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Sample records for bmr operator binding

  1. Structures of BmrR-Drug Complexes Reveal a Rigid Multidrug Binding Pocket And Transcription Activation Through Tyrosine Expulsion

    Energy Technology Data Exchange (ETDEWEB)

    Newberry, K.J.; Huffman, J.L.; Miller, M.C.; Vazquez-Laslop, N.; Neyfakh, A.A.; Brennan, R.G.

    2009-05-22

    BmrR is a member of the MerR family and a multidrug binding transcription factor that up-regulates the expression of the bmr multidrug efflux transporter gene in response to myriad lipophilic cationic compounds. The structural mechanism by which BmrR binds these chemically and structurally different drugs and subsequently activates transcription is poorly understood. Here, we describe the crystal structures of BmrR bound to rhodamine 6G (R6G) or berberine (Ber) and cognate DNA. These structures reveal each drug stacks against multiple aromatic residues with their positive charges most proximal to the carboxylate group of Glu-253 and that, unlike other multidrug binding pockets, that of BmrR is rigid. Substitution of Glu-253 with either alanine (E253A) or glutamine (E253Q) results in unpredictable binding affinities for R6G, Ber, and tetraphenylphosphonium. Moreover, these drug binding studies reveal that the negative charge of Glu-253 is not important for high affinity binding to Ber and tetraphenylphosphonium but plays a more significant, but unpredictable, role in R6G binding. In vitro transcription data show that E253A and E253Q are constitutively active, and structures of the drug-free E253A-DNA and E253Q-DNA complexes support a transcription activation mechanism requiring the expulsion of Tyr-152 from the multidrug binding pocket. In sum, these data delineate the mechanism by which BmrR binds lipophilic, monovalent cationic compounds and suggest the importance of the redundant negative electrostatic nature of this rigid drug binding pocket that can be used to discriminate against molecules that are not substrates of the Bmr multidrug efflux pump.

  2. The Structure and Dynamics of BmR1 Protein from Brugia malayi: In Silico Approaches

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    Bee Yin Khor

    2014-06-01

    Full Text Available Brugia malayi is a filarial nematode, which causes lymphatic filariasis in humans. In 1995, the disease has been identified by the World Health Organization (WHO as one of the second leading causes of permanent and long-term disability and thus it is targeted for elimination by year 2020. Therefore, accurate filariasis diagnosis is important for management and elimination programs. A recombinant antigen (BmR1 from the Bm17DIII gene product was used for antibody-based filariasis diagnosis in “Brugia Rapid”. However, the structure and dynamics of BmR1 protein is yet to be elucidated. Here we study the three dimensional structure and dynamics of BmR1 protein using comparative modeling, threading and ab initio protein structure prediction. The best predicted structure obtained via an ab initio method (Rosetta was further refined and minimized. A total of 5 ns molecular dynamics simulation were performed to investigate the packing of the protein. Here we also identified three epitopes as potential antibody binding sites from the molecular dynamics average structure. The structure and epitopes obtained from this study can be used to design a binder specific against BmR1, thus aiding future development of antigen-based filariasis diagnostics to complement the current diagnostics.

  3. The allometry of parrot BMR: seasonal data for the Greater Vasa Parrot, Coracopsis vasa, from Madagascar.

    Science.gov (United States)

    Lovegrove, Barry G; Perrin, Mike R; Brown, Mark

    2011-12-01

    In this study we examined the allometry of basal metabolic rate (BMR) of 31 parrot species. Unlike previous reports, we show that parrots per se do not display BMRs that are any different to other captive-raised birds of their body size. An ordinary least squares regression fitted the data best and body mass explained 95% of the variation in BMR. There was no phylogenetic signal in the BMR data. We also provide new data for the Greater Vasa Parrot (Coracopsis vasa) of Madagascar. We tested the hypotheses that C. vasa may, because of its insular existence, display conservative energetic traits (low BMR, use of adaptive heterothermy) similar to those observed in several Malagasy mammals. However, this was not the case. C. vasa had a higher BMR than other parrots, especially during summer, when BMR was up-regulated by 50.5% and was 95.7% higher than predicted from an ordinary least squares (OLS) allometry of parrots (BMR = 0.042M (b) (0.649) , BMR in Watts, M (b) in grammes). Compared with BMR data for 94 captive-raised bird species, the winter and summer BMRs were, respectively, 45.5 and 117.8% higher than predicted by a phylogenetic generalised least squares (PGLS) allometry (BMR = 0.030M (b) (0.687) , BMR in Watts, M (b) in grammes). The summer up-regulation of BMR is the highest recorded for a bird of any size to date. We suggest that the costs of a high summer BMR may be met by the unusual cooperative breeding system of C. vasa in which groups of males feed the female and share paternity. The potential breeding benefits of a high summer BMR are unknown.

  4. Map-based cloning and expression analysis of BMR-6 in sorghum

    Indian Academy of Sciences (India)

    Jieqin Li; Lihua Wang; Qiuwen Zhan; Yanlong Liu

    2015-09-01

    Brown midrib mutants in sorghum are associated with reduced lignin content and increased cell wall digestibility. In this study, we characterized a bmr-6 sorghum mutant, which shows reddish pigment in the midrib and stem after the fifth-leaf stage. Compared to wild type, Kalson lignin content of bmr-6 is decreased significantly. We used histological analysis to determine that the mutant exhibited a modified pattern of lignin staining and found an increased polysaccharide content. We cloned BMR-6 gene, a gene encoded a cinnamyl alcohol dehydrogenase (CAD), using a map-based cloning approach. Genetic complementation confirmed that CAD is responsible for the BMR-6 phenotype. BMR-6 gene was expressed in all tested sorghum tissues, with the highest being in midrib and stem. Transient expression assays in Nicotiana benthamiana leaves demonstrated cytomplasmic localization of BMR-6. We found that the expression level of bmr-6 was significantly decreased in the mutant but expression of SbCAD3 and SbCAD5 were significantly increased. Our results indicate that BMR-6 not only affects the distribution of lignin but also the biosynthesis of lignin in sorghum.

  5. Metabolic risk factors in mice divergently selected for BMR fed high fat and high carb diets.

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    Sadowska, Julita; Gębczyński, Andrzej K; Konarzewski, Marek

    2017-01-01

    Factors affecting contribution of spontaneous physical activity (SPA; activity associated with everyday tasks) to energy balance of humans are not well understood, as it is not clear whether low activity is related to dietary habits, precedes obesity or is a result of thereof. In particular, human studies on SPA and basal metabolic rates (BMR, accounting for >50% of human energy budget) and their associations with diet composition, metabolic thrift and obesity are equivocal. To clarify these ambiguities we used a unique animal model-mice selected for divergent BMR rates (the H-BMR and L-BMR line type) presenting a 50% between-line type difference in the primary selected trait. Males of each line type were divided into three groups and fed either a high fat, high carb or a control diet. They then spent 4 months in individual cages under conditions emulating human "sedentary lifestyle", with SPA followed every month and measurements of metabolic risk indicators (body fat mass %, blood lipid profile, fasting blood glucose levels and oxidative damage in the livers, kidneys and hearts) taken at the end of study. Mice with genetically determined high BMR assimilated more energy and had higher SPA irrespective of type of diet. H-BMR individuals were characterized by lower dry body fat mass %, better lipid profile and lower fasting blood glucose levels, but higher oxidative damage in the livers and hearts. Genetically determined high BMR may be a protective factor against diet-induced obesity and most of the metabolic syndrome indicators. Elevated spontaneous activity is correlated with high BMR, and constitutes an important factor affecting individual capability to sustain energy balance even under energy dense diets.

  6. SbCOMT (Bmr12) is involved in the biosynthesis of tricin-lignin in sorghum.

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    Eudes, Aymerick; Dutta, Tanmoy; Deng, Kai; Jacquet, Nicolas; Sinha, Anagh; Benites, Veronica T; Baidoo, Edward E K; Richel, Aurore; Sattler, Scott E; Northen, Trent R; Singh, Seema; Simmons, Blake A; Loqué, Dominique

    2017-01-01

    Lignin in plant biomass represents a target for engineering strategies towards the development of a sustainable bioeconomy. In addition to the conventional lignin monomers, namely p-coumaryl, coniferyl and sinapyl alcohols, tricin has been shown to be part of the native lignin polymer in certain monocot species. Because tricin is considered to initiate the polymerization of lignin chains, elucidating its biosynthesis and mechanism of export to the cell wall constitute novel challenges for the engineering of bioenergy crops. Late steps of tricin biosynthesis require two methylation reactions involving the pathway intermediate selgin. It has recently been demonstrated in rice and maize that caffeate O-methyltransferase (COMT) involved in the synthesis syringyl (S) lignin units derived from sinapyl alcohol also participates in the synthesis of tricin in planta. In this work, we validate in sorghum (Sorghum bicolor L.) that the O-methyltransferase responsible for the production of S lignin units (SbCOMT / Bmr12) is also involved in the synthesis of lignin-linked tricin. In particular, we show that biomass from the sorghum bmr12 mutant contains lower level of tricin incorporated into lignin, and that SbCOMT can methylate the tricin precursors luteolin and selgin. Our genetic and biochemical data point toward a general mechanism whereby COMT is involved in the synthesis of both tricin and S lignin units.

  7. Recognition rules for binding of homeodomains to operator DNA.

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    Chirgadze, Yu N; Sivozhelezov, V S; Polozov, R V; Stepanenko, V A; Ivanov, V V

    2012-01-01

    The spatial arrangement of interfaces between homeodomain transcription factors and operator DNA has been considered. We analyzed the binding contacts for a representative set of 22 complexes of homeodomain transcription factors with a double-stranded operator DNA in the region of the major groove. It was shown that the recognition of DNA by the recognizing _-helix of protein is governed by two contact groups. Invariant protein-DNA group of contacts includes six contacts, formed by atomic groups of coding and non-coding DNA chains with the groups of amino acids. The recognizing _-helix forms contacts by polar groups of residues Trp2 (NE1), Asn5, and Lys9 with the canonical sequence T(1)A(2)A(3)T(4) of the coding DNA chain, and contacts by residues Lys0, Arg7 and Lys11 with the sequence A(4)X(5)X(6)X(7) of a non-coding DNA chain, where X is any nucleotide. Variable protein-DNA group of contacts comprises two groups bound with the sequence T(3)A(4)X(5)X(6) of the non- coding DNA-chain. These contacts are mainly with the bases and specify the binding pattern of individual homeodomains. The invariant contact group represents a recognition pattern for transcription factors of the homeodomain family: multiple adenine-asparagine contact and six position-specific phosphate contacts mainly with lysine or arginine. Within this group, we have found three most significant invariant contacts which allow deducing the recognition rules for homeodomains. These rules are inherent for different taxonomic groups of the homeodomain family and can distinguishing members of this family from any other family of transcription factors.

  8. Emission Inventory of On-Road Transport in Bangkok Metropolitan Region (BMR Development during 2007 to 2015 Using the GAINS Model

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    Penwadee Cheewaphongphan

    2017-09-01

    Full Text Available Bangkok Metropolitan Region (BMR, including the capital city and five adjacent provinces, constitutes one of the top 10 megacities experiencing serious traffic congestion in the world, leading to air quality problems with significant adverse human health risks. Previously, there have been many operations planned to influence the fuel consumption and emissions from the on-road transport sector in the BMR area. It is necessary to estimate emissions using detailed information in order to thoroughly understand the reason for changes in emission levels and their impact on air quality. This paper aims to determine the successful implementation of energy and air pollution control policies in Thailand through an investigation of the emissions inventory of on-road transport in BMR, including ozone precursors (CO, NOX, Non-methane volatile organic compounds (NMVOCs , greenhouse gases (CO2, CH4, N2O, acidic substances (SO2 and NH3, and particulate matters (PM2.5, PM10, Black Carbon (BC, Organic Carbon (OC during the period from 2007 to 2015, using the Greenhouse Gas and Air Pollution Interactions and Synergies (GAINS model based on the country-specific activity data together with the emission factor from the GAINS-Asia database. This study found that the amount of exhaust emissions over the BMR area in the year 2015 (and the trend during the period from 2007 to 2015 is approximately 139 kt of CO (−7.9%, 103 kt of NOX (−4.1%, 19.9 kt of NMVOC (−6.7%, 15 kt of CO2 (+1.6%, 8.6 kt of CH4 (+6.8%, 0.59 kt of N2O (+1.3%, 0.87 kt of SO2 (−25.8%, 1.1 kt of NH3 (+7.8%, 4.9 kt of PM2.5 (−5.5%, 5.1 kt of PM10 (−7.9%, 3.1 kt of BC (−2.5%, and 1.4 kt of OC (−7.7%. The change in emissions in each pollutant is a result of the more stringent control of fuel and engine standards, the shift in the fuel type used, and the effects of controlling some emissions. Light duty car gasoline fuel is identified as a major contributor of CO, NH3, N2O, and NMVOC, whereas

  9. PEMERIKSAAN CEMARAN PESTISIDA DALAM KOMODITI CABAl MERAH BESAR DAN CABAI MERAH KERITING DI BEBERAPA KOTA DALAM UPAYA PENETAPAN BMR (BATAS MAKSIMUM RESIDU

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    D. Mutiatikum

    2012-10-01

    Full Text Available Telah dilakukan penelitian terhadap residu pestisida dalam komoditi cabai merah besar dan cabai merah keriting yang berasal dari pasar di kota Cianjur, Semarang dan Surabaya. Pengujian dilakukan menggunakan alat KCKT (Kromatografi Cair Kinerja Tinggi. Hasil pengujian terhadap beberapa golongan pestisida kemudian dikaji kembali berdasarkan pola konsumsi cabai orang Indonesia dan dihitung BMR-nya dan dibandingkan terhadap BMR pustaka. Dari hasil pemeriksaan terdeteksi pestisida golongan organoklorin seperti lindon, aldrin, heptaklor, endosulfon. Golongan organofosfat yang terdeteksi adalah paration, klorpirifos, dimethoat, profenofos, protiofos. Golongan karbamat yang terdeteksi adalah karbofuran, sedangkan golongan piretrin tidak terdeteksi, hasil perhitungan lebih kecil dari BMR pustaka.   Kata kunci : Pestisida, cabai

  10. 枯草杆菌耐药转运蛋白Bmr及其基因bmr的表达调控研究进展%Advances in multidrug resistance transporter Bmr of Bacillus subtilis and transcriptional regulation mechanism of its gene bmr

    Institute of Scientific and Technical Information of China (English)

    关维; 陈仪本

    2012-01-01

    Multidrug transporter Bmr is one of the main drug resistance efflux proteins in Ba-cillus subtilis. It's encoded by bmr gene which is located in the genome, and it mediates theresistance to a wide range of drugs such as antibiotics and antimicrobials, etc. The expression of bmr gene is regulated by BmrR and MtaN, both of which are transcriptional regulator from the MerR family. This paper reviewed the study of structure, physiological function and the action mechanism of Bmr and the regulatory protein BmrR and MtaN in recent years.%枯草杆菌多重耐药转运蛋白Bmr是其主要的耐药外排蛋白之一,由位于基因组DNA的bmr基因编码,介导对多种抗生素、杀菌剂等药物的耐药性.bmr基因的表达受到BmrR及MtaN的转录调控,二者均属于MerR家族调节子.关于近年对多重耐药转运蛋白Bmr和调节蛋白BmrR、MtaN的结构、生理功能及作用机制等研究情况进行综述.

  11. PEMERIKSAAN RESIDU PESTISIDA DALAM KOMODITI BERAS YANG BERASAL DARI BEBERAPA KOTA DALAM UPAYA PENETAPAN BATAS MAKSIMUM PESTISIDA (BMR

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    D. Mutiatikum

    2012-09-01

    Full Text Available It has researched that the residual pesticide in rice commodities with come from Cianjur, Semarang and Surabaya markets. The test examined using HPLC (High Pressure Liquid Chromatography method. The result of the test that come from some kind of Indonesia people and is calculated  pattern of Indonesia people. The result of test, the karbofuran has detected 0,0296 - 0,0755 mg/kg and according to BMR level allowable minimum consume around 0,02 mg/kglday, which is ADI level 0,01 mg/kg/day from cereal.   Kata Kunci : Residual pesticide, Rice

  12. Microbial inoculant effects on silage and in vitro ruminal fermentation, and microbial biomass estimation for alfalfa, bmr corn, and corn silages

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    Third cut alfalfa, brown mid-rib (bmr) corn, and corn were chopped and inoculated with one of four different strains of lactic acid bacteria (LAB). Uninoculated silage was the control treatment. For each crop, four mini-silos 1-L glass jars were ensiled per treatment. All silos were fermented for 60...

  13. Blepharophimosis and mental retardation (BMR) phenotypes caused by chromosomal rearrangements: description in a boy with partial trisomy 10q and monosomy 4q and review of the literature.

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    Bartholdi, Deborah; Toelle, Sandra P; Steiner, Bernhard; Boltshauser, Eugen; Schinzel, Albert; Riegel, Mariluce

    2008-01-01

    Blepharophimosis is a rare congenital anomaly of the palpebral fissure which is often associated with mental retardation and additional malformations. We report on a boy with blepharophimosis, ptosis and severe mental retardation carrying an unbalanced 4;10 translocation with terminal duplication of 10q [dup(10)(q25.1-->qter)] and monosomy of a small terminal segment of chromosome 4q [del(4)(34.3-->qter)]. Detailed clinical examination and review of the literature showed that the phenotype of the patient was mainly determined by the dup(10q). This paper reviews the chromosomal aberrations associated with BMR (blepharophimosis mental retardation) phenotypes. Searching different databases and reviewing the literature revealed 14 microscopically visible aberrations (among them UPD(14)pat) and two submicroscopic rearrangements causing blepharophimosis and mental retardation (BMR) syndrome. Some of these rearrangements-like the terminal dup(10q) identified in our patient or interstitial del(2q)-are associated with clearly defined phenotypes and can be well distinguished from each other on basis of clinical examination. This paper should assist clinicians and cytogeneticists when evaluating patients with BMR syndrome.

  14. Glutamine synthetase stabilizes the binding of GlnR to nitrogen fixation gene operators.

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    Fernandes, Gabriela de C; Hauf, Ksenia; Sant'Anna, Fernando H; Forchhammer, Karl; Passaglia, Luciane M P

    2017-03-01

    Biological nitrogen fixation (BNF) is a high energy demanding process carried out by diazotrophic microorganisms that supply combined nitrogen to the biosphere. The genes related to BNF are strictly regulated, but these mechanisms are poorly understood in gram-positive bacteria. The transcription factor GlnR was proposed to regulate nitrogen fixation-related genes based on Paenibacillus comparative genomics. In order to validate this proposal, we investigated BNF regulatory sequences in Paenibacillus riograndensis SBR5(T) genome. We identified GlnR-binding sites flanking σ(A) -binding sites upstream from BNF-related genes. GlnR binding to these sites was demonstrated by surface plasmon resonance spectroscopy. GlnR-DNA affinity is greatly enhanced when GlnR is in complex with feedback-inhibited (glutamine-occupied) glutamine synthetase (GS). GlnR-GS complex formation is also modulated by ATP and AMP. Thereby, gene repression exerted by the GlnR-GS complex is coupled with nitrogen (glutamine levels) and energetic status (ATP and AMP). Finally, we propose a DNA-looping model based on multiple operator sites that represents a strong and strict regulation for these genes. © 2017 Federation of European Biochemical Societies.

  15. Exploration of Energy Metabolism in the Mouse Using Indirect Calorimetry: Measurement of Daily Energy Expenditure (DEE) and Basal Metabolic Rate (BMR).

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    Meyer, Carola W; Reitmeir, Peter; Tschöp, Matthias H

    2015-09-01

    Current comprehensive mouse metabolic phenotyping involves studying energy balance in cohorts of mice via indirect calorimetry, which determines heat release from changes in respiratory air composition. Here, we describe the measurement of daily energy expenditure (DEE) and basal metabolic rate (BMR) in mice. These well-defined metabolic descriptors serve as meaningful first-line read-outs for metabolic phenotyping and should be reported when exploring energy expenditure in mice. For further guidance, the issue of appropriate sample sizes and the frequency of sampling of metabolic measurements is also discussed.

  16. Recognition rules for binding of Zn-Cys2His2 transcription factors to operator DNA.

    Science.gov (United States)

    Polozov, R V; Sivozhelezov, V S; Chirgadze, Yu N; Ivanov, V V

    2015-01-01

    The molecules of Zn-finger transcription factors consist of several similar small protein units. We analyzed the crystal structures 46 basic units of 22 complexes of Zn-Cys2His2 family with the fragments of operator DNA. We showed that the recognition of DNA occurs via five protein contacts. The canonical binding positions of the recognizing α-helix were -1, 3, 6, and 7, which make contacts with the tetra-nucleotide sequence ZXYZ of the coding DNA strand; here the canonical binding triplet is underlined. The non-coding DNA strand forms only one contact at α-helix position 2. We have discovered that there is a single highly conservative contact His7α with the phosphate group of nucleotide Z, which precedes each triplet XYZ of the coding DNA chain. This particular contact is invariant for the all Zn-Cys2His2 family with high frequency of occurrence 83%, which we considered as an invariant recognition rule. We have also selected a previously unreported Zn-Cys2His2-Arg subfamily of 21 Zn-finger units bound with DNA triplets, which make two invariant contacts with residues Arg6α and His7α with the coding DNA chain. These contacts show frequency of occurrence 100 and 90%, and are invariant recognition rule. Three other variable protein-DNA contacts are formed mainly with the bases and specify the recognition patterns of individual factor units. The revealed recognition rules are inherent for the Zn-Cys2His2 family and Zn-Cys2His2-Arg subfamily of different taxonomic groups and can distinguish members of these families from any other family of transcription factors.

  17. Investigation of Changes in Tetracycline Repressor Binding upon Mutations in the Tetracycline Operator.

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    Bolintineanu, Dan S; Volzing, Katherine; Vivcharuk, Victor; Sayyed-Ahmad, Abdallah; Srivastava, Poonam; Kaznessis, Yiannis N

    2014-10-01

    The tetracycline operon is an important gene network component, commonly used in synthetic biology applications because of its switch-like character. At the heart of this system is the highly specific interaction of the tet repressor protein (TetR) with its cognate DNA sequence (tetO). TetR binding on tetO practically stops expression of genes downstream of tetO by excluding RNA polymerase from binding the promoter and initiating transcription. Mutating the tetO sequence alters the strength of TetR-tetO binding and thus provides a tool to synthetic biologists to manipulate gene expression levels. We employ molecular dynamics (MD) simulations coupled with the free energy perturbation method to investigate the binding affinity of TetR to different tetO mutants. We also carry out in vivo tests in Escherichia coli for a series of promoters based on these mutants. We obtain reasonable agreement between experimental green fluorescent protein (GFP) repression levels and binding free energy differences computed from molecular simulations. In all cases, the wild-type tetO sequence yields the strongest TetR binding, which is observed both experimentally, in terms of GFP levels, and in simulation, in terms of free energy changes. Two of the four tetO mutants we tested yield relatively strong binding, whereas the other two mutants tend to be significantly weaker. The clustering and relative ranking of this subset of tetO mutants is generally consistent between our own experimental data, previous experiments with different systems and the free energy changes computed from our simulations. Overall, this work offers insights into an important synthetic biological system and demonstrates the potential, as well as limitations of molecular simulations to quantitatively explain biologically relevant behavior.

  18. HYSTERECTOMY OPERATION FOR THE TREATMENT OF THE EGG BINDING IN THE LOVEBiRD (AGAPORNIS COMPRISE): CASE REPORT

    OpenAIRE

    GÜNDÜZ, Mehmet Can; TOYDEMİR, Seval; APAYDIN ENGİNLER, Sinem Özlem; Turna YILMAZ, Özge; YİGİT, Funda; UÇMAK, Melih

    2012-01-01

    ABSTRACT The case material is a 15 months-old lovebird who performed hysteretomy operation for egg binding three months ago. Calcium gluconate (0.5 mg/100 g) and oxytocin (1 unit/kg) were administered intramuscularly after the lubrication of the cloacal opening. These applications yielded no results and attempts were made to remove the egg manually as a result of which the egg shell was broken. By considering the case's current condition and future life, treatment by hysterectomy was pre...

  19. Structural basis of operator sites recognition and effector binding in the TetR family transcription regulator FadR.

    Science.gov (United States)

    Yeo, Hyun Ku; Park, Young Woo; Lee, Jae Young

    2017-04-20

    FadR is a fatty acyl-CoA dependent transcription factor that regulates genes encoding proteins involved in fatty-acid degradation and synthesis pathways. In this study, the crystal structures of Bacillus halodurans FadR, which belong to the TetR family, have been determined in three different forms: ligand-bound, ligand-free and DNA-bound at resolutions of 1.75, 2.05 and 2.80 Å, respectively. Structural and functional data showed that B. halodurans FadR was bound to its operator site without fatty acyl-CoAs. Structural comparisons among the three different forms of B. halodurans FadR revealed that the movement of DNA binding domains toward the operator DNA was blocked upon binding of ligand molecules. These findings suggest that the TetR family FadR negatively regulates the genes involved in fatty acid metabolism by binding cooperatively to the operator DNA as a dimer of dimers. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Operating mechanism and molecular dynamics of pheromone-binding protein ASP1 as influenced by pH.

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    Lei Han

    Full Text Available Odorant binding protein (OBP is a vital component of the olfactory sensation system. It performs the specific role of ferrying odorant molecules to odorant receptors. OBP helps insects and types of animal to sense and transport stimuli molecules. However, the molecular details about how OBPs bind or release its odorant ligands are unclear. For some OBPs, the systems' pH level is reported to impact on the ligands' binding or unbinding capability. In this work we investigated the operating mechanism and molecular dynamics in bee antennal pheromone-binding protein ASP1 under varying pH conditions. We found that conformational flexibility is the key factor for regulating the interaction of ASP1 and its ligands, and the odorant binds to ASP1 at low pH conditions. Dynamics, once triggered by pH changes, play the key roles in coupling the global conformational changes with the odorant release. In ASP1, the C-terminus, the N-terminus, helix α2 and the region ranging from helices α4 to α5 form a cavity with a novel 'entrance' of binding. These are the major regions that respond to pH change and regulate the ligand release. Clearly there are processes of dynamics and hydrogen bond network propagation in ASP1 in response to pH stimuli. These findings lead to an understanding of the mechanism and dynamics of odorant-OBP interaction in OBP, and will benefit chemsensory-related biotech and agriculture research and development.

  1. dREAM co-operates with insulator-binding proteins and regulates expression at divergently paired genes.

    Science.gov (United States)

    Korenjak, Michael; Kwon, Eunjeong; Morris, Robert T; Anderssen, Endre; Amzallag, Arnaud; Ramaswamy, Sridhar; Dyson, Nicholas J

    2014-08-01

    dREAM complexes represent the predominant form of E2F/RBF repressor complexes in Drosophila. dREAM associates with thousands of sites in the fly genome but its mechanism of action is unknown. To understand the genomic context in which dREAM acts we examined the distribution and localization of Drosophila E2F and dREAM proteins. Here we report a striking and unexpected overlap between dE2F2/dREAM sites and binding sites for the insulator-binding proteins CP190 and Beaf-32. Genetic assays show that these components functionally co-operate and chromatin immunoprecipitation experiments on mutant animals demonstrate that dE2F2 is important for association of CP190 with chromatin. dE2F2/dREAM binding sites are enriched at divergently transcribed genes, and the majority of genes upregulated by dE2F2 depletion represent the repressed half of a differentially expressed, divergently transcribed pair of genes. Analysis of mutant animals confirms that dREAM and CP190 are similarly required for transcriptional integrity at these gene pairs and suggest that dREAM functions in concert with CP190 to establish boundaries between repressed/activated genes. Consistent with the idea that dREAM co-operates with insulator-binding proteins, genomic regions bound by dREAM possess enhancer-blocking activity that depends on multiple dREAM components. These findings suggest that dREAM functions in the organization of transcriptional domains. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  2. LabVIEW-operated novel nanoliter osmometer for ice binding protein investigations.

    Science.gov (United States)

    Braslavsky, Ido; Drori, Ran

    2013-02-04

    Ice-binding proteins (IBPs), including antifreeze proteins, ice structuring proteins, thermal hysteresis proteins, and ice recrystallization inhibition proteins, are found in cold-adapted organisms and protect them from freeze injuries by interacting with ice crystals. IBPs are found in a variety of organism, including fish(1), plants(2, 3), arthropods(4, 5), fungi(6), and bacteria(7). IBPs adsorb to the surfaces of ice crystals and prevent water molecules from joining the ice lattice at the IBP adsorption location. Ice that grows on the crystal surface between the adsorbed IBPs develops a high curvature that lowers the temperature at which the ice crystals grow, a phenomenon referred to as the Gibbs-Thomson effect. This depression creates a gap (thermal hysteresis, TH) between the melting point and the nonequilibrium freezing point, within which ice growth is arrested(8-10), see Figure 1. One of the main tools used in IBP research is the nanoliter osmometer, which facilitates measurements of the TH activities of IBP solutions. Nanoliter osmometers, such as the Clifton instrument (Clifton Technical Physics, Hartford, NY,) and Otago instrument (Otago Osmometers, Dunedin, New Zealand), were designed to measure the osmolarity of a solution by measuring the melting point depression of droplets with nanoliter volumes. These devices were used to measure the osmolarities of biological samples, such as tears(11), and were found to be useful in IBP research. Manual control over these nanoliter osmometers limited the experimental possibilities. Temperature rate changes could not be controlled reliably, the temperature range of the Clifton instrument was limited to 4,000 mOsmol (about -7.5 °C), and temperature recordings as a function of time were not an available option for these instruments. We designed a custom-made computer-controlled nanoliter osmometer system using a LabVIEW platform (National Instruments). The cold stage, described previously(9, 10), contains a metal

  3. 1H NMR study of the interaction of bacteriophage lambda Cro protein with the OR3 operator. Evidence for a change of the conformation of the OR3 operator on binding.

    Science.gov (United States)

    Kirpichnikov, M P; Hahn, K D; Buck, F; Rüterjans, H; Chernov, B K; Kurochkin, A V; Skryabin, K G; Bayev, A A

    1984-01-01

    The specific complex between the lambda phage OR3 operator and the Cro protein has been studied by proton NMR spectroscopy at 500 MHz. The DNA imino proton resonances of this complex have been assigned to specific base pairs using the known assignments of these resonances for the free operator. Increase of the protein/DNA ratio to complete saturation of the OR3 operator with the Cro protein made it possible to follow the shift changes of the resonances. Ambiguities were resolved by nuclear Overhauser effect measurements on the complex. The shifts of the imino proton resonance positions provide information on the changes induced in the conformation of the operator upon complex formation with a dimer of the Cro protein. The most striking shift occurs for the central (GC 9) base pair, which is known to have no direct contacts with the Cro protein. This shift may be induced by a bend in the OR3 operator DNA at the GC 9 base pair to accommodate the operator for the binding of the Cro protein dimer. The imino proton resonances of two additional base pairs can be observed in the complex, demonstrating an overall stabilization of the DNA structure by the binding of the Cro protein. PMID:6233535

  4. Identification of the Zn2+ binding site and mode of operation of a mammalian Zn2+ transporter.

    Science.gov (United States)

    Ohana, Ehud; Hoch, Eitan; Keasar, Chen; Kambe, Taiho; Yifrach, Ofer; Hershfinkel, Michal; Sekler, Israel

    2009-06-26

    Vesicular zinc transporters (ZnTs) play a critical role in regulating Zn2+ homeostasis in various cellular compartments and are linked to major diseases ranging from Alzheimer disease to diabetes. Despite their importance, the intracellular localization of ZnTs poses a major challenge for establishing the mechanisms by which they function and the identity of their ion binding sites. Here, we combine fluorescence-based functional analysis and structural modeling aimed at elucidating these functional aspects. Expression of ZnT5 was followed by both accelerated removal of Zn2+ from the cytoplasm and its increased vesicular sequestration. Further, activity of this zinc transport was coupled to alkalinization of the trans-Golgi network. Finally, structural modeling of ZnT5, based on the x-ray structure of the bacterial metal transporter YiiP, identified four residues that can potentially form the zinc binding site on ZnT5. Consistent with this model, replacement of these residues, Asp599 and His451, with alanine was sufficient to block Zn2+ transport. These findings indicate, for the first time, that Zn2+ transport mediated by a mammalian ZnT is catalyzed by H+/Zn2+ exchange and identify the zinc binding site of ZnT proteins essential for zinc transport.

  5. The Molecular Switch of Telomere Phages: High Binding Specificity of the PY54 Cro Lytic Repressor to a Single Operator Site

    Directory of Open Access Journals (Sweden)

    Jens Andre Hammerl

    2015-06-01

    Full Text Available Temperate bacteriophages possess a molecular switch, which regulates the lytic and lysogenic growth. The genomes of the temperate telomere phages N15, PY54 and ɸKO2 harbor a primary immunity region (immB comprising genes for the prophage repressor, the lytic repressor and a putative antiterminator. The roles of these products are thought to be similar to those of the lambda proteins CI, Cro and Q, respectively. Moreover, the gene order and the location of several operator sites in the prototype telomere phage N15 and in ɸKO2 are also reminiscent of lambda-like phages. By contrast, in silico analyses revealed the presence of only one operator (O\\(_{\\rm{R}}\\3 in PY54. The purified PY54 Cro protein was used for EMSA studies demonstrating that it exclusively binds to a 16-bp palindromic site (O\\(_{\\rm{R}}\\3 upstream of the prophage repressor gene. The O\\(_{\\rm{R}}\\3 operator sequences of PY54 and ɸKO2/N15 only differ by their peripheral base pairs, which are responsible for Cro specificity. PY54 cI and cro transcription is regulated by highly active promoters initiating the synthesis of a homogenious species of leaderless mRNA. The location of the PY54 Cro binding site and of the identified promoters suggests that the lytic repressor suppresses cI transcription but not its own synthesis. The results indicate an unexpected diversity of the growth regulation mechanisms in lambda-related phages.

  6. Optimized Standard Operating Procedures for the Analysis of Cerebrospinal Fluid Aβ42 and the Ratios of Aβ Isoforms Using Low Protein Binding Tubes

    Science.gov (United States)

    Vanderstichele, Hugo Marcel Johan; Janelidze, Shorena; Demeyer, Leentje; Coart, Els; Stoops, Erik; Herbst, Victor; Mauroo, Kimberley; Brix, Britta; Hansson, Oskar

    2016-01-01

    Background: Reduced cerebrospinal fluid (CSF) concentration of amyloid-β1-42 (Aβ1-42) reflects the presence of amyloidopathy in brains of subjects with Alzheimer’s disease (AD). Objective: To qualify the use of Aβ1-42/Aβ1-40 for improvement of standard operating procedures (SOP) for measurement of CSF Aβ with a focus on CSF collection, storage, and analysis. Methods: Euroimmun ELISAs for CSF Aβ isoforms were used to set up a SOP with respect to recipient properties (low binding, polypropylene), volume of tubes, freeze/thaw cycles, addition of detergents (Triton X-100, Tween-20) in collection or storage tubes or during CSF analysis. Data were analyzed with linear repeated measures and mixed effects models. Results: Optimization of CSF analysis included a pre-wash of recipients (e.g., tubes, 96-well plates) before sample analysis. Using the Aβ1-42/Aβ1-40 ratio, in contrast to Aβ1-42, eliminated effects of tube type, additional freeze/thaw cycles, or effect of CSF volumes for polypropylene storage tubes. ‘Low binding’ tubes reduced the loss of Aβ when aliquoting CSF or in function of additional freeze/thaw cycles. Addition of detergent in CSF collection tubes resulted in an almost complete absence of variation in function of collection procedures, but affected the concentration of Aβ isoforms in the immunoassay. Conclusion: The ratio of Aβ1-42/Aβ1-40 is a more robust biomarker than Aβ1-42 toward (pre-) analytical interfering factors. Further, ‘low binding’ recipients and addition of detergent in collection tubes are able to remove effects of SOP-related confounding factors. Integration of the Aβ1-42/Aβ1-40 ratio and ‘low-binding tubes’ into guidance criteria may speed up worldwide standardization of CSF biomarker analysis. PMID:27258423

  7. The Escherichia coli metallo-regulator RcnR represses rcnA and rcnR transcription through binding on a shared operator site: Insights into regulatory specificity towards nickel and cobalt.

    Science.gov (United States)

    Blaha, Didier; Arous, Safia; Blériot, Camille; Dorel, Corinne; Mandrand-Berthelot, Marie-Andrée; Rodrigue, Agnès

    2011-03-01

    RcnA is an efflux pump responsible for Ni and Co detoxification in Escherichia coli. The expression of rcnA is induced by Ni and Co via the metallo-regulator RcnR. In the present work, the functioning of the promoter-operator region of rcnR and rcnA was investigated using primer extension and DNAse I footprinting experiments. We show that the promoters of rcnR and rcnA are convergent and that apo-RcnR binds on symmetrically located sequences in this intergenic region. Moreover, RcnR DNA binding is specifically modulated by one Ni or Co equivalent and not by other metals. In addition to rcnA, RcnR controls expression of its own gene in response to Ni and Co, but the two genes are differentially expressed.

  8. Co-operative intra-protein structural response due to protein-protein complexation revealed through thermodynamic quantification: study of MDM2-p53 binding

    Science.gov (United States)

    Samanta, Sudipta; Mukherjee, Sanchita

    2017-09-01

    The p53 protein activation protects the organism from propagation of cells with damaged DNA having oncogenic mutations. In normal cells, activity of p53 is controlled by interaction with MDM2. The well understood p53-MDM2 interaction facilitates design of ligands that could potentially disrupt or prevent the complexation owing to its emergence as an important objective for cancer therapy. However, thermodynamic quantification of the p53-peptide induced structural changes of the MDM2-protein remains an area to be explored. This study attempts to understand the conformational free energy and entropy costs due to this complex formation from the histograms of dihedral angles generated from molecular dynamics simulations. Residue-specific quantification illustrates that, hydrophobic residues of the protein contribute maximum to the conformational thermodynamic changes. Thermodynamic quantification of structural changes of the protein unfold the fact that, p53 binding provides a source of inter-element cooperativity among the protein secondary structural elements, where the highest affected structural elements (α2 and α4) found at the binding site of the protein affects faraway structural elements (β1 and Loop1) of the protein. The communication perhaps involves water mediated hydrogen bonded network formation. Further, we infer that in inhibitory F19A mutation of P53, though Phe19 is important in the recognition process, it has less prominent contribution in the stability of the complex. Collectively, this study provides vivid microscopic understanding of the interaction within the protein complex along with exploring mutation sites, which will contribute further to engineer the protein function and binding affinity.

  9. Binding Procurement

    Science.gov (United States)

    Rao, Gopalakrishna M.; Vaidyanathan, Hari

    2007-01-01

    This viewgraph presentation reviews the use of the binding procurement process in purchasing Aerospace Flight Battery Systems. NASA Engineering and Safety Center (NESC) requested NASA Aerospace Flight Battery Systems Working Group to develop a set of guideline requirements document for Binding Procurement Contracts.

  10. Crystal Structure of an Integron Gene Cassette-Associated Protein from Vibrio cholerae Identifies a Cationic Drug-Binding Module

    Energy Technology Data Exchange (ETDEWEB)

    Deshpande, Chandrika N.; Harrop, Stephen J.; Boucher, Yan; Hassan, Karl A.; Di Leo, Rosa; Xu, Xiaohui; Cui, Hong; Savchenko, Alexei; Chang, Changsoo; Labbate, Maurizio; Paulsen, Ian T.; Stokes, H.W.; Curmi, Paul M.G.; Mabbutt, Bridget C. (MIT); (UT-Australia); (Macquarie); (Toronto); (New South)

    2012-02-15

    The direct isolation of integron gene cassettes from cultivated and environmental microbial sources allows an assessment of the impact of the integron/gene cassette system on the emergence of new phenotypes, such as drug resistance or virulence. A structural approach is being exploited to investigate the modularity and function of novel integron gene cassettes. We report the 1.8 {angstrom} crystal structure of Cass2, an integron-associated protein derived from an environmental V. cholerae. The structure defines a monomeric beta-barrel protein with a fold related to the effector-binding portion of AraC/XylS transcription activators. The closest homologs of Cass2 are multi-drug binding proteins, such as BmrR. Consistent with this, a binding pocket made up of hydrophobic residues and a single glutamate side chain is evident in Cass2, occupied in the crystal form by polyethylene glycol. Fluorescence assays demonstrate that Cass2 is capable of binding cationic drug compounds with submicromolar affinity. The Cass2 module possesses a protein interaction surface proximal to its drug-binding cavity with features homologous to those seen in multi-domain transcriptional regulators. Genetic analysis identifies Cass2 to be representative of a larger family of independent effector-binding proteins associated with lateral gene transfer within Vibrio and closely-related species. We propose that the Cass2 family not only has capacity to form functional transcription regulator complexes, but represents possible evolutionary precursors to multi-domain regulators associated with cationic drug compounds.

  11. Crystal structure of an integron gene cassette-associated protein from Vibrio cholerae identifies a cationic drug-binding module.

    Directory of Open Access Journals (Sweden)

    Chandrika N Deshpande

    Full Text Available The direct isolation of integron gene cassettes from cultivated and environmental microbial sources allows an assessment of the impact of the integron/gene cassette system on the emergence of new phenotypes, such as drug resistance or virulence. A structural approach is being exploited to investigate the modularity and function of novel integron gene cassettes.We report the 1.8 Å crystal structure of Cass2, an integron-associated protein derived from an environmental V. cholerae. The structure defines a monomeric beta-barrel protein with a fold related to the effector-binding portion of AraC/XylS transcription activators. The closest homologs of Cass2 are multi-drug binding proteins, such as BmrR. Consistent with this, a binding pocket made up of hydrophobic residues and a single glutamate side chain is evident in Cass2, occupied in the crystal form by polyethylene glycol. Fluorescence assays demonstrate that Cass2 is capable of binding cationic drug compounds with submicromolar affinity. The Cass2 module possesses a protein interaction surface proximal to its drug-binding cavity with features homologous to those seen in multi-domain transcriptional regulators.Genetic analysis identifies Cass2 to be representative of a larger family of independent effector-binding proteins associated with lateral gene transfer within Vibrio and closely-related species. We propose that the Cass2 family not only has capacity to form functional transcription regulator complexes, but represents possible evolutionary precursors to multi-domain regulators associated with cationic drug compounds.

  12. Analyzing binding data.

    Science.gov (United States)

    Motulsky, Harvey J; Neubig, Richard R

    2010-07-01

    Measuring the rate and extent of radioligand binding provides information on the number of binding sites, and their affinity and accessibility of these binding sites for various drugs. This unit explains how to design and analyze such experiments.

  13. Membrane binding domains

    OpenAIRE

    Hurley, James H.

    2006-01-01

    Eukaryotic signaling and trafficking proteins are rich in modular domains that bind cell membranes. These binding events are tightly regulated in space and time. The structural, biochemical, and biophysical mechanisms for targeting have been worked out for many families of membrane binding domains. This review takes a comparative view of seven major classes of membrane binding domains, the C1, C2, PH, FYVE, PX, ENTH, and BAR domains. These domains use a combination of specific headgroup inter...

  14. Analyzing radioligand binding data.

    Science.gov (United States)

    Motulsky, Harvey; Neubig, Richard

    2002-08-01

    Radioligand binding experiments are easy to perform, and provide useful data in many fields. They can be used to study receptor regulation, discover new drugs by screening for compounds that compete with high affinity for radioligand binding to a particular receptor, investigate receptor localization in different organs or regions using autoradiography, categorize receptor subtypes, and probe mechanisms of receptor signaling, via measurements of agonist binding and its regulation by ions, nucleotides, and other allosteric modulators. This unit reviews the theory of receptor binding and explains how to analyze experimental data. Since binding data are usually best analyzed using nonlinear regression, this unit also explains the principles of curve fitting with nonlinear regression.

  15. Mediaeval manuscript bindings

    Directory of Open Access Journals (Sweden)

    Jedert Vodopivec

    1999-01-01

    Full Text Available The present article represents an excerpt from the final chapters of the research study titled "The development of structures in mediaeval manuscript bindings - interdependence with conservatory methods". In it, aims, methods of work, archive and library materials used and directions for conservatory methods are presented. Besides, the research study includes also a historcial overview of book bindings, detailed analysis of separate structural elements in Slovenian mediaeval bindings, comprehensive presentation of separate structures, the techniques of binding and materials of the preserved mediaeval bindings in Slovenian public archives and libraries, terminological dictionary of specific professional terms related to binding as a segment of a book, and a catalogue of all analysed bindings, containing a survey of ajI detectable data, sketches,graphite prints and photographs.

  16. Ureaplasma urealyticum binds mannose-binding lectin.

    Science.gov (United States)

    Benstein, Barbara D; Ourth, Donald D; Crouse, Dennis T; Shanklin, D Radford

    2004-10-01

    Mannose-binding C-type lectin (MBL) is an important component of innate immunity in mammals. Mannose-binding lectin (MBL), an acute phase protein, acts as an opsonin for phagocytosis and also activates the mannan-binding lectin complement pathway. It may play a particularly significant role during infancy before adequate specific protection can be provided by the adaptive immune system. Ureaplasma urealyticum has been linked to several diseases including pneumonia and chronic lung disease (CLD) in premature infants. We therefore investigated the ability of U. urealyticum to bind MBL. A guinea pig IgG anti-rabbit-MBL antiserum was produced. An immunoblot (dot-blot) assay done on nitrocellulose membrane determined that the anti-MBL antibody had specificity against both rabbit and human MBL. Pure cultures of U. urealyticum, serotype 3, were used to make slide preparations. The slides containing the organisms were then incubated with nonimmune rabbit serum containing MBL. Ureaplasma was shown to bind rabbit MBL with an immunocytochemical assay using the guinea pig IgG anti-rabbit MBL antiserum. Horseradish peroxidase (HRP)-labeled anti-guinea pig IgG was used to localize the reaction. The anti-MBL antiserum was also used in an immunocytochemical assay to localize U. urealyticum in histological sections of lungs from mice specifically infected with this organism. The same method also indicated binding of MBL by ureaplasma in human lung tissue obtained at autopsy from culture positive infants. Our results demonstrate that ureaplasma has the capacity to bind MBL. The absence of MBL may play a role in the predisposition of diseases related to this organism.

  17. Ligand binding mechanics of maltose binding protein.

    Science.gov (United States)

    Bertz, Morten; Rief, Matthias

    2009-11-13

    In the past decade, single-molecule force spectroscopy has provided new insights into the key interactions stabilizing folded proteins. A few recent studies probing the effects of ligand binding on mechanical protein stability have come to quite different conclusions. While some proteins seem to be stabilized considerably by a bound ligand, others appear to be unaffected. Since force acts as a vector in space, it is conceivable that mechanical stabilization by ligand binding is dependent on the direction of force application. In this study, we vary the direction of the force to investigate the effect of ligand binding on the stability of maltose binding protein (MBP). MBP consists of two lobes connected by a hinge region that move from an open to a closed conformation when the ligand maltose binds. Previous mechanical experiments, where load was applied to the N and C termini, have demonstrated that MBP is built up of four building blocks (unfoldons) that sequentially detach from the folded structure. In this study, we design the pulling direction so that force application moves the two MBP lobes apart along the hinge axis. Mechanical unfolding in this geometry proceeds via an intermediate state whose boundaries coincide with previously reported MBP unfoldons. We find that in contrast to N-C-terminal pulling experiments, the mechanical stability of MBP is increased by ligand binding when load is applied to the two lobes and force breaks the protein-ligand interactions directly. Contour length measurements indicate that MBP is forced into an open conformation before unfolding even if ligand is bound. Using mutagenesis experiments, we demonstrate that the mechanical stabilization effect is due to only a few key interactions of the protein with its ligand. This work illustrates how varying the direction of the applied force allows revealing important details about the ligand binding mechanics of a large protein.

  18. Protein Binding Pocket Dynamics.

    Science.gov (United States)

    Stank, Antonia; Kokh, Daria B; Fuller, Jonathan C; Wade, Rebecca C

    2016-05-17

    The dynamics of protein binding pockets are crucial for their interaction specificity. Structural flexibility allows proteins to adapt to their individual molecular binding partners and facilitates the binding process. This implies the necessity to consider protein internal motion in determining and predicting binding properties and in designing new binders. Although accounting for protein dynamics presents a challenge for computational approaches, it expands the structural and physicochemical space for compound design and thus offers the prospect of improved binding specificity and selectivity. A cavity on the surface or in the interior of a protein that possesses suitable properties for binding a ligand is usually referred to as a binding pocket. The set of amino acid residues around a binding pocket determines its physicochemical characteristics and, together with its shape and location in a protein, defines its functionality. Residues outside the binding site can also have a long-range effect on the properties of the binding pocket. Cavities with similar functionalities are often conserved across protein families. For example, enzyme active sites are usually concave surfaces that present amino acid residues in a suitable configuration for binding low molecular weight compounds. Macromolecular binding pockets, on the other hand, are located on the protein surface and are often shallower. The mobility of proteins allows the opening, closing, and adaptation of binding pockets to regulate binding processes and specific protein functionalities. For example, channels and tunnels can exist permanently or transiently to transport compounds to and from a binding site. The influence of protein flexibility on binding pockets can vary from small changes to an already existent pocket to the formation of a completely new pocket. Here, we review recent developments in computational methods to detect and define binding pockets and to study pocket dynamics. We introduce five

  19. Python bindings for libcloudph++

    OpenAIRE

    Jarecka, Dorota; Arabas, Sylwester; Del Vento, Davide

    2015-01-01

    This technical note introduces the Python bindings for libcloudph++. The libcloudph++ is a C++ library of algorithms for representing atmospheric cloud microphysics in numerical models. The bindings expose the complete functionality of the library to the Python users. The bindings are implemented using the Boost.Python C++ library and use NumPy arrays. This note includes listings with Python scripts exemplifying the use of selected library components. An example solution for using the Python ...

  20. DNS & Bind Cookbook

    CERN Document Server

    Liu, Cricket

    2011-01-01

    The DNS & BIND Cookbook presents solutions to the many problems faced by network administrators responsible for a name server. Following O'Reilly's popular problem-and-solution cookbook format, this title is an indispensable companion to DNS & BIND, 4th Edition, the definitive guide to the critical task of name server administration. The cookbook contains dozens of code recipes showing solutions to everyday problems, ranging from simple questions, like, "How do I get BIND?" to more advanced topics like providing name service for IPv6 addresses. It's full of BIND configuration files that yo

  1. Python bindings for libcloudph++

    CERN Document Server

    Jarecka, Dorota; Del Vento, Davide

    2015-01-01

    This technical note introduces the Python bindings for libcloudph++. The libcloudph++ is a C++ library of algorithms for representing atmospheric cloud microphysics in numerical models. The bindings expose the complete functionality of the library to the Python users. The bindings are implemented using the Boost.Python C++ library and use NumPy arrays. This note includes listings with Python scripts exemplifying the use of selected library components. An example solution for using the Python bindings to access libcloudph++ from Fortran is presented.

  2. On Binding Domains

    NARCIS (Netherlands)

    Everaert, M.B.H.

    2005-01-01

    In this paper I want to explore reasons for replacing Binding Theory based on the anaphor-pronoun dichotomy by a Binding Theory allowing more domains restricting/defining anaphoric dependencies. This will, thus, have consequences for the partitioning of anaphoric elements, presupposing more types of

  3. Melanin-binding radiopharmaceuticals

    Energy Technology Data Exchange (ETDEWEB)

    Packer, S; Fairchild, R G; Watts, K P; Greenberg, D; Hannon, S J

    1980-01-01

    The scope of this paper is limited to an analysis of the factors that are important to the relationship of radiopharmaceuticals to melanin. While the authors do not attempt to deal with differences between melanin-binding vs. melanoma-binding, a notable variance is assumed. (PSB)

  4. DNS BIND Server Configuration

    Directory of Open Access Journals (Sweden)

    Radu MARSANU

    2011-01-01

    Full Text Available After a brief presentation of the DNS and BIND standard for Unix platforms, the paper presents an application which has a principal objective, the configuring of the DNS BIND 9 server. The general objectives of the application are presented, follow by the description of the details of designing the program.

  5. Thermodynamics of fragment binding.

    Science.gov (United States)

    Ferenczy, György G; Keserű, György M

    2012-04-23

    The ligand binding pockets of proteins have preponderance of hydrophobic amino acids and are typically within the apolar interior of the protein; nevertheless, they are able to bind low complexity, polar, water-soluble fragments. In order to understand this phenomenon, we analyzed high resolution X-ray data of protein-ligand complexes from the Protein Data Bank and found that fragments bind to proteins with two near optimal geometry H-bonds on average. The linear extent of the fragment binding site was found not to be larger than 10 Å, and the H-bonding region was found to be restricted to about 5 Å on average. The number of conserved H-bonds in proteins cocrystallized with multiple different fragments is also near to 2. These fragment binding sites that are able to form limited number of strong H-bonds in a hydrophobic environment are identified as hot spots. An estimate of the free-energy gain of H-bond formation versus apolar desolvation supports that fragment sized compounds need H-bonds to achieve detectable binding. This suggests that fragment binding is mostly enthalpic that is in line with their observed binding thermodynamics documented in Isothermal Titration Calorimetry (ITC) data sets and gives a thermodynamic rationale for fragment based approaches. The binding of larger compounds tends to more rely on apolar desolvation with a corresponding increase of the entropy content of their binding free-energy. These findings explain the reported size-dependence of maximal available affinity and ligand efficiency both behaving differently in the small molecule region featured by strong H-bond formation and in the larger molecule region featured by apolar desolvation.

  6. Operational amplifiers

    CERN Document Server

    Dostal, Jiri

    1993-01-01

    This book provides the reader with the practical knowledge necessary to select and use operational amplifier devices. It presents an extensive treatment of applications and a practically oriented, unified theory of operational circuits.Provides the reader with practical knowledge necessary to select and use operational amplifier devices. Presents an extensive treatment of applications and a practically oriented, unified theory of operational circuits

  7. The biotin repressor: thermodynamic coupling of corepressor binding, protein assembly, and sequence-specific DNA binding.

    Science.gov (United States)

    Streaker, Emily D; Gupta, Aditi; Beckett, Dorothy

    2002-12-03

    The Escherichia coli biotin repressor, an allosteric transcriptional regulator, is activated for binding to the biotin operator by the small molecule biotinyl-5'-AMP. Results of combined thermodynamic, kinetic, and structural studies of the protein have revealed that corepressor binding results in disorder to order transitions in the protein monomer that facilitate tighter dimerization. The enhanced stability of the dimer leads to stabilization of the resulting biotin repressor-biotin operator complex. It is not clear, however, that the allosteric response in the system is transmitted solely through the protein-protein interface. In this work, the allosteric mechanism has been quantitatively probed by measuring the biotin operator binding and dimerization properties of three biotin repressor species: the apo or unliganded form, the biotin-bound form, and the holo or bio-5'-AMP-bound form. Comparisons of the pairwise differences in the bioO binding and dimerization energetics for the apo and holo species reveal that the enhanced DNA binding energetics resulting from adenylate binding track closely with the enhanced assembly energetics. However, when the results for repressor pairs that include the biotin-bound species are compared, no such equivalence is observed.

  8. SHBG (Sex Hormone Binding Globulin)

    Science.gov (United States)

    ... as: Testosterone-estrogen Binding Globulin; TeBG Formal name: Sex Hormone Binding Globulin Related tests: Testosterone , Free Testosterone, ... I should know? How is it used? The sex hormone binding globulin (SHBG) test may be used ...

  9. Supramolecular electron transfer by anion binding.

    Science.gov (United States)

    Fukuzumi, Shunichi; Ohkubo, Kei; D'Souza, Francis; Sessler, Jonathan L

    2012-10-11

    Anion binding has emerged as an attractive strategy to construct supramolecular electron donor-acceptor complexes. In recent years, the level of sophistication in the design of these systems has advanced to the point where it is possible to create ensembles that mimic key aspects of the photoinduced electron-transfer events operative in the photosynthetic reaction centre. Although anion binding is a reversible process, kinetic studies on anion binding and dissociation processes, as well as photoinduced electron-transfer and back electron-transfer reactions in supramolecular electron donor-acceptor complexes formed by anion binding, have revealed that photoinduced electron transfer and back electron transfer occur at time scales much faster than those associated with anion binding and dissociation. This difference in rates ensures that the linkage between electron donor and acceptor moieties is maintained over the course of most forward and back electron-transfer processes. A particular example of this principle is illustrated by electron-transfer ensembles based on tetrathiafulvalene calix[4]pyrroles (TTF-C4Ps). In these ensembles, the TTF-C4Ps act as donors, transferring electrons to various electron acceptors after anion binding. Competition with non-redox active substrates is also observed. Anion binding to the pyrrole amine groups of an oxoporphyrinogen unit within various supramolecular complexes formed with fullerenes also results in acceleration of the photoinduced electron-transfer process but deceleration of the back electron transfer; again, this is ascribed to favourable structural and electronic changes. Anion binding also plays a role in stabilizing supramolecular complexes between sulphonated tetraphenylporphyrin anions ([MTPPS](4-): M = H(2) and Zn) and a lithium ion encapsulated C(60) (Li(+)@C(60)); the resulting ensemble produces long-lived charge-separated states upon photoexcitation of the porphyrins.

  10. Operational calculus

    CERN Document Server

    Boehme, Thomas K

    1987-01-01

    Operational Calculus, Volume II is a methodical presentation of operational calculus. An outline of the general theory of linear differential equations with constant coefficients is presented. Integral operational calculus and advanced topics in operational calculus, including locally integrable functions and convergence in the space of operators, are also discussed. Formulas and tables are included.Comprised of four sections, this volume begins with a discussion on the general theory of linear differential equations with constant coefficients, focusing on such topics as homogeneous and non-ho

  11. Operating systems

    CERN Document Server

    Tsichritzis, Dionysios C; Rheinboldt, Werner

    1974-01-01

    Operating Systems deals with the fundamental concepts and principles that govern the behavior of operating systems. Many issues regarding the structure of operating systems, including the problems of managing processes, processors, and memory, are examined. Various aspects of operating systems are also discussed, from input-output and files to security, protection, reliability, design methods, performance evaluation, and implementation methods.Comprised of 10 chapters, this volume begins with an overview of what constitutes an operating system, followed by a discussion on the definition and pr

  12. CARBOHYDRATE-CONTAINING COMPOUNDS WHICH BIND TO CARBOHYDRATE BINDING RECEPTORS

    DEFF Research Database (Denmark)

    1995-01-01

    Carbohydrate-containing compounds which contain saccharides or derivatives thereof and which bind to carbohydrate binding receptors are useful in pharmaceutical products for treatment of inflammatory diseases and other diseases.......Carbohydrate-containing compounds which contain saccharides or derivatives thereof and which bind to carbohydrate binding receptors are useful in pharmaceutical products for treatment of inflammatory diseases and other diseases....

  13. Schwartz operators

    Science.gov (United States)

    Keyl, M.; Kiukas, J.; Werner, R. F.

    2016-05-01

    In this paper, we introduce Schwartz operators as a non-commutative analog of Schwartz functions and provide a detailed discussion of their properties. We equip them, in particular, with a number of different (but equivalent) families of seminorms which turns the space of Schwartz operators into a Fréchet space. The study of the topological dual leads to non-commutative tempered distributions which are discussed in detail as well. We show, in particular, that the latter can be identified with a certain class of quadratic forms, therefore making operations like products with bounded (and also some unbounded) operators and quantum harmonic analysis available to objects which are otherwise too singular for being a Hilbert space operator. Finally, we show how the new methods can be applied by studying operator moment problems and convergence properties of fluctuation operators.

  14. Transition Operators

    CERN Document Server

    Alcock-Zeilinger, Judith

    2016-01-01

    In this paper, we give a generic algorithm of the transition operators between Hermitian Young projection operators corresponding to equivalent irreducible representations of SU(N), using the compact expressions of Hermitian Young projection operators derived in a companion paper. We show that the Hermitian Young projection operators together with their transition operators constitute a fully orthogonal basis for the algebra of invariants of $V^{\\otimes m}$ that exhibits a systematically simplified multiplication table. We discuss the full algebra of invariants over $V^{\\otimes 3}$ and $V^{\\otimes 4}$ as explicit examples. In our presentation we make use of various standard concepts such as Young projection operators, Clebsch-Gordan operators, and invariants (in birdtrack notation). We tie these perspectives together and use them to shed light on each other.

  15. Spacecraft operations

    CERN Document Server

    Sellmaier, Florian; Schmidhuber, Michael

    2015-01-01

    The book describes the basic concepts of spaceflight operations, for both, human and unmanned missions. The basic subsystems of a space vehicle are explained in dedicated chapters, the relationship of spacecraft design and the very unique space environment are laid out. Flight dynamics are taught as well as ground segment requirements. Mission operations are divided into preparation including management aspects, execution and planning. Deep space missions and space robotic operations are included as special cases. The book is based on a course held at the German Space Operation Center (GSOC).

  16. Terms of Binding

    NARCIS (Netherlands)

    Sevcenco, A.

    2006-01-01

    The present dissertation aimed at achieving two goals. First, it constitutes an attempt to widen the search for phenomena that bear relevance to the idea that binding has a syntactic residue and is not, therefore, an exclusively semantic matter. Second, it tried to provide the technical means to acc

  17. Cellulose binding domain proteins

    Science.gov (United States)

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc; Doi, Roy

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  18. MD-2 binds cholesterol.

    Science.gov (United States)

    Choi, Soo-Ho; Kim, Jungsu; Gonen, Ayelet; Viriyakosol, Suganya; Miller, Yury I

    2016-02-19

    Cholesterol is a structural component of cellular membranes, which is transported from liver to peripheral cells in the form of cholesterol esters (CE), residing in the hydrophobic core of low-density lipoprotein. Oxidized CE (OxCE) is often found in plasma and in atherosclerotic lesions of subjects with cardiovascular disease. Our earlier studies have demonstrated that OxCE activates inflammatory responses in macrophages via toll-like receptor-4 (TLR4). Here we demonstrate that cholesterol binds to myeloid differentiation-2 (MD-2), a TLR4 ancillary molecule, which is a binding receptor for bacterial lipopolysaccharide (LPS) and is indispensable for LPS-induced TLR4 dimerization and signaling. Cholesterol binding to MD-2 was competed by LPS and by OxCE-modified BSA. Furthermore, soluble MD-2 in human plasma and MD-2 in mouse atherosclerotic lesions carried cholesterol, the finding supporting the biological significance of MD-2 cholesterol binding. These results help understand the molecular basis of TLR4 activation by OxCE and mechanisms of chronic inflammation in atherosclerosis.

  19. Binding and Bulgarian

    NARCIS (Netherlands)

    Schürcks-Grozeva, Lilia Lubomirova

    2003-01-01

    In haar proefschrift analyseert Lilia Schürcks de anaforische verschijnselen in de Bulgaarse taal. Het gaat dan om wederkerende aspecten, uitgedrukt bij woorden als ‘zich’ en ‘elkaar’. De situatie in het Bulgaars blijkt moeilijk in te passen in de klassieke Binding Theory van Noam Chomsky. Bron: RUG

  20. Sequential memory: Binding dynamics

    Science.gov (United States)

    Afraimovich, Valentin; Gong, Xue; Rabinovich, Mikhail

    2015-10-01

    Temporal order memories are critical for everyday animal and human functioning. Experiments and our own experience show that the binding or association of various features of an event together and the maintaining of multimodality events in sequential order are the key components of any sequential memories—episodic, semantic, working, etc. We study a robustness of binding sequential dynamics based on our previously introduced model in the form of generalized Lotka-Volterra equations. In the phase space of the model, there exists a multi-dimensional binding heteroclinic network consisting of saddle equilibrium points and heteroclinic trajectories joining them. We prove here the robustness of the binding sequential dynamics, i.e., the feasibility phenomenon for coupled heteroclinic networks: for each collection of successive heteroclinic trajectories inside the unified networks, there is an open set of initial points such that the trajectory going through each of them follows the prescribed collection staying in a small neighborhood of it. We show also that the symbolic complexity function of the system restricted to this neighborhood is a polynomial of degree L - 1, where L is the number of modalities.

  1. Optical binding between dielectric nanowires (Conference Presentation)

    Science.gov (United States)

    Hanna, Simon; Simpson, Stephen H.

    2016-09-01

    Optical binding occurs when micron-sized particles interact through the exchange of scattered photons. It has been observed both in systems of colloidal dielectric particles and between metallic nanoparticles, and can result in the formation of clusters and coupled dynamical behaviour. Optical binding between spherical particles has been studied in some detail, but little work has appeared in the literature to describe binding effects in lower symmetry systems. In the present paper we discuss recent theoretical work and computer simulations of optical binding effects operating between dielectric nanowires in counter propagating beams. The reduction in symmetry from simple spheres introduces new opportunities for binding, including different types of orientational ordering and anisotropies in the spatial arrangements that are possible for the bound particles. Various ordered configurations are possible, including ladder-like structures and oriented lattices. The stability of these structures to thermal perturbations will be discussed. Asymmetric arrangements of the nanowires are also possible, as a consequence of interactions between the nanowires and the underlying counter-propagating laser field. These configurations lead to a diversity of non-conservative effects, including uniform translation in linearly polarised beams and synchronous rotations in circularly polarised beams, suggesting potential applications of such bound structures in micro-machines.

  2. Operation Zeus

    DEFF Research Database (Denmark)

    Laursen, Johnny

    Dette bind redegør for den yderste højrefløj og PET's overvågning af grupperinger og partier inden for dette felt. Undersøgelsen, som er kronologisk og tematisk opbygget, tegner et billede af nazismens og den yderste højrefløjs udvikling fra 1945 til 1989. Der redegøres udførligt for PET's overvå...

  3. Operation REDWING

    Science.gov (United States)

    1956-07-31

    only 16mm cinemascope films would be available after 1 August 1956t Act- tion was taken to modify the screens of the Terrace and Starlite theaters...approximately 900, was in operation throughout the interim and operational period. The Starlite Theater, which seats approximately 600, opened in

  4. OPERATION ASKARI

    African Journals Online (AJOL)

    operation using conventional arms against Swapo Plan, while they were still massed in their .... stationed there was no real threat to our planned operation. the idea was to sow confusion in the minds ...... A four by four transport vehi- cle, based ...

  5. Operational Sequencing

    DEFF Research Database (Denmark)

    Nielsen, Thomas Rosendal; Hustvedt, Kjersti

    2016-01-01

    by Bakhtinian theory, Brian Edmiston developed a solution to this in the 1990s: the principle of ‘dialogic sequencing’. Aiming to escape the conflict between relativism and absolutism, we present an alternative to Edmiston’s approach, based on Niklas Luhmann’s theory of ‘operational closure’: operational...

  6. Business & Operations

    Science.gov (United States)

    Agron, Joe

    2007-01-01

    This article presents an interview with John D. Musso, executive director of the Association of School Business Officials (ASBO) International. Musso talks about trends and issues that will most affect school business and operations in 2007 and beyond. Despite the challenges facing school operations, he believes that the key to being successful at…

  7. Operation crosscheck

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert, F. C.

    1964-11-06

    This report consists of three sections covering the three major areas of Lawrence Livermore Laboratory`s participation in Operation Crosscheck. These areas are: Diagnostic Aircraft; Radiochemical Sampling; and Device Assembly and Handling, Barbers Point. The information contained in these sections has been extracted from Crosscheck post-operation reports.

  8. Operational Amplifiers.

    Science.gov (United States)

    Foxcroft, G. E.

    1986-01-01

    Addresses the introduction of low cost equipment into high school and college physical science classes. Examines the properties of an "ideal" operational amplifier and discusses how it might be used under saturated and non-saturated conditions. Notes the action of a "real" operational amplifier. (TW)

  9. Megalin binds and mediates cellular internalization of folate binding protein

    DEFF Research Database (Denmark)

    Birn, Henrik; Zhai, Xiaoyue; Holm, Jan

    2005-01-01

    Folate is an essential vitamin involved in a number of biological processes. High affinity folate binding proteins (FBPs) exist both as glycosylphosphatidylinositol-linked, membrane associated folate binding proteins and as soluble FBPs in plasma and some secretory fluids such as milk, saliva...... to bind and mediate cellular uptake of FBP. Surface plasmon resonance analysis shows binding of bovine and human milk FBP to immobilized megalin, but not to low density lipoprotein receptor related protein. Binding of (125)I-labeled folate binding protein (FBP) to sections of kidney proximal tubule, known...

  10. Reactor operation

    CERN Document Server

    Shaw, J

    2013-01-01

    Reactor Operation covers the theoretical aspects and design information of nuclear reactors. This book is composed of nine chapters that also consider their control, calibration, and experimentation.The opening chapters present the general problems of reactor operation and the principles of reactor control and operation. The succeeding chapters deal with the instrumentation, start-up, pre-commissioning, and physical experiments of nuclear reactors. The remaining chapters are devoted to the control rod calibrations and temperature coefficient measurements in the reactor. These chapters also exp

  11. Operator programs and operator processes

    NARCIS (Netherlands)

    Bergstra, J.A.; Walters, P.

    2003-01-01

    We define a notion of program which is not a computer program but an operator program: a detailed description of actions performed and decisions taken by a human operator (computer user) performing a task to achieve a goal in a simple setting consisting of that user, one or more computers and a

  12. Operator programs and operator processes

    NARCIS (Netherlands)

    Bergstra, J.A.; Walters, P.

    2003-01-01

    We define a notion of program which is not a computer program but an operator program: a detailed description of actions performed and decisions taken by a human operator (computer user) performing a task to achieve a goal in a simple setting consisting of that user, one or more computers and a work

  13. Pressure locking and thermal binding of gate valves

    Energy Technology Data Exchange (ETDEWEB)

    Kelly, E.M.

    1996-12-01

    Pressure locking and thermal binding represent potential common mode failure mechanisms that can cause safety-related power-operated gate valves to fail in the closed position, thus rendering redundant safety-related systems incapable of performing their safety functions. Supplement 6 to Generic Letter 89-10, {open_quotes}Safety-Related Motor-Operated Gate Valve Testing and Surveillance,{close_quotes} provided an acceptable approach to addressing pressure locking and thermal binding of gate valves. More recently, the NRC has issued Generic Letter 95-07, {open_quotes}Pressure Locking and Thermal Binding of Safety-Related Power-Operated Gate Valves,{close_quotes} to request that licensees take certain actions to ensure that safety-related power-operated gate valves that are susceptible to pressure locking or thermal binding are capable of performing their safety functions within the current licensing bases. Over the past two years, several plants in Region I determined that valves in certain systems were potentially susceptible to pressure locking and thermal binding, and have taken various corrective actions. The NRC Region I Systems Engineering Branch has been actively involved in the inspection of licensee actions in response to the pressure locking and thermal binding issue. Region I continues to maintain an active involvement in this area, including participation with the Office of Nuclear Reactor Regulation in reviewing licensee responses to Generic Letter 95-07.

  14. Net Operations

    Institute of Scientific and Technical Information of China (English)

    蒋昌俊; 吴哲辉

    1992-01-01

    Two kinds of net operations.addition and Cartesian production of P/T nets,are introduced.They are defined on the set of underlying net of P/T systems.The conditions for preserving structural properties of Petri net after these operations are discussed.It is shown that the set of P/T nets forms and Abelian group for net addition operation and the inverse net of a P/T net in usual meaning of net theory is exactly the inverse of this P/T net as an element of the P/T net group;and that the set of P/T nets forms an Abelian ring for net addition and Caresian product operations.

  15. Operable Units

    Data.gov (United States)

    U.S. Environmental Protection Agency — This dataset consists of operable unit data from multiple Superfund sites in U.S. EPA Region 8. These data were acquired from multiple sources at different times and...

  16. Operator theory

    CERN Document Server

    2015-01-01

    A one-sentence definition of operator theory could be: The study of (linear) continuous operations between topological vector spaces, these being in general (but not exclusively) Fréchet, Banach, or Hilbert spaces (or their duals). Operator theory is thus a very wide field, with numerous facets, both applied and theoretical. There are deep connections with complex analysis, functional analysis, mathematical physics, and electrical engineering, to name a few. Fascinating new applications and directions regularly appear, such as operator spaces, free probability, and applications to Clifford analysis. In our choice of the sections, we tried to reflect this diversity. This is a dynamic ongoing project, and more sections are planned, to complete the picture. We hope you enjoy the reading, and profit from this endeavor.

  17. Binding Principles A and B

    Institute of Scientific and Technical Information of China (English)

    陈源

    2014-01-01

    This paper focuses on the discussion of how Binding Principle A and Binding Principe B help with the interpretation of reference in English and Chinese. They are supposedly universal across languages.

  18. Applied Operations Research: Operator's Assistant

    Science.gov (United States)

    Cole, Stuart K.

    2015-01-01

    NASA operates high value critical equipment (HVCE) that requires trouble shooting, periodic maintenance and continued monitoring by Operations staff. The complexity HVCE and information required to maintain and trouble shoot HVCE to assure continued mission success as paper is voluminous. Training on new HVCE is commensurate with the need for equipment maintenance. LaRC Research Directorate has undertaken a proactive research to support Operations staff by initiation of the development and prototyping an electronic computer based portable maintenance aid (Operator's Assistant). This research established a goal with multiple objectives and a working prototype was developed. The research identified affordable solutions; constraints; demonstrated use of commercial off the shelf software; use of the US Coast Guard maintenance solution; NASA Procedure Representation Language; and the identification of computer system strategies; where these demonstrations and capabilities support the Operator, and maintenance. The results revealed validation against measures of effectiveness and overall proved a substantial training and capability sustainment tool. The research indicated that the OA could be deployed operationally at the LaRC Compressor Station with an expectation of satisfactorily results and to obtain additional lessons learned prior to deployment at other LaRC Research Directorate Facilities. The research revealed projected cost and time savings.

  19. Carboplatin binding to histidine

    Energy Technology Data Exchange (ETDEWEB)

    Tanley, Simon W. M. [University of Manchester, Brunswick Street, Manchester M13 9PL (United Kingdom); Diederichs, Kay [University of Konstanz, D-78457 Konstanz (Germany); Kroon-Batenburg, Loes M. J. [Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands); Levy, Colin [University of Manchester, 131 Princess Street, Manchester M1 7DN (United Kingdom); Schreurs, Antoine M. M. [Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands); Helliwell, John R., E-mail: john.helliwell@manchester.ac.uk [University of Manchester, Brunswick Street, Manchester M13 9PL (United Kingdom)

    2014-08-29

    An X-ray crystal structure showing the binding of purely carboplatin to histidine in a model protein has finally been obtained. This required extensive crystallization trials and various novel crystal structure analyses. Carboplatin is a second-generation platinum anticancer agent used for the treatment of a variety of cancers. Previous X-ray crystallographic studies of carboplatin binding to histidine (in hen egg-white lysozyme; HEWL) showed the partial conversion of carboplatin to cisplatin owing to the high NaCl concentration used in the crystallization conditions. HEWL co-crystallizations with carboplatin in NaBr conditions have now been carried out to confirm whether carboplatin converts to the bromine form and whether this takes place in a similar way to the partial conversion of carboplatin to cisplatin observed previously in NaCl conditions. Here, it is reported that a partial chemical transformation takes place but to a transplatin form. Thus, to attempt to resolve purely carboplatin binding at histidine, this study utilized co-crystallization of HEWL with carboplatin without NaCl to eliminate the partial chemical conversion of carboplatin. Tetragonal HEWL crystals co-crystallized with carboplatin were successfully obtained in four different conditions, each at a different pH value. The structural results obtained show carboplatin bound to either one or both of the N atoms of His15 of HEWL, and this particular variation was dependent on the concentration of anions in the crystallization mixture and the elapsed time, as well as the pH used. The structural details of the bound carboplatin molecule also differed between them. Overall, the most detailed crystal structure showed the majority of the carboplatin atoms bound to the platinum centre; however, the four-carbon ring structure of the cyclobutanedicarboxylate moiety (CBDC) remained elusive. The potential impact of the results for the administration of carboplatin as an anticancer agent are described.

  20. Operational Circulars

    CERN Multimedia

    2003-01-01

    Operational Circular N° 4 - April 2003 Conditions for use by members of the CERN personnel of vehicles belonging to or rented by CERN - This circular has been drawn up. Operational Circular N° 5 - October 2000 Use of CERN computing facilities - Further details on the personal use of CERN computing facilities Operational Circular N° 5 and its Subsidiary Rules http://cern.ch/ComputingRules defines the rules for the use of CERN computing facilities. One of the basic principles governing such use is that it must come within the professional duties of the user concerned, as defined by the user's divisional hierarchy. However, personal use of the computing facilities is tolerated or allowed provided : a) It is in compliance with Operational Circular N° 5 and not detrimental to official duties, including those of other users; b) the frequency and duration is limited and there is a negligible use of CERN resources; c) it does not constitute a political, commercial and/or profit-making activity; d) it is not...

  1. Operative links

    DEFF Research Database (Denmark)

    Wistoft, Karen

    2010-01-01

    as networks: second, a semantic perspective on discourses and concepts of health, and, third, a health pedagogical perspective on participation, intervention, and roles. This paper argues for the importance of 'operative links' between different levels in health strategies. It is proposed that such links...

  2. Operation Context

    DEFF Research Database (Denmark)

    Stüben, Henning; Tietjen, Anne

    2006-01-01

    Abstract: This paper seeks to challenge the notion of context from an operational perspective. Can we grasp the forces that shape the complex conditions for an architectural or urban design within the notion of context? By shifting the gaze towards the agency of architecture, contextual analysis...

  3. Evaluation of binding strength depending on the adhesive binding methods

    Directory of Open Access Journals (Sweden)

    Suzana Pasanec Preprotić

    2015-05-01

    Full Text Available A book with a personal value is worth remembering since it represents specific interests of an individual - author of the book. Therefore the original is the first issue of a book which is always bound manually. Due to cost-effectiveness, adhesive binding is most commonly used in author’s edition in paperback and hardback. Adhesive binding methods differ only if a paper leaf is a binding unit in adhesive binding form. The subject of the research is the quality of book block binding for two binding methods with/without mull fabric. The assumption is that double-fan adhesive binding method shows an extraordinary binding quality as compared to the rough spine method. For the needs of this research book block parameters remained unaltered: paper type, size and book volume. The results related to strength were obtained by using an experimental method of tensile strength for individual paper leaves. The rating of book block quality was conducted in accordance with FOGRA Nr.71006 guidelines for page pull-test. Furthermore, strength results for both methods were compared in order to evaluate the importance of changing the quality of adhesive binding. Statistical method ANOVA analysis of variance and Fisher’s F-test were used to evaluate the quality of book block binding.

  4. Your Lung Operation: After Your Operation

    Medline Plus

    Full Text Available ... Surgeons Education Patients and Family Skills Programs Your Lung Operation Your Lung Operation DVD After Your Operation Back to Your Lung Operation Your Lung Operation DVD Welcome Your Lung ...

  5. Operation Poorman

    Energy Technology Data Exchange (ETDEWEB)

    Pruvost, N.; Tsitouras, J.

    1981-03-18

    The objectives of Operation Poorman were to design and build a portable seismic system and to set up and use this system in a cold-weather environment. The equipment design uses current technology to achieve a low-power, lightweight system that is configured into three modules. The system was deployed in Alaska during wintertime, and the results provide a basis for specifying a mission-ready seismic verification system.

  6. Joint Operations

    Science.gov (United States)

    2006-09-17

    Unified Task Force (UNITAF) Somalia was formed with forces from France, Italy, Canada, Belgium, Egypt , Turkey, Saudi Arabia, and the United States...military presence, open-source intelligence ( OSINT ) may be the best immediately available information to prepare US forces to operate in a foreign...country. OSINT from radio broadcasts, newspapers, and periodicals often provide tip-offs for HUMINT and other intelligence and information collection

  7. Analytic QCD Binding Potentials

    CERN Document Server

    Fried, H M; Grandou, T; Sheu, Y -M

    2011-01-01

    This paper applies the analytic forms of a recent non-perturbative, manifestly gauge- and Lorentz-invariant description (of the exchange of all possible virtual gluons between quarks ($Q$) and/or anti-quarks ($\\bar{Q}$) in a quenched, eikonal approximation) to extract analytic forms for the binding potentials generating a model $Q$-$\\bar{Q}$ "pion", and a model $QQQ$ "nucleon". Other, more complicated $Q$, $\\bar{Q}$ contributions to such color-singlet states may also be identified analytically. An elementary minimization technique, relevant to the ground states of such bound systems, is adopted to approximate the solutions to a more proper, but far more complicated Schroedinger/Dirac equation; the existence of possible contributions to the pion and nucleon masses due to spin, angular momentum, and "deformation" degrees of freedom is noted but not pursued. Neglecting electromagnetic and weak interactions, this analysis illustrates how the one new parameter making its appearance in this exact, realistic formali...

  8. Identification of consensus binding sites clarifies FMRP binding determinants.

    Science.gov (United States)

    Anderson, Bart R; Chopra, Pankaj; Suhl, Joshua A; Warren, Stephen T; Bassell, Gary J

    2016-08-19

    Fragile X mental retardation protein (FMRP) is a multifunctional RNA-binding protein with crucial roles in neuronal development and function. Efforts aimed at elucidating how FMRP target mRNAs are selected have produced divergent sets of target mRNA and putative FMRP-bound motifs, and a clear understanding of FMRP's binding determinants has been lacking. To clarify FMRP's binding to its target mRNAs, we produced a shared dataset of FMRP consensus binding sequences (FCBS), which were reproducibly identified in two published FMRP CLIP sequencing datasets. This comparative dataset revealed that of the various sequence and structural motifs that have been proposed to specify FMRP binding, the short sequence motifs TGGA and GAC were corroborated, and a novel TAY motif was identified. In addition, the distribution of the FCBS set demonstrates that FMRP preferentially binds to the coding region of its targets but also revealed binding along 3' UTRs in a subset of target mRNAs. Beyond probing these putative motifs, the FCBS dataset of reproducibly identified FMRP binding sites is a valuable tool for investigating FMRP targets and function. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. Suspended Operations

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    A ship from China’s State Oceanic Administration (SOA) evaluates ConocoPhillips’s clean-up efforts in the Bohai Bay on September 2.That day, the SOA ordered the U.S. oil giant to cease all operations on the Penglai 19-3 Oilfield after the company failed to plug leaks in the oilfield by the administration’s August 31 deadline.The oil leaking from the oilfield caused by ConocoPhillips at the Penglai 19-3 Oilfield in the Bohai Bay was first spotted in June. The oil has since spread to beaches in China’s Hebei and Liaoning provinces, causing huge losses in the provinces’ tourism and aquatic farming industries.On September 7, ConocoPhillips said it will establish a fund to compensate victims of the oil spill in line with Chinese laws and to benefit the general environment of the Bohai Bay.

  10. SUMO-1 possesses DNA binding activity

    Directory of Open Access Journals (Sweden)

    Wieruszeski Jean-Michel

    2010-05-01

    Full Text Available Abstract Background Conjugation of small ubiquitin-related modifiers (SUMOs is a frequent post-translational modification of proteins. SUMOs can also temporally associate with protein-targets via SUMO binding motifs (SBMs. Protein sumoylation has been identified as an important regulatory mechanism especially in the regulation of transcription and the maintenance of genome stability. The precise molecular mechanisms by which SUMO conjugation and association act are, however, not understood. Findings Using NMR spectroscopy and protein-DNA cross-linking experiments, we demonstrate here that SUMO-1 can specifically interact with dsDNA in a sequence-independent fashion. We also show that SUMO-1 binding to DNA can compete with other protein-DNA interactions at the example of the regulatory domain of Thymine-DNA Glycosylase and, based on these competition studies, estimate the DNA binding constant of SUMO1 in the range 1 mM. Conclusion This finding provides an important insight into how SUMO-1 might exert its activity. SUMO-1 might play a general role in destabilizing DNA bound protein complexes thereby operating in a bottle-opener way of fashion, explaining its pivotal role in regulating the activity of many central transcription and DNA repair complexes.

  11. Binding Energy and Enzymatic Catalysis.

    Science.gov (United States)

    Hansen, David E.; Raines, Ronald T.

    1990-01-01

    Discussed is the fundamental role that the favorable free energy of binding of the rate-determining transition state plays in catalysis. The principle that all of the catalytic factors discussed are realized by the use of this binding energy is reviewed. (CW)

  12. Competing binding of metal ions with protein studied by microdialysis

    Institute of Scientific and Technical Information of China (English)

    GUO; Ming(郭明); KONG; Liang(孔亮); MAO; Xiqin(毛希琴); LI; Xin(历欣); ZOU; Hanfa(邹汉法)

    2002-01-01

    A method has been established to study the competing binding of metal ions with protein by a combined technique of microdialysis with high performance liquid chromatography (HPLC). Ni2+, Cd2+, Zn2+, Cu2+ and human serum albumin (HSA) were chosen as model metal ions and protein. The experimental results show that Ni2+ and Cu2+ share a common primary binding site on HSA, and Zn2+ and Cd2+ share a different common primary binding site from them, but there is a common multi-metal binding site for all of those four metal ions. This method show advantages of fast sampling, easily to be operated and especially to be useful when ideal spectroscopic probes are not available for the study of interaction between protein and metal ions.

  13. Use of binding enthalpy to drive an allosteric transition.

    Science.gov (United States)

    Brown, Patrick H; Beckett, Dorothy

    2005-03-01

    The Escherichia coli biotin repressor is an allosteric DNA binding protein and is activated by the small molecule bio-5'-AMP. Binding of this small molecule promotes transcription repression complex assembly between the repressor and the biotin operator of the biotin biosynthetic operon. The ability of the adenylate to activate the assembly process reflects its effect on biotin repressor dimerization. Thus concomitant with small molecule binding the free energy of repressor dimerization becomes more favorable by approximately -4 kcal/mol. The structural, dynamic, and energetic changes in the repressor monomer that accompany allosteric activation are not known. In this work the thermodynamics of binding of four allosteric activators to the repressor have been characterized by isothermal titration calorimetry. While binding of two of the effectors results in relatively modest activation of the dimerization process, binding of the other two small molecules, including the physiological effector, leads to large changes in repressor dimerization energetics. Results of the calorimetric measurements indicate that strong effector binding is accompanied by an enthalpically costly transition in the protein. This transition is "paid for" by the enthalpy that would have otherwise been realized from the formation of noncovalent bonds between the ligand and repressor monomer.

  14. Characterization of 6-mercaptopurine binding to bovine serum albumin and its displacement from the binding sites by quercetin and rutin

    Energy Technology Data Exchange (ETDEWEB)

    Ehteshami, Mehdi [Nutrition Research Center, School of Health and Nutrition, Tabriz University of Medical Sciences, Tabriz 51644-14766 (Iran, Islamic Republic of); Rasoulzadeh, Farzaneh [Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz 51644-14766 (Iran, Islamic Republic of); Mahboob, Soltanali [Nutrition Research Center, School of Health and Nutrition, Tabriz University of Medical Sciences, Tabriz 51644-14766 (Iran, Islamic Republic of); Rashidi, Mohammad-Reza, E-mail: rashidi@tbzmed.ac.ir [Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz 51644-14766 (Iran, Islamic Republic of)

    2013-03-15

    Binding of a drug to the serum albumins as major serum transport proteins can be influenced by other ligands leading to alteration of its pharmacological properties. In the present study, binding characteristics of 6-mercaptopurine (6-MP) with bovine serum albumin (BSA) together with its displacement from its binding site by quercetin and rutin have been investigated by the spectroscopic method. According to the binding parameters, a static quenching component in overall dynamic quenching process is operative in the interaction between 6-MP and BSA. The binding of 6-MP to BSA occurred spontaneously due to entropy-driven hydrophobic interactions. The synchronous fluorescence spectroscopy study revealed that the secondary structure of BSA is changed in the presence of 6-MP and both Tyr and Trp residues participate in the interaction between 6-MP and BSA with the later one being more dominant. The binding constant value of 6-MP-BSA in the presence of quercetin and rutin increased. 6-MP was displaced by ibuprofen indicating that the binding site of 6-MP on albumin is site II. Therefore, the change of the pharmacokinetic and pharmacodynamic properties of 6-MP by quercetin and rutin through alteration of binding capacity of 6-MP to the serum albumin cannot be ruled out. In addition, the displacement study showed that 6-MP is located in site II of BSA. - Highlights: Black-Right-Pointing-Pointer Participation of both Tyr and particularly Trp residues in the interaction between 6-MP and BSA. Black-Right-Pointing-Pointer Involvement of a static quenching component in an overall dynamic quenching process. Black-Right-Pointing-Pointer Ability of quercetin and rutin to change the binding constants of 6-MP-BSA complex. Black-Right-Pointing-Pointer Binding of 6-MP to BSA through entropy-driven hydrophobic interactions.

  15. Cooperative binding: a multiple personality.

    Science.gov (United States)

    Martini, Johannes W R; Diambra, Luis; Habeck, Michael

    2016-06-01

    Cooperative binding has been described in many publications and has been related to or defined by several different properties of the binding behavior of the ligand to the target molecule. In addition to the commonly used Hill coefficient, other characteristics such as a sigmoidal shape of the overall titration curve in a linear plot, a change of ligand affinity of the other binding sites when a site of the target molecule becomes occupied, or complex roots of the binding polynomial have been used to define or to quantify cooperative binding. In this work, we analyze how the different properties are related in the most general model for binding curves based on the grand canonical partition function and present several examples which highlight differences between the cooperativity characterizing properties which are discussed. Our results mainly show that among the presented definitions there are not two which fully coincide. Moreover, this work poses the question whether it can make sense to distinguish between positive and negative cooperativity based on the macroscopic binding isotherm only. This article shall emphasize that scientists who investigate cooperative effects in biological systems could help avoiding misunderstandings by stating clearly which kind of cooperativity they discuss.

  16. The Accountability Bind

    Directory of Open Access Journals (Sweden)

    Katrina Bulkley

    2001-10-01

    Full Text Available Charter schools involve a trading of autonomy for accountability. This accountability comes through two forces—markets through the choices of parents and students, and accountability to government through the writing of contracts that must be renewed for schools to continue to operate. Charter schools are supposed to be more accountable for educational performance than traditional public schools because authorizers have the ability to revoke charter contracts. Here, I focus on one central component of accountability to government: performance accountability or accountability for educational outcomes to charter school authorizers through the revocation or non-renewal of charter contracts. In this paper, I suggest that contract-based accountability for educational performance in charter schools may not be working as proponents argued it would. This article explores some explanations for why there are very few examples of charter schools that have been closed primarily because of failure to demonstrate educational performance or improvement. Future work will need to test if these challenges for authorizers hold in a variety of contexts. The conclusion examines the implications of these findings for the future of charter school accountability.

  17. Asymmetric cation-binding catalysis

    DEFF Research Database (Denmark)

    Oliveira, Maria Teresa; Lee, Jiwoong

    2017-01-01

    and KCN, are selectively bound to the catalyst, providing exceptionally high enantioselectivities for kinetic resolutions, elimination reactions (fluoride base), and Strecker synthesis (cyanide nucleophile). Asymmetric cation-binding catalysis was recently expanded to silicon-based reagents, enabling...... solvents, thus increasing their applicability in synthesis. The expansion of this concept to chiral polyethers led to the emergence of asymmetric cation-binding catalysis, where chiral counter anions are generated from metal salts, particularly using BINOL-based polyethers. Alkali metal salts, namely KF...

  18. Your Lung Operation: After Your Operation

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  20. Operator theory, operator algebras and applications

    CERN Document Server

    Lebre, Amarino; Samko, Stefan; Spitkovsky, Ilya

    2014-01-01

    This book consists of research papers that cover the scientific areas of the International Workshop on Operator Theory, Operator Algebras and Applications, held in Lisbon in September 2012. The volume particularly focuses on (i) operator theory and harmonic analysis (singular integral operators with shifts; pseudodifferential operators, factorization of almost periodic matrix functions; inequalities; Cauchy type integrals; maximal and singular operators on generalized Orlicz-Morrey spaces; the Riesz potential operator; modification of Hadamard fractional integro-differentiation), (ii) operator algebras (invertibility in groupoid C*-algebras; inner endomorphisms of some semi group, crossed products; C*-algebras generated by mappings which have finite orbits; Folner sequences in operator algebras; arithmetic aspect of C*_r SL(2); C*-algebras of singular integral operators; algebras of operator sequences) and (iii) mathematical physics (operator approach to diffraction from polygonal-conical screens; Poisson geo...

  1. Your Lung Operation: After Your Operation

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  2. Influence of binding pH and protein solubility on the dynamic binding capacity in hydrophobic interaction chromatography.

    Science.gov (United States)

    Baumann, Pascal; Baumgartner, Kai; Hubbuch, Jürgen

    2015-05-29

    Hydrophobic interaction chromatography (HIC) is one of the most frequently used purification methods in biopharmaceutical industry. A major drawback of HIC, however, is the rather low dynamic binding capacity (DBC) obtained when compared to e.g. ion exchange chromatography (IEX). The typical purification procedure for HIC includes binding at neutral pH, independently of the proteins nature and isoelectric point. Most approaches to process intensification are based on resin and salt screenings. In this paper a combination of protein solubility data and varying binding pH leads to a clear enhancement of dynamic binding capacity. This is shown for three proteins of acidic, neutral, and alkaline isoelectric points. High-throughput solubility screenings as well as miniaturized and parallelized breakthrough curves on Media Scout RoboColumns (Atoll, Germany) were conducted at pH 3-10 on a fully automated robotic workstation. The screening results show a correlation between the DBC and the operational pH, the protein's isoelectric point and the overall solubility. Also, an inverse relationship of DBC in HIC and the binding kinetics was observed. By changing the operational pH, the DBC could be increased up to 30% compared to the standard purification procedure performed at neutral pH. As structural changes of the protein are reported during HIC processes, the applied samples and the elution fractions were proven not to be irreversibly unfolded. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Ion binding to biological macromolecules.

    Science.gov (United States)

    Petukh, Marharyta; Alexov, Emil

    2014-11-01

    Biological macromolecules carry out their functions in water and in the presence of ions. The ions can bind to the macromolecules either specifically or non-specifically, or can simply to be a part of the water phase providing physiological gradient across various membranes. This review outlines the differences between specific and non-specific ion binding in terms of the function and stability of the corresponding macromolecules. Furthermore, the experimental techniques to identify ion positions and computational methods to predict ion binding are reviewed and their advantages compared. It is indicated that specifically bound ions are relatively easier to be revealed while non-specifically associated ions are difficult to predict. In addition, the binding and the residential time of non-specifically bound ions are very much sensitive to the environmental factors in the cells, specifically to the local pH and ion concentration. Since these characteristics differ among the cellular compartments, the non-specific ion binding must be investigated with respect to the sub-cellular localization of the corresponding macromolecule.

  4. The prion protein binds thiamine.

    Science.gov (United States)

    Perez-Pineiro, Rolando; Bjorndahl, Trent C; Berjanskii, Mark V; Hau, David; Li, Li; Huang, Alan; Lee, Rose; Gibbs, Ebrima; Ladner, Carol; Dong, Ying Wei; Abera, Ashenafi; Cashman, Neil R; Wishart, David S

    2011-11-01

    Although highly conserved throughout evolution, the exact biological function of the prion protein is still unclear. In an effort to identify the potential biological functions of the prion protein we conducted a small-molecule screening assay using the Syrian hamster prion protein [shPrP(90-232)]. The screen was performed using a library of 149 water-soluble metabolites that are known to pass through the blood-brain barrier. Using a combination of 1D NMR, fluorescence quenching and surface plasmon resonance we identified thiamine (vitamin B1) as a specific prion ligand with a binding constant of ~60 μM. Subsequent studies showed that this interaction is evolutionarily conserved, with similar binding constants being seen for mouse, hamster and human prions. Various protein construct lengths, both with and without the unstructured N-terminal region in the presence and absence of copper, were examined. This indicates that the N-terminus has no influence on the protein's ability to interact with thiamine. In addition to thiamine, the more biologically abundant forms of vitamin B1 (thiamine monophosphate and thiamine diphosphate) were also found to bind the prion protein with similar affinity. Heteronuclear NMR experiments were used to determine thiamine's interaction site, which is located between helix 1 and the preceding loop. These data, in conjunction with computer-aided docking and molecular dynamics, were used to model the thiamine-binding pharmacophore and a comparison with other thiamine binding proteins was performed to reveal the common features of interaction.

  5. Cholesterol binding to ion channels

    Directory of Open Access Journals (Sweden)

    Irena eLevitan

    2014-02-01

    Full Text Available Numerous studies demonstrated that membrane cholesterol is a major regulator of ion channel function. The goal of this review is to discuss significant advances that have been recently achieved in elucidating the mechanisms responsible for cholesterol regulation of ion channels. The first major insight that comes from growing number of studies that based on the sterol specificity of cholesterol effects, show that several types of ion channels (nAChR, Kir, BK, TRPV are regulated by specific sterol-protein interactions. This conclusion is supported by demonstrating direct saturable binding of cholesterol to a bacterial Kir channel. The second major advance in the field is the identification of putative cholesterol binding sites in several types of ion channels. These include sites at locations associated with the well-known cholesterol binding motif CRAC and its reversed form CARC in nAChR, BK, and TRPV, as well as novel cholesterol binding regions in Kir channels. Notably, in the majority of these channels, cholesterol is suggested to interact mainly with hydrophobic residues in non-annular regions of the channels being embedded in between transmembrane protein helices. We also discuss how identification of putative cholesterol binding sites is an essential step to understand the mechanistic basis of cholesterol-induced channel regulation. Clearly, however, these are only the first few steps in obtaining a general understanding of cholesterol-ion channels interactions and their roles in cellular and organ functions.

  6. Electrochemical binding and wiring in battery materials

    Energy Technology Data Exchange (ETDEWEB)

    Pejovnik, S. [National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana (Slovenia); Faculty of Chemistry and Chemical Technology, Askerceva 5, SI-1000 Ljubljana (Slovenia); Dominko, R.; Bele, M.; Gaberscek, M.; Jamnik, J. [National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana (Slovenia)

    2008-10-01

    Binders in battery electrodes not only provide mechanical cohesiveness during battery operation but can also affect the electrode properties via the surface modification. Using atomic force microscopy (AFM), we study the surface structuring of three binders: polyvinylidene fluoride (PVdF), carboxymethyl cellulose (CMC) and gelatin. We try to find correlation between the observed structures and the measured electrochemical charge-discharge characteristics. We further measure the binding ability of gelatin adsorbed from solutions of different pHs. While the best binding ability of gelatin is obtained at pH about 9, the least polarization is observed at pH 12. Both properties are explained based on the observed gelatin structuring as a function of pH. In the second part of this study, gelatin is used as a surface agent that dictates the organization of nanometre-sized carbon black particles around micrometre-sized cathodic active particles. Using microcontact impedance measurements on polished pellets we show that using gelatin-forced carbon black deposition the average electronic resistance around LiMn{sub 2}O{sub 4} particles is decreased by more than two orders of magnitude. We believe that it is this decrease in resistance that improves significantly the rate performance of various cathode materials, such as LiMn{sub 2}O{sub 4} and LiCoO{sub 2}. (author)

  7. Galectin-3-Binding and Metastasis

    Science.gov (United States)

    Nangia-Makker, Pratima; Balan, Vitaly; Raz, Avraham

    2013-01-01

    i. Summary Galectin-3 is a member of a family of carbohydrate-binding proteins. It is present in the nucleus, the cytoplasm and also extracellular matrix of many normal and neoplastic cell types. Arrays of reports show an upregulation of this protein in transformed and metastatic cell lines (1, 2). Moreover, in many human carcinomas, an increased expression of galectin-3 correlates with progressive tumor stages (3–6). Several lines of analysis have demonstrated that the galectins participate in cell-cell and cell-matrix interactions by recognizing and binding complimentary glycoconjugates and thereby play a crucial role in normal and pathological processes. Elevated expression of the protein is associated with an increased capacity for anchorage-independent growth, homotypic aggregation, and tumor cell lung colonization (7–9). In this chapter we describe the methods of purification of galectin-3 from transformed E. coli and some of the commonly used functional assays for analyzing galectin-3 binding. PMID:22674139

  8. Computational Prediction of RNA-Binding Proteins and Binding Sites

    Directory of Open Access Journals (Sweden)

    Jingna Si

    2015-11-01

    Full Text Available Proteins and RNA interaction have vital roles in many cellular processes such as protein synthesis, sequence encoding, RNA transfer, and gene regulation at the transcriptional and post-transcriptional levels. Approximately 6%–8% of all proteins are RNA-binding proteins (RBPs. Distinguishing these RBPs or their binding residues is a major aim of structural biology. Previously, a number of experimental methods were developed for the determination of protein–RNA interactions. However, these experimental methods are expensive, time-consuming, and labor-intensive. Alternatively, researchers have developed many computational approaches to predict RBPs and protein–RNA binding sites, by combining various machine learning methods and abundant sequence and/or structural features. There are three kinds of computational approaches, which are prediction from protein sequence, prediction from protein structure, and protein-RNA docking. In this paper, we review all existing studies of predictions of RNA-binding sites and RBPs and complexes, including data sets used in different approaches, sequence and structural features used in several predictors, prediction method classifications, performance comparisons, evaluation methods, and future directions.

  9. Computational Prediction of RNA-Binding Proteins and Binding Sites.

    Science.gov (United States)

    Si, Jingna; Cui, Jing; Cheng, Jin; Wu, Rongling

    2015-01-01

    Proteins and RNA interaction have vital roles in many cellular processes such as protein synthesis, sequence encoding, RNA transfer, and gene regulation at the transcriptional and post-transcriptional levels. Approximately 6%-8% of all proteins are RNA-binding proteins (RBPs). Distinguishing these RBPs or their binding residues is a major aim of structural biology. Previously, a number of experimental methods were developed for the determination of protein-RNA interactions. However, these experimental methods are expensive, time-consuming, and labor-intensive. Alternatively, researchers have developed many computational approaches to predict RBPs and protein-RNA binding sites, by combining various machine learning methods and abundant sequence and/or structural features. There are three kinds of computational approaches, which are prediction from protein sequence, prediction from protein structure, and protein-RNA docking. In this paper, we review all existing studies of predictions of RNA-binding sites and RBPs and complexes, including data sets used in different approaches, sequence and structural features used in several predictors, prediction method classifications, performance comparisons, evaluation methods, and future directions.

  10. Synthetic heparin-binding growth factor analogs

    Science.gov (United States)

    Pena, Louis A.; Zamora, Paul; Lin, Xinhua; Glass, John D.

    2007-01-23

    The invention provides synthetic heparin-binding growth factor analogs having at least one peptide chain that binds a heparin-binding growth factor receptor, covalently bound to a hydrophobic linker, which is in turn covalently bound to a non-signaling peptide that includes a heparin-binding domain. The synthetic heparin-binding growth factor analogs are useful as soluble biologics or as surface coatings for medical devices.

  11. Workshop on gate valve pressure locking and thermal binding

    Energy Technology Data Exchange (ETDEWEB)

    Brown, E.J.

    1995-07-01

    The purpose of the Workshop on Gate Valve Pressure Locking and Thermal Binding was to discuss pressure locking and thermal binding issues that could lead to inoperable gate valves in both boiling water and pressurized water reactors. The goal was to foster exchange of information to develop the technical bases to understand the phenomena, identify the components that are susceptible, discuss actual events, discuss the safety significance, and illustrate known corrective actions that can prevent or limit the occurrence of pressure locking or thermal binding. The presentations were structured to cover U.S. Nuclear Regulatory Commission staff evaluation of operating experience and planned regulatory activity; industry discussions of specific events, including foreign experience, and efforts to determine causes and alleviate the affects; and valve vendor experience and recommended corrective action. The discussions indicated that identifying valves susceptible to pressure locking and thermal binding was a complex process involving knowledge of components, systems, and plant operations. The corrective action options are varied and straightforward.

  12. Cellulose binding domain fusion proteins

    Science.gov (United States)

    Shoseyov, Oded; Shpiegl, Itai; Goldstein, Marc A.; Doi, Roy H.

    1998-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  13. Bacterial oligopeptide-binding proteins.

    Science.gov (United States)

    Monnet, V

    2003-10-01

    This review focuses on bacterial oligopeptide-binding proteins, which form part of the oligopeptide transport system belonging to the ATP-binding cassette family of transporters. Depending on the bacterial species, these binding proteins (OppA) capture peptides ranging in size from 2 to 18 amino acids from the environment and pass them on to the other components of the oligopeptide transport system for internalisation. Bacteria have developed several strategies to produce these binding proteins, which are periplasmic in Gram- bacteria and membrane-anchored in Gram+, with a higher stoichiometry (probably necessary for efficient transport) than the other components in the transport system. The expression of OppA-encoding genes is clearly modulated by external factors, especially nitrogen compounds, but the mechanisms of regulation are not always clear. The best-understood roles played by OppAs are internalisation of peptides for nutrition and recycling of muropeptides. It has, however, recently become clear that OppAs are also involved in sensing the external medium via specific or non-specific peptides.

  14. Genome-Wide Motif Statistics are Shaped by DNA Binding Proteins over Evolutionary Time Scales

    Science.gov (United States)

    Qian, Long; Kussell, Edo

    2016-10-01

    The composition of a genome with respect to all possible short DNA motifs impacts the ability of DNA binding proteins to locate and bind their target sites. Since nonfunctional DNA binding can be detrimental to cellular functions and ultimately to organismal fitness, organisms could benefit from reducing the number of nonfunctional DNA binding sites genome wide. Using in vitro measurements of binding affinities for a large collection of DNA binding proteins, in multiple species, we detect a significant global avoidance of weak binding sites in genomes. We demonstrate that the underlying evolutionary process leaves a distinct genomic hallmark in that similar words have correlated frequencies, a signal that we detect in all species across domains of life. We consider the possibility that natural selection against weak binding sites contributes to this process, and using an evolutionary model we show that the strength of selection needed to maintain global word compositions is on the order of point mutation rates. Likewise, we show that evolutionary mechanisms based on interference of protein-DNA binding with replication and mutational repair processes could yield similar results and operate with similar rates. On the basis of these modeling and bioinformatic results, we conclude that genome-wide word compositions have been molded by DNA binding proteins acting through tiny evolutionary steps over time scales spanning millions of generations.

  15. Your Lung Operation: After Your Operation

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  16. Your Lung Operation: After Your Operation

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  17. Your Lung Operation: After Your Operation

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  18. Protein binding assay for hyaluronate

    Energy Technology Data Exchange (ETDEWEB)

    Lacy, B.E.; Underhill, C.B.

    1986-11-01

    A relatively quick and simple assay for hyaluronate was developed using the specific binding protein, hyaluronectin. The hyaluronectin was obtained by homogenizing the brains of Sprague-Dawley rats, and then centrifuging the homogenate. The resulting supernatant was used as a source of crude hyaluronectin. In the binding assay, the hyaluronectin was mixed with (/sup 3/H)hyaluronate, followed by an equal volume of saturated (NH/sub 4/)/sub 2/SO/sub 4/, which precipitated the hyaluronectin and any (/sup 3/H)hyaluronate associated with it, but left free (/sup 3/H)hyaluronate in solution. The mixture was then centrifuged, and the amount of bound (/sup 3/H)hyaluronate in the precipitate was determined. Using this assay, the authors found that hyaluronectin specifically bound hyaluronate, since other glycosaminoglycans failed to compete for the binding protein. In addition, the interaction between hyaluronectin and hyaluronate was of relatively high affinity, and the size of the hyaluronate did not appear to substantially alter the amount of binding. To determine the amount of hyaluronate in an unknown sample, they used a competition assay in which the binding of a set amount of (/sup 3/H)hyaluronate was blocked by the addition of unlabeled hyaluronate. By comparing the degree of competition of the unknown samples with that of known amounts of hyaluronate, it was possible to determine the amount of hyaluronate in the unknowns. They have found that this method is sensitive to 1 ..mu..g or less of hyaluronate, and is unaffected by the presence of proteins.

  19. Intelligence service binding architecture for interoperability between home network devices

    Institute of Scientific and Technical Information of China (English)

    Seung-Ryun Lee; Dae-Ho Bae; Soon Ju Kang

    2007-01-01

    Existing home devices in home network provides only independent services limited on a homogeneous protocol and/or do not fully support an intelligent service provided by cooperating among heterogeneous protocol devices. This paper proposes an intelligent and integrated service binding architecture which allow the users to figure out the status of devices and to cooperate among home network devices regardless of supported protocols or operational characteristics.

  20. Poly-infix operators and operator families

    OpenAIRE

    Bergstra, Jan A.; Ponse, Alban

    2015-01-01

    Poly-infix operators and operator families are introduced as an alternative for working modulo associativity and the corresponding bracket deletion convention. Poly-infix operators represent the basic intuition of repetitively connecting an ordered sequence of entities with the same connecting primitive.

  1. Space station operations management

    Science.gov (United States)

    Cannon, Kathleen V.

    1989-01-01

    Space Station Freedom operations management concepts must be responsive to the unique challenges presented by the permanently manned international laboratory. Space Station Freedom will be assembled over a three year period where the operational environment will change as significant capability plateaus are reached. First Element Launch, Man-Tended Capability, and Permanent Manned Capability, represent milestones in operational capability that is increasing toward mature operations capability. Operations management concepts are being developed to accomodate the varying operational capabilities during assembly, as well as the mature operational environment. This paper describes operations management concepts designed to accomodate the uniqueness of Space Station Freedoom, utilizing tools and processes that seek to control operations costs.

  2. Human plasminogen binding protein tetranectin

    DEFF Research Database (Denmark)

    Kastrup, J S; Rasmussen, H; Nielsen, B B;

    1997-01-01

    The recombinant human plasminogen binding protein tetranectin (TN) and the C-type lectin CRD of this protein (TN3) have been crystallized. TN3 crystallizes in the tetragonal space group P4(2)2(1)2 with cell dimensions a = b = 64.0, c = 75.7 A and with one molecule per asymmetric unit. The crystals...... to at least 2.5 A. A full data set has been collected to 3.0 A. The asymmetric unit contains one monomer of TN. Molecular replacement solutions for TN3 and TN have been obtained using the structure of the C-type lectin CRD of rat mannose-binding protein as search model. The rhombohedral space group indicates...

  3. Probing protein phosphatase substrate binding

    DEFF Research Database (Denmark)

    Højlys-Larsen, Kim B.; Sørensen, Kasper Kildegaard; Jensen, Knud Jørgen;

    2012-01-01

    Proteomics and high throughput analysis for systems biology can benefit significantly from solid-phase chemical tools for affinity pull-down of proteins from complex mixtures. Here we report the application of solid-phase synthesis of phosphopeptides for pull-down and analysis of the affinity...... around the phosphorylated residue are important for the binding affinity of ILKAP. We conclude that solid-phase affinity pull-down of proteins from complex mixtures can be applied in phosphoproteomics and systems biology....

  4. BINDING ISOTHERMS SURFACTANT-PROTEINS

    Directory of Open Access Journals (Sweden)

    Elena Irina Moater

    2011-12-01

    Full Text Available The interactions between surfactants and proteins shows some similarities with interactions between surfactants and polymers, but the hydrophobic amphoteric nature of proteins and their secondary and tertiary structure components make them different from conventional polymer systems. Many studies from the past about surfactant - proteins bonding used the dialysis techniques. Other techniques used to determine the binding isotherm, included ultrafiltration, ultracentrifugation, potentiometry, ion-selective electrode method and surface tension. High affinity isotherms which are typical of an anionic surfactant - protein bonding, exhibit an initial increase steep followed by a slow growth region and then a vertical growth above a certain concentration. This isotherm is typical of ionic surfactant to protein binding. Often the high affinity initial bond appears at very low concentrations of surfactant and therefore in some protein-surfactant systems, the exact shape of the isotherm in this region may be missing. The surfactant - protein binding is influenced by a number of variables such as the nature and chain length of surfactant, pH, ionic strength, temperature, nature of this protein and additives.

  5. Anion binding in biological systems

    Energy Technology Data Exchange (ETDEWEB)

    Feiters, Martin C [Department of Organic Chemistry, Institute for Molecules and Materials, Faculty of Science, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen (Netherlands); Meyer-Klaucke, Wolfram [EMBL Hamburg Outstation at DESY, Notkestrasse 85, D-22607 Hamburg (Germany); Kostenko, Alexander V; Soldatov, Alexander V [Faculty of Physics, Southern Federal University, Sorge 5, Rostov-na-Donu, 344090 (Russian Federation); Leblanc, Catherine; Michel, Gurvan; Potin, Philippe [Centre National de la Recherche Scientifique and Universite Pierre et Marie Curie Paris-VI, Station Biologique de Roscoff, Place Georges Teissier, BP 74, F-29682 Roscoff cedex, Bretagne (France); Kuepper, Frithjof C [Scottish Association for Marine Science, Dunstaffnage Marine Laboratory, Oban, Argyll PA37 1QA, Scotland (United Kingdom); Hollenstein, Kaspar; Locher, Kaspar P [Institute of Molecular Biology and Biophysics, ETH Zuerich, Schafmattstrasse 20, Zuerich, 8093 (Switzerland); Bevers, Loes E; Hagedoorn, Peter-Leon; Hagen, Wilfred R, E-mail: m.feiters@science.ru.n [Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft (Netherlands)

    2009-11-15

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L{sub 3} (2p{sub 3/2}) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  6. Anion binding in biological systems

    Science.gov (United States)

    Feiters, Martin C.; Meyer-Klaucke, Wolfram; Kostenko, Alexander V.; Soldatov, Alexander V.; Leblanc, Catherine; Michel, Gurvan; Potin, Philippe; Küpper, Frithjof C.; Hollenstein, Kaspar; Locher, Kaspar P.; Bevers, Loes E.; Hagedoorn, Peter-Leon; Hagen, Wilfred R.

    2009-11-01

    We compare aspects of biological X-ray absorption spectroscopy (XAS) studies of cations and anions, and report on some examples of anion binding in biological systems. Brown algae such as Laminaria digitata (oarweed) are effective accumulators of I from seawater, with tissue concentrations exceeding 50 mM, and the vanadate-containing enzyme haloperoxidase is implicated in halide accumulation. We have studied the chemical state of iodine and its biological role in Laminaria at the I K edge, and bromoperoxidase from Ascophyllum nodosum (knotted wrack) at the Br K edge. Mo is essential for many forms of life; W only for certain archaea, such as Archaeoglobus fulgidus and the hyperthermophilic archaeon Pyrococcus furiosus, and some bacteria. The metals are bound and transported as their oxo-anions, molybdate and tungstate, which are similar in size. The transport protein WtpA from P. furiosus binds tungstate more strongly than molybdate, and is related in sequence to Archaeoglobus fulgidus ModA, of which a crystal structure is known. We have measured A. fulgidus ModA with tungstate at the W L3 (2p3/2) edge, and compared the results with the refined crystal structure. XAS studies of anion binding are feasible even if only weak interactions are present, are biologically relevant, and give new insights in the spectroscopy.

  7. Animal Feeding Operations

    Science.gov (United States)

    ... What's this? Submit Button Healthy Water Home Animal Feeding Operations Recommend on Facebook Tweet Share Compartir On ... Concentrated Animal Feeding Operations (CAFOs) What are Animal Feeding Operations (AFOs)? According to the United States Environmental ...

  8. Engineering cofactor and ligand binding in an artificial neuroglobin

    Science.gov (United States)

    Zhang, Lei

    HP-7 is one artificial mutated oxygen transport protein, which operates via a mechanism akin to human neuroglobin and cytoglobin. This protein destabilizes one of two heme-ligating histidine residues by coupling histidine side chain ligation with the burial of three charged glutamate residues on the same helix. Replacement of these glutamate residues with alanine, which has a neutral hydrophobicity, slows gaseous ligand binding 22-fold, increases the affinity of the distal histidine ligand by a factor of thirteen, and decreases the binding affinity of carbon monoxide, a nonreactive oxygen analogue, three-fold. Paradoxically, it also decreases heme binding affinity by a factor of three in the reduced state and six in the oxidized state. Application of a two-state binding model, in which an initial pentacoordinate binding event is followed by a protein conformational change to hexacoordinate, provides insight into the mechanism of this seemingly counterintuitive result: the initial pentacoordinate encounter complex is significantly destabilized by the loss of the glutamate side chains, and the increased affinity for the distal histidine only partially compensates. These results point to the importance of considering each oxidation and conformational state in the design of functional artificial proteins. We have also examined the effects these mutations have on function. The K d of the nonnreactive oxygen analogue carbon monoxide (CO) is only decreased three-fold, despite the large increase in distal histidine affinity engendered by the 22-fold decrease in the histidine ligand off-rate. This is a result of the four-fold increase in affinity for CO binding to the pentacoordinate state. Oxygen binds to HP7 with a Kd of 117 µM, while the mutant rapidly oxidizes when exposed to oxygen. EPR analysis of both ferric hemoproteins demonstrates that the mutation increases disorder at the heme binding site. NMR-detected deuterium exchange demonstrates that the mutation causes a

  9. Saxton Transportation Operations Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — The Saxton Transportation Operations Laboratory (Saxton Laboratory) is a state-of-the-art facility for conducting transportation operations research. The laboratory...

  10. Foreign Operation Methods

    DEFF Research Database (Denmark)

    Welch, Lawrence S.; Benito, Gabriel R. G.; Petersen, Bent

    Introduction and theory -- Introduction -- Theoretical approaches -- Modes of operation -- Franchising -- Licensing -- Management contracts -- International subcontracting -- Project operations -- Exports -- Alliances -- Foreign direct investment -- Strategies -- Mode switching and stretching...

  11. Foreign Operation Methods

    DEFF Research Database (Denmark)

    Welch, Lawrence S.; Benito, Gabriel R. G.; Petersen, Bent

    Introduction and theory -- Introduction -- Theoretical approaches -- Modes of operation -- Franchising -- Licensing -- Management contracts -- International subcontracting -- Project operations -- Exports -- Alliances -- Foreign direct investment -- Strategies -- Mode switching and stretching...

  12. Nilpotent operators similar to irreducible operators

    Institute of Scientific and Technical Information of China (English)

    JIANG; Chunlan

    2001-01-01

    [1]Halmos, P. R., A Hilbert Space Problem Book, Princeton, New Jersey: D Van Nostrand, 1967.[2]Halmos, P. R., Irreducible operators, Mich. Math. J., 1968, 15: 215—223.[3]Voiculescu, D., A non-commutative Weyl-Von Neuwann theorem, Rev. Roum. Math. Pures et, 1976, Appl. 21: 97—113.[4]Gilfeather, F., Strong reducibility of operators., Indiana Univ. Math. J., 1972, 22: 393—397.[5]Jiang, Z. J., Sun, S. L., On completely irreducible operators, Acta Sci. Natur. Univ. Jilin (in Chinese), 1992, 4: 20—29.[6]Fong, C. K., Jiang, C. L., Normal operators similar to irreducible operators, Acta Math. Sinica, New series, 1994, 10: 192—205.[7]Jiang, C. L., Li, X., The irreducible decomposition of Cowen-Douglas operators and operator weighted shifts, Acta Sci. Math. (Szeged), 2000, 48: 1—18.[8]Jiang, C. L., Wu, P. Y., Sums of strongly irreducible operator, Houston. J. Math., 1998, 24: 467—481.[9]Davidson, K. R., Herrero, D. A., The Jordan form of a bitriangular operator., J. Funct. Anal., 1990, 94: 27—73.[10]Herrero, D. A., Approximation of Hilbert Space Operators Research Notes in Math 224, Harlow, Essex: Longman, 1990.[11]Jiang Chunlan, Wang Zongyao, Strongly irreducible operators on Hilbert space, Research Notes in Math 389, Harlow, Essex: Longman, 1998.[12]Tosio Kato, Perturbation Theory for Linear Operators, Berlin, Heidelberg, New York, Tokyo: Springer-Verlag, 1984.

  13. Engineering RNA-binding proteins for biology

    OpenAIRE

    Chen,Yu; Varani, Gabriele

    2013-01-01

    RNA-binding proteins play essential roles in the regulation of gene expression. Many have modular structures and combine relatively few common domains in various arrangements to recognize RNA sequences and/or structures. Recent progress in engineering the specificity of the PUF class RNA-binding proteins has shown that RNA-binding domains may be combined with various effector or functional domains to regulate the metabolism of targeted RNAs. Designer RNA-binding proteins with tailored sequenc...

  14. Rat Mannose-Binding Protein A Binds CD14

    OpenAIRE

    Chiba, Hirofumi; Sano, Hitomi; Iwaki, Daisuke; Murakami, Seiji; Mitsuzawa, Hiroaki; Takahashi, Toru; Konishi, Masanori; Takahashi, Hiroki; Kuroki, Yoshio

    2001-01-01

    Lipopolysaccharide (LPS) has been known to induce inflammation by interacting with CD14, which serves as a receptor for LPS. Mannose-binding protein (MBP) belongs to the collectin subgroup of the C-type lectin superfamily, along with surfactant proteins SP-A and SP-D. We have recently demonstrated that SP-A modulates LPS-induced cellular responses by interaction with CD14 (H. Sano, H. Sohma, T. Muta, S. Nomura, D. R. Voelker, and Y. Kuroki, J. Immunol. 163:387–395, 2000) and that SP-D also in...

  15. Feature-Based Binding and Phase Theory

    Science.gov (United States)

    Antonenko, Andrei

    2012-01-01

    Current theories of binding cannot provide a uniform account for many facts associated with the distribution of anaphors, such as long-distance binding effects and the subject-orientation of monomorphemic anaphors. Further, traditional binding theory is incompatible with minimalist assumptions. In this dissertation I propose an analysis of…

  16. Comparison and correlation of binding mode of ATP in the kinase domains of Hexokinase family

    Science.gov (United States)

    Kumar, Yellapu Nanda; Kumar, Pasupuleti Santhosh; Sowjenya, Gopal; Rao, Valasani Koteswara; Yeswanth, Sthanikam; Prasad, Uppu Venkateswara; Pradeepkiran, Jangampalli Adi; Sarma, PVGK; Bhaskar, Matcha

    2012-01-01

    Hexokinases (HKs) are the enzymes that catalyses the ATP dependent phosphorylation of Hexose sugars to Hexose-6-Phosphate (Hex-6-P). There exist four different forms of HKs namely HK-I, HK-II, HK-III and HK-IV and all of them share a common ATP binding site core surrounded by more variable sequence that determine substrate affinities. Although they share a common binding site but they differ in their kinetic functions, hence the present study is aimed to analyze the binding mode of ATP. The analysis revealed that the four ATP binding domains are showing 13 identical, 7 similar and 6 dissimilar residues with similar structural conformation. Molecular docking of ATP into the kinase domains using Molecular Operating Environment (MOE) soft ware tool clearly showed the variation in the binding mode of ATP with variable docking scores. This probably explains the variable phosphorylation rates among hexokinases family. PMID:22829728

  17. A method for evaluating pressure locking and thermal binding of gate valves

    Energy Technology Data Exchange (ETDEWEB)

    Dogan, T.

    1996-12-01

    A method is described to evaluate the susceptibility of gate valves to pressure locking and thermal binding. Binding of the valve disc in the closed position due to high pressure water trapped in the bonnet cavity (pressure locking) or differential thermal expansion of the disk in the seat (thermal binding) represents a potential mechanism that can prevent safety-related systems from functioning when called upon. The method described here provides a general equation that can be applied to a given gate valve design and set of operating conditions to determine the susceptibility of the valve to fail due to disc binding. The paper is organized into three parts. The first part discusses the physical mechanisms that cause disc binding. The second part describes the mathematical equations. The third part discusses the conclusions.

  18. Detection of Binding Site Molecular Interaction Field Similarities.

    Science.gov (United States)

    Chartier, Matthieu; Najmanovich, Rafael

    2015-08-24

    Protein binding-site similarity detection methods can be used to predict protein function and understand molecular recognition, as a tool in drug design for drug repurposing and polypharmacology, and for the prediction of the molecular determinants of drug toxicity. Here, we present IsoMIF, a method able to identify binding site molecular interaction field similarities across protein families. IsoMIF utilizes six chemical probes and the detection of subgraph isomorphisms to identify geometrically and chemically equivalent sections of protein cavity pairs. The method is validated using six distinct data sets, four of those previously used in the validation of other methods. The mean area under the receiver operator curve (AUC) obtained across data sets for IsoMIF is higher than those of other methods. Furthermore, while IsoMIF obtains consistently high AUC values across data sets, other methods perform more erratically across data sets. IsoMIF can be used to predict function from structure, to detect potential cross-reactivity or polypharmacology targets, and to help suggest bioisosteric replacements to known binding molecules. Given that IsoMIF detects spatial patterns of molecular interaction field similarities, its predictions are directly related to pharmacophores and may be readily translated into modeling decisions in structure-based drug design. IsoMIF may in principle detect similar binding sites with distinct amino acid arrangements that lead to equivalent interactions within the cavity. The source code to calculate and visualize MIFs and MIF similarities are freely available.

  19. Biodiscovery of Aluminum Binding Peptides

    Science.gov (United States)

    2013-08-01

    for an additional 35-45 min. After induction, 5 µL cells were added to 25µL 250 nM YPet-Mona for 45 min. on ice. Cells were then pelleted and...binding mechanism of phage particles displaying a constrained heptapeptide with specific affinity to SiO2 and TiO2 ," Anal. Chem. 78(14), 4872-4879 (2006...hydroxyapatite crystals," Langmuir 27(12), 7620-7628 (2011). [15] Dickerson, M. B. A., et al., Peptide-induced room temperature formation of nanostructured TiO2

  20. Statistics for Transcription Factor Binding Sites

    OpenAIRE

    2008-01-01

    Transcription factors (TFs) play a key role in gene regulation. They interact with specific binding sites or motifs on the DNA sequence and regulate expression of genes downstream of these binding sites. In silico prediction of potential binding of a TF to a binding site is an important task in computational biology. From a statistical point of view, the DNA sequence is a long text consisting of four different letters ('A','C','G', and 'T'). The binding of a TF to the sequence corresponds to ...

  1. Defining Starch Binding by Glucan Phosphatases

    DEFF Research Database (Denmark)

    Auger, Kyle; Raththagala, Madushi; Wilkens, Casper

    2015-01-01

    phosphatases. The main objective of this study was to quantify the binding affinity of different enzymes that are involved in this cyclic process. We established a protocol to quickly, reproducibly, and quantitatively measure the binding of the enzymes to glucans utilizing Affinity Gel Electrophoresis (AGE...... glucan phosphatases showed similar affinities for the short oligosaccharide β-cyclodextrin. We performed structure-guided mutagenesis to define the mechanism of these differences. We found that the carbohydrate binding module (CBM) domain provided a stronger binding affinity compared to surface binding...

  2. Synthetic heparin-binding factor analogs

    Science.gov (United States)

    Pena, Louis A.; Zamora, Paul O.; Lin, Xinhua; Glass, John D.

    2010-04-20

    The invention provides synthetic heparin-binding growth factor analogs having at least one peptide chain, and preferably two peptide chains branched from a dipeptide branch moiety composed of two trifunctional amino acid residues, which peptide chain or chains bind a heparin-binding growth factor receptor and are covalently bound to a non-signaling peptide that includes a heparin-binding domain, preferably by a linker, which may be a hydrophobic linker. The synthetic heparin-binding growth factor analogs are useful as pharmaceutical agents, soluble biologics or as surface coatings for medical devices.

  3. DBD2BS: connecting a DNA-binding protein with its binding sites

    OpenAIRE

    2012-01-01

    By binding to short and highly conserved DNA sequences in genomes, DNA-binding proteins initiate, enhance or repress biological processes. Accurately identifying such binding sites, often represented by position weight matrices (PWMs), is an important step in understanding the control mechanisms of cells. When given coordinates of a DNA-binding domain (DBD) bound with DNA, a potential function can be used to estimate the change of binding affinity after base substitutions, where the changes c...

  4. Infinite sets and double binds.

    Science.gov (United States)

    Arden, M

    1984-01-01

    There have been many attempts to bring psychoanalytical theory up to date. This paper approaches the problem by discussing the work of Gregory Bateson and Ignacio Matte-Blanco, with particular reference to the use made by these authors of Russell's theory of logical types. Bateson's theory of the double bind and Matte-Blanco's bilogic are both based on concepts of logical typing. It is argued that the two theories can be linked by the idea that neurotic symptoms are based on category errors in thinking. Clinical material is presented from the analysis of a middle-aged woman. The intention is to demonstrate that the process of making interpretations can be thought of as revealing errors in thinking. Changes in the patient's inner world are then seen to be the result of clarifying childhood experiences based on category errors. Matte-Blanco's theory of bilogic and infinite experiences is a re-evaluation of the place of the primary process in mental life. It is suggested that a combination of bilogic and double bind theory provides a possibility of reformulating psychoanalytical theory.

  5. Elementary operators on self-adjoint operators

    Science.gov (United States)

    Molnar, Lajos; Semrl, Peter

    2007-03-01

    Let H be a Hilbert space and let and be standard *-operator algebras on H. Denote by and the set of all self-adjoint operators in and , respectively. Assume that and are surjective maps such that M(AM*(B)A)=M(A)BM(A) and M*(BM(A)B)=M*(B)AM*(B) for every pair , . Then there exist an invertible bounded linear or conjugate-linear operator and a constant c[set membership, variant]{-1,1} such that M(A)=cTAT*, , and M*(B)=cT*BT, .

  6. Multisensory Illusions and the Temporal Binding Window

    Directory of Open Access Journals (Sweden)

    Ryan A Stevenson

    2011-10-01

    Full Text Available The ability of our sensory systems to merge sensory information from distinct modalities is remarkable. One stimulus characteristic utilized in this operation is temporal coincidence. Auditory and visual information are integrated within a narrow range of temporal offsets, known as the temporal binding window (TBW, which varies between individuals, stimulus type, and task. In this series of experiments, we assessed the relationship within individuals between the width of their TBW and their ability to integrate audiovisual information. The TBW was measured through a perceived subjective simultaneity task. In conjunction with this, we measured each individual's ability to integrate auditory and visual information with two multisensory illusions, the McGurk effect and Flashbeep illusion. The results from these studies demonstrate that the TBW is highly correlated with the individual's ability to integrate. These relationships were seen in only the right TBW, in which visual presentations preceded auditory presentations, a finding that is ecologically logical. However, differences were seen between the two illusory conditions, where the McGurk effect was stronger in individuals with narrow TBWs, again, an ecologically logical finding. The opposite relationship was seen with flashbeep illusion, possibly due to inherent asynchronies in the illusion.

  7. Glucose Binding Protein as a Novel Optical Glucose Nanobiosensor

    Directory of Open Access Journals (Sweden)

    Majed DWEIK

    2009-11-01

    Full Text Available Development of an in vivo optical sensor requires the utilization of Near Infra Red (NIR fluorophores due to their ability to operate within the biological tissue window. Alexa Fluor 750 (AF750 and Alexa Fluor 680 (AF680 were examined as potential NIR fluorophores for an in vivo fluorescence resonance energy transfer (FRET glucose biosensor. AF680 and AF750 found to be a FRET pair and percent energy transfer was calculated. Next, the tested dye pair was utilized in a competitive binding assay in order to detect glucose. Concanavalin A (Con A and dextran have binding affinity, but in the presence of glucose, glucose displaces dextran due to its higher affinity to Con A than dextran. Finally, the percent signal transfer through porcine skin was examined. The results showed with approximately 4.0 mm porcine skin thickness, 1.98 % of the fluorescence was transmitted and captured by the detector.

  8. Nonlocal Operational Calculi for Dunkl Operators

    Directory of Open Access Journals (Sweden)

    Ivan H. Dimovski

    2009-03-01

    Full Text Available The one-dimensional Dunkl operator $D_k$ with a non-negative parameter $k$, is considered under an arbitrary nonlocal boundary value condition. The right inverse operator of $D_k$, satisfying this condition is studied. An operational calculus of Mikusinski type is developed. In the frames of this operational calculi an extension of the Heaviside algorithm for solution of nonlocal Cauchy boundary value problems for Dunkl functional-differential equations $P(D_ku = f$ with a given polynomial $P$ is proposed. The solution of these equations in mean-periodic functions reduces to such problems. Necessary and sufficient condition for existence of unique solution in mean-periodic functions is found.

  9. Your Lung Operation: After Your Operation

    Medline Plus

    Full Text Available ... Life Support Advanced Trauma Operative Management Basic Endovascular Skills for Trauma Disaster Management and Emergency Preparedness Rural Trauma Team Development Course Trauma Evaluation and Management Trauma CME Nora ...

  10. Your Lung Operation: After Your Operation

    Medline Plus

    Full Text Available ... Online Guide to Choosing a Surgical Residency Practice Management Workshops Patients and Family Patient Education Patient Education ... Trauma Advanced Trauma Life Support Advanced Trauma Operative Management Basic Endovascular Skills for Trauma Disaster Management and ...

  11. Your Lung Operation: After Your Operation

    Medline Plus

    Full Text Available ... Stay Up to Date with ACS Association Management Jobs Events Find a Surgeon Patients and Family Contact My Profile Shop/Donate ( 0 ) Items American College of Surgeons Education Patients and Family Skills Programs Your Lung Operation ...

  12. Your Lung Operation: After Your Operation

    Medline Plus

    Full Text Available ... Online Guide to Choosing a Surgical Residency Practice Management Workshops Patients and Family Patient Education Patient Education ... Trauma Advanced Trauma Life Support Advanced Trauma Operative Management Basic Endovascular Skills for Trauma Disaster Management and ...

  13. Computer algebra and operators

    Science.gov (United States)

    Fateman, Richard; Grossman, Robert

    1989-01-01

    The symbolic computation of operator expansions is discussed. Some of the capabilities that prove useful when performing computer algebra computations involving operators are considered. These capabilities may be broadly divided into three areas: the algebraic manipulation of expressions from the algebra generated by operators; the algebraic manipulation of the actions of the operators upon other mathematical objects; and the development of appropriate normal forms and simplification algorithms for operators and their actions. Brief descriptions are given of the computer algebra computations that arise when working with various operators and their actions.

  14. Renormalization of composite operators

    CERN Document Server

    Polonyi, J

    2001-01-01

    The blocked composite operators are defined in the one-component Euclidean scalar field theory, and shown to generate a linear transformation of the operators, the operator mixing. This transformation allows us to introduce the parallel transport of the operators along the RG trajectory. The connection on this one-dimensional manifold governs the scale evolution of the operator mixing. It is shown that the solution of the eigenvalue problem of the connection gives the various scaling regimes and the relevant operators there. The relation to perturbative renormalization is also discussed in the framework of the $\\phi^3$ theory in dimension $d=6$.

  15. Operating System Security

    CERN Document Server

    Jaeger, Trent

    2008-01-01

    Operating systems provide the fundamental mechanisms for securing computer processing. Since the 1960s, operating systems designers have explored how to build "secure" operating systems - operating systems whose mechanisms protect the system against a motivated adversary. Recently, the importance of ensuring such security has become a mainstream issue for all operating systems. In this book, we examine past research that outlines the requirements for a secure operating system and research that implements example systems that aim for such requirements. For system designs that aimed to

  16. Operation Anaconda. Lessons for Joint Operations

    Science.gov (United States)

    2009-03-01

    joint battle plan and commanded accordingly. For all services, fast-paced joint operations in the information era require well-honed skills that...communications. Accompanying Lessons: To carry out information - era operations, excellent joint communications at all levels are vital, as are...to employ their information - era assets to full advantage. 39 Accompanying Lessons: Modern combat requires great skill and high-speed

  17. Adaptive evolution of transcription factor binding sites

    Directory of Open Access Journals (Sweden)

    Berg Johannes

    2004-10-01

    Full Text Available Abstract Background The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks in the evolution of complex regulatory networks. We study a theoretical model for the sequence evolution of binding sites by point mutations. The approach is based on biophysical models for the binding of transcription factors to DNA. Hence we derive empirically grounded fitness landscapes, which enter a population genetics model including mutations, genetic drift, and selection. Results We show that the selection for factor binding generically leads to specific correlations between nucleotide frequencies at different positions of a binding site. We demonstrate the possibility of rapid adaptive evolution generating a new binding site for a given transcription factor by point mutations. The evolutionary time required is estimated in terms of the neutral (background mutation rate, the selection coefficient, and the effective population size. Conclusions The efficiency of binding site formation is seen to depend on two joint conditions: the binding site motif must be short enough and the promoter region must be long enough. These constraints on promoter architecture are indeed seen in eukaryotic systems. Furthermore, we analyse the adaptive evolution of genetic switches and of signal integration through binding cooperativity between different sites. Experimental tests of this picture involving the statistics of polymorphisms and phylogenies of sites are discussed.

  18. Actin binding proteins and spermiogenesis

    Science.gov (United States)

    Mruk, Dolores D

    2011-01-01

    Drebrin E, an actin-binding protein lacking intrinsic activity in the regulation of actin dynamics (e.g., polymerization, capping, nucleation, branching, cross-linking, bundling and severing), is known to recruit actin regulatory proteins to a specific cellular site. Herein, we critically evaluate recent findings in the field which illustrate that drebrin E works together with two other actin-binding proteins, namely Arp3 (actin-related protein 3, a component of the Arp2/3 complex that simultaneously controls actin nucleation for polymerization and branching of actin filaments) and Eps8 (epidermal growth factor receptor pathway substrate 8 that controls capping of the barbed ends of actin filaments, as well as actin filament bundling) to regulate the homeostasis of F-actin filament bundles at the ectoplasmic specialization (ES), a testis-specific atypical adherens junction (AJ) in the seminiferous epithelium. This is mediated by the strict temporal and spatial expression of these three actin-binding proteins at the apical and basal ES at the Sertoli cell-spermatid (step 8–19) and Sertoli-Sertoli cell interface, respectively, during the seminiferous epithelial cycle of spermatogenesis. In this Commentary, we put forth a possible model by which drebrin E may be acting as a platform upon which proteins (e.g., Arp3) that are needed to alter the conformation of actin filament bundles at the ES can be recruited to the site, thus facilitating changes in cell shape and cell position in the epithelium during spermiogenesis and spermiation. In short, drebrin E may be acting as a “logistic” distribution center to manage different regulatory proteins at the apical ES, thereby regulating the dynamics of actin filament bundles and modulating the plasticity of the apical ES. This would allow adhesion to be altered continuously throughout the epithelial cycle to accommodate spermatid movement in the seminiferous epithelium during spermiogenesis and spermiation. We also

  19. On completely irreducible operators

    Institute of Scientific and Technical Information of China (English)

    JIANG Zejian; SUN Shanli

    2006-01-01

    Let T be a bounded linear operator on Hilbert space H,M an invariant subspace of T.If there exists another invariant subspace N of T such that H=M+N and M ∩ N=0,then M is said to be a completely reduced subspace of T.If T has a nontrivial completely reduced subspace,then T is said to be completely reducible;otherwise T is said to be completely irreducible.In the present paper we briefly sum up works on completely irreducible operators that have been done by the Functional Analysis Seminar of Jilin University in the past ten years and more.The paper contains four sections.In section 1 the background of completely irreducible operators is given in detail.Section 2 shows which operator in some well-known classes of operators,for example,weighted shifts,Toeplitz operators,etc.,is completely irreducible.In section 3 it is proved that every bounded linear operator on the Hilbert space can be approximated by the finite direct sum of completely irreducible operators.It is clear that a completely irreducible operator is a rather suitable analogue of Jordan blocks in L(H),the set of all bounded linear operators on Hilbert space H.In section 4 several questions concerning completely irreducible operators are discussed and it is shown that some properties of completely irreducible operators are different from properties of unicellular operators.

  20. Sex hormone binding globulin phenotypes

    DEFF Research Database (Denmark)

    Cornelisse, M M; Bennett, Patrick; Christiansen, M

    1994-01-01

    Human sex hormone binding globulin (SHBG) is encoded by a normal and a variant allele. The resulting SHBG phenotypes (the homozygous normal SHBG, the heterozygous SHBG and the homozygous variant SHBG phenotype) can be distinguished by their electrophoretic patterns. We developed a novel detection....... This method of detection was used to determine the distribution of SHBG phenotypes in healthy controls of both sexes and in five different pathological conditions characterized by changes in the SHBG level or endocrine disturbances (malignant and benign ovarian neoplasms, hirsutism, liver cirrhosis...... on the experimental values. Differences in SHBG phenotypes do not appear to have any clinical significance and no sex difference was found in the SHBG phenotype distribution....

  1. Gamma Oscillations and Visual Binding

    Science.gov (United States)

    Robinson, Peter A.; Kim, Jong Won

    2006-03-01

    At the root of visual perception is the mechanism the brain uses to analyze features in a scene and bind related ones together. Experiments show this process is linked to oscillations of brain activity in the 30-100 Hz gamma band. Oscillations at different sites have correlation functions (CFs) that often peak at zero lag, implying simultaneous firing, even when conduction delays are large. CFs are strongest between cells stimulated by related features. Gamma oscillations are studied here by modeling mm-scale patchy interconnections in the visual cortex. Resulting predictions for gamma responses to stimuli account for numerous experimental findings, including why oscillations and zero-lag synchrony are associated, observed connections with feature preferences, the shape of the zero-lag peak, and variations of CFs with attention. Gamma waves are found to obey the Schroedinger equation, opening the possibility of cortical analogs of quantum phenomena. Gamma instabilities are tied to observations of gamma activity linked to seizures and hallucinations.

  2. DNA binding hydroxyl radical probes

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Vicky J.; Konigsfeld, Katie M.; Aguilera, Joe A. [Department of Radiology, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0610 (United States); Milligan, Jamie R., E-mail: jmilligan@ucsd.edu [Department of Radiology, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0610 (United States)

    2012-01-15

    The hydroxyl radical is the primary mediator of DNA damage by the indirect effect of ionizing radiation. It is a powerful oxidizing agent produced by the radiolysis of water and is responsible for a significant fraction of the DNA damage associated with ionizing radiation. There is therefore an interest in the development of sensitive assays for its detection. The hydroxylation of aromatic groups to produce fluorescent products has been used for this purpose. We have examined four different chromophores, which produce fluorescent products when hydroxylated. Of these, the coumarin system suffers from the fewest disadvantages. We have therefore examined its behavior when linked to a cationic peptide ligand designed to bind strongly to DNA. - Highlights: > Examined four aromatic groups as a means to detect hydroxyl radicals by fluorescence. > Coumarin system suffers from the fewest disadvantages. > Characterized its reactivity when linked to a hexa-arginine peptide.

  3. Why tight-binding theory?

    Science.gov (United States)

    Harrison, Walter A.

    2002-12-01

    In the context of computational physics other methods are more accurate, but tight-binding theory allows very direct physical interpretation and is simple enough to allow much more realistic treatments beyond the local density approximation. We address several important questions of this last category: How does the gap enhancement from Coulomb correlations vary from material to material? Should the enhanced gap be used for calculating the dielectric constant? For calculating the effective mass in k-dot-p theory? How valid is the scissors approximation? How does one line up bands at an interface? How should we match the envelope function at interfaces in effective-mass theory? Why can the resulting quantum-well states seem to violate the uncertainty principle? How should f-shell electrons be treated when they are intermediate between band-like and core-like? The answers to all of these questions are given and discussed.

  4. Boiler operator's handbook

    CERN Document Server

    Heselton, Ken

    2004-01-01

    Containing key information for operators and managers of large and small plants, this is an indispensable guide for those at advanced and early stages of their careers, as well as for managers interested in reducing operating expenses.

  5. Crew Transportation Operations Standards

    Science.gov (United States)

    Mango, Edward J.; Pearson, Don J. (Compiler)

    2013-01-01

    The Crew Transportation Operations Standards contains descriptions of ground and flight operations processes and specifications and the criteria which will be used to evaluate the acceptability of Commercial Providers' proposed processes and specifications.

  6. Ranking Operations Management Conferences

    NARCIS (Netherlands)

    Steenhuis, Harm-Jan; Bruijn, de Erik Joost; Gupta, Sushil; Laptaned, U.

    2007-01-01

    Several publications have appeared in the field of Operations Management which rank Operations Management related journals. Several ranking systems exist for journals based on , for example, perceived relevance and quality, citation, and author affiliation. Many academics also publish at conferences

  7. Vessel Operator System

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Operator cards are required for any operator of a charter/party boat and or a commercial vessel (including carrier and processor vessels) issued a vessel permit from...

  8. Major operations and activities

    Energy Technology Data Exchange (ETDEWEB)

    Black, D.G.

    1995-06-01

    This section of the 1994 Hanford Site Environmental Report summarizes the major operations and activities on the site. These operations and activities include site management, waste management, environmental restoration and corrective actions, and research and technology development.

  9. Synthetic LPS-Binding Polymer Nanoparticles

    Science.gov (United States)

    Jiang, Tian

    Lipopolysaccharide (LPS), one of the principal components of most gram-negative bacteria's outer membrane, is a type of contaminant that can be frequently found in recombinant DNA products. Because of its strong and even lethal biological effects, selective LPS removal from bioproducts solution is of particular importance in the pharmaceutical and health care industries. In this thesis, for the first time, a proof-of-concept study on preparing LPS-binding hydrogel-like NPs through facile one-step free-radical polymerization was presented. With the incorporation of various hydrophobic (TBAm), cationic (APM, GUA) monomers and cross-linkers (BIS, PEG), a small library of NPs was constructed. Their FITC-LPS binding behaviors were investigated and compared with those of commercially available LPS-binding products. Moreover, the LPS binding selectivity of the NPs was also explored by studying the NPs-BSA interactions. The results showed that all NPs obtained generally presented higher FITC-LPS binding capacity in lower ionic strength buffer than higher ionic strength. However, unlike commercial poly-lysine cellulose and polymyxin B agarose beads' nearly linear increase of FITC-LPS binding with particle concentration, NPs exhibited serious aggregation and the binding quickly saturated or even decreased at high particle concentration. Among various types of NPs, higher FITC-LPS binding capacity was observed for those containing more hydrophobic monomers (TBAm). However, surprisingly, more cationic NPs with higher content of APM exhibited decreased FITC-LPS binding in high ionic strength conditions. Additionally, when new cationic monomer and cross-linker, GUA and PEG, were applied to replace APM and BIS, the obtained NPs showed improved FITC-LPS binding capacity at low NP concentration. But compared with APM- and BIS-containing NPs, the FITC-LPS binding capacity of GUA- and PEG-containing NPs saturated earlier. To investigate the NPs' binding to proteins, we tested the NPs

  10. Essentially slant Toeplitz operators

    OpenAIRE

    2009-01-01

    The notion of an essentially slant Toeplitz operator on the space $L^2$ is introduced and some of the properties of the set ${\\rm ESTO}(L^2)$, the set of all essentially slant Toeplitz operators on $L^2$, are investigated. In particular the conditions under which the product of two operators in ${\\rm ESTO}(L^2)$ is in ${\\rm ESTO}(L^2)$ are discussed. The notion is generalized to $k$th-order essentially slant Toeplitz operators.

  11. Star operations and Pullbacks

    OpenAIRE

    Fontana, Marco; Park, Mi Hee

    2003-01-01

    In this paper we study the star operations on a pullback of integral domains. In particular, we characterize the star operations of a domain arising from a pullback of ``a general type'' by introducing new techniques for ``projecting'' and ``lifting'' star operations under surjective homomorphisms of integral domains. We study the transfer in a pullback (or with respect to a surjective homomorphism) of some relevant classes or distinguished properties of star operations such as $v-, t-, w-, b...

  12. Unix operating system

    CERN Document Server

    Liu, Yukun; Guo, Liwei

    2011-01-01

    ""UNIX Operating System: The Development Tutorial via UNIX Kernel Services"" introduces the hierarchical structure, principles, applications, kernel, shells, development, and management of the UNIX operation systems multi-dimensionally and systematically. It clarifies the natural bond between physical UNIX implementation and general operating system and software engineering theories, and presents self-explanatory illustrations for readers to visualize and understand the obscure relationships and intangible processes in UNIX operating system. This book is intended for engineers and researchers

  13. Peptide binding specificity of the chaperone calreticulin

    DEFF Research Database (Denmark)

    Sandhu, N.; Duus, K.; Jorgensen, C.S.;

    2007-01-01

    Calreticulin is a molecular chaperone with specificity for polypeptides and N-linked monoglucosylated glycans. In order to determine the specificity of polypeptide binding, the interaction of calreticulin with polypeptides was investigated using synthetic peptides of different length and composit......Calreticulin is a molecular chaperone with specificity for polypeptides and N-linked monoglucosylated glycans. In order to determine the specificity of polypeptide binding, the interaction of calreticulin with polypeptides was investigated using synthetic peptides of different length...... and composition. A large set of available synthetic peptides (n=127) was tested for binding to calreticulin and the results analysed by multivariate data analysis. The parameter that correlated best with binding was hydrophobicity while beta-turn potential disfavoured binding. Only hydrophobic peptides longer...... a peptide-binding specificity for hydrophobic sequences and delineate the fine specificity of calreticulin for hydrophobic amino acid residues....

  14. An RNA motif that binds ATP

    Science.gov (United States)

    Sassanfar, M.; Szostak, J. W.

    1993-01-01

    RNAs that contain specific high-affinity binding sites for small molecule ligands immobilized on a solid support are present at a frequency of roughly one in 10(10)-10(11) in pools of random sequence RNA molecules. Here we describe a new in vitro selection procedure designed to ensure the isolation of RNAs that bind the ligand of interest in solution as well as on a solid support. We have used this method to isolate a remarkably small RNA motif that binds ATP, a substrate in numerous biological reactions and the universal biological high-energy intermediate. The selected ATP-binding RNAs contain a consensus sequence, embedded in a common secondary structure. The binding properties of ATP analogues and modified RNAs show that the binding interaction is characterized by a large number of close contacts between the ATP and RNA, and by a change in the conformation of the RNA.

  15. The helical structure of DNA facilitates binding

    Science.gov (United States)

    Berg, Otto G.; Mahmutovic, Anel; Marklund, Emil; Elf, Johan

    2016-09-01

    The helical structure of DNA imposes constraints on the rate of diffusion-limited protein binding. Here we solve the reaction-diffusion equations for DNA-like geometries and extend with simulations when necessary. We find that the helical structure can make binding to the DNA more than twice as fast compared to a case where DNA would be reactive only along one side. We also find that this rate advantage remains when the contributions from steric constraints and rotational diffusion of the DNA-binding protein are included. Furthermore, we find that the association rate is insensitive to changes in the steric constraints on the DNA in the helix geometry, while it is much more dependent on the steric constraints on the DNA-binding protein. We conclude that the helical structure of DNA facilitates the nonspecific binding of transcription factors and structural DNA-binding proteins in general.

  16. Convolution Operators on Groups

    CERN Document Server

    Derighetti, Antoine

    2011-01-01

    This volume is devoted to a systematic study of the Banach algebra of the convolution operators of a locally compact group. Inspired by classical Fourier analysis we consider operators on Lp spaces, arriving at a description of these operators and Lp versions of the theorems of Wiener and Kaplansky-Helson.

  17. Operations and maintenance philosophy

    Energy Technology Data Exchange (ETDEWEB)

    DUNCAN, G.P.

    1999-10-28

    This Operations and Maintenance (O&M) Philosophy document is intended to establish a future O&M vision, with an increased focus on minimizing worker exposure, ensuring uninterrupted retrieval operations, and minimizing operation life-cycle cost. It is intended that this document would incorporate O&M lessons learned into on-going and future project upgrades.

  18. Open Verlinde line operators

    CERN Document Server

    Gaiotto, Davide

    2014-01-01

    We reformulate the action of Verlinde line operators on conformal blocks in a 3d TFT language and extend it to line operators labelled by open paths joining punctures on the Riemann surface. We discuss the possible applications of open Verlinde line operators to quantum Teichm\\"uller theory, supersymmetric gauge theory and quantum groups

  19. Sources of Operating Costs

    OpenAIRE

    Mackie, Peter; Nellthorp, John; Laird, James

    2005-01-01

    Historically, road vehicle operating costs have tended to dominate highway economic appraisals in developing countries, due to the poor road surfaces that can occur there. The operating costs of railways and ports are also substantial, and form key components of cost benefit analyses of their associated infrastructure. The definition of operating costs for Bank projects is therefore important ...

  20. Binding of TH-iloprost to rat gastric mucosa: a pitfall in performing radioligand binding assays

    Energy Technology Data Exchange (ETDEWEB)

    Beinborn, M.; Kromer, W.; Staar, U.; Sewing, K.F.

    1985-09-01

    Binding of TH-iloprost was studied in a 20,000 x g sediment of the rat gastric mucosa. When pH in both test tubes for total and non-specific binding was kept identical, no displaceable binding of iloprost could be detected. When no care was taken to keep the pH identical in corresponding test tubes of the binding assay, changes in pH simulated specific and displaceable binding of iloprost. Therefore it is concluded that - in contrast to earlier reports - it is not possible to demonstrate specific iloprost binding using the given method.

  1. LEGRI Science Operation Center. Architecture and Operations

    Science.gov (United States)

    Blay, Pere; Suso, Julia; Robert, Almudena; Luis Requena, Jose; Alamo, Jorge; Reglero, Victor; Eyles, Chris J.

    2001-03-01

    The LEGRI Science Operation Center (SOC) is the single contact point between the MINISAT-01 Centro de Operaciones Científicas (COC) located at Villafranca del Castillo (Madrid) and the LEGRI Consortium. Its architecture, operational procedures and associated software has been developed at the Universities of Valencia and Birmingham on the scope to define a integrated Data Analysis System, able to perform the daily follow-up of the instrument health, raw data files decompression and archiving activities (on-line and historical). Pointing and telecommand files generation is also a SOC responsibility. The aim of this paper is to report the SOC activities during the two years of LEGRI operations. Conclusions about the SOC architecture and procedures evolution on how to handle the operations for space-borne instrumentation, are also presented. Special attention has been paid to the operative evaluation of the pointing reconstruction solutions from the MINISAT-01 Attitude Control System by comparing them with those obtained with the LEGRI Star Sensor. The analysis of one year of observations shows the good agreement between both sets of data. No systematic deviations have been found with an averaged standard deviation of 1 degree in alpha and delta coordinates. For most of the time the MINISAT pointing system is working slightly better than expected and within specifications.

  2. Predicted metal binding sites for phytoremediation

    OpenAIRE

    Sharma, Ashok; Roy, Sudeep; Tripathi, Kumar Parijat; Roy, Pratibha; Mishra, Manoj; Khan, Feroz; Meena, Abha

    2009-01-01

    Metal ion binding domains are found in proteins that mediate transport, buffering or detoxification of metal ions. The objective of the study is to design and analyze metal binding motifs against the genes involved in phytoremediation. This is being done on the basis of certain pre-requisite amino-acid residues known to bind metal ions/metal complexes in medicinal and aromatic plants (MAP's). Earlier work on MAP's have shown that heavy metals accumulated by aromatic and medicinal plants do no...

  3. A computational model for feature binding

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The "Binding Problem" is an important problem across many disciplines, including psychology, neuroscience, computational modeling, and even philosophy. In this work, we proposed a novel computational model, Bayesian Linking Field Model, for feature binding in visual perception, by combining the idea of noisy neuron model, Bayesian method, Linking Field Network and competitive mechanism. Simulation Experiments demonstrated that our model perfectly fulfilled the task of feature binding in visual perception and provided us some enlightening idea for future research.

  4. A computational model for feature binding

    Institute of Scientific and Technical Information of China (English)

    SHI ZhiWei; SHI ZhongZhi; LIU Xi; SHI ZhiPing

    2008-01-01

    The "Binding Problem" is an important problem across many disciplines, including psychology, neuroscience, computational modeling, and even philosophy. In this work, we proposed a novel computational model, Bayesian Linking Field Model, for feature binding in visual perception, by combining the idea of noisy neuron model, Bayesian method, Linking Field Network and competitive mechanism.Simulation Experiments demonstrated that our model perfectly fulfilled the task of feature binding in visual perception and provided us some enlightening idea for future research.

  5. Characterization of feline serum-cobalt binding.

    Science.gov (United States)

    Schnelle, Amy N; Barger, Anne M; MacNeill, Amy L; Mitchell, Mark M; Solter, Philip

    2015-06-01

    Oxidative stress inhibits albumin's ability to complex with cobalt. Feline serum-cobalt binding has not been described. The objective was to develop a cobalt binding test for use with feline serum, and correlate the results with other biochemical and cellular constituents in blood, and with clinical diseases of cats. A colorimetric test of cobalt binding, based on the oxidation-reduction reaction of Co(+2) and dithiothreitol, was developed using feline serum. The test was used to measure cobalt binding in stored serum from 176 cats presented to the University of Illinois Veterinary Teaching Hospital for a variety of disease conditions. Time-matched hematology and biochemical data, and clinical information, were obtained from the medical record of each cat and correlated with the serum-cobalt binding results. Serial dilution of feline serum with phosphate-buffered saline resulted in a highly linear decrease in serum-cobalt binding (r(2)  = .9984). Serum-cobalt binding of the clinical samples also correlated with albumin concentrations in a stepwise linear regression model (r(2)  = .425), and both cobalt binding and albumin were significantly decreased in cases of inflammation. Albumin and cobalt binding also shared significant correlations with several erythron variables, and serum concentration of total calcium and bilirubin. The correlation of cobalt binding measured by a colorimetric test with albumin concentration in the clinical samples and with serum dilution is consistent with feline albumin-cobalt complex formation. Hypoalbuminemia is the likely cause of reduced serum-cobalt binding in inflammation and the correlations observed between cobalt binding and other variables. © 2015 American Society for Veterinary Clinical Pathology.

  6. Norfloxacin binds to human fecal material.

    Science.gov (United States)

    Edlund, C; Lindqvist, L; Nord, C E

    1988-01-01

    Earlier studies have reported very high (120 to 2,700 mg/kg) concentrations of norfloxacin in feces after therapeutic doses. MICs for fecal microorganisms are with few exceptions far below these levels. Nevertheless, clinical investigations show that the main part of the aerobic gram-positive and the anaerobic microflora remains unaffected after norfloxacin administration. In this study, the binding of [14C]norfloxacin to fecal material was analyzed. The binding of a group of nonlabeled quinolones to feces and the interactions between Enterococcus faecium, Bacteroides fragilis, and norfloxacin were also investigated. The results showed that norfloxacin has the ability to bind to feces. The specific binding was reversible, saturated after 90 min of incubation at 37 degrees C, and increased linearly with fecal concentration. Scatchard plots and nonlinear regression computer analyses revealed two different binding classes. The primary specific binding had a dissociation constant (KD) of 1.0 microM and a maximal binding capacity (Bmax) of 0.12 mumol/g of feces. The KD and Bmax of the secondary, more unspecific binding were 450 microM and 11.8 mumol/g of feces, respectively. The binding of unlabeled ciprofloxacin, enoxacin, ofloxacin, pefloxacin, and norfloxacin to feces was comparable to that of [14C]norfloxacin. The results of norfloxacin binding to suspensions of B. fragilis suggested that the main part of the binding is to the bacterial fraction of feces. In the presence of 8.0 g (dry weight) of B. fragilis per liter, the MBC of norfloxacin for E. faecium increased from 8 to 256 micrograms/ml. The finding of the present study indicated that binding of norfloxacin to feces may explain the paradox of high fecal concentrations of norfloxacin versus the actual effect on the normal gastrointestinal microflora. PMID:2854456

  7. Drug binding properties of neonatal albumin

    DEFF Research Database (Denmark)

    Brodersen, R; Honoré, B

    1989-01-01

    Neonatal and adult albumin was isolated by gel chromatography on Sephacryl S-300, from adult and umbilical cord serum, respectively. Binding of monoacetyl-diamino-diphenyl sulfone, warfarin, sulfamethizole, and diazepam was studied by means of equilibrium dialysis and the binding data were analyzed...... by the method of several acceptable fitted curves. It was found that the binding affinity to neonatal albumin is less than to adult albumin for monoacetyl-diamino-diphenyl sulfone and warfarin. Sulfamethizole binding to the neonatal protein is similarly reduced when more than one molecule of the drug is bound...

  8. Advances on Plant Pathogenic Mycotoxin Binding Proteins

    Institute of Scientific and Technical Information of China (English)

    WANG Chao-hua; DONG Jin-gao

    2002-01-01

    Toxin-binding protein is one of the key subjects in plant pathogenic mycotoxin research. In this paper, new advances in toxin-binding proteins of 10 kinds of plant pathogenic mycotoxins belonging to Helminthosporium ,Alternaria ,Fusicoccum ,Verticillium were reviewed, especially the techniques and methods of toxin-binding proteins of HS-toxin, HV-toxin, HMT-toxin, HC-toxin. It was proposed that the isotope-labeling technique and immunological chemistry technique should be combined together in research of toxin-binding protein, which will be significant to study the molecular recognition mechanism between host and pathogenic fungus.

  9. Lead-Binding Proteins: A Review

    Directory of Open Access Journals (Sweden)

    Harvey C. Gonick

    2011-01-01

    Full Text Available Lead-binding proteins are a series of low molecular weight proteins, analogous to metallothionein, which segregate lead in a nontoxic form in several organs (kidney, brain, lung, liver, erythrocyte. Whether the lead-binding proteins in every organ are identical or different remains to be determined. In the erythrocyte, delta-aminolevulinic acid dehydratase (ALAD isoforms have commanded the greatest attention as proteins and enzymes that are both inhibitable and inducible by lead. ALAD-2, although it binds lead to a greater degree than ALAD-1, appears to bind lead in a less toxic form. What may be of greater significance is that a low molecular weight lead-binding protein, approximately 10 kDa, appears in the erythrocyte once blood lead exceeds 39 μg/dL and eventually surpasses the lead-binding capacity of ALAD. In brain and kidney of environmentally exposed humans and animals, a cytoplasmic lead-binding protein has been identified as thymosin β4, a 5 kDa protein. In kidney, but not brain, another lead-binding protein has been identified as acyl-CoA binding protein, a 9 kDa protein. Each of these proteins, when coincubated with liver ALAD and titrated with lead, diminishes the inhibition of ALAD by lead, verifying their ability to segregate lead in a nontoxic form.

  10. Operational symmetries basic operations in physics

    CERN Document Server

    Saller, Heinrich

    2017-01-01

    This book describes the endeavour to relate the particle spectrum with representations of operational electroweak spacetime, in analogy to the atomic spectrum as characterizing representations of hyperbolic space. The spectrum of hyperbolic position space explains the properties of the nonrelativistic atoms; the spectrum of electroweak spacetime is hoped to explain those of the basic interactions and elementary particles. In this book, the theory of operational symmetries is developed from the numbers, from Plato’s and Kepler’s symmetries over the simple Lie groups to their applications in nonrelativistic, special relativistic and general relativistic quantum theories with the atomic spectrum for hyperbolic position and, in first attempts, the particle spectrum for electroweak spacetime. The standard model of elementary particles and interactions is characterized by a symmetry group. In general, as initiated by Weyl and stressed by Heisenberg, quantum theory can be built as a theory of operation groups an...

  11. Retinoid-binding proteins: similar protein architectures bind similar ligands via completely different ways.

    Directory of Open Access Journals (Sweden)

    Yu-Ru Zhang

    Full Text Available BACKGROUND: Retinoids are a class of compounds that are chemically related to vitamin A, which is an essential nutrient that plays a key role in vision, cell growth and differentiation. In vivo, retinoids must bind with specific proteins to perform their necessary functions. Plasma retinol-binding protein (RBP and epididymal retinoic acid binding protein (ERABP carry retinoids in bodily fluids, while cellular retinol-binding proteins (CRBPs and cellular retinoic acid-binding proteins (CRABPs carry retinoids within cells. Interestingly, although all of these transport proteins possess similar structures, the modes of binding for the different retinoid ligands with their carrier proteins are different. METHODOLOGY/PRINCIPAL FINDINGS: In this work, we analyzed the various retinoid transport mechanisms using structure and sequence comparisons, binding site analyses and molecular dynamics simulations. Our results show that in the same family of proteins and subcellular location, the orientation of a retinoid molecule within a binding protein is same, whereas when different families of proteins are considered, the orientation of the bound retinoid is completely different. In addition, none of the amino acid residues involved in ligand binding is conserved between the transport proteins. However, for each specific binding protein, the amino acids involved in the ligand binding are conserved. The results of this study allow us to propose a possible transport model for retinoids. CONCLUSIONS/SIGNIFICANCE: Our results reveal the differences in the binding modes between the different retinoid-binding proteins.

  12. Comparative Ellipsis and Variable Binding

    CERN Document Server

    Lerner, J; Lerner, Jan; Pinkal, Manfred

    1995-01-01

    In this paper, we discuss the question whether phrasal comparatives should be given a direct interpretation, or require an analysis as elliptic constructions, and answer it with Yes and No. The most adequate analysis of wide reading attributive (WRA) comparatives seems to be as cases of ellipsis, while a direct (but asymmetric) analysis fits the data for narrow scope attributive comparatives. The question whether it is a syntactic or a semantic process which provides the missing linguistic material in the complement of WRA comparatives is also given a complex answer: Linguistic context is accessed by combining a reconstruction operation and a mechanism of anaphoric reference. The analysis makes only few and straightforward syntactic assumptions. In part, this is made possible because the use of Generalized Functional Application as a semantic operation allows us to model semantic composition in a flexible way.

  13. Tissue specificity of endothelin binding sites

    Energy Technology Data Exchange (ETDEWEB)

    Bolger, G.T.; Liard, F.; Krogsrud, R.; Thibeault, D.; Jaramillo, J. (BioMega, Inc., Laval, Quebec (Canada))

    1990-09-01

    A measurement was made of the binding of 125I-labeled endothelin (125I-ET) to crude membrane fractions prepared from rat aorta, atrium, ventricle, portal vein, trachea, lung parenchyma, vas deferens, ileum, bladder, and guinea-pig taenia coli and lung parenchyma. Scatchard analysis of 125I-ET binding in all tissues indicated binding to a single class of saturable sites. The affinity and density of 125I-ET binding sites varied between tissues. The Kd of 125I-ET binding was approximately 0.5 nM for rat aorta, trachea, lung parenchyma, ventricle, bladder, and vas deferens, and guinea-pig taenia coli and lung parenchyma, 1.8 nM for rat portal vein and atrium, and 3.3 nM for ileum. The Bmax of 125I-ET binding had the following rank order of density in rat tissues: trachea greater than lung parenchyma = vas deferens much greater than aorta = portal vein = atrium greater than bladder greater than ventricle = ileum. The properties of 125I-ET endothelin binding were characterized in rat ventricular membranes. 125I-ET binding was time dependent, reaching a maximum within 45-60 min at 25 degrees C. The calculated microassociation constant was 9.67 x 10(5) s-1 M-1. Only 15-20% of 125I-ET dissociated from its binding site even when dissociation was studied as long as 3 h. Preincubation of ventricular membranes with ET prevented binding of 125I-ET. 125I-ET binding was destroyed by boiling of ventricular membranes and was temperature, pH, and cation (Ca2+, Mg2+, and Na+) dependent.

  14. Your Lung Operation: After Your Operation

    Medline Plus

    Full Text Available ... Want to Be a RAS-ACS Leader International Exchange Scholar Program Resources RAS E-News Operation Giving ... E-Learning Evidence-Based Decisions in Surgery Medical Student Resources So You Want to Be a Surgeon ...

  15. Unconventional Operations Forces of Special Operations

    Science.gov (United States)

    1993-04-15

    neighbors. 28. Samuel Huntington is an Eaton Professor of the Science of Government and Director of the John M. Olin Institute of Strategic Studies at the...1944. Special Operations in US Strategy. Ed by Frank R. Barnett, B. Hugh Tovar and Richard H. Shultz. Washington: National Defense University Press

  16. Hermeneutic operative calculus

    Science.gov (United States)

    Ramakrishnan, Sivakumar; Isawasan, Pradeep; Mohanan, Vasuky

    2014-07-01

    The predicate calculus used currently by mathematical logic in computer science, philosophy and linguistic was found to be too restrictive and inadequate for describing the grammar of natural and artificial language. Therefore many higher order logics have been developed to overcome the limitation of predicate calculus. In this paper a new representation of logic using mathematical principles has been developed for the natural language called Hermeneutic Operative Calculus. This Hermeneutic Operative Calculus is a new language interpretive calculus developed to account for the syntactic, semantic and pragmatic features of natural language and allows removing the restrictions of any particular natural language in the semantic field its map out. The logic of Hermeneutic Operative Calculus capable of represent the syntactic and semantic of factual information of a natural language precisely in any language. The logic of this Hermeneutic Operative Calculus has two different forms of operations called object and meta-operations. The object operation allow for listing the various objects, picturing the various propositions and so forth. The meta-operation would specify what cannot be specified by the object operation like semantical stances of a proposition. The basic operative processes of linguistics and cognitive logic will be mathematically conceptualized and elaborated in this paper.

  17. Biodiscovery of aluminum binding peptides

    Science.gov (United States)

    Adams, Bryn L.; Sarkes, Deborah A.; Finch, Amethist S.; Hurley, Margaret M.; Stratis-Cullum, Dimitra

    2013-05-01

    Cell surface peptide display systems are large and diverse libraries of peptides (7-15 amino acids) which are presented by a display scaffold hosted by a phage (virus), bacteria, or yeast cell. This allows the selfsustaining peptide libraries to be rapidly screened for high affinity binders to a given target of interest, and those binders quickly identified. Peptide display systems have traditionally been utilized in conjunction with organic-based targets, such as protein toxins or carbon nanotubes. However, this technology has been expanded for use with inorganic targets, such as metals, for biofabrication, hybrid material assembly and corrosion prevention. While most current peptide display systems employ viruses to host the display scaffold, we have recently shown that a bacterial host, Escherichia coli, displaying peptides in the ubiquitous, membrane protein scaffold eCPX can also provide specific peptide binders to an organic target. We have, for the first time, extended the use of this bacterial peptide display system for the biodiscovery of aluminum binding 15mer peptides. We will present the process of biopanning with macroscopic inorganic targets, binder enrichment, and binder isolation and discovery.

  18. Binding of (/sup 3/H)imipramine to human platelet membranes with compensation for saturable binding to filters and its implication for binding studies with brain membranes

    Energy Technology Data Exchange (ETDEWEB)

    Phillips, O.M.; Wood, K.M.; Williams, D.C.

    1984-08-01

    Apparent specific binding of (/sup 3/H)imipramine to human platelet membranes at high concentrations of imipramine showed deviation from that expected of a single binding site, a result consistent with a low-affinity binding site. The deviation was due to displaceable, saturable binding to the glass fibre filters used in the assays. Imipramine, chloripramine, desipramine, and fluoxetine inhibited binding to filters whereas 5-hydroxytryptamine and ethanol were ineffective. Experimental conditions were developed that eliminated filter binding, allowing assay of high- and low-affinity binding to membranes. Failure to correct for filter binding may lead to overestimation of binding parameters, Bmax and KD for high-affinity binding to membranes, and may also be misinterpreted as indicating a low-affinity binding component in both platelet and brain membranes. Low-affinity binding (KD less than 2 microM) of imipramine to human platelet membranes was demonstrated and its significance discussed.

  19. Binding Principle for Long-Distance Anaphors.

    Science.gov (United States)

    Choi, Dong-Ik

    1997-01-01

    An analysis of long-distance anaphora, a binding phenomenon in which reflexives find their antecedents outside their local domain, is presented, using data from English, Chinese, Japanese, Korean, Russian, Icelandic, and Italian. It is found that no approach deals with long-distance anaphors exclusively and elegantly. The binding domain…

  20. Triazatriangulene as binding group for molecular electronics

    DEFF Research Database (Denmark)

    Wei, Zhongming; Wang, Xintai; Borges, Anders

    2014-01-01

    The triazatriangulene (TATA) ring system was investigated as a binding group for tunnel junctions of molecular wires on gold surfaces. Self-assembled monolayers (SAMs) of TATA platforms with three different lengths of phenylene wires were fabricated, and their electrical conductance was recorded ...... with its high stability and directionality make this binding group very attractive for molecular electronic measurements and devices. (Figure Presented)....

  1. Localization-enhanced biexciton binding in semiconductors

    DEFF Research Database (Denmark)

    Langbein, Wolfgang Werner; Hvam, Jørn Märcher

    1999-01-01

    The influence of excitonic localization on the binding energy of biexcitons is investigated for quasi-three-dimensional and quasi-two-dimensional AlxGa1-xAs structures. An increase of the biexciton binding energy is observed for localization energies comparable to or larger than the free biexcito...

  2. CTCF Binding Polarity Determines Chromatin Looping

    NARCIS (Netherlands)

    de Wit, Elzo; Vos, Erica S M; Holwerda, Sjoerd J B|info:eu-repo/dai/nl/344682218; Valdes-Quezada, Christian; Verstegen, Marjon J A M; Teunissen, Hans; Splinter, Erik; Wijchers, Patrick J; Krijger, Peter H L; de Laat, Wouter|info:eu-repo/dai/nl/169934497

    2015-01-01

    CCCTC-binding factor (CTCF) is an architectural protein involved in the three-dimensional (3D) organization of chromatin. In this study, we assayed the 3D genomic contact profiles of a large number of CTCF binding sites with high-resolution 4C-seq. As recently reported, our data also suggest that ch

  3. Binding of anandamide to bovine serum albumin

    DEFF Research Database (Denmark)

    Bojesen, I.N.; Hansen, Harald S.

    2003-01-01

    The endocannabinoid anandamide is of lipid nature and may thus bind to albumin in the vascular system, as do fatty acids. The knowledge of the free water-phase concentration of anandamide is essential for the investigations of its transfer from the binding protein to cellular membranes, because...

  4. Multiple binding modes of ibuprofen in human serum albumin identified by absolute binding free energy calculations

    KAUST Repository

    Evoli, Stefania

    2016-11-10

    Human serum albumin possesses multiple binding sites and transports a wide range of ligands that include the anti-inflammatory drug ibuprofen. A complete map of the binding sites of ibuprofen in albumin is difficult to obtain in traditional experiments, because of the structural adaptability of this protein in accommodating small ligands. In this work, we provide a set of predictions covering the geometry, affinity of binding and protonation state for the pharmaceutically most active form (S-isomer) of ibuprofen to albumin, by using absolute binding free energy calculations in combination with classical molecular dynamics (MD) simulations and molecular docking. The most favorable binding modes correctly reproduce several experimentally identified binding locations, which include the two Sudlow\\'s drug sites (DS2 and DS1) and the fatty acid binding sites 6 and 2 (FA6 and FA2). Previously unknown details of the binding conformations were revealed for some of them, and formerly undetected binding modes were found in other protein sites. The calculated binding affinities exhibit trends which seem to agree with the available experimental data, and drastically degrade when the ligand is modeled in a protonated (neutral) state, indicating that ibuprofen associates with albumin preferentially in its charged form. These findings provide a detailed description of the binding of ibuprofen, help to explain a wide range of results reported in the literature in the last decades, and demonstrate the possibility of using simulation methods to predict ligand binding to albumin.

  5. Thermodynamics of ligand binding to acyl-coenzyme A binding protein studied by titration calorimetry

    DEFF Research Database (Denmark)

    Færgeman, Nils J.; Sigurskjold, B W; Kragelund, B B

    1996-01-01

    Ligand binding to recombinant bovine acyl-CoA binding protein (ACBP) was examined using isothermal microcalorimetry. Microcalorimetric measurements confirm that the binding affinity of acyl-CoA esters for ACBP is strongly dependent on the length of the acyl chain with a clear preference for acyl-...

  6. Acyl-CoA-binding protein/diazepam-binding inhibitor gene and pseudogenes

    DEFF Research Database (Denmark)

    Mandrup, S; Hummel, R; Ravn, S

    1992-01-01

    Acyl-CoA-binding protein (ACBP) is a 10 kDa protein isolated from bovine liver by virtue of its ability to bind and induce the synthesis of medium-chain acyl-CoA esters. Surprisingly, it turned out to be identical to a protein named diazepam-binding Inhibitor (DBI) claimed to be an endogenous mod...

  7. Cask fleet operations study

    Energy Technology Data Exchange (ETDEWEB)

    1988-01-01

    The Nuclear Waste Policy Act of 1982 assigned to the Department of Energy's (DOE) Office of Civilian Waste Management the responsibility for disposing of high-level waste and spent fuel. A significant part of that responsibility involves transporting nuclear waste materials within the federal waste management system; that is, from the waste generator to the repository. The lead responsibility for transportation operations has been assigned to Oak Ridge Operations, with Oak Ridge National Laboratory (ORNL) providing technical support through the Transportation Operations Support Task Group. One of the ORNL support activities involves assessing what facilities, equipment and services are required to assure that an acceptable, cost-effective and safe transportation operations system can be designed, operated and maintained. This study reviews, surveys and assesses the experience of Nuclear Assurance Corporation (NAC) in operating a fleet of spent-fuel shipping casks to aid in developing the spent-fuel transportation system.

  8. Operations management system

    Science.gov (United States)

    Brandli, A. E.; Eckelkamp, R. E.; Kelly, C. M.; Mccandless, W.; Rue, D. L.

    1990-01-01

    The objective of an operations management system is to provide an orderly and efficient method to operate and maintain aerospace vehicles. Concepts are described for an operations management system and the key technologies are highlighted which will be required if this capability is brought to fruition. Without this automation and decision aiding capability, the growing complexity of avionics will result in an unmanageable workload for the operator, ultimately threatening mission success or survivability of the aircraft or space system. The key technologies include expert system application to operational tasks such as replanning, equipment diagnostics and checkout, global system management, and advanced man machine interfaces. The economical development of operations management systems, which are largely software, will require advancements in other technological areas such as software engineering and computer hardware.

  9. Probing the binding of fluoxetine hydrochloride to human serum albumin by multispectroscopic techniques

    Science.gov (United States)

    Katrahalli, Umesha; Jaldappagari, Seetharamappa; Kalanur, Shankara S.

    2010-01-01

    The interaction between human serum albumin (HSA) and fluoxetine hydrochloride (FLX) have been studied by using different spectroscopic techniques viz., fluorescence, UV-vis absorption, circular dichroism and FTIR under simulated physiological conditions. Fluorescence results revealed the presence of static type of quenching mechanism in the binding of FLX to HSA. The values of binding constant, K of FLX-HSA were evaluated at 289, 300 and 310 K and were found to be 1.90 × 10 3, 1.68 × 10 3 and 1.45 × 10 3 M -1, respectively. The number of binding sites, n was noticed to be almost equal to unity thereby indicating the presence of a single class of binding site for FLX on HSA. Based on the thermodynamic parameters, Δ H0 and Δ S0 nature of binding forces operating between HSA and FLX were proposed. Spectral results revealed the conformational changes in protein upon interaction. Displacement studies indicated the site I as the main binding site for FLX on HSA. The effect of common ions on the binding of FLX to HSA was also investigated.

  10. Operational Modal Analysis Tutorial

    OpenAIRE

    Brincker, Rune; Andersen, Palle

    2007-01-01

    In this paper the basic principles in operational modal testing and analysis are presented and discussed. A brief review of the techniques for operational modal testing and identification is presented, and it is argued, that there is now a wide range of techniques for effective identification of modal parameters of practical interest - including the mode shape scaling factor - with a high degree of accuracy. It is also argued that the operational technology offers the user a number of advanta...

  11. Relativistic Spin Operators

    Institute of Scientific and Technical Information of China (English)

    ZHANG Peng-Fei; RUAN Tu-Nan

    2001-01-01

    A systematic theory on the appropriate spin operators for the relativistic states is developed. For a massive relativistic particle with arbitrary nonzero spin, the spin operator should be replaced with the relativistic one, which is called in this paper as moving spin. Further the concept of moving spin is discussed in the quantum field theory. A new is constructed. It is shown that, in virtue of the two operators, problems in quantum field concerned spin can be neatly settled.

  12. Lax operator algebras

    OpenAIRE

    Krichever, Igor M.; Sheinman, Oleg K.

    2007-01-01

    In this paper we develop a general concept of Lax operators on algebraic curves introduced in [1]. We observe that the space of Lax operators is closed with respect to their usual multiplication as matrix-valued functions. We construct the orthogonal and symplectic analogs of Lax operators, prove that they constitute almost graded Lie algebras and construct local central extensions of those Lie algebras.

  13. 2015 Special Operations Essays

    Science.gov (United States)

    2015-05-01

    stability operations in Afghanistan.19 27 Goldstein: The First Women in SOF The persistent cultural stereotype of the female spy is of a hyper-sexual...outreach, and research in the science and art of joint special operations. JSOU provides education to the men and women of SOF and to those who...Human Domain in Warfare ................................ 11 The First Women in SOF: Women Operatives in the OSS and SOE as a Framework for the

  14. Network operating system

    Science.gov (United States)

    1985-01-01

    Long-term and short-term objectives for the development of a network operating system for the Space Station are stated. The short-term objective is to develop a prototype network operating system for a 100 megabit/second fiber optic data bus. The long-term objective is to establish guidelines for writing a detailed specification for a Space Station network operating system. Major milestones are noted. Information is given in outline form.

  15. Naive Realism about Operators

    OpenAIRE

    Daumer, Martin; Dürr, Detlef; Goldstein, Sheldon; Zanghì, Nino

    1996-01-01

    A source of much difficulty and confusion in the interpretation of quantum mechanics is a ``naive realism about operators.'' By this we refer to various ways of taking too seriously the notion of operator-as-observable, and in particular to the all too casual talk about ``measuring operators'' that occurs when the subject is quantum mechanics. Without a specification of what should be meant by ``measuring'' a quantum observable, such an expression can have no clear meaning. A definite specifi...

  16. Lattice Trace Operators

    Directory of Open Access Journals (Sweden)

    Brian Jefferies

    2014-01-01

    Full Text Available A bounded linear operator T on a Hilbert space ℋ is trace class if its singular values are summable. The trace class operators on ℋ form an operator ideal and in the case that ℋ is finite-dimensional, the trace tr(T of T is given by ∑jajj for any matrix representation {aij} of T. In applications of trace class operators to scattering theory and representation theory, the subject is complicated by the fact that if k is an integral kernel of the operator T on the Hilbert space L2(μ with μ a σ-finite measure, then k(x,x may not be defined, because the diagonal {(x,x} may be a set of (μ⊗μ-measure zero. The present note describes a class of linear operators acting on a Banach function space X which forms a lattice ideal of operators on X, rather than an operator ideal, but coincides with the collection of hermitian positive trace class operators in the case of X=L2(μ.

  17. Operators on Hilbert space

    CERN Document Server

    Sunder, V S

    2016-01-01

    The primarily objective of the book is to serve as a primer on the theory of bounded linear operators on separable Hilbert space. The book presents the spectral theorem as a statement on the existence of a unique continuous and measurable functional calculus. It discusses a proof without digressing into a course on the Gelfand theory of commutative Banach algebras. The book also introduces the reader to the basic facts concerning the various von Neumann–Schatten ideals, the compact operators, the trace-class operators and all bounded operators. .

  18. Operator interface for vehicles

    Science.gov (United States)

    Bissontz, Jay E

    2015-03-10

    A control interface for drivetrain braking provided by a regenerative brake and a non-regenerative brake is implemented using a combination of switches and graphic interface elements. The control interface comprises a control system for allocating drivetrain braking effort between the regenerative brake and the non-regenerative brake, a first operator actuated control for enabling operation of the drivetrain braking, and a second operator actuated control for selecting a target braking effort for drivetrain braking. A graphic display displays to an operator the selected target braking effort and can be used to further display actual braking effort achieved by drivetrain braking.

  19. Miscellaneous Industrial Mineral Operations

    Data.gov (United States)

    Department of Homeland Security — This map layer includes miscellaneous industrial minerals operations in the United States. The data represent commodities covered by the Minerals Information Team...

  20. Implications for operations

    CERN Document Server

    Arduini, G; Pieloni, T; Rumolo, G

    2015-01-01

    The HL-LHC will introduce a number of novel operational features and challenges including luminosity leveling. After a brief recap of the possible leveling techniques, the potential impact of the operational regime on overall efficiency is discussed. A breakdown of the operational cycle and the standard operational year, together with a discussion of fault time is presented. The potential performance is then explored and estimates of the required machine availability and efficiency for 250 fb−1 per year are given. Finally the e-cloud challenges, scrubbing runs requirements, and machine development potential are outlined.

  1. Airline Operation Center Workstation

    Data.gov (United States)

    Department of Transportation — The Airline Operation Center Workstation (AOC Workstation) represents equipment available to users of the National Airspace system, outside of the FAA, that enables...

  2. Cyberspace Operations in Support of Counterinsurgency Operations

    Science.gov (United States)

    2013-04-10

    probability it is being used for strategic communication, information operations (io), advertisement for recruits, so- licitation of funding and ongoing...reliability. implementation plans and advertising exist for 3G- and General Packet Radio Service-based networks, which will mark a significant jump in...substantial role in contributing to the coordination efforts of protestors. Websites such as facebook and twitter, various blogs and the use of text messages

  3. Operational Transformation In Co-Operative Editing

    Directory of Open Access Journals (Sweden)

    Mandeep Kaur

    2015-08-01

    Full Text Available Cooperative Editing Systems in real-time allows a virtual team to view and edit a shared document at the same time. The document shared must be synchronized in order to ensure consistency for all the participants. This paper describes the Operational Transformation the evolution of its techniques its various applications major issues and achievements. In addition this paper will present working of a platform where two users can edit a code programming file at the same time.

  4. Operational Transformation In Co-Operative Editing

    OpenAIRE

    Mandeep Kaur; Manpreet Singh; Harneet Kaur; Simran Kaur

    2015-01-01

    Cooperative Editing Systems in real-time allows a virtual team to view and edit a shared document at the same time. The document shared must be synchronized in order to ensure consistency for all the participants. This paper describes the Operational Transformation the evolution of its techniques its various applications major issues and achievements. In addition this paper will present working of a platform where two users can edit a code programming file at the same time.

  5. Bacterial periplasmic sialic acid-binding proteins exhibit a conserved binding site

    Energy Technology Data Exchange (ETDEWEB)

    Gangi Setty, Thanuja [Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065 (India); Cho, Christine [Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109 (United States); Govindappa, Sowmya [Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065 (India); Apicella, Michael A. [Carver College of Medicine, University of Iowa, Iowa City, IA 52242-1109 (United States); Ramaswamy, S., E-mail: ramas@instem.res.in [Institute for Stem Cell Biology and Regenerative Medicine, NCBS Campus, GKVK Post, Bangalore, Karnataka 560 065 (India)

    2014-07-01

    Structure–function studies of sialic acid-binding proteins from F. nucleatum, P. multocida, V. cholerae and H. influenzae reveal a conserved network of hydrogen bonds involved in conformational change on ligand binding. Sialic acids are a family of related nine-carbon sugar acids that play important roles in both eukaryotes and prokaryotes. These sialic acids are incorporated/decorated onto lipooligosaccharides as terminal sugars in multiple bacteria to evade the host immune system. Many pathogenic bacteria scavenge sialic acids from their host and use them for molecular mimicry. The first step of this process is the transport of sialic acid to the cytoplasm, which often takes place using a tripartite ATP-independent transport system consisting of a periplasmic binding protein and a membrane transporter. In this paper, the structural characterization of periplasmic binding proteins from the pathogenic bacteria Fusobacterium nucleatum, Pasteurella multocida and Vibrio cholerae and their thermodynamic characterization are reported. The binding affinities of several mutations in the Neu5Ac binding site of the Haemophilus influenzae protein are also reported. The structure and the thermodynamics of the binding of sugars suggest that all of these proteins have a very well conserved binding pocket and similar binding affinities. A significant conformational change occurs when these proteins bind the sugar. While the C1 carboxylate has been identified as the primary binding site, a second conserved hydrogen-bonding network is involved in the initiation and stabilization of the conformational states.

  6. Specific insulin binding in bovine chromaffin cells; demonstration of preferential binding to adrenalin-storing cells

    Energy Technology Data Exchange (ETDEWEB)

    Serck-Hanssen, G.; Soevik, O.

    1987-12-28

    Insulin binding was studied in subpopulations of bovine chromaffin cells enriched in adrenalin-producing cells (A-cells) or noradrenalin-producing cells (NA-cells). Binding of /sup 125/I-insulin was carried out at 15/sup 0/C for 3 hrs in the absence or presence of excess unlabeled hormone. Four fractions of cells were obtained by centrifugation on a stepwise bovine serum albumin gradient. The four fractions were all shown to bind insulin in a specific manner and the highest binding was measured in the cell layers of higher densities, containing mainly A-cells. The difference in binding of insulin to the four subpopulations of chromaffin cells seemed to be related to differences in numbers of receptors as opposed to receptor affinities. The authors conclude that bovine chromaffin cells possess high affinity binding sites for insulin and that these binding sites are mainly confined to A-cells. 24 references, 2 figures, 1 table.

  7. Mission Operations Assurance

    Science.gov (United States)

    Faris, Grant

    2012-01-01

    Integrate the mission operations assurance function into the flight team providing: (1) value added support in identifying, mitigating, and communicating the project's risks and, (2) being an essential member of the team during the test activities, training exercises and critical flight operations.

  8. Boolean Operator Fuzzy Logic

    Institute of Scientific and Technical Information of China (English)

    刘叙华; 邓安生

    1994-01-01

    A new approach of operator fuzzy logic, Boolean operator fuzzy logic (BOFL) based on Boolean algebra, is presented. The resolution principle is also introduced into BOFL. BOFL is a natural generalization of classical logic and can be applied to the qualitative description of fuzzy knowledge.

  9. operation zitadelle (kursk)

    African Journals Online (AJOL)

    Administrator

    military technology (command language) will ensure proper communication within the framework ... The use of military power must be understood within this framework. Baucom ... European, Mediterranean and Russian theatres of operation. ... operations to accomplish a common objective, normally within a given time and.

  10. About Some Linear Operators

    Directory of Open Access Journals (Sweden)

    Ovidiu T. Pop

    2007-01-01

    Full Text Available Using the method of Jakimovski and Leviatan from their work in 1969, we construct a general class of linear positive operators. We study the convergence, the evaluation for the rate of convergence in terms of the first modulus of smoothness and we give a Voronovskaja-type theorem for these operators.

  11. Operating room manager game

    NARCIS (Netherlands)

    Hans, Erwin W.; Nieberg, Tim

    2007-01-01

    The operating room (OR) department of a hospital forms the heart of the organization, where the single largest cost is incurred. This document presents and reports on the “Operating Room Manager Game,” developed to give insight into managing a large hospital's OR department at various levels of cont

  12. On Real Operator Spaces

    Institute of Scientific and Technical Information of China (English)

    Zhong Jin RUAN (Zhong-Jin Ruan)

    2003-01-01

    During the last ten to fifteen years , a lot of progress has been achieved in the study ofcomplex operator spaces. In this paper, we show that a corresponding theory can be developed forreal operator spaces. With some appropriate modifications, many complex results still hold for realoperator spaces.

  13. Health care operations management

    NARCIS (Netherlands)

    Carter, M.W.; Hans, Elias W.; Kolisch, R.

    2012-01-01

    Health care operations management has become a major topic for health care service providers and society. Operations research already has and further will make considerable contributions for the effective and efficient delivery of health care services. This special issue collects seven carefully

  14. Custodial Operations: Green & Sustainable

    Science.gov (United States)

    Campbell, J. Kirk

    2008-01-01

    Custodial Operations can have a significant impact on institutional green and sustainable goals if given the proper support and challenge. This article describes the green and sustainable custodial operations in place at Carleton College in Northfield, Minnesota. The article reviews the college's sustainable efforts on biodegradables, packaging,…

  15. Operation plan : Alviso System

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This is the operation plan for ponds A2W, A3W, A7, A14, and A16 in the Alviso System at San Francisco Bay NWR Complex. Operating instructions for both winter and...

  16. Predicted metal binding sites for phytoremediation.

    Science.gov (United States)

    Sharma, Ashok; Roy, Sudeep; Tripathi, Kumar Parijat; Roy, Pratibha; Mishra, Manoj; Khan, Feroz; Meena, Abha

    2009-09-05

    Metal ion binding domains are found in proteins that mediate transport, buffering or detoxification of metal ions. The objective of the study is to design and analyze metal binding motifs against the genes involved in phytoremediation. This is being done on the basis of certain pre-requisite amino-acid residues known to bind metal ions/metal complexes in medicinal and aromatic plants (MAP's). Earlier work on MAP's have shown that heavy metals accumulated by aromatic and medicinal plants do not appear in the essential oil and that some of these species are able to grow in metal contaminated sites. A pattern search against the UniProtKB/Swiss-Prot and UniProtKB/TrEMBL databases yielded true positives in each case showing the high specificity of the motifs designed for the ions of nickel, lead, molybdenum, manganese, cadmium, zinc, iron, cobalt and xenobiotic compounds. Motifs were also studied against PDB structures. Results of the study suggested the presence of binding sites on the surface of protein molecules involved. PDB structures of proteins were finally predicted for the binding sites functionality in their respective phytoremediation usage. This was further validated through CASTp server to study its physico-chemical properties. Bioinformatics implications would help in designing strategy for developing transgenic plants with increased metal binding capacity. These metal binding factors can be used to restrict metal update by plants. This helps in reducing the possibility of metal movement into the food chain.

  17. [Binding to chicken liver lactatedehydrogenase (author's transl)].

    Science.gov (United States)

    Lluís, C; Bozal, J

    1976-06-01

    Some information about the lactate dehydrogenase NAD binding site has been obtained by working with coenzymes analogs of incomplete molecules. 5'AMP, 5'-ADP, ATP, 5'-c-AMP and 3'(2)-AMP inhibit chicken liver LDH activity competitively with NADH. 5"-AMP and 5'-ADP show a stronger inhibition power than ATP, suggesting that the presence of one or two phosphate groups at the 5' position of adenosine, is essential for the binding of the coenzyme analogs at the enzyme binding site. Ribose and ribose-5'-P do not appear to inhibit the LDH activity, proving that purine base lacking mononucleotides do not bind to the enzyme. 5"-ADPG inhibits LDH activity in the exactly as 5'-ADP, showing that ribose moiety may be replaced by glucose, without considerable effects on the coenzyme analog binding. 2'-desoxidenosin-5'-phosphate proves to be a poorer inhibitor of the LDH activity than 5'-AMP, indicating that an interaction between the--OH groups and the amino-acids of the LDH active center takes place. Nicotinamide does not produce any inhibition effect, while NMN and CMP induce a much weaker inhibition than the adenine analogues, thus indicating a lesser binding capacity to the enzyme. Therefore, the LDH binding site seems to show some definite specificity towards the adenina groups of the coenzyme.

  18. Operation of Reactor

    Institute of Scientific and Technical Information of China (English)

    1996-01-01

    3.1 Annual Report of SPR Operation Chu Shaochu Having overseen by National Nuclear Safety Administration and specialists, the reactor restarted up successfully after Safety renovation on April 16, 1996. In August 1996 the normal operation of SPR was approved by the authorities of Naitonal Nuclear Safety Administration. 1 Operation status In 1996, the reactor operated safely for 40 d and the energy released was about 137.3 MW·d. The operation status of SPR is shown in table 1. The reactor started up to higher power (power more than 1 MW) and lower power (for physics experiments) 4 times and 14 times respectively. Measurement of control rod efficiency and other measurement tasks were 2 times and 5 times respectively.

  19. Sustainable Building Operation

    DEFF Research Database (Denmark)

    Jensen, Jesper Ole

    2009-01-01

    Energy-savings in the existing building stock have becomes a main goal in national and international policies. Often focus is on building-renovations, whereas the potential of sustainable building operation to a large extent has been neglected. Nevertheless, international research as well...... as practical experiences from Danish housing estates indicates that there are large potentials for energy savings by focusing on the operation of the buildings. We suggest that in order to achieve sustainability in the existing housing, renovation and operations should be seen as integrated parts...... building operation as an 'umbrella' for various ways of reducing flows of energy, water and waste in the daily operation of the buildings, for instance by regular monitoring the consumption, by using 'green accounting', by applying policies for sustainability etc. The paper is based on case studies...

  20. Operations Between Functions

    DEFF Research Database (Denmark)

    Gardner, Richard J.; Kiderlen, Markus

    A structural theory of operations between real-valued (or extended-real-valued) functions on a nonempty subset A of Rn is initiated. It is shown, for example, that any operation ∗ on a cone of functions containing the constant functions, which is pointwise, positively homogeneous, monotonic......, and associative, must be one of 40 explicitly given types. In particular, this is the case for operations between pairs of arbitrary, or continuous, or differentiable functions. The term pointwise means that (f ∗g)(x) = F(f(x), g(x)), for all x ∈ A and some function F of two variables. Several results in the same...... spirit are obtained for operations between convex functions or between support functions. For example, it is shown that ordinary addition is the unique pointwise operation between convex functions satisfying the identity property, i.e., f ∗ 0 = 0 ∗ f = f, for all convex f, while other results classify Lp...

  1. Assessing Operational Situations

    DEFF Research Database (Denmark)

    Zhang, Xinxin

    different perspectives on situation awareness in the human factor studies and uses the knowledge reflectively for system representation and analysis. The human cognitive activities during complex plant operation and how they perceive a situation and what kind of knowledge has to be established in the human...... operators to perceive and understand the operational situation. The research domain of situation awareness approaches the operational challenges from the human cognition perspective while the presented thesis aims at supporting situation assessment from the system perspective. The thesis has reviewed...... mental model for the operators to be aware of the situations has motivated the utilization of functional representation in system level of situation assessment. The thesis has summarized the MFM syntax and provides detail instructions of how to model by using the modeling technique. A PWR primary system...

  2. Modern operating systems

    CERN Document Server

    Tanenbaum, Andrew S

    2015-01-01

    Modern Operating Systems, Fourth Edition, is intended for introductory courses in Operating Systems in Computer Science, Computer Engineering, and Electrical Engineering programs. It also serves as a useful reference for OS professionals ' The widely anticipated revision of this worldwide best-seller incorporates the latest developments in operating systems (OS) technologies. The Fourth Edition includes up-to-date materials on relevant'OS. Tanenbaum also provides information on current research based on his experience as an operating systems researcher. ' Modern Operating Systems, Third Editionwas the recipient of the 2010 McGuffey Longevity Award. The McGuffey Longevity Award recognizes textbooks whose excellence has been demonstrated over time.'http://taaonline.net/index.html " Teaching and Learning Experience This program will provide a better teaching and learning experience-for you and your students. It will help: ' *Provide Practical Detail on the Big Picture Concepts: A clear and entertaining writing s...

  3. Noncommutative operational calculus

    Directory of Open Access Journals (Sweden)

    Henry E. Heatherly

    1999-12-01

    Full Text Available Oliver Heaviside's operational calculus was placed on a rigorous mathematical basis by Jan Mikusinski, who constructed an algebraic setting for the operational methods. In this paper, we generalize Mikusi'{n}ski's methods to solve linear ordinary differential equations in which the unknown is a matrix- or linear operator-valued function. Because these functions can be zero-divisors and do not necessarily commute, Mikusi'{n}ski's one-dimensional calculus cannot be used. The noncommuative operational calculus developed here,however, is used to solve a wide class of such equations. In addition, we provide new proofs of existence and uniqueness theorems for certain matrix- and operator valued Volterra integral and integro-differential equations. Several examples are given which demonstrate these new methods.

  4. Aircraft operations management manual

    Science.gov (United States)

    1992-01-01

    The NASA aircraft operations program is a multifaceted, highly diverse entity that directly supports the agency mission in aeronautical research and development, space science and applications, space flight, astronaut readiness training, and related activities through research and development, program support, and mission management aircraft operations flights. Users of the program are interagency, inter-government, international, and the business community. This manual provides guidelines to establish policy for the management of NASA aircraft resources, aircraft operations, and related matters. This policy is an integral part of and must be followed when establishing field installation policy and procedures covering the management of NASA aircraft operations. Each operating location will develop appropriate local procedures that conform with the requirements of this handbook. This manual should be used in conjunction with other governing instructions, handbooks, and manuals.

  5. Naive realism about operators

    CERN Document Server

    Daumer, M; Goldstein, S; Zanghì, N; Daumer, Martin; Durr, Detlef; Goldstein, Sheldon; Zangh, Nino

    1996-01-01

    A source of much difficulty and confusion in the interpretation of quantum mechanics is a ``naive realism about operators.'' By this we refer to various ways of taking too seriously the notion of operator-as-observable, and in particular to the all too casual talk about ``measuring operators'' that occurs when the subject is quantum mechanics. Without a specification of what should be meant by ``measuring'' a quantum observable, such an expression can have no clear meaning. A definite specification is provided by Bohmian mechanics, a theory that emerges from Sch\\"rodinger's equation for a system of particles when we merely insist that ``particles'' means particles. Bohmian mechanics clarifies the status and the role of operators as observables in quantum mechanics by providing the operational details absent from standard quantum mechanics. It thereby allows us to readily dismiss all the radical claims traditionally enveloping the transition from the classical to the quantum realm---for example, that we must a...

  6. The Verrucomicrobia LexA-binding Motif: Insights into the Evolutionary Dynamics of the SOS Response

    Directory of Open Access Journals (Sweden)

    Ivan Erill

    2016-07-01

    Full Text Available The SOS response is the primary bacterial mechanism to address DNA damage, coordinating multiple cellular processes that include DNA repair, cell division and translesion synthesis. In contrast to other regulatory systems, the composition of the SOS genetic network and the binding motif of its transcriptional repressor, LexA, have been shown to vary greatly across bacterial clades, making it an ideal system to study the co-evolution of transcription factors and their regulons. Leveraging comparative genomics approaches and prior knowledge on the core SOS regulon, here we define the binding motif of the Verrucomicrobia, a recently described phylum of emerging interest due to its association with eukaryotic hosts. Site directed mutagenesis of the Verrucomicrobium spinosum recA promoter confirms that LexA binds a 14 bp palindromic motif with consensus sequence TGTTC-N4-GAACA. Computational analyses suggest that recognition of this novel motif is determined primarily by changes in base-contacting residues of the third alpha helix of the LexA helix-turn-helix DNA binding motif. In conjunction with comparative genomics analysis of the LexA regulon in the Verrucomicrobia phylum, electrophoretic shift assays reveal that LexA binds to operators in the promoter region of DNA repair genes and a mutagenesis cassette in this organism, and identify previously unreported components of the SOS response. The identification of tandem LexA-binding sites generating instances of other LexA-binding motifs in the lexA gene promoter of Verrucomicrobia species leads us to postulate a novel mechanism for LexA-binding motif evolution. This model, based on gene duplication, successfully addresses outstanding questions in the intricate co-evolution of the LexA protein, its binding motif and the regulatory network it controls.

  7. The Verrucomicrobia LexA-Binding Motif: Insights into the Evolutionary Dynamics of the SOS Response.

    Science.gov (United States)

    Erill, Ivan; Campoy, Susana; Kılıç, Sefa; Barbé, Jordi

    2016-01-01

    The SOS response is the primary bacterial mechanism to address DNA damage, coordinating multiple cellular processes that include DNA repair, cell division, and translesion synthesis. In contrast to other regulatory systems, the composition of the SOS genetic network and the binding motif of its transcriptional repressor, LexA, have been shown to vary greatly across bacterial clades, making it an ideal system to study the co-evolution of transcription factors and their regulons. Leveraging comparative genomics approaches and prior knowledge on the core SOS regulon, here we define the binding motif of the Verrucomicrobia, a recently described phylum of emerging interest due to its association with eukaryotic hosts. Site directed mutagenesis of the Verrucomicrobium spinosum recA promoter confirms that LexA binds a 14 bp palindromic motif with consensus sequence TGTTC-N4-GAACA. Computational analyses suggest that recognition of this novel motif is determined primarily by changes in base-contacting residues of the third alpha helix of the LexA helix-turn-helix DNA binding motif. In conjunction with comparative genomics analysis of the LexA regulon in the Verrucomicrobia phylum, electrophoretic shift assays reveal that LexA binds to operators in the promoter region of DNA repair genes and a mutagenesis cassette in this organism, and identify previously unreported components of the SOS response. The identification of tandem LexA-binding sites generating instances of other LexA-binding motifs in the lexA gene promoter of Verrucomicrobia species leads us to postulate a novel mechanism for LexA-binding motif evolution. This model, based on gene duplication, successfully addresses outstanding questions in the intricate co-evolution of the LexA protein, its binding motif and the regulatory network it controls.

  8. Transcription factor binding site positioning in yeast: proximal promoter motifs characterize TATA-less promoters.

    Science.gov (United States)

    Erb, Ionas; van Nimwegen, Erik

    2011-01-01

    The availability of sequence specificities for a substantial fraction of yeast's transcription factors and comparative genomic algorithms for binding site prediction has made it possible to comprehensively annotate transcription factor binding sites genome-wide. Here we use such a genome-wide annotation for comprehensively studying promoter architecture in yeast, focusing on the distribution of transcription factor binding sites relative to transcription start sites, and the architecture of TATA and TATA-less promoters. For most transcription factors, binding sites are positioned further upstream and vary over a wider range in TATA promoters than in TATA-less promoters. In contrast, a group of 6 'proximal promoter motifs' (GAT1/GLN3/DAL80, FKH1/2, PBF1/2, RPN4, NDT80, and ROX1) occur preferentially in TATA-less promoters and show a strong preference for binding close to the transcription start site in these promoters. We provide evidence that suggests that pre-initiation complexes are recruited at TATA sites in TATA promoters and at the sites of the other proximal promoter motifs in TATA-less promoters. TATA-less promoters can generally be classified by the proximal promoter motif they contain, with different classes of TATA-less promoters showing different patterns of transcription factor binding site positioning and nucleosome coverage. These observations suggest that different modes of regulation of transcription initiation may be operating in the different promoter classes. In addition we show that, across all promoter classes, there is a close match between nucleosome free regions and regions of highest transcription factor binding site density. This close agreement between transcription factor binding site density and nucleosome depletion suggests a direct and general competition between transcription factors and nucleosomes for binding to promoters.

  9. Transcription factor binding site positioning in yeast: proximal promoter motifs characterize TATA-less promoters.

    Directory of Open Access Journals (Sweden)

    Ionas Erb

    Full Text Available The availability of sequence specificities for a substantial fraction of yeast's transcription factors and comparative genomic algorithms for binding site prediction has made it possible to comprehensively annotate transcription factor binding sites genome-wide. Here we use such a genome-wide annotation for comprehensively studying promoter architecture in yeast, focusing on the distribution of transcription factor binding sites relative to transcription start sites, and the architecture of TATA and TATA-less promoters. For most transcription factors, binding sites are positioned further upstream and vary over a wider range in TATA promoters than in TATA-less promoters. In contrast, a group of 6 'proximal promoter motifs' (GAT1/GLN3/DAL80, FKH1/2, PBF1/2, RPN4, NDT80, and ROX1 occur preferentially in TATA-less promoters and show a strong preference for binding close to the transcription start site in these promoters. We provide evidence that suggests that pre-initiation complexes are recruited at TATA sites in TATA promoters and at the sites of the other proximal promoter motifs in TATA-less promoters. TATA-less promoters can generally be classified by the proximal promoter motif they contain, with different classes of TATA-less promoters showing different patterns of transcription factor binding site positioning and nucleosome coverage. These observations suggest that different modes of regulation of transcription initiation may be operating in the different promoter classes. In addition we show that, across all promoter classes, there is a close match between nucleosome free regions and regions of highest transcription factor binding site density. This close agreement between transcription factor binding site density and nucleosome depletion suggests a direct and general competition between transcription factors and nucleosomes for binding to promoters.

  10. Measuring Binding Affinity of Protein-Ligand Interaction Using Spectrophotometry: Binding of Neutral Red to Riboflavin-Binding Protein

    Science.gov (United States)

    Chenprakhon, Pirom; Sucharitakul, Jeerus; Panijpan, Bhinyo; Chaiyen, Pimchai

    2010-01-01

    The dissociation constant, K[subscript d], of the binding of riboflavin-binding protein (RP) with neutral red (NR) can be determined by titrating RP to a fixed concentration of NR. Upon adding RP to the NR solution, the maximum absorption peak of NR shifts to 545 nm from 450 nm for the free NR. The change of the absorption can be used to determine…

  11. Inverse Temperature Dependence in Static Quenching versus Calorimetric Exploration: Binding Interaction of Chloramphenicol to β-Lactoglobulin.

    Science.gov (United States)

    Ghosh, Narayani; Mondal, Ramakanta; Mukherjee, Saptarshi

    2015-07-28

    The binding interaction between the whey protein bovine β-lactoglobulin (βLG) with the well-known antibiotic chloramphenicol (Clp) is explored by monitoring the intrinsic fluorescence of βLG. Steady-state and time-resolved fluorescence spectral data reveal that quenching of βLG fluorescence proceeds through ground state complex formation, i.e., static quenching mechanism. However, the drug-protein binding constant is found to vary proportionately with temperature. This anomalous result is explained on the basis of the Arrhenius theory which states that the rate constant varies proportionally with temperature. Thermodynamic parameters like ΔH, ΔS, ΔG, and the stoichiometry for the binding interaction have been estimated by isothermal titration calorimetric (ITC) study. Thermodynamic data show that the binding phenomenon is mainly an entropy driven process suggesting the major role of hydrophobic interaction forces in the Clp-βLG binding. Constant pressure heat capacity change (ΔCp) has been calculated from enthalpy of binding at different temperatures which reveals that hydrophobic interaction is the major operating force. The inverse temperature dependence in static quenching is however resolved from ITC data which show that the binding constant regularly decreases with increase in temperature. The modification of native protein conformation due to binding of drug has been monitored by circular dichroism (CD) spectroscopy. The probable binding location of Clp inside βLG is explored from AutoDock based blind docking simulation.

  12. Stirling machine operating experience

    Energy Technology Data Exchange (ETDEWEB)

    Ross, B. [Stirling Technology Co., Richland, WA (United States); Dudenhoefer, J.E. [Lewis Research Center, Cleveland, OH (United States)

    1994-09-01

    Numerous Stirling machines have been built and operated, but the operating experience of these machines is not well known. It is important to examine this operating experience in detail, because it largely substantiates the claim that stirling machines are capable of reliable and lengthy operating lives. The amount of data that exists is impressive, considering that many of the machines that have been built are developmental machines intended to show proof of concept, and are not expected to operate for lengthy periods of time. Some Stirling machines (typically free-piston machines) achieve long life through non-contact bearings, while other Stirling machines (typically kinematic) have achieved long operating lives through regular seal and bearing replacements. In addition to engine and system testing, life testing of critical components is also considered. The record in this paper is not complete, due to the reluctance of some organizations to release operational data and because several organizations were not contacted. The authors intend to repeat this assessment in three years, hoping for even greater participation.

  13. Basic operator theory

    CERN Document Server

    Gohberg, Israel

    2001-01-01

    rii application of linear operators on a Hilbert space. We begin with a chapter on the geometry of Hilbert space and then proceed to the spectral theory of compact self adjoint operators; operational calculus is next presented as a nat­ ural outgrowth of the spectral theory. The second part of the text concentrates on Banach spaces and linear operators acting on these spaces. It includes, for example, the three 'basic principles of linear analysis and the Riesz­ Fredholm theory of compact operators. Both parts contain plenty of applications. All chapters deal exclusively with linear problems, except for the last chapter which is an introduction to the theory of nonlinear operators. In addition to the standard topics in functional anal­ ysis, we have presented relatively recent results which appear, for example, in Chapter VII. In general, in writ­ ing this book, the authors were strongly influenced by re­ cent developments in operator theory which affected the choice of topics, proofs and exercises. One ...

  14. General purpose operator interface

    Energy Technology Data Exchange (ETDEWEB)

    Bennion, S. I.

    1979-07-01

    The Hanford Engineering Development Laboratory in Richland, Washington is developing a general-purpose operator interface for controlling set-point driven processes. The interface concept is being developed around graphics display devices with touch-sensitive screens for direct interaction with the displays. Additional devices such as trackballs and keyboards are incorporated for the operator's convenience, but are not necessary for operation. The hardware and software are modular; only those capabilities needed for a particular application need to be used. The software is written in FORTRAN IV with minimal use of operating system calls to increase portability. Several ASCII files generated by the user define displays and correlate the display variables with the process parameters. It is also necessary for the user to build an interface routine which translates the internal graphics commands into device-specific commands. The interface is suited for both continuous flow processes and unit operations. An especially useful feature for controlling unit operations is the ability to generate and execute complex command sequences from ASCII files. This feature relieves operators of many repetitive tasks. 2 figures.

  15. Magellan Telescopes operations 2008

    Science.gov (United States)

    Osip, David J.; Phillips, Mark M.; Palunas, Povilas; Perez, Frank; Leroy, M.

    2008-07-01

    The twin 6.5m Magellan Telescopes have been in routine operations at the Las Campanas Observatory in the Chilean Andes since 2001 and 2002 respectively. The telescopes are owned and operated by Carnegie for the benefit of the Magellan consortium members (Carnegie Institution of Washington, Harvard University, the University of Arizona, Massachusetts Institute of Technology, and the University of Michigan). This paper provides an up to date review of the scientific, technical, and administrative structure of the 'Magellan Model' for observatory operations. With a modest operations budget and a reasonably small staff, the observatory is operated in the "classical" mode, wherein the visiting observer is a key member of the operations team. Under this model, all instrumentation is supplied entirely by the consortium members and the various instrument teams continue to play a critical support role beyond initial deployment and commissioning activities. Here, we present a critical analysis of the Magellan operations model and suggest lessons learned and changes implemented as we continue to evolve an organizational structure that can efficiently deliver a high scientific return for the investment of the partners.

  16. Hydropower Reservoir Operation using Standard Operating and Standard Hedging Policies

    OpenAIRE

    T.R. Neelakantan; K. Sasireka

    2013-01-01

    Standard operating policy and hedging policies are commonly used for reservoir operation for municipal or irrigation water supply. Application of these policies to hydropower reservoir operation is complex. In this paper, new standard operating policies and standard hedging policy are proposed for hydropower reservoir operation. The newly proposed policies were applied to the operation of Indira Sagar reservoir in India and demonstrated.

  17. Low enriched uranium foil targets with different geometries for the production of Molybdenum-99 in the BMR (Brazilian Multipurpose Reactor)

    Energy Technology Data Exchange (ETDEWEB)

    Domingos, Douglas B.; Silva, Antonio T. e; Joao, Thiago G.; Muniz, Rafael O.R.; Coelho, Talita S., E-mail: teixeira@ipen.b [Instituto de Pesquisas Energeticas e Nucleares (IPEN/CNEN-SP), Sao Paulo, SP (Brazil)

    2011-07-01

    A new research reactor is being planned in Brazil to take care of the demand of radiopharmaceuticals in the country and conduct research in various areas. This new reactor, the Brazilian Multipurpose Reactor (RMB), planned for 30 MW, is now in the conception design phase. Two low enriched (<20% {sup 235}U) metallic uranium foil targets (cylinder and plate geometries) are being considered for production of Molybdenum-99 ({sup 99}Mo) by fission. Neutronic and thermal-hydraulics calculations were performed to compare the production of {sup 99}Mo for these targets in the RMB and to determine the temperatures achieved in the targets. For the neutronic calculations were utilized the computer codes HAMMER-TECHNION, CITATION and SCALE and for the thermal-hydraulics calculations were utilized the computer codes MTRCR-IEA-R1 and ANSYS CFX. (author)

  18. Estradiol Binds to Insulin and Insulin Receptor Decreasing Insulin Binding in vitro

    Directory of Open Access Journals (Sweden)

    Robert eRoot-Bernstein

    2014-07-01

    Full Text Available Rationale: Insulin resistance associated with hyperestrogenemias occurs in gestational diabetes mellitus, polycystic ovary syndrome, ovarian hyperstimulation syndrome, estrogen therapies, metabolic syndrome and obesity. The mechanism by which insulin and estrogen interact is unknown. We hypothesize that estrogen binds directly to insulin and the insulin receptor producing insulin resistance.Objectives: To determine the binding constants of steroid hormones to insulin, the insulin receptor, and insulin-like peptides derived from the insulin receptor; and to investigate the effect of estrogens on the binding of insulin to its receptor.Methods: Ultraviolet spectroscopy, capillary electrophoresis and NMR demonstrated estrogen binding to insulin and its receptor. Horse-radish peroxidase-linked insulin was used in an ELISA-like procedure to measure the effect of estradiol on binding of insulin to its receptor. Measurements: Binding constants for estrogens to insulin and the insulin receptor were determined by concentration-dependent spectral shifts. The effect of estradiol on insulin-HRP binding to its receptor was determined by shifts in the insulin binding curve. Main Results: Estradiol bound to insulin with a Kd of 12 x 10-9 M and to the insulin receptor with a Kd of 24 x 10-9 M, while other hormones had significantly less affinity. 200 nM estradiol shifted the binding curve of insulin to its receptor 0.8 log units to the right. Conclusions: Estradiol concentrations in many hyperestrogenemic syndromes are sufficient to interfere with insulin binding to its receptor producing significant insulin resistance.

  19. Computer system operation

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Young Jae; Lee, Hae Cho; Lee, Ho Yeun; Kim, Young Taek; Lee, Sung Kyu; Park, Jeong Suk; Nam, Ji Wha; Kim, Soon Kon; Yang, Sung Un; Sohn, Jae Min; Moon, Soon Sung; Park, Bong Sik; Lee, Byung Heon; Park, Sun Hee; Kim, Jin Hee; Hwang, Hyeoi Sun; Lee, Hee Ja; Hwang, In A. [Korea Atomic Energy Research Institute, Taejon (Korea, Republic of)

    1993-12-01

    The report described the operation and the trouble shooting of main computer and KAERINet. The results of the project are as follows; 1. The operation and trouble shooting of the main computer system. (Cyber 170-875, Cyber 960-31, VAX 6320, VAX 11/780). 2. The operation and trouble shooting of the KAERINet. (PC to host connection, host to host connection, file transfer, electronic-mail, X.25, CATV etc.). 3. The development of applications -Electronic Document Approval and Delivery System, Installation the ORACLE Utility Program. 22 tabs., 12 figs. (Author) .new.

  20. Differences in Fusarium species in brown midrib sorghum and in air populations in production fields.

    Science.gov (United States)

    Funnell-Harris, Deanna Lillian; Scully, Erin D; Sattler, Scott E; French, Roy C; O'Neill, Patrick M; Pedersen, Jeffrey F

    2017-07-07

    Several Fusarium species cause sorghum [Sorghum bicolor (L.) Moench] grain mold, resulting in deterioration and mycotoxin production in the field and during storage. Fungal isolates from air (2005-2006), and from leaves and grain from wild-type and brown midrib (bmr)-6 and bmr12 plants (2002-2003), were collected from two locations. Compared with wild-type, bmr plants have reduced lignin content, altered cell wall composition and different levels of phenolic intermediates. Multilocus maximum likelihood analysis identified two Fusarium thapsinum operational taxonomic units (OTUs). One was identified at greater frequency in grain and leaves of bmr and wild-type plants, but was infrequently detected in air. Nine Fusarium graminearum OTUs were identified: one was detected at low levels in grain and leaves while the rest were only detected in air. Wright's F-statistic (FST) indicated that Fusarium air populations differentiated between locations during crop anthesis, but did not differ during vegetative growth, grain development and maturity. FST also indicated that Fusarium populations from wild-type grain were differentiated from those in bmr6 or bmr12 grain at one location but at the second location, populations from wild-type and bmr6 grain were more similar. Thus, impairing monolignol biosynthesis substantially effected Fusarium populations but environment had a strong influence.

  1. On Reflexive Binding in North Sami

    Directory of Open Access Journals (Sweden)

    Hanna Outakoski

    2004-01-01

    Full Text Available Principle A of the Binding Theory states that an anaphor must be A-bound in the local domain containing it, its governor and an accessible subject. However, if the anaphor is contained in an infinitival complement clause, it may, in North Sami, be bound either by the clause-mate subject or by the subject of the tensed clause. Thus, it appears that there is a larger binding domain for anaphors in addition to that determined by the condition A of standard binding theory. This domain can in some languages, as in North Sami, be defined by the notion of Tense whereas in other languages this need not be case, as in English. This supports the approach that the characterization of binding domains is parameterized and that languages pick different values of the parameter.

  2. Tau Induces Cooperative Taxol Binding to Microtubules

    Science.gov (United States)

    Ross, Jennifer; Santangelo, Christian; Victoria, Makrides; Fygenson, Deborah

    2004-03-01

    Taxol and tau are two ligands which stabilize the microtubule (MT) lattice. Taxol is an anti-mitotic drug that binds β tubulin in the MT interior. Tau is a MT-associated protein that binds both α and β tubulin on the MT exterior. Both taxol and tau reduce MT dynamics and promote tubulin polymerization. Tau alone also acts as a buttress to bundle, stiffen, and space MTs. A structural study recently suggested that taxol and tau may interact by binding to the same site. Using fluorescence recovery after photobleaching, we find that tau induces taxol to bind MTs cooperatively depending on the tau concentration. We develop a model that correctly fits the data in the absence of tau and yields a measure of taxol cooperativity when tau is present.

  3. Motion transparency promotes synchronous perceptual binding.

    Science.gov (United States)

    Clifford, Colin W G; Spehar, Branka; Pearson, Joel

    2004-12-01

    While identified regions of human extrastriate visual cortex are functionally specialized for processing different attributes of an object, the cognitive and neural mechanisms by which these attributes are dynamically bound into integrated percepts are still largely mysterious. Here, we report that perceptual organization influences the dynamics of binding. Specifically, the perception of motion transparency promotes the synchronous perceptual binding of colour and motion, which otherwise exhibits considerable asynchronies. In addition, we demonstrate that perceptual asynchrony can be reinstated by manipulating stereoscopic disparity or speed within the stimulus. Our findings suggest that the phenomenology of colour-motion binding parallels the known physiology of motion processing in area MT of primate visual cortex, supporting the view that the dynamics of perceptual binding is a direct reflection of the time course of the underlying neural processing.

  4. System Support for Managing Invalid Bindings

    CERN Document Server

    Das, Lachhman; Shah, Azhar; Khoumbati, Khalil; 10.5121/iju.2011.2303

    2011-01-01

    Context-aware adaptation is a central aspect of pervasive computing applications, enabling them to adapt and perform tasks based on contextual information. One of the aspects of context-aware adaptation is reconfiguration in which bindings are created between application component and remote services in order to realize new behaviour in response to contextual information. Various research efforts provide reconfiguration support and allow the development of adaptive context-aware applications from high-level specifications, but don't consider failure conditions that might arise during execution of such applications, making bindings between application and remote services invalid. To this end, we propose and implement our design approach to reconfiguration to manage invalid bindings. The development and modification of adaptive context-aware applications is a complex task, and an issue of an invalidity of bindings further complicates development efforts. To reduce the development efforts, our approach provides ...

  5. Receptor binding profile of Otilonium bromide.

    Science.gov (United States)

    Evangelista, S; Giachetti, A; Chapelain, B; Neliat, G; Maggi, C A

    1998-08-01

    The interaction of Otilonium bromide (OB) with binding sites for 63 different receptors and ion channels in appropriate preparations has been investigated. Experiments were also performed in rat colon, the preferred tissue for OB 'in vivo' uptake after oral administration. Among the receptors investigated OB binds with sub microM affinity to muscarinic M1, M2, M4, M5 and PAF receptors and with microM affinity to the diltiazem binding site on L type Ca2+ channels. In the rat colon OB shows competitive interaction with the verapamil binding site on L type Ca2+ channels and with muscarinic M2 receptors with IC50 of 1020 and 1220 nM, respectively. These findings provide a molecular rationale to explain the spasmolytic action exerted by OB on intestinal smooth muscle. In particular, a combination of antimuscarinic and Ca2+ channel blocker properties seems to best account for the action of this compound.

  6. HEAVY QUARK POTENTIALS AND QUARKONIA BINDING.

    Energy Technology Data Exchange (ETDEWEB)

    PETRECZKY,P.

    2004-11-04

    The author reviews recent progress in studying in-medium modification of inter-quark forces at finite temperature in lattice QCD. Some applications to the problem of quarkonium binding in potential models is also discussed.

  7. Hardware device binding and mutual authentication

    Energy Technology Data Exchange (ETDEWEB)

    Hamlet, Jason R; Pierson, Lyndon G

    2014-03-04

    Detection and deterrence of device tampering and subversion by substitution may be achieved by including a cryptographic unit within a computing device for binding multiple hardware devices and mutually authenticating the devices. The cryptographic unit includes a physically unclonable function ("PUF") circuit disposed in or on the hardware device, which generates a binding PUF value. The cryptographic unit uses the binding PUF value during an enrollment phase and subsequent authentication phases. During a subsequent authentication phase, the cryptographic unit uses the binding PUF values of the multiple hardware devices to generate a challenge to send to the other device, and to verify a challenge received from the other device to mutually authenticate the hardware devices.

  8. Adjustment of legally binding local plans

    DEFF Research Database (Denmark)

    Hvingel, Line Træholt; Aunsborg, Christian; Christensen, Finn Kjær

    2012-01-01

    Traditionally, and by law, new urban areas in Denmark are regulated and planned through legally binding local plans. Recently a tendency has occurred: The municipalities make the legally binding local plans quite open for future adjustment, and they are using a substantial amount of ‘empowerment......, which seem to be beyond the scope of the Danish Planning Act. This paper deals with this problem through case studies and a legal analysis of present law. If the combination of the legally binding local plan and subsequent added requirements is misused, it will weaken the legal rights of the citizens...... the considerations of legal rights, the extend of the legal use of empowerment provisions and the combination of the use of legal binding local plans and other legal instruments such as easements and sales agreements....

  9. Imidazole binding to human serum albumin.

    Science.gov (United States)

    Rodrigo, M C; Ceballos, A; Mariño, E; Cachaza, J M; Domínguez-Gil, A; Kuemmerle, H P

    1988-06-01

    Imidazole is a substance released by the organism when a new salicylate derivative, imidazole salicylate is administered. A study was made of the binding of imidazole to human serum albumin by an in vitro assay employing an ultrafiltration technique. For the concentration range that imidazole was found in plasma following administration of the drug to healthy volunteers, the mean binding percentages were: 12.1 +/- 1.8 and 19.7 +/- 3.1 at 37 degrees C and 25 degrees C, respectively. The results obtained in the study follow a model entailing three equal and independent binding sites of imidazole to serum albumin and the values of the corresponding constants were determined. Apparently, the presence in the plasma samples of sodium salicylate at a concentration of 100 micrograms/ml does not affect the binding of imidazole to human serum albumin.

  10. Acyl-coenzyme A binding protein, ACBP

    DEFF Research Database (Denmark)

    Kragelund, Birthe Brandt; Knudsen, J.; Poulsen, Flemming

    1999-01-01

    Acyl-coenzyme A binding proteins are known from a large group of eukaryote species and to bind a long chain length acyl-CoA ester with very high affinity. Detailed biochemical mapping of ligand binding properties has been obtained as well as in-depth structural studies on the bovine apo-protein...... and of the complex with palmitoyl-CoA using NMR spectroscopy. In the four a-helix bundle structure, a set of 21 highly conserved residues present in more that 90% of all known sequences of acyl-coenzyme A binding proteins constitutes three separate mini-cores. These residues are predominantly located at the helix......-helix interfaces. From studies of a large set of mutant proteins the role of the conserved residues has been related to structure, function, folding and stability....

  11. Acyl-coenzyme A binding protein (ACBP)

    DEFF Research Database (Denmark)

    Kragelund, B B; Knudsen, J; Poulsen, F M

    1999-01-01

    and of the complex with palmitoyl-CoA using NMR spectroscopy. In the four alpha-helix bundle structure, a set of 21 highly conserved residues present in more that 90% of all known sequences of acyl-coenzyme A binding proteins constitutes three separate mini-cores. These residues are predominantly located......Acyl-coenzyme A binding proteins are known from a large group of eukaryote species and to bind a long chain length acyl-CoA ester with very high affinity. Detailed biochemical mapping of ligand binding properties has been obtained as well as in-depth structural studies on the bovine apo-protein...... at the helix-helix interfaces. From studies of a large set of mutant proteins the role of the conserved residues has been related to structure, function, folding and stability....

  12. Commercialization in NASA Space Operations

    Science.gov (United States)

    Gilbert, Charlene E.

    1998-01-01

    Various issues associated with commercialization in NASA space operations are presented in viewgraph form. Specific topics include: 1) NASA's financial outlook; 2) Space operations; 3) Space operations technology; and 4) Strategies associated with these operations.

  13. Binding capacity: cooperativity and buffering in biopolymers.

    Science.gov (United States)

    Di Cera, E; Gill, S J; Wyman, J

    1988-01-01

    The group of linkage potentials resulting from the energy of a physicochemical system expressed per mol of a reference component, say a polyfunctional macromolecule, leads to the concept of binding capacity. This concept applies equally to both chemical and physical ligands and opens the way to consideration of higher-order linkage relationships. It provides a means of exploring the consequences of thermodynamic stability on generalized binding phenomena in biopolymers. PMID:3422436

  14. Predicting zinc binding at the proteome level

    Directory of Open Access Journals (Sweden)

    Rosato Antonio

    2007-02-01

    Full Text Available Abstract Background Metalloproteins are proteins capable of binding one or more metal ions, which may be required for their biological function, for regulation of their activities or for structural purposes. Metal-binding properties remain difficult to predict as well as to investigate experimentally at the whole-proteome level. Consequently, the current knowledge about metalloproteins is only partial. Results The present work reports on the development of a machine learning method for the prediction of the zinc-binding state of pairs of nearby amino-acids, using predictors based on support vector machines. The predictor was trained using chains containing zinc-binding sites and non-metalloproteins in order to provide positive and negative examples. Results based on strong non-redundancy tests prove that (1 zinc-binding residues can be predicted and (2 modelling the correlation between the binding state of nearby residues significantly improves performance. The trained predictor was then applied to the human proteome. The present results were in good agreement with the outcomes of previous, highly manually curated, efforts for the identification of human zinc-binding proteins. Some unprecedented zinc-binding sites could be identified, and were further validated through structural modelling. The software implementing the predictor is freely available at: http://zincfinder.dsi.unifi.it Conclusion The proposed approach constitutes a highly automated tool for the identification of metalloproteins, which provides results of comparable quality with respect to highly manually refined predictions. The ability to model correlations between pairwise residues allows it to obtain a significant improvement over standard 1D based approaches. In addition, the method permits the identification of unprecedented metal sites, providing important hints for the work of experimentalists.

  15. Fractal aspects of calcium binding protein structures

    Energy Technology Data Exchange (ETDEWEB)

    Isvoran, Adriana [West University of Timisoara, Department of Chemistry, Pestalozzi 16, 300115 Timisoara (Romania)], E-mail: aisvoran@cbg.uvt.ro; Pitulice, Laura [West University of Timisoara, Department of Chemistry, Pestalozzi 16, 300115 Timisoara (Romania); Craescu, Constantin T. [INSERM U759/Institute Curie-Recherche, Centre Universitaire Paris-Sud, Batiment 112, 91405 Orsay (France); Chiriac, Adrian [West University of Timisoara, Department of Chemistry, Pestalozzi 16, 300115 Timisoara (Romania)

    2008-03-15

    The structures of EF-hand calcium binding proteins may be classified into two distinct groups: extended and compact structures. In this paper we studied 20 different structures of calcium binding proteins using the fractal analysis. Nine structures show extended shapes, one is semi-compact and the other 10 have compact shapes. Our study reveals different fractal characteristics for protein backbones belonging to different structural classes and these observations may be correlated to the physicochemical forces governing the protein folding.

  16. Ligand Binding to Macromolecules: Allosteric and Sequential Models of Cooperativity.

    Science.gov (United States)

    Hess, V. L.; Szabo, Attila

    1979-01-01

    A simple model is described for the binding of ligands to macromolecules. The model is applied to the cooperative binding by hemoglobin and aspartate transcarbamylase. The sequential and allosteric models of cooperative binding are considered. (BB)

  17. Nuclear material operations manual

    Energy Technology Data Exchange (ETDEWEB)

    Tyler, R.P.

    1981-02-01

    This manual provides a concise and comprehensive documentation of the operating procedures currently practiced at Sandia National Laboratories with regard to the management, control, and accountability of nuclear materials. The manual is divided into chapters which are devoted to the separate functions performed in nuclear material operations-management, control, accountability, and safeguards, and the final two chapters comprise a document which is also issued separately to provide a summary of the information and operating procedures relevant to custodians and users of radioactive and nuclear materials. The manual also contains samples of the forms utilized in carrying out nuclear material activities. To enhance the clarity of presentation, operating procedures are presented in the form of playscripts in which the responsible organizations and necessary actions are clearly delineated in a chronological fashion from the initiation of a transaction to its completion.

  18. Operating plan FY 1998

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-10-01

    This document is the first edition of Argonne`s new Operating Plan. The Operating Plan complements the strategic planning in the Laboratory`s Institutional Plan by focusing on activities that are being pursued in the immediate fiscal year, FY 1998. It reflects planning that has been done to date, and it will serve in the future as a resource and a benchmark for understanding the Laboratory`s performance. The heart of the Institutional Plan is the set of major research initiatives that the Laboratory is proposing to implement in future years. In contrast, this Operating Plan focuses on Argonne`s ongoing R&D programs, along with cost-saving measures and other improvements being implemented in Laboratory support operations.

  19. Operation of monetary policy

    National Research Council Canada - National Science Library

    1984-01-01

    ... stocks Per cent per annum 10 15 20 30 50 Years to maturity 13 Operation of monetary policy This article covers the three months mid-November 1983 to mid-February 1984. The behaviour of the moneta...

  20. LCOGT Network Observatory Operations

    CERN Document Server

    Pickles, Andrew; Boroson, Todd; Burleson, Ben; Conway, Patrick; de Vera, Jon; Elphick, Mark; Haworth, Brian; Rosing, Wayne; Saunders, Eric; Thomas, Doug; White, Gary; Willis, Mark; Walker, Zach

    2014-01-01

    We describe the operational capabilities of the Las Cumbres Observatory Global Telescope Network. We summarize our hardware and software for maintaining and monitoring network health. We focus on methodologies to utilize the automated system to monitor availability of sites, instruments and telescopes, to monitor performance, permit automatic recovery, and provide automatic error reporting. The same jTCS control system is used on telescopes of apertures 0.4m, 0.8m, 1m and 2m, and for multiple instruments on each. We describe our network operational model, including workloads, and illustrate our current tools, and operational performance indicators, including telemetry and metrics reporting from on-site reductions. The system was conceived and designed to establish effective, reliable autonomous operations, with automatic monitoring and recovery - minimizing human intervention while maintaining quality. We illustrate how far we have been able to achieve that.

  1. CH Packaging Operations Manual

    Energy Technology Data Exchange (ETDEWEB)

    Washington TRU Solutions LLC

    2005-06-13

    This procedure provides instructions for assembling the CH Packaging Drum payload assembly, Standard Waste Box (SWB) assembly, Abnormal Operations and ICV and OCV Preshipment Leakage Rate Tests on the packaging seals, using a nondestructive Helium (He) Leak Test.

  2. South African Airborne Operations

    African Journals Online (AJOL)

    South Africa carried out numerous airborne operations during the latter part ofthe last century. .... Watch, an engineer unit under command of Commandant Louw, which had been ..... locals, to transport weapons, food and other supplies.

  3. Intelligence Operations Manual

    Directory of Open Access Journals (Sweden)

    Karla Andrade

    2016-02-01

    Full Text Available This Manual was an important document for the development of intelligence units in El Salvador´s police. It is a guiding document for intelligence operations where relevant aspects on overall information management are detailed.

  4. Construction Minerals Operations

    Data.gov (United States)

    Department of Homeland Security — This map layer includes construction minerals operations in the United States. The data represent commodities covered by the Minerals Information Team (MIT) of the...

  5. Sand and Gravel Operations

    Data.gov (United States)

    Department of Homeland Security — This map layer includes sand and gravel operations in the United States. These data were obtained from information reported voluntarily to the USGS by the aggregate...

  6. Agricultural Minerals Operations

    Data.gov (United States)

    Department of Homeland Security — This map layer includes agricultural minerals operations in the United States. The data represent commodities covered by the Minerals Information Team (MIT) of the...

  7. Information Operations Primer

    Science.gov (United States)

    2010-11-01

    Director, Information Operations & Strategic Studies Rosemary Wenchel DISES Requirements & Programs IO Intelligence Integration Plans & Policy...competitive civil service selection process. Mr. Mark H. Johnson ( DISES ) is the Director of JIOWC, and USAR Colonel Vincent D. Crabb is the Deputy

  8. Operable Unit Boundaries

    Data.gov (United States)

    U.S. Environmental Protection Agency — This dataset consists of operable unit data from multiple Superfund sites in U.S. EPA Region 8. These data were acquired from multiple sources at different times and...

  9. Administrative & Operational Circulars - Reminder

    CERN Multimedia

    HR Department

    2011-01-01

    All Administrative and Operational Circulars are available on the intranet site of the Human Resources Department at the following address: http://cern.ch/hr-docs/admincirc/admincirc.asp Department Head Office  

  10. Dialectic operator fuzzy logic

    Institute of Scientific and Technical Information of China (English)

    程晓春; 姜云飞; 刘叙华

    1996-01-01

    Dialectic operator fuzzy logic (DOFL) is presented which is relevant,paraconsistent and nonmonotonic.DOFL can vividly describe the belief revision in the cognitive process and can infer reasonably well while the knowledge is inconsistent,imprecise or incomplete.

  11. Crushed Stone Operations

    Data.gov (United States)

    Department of Homeland Security — This map layer includes crushed stone operations in the United States. These data were obtained from information reported voluntarily to the USGS by the aggregate...

  12. Landfills - Municipal Waste Operations

    Data.gov (United States)

    NSGIC GIS Inventory (aka Ramona) — A Municipal Waste Operation is a DEP primary facility type related to the Waste Management Municipal Waste Program. The sub-facility types related to Municipal Waste...

  13. Payroll Operational Data Store

    Data.gov (United States)

    Social Security Administration — The Payroll ODS will provide a single repository of payroll data to produce accurate and timely financial reports to support operating, budget, and policy decisions.

  14. Adaptively Compressed Exchange Operator

    CERN Document Server

    Lin, Lin

    2016-01-01

    The Fock exchange operator plays a central role in modern quantum chemistry. The large computational cost associated with the Fock exchange operator hinders Hartree-Fock calculations and Kohn-Sham density functional theory calculations with hybrid exchange-correlation functionals, even for systems consisting of hundreds of atoms. We develop the adaptively compressed exchange operator (ACE) formulation, which greatly reduces the computational cost associated with the Fock exchange operator without loss of accuracy. The ACE formulation does not depend on the size of the band gap, and thus can be applied to insulating, semiconducting as well as metallic systems. In an iterative framework for solving Hartree-Fock-like systems, the ACE formulation only requires moderate modification of the code, and can be potentially beneficial for all electronic structure software packages involving exchange calculations. Numerical results indicate that the ACE formulation can become advantageous even for small systems with tens...

  15. The readiness potential reflects intentional binding

    Directory of Open Access Journals (Sweden)

    Han-Gue eJo

    2014-06-01

    Full Text Available When a voluntary action is causally linked with a sensory outcome, the action and its consequent effect are perceived as being closer together in time. This effect is called intentional binding. Although many experiments were conducted on this phenomenon, the underlying neural mechanisms are not well understood. While intentional binding is specific to voluntary action, we presumed that preconscious brain activity (the readiness potential, RP, which occurs before an action is made, might play an important role in this binding effect. In this study, the brain dynamics were recorded with electroencephalography (EEG and analyzed in single-trials in order to estimate whether intentional binding is correlated with the early neural processes. Moreover, we were interested in different behavioral performance between meditators and non-meditators since meditators are expected to be able to keep attention more consistently on a task. Thus, we performed the intentional binding paradigm with twenty mindfulness meditators and compared them to matched controls. Although, we did not observe a group effect on either behavioral data or EEG recordings, we found that self-initiated movements following ongoing negative deflections of slow cortical potentials (SCPs result in a stronger binding effect compared to positive potentials, especially regarding the perceived time of the consequent effect. Our results provide the first direct evidence that the early neural activity within the range of SCPs affects perceived time of a sensory outcome that is caused by intentional action.

  16. Comparative serum protein binding of anthracycline derivatives.

    Science.gov (United States)

    Chassany, O; Urien, S; Claudepierre, P; Bastian, G; Tillement, J P

    1996-01-01

    The binding of doxorubicin, iododoxorubicin, daunorubicin, epirubicin, pirarubicin, zorubicin, aclarubicin, and mitoxantrone to 600 microM human serum albumin and 50 microM alpha 1-acid glycoprotein was studied by ultrafiltration at 37 degrees C and pH 7.4. Anthracycline concentrations (total and free) were determined by high-performance liquid chromatography (HPLC) with fluorometric detection. Binding to albumin (600 microM) varied from 61% (daunorubicin) to 94% (iododoxorubicin). The binding to alpha 1-acid glycoprotein (50 microM) was more variable, ranging from 31% (epirubicin) to 64% (zorubicin), and was essentially related to the hydrophobicity of the derivatives. Simulations showed that the total serum binding varied over a broad range from 71% (doxorubicin) to 96% (iododoxorubicin). We recently reported that the binding to lipoproteins of a series of eight anthracycline analogues could be ascribed to chemicophysical determinants of lipophilicity [2]. The present study was conducted to evaluate in vitro the contribution of albumin and alpha 1-acid glycoprotein to the total serum binding of these drugs.

  17. Zinc Binding by Lactic Acid Bacteria

    Directory of Open Access Journals (Sweden)

    Jasna Mrvčić

    2009-01-01

    Full Text Available Zinc is an essential trace element in all organisms. A common method for the prevention of zinc deficiency is pharmacological supplementation, especially in a highly available form of a metalloprotein complex. The potential of different microbes to bind essential and toxic heavy metals has recently been recognized. In this work, biosorption of zinc by lactic acid bacteria (LAB has been investigated. Specific LAB were assessed for their ability to bind zinc from a water solution. Significant amount of zinc ions was bound, and this binding was found to be LAB species-specific. Differences among the species in binding performance at a concentration range between 10–90 mg/L were evaluated with Langmuir model for biosorption. Binding of zinc was a fast process, strongly influenced by ionic strength, pH, biomass concentration, and temperature. The most effective metal-binding LAB species was Leuconostoc mesenteroides (27.10 mg of Zn2+ per gram of dry mass bound at pH=5 and 32 °C, during 24 h. FT-IR spectroscopy analysis and electron microscopy demonstrated that passive adsorption and active uptake of the zinc ions were involved.

  18. DNA-Aptamers Binding Aminoglycoside Antibiotics

    Directory of Open Access Journals (Sweden)

    Nadia Nikolaus

    2014-02-01

    Full Text Available Aptamers are short, single stranded DNA or RNA oligonucleotides that are able to bind specifically and with high affinity to their non-nucleic acid target molecules. This binding reaction enables their application as biorecognition elements in biosensors and assays. As antibiotic residues pose a problem contributing to the emergence of antibiotic-resistant pathogens and thereby reducing the effectiveness of the drug to fight human infections, we selected aptamers targeted against the aminoglycoside antibiotic kanamycin A with the aim of constructing a robust and functional assay that can be used for water analysis. With this work we show that aptamers that were derived from a Capture-SELEX procedure targeting against kanamycin A also display binding to related aminoglycoside antibiotics. The binding patterns differ among all tested aptamers so that there are highly substance specific aptamers and more group specific aptamers binding to a different variety of aminoglycoside antibiotics. Also the region of the aminoglycoside antibiotics responsible for aptamer binding can be estimated. Affinities of the different aptamers for their target substance, kanamycin A, are measured with different approaches and are in the micromolar range. Finally, the proof of principle of an assay for detection of kanamycin A in a real water sample is given.

  19. Electrostatically biased binding of kinesin to microtubules.

    Directory of Open Access Journals (Sweden)

    Barry J Grant

    2011-11-01

    Full Text Available The minimum motor domain of kinesin-1 is a single head. Recent evidence suggests that such minimal motor domains generate force by a biased binding mechanism, in which they preferentially select binding sites on the microtubule that lie ahead in the progress direction of the motor. A specific molecular mechanism for biased binding has, however, so far been lacking. Here we use atomistic Brownian dynamics simulations combined with experimental mutagenesis to show that incoming kinesin heads undergo electrostatically guided diffusion-to-capture by microtubules, and that this produces directionally biased binding. Kinesin-1 heads are initially rotated by the electrostatic field so that their tubulin-binding sites face inwards, and then steered towards a plus-endwards binding site. In tethered kinesin dimers, this bias is amplified. A 3-residue sequence (RAK in kinesin helix alpha-6 is predicted to be important for electrostatic guidance. Real-world mutagenesis of this sequence powerfully influences kinesin-driven microtubule sliding, with one mutant producing a 5-fold acceleration over wild type. We conclude that electrostatic interactions play an important role in the kinesin stepping mechanism, by biasing the diffusional association of kinesin with microtubules.

  20. The readiness potential reflects intentional binding.

    Science.gov (United States)

    Jo, Han-Gue; Wittmann, Marc; Hinterberger, Thilo; Schmidt, Stefan

    2014-01-01

    When a voluntary action is causally linked with a sensory outcome, the action and its consequent effect are perceived as being closer together in time. This effect is called intentional binding. Although many experiments were conducted on this phenomenon, the underlying neural mechanisms are not well understood. While intentional binding is specific to voluntary action, we presumed that preconscious brain activity (the readiness potential, RP), which occurs before an action is made, might play an important role in this binding effect. In this study, the brain dynamics were recorded with electroencephalography (EEG) and analyzed in single-trials in order to estimate whether intentional binding is correlated with the early neural processes. Moreover, we were interested in different behavioral performance between meditators and non-meditators since meditators are expected to be able to keep attention more consistently on a task. Thus, we performed the intentional binding paradigm with 20 mindfulness meditators and compared them to matched controls. Although, we did not observe a group effect on either behavioral data or EEG recordings, we found that self-initiated movements following ongoing negative deflections of slow cortical potentials (SCPs) result in a stronger binding effect compared to positive potentials, especially regarding the perceived time of the consequent effect. Our results provide the first direct evidence that the early neural activity within the range of SCPs affects perceived time of a sensory outcome that is caused by intentional action.

  1. Operational waste volume projection

    Energy Technology Data Exchange (ETDEWEB)

    Koreski, G.M.

    1996-09-20

    Waste receipts to the double-shell tank system are analyzed and wastes through the year 2015 are projected based on generation trends of the past 12 months. A computer simulation of site operations is performed, which results in projections of tank fill schedules, tank transfers, evaporator operations, tank retrieval, and aging waste tank usage. This projection incorporates current budget planning and the clean-up schedule of the Tri-Party Agreement. Assumptions were current as of June 1996.

  2. Joint Operations. Change 1

    Science.gov (United States)

    2008-02-13

    Egypt , Turkey, Saudi Arabia, and the United States, as well as other nations. On 9 December 1992, under UN auspices, US special operations forces and...collection to produce the most accurate intelligence products. (2) Where there is little USG or US military presence, open-source intelligence ( OSINT ) may...be the best immediately available information to prepare US forces to operate in a foreign country. OSINT from radio broadcasts, newspapers, and

  3. Somalia Operations: Lessons Learned

    Science.gov (United States)

    1995-01-01

    are the only other • .o" ’" "- THE OPERATIONAL COwnTEX FI(GUM1, EI Smoall Gulf of Aden DJIEBO U.S. and SomaMa Flelol Sin 12 SOMALIA OPERATIONS: LESSONS...demeanor that sawess q-d let diplomacy and reasuing wMii achiev- more than arogance. anger, disdain. coon. or sarcasm . PmmmeI mut be able to cope pq

  4. Quality in drilling operations

    Energy Technology Data Exchange (ETDEWEB)

    Duncan, E.; Gervais, I. [Sedco Forex Jacintoport Facility, Channelview, TX (United States); Le Moign, Y.; Pangarkar, S.; Stibbs, B. [Sedco Forex, Montrouge (France); McMorran, P. [Sedco Forex, Pau (France); Nordquist, E. [Dubai Petroleum Company, Dubai (United Arab Emirates); Pittman, T. [Sedco Forex, Perth (Australia); Schindler, H. [Sedco Forex, Dubai (United Arab Emirates); Scott, P. [Woodside Offshore Petroleum Pty. Ltd., Perth (Australia)

    1996-12-31

    Driven by cost and profitability pressures, quality has taken on new meaning and importance in the oil field during the past decade. In drilling operations, new initiatives have led to cooperative team efforts between operators and drilling contractors to enhance quality. In this article examples are given of how one drilling contractor, by adopting a quality culture, is reaping major benefits for its clients as well as its employees. 22 figs., 19 refs.

  5. Operational Logistics Wargame

    Science.gov (United States)

    2001-12-01

    Gettysburg CG 64 Ticonderoga 0 40 3 Nicholson DD 982 Spruance 20 0 4 Cole DDG 67 Arleigh Burke 60 20 5 Rueben James FFG 57 Perry 0 20 6 Halyburton FFG 40...the Operational Logistics Wargame and depicted in this document were obtained from a variety of sources including theses by Lt J.R. Sterba and Lt A.W...Consumption: Update, NPS, July 1996. Sterba , J. R., Operational Maneuver from the Sea Logistics Training Aid, NPS, September 1999, Troxell, A

  6. Stochastic power system operation

    OpenAIRE

    Power, Michael

    2010-01-01

    This paper outlines how to economically and reliably operate a power system with high levels of renewable generation which are stochastic in nature. It outlines the challenges for system operators, and suggests tools and methods for meeting this challenge, which is one of the most fundamental since large scale power networks were instituted. The Ireland power system, due to its nature and level of renewable generation, is considered as an example in this paper.

  7. Operational Risk Modeling

    Directory of Open Access Journals (Sweden)

    Gabriela ANGHELACHE

    2011-06-01

    Full Text Available Losses resulting from operational risk events from a complex interaction between organizational factors, personal and market participants that do not fit a simple classification scheme. Taking into account past losses (ex. Barings, Daiwa, etc. we can say that operational risk is a major financial losses in the banking sector, although until recently have been underestimated, considering that they are generally minor, note setting survival of a bank.

  8. To Bind or not to Bind: It’s in the Contract

    DEFF Research Database (Denmark)

    Tvarnø, Christina D.

    2015-01-01

    discusses, in a theoretical perspective, the legal reasoning behind the different partnering approaches, both from a historical and contract law perspective, and furthermore applies a game theoretical approach in evaluating binding versus non-binding partnering contracts. The analysis focuses on private......This article discusses the formalization of collaboration through partnering contracts in the construction industry in the USA, Great Britain and Denmark. The article compares the different types of collaborative partnering contracts in the three countries, and provides a conclusion on whether...... the collaborative partnering contract should be binding or non-binding, based on the three empirical contracts analyzed in this article. The partnering contracts in Great Britain and Denmark are legally binding, while in the USA the partnering agreements are non-binding charters or letters of intent. This article...

  9. Theoretical studies of binding of mannose-binding protein to monosaccharides

    Science.gov (United States)

    Aida-Hyugaji, Sachiko; Takano, Keiko; Takada, Toshikazu; Hosoya, Haruo; Kojima, Naoya; Mizuochi, Tsuguo; Inoue, Yasushi

    2004-11-01

    Binding properties of mannose-binding protein (MBP) to monosaccharides are discussed based on ab initio molecular orbital calculations for cluster models constructed. The calculated binding energies indicate that MBP has an affinity for N-acetyl- D-glucosamine, D-mannose, L-fucose, and D-glucose rather than D-galactose and N-acetyl- D-galactosamine, which is consistent with the biochemical experimental results. Electrostatic potential surfaces at the binding site of four monosaccharides having binding properties matched well with that of MBP. A vacant frontier orbital was found to be localized around the binding site of MBP, suggesting that MBP-monosaccharide interaction may occur through electrostatic and orbital interactions.

  10. Mannose-Binding Lectin Binds to Amyloid Protein and Modulates Inflammation

    Directory of Open Access Journals (Sweden)

    Mykol Larvie

    2012-01-01

    Full Text Available Mannose-binding lectin (MBL, a soluble factor of the innate immune system, is a pattern recognition molecule with a number of known ligands, including viruses, bacteria, and molecules from abnormal self tissues. In addition to its role in immunity, MBL also functions in the maintenance of tissue homeostasis. We present evidence here that MBL binds to amyloid β peptides. MBL binding to other known carbohydrate ligands is calcium-dependent and has been attributed to the carbohydrate-recognition domain, a common feature of other C-type lectins. In contrast, we find that the features of MBL binding to Aβ are more similar to the reported binding characteristics of the cysteine-rich domain of the unrelated mannose receptor and therefore may involve the MBL cysteine-rich domain. Differences in MBL ligand binding may contribute to modulation of inflammatory response and may correlate with the function of MBL in processes such as coagulation and tissue homeostasis.

  11. NRC staff review of licensee responses to pressure-locking and thermal-binding issue

    Energy Technology Data Exchange (ETDEWEB)

    Rathbun, H.J.

    1996-12-01

    Commercial nuclear power plant operating experience has indicated that pressure locking and thermal binding represent potential common mode failure mechanisms that can cause safety-related power-operated gate valves to fail in the closed position, thus rendering redundant safety-related systems incapable of performing their safety functions. In Generic Letter (GL) 95-07, {open_quotes}Pressure Locking and Thermal Binding of Safety-Related Power-Operated Gate Valves,{close_quotes} the U.S. Nuclear Regulatory Commission (NRC) staff requested that nuclear power plant licensees take certain actions to ensure that valves susceptible to pressure locking or thermal binding are capable of performing their safety functions within the current licensing bases of the facility. The NRC staff has received summary information from licensees in response to GL 95-07 describing actions they have taken to prevent the occurrence of pressure locking and thermal binding. The NRC staff has developed a systematic process to help ensure uniform and consistent review of licensee submittals in response to GL 95-07.

  12. Ca2+ and Mg2+ binding induce conformational stability of Calfumirin-1 from Dictyostelium discoideum

    Indian Academy of Sciences (India)

    Bairagi C Mallick; Sa-Ouk Kang; Suman Jha

    2014-05-01

    The apo-Calfumirin-1 (CAF-1) binds to Ca2+ with high affinity and also to Mg2+ with high positive cooperativity. The thermal unfolding curves of wtCAF-1 monitored at neutral pH by CD spectroscopy are reversible and show different thermal stabilities in the absence or presence of Ca2+ and Mg2+ ions. Metalfree wtCAF-1 shows greater thermal stability than EF-IV mutant protein. We observed that GdnHCl-induced unfolding of apo-wtCAF-1 monitored by CD and fluorescence spectroscopies increases co-operative folding with approximately same C values. Binding of Ca2+ and Mg2+ ions to CAF-1 dramatically altered the fluorescence and CD spectra, indicating metal ion-induced conformational changes both in the wild-type and mutant proteins. The hydrophobic probe, ANS is used to observe alteration in surface hydrophobicity of the protein in different ligation states. In apo-wtCAF-1, the exposed hydrophobic surfaces are able to bind ANS which is in contrast to the unfolded or the metal ions ligated conformations. Isothermal titration calorimetry (ITC) resultsshow two possible independent binding sites of comparable affinity for the metal ions. However, their binding to the EF-IV E helix-loop-F helix mutant apo-protein happens with different affinities. The present study demonstrates that Ca2+ or Mg2+ binding plays a possible role in the conformational stability of the protein.

  13. Solution Structure and Backbone Dynamics of Human Liver Fatty Acid Binding Protein: Fatty Acid Binding Revisited

    OpenAIRE

    Cai, Jun; Lücke, Christian; Chen, Zhongjing; Qiao, Ye; Klimtchuk, Elena; Hamilton, James A.

    2012-01-01

    Liver fatty acid binding protein (L-FABP), a cytosolic protein most abundant in liver, is associated with intracellular transport of fatty acids, nuclear signaling, and regulation of intracellular lipolysis. Among the members of the intracellular lipid binding protein family, L-FABP is of particular interest as it can i), bind two fatty acid molecules simultaneously and ii), accommodate a variety of bulkier physiological ligands such as bilirubin and fatty acyl CoA. To better understand the p...

  14. Automatic Binding Time Analysis for a Typed Lambda-Calculus

    DEFF Research Database (Denmark)

    Nielson, Hanne Riis; Nielson, Flemming

    1988-01-01

    analysis of the binding times of a typed lambda-calculus with products, sums, lists and general recursive types. Given partial information about the binding times of some of the subexpressions it will complete that information such that (i) early bindings may be turned into late bindings but not vice versa......, (ii) the resulting two-level lambda-expression reflects our intuition about binding times, e.g. that early bindings are performed before late bindings, and (iii) as few changes as possible have been made compared with the initial binding information. The results can be applied in the implementation...

  15. Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species.

    Directory of Open Access Journals (Sweden)

    Robert K Bradley

    2010-03-01

    Full Text Available Changes in gene expression play an important role in evolution, yet the molecular mechanisms underlying regulatory evolution are poorly understood. Here we compare genome-wide binding of the six transcription factors that initiate segmentation along the anterior-posterior axis in embryos of two closely related species: Drosophila melanogaster and Drosophila yakuba. Where we observe binding by a factor in one species, we almost always observe binding by that factor to the orthologous sequence in the other species. Levels of binding, however, vary considerably. The magnitude and direction of the interspecies differences in binding levels of all six factors are strongly correlated, suggesting a role for chromatin or other factor-independent forces in mediating the divergence of transcription factor binding. Nonetheless, factor-specific quantitative variation in binding is common, and we show that it is driven to a large extent by the gain and loss of cognate recognition sequences for the given factor. We find only a weak correlation between binding variation and regulatory function. These data provide the first genome-wide picture of how modest levels of sequence divergence between highly morphologically similar species affect a system of coordinately acting transcription factors during animal development, and highlight the dominant role of quantitative variation in transcription factor binding over short evolutionary distances.

  16. Crystal Structure of the Botulinum Neurotoxin Type G Binding Domain: Insight into Cell Surface Binding

    Energy Technology Data Exchange (ETDEWEB)

    Stenmark, Pål; Dong, Min; Dupuy, Jérôme; Chapman, Edwin R.; Stevens, Raymond C. (Scripps); (UW)

    2011-11-02

    Botulinum neurotoxins (BoNTs) typically bind the neuronal cell surface via dual interactions with both protein receptors and gangliosides. We present here the 1.9-{angstrom} X-ray structure of the BoNT serotype G (BoNT/G) receptor binding domain (residues 868-1297) and a detailed view of protein receptor and ganglioside binding regions. The ganglioside binding motif (SxWY) has a conserved structure compared to the corresponding regions in BoNT serotype A and BoNT serotype B (BoNT/B), but several features of interactions with the hydrophilic face of the ganglioside are absent at the opposite side of the motif in the BoNT/G ganglioside binding cleft. This may significantly reduce the affinity between BoNT/G and gangliosides. BoNT/G and BoNT/B share the protein receptor synaptotagmin (Syt) I/II. The Syt binding site has a conserved hydrophobic plateau located centrally in the proposed protein receptor binding interface (Tyr1189, Phe1202, Ala1204, Pro1205, and Phe1212). Interestingly, only 5 of 14 residues that are important for binding between Syt-II and BoNT/B are conserved in BoNT/G, suggesting that the means by which BoNT/G and BoNT/B bind Syt diverges more than previously appreciated. Indeed, substitution of Syt-II Phe47 and Phe55 with alanine residues had little effect on the binding of BoNT/G, but strongly reduced the binding of BoNT/B. Furthermore, an extended solvent-exposed hydrophobic loop, located between the Syt binding site and the ganglioside binding cleft, may serve as a third membrane association and binding element to contribute to high-affinity binding to the neuronal membrane. While BoNT/G and BoNT/B are homologous to each other and both utilize Syt-I/Syt-II as their protein receptor, the precise means by which these two toxin serotypes bind to Syt appears surprisingly divergent.

  17. Lessons Learned in Building VO Resources: Binding Together Several VO Standards into an Operational Service

    Science.gov (United States)

    Chilingarian, I.; Bonnarel, F.; Louys, M.; Le Sidaner, P.

    2012-09-01

    The International Virtual Observatory Alliance (IVOA) developed numerous interoperability standards during the last several years. Most of them are quite simple to implement from the technical point of view and even contain “SIMPLE” in the title. Does it mean that it is also simple to build a working VO resource using those standards? Yes and no. “Yes” because the standards are indeed simple, and “no” because usually one needs to implement a lot more than it was thought in the beginning of the project so the time management of the team becomes difficult. In our presentation we will start with a basic case of a simple spectral data collection. Then we will describe several examples of “small” technologically advanced VO resources built in CDS and VO-Paris and will show that many standards are hidden from managers' eyes at the initial stage of the project development. The projects will be: (1) the GalMer database providing access to the results of numerical simulations of galaxy interactions; (2) the full spectrum fitting service that allows one to extract internal kinematics and stellar populations from spectra of galaxies available in the VO. We conclude that: (a) with the existing set of IVOA standards one can already build very advanced VO-enabled archives and tools useful for scientists; (b) managers have to be very careful when estimating the project development timelines for VO-enabled resources.

  18. Operator Spin Foam Models

    CERN Document Server

    Bahr, Benjamin; Kamiński, Wojciech; Kisielowski, Marcin; Lewandowski, Jerzy

    2010-01-01

    The goal of this paper is to introduce a systematic approach to spin foams. We define operator spin foams, that is foams labelled by group representations and operators, as the main tool. An equivalence relation we impose in the set of the operator spin foams allows to split the faces and the edges of the foams. The consistency with that relation requires introduction of the (familiar for the BF theory) face amplitude. The operator spin foam models are defined quite generally. Imposing a maximal symmetry leads to a family we call natural operator spin foam models. This symmetry, combined with demanding consistency with splitting the edges, determines a complete characterization of a general natural model. It can be obtained by applying arbitrary (quantum) constraints on an arbitrary BF spin foam model. In particular, imposing suitable constraints on Spin(4) BF spin foam model is exactly the way we tend to view 4d quantum gravity, starting with the BC model and continuing with the EPRL or FK models. That makes...

  19. CaMELS: In silico prediction of calmodulin binding proteins and their binding sites.

    Science.gov (United States)

    Abbasi, Wajid Arshad; Asif, Amina; Andleeb, Saiqa; Minhas, Fayyaz Ul Amir Afsar

    2017-09-01

    Due to Ca(2+) -dependent binding and the sequence diversity of Calmodulin (CaM) binding proteins, identifying CaM interactions and binding sites in the wet-lab is tedious and costly. Therefore, computational methods for this purpose are crucial to the design of such wet-lab experiments. We present an algorithm suite called CaMELS (CalModulin intEraction Learning System) for predicting proteins that interact with CaM as well as their binding sites using sequence information alone. CaMELS offers state of the art accuracy for both CaM interaction and binding site prediction and can aid biologists in studying CaM binding proteins. For CaM interaction prediction, CaMELS uses protein sequence features coupled with a large-margin classifier. CaMELS models the binding site prediction problem using multiple instance machine learning with a custom optimization algorithm which allows more effective learning over imprecisely annotated CaM-binding sites during training. CaMELS has been extensively benchmarked using a variety of data sets, mutagenic studies, proteome-wide Gene Ontology enrichment analyses and protein structures. Our experiments indicate that CaMELS outperforms simple motif-based search and other existing methods for interaction and binding site prediction. We have also found that the whole sequence of a protein, rather than just its binding site, is important for predicting its interaction with CaM. Using the machine learning model in CaMELS, we have identified important features of protein sequences for CaM interaction prediction as well as characteristic amino acid sub-sequences and their relative position for identifying CaM binding sites. Python code for training and evaluating CaMELS together with a webserver implementation is available at the URL: http://faculty.pieas.edu.pk/fayyaz/software.html#camels. © 2017 Wiley Periodicals, Inc.

  20. Operations management for construction

    CERN Document Server

    March, Chris

    2009-01-01

    Students studying construction management and related subjects need to have a broad understanding of the major aspects of controlling the building processes. Operations Management for Construction is one of three textbooks (Business Organisation, Operations Management and Finance Control) written to systematically cover the field. Focusing on construction sites and operations which are challenging to run, Chris March explores issues such as the setting up of the site, the deciding of the methodology of construction, and the sequence of work and resourcing. As changing and increasing regulations affect the way sites are managed, he also considers the issues and methods of successful administering, safety, quality and environment. Finally, the contractor's responsibility to the environment, including relationships with third parties, selection of materials, waste management and sustainability is discussed. Chris March has a wealth of practical experience in the construction industry, as well as considerable exp...

  1. Operations Strategy in practice

    DEFF Research Database (Denmark)

    Rytter, Niels Gorm; Koch, Christian; Boer, Harry

    2005-01-01

    In this paper, we describe and illustrate a new, action-based longitudinal case study approach, which aims at helping scholars narrow the gap between the theory and practice of Operations Strategy (OS). First, we elaborate on the need for new research methods for studying OS in practice. Then, we...... present the two research strategies underpinning the approach proposed here: action research and longitudinal case study. Next, we illustrate the use of the method and exemplify it using a recent study of OS in practice. Then, based on this experience we present and discuss the advantages...... and disadvantages of the method. Finally, we draw conclusions on its potential for operations strategy and operations management studies....

  2. About APPLE II Operation

    Science.gov (United States)

    Schmidt, T.; Zimoch, D.

    2007-01-01

    The operation of an APPLE II based undulator beamline with all its polarization states (linear horizontal and vertical, circular and elliptical, and continous variation of the linear vector) requires an effective description allowing an automated calculation of gap and shift parameter as function of energy and operation mode. The extension of the linear polarization range from 0 to 180° requires 4 shiftable magnet arrrays, permitting use of the APU (adjustable phase undulator) concept. Studies for a pure fixed gap APPLE II for the SLS revealed surprising symmetries between circular and linear polarization modes allowing for simplified operation. A semi-analytical model covering all types of APPLE II and its implementation will be presented.

  3. Theory of linear operations

    CERN Document Server

    Banach, S

    1987-01-01

    This classic work by the late Stefan Banach has been translated into English so as to reach a yet wider audience. It contains the basics of the algebra of operators, concentrating on the study of linear operators, which corresponds to that of the linear forms a1x1 + a2x2 + ... + anxn of algebra.The book gathers results concerning linear operators defined in general spaces of a certain kind, principally in Banach spaces, examples of which are: the space of continuous functions, that of the pth-power-summable functions, Hilbert space, etc. The general theorems are interpreted in various mathematical areas, such as group theory, differential equations, integral equations, equations with infinitely many unknowns, functions of a real variable, summation methods and orthogonal series.A new fifty-page section (``Some Aspects of the Present Theory of Banach Spaces'''') complements this important monograph.

  4. Annual Report on SPR Operation in 2011

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    1 Information of operation Operation person: present chief operators are 11 persons, operators are 6 persons; new chief operators are 3 persons, new operator is 1 person; training chief operators are 3 persons, training operators are 1 persons;

  5. Interpolating Operators for Multiapproximation

    Directory of Open Access Journals (Sweden)

    Eman S. Bhaya

    2010-01-01

    Full Text Available Problem statement: There are no simple definitions of operators for best multiapproximation and best one sided multiapproximation which work for any measurable function in Lp for, p>0. This study investigated operators that are good for best multiapproximation and best one sided multiapproximation. Approach: We first introduced some direct results related to the approximation problem of continuous functions by Hermit-Fejer interpolation based on the zeros of Chebyshev polynomials of the first or second kind in terms of the usual modulus of continuity. They were then improved to spaces Lp for pn(f of measurable functions, that operator based on the zeros of Chepyshev polynomials of the first kind and prove that for any measurable function defined on Lp[-1,1 ]d the sequence Hn(f converges uniformly to f. Results: The resulting operators were defined for functions f such that f(k, k = 0,1,… is of bounded variation. Then, the order of best onesided trigonometric approximation to bounded measurable functions in terms of the average modulus of smoothness was characterized. Estimates characterizing the order of best onesided approximation in terms of the k-th averaged modulus of smoothness for any function in spaces Lp, pp[-1,1]d by defining a new operator for onesided approximation and prove a direct theorem for best one sided multiapproximation in terms of the first order averaged moduli of smoothness. Conclusion: The proposed method successfully construct operators for best multi approximation and best one sided multiapproximation for any measurable function in Lp for, p>0.

  6. Characterization of the hormone-binding domain of the chicken c-erbA/thyroid hormone receptor protein

    DEFF Research Database (Denmark)

    Muñoz, A; Zenke, M; Gehring, U

    1988-01-01

    mutations present in the carboxy-terminal half of P75gag-v-erbA co-operate in abolishing hormone binding, and that the ligand-binding domain resides in a position analogous to that of steroid receptors. Furthermore, a point mutation that is located between the putative DNA and ligand-binding domains of P75......To identify and characterize the hormone-binding domain of the thyroid hormone receptor, we analyzed the ligand-binding capacities of proteins representing chimeras between the normal receptor and P75gag-v-erbA, the retrovirus-encoded form deficient in binding ligand. Our results show that several......gag-v-erbA and that renders it biologically inactive fails to affect hormone binding by the c-erbA protein. These results suggest that the mutation changed the ability of P75gag-v-erbA to affect transcription since it also had no effect on DNA binding. Our data also suggest that hormone...

  7. Competitive binding of fluoroquinolone antibiotics and some other drugs to human serum albumin: a luminescence spectroscopic study.

    Science.gov (United States)

    Seedher, Neelam; Agarwal, Pooja

    2013-01-01

    Co-administration of several drugs in multidrug therapy may alter the binding of each to human serum albumin (HSA) and hence their pharmacological activity. Thirty-two frequently prescribed drug combinations, consisting of four fluoroquinolone antibiotics and eight competing drugs, have been studied using fluorescence and circular dichroism spectroscopic techniques. Competitive binding studies on the drug combinations are not available in the literature. In most cases, the presence of competing drug decreased the binding affinity of fluoroquinolone, resulting in an increase in the concentration of free pharmacologically active drug. The competitive binding mechanism involved could be interpreted in terms of the site specificity of the binding and competing drugs. For levofloxacin, the change in the binding affinity was small because in the presence of site II-specific competing drugs, levofloxacin mainly occupied site I. A competitive interference mechanism was operative for sparfloxacin, whereas competitive interference as well as site-to-site displacement of competing drugs was observed in the case of ciprofloxacin hydrochloride. For enrofloxacin, a different behavior was observed for different combinations; site-to-site displacement and conformational changes as well as independent binding has been observed for various drug combinations. Circular dichroism spectral studies showed that competitive binding did not cause any major structural changes in the HSA molecule. Copyright © 2013 John Wiley & Sons, Ltd.

  8. Computational search for aflatoxin binding proteins

    Science.gov (United States)

    Wang, Ying; Liu, Jinfeng; Zhang, Lujia; He, Xiao; Zhang, John Z. H.

    2017-10-01

    Aflatoxin is one of the mycotoxins that contaminate various food products. Among various aflatoxin types (B1, B2, G1, G2 and M1), aflatoxin B1 is the most important and the most toxic one. In this study, through computational screening, we found that several proteins may bind specifically with different type of aflatoxins. Combination of theoretical methods including target fishing, molecular docking, molecular dynamics (MD) simulation, MM/PBSA calculation were utilized to search for new aflatoxin B1 binding proteins. A recently developed method for calculating entropic contribution to binding free energy called interaction entropy (IE) was employed to compute the binding free energy between the protein and aflatoxin B1. Through comprehensive comparison, three proteins, namely, trihydroxynaphthalene reductase, GSK-3b, and Pim-1 were eventually selected as potent aflatoxin B1 binding proteins. GSK-3b and Pim-1 are drug targets of cancers or neurological diseases. GSK-3b is the strongest binder for aflatoxin B1.

  9. Haptenation: Chemical Reactivity and Protein Binding

    Directory of Open Access Journals (Sweden)

    Itai Chipinda

    2011-01-01

    Full Text Available Low molecular weight chemical (LMW allergens are commonly referred to as haptens. Haptens must complex with proteins to be recognized by the immune system. The majority of occupationally related haptens are reactive, electrophilic chemicals, or are metabolized to reactive metabolites that form covalent bonds with nucleophilic centers on proteins. Nonelectrophilic protein binding may occur through disulfide exchange, coordinate covalent binding onto metal ions on metalloproteins or of metal allergens, themselves, to the major histocompatibility complex. Recent chemical reactivity kinetic studies suggest that the rate of protein binding is a major determinant of allergenic potency; however, electrophilic strength does not seem to predict the ability of a hapten to skew the response between Th1 and Th2. Modern proteomic mass spectrometry methods that allow detailed delineation of potential differences in protein binding sites may be valuable in predicting if a chemical will stimulate an immediate or delayed hypersensitivity. Chemical aspects related to both reactivity and protein-specific binding are discussed.

  10. Conformational heterogeneity of the calmodulin binding interface

    Science.gov (United States)

    Shukla, Diwakar; Peck, Ariana; Pande, Vijay S.

    2016-04-01

    Calmodulin (CaM) is a ubiquitous Ca2+ sensor and a crucial signalling hub in many pathways aberrantly activated in disease. However, the mechanistic basis of its ability to bind diverse signalling molecules including G-protein-coupled receptors, ion channels and kinases remains poorly understood. Here we harness the high resolution of molecular dynamics simulations and the analytical power of Markov state models to dissect the molecular underpinnings of CaM binding diversity. Our computational model indicates that in the absence of Ca2+, sub-states in the folded ensemble of CaM's C-terminal domain present chemically and sterically distinct topologies that may facilitate conformational selection. Furthermore, we find that local unfolding is off-pathway for the exchange process relevant for peptide binding, in contrast to prior hypotheses that unfolding might account for binding diversity. Finally, our model predicts a novel binding interface that is well-populated in the Ca2+-bound regime and, thus, a candidate for pharmacological intervention.

  11. Endocytosis of Integrin-Binding Human Picornaviruses

    Directory of Open Access Journals (Sweden)

    Pirjo Merilahti

    2012-01-01

    Full Text Available Picornaviruses that infect humans form one of the largest virus groups with almost three hundred virus types. They include significant enteroviral pathogens such as rhino-, polio-, echo-, and coxsackieviruses and human parechoviruses that cause wide range of disease symptoms. Despite the economic importance of picornaviruses, there are no antivirals. More than ten cellular receptors are known to participate in picornavirus infection, but experimental evidence of their role in cellular infection has been shown for only about twenty picornavirus types. Three enterovirus types and one parechovirus have experimentally been shown to bind and use integrin receptors in cellular infection. These include coxsackievirus A9 (CV-A9, echovirus 9, and human parechovirus 1 that are among the most common and epidemic human picornaviruses and bind to αV-integrins via RGD motif that resides on virus capsid. In contrast, echovirus 1 (E-1 has no RGD and uses integrin α2β1 as cellular receptor. Endocytosis of CV-A9 has recently been shown to occur via a novel Arf6- and dynamin-dependent pathways, while, contrary to collagen binding, E-1 binds inactive β1 integrin and enters via macropinocytosis. In this paper, we review what is known about receptors and endocytosis of integrin-binding human picornaviruses.

  12. An extended database of keratin binding.

    Science.gov (United States)

    Hansen, Steffi; Selzer, Dominik; Schaefer, Ulrich F; Kasting, Gerald B

    2011-05-01

    Diffusion modeling of dermal absorption relies in large part on high quality input data. Currently, estimates of corneocyte-phase partitioning are based on an analysis of a dataset of limited size and diversity. Therefore, we have updated and broadened the analysis. For this purpose, binding coefficients to different keratins, namely, bovine hoof and horn, human delipidized callus, human delipidized stratum corneum (SC), human nail, human hair, and sheep wool were collected from the literature. In addition, binding coefficients to hoof/horn and delipidized SC were measured for eight hydrophilic compounds including three ionizable compounds that were measured at different pH values. Important results are: (i) only hoof/horn, callus, and delipidized SC are suitable keratins for estimating corneocyte protein binding; (ii) binding coefficients to hoof/horn, callus, and delipidized SC can be predicted from the octanol-water partition coefficients log K(o/w) confirming the analysis of the limited dataset; (iii) binding of ionizable compounds can be predicted by correcting log K(o/w) for pH; (iv) the correlation derived for the extended database is steeper than the relationship derived for the limited dataset. This has consequences for the estimates of SC partition and diffusion coefficients for diffusion modeling of dermal absorption. .

  13. Endocytosis of integrin-binding human picornaviruses.

    Science.gov (United States)

    Merilahti, Pirjo; Koskinen, Satu; Heikkilä, Outi; Karelehto, Eveliina; Susi, Petri

    2012-01-01

    Picornaviruses that infect humans form one of the largest virus groups with almost three hundred virus types. They include significant enteroviral pathogens such as rhino-, polio-, echo-, and coxsackieviruses and human parechoviruses that cause wide range of disease symptoms. Despite the economic importance of picornaviruses, there are no antivirals. More than ten cellular receptors are known to participate in picornavirus infection, but experimental evidence of their role in cellular infection has been shown for only about twenty picornavirus types. Three enterovirus types and one parechovirus have experimentally been shown to bind and use integrin receptors in cellular infection. These include coxsackievirus A9 (CV-A9), echovirus 9, and human parechovirus 1 that are among the most common and epidemic human picornaviruses and bind to αV-integrins via RGD motif that resides on virus capsid. In contrast, echovirus 1 (E-1) has no RGD and uses integrin α2β1 as cellular receptor. Endocytosis of CV-A9 has recently been shown to occur via a novel Arf6- and dynamin-dependent pathways, while, contrary to collagen binding, E-1 binds inactive β1 integrin and enters via macropinocytosis. In this paper, we review what is known about receptors and endocytosis of integrin-binding human picornaviruses.

  14. DNA binding studies of tartrazine food additive.

    Science.gov (United States)

    Kashanian, Soheila; Zeidali, Sahar Heidary

    2011-07-01

    The interaction of native calf thymus DNA with tartrazine in 10 mM Tris-HCl aqueous solution at neutral pH 7.4 was investigated. Tartrazine is a nitrous derivative and may cause allergic reactions, with a potential of toxicological risk. Also, tartrazine induces oxidative stress and DNA damage. Its DNA binding properties were studied by UV-vis and circular dichroism spectra, competitive binding with Hoechst 33258, and viscosity measurements. Tartrazine molecules bind to DNA via groove mode as illustrated by hyperchromism in the UV absorption band of tartrazine, decrease in Hoechst-DNA solution fluorescence, unchanged viscosity of DNA, and conformational changes such as conversion from B-like to C-like in the circular dichroism spectra of DNA. The binding constants (K(b)) of DNA with tartrazine were calculated at different temperatures. Enthalpy and entropy changes were calculated to be +37 and +213 kJ mol(-1), respectively, according to the Van't Hoff equation, which indicated that the reaction is predominantly entropically driven. Also, tartrazine does not cleave plasmid DNA. Tartrazine interacts with calf thymus DNA via a groove interaction mode with an intrinsic binding constant of 3.75 × 10(4) M(-1).

  15. Operative management of appendicitis.

    Science.gov (United States)

    St Peter, Shawn D; Snyder, Charles L

    2016-08-01

    Appendectomy has been the standard of care for appendicitis since the late 1800s, and remains one of the most common operations performed in children. The advent of data-driven medicine has led to questions about every aspect of the operation-whether appendectomy is even necessary, when it should be performed (timing), how the procedure is done (laparoscopic variants versus open and irrigation versus no irrigation), length of hospital stay, and antibiotic duration. The goal of this analysis is to review the current status of, and available data regarding, the surgical management of appendicitis in children. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. HIRFL Operation and Upgrade

    Institute of Scientific and Technical Information of China (English)

    ZhaoHongwei; WangYifang; ZhanWenlong; WeiBaowen; HIRFLTeam

    2003-01-01

    After almost one year shutdown for upgrading the vacuum chamber of the iniector SFC,SFC has been in operation separately since May 2003. The SFC operation statistics and accelerated heams from May to December 2003 are shown in Table 1 and 2. The main cyclotron SSC has beenfor still shut down in 2003 for upgrading the SSC power supply system, control and diagnostic system, and themain experimental area, LECR3, an ECR ion source dedicated for atomic physics and surface physics research, has provided 2488 hours beams for experiments of atomic physics research.

  17. Alkaline battery operational methodology

    Science.gov (United States)

    Sholklapper, Tal; Gallaway, Joshua; Steingart, Daniel; Ingale, Nilesh; Nyce, Michael

    2016-08-16

    Methods of using specific operational charge and discharge parameters to extend the life of alkaline batteries are disclosed. The methods can be used with any commercial primary or secondary alkaline battery, as well as with newer alkaline battery designs, including batteries with flowing electrolyte. The methods include cycling batteries within a narrow operating voltage window, with minimum and maximum cut-off voltages that are set based on battery characteristics and environmental conditions. The narrow voltage window decreases available capacity but allows the batteries to be cycled for hundreds or thousands of times.

  18. Energy Operation Model

    Energy Technology Data Exchange (ETDEWEB)

    2017-04-27

    Energy Operation Model (EOM) simulates the operation of the electric grid at the zonal scale, including inter-zonal transmission constraints. It generates the production cost, power generation by plant and category, fuel usage, and locational marginal price (LMP) with a flexible way to constrain the power production by environmental constraints, e.g. heat waves, drought conditions). Different from commercial software such as PROMOD IV where generator capacity and heat rate efficiency can only be adjusted on a monthly basis, EOM calculates capacity impacts and plant efficiencies based on hourly ambient conditions (air temperature and humidity) and cooling water availability for thermal plants. What is missing is a hydro power dispatch.

  19. Operational Modal Analysis Tutorial

    DEFF Research Database (Denmark)

    Brincker, Rune; Andersen, Palle

    analysis in an easier way and in many cases more effectively than traditional modal analysis methods. It can be applied for modal testing and analysis on a wide range of structures and not only for problems generally investigated using traditional modal analysis, but also for those requiring load......In this paper the basic principles in operational modal testing and analysis are presented and discussed. A brief review of the techniques for operational modal testing and identification is presented, and it is argued, that there is now a wide range of techniques for effective identification...... estimation, vibration level estimation and fatigue analysis....

  20. Cohomological vertex operators

    CERN Document Server

    Viña, Andrés

    2016-01-01

    Given a Calabi-Yau manifold and considering the $B$-branes on it as objects in the derived category of coherent sheaves, we identify the vertex operators for strings between two branes with elements of the cohomology groups of Ext sheaves. We define the correlation functions for these general vertex operators. Strings stretching between two coherent sheaves are studied as homological extensions of the corresponding branes. In this context, we relate strings between different pairs of branes when there are maps between these branes. We also interpret some strings with ghost number $k$ as obstructions for lifts or extensions of strings with ghost number $k-1$.

  1. Operation for gigantincisionalhernie

    DEFF Research Database (Denmark)

    Eriksson, Axelina; Krag, Christen; Jørgensen, Lars Nannestad;

    2014-01-01

    Incisional hernia is a common complication to laparotomy impacting negatively on quality of life, risk of emergency surgery and cosmesis. The operation of giant incisional hernia (cross diameter of hernia defect > 20 cm) is a high risk procedure and the surgical techniques are not based on high...... level evidence. Mesh placement is possible onlay, inlay, sublay or intraperitoneal. These operations are most often performed as open procedures, or in combination with endoscopic techniques. These procedures should be centralized to few centers to improve quality and allow robust research....

  2. Topics in Operator Theory

    CERN Document Server

    Ball, Joseph A; Helton, JWilliam; Rodman, Leiba; Spitkovsky, Iiya

    2010-01-01

    This is the first volume of a collection of original and review articles on recent advances and new directions in a multifaceted and interconnected area of mathematics and its applications. It encompasses many topics in theoretical developments in operator theory and its diverse applications in applied mathematics, physics, engineering, and other disciplines. The purpose is to bring in one volume many important original results of cutting edge research as well as authoritative review of recent achievements, challenges, and future directions in the area of operator theory and its applications.

  3. A VIRTUAL OPERATING SYSTEM

    Energy Technology Data Exchange (ETDEWEB)

    Hall, Dennis E.; Scherrer, Deborah K.; Sventek, Joseph S.

    1980-05-01

    Significant progress toward disentangling computing environments from their under lying operating systern has been made. An approach is presented that achieves inter-system uniformity at all three levels of user interface - virtual machine, utilities, and command language. Under specifiable conditions, complete uniformity is achievable without disturbing the underlying operating system. The approach permits accurate computation of the cost to move both people and software to a new system. The cost of moving people is zero, and the cost of moving software is equal to the cost of implementing a virtual machine. Efficiency is achieved through optimization of the primitive functions.

  4. Transitive spaces of operators

    CERN Document Server

    Davidson, K R; Radjavi, H

    2007-01-01

    We investigate algebraic and topological transitivity and, more generally, k-transitivity for linear spaces of operators. In finite dimensions, we determine minimal dimensions of k-transitive spaces for every k, and find relations between the degree of transitivity of a product or tensor product on the one hand and those of the factors on the other. We present counterexamples to some natural conjectures. Some infinite dimensional analogues are discussed. A simple proof is given of Arveson's result on the weak-operator density of transitive spaces that are masa bimodules.

  5. An entropic mechanism of generating selective ion binding in macromolecules.

    Directory of Open Access Journals (Sweden)

    Michael Thomas

    Full Text Available Several mechanisms have been proposed to explain how ion channels and transporters distinguish between similar ions, a process crucial for maintaining proper cell function. Of these, three can be broadly classed as mechanisms involving specific positional constraints on the ion coordinating ligands which arise through: a "rigid cavity", a 'strained cavity' and 'reduced ligand fluctuations'. Each operates in subtly different ways yet can produce markedly different influences on ion selectivity. Here we expand upon preliminary investigations into the reduced ligand fluctuation mechanism of ion selectivity by simulating how a series of model systems respond to a decrease in ligand thermal fluctuations while simultaneously maintaining optimal ion-ligand binding distances. Simple abstract-ligand models, as well as simple models based upon the ion binding sites in two amino acid transporters, show that limiting ligand fluctuations can create ion selectivity between Li(+, Na(+ and K(+ even when there is no strain associated with the molecular framework accommodating the different ions. Reducing the fluctuations in the position of the coordinating ligands contributes to selectivity toward the smaller of two ions as a consequence of entropic differences.

  6. On the Orientation Problem in Korean 'CAKI' Binding and the Typology of X Reflexive Binding.

    Science.gov (United States)

    Cho, Mi-Hui

    1994-01-01

    The purpose of this paper is to demonstrate the existence of nonsubject binding of the so-called long distance anaphor in languages like Korean and Japanese and to give a principled account of why and when it happens. The Korean reflexive pronoun "caki" ('self') is bound by local and long-distance antecedents. Nonsubject binding occurs…

  7. CTCF: the protein, the binding partners, the binding sites and their chromatin loops

    NARCIS (Netherlands)

    Holwerda, S.J.; de Laat, W.

    2013-01-01

    CTCF has it all. The transcription factor binds to tens of thousands of genomic sites, some tissue-specific, others ultra-conserved. It can act as a transcriptional activator, repressor and insulator, and it can pause transcription. CTCF binds at chromatin domain boundaries, at enhancers and gene pr

  8. The interrelationship between ligand binding and self-association of the folate binding protein

    DEFF Research Database (Denmark)

    Holm, Jan; Schou, Christian; Babol, Linnea N.

    2011-01-01

    The folate binding protein (FBP) regulates homeostasis and intracellular trafficking of folic acid, a vitamin of decisive importance in cell division and growth. We analyzed whether interrelationship between ligand binding and self-association of FBP plays a significant role in the physiology...

  9. Ancestral Protein Reconstruction Yields Insights into Adaptive Evolution of Binding Specificity in Solute-Binding Proteins.

    Science.gov (United States)

    Clifton, Ben E; Jackson, Colin J

    2016-02-18

    The promiscuous functions of proteins are an important reservoir of functional novelty in protein evolution, but the molecular basis for binding promiscuity remains elusive. We used ancestral protein reconstruction to experimentally characterize evolutionary intermediates in the functional expansion of the polar amino acid-binding protein family, which has evolved to bind a variety of amino acids with high affinity and specificity. High-resolution crystal structures of an ancestral arginine-binding protein in complex with l-arginine and l-glutamine show that the promiscuous binding of l-glutamine is enabled by multi-scale conformational plasticity, water-mediated interactions, and selection of an alternative conformational substate productive for l-glutamine binding. Evolution of specialized glutamine-binding proteins from this ancestral protein was achieved by displacement of water molecules from the protein-ligand interface, reducing the entropic penalty associated with the promiscuous interaction. These results provide a structural and thermodynamic basis for the co-option of a promiscuous interaction in the evolution of binding specificity.

  10. Asporin competes with decorin for collagen binding, binds calcium and promotes osteoblast collagen mineralization

    DEFF Research Database (Denmark)

    Kalamajski, Sebastian; Aspberg, Anders; Lindblom, Karin

    2009-01-01

    The interactions of the ECM (extracellular matrix) protein asporin with ECM components have previously not been investigated. Here, we show that asporin binds collagen type I. This binding is inhibited by recombinant asporin fragment LRR (leucine-rich repeat) 10-12 and by full-length decorin, but...

  11. Opioid binding sites in the guinea pig and rat kidney: Radioligand homogenate binding and autoradiography

    Energy Technology Data Exchange (ETDEWEB)

    Dissanayake, V.U.; Hughes, J.; Hunter, J.C. (Parke-Davis Research Unit, Addenbrookes Hospital Site, Cambridge (England))

    1991-07-01

    The specific binding of the selective {mu}-, {delta}-, and {kappa}-opioid ligands (3H)(D-Ala2,MePhe4,Gly-ol5)enkephalin ((3H) DAGOL), (3H)(D-Pen2,D-Pen5)enkephalin ((3H)DPDPE), and (3H)U69593, respectively, to crude membranes of the guinea pig and rat whole kidney, kidney cortex, and kidney medulla was investigated. In addition, the distribution of specific 3H-opioid binding sites in the guinea pig and rat kidney was visualized by autoradiography. Homogenate binding and autoradiography demonstrated the absence of {mu}- and {kappa}-opioid binding sites in the guinea pig kidney. No opioid binding sites were demonstrable in the rat kidney. In the guinea pig whole kidney, cortex, and medulla, saturation studies demonstrated that (3H)DPDPE bound with high affinity (KD = 2.6-3.5 nM) to an apparently homogeneous population of binding sites (Bmax = 8.4-30 fmol/mg of protein). Competition studies using several opioid compounds confirmed the nature of the {delta}-opioid binding site. Autoradiography experiments demonstrated that specific (3H)DPDPE binding sites were distributed radially in regions of the inner and outer medulla and at the corticomedullary junction of the guinea pig kidney. Computer-assisted image analysis of saturation data yielded KD values (4.5-5.0 nM) that were in good agreement with those obtained from the homogenate binding studies. Further investigation of the {delta}-opioid binding site in medulla homogenates, using agonist ((3H)DPDPE) and antagonist ((3H)diprenorphine) binding in the presence of Na+, Mg2+, and nucleotides, suggested that the {delta}-opioid site is linked to a second messenger system via a GTP-binding protein. Further studies are required to establish the precise localization of the {delta} binding site in the guinea pig kidney and to determine the nature of the second messenger linked to the GTP-binding protein in the medulla.

  12. ABP: a novel AMPA receptor binding protein.

    Science.gov (United States)

    Srivastava, S; Ziff, E B

    1999-04-30

    We review the cloning of a novel AMPA receptor binding protein (ABP) that interacts with GluR2/3 and is homologous to GRIP. ABP is enriched in the PSD with GluR2 and is localized to the PSD by EM. ABP binds GluR2 via the C-terminal VXI motif through a Class I PDZ interaction. ABP and GRIP can also homo- and heteromultimerize. Thus, ABP and GRIP may be involved in AMPA receptor regulation and localization, by linking it to other cytoskeletal or signaling molecules. We suggest that the ABP/GRIP and PSD-95 families form distinct scaffolds that anchor, respectively, AMPA and NMDA receptors. We are currently investigating proteins that bind ABP and that may regulate the AMPA receptor.

  13. Arsenic binding to Fucus vesiculosus metallothionein.

    Science.gov (United States)

    Merrifield, Maureen E; Ngu, Thanh; Stillman, Martin J

    2004-11-05

    The seaweed Fucus vesiculosus is a member of the brown algae family. Kille and co-workers [Biochem. J. 338 (1999) 553] reported that this species contains the gene for metallothionein. Metallothionein is a metalloprotein having low molecular weight, and high cysteine content, which binds a range of metals. F. vesiculosus bioaccumulates arsenic from the aquatic environment [Mar. Chem. 18 (1986) 321]. In this paper we describe arsenic binding to F. vesiculosus metallothionein, characterized by electrospray ionization mass spectrometry. Five arsenic-MT species were detected with increasing As to protein ratios. These results provide important information about the metal-chelation behaviour of this novel algal metallothionein which is a putative model for arsenic binding to F. vesiculosus in vivo.

  14. Asymmetry of calmodulin revealed by peptide binding.

    Science.gov (United States)

    Leclerc, E; Leclerc, L; Marden, M C

    1993-03-01

    The binding of amphiphilic peptides to calmodulin has been studied using fluorescence energy transfer techniques. Calmodulin has no tryptophan residues but possesses two tyrosines (at positions 99 and 138) in the C-terminal half of the protein. The peptides have a single tryptophan which serves as energy acceptor for the protein tyrosine fluorescence. For the binding of mastoparan or peptide Baa17, with a tryptophan at position 3, the observed quenching of the tyrosine fluorescence of over a factor of 2 corresponds to an average tyrosine-trytophan distance of less than 14 Å. These results indicate that the peptides binds preferentially with the tryptophan in the C-terminal half of the protein.

  15. A review of albumin binding in CKD.

    Science.gov (United States)

    Meijers, Björn K I; Bammens, Bert; Verbeke, Kristin; Evenepoel, Pieter

    2008-05-01

    Hypoalbuminemia is associated with excess mortality in patients with kidney disease. Albumin is an important oxidant scavenger and an abundant carrier protein for numerous endogenous and exogenous compounds. Several specific binding sites for anionic, neutral, and cationic ligands were described. Overall, the extent of binding depends on the ligand and albumin concentration, albumin-binding affinity, and presence of competing ligands. Chronic kidney disease affects all these determinants. This may result in altered pharmacokinetics and increased risk of toxicity. Renal clearance of albumin-bound solutes mainly depends on tubular clearance. Dialytic clearance by means of conventional hemodialysis/hemofiltration and peritoneal dialysis is limited. Other epuration techniques combining hemodialysis with adsorption have been developed. However, the benefit of these techniques remains to be proved.

  16. Conformation-controlled binding kinetics of antibodies

    Science.gov (United States)

    Galanti, Marta; Fanelli, Duccio; Piazza, Francesco

    2016-01-01

    Antibodies are large, extremely flexible molecules, whose internal dynamics is certainly key to their astounding ability to bind antigens of all sizes, from small hormones to giant viruses. In this paper, we build a shape-based coarse-grained model of IgG molecules and show that it can be used to generate 3D conformations in agreement with single-molecule Cryo-Electron Tomography data. Furthermore, we elaborate a theoretical model that can be solved exactly to compute the binding rate constant of a small antigen to an IgG in a prescribed 3D conformation. Our model shows that the antigen binding process is tightly related to the internal dynamics of the IgG. Our findings pave the way for further investigation of the subtle connection between the dynamics and the function of large, flexible multi-valent molecular machines.

  17. Heavy quark interactions and quarkonium binding

    Science.gov (United States)

    Satz, Helmut

    2009-06-01

    We consider heavy quark interactions in quenched and unquenched lattice QCD. In a region just above the deconfinement point, non-Abelian gluon polarization leads to a strong increase in the binding. Comparing quark-antiquark and quark-quark interaction, the dependence of the binding on the separation distance r is found to be the same for the colorless singlet Q{\\skew3\\bar{Q}} and the colored anti-triplet QQ state. In a potential model description of in-medium J/ψ behavior, this enhancement of the binding leads to a survival up to temperatures of 1.5 Tc or higher; it could also result in J/ψ flow. Based on joint work with O Kaczmarek and F Karsch.

  18. Defining Starch Binding by Glucan Phosphatases

    DEFF Research Database (Denmark)

    Auger, Kyle; Raththagala, Madushi; Wilkens, Casper;

    2015-01-01

    Starch is a vital energy molecule in plants that has a wide variety of uses in industry, such as feedstock for biomaterial processing and biofuel production. Plants employ a three enzyme cyclic process utilizing kinases, amylases, and phosphatases to degrade starch in a diurnal manner. Starch...... is comprised of the branched glucan amylopectin and the more linear glucan amylose. Our lab has determined the first structures of these glucan phosphatases and we have defined their enzymatic action. Despite this progress, we lacked a means to quickly and efficiently quantify starch binding to glucan...... phosphatases. The main objective of this study was to quantify the binding affinity of different enzymes that are involved in this cyclic process. We established a protocol to quickly, reproducibly, and quantitatively measure the binding of the enzymes to glucans utilizing Affinity Gel Electrophoresis (AGE...

  19. Adjustment of legally binding local plans

    DEFF Research Database (Denmark)

    Hvingel, Line Træholt; Aunsborg, Christian; Christensen, Finn Kjær

    2012-01-01

    Traditionally, and by law, new urban areas in Denmark are regulated and planned through legally binding local plans. Recently a tendency has occurred: The municipalities make the legally binding local plans quite open for future adjustment, and they are using a substantial amount of ‘empowerment...... provisions’ which empower the municipalities to later ruling. This way of making plans postpones the actual regulation of an area (i.e. the planning permission) making it an individual ruling for instance at the application of building permits. Case studies show examples of this way of regulating an area......, which seem to be beyond the scope of the Danish Planning Act. This paper deals with this problem through case studies and a legal analysis of present law. If the combination of the legally binding local plan and subsequent added requirements is misused, it will weaken the legal rights of the citizens...

  20. Predicting binding free energies in solution

    CERN Document Server

    Jensen, Jan H

    2015-01-01

    Recent predictions of absolute binding free energies of host-guest complexes in aqueous solution using electronic structure theory have been encouraging for some systems, while other systems remain problematic for others. In paper I summarize some of the many factors that could easily contribute 1-3 kcal/mol errors at 298 K: three-body dispersion effects, molecular symmetry, anharmonicity, spurious imaginary frequencies, insufficient conformational sampling, wrong or changing ionization states, errors in the solvation free energy of ions, and explicit solvent (and ion) effects that are not well-represented by continuum models. While the paper is primarily a synthesis of previously published work there are two new results: the adaptation of Legendre transformed free energies to electronic structure theory and a use of water clusters that maximizes error cancellation in binding free energies computed using explicit solvent molecules. While I focus on binding free energies in aqueous solution the approach also a...

  1. Mercury-binding proteins of Mytilus edulis

    Energy Technology Data Exchange (ETDEWEB)

    Roesijadi, G.; Morris, J. E.; Calabrese, A.

    1981-11-01

    Mytilus edulis possesses low molecular weight, mercury-binding proteins. The predominant protein isolated from gill tissue is enriched in cysteinyl residues (8%) and possesses an amino acid composition similar to cadmium-binding proteins of mussels and oysters. Continuous exposure of mussels to 5 ..mu..g/l mercury results in spillover of mercury from these proteins to high molecular weight proteins. Antibodies to these proteins have been isolated, and development of immunoassays is presently underway. Preliminary studies to determine whether exposure of adult mussels to mercury will result in induction of mercury-binding proteins in offspring suggest that such proteins occur in larvae although additional studies are indicated for a conclusive demonstration.

  2. Presence of a highly efficient binding to bacterial contamination can distort data from binding studies

    Energy Technology Data Exchange (ETDEWEB)

    Balcar, V.J. (Department of Anatomy, University of Sydney, N.S.W. (Australia))

    1990-12-01

    {sup 3}HGABA at low concentrations (5-10 nM) was bound by what appeared to be a GABA receptor binding site in bacterial contamination originating from a batch of distilled water. Under experimental conditions similar to those usually employed in {sup 3}HGABA binding studies, the apparent binding displayed a very high specific component and a high efficiency in terms of {sup 3}HGABA bound per mg of protein. The binding was blocked by muscimol but not by isoguvacine, SR95531 and nipecotic acid. These characteristics suggest that the presence of such spurious binding in the experiments using 3H-labeled ligands in brain homogenates may not always be very obvious and, moreover, it can result in subtle, but serious, distortions of data from such studies, which may not be immediately recognized.

  3. Space Operations Learning Center

    Science.gov (United States)

    Lui, Ben; Milner, Barbara; Binebrink, Dan; Kuok, Heng

    2012-01-01

    The Space Operations Learning Center (SOLC) is a tool that provides an online learning environment where students can learn science, technology, engineering, and mathematics (STEM) through a series of training modules. SOLC is also an effective media for NASA to showcase its contributions to the general public. SOLC is a Web-based environment with a learning platform for students to understand STEM through interactive modules in various engineering topics. SOLC is unique in its approach to develop learning materials to teach schoolaged students the basic concepts of space operations. SOLC utilizes the latest Web and software technologies to present this educational content in a fun and engaging way for all grade levels. SOLC uses animations, streaming video, cartoon characters, audio narration, interactive games and more to deliver educational concepts. The Web portal organizes all of these training modules in an easily accessible way for visitors worldwide. SOLC provides multiple training modules on various topics. At the time of this reporting, seven modules have been developed: Space Communication, Flight Dynamics, Information Processing, Mission Operations, Kids Zone 1, Kids Zone 2, and Save The Forest. For the first four modules, each contains three components: Flight Training, Flight License, and Fly It! Kids Zone 1 and 2 include a number of educational videos and games designed specifically for grades K-6. Save The Forest is a space operations mission with four simulations and activities to complete, optimized for new touch screen technology. The Kids Zone 1 module has recently been ported to Facebook to attract wider audience.

  4. Beyond an Operational Reserve

    Science.gov (United States)

    2013-05-01

    equipment, electronics and wheeled vehicles, as well as personnel shortages in critical specialty areas such as doctors and nurses . The report concluded... intervention in Korea. The President’s declaration called for additional military forces, including four ARNG divisions, to provide a deterrence to...regional conflicts, the new strategy emphasizes the need for strong capabilities to conduct smaller scale intervention operations like peace

  5. Invariant differential operators

    CERN Document Server

    Dobrev, Vladimir K

    2016-01-01

    With applications in quantum field theory, elementary particle physics and general relativity, this two-volume work studies invariance of differential operators under Lie algebras, quantum groups, superalgebras including infinite-dimensional cases, Schrödinger algebras, applications to holography. This first volume covers the general aspects of Lie algebras and group theory.

  6. Oscillators and operational amplifiers

    DEFF Research Database (Denmark)

    Lindberg, Erik

    2005-01-01

    A generalized approach to the design of oscillators using operational amplifiers as active elements is presented. A piecewise-linear model of the amplifier is used so that it make sense to investigate the eigenvalues of the Jacobian of the differential equations. The characteristic equation...

  7. Resilient Grid Operational Strategies

    Energy Technology Data Exchange (ETDEWEB)

    Pasqualini, Donatella [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2017-03-01

    Extreme weather-related disturbances, such as hurricanes, are a leading cause of grid outages historically. Although physical asset hardening is perhaps the most common way to mitigate the impacts of severe weather, operational strategies may be deployed to limit the extent of societal and economic losses associated with weather-related physical damage.1 The purpose of this study is to examine bulk power-system operational strategies that can be deployed to mitigate the impact of severe weather disruptions caused by hurricanes, thereby increasing grid resilience to maintain continuity of critical infrastructure during extreme weather. To estimate the impacts of resilient grid operational strategies, Los Alamos National Laboratory (LANL) developed a framework for hurricane probabilistic risk analysis (PRA). The probabilistic nature of this framework allows us to estimate the probability distribution of likely impacts, as opposed to the worst-case impacts. The project scope does not include strategies that are not operations related, such as transmission system hardening (e.g., undergrounding, transmission tower reinforcement and substation flood protection) and solutions in the distribution network.

  8. Novel operative treatment options.

    Science.gov (United States)

    Ricketts, D N J; Pitts, N B

    2009-01-01

    There are an increasing number of more novel options available for operative intervention. This chapter outlines a series of operative treatment options which are available to the modern clinician to select from once a decision has been made to treat a carious lesion operatively. A series of novel methods of caries removal have been described; including chemomechanical caries removal, air abrasion, sono-abrasion, polymer rotary burs and lasers. There are also novel approaches to ensure complete caries removal and novel approaches for the management of deep caries. A novel question increasingly asked by clinicians is: does all the caries need to be removed? Operative management options here include: therapeutic fissure sealants, ultraconservative caries removal, stepwise excavation and the Hall technique. In conclusion, there is now a growing wealth of evidence that questions the traditional methods of caries removal and restoring the tooth. In parallel, there is a growing movement exploring the merits of therapeutically sealing caries into the tooth. This philosophy is alien to many of today's dentists and, until further randomized controlled trials are carried out in primary care, prudent caution must be exercised with this promising approach. Research is required into techniques which will allow monitoring of sealed caries to detect any rare, but insidious, failures. These novel techniques are an alternative way of managing the later stages of the caries process from a sounder biological basis and have marked potential benefits to patients from treatment, pain and outcome perspectives. Copyright 2009 S. Karger AG, Basel

  9. Snow-clearing operations

    CERN Multimedia

    EN Department

    2010-01-01

    To facilitate snow clearing operations, which commence at 4.30 in the morning, all drivers of CERN cars are kindly requested to park them together in groups. This will help us greatly assist us in our work. Thank-you for your help. Transport Group / EN-HE Tel. 72202

  10. UN Peacebuilding Operations

    African Journals Online (AJOL)

    Civil-Military Coordination and UN Peacebuilding Operations actors, including but not ..... (b) the military unit is deployed as part of an integrated civilian-military- ..... ians and those no longer taking part in hostilities, and the provision of food, water .... providing transport and manpower, engineering support, equipment like.

  11. Basic Water Treatment Operation.

    Science.gov (United States)

    Ontario Ministry of the Environment, Toronto.

    This manual was developed for use at workshops designed to introduce the fundamentals of water treatment plant operations. The course consists of lecture-discussions and hands-on activities. Each of the fourteen lessons in this document has clearly stated behavioral objectives to tell the trainee what he should know or do after completing that…

  12. Sales and operations planning

    DEFF Research Database (Denmark)

    Kjellsdotter, Linea; Dukovska-Popovska, Iskra; Kaipia, Riikka

    2015-01-01

    This paper investigates sales and operations planning (S&OP) at four Scandinavian industrial food producers in order to explore how the use of S&OP might help leaders to deal with the challenges set by the planning environment. Variables connected to the product and market, e.g., frequency of new...

  13. Sales and operations planning

    DEFF Research Database (Denmark)

    Kjellsdotter, Linea; Dukovska-Popovska, Iskra; Kaipia, Riikka

    2013-01-01

    This paper explores how the use of sales and operations planning (S&OP) may deal with the challenges set by the planning environment by investigating S&OP at four Scandinavian industrial food producers. Variables connected to the product and market, e.g. perishability, customer service elements...

  14. Operations Strategy in practice

    DEFF Research Database (Denmark)

    Rytter, Niels Gorm; Koch, Christian; Boer, Harry

    2005-01-01

    In this paper, we describe and illustrate a new, action-based longitudinal case study approach, which aims at helping scholars narrow the gap between the theory and practice of Operations Strategy (OS). First, we elaborate on the need for new research methods for studying OS in practice. Then, we...... and disadvantages of the method. Finally, we draw conclusions on its potential for operations strategy and operations management studies.......In this paper, we describe and illustrate a new, action-based longitudinal case study approach, which aims at helping scholars narrow the gap between the theory and practice of Operations Strategy (OS). First, we elaborate on the need for new research methods for studying OS in practice. Then, we...... present the two research strategies underpinning the approach proposed here: action research and longitudinal case study. Next, we illustrate the use of the method and exemplify it using a recent study of OS in practice. Then, based on this experience we present and discuss the advantages...

  15. Operational Area Environmental Evaluations

    Energy Technology Data Exchange (ETDEWEB)

    Bailey-White, Brenda Eileen [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Nagy, Michael David [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Wagner, Katrina Marie [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Goodman, Thomas Richard [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Herring, Allen [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Catechis, Christopher S. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Kinghorn, Aubrianna Nicole [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Johnson, Ellie [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Barthel, Michael David [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Casaus, Benito [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2017-08-01

    The Operational Area Environmental Evaluation update provides a description of activities that have the potential to adversely affect natural and cultural resources, including soil, air, water, biological, ecological, and historical resources. The environmental sensitivity of an area is evaluated and summarized, which may facilitate informed management decisions as to where development may be prohibited, restricted, or subject to additional requirements.

  16. Variability as an Operant?

    Science.gov (United States)

    Holth, Per

    2012-01-01

    A series of experiments on operant variability by Neuringer and colleagues (e.g., Neuringer, 1986, 2002; Page & Neuringer, 1985) have been repeatedly cited as showing that behavioral variability can be reinforced by making reinforcement contingent on it. They showed that the degree of variability in pigeons' eight-peck sequences, as measured by U…

  17. The Operations Process

    Science.gov (United States)

    2010-03-26

    particular operation or exercise, place a nickname or code words before the letter, such as BALD EAGLE (D-day) or ANVIL EXPRESS (M-day). EXPRESSING TIME E...York: Vintage Books, 1991. Fuller, J. F. C. Generalship: Its Diseases and Their Cure . Harrisburg, PA: Military Service Publishing Co., 1936

  18. Distributed operating systems

    NARCIS (Netherlands)

    Mullender, Sape J.

    1987-01-01

    In the past five years, distributed operating systems research has gone through a consolidation phase. On a large number of design issues there is now considerable consensus between different research groups. In this paper, an overview of recent research in distributed systems is given. In turn, th

  19. Sales and operations planning

    DEFF Research Database (Denmark)

    Kjellsdotter, Linea; Dukovska-Popovska, Iskra; Kaipia, Riikka

    2013-01-01

    This paper explores how the use of sales and operations planning (S&OP) may deal with the challenges set by the planning environment by investigating S&OP at four Scandinavian industrial food producers. Variables connected to the product and market, e.g. perishability, customer service elements...

  20. Global Operations Coevolution

    DEFF Research Database (Denmark)

    Slepniov, Dmitrij; Wæhrens, Brian Vejrum; Gubi, Ebbe

    2013-01-01

    Companies are actively seeking competitive advantage through their choice of location and ownership of operations. The purpose of this chapter is to uncover hidden effects of this development and propose how companies can respond to them. The chapter draws on a case study of a Danish industrial e...... of analysis and involving temporal adaptations. In terms of managerial implications, the study provides managers with lessons for designing a robust system of globally dispersed operations.......Companies are actively seeking competitive advantage through their choice of location and ownership of operations. The purpose of this chapter is to uncover hidden effects of this development and propose how companies can respond to them. The chapter draws on a case study of a Danish industrial...... equipment firm and describes how its operations configuration has been changing over time. The chapter identifies the key determinants of this change and uncovers some of its hidden effects. The chapter closes with propositions for how to respond to these effects through the development of a distinct...

  1. Mission operations management

    Science.gov (United States)

    Rocco, David A.

    1994-01-01

    Redefining the approach and philosophy that operations management uses to define, develop, and implement space missions will be a central element in achieving high efficiency mission operations for the future. The goal of a cost effective space operations program cannot be realized if the attitudes and methodologies we currently employ to plan, develop, and manage space missions do not change. A management philosophy that is in synch with the environment in terms of budget, technology, and science objectives must be developed. Changing our basic perception of mission operations will require a shift in the way we view the mission. This requires a transition from current practices of viewing the mission as a unique end product, to a 'mission development concept' built on the visualization of the end-to-end mission. To achieve this change we must define realistic mission success criteria and develop pragmatic approaches to achieve our goals. Custom mission development for all but the largest and most unique programs is not practical in the current budget environment, and we simply do not have the resources to implement all of our planned science programs. We need to shift our management focus to allow us the opportunity make use of methodologies and approaches which are based on common building blocks that can be utilized in the space, ground, and mission unique segments of all missions.

  2. Operational Amplifer Integrator

    NARCIS (Netherlands)

    van Tuijl, Adrianus Johannes Maria

    2003-01-01

    An integrator circuit comprises an operational amplifier which has a transistor stage (1) with an input terminal (4) and an output terminal (3), a feedback capacitor (2) connected between the input terminal (4) and the output terminal (3), and a resistor (5) connected to the input terminal (4), and

  3. Education of Operational Art

    Science.gov (United States)

    2012-12-06

    Arab movement were only achievable in a protracted war, inflicting an intolerable amount of casualties against Israel and the West. To accomplish this...functioning rice as well as wheat mill with adequate storage and production capacity, the 3/2 SBCT coordinated with higher division, corps, multinational...168 Ibid. 169 Ibid. 63 repair of silos and wheat and rice processing factories. Operation

  4. Concept of Operations: Essence

    Energy Technology Data Exchange (ETDEWEB)

    Hutton, William J.

    2014-04-01

    This concept of operations is designed to give the reader a brief overview of the National Rural Electric Cooperative Association’s Essence project and a description of the Essence device design. The data collected by the device, how the data are used, and how the data are protected are also discussed in this document.

  5. Splunk operational intelligence cookbook

    CERN Document Server

    Diakun, Josh; Mock, Derek

    2014-01-01

    This book is intended for users of all levels who are looking to leverage the Splunk Enterprise platform as a valuable operational intelligence tool. The recipes provided in this book will appeal to individuals from all facets of a business - IT, Security, Product, Marketing, and many more!

  6. Cyberwarfare and Operational Art

    Science.gov (United States)

    2017-05-25

    the Cambridge scene [.]…And it was because of the greater difficulties of dealing with the Enigma that it had to be that powerful… [I]n particular it...irregular forces, air-defense, and field artillery. Finally, cyber-attacks to neutralize the western Ukraine electrical grid extend operational

  7. Intelligent Potroom Operation

    Energy Technology Data Exchange (ETDEWEB)

    Jan Berkow; Larry Banta

    2003-07-29

    The Intelligent Potroom Operation project focuses on maximizing the performance of an aluminum smelter by innovating components for an intelligent manufacturing system. The Intelligent Potroom Advisor (IPA) monitors process data to identify reduction cells exhibiting behaviors that require immediate attention. It then advises operational personnel on those heuristic-based actions to bring the cell back to an optimal operating state in order to reduce the duration and frequency of substandard reduction cell performance referred to as ''Off-Peak Modes'' (OPMs). Techniques developed to identify cells exhibiting OPMs include the use of a finite element model-based cell state estimator for defining the cell's current operating state via advanced cell noise analyses. In addition, rule induction was also employed to identify statistically significant complex behaviors that occur prior to OPMs. The intelligent manufacturing system design, concepts and formalisms developed in this project w ere used as a basis for an intelligent manufacturing system design. Future research will incorporate an adaptive component to automate continuous process improvement, a technology platform with the potential to improve process performance in many of the other Industries of the Future applications as well.

  8. Camera Operator and Videographer

    Science.gov (United States)

    Moore, Pam

    2007-01-01

    Television, video, and motion picture camera operators produce images that tell a story, inform or entertain an audience, or record an event. They use various cameras to shoot a wide range of material, including television series, news and sporting events, music videos, motion pictures, documentaries, and training sessions. Those who film or…

  9. Operations Mercury and Husky: Contemporary Art of Operations and their Relevance for Operational Art

    Science.gov (United States)

    2016-04-07

    Operations Mercury and Husky: Contemporary Art of Operations and their Relevance for Operational Art A Monograph by LTC (GS...Operations Mercury and Husky: Contemporary Art of Operations and their Relevance for Operational Art 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c...operational art fulfi l ls a bridging role between strategic objectives and tactical action. The German Wehrmacht and the US Army applied their contemporary

  10. The repertoire of DNA-binding transcription factors in prokaryotes: functional and evolutionary lessons.

    Science.gov (United States)

    Perez-Rueda, Ernesto; Martinez-Nuñez, Mario Alberto

    2012-01-01

    The capabilities of organisms to contend with environmental changes depend on their genes and their ability to regulate their expression. DNA-binding transcription factors (TFs) play a central role in this process, because they regulate gene expression positively and/or negatively, depending on the operator context and ligand-binding status. In this review, we summarise recent findings regarding the function and evolution of TFs in prokaryotes. We consider the abundance of TFs in bacteria and archaea, the role of DNA-binding domains and their partner domains, and the effects of duplication events in the evolution of regulatory networks. Finally, a comprehensive picture for how regulatory networks have evolved in prokaryotes is provided.

  11. Potential of goat probiotic to bind mutagens.

    Science.gov (United States)

    Apás, Ana Lidia; González, Silvia Nelina; Arena, Mario Eduardo

    2014-08-01

    The mutagen binding ability of the goat probiotics (Lactobacillus reuteri DDL 19, Lactobacillus alimentarius DDL 48, Enterococcus faecium DDE 39, and Bifidobacterium bifidum DDBA) was evaluated. The oral administration of these probiotics reduced fecal mutagens and intestinal cancer markers in goats. Secondly, the effects of probiotics against the mutagenesis induced by sodium azide (SA), and Benzopyrene (B[α]P) by performing the modified Ames test using Salmonella typhimurium TA 100 was investigated. The capacity to bind benzopyrene and the stability of the bacterial-mutagen complex was analyzed by HPLC. The dismutagenic potential against both mutagens was proportional to probiotic concentration. Results showed that probiotic antimutagenic capacity against SA was ranging from 13 to 78%. The mixture of four goat probiotics (MGP) displayed higher antimutagenic activity against SA than any individual strains at the same cell concentration. This study shows that the highest diminution of mutagenicity in presence of B[α]P (74%) was observed in presence of MGP. The antimutagenic activity of nearly all the individual probiotic and the MGP were in concordance with the B[α]P binding determined by HPLC. According to our results, the B[α]P binding to probiotic was irreversible still after being washed with DMSO solution. The stability of the toxic compounds-bacterial cell binding is a key consideration when probiotic antimutagenic property is evaluated. MGP exhibits the ability to bind and detoxify potent mutagens, and this property can be useful in supplemented foods for goats since it can lead to the removal of potent mutagens and protect and enhance ruminal health and hence food safety of consumers.

  12. Binding of alkylpyridinium chloride surfactants to sodium polystyrene sulfonate

    NARCIS (Netherlands)

    Ishiguro, M.; Koopal, L.K.

    2009-01-01

    Binding of cationic surfactants to anionic polymers is well studied. However, the surfactant binding characteristics at very low concentration near the start of binding and at high concentration, where charge compensation may Occur. are less well known. Therefore, the binding characteristics of

  13. Rhadinovirus host entry by co-operative infection.

    Directory of Open Access Journals (Sweden)

    Clara Lawler

    2015-03-01

    Full Text Available Rhadinoviruses establish chronic infections of clinical and economic importance. Several show respiratory transmission and cause lung pathologies. We used Murid Herpesvirus-4 (MuHV-4 to understand how rhadinovirus lung infection might work. A primary epithelial or B cell infection often is assumed. MuHV-4 targeted instead alveolar macrophages, and their depletion reduced markedly host entry. While host entry was efficient, alveolar macrophages lacked heparan - an important rhadinovirus binding target - and were infected poorly ex vivo. In situ analysis revealed that virions bound initially not to macrophages but to heparan⁺ type 1 alveolar epithelial cells (AECs. Although epithelial cell lines endocytose MuHV-4 readily in vitro, AECs did not. Rather bound virions were acquired by macrophages; epithelial infection occurred only later. Thus, host entry was co-operative - virion binding to epithelial cells licensed macrophage infection, and this in turn licensed AEC infection. An antibody block of epithelial cell binding failed to block host entry: opsonization provided merely another route to macrophages. By contrast an antibody block of membrane fusion was effective. Therefore co-operative infection extended viral tropism beyond the normal paradigm of a target cell infected readily in vitro; and macrophage involvement in host entry required neutralization to act down-stream of cell binding.

  14. High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints.

    Directory of Open Access Journals (Sweden)

    Yuchun Guo

    Full Text Available An essential component of genome function is the syntax of genomic regulatory elements that determine how diverse transcription factors interact to orchestrate a program of regulatory control. A precise characterization of in vivo spacing constraints between key transcription factors would reveal key aspects of this genomic regulatory language. To discover novel transcription factor spatial binding constraints in vivo, we developed a new integrative computational method, genome wide event finding and motif discovery (GEM. GEM resolves ChIP data into explanatory motifs and binding events at high spatial resolution by linking binding event discovery and motif discovery with positional priors in the context of a generative probabilistic model of ChIP data and genome sequence. GEM analysis of 63 transcription factors in 214 ENCODE human ChIP-Seq experiments recovers more known factor motifs than other contemporary methods, and discovers six new motifs for factors with unknown binding specificity. GEM's adaptive learning of binding-event read distributions allows it to further improve upon previous methods for processing ChIP-Seq and ChIP-exo data to yield unsurpassed spatial resolution and discovery of closely spaced binding events of the same factor. In a systematic analysis of in vivo sequence-specific transcription factor binding using GEM, we have found hundreds of spatial binding constraints between factors. GEM found 37 examples of factor binding constraints in mouse ES cells, including strong distance-specific constraints between Klf4 and other key regulatory factors. In human ENCODE data, GEM found 390 examples of spatially constrained pair-wise binding, including such novel pairs as c-Fos:c-Jun/USF1, CTCF/Egr1, and HNF4A/FOXA1. The discovery of new factor-factor spatial constraints in ChIP data is significant because it proposes testable models for regulatory factor interactions that will help elucidate genome function and the

  15. High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints.

    Science.gov (United States)

    Guo, Yuchun; Mahony, Shaun; Gifford, David K

    2012-01-01

    An essential component of genome function is the syntax of genomic regulatory elements that determine how diverse transcription factors interact to orchestrate a program of regulatory control. A precise characterization of in vivo spacing constraints between key transcription factors would reveal key aspects of this genomic regulatory language. To discover novel transcription factor spatial binding constraints in vivo, we developed a new integrative computational method, genome wide event finding and motif discovery (GEM). GEM resolves ChIP data into explanatory motifs and binding events at high spatial resolution by linking binding event discovery and motif discovery with positional priors in the context of a generative probabilistic model of ChIP data and genome sequence. GEM analysis of 63 transcription factors in 214 ENCODE human ChIP-Seq experiments recovers more known factor motifs than other contemporary methods, and discovers six new motifs for factors with unknown binding specificity. GEM's adaptive learning of binding-event read distributions allows it to further improve upon previous methods for processing ChIP-Seq and ChIP-exo data to yield unsurpassed spatial resolution and discovery of closely spaced binding events of the same factor. In a systematic analysis of in vivo sequence-specific transcription factor binding using GEM, we have found hundreds of spatial binding constraints between factors. GEM found 37 examples of factor binding constraints in mouse ES cells, including strong distance-specific constraints between Klf4 and other key regulatory factors. In human ENCODE data, GEM found 390 examples of spatially constrained pair-wise binding, including such novel pairs as c-Fos:c-Jun/USF1, CTCF/Egr1, and HNF4A/FOXA1. The discovery of new factor-factor spatial constraints in ChIP data is significant because it proposes testable models for regulatory factor interactions that will help elucidate genome function and the implementation of combinatorial

  16. Binding energies of hypernuclei and hypernuclear interactions

    Energy Technology Data Exchange (ETDEWEB)

    Bodmer, A.R. [Argonne National Lab., IL (United States)]|[Univ. of Illinois, Chicago, IL (United States). Dept. of Physics; Murali, S.; Usmani, Q.N. [Jamia Millia Islamia, New Delhi (India). Dept. of Physics

    1996-05-01

    In part 1 the effect of nuclear core dynamics on the binding energies of {Lambda} hypernuclei is discussed in the framework of variational correlated wave functions. In particular, the authors discuss a new rearrangement energy contribution and its effect on the core polarization. In part 2 they consider the interpretation of the {Lambda} single-particle energy in terms of basic {Lambda}-nuclear interactions using a local density approximation based on a Fermi hypernetted chain calculation of the A binding to nuclear matter. To account for the data strongly repulsive 3-body {Lambda}NN forces are required. Also in this framework they discuss core polarization for medium and heavier hypernuclei.

  17. The binding energy and bonding in dialane.

    Science.gov (United States)

    Goebbert, Daniel J; Hernandez, Heriberto; Francisco, Joseph S; Wenthold, Paul G

    2005-08-24

    The binding energy of dialane, Al2H6, has been measured using mass spectrometric techniques to be 33 +/- 5 kcal/mol. This represents the first measurement of the thermochemical properties of dialane, which has only recently been observed in low-temperature matricies. High-level quantum mechanical calculations give a binding energy in agreement with the measured value. Experimental and quantum mechanical calculations show that dialane is chemically similar to diborane, B2H6, even though the bonding for these two systems shows significant differences.

  18. Perceptual-binding and persistent surface segregation.

    Science.gov (United States)

    Moradi, Farshad; Shimojo, Shinsuke

    2004-11-01

    Visual input is segregated in the brain into subsystems that process different attributes such as motion and color. At the same time, visual information is perceptually segregated into objects and surfaces. Here we demonstrate that perceptual segregation of visual entities based on a transparency cue precedes and affects perceptual binding of attributes. Adding an irrelevant transparency cue paradoxically improved the pairing of color and motion for rapidly alternating surfaces. Subsequent experiments show: (1) Attributes are registered over the temporal window defined by the perceptual persistence of segregation, resulting in asynchrony in binding, and (2) attention is necessary for correct registration of attributes in the presence of ambiguity.

  19. Binding energy of two-dimensional biexcitons

    DEFF Research Database (Denmark)

    Singh, Jai; Birkedal, Dan; Vadim, Lyssenko;

    1996-01-01

    Using a model structure for a two-dimensional (2D) biexciton confined in a quantum well, it is shown that the form of the Hamiltonian of the 2D biexciton reduces into that of an exciton. The binding energies and Bohr radii of a 2D biexciton in its various internal energy states are derived...... analytically using the fractional dimension approach. The ratio of the binding energy of a 2D biexciton to that of a 2D exciton is found to be 0.228, which agrees very well with the recent experimental value. The results of our approach are compared with those of earlier theories....

  20. Binding Energy Distribution Analysis Method: Hamiltonian Replica Exchange with Torsional Flattening for Binding Mode Prediction and Binding Free Energy Estimation.

    Science.gov (United States)

    Mentes, Ahmet; Deng, Nan-Jie; Vijayan, R S K; Xia, Junchao; Gallicchio, Emilio; Levy, Ronald M

    2016-05-10

    Molecular dynamics modeling of complex biological systems is limited by finite simulation time. The simulations are often trapped close to local energy minima separated by high energy barriers. Here, we introduce Hamiltonian replica exchange (H-REMD) with torsional flattening in the Binding Energy Distribution Analysis Method (BEDAM), to reduce energy barriers along torsional degrees of freedom and accelerate sampling of intramolecular degrees of freedom relevant to protein-ligand binding. The method is tested on a standard benchmark (T4 Lysozyme/L99A/p-xylene complex) and on a library of HIV-1 integrase complexes derived from the SAMPL4 blind challenge. We applied the torsional flattening strategy to 26 of the 53 known binders to the HIV Integrase LEDGF site found to have a binding energy landscape funneled toward the crystal structure. We show that our approach samples the conformational space more efficiently than the original method without flattening when starting from a poorly docked pose with incorrect ligand dihedral angle conformations. In these unfavorable cases convergence to a binding pose within 2-3 Å from the crystallographic pose is obtained within a few nanoseconds of the Hamiltonian replica exchange simulation. We found that torsional flattening is insufficient in cases where trapping is due to factors other than torsional energy, such as the formation of incorrect intramolecular hydrogen bonds and stacking. Work is in progress to generalize the approach to handle these cases and thereby make it more widely applicable.

  1. On the Neuberger overlap operator

    Science.gov (United States)

    Boriçi, Artan

    1999-04-01

    We compute Neuberger's overlap operator by the Lanczos algorithm applied to the Wilson-Dirac operator. Locality of the operator for quenched QCD data and its eigenvalue spectrum in an instanton background are studied.

  2. Toeplitz Operators on Dirichlet Spaces

    Institute of Scientific and Technical Information of China (English)

    Yu Feng LU; Shun Hua SUN

    2001-01-01

    In this paper we study Toeplitz operators on Dirichlet spaces and describe the boundedness and compactness of Toeplitz operators on Dirichlet spaces. Meanwhile. we give density theorems for Toeplitz operators on Dirichlet spaces

  3. Gyrokinetic linearized Landau collision operator

    DEFF Research Database (Denmark)

    Madsen, Jens

    2013-01-01

    The full gyrokinetic electrostatic linearized Landau collision operator is calculated including the equilibrium operator, which represents the effect of collisions between gyrokinetic Maxwellian particles. First, the equilibrium operator describes energy exchange between different plasma species...

  4. Cohering power of quantum operations

    Energy Technology Data Exchange (ETDEWEB)

    Bu, Kaifeng, E-mail: bkf@zju.edu.cn [School of Mathematical Sciences, Zhejiang University, Hangzhou 310027 (China); Kumar, Asutosh, E-mail: asukumar@hri.res.in [Harish-Chandra Research Institute, Chhatnag Road, Jhunsi, Allahabad 211019 (India); Homi Bhabha National Institute, Anushaktinagar, Mumbai 400094 (India); Zhang, Lin, E-mail: linyz@zju.edu.cn [Institute of Mathematics, Hangzhou Dianzi University, Hangzhou 310018 (China); Wu, Junde, E-mail: wjd@zju.edu.cn [School of Mathematical Sciences, Zhejiang University, Hangzhou 310027 (China)

    2017-05-18

    Highlights: • Quantum coherence. • Cohering power: production of quantum coherence by quantum operations. • Study of cohering power and generalized cohering power, and their comparison for differentmeasures of quantum coherence. • Operational interpretation of cohering power. • Bound on cohering power of a generic quantum operation. - Abstract: Quantum coherence and entanglement, which play a crucial role in quantum information processing tasks, are usually fragile under decoherence. Therefore, the production of quantum coherence by quantum operations is important to preserve quantum correlations including entanglement. In this paper, we study cohering power–the ability of quantum operations to produce coherence. First, we provide an operational interpretation of cohering power. Then, we decompose a generic quantum operation into three basic operations, namely, unitary, appending and dismissal operations, and show that the cohering power of any quantum operation is upper bounded by the corresponding unitary operation. Furthermore, we compare cohering power and generalized cohering power of quantum operations for different measures of coherence.

  5. Whether metal (Pb, Cd, Zn) binding property of natural organic matter is source-dependent-A study based on spectroscopy, potentiometry, and voltammetry

    Science.gov (United States)

    Chen, W.; Gueguen, C.; Smith, S.

    2016-02-01

    Natural organic matter (NOM) is a complex molecule of diverse ligands that essentially regulates metal speciation and toxicity. NOM source is heterogeneous, but can be operationally classified into allochthonous, autochthonous, and intermediate between these two groups. Whether the metal binding property (i.e. affinity and capacity) is NOM-source dependent however, remains unclear. The answer of this question is helpful for environmental modeling. If metal binding properties are sensitive to NOM source, then models used to determine metal speciation will need to be revised to take some measurement of NOM quality into consideration. In this study, different sources of NOM were collected for the study of Pb, Cd, and Zn binding. The NOM properties were characterized by different techniques from different chemistry indexes, including acidity chemistry, optical spectroscopy for component and structure, and cathodic stripping voltammetry for thiol determination. Absence of Gradient and Nernstian Equilibrium Stripping was used to selectively determine the concentration of free metal ion for binding isotherm. A model based on continuous site distribution was used to describe this binding isotherm. By best fitting the binding isotherm into the model using a regularized optimization, a conditional affinity spectrum was derived. Comparing binding isotherm and affinity spectrum between NOM samples showed that Pb binding was more dependent on NOM sources than Cd and Zn binding. Under the same binding condition (i.e. DOC, pH and ionic strength), allochthonous NOM mostly showed higher binding level (i.e. up to 3 log unit of bound species concentration) and stronger binding affinity for Pb than autochthonous NOM. This tendency however, was not obvious for Cd and Zn. Humic-like content probably contributed the most significant factor for Pb binding discrimination. Thiol content may be another important factor to differentiate metal binding affinity and capacity between NOM samples.

  6. Train operation in emergencies

    CERN Document Server

    Jia, Limin; Qin, Yong

    2017-01-01

    This book presents the latest findings on train operation theories and methods in the context of emergencies. It examines and assesses a range of aspects—including the definition of a railway emergency, transport organization modes in emergencies, calculating railway transport capacity in emergencies, line planning in emergencies, train re-pathing in emergencies and train re-scheduling in emergencies—that are urgently needed in the railway transportation field, which faces the serious challenge of dealing with emergencies worldwide. The book highlights the latest research results in an integrated and systematic way, and the methodology presented is oriented on real-world problems, allowing it to be used not only directly in railway operational management, but also as the point of departure for further applications or theoretical research. As such, the book will be of considerable interest to graduate students and researchers in the field of traffic and transportation engineering.>.

  7. ATLAS IBL operational experience

    CERN Document Server

    Takubo, Yosuke; The ATLAS collaboration

    2016-01-01

    The Insertable B-Layer (IBL) is the inner most pixel layer in the ATLAS experiment, which was installed at 3.3 cm radius from the beam axis in 2014 to improve the tracking performance. To cope with the high radiation and hit occupancy due to proximity to the interaction point, a new read-out chip and two different silicon sensor technologies (planar and 3D) have been developed for the IBL. After the long shut-down period over 2013 and 2014, the ATLAS experiment started data-taking in May 2015 for Run-2 of the Large Hadron Collider (LHC). The IBL has been operated successfully since the beginning of Run-2 and shows excellent performance with the low dead module fraction, high data-taking efficiency and improved tracking capability. The experience and challenges in the operation of the IBL is described as well as its performance.

  8. NICMOS FOM Operation Test

    Science.gov (United States)

    Noll, Keith

    2001-07-01

    This test verifies the FOM's mechanical operation. A 7 x 1 grid of points will be made by moving the FOM in steps of 6.5 from -20 to +19 arcsec relative to the 0 position {-36 to +3 relative to the default NIC3 FOM position of +16 arcsec}. We also have an additional FOM position at the default NIC3 position. These exposures all use the F166N filter. At the end of this sequence we will take F222M exposures at three additional FOM positions, the default position {+16 arcsec relative to the center point of the FOM mechanical range} and +/- 2 arcsec. This is to test for vignetting. Prerequisites for this test are cool down to nominal operating temperature {cold and stable, near the expected final temperature set point, but not necessarily the final temperature set point} and the filter wheel minifunctional and the filter wheel tests {proposals 8944 and 8972}.

  9. Global Operations Networks

    DEFF Research Database (Denmark)

    of global operations and operations strategy. This summative volume utilises the rich and diverse empirical foundation generated during the project activities in Denmark, Sweden and Finland. Chapters of the book are based on quantitative data and multiple case studies which the project partners have been......In the current context of global economic liberalisation and technological advancements, industrial companies are less likely to generate value in the traditional vertically integrated chain. Instead, they are doing so by means of elaborate cross-border and cross-organisational networks. As a rule......, these networks are configured on a global basis and consist of diverse and interdependent affiliates (linked both through ownership and non-equity relationships), which are engaged in an exchange of goods, services and information. The Scandinavian context is no exception to this trend. Nevertheless...

  10. Airline Operations Aid

    Science.gov (United States)

    1993-01-01

    C Language Integrated Production System (CLIPS), a NASA-developed expert systems program, is used by American Airlines for three purposes: as a rapid prototyping tool; to develop production prototypes; and to develop production application. An example of the latter is CLIPS' use in "Hub S1AAshing," a knowledge based system that recommends contingency plans when severe schedule reductions must be made. Hub S1AAshing has replaced a manual, labor intensive process. It saves time and allows Operations Control Coordinators to handle more difficult situations. Because the system assimilates much of the information necessary to facilitate educated decision making, it minimizes negative impact in situations where it is impossible to operate all flights.

  11. TOKM hardware operation manual

    Energy Technology Data Exchange (ETDEWEB)

    Menlove, H.O.; Halbig, J.K.; Klosterbuer, S.F.; Bosler, G.E. [Los Alamos National Lab., NM (United States); Abedin-Zadeh, R.; Syed-Azmi, B. [International Atomic Energy Agency, Wagramerstrasse, Vienna (Austria)

    1995-08-01

    This manual describes the detector design features, performance, and operating characteristics of the Tokai-1 spent fuel monitor. The system includes a pair of monitors-one for the primary (normal) fuel transfer chute and one for the by-pass fuel transfer chute. Each monitor contains four independent detector tubes to provide direction of travel and redundancy. There are two ion chambers and two {sup 3}He tubes inside each detector package. All of the detectors are used to monitor the presence of spent-fuel gamma rays as the fuel rods pass alongside the detector package. Gamma-ray and neutron detector (GRAND) electronics supply power to the ion chambers and {sup 3}He tubes, and the data is collected in the GRAND and the Kontron computer. The system is designed to operate unattended with data pickup by the inspectors on a 90-day period. This manual gives the performance and calibration parameters.

  12. Operational discipline and microenterprises

    Directory of Open Access Journals (Sweden)

    Francisca Rosales Gómez

    2015-06-01

    Full Text Available The aim of this study is to identify the elements of the operational Discipline in the business of micro-enterprises in Coatzacoalcos, Mexico. For the analysis an instrument is designed and applied to 20 companies which fulfill the suggested recommendations in research such as caution in the use of hazardous materials, use of equipment with simple specifications and easily accessible to employees, monitoring of some standard to identify risks, good environmental management, among others. We conclude that despite the findings in the application of the methodology of Operational Discipline, it is generally suffers from many important practices, and can be considered as construction companies of the city of Coatzacoalcos no mandatory environmental care this activity.

  13. Solution structure and binding specificity of the p63 DNA binding domain.

    Science.gov (United States)

    Enthart, Andreas; Klein, Christian; Dehner, Alexander; Coles, Murray; Gemmecker, Gerd; Kessler, Horst; Hagn, Franz

    2016-05-26

    p63 is a close homologue of p53 and, together with p73, is grouped into the p53 family of transcription factors. p63 is known to be involved in the induction of controlled apoptosis important for differentiation processes, germ line integrity and development. Despite its high homology to p53, especially within the DNA binding domain (DBD), p63-DBD does not show cooperative DNA binding properties and is significantly more stable against thermal and chemical denaturation. Here, we determined the solution structure of p63-DBD and show that it is markedly less dynamic than p53-DBD. In addition, we also investigate the effect of a double salt bridge present in p53-DBD, but not in p63-DBD on the cooperative binding behavior and specificity to various DNA sites. Restoration of the salt bridges in p63-DBD by mutagenesis leads to enhanced binding affinity to p53-specific, but not p63-specific response elements. Furthermore, we show that p63-DBD is capable of binding to anti-apoptotic BclxL via its DNA binding interface, a feature that has only been shown for p53 so far. These data suggest that all p53 family members - despite alterations in the specificity and binding affinity - are capable of activating pro-apoptotic pathways in a tissue specific manner.

  14. Generation of metal-binding staphylococci through surface display of combinatorially engineered cellulose-binding domains.

    Science.gov (United States)

    Wernérus, H; Lehtiö, J; Teeri, T; Nygren, P A; Ståhl, S

    2001-10-01

    Ni(2+)-binding staphylococci were generated through surface display of combinatorially engineered variants of a fungal cellulose-binding domain (CBD) from Trichoderma reesei cellulase Cel7A. Novel CBD variants were generated by combinatorial protein engineering through the randomization of 11 amino acid positions, and eight potentially Ni(2+)-binding CBDs were selected by phage display technology. These new variants were subsequently genetically introduced into chimeric surface proteins for surface display on Staphylococcus carnosus cells. The expressed chimeric proteins were shown to be properly targeted to the cell wall of S. carnosus cells, since full-length proteins could be extracted and affinity purified. Surface accessibility for the chimeric proteins was demonstrated, and furthermore, the engineered CBDs, now devoid of cellulose-binding capacity, were shown to be functional with regard to metal binding, since the recombinant staphylococci had gained Ni(2+)-binding capacity. Potential environmental applications for such tailor-made metal-binding bacteria as bioadsorbents in biofilters or biosensors are discussed.

  15. The requirement of the glutamic acid residue at the third position from the carboxyl termini of the laminin gamma chains in integrin binding by laminins.

    Science.gov (United States)

    Ido, Hiroyuki; Nakamura, Aya; Kobayashi, Reiko; Ito, Shunsuke; Li, Shaoliang; Futaki, Sugiko; Sekiguchi, Kiyotoshi

    2007-04-13

    Laminins are the major cell-adhesive proteins in the basement membrane, consisting of three subunits termed alpha, beta, and gamma. The putative binding site for integrins has been mapped to the G domain of the alpha chain, although trimerization with beta and gamma chains is necessary for the G domain to exert its integrin binding activity. The mechanism underlying the requirement of beta and gamma chains in integrin binding by laminins remains poorly understood. Here, we show that the C-terminal region of the gamma chain is involved in modulation of the integrin binding activity of laminins. We found that deletion of the C-terminal three but not two amino acids within the gamma1 chain completely abrogated the integrin binding activity of laminin-511. Furthermore, substitution of Gln for Glu-1607, the amino acid residue at the third position from the C terminus of the gamma1 chain, also abolished the integrin binding activity, underscoring the role of Glu-1607 in integrin binding by the laminin. We also found that the conserved Glu residue of the gamma2 chain is necessary for integrin binding by laminin-332, suggesting that the same mechanism operates in the modulation of the integrin binding activity of laminins containing either gamma1 or gamma2 chains. However, the peptide segment modeled after the C-terminal region of gamma1 chain was incapable of either binding to integrin or inhibiting integrin binding by laminin-511, making it unlikely that the Glu residue is directly recognized by integrin. These results, together, indicate a novel mechanism operating in ligand recognition by laminin binding integrins.

  16. Cyber Operations Virtual Environment

    Science.gov (United States)

    2010-09-01

    attacks within the context of special assignment airlift missions (E. Kean (AFRL/ RISA ), personal communication, April 12, 2010). Similarly, systems...which classes of cyber attack vectors may be implemented to facilitate TTP development (E. Kean (AFRL/ RISA ), personal communication, April 12, 2010...related scenarios for air mobility operations (E. Kean (AFRL/ RISA ), personal communication, April 11, 2010). Data of this nature has its advantages

  17. Operation Brain Trauma Therapy

    Science.gov (United States)

    2012-10-01

    seizures in rats with brain injured at different developmental stages. Epilepsy Res. 2004;61:63–72. 29. Tikka T, Fiebich BL, Goldsteins G, Keinanen R...intrahippocampal transplantation of adult neural stem cells and intraventricular erythropoietin-infusion ameliorates spontaneous recurrent seizures by...brain injury (TBI) is a leading cause of morbid-ity and mortality in Operation Iraqi Freedom largely due to the emergence of blast-injury from

  18. Operations (Field Manual)

    Science.gov (United States)

    2008-02-27

    ability to learn and adapt. German Field Marshal Erwin Rommel observed that American Soldiers were initially inexperienced but learned and adapted...quickly and well. Even though the Army is much more experienced than it was in North Africa in World War II, today’s complex environment requires or...strategic distance include the 1942 invasion of North Africa and the 1992 intervention in Somalia. These operations involved forces projected from the

  19. Pre-operative anaemia.

    Science.gov (United States)

    Clevenger, B; Richards, T

    2015-01-01

    Pre-operative anaemia is a relatively common finding, affecting a third of patients undergoing elective surgery. Traditionally associated with chronic disease, management has historically focused on the use of blood transfusion as a solution for anaemia in the peri-operative period. Data from large series now suggest that anaemia is an independent risk associated with poor outcome in both cardiac and non-cardiac surgery. Furthermore, blood transfusion does not appear to ameliorate this risk, and in fact may increase the risk of postoperative complications and hospital length of stay. Consequently, there is a need to identify, diagnose and manage pre-operative anaemia to reduce surgical risk. Discoveries in the pathways of iron metabolism have found that chronic disease can cause a state of functional iron deficiency leading to anaemia. The key iron regulatory protein hepcidin, activated in response to inflammation, inhibits absorption of iron from the gastrointestinal tract and further reduces bioavailability of iron stores for red cell production. Consequently, although iron stores (predominantly ferritin) may be normal, the transport of iron either from the gastrointestinal tract or iron stores to the bone marrow is inhibited, leading to a state of 'functional' iron deficiency and subsequent anaemia. Since absorption from the gastrointestinal tract is blocked, increasing oral iron intake is ineffective, and studies are now looking at the role of intravenous iron to treat anaemia in the surgical setting. In this article, we review the incidence and impact of anaemia on the pre-operative patient. We explain how anaemia may be caused by functional iron deficiency, and how iron deficiency anaemia may be diagnosed and treated.

  20. Operation of the accelerator

    Energy Technology Data Exchange (ETDEWEB)

    Pardo, R.C.; Batzka, B.; Billquist, P.J. [and others

    1995-08-01

    Fiscal Year 1994 was the first year of seven-day operation since ATLAS became a national user facility in 1985. ATLