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Sample records for bound receptor based

  1. 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.

  2. Mutually Unbiased Bases and Bound Entanglement

    OpenAIRE

    Hiesmayr, Beatrix C.; Löffler, Wolfgang

    2013-01-01

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

  3. Co-Immunoprecipitation of Membrane-Bound Receptors

    Science.gov (United States)

    Avila, Julian R.; Lee, Jin Suk; Torii, Keiko U.

    2015-01-01

    The study of cell-surface receptor dynamics is critical for understanding how cells sense and respond to changing environments. Therefore, elucidating the mechanisms by which signals are perceived and communicated into the cell is necessary to understand immunity, development, and stress. Challenges in testing interactions of membrane-bound proteins include their dynamic nature, their abundance, and the complex dual environment (lipid/soluble) in which they reside. Co-Immunoprecipitation (Co-IP) of tagged membrane proteins is a widely used approach to test protein-protein interaction in vivo. In this protocol we present a method to perform Co-IP using enriched membrane proteins in isolated microsomal fractions. The different variations of this protocol are highlighted, including recommendations and troubleshooting guides in order to optimize its application. This Co-IP protocol has been developed to test the interaction of receptor-like kinases, their interacting partners, and peptide ligands in stable Arabidopsis thaliana lines, but can be modified to test interactions in transiently expressed proteins in tobacco, and potentially in other plant models, or scaled for large-scale protein-protein interactions at the membrane. PMID:26097438

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

    Energy Technology Data Exchange (ETDEWEB)

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

    1993-01-01

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

  5. Kinetics of Carbamylcholine Binding to Membrane-Bound Acetylcholine Receptor Monitored by Fluorescence Changes of a Covalently Bound Probe

    OpenAIRE

    Dunn, Susan M.J.; Blanchard, Steven G.; Raftery, Michael A.

    1980-01-01

    The fluorescent probe 5-(iodoacetamido)salicylic acid has been used to alkylate acetylcholine receptor enriched membrane fragments from Torpedo californica following their reduction with low concentrations of dithiothreitol. This modification did not affect the equilibrium binding of carbamylcholine to the receptor. The fluorescence of bound 5-(iodoacetamido)salicylic acid was enhanced when the labeled membrane fragments were mixed with carbamylcholine. This increase in fluorescence was ab...

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

    OpenAIRE

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

    2015-01-01

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

  7. Bounds on Codes Based on Graph Theory

    CERN Document Server

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

    2008-01-01

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

  8. Structure of adenovirus bound to cellular receptor car

    Science.gov (United States)

    Freimuth, Paul I.

    2007-01-02

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

  9. Bounds on Codes Based on Graph Theory

    OpenAIRE

    Rouayheb, Salim Y. El; Georghiades, C. N.; Soljanin, E.; Sprintson, A.

    2008-01-01

    Let $A_q(n,d)$ be the maximum order (maximum number of codewords) of a $q$-ary code of length $n$ and Hamming distance at least $d$. And let $A(n,d,w)$ that of a binary code of constant weight $w$. Building on results from algebraic graph theory and Erd\\H{o}s-ko-Rado like theorems in extremal combinatorics, we show how several known bounds on $A_q(n,d)$ and $A(n,d,w)$ can be easily obtained in a single framework. For instance, both the Hamming and Singleton bounds can derived as an applicatio...

  10. Upper bounds for reversible circuits based on Young subgroups

    DEFF Research Database (Denmark)

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

    2014-01-01

    We present tighter upper bounds on the number of Toffoli gates needed in reversible circuits. Both multiple controlled Toffoli gates and mixed polarity Toffoli gates have been considered for this purpose. The calculation of the bounds is based on a synthesis approach based on Young subgroups that...

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    2016-01-01

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

  13. 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.

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

    International Nuclear Information System (INIS)

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

  15. 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; Jørgensen, Flemming Steen; Gloriam, David Erik Immanuel

    2011-01-01

    A 5-HT(2A) receptor model was constructed by homology modeling based on the ß(2)-adrenergic receptor and the G protein-bound opsin crystal structures. The 5-HT(2A) receptor model was transferred into an active conformation by an agonist ligand and a G(aq) peptide in four subsequent steered...... 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 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...

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

    DEFF Research Database (Denmark)

    Pless, Stephan Alexander; Lynch, Joseph W

    2009-01-01

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

  17. Confidence bounds of recurrence-based complexity measures

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-06-15

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

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

    Science.gov (United States)

    Rodríguez, David; Ranganathan, Anirudh; Carlsson, Jens

    2014-07-28

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

  19. Negative correlation between the conversion of thyrotropin receptor-bound blocking type thyrotropin receptor antibody to the stimulating type by anti-human IgG antibodies and the biological activity of blocking type thyrotropin receptor antibody.

    OpenAIRE

    Cho, B. Y.; Shong, M. H.; Chung, J. H.; Lee, H. K.; Koh, C S; Min, H. K.

    1993-01-01

    It has been reported that receptor-bound blocking type TSH receptor antibody (TRAb) can be converted to the stimulating type by anti-human IgG antibodies. To evaluate the relationship between the conversion of receptor-bound blocking type TRAb to the stimulating type and the biological activity of blocking type TRAb, we compared converting activities of blocking type TRAb from 10 patients with primary nongoitrous hypothyroidism with both the doses of blocking type TRAb which show 50% inhibiti...

  20. Trajectory based models. Evaluation of minmax pricing bounds

    OpenAIRE

    Degano, Ivan; Ferrando, Sebastian; Gonzalez, Alfredo

    2015-01-01

    The paper studies market models based on trajectory spaces, properties of such models are obtained without recourse to probabilistic assumptions. For a given European option, an interval of rational prices exists under a more general condition than the usual no-arbitrage requirement. The paper develops computational results in order to evaluate the option bounds; the global minmax optimization, defining the price interval, is reduced to a local minmax optimization via dynamic programming. A g...

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

    OpenAIRE

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

    2013-01-01

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

  2. Flexibility in the Insulin Receptor Ectodomain Enables Docking of Insulin in Crystallographic Conformation Observed in a Hormone-Bound Microreceptor

    OpenAIRE

    Harish Vashisth

    2014-01-01

    Insulin binding to the insulin receptor (IR) is the first key step in initiating downstream signaling cascades for glucose homeostasis in higher organisms. The molecular details of insulin recognition by IR are not yet completely understood, but a picture of hormone/receptor interactions at one of the epitopes (Site 1) is beginning to emerge from recent structural evidence. However, insulin-bound structures of truncated IR suggest that crystallographic conformation of insulin cannot be accomm...

  3. Construction of bound entangled states based on permutation operators

    Science.gov (United States)

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

    2016-04-01

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

  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...... 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....

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

    Directory of Open Access Journals (Sweden)

    Ruonan Rao

    2010-01-01

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

  6. Receptor-Bound Targets of Selective Autophagy Use a Scaffold Protein to Activate the Atg1 Kinase.

    Science.gov (United States)

    Kamber, Roarke A; Shoemaker, Christopher J; Denic, Vladimir

    2015-08-01

    Selective autophagy eliminates protein aggregates, damaged organelles, and other targets that otherwise accumulate and cause disease. Autophagy receptors mediate selectivity by connecting targets to the autophagosome membrane. It has remained unknown whether receptors perform additional functions. Here, we show that in yeast certain receptor-bound targets activate Atg1, the kinase that controls autophagosome formation. Specifically, we found that in nutrient-rich conditions, Atg1 is active only in a multisubunit complex comprising constitutive protein aggregates, their autophagy receptor, and a scaffold protein, Atg11. Development of a cell-free assay for Atg1-mediated phosphorylation enabled us to activate Atg1 with purified receptor-bound aggregates and Atg11. Another target, damaged peroxisomes, also activated Atg1 using Atg11 with a distinct receptor. Our work reveals that receptor-target complexes activate Atg1 to drive formation of selective autophagosomes. This regulatory logic is a key similarity between selective autophagy and bulk autophagy, which is initiated by a distinct Atg1 activation mechanism during starvation. PMID:26166702

  7. Abnormal gene expression of proinflammatory cytokines and their membrane-bound receptors in the lymphocytes of depressed patients.

    Science.gov (United States)

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

    2016-06-30

    Abnormalities of protein levels of proinflammatory cytokines and their soluble receptors have been reported in plasma of depressed patients. In this study, we examined the role of cytokines and their membrane-bound receptors in major depressive disorder (MDD). We determined the protein and mRNA expression of proinflammatory cytokines, interleukin (IL)-1β, IL-6, tumor necrosis factor (TNF)-α, and mRNA expression of their membrane-bound receptors in the lymphocytes from 31 hospitalized MDD patients and 30 non-hospitalized normal control (NC) subjects. The subjects were diagnosed according to DSM-IV criteria. Protein levels of cytokines were determined by ELISA, and mRNA levels in lymphocytes were determined by the qPCR method. We found that the mean mRNA levels of the proinflammatory cytokines IL-1β, IL-6, TNF-α, their receptors, TNFR1, TNFR2, IL-1R1 and the antagonist IL-1RA were significantly increased in the lymphocytes of MDD patients compared with NC. No significant differences in the lymphocyte mRNA levels of IL-1R2, IL-6R, and Gp130 were observed between MDD patients and NC. These studies suggest abnormal gene expression of these cytokines and their membrane-bound receptors in the lymphocytes of MDD patients, and that their mRNA expression levels in the lymphocytes could be a useful biomarker for depression. PMID:27138824

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

    CERN Document Server

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

    2010-01-01

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

  9. Ebola Viral Glycoprotein Bound to Its Endosomal Receptor Niemann-Pick C1.

    Science.gov (United States)

    Wang, Han; Shi, Yi; Song, Jian; Qi, Jianxun; Lu, Guangwen; Yan, Jinghua; Gao, George F

    2016-01-14

    Filoviruses, including Ebola and Marburg, cause fatal hemorrhagic fever in humans and primates. Understanding how these viruses enter host cells could help to develop effective therapeutics. An endosomal protein, Niemann-Pick C1 (NPC1), has been identified as a necessary entry receptor for this process, and priming of the viral glycoprotein (GP) to a fusion-competent state is a prerequisite for NPC1 binding. Here, we have determined the crystal structure of the primed GP (GPcl) of Ebola virus bound to domain C of NPC1 (NPC1-C) at a resolution of 2.3 Å. NPC1-C utilizes two protruding loops to engage a hydrophobic cavity on head of GPcl. Upon enzymatic cleavage and NPC1-C binding, conformational change in the GPcl further affects the state of the internal fusion loop, triggering membrane fusion. Our data therefore provide structural insights into filovirus entry in the late endosome and the molecular basis for design of therapeutic inhibitors of viral entry. PMID:26771495

  10. Image Distortion Metric Based on Total Bounded Variation

    Institute of Scientific and Technical Information of China (English)

    Cheng Xiaogang; An Mingwei; Chen Qimei

    2012-01-01

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

  11. Persistence-Based Branch Misprediction Bounds for WCET Analysis

    DEFF Research Database (Denmark)

    Puffitsch, Wolfgang

    Branch prediction is an important feature of pipelined processors to achieve high performance. However, it can lead to overly pessimistic worst-case execution time (WCET) bounds when being modeled too conservatively. This paper presents bounds on the number of branch mispredictions for local...... 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...... 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....

  12. 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.

  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; Espersen, Torben Grønvall

    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...... general bounding procedure based on the dual of the linearization of Adams and Johnson. The new procedure has been applied to problems of dimension up to...

  14. Bound of Noncommutativity Parameter Based on Black Hole Entropy

    OpenAIRE

    Kim, Wontae; Lee, Daeho

    2010-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Reinhold Egger

    2013-01-01

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

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

    OpenAIRE

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

    2008-01-01

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

  17. Efficient Amide Based Halogenide Anion Receptors

    Institute of Scientific and Technical Information of China (English)

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

    2005-01-01

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

  18. 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

    The specific cellular receptor for urokinase-type plasminogen activator (uPA) is found on a variety of cell types and has been postulated to play a central role in the mediation of pericellular proteolytic activity. We have studied the kinetics of plasminogen (Plg) activation catalyzed by uPA spe...

  19. Subunit structure of the follitropin (FSH) receptor. Photoaffinity labeling of the membrane-bound receptor follitropin complex in situ

    International Nuclear Information System (INIS)

    Human follicle-stimulating hormone (hFSH) was acylated with N-hydroxysuccinimidyl-4-azidobenzoate (HSAB) and radioiodinated (55 microCi/micrograms) for use as a photoaffinity probe to investigate the subunit structure of the FSH receptor in calf testis. After incubation with the photoaffinity probe and photolysis with UV light, the cross-linked hormone-receptor complex was solubilized from the membrane and subjected to sodium dodecyl sulfate-polyacrylamide gel electrophoresis in the presence and absence of the reducing agent dithiothreitol. Autoradiography of the polyacrylamide gels revealed two major bands, 64 kDa and 84 kDa. These were equivalent in molecular mass to those observed in a previous study in which performed hormone-receptor complexes were solubilized with detergent prior to formation of covalent cross-linkages through the use of homobifunctional cross-linking reagents. Reduction with dithiothreitol resulted in the loss of radioactivity from the 84-kDa band with a concomitant increase in the intensity of the 64-kDa band. Since dithiothreitol increases the dissociation of intact radioiodinated azidobenzoyl-FSH into subunits, it is suggested that the conversion of the 84-kDa band to the 64-kDa band by dithiothreitol is due to the loss of non-cross-linked hFSH subunit from the 84-kDa band and that the two bands observed after photoaffinity labeling arise from covalent bond formation between hFSH and a receptor subunit having a relative molecular weight (Mr) of 48,000. In addition to the predominant photolabeling of the receptor to yield the 64-kDa and 84-kDa bands, several other, less intense bands (54 kDa, 76 kDa, 97 kDa, and 116 kDa) were also consistently observed on autoradiographs

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

    OpenAIRE

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

    2008-01-01

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

  1. Two unrelated putative membrane-bound progestin receptors, progesterone membrane receptor component 1 (PGMRC1 and membrane progestin receptor (mPR beta, are expressed in the rainbow trout oocyte and exhibit similar ovarian expression patterns

    Directory of Open Access Journals (Sweden)

    Fostier Alexis

    2006-02-01

    Full Text Available Abstract Background In lower vertebrates, steroid-induced oocyte maturation is considered to involve membrane-bound progestin receptors. Two totally distinct classes of putative membrane-bound progestin receptors have been reported in vertebrates. A first class of receptors, now termed progesterone membrane receptor component (PGMRC; subtypes 1 and 2 has been studied since 1996 but never studied in a fish species nor in the oocyte of any animal species. A second class of receptors, termed membrane progestin receptors (mPR; subtypes alpha, beta and gamma, was recently described in vertebrates and implicated in the progestin-initiated induction of oocyte maturation in fish. Methods In the present study, we report the characterization of the full coding sequence of rainbow trout PGMRC1 and mPR beta cDNAs, their tissue distribution, their ovarian expression profiles during oogenesis, their hormonal regulation in the full grown ovary and the in situ localization of PGMRC1 mRNA in the ovary. Results Our results clearly show, for the first time in any animal species, that rainbow trout PGMRC1 mRNA is present in the oocyte and has a strong expression in ovarian tissue. In addition, we show that both mPR beta and PGMRC1, two members of distinct membrane-bound progestin receptor classes, exhibit highly similar ovarian expression profiles during the reproductive cycle with maximum levels during vitellogenesis and a down-expression during late vitellogenesis. In addition, the mRNA abundance of both genes is not increased after in vitro hormonal stimulation of full grown follicles by maturation inducing hormones. Conclusion Together, our findings suggest that PGMRC1 is a new possible participant in the progestin-induced oocyte maturation in fish. However, its participation in the process of oocyte maturation, which remains to be confirmed, would occur at post-transcriptional levels.

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

    OpenAIRE

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

    2015-01-01

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

  3. An improved lower bound for the asymmetric traveling salesman problem based on the assignment problem

    OpenAIRE

    Ramires, Ana; Soares, João

    2005-01-01

    In this article we decribe how to compute a lower bound for the asymmetric traveling salesman problem that dominates the bound that comes from the assignment relaxation, through the solving of a sequence of assignment problems. The algorithm that we propose is a first-order method based on the exponential penalty function. Directions of movement are derived from a disjunctive relaxation that we proposed as being one of two possible classes, one based on cycles, the other based on cliques.

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

    OpenAIRE

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2005-12-20

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

  6. Computing bounds for kernel-based policy evaluation in reinforcement learning

    OpenAIRE

    Fonteneau, Raphaël; Murphy, Susan A.; Wehenkel, Louis; Ernst, Damien

    2010-01-01

    This technical report proposes an approach for computing bounds on the finite-time return of a policy using kernel-based approximators from a sample of trajectories in a continuous state space and deterministic framework.

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

    Science.gov (United States)

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

    2010-05-01

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

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

    International Nuclear Information System (INIS)

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

  9. A complexity lower bound based on software engineering concepts

    OpenAIRE

    Rojas Paredes, Andrés

    2013-01-01

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

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

    OpenAIRE

    Ruonan Rao; Shuyin Liang; Jinyuan You

    2010-01-01

    Geographic-based routing allows routing in mobile ad hoc networks (MANETs) yet avoiding the overhead for maintaining the topology changes in MANETs. A critical challenge in geographic routing protocols is the design of a scalable distributed location services that tracks the locations of mobile nodes in MANETs. Although a number of location services have been proposed, in typical works, the performance is not satisfactory when it comes to locality problem, which introduce high overhead in upd...

  11. Calixarene-based receptors for molecular recognition

    OpenAIRE

    YILMAZ, Mustafa; ERDEMİR, Serkan

    2013-01-01

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

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

    Science.gov (United States)

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

    2016-10-01

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

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

    KAUST Repository

    Rungta, Meha

    2013-08-02

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-10-22

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

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

    Science.gov (United States)

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

    2016-04-26

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

  16. A methodology for computing uncertainty bounds of multivariable systems based on sector stability theory concepts

    Science.gov (United States)

    Waszak, Martin R.

    1992-01-01

    The application of a sector-based stability theory approach to the formulation of useful uncertainty descriptions for linear, time-invariant, multivariable systems is explored. A review of basic sector properties and sector-based approach are presented first. The sector-based approach is then applied to several general forms of parameter uncertainty to investigate its advantages and limitations. The results indicate that the sector uncertainty bound can be used effectively to evaluate the impact of parameter uncertainties on the frequency response of the design model. Inherent conservatism is a potential limitation of the sector-based approach, especially for highly dependent uncertain parameters. In addition, the representation of the system dynamics can affect the amount of conservatism reflected in the sector bound. Careful application of the model can help to reduce this conservatism, however, and the solution approach has some degrees of freedom that may be further exploited to reduce the conservatism.

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

    Science.gov (United States)

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

    2015-10-01

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

  18. Upper Bounding Service Capacity in Multihop Wireless SSMA-Based Ad Hoc Networks

    Science.gov (United States)

    Du, Shirong; Daigle, John N.; Alidaee, Bahram

    Upper bounds on the service carrying capacity of a multihop, wireless, SSMA-based ad hoc network are considered herein. The network has a single radio band for transmission and reception. Each node can transmit to, or receive from, multiple nodes simultaneously. We formulate the scheduling of transmissions and control of transmit powers as a joint, mixed-integer, nonlinear optimization problem that yields maximum return at minimum power subject to SINR constraints. We present an efficient tabu search-based heuristic algorithm to solve the optimization problem and rigorously assess the quality of the results. Through analysis and simulation, we establish upper bounds on the VoIP call carrying capacity of the network as function of various parameters. We discuss the pros and cons of using SSMA as a spectrum sharing technique in wireless ad hoc networks

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

    OpenAIRE

    Kohei Arai

    2012-01-01

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

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

    OpenAIRE

    Mahdi Azizi; Abdolrasol Mirgadri; Nasour Bagheri

    2012-01-01

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

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

    International Nuclear Information System (INIS)

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-12-11

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

  3. SMT-Based Bounded Model Checking for Embedded ANSI-C Software

    CERN Document Server

    Cordeiro, Lucas; Marques-Silva, Joao

    2009-01-01

    Propositional bounded model checking has been applied successfully to verify embedded software but is limited by the increasing propositional formula size and the loss of structure during the translation. These limitations can be reduced by encoding word-level information in theories richer than propositional logic and using SMT solvers for the generated verification conditions. Here, we investigate the application of different SMT solvers to the verification of embedded software written in ANSI-C. We have extended the encodings from previous SMT-based bounded model checkers to provide more accurate support for finite variables, bit-vector operations, arrays, structures, unions and pointers. We have integrated the CVC3, Boolector, and Z3 solvers with the CBMC front-end and evaluated them using both standard software model checking benchmarks and typical embedded applications from telecommunications, control systems and medical devices. The experiments show that our approach can analyze larger problems and sub...

  4. 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.

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

    International Nuclear Information System (INIS)

    Estrogen receptor alpha (ERα), a ligand controlled transcription factor, plays an important role in breast cancer growth and endocrine therapy. Tamoxifen (TAM) antagonizes ERα activity and has been applied in breast cancer treatment. TAM-bound ERα associates with nuclear receptor-corepressors. Mitogen-activated protein kinase (MAPK) has been elucidated to result in cross-talk between growth factor and ERα mediated signaling. We show that activated MAPK represses interaction of TAM-bound ERα with silencing mediator for retinoid and thyroid hormone receptors (SMRT) and inhibits the recruitment of SMRT by ERα to certain estrogen target genes. Blockade of MAPK signaling cascade with MEK inhibitor U0126 promotes the interaction and subsequently inhibits ERα activity via enhanced recruitment of SMRT, leading to reduced expression of ERα 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 ERα, suggesting corepressor mediates inhibition of ERα 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.

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

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

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

  7. 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...... 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....

  8. Ligand modulates the conversion of DNA-bound vitamin D3 receptor (VDR) homodimers into VDR-retinoid X receptor heterodimers.

    OpenAIRE

    Cheskis, B; Freedman, L P

    1994-01-01

    Protein dimerization facilitates cooperative, high-affinity interactions with DNA. Nuclear hormone receptors, for example, bind either as homodimers or as heterodimers with retinoid X receptors (RXR) to half-site repeats that are stabilized by protein-protein interactions mediated by residues within both the DNA- and ligand-binding domains. In vivo, ligand binding among the subfamily of steroid receptors unmasks the nuclear localization and DNA-binding domains from a complex with auxiliary fa...

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

    OpenAIRE

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

    2013-01-01

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

  10. A drug will not function unless it is bound to a receptor: a longstanding confusion in basic pharmacology

    Directory of Open Access Journals (Sweden)

    Partha S. Saha

    2013-12-01

    Full Text Available The disparity between the general definition of a ‘drug’ and the wide-spread mechanism of actions of receptor-dependent drugs may often mislead to believe that a drug-receptor interaction is always indispensable for a drug to exert its action. This short review is intended to rectify this basic misconception in pharmacology with the aid of a list of examples of several receptor-independent drugs in context to their mode of actions. [Int J Basic Clin Pharmacol 2013; 2(6.000: 693-695

  11. Nanobiosensors based on individual olfactory receptors

    CERN Document Server

    Pajot-Augy, E

    2008-01-01

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

  12. 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.

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

    Institute of Scientific and Technical Information of China (English)

    Shu-Tao Zhou; Ying-Hua Liu

    2012-01-01

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

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

    Science.gov (United States)

    Zhou, Shu-Tao; Liu, Ying-Hua

    2012-10-01

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

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

    Science.gov (United States)

    Kurics, Tamás; Menshykau, Denis; Iber, Dagmar

    2014-08-01

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

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

    CERN Document Server

    Gupta, Sandeep

    2012-01-01

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

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

    CERN Document Server

    Cordeiro, Lucas; Marques-Silva, Joao

    2009-01-01

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

  18. Nanoscale patterning of membrane-bound proteins formed through curvature-induced partitioning of phase-specific receptor lipids.

    Science.gov (United States)

    Ogunyankin, Maria O; Huber, Dale L; Sasaki, Darryl Y; Longo, Marjorie L

    2013-05-21

    This work describes a technique for forming high-density arrays and patterns of membrane-bound proteins through binding to a curvature-organized compositional pattern of metal-chelating lipids (Cu(2+)-DOIDA or Cu(2+)-DSIDA). In this bottom-up approach, the underlying support is an e-beam formed, square lattice pattern of hemispheres. This curvature pattern sorts Cu(2+)-DOIDA to the 200 nm hemispherical lattice sites of a 600 nm × 600 nm unit cell in Ld - Lo phase separated lipid multibilayers. Binding of histidine-tagged green fluorescent protein (His-GFP) creates a high density array of His-GFP-bound pixels localized to the square lattice sites. In comparison, the negative pixel pattern is created by sorting Cu(2+)-DSIDA in Ld - Lβ' phase separated lipid multibilayers to the flat grid between the lattice sites followed by binding to His-GFP. Lattice defects in the His-GFP pattern lead to interesting features such as pattern circularity. We also observe defect-free arrays of His-GFP that demonstrate perfect arrays can be formed by this method suggesting the possibility of using this approach for the localization of various active molecules to form protein, DNA, or optically active molecular arrays. PMID:23642033

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

    Directory of Open Access Journals (Sweden)

    Jennifer L Miller-Gallacher

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

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

    CERN Document Server

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

    2012-01-01

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

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

    OpenAIRE

    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 lower bound. In the first part of this thesis, we analyze promising old and new semidefinite programming (SDP) relaxations. In particular, we focus on their complexity, the strength of the respect...

  2. Binding affinity prediction of novel estrogen receptor ligands using receptor-based 3-D QSAR methods.

    Science.gov (United States)

    Sippl, Wolfgang

    2002-12-01

    We have recently reported the development of a 3-D QSAR model for estrogen receptor ligands showing a significant correlation between calculated molecular interaction fields and experimentally measured binding affinity. The ligand alignment obtained from docking simulations was taken as basis for a comparative field analysis applying the GRID/GOLPE program. Using the interaction field derived with a water probe and applying the smart region definition (SRD) variable selection procedure, a significant and robust model was obtained (q(2)(LOO)=0.921, SDEP=0.345). To further analyze the robustness and the predictivity of the established model several recently developed estrogen receptor ligands were selected as external test set. An excellent agreement between predicted and experimental binding data was obtained indicated by an external SDEP of 0.531. Two other traditionally used prediction techniques were applied in order to check the performance of the receptor-based 3-D QSAR procedure. The interaction energies calculated on the basis of receptor-ligand complexes were correlated with experimentally observed affinities. Also ligand-based 3-D QSAR models were generated using program FlexS. The interaction energy-based model, as well as the ligand-based 3-D QSAR models yielded models with lower predictivity. The comparison with the interaction energy-based model and with the ligand-based 3-D QSAR models, respectively, indicates that the combination of receptor-based and 3-D QSAR methods is able to improve the quality of prediction. PMID:12413831

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

    OpenAIRE

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

    2005-01-01

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

  4. Wash-resistantly bound xanomeline inhibits acetylcholine release by persistent activation of presynaptic M2 and M4 muscarinic receptors

    Czech Academy of Sciences Publication Activity Database

    Machová, Eva; Jakubík, Jan; El-Fakahany, E. E.; Doležal, Vladimír

    Praha : 2.Lékařská fakulta UK, 2007. s. 55-55. [Vědecká konference 2007 - věda, sport a rock ´n´roll. 25.04.2007-26.04.2007, Praha] R&D Projects: GA ČR(CZ) GA305/05/0452; GA MŠk(CZ) LC554 Grant ostatní: NIH(US) NS25732 Institutional research plan: CEZ:AV0Z50110509 Keywords : spo2 * xanomeline * acetylcholine * presynaptic muscarinic receptors Subject RIV: FH - Neurology

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

    Science.gov (United States)

    Kim, Sung Kuk; Sessler, Jonathan L

    2014-08-19

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

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

    Science.gov (United States)

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

    2016-01-01

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

  7. Bounded Earthquakes

    OpenAIRE

    Saric, Dragomir

    2006-01-01

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

  8. Biophysics of risk aversion based on neurotransmitter receptor theory

    OpenAIRE

    Takahashi, Taiki

    2011-01-01

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

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

    Science.gov (United States)

    Evers, Andreas; Klebe, Gerhard

    2004-10-21

    The neurokinin-1 (NK1) receptor belongs to the family of G-protein-coupled receptors (GPCRs), which represents one of the most relevant target families in small-molecule drug design. In this paper, we describe a homology modeling of the NK1 receptor based on the high-resolution X-ray structure of rhodopsin and the successful virtual screening based on this protein model. The NK1 receptor model has been generated using our new MOBILE (modeling binding sites including ligand information explicitly) approach. Starting with preliminary homology models, it generates improved models of the protein binding pocket together with bound ligands. Ligand information is used as an integral part in the homology modeling process. For the construction of the NK1 receptor, antagonist CP-96345 was used to restrain the modeling. The quality of the obtained model was validated by probing its ability to accommodate additional known NK1 antagonists from structurally diverse classes. On the basis of the generated model and on the analysis of known NK1 antagonists, a pharmacophore model was deduced, which subsequently guided the 2D and 3D database search with UNITY. As a following step, the remaining hits were docked into the modeled binding pocket of the NK1 receptor. Finally, seven compounds were selected for biochemical testing, from which one showed affinity in the submicromolar range. Our results suggest that ligand-supported homology models of GPCRs may be used as effective platforms for structure-based drug design. PMID:15481976

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

    Directory of Open Access Journals (Sweden)

    Christina Koers-Wunrau

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

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

    Science.gov (United States)

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

    2016-08-01

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

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

    International Nuclear Information System (INIS)

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

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

    NARCIS (Netherlands)

    Boesten, J.J.T.I.

    2016-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2004-06-24

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

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

    OpenAIRE

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

    2015-01-01

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

  17. A Lagrangian Dual-Based Branch-and-Bound Algorithm for the Generalized Multi-Assignment Problem

    OpenAIRE

    June S. Park; Byung Ha Lim; Youngho Lee

    1998-01-01

    This paper develops a Lagrangian dual-based branch-and-bound algorithm for the generalized multi-assignment problem (GMAP) which includes the well-known generalized assignment problem (GAP) as a special case. In GMAP, an object may be required to be duplicated in multiple locations. We develop a Lagrangian dual ascent algorithm for GMAP. This dual ascent and the subgradient search each possess advantages that can be combined to develop a new Lagrangian dual search algorithm. The latter algori...

  18. Hybrid procedure based on Bounded Dynamic Programming and Linear Programming for solving a variant of the MMSP-W

    OpenAIRE

    Bautista Valhondo, Joaquín; Cano Pérez, Alberto; Alfaro Pozo, Rocío; Batalla García, Cristina

    2013-01-01

    n this paper, we propose a hybrid procedure based on Bounded Dynamic Programming ( BDP ) and linear programming to solve the Mixed - Model Se quencing Problem with Workload Minimization ( MMSP - W ), with serial workstations, free interruption of the operations and production mix restrictions. We performed a computational experiment with 225 instances from the literature. The results of our proposal are compared with those obtained through the Guro...

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

    Directory of Open Access Journals (Sweden)

    Ellis L Reinherz

    2014-09-01

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

  20. 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).

