from the local emissions, north and south of Wuhan were the potential sources contributing to the high PM2.5 concentrations in Wuhan, such as Baoding and Handan in Hebei province, Zhumadian

  3. Molecular dynamics simulation study of PTP1B with allosteric inhibitor and its application in receptor based pharmacophore modeling

    Science.gov (United States)

    Bharatham, Kavitha; Bharatham, Nagakumar; Kwon, Yong Jung; Lee, Keun Woo

    2008-12-01

    Allosteric inhibition of protein tyrosine phosphatase 1B (PTP1B), has paved a new path to design specific inhibitors for PTP1B, which is an important drug target for the treatment of type II diabetes and obesity. The PTP1B1-282-allosteric inhibitor complex crystal structure lacks α7 (287-298) and moreover there is no available 3D structure of PTP1B1-298 in open form. As the interaction between α7 and α6-α3 helices plays a crucial role in allosteric inhibition, α7 was modeled to the PTP1B1-282 in open form complexed with an allosteric inhibitor (compound-2) and a 5 ns MD simulation was performed to investigate the relative orientation of the α7-α6-α3 helices. The simulation conformational space was statistically sampled by clustering analyses. This approach was helpful to reveal certain clues on PTP1B allosteric inhibition. The simulation was also utilized in the generation of receptor based pharmacophore models to include the conformational flexibility of the protein-inhibitor complex. Three cluster representative structures of the highly populated clusters were selected for pharmacophore model generation. The three pharmacophore models were subsequently utilized for screening databases to retrieve molecules containing the features that complement the allosteric site. The retrieved hits were filtered based on certain drug-like properties and molecular docking simulations were performed in two different conformations of protein. Thus, performing MD simulation with α7 to investigate the changes at the allosteric site, then developing receptor based pharmacophore models and finally docking the retrieved hits into two distinct conformations will be a reliable methodology in identifying PTP1B allosteric inhibitors.

  4. A Note on the W-S Lower Bound of the MEE Estimation

    Directory of Open Access Journals (Sweden)

    Badong Chen

    2014-02-01

    Full Text Available The minimum error entropy (MEE estimation is concerned with the estimation of a certain random variable (unknown variable based on another random variable (observation, so that the entropy of the estimation error is minimized. This estimation method may outperform the well-known minimum mean square error (MMSE estimation especially for non-Gaussian situations. There is an important performance bound on the MEE estimation, namely the W-S lower bound, which is computed as the conditional entropy of the unknown variable given observation. Though it has been known in the literature for a considerable time, up to now there is little study on this performance bound. In this paper, we reexamine the W-S lower bound. Some basic properties of the W-S lower bound are presented, and the characterization of Gaussian distribution using the W-S lower bound is investigated.

  5. Dioxin increases the interaction between aryl hydrocarbon receptor and estrogen receptor alpha at human promoters

    DEFF Research Database (Denmark)

    Ahmed, Shaaima; Valen, Eivind; Sandelin, Albin Gustav

    2009-01-01

    Recent studies have shown that activated aryl hydrocarbon receptor (AHR) induced the recruitment of estrogen receptor- (ER ) to AHR-regulated genes and that AHR is recruited to ER -regulated genes. However, these findings were limited to a small number of well-characterized AHR- or ER -responsive...... regions bound by both AHR and ER . Conventional and sequential ChIPs confirmed the recruitment of AHR and ER to many of the identified regions. Transcription factor binding site analysis revealed an overrepresentation of aryl hydrocarbon receptor response elements in regions bound by both AHR and ER...

  6. Ligands specify estrogen receptor alpha nuclear localization and degradation

    OpenAIRE

    Caze-Subra Stéphanie; Mazaheri Mahta; Kocanova Silvia; Bystricky Kerstin

    2010-01-01

    Abstract Background The estrogen receptor alpha (ERα) is found predominately in the nucleus, both in hormone stimulated and untreated cells. Intracellular distribution of the ERα changes in the presence of agonists but the impact of different antiestrogens on the fate of ERα is a matter of debate. Results A MCF-7 cell line stably expressing GFP-tagged human ERα (SK19 cell line) was created to examine the localization of ligand-bound GFP-ERα. We combined digitonin-based cell fractionation anal...

  7. The neural basis of bounded rational behavior

    Directory of Open Access Journals (Sweden)

    Coricelli, Giorgio

    2012-03-01

    Full Text Available Bounded rational behaviour is commonly observed in experimental games and in real life situations. Neuroeconomics can help to understand the mental processing underlying bounded rationality and out-of-equilibrium behaviour. Here we report results from recent studies on the neural basis of limited steps of reasoning in a competitive setting —the beauty contest game. We use functional magnetic resonance imaging (fMRI to study the neural correlates of human mental processes in strategic games. We apply a cognitive hierarchy model to classify subject’s choices in the experimental game according to the degree of strategic reasoning so that we can identify the neural substrates of different levels of strategizing. We found a correlation between levels of strategic reasoning and activity in a neural network related to mentalizing, i.e. the ability to think about other’s thoughts and mental states. Moreover, brain data showed how complex cognitive processes subserve the higher level of reasoning about others. We describe how a cognitive hierarchy model fits both behavioural and brain data.

    La racionalidad limitada es un fenómeno observado de manera frecuente tanto en juegos experimentales como en situaciones cotidianas. La Neuroeconomía puede mejorar la comprensión de los procesos mentales que caracterizan la racionalidad limitada; en paralelo nos puede ayudar a comprender comportamientos que violan el equilibrio. Nuestro trabajo presenta resultados recientes sobre la bases neuronales del razonamiento estratégico (y sus límite en juegos competitivos —como el juego del “beauty contest”. Estudiamos las bases neuronales del comportamiento estratégico en juegos con interacción entre sujetos usando resonancia magnética funcional (fMRI. Las decisiones de los participantes se clasifican acorde al grado de razonamiento estratégico: el llamado modelo de Jerarquías Cognitivas. Los resultados muestran una correlación entre niveles de

  8. Sound velocity bound and neutron stars.

    Science.gov (United States)

    Bedaque, Paulo; Steiner, Andrew W

    2015-01-23

    It has been conjectured that the velocity of sound in any medium is smaller than the velocity of light in vacuum divided by sqrt[3]. Simple arguments support this bound in nonrelativistic and/or weakly coupled theories. The bound has been demonstrated in several classes of strongly coupled theories with gravity duals and is saturated only in conformal theories. We point out that the existence of neutron stars with masses around two solar masses combined with the knowledge of the equation of state of hadronic matter at "low" densities is in strong tension with this bound.

  9. Lability of copper bound to humic acid

    OpenAIRE

    Mao, Lingchen; Young, Scott D.; Bailey, Liz

    2015-01-01

    Geochemical speciation models generally include the assumption that all metal bound to humic acid and fulvic acid (HA, FA) is labile. However, in the current study, we determined the presence of a soluble ‘non-labile’ Cu fraction bound to HA extracted from grassland and peat soils. This was quantified by determining isotopically-exchangeable Cu (E-value) and EDTA-extraction of HA-bound Cu, separated by size-exclusion chromatography (SEC) and assayed by coupled ICP-MS. Evidence of time-depend...

  10. Positivity bounds on double parton distributions

    Energy Technology Data Exchange (ETDEWEB)

    Diehl, Markus; Kasemets, Tomas

    2013-03-15

    Double hard scattering in proton-proton collisions is described in terms of double parton distributions. We derive bounds on these distributions that follow from their interpretation as probability densities, taking into account all possible spin correlations between two partons in an unpolarized proton. These bounds constrain the size of the polarized distributions and can for instance be used to set upper limits on the effects of spin correlations in double hard scattering. We show that the bounds are stable under leading-order DGLAP evolution to higher scales.

  11. Lower bound for the nuclear kinetic energy

    Energy Technology Data Exchange (ETDEWEB)

    Dehesa, J.S. (Granada Univ. (Spain). Dept. de Fisica Nuclear); Galvez, F.J. (Granada Univ. (Spain). Dept. de Fisica Teorica)

    1985-06-27

    We argue that the kinetic energy of a many-fermion system is bounded from below by Kqsup(-2/3)A sup(5/3) / , with K = 0.565 where q is the number of spin states available to each particle and sup(1/2) is the root mean square radius of the single-particle density. A simple lower bound for the nuclear kinetic energy is found. Numerical values of the bound for several nuclei are shown, and a comparison with some self-consistent calculations and some pseudo-empirical values is made.

  12. Continuous bounded cohomology of locally compact groups

    CERN Document Server

    2001-01-01

    Recent research has repeatedly led to connections between important rigidity questions and bounded cohomology. However, the latter has remained by and large intractable. This monograph introduces the functorial study of the continuous bounded cohomology for topological groups, with coefficients in Banach modules. The powerful techniques of this more general theory have successfully solved a number of the original problems in bounded cohomology. As applications, one obtains, in particular, rigidity results for actions on the circle, for representations on complex hyperbolic spaces and on Teichmüller spaces. A special effort has been made to provide detailed proofs or references in quite some generality.

  13. Mechanism-Based Mathematical Model for Gating of Ionotropic Glutamate Receptors.

    Science.gov (United States)

    Dai, Jian; Wollmuth, Lonnie P; Zhou, Huan-Xiang

    2015-08-27

    We present a mathematical model for ionotropic glutamate receptors (iGluR's) that is built on mechanistic understanding and yields a number of thermodynamic and kinetic properties of channel gating. iGluR's are ligand-gated ion channels responsible for the vast majority of fast excitatory neurotransmission in the central nervous system. The effects of agonist-induced closure of the ligand-binding domain (LBD) are transmitted to the transmembrane channel (TMC) via interdomain linkers. Our model demonstrates that, relative to full agonists, partial agonists may reduce either the degree of LBD closure or the curvature of the LBD free energy basin, leading to less stabilization of the channel open state and hence lower channel open probability. A rigorous relation is derived between the channel closed-to-open free energy difference and the tension within the linker. Finally, by treating LBD closure and TMC opening as diffusive motions, we obtain gating trajectories that resemble stochastic current traces from single-channel recordings and calculate the rate constants for transitions between the channel open and closed states. Our model can be implemented by molecular dynamics simulations to realistically depict iGluR gating and may guide functional experiments in gaining deeper insight into this essential family of channel proteins.

  14. Treating Diabetes Mellitus: Pharmacophore Based Designing of Potential Drugs from Gymnema sylvestre against Insulin Receptor Protein

    Directory of Open Access Journals (Sweden)

    Mohammad Uzzal Hossain

    2016-01-01

    Full Text Available Diabetes mellitus (DM is one of the most prevalent metabolic disorders which can affect the quality of life severely. Injectable insulin is currently being used to treat DM which is mainly associated with patient inconvenience. Small molecules that can act as insulin receptor (IR agonist would be better alternatives to insulin injection. Herein, ten bioactive small compounds derived from Gymnema sylvestre (G. sylvestre were chosen to determine their IR binding affinity and ADMET properties using a combined approach of molecular docking study and computational pharmacokinetic elucidation. Designing structural analogues were also performed for the compounds associated with toxicity and less IR affinity. Among the ten parent compounds, six were found to have significant pharmacokinetic properties with considerable binding affinity towards IR while four compounds were associated with toxicity and less IR affinity. Among the forty structural analogues, four compounds demonstrated considerably increased binding affinity towards IR and less toxicity compared with parent compounds. Finally, molecular interaction analysis revealed that six parent compounds and four analogues interact with the active site amino acids of IR. So this study would be a way to identify new therapeutics and alternatives to insulin for diabetic patients.

  15. Role of Leukotriene receptor antagonist Montelukast in the treatment of chronic urticaria: A hospital based study

    Directory of Open Access Journals (Sweden)

    Iffat Hassan

    2012-01-01

    Full Text Available Introduction: Chronic urticaria is a disabling disease which may be refractory to standard therapies. Leukotriene receptor antagonists like montelukast have been tried in allergic diseases like asthma and find mention as a therapeutic option in chronic urticaria. Purposes: A randomized single-blinded non-placebo controlled study to evaluate the role of montelukast, in addition to the adjunctive role of non-sedating antihistamine levocetirizine (H1, was conducted in patients with chronic urticaria.Methods: Thirty-five patients with chronic urticaria were enrolled. Medication was given for a period of twelve weeks. Montelukast 10mg/day in an adult and 5mg in the age group 6-13 years,4 mg 2-6 years and levocetirizine 5 mg once a day was added, if patient had new weals while on therapy. The improvement was monitored by estimating the episodes of wheals and pruritus in any two weeks period.Results: Twenty-two patients showed a good response with occasional wheals at the end of 2 weeks and no weals at the end of 12 weeks. These included all 8 patients on non-steroidal anti-inflammatory drugs (NSAIDS. Four of these patients relapsed on discontinuation of therapy.Conclusion: Montelukast is effective in chronic refractory urticaria especially in patients on non-steroidal anti-inflammatory drugs with occasional add-on use of a non-sedating anti-histamine.

  16. Combined Ligand/Structure-Based Virtual Screening and Molecular Dynamics Simulations of Steroidal Androgen Receptor Antagonists

    Directory of Open Access Journals (Sweden)

    Yuwei Wang

    2017-01-01

    Full Text Available The antiandrogens, such as bicalutamide, targeting the androgen receptor (AR, are the main endocrine therapies for prostate cancer (PCa. But as drug resistance to antiandrogens emerges in advanced PCa, there presents a high medical need for exploitation of novel AR antagonists. In this work, the relationships between the molecular structures and antiandrogenic activities of a series of 7α-substituted dihydrotestosterone derivatives were investigated. The proposed MLR model obtained high predictive ability. The thoroughly validated QSAR model was used to virtually screen new dihydrotestosterones derivatives taken from PubChem, resulting in the finding of novel compounds CID_70128824, CID_70127147, and CID_70126881, whose in silico bioactivities are much higher than the published best one, even higher than bicalutamide. In addition, molecular docking, molecular dynamics (MD simulations, and MM/GBSA have been employed to analyze and compare the binding modes between the novel compounds and AR. Through the analysis of the binding free energy and residue energy decomposition, we concluded that the newly discovered chemicals can in silico bind to AR with similar position and mechanism to the reported active compound and the van der Waals interaction is the main driving force during the binding process.

  17. Combined Ligand/Structure-Based Virtual Screening and Molecular Dynamics Simulations of Steroidal Androgen Receptor Antagonists.

    Science.gov (United States)

    Wang, Yuwei; Han, Rui; Zhang, Huimin; Liu, Hongli; Li, Jiazhong; Liu, Huanxiang; Gramatica, Paola

    2017-01-01

    The antiandrogens, such as bicalutamide, targeting the androgen receptor (AR), are the main endocrine therapies for prostate cancer (PCa). But as drug resistance to antiandrogens emerges in advanced PCa, there presents a high medical need for exploitation of novel AR antagonists. In this work, the relationships between the molecular structures and antiandrogenic activities of a series of 7α-substituted dihydrotestosterone derivatives were investigated. The proposed MLR model obtained high predictive ability. The thoroughly validated QSAR model was used to virtually screen new dihydrotestosterones derivatives taken from PubChem, resulting in the finding of novel compounds CID_70128824, CID_70127147, and CID_70126881, whose in silico bioactivities are much higher than the published best one, even higher than bicalutamide. In addition, molecular docking, molecular dynamics (MD) simulations, and MM/GBSA have been employed to analyze and compare the binding modes between the novel compounds and AR. Through the analysis of the binding free energy and residue energy decomposition, we concluded that the newly discovered chemicals can in silico bind to AR with similar position and mechanism to the reported active compound and the van der Waals interaction is the main driving force during the binding process.

  18. Structure-based Design Targeted at LOX-1, a Receptor for Oxidized Low-Density Lipoprotein

    Science.gov (United States)

    Thakkar, Shraddha; Wang, Xianwei; Khaidakov, Magomed; Dai, Yao; Gokulan, Kuppan; Mehta, Jawahar L.; Varughese, Kottayil I.

    2015-11-01

    Atherosclerosis related cardiovascular diseases continue to be the primary cause of mortality in developed countries. The elevated level of low density lipoprotein (LDL) is generally considered to be the driver of atherosclerosis, but recent years have seen a shift in this perception in that the vascular plaque buildup is mainly caused by oxidized LDL (ox-LDL) rather than native-LDL. The scavenger receptor LOX-1 found in endothelial cells binds and internalizes ox-LDL which leads to the initiation of plaque formation in arteries. Using virtual screening techniques, we identified a few potential small molecule inhibitors of LOX-1 and tested their inhibitory potential using differential scanning fluorimetry and various cellular assays. Two of these molecules significantly reduced the uptake of ox-LDL by human endothelial cells, LOX-1 transcription and the activation of ERK1/2 and p38 MAPKs in human endothelial cells. In addition, these molecules suppressed ox-LDL-induced VCAM-1 expression and monocyte adhesion onto human endothelial cells demonstrating their therapeutic potential.

  19. Target-based biomarker selection - Mineralocorticoid receptor-related biomarkers and treatment outcome in major depression.

    Science.gov (United States)

    Büttner, Matthias; Jezova, Daniela; Greene, Brandon; Konrad, Carsten; Kircher, Tilo; Murck, Harald

    2015-01-01

    Aldosterone and mineralocorticoid receptor (MR)-function have been related to depression. We examined central and peripheral parameters of MR-function in order to characterize their relationship to clinical treatment outcome after six weeks in patients with acute depression. 30 patients with a diagnosis of major depression were examined 3 times over a 6 week period. Aldosterone and cortisol salvia samples were taken at 7.00 a.m. before patients got out of bed. Easy to use e-devices were used to measure markers of central MR function, i.e. slow wave sleep (SWS) and heart-rate variability (HRV). Salt-taste intensity (STI) and salt pleasantness (SP) of a 0.9% salt solution were determined by a newly developed scale. In addition, systolic blood pressure (SBP) and plasma electrolytes were determined as markers for peripheral MR activity. The relationship between the levels of these biomarkers at baseline and the change in clinical outcome parameters (Hamilton depression rating scale (HDRS)-21, anxiety, QIDS and BDI) after 6 weeks of treatment was investigated. A higher aldosterone/cortisol ratio (Aldo/Cort) (n = 17 due to missing values; p depression. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Improved Bounds for Hybrid Flow Shop Scheduling with Multiprocessor Tasks

    OpenAIRE

    Lahimer, Asma; Lopez, Pierre; Haouari, Mohamed

    2013-01-01

    Accepté à 'Computers & Industrial Engineering'; International audience; In this paper, we investigate the problem of minimizing makespan in a multistage hybrid flow-shop scheduling with multiprocessor tasks. To generate high-quality approximate solutions to this challenging NP-hard problem, we propose a discrepancy search heuristic that is based on the new concept of adjacent discrepancies. Moreover, we describe a new lower bound based on the concept of dual feasible functions. The proposed l...

  1. Establishing a cellular FRET-based fluorescence plate reader assay to monitor proNGF-induced cross-linking of sortilin and the neurotrophin receptor p75(NTR)

    DEFF Research Database (Denmark)

    Skeldal, Sune; Kjaergaard, Maj M; Alwasel, Saleh

    2015-01-01

    the vps10p domain receptor sortilin and the neurotrophin receptor p75(NTR). However, proNGF-induced receptor complex formation has been difficult to directly assess other than by western blotting. We here describe a fluorescence resonance energy transfer (FRET) based fluorescence plate reader assay...... to monitor the interaction between fluorescently tagged sortilin and p75(NTR) in live cells. The method is based on a standard fluorescent plate reader found in many biochemical laboratories and the results are evaluated using a microscopy-based quantified sensitized acceptor emission FRET approach making...... use of a pair of FRET standard constructs. As a result, the effect of proNGF on the interaction between sortilin and p75(NTR) can be evaluated in live cells allowing for screening and selection of therapeutic compounds interfering with proNGF-induced cell death....

  2. The significance of transferrin receptors in oncology: the development of functional nano-based drug delivery systems.

    Science.gov (United States)

    Tortorella, Stephanie; Karagiannis, Tom C

    2014-01-01

    Anticancer therapeutic research aims to improve clinical management of the disease through the development of strategies that involve currently-relevant treatment options and targeted delivery. Tumour-specific and -targeted delivery of compounds to the site of malignancy allows for enhanced cellular uptake, increased therapeutic benefit with high intratumoural drug concentrations, and decreased systemic exposure. Due to the upregulation of transferrin receptor expression in a wide variety of cancers, its function and its highly efficient recycling pathway, strategies involving the selective targeting of the receptor are well documented. Direct conjugation and immunotoxin studies using the transferrin peptide or anti-transferrin receptor antibodies as the targeting moiety have established the capacity to enhance cellular uptake, cross the blood brain barrier, limit systemic toxicity and reverse multi-drug resistance. Limitations in direct conjugation, including the difficulty in linking an adequate amount of therapeutic compound to the ligand or antibody have identified the requirement to develop novel delivery methods. The application of nanoparticulate theory in the development of functional drug delivery systems has proven to be most promising, with the ability to selectively modify size-dependent properties and surface chemistry. The transferrin modification on a range of nanoparticle formulations enhances selective cellular uptake through transferrin-mediated processes, and increases therapeutic benefit through the ability to encapsulate high concentrations of relevant drug to the tumour site. Although ineffective in crossing the blood brain barrier in its free form, chemotherapeutic compounds including doxorubicin, may be loaded into transferrin-conjugated nanocarriers and impart cytotoxic effects in glioma cells in vitro and in vivo. Additionally, transferrin-targeted nanoparticles may be used in selective diagnostic applications with enhanced selectivity and

  3. Parallel Branch-and-Bound Methods for the Job Shop Scheduling

    DEFF Research Database (Denmark)

    Clausen, Jens; Perregaard, Michael

    1998-01-01

    Job-shop scheduling (JSS) problems are among the more difficult to solve in the class of NP-complete problems. The only successful approach has been branch-and-bound based algorithms, but such algorithms depend heavily on good bound functions. Much work has been done to identify such functions...

  4. Fitness levels with tail bounds for the analysis of randomized search heuristics

    DEFF Research Database (Denmark)

    Witt, Carsten

    2014-01-01

    The fitness-level method, also called the method of f-based partitions, is an intuitive and widely used technique for the running time analysis of randomized search heuristics. It was originally defined to prove upper and lower bounds on the expected running time. Recently, upper tail bounds were...

  5. 77 FR 43561 - Proposed Eligibility Criteria for Bound Printed Matter Parcels

    Science.gov (United States)

    2012-07-25

    ... criterion for eligibility of Bound Printed Matter (BPM) parcels by adding a physical density threshold for....gov , with a subject line of ``New Eligibility for BPM Parcels.'' Faxed comments are not accepted. FOR.... SUPPLEMENTARY INFORMATION: BPM parcels is an economical ground-based product containing qualifying bound printed...

  6. New estradiol based {sup 111}In complex towards the estrogen receptor

    Energy Technology Data Exchange (ETDEWEB)

    Vultos, Filipe; Cunha, Susana; Fernandes, Celia; Oliveira, Maria Cristina; Marques, Fernanda; Santos, Isabel; Gano, Lurdes [Universidade de Lisboa, Bobadela (Portugal). Centro de Ciencias e Tecnologias Nucleares C2TN; Botelho, Maria Filomena [Universidade de Coimbra (Portugal). Inst. de Biofisica/Biomatematica

    2015-07-01

    The oestrogen receptor (ER) is an important tumour target for molecular imaging and radionuclide therapy due to its overexpression in many malignant cells as compared to normal cells. Aiming to find new functional molecular imaging/therapeutic agents for ER positive tumours, we have synthesized a new estradiol derivative substituted at the 16-α position with a diethylene triamine tetraacetic acid (DTTA)-like chelating ligand through a four-carbon spacer. The new bioconjugate (H{sub 4}L), was used to synthesize the corresponding indium complexes (InL/[{sup 111}In]L). The radioactive complex [{sup 111}In]L was prepared in high yield (>98%) at final concentrations of 1 x 10{sup -4} M and its chemical identity was ascertained by comparing its HPLC gamma-chromatogram to the HPLC UV-vis-chromatogram of the InL analogue. [{sup 111}In]L is hydrophilic and kinetically stable in the presence of an excess of apo-transferrin and in human blood serum. Cellular studies in breast cancer cells (MCF-7 and MDA-MB-431) suggest that [{sup 111}In]L uptake may be mediated by an ER dependent mechanism. Biodistribution studies were performed in mice indicating a rapid clearance from most organs and a slow total excretion that occurs mainly by hepatobiliar pathway. High in vivo stability of [{sup 111}In]L was confirmed by HPLC analysis of urine and blood samples. Nevertheless, the hydrophilicity, the low ER affinity and the biodistribution of [{sup 111}In]L indicate that structural modifications are required to improve its behaviour for ER targeting in vivo.

  7. A rapid conductometric sensor for the analysis of cyanide using imidazole based receptor.

    Science.gov (United States)

    Paul, Anirban; Perween, Mosarrat; Saha, Sukdeb; Srivastava, Divesh N; Das, Amitava

    2015-10-28

    A specific and efficient hydrogen bonding interaction between cyanide and the HN-H [imidazole] in an aqueous medium has been utilized for the selective recognition of cyanide under physiological conditions. The possibility of utilizing such an interaction for developing any practical device for the specific detection of cyanide in an aqueous environment has not been explored to date. We now report a simple dip and read conductometric sensor for cyanide ions using a tailored electrode in aqueous media. The purpose built reagent, 2-phenyl-1H-anthra-[2,3-d]-immidazole-5,10 dione was immobilized in a polyaniline matrix to fabricate this conductometric device. The homogeneous immobilization of the receptor in polyaniline was confirmed by FT-IR mapping. The proposed transduction mechanism is charge neutralization on the polyaniline moiety, which ultimately inhibits the protonation resulting in a decrease in the conductance of polyaniline. The sensor response was measured in three ranges of cyanide concentration (10(-10) M to 10(-8) M; 10(-8) M to 10(-6) M and 10(-6) M to 10(-3) M). Whereas the device is found insensitive in the first range, it acts as a detector in the second range and as a proportional sensor in the third range. The minimum detection limit of this device was found to be 10 nmol L(-1) (2.6 ppt), which is significantly less than the WHO guideline values. The responses have been investigated under various conditions such as different pH and the electrochemical state of the polymer. The current device has been found to be better close to neutral pH and at a 400 mV vs. Ag/AgCl potential. The reproducibility and repeatability of the sensor was investigated and interference studies were performed.

  8. Redshift-space limits of bound structures

    NARCIS (Netherlands)

    Duenner, Rolando; Reisenegger, Andreas; Meza, Andres; Araya, Pablo A.; Quintana, Hernan

    2007-01-01

    An exponentially expanding Universe, possibly governed by a cosmological constant, forces gravitationally bound structures to become more and more isolated, eventually becoming causally disconnected from each other and forming so-called 'island universes'. This new scenario reformulates the question

  9. Learning in Leaps and Bounds

    Science.gov (United States)

    Pica, Rae

    2006-01-01

    Gardner's theory of multiple intelligences (1993) identifies several ways of "learning and knowing." Among these are the logical/mathematical and linguistic intelligence--the two most validated by society and on which all standardized tests are based. Therefore, physical education specialist are facing more pressure than ever to advocate for their…

  10. New Spectral Features from Bound Dark Matter

    DEFF Research Database (Denmark)

    Catena, Riccardo; Kouvaris, Chris

    2016-01-01

    We demonstrate that dark matter particles gravitationally bound to the Earth can induce a characteristic nuclear recoil signal at low energies in direct detection experiments. The new spectral feature we predict can provide the ultimate smoking gun for dark matter discovery for experiments...... with positive signal but unclear background. The new feature is universal, in that the ratio of bound over halo dark matter event rates at detectors is independent of the dark matter-nucleon cross section....

  11. On bounds for symmetric divergence measures

    Science.gov (United States)

    Furuichi, S.; Yanagi, K.; Kuriyama, K.

    2017-06-01

    In the paper [1], tight bounds for symmetric divergence measures applying the results established by G.L.Gilardoni. In this article, we report on two kinds of extensions for the Sason's results, namely a classical q-extension and a non-commutative(quantum) extension. Especially, we improve Sason's bound of the summation of the absolute value for the difference between two probability distributions, applying the parameter q of Tsallis entropy, under a certain assumption.

  12. Stable Bound States of Asymmetric Dark Matter

    OpenAIRE

    Wise, Mark B.; Zhang, Yue

    2014-01-01

    The simplest renormalizable effective field theories with asymmetric dark matter bound states contain two additional gauge singlet fields one being the dark matter and the other a mediator particle that the dark matter annihilates into. We examine the physics of one such model with a Dirac fermion as the dark matter and a real scalar mediator. For a range of parameters the Yukawa coupling of the dark matter to the mediator gives rise to stable asymmetric dark matter bound states. We derive pr...

  13. Malabsorption of protein bound vitamin B12.

    OpenAIRE

    Dawson, D W; Sawers, A H; Sharma, R K

    1984-01-01

    Patients with subnormal serum vitamin B12 concentrations were tested for absorption of protein bound vitamin B12 and compared with controls. Absorption of the protein bound vitamin appeared to decrease with increasing age in healthy subjects. Differences between the result of this test and the result of the Schilling test in patients who had undergone gastric surgery were confirmed; such differences were also seen in some patients who had iron deficiency anaemia, an excessive alcohol intake, ...

  14. Dynamic optimization problems with bounded terminal conditions

    Science.gov (United States)

    Lee, A. Y.

    1987-01-01

    Bounded terminal conditions of nonlinear optimization problems are converted to equality terminal conditions via Valentine's device. In so doing, additional unknown parameters are introduced into the problem. The transformed problems can still be easily solved using the sequential gradient-restoration algorithm (SGRA) via a simple augmentation of the unknown parameter vector pi. Three example problems with bounded terminal conditions are solved to verify this technique.

  15. NITRO MUSK BOUND TO CARP HEMOGLOBIN ...

    Science.gov (United States)

    Nitroaromatic compounds including synthetic nitro musks are important raw materials and intermediates in the synthesis of explosives, dyes, and pesticides, pharmaceutical and personal care-products (PPCPs). The nitro musks such as musk xylene (MX) and musk ketone (MK) are extensively used as fragrance ingredients in PPCPs and other commercial toiletries. Identification and quantification of a bound 4-amino-MX (4-AMX) metabolite as well as a 2- amino-MK (2-AMK) metabolite were carried out by gas chromatography-mass spectrometry' (GC/MS), with selected ion monitoring (SIM) in both the electron ionization (ElMS) and electron capture (EC) negative ion chemical ionization (NICIMS) modes. Detection of 4-AMX and 2-AMK occurred after the cysteine adducts in carp hemoglobin, derived from the nitroso metabolites, were released by alkaline hydrolysis. The released metabolites were extracted into n-hexane. The extract was preconcentrated by evaporation, and analyzed by GC-SIM-MS. A comparison between the El and EC approaches was made. EC NICIMS detected both metabolites whereas only 4-AMX was detected by ElMS. The EC NICIMS approach exhibited fewer matrix responses and provided a lower detection limit. Quantitation in both approaches was based on internal standard and a calibration plot. The research focused on in the subtasks is the development and application of state-of the-art technologies to meet the needs of the public, Office of Water, and ORD in the area of Water Q

  16. Iodide and triiodide anion complexes involving anion-π interactions with a tetrazine-based receptor.

    Science.gov (United States)

    Savastano, Matteo; Bazzicalupi, Carla; García, Celeste; Gellini, Cristina; López de la Torre, María Dolores; Mariani, Palma; Pichierri, Fabio; Bianchi, Antonio; Melguizo, Manuel

    2017-04-05

    Protonated forms of the tetrazine ligand L2 (3,6-bis(morpholin-4-ylethyl)-1,2,4,5-tetrazine) interact with iodide in aqueous solution forming relatively stable complexes (ΔG° = -11.6(4) kJ mol(-1) for HL2(+) + I(-) = (HL2)I and ΔG° = -13.4(2) kJ mol(-1) for H2L2(2+) + I(-) = [(H2L2)I](+)). When solutions of [(H2L2)I](+) are left in contact with air, crystals of the oxidation product (H2L2)2(I3)3I·4H2O are formed. Unfortunately, the low solubility of I3(-) complexes prevents the determination of their stability constants. The crystal structures of H2L2I2·H2O (1), H2L2(I3)2·2H2O (2) and (H2L2)2(I3)3I·4H2O (3) were determined by means of X-ray diffraction analyses. In all crystal structures, it was found that the interaction between I(-) and I3(-) with H2L2(2+) is dominated by anion interactions with the π electron density of the receptor. Only in the case of 1, the iodide anions involved in close anion-π interactions with the ligand tetrazine ring form an additional H-bond with the protonated morpholine nitrogen of an adjacent ligand molecule. Conversely, in crystals of 2 and 3 there are alternate segregated planes which contain only protonated ligands hydrogen-bonded to cocrystallized water molecules or I3(-) and I(-) forming infinite two-dimensional networks established through short interhalogen contacts, making these crystalline products good candidates to behave as solid conductors. In the solid complexes, the triiodide anion displays both end-on and side-on interaction modes with the tetrazine ring, in agreement with density functional theory calculations indicating a preference for the alignment of the I3(-) molecular axis with the molecular axis of the ligand. Further information about geometries and structures of triiodide anions in 2 and 3 was acquired by the analysis of their Raman spectra.

  17. Switch strategies in the management of hypertension: a cost minimisation analysis of angiotensin receptor blocker based regimen.

    Science.gov (United States)

    Belsey, J D

    2008-02-01

    Budgetary pressures within health care systems have led many health care providers to consider the switching of patients on long term anti hypertensive medication to agents with the lowest acquisition price. The long term success of this strategy hinges on price differentials remaining stable, an assumption that may not be valid in drug classes where patent expiry times vary. The treatment of hypertension using angiotensin receptor blockers (ARBs) represents just such a case. The present study, therefore, modelled the 5-year cost consequences of treatment based on losartan, candesartan, valsartan and irbesartan, based on expected patent expiry dates. A Markov model was constructed, applying dose-specific blood-pressure lowering and costs to a cohort of uncontrolled mild-moderate hypertensive patients and assessing the anticipated cost of treatment over a 5 year period. A probabilistic approach was adopted to account for between-patient and between-treatment differences. For both undiscounted and discounted models, a losartan-based regimen represents the least costly option of the four agents tested. Median (IQR) discounted expenditure per patient for each agent was: losartan: pound 506 ( pound 441- pound 650), candesartan: pound 610 ( pound 542- pound 766), valsartan: pound 809 ( pound 796- pound 1078), irbesartan pound 696 ( pound 694- pound 934). Switching hypertensive patients taking ARBs to the agent with the lowest current acquisition cost may yield only transient budgetary savings. Once patent expiry is taken into account, this model suggests that maintaining or switching patients to losartan would yield considerably greater savings over 5 years.

  18. Family and population-based studies of variation within the ghrelin receptor locus in relation to measures of obesity.

    Directory of Open Access Journals (Sweden)

    Anette P Gjesing

    Full Text Available BACKGROUND: The growth hormone secretagogue receptor (GHSR is mediating hunger sensation when stimulated by its natural ligand ghrelin. In the present study, we tested the hypothesis that common and rare variation in the GHSR locus are related to increased prevalence of obesity and overweight among Whites. METHODOLOGY/PRINCIPAL FINDINGS: In a population-based study sample of 15,854 unrelated, middle-aged Danes, seven variants were genotyped to capture common variation in an 11 kbp region including GHSR. These were investigated for their individual and haplotypic association with obesity. None of these analyses revealed consistent association with measures of obesity. A -151C/T promoter mutation in the GHSR was found in two unrelated obese patients. One family presented with complete co-segregation, but the other with incomplete co-segregation. The mutation resulted in an increased transcriptional activity (p0.05 could be shown. CONCLUSIONS/SIGNIFICANCE: In a population-based study sample of 15,854 Danes no association between GHSR genotypes and measures of obesity and overweight was found. Also, analyses of GHSR haplotypes lack consistent associations with obesity related traits. A rare functional GHSR promoter mutation variant was identified, yet there was no consistent relationship with obesity in neither family- nor population-based studies.

  19. Receptor Expression in Rat Skeletal Muscle Cell Cultures

    Science.gov (United States)

    Young, Ronald B.

    1996-01-01

    One on the most persistent problems with long-term space flight is atrophy of skeletal muscles. Skeletal muscle is unique as a tissue in the body in that its ability to undergo atrophy or hypertrophy is controlled exclusively by cues from the extracellular environment. The mechanism of communication between muscle cells and their environment is through a group of membrane-bound and soluble receptors, each of which carries out unique, but often interrelated, functions. The primary receptors include acetyl choline receptors, beta-adrenergic receptors, glucocorticoid receptors, insulin receptors, growth hormone (i.e., somatotropin) receptors, insulin-like growth factor receptors, and steroid receptors. This project has been initiated to develop an integrated approach toward muscle atrophy and hypertrophy that takes into account information on the populations of the entire group of receptors (and their respective hormone concentrations), and it is hypothesized that this information can form the basis for a predictive computer model for muscle atrophy and hypertrophy. The conceptual basis for this project is illustrated in the figure below. The individual receptors are shown as membrane-bound, with the exception of the glucocorticoid receptor which is a soluble intracellular receptor. Each of these receptors has an extracellular signalling component (e.g., innervation, glucocorticoids, epinephrine, etc.), and following the interaction of the extracellular component with the receptor itself, an intracellular signal is generated. Each of these intracellular signals is unique in its own way; however, they are often interrelated.

  20. Functional analysis of Torpedo californica nicotinic acetylcholine receptors in multiple activation states by SSM-based electrophysiology.

    Science.gov (United States)

    Niessen, K V; Muschik, S; Langguth, F; Rappenglück, S; Seeger, T; Thiermann, H; Worek, F

    2016-04-15

    Organophosphorus compounds (OPC), i.e. nerve agents or pesticides, are highly toxic due to their strong inhibition potency against acetylcholinesterase (AChE). Inhibited AChE results in accumulation of acetylcholine in the synaptic cleft and thus the desensitisation of the nicotinic acetylcholine receptor (nAChR) in the postsynaptic membrane is provoked. Direct targeting of nAChR to reduce receptor desensitisation might be an alternative therapeutic approach. For drug discovery, functional properties of potent therapeutic candidates need to be investigated in addition to affinity properties. Solid supported membrane (SSM)-based electrophysiology is useful for functional characterisation of ligand-gated ion channels like nAChRs, as charge translocations via capacitive coupling of the supporting membrane can be measured. By varying the agonist (carbamoylcholine) concentration, different functional states of the nAChR were initiated. Using plasma membrane preparations obtained from Torpedo californica electric organ, functional properties of selected nAChR ligands and non-oxime bispyridinium compounds were investigated. Depending on overall-size, the bispyridinium compounds enhanced or inhibited cholinergic signals induced by 100 μM carbamoylcholine. Applying excessive concentrations of the agonist carbamoylcholine provoked desensitisation of the nAChRs, whereas addition of bispyridinium compounds bearing short alkyl linkers exhibited functional recovery of previously desensitised nAChRs. The results suggest that these non-oxime bispyridinium compounds possibly interacted with nAChR subtypes in a manner of a positive allosteric modulator (PAM). The described newly developed functional assay is a valuable tool for the assessment of functional properties of potential compounds such as nAChR modulating ligands, which might be a promising approach in the therapeutically treatment of OPC-poisonings. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.