  1. 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

  2. Material growth and device fabrication of terahertz quantum-cascade laser based on bound-to-continuum structure

    International Nuclear Information System (INIS)

    The terahertz quantum-cascade laser (THz QCL) based on bound-to-continuum structure is demonstrated. The X-ray diffraction measurement of the material shows a high crystalline quality of the active region. A THz QCL device was fabricated with semi-insulating surface-plasmon waveguide. The test device is lasing at about 3 THz and operating up to 60 K. It shows a single frequency property under different drive currents and temperatures. At 9 K, the maximum output power is greater than 2 mW with a threshold current density of 159 A/cm2. (electromagnetism, optics, acoustics, heat transfer, classical mechanics, and fluid dynamics)

  3. 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

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

    Directory of Open Access Journals (Sweden)

    Gérard Tchouassi

    2014-06-01

    Full Text Available Using time series, autoregressive distributed lags (ARDL-bound test approach and error-correction model (ECM, this paper aims to analyze how private capital and investment climate contribute to economic growth in African countries: Cameroon, Côte d’Ivoire, Tunisia, South Africa and Zambia. We find that in short-run there is a significant relationship between private capital, economic freedom and economic growth in Cameroon, in Côte d’Ivoire, in South Africa and in Zambia. In long run, we establish that a long term relationship exists between the variables. This implies that there is a long run cointegration relationship among the variables in some equations in Cameroon, Côte d’Ivoire, South Africa and Zambia. Employing the appropriate order of the ARDL specification and multidimensional economic freedom proxies to examine this linkage, the results obtained are not all significant.  JEL Classifications: C13, C22, E22, F43, O11, O47 Key-Words: Private capital, Investment climate, Economic freedom, Economic growth, Time series, ARDL bound test approach, Error-Correction Model. Normal 0 14 false false false IT X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Tabella normale"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-qformat:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:11.0pt; font-family:"Calibri","sans-serif"; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-fareast-font-family:"Times New Roman"; mso-fareast-theme-font:minor-fareast; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:"Times New Roman"; mso-bidi-theme-font:minor-bidi;}

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

    International Nuclear Information System (INIS)

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

  6. LDPC-Based Iterative Algorithm for Compression of Correlated Sources at Rates Approaching the Slepian-Wolf Bound

    CERN Document Server

    Daneshgaran, F; Mondin, M

    2007-01-01

    This article proposes a novel iterative algorithm based on Low Density Parity Check (LDPC) codes for compression of correlated sources at rates approaching the Slepian-Wolf bound. The setup considered in the article looks at the problem of compressing one source at a rate determined based on the knowledge of the mean source correlation at the encoder, and employing the other correlated source as side information at the decoder which decompresses the first source based on the estimates of the actual correlation. We demonstrate that depending on the extent of the actual source correlation estimated through an iterative paradigm, significant compression can be obtained relative to the case the decoder does not use the implicit knowledge of the existence of correlation.

  7. Generalized Sphere Packing Bound

    OpenAIRE

    Fazeli, Arman; Vardy, Alexander; Yaakobi, Eitan

    2014-01-01

    Kulkarni and Kiyavash recently introduced a new method to establish upper bounds on the size of deletion-correcting codes. This method is based upon tools from hypergraph theory. The deletion channel is represented by a hypergraph whose edges are the deletion balls (or spheres), so that a deletion-correcting code becomes a matching in this hypergraph. Consequently, a bound on the size of such a code can be obtained from bounds on the matching number of a hypergraph. Classical results in hyper...

  8. Development of gene diagnosis for diabetes and cholecystis based on gene analysis of CCK-A receptor

    International Nuclear Information System (INIS)

    The gene structures of CCK, A type receptor in human, the rat and the mouse were investigated aiming to clarify that the aberration of the gene is involved in the incidences of diabetes and cholecystis. In this fiscal year, 1997, the normal structure of the gene and the accurate base sequence were analyzed using DNA fragments bound to 32P-labelled cDNA of human CCKAR originated from the gene library of leucocyte. This gene contained about 2.2 x 105 base pairs and the base sequence was completely determined and registered to Japan DNA data bank (D85606). In addition, the genome structures and base sequences of mouse and rat CCKAR were analyzed and registered (D 85605 and D 50608, respectively). The differences in the base sequence of CCKAR among the species were found in the promotor region and the intron regions, suggesting that there might be differences in splicing among species. (M.N.)

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

    NARCIS (Netherlands)

    Viel, Gerhard Theodoor

    1999-01-01

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

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

    NARCIS (Netherlands)

    Viel, Gerhard Theodoor

    1999-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2012-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Takashi Morii

    2010-02-01

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

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

    DEFF Research Database (Denmark)

    Adamsen, Billy; Thomsen, Svend Erik

    This study applies an agent-based modeling approach to explore some aspects of an important managerial task: finding and cultivating talented individuals capable of creating value for their organization at some future state. Given that the term talent in talent management is an empty signifier...... of past success will provide failure rather than success in the future (Capelli.2008). Finally, we model the talent selection process either as a collective decision making process made by a group of managers or a decision process made by a single manager.It is argued that agent-based modeling is a useful...... 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...

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

    DEFF Research Database (Denmark)

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

    2014-01-01

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

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

    CERN Document Server

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

    2015-01-01

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

  16. 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.

  17. Alterations of the membrane-bound adenyl-cyclase enzyme and beta-receptors in developing glia- and neuron tissue cultures

    International Nuclear Information System (INIS)

    The development of beta-receptors was investigated on the basis of specific 3H-L-dihydro-alprenolol (DHA) binding. The dependence of the binding on time and concentration the dissociation constant and the number of receptor sites on one cell were determined. It is concluded that the number of 3H-DHA binding sites significantly increases after preincubation with beta-agonists and in mixed glia-neuron cultures. (L.E.)

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

    Science.gov (United States)

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

    2015-09-01

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

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

    Directory of Open Access Journals (Sweden)

    Niedermeier Rolf

    2011-08-01

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

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

    CERN Document Server

    Einolghozati, Arash; Fekri, Faramarz

    2012-01-01

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

  1. 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.

  2. 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; Karlsen, Jesper Lykkegaard; Rahbek-Nielsen, Henrik; Paludan, Søren Riis; Hjorth, Siv A; Bondensgaard, Kent; Hartmann, Rune

    2012-01-01

    the class I cytokine receptor signature motif (WSXWS). The exact role of this motif has not been determined yet, however, it has been implicated in diverse functions including ligand binding, receptor internalization, proper folding, and export as well as signal transduction. Furthermore, the WXXW is...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-01-15

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

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

    Institute of Scientific and Technical Information of China (English)

    Zheng Yingren; Deng Chujian; Wang Jinglin

    2010-01-01

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

  5. Information, Utility & Bounded Rationality

    CERN Document Server

    Ortega, Pedro A

    2011-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    姜继娇

    2005-01-01

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

  7. Crystallization and preliminary X-ray diffraction analysis of human IL-22 bound to its soluble decoy receptor IL-22BP

    International Nuclear Information System (INIS)

    The human cytokine IL-22 has been crystallized in complex with its soluble decoy receptor IL-22BP. Diffraction data were collected to 2.75 Å resolution; the crystals belonged to the tetragonal space group P41. Interleukin-22 (IL-22) is a pleiotropic cytokine that is involved in inflammatory responses. Human IL-22 was incubated with its soluble decoy receptor IL-22BP (IL-22 binding protein) and the IL-22–IL-22BP complex was crystallized in hanging drops using the vapour-diffusion method. Suitable crystals were obtained from polyethylene glycol solutions and diffraction data were collected to 2.75 Å resolution. The crystal belonged to the tetragonal space group P41, with unit-cell parameters a = b = 67.9, c = 172.5 Å, and contained two IL-22–IL-22BP complexes per asymmetric unit

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-12-12

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-10-01

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

  10. 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.

  11. Stamping Vital Cells—a Force-Based Ligand Receptor Assay

    OpenAIRE

    Wienken, Uta; Gaub, Hermann E.

    2013-01-01

    Gaining information about receptor profiles on cells, and subsequently finding the most efficient ligands for these signaling receptors, remain challenging tasks in stem cell and cancer research as well as drug development. We introduce a live-cell method with great potential in both screening for surface receptors and analysing binding forces of different ligands. The technique is based on the molecular force assay, a parallel-format, high-throughput experiment on a single-molecule level. On...

  12. Combinatorial Consensus Scoring for Ligand-Based Virtual Fragment Screening: A Comparative Case Study for Serotonin 5-HT(3)A, Histamine H(1), and Histamine H(4) Receptors.

    Science.gov (United States)

    Schultes, Sabine; Kooistra, Albert J; Vischer, Henry F; Nijmeijer, Saskia; Haaksma, Eric E J; Leurs, Rob; de Esch, Iwan J P; de Graaf, Chris

    2015-05-26

    In the current study we have evaluated the applicability of ligand-based virtual screening (LBVS) methods for the identification of small fragment-like biologically active molecules using different similarity descriptors and different consensus scoring approaches. For this purpose, we have evaluated the performance of 14 chemical similarity descriptors in retrospective virtual screening studies to discriminate fragment-like ligands of three membrane-bound receptors from fragments that are experimentally determined to have no affinity for these proteins (true inactives). We used a complete fragment affinity data set of experimentally determined ligands and inactives for two G protein-coupled receptors (GPCRs), the histamine H1 receptor (H1R) and the histamine H4 receptor (H4R), and one ligand-gated ion channel (LGIC), the serotonin receptor (5-HT3AR), to validate our retrospective virtual screening studies. We have exhaustively tested consensus scoring strategies that combine the results of multiple actives (group fusion) or combine different similarity descriptors (similarity fusion), and for the first time systematically evaluated different combinations of group fusion and similarity fusion approaches. Our studies show that for these three case study protein targets both consensus scoring approaches can increase virtual screening enrichments compared to single chemical similarity search methods. Our cheminformatics analyses recommend to use a combination of both group fusion and similarity fusion for prospective ligand-based virtual fragment screening. PMID:25815783

  13. 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

    apparently intact form in the medium or was still cell associated. The degradation could be inhibited by inhibitors of vesicle transport and lysosomal hydrolases. By electron microscopic autoradiography, both 125I-u-PA and 125I-u-PA-inhibitor complexes were located over the cell membrane at 4 degrees C, with...... the highest density of grains over the membrane at cell-cell interphases, but, after incubation at 37 degrees C, 17 and 27% of the grains for u-PA and u-PA-PAI-1 complexes, respectively, appeared over lysosomal-like bodies. These findings suggest that the u-PA receptor possesses a clearance function...

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

    DEFF Research Database (Denmark)

    Venskutonyte, Raminta; Frydenvang, Karla; Valadés, Elena Antón; Szymanska, Ewa Monika; Johansen, Tommy N; Kastrup, Jette S; Pickering, Darryl S

    2012-01-01

    Continued efforts into the discovery of ligands that target ionotropic glutamate receptors (iGluRs) are important for studies of the physiological roles of the various iGluR subtypes as well as for the search for drugs that can be used in the treatment of diseases of the central nervous system. A...

  15. An Arabidopsis MADS-box protein, AGL24, is specifically bound to and phosphorylated by meristematic receptor-like kinase (MRLK).

    Science.gov (United States)

    Fujita, Hidetomo; Takemura, Miho; Tani, Emi; Nemoto, Kyoko; Yokota, Akiho; Kohchi, Takayuki

    2003-07-01

    Intercellular signaling mediated by receptor-like kinases (RLKs) is important for diverse processes in plant development, although downstream intracellular signaling pathways remain poorly understood. Proteins interacting directly with RLK were screened for by yeast two-hybrid assay with the kinase domain as bait. A MADS-box protein, AGL24 was identified as a candidate substrate of MRLK (Meristematic Receptor-Like Kinase), which was named for its spatial expression in shoot and root apical meristems in Arabidopsis: The AGL24 protein specifically interacted with, and was phosphorylated by, the MRLK kinase domain in in vitro assays. The simultaneous expression of AGL24 and MRLK in shoot apices during floral transition suggested that the interaction occurs in plants. Using plants constitutively expressing a fusion protein of AGL24 and green fluorescent protein, the subcellular localization of AGL24 protein was observed exclusively in the nucleus in apical tissues where MRLK was expressed, while AGL24 was localized in both the cytoplasm and the nucleus in tissues where no MRLK expression was detectable. These results suggest that MRLK signaling promotes translocation of AGL24 from the cytoplasm to the nucleus. We propose that the RLK signaling pathway involves phosphorylation of a MADS-box transcription factor. PMID:12881501

  16. Photolabeling of membrane-bound Torpedo nicotinic acetylcholine receptor with the hydrophobic probe 3-trifluoromethyl-3-(m-[125I]iodophenyl)diazirine

    International Nuclear Information System (INIS)

    The hydrophobic, photoactivatable probe 3-trifluoromethyl-3-(m-[125I]iodophenyl)diazirine ([125I]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 γ-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 α-bungarotoxin and the noncompetitive antagonist phencyclidine had only modest effect on [125I]TID labeling of the AChR. The regions of the AChR α-subunit that incorporate [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 [125I]TID but in a carbamylcholine-insensitive manner. Two further cleavage fragments, which together span about one-third of the α-subunit amino terminus, incorporated no detectable [125I]TID. The mapping results place constraints on suggested models of AChR subunit topology

  17. Receptor-based 3D QSAR analysis of estrogen receptor ligands--merging the accuracy of receptor-based alignments with the computational efficiency of ligand-based methods.

    Science.gov (United States)

    Sippl, W

    2000-08-01

    One of the major challenges in computational approaches to drug design is the accurate prediction of binding affinity of biomolecules. In the present study several prediction methods for a published set of estrogen receptor ligands are investigated and compared. The binding modes of 30 ligands were determined using the docking program AutoDock and were compared with available X-ray structures of estrogen receptor-ligand complexes. On the basis of the docking results an interaction energy-based model, which uses the information of the whole ligand-receptor complex, was generated. Several parameters were modified in order to analyze their influence onto the correlation between binding affinities and calculated ligand-receptor interaction energies. The highest correlation coefficient (r2 = 0.617, q2Loo = 0.570) was obtained considering protein flexibility during the interaction energy evaluation. The second prediction method uses a combination of receptor-based and 3D quantitative structure-activity relationships (3D QSAR) methods. The ligand alignment obtained from the docking simulations was taken as basis for a comparative field analysis applying the GRID/GOLPE program. Using the interaction field derived with a water probe and applying the smart region definition (SRD) variable selection, a significant and robust model was obtained (r2 = 0.991, q2LOO = 0.921). The predictive ability of the established model was further evaluated by using a test set of six additional compounds. The comparison with the generated interaction energy-based model and with a traditional CoMFA model obtained using a ligand-based alignment (r2 = 0.951, q2L00 = 0.796) indicates that the combination of receptor-based and 3D QSAR methods is able to improve the quality of the underlying model. PMID:10921772

  18. 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”.

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

    Directory of Open Access Journals (Sweden)

    I. Cheng

    2015-02-01

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

  20. 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...

  1. Complex bounds for multimodal maps: bounded combinatorics

    OpenAIRE

    Smania, Daniel

    2000-01-01

    We proved the so called complex bounds for multimodal, infinitely renormalizable analytic maps with bounded combinatorics: deep renormalizations have polynomial-like extensions with definite modulus. The complex bounds is the first step to extend the renormalization theory of unimodal maps to multimodal maps.

  2. Bounded Tamper Resilience

    DEFF Research Database (Denmark)

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

    Related key attacks (RKAs) are powerful cryptanalytic attacks where an adversary can change the secret key and observe the effect of such changes at the output. The state of the art in RKA security protects against an a-priori unbounded number of certain algebraic induced key relations, e...... 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...

  3. Deeply bound $\\Xi$ tribaryon

    CERN Document Server

    Garcilazo, H

    2016-01-01

    We have used realistic local interactions based on the recent update of the strangeness $-2$ Nijmegen ESC08c potential to calculate the bound state problem of the $\\Xi NN$ system in the $(I)J^P=(\\frac{1}{2})\\frac{3}{2}^+$ state. We found that this system presents a deeply bound state lying $13.5$ MeV below the $\\Xi d$ threshold. Since in lowest order, pure S$-$wave configuration, this system can not decay into the open $\\Lambda\\Lambda N$ channel, its decay width is expected to be very small. We have also recalculated the $(I)J^P=(\\frac{3}{2})\\frac{1}{2}^+$ state and we have compared with results of quark-model based potentials.

  4. Calculations of K{sup -} nuclear quasi-bound states based on chiral meson-baryon amplitudes

    Energy Technology Data Exchange (ETDEWEB)

    Gazda, Daniel [Nuclear Physics Institute, 250 68 Rez (Czech Republic); Mares, Jiri, E-mail: mares@ujf.cas.cz [Nuclear Physics Institute, 250 68 Rez (Czech Republic)

    2012-05-01

    In-medium K{sup Macron}N scattering amplitudes developed within a new chirally motivated coupled-channel model due to Cieply and Smejkal that fits the recent SIDDHARTA kaonic hydrogen 1s level shift and width are used to construct K{sup -} nuclear potentials for calculations of K{sup -} nuclear quasi-bound states. The strong energy and density dependence of scattering amplitudes at and near threshold leads to K{sup -} potential depths -ReV{sub K} Almost-Equal-To 80-120 MeV. Self-consistent calculations of all K{sup -} nuclear quasi-bound states, including excited states, are reported. Model dependence, polarization effects, the role of p-wave interactions, and two-nucleon K{sup -}NN{yields}YN absorption modes are discussed. The K{sup -} absorption widths {Gamma}{sub K} are comparable or even larger than the corresponding binding energies B{sub K} for allK{sup -} nuclear quasi-bound states, exceeding considerably the level spacing. This discourages search for K{sup -} nuclear quasi-bound states in any but the lightest nuclear systems.

  5. A Cholesterol-Based Allostery Model of T Cell Receptor Phosphorylation.

    Science.gov (United States)

    Swamy, Mahima; Beck-Garcia, Katharina; Beck-Garcia, Esmeralda; Hartl, Frederike A; Morath, Anna; Yousefi, O Sascha; Dopfer, Elaine Pashupati; Molnár, Eszter; Schulze, Anna K; Blanco, Raquel; Borroto, Aldo; Martín-Blanco, Nadia; Alarcon, Balbino; Höfer, Thomas; Minguet, Susana; Schamel, Wolfgang W A

    2016-05-17

    Signaling through the T cell receptor (TCR) controls adaptive immune responses. Antigen binding to TCRαβ transmits signals through the plasma membrane to induce phosphorylation of the CD3 cytoplasmic tails by incompletely understood mechanisms. Here we show that cholesterol bound to the TCRβ transmembrane region keeps the TCR in a resting, inactive conformation that cannot be phosphorylated by active kinases. Only TCRs that spontaneously detached from cholesterol could switch to the active conformation (termed primed TCRs) and then be phosphorylated. Indeed, by modulating cholesterol binding genetically or enzymatically, we could switch the TCR between the resting and primed states. The active conformation was stabilized by binding to peptide-MHC, which thus controlled TCR signaling. These data are explained by a model of reciprocal allosteric regulation of TCR phosphorylation by cholesterol and ligand binding. Our results provide both a molecular mechanism and a conceptual framework for how lipid-receptor interactions regulate signal transduction. PMID:27192576

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

    Science.gov (United States)

    Yan, Zheng; Wang, Jun

    2014-03-01

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

  7. Stochastic bounded consensus tracking of leader-follower multi-agent systems with measurement noises based on sampled data with general sampling delay

    International Nuclear Information System (INIS)

    In this paper we provide a unified framework for consensus tracking of leader-follower multi-agent systems with measurement noises based on sampled data with a general sampling delay. First, a stochastic bounded consensus tracking protocol based on sampled data with a general sampling delay is presented by employing the delay decomposition technique. Then, necessary and sufficient conditions are derived for guaranteeing leader-follower multi-agent systems with measurement noises and a time-varying reference state to achieve mean square bounded consensus tracking. The obtained results cover no sampling delay, a small sampling delay and a large sampling delay as three special cases. Last, simulations are provided to demonstrate the effectiveness of the theoretical results. (interdisciplinary physics and related areas of science and technology)

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

    Science.gov (United States)

    Petre-Lazar, S.; Popeea, G.

    1974-01-01

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

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

    OpenAIRE

    Mønness, Erik Neslein

    2013-01-01

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

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

    OpenAIRE

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

    2014-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2005-01-01

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

  12. Optimization of amide-based EP3 receptor antagonists.

    Science.gov (United States)

    Lee, Esther C Y; Futatsugi, Kentaro; Arcari, Joel T; Bahnck, Kevin; Coffey, Steven B; Derksen, David R; Kalgutkar, Amit S; Loria, Paula M; Sharma, Raman

    2016-06-01

    Prostaglandin E receptor subtype 3 (EP3) antagonism may treat a variety of symptoms from inflammation to cardiovascular and metabolic diseases. Previously, most EP3 antagonists were large acidic ligands that mimic the substrate, prostaglandin E2 (PGE2). This manuscript describes the optimization of a neutral small molecule amide series with improved lipophilic efficiency (LipE) also known as lipophilic ligand efficiency (LLE) ((a) Nat. Rev. Drug Disc.2007, 6, 881; (b) Annu. Rep. Med. Chem.2010, 45, 380). PMID:27107947

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

    Science.gov (United States)

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

    2015-07-01

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

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

    Science.gov (United States)

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

    2015-02-25

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

  15. Structure-Based Virtual Screening for Dopamine D2 Receptor Ligands as Potential Antipsychotics.

    Science.gov (United States)

    Kaczor, Agnieszka A; Silva, Andrea G; Loza, María I; Kolb, Peter; Castro, Marián; Poso, Antti

    2016-04-01

    Structure-based virtual screening using a D2 receptor homology model was performed to identify dopamine D2 receptor ligands as potential antipsychotics. From screening a library of 6.5 million compounds, 21 were selected and were subjected to experimental validation. From these 21 compounds tested, ten D2 ligands were identified (47.6 % success rate, among them D2 receptor antagonists, as expected) that have additional affinity for other receptors tested, in particular 5-HT2A receptors. The affinity (Ki values) of the compounds ranged from 58 nm to about 24 μm. Similarity and fragment analysis indicated a significant degree of structural novelty among the identified compounds. We found one D2 receptor antagonist that did not have a protonatable nitrogen atom, which is a key structural element of the classical D2 pharmacophore model necessary for interaction with the conserved Asp(3.32) residue. This compound exhibited greater than 20-fold binding selectivity for the D2 receptor over the D3 receptor. We provide additional evidence that the amide hydrogen atom of this compound forms a hydrogen bond with Asp(3.32), as determined by tests of its derivatives that cannot maintain this interaction. PMID:26990027

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

    International Nuclear Information System (INIS)

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

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

    Science.gov (United States)

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

    2016-05-01

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

  18. Circuit lower bounds in bounded arithmetics

    Czech Academy of Sciences Publication Activity Database

    Pich, Ján

    2015-01-01

    Roč. 166, č. 1 (2015), s. 29-45. ISSN 0168-0072 R&D Projects: GA AV ČR IAA100190902 Keywords : bounded arithmetic * circuit lower bounds Subject RIV: BA - General Mathematics Impact factor: 0.548, year: 2014 http://www.sciencedirect.com/science/article/pii/S0168007214000888

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

    Institute of Scientific and Technical Information of China (English)

    YANG Xu-dong; JIN Liang-liang

    2011-01-01

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

  20. A bound on chaos

    CERN Document Server

    Maldacena, Juan; Stanford, Douglas

    2015-01-01

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

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

    International Nuclear Information System (INIS)

    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 λphage after fragmentation to construct the gene library of OLETF. Then, λphage 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, F2 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 F2 (CCKAR,-/-) as well as the parent OLETF rat than hetero-mutant F2 (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.)

  2. A Causal Entropy Bound

    CERN Document Server

    Brustein, Ram

    2000-01-01

    The identification of a causal-connection scale motivates us to propose a new covariant bound on entropy within a generic space-like region. This "causal entropy bound", scaling as the square root of EV, and thus lying around the geometric mean of Bekenstein's S/ER and holographic S/A bounds, is checked in various "critical" situations. In the case of limited gravity, Bekenstein's bound is the strongest while naive holography is the weakest. In the case of strong gravity, our bound and Bousso's holographic bound are stronger than Bekenstein's, while naive holography is too tight, and hence typically wrong.

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

    Science.gov (United States)

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

    2016-01-01

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

  4. Scattering by bound nucleons

    International Nuclear Information System (INIS)

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

  5. Variance bounding Markov chains

    OpenAIRE

    Roberts, Gareth O.; Jeffrey S. Rosenthal

    2008-01-01

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

  6. Bound states and the Bekenstein bound

    CERN Document Server

    Bousso, R

    2004-01-01

    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 a. 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.

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

    OpenAIRE

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

    2006-01-01

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

  8. Structures of native and affinity-enhanced WT1 epitopes bound to HLA-A*0201: implications for WT1-based cancer therapeutics

    OpenAIRE

    Borbulevych, Oleg Y.; Do, Priscilla; Baker, Brian M.

    2010-01-01

    Presentation of peptides by class I or class II major histocompatibility complex (MHC) molecules is required for the initiation and propagation of a T cell-mediated immune response. Peptides from the Wilms Tumor 1 transcription factor (WT1), upregulated in many hematopoetic and solid tumors, can be recognized by T cells and numerous efforts are underway to engineer WT1-based cancer vaccines. Here we determined the structures of the class I MHC molecule HLA-A*0201 bound to the native 126–134 e...

  9. FTIR Studies of Internal Water Molecules of Bacteriorhodopsin: Structural Analysis of Halide-bound D85S and D212N Mutants in the Schiff Base Region

    Science.gov (United States)

    Shibata, Mikihiro; Kandori, Hideki

    2007-12-01

    Bacteriorhodopsin (BR), a membrane protein found in Halobacterium salinarum, functions as a light-driven proton pump. The Schiff base region has a quadropolar structure with positive charges located at the protonated Schiff base and Arg82, and counterbalancing negative charges located at Asp85 and Asp212 (Figure 1A). It is known that BR lacks a proton-pumping activity if Asp85 or Asp212 is neutralized by mutation. On the other hand, binding of C1- brings different effects for pumping functions in mutants at D85 and D212 position. While C1--bound D85T and D85S pump C1-, photovoltage measurements suggested that C1--bound D212N pumps protons at low pH. In this study, we measured low-temperature FTIR spectra of D85S and D212N containing various halides to compare the halide binding site of both proteins. In the case of D85S, the N-D stretching vibrations of the Schiff base were halide-dependent. This result suggests that the halide is a hydrogen-bond acceptor of the Schiff base, being consistent with the X-ray crystal structure. On the other hand, no halide dependence was observed for vibrational bands of the retinal skeleton and the Schiff base in the D212N mutant. This result suggests that the halide does not form a hydrogen bond with the Schiff base directly, unlike the mutation at D85 position. Halide-dependent water bands in the Schiff base region also differ between D85S and D212N. From these results, halide binding site of both proteins and role of two negative charges in BR will be discussed.

  10. A Causal Entropy Bound

    OpenAIRE

    Brustein, R; Veneziano, G

    1999-01-01

    The identification of a causal-connection scale motivates us to propose a new covariant bound on entropy within a generic space-like region. This "causal entropy bound", scaling as the square root of EV, and thus lying around the geometric mean of Bekenstein's S/ER and holographic S/A bounds, is checked in various "critical" situations. In the case of limited gravity, Bekenstein's bound is the strongest while naive holography is the weakest. In the case of strong gravity, our bound and Bousso...

  11. A matrix lower bound

    Energy Technology Data Exchange (ETDEWEB)

    Grcar, Joseph F.

    2002-02-04

    A matrix lower bound is defined that generalizes ideas apparently due to S. Banach and J. von Neumann. The matrix lower bound has a natural interpretation in functional analysis, and it satisfies many of the properties that von Neumann stated for it in a restricted case. Applications for the matrix lower bound are demonstrated in several areas. In linear algebra, the matrix lower bound of a full rank matrix equals the distance to the set of rank-deficient matrices. In numerical analysis, the ratio of the matrix norm to the matrix lower bound is a condition number for all consistent systems of linear equations. In optimization theory, the matrix lower bound suggests an identity for a class of min-max problems. In real analysis, a recursive construction that depends on the matrix lower bound shows that the level sets of continuously differential functions lie asymptotically near those of their tangents.

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

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

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

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

    CERN Document Server

    Lucarini, Valerio

    2010-01-01

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

  14. Low potential biofuel cell anodes based on redox polymers with covalently bound phenothiazine derivatives for wiring flavin adenine dinucleotide-dependent enzymes

    International Nuclear Information System (INIS)

    The design of biofuel cell anodes with substantially decreased potential is a prerequisite for the development of biofuel cells with large open-circuit voltage and power density. Redox polymers with covalently attached phenothiazine derivatives such of thionine acetate, toluidine blue, azure B simultaneously providing epoxide functions for covalent binding to suitably modified electrode surfaces and crosslinking were synthesized and evaluated for their ability to transfer electrons from the FAD cofactor of the flavodehydrogenase domain of cellobiose dehydrogenase from Myriococcum thermophilum (FAD-MtCDH), the flavodehydrogenase domain of cellobiose dehydrogenase from Corynascus thermophilus (FAD-CtCDH), or glucose oxidase from Aspergillus niger (GOx). Polymer/enzyme films were covalently bound via polymer bound epoxy groups to terminal amino functions introduced to graphite electrode surfaces by electrochemically induced grafting of diaminoheptane or Boc-protected ethylene diamine (EDA). The electrodes were optimized for biocatalytic glucose oxidation with respect to the hydrophilicity of the polymer backbone, the nature of the phenothiazine derivative, the pH value, as well as the relative amount of enzyme, polymer and crosslinker. Biofuel cells based on toluidine blue-modified redox polymers with integrated FAD-MtCDH, FAD-CtCDH, or GOx in combination with a bilirubin oxidase based biocathode exhibited open-circuit voltages of more than 0.7 V and maximum power densities in the range of 4 to 6 μW cm−2 at a pH value of 7.8

  15. Consistent, multi-instrument single tube quantification of CD20 in antibody bound per cell based on CD4 reference.

    Science.gov (United States)

    Degheidy, Heba; Abbasi, Fatima; Mostowski, Howard; Gaigalas, Adolfas K; Marti, Gerald; Bauer, Steven; Wang, Lili

    2016-03-01

    Detecting changes in the expression levels of cell antigens could provide critical information for the diagnosis of many diseases, for example, leukemia, lymphoma, and immunodeficiency diseases, detecting minimal residual disease, monitoring immunotherapies and discovery of meaningful clinical disease markers. One of the most significant challenges in flow cytometry is how to best ensure measurement quality and generate consistent and reproducible inter-laboratory and intra-laboratory results across multiple cytometer platforms and locations longitudinally over time. In a previous study, we developed a procedure for instrument standardization across four different flow cytometer platforms from the same manufacturer. CD19 quantification was performed on three of the standardized instruments relative to CD4 expression on T lymphocytes with a known amount of antibody bound per cell (ABC) as a quantification standard. Consistent and reliable measures of CD19 expression were obtained independent of fluorochrome used demonstrating the utility of this approach. In the present investigation, quantification of CD20 relative to CD4 reference marker was implemented within a single tube containing both antibodies. Relative quantification of CD20 was performed using anti-CD20 antibody (clone L27) in three different fluorochromes relative to anti-CD4 antibody (clone SK3). Our results demonstrated that cell surface marker quantification can be performed robustly using the single tube assay format with novel gating strategies. The ABC values obtained for CD20 expression levels using PE, APC, or PerCP Cy5.5 are consistent over the five different instrument platforms for any given apparently healthy donor independent of the fluorochrome used. © 2015 International Clinical Cytometry Society. PMID:26013593

  16. 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.

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

    OpenAIRE

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

    2011-01-01

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

  18. 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.

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

    Science.gov (United States)

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

    2016-03-01

    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 (BMAA was found in a trichloroacetic acid soluble, bound form and we recommend including this fraction during analysis. PMID:26938542

  20. 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.

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

    DEFF Research Database (Denmark)

    Fidom, Kimberley; Isberg, Vignir; Hauser, Alexander Sebastian; Mordalski, Stefan; Lehto, Thomas; Bojarski, Andrzej J; Gloriam, David E

    2015-01-01

    We have developed a new method for the building of pharmacophores for G protein-coupled receptors, a major drug target family. The method is a combination of the ligand- and target-based pharmacophore methods and founded on the extraction of structural fragments, interacting ligand moiety and...... ligands are known. 47% of the class A G protein-coupled receptors can be targeted with at least four-element pharmacophores. The fragment libraries can also be used to grow known ligands or for rotamer refinement of homology models. Researchers can download the complete fragment library or a subset...... 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 for...

  2. Discoidin domain receptor 1 (DDR1) kinase as target for structure-based drug discovery.

    Science.gov (United States)

    Kothiwale, Sandeepkumar; Borza, Corina M; Lowe, Edward W; Pozzi, Ambra; Meiler, Jens

    2015-02-01

    Discoidin domain receptor (DDR) 1 and 2 are transmembrane receptors that belong to the family of receptor tyrosine kinases (RTK). Upon collagen binding, DDRs transduce cellular signaling involved in various cell functions, including cell adhesion, proliferation, differentiation, migration, and matrix homeostasis. Altered DDR function resulting from either mutations or overexpression has been implicated in several types of disease, including atherosclerosis, inflammation, cancer, and tissue fibrosis. Several established inhibitors, such as imatinib, dasatinib, and nilotinib, originally developed as Abelson murine leukemia (Abl) kinase inhibitors, have been found to inhibit DDR kinase activity. As we review here, recent discoveries of novel inhibitors and their co-crystal structure with the DDR1 kinase domain have made structure-based drug discovery for DDR1 amenable. PMID:25284748

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

    Directory of Open Access Journals (Sweden)

    Liqiang XU

    2011-09-01

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

  4. Dopamine D2/3 receptor antagonism reduces activity-based anorexia.

    Science.gov (United States)

    Klenotich, S J; Ho, E V; McMurray, M S; Server, C H; Dulawa, S C

    2015-01-01

    Anorexia nervosa (AN) is an eating disorder characterized by severe hypophagia and weight loss, and an intense fear of weight gain. Activity-based anorexia (ABA) refers to the weight loss, hypophagia and paradoxical hyperactivity that develops in rodents exposed to running wheels and restricted food access, and provides a model for aspects of AN. The atypical antipsychotic olanzapine was recently shown to reduce both AN symptoms and ABA. We examined which component of the complex pharmacological profile of olanzapine reduces ABA. Mice received 5-HT(2A/2C), 5-HT3, dopamine D1-like, D2, D3 or D2/3 antagonist treatment, and were assessed for food intake, body weight, wheel running and survival in ABA. D2/3 receptor antagonists eticlopride and amisulpride reduced weight loss and hypophagia, and increased survival during ABA. Furthermore, amisulpride produced larger reductions in weight loss and hypophagia than olanzapine. Treatment with either D3 receptor antagonist SB277011A or D2 receptor antagonist L-741,626 also increased survival. All the other treatments either had no effect or worsened ABA. Overall, selective antagonism of D2 and/or D3 receptors robustly reduces ABA. Studies investigating the mechanisms by which D2 and/or D3 receptors regulate ABA, and the efficacy for D2/3 and/or D3 antagonists to treat AN, are warranted. PMID:26241351

  5. Asymptotic Entropy Bounds

    CERN Document Server

    Bousso, Raphael

    2016-01-01

    We show that known entropy bounds constrain the information carried off by radiation to null infinity. We consider distant, planar null hypersurfaces in asymptotically flat spacetime. Their focussing and area loss can be computed perturbatively on a Minkowski background, yielding entropy bounds in terms of the energy flux of the outgoing radiation. In the asymptotic limit, we obtain boundary versions of the Quantum Null Energy Condition, of the Generalized Second Law, and of the Quantum Bousso Bound.

  6. Bound soliton fiber laser

    OpenAIRE

    Tang, D. Y.; B. Zhao; Shen, D. Y.; Lu, C.

    2009-01-01

    Experimental study on the soliton dynamics of a passively mode locked fiber ring laser firstly revealed a state of bound soliton operation in the laser, where two solitons bind together tightly with fixed pulse separation. We further report on the properties of the bound-soliton emission of the laser. In particular, we demonstrate both experimentally and numerically that, like the single pulse soliton operation of the laser, the bound soliton emission is another intrinsic feature of the laser.

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

    OpenAIRE

    Santi, Paolo

    2002-01-01

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

  8. Bound anionic states of adenine

    OpenAIRE

    Harańczyk, Maciej; Gutowski, Maciej; Li, Xiang; Bowen, Kit H.

    2007-01-01

    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...

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

    Science.gov (United States)

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

    2016-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Jieun Han

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

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

    Directory of Open Access Journals (Sweden)

    Vincent eZoete

    2013-09-01

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

  12. Nanopore-Based Sensors for Ligand-Receptor Lead Optimization.

    Science.gov (United States)

    Luan, Binquan; Huynh, Tien; Zhou, Ruhong

    2015-02-01

    Developing a low-cost and high-efficacy method to optimize prescreened or designed drug candidates will facilitate drug discovery and biomedical research in general. Current methods of drug screening usually involve tedious sample preparation and costly biological/chemical assays. Here, through all-atom molecular dynamics simulations, we propose a new drug optimization method, based on the nanopore force spectroscopy, to electrically detect the binding strength between a drug molecule and a target protein. Simulation results demonstrate that the drug-protein complex can be electrophoretically driven into a nanopore, which is followed by the rupture of the complex at a critical biasing voltage. The latter determines the binding strength of the tested drug molecule. It is expected that the application of this single-molecule technology could help to accelerate the drug discovery, particularly for processes of the narrow screening and further lead optimization. PMID:26261942

  13. 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.)

  14. Call packing bounds for overflow queues

    OpenAIRE

    van Dijk; Sluis, van der, B.

    2004-01-01

    Finite queueing loss systems are studied with overflow. For these systems there is no simple analytic expression for the loss probability or throughput. This paper aims to prove and promote easily computable bounds as based upon the so-called call packing principle. Under call packing a standard product form expression is available. It is proven that call packing leads to a guaranteed upper bound for the loss probability. In addition, an analytic error bound for the accuracy is derived which ...

  15. Bounded rationality and learning in market competition

    OpenAIRE

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

    2015-01-01

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

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

    International Nuclear Information System (INIS)

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

  17. 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...

  18. Graviton Mass Bounds

    CERN Document Server

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

    2016-01-01

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

  19. Energy transfer in solution-based complexes of CdTe nanocrystals electrostatically bound by calcium ions

    International Nuclear Information System (INIS)

    Colloidal semiconductor nanocrystals with controllable surface properties are attractive objects for use as building blocks in different functional structures within the bottom-up assembly approach. We produced stable complexes from differently-sized water soluble CdTe nanocrystals capped by mercaptoacid stabilizers through electrostatic interactions of negatively charged carboxylic groups of capping ligands with positively charged Ca(II) cations. Energy transfer between smaller nanocrystals (donors) and larger nanocrystals (acceptors) in fabricated complexes is demonstrated by means of steady-state and time-resolved photoluminescence spectroscopy, paving the way to nanocrystal-based light harvesting structures

  20. Changes in dynamical behavior of the retinoid X receptor DNA-binding domain upon binding to a 14 base-pair DNA half site.

    Science.gov (United States)

    van Tilborg, P J; Czisch, M; Mulder, F A; Folkers, G E; Bonvin, A M; Nair, M; Boelens, R; Kaptein, R

    2000-08-01

    The retinoid X receptor (RXR) is a prominent member of the nuclear receptor family of ligand-inducible transcription factors. Many proteins of this family exert their function as heterodimers with RXR as a common upstream partner. Studies of the DNA-binding domains of several nuclear receptors reveal differences in structure and dynamics, both between the different proteins and between the free- and DNA-bound receptor DBDs. We investigated the differences in dynamics between RXR free in solution and in complex with a 14 base-pair oligonucleotide, using (1)H and (15)N relaxation studies. Nano- to picosecond dynamics were probed on (15)N, employing Lipari-Szabo analysis with an axially symmetric tumbling model to estimate the exchange contributions to the transverse relaxation rates. Furthermore, milli- to microsecond dynamics were estimated qualitatively for (1)H and (15)N, using CPMG-HSQC and CPMG-T(2) measurements with differential pulse spacing. RXR shows hardly any nano- to picosecond time-scale internal motion. Upon DNA binding, the order parameters show a tiny increase. Dynamics in the milli- to microsecond time scale is more prevalent. It is localized in the first and second zinc fingers of the free RXR. Upon DNA-binding, exchange associated with specific/aspecific DNA-binding of RXR is observed throughout the sequence, whereas conformational flexibility of the D-box and the second zinc finger of RXR is greatly reduced. Since this DNA-binding induced folding transition occurs remote from the DNA in a region which is involved in protein-protein interactions, it may very well be related to the cooperativity of dimeric DNA binding. PMID:10913286

  1. Novel Receptor-Based Countermeasures to Microgravity-Induced Bone Loss

    Science.gov (United States)

    OMalley, Bert W.

    1999-01-01

    The biological actions mediated by the estrogen receptor (ER), vitamin D receptor (VDR) and Ca(sup 2+) (sub o) -sensing receptor (CaR) play key roles in the normal control of bone growth and skeletal turnover that is necessary for skeletal health. These receptors act by controlling the differentiation and/or function of osteoblasts and osteoclasts, and other cell types within the bone and bone marrow microenvironment. The appropriate use of selective ER modulators (SERMS) which target bone, vitamin D analogs that favor bone formation relative to resorption, and CaR agonists may both stimulate osteoblastogenesis and inhibit osteoclastogenesis and the function of mature osteoclasts, should make it possible to prevent the reduction in bone formation and increase in bone resorption that normally contribute to the bone loss induced by weightlessness. Indeed, there may be synergistic interactions among these receptors that enhance the actions of any one used alone. Therefore, we proposed to: 1) assess the in vitro ability of novel ER, VDR and CaR agonists, alone or in combination, to modulate osteoblastogenesis and mature osteoblast function under conditions of 1g and simulated microgravity; 2) assess the in vitro ability of novel ER, VDR and CaR agonists, alone or in combination, to modulate osteoclastogenesis and bone resorption under conditions of lg and simulated microgravity; and 3) carry out baseline studies on the skeletal localization of the CaR in normal rat bone as well as the in vivo actions of our novel ER- and VDR-based therapeutics in the rat in preparation for their use, alone or in combination, in well-established ground-based models of microgravity and eventually in space flight.

  2. Spontaneous R-Parity violation bounds

    CERN Document Server

    Frank, M

    2001-01-01

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

  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.

    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

  5. 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.

  6. Deeply bound pionic atom

    International Nuclear Information System (INIS)

    The standard method of pionic atom formation does not produce deeply bound pionic atoms. A study is made on the properties of deeply bound pionic atom states by using the standard pion-nucleus optical potential. Another study is made to estimate the cross sections of the formation of ls pionic atom states by various methods. The pion-nucleus optical potential is determined by weakly bound pionic atom states and pion nucleus scattering. Although this potential may not be valid for deeply bound pionic atoms, it should provide some hint on binding energies and level widths of deeply bound states. The width of the ls state comes out to be 0.3 MeV and is well separated from the rest. The charge dependence of the ls state is investigated. The binding energies and the widths increase linearly with Z azbove a Z of 30. The report then discusses various methods to populate deeply bound pionic atoms. In particular, 'pion exchange' reactions are proposed. (n, pπ) reaction is discussed first. The cross section is calculated by assuming the in- and out-going nucleons on-shell and the produced pion in (n1) pionic atom states. Then, (n, dπ-) cross sections are estimated. (p, 2Heπ-) reaction would have cross sections similar to the cross section of (n, dπ-) reaction. In conclusion, it seems best to do (n, p) experiment on heavy nuclei for deeply bound pionic atom. (Nogami, K.)

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

    Science.gov (United States)

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

    2012-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    周雪瑞

    2001-01-01

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

  9. Organization of the Human Inferior Parietal Lobule Based on Receptor Architectonics

    OpenAIRE

    Caspers, S.; Schleicher, A.; Bacha-Trams, M.; Palomero-Gallagher, N.; Amunts, K.; Zilles, K

    2012-01-01

    Human inferior parietal lobule (IPL) plays a key role in various cognitive functions. Its functional diversity, including attention, language, and action processing, is reflected by its structural segregation into 7 cytoarchitectonically distinct areas, each with characteristic connectivity patterns. We hypothesized that commonalities of the cytoarchitectonic, connectional, and functional diversity of the IPL should be reflected by a correlated transmitter receptor-based organization. Since t...

  10. 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. PMID:23828307

  11. Quantum Lower Bounds by Entropy Numbers

    OpenAIRE

    Heinrich, Stefan

    2006-01-01

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

  12. 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. PMID:24583195

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

    Science.gov (United States)

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

    2016-09-01

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

  14. Deeply bound pionic states

    International Nuclear Information System (INIS)

    We discuss the structure and formation of deeply bound π- states in heavy nuclei, which are expected to be narrow due to the repulsive π--nucleus interaction. Possible experiments to produce those states are described. (author)

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

    Science.gov (United States)

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

    2015-01-01

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

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

    OpenAIRE

    Wang, Jian; She, Yongxin; Wang, Miao; Jin, Maojun; Li, Yongfei; Wang, Jing; Liu, Yuan

    2015-01-01

    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...

  17. 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.

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

    Institute of Scientific and Technical Information of China (English)

    栾琨; 傅忠宁; 隽志才

    2016-01-01

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

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

    OpenAIRE

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

    2014-01-01

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

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

    2010-01-01

    NMDA receptor function, including the histamine H3 receptor antagonists clobenpropit and iodophenpropit, as well as the vanilloid receptor transient receptor potential cation channel, subfamily V, member 1 (TRPV1) antagonist capsazepine. These compounds are noncompetitive antagonists and the histamine...

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

    Science.gov (United States)

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

    2016-07-01

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

  2. Lectures on Bound states

    CERN Document Server

    Hoyer, Paul

    2016-01-01

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

  3. Bounding species distribution models

    Institute of Scientific and Technical Information of China (English)

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

    2011-01-01

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

  4. Structures of native and affinity-enhanced WT1 epitopes bound to HLA-A*0201: Implications for WT1-based cancer therapeutics

    Energy Technology Data Exchange (ETDEWEB)

    Borbulevych, Oleg Y.; Do, Priscilla; Baker, Brian M. (Notre)

    2010-09-07

    Presentation of peptides by class I or class II major histocompatibility complex (MHC) molecules is required for the initiation and propagation of a T cell-mediated immune response. Peptides from the Wilms Tumor 1 transcription factor (WT1), upregulated in many hematopoetic and solid tumors, can be recognized by T cells and numerous efforts are underway to engineer WT1-based cancer vaccines. Here we determined the structures of the class I MHC molecule HLA-A*0201 bound to the native 126-134 epitope of the WT1 peptide and a recently described variant (R1Y) with improved MHC binding. The R1Y variant, a potential vaccine candidate, alters the positions of MHC charged side chains near the peptide N-terminus and significantly reduces the peptide/MHC electrostatic surface potential. These alterations indicate that the R1Y variant is an imperfect mimic of the native WT1 peptide, and suggest caution in its use as a therapeutic vaccine. Stability measurements revealed how the R1Y substitution enhances MHC binding affinity, and together with the structures suggest a strategy for engineering WT1 variants with improved MHC binding that retain the structural features of the native peptide/MHC complex.

  5. Structures of native and affinity-enhanced WT1 epitopes bound to HLA-A*0201: implications for WT1-based cancer therapeutics.

    Science.gov (United States)

    Borbulevych, Oleg Y; Do, Priscilla; Baker, Brian M

    2010-09-01

    Presentation of peptides by class I or class II major histocompatibility complex (MHC) molecules is required for the initiation and propagation of a T cell-mediated immune response. Peptides from the Wilms Tumor 1 transcription factor (WT1), upregulated in many hematopoetic and solid tumors, can be recognized by T cells and numerous efforts are underway to engineer WT1-based cancer vaccines. Here we determined the structures of the class I MHC molecule HLA-A*0201 bound to the native 126-134 epitope of the WT1 peptide and a recently described variant (R1Y) with improved MHC binding. The R1Y variant, a potential vaccine candidate, alters the positions of MHC charged side chains near the peptide N-terminus and significantly reduces the peptide/MHC electrostatic surface potential. These alterations indicate that the R1Y variant is an imperfect mimic of the native WT1 peptide, and suggest caution in its use as a therapeutic vaccine. Stability measurements revealed how the R1Y substitution enhances MHC binding affinity, and together with the structures suggest a strategy for engineering WT1 variants with improved MHC binding that retain the structural features of the native peptide/MHC complex. PMID:20619457

  6. 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.

  7. Studies of glutathione transferase P1-1 bound to a platinum(IV)-based anticancer compound reveal the molecular basis of its activation.

    Science.gov (United States)

    Parker, Lorien J; Italiano, Louis C; Morton, Craig J; Hancock, Nancy C; Ascher, David B; Aitken, Jade B; Harris, Hugh H; Campomanes, Pablo; Rothlisberger, Ursula; De Luca, Anastasia; Lo Bello, Mario; Ang, Wee Han; Dyson, Paul J; Parker, Michael W

    2011-07-01

    Platinum-based cancer drugs, such as cisplatin, are highly effective chemotherapeutic agents used extensively for the treatment of solid tumors. However, their effectiveness is limited by drug resistance, which, in some cancers, has been associated with an overexpression of pi class glutathione S-transferase (GST P1-1), an important enzyme in the mercapturic acid detoxification pathway. Ethacraplatin (EA-CPT), a trans-Pt(IV) carboxylate complex containing ethacrynate ligands, was designed as a platinum cancer metallodrug that could also target cytosolic GST enzymes. We previously reported that EA-CPT was an excellent inhibitor of GST activity in live mammalian cells compared to either cisplatin or ethacrynic acid. In order to understand the nature of the drug-protein interactions between EA-CPT and GST P1-1, and to obtain mechanistic insights at a molecular level, structural and biochemical investigations were carried out, supported by molecular modeling analysis using quantum mechanical/molecular mechanical methods. The results suggest that EA-CPT preferentially docks at the dimer interface at GST P1-1 and subsequent interaction with the enzyme resulted in docking of the ethacrynate ligands at both active sites (in the H-sites), with the Pt moiety remaining bound at the dimer interface. The activation of the inhibitor by its target enzyme and covalent binding accounts for the strong and irreversible inhibition of enzymatic activity by the platinum complex. PMID:21681839

  8. Epidermal growth factor (EGF) receptor gene transcription

    International Nuclear Information System (INIS)

    The authors have studied in vitro transcription of the human epidermal growth factor (EGF) receptor proto-oncogene using nuclear extracts of A431 human epidermoid carcinoma cells, which overproduce the EGF receptor. With the in vitro system we found that Sp1 and other trans-acting factors bound to the EGF receptor promoter regions and are required for maximal expression. Fractionation showed that a DEAE-Sepharose fraction (BA) contained a novel factor, which specifically stimulated EGF receptor transcription 5- to 10-fold. The molecular mass of the native form of the factor is about 270-kDa based on its migration on Sephacryl S-300. This factor may activate transcription of the proto-oncogene through a weak or indirect interaction with the DNA template

  9. 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.

  10. Thermostabilisation of the neurotensin receptor NTS1

    OpenAIRE

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

    2009-01-01

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

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

    OpenAIRE

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

    2014-01-01

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

  12. 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.

  13. 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.

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

    Science.gov (United States)

    Kakarala, Kavita Kumari; Jamil, Kaiser

    2014-05-01

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

  15. The Fitness Level Method with Tail Bounds

    OpenAIRE

    Witt, Carsten

    2013-01-01

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

  16. Asynchronous Bounded Expected Delay Networks

    OpenAIRE

    Bakhshi, Rena; Endrullis, Jörg; Fokkink, Wan; Pang, Jun

    2010-01-01

    The commonly used asynchronous bounded delay (ABD) network models assume a fixed bound on message delay. We propose a probabilistic network model, called asynchronous bounded expected delay (ABE) model. Instead of a strict bound, the ABE model requires only a bound on the expected message delay. While the conditions of ABD networks restrict the set of possible executions, in ABE networks all asynchronous executions are possible, but executions with extremely long delays are less probable. In ...

  17. On Entropy Bounds and Holography

    CERN Document Server

    Halyo, Edi

    2009-01-01

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

  18. Artificial Avidin-Based Receptors for a Panel of Small Molecules.

    Science.gov (United States)

    Lehtonen, Soili I; Tullila, Antti; Agrawal, Nitin; Kukkurainen, Sampo; Kähkönen, Niklas; Koskinen, Masi; Nevanen, Tarja K; Johnson, Mark S; Airenne, Tomi T; Kulomaa, Markku S; Riihimäki, Tiina A; Hytönen, Vesa P

    2016-01-15

    Proteins with high specificity, affinity, and stability are needed for biomolecular recognition in a plethora of applications. Antibodies are powerful affinity tools, but they may also suffer from limitations such as low stability and high production costs. Avidin and streptavidin provide a promising scaffold for protein engineering, and due to their ultratight binding to D-biotin they are widely used in various biotechnological and biomedical applications. In this study, we demonstrate that the avidin scaffold is suitable for use as a novel receptor for several biologically active small molecules: Artificial, chicken avidin-based proteins, antidins, were generated using a directed evolution method for progesterone, hydrocortisone, testosterone, cholic acid, ketoprofen, and folic acid, all with micromolar to nanomolar affinity and significantly reduced biotin-binding affinity. We also describe the crystal structure of an antidin, sbAvd-2(I117Y), a steroid-binding avidin, which proves that the avidin scaffold can tolerate significant modifications without losing its characteristic tetrameric beta-barrel structure, helping us to further design avidin-based small molecule receptors. PMID:26550684

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

    Science.gov (United States)

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

    2006-02-15

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

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

    CERN Document Server

    Ter-Sarkisov, Aram

    2012-01-01

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

  1. Redshift-space limits of bound structures

    CERN Document Server

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

    2006-01-01

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

  2. Petawatt laser absorption bounded

    CERN Document Server

    Levy, Matthew C; Tabak, Max; Libby, Stephen B; Baring, Matthew G

    2014-01-01

    The interaction of petawatt ($10^{15}\\ \\mathrm{W}$) lasers with solid matter forms the basis for advanced scientific applications such as table-top particle accelerators, ultrafast imaging systems and laser fusion. Key metrics for these applications relate to absorption, yet conditions in this regime are so nonlinear that it is often impossible to know the fraction of absorbed light $f$, and even the range of $f$ is unknown. Here using a relativistic Rankine-Hugoniot-like analysis, we show for the first time that $f$ exhibits a theoretical maximum and minimum. These bounds constrain nonlinear absorption mechanisms across the petawatt regime, forbidding high absorption values at low laser power and low absorption values at high laser power. For applications needing to circumvent the absorption bounds, these results will accelerate a shift from solid targets, towards structured and multilayer targets, and lead the development of new materials.

  3. Refined Error Bounds for Several Learning Algorithms

    OpenAIRE

    Hanneke, Steve

    2015-01-01

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

  4. 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.

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

    Science.gov (United States)

    Wang, Jian; She, Yongxin; Wang, Miao; Jin, Maojun; Li, Yongfei; Wang, Jing; Liu, Yuan

    2015-01-01

    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. PMID:26422475

  6. Towards Secure Distance Bounding

    OpenAIRE

    Boureanu, Ioana; Mitrokotsa, Aikaterini; Vaudenay, Serge

    2013-01-01

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

  7. Maps of Bounded Rationality

    OpenAIRE

    Kahneman, Daniel

    2002-01-01

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

  8. Bounded Active Perception

    OpenAIRE

    KETENCI, Uktu Gorkem; Bremond, Roland; Auberlet, Jean Michel; GRISLIN, Emmanuelle

    2010-01-01

    There are two kinds of perception : active and passive. This paper is an attempt to take advantage of active perception to improve the agent's perception of relevant information. Through the data filtering capacity, active perception is a useful tool for modeling human-like bounded perception. Using such filters, either the agent or the environment take an active role. We determine several unsolved issues in active perception and do several proposals to implement our concept on the active per...

  9. Bounded Discrete Walks

    OpenAIRE

    Banderier, Cyril; Nicodeme, Pierre

    2010-01-01

    This article tackles the enumeration and asymptotics of directed lattice paths (that are isomorphic to unidimensional paths) of bounded height (walks below one wall, or between two walls, for \\emphany finite set of jumps). Thus, for any lattice paths, we give the generating functions of bridges (``discrete'' Brownian bridges) and reflected bridges (``discrete'' reflected Brownian bridges) of a given height. It is a new success of the ``kernel method'' that the generating functions of such wal...

  10. Reflecting Magnon Bound States

    CERN Document Server

    Ahn, C; Rey, S J

    2008-01-01

    In N=4 super Yang-Mills spin chain, we compute reflection amplitudes of magnon bound-state off giant graviton. We first compute the reflection amplitude off Y=0 brane boundary and compare it with the scattering amplitude between two magnon bound-states in the bulk. We find that analytic structure of the two amplitudes are intimately related each other: the boundary reflection amplitude is a square-root of the bulk scattering amplitude. Using such relation as a guide and taking known results at weak and strong coupling limits as inputs, we find the reflection amplitude of an elementary magnon off Z=0 giant graviton boundary. The reflection phase factor is shown to solve crossing and unitarity relations. We then compute the reflection amplitude of magnon bound-state off the Z=0 brane boundary and observe that its analytic structures are again intimately related to the bulk scattering and the Y=0 boundary reflection amplitudes. We also take dyonic giant magnon limit of these reflection amplitudes and confirm tha...

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

    OpenAIRE

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2016-01-01

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

  13. 3D-QSAR and docking studies of estrogen compounds based on estrogen receptor β

    Institute of Scientific and Technical Information of China (English)

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

    2009-01-01

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

  14. 3D-QSAR and docking studies of estrogen compounds based on estrogen receptor β

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

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

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

    Science.gov (United States)

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

    2011-11-10

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

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

    Directory of Open Access Journals (Sweden)

    Kiattawee Choowongkomon

    2010-06-01

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

  17. 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

  18. Regularity of Bound States

    DEFF Research Database (Denmark)

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

    2011-01-01

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

  19. Tight Bernoulli tail probability bounds

    OpenAIRE

    Dzindzalieta, Dainius

    2014-01-01

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

  20. Bounded Rationality in Transposition Processes

    DEFF Research Database (Denmark)

    Vollaard, Hans; Martinsen, Dorte Sindbjerg

    2014-01-01

    concerns the organisation and financing of national healthcare systems. This article applies the perspective of bounded rationality to explain (irregularities in) the timely and correct transposition of EU directives. The cognitive and organisational constraints long posited by the bounded rationality...... 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....

  1. Novel Bounds on Marginal Probabilities

    OpenAIRE

    Mooij, Joris M.; Kappen, Hilbert J

    2008-01-01

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

  2. Separable subgroups have bounded packing

    CERN Document Server

    Yang, Wen-yuan

    2010-01-01

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

  3. On bound entanglement assisted distillation

    OpenAIRE

    Vedral, V.

    1999-01-01

    We investigate asymptotic distillation of entanglement in the presence of an unlimited amount of bound entanglement for bi-partite systems. We show that the distillability is still bounded by the relative entropy of entanglement. This offers a strong support to the fact that bound entanglement does not improve distillation of entanglement.

  4. 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; Larsen, Inna; Kuhne, Sebastiaan; Gloriam, David E; Bräuner-Osborne, Hans; Sejer Pedersen, Daniel

    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....

  5. Towards Bounded Infeasible Code Detection

    CERN Document Server

    Christ, Jürgen; Schäf, Martin

    2012-01-01

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

  6. Sequence, Structure and Ligand Binding Evolution of Rhodopsin-Like G Protein-Coupled Receptors: A Crystal Structure-Based Phylogenetic Analysis

    OpenAIRE

    Wolf, Steffen; Grünewald, Stefan

    2015-01-01

    G protein-coupled receptors (GPCRs) form the largest family of membrane receptors in the human genome. Advances in membrane protein crystallization so far resulted in the determination of 24 receptors available as high-resolution atomic structures. We performed the first phylogenetic analysis of GPCRs based on the available set of GPCR structures. We present a new phylogenetic tree of known human rhodopsin-like GPCR sequences based on this structure set. We can distinguish the three separate ...

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

    Science.gov (United States)

    Sekuła, Karolina; Zuba, Dariusz; Stanaszek, Roman

    2012-05-01

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

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

    Institute of Scientific and Technical Information of China (English)

    张静; 李云松; 郭杰; 王柯俨; 吴成柯

    2012-01-01

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

  9. Experimental and theoretical study on the cooperative interaction of the ethanolammonium cation with a hexaarylbenzene-based receptor

    Czech Academy of Sciences Publication Activity Database

    Makrlík, E.; Toman, Petr; Vaňura, P.; Rathore, R.

    2012-01-01

    Roč. 406, 8 October (2012), s. 86-90. ISSN 0301-0104 R&D Projects: GA ČR(CZ) GAP205/10/2280 Institutional research plan: CEZ:AV0Z40500505 Institutional support: RVO:61389013 Keywords : ethanolammonium cation * hexaarylbenzene-based receptor * complexation Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.957, year: 2012

  10. A "turn-on" silver nanocluster based fluorescent sensor for folate receptor detection and cancer cell imaging under visual analysis.

    Science.gov (United States)

    Jiang, Hong; Xu, Gang; Sun, Yimin; Zheng, Weiwei; Zhu, Xiangxiang; Wang, Baojuan; Zhang, Xiaojun; Wang, Guangfeng

    2015-07-28

    A novel terminal protection based label-free and "turn-on" fluorescent sensor for detection of folate receptors (FRs) and HeLa cells is developed by fluorescence resonance energy transfer (FRET) between single-walled carbon nanotubes (SWCNTs) and silver nanoclusters (AgNCs). Multilevel visual analysis (m(2)VA) was firstly proposed and applied in optimizing the experimental parameters. PMID:26108636

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

    NARCIS (Netherlands)

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

    2011-01-01

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

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

    DEFF Research Database (Denmark)

    Dietrich, J; Geisler, C

    1998-01-01

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

  13. Strongly Bounded Partial Sums

    Directory of Open Access Journals (Sweden)

    Charles Swartz

    2014-06-01

    Full Text Available If λ is a scalar sequence space, a series P Zj in a topological vector space Z is λ multiplier convergent in Z if the series P ∞J =1 tj Zj converges in Z for every t = {tj} ∈ λ-If λ satisfies appropriate conditions, a series in a locally convex space X which is λ multiplier convergent in the weak topology is λ multiplier convergent in the original topology ofthe space (the Orlicz-Pettis Theorem but may fail to be λ multiplier convergent in the strong topology of the space. However, we show under apprpriate conditions on the multiplier space λ that the series will have strongly bounded partial sums.

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

    DEFF Research Database (Denmark)

    Jensen, Anders A.

    2005-01-01

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

  15. 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

    discovery is described, and proof-of-concept data from a pilot screen with a CXCR4 assay are presented. This chemokine receptor is a highly relevant drug target which plays an important role in the pathogenesis of inflammatory disease and also has been shown to be a co-receptor for entry of HIV into cells...

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

    Science.gov (United States)

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

    2016-06-01

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

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

    Science.gov (United States)

    Helsing, Johan

    1993-02-01

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

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

    DEFF Research Database (Denmark)

    Beelen, Peter

    A one-point AG-code is an algebraic geometry code based on a divisor whose support consists of one point. Since the discovery of the Feng-Rao lower bound for the minimum distance, there has been a renewed interest in such codes. This lower bound is also called the order bound. An alternative...... description of these codes in terms of order domains has been found. In my talk I will indicate how one can use the ideas behind the order bound to obtain a lower bound for the minimum distance of any AG-code. After this I will compare this generalized order bound with other known lower bounds, such as the...

  19. 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

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

    Directory of Open Access Journals (Sweden)

    M. L. McGuire

    2011-03-01

    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 were 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 caused in part 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

  1. Information bounds for Gaussian copulas

    CERN Document Server

    Hoff, Peter D; Wellner, Jon A

    2011-01-01

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

  2. Performance Bounds of Quaternion Estimators.

    Science.gov (United States)

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

    2015-12-01

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

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

    Directory of Open Access Journals (Sweden)

    Creamer Matthew S

    2012-08-01

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

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

    Science.gov (United States)

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

    2014-01-01

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

  5. 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. PMID:24853343

  6. 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.

  7. 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.

  8. 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.

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

    Science.gov (United States)

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

    2016-08-23

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

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

    Science.gov (United States)

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

    2011-04-01

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

  11. 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

  12. Call packing bound for overflow loss systems

    NARCIS (Netherlands)

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

    2009-01-01

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

  13. Call packing bounds for overflow queues

    NARCIS (Netherlands)

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

    2004-01-01

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

  14. On Quantum Capacity and its Bound

    OpenAIRE

    Ohya, Masanori; Volovich, Igor V.

    2004-01-01

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

  15. AT1 receptors as mechanosensors.

    Science.gov (United States)

    Mederos y Schnitzler, Michael; Storch, Ursula; Gudermann, Thomas

    2011-04-01

    G-protein-coupled receptors are appreciated as central components of neurohormonal signaling. Recently, it turned out that they may also play a role in mechanotransduction. The angiotensin II AT(1) receptor was the first G-protein-coupled receptor claimed to be a mechanosensor. In the meantime, several other G(q/11)-coupled receptors were found to be sensitive to mechanical stimuli. Furthermore, there is first evidence to support the concept that G(i/o)-coupled receptors are susceptible to mechanical stimulation as well. Mechanical receptor activation appears to be agonist-independent and is initiated by a conformational change of the receptor protein discernible from agonist-bound conformations. Mechanically induced receptor activation plays a physiological role for myogenic vasoconstriction and is involved in the pathogenesis of cardiac hypertrophy. PMID:21147033

  16. 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.

  17. Tight Bounds for Distributed Functional Monitoring

    DEFF Research Database (Denmark)

    Woodruff, David P.; Zhang, Qin

    2011-01-01

    $, our bound resolves their main open question. Our lower bounds are based on new direct sum theorems for approximate majority, and yield significant improvements to problems in the data stream model, improving the bound for estimating $F_p, p > 2,$ in $t$ passes from $\\tilde{\\Omega}(n^{1-2/p}/(\\eps^{2/p......We resolve several fundamental questions in the area of distributed functional monitoring, initiated by Cormode, Muthukrishnan, and Yi (SODA, 2008). In this model there are $k$ sites each tracking their input and communicating with a central coordinator that continuously maintain an approximate......-polynomial communication, partly answering Question 25 in the Open Problems in Data Streams list....

  18. Lower Bounds for External Memory Dictionaries

    DEFF Research Database (Denmark)

    Brodal, Gerth Stølting; Fagerberg, Rolf

    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 < M insertions perform at most δ · N/B I/Os, then...... (1) there exists a query requiring N/(M. ·~O(δ)) I/Os, and (2) there exists a query requiring Ω(logδlog2N ~ I/Os when δ is O(B/log3 N) and N is at least M2. For both lower bound we describe data structures which give matching upper bounds for a wide range of parameters, thereby showing the lower...

  19. 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.

  20. Bounded link prediction in very large networks

    Science.gov (United States)

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

    2016-09-01

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

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

    OpenAIRE

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

    2014-01-01

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

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

    Science.gov (United States)

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

    2014-05-01

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

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

    OpenAIRE

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

    2011-01-01

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

  4. Different angiotensin receptor blockers and incidence of diabetes: a nationwide population-based cohort study

    OpenAIRE

    Chang, Chia-Hsuin; Chang, Yi-Cheng; Wu, Li-Chiu; Lin, Jou-Wei; Chuang, Lee-Ming; Lai, Mei-Shu

    2014-01-01

    Background Angiotensin receptor blockers (ARBs) have been shown to exert various peroxisome proliferator-activated receptor gamma (PPARγ) binding activities and insulin-sensitizing effects. The objective of this study was to investigate the association of different ARBs with new-onset diabetes mellitus. Methods In the respective cohort, a total of 492,530 subjects who initiated ARB treatment between January 2004 and December 2009 were identified from Taiwan National Health Insurance Database....

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

    OpenAIRE

    Frank, Michael J.; Hutchison, Kent

    2009-01-01

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

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

    OpenAIRE

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

    2016-01-01

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

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

    OpenAIRE

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

    2015-01-01

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

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

    OpenAIRE

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

    2013-01-01

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

  9. Scattering theory methods for bound state problems

    International Nuclear Information System (INIS)

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

  10. 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.

  11. A Lower Bound on Concurrence

    Institute of Scientific and Technical Information of China (English)

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

    2009-01-01

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

  12. Extraction and DFT study on the complexation of the TRIS+ cation with a hexaarylbenzene-based receptor

    Czech Academy of Sciences Publication Activity Database

    Makrlík, E.; Toman, Petr; Vaňura, P.; Rathore, R.

    2012-01-01

    Roč. 59, č. 4 (2012), s. 944-948. ISSN 1318-0207 R&D Projects: GA ČR(CZ) GAP205/10/2280 Institutional research plan: CEZ:AV0Z40500505 Institutional support: RVO:61389013 Keywords : TRIS+ * hexaarylbenzene–based receptor * complexation Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.135, year: 2012 http://acta.chem-soc.si/59/59-4-944.pdf

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

    OpenAIRE

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

    1989-01-01

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

  14. 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

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

    CERN Document Server

    Eldering, J

    2012-01-01

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

  16. Distribution Network Planning and Design Using Branch and Bound Methods

    Directory of Open Access Journals (Sweden)

    Jalal Abdallah

    2005-01-01

    Full Text Available This study presents implementation of the bound and branch methods as an optimization mathematical device for distribution network planning. A development technology concentrates on minimizing the total costs and provides extended opportunities for improvement of network operation, from the initial planning stage. The study illustrate the mathematical and the algorithm of the branch and bound method with an example to indicate the efficiency of the branch and bound in planning and design processes. It also shows that the optimal configuration strongly depends on the branching rule and on the bound calculation bases.

  17. On the Applicability of Lower Bounds for Solving Rectilinear

    DEFF Research Database (Denmark)

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

    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. Rec...... Branch-and-Bound code solving large scale QAPs.......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...

  18. Antibody-bound amyloid precursor protein upregulates ornithine decarboxylase expression

    DEFF Research Database (Denmark)

    Nilsson, Tatjana; Malkiewicz, Katarzyna; Gabrielsson, Maria;

    2006-01-01

    Alzheimer's disease is a neurodegenerative disorder characterised by extracellular accumulation of the Abeta peptide, derived from the amyloid precursor protein (APP). The function of APP as a cell surface receptor was examined by ligand-mimicking using an antibody against the APP extracellular...... signalling events. This study shows that antibody-bound APP leads to altered gene expression that may be relevant to AD....... domain. Alterations in gene expression evoked by antibody-bound APP were analysed using human pathway-finder gene arrays and the largest change in expression levels was found for ornithine decarboxylase (ODC). These results were confirmed by Western blotting which showed even higher upregulation on the...

  19. A PSL Bounded Model Checking Method

    Institute of Scientific and Technical Information of China (English)

    YU Lei; ZHAO Zongtao

    2012-01-01

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

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

    Science.gov (United States)

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

    2015-09-01

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

  1. Design of a new serotonin receptor 5-HT1A imaging agent based on 99mTc

    International Nuclear Information System (INIS)

    Serotonin is one of the neurotransmitters found in the brain and mediates brain functions. It is very well known that serotonin related brain abnormalities are exerted mainly via serotonin receptors in a similar manner to other neurotransmitters found in the brain. Recently, it has also been found that serotonin is involved in Alzheimer's disease either directly or indirectly by its actions on serotonergic neurons. To understand and treat the diseases caused by abnormalities in the serotonergic system in the brain, it is certain that its mechanism of function has to be well investigated. So far several 5-HT receptors and receptor subtypes have been well characterized. Moreover, serotonin agonists and antagonists acting on specific receptors are chemically synthesized and are now available for the prevention or treatment of serotonergic related diseases. In recent years, a great demand for developing neuroimaging agents has emerged for the diagnosis of abnormal brain functions in the area of nuclear medicine. Since arylpiperazine, WAY 100635, in the present investigation, has been recognized as a highly selective ligand for the 5-HT1A receptor, it has been used for the development of brain imaging agents based on serotonin receptors. First, S,S'-bis(trityl) monoamide monoamine (MAMA-Tr2) was synthesized, followed by synthesis of an arylpiperazine ligand. The synthesis of the analogue of WAY 100635 was completed and it lead to successful labelling with 99mTc without a by-product. Deprotection of the S,S-Tr2 group of MAMA-Tr2 was efficiently conducted by incubation at 100 deg. C for 1 h under acidic conditions (pH2-3), followed by labelling with 99mTc. Its radiochemical purity was checked by high performance liquid chromatography, and a labelled compound of >99% radiochemical purity was used for an in vivo bioavailability study using a gamma ray camera. An animal biodistribution study was also conducted to ascertain the serotonergic neuronal imaging effect of 99m

  2. 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.

  3. 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.

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

    Science.gov (United States)

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

    2016-08-01

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

  5. A CXCL8 receptor antagonist based on the structure of N-Acetyl-Proline-Glycine-Proline

    OpenAIRE

    Jackson, Patricia L; Noerager, Brett D.; Jablonsky, Michael J; Hardison, Matthew T.; Cox, Bryan D; Patterson, James C.; Dhanapal, Boopathy; Blalock, J Edwin; Muccio, Donald D

    2011-01-01

    A role for the collagen-derived tripeptide, N-acetyl proline-glycine-proline (NAc-PGP), in neutrophil recruitment in chronic airway inflammatory diseases, including COPD and cystic fibrosis, has recently been delineated. Due to structural similarity to an important motif for interleukin-8 (CXCL8) binding to its receptor, NAc-PGP binds to CXCR1/2 receptors, leading to neutrophil activation and chemotaxis. In an effort to develop novel CXCL8 antagonists, we describe the synthesis of four chiral...

  6. Fluctuation bounds for entropy production estimators in Gibbs measures

    Science.gov (United States)

    Maldonado, Cesar

    2015-01-01

    We give bounds for the fluctuations of estimators of the mean entropy production in Gibbsian sources. These bounds are valid for every n, where n denotes the size-length of the sample. We consider two estimators which are based on waiting and hitting times.

  7. Fluctuation bounds for entropy production estimators in Gibbs measures

    International Nuclear Information System (INIS)

    We give bounds for the fluctuations of estimators of the mean entropy production in Gibbsian sources. These bounds are valid for every n, where n denotes the size-length of the sample. We consider two estimators which are based on waiting and hitting times. (paper)

  8. 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.

  9. Bounded Model Checking of CTL

    Institute of Scientific and Technical Information of China (English)

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

    2007-01-01

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

  10. Bounded link prediction for very large networks

    CERN Document Server

    Cui, Wei; Xu, Zhongqi

    2015-01-01

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

  11. Novel Receptors Based on the Porphyrin-Calix[4]Arene Conjugates

    Czech Academy of Sciences Publication Activity Database

    Dudic, M.; Lang, Kamil

    Leuven: Global Supramolecular Chemistry Network, 2000. s. 88 [International Conference on Supramolecular Science & Technology /2./. 10.09.2000-14.09.2000, Leuven] Institutional research plan: CEZ:AV0Z4032918 Keywords : porphyrin * receptors * calix[4]arene Subject RIV: CA - Inorganic Chemistry

  12. Scavenger receptor AI/II truncation, lung function and COPD: a large population-based study

    DEFF Research Database (Denmark)

    Thomsen, M; Nordestgaard, B G; Tybjærg-Hansen, Anne;

    2011-01-01

    The scavenger receptor A-I/II (SRA-I/II) on alveolar macrophages is involved in recognition and clearance of modified lipids and inhaled particulates. A rare variant of the SRA-I/II gene, Arg293X, truncates the distal collagen-like domain, which is essential for ligand recognition. We tested whet...

  13. Anion Receptors based on Ureidocalix[4]arenes Immobilised in the Partial cone Conformation

    Czech Academy of Sciences Publication Activity Database

    Hudeček, O.; Budka, J.; Dvořáková, H.; Cuřínová, Petra; Císařová, I.; Lhoták, P.

    2013-01-01

    Roč. 37, č. 1 (2013), s. 220-227. ISSN 1144-0546 R&D Projects: GA ČR GA203/09/0691; GA AV ČR IAAX08240901 Institutional support: RVO:67985858 Keywords : anion receptors * ureidocalix[4]arenes * partial cone conformation Subject RIV: CC - Organic Chemistry Impact factor: 3.159, year: 2013

  14. Identification of small-molecule agonists of human relaxin family receptor 1 (RXFP1) by using a homogenous cell-based cAMP assay.

    Science.gov (United States)

    Chen, Catherine Z; Southall, Noel; Xiao, Jingbo; Marugan, Juan J; Ferrer, Marc; Hu, Xin; Jones, Raisa E; Feng, Shu; Agoulnik, Irina U; Zheng, Wei; Agoulnik, Alexander I

    2013-07-01

    The relaxin hormone is involved in a variety of biological functions, including female reproduction and parturition, as well as regulation of cardiovascular, renal, pulmonary, and hepatic functions. It regulates extracellular matrix remodeling, cell invasiveness, proliferation, differentiation, and overall tissue homeostasis. The G protein-coupled receptor (GPCR) relaxin family receptor 1 (RXFP1) is a cognate relaxin receptor that mainly signals through cyclic AMP second messenger. Although agonists of the receptor could have a wide range of pharmacologic utility, until now there have been no reported small-molecule agonists for relaxin receptors. Here, we report the development of a quantitative high-throughput platform for an RXFP1 agonist screen based on homogenous cell-based HTRF cyclic AMP (cAMP) assay technology. Two small molecules of similar structure were independently identified from a screen of more than 365 677 compounds. Neither compound showed activity in a counterscreen with HEK293T cells transfected with an unrelated GPCR vasopressin 1b receptor. These small-molecule agonists also demonstrated selectivity against the RXFP2 receptor, providing a basis for future medicinal chemistry optimization of selective relaxin receptor agonists. PMID:23212924

  15. Bound states in string nets

    CERN Document Server

    Schulz, M D; Vidal, J

    2016-01-01

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

  16. Curvature bounds for configuration spaces

    OpenAIRE

    Erbar, Matthias; Huesmann, Martin

    2014-01-01

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

  17. Entropy bounds for uncollapsed matter

    Energy Technology Data Exchange (ETDEWEB)

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

    2011-09-22

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

  18. Finite Domain Bounds Consistency Revisited

    OpenAIRE

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

    2004-01-01

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

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

    Science.gov (United States)

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

    2006-02-01

    Standard solution Gibbs energies, DeltasG degrees, of the resorcarene-based receptor 5,11,17,23-ethylthiomethylated calix[4]resorcarene, (characterized by 1H NMR and X-ray diffraction studies) in its monomeric state (established through partition experiments) in various solvents are for the first time reported in the area of resorcarene chemistry. Transfer Gibbs energies of from hexane (reference solvent) to other medium are calculated. Agreement between DeltatG degrees (referred to the pure solvents) and standard partition Gibbs energies, DeltapG degrees (solvent mutually saturated) is found. Cation-ligand interactions were investigated through 1H NMR (CD3CN and CD3OD) and conductometric titrations in acetonitrile and methanol. 1H NMR data revealed the sites of interaction of with the metal cation. The composition of the metal-ion complexes (Ag+ and Pb2+ in acetonitrile and Ag+ and Cu2+ in methanol) was established through conductometric titrations. Thus, complexes of 1:1 stoichiometry were formed between and Ag+ and Pb2+ in acetonitrile and Cu2+ in methanol. However, in moving from acetonitrile to methanol, the composition of the silver complex was altered. Thus, two metal cations are hosted by a unit of the ligand. As far as Cu2+ and in acetonitrile is concerned, conductance data suggest that metalates are formed in which up to four units of Cu2+ are taken up per unit of resorcarene. The contrasting behavior of with Cu2+ in acetonitrile relative to methanol is discussed. As far as mercury (II) is concerned, the unusual jump in conductance observed in the titration of Hg2+ with in acetonitrile and methanol after the formation of a multicharged complex (undefined composition) is attributed to the presence of highly charged smaller units (higher mobility) resulting from the departure of pendant arms from the resorcarene backbone. Isolation of these species followed by X-ray diffraction studies corroborated this statement. The thermodynamic characterization of metal

  20. Enhanced lower entropy bounds with application to constructive learning

    Energy Technology Data Exchange (ETDEWEB)

    Beiu, V.

    1997-04-01

    In this paper the authors prove two new lower bounds for the number-of-bits required by neural networks for classification problems defined by m examples from R{sup n}. Because they are obtained in a constructive way, they can be used for designing a constructive algorithm. These results rely on techniques used for determining tight upper bounds, which start by upper bounding the space with an n-dimensional ball. Very recently, a better upper bound has been detailed by showing that the volume of the ball can always be replaced by the volume of the intersection of two balls. A first lower bound for the case of integer weights in the range [{minus}p,p] has been detailed: it is based on computing the logarithm of the quotient between the volume of the ball containing all the examples (rough approximation) and the maximum volume of a polyhedron. A first improvement over that bound will come from a tighter upper bound of the maximum volume of the polyhedron by two n-dimensional cones. An even tighter bound will be obtained by upper bounding the space by the intersection of two balls.

  1. 3D Structure Prediction of Human β1-Adrenergic Receptor via Threading-Based Homology Modeling for Implications in Structure-Based Drug Designing

    OpenAIRE

    Ul-Haq, Zaheer; Saeed, Maria; Halim, Sobia Ahsan; Khan, Waqasuddin

    2015-01-01

    Dilated cardiomyopathy is a disease of left ventricular dysfunction accompanied by impairment of the β1-adrenergic receptor (β1-AR) signal cascade. The disturbed β1-AR function may be based on an elevated sympathetic tone observed in patients with heart failure. Prolonged adrenergic stimulation may induce metabolic and electrophysiological disturbances in the myocardium, resulting in tachyarrhythmia that leads to the development of heart failure in human and sudden death. Hence, β1-AR is cons...

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

    OpenAIRE

    Awad, M M; Muzychka, Y. S.

    2014-01-01

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

  3. On Shrinking and Boundedly Complete Schauder Frames of Banach spaces

    OpenAIRE

    Liu, Rui

    2009-01-01

    This paper studies Schauder frames in Banach spaces, a concept which is a natural generalization of frames in Hilbert spaces and Schauder bases in Banach spaces. The associated minimal and maximal spaces are introduced, as are shrinking and boundedly complete Schauder frames. Our main results extend the classical duality theorems on bases to the situation of Schauder frames. In particular, we will generalize James' results on shrinking and boundedly complete bases to frames. Secondly we will ...

  4. Macrocyclic chelator-coupled gastrin-based radiopharmaceuticals for targeting of gastrin receptor-expressing tumours

    International Nuclear Information System (INIS)

    Diethylenetriamine-pentaacetic acid (DTPA)-coupled minigastrins are unsuitable for therapeutic application with the available β-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 111In-labelled derivatives. Gastrin derivatives with decreasing numbers of glutamic acids were synthesised using 111In as surrogate for therapeutic radiometals for in vitro and in vivo studies. Gastrin receptor affinities of the natIn-metallated compounds were determined by receptor autoradiography using 125I-CCK as radioligand. Internalisation was evaluated in AR4-2J cells. Enzymatic stability was determined by incubating the 111In-labelled peptides in human serum. Biodistribution was performed in AR4-2J-bearing Lewis rats. IC50 values of the natIn-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 (IC50 between 9.9 and 1,195 nmol/L). All cholecystokinin receptor affinities were >100 nmol/L. All 111In-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 111In-labelled macrocyclic chelator conjugates showed higher tumour-to-kidney ratios after 24 h (0.37-0.99) compared to 111In-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 lower metabolic stability. The properties of the macrocyclic chelator

  5. A yellow fluorescent protein-based assay for high-throughput screening of glycine and GABAA receptor chloride channels.

    Science.gov (United States)

    Kruger, Wade; Gilbert, Daniel; Hawthorne, Rebecca; Hryciw, Deanne H; Frings, Stephan; Poronnik, Philip; Lynch, Joseph W

    2005-06-01

    There is a significant clinical need to identify novel ligands with high selectivity and potency for GABA(A), GABA(C) and glycine receptor Cl- channels. Two recently developed, yellow fluorescent protein variants (YFP-I152L and YFP-V163S) are highly sensitive to quench by small anions and are thus suited to reporting anionic influx into cells. The aim of this study was to establish the optimal conditions for using these constructs for high-throughput screening of GABA(A), GABA(C) and glycine receptors transiently expressed in HEK293 cells. We found that a 70% fluorescence reduction was achieved by quenching YFP-I152L with a 10 s influx of I- ions, driven by an external I- concentration of at least 50 mM. The fluorescence quench was rapid, with a mean time constant of 3 s. These responses were similar for all anion receptor types studied. We also show the assay is sufficiently sensitive to measure agonist and antagonist concentration-responses using either imaging- or photomultiplier-based detection systems. The robustness, sensitivity and low cost of this assay render it suited for high-throughput screening of transiently expressed anionic ligand-gated channels. PMID:15862914

  6. Detection of marine microalgal biotoxins using bioassays based on functional expression of tunicate xenobiotic receptors in yeast.

    Science.gov (United States)

    Richter, Ingrid; Fidler, Andrew E

    2015-03-01

    Marine microalgae can produce biotoxins that cause widespread poisoning in marine ecosystems and may also affect human health. While established microalgal biotoxins are detectable using chemical methods, a need remains for robust, inexpensive bioassays. Ligand-binding domains (LBDs) from a tunicate nuclear receptor, VDR/PXRα, which is orthologous to both the vertebrate pregnane X receptor (PXR) and the vitamin D receptor (VDR), can be activated by microalgal biotoxins when expressed in mammalian cell lines. Building on this observation, we developed a generic recombinant yeast bioassay platform that expresses chimeric proteins containing tunicate VDR/PXRα LBDs which mediate ligand-dependent transcription of a reporter gene (lacZ) encoding an easily assayed enzyme (β-galactosidase). Recombinant yeast strains expressing VDR/PXRα LBDs from two tunicate species, Ciona intestinalis and Botryllus schlosseri, were exposed to both synthetic and natural toxins. Structurally simple synthetic chemicals (n-butyl-p-aminobenzoate, carbamazepine, p-aminobenzoic acid, and bisphenol-A) generated EC50 values in the μM range, while more structurally complex marine biotoxins (okadaic acid, pectenotoxin-11, and portimine) activated the assays in the nM range. Given the large number of tunicate species, we propose that tunicate VDR/PXR LBDs may be used as 'sensor elements' in similar yeast-based high-throughput bioassays for detection of established microalgal biotoxins and uncharacterised marine bioactive compounds. PMID:25549942

  7. 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.

  8. 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...

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

    Directory of Open Access Journals (Sweden)

    R Barcia

    2011-03-01

    Full Text Available In molluscs, hemocytes perform the molecular mechanisms related to immunity. These cells have the ability to respond to the different varieties of stress by modulating their responses. The stressors may be bacterial toxins, cytokines or growth factors, and even physical agents such as changes in temperature or oxygen partial pressure. In the first place, hemocytes synthesise catecholamines, which, in turn, modify the immune response in terms of phagocytosis or nitric oxide synthesis. According to studies on the hemocytes of the mussel Mytilus galloprovincialis, we propose a model for a sequential action where the IL-2 receptor and its wide agonist specificity play an important role. Also, α and β-adrenergic receptors suggest the functioning of a return-to-hemocyte mechanism. The model is proposed taking into account the possible relationship between the pathways mediated by cAMP-activated protein kinase and protein kinase C in hemocytes.

  10. Diversity in anti-N-methyl-D-aspartate receptor encephalitis: case-based evidence

    OpenAIRE

    Pinho, J; Rocha, J.; Rodrigues, M.; Pereira, J.; Maré, R; Ferreira, C; Lourenço, E; Beleza, P

    2012-01-01

    Antibodies against N-methyl-D-aspartate receptor (NMDAR) are identified in the form of immune-mediated encephalitis in which typical manifestations include neuropsychiatric symptoms, seizures, abnormal movements, dysautonomia and hypoventilation. The authors report two cases of anti-NMDAR encephalitis with different presentations and patterns of progression. The first patient presented with status epilepticus and later developed psychosis, pyramidal signs and diffuse encephalopathy. The secon...

  11. On a Generalization of Kingman's Bounds

    OpenAIRE

    Liu, Zhen; Nain, Philippe; Towsley, Don

    1994-01-01

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

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

    Directory of Open Access Journals (Sweden)

    V. K. Sahu

    2008-01-01

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

  13. Fluorescence-based optimization of human bitter taste receptor expression in Saccharomyces cerevisiae

    Energy Technology Data Exchange (ETDEWEB)

    Sugawara, Taishi; Ito, Keisuke [Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657 (Japan); Shiroishi, Mitsunori [Iwata Human Receptor Crystallography Project, ERATO, JST, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501 (Japan); Tokuda, Natsuko [Department of Medical Chemistry, Kyoto University Faculty of Medicine, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501 (Japan); Asada, Hidetsugu; Yurugi-Kobayashi, Takami; Shimamura, Tatsuro [Iwata Human Receptor Crystallography Project, ERATO, JST, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501 (Japan); Misaka, Takumi [Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657 (Japan); Nomura, Norimichi [Iwata Human Receptor Crystallography Project, ERATO, JST, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501 (Japan); Murata, Takeshi [Iwata Human Receptor Crystallography Project, ERATO, JST, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501 (Japan); Department of Medical Chemistry, Kyoto University Faculty of Medicine, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501 (Japan); Abe, Keiko [Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657 (Japan); Iwata, So, E-mail: s.iwata@mfour.med.kyoto-u.ac.jp [Iwata Human Receptor Crystallography Project, ERATO, JST, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501 (Japan); Department of Medical Chemistry, Kyoto University Faculty of Medicine, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501 (Japan); Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College London, London SW7 2AZ (United Kingdom); Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Chilton, Oxfordshire OX11 0DE (United Kingdom); and others

    2009-05-15

    Human TAS2 receptors (hTAS2Rs) perceive bitter tastants, but few studies have explored the structure-function relationships of these receptors. In this paper, we report our trials on the large-scale preparations of hTAS2Rs for structural analysis. Twenty-five hTAS2Rs were expressed using a GFP-fusion yeast system in which the constructs and the culture conditions (e.g., the signal sequence, incubation time and temperature after induction) were optimized by measuring GFP fluorescence. After optimization, five hTAS2Rs (hTAS2R7, hTAS2R8, hTAS2R16, hTAS2R41, and hTAS2R48) were expressed at levels greater than 1 mg protein/L of culture, which is a preferable level for purification and crystallization. Among these five bitter taste receptors, hTAS2R41 exhibited the highest detergent solubilization efficiency of 87.1% in n-dodecyl-{beta}-D-maltopyranoside (DDM)/cholesteryl hemisuccinate (CHS). Fluorescence size-exclusion chromatography showed that hTAS2R41 exhibited monodispersity in DDM/CHS without aggregates, suggesting that hTAS2R41 is a good target for future crystallization trials.

  14. Fluorescence-based optimization of human bitter taste receptor expression in Saccharomyces cerevisiae

    International Nuclear Information System (INIS)

    Human TAS2 receptors (hTAS2Rs) perceive bitter tastants, but few studies have explored the structure-function relationships of these receptors. In this paper, we report our trials on the large-scale preparations of hTAS2Rs for structural analysis. Twenty-five hTAS2Rs were expressed using a GFP-fusion yeast system in which the constructs and the culture conditions (e.g., the signal sequence, incubation time and temperature after induction) were optimized by measuring GFP fluorescence. After optimization, five hTAS2Rs (hTAS2R7, hTAS2R8, hTAS2R16, hTAS2R41, and hTAS2R48) were expressed at levels greater than 1 mg protein/L of culture, which is a preferable level for purification and crystallization. Among these five bitter taste receptors, hTAS2R41 exhibited the highest detergent solubilization efficiency of 87.1% in n-dodecyl-β-D-maltopyranoside (DDM)/cholesteryl hemisuccinate (CHS). Fluorescence size-exclusion chromatography showed that hTAS2R41 exhibited monodispersity in DDM/CHS without aggregates, suggesting that hTAS2R41 is a good target for future crystallization trials.

  15. 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.

  16. Prediction of binding affinity and efficacy of thyroid hormone receptor ligands using QSAR and structure-based modeling methods

    International Nuclear Information System (INIS)

    The thyroid hormone receptor (THR) is an important member of the nuclear receptor family that can be activated by endocrine disrupting chemicals (EDC). Quantitative Structure–Activity Relationship (QSAR) models have been developed to facilitate the prioritization of THR-mediated EDC for the experimental validation. The largest database of binding affinities available at the time of the study for ligand binding domain (LBD) of THRβ was assembled to generate both continuous and classification QSAR models with an external accuracy of R2 = 0.55 and CCR = 0.76, respectively. In addition, for the first time a QSAR model was developed to predict binding affinities of antagonists inhibiting the interaction of coactivators with the AF-2 domain of THRβ (R2 = 0.70). Furthermore, molecular docking studies were performed for a set of THRβ ligands (57 agonists and 15 antagonists of LBD, 210 antagonists of the AF-2 domain, supplemented by putative decoys/non-binders) using several THRβ structures retrieved from the Protein Data Bank. We found that two agonist-bound THRβ conformations could effectively discriminate their corresponding ligands from presumed non-binders. Moreover, one of the agonist conformations could discriminate agonists from antagonists. Finally, we have conducted virtual screening of a chemical library compiled by the EPA as part of the Tox21 program to identify potential THRβ-mediated EDCs using both QSAR models and docking. We concluded that the library is unlikely to have any EDC that would bind to the THRβ. Models developed in this study can be employed either to identify environmental chemicals interacting with the THR or, conversely, to eliminate the THR-mediated mechanism of action for chemicals of concern. - Highlights: • This is the largest curated dataset for ligand binding domain (LBD) of the THRβ. • We report the first QSAR model for antagonists of AF-2 domain of THRβ. • A combination of QSAR and docking enables prediction of both

  17. Prediction of binding affinity and efficacy of thyroid hormone receptor ligands using QSAR and structure-based modeling methods

    Energy Technology Data Exchange (ETDEWEB)

    Politi, Regina [Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina, Chapel Hill, NC 27599 (United States); Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC 27599 (United States); Rusyn, Ivan, E-mail: iir@unc.edu [Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC 27599 (United States); Tropsha, Alexander, E-mail: alex_tropsha@unc.edu [Laboratory for Molecular Modeling, Division of Chemical Biology and Medicinal Chemistry, University of North Carolina, Chapel Hill, NC 27599 (United States)

    2014-10-01

    The thyroid hormone receptor (THR) is an important member of the nuclear receptor family that can be activated by endocrine disrupting chemicals (EDC). Quantitative Structure–Activity Relationship (QSAR) models have been developed to facilitate the prioritization of THR-mediated EDC for the experimental validation. The largest database of binding affinities available at the time of the study for ligand binding domain (LBD) of THRβ was assembled to generate both continuous and classification QSAR models with an external accuracy of R{sup 2} = 0.55 and CCR = 0.76, respectively. In addition, for the first time a QSAR model was developed to predict binding affinities of antagonists inhibiting the interaction of coactivators with the AF-2 domain of THRβ (R{sup 2} = 0.70). Furthermore, molecular docking studies were performed for a set of THRβ ligands (57 agonists and 15 antagonists of LBD, 210 antagonists of the AF-2 domain, supplemented by putative decoys/non-binders) using several THRβ structures retrieved from the Protein Data Bank. We found that two agonist-bound THRβ conformations could effectively discriminate their corresponding ligands from presumed non-binders. Moreover, one of the agonist conformations could discriminate agonists from antagonists. Finally, we have conducted virtual screening of a chemical library compiled by the EPA as part of the Tox21 program to identify potential THRβ-mediated EDCs using both QSAR models and docking. We concluded that the library is unlikely to have any EDC that would bind to the THRβ. Models developed in this study can be employed either to identify environmental chemicals interacting with the THR or, conversely, to eliminate the THR-mediated mechanism of action for chemicals of concern. - Highlights: • This is the largest curated dataset for ligand binding domain (LBD) of the THRβ. • We report the first QSAR model for antagonists of AF-2 domain of THRβ. • A combination of QSAR and docking enables

  18. Invited review: Growth-promoting effects of colostrum in calves based on interaction with intestinal cell surface receptors and receptor-like transporters.

    Science.gov (United States)

    Ontsouka, Edgar C; Albrecht, Christiane; Bruckmaier, Rupert M

    2016-06-01

    The postnatal development and maturation of the gastrointestinal (GI) tract of neonatal calves is crucial for their survival. Major morphological and functional changes in the calf's GI tract initiated by colostrum bioactive substances promote the establishment of intestinal digestion and absorption of food. It is generally accepted that colostrum intake provokes the maturation of organs and systems in young calves, illustrating the significance of the cow-to-calf connection at birth. These postnatal adaptive changes of the GI tissues in neonatal calves are especially induced by the action of bioactive substances such as insulin-like growth factors, hormones, or cholesterol carriers abundantly present in colostrum. These substances interact with specific cell-surface receptors or receptor-like transporters expressed in the GI wall of neonatal calves to elicit their biological effects. Therefore, the abundance and activity of cell surface receptors and receptor-like transporters binding colostral bioactive substances are a key aspect determining the effects of the cow-to-calf connection at birth. The present review compiles the information describing the effects of colostrum feeding on selected serum metabolic and endocrine traits in neonatal calves. In this context, the current paper discusses specifically the consequences of colostrum feeding on the GI expression and activity of cell-receptors and receptor-like transporters binding growth hormone, insulin-like growth factors, insulin, or cholesterol acceptors in neonatal calves. PMID:26874414

  19. Family and population-based studies of variation within the ghrelin receptor locus in relation to measures of obesity

    DEFF Research Database (Denmark)

    Gjesing, Anette P.; Larsen, Lesli Hingstrup; Torekov, Signe Sørensen; Hainerová, Irena Aldhoon; Kapur, Rahul; Johansen, Anders; Albrechtsen, Anders; Boj, Sylvia; Holst, Birgitte; Harper, Angela; Urhammer, Søren A.; Borch-Johnsen, Knut; Pisinger, Charlotta Holm; Echwald, Søren M; Eiberg, Hans Rudolf Lytchoff; Astrup, Arne; Lebl, Jan; Ferrer, Jorge; Schwartz, Thue W.; Hansen, Torben; Pedersen, Oluf

    2010-01-01

    BACKGROUND: The growth hormone secretagogue receptor (GHSR) is mediating hunger sensation when stimulated by its natural ligand ghrelin. In the present study, we tested the hypothesis that common and rare variation in the GHSR locus are related to increased prevalence of obesity and overweight......-carriers (mean BMI: 28+/-5 kg/m(2)) (p>0.05) 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...

  20. 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.

  1. 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

  2. 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.

  3. Bounded solutions for fuzzy differential and integral equations

    Energy Technology Data Exchange (ETDEWEB)

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

    2006-03-01

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

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

    International Nuclear Information System (INIS)

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

  5. 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.

  6. Quantitative analysis of G-protein-coupled receptor internalization using DnaE intein-based assay.

    Science.gov (United States)

    Lu, Bin; Chen, Linjie; Zhang, Yaping; Shi, Ying; Zhou, Naiming

    2016-01-01

    G-protein-coupled receptors (GPCRs), the largest family of cell surface receptors, are involved in many physiological processes. They represent highly important therapeutic targets for drug discovery. Currently, there are numerous cell-based assays developed for the pharmacological profiling of GPCRs and the identification of novel agonists and antagonists. However, the development of new, faster, easier, and more cost-effective approaches to detect GPCR activity remains highly desirable. β-arrestin-dependent internalization has been demonstrated to be a common mechanism for most GPCRs. Here we describe a novel assay for quantitative analysis of GPCR internalization based on DnaE intein-mediated reconstitution of fragmented Renilla luciferase or Firefly luciferase when activated GPCRs interact with β-arrestin2 or Rab5. Further validation, using functionally divergent GPCRs, showed that EC50 values obtained for the known agonists and antagonists were in close agreement with the results of previous reports. This suggests that this assay is sensitive enough to permit quantification of GPCR internalization. Compared with conventional assays, this novel assay system is cost-effective, rapid, and easy to manipulate. These advantages may allow this assay to be used universally as a functional cell-based system for GPCR characterization and in the screening process of drug discovery. PMID:26928549

  7. Interaction of magnetite-based receptors in the beak with the visual system underlying 'fixed direction' responses in birds

    Directory of Open Access Journals (Sweden)

    Wiltschko Roswitha

    2010-08-01

    Full Text Available Abstract Background European robins, Erithacus rubecula, show two types of directional responses to the magnetic field: (1 compass orientation that is based on radical pair processes and lateralized in favor of the right eye and (2 so-called 'fixed direction' responses that originate in the magnetite-based receptors in the upper beak. Both responses are light-dependent. Lateralization of the 'fixed direction' responses would suggest an interaction between the two magnetoreception systems. Results Robins were tested with either the right or the left eye covered or with both eyes uncovered for their orientation under different light conditions. With 502 nm turquoise light, the birds showed normal compass orientation, whereas they displayed an easterly 'fixed direction' response under a combination of 502 nm turquoise with 590 nm yellow light. Monocularly right-eyed birds with their left eye covered were oriented just as they were binocularly as controls: under turquoise in their northerly migratory direction, under turquoise-and-yellow towards east. The response of monocularly left-eyed birds differed: under turquoise light, they were disoriented, reflecting a lateralization of the magnetic compass system in favor of the right eye, whereas they continued to head eastward under turquoise-and-yellow light. Conclusion 'Fixed direction' responses are not lateralized. Hence the interactions between the magnetite-receptors in the beak and the visual system do not seem to involve the magnetoreception system based on radical pair processes, but rather other, non-lateralized components of the visual system.

  8. Improved Range Searching Lower Bounds

    DEFF Research Database (Denmark)

    Larsen, Kasper Green; Nguyen, Huy L.

    2012-01-01

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

  9. Simulation bounds for system availability

    International Nuclear Information System (INIS)

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

  10. Polymerase chain reaction of Au nanoparticle-bound primers

    Institute of Scientific and Technical Information of China (English)

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

    2005-01-01

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

  11. Classical and quantum partition bound and detector inefficiency

    CERN Document Server

    Laplante, S; Roland, J

    2012-01-01

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

  12. Higher-order Boltzmann machines and entropy bounds

    Science.gov (United States)

    Apolloni, Bruno; Battistini, Egidio; de Falco, Diego

    1999-07-01

    We examine some aspects of the interface area between mathematical statistics and statistical physics relevant to the study of Boltzmann machines. The Boltzmann machine learning algorithm is based on a variational principle (Gibbs' lemma for relative entropy). This fact suggests the possibility of a scheme of successive approximations: here we consider successive approximations parametrized by the order of many-body interactions among individual units. We prove bounds on the gain in relative entropy in the crucial step of adding, and estimating by Hebb's rule, a new parameter. We address the problem of providing, on the basis of local observations, upper and lower bounds on the entropy. While upper bounds are easily obtained by subadditivity, lower bounds involve localization of Hirschman bounds on a dual quantum system.

  13. Tsh receptor

    OpenAIRE

    Frauman, Albert

    2013-01-01

    The TSH receptor is a member of the G protein-coupled receptor(GPCR)family. It is one of the glycoprotein hormone receptors, which also includes the FSH and LH/CG receptors. The TSH receptor mediates the action of the pituitary-derived glycoprotein, TSH (thyroid stimulating hormone, thyrotropin or thyrotrophin). TSH binds to the TSH receptor which is located on thyroid follicular cells (but is also expressed in extrathyroidal sites). Glycosylation of the TSH receptor occurs, as does cleavage ...

  14. Mutual information rate and bounds for it.

    Directory of Open Access Journals (Sweden)

    Murilo S Baptista

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

  15. Mutual information rate and bounds for it.

    Science.gov (United States)

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

    2012-01-01

    The amount of information exchanged per unit of time between two nodes in a dynamical network or between two data sets is a powerful concept for analysing complex systems. This quantity, known as the mutual information rate (MIR), is calculated from the mutual information, which is rigorously defined only for random systems. Moreover, the definition of mutual information is based on probabilities of significant events. This work offers a simple alternative way to calculate the MIR in dynamical (deterministic) networks or between two time series (not fully deterministic), and to calculate its upper and lower bounds without having to calculate probabilities, but rather in terms of well known and well defined quantities in dynamical systems. As possible applications of our bounds, we study the relationship between synchronisation and the exchange of information in a system of two coupled maps and in experimental networks of coupled oscillators. PMID:23112809

  16. REE bound DNA in natural plant

    Institute of Scientific and Technical Information of China (English)

    王玉琦; 江平; 郭繁清; 张智勇; 孙景信; 许雷; 曹国印

    1999-01-01

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

  17. Refining Castelnuovo-Halphen bounds

    CERN Document Server

    Di Gennaro, Vincenzo

    2011-01-01

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

  18. Space-bounded communication complexity

    DEFF Research Database (Denmark)

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

    2013-01-01

    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...

  19. Bounding solutions of Pfaff equations

    OpenAIRE

    Esteves, E.; Kleiman, S

    2003-01-01

    Let \\omega be a Pfaff system of differential forms on a projective space. Let S be its singular locus, and Y a solution of \\omega=0. We prove Y\\cap S is of codimension at most 1 in Y, just as Jouanolou suspected; he proved this result assuming \\omega is completely integrable, and asked if the integrability is, in fact, needed. Furthermore, we prove a lower bound on the Castelnuovo--Mumford regularity of Y\\cap S. As in two related articles, we derive upper bounds on numerical invariants of Y, ...

  20. Bound orbits and gravitational theory

    OpenAIRE

    Dadhich, Naresh; Ghosh, Sushant G.(School of Mathematical Sciences, University of KwaZulu-Natal, Westville, 4000, Durban, South Africa); Jhingan, Sanjay

    2013-01-01

    It can be easily shown that bound orbits around a static source can exist only in 4 dimension and in none else for any long range force. This is so not only for Maxwell's electromagnetic and Newton's gravity but also for Einstein's gravitation theory. In contrast to Maxwell's electrodynamics and Newton's gravity, GR has a natural higher dimensional generalization in Lovelock gravity which remarkably admits bound orbits around a static black hole in all even d=2N+2 dimensions where $N$ is degr...

  1. Profiling epidermal growth factor receptor and heregulin receptor 3 heteromerization using receptor tyrosine kinase heteromer investigation technology.

    Directory of Open Access Journals (Sweden)

    Mohammed Akli Ayoub

    Full Text Available Heteromerization can play an important role in regulating the activation and/or signal transduction of most forms of receptors, including receptor tyrosine kinases (RTKs. The study of receptor heteromerization has evolved extensively with the emergence of resonance energy transfer based approaches such as bioluminescence resonance energy transfer (BRET. Here, we report an adaptation of our Receptor-Heteromer Investigation Technology (Receptor-HIT that has recently been published as the G protein-coupled receptor (GPCR Heteromer Identification Technology (GPCR-HIT. We now demonstrate the utility of this approach for investigating RTK heteromerization by examining the functional interaction between the epidermal growth factor (EGF receptor (EGFR; also known as erbB1/HER1 and heregulin (HRG receptor 3 (HER3; also known as erbB3 in live HEK293FT cells using recruitment of growth factor receptor-bound protein 2 (Grb2 to the activated receptors. We found that EGFR and HER3 heteromerize specifically as demonstrated by HRG inducing a BRET signal between EGFR/Rluc8 and Grb2/Venus only when HER3 was co-expressed. Similarly, EGF stimulation promoted a specific BRET signal between HER3/Rluc8 and Grb2/Venus only when EGFR was co-expressed. Both EGF and HRG effects on Grb2 interaction are dose-dependent, and specifically blocked by EGFR inhibitor AG-1478. Furthermore, truncation of HER3 to remove the putative Grb2 binding sites appears to abolish EGF-induced Grb2 recruitment to the EGFR-HER3 heteromer. Our results support the concept that EGFR interacts with Grb2 in both constitutive and EGF-dependent manners and this interaction is independent of HER3 co-expression. In contrast, HER3-Grb2 interaction requires the heteromerization between EGFR and HER3. These findings clearly indicate the importance of EGFR-HER3 heteromerization in HER3-mediated Grb2-dependent signaling pathways and supports the central role of HER3 in the diversity and regulation of HER

  2. Multiscale design of coarse-grained elastic network-based potentials for the μ opioid receptor.

    Science.gov (United States)

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

    2016-09-01

    Despite progress in computer modeling, most biological processes are still out of reach when using all-atom (AA) models. Coarse-grained (CG) models allow classical molecular dynamics (MD) simulations to be accelerated. Although simplification of spatial resolution at different levels is often investigated, simplification of the CG potential in itself has been less common. CG potentials are often similar to AA potentials. In this work, we consider the design and reliability of purely mechanical CG models of the μ opioid receptor (μOR), a G protein-coupled receptor (GPCR). In this sense, CG force fields (FF) consist of a set of holonomic constraints guided by an elastic network model (ENM). Even though ENMs are used widely to perform normal mode analysis (NMA), they are not often implemented as a single FF in the context of MD simulations. In this work, various ENM-like potentials were investigated by varying their force constant schemes and connectivity patterns. A method was established to systematically parameterize ENM-like potentials at different spatial resolutions by using AA data. To do so, new descriptors were introduced. The choice of conformation descriptors that also include flexibility information is important for a reliable parameterization of ENMs with different degrees of sensitivity. Hence, ENM-like potentials, with specific parameters, can be sufficient to accurately reproduce AA MD simulations of μOR at highly coarse-grained resolutions. Therefore, the essence of the flexibility properties of μOR can be captured with simple models at different CG spatial resolutions, opening the way to mechanical approaches to understanding GPCR functions. Graphical Abstract All atom structure, residue interaction network and coarse-grained elastic network models of the μ opioid receptor (μOR). PMID:27566318

  3. Somatostatin receptor expression and biological functions in endocrine pancreatic cells: review based on a doctoral thesis.

    Science.gov (United States)

    Ludvigsen, Eva

    2007-01-01

    Type 1 diabetes is resulting from the selective destruction of insulin-producing betacells within the pancreatic islets. Somatostatin acts as an inhibitor of hormone secretion through specific receptors (sst1-5). All ssts were expressed in normal rat and mouse pancreatic islets, although the expression intensity and the co-expression pattern varied between ssts as well as between species. This may reflect a difference in response to somatostatin in islet cells of the two species. The Non-Obese Diabetic (NOD) mouse model is an experimental model of type 1 diabetes, with insulitis accompanied by spontaneous hyperglycaemia. Pancreatic specimens from NOD mice at different age and stage of disease were stained for ssts. The islet cells of diabetic NOD mice showed increased islet expression of sst2-5 compared to normoglycemic NOD mice. The increase in sst2-5 expression in the islets cells may suggest either a contributing factor in the process leading to diabetes, or a defense response against ongoing beta-cell destruction. Somatostatin analogues were tested on a human endocrine pancreatic tumour cell line and cultured pancreatic islets. Somatostatin analogues had an effect on cAMP accumulation, chromogranin A secretion and MAP kinase activity in the cell line. Treatment of rat pancreatic islets with somatostatin analogues with selective receptor affinity was not sufficient to induce an inhibition of insulin and glucagon secretion. However, a combination of selective analogues or non-selective analogues via costimulation of receptors can cause inhibition of hormone production. For insulin and glucagon, combinations of sst2 + sst5 and sst1 + sst2, respectively, showed a biological effect. In summary, knowledge of islet cell ssts expression and the effect of somatostatin analogues with high affinity to ssts may be valuable in the future attempts to influence beta-cell function in type 1 diabetes mellitus, since down-regulation of beta-cell function may promote survival of

  4. Targeted cancer therapies based on antibodies directed against epidermal growth factor receptor: status and perspectives

    Institute of Scientific and Technical Information of China (English)

    Zhenping ZHU

    2007-01-01

    Compelling experimental and clinical evidence suggests that epidermal growth factor receptor (EGFR) plays an important role in the pathogenesis of a variety of human cancers; thus, providing a strong rationale for the development of receptor antagonists as effective and specific therapeutic strategies for the treatment of EGFR-expressing cancers. Monoclonal antibodies (mAb), owing to their high specificity towards a given target, represent a unique class of novel cancer therapeutics. A number of anti-EGFR mAb are currently being developed in our clinic, including two that have been approved by the United States Food and Drug Administration for the treatment of refractory metastatic colorectal cancer (mCRC) and squamous cell carcinomas of the head and neck (SCCHN). Cetuximab (Erbitux, IMC-C225), an IgG 1 mAb, has demonstrated significant antitumor activity,both as a single agent and in combination with chemotherapeutics and radiation,in patients with refractory mCRC and SCCHN, respectively. Panitumumab(Vectibix), an IgG2 mAb, has been approved as a single agent for the treatment of patients with refractory mCRC. These mAb, via blocking ligand/receptor interactions, exert their biological activity via multiple mechanisms, includinginhibition of cell cycle progression, potentiation of cell apoptosis, inhibition of DNA repair, inhibition of angiogenesis, tumor cell invasion and metastasis and,potentially, induction of immunological effector mechanisms. Anti-EGFR anti-bodies have demonstrated good safety profiles and potent anticancer activity in our clinic and may prove to be efficacious agents in the treatment of a variety of human malignancies.

  5. Functional characterisation of homomeric ionotropic glutamate receptors GluR1-GluR6 in a fluorescence-based high throughput screening assay

    DEFF Research Database (Denmark)

    Strange, Mette; Bräuner-Osborne, Hans; Jensen, Anders A.

    2006-01-01

    We have constructed stable HEK293 cell lines expressing the rat ionotropic glutamate receptor subtypes GluR1(i), GluR2Q(i), GluR3(i), GluR4(i), GluR5Q and GluR6Q and characterised the pharmacological profiles of the six homomeric receptors in a fluorescence-based high throughput screening assay...

  6. Characterization and Modulation of the Bitterness of Polymethoxyflavones Using Sensory and Receptor-Based Methods.

    Science.gov (United States)

    Batenburg, A Max; de Joode, Teun; Gouka, Robin J

    2016-03-30

    An obstacle in the application of many "health ingredients" is their alleged off-flavor. We used a combination of chemical, sensory, and biological analyses to identify the bitter components in citrus peel-derived polymethoxyflavone preparations, claimed to be functional in the lowering of cholesterol. Nobiletin (56-81%) and tangeretin (10-33%) were found to be the main bitter components. Using in vitro receptor assays, hTAS2R14 was shown to be the main bitter receptor involved in their perception, with EC50 values of 14 and 63 μM, respectively. Our analysis provided several routes for off-flavor reduction. Purification is an option because a purified, single PMF species proved to be considerably less bitter upon application in emulsified foods, due to limited solubility in the aqueous phase. A second route, also demonstrated in vivo, is C5-specific demethoxylation, in line with the finding that 5-desmethylnobiletin does not activate hTAS2R14. A third route could be the use of TAS2R14 antagonists. As a proof of principle, several antagonists, with IC50 values ranging from 10 to 50 μM, were identified. PMID:26934534

  7. Biomimetic infrared sensors based on the infrared receptors of pyrophilous insects

    Science.gov (United States)

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

    2011-04-01

    Beetles of the genus Melanophila and certain flat bugs of the genus Aradus approach forest fires. For the detection of fires and of hot surfaces the pyrophilous species of both genera have developed infrared (IR) receptors, which have developed from common hair mechanoreceptors. Thus this type of insect IR receptor has been termed photomechanic and shows the following two special features: (i) the formation of a complex cuticular sphere consisting of an outer exocuticular shell as well as of a cavernous microfluidic core. (ii) The enclosure of the dendritic tip of a mechanosensitive neuron inside the core in a liquid-filled chamber. Most probably a photomechanic IR sensillum acts as a microfluidic converter of infrared radiation into an increase in internal pressure inside the sphere, which is measured by a mechanosensitive neuron. A simple model for this biological IR sensor is the Golay sensor, which is filled with a liquid instead of gas. Here the absorbed IR radiation results in a pressure increase of the liquid and the deflection of a thin membrane. For the evaluation of this model analytical formulas are presented, which permits the calculation of the pressure increase in the cavity, the deformation of the membrane and the time constant of an artificial leak to compensate ambient temperature changes. Some organic liquids with high thermal expansion coefficients may improve the deflection of the membrane compared to water.

  8. Predicting kinase activity in angiotensin receptor phosphoproteomes based on sequence-motifs and interactions.

    Directory of Open Access Journals (Sweden)

    Rikke Bøgebo

    Full Text Available Recent progress in the understanding of seven-transmembrane receptor (7TMR signalling has promoted the development of a new generation of pathway selective ligands. The angiotensin II type I receptor (AT1aR is one of the most studied 7TMRs with respect to selective activation of the β-arrestin dependent signalling. Two complimentary global phosphoproteomics studies have analyzed the complex signalling induced by the AT1aR. Here we integrate the data sets from these studies and perform a joint analysis using a novel method for prediction of differential kinase activity from phosphoproteomics data. The method builds upon NetworKIN, which applies sophisticated linear motif analysis in combination with contextual network modelling to predict kinase-substrate associations with high accuracy and sensitivity. These predictions form the basis for subsequently nonparametric statistical analysis to identify likely activated kinases. This suggested that AT1aR-dependent signalling activates 48 of the 285 kinases detected in HEK293 cells. Of these, Aurora B, CLK3 and PKG1 have not previously been described in the pathway whereas others, such as PKA, PKB and PKC, are well known. In summary, we have developed a new method for kinase-centric analysis of phosphoproteomes to pinpoint differential kinase activity in large-scale data sets.

  9. Nicotinic acetylcholine receptor-based blockade: applications of molecular targets for cancer therapy.

    Science.gov (United States)

    Wu, Chih-Hsiung; Lee, Chia-Hwa; Ho, Yuan-Soon

    2011-06-01

    The nicotinic acetylcholine receptor (nAChR) was first characterized in 1970 as a membrane receptor of a neurotransmitter and an ion channel. nAChRs have been shown to be involved in smoking-induced cancer formation in multiple types of human cancer cells. In vitro and in vivo animal studies have shown that homopentameric nAChR inhibitors, such as methyllycaconitine and α-Bgtx, can attenuate nicotine-induced proliferative, angiogenic, and metastatic effects in lung, colon, and bladder cancer cells. Recent publications have shown that α9-nAChR is important for breast cancer formation, and in many in vivo studies, α9-nAChR-specific antagonists (e.g., α-ImI, α-ImI, Vc1.1, RgIA, and It14a) produced an analgesic effect. Vc1.1 functions in a variety of animal pain models and currently has entered phase II clinical trials. For cancer therapy, natural compounds such as garcinol and EGCG have been found to block nicotine- and estrogen-induced breast cancer cell proliferation through inhibition of the α9-nAChR signaling pathway. A detailed investigation of the carcinogenic effects of nAChRs and their specific antagonists would enhance our understanding of their value as targets for clinical translation. PMID:21444681

  10. Bound states of 'dressed' particles

    International Nuclear Information System (INIS)

    A new approach to the problem of bound states in relativistic quantum field theories is suggested. It uses the creation - destruction operators of 'dresses' particles which have been granted by Faddeev's (1963) 'dressing' formalism. Peculiarities of the proposed approach as compared to the known ones are discussed. 8 refs. (author)

  11. 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...

  12. Semiclassical bounds in magnetic bottles

    Czech Academy of Sciences Publication Activity Database

    Barseghyan, Diana; Exner, Pavel; Kovařík, H.; Weidl, T.

    2016-01-01

    Roč. 28, č. 1 (2016), s. 1650002. ISSN 0129-055X R&D Projects: GA ČR(CZ) GA14-06818S Institutional support: RVO:61389005 Keywords : magnetic Laplacian * discrete spectrum * eigenvalue bounds Subject RIV: BE - Theoretical Physics Impact factor: 1.329, year: 2014

  13. Unconditional lower bounds against advice

    NARCIS (Netherlands)

    H. Buhrman; L. Fortnow; R. Santhanam

    2009-01-01

    We show several unconditional lower bounds for exponential time classes against polynomial time classes with advice, including: (1) For any constant c, NEXP not in P^{NP[n^c]} (2) For any constant c, MAEXP not in MA/n^c (3) BPEXP not in BPP/n^{o(1)}. It was previously unknown even whether NEXP in NP

  14. Bounded Fixed-Point Iteration

    DEFF Research Database (Denmark)

    Nielson, Hanne Riis; Nielson, Flemming

    1992-01-01

    In the context of abstract interpretation the authors study the number of times a functional needs to be unfolded in order to give the least fixed point. For the cases of total or monotone functions they obtain an exponential bound and in the case of strict and additive (or distributive) functions...

  15. Market Access through Bound Tariffs

    DEFF Research Database (Denmark)

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

    WTO negotiations deal predominantly with bound - besides applied - tariff rates. But, how can reductions in tariffs ceilings, i.e. tariff rates that no exporter may ever actually be confronted with, generate market access? The answer to this question relates to the effects of tariff bindings on t...

  16. Market access through bound tariffs

    DEFF Research Database (Denmark)

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

    2010-01-01

    WTO negotiations deal predominantly with bound - besides applied - tariff rates. But, how can reductions in tariffs ceilings, i.e. tariff rates that no exporter may ever actually be confronted with, generate market access? The answer to this question relates to the effects of tariff bindings on t...

  17. Improved Bounds for Geometric Permutations

    CERN Document Server

    Rubin, Natan; Sharir, Micha

    2010-01-01

    We show that the number of geometric permutations of an arbitrary collection of $n$ pairwise disjoint convex sets in $\\mathbb{R}^d$, for $d\\geq 3$, is $O(n^{2d-3}\\log n)$, improving Wenger's 20 years old bound of $O(n^{2d-2})$.

  18. 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

  19. Peptide-based biosensor for the prostate-specific antigen using magnetic particle-bound invertase and a personal glucose meter for readout

    International Nuclear Information System (INIS)

    We describe a highly sensitive and selective peptide-based biosensor for the prostate-specific antigen (PSA). The biotinylated peptide biotin-EHSSKLQKC served as a molecular recognition element. It was self-assembled on the surface of the wells of a 96-well microtiter plate modified with gold nanoparticles (AuNPs). In parallel, streptavidin-coated magnetic beads (strep-MBs) were modified with the enzyme invertase and then added to the peptide-modified wells upon which the modified strep-MBs bind to the peptide via biotin/streptavidin interaction. If a sample containing PSA is placed in the well, PSA will cause the cleavage of the peptide, and a respective quantity of invertase-modified strep-MBs will be released. The supernatant containing the invertase-modified strep-MBs is taken out and sucrose is added which is enzymatically cleaved by invertase. The concentration of the glucose formed after 1 h is quantified with a personal glucose meter. It is linearly related to the concentration of PSA in the range from 80 pg to 7 ng∙mL−1. The detection limit is 30 pg∙mL−1 and the relative standard deviation is 3.7 % (at a level of 500 pg∙mL−1 and for n = 7). The method was successfully applied to the determination of PSA in spiked real human urine. Due to its simplicity, sensitivity and selectivity, this bioassay offers a promising approach to the detection of PSA and other biomolecules. (author)

  20. Universal Entropy Bound for Rotating Systems

    OpenAIRE

    Hod, Shahar

    1999-01-01

    We conjecture a universal upper bound to the entropy of a rotating system. The entropy bound follows from application of the generalized second law of thermodynamics to an idealized gedanken experiment in which an entropy-bearing rotating system falls into a black hole. This bound is stronger than the Bekenstein entropy bound for non-rotating systems.

  1. Dosimetric accuracy of a deterministic radiation transport based 192Ir brachytherapy treatment planning system. Part I: Single sources and bounded homogeneous geometries

    International Nuclear Information System (INIS)

    Purpose: The aim of this work is to validate a deterministic radiation transport based treatment planning system (TPS) for single 192Ir brachytherapy source dosimetry in homogeneous water geometries. Methods: TPS results were obtained using the deterministic radiation transport option of a BRACHYVISION v. 8.8 system for three characteristic source designs (VS2000, GMPlus HDR, and GMPlus PDR) with each source either centered in a 15 cm radius spherical water phantom, or positioned at varying distance away from the phantom center. Corresponding MC simulations were performed using the MCNPX code v.2.5.0 and source geometry models prepared using information provided by the manufacturers. Results: Comparison in terms of the AAPM TG-43 dosimetric formalism quantities, as well as dose rate distributions per unit air kerma strength with a spatial resolution of 0.1 cm, yielded close agreement between TPS and MC results for the sources centered in the phantom. Besides some regions close to the source longitudinal axes where discrepancies could be characterized as systematic, overall agreement for all three sources studied is comparable to the statistical (type A) uncertainty of MC simulations (1% at the majority of points in the geometry increasing to 2%-3% at points lying both away from the source center and close to the source longitudinal axis). A corresponding good agreement was also found between TPS and MC results for the sources positioned away from the phantom center. Conclusions: Results of this work attest the capability of the TPS to accurately account for the scatter conditions regardless of the size or shape of a given geometry of dosimetric interest, and the position of a source within it. This is important since, as shown in the literature and summarized also in this work, these factors could introduce a significant dosimetric effect that is currently ignored in clinical treatment planning. It is concluded that the implementation of the deterministic radiation

  2. Self-assembled tetra- and pentanuclear nickel(II) aggregates from phenoxido-based ligand -bound {Ni2} fragments: carboxylate bridge controlled structures.

    Science.gov (United States)

    Ghosh, Aloke Kumar; Shatruk, Michael; Bertolasi, Valerio; Pramanik, Kausikisankar; Ray, Debashis

    2013-12-16

    Three different carboxylato bridges (R = C2H5, CF3, and PhCH2 in RCO2(-)) have been used to obtain the supramolecular aggregates [Ni5(μ-H2bpmp)2(μ3-OH)2(μ1,3-O2CC2H5)6]·2H2O·4DMF (1·2H2O·4DMF), [Ni4(μ3-H2bpmp)2(μ3-OH)2(μ1,3-O2CCF3)2](CF3CO2)2·H2O (2·H2O), and [Ni4(μ3-H2bpmp)2(μ3-OH)2(μ1,3-O2CCH2Ph)2](PhCH2CO2)2·4H2O (3·4H2O) (H3bpmp =2,6-bis-[(3-hydroxy-propylimino)-methyl]-4-methyl-phenol) from the hydroxido-bridged dinuclear motif [Ni2(μ-H2bpmp)(OH)](2+). These complexes have been characterized by X-ray crystallography and magnetic measurements. A change from propanoate group to trifluoroacetate and phenylaceate groups provided different course of cluster assembly based on Ni2(μ-H2bpmp)2 fragments. The {Ni5(μ3-OH)2(μ1,3-O2CC2H5)6}(2+) core in 1 contains five Ni(II) ions in an hourglass (pentanuclear vertex-shared double cubane) arrangement. These compounds are new examples of [Ni5] and [Ni4] complexes where aggregation of the building motifs are guided by the nature of the carboxylate anions, which allows an effective tuning of the self-aggregate process within same ligand environment. The study of the magnetic properties reveals that 1 exhibits an S = 3 ground state. Nevertheless, the magnetization increases above the expected saturation value of 6 μB at higher fields, because of the suppression of antiferromagnetic exchange between the central and peripheral Ni(II) ions. Complexes 2 and 3 exhibit ferromagnetic exchange interactions that result in the S = 4 ground state. Examination of AC magnetic susceptibility showed that complex 2 in finely ground form behaves as spin glass with the spin-freezing temperature of ∼5.5 K. This behavior was attributed to the collapse of the structure upon the loss of interstitial solvent. Such property was not observed for complex 3, in which the bulkier carboxylate ligands provide for a more robust crystal packing and larger separation between the [Ni4O4] clusters. PMID:24295223

  3. 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.

  4. 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. PMID:25405348

  5. Research Resource: Real-Time Analysis of Somatostatin and Dopamine Receptor Signaling in Pituitary Cells Using a Fluorescence-Based Membrane Potential Assay.

    Science.gov (United States)

    Günther, Thomas; Culler, Michael; Schulz, Stefan

    2016-04-01

    Stable somatostatin analogues and dopamine receptor agonists are the mainstay for the pharmacological treatment of functional pituitary adenomas; however, only a few cellular assays have been developed to detect receptor activation of novel compounds without disrupting cells to obtain the second messenger content. Here, we adapted a novel fluorescence-based membrane potential assay to characterize receptor signaling in a time-dependent manner. This minimally invasive technique provides a robust and reliable read-out for ligand-induced receptor activation in permanent and primary pituitary cells. The mouse corticotropic cell line AtT-20 endogenously expresses both the somatostatin receptors 2 (sst2) and 5 (sst5). Exposure of wild-type AtT-20 cells to the sst2- and sst5-selective agonists BIM-23120 and BIM-23268, respectively, promoted a pertussis toxin- and tertiapin-Q-sensitive reduction in fluorescent signal intensity, which is indicative of activation of G protein-coupled inwardly rectifying potassium (GIRK) channels. After heterologous expression, sst1, sst3, and sst4 receptors also coupled to GIRK channels in AtT-20 cells. Similar activation of GIRK channels by dopamine required overexpression of dopamine D2 receptors (D2Rs). Interestingly, the presence of D2Rs in AtT-20 cells strongly facilitated GIRK channel activation elicited by the sst2-D2 chimeric ligand BIM-23A760, suggesting a synergistic action of sst2 and D2Rs. Furthermore, stable somatostatin analogues produced strong responses in primary pituitary cultures from wild-type mice; however, in cultures from sst2 receptor-deficient mice, only pasireotide and somatoprim, but not octreotide, induced a reduction in fluorescent signal intensity, suggesting that octreotide mediates its pharmacological action primarily via the sst2 receptor. PMID:26967369

  6. Complete manifolds with bounded curvature and spectral gaps

    Science.gov (United States)

    Schoen, Richard; Tran, Hung

    2016-08-01

    We study the spectrum of complete noncompact manifolds with bounded curvature and positive injectivity radius. We give general conditions which imply that their essential spectrum has an arbitrarily large finite number of gaps. In particular, for any noncompact covering of a compact manifold, there is a metric on the base so that the lifted metric has an arbitrarily large finite number of gaps in its essential spectrum. Also, for any complete noncompact manifold with bounded curvature and positive injectivity radius we construct a metric uniformly equivalent to the given one (also of bounded curvature and positive injectivity radius) with an arbitrarily large finite number of gaps in its essential spectrum.

  7. Affinity- and topology-dependent bound on current fluctuations

    CERN Document Server

    Pietzonka, Patrick; Seifert, Udo

    2016-01-01

    We provide a proof of a recently conjectured universal bound on current fluctuations in Markovian processes. This bound establishes a link between the fluctuations of an individual observable current, the cycle affinities driving the system into a non-equilibrium steady state, and the topology of the network. The proof is based on a decomposition of the network into independent cycles with both positive affinity and positive stationary cycle current. This formalism allows for a refinement of the bound for systems in equilibrium or with locally vanishing affinities.

  8. Design of planar articulated mechanisms using branch and bound

    DEFF Research Database (Denmark)

    Stolpe, Mathias; Kawamoto, Atsushi

    2005-01-01

    that buckling is prevented. The feasible set of the design problem is described by nonlinear differentiable and non-differentiable constraints as well as nonlinear matrix inequalities. To solve the mechanism design problem a branch and bound method based on convex relaxations is developed. To guarantee...... convergence of the method, two different types of convex relaxations are derived. The relaxations are strengthened by adding valid inequalities to the feasible set and by solving bound contraction sub-problems. Encouraging computational results indicate that the branch and bound method can reliably solve...

  9. Design of planar articulated mechanisms using branch and bound

    DEFF Research Database (Denmark)

    Stolpe, Mathias; Kawamoto, Atsushi

    2004-01-01

    that buckling is prevented. The feasible set of the design problem is described by nonlinear differentiable and non-differentiable constraints as well as nonlinear matrix inequalities. To solve the mechanism design problem a branch and bound method based on convex relaxations is developed. To guarantee...... convergence of the method, two different types of convex relaxations are derived. The relaxations are strengthened by adding valid inequalities to the feasible set and by solving bound contraction sub-problems. Encouraging computational results indicate that the branch and bound method can reliably solve...

  10. Somatostatin Receptor-Based Molecular Imaging and Therapy for Neuroendocrine Tumors

    Directory of Open Access Journals (Sweden)

    Ling Wang

    2013-01-01

    Full Text Available Neuroendocrine tumors (NETs are tumors originated from neuroendocrine cells in the body. The localization and the detection of the extent of NETs are important for diagnosis and treatment, which should be individualized according to the tumor type, burden, and symptoms. Molecular imaging of NETs with high sensitivity and specificity is achieved by nuclear medicine method using single photon-emitting and positron-emitting radiopharmaceuticals. Somatostatin receptor imaging (SRI using SPECT or PET as a whole-body imaging technique has become a crucial part of the management of NETs. The radiotherapy with somatostatin analogues labeled with therapeutic beta emitters, such as lutetium-177 or yttrium-90, has been proved to be an option of therapy for patients with unresectable and metastasized NETs. Molecular imaging can deliver an important message to improve the outcome for patients with NETs by earlier diagnosis, better choice of the therapeutic method, and evaluation of the therapeutic response.

  11. The Role of the Enterohepatic Circulation of Bile Salts and Nuclear Hormone Receptors in the Regulation of Cholesterol Homeostasis: Bile Salts as Ligands for Nuclear Hormone Receptors

    OpenAIRE

    Redinger, Richard N.

    2003-01-01

    The coordinated effect of lipid activated nuclear hormone receptors; liver X receptor (LXR), bound by oxysterol ligands and farnesoid X receptor (FXR), bound by bile acid ligands, act as genetic transcription factors to cause feed-forward cholesterol catabolism to bile acids and feedback repression of bile acid synthesis, respectively. It is the coordinated action of LXR and FXR, each dimerized to retinoid X receptor, that signal nuclear DNA response elements to encode proteins that prevent e...

  12. The Construction of Chimeric T-Cell Receptor with Spacer Base of Modeling Study of VHH and MUC1 Interaction

    OpenAIRE

    Nazanin Pirooznia; Sadegh Hasannia; Majid Taghdir; Fatemeh Rahbarizadeh; Morteza Eskandani

    2011-01-01

    Adaptive cell immunotherapy with the use of chimeric receptors leads to the best and most specific response against tumors. Chimeric receptors consist of a signaling fragment, extracellular spacer, costimulating domain, and an antibody. Antibodies cause immunogenicity; therefore, VHH is a good replacement for ScFv in chimeric receptors. Since peptide sequences have an influence on chimeric receptors, the effect of peptide domains on each other's conformation were investigated. CD3Zeta, CD28, ...

  13. 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.

  14. Synthesis and studies of boron based anion receptors and their use in non-aqueous electrolytes for lithium batteries

    Energy Technology Data Exchange (ETDEWEB)

    Sun, X.; Yang, X.Q.; Lee, H.S.; McBreen, J. [Brookhaven National Lab., Upton, NY (United States); Choi, L.S. [Naval Research Lab., Washington, DC (United States)

    1998-12-31

    A new family of anion receptors based on boron compounds has been synthesized. These compounds can be used as anion receptors in lithium battery electrolytes and can greatly increase solubility and ionic conductivities of various lithium salts, such as LiF, LiCl, CF{sub 3}COOLi and C{sub 2}F{sub 5}COOLi, in DME solutions. Near Edge X-ray Absorption Fine Structure (NEXAFS) spectroscopy studies show that Cl{sup {minus}} anions of LiCl are complexed with these compounds in DME solutions. The electrochemical stability of lithium salts and one of the boron compounds in deferent solvents was studied. For the first time, LiF has been successfully used as conducting salt in a novel electrolyte with this boron compound as an additive in DME. A rechargeable Li/LiMn{sub 2}O{sub 4} cell using this electrolyte was successfully cycled 51 times. However, the capacity fades with cycling due to decomposition of the solvent. The cycling performance of the battery was greatly improved by replacing DME with PC-EC-DMC as the solvent.

  15. Research on Risk Behavior for the Strategic Decision-making of Entrepreneur Based on Bounded Rationality%基于有限理性的企业家战略决策风险行为研究

    Institute of Scientific and Technical Information of China (English)

    任静; 刘升福

    2014-01-01

    企业家认知的有限性决定了企业家在有限理性的状态下进行战略决策。基于行为经济学和决策行为理论,研究有限理性下企业家战略决策风险行为及其影响因素。通过建立模型和实证研究来探讨企业家战略决策风险行为及其影响因素对战略决策风险行为的影响,从而为企业家战略决策风险行为管理提供依据。%The limitation of Entrepreneurs′cognition decides that entrepreneurs make strategic decisions under the limited rational state.The paper,based on the theory of behavioral economics and the decision-making behavior,studies the entrepreneur strategic decision deviation behavior based on bounded rationality and its influencing factors.Through the questionnaire,interviews and the empirical research,the paper explores the various influencing factors of entrepreneur strategic decision-making risk behavior influence on strategic decision-making risk behaviors,so as to provide the basis for entrepreneurs strategic decision-making risk behavior management.

  16. A Branch and Bound Algorithm for the Global Optimization of Hessian Lipschitz Continuous Functions

    OpenAIRE

    Fowkes, J. M.; Gould, N. I. M.; Farmer, C.L.

    2012-01-01

    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 num...

  17. Ligand similarity guided receptor selection enhances docking accuracy and recall for non-nucleoside HIV reverse transcriptase inhibitors.

    Science.gov (United States)

    Stanton, Richard A; Nettles, James H; Schinazi, Raymond F

    2015-11-01

    Non-nucleoside reverse transcriptase inhibitors (NNRTI) are allosteric inhibitors of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT), a viral polymerase essential to infection. Despite the availability of >150 NNRTI-bound RT crystal structures, rational design of new NNRTI remains challenging because of the variability of their induced fit, hydrophobic binding patterns. Docking NNRTI yields inconsistent results that vary markedly depending on the receptor structure used, as only 27% of the >20k cross-docking calculations we performed using known NNRTI were accurate. In order to determine if a hospitable receptor for docking could be selected a priori, we evaluated more than 40 chemical descriptors for their ability to pre-select a best receptor for NNRTI cross-docking. The receptor selection was based on similarity scores between the bound- and target-ligands generated by each descriptor. The top descriptors were able to double the probability of cross-docking accuracy over random receptor selection. Additionally, recall of known NNRTI from a large library of similar decoys was increased using the same approach. The results demonstrate the utility of pre-selecting receptors when docking into difficult targets. Graphical Abstract Cross-docking accuracy increases when using chemical descriptors to determine the NNRTI with maximum similarity to the new compound and then docking into its respective receptor. PMID:26450349

  18. (64)Cu- and (68)Ga-Based PET Imaging of Folate Receptor-Positive Tumors: Development and Evaluation of an Albumin-Binding NODAGA-Folate.

    Science.gov (United States)

    Farkas, Renáta; Siwowska, Klaudia; Ametamey, Simon M; Schibli, Roger; van der Meulen, Nicholas P; Müller, Cristina

    2016-06-01

    A number of folate-based radioconjugates have been synthesized and evaluated for nuclear imaging purposes of folate receptor (FR)-positive tumors and potential therapeutic application. A common shortcoming of radiofolates is, however, a significant accumulation of radioactivity in the kidneys. This situation has been faced by modifying the folate conjugate with an albumin-binding entity to increase the circulation time of the radiofolate, which led to significantly improved tumor-to-kidney ratios. The aim of this study was to develop an albumin-binding folate conjugate with a NODAGA-chelator (rf42) for labeling with (64)Cu and (68)Ga, allowing application for PET imaging. The folate conjugate rf42 was synthesized in 8 steps, with an overall yield of 5%. Radiolabeling with (64)Cu and (68)Ga was carried out at room temperature within 10 min resulting in (64)Cu-rf42 and (68)Ga-rf42 with >95% radiochemical purity. (64)Cu-rf42 and (68)Ga-rf42 were stable (>95% intact) in phosphate-buffered saline over more than 4 half-lives of the corresponding radionuclide. In vitro, the plasma protein-bound fraction of (64)Cu-rf42 and (68)Ga-rf42 was determined to be >96%. Cell experiments proved FR-specific uptake of both radiofolates, as it was reduced to DOTA-folate conjugate (cm10) clearly proved the superiority of NODAGA for stable coordination of (64)Cu. (64)Cu-cm10 showed high liver uptake, most probably as a consequence of released (64)Cu(2+). The data reported in this study clearly proved the promising features of (64)Cu-rf42, particularly in terms of favorable tumor-to-kidney ratios. The relatively long half-life of (64)Cu (T1/2 = 12.7 h) matches well with the enhanced circulation time of the albumin-binding NODAGA-folate, allowing PET imaging at longer time points after injection than is possible when using (68)Ga (T1/2 = 68 min). PMID:27145400

  19. Physics with loosely bound nuclei

    Indian Academy of Sciences (India)

    Chhanda Samanta

    2001-08-01

    The essential aspect of contemporary physics is to understand properties of nucleonic matter that constitutes the world around us. Over the years research in nuclear physics has provided strong guidance in understanding the basic principles of nuclear interactions. But, the scenario of nuclear physics changed drastically as the new generation of accelerators started providing more and more rare isotopes, which are away from the line of stability. These weakly bound nuclei are found to exhibit new forms of nuclear matter and unprecedented exotic behaviour. The low breakup thresholds of these rare nuclei are posing new challenges to both theory and experiments. Fortunately, nature has provided a few loosely bound stable nuclei that have been studied thoroughly for decades. Attempts are being made to find a consistent picture for the unstable nuclei starting from their stable counterparts. Some significant differences in the structure and reaction mechanisms are found.

  20. Concentration Bounds for Stochastic Approximations

    CERN Document Server

    Frikha, Noufel

    2012-01-01

    We obtain non asymptotic concentration bounds for two kinds of stochastic approximations. We first consider the deviations between the expectation of a given function of the Euler scheme of some diffusion process at a fixed deterministic time and its empirical mean obtained by the Monte-Carlo procedure. We then give some estimates concerning the deviation between the value at a given time-step of a stochastic approximation algorithm and its target. Under suitable assumptions both concentration bounds turn out to be Gaussian. The key tool consists in exploiting accurately the concentration properties of the increments of the schemes. For the first case, as opposed to the previous work of Lemaire and Menozzi (EJP, 2010), we do not have any systematic bias in our estimates. Also, no specific non-degeneracy conditions are assumed.

  1. Towards a taxonomy of parallel branch and bound algorithms

    OpenAIRE

    Trienekens, H.W.J.M.; Bruin, Arie

    1992-01-01

    textabstractIn this paper we present a classification of parallel branch and bound algorithms, and elaborate on the consequences of particular parameter settings. The taxonomy is based upon how the algorithms handle the knowledge about the problem instance to be solved, generated during execution. The starting point of the taxonomy is the generally accepted description of the sequential branch and bound algorithm, as presented in, for example, [Mitten 1970] and [Ibaraki 1976a, 1976b, 1977a, 1...

  2. Bounds for Regularity and Coregularity of Graded Modules

    Indian Academy of Sciences (India)

    Reza Sazeedeh

    2007-11-01

    Let be a finitely generated graded module over a Noetherian homogeneous ring with local base ring $(R_0,\\mathfrak{m}_0)$. If 0 is of dimension one, then we show that $\\mathrm{reg}^i+1(M)$ and $\\mathrm{coreg}^{i+1}(M)$ are bounded for all $i\\in\\mathbb{N}_0$. We improve these bounds, if in addition, 0 is either regular or analytically irreducible of unequal characteristic.

  3. Lipschitz bounds for noise robustness in compressive sensing: two algorithms

    OpenAIRE

    Nicodème, Marc; Dossal, Charles; Turcu, Flavius; Berthoumieu, Yannick

    2014-01-01

    The paper deals with estimating the local noise robustness in a compressive sensing framework. We provide two algorithms which estimate, for each vector x that can be recovered by $\\ell^1$ minimization, the Lipschitz bounds relating the $\\ell^1$-reconstruction error to the measurement error (or noise) for a given sensing matrix. Classical theoretical estimations, such as those based on the restricted isometry property, theoretically give error bounds estimates depending on RIP constants. Unfo...

  4. The bound mu+ mu- system

    OpenAIRE

    Jentschura, U.; Soff, G.; Ivanov, V.; Karshenboim, S.

    1997-01-01

    We consider the hyperfine structure, the atomic spectrum and the decay channels of the bound mu+ mu- system (dimuonium). The annihilation lifetimes of low-lying atomic states of the system lie in the nanosecond range range. The decay rates could be measured by detection of the decay products (high energy photons or electron-positron pairs). The hyperfine structure splitting of the dimuonic system and its decay rate are influenced by electronic vacuum polarization effects in the far time-like ...

  5. Provably Bounded-Optimal Agents

    OpenAIRE

    Russell, S J; Subramanian, D.

    1995-01-01

    Since its inception, artificial intelligence has relied upon a theoretical foundation centered around perfect rationality as the desired property of intelligent systems. We argue, as others have done, that this foundation is inadequate because it imposes fundamentally unsatisfiable requirements. As a result, there has arisen a wide gap between theory and practice in AI, hindering progress in the field. We propose instead a property called bounded optimality. Roughly speaking, an agent is boun...

  6. UPPER BOUND ANALYSIS OF HORIZONTALLY EMBEDDED ANCHORS BASED ON BLOCK SET MECHANISM%基于组合块体集的浅埋条形锚板上限分析

    Institute of Scientific and Technical Information of China (English)

    余生兵; 黄茂松

    2011-01-01

    基于极限分析法的基本原理以及集成与组合的思路,推导组合块体集的内能耗散和重力做功,运用组合的思想构造斜坡地形下浅埋水平条形锚板的运动许可速度场.首先分析地表水平条件下法向受力水平条形锚板抗拔承载力,并与文献中已有解和模型试验进行对比,验证块体集上限法的优越性.然后详细研究斜坡地形条件下土体重度、不排水抗剪强度、斜坡倾角等因素对条形锚板抗拔承载力和破坏面形状的影响.分析结果表明:重力叠加法并不适用于斜坡地形情况;随着斜坡倾角的增大,锚板的破坏面向坡角方向倾斜;锚板埋深比越大,斜坡倾角的影响也越显著.块体集上限分析方法构造简单,求解快捷,能够为工程设计提供依据.%Based on the bound theorems of limit analysis, admissible velocity field of horizontal strip anchor is constructed by using a combination of several rotational block sets. An application to upper bound analysis of vertically loaded strip anchors on horizontal ground surface is given first to illustrate the utility and effectiveness of the proposed method, and include detailed comparisons with results obtained from other approaches. Then the pull-out capacities of strip anchors in undrained clay with sloping ground surface are analyzed. Pull-out capacity and failure surface characteristics under different embedment ratios, undrained strength, inclined angles of slopes and weight of soil are studied. The results show that the superposition of gravity is not applicable to the case of sloping ground surface. The variation of slope angle has a significant impact on failure surface. The block set mechanism is based on a very simple concept which is integration and combination and can be a reference for the practical design.

  7. 循环荷载作用下基于隶属度函数的边界面模型%Bounding surface model based on membership function under cyclic loading

    Institute of Scientific and Technical Information of China (English)

    王喜刚; 扶名福; 胡小荣

    2015-01-01

    A membership function was imported into the bounding surface model to solve accumulated and continu-ous plastic strain under cyclic loading.A new three-dimensional cone was constructed based on the two-dimensional critical soil model figure.The relationship between the membership function and the loading surface was established based on the new three-dimensional cone.The membership function was used to modify the plastic flow criteria, so that the maximum stress of model was partially memorized;the damage parameters were adopted to deduce a fuzzy bounding surface model.A dynamic triaxial experiment was adopted to determine the parameters of the model.The numerical prediction matches the experiment results, proving the model is reasonable.%为了反映土体在循环荷载作用下塑性应变的累积特性和连续性,将隶属度函数引入到边界面模型中,在二维临界土力学模型图基础上,构造了一个新三维空间锥体,利用该锥体建立了加载面与隶属度函数的一一对应关系。根据隶属度函数修正了塑性流动法则,使得模型对最大预应力具有部分记忆功能,并引入损伤参数,推导得到了模糊边界面模型,通过动三轴实验确定了该模型的参数。利用有限元的二次开发功能,将该模型引入到有限元中,得到了模型的数值结果,通过与动三轴实验结果对比,发现两者吻合较好,证明了模型的合理性。

  8. 78 FR 18326 - Agency Information Collection Activities; Comment Request; Upward Bound and Upward Bound Math...

    Science.gov (United States)

    2013-03-26

    ... Agency Information Collection Activities; Comment Request; Upward Bound and Upward Bound Math Science... Upward Bound Math Science Annual Performance Report. OMB Control Number: 1840-NEW. Type of Review: New... under the regular Upward Bound (UB) and Upward Bound Math and Science (UBMS) Programs. The Department...

  9. The Cost of Bounded Curvature

    CERN Document Server

    Kim, Hyo-Sil

    2011-01-01

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

  10. Granger causality in wall-bounded turbulence

    International Nuclear Information System (INIS)

    Granger causality is based on the idea that if a variable helps to predict another one, then they are probably involved in a causality relationship. This technique is based on the identification of a predictive model for causality detection. The aim of this paper is to use Granger causality to study the dynamics and the energy redistribution between scales and components in wall-bounded turbulent flows. In order to apply it on flows, Granger causality is generalized for snapshot-based observations of large size using linear-model identification methods coming from model reduction. Optimized DMD, a variant of the Dynamic Mode Decomposition, is considered for building a linear model based on snapshots. This method is used to link physical events and extract physical mechanisms associated to the bursting process in the logarithmic layer of a turbulent channel flow.

  11. 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.

  12. Ligand fishing using new chitosan based functionalized Androgen Receptor magnetic particles.

    Science.gov (United States)

    Marszałł, Michał Piotr; Sroka, Wiktor Dariusz; Sikora, Adam; Chełminiak, Dorota; Ziegler-Borowska, Marta; Siódmiak, Tomasz; Moaddel, Ruin

    2016-08-01

    Superparamagnetic nanoparticles with chemically modified chitosan has been proposed as a potential support for the immobilization of the androgen receptor (AR). The study involved comparison of different AR carriers like commercially available magnetic beads coated with silica (BcMag) and chitosan coated nanoparticles with different amount of amino groups. The immobilization was carried out through covalent immobilization of the AR through the terminal amino group or through available carboxylic acids. The initial characterization of the AR coated magnetic beads was carried out with dihydrotestosterone, a known AR ligand. Subsequently, chitosan modified nanporticles with long-distanced primary amino groups (Fe3O4CS-(NH2)3) (upto 8.34mM/g) were used for further study to isolate known AR ligands (bicalutamide, flutamide, hydroxyflutamide and levonogestrel) from a mixture of tested compounds in ammonium acetate buffer [10mM, pH 7.4]. The results showed that the selected nanoparticles are a promising semi-quantitative tool for the identification of high affinity compounds to AR and might be of special importance in the identification of novel agonists or antiandrogens. PMID:27156644

  13. Discovery of a sulfamate-based steroid sulfatase inhibitor with intrinsic selective estrogen receptor modulator properties.

    Science.gov (United States)

    Ouellet, Charles; Maltais, René; Ouellet, Étienne; Barbeau, Xavier; Lagüe, Patrick; Poirier, Donald

    2016-08-25

    Steroid sulfatase (STS), the enzyme which converts inactive sulfated steroid precursors into active hormones, is a promising therapeutic target for the treatment of estrogen-sensitive breast cancer. We report herein the synthesis and in vitro study of dual-action STS inhibitors with selective estrogen-receptor modulator (SERM) effects. A library of tetrahydroisoquinoline-N-substituted derivatives (phenolic compounds) was synthesized by solid-phase chemistry and tested on estrogen-sensitive breast cancer T-47D cells. Three phenolic compounds devoid of estrogenic activity and toxicity emerged from this screening. Their sulfamate analogs were then synthesized, tested in STS-transfected HEK-293 cells, and found to be potent inhibitors of the enzyme (IC50 of 3.9, 8.9, and 16.6 nM). When tested in T-47D cells they showed no estrogenic activity and produced a moderate antiestrogenic activity. The compounds were further tested on osteoblast-like Saos-2 cells and found to significantly stimulate their proliferation as well as their alkaline phosphatase activity, thus suggesting a SERM activity. These results are supported by molecular docking experiments. PMID:27155470

  14. First pharmacophore-based identification of androgen receptor down-regulating agents: discovery of potent anti-prostate cancer agents.

    Science.gov (United States)

    Purushottamachar, Puranik; Khandelwal, Aakanksha; Chopra, Pankaj; Maheshwari, Neha; Gediya, Lalji K; Vasaitis, Tadas S; Bruno, Robert D; Clement, Omoshile O; Njar, Vincent C O

    2007-05-15

    A qualitative 3D pharmacophore model (a common feature based model or Catalyst HipHop algorithm) was developed for well-known natural product androgen receptor down-regulating agents (ARDAs). The four common chemical features identified included: one hydrophobic group, one ring aromatic group, and two hydrogen bond acceptors. This model served as a template in virtual screening of the Maybridge and NCI databases that resulted in identification of six new ARDAs (EC(50) values 17.5-212 microM). Five of these molecules strongly inhibited the growth of human prostate LNCaP cells. These novel compounds may be used as leads to develop other novel anti-prostate cancer agents. PMID:17383188

  15. Design and Synthesis of Novel Schiff Base-Benzothiazole Hybrids as Potential Epidermal Growth Factor Receptor (EGFR) Inhibitors.

    Science.gov (United States)

    Singh, Meenakshi; Singh, Sudhir Kumar; Thakur, Bhushan; Ray, Pritha; Singh, Sushil K

    2016-01-01

    A series of novel Schiff bases -benzothiazole hybrids was designed, synthesized and evaluated for their anticancer activity by MTT assay and western blot method. Antiproliferative screening indicated that compound containing dihydroxy substituents had potent inhibitory activity with IC50 value 34µg/ml against SKOV3, A2780-S and A2780-CR cell lines. It showed more potent cytotoxicity in combination with cisplatin and paclitaxel than alone in the selected cell lines (SKOV3, A2780 and A2780-CR models). The in vitro cytotoxicity of the compounds on IOSE 364 cell line was evaluated to establish the selectivity. Molecular docking study exhibited good binding against epidermal growth factor receptor, which was further ascertained by immunoblot assay using specific antibody against phosphorylated EGFR, and thus unravelling the targeted anticancer mechanism. PMID:26443027

  16. 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.

  17. Glucocorticoid receptor transformation and DNA binding

    International Nuclear Information System (INIS)

    The overall goal is to probe the mechanism whereby glucocorticoid receptors are transformed from a non-DNA-binding form to their active DNA-binding form. The author has examined the effect of an endogenous inhibitor purified from rat liver cytosol on receptor binding to DNA. The inhibitor binds to transformed receptors in whole cytosol and prevent their binding to DNA. He also examined the role of sulfhydryl groups in determining the DNA binding activity of the transformed receptor and in determining the transformation process. Treatment of rat liver cytosol containing temperature-transformed, [3H]dexamethasone-bound receptors at 00C with the sulfhydryl modifying reagent methyl methanethiosulfonate inhibits the DNA-binding activity of the receptor, and DNA-binding activity is restored after addition of dithiothreitol. In addition, he has examined the relationship between receptor phosphorylation and DNA binding. Untransformed receptor complexes purified from cytosol prepared from mouse L cells grown in medium containing [32P]orthophosphate contain two components, a 100 k-Da and a 90-kDa subunit, both of which are phosphoproteins. On transformation, the receptor dissociates from the 90-kDa protein. Transformation of the complex under cell free conditions does not result in a dephosphorylation of the 100-kDa steroid-binding protein. Transformed receptor that has been bound to DNA and purified by monoclonal antibody is still in a phosphorylated form. These results suggest that dephosphorylation is not required for receptor binding to DNA

  18. Causal Entropy Bound for a Spacelike Region

    Science.gov (United States)

    Brustein, R.; Veneziano, G.

    2000-06-01

    The identification of a causal-connection scale motivates us to propose a new covariant bound on entropy within a generic spacelike region. This ``causal entropy bound,'' scaling as EV, and thus lying around the geometric mean of Bekenstein's S/ER and holographic S/A bounds, is checked in various ``critical'' situations. In the case of limited gravity, Bekenstein's bound is the strongest while naive holography is the weakest. In the case of strong gravity, our bound and Bousso's holographic bound are stronger than Bekenstein's, while naive holography is too tight, and hence typically wrong.

  19. Pharmacokinetic digital phantoms for accuracy assessment of image-based dosimetry in 177Lu-DOTATATE peptide receptor radionuclide therapy

    International Nuclear Information System (INIS)

    Patient-specific image-based dosimetry is considered to be a useful tool to limit toxicity associated with peptide receptor radionuclide therapy (PRRT). To facilitate the establishment and reliability of absorbed-dose response relationships, it is essential to assess the accuracy of dosimetry in clinically realistic scenarios. To this end, we developed pharmacokinetic digital phantoms corresponding to patients treated with 177Lu-DOTATATE. Three individual voxel phantoms from the XCAT population were generated and assigned a dynamic activity distribution based on a compartment model for 177Lu-DOTATATE, designed specifically for this purpose. The compartment model was fitted to time-activity data from 10 patients, primarily acquired using quantitative scintillation camera imaging. S values for all phantom source-target combinations were calculated based on Monte-Carlo simulations. Combining the S values and time-activity curves, reference values of the absorbed dose to the phantom kidneys, liver, spleen, tumours and whole-body were calculated. The phantoms were used in a virtual dosimetry study, using Monte-Carlo simulated gamma-camera images and conventional methods for absorbed-dose calculations. The characteristics of the SPECT and WB planar images were found to well represent those of real patient images, capturing the difficulties present in image-based dosimetry. The phantoms are expected to be useful for further studies and optimisation of clinical dosimetry in 177Lu PRRT. (paper)

  20. Pharmacokinetic digital phantoms for accuracy assessment of image-based dosimetry in 177Lu-DOTATATE peptide receptor radionuclide therapy

    Science.gov (United States)

    Brolin, Gustav; Gustafsson, Johan; Ljungberg, Michael; Sjögreen Gleisner, Katarina

    2015-08-01

    Patient-specific image-based dosimetry is considered to be a useful tool to limit toxicity associated with peptide receptor radionuclide therapy (PRRT). To facilitate the establishment and reliability of absorbed-dose response relationships, it is essential to assess the accuracy of dosimetry in clinically realistic scenarios. To this end, we developed pharmacokinetic digital phantoms corresponding to patients treated with 177Lu-DOTATATE. Three individual voxel phantoms from the XCAT population were generated and assigned a dynamic activity distribution based on a compartment model for 177Lu-DOTATATE, designed specifically for this purpose. The compartment model was fitted to time-activity data from 10 patients, primarily acquired using quantitative scintillation camera imaging. S values for all phantom source-target combinations were calculated based on Monte-Carlo simulations. Combining the S values and time-activity curves, reference values of the absorbed dose to the phantom kidneys, liver, spleen, tumours and whole-body were calculated. The phantoms were used in a virtual dosimetry study, using Monte-Carlo simulated gamma-camera images and conventional methods for absorbed-dose calculations. The characteristics of the SPECT and WB planar images were found to well represent those of real patient images, capturing the difficulties present in image-based dosimetry. The phantoms are expected to be useful for further studies and optimisation of clinical dosimetry in 177Lu PRRT.

  1. Affinity-Based Screening of Tetravalent Peptides Identifies Subtype-Selective Neutralizers of Shiga Toxin 2d, a Highly Virulent Subtype, by Targeting a Unique Amino Acid Involved in Its Receptor Recognition.

    Science.gov (United States)

    Mitsui, Takaaki; Watanabe-Takahashi, Miho; Shimizu, Eiko; Zhang, Baihao; Funamoto, Satoru; Yamasaki, Shinji; Nishikawa, Kiyotaka

    2016-09-01

    Shiga toxin (Stx), a major virulence factor of enterohemorrhagic Escherichia coli (EHEC), can be classified into two subgroups, Stx1 and Stx2, each consisting of various closely related subtypes. Stx2 subtypes Stx2a and Stx2d are highly virulent and linked with serious human disorders, such as acute encephalopathy and hemolytic-uremic syndrome. Through affinity-based screening of a tetravalent peptide library, we previously developed peptide neutralizers of Stx2a in which the structure was optimized to bind to the B-subunit pentamer. In this study, we identified Stx2d-selective neutralizers by targeting Asn16 of the B subunit, an amino acid unique to Stx2d that plays an essential role in receptor binding. We synthesized a series of tetravalent peptides on a cellulose membrane in which the core structure was exactly the same as that of peptides in the tetravalent library. A total of nine candidate motifs were selected to synthesize tetravalent forms of the peptides by screening two series of the tetravalent peptides. Five of the tetravalent peptides effectively inhibited the cytotoxicity of Stx2a and Stx2d, and notably, two of the peptides selectively inhibited Stx2d. These two tetravalent peptides bound to the Stx2d B subunit with high affinity dependent on Asn16. The mechanism of binding to the Stx2d B subunit differed from that of binding to Stx2a in that the peptides covered a relatively wide region of the receptor-binding surface. Thus, this highly optimized screening technique enables the development of subtype-selective neutralizers, which may lead to more sophisticated treatments of infections by Stx-producing EHEC. PMID:27382021

  2. Evaluation of a new calix[4]arene based molecular receptor for sensitive and selective recognition of F{sup −} and Cu{sup 2+} ions

    Energy Technology Data Exchange (ETDEWEB)

    Chawla, Har Mohindra, E-mail: hmchawla@chemistry.iitd.ernet.in; Gupta, Tanu

    2014-10-15

    Design and evaluation of a single molecular receptor for multiple analytes reveal that calix[4]arene based molecular receptor 4 shows a highly selective response towards Cu{sup 2+} and F{sup −} ions with detection limits of 0.5 µM and 0.7 µM respectively when examined through UV–vis, fluorescence and {sup 1}H NMR spectroscopy. Simultaneous binding studies on 4 towards metal ion and fluoride reveal that it exhibits a negative allosteric effect towards Cu{sup 2+}/F{sup −}. - Highlights: • New calixarene based receptor for selective sensing of both F{sup −} and Cu{sup 2+}. • The LOD values for Cu{sup 2+} and F{sup −} are 0.5 μM and 0.7 μM respectively. • Simultaneous binding studies revealed negative allosterism towards Cu{sup 2+}/F{sup −} binding.

  3. Dopaminergic receptor-ligand binding assays based on molecularly imprinted polymers on quartz crystal microbalance sensors.

    Science.gov (United States)

    Naklua, Wanpen; Suedee, Roongnapa; Lieberzeit, Peter A

    2016-07-15

    Molecularly imprinted polymers (MIPs) have been successfully applied as selective materials for assessing the binding activity of agonist and antagonist of dopamine D1 receptor (D1R) by using quartz crystal microbalance (QCM). In this study, D1R derived from rat hypothalamus was used as a template and thus self-organized on stamps. Those were pressed into an oligomer film consisting of acrylic acid: N-vinylpyrrolidone: N,N'-(1,2-dihydroxyethylene) bis-acrylamide in a ratio of 2:3:12 spin coated onto a dual electrode QCM. Such we obtained one D1R-MIP-QCM electrode, whereas the other electrode carried the non-imprinted control polymer (NIP) that had remained untreated. Successful imprinting of D1R was confirmed by AFM. The polymer can re-incorporate D1R leading to frequency responses of 100-1200Hz in a concentration range of 5.9-47.2µM. In a further step such frequency changes proved inherently useful for examining the binding properties of test ligands to D1R. The resulting mass-sensitive measurements revealed Kd of dopamine∙HCl, haloperidol, and (+)-SCH23390 at 0.874, 25.6, and 0.004nM, respectively. These results correlate well with the values determined in radio ligand binding assays. Our experiments revealed that D1R-MIP sensors are useful for estimating the strength of ligand binding to the active single site. Therefore, we have developed a biomimetic surface imprinting strategy for QCM studies of D1R-ligand binding and presented a new method to ligand binding assay for D1R. PMID:26926593

  4. 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.

  5. Higgs interchange and bound states of superheavy fermions

    Indian Academy of Sciences (India)

    M De Sanctis

    2013-09-01

    Hypothetical superheavy fourth-generation fermions with a very small coupling with the rest of the Standard Model can give rise to long enough lived bound states. The production and the detection of these bound states would be experimentally feasible at the LHC. Extending, in the present study, the analysis of other authors, a semirelativistic wave equation is solved using an accurate numerical method to determine the binding energies of these possible superheavy fermion-bound states. The interaction given by the Yukawa potential of the Higgs boson exchange is considered; the corresponding relativistic corrections are calculated by means of a model based on the covariance properties of the Hamiltonian. We study the effects given by the Coulomb force. Moreover, we calculate the contributions given by the Coulombic and confining terms of the strong interaction in the case of superheavy quark bound states. The results of the model are critically analysed.

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

    CERN Document Server

    Williams, Ryan

    2010-01-01

    A fertile area of recent research has demonstrated concrete polynomial time lower bounds for solving natural hard problems on restricted computational models. Among these problems are Satisfiability, Vertex Cover, Hamilton Path, Mod6-SAT, Majority-of-Majority-SAT, and Tautologies, to name a few. The proofs of these lower bounds follow a certain proof-by-contradiction strategy that we call alternation-trading. An important open problem is to determine how powerful such proofs can possibly be. We propose a methodology for studying these proofs that makes them amenable to both formal analysis and automated theorem proving. We prove that the search for better lower bounds can often be turned into a problem of solving a large series of linear programming instances. Implementing a small-scale theorem prover based on this result, we extract new human-readable time lower bounds for several problems. This framework can also be used to prove concrete limitations on the current techniques.

  7. Leucine-based receptor sorting motifs are dependent on the spacing relative to the plasma membrane

    DEFF Research Database (Denmark)

    Geisler, C; Dietrich, J; Nielsen, B L;

    1998-01-01

    amino acid, is constitutively active. In this study, we have investigated how the spacing relative to the plasma membrane affects the function of both types of leucine-based motifs. For phosphorylation-dependent leucine-based motifs, a minimal spacing of 7 residues between the plasma membrane and the...... phospho-acceptor was required for phosphorylation and thereby activation of the motifs. For constitutively active leucine-based motifs, a minimal spacing of 6 residues between the plasma membrane and the acidic residue was required for optimal activity of the motifs. In addition, we found that the acidic......Many integral membrane proteins contain leucine-based motifs within their cytoplasmic domains that mediate internalization and intracellular sorting. Two types of leucine-based motifs have been identified. One type is dependent on phosphorylation, whereas the other type, which includes an acidic...

  8. Encompassing receptor flexibility in virtual screening using ensemble docking-based hybrid QSAR: discovery of novel phytochemicals for BACE1 inhibition.

    Science.gov (United States)

    Chakraborty, Sandipan; Ramachandran, Balaji; Basu, Soumalee

    2014-10-01

    Mimicking receptor flexibility during receptor-ligand binding is a challenging task in computational drug design since it is associated with a large increase in the conformational search space. In the present study, we have devised an in silico design strategy incorporating receptor flexibility in virtual screening to identify potential lead compounds as inhibitors for flexible proteins. We have considered BACE1 (β-secretase), a key target protease from a therapeutic perspective for Alzheimer's disease, as the highly flexible receptor. The protein undergoes significant conformational transitions from open to closed form upon ligand binding, which makes it a difficult target for inhibitor design. We have designed a hybrid structure-activity model containing both ligand based descriptors and energetic descriptors obtained from molecular docking based on a dataset of structurally diverse BACE1 inhibitors. An ensemble of receptor conformations have been used in the docking study, further improving the prediction ability of the model. The designed model that shows significant prediction ability judged by several statistical parameters has been used to screen an in house developed 3-D structural library of 731 phytochemicals. 24 highly potent, novel BACE1 inhibitors with predicted activity (Ki) ≤ 50 nM have been identified. Detailed analysis reveals pharmacophoric features of these novel inhibitors required to inhibit BACE1. PMID:25088750

  9. Oxytocin and Vasopressin Receptor Gene Variation as a Proximate Base for Inter- and Intraspecific Behavioral Differences in Bonobos and Chimpanzees

    OpenAIRE

    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 pros...

  10. Monotonicity of the quantum linear programming bound

    OpenAIRE

    Eric M. Rains

    1998-01-01

    The most powerful technique known at present for bounding the size of quantum codes of prescribed minimum distance is the quantum linear programming bound. Unlike the classical linear programming bound, it is not immediately obvious that if the quantum linear programming constraints are satisfiable for dimension K, that the constraints can be satisfied for all lower dimensions. We show that the quantum linear programming bound is indeed monotonic in this sense, and give an explicitly monotoni...

  11. The Hallucinogen N,N-Dimethyltryptamine (DMT) Is an Endogenous Sigma-1 Receptor Regulator

    OpenAIRE

    Fontanilla, Dominique; Johannessen, Molly; Hajipour, Abdol R.; Cozzi, Nicholas V; Jackson, Meyer B.; Ruoho, Arnold E.

    2009-01-01

    The sigma-1 receptor is widely distributed in the central nervous system and periphery. Originally mischaracterized as an opioid receptor, the sigma-1 receptor binds a vast number of synthetic compounds but does not bind opioid peptides; it is currently considered an orphan receptor. The sigma-1 receptor pharmacophore includes an alkylamine core, also found in the endogenous compound N,N-dimethyltryptamine (DMT). DMT acts as a hallucinogen, but its receptor target has been unclear. DMT bound ...

  12. Graphene in inhomogeneous magnetic fields: bound, quasi-bound and scattering states

    Energy Technology Data Exchange (ETDEWEB)

    Ramezani Masir, M; Peeters, F M [Departement Fysica, Universiteit Antwerpen Groenenborgerlaan 171, B-2020 Antwerpen (Belgium); Vasilopoulos, P, E-mail: mrmphys@gmail.com, E-mail: takis@alcor.concordia.ca, E-mail: francois.peeters@ua.ac.be [Department of Physics, Concordia University, Montreal, Quebec, H4B 1R6 (Canada)

    2011-08-10

    The electron states in graphene-based magnetic dot and magnetic ring structures and combinations of both are investigated. The corresponding spectra are studied as a function of the radii, the strengths of the inhomogeneous magnetic field and of a uniform background field, the strength of an electrostatic barrier and the angular momentum quantum number. In the absence of an external magnetic field we have only long-lived quasi-bound and scattering states and we assess their influence on the density of states. In addition, we consider elastic electron scattering by a magnetic dot, whose average B vanishes, and show that the Hall and longitudinal resistivities, as a function of the Fermi energy, exhibit a pronounced oscillatory structure due to the presence of quasi-bound states. Depending on the dot parameters this oscillatory structure differs substantially for energies below and above the first Landau level.

  13. Bound entangled states invariant under Ux

    Institute of Scientific and Technical Information of China (English)

    Wang Zhen; Wang Zhi-Xi

    2008-01-01

    This paper obtains an entangled condition for isotropic-like states by using an atomic map. It constructs a class of bound entangled states from the entangled condition and shows that the partial transposition of the state from the constructed bound entangled class is an edge bound entangled state by using range criterion.

  14. Bounded rationality and heterogeneous expectations in macroeconomics

    NARCIS (Netherlands)

    D. Massaro

    2012-01-01

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

  15. 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. The...... approximations of a standard (strictly concave)growth model.KEYWORDS: Numerical approximation errors, Bellman contractions, Error bounds...

  16. Class-specific Error Bounds for Ensemble Classifiers

    Energy Technology Data Exchange (ETDEWEB)

    Prenger, R; Lemmond, T; Varshney, K; Chen, B; Hanley, W

    2009-10-06

    The generalization error, or probability of misclassification, of ensemble classifiers has been shown to be bounded above by a function of the mean correlation between the constituent (i.e., base) classifiers and their average strength. This bound suggests that increasing the strength and/or decreasing the correlation of an ensemble's base classifiers may yield improved performance under the assumption of equal error costs. However, this and other existing bounds do not directly address application spaces in which error costs are inherently unequal. For applications involving binary classification, Receiver Operating Characteristic (ROC) curves, performance curves that explicitly trade off false alarms and missed detections, are often utilized to support decision making. To address performance optimization in this context, we have developed a lower bound for the entire ROC curve that can be expressed in terms of the class-specific strength and correlation of the base classifiers. We present empirical analyses demonstrating the efficacy of these bounds in predicting relative classifier performance. In addition, we specify performance regions of the ROC curve that are naturally delineated by the class-specific strengths of the base classifiers and show that each of these regions can be associated with a unique set of guidelines for performance optimization of binary classifiers within unequal error cost regimes.

  17. Atoms as Qed bound atoms

    International Nuclear Information System (INIS)

    The relevance of Quantum Electrodynamics (Qed) in contemporary atomic structure theory is reviewed. Recent experimental advances allow both the production of heavy ions of high charge as well as the measurement of atomic properties with a precision never achieved before. The description of heavy atoms with few electrons via the successive incorporation of one, two, etcetera photons in a rigorous manner and within the bound state Furry representation of Qed is technically feasible. For many-electron atoms the many-body (correlation) effects are very important and it is practically impossible to evaluate all the relevant Feynman diagrams to the required accuracy. Thus, it is necessary to develop a theoretical scheme in which the radiative and nonradiative effects are taken into account in an effective way making emphasis in electronic correlation. Preserving gauge invariance, and avoiding both continuum dissolution and variational collapse are basic problems that must be solved when using effective potential methods and finite-basis representations of them. In this context, we shall discuss advances and problems in the description of atoms as Qed bound states. (Author)

  18. The effects of a 5-HT5A receptor antagonist in a ketamine-based rat model of cognitive dysfunction and the negative symptoms of schizophrenia.

    Science.gov (United States)

    Nikiforuk, Agnieszka; Hołuj, Małgorzata; Kos, Tomasz; Popik, Piotr

    2016-06-01

    Serotonin (5-HT) receptors still represent promising targets for the development of novel multireceptor or stand-alone antipsychotic drugs with a potential to ameliorate cognitive impairments and negative symptoms in schizophrenia. The 5-HT5A receptor, one of the least known members of the serotonin receptor family, has also drawn attention in this regard. Although the antipsychotic efficacy of 5-HT5A antagonists is still equivocal, recent experimental data suggest the cognitive-enhancing activity of this strategy. The aim of the present study was to evaluate pro-cognitive and pro-social efficacies of the 5-HT5A receptor antagonist in a rat pharmacological model of schizophrenia employing the administration of the NMDA receptor antagonist, ketamine. The ability of SB-699551 to reverse ketamine-induced cognitive deficits in the attentional set-shifting task (ASST) and novel object recognition task (NORT) was examined. The compound's efficacy against ketamine-induced social withdrawal was assessed in the social interaction test (SIT) and in the social choice test (SCT). The results demonstrated the efficacy of SB-699551 in ameliorating ketamine-induced impairments on the ASST and NORT. Moreover, the tested compound also enhanced set-shifting performance in cognitively unimpaired control rats and improved object recognition memory in conditions of delay-induced natural forgetting. The pro-social activity of SB-699551 was demonstrated on both employed paradigms, the SIT and SCT. The present study suggests the preclinical efficacy of a strategy based on the blockade of 5-HT5A receptors against schizophrenia-like cognitive deficits and negative symptoms. The utility of this receptor as a target for improvement of cognitive and social dysfunctions warrants further studies. PMID:26826431

  19. 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.

  20. Identification of potent and selective retinoic acid receptor gamma (RARγ) antagonists for the treatment of osteoarthritis pain using structure based drug design.

    Science.gov (United States)

    Hughes, Norman E; Bleisch, Thomas J; Jones, Scott A; Richardson, Timothy I; Doti, Robert A; Wang, Yong; Stout, Stephanie L; Durst, Gregory L; Chambers, Mark G; Oskins, Jennifer L; Lin, Chaohua; Adams, Lisa A; Page, Todd J; Barr, Robert J; Zink, Richard W; Osborne, Harold; Montrose-Rafizadeh, Chahrzad; Norman, Bryan H

    2016-07-15

    A series of triaryl pyrazoles were identified as potent pan antagonists for the retinoic acid receptors (RARs) α, β and γ. X-ray crystallography and structure-based drug design were used to improve selectivity for RARγ by targeting residue differences in the ligand binding pockets of these receptors. This resulted in the discovery of novel antagonists which maintained RARγ potency but were greater than 500-fold selective versus RARα and RARβ. The potent and selective RARγ antagonist LY2955303 demonstrated good pharmacokinetic properties and was efficacious in the MIA model of osteoarthritis-like joint pain. This compound demonstrated an improved margin to RARα-mediated adverse effects. PMID:27261179

  1. Physical bounds for antenna radiation efficiency

    CERN Document Server

    Shahpari, Morteza

    2016-01-01

    Small volume, reduced conductivity and high frequencies are major imperatives in the design of communications infrastructure. The radiation efficiency $\\eta_r$ impacts on the optimal gain, quality factor, and bandwidth. The current efficiency limit applies to structures confined to a radian sphere $ka$ ($k$ is the wave number, $a$ is the radius). Here we present new absolute limits to $\\eta_r$ for arbitrary antenna shapes based on $k^2S$ where $S$ is the conductor surface area. For an electrical length of $10^{-5}$ our result is four orders of magnitude closer to the analytical solution. The improved bound on $\\eta_r$ is more accurate, more general, and easier to calculate than other limits. It is based on the total surface area of the conductors and provides greatly improved estimations for electrically small radiators at very low frequencies. The work is of great benefit to antenna designers assessing new materials such as conductive polymers.

  2. Bound on viscosity and the generalized second law of thermodynamics

    International Nuclear Information System (INIS)

    We describe a new paradox for ideal fluids. It arises in the accretion of an ideal fluid onto a black hole, where, under suitable boundary conditions, the flow can violate the generalized second law of thermodynamics. The paradox indicates that there is in fact a lower bound to the correlation length of any real fluid, the value of which is determined by the thermodynamic properties of that fluid. We observe that the universal bound on entropy, itself suggested by the generalized second law, puts a lower bound on the correlation length of any fluid in terms of its specific entropy. With the help of a new, efficient estimate for the viscosity of liquids, we argue that this also means that viscosity is bounded from below in a way reminiscent of the conjectured Kovtun-Son-Starinets lower bound on the ratio of viscosity to entropy density. We conclude that much light may be shed on the Kovtun-Son-Starinets bound by suitable arguments based on the generalized second law

  3. Development of genetic diagnosing method 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)

    2000-02-01

    Based on the gene analysis of cholecystokinin type A receptor (CCKAR) from normal mouse and its sequence analysis in the previous year, CCKAR knock-out gene which allows mRNA expression of {beta}-galactosidase gene in stead of CCKAR gene was constructed. Since some abnormality in CCKAR gene is thought to be a causal factor of diabetes and cholecystitis, a knock-out mouse that expressed LacZ but not CCKAR was constructed to investigate the correlation between the clinical features of diabetes and cholecystitis, and CCKAR gene abnormalities. F2 mice that had mutations in CCKAR gene were born according to the Mendel's low. The expression of CCKAR gene was investigated in detail based on the expression of LacZ gene in various tissues of homo (-/-) and hetero (-/+) knockout mice. Comparative study on blood sugar level, blood insulin level, the formation of biliary calculus, etc. is underway with the wild mouse, hetero and homo knockout mouse. (M.N.)

  4. Rational Structure-Based Rescaffolding Approach to De Novo Design of Interleukin 10 (IL-10) Receptor-1 Mimetics.

    Science.gov (United States)

    Ruiz-Gómez, Gloria; Hawkins, John C; Philipp, Jenny; Künze, Georg; Wodtke, Robert; Löser, Reik; Fahmy, Karim; Pisabarro, M Teresa

    2016-01-01

    Tackling protein interfaces with small molecules capable of modulating protein-protein interactions remains a challenge in structure-based ligand design. Particularly arduous are cases in which the epitopes involved in molecular recognition have a non-structured and discontinuous nature. Here, the basic strategy of translating continuous binding epitopes into mimetic scaffolds cannot be applied, and other innovative approaches are therefore required. We present a structure-based rational approach involving the use of a regular expression syntax inspired in the well established PROSITE to define minimal descriptors of geometric and functional constraints signifying relevant functionalities for recognition in protein interfaces of non-continuous and unstructured nature. These descriptors feed a search engine that explores the currently available three-dimensional chemical space of the Protein Data Bank (PDB) in order to identify in a straightforward manner regular architectures containing the desired functionalities, which could be used as templates to guide the rational design of small natural-like scaffolds mimicking the targeted recognition site. The application of this rescaffolding strategy to the discovery of natural scaffolds incorporating a selection of functionalities of interleukin-10 receptor-1 (IL-10R1), which are relevant for its interaction with interleukin-10 (IL-10) has resulted in the de novo design of a new class of potent IL-10 peptidomimetic ligands. PMID:27123592

  5. Rational Structure-Based Rescaffolding Approach to De Novo Design of Interleukin 10 (IL-10 Receptor-1 Mimetics.

    Directory of Open Access Journals (Sweden)

    Gloria Ruiz-Gómez

    Full Text Available Tackling protein interfaces with small molecules capable of modulating protein-protein interactions remains a challenge in structure-based ligand design. Particularly arduous are cases in which the epitopes involved in molecular recognition have a non-structured and discontinuous nature. Here, the basic strategy of translating continuous binding epitopes into mimetic scaffolds cannot be applied, and other innovative approaches are therefore required. We present a structure-based rational approach involving the use of a regular expression syntax inspired in the well established PROSITE to define minimal descriptors of geometric and functional constraints signifying relevant functionalities for recognition in protein interfaces of non-continuous and unstructured nature. These descriptors feed a search engine that explores the currently available three-dimensional chemical space of the Protein Data Bank (PDB in order to identify in a straightforward manner regular architectures containing the desired functionalities, which could be used as templates to guide the rational design of small natural-like scaffolds mimicking the targeted recognition site. The application of this rescaffolding strategy to the discovery of natural scaffolds incorporating a selection of functionalities of interleukin-10 receptor-1 (IL-10R1, which are relevant for its interaction with interleukin-10 (IL-10 has resulted in the de novo design of a new class of potent IL-10 peptidomimetic ligands.

  6. Development of genetic diagnosing method for diabetes and cholecystitis based on gene analysis of CCK-A receptor

    International Nuclear Information System (INIS)

    Based on the gene analysis of cholecystokinin type A receptor (CCKAR) from normal mouse and its sequence analysis in the previous year, CCKAR knock-out gene which allows mRNA expression of β-galactosidase gene in stead of CCKAR gene was constructed. Since some abnormality in CCKAR gene is thought to be a causal factor of diabetes and cholecystitis, a knock-out mouse that expressed LacZ but not CCKAR was constructed to investigate the correlation between the clinical features of diabetes and cholecystitis, and CCKAR gene abnormalities. F2 mice that had mutations in CCKAR gene were born according to the Mendel's low. The expression of CCKAR gene was investigated in detail based on the expression of LacZ gene in various tissues of homo (-/-) and hetero (-/+) knockout mice. Comparative study on blood sugar level, blood insulin level, the formation of biliary calculus, etc. is underway with the wild mouse, hetero and homo knockout mouse. (M.N.)

  7. 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.

  8. Bounded generalized Harish-Chandra modules

    OpenAIRE

    Penkov, Ivan; Serganova, Vera

    2007-01-01

    Let $\\gg$ be a complex reductive Lie algebra and $\\kk\\subset\\gg$ be any reductive in $\\gg$ subalgebra. We call a $(\\gg,\\kk)$-module $M$ bounded if the $\\kk$-multiplicities of $M$ are uniformly bounded. In this paper we initiate a general study of simple bounded $(\\gg,\\kk)$-modules. We prove a strong necessary condition for a subalgebra $\\kk$ to be bounded (Corollary \\ref{cor1.6}), i.e. to admit an infinite-dimensional simple bounded $(\\gg,\\kk)$-module, and then establish a sufficient conditio...

  9. Higgs mass bounds from the functional RG

    International Nuclear Information System (INIS)

    We investigate a Top-Yukawa toy model to study Higgs mass bounds in the framework of the functional renormalization group (RG). Starting the calculations with a quartic ultraviolet (UV) potential we get a finite range of values for the Higgs mass in the infrared for a given cutoff. The bounds appear in a natural way as a consequence of the RG flow. The lower mass bound is approached for a vanishing UV quartic coupling. Furthermore, we study the influence of higher-dimensional operators on the lower Higgs mass bound. We find that even seemingly RG irrelevant interactions can take a substantial influence on the lower bound for the Higgs mass.

  10. Association of the insulin-receptor variant Met-985 with hyperglycemia and non-insulin-dependent diabetes mellitus in the Netherlands: A population-based study

    Energy Technology Data Exchange (ETDEWEB)

    `t Hart, L.M.; Maassen, J.A. [Leiden Univ. (Netherlands); Does, F.E.E. van der [Free Univ., Amsterdam (Netherlands)] [and others

    1996-11-01

    One of the characteristics of non-insulin-dependent diabetes mellitus (NIDDM) is the presence of insulin. Most NIDDM patients have a normal sequence of the insulin receptor, indicating that, if insulin-receptor mutations contribute to the development of NIDDM, they will be present only in a minor fraction of the NIDDM population. The goal of the present study was to examine whether insulin-receptor mutations contribute to the development of NIDDM. We examined 161 individuals with NIDDM and 538 healthy controls from the population-based Rotterdam study for the presence of mutations in the insulin-receptor gene by SSCP. A heterozygous mutation changing valine-985 into methionine was detected in 5.6% of diabetic subjects and in 1.3% of individuals with normal oral glucose tolerance test. Adjusted for age, gender, and body-mass index, this revealed a relative risk for diabetes of 4.49 (95% confidence interval 1.59-12.25) for Met-985 carriers. When the total study group was analyzed, the prevalence of the mutation increased with increasing serum glucose levels (test for trend P < .005). We conclude that the Met-985 insulin-receptor variant associates with hyperglycemia and represents a risk factor for NIDDM. 30 refs., 3 figs., 1 tab.

  11. Triazolam-induced modulation of muscarinic acetylcholine receptor in living brain slices as revealed by a new positron-based imaging technique

    International Nuclear Information System (INIS)

    The effect of triazolam, a potent benzodiazepine (BZ) agonist, on muscarinic acetylcholinergic receptor (mAChR) binding was investigated in living brain slices by use of a novel positron-based imaging technique. Fresh rat brain slices were incubated with [11C]N-methyl-4-piperidylbenzilate ([11C]NMPB), a mAChR antagonist, in oxygenated Krebs-Ringer solution at 37 degree C. During incubation, time-resolved imaging of [11C]NMPB binding in the slices was constructed on the storage phosphor screens. Addition of triazolam (1 μM) plus muscimol (30 μM), a GABAA receptor agonist, to the incubation mixture decreased the specific binding of [11C]NMPB. Ro15-1788, a BZ receptor antagonist, prevented this effect, indicating that the effect was exerted through the GABAA/BZ receptor complex. These results demonstrated that stimulation of the GABAA/BZ receptor lowers the affinity of the mAChR for its ligand, which may underlie the BZ-induced amnesia, a serious clinical side effect of BZ. No such effect in the P2-fraction instead implies that the integrity of the neuronal cells and/or their environment is prerequisite for the modulation of mAChR by GABAA/BZ stimulation. (author)

  12. Radiocarbon-based source apportionment of elemental carbon aerosols at two South Asian receptor observatories over a full annual cycle

    International Nuclear Information System (INIS)

    Black carbon (BC) aerosols impact climate and air quality. Since BC from fossil versus biomass combustion have different optical properties and different abilities to penetrate the lungs, it is important to better understand their relative contributions in strongly affected regions such as South Asia. This study reports the first year-round 14C-based source apportionment of elemental carbon (EC), the mass-based correspondent to BC, using as regional receptor sites the international Maldives Climate Observatory in Hanimaadhoo (MCOH) and the mountaintop observatory of the Indian Institute of Tropical Meteorology in Sinhagad, India (SINH). For the highly-polluted winter season (December–March), the fractional contribution to EC from biomass burning (fbio) was 53 ± 5% (n = 6) at MCOH and 56 ± 3% at SINH (n = 5). The fbio for the non-winter remainder was 53 ± 11% (n = 6) at MCOH and 48 ± 8% (n = 7) at SINH. This observation-based constraint on near-equal contributions from biomass burning and fossil fuel combustion at both sites compare with predictions from eight technology-based emission inventory (EI) models for India of (fbio)EI spanning 55–88%, suggesting that most current EI for Indian BC systematically under predict the relative contribution of fossil fuel combustion. A continued iterative testing of bottom-up EI with top-down observational source constraints has the potential to lead to reduced uncertainties regarding EC sources and emissions to the benefit of both models of climate and air quality as well as guide efficient policies to mitigate emissions. (letter)

  13. Structure-based drug design targeting the cell membrane receptor GPBAR1: exploiting the bile acid scaffold towards selective agonism

    Science.gov (United States)

    Di Leva, Francesco Saverio; Festa, Carmen; Renga, Barbara; Sepe, Valentina; Novellino, Ettore; Fiorucci, Stefano; Zampella, Angela; Limongelli, Vittorio

    2015-01-01

    Bile acids can regulate nutrient metabolism through the activation of the cell membrane receptor GPBAR1 and the nuclear receptor FXR. Developing an exogenous control over these receptors represents an attractive strategy for the treatment of enterohepatic and metabolic disorders. A number of dual GPBAR1/FXR agonists are known, however their therapeutic use is limited by multiple unwanted effects due to activation of the diverse downstream signals controlled by the two receptors. On the other hand, designing selective GPBAR1 and FXR agonists is challenging since the two proteins share similar structural requisites for ligand binding. Here, taking advantage of our knowledge of the two targets, we have identified through a rational drug design study a series of amine lithocholic acid derivatives as selective GPBAR1 agonists. The presence of the 3α-NH2 group on the steroidal scaffold is responsible for the selectivity over FXR unveiling unprecedented structural insights into bile acid receptors activity modulation. PMID:26567894

  14. Structure-based drug design targeting the cell membrane receptor GPBAR1: exploiting the bile acid scaffold towards selective agonism

    Science.gov (United States)

    di Leva, Francesco Saverio; Festa, Carmen; Renga, Barbara; Sepe, Valentina; Novellino, Ettore; Fiorucci, Stefano; Zampella, Angela; Limongelli, Vittorio

    2015-11-01

    Bile acids can regulate nutrient metabolism through the activation of the cell membrane receptor GPBAR1 and the nuclear receptor FXR. Developing an exogenous control over these receptors represents an attractive strategy for the treatment of enterohepatic and metabolic disorders. A number of dual GPBAR1/FXR agonists are known, however their therapeutic use is limited by multiple unwanted effects due to activation of the diverse downstream signals controlled by the two receptors. On the other hand, designing selective GPBAR1 and FXR agonists is challenging since the two proteins share similar structural requisites for ligand binding. Here, taking advantage of our knowledge of the two targets, we have identified through a rational drug design study a series of amine lithocholic acid derivatives as selective GPBAR1 agonists. The presence of the 3α-NH2 group on the steroidal scaffold is responsible for the selectivity over FXR unveiling unprecedented structural insights into bile acid receptors activity modulation.

  15. Limit Analysis on Mechanism of Low-angle Submarine Landslide Based on Upper Bound Energy Method%基于能量上限法的海底缓边坡滑坡机理分析

    Institute of Scientific and Technical Information of China (English)

    安晨歌; 张建红; 周敏; 朱政

    2011-01-01

    海床中的天然气水合物分解后由固体变为气体,将直接提高孔隙水压力,减小边坡内有效应力,导致边坡稳定性下降.本文以能量上限定理为理论基础,采用二维极限分析方法分析海底缓倾角边坡的滑坡机理,研究由于水合物分解形成的软弱夹层对边坡稳定性的影响.分析表明,软弱夹层的埋深和海床土体内摩擦角会对边坡的稳定性产生直接影响.由于水合物分解而产生的膨胀压力也会降低海底缓倾角边坡的稳定性.%It is indicated by some experimental and theoretical data that the disassociation of gas hydrate could directly increase pore water pressure, decrease effective stresses in the submarine slope, reduce the friction coefficient between different soil layers in slope, and in consequence the slope stability will be weakened. In this paper, a two-dimensional numerical limit analysis, incorporating the upper-bound energy method, is presented to improve the understanding of the failure mechanism of submarine low-angle slope. Based on the analysis, it is found that the internal friction angle and the burial depth of weak layer affect the slope stability. It is also found that the expansion pressure due to gas hydrate disassociation in weak layer can affect the stability also.

  16. Analysis of imbalanced weather data based on branch-and-bound approach%基于分支限界的不平衡气象数据晴雨分析

    Institute of Scientific and Technical Information of China (English)

    王剑辉; 梁路; 王彪

    2016-01-01

    This paper proposed the modified cost-sensitive learning methods to preprocess the imbalance weather data.Con-sidering about the specialty of weather data,it made the value of rainfall per unit time as the cost value.So the data could be divided into two types of rain and non-rain effectively and reasonably.And then it used logic-based approach to analysie the data processed,used branch-and-bound approach to derive a Boolean classifier.Experimental results show that this method is feasible and effective.What’s more,it’s valid to perform any further logic calculation or logic operation on the result of the Boolean classifiers,achieving more flexibility.%提出基于修改的代价敏感学习的方法对不平衡的天气数据进行预处理,结合天气数据自身的特点,以单位时间的降雨量为成本的值,将数据合理有效地区分为下雨和非下雨两类;进而运用基于逻辑的方法对处理完的数据进行分析,运用分支限界算法得出布尔分类器。实验结果表明此方法可行有效,该方法可进一步对布尔分类器结果进行逻辑运算,从而达到更加灵活的操作分类器的效果。

  17. 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.

  18. 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...

  19. Antibaryon-nucleus bound states

    CERN Document Server

    Hrtánková, J

    2014-01-01

    We calculated antibaryon ($\\bar{B}$ = $\\bar{p}$, $\\bar{\\Lambda}$, $\\bar{\\Sigma}$, $\\bar{\\Xi}$) bound states in selected nuclei within the relativistic mean-field (RMF) model. The G-parity motivated $\\bar{B}$-meson coupling constants were scaled to yield corresponding potentials consistent with available experimental data. Large polarization of the nuclear core caused by $\\bar{B}$ was confirmed. The $\\bar{p}$ annihilation in the nuclear medium was incorporated by including a phenomenological imaginary part of the optical potential. The calculations using a complex $\\bar{p}$-nucleus potential were performed fully self-consistently. The $\\bar{p}$ widths significantly decrease when the phase space reduction is considered for $\\bar{p}$ annihilation products, but they still remain sizeable for potentials consistent with $\\bar{p}$-atom data.

  20. Role of serotonin 5-HT2C and histamine H1 receptors in antipsychotic-induced diabetes: A pharmacoepidemiological-pharmacodynamic study in VigiBase.

    Science.gov (United States)

    Montastruc, François; Palmaro, Aurore; Bagheri, Haleh; Schmitt, Laurent; Montastruc, Jean-Louis; Lapeyre-Mestre, Maryse

    2015-10-01

    Pharmacodynamic mechanisms of diabetes induced by antipsychotic drugs remain unclear, while numerous receptors have been suspected to be involved in the genesis of this Adverse Drug Reaction (ADR). We investigated potential relationships between antipsychotics׳ receptor occupancy (serotonin 5-HT1A, 5-HT2A, 5-HT2C, histamine H1, muscarinic M3, adrenergic α1, α2 or dopaminergic D2 D3 occupancies) and reports of diabetes using VigiBase(®), the World Health Organization (WHO) global Individual Case Safety Report (ICSR) database. All ADR reports from 15 first and second generation antipsychotic drugs recorded in VigiBase(®) were extracted. Logistic regression models, completed by disproportionality analysis, were used to determine the associations between antipsychotics׳ receptor occupancy and ICSRs of diabetes on VigiBase(®). During the study period, 94,460 ICSRs involved at least one of the 15 antipsychotics of interest. Diabetes was reported in 1799 (1.9%) patients. Clozapine was the most frequently suspected drug (n=953; 53.0%). A significant and positive association was found between histamine H1, muscarinic M3 and serotonin 5-HT2C, 5-HT2A receptor occupancies and reports of diabetes. A multivariable stepwise regression model showed that only serotonin 5-HT2c (AOR=2.13, CI 95% 1.72-2.64) and histamine H1 (AOR=1.91, CI 95% 1.38-2.64) predicted the risk for diabetes mellitus (p<0.001). Using an original pharmacoepidemiology-pharmacodynamic (PE-PD) approach, our study supports that antipsychotic drugs blocking simultaneously histamine H1 and serotonin 5-HT2C receptors are more frequently associated with diabetes reports in VigiBase(®) than other antipsychotics. These findings should encourage investigation of histamine H1 and serotonin 5-HT2C properties for predicting the risk of glycemic effects in candidate antipsychotics. PMID:26256010

  1. Expression cloning of a cDNA encoding the murine interleukin 4 receptor based on ligand binding

    Energy Technology Data Exchange (ETDEWEB)

    Harada, N.; Castle, B.E.; Gorman, D.M.; Itoh, A.; Schreurs, J.; Barrett, R.L.; Howard, M.; Miyajima, A. (DNAX Research Institute of Molecular and Cellular Biology, Palo Alto, CA (USA))

    1990-02-01

    Interleukin 4 (IL-4) is a potent mediator of growth and differentiation for various lymphoid and myeloid cells. To isolate a cDNA encoding the murine IL-4 receptor, the authors have developed an expression cloning method that uses biotinylated ligand as a probe and that may be generally applicable to cloning of receptor genes. COS-7 cells transiently transfected with the cloned full-length cDNA bind murine IL-4 specifically with a K{sub d} = 165 pM. Crosslinking of {sup 125}I-labeled IL-4 to COS-7 cells transfected with the cDNA reveals binding to proteins of 120-140 kDa. IL-4-responsive cells also express IL-4-binding proteins of 120-140 kDa but show additional bands at 60-70 kDa; the relationship of the smaller proteins to the larger ones is unclear. The nucleotide sequence indicates that the full-length cDNA encodes 810 amino acids including the signal sequence. While no consensus sequence for protein kinases is present in the cytoplasmic domain, a sequence comparison with the erythropoietin receptor, the IL-6 receptor, and the {beta} chain of the IL-2 receptor reveals a significant homology in the extracellular domain, indicating that the IL-4 receptor is a member of a cytokine receptor family.

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

    Science.gov (United States)

    Nakayama, Yu

    2016-07-01

    The recent work by Iha et al. shows an upper bound on mass anomalous dimension γ m of multi-flavor massless QCD at the renormalization group fixed point from the conformal bootstrap in SU( N F ) V symmetric conformal field theories under the assumption that the fixed point is realizable with the lattice regularization based on staggered fermions. We show that the almost identical but slightly stronger bound applies to the regularization based on Wilson fermions (or domain wall fermions) by studying the conformal bootstrap in SU( N f ) L × SU( N f ) R symmetric conformal field theories. For N f = 8, our bound implies γ m < 1 .31 to avoid dangerously irrelevant operators that are not compatible with the lattice symmetry.

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

    CERN Document Server

    Nakayama, Yu

    2016-01-01

    The recent work by Iha et al shows an upper bound on mass anomalous dimension $\\gamma_m$ of multi-flavor massless QCD at the renormalization group fixed point from the conformal bootstrap in $SU(N_F)_V$ symmetric conformal field theories under the assumption that the fixed point is realizable with the lattice regularization based on staggered fermions. We show that the almost identical but slightly stronger bound applies to the regularization based on Wilson fermions (or domain wall fermions) by studying the conformal bootstrap in $SU(N_f)_L \\times SU(N_f)_R$ symmetric conformal field theories. For $N_f=8$, our bound implies $\\gamma_m < 1.31$ to avoid dangerously irrelevant operators that are not compatible with the lattice symmetry.

  4. Molecularly imprinted polymers as biomimetic receptors for fluorescence-based optical sensors

    Science.gov (United States)

    Moreno-Bondi, María C.; Urraca, Javier L.; Benito-Peña, Elena; Navarro-Villoslada, Fernando; Martins, Sofía A.; Orellana, Guillermo; Sellergren, Börje

    2007-07-01

    Molecularly imprinted polymers (MIPs), human-made polymers capable of recognizing a particular molecule in the presence of others due to the selective cavities of the material, have been successfully applied to the development of chromatographic and solid phase extraction methods. They have also been applied to the development of electrochemical, piezoelectrical and optical sensors. In parallel with the classification of biosensors, MIP-based devices can work according to two different detection schemes: (1) affinity sensors ("plastic-bodies") and, (2) catalytic sensors ("plastic-enzymes"). In the first case the change in a characteristic optical property, most frequently fluorescence, of the analyte or of the polymer is monitored, upon their mutual interaction. Alternatively, a fluorescent analogue of the target analyte can also be used to develop sensors based on competitive assays (MIAs). Optimization of the polymer composition and, in particular, a proper choice of the nature of the functional monomers involved in the polymerization process, is critical to prepare materials able to selectively interact with the analyte in aqueous media and with the fast kinetics required for analytical applications. Moreover, a rational design of fluorescent analogues of non-naturally fluorescent templates or of fluorescent monomers able to change its property upon interaction with the analyte, is also a bottle neck for wide application of this recognition elements in optical sensing. In this paper we present several approaches to address these issues namely the optimization of MIP composition and the design and synthesis of novel fluorophores for the analysis of antibiotics and mycotoxins in real samples.

  5. Droplet Digital PCR Based Androgen Receptor Variant 7 (AR-V7) Detection from Prostate Cancer Patient Blood Biopsies

    Science.gov (United States)

    Ma, Yafeng; Luk, Alison; Young, Francis P.; Lynch, David; Chua, Wei; Balakrishnar, Bavanthi; de Souza, Paul; Becker, Therese M.

    2016-01-01

    Androgen receptor splice variant V7 (AR-V7) was recently identified as a valuable predictive biomarker in metastatic castrate-resistant prostate cancer. Here, we report a new, sensitive and accurate screen for AR-V7 mRNA expression directly from circulating tumor cells (CTCs): We combined EpCAM-based immunomagnetic CTC isolation using the IsoFlux microfluidic platform with droplet digital polymerase chain reaction (ddPCR) to analyze total AR and AR-V7 expression from prostate cancer patients CTCs. We demonstrate that AR-V7 is reliably detectable in enriched CTC samples with as little as five CTCs, even considering tumor heterogeneity, and confirm detection of AR-V7 in CTC samples from advanced prostate cancer (PCa) patients with AR-V7 detection limited to castrate resistant disease status in our sample set. Sensitive molecular analyses of circulating tumor cells (CTCs) or circulating tumor nucleic acids present exciting strategies to detect biomarkers, such as AR-V7 from non-invasive blood samples, so-called blood biopsies. PMID:27527157

  6. Calix[4]pyrrole derivative: recognition of fluoride and mercury ions and extracting properties of the receptor-based new material.

    Science.gov (United States)

    de Namor, Angela F Danil; Khalife, Rasha

    2008-12-11

    A calix[4]pyrrole derivative, namely, meso-tetramethyl tetrakis (4-phenoxy methyl ketone) calix[4]pyrrole, 1, was synthesized and structurally (1H NMR) and thermodynamically characterized. The complexing properties of this receptor with a wide variety of anions and cations in dipolar aprotic media (acetonitrile, propylene carbonate, and dimethyl sulfoxide) were investigated through 1H NMR and conductance studies. The former technique was used to assess whether or not complexation occurs and if so to identify the active sites of interaction of 1 with ions. The composition of the complexes was established by conductance measurements. It was found that in dipolar aprotic solvents, 1 interacts only with two polluting ions (fluoride and mercury). The complexation thermodynamics of 1 and these ions in these solvents is reported. The medium effect on the binding process involving the fluoride ion is discussed taking into account the solvation properties of reactants and the product. Complexes of moderate stability are found. Given that this is an important factor to consider for the recycling of the loaded material in extraction processes, 1 was treated with formaldehyde in basic medium leading to the production of a calix[4]pyrrole based material able to extract fluoride and mercury (II) ions from water. Thus the optimum conditions for the extraction of these ions from aqueous solutions were established. The material is easily recyclable using an organic acid. Final conclusions are given. PMID:19053691

  7. Using Molecular Initiating Events to Develop a Structural Alert Based Screening Workflow for Nuclear Receptor Ligands Associated with Hepatic Steatosis.

    Science.gov (United States)

    Mellor, Claire L; Steinmetz, Fabian P; Cronin, Mark T D

    2016-02-15

    In silico models are essential for the development of integrated alternative methods to identify organ level toxicity and lead toward the replacement of animal testing. These models include (quantitative) structure-activity relationships ((Q)SARs) and, importantly, the identification of structural alerts associated with defined toxicological end points. Structural alerts are able both to predict toxicity directly and assist in the formation of categories to facilitate read-across. They are particularly important to decipher the myriad mechanisms of action that result in organ level toxicity. The aim of this study was to develop novel structural alerts for nuclear receptor (NR) ligands that are associated with inducing hepatic steatosis and to show the vast number of existing data that are available. Current knowledge on NR agonists was extended with data from the ChEMBL database (12,713 chemicals in total) of bioactive molecules and from studying NR ligand-binding interactions within the protein database (PDB, 624 human NR structure files). A computational structural alert based workflow was developed using KNIME from these data using molecular fragments and other relevant chemical features. In total, 214 structural features were recorded computationally as SMARTS strings, and therefore, they can be used for grouping and screening during drug development and hazard assessment and provide knowledge to anchor adverse outcome pathways (AOPs) via their molecular initiating events (MIEs). PMID:26787004

  8. Droplet Digital PCR Based Androgen Receptor Variant 7 (AR-V7 Detection from Prostate Cancer Patient Blood Biopsies

    Directory of Open Access Journals (Sweden)

    Yafeng Ma

    2016-08-01

    Full Text Available Androgen receptor splice variant V7 (AR-V7 was recently identified as a valuable predictive biomarker in metastatic castrate-resistant prostate cancer. Here, we report a new, sensitive and accurate screen for AR-V7 mRNA expression directly from circulating tumor cells (CTCs: We combined EpCAM-based immunomagnetic CTC isolation using the IsoFlux microfluidic platform with droplet digital polymerase chain reaction (ddPCR to analyze total AR and AR-V7 expression from prostate cancer patients CTCs. We demonstrate that AR-V7 is reliably detectable in enriched CTC samples with as little as five CTCs, even considering tumor heterogeneity, and confirm detection of AR-V7 in CTC samples from advanced prostate cancer (PCa patients with AR-V7 detection limited to castrate resistant disease status in our sample set. Sensitive molecular analyses of circulating tumor cells (CTCs or circulating tumor nucleic acids present exciting strategies to detect biomarkers, such as AR-V7 from non-invasive blood samples, so-called blood biopsies.

  9. Chernoff Bound Based Approximate Frequent Itemset Mining Method over Streams%一种基于Chernoff Bound的数据流上近似频繁项集的挖掘方法

    Institute of Scientific and Technical Information of China (English)

    李海峰; 章宁

    2011-01-01

    数据流高速、无限和动态的特点决定了必须在有限的内存中以尽快的计算速度完成流数据上的频繁项集挖掘.将数据流中的数据按照段进行划分,采用二元组列表的数据结构进行保存,提出了一种基于滑动窗口的近似频繁项集挖掘方法AFIoDS,以实时获取频繁项集集合的真子集,并引入了概率参数,利用Chernoff Bound来动态改变支持度的近似值,保证真子集中的频繁项集被限制在一定的误差范围之内.此外,为了进一步节省内存,AFIoDS采用闭合项集的形式压缩每个段中获取的频繁项集.通过在3种真实数据集上的实验表明,AFIoDS算法与现有算法相比,在精度没有下降的情况下,具有更快的处理速度,同时其存储开销大大降低.%A data stream is fast, unlimited and dynamic, these characteristics constraint the computational resources and storages when mining frequent itemsets. This paper addressed this problem and proposed a simple and effective algorithrn AFIoDS, AFIoDS is an approximate algorithm based on sliding window model,which splits stream data into batches and maintains them with 2-tuple lists;thus,a false negative result can be obtained using a probabilistic parameter based on chernoff bound. The approximation will be changed dynamically to guarantee the mining frequent itemsets are error controllable. Plus, a compression of frequent itemsets, the closed frequent itemsets, are employed to represent the results of each batch for further memory saving. Our experimental results on 3 real world data show that without precision reduction, AFIoDS achieves a faster speed and a much reduced memory cost in comparison with the state-of-the-art algorithrna.

  10. Molecular Characterization and Differential Expression of an Olfactory Receptor Gene Family in the White-Backed Planthopper Sogatella furcifera Based on Transcriptome Analysis.

    Directory of Open Access Journals (Sweden)

    Ming He

    Full Text Available The white-backed planthopper, Sogatella furcifera, a notorious rice pest in Asia, employs host plant volatiles as cues for host location. In insects, odor detection is mediated by two types of olfactory receptors: odorant receptors (ORs and ionotropic receptors (IRs. In this study, we identified 63 SfurORs and 14 SfurIRs in S. furcifera based on sequences obtained from the head transcriptome and bioinformatics analysis. The motif-pattern of 130 hemiptera ORs indicated an apparent differentiation in this order. Phylogenetic trees of the ORs and IRs were constructed using neighbor-joining estimates. Most of the ORs had orthologous genes, but a specific OR clade was identified in S. furcifera, which suggests that these ORs may have specific olfactory functions in this species. Our results provide a basis for further investigations of how S. furcifera coordinates its olfactory receptor genes with its plant hosts, thereby providing a foundation for novel pest management approaches based on these genes.

  11. New molecular scaffolds for the design of Mycobacterium tuberculosis type II dehydroquinase inhibitors identified using ligand and receptor based virtual screening.

    Science.gov (United States)

    Kumar, Ashutosh; Siddiqi, Mohammad Imran; Miertus, Stanislav

    2010-04-01

    Using ligand and receptor based virtual screening approaches we have identified potential virtual screening hits targeting type II dehydroquinase from Mycobacterium tuberculosis, an effective and validated anti-mycobacterial target. Initially, we applied a virtual screening workflow based on a combination of 2D structural fingerprints, 3D pharmacophore and molecular docking to identify compounds that rigidly match specific aspects of ligand bioactive conformation. Subsequently, the resulting compounds were ranked and prioritized using receptor interaction fingerprint based scoring and quantitative structure activity relationship model developed using already known actives. The virtual screening hits prioritized belong to several classes of molecular scaffolds with several available substitution positions that could allow chemical modification to enhance binding affinity. Finally, identified hits may be useful to a medicinal chemist or combinatorial chemist to pick up the new molecular starting points for medicinal chemistry optimization for the design of novel type II dehydroquinase inhibitors. PMID:19816720

  12. Holographic bound in covariant loop quantum gravity

    CERN Document Server

    Tamaki, Takashi

    2016-01-01

    We investigate puncture statistics based on the covariant area spectrum in loop quantum gravity. First, we consider Maxwell-Boltzmann statistics with a Gibbs factor for punctures. We establish formulae which relate physical quantities such as horizon area to the parameter characterizing holographic degrees of freedom. We also perform numerical calculations and obtain consistency with these formulae. These results tell us that the holographic bound is satisfied in the large area limit and correction term of the entropy-area law can be proportional to the logarithm of the horizon area. Second, we also consider Bose-Einstein statistics and show that the above formulae are also useful in this case. By applying the formulae, we can understand intrinsic features of Bose-Einstein condensate which corresponds to the case when the horizon area almost consists of punctures in the ground state. When this phenomena occurs, the area is approximately constant against the parameter characterizing the temperature. When this ...

  13. Circulating Ghrelin, Leptin, and Soluble Leptin Receptor Concentrations and Cardiometabolic Risk Factors in a Community-Based Sample

    OpenAIRE

    Ingelsson, Erik; Larson, Martin G.; Yin, Xiaoyan; Wang, Thomas J.; Meigs, James B; Lipinska, Izabella; Benjamin, Emelia J.; Keaney, John F.; Vasan, Ramachandran S.

    2008-01-01

    Context: The conjoint effects and relative importance of ghrelin, leptin, and soluble leptin receptor (sOB-R), adipokines involved in appetite control and energy expenditure in mediating cardiometabolic risk, is unknown.

  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. Thermodynamic law from the entanglement entropy bound

    Science.gov (United States)

    Park, Chanyong

    2016-04-01

    From black hole thermodynamics, the Bekenstein bound has been proposed as a universal thermal entropy bound. It has been further generalized to an entanglement entropy bound which is valid even in a quantum system. In a quantumly entangled system, the non-negativity of the relative entropy leads to the entanglement entropy bound. When the entanglement entropy bound is saturated, a quantum system satisfies the thermodynamicslike law with an appropriately defined entanglement temperature. We show that the saturation of the entanglement entropy bound accounts for a universal feature of the entanglement temperature proportional to the inverse of the system size. In addition, we show that the deformed modular Hamiltonian under a global quench also satisfies the generalized entanglement entropy boundary after introducing a new quantity called the entanglement chemical potential.

  16. Preparation and physico-chemical characterization of supramolecular fluoride receptors based on uranyl-salophen complexes incorporated within micelles

    OpenAIRE

    De Bernardin, Paolo

    2012-01-01

    The development of selective and sensitive sensors for anionic species in water is a growing field of research. In particular, the detection of fluoride in aqueous samples is of great interest because of health related problems attributed to this anion. Furthermore its small size and its high hydration energy make it a particularly challenging species to recognize in water. Uranyl-salophen receptors have shown to be good receptors for this anion in organic solvents due to their hard Lewis aci...

  17. 3D structure prediction of human β1-adrenergic receptor via threading-based homology modeling for implications in structure-based drug designing.

    Directory of Open Access Journals (Sweden)

    Zaheer Ul-Haq

    Full Text Available Dilated cardiomyopathy is a disease of left ventricular dysfunction accompanied by impairment of the β1-adrenergic receptor (β1-AR signal cascade. The disturbed β1-AR function may be based on an elevated sympathetic tone observed in patients with heart failure. Prolonged adrenergic stimulation may induce metabolic and electrophysiological disturbances in the myocardium, resulting in tachyarrhythmia that leads to the development of heart failure in human and sudden death. Hence, β1-AR is considered as a promising drug target but attempts to develop effective and specific drug against this tempting pharmaceutical target is slowed down due to the lack of 3D structure of Homo sapiens β1-AR (hsβADR1. This study encompasses elucidation of 3D structural and physicochemical properties of hsβADR1 via threading-based homology modeling. Furthermore, the docking performance of several docking programs including Surflex-Dock, FRED, and GOLD were validated by re-docking and cross-docking experiments. GOLD and Surflex-Dock performed best in re-docking and cross docking experiments, respectively. Consequently, Surflex-Dock was used to predict the binding modes of four hsβADR1 agonists. This study provides clear understanding of hsβADR1 structure and its binding mechanism, thus help in providing the remedial solutions of cardiovascular, effective treatment of asthma and other diseases caused by malfunctioning of the target protein.

  18. Molecular Characterization and Sex Distribution of Chemosensory Receptor Gene Family Based on Transcriptome Analysis of Scaeva pyrastri

    Science.gov (United States)

    Li, Xiao-Ming; Zhu, Xiu-Yun; He, Peng; Xu, Lu; Sun, Liang; Chen, Li; Wang, Zhi-Qiang; Deng, Dao-Gui

    2016-01-01

    Chemosensory receptors play key roles in insect behavior. Thus, genes encoding these receptors have great potential for use in integrated pest management. The hover fly Scaeva pyrastri (L.) is an important pollinating insect and a natural enemy of aphids, mainly distributed in the Palearctic and Nearctic regions. However, a systematic identification of their chemosensory receptor genes in the antennae has not been reported. In the present study, we assembled the antennal transcriptome of S. pyrastri by using Illumina sequencing technology. Analysis of the transcriptome data identified 60 candidate chemosensory genes, including 38 for odorant receptors (ORs), 16 for ionotropic receptors (IRs), and 6 for gustatory receptors (GRs). The numbers are similar to those of other Diptera species, suggesting that we were able to successfully identify S. pyrastri chemosensory genes. We analyzed the expression patterns of all genes by using reverse transcriptase PCR (RT-PCR), and found that some genes exhibited sex-biased or sex-specific expression. These candidate chemosensory genes and their tissue expression profiles provide information for further studies aimed at fully understanding the molecular basis behind chemoreception-related behaviors in S. pyrastri. PMID:27171401

  19. Volume bounds of conic 2-spheres

    OpenAIRE

    Fang, Hao; Lai, Mijia

    2016-01-01

    We obtain sharp volume bound for a conic 2-sphere in terms of its Gaussian curvature bound. We also give the geometric models realizing the extremal volume. In particular, when the curvature is bounded in absolute value by $1$, we compute the minimal volume of a conic sphere in the sense of Gromov. In order to apply the level set analysis and iso-perimetric inequality as in our previous works, we develop some new analytical tools to treat regions with vanishing curvature.

  20. Fuzzy upper bounds and their applications

    International Nuclear Information System (INIS)

    This paper considers the concept of fuzzy upper bounds and provides some relevant applications. Considering a fuzzy DEA model, the existence of a fuzzy upper bound for the objective function of the model is shown and an effective approach to solve that model is introduced. Some dual interpretations are provided, which are useful for practical purposes. Applications of the concept of fuzzy upper bounds in two physical problems are pointed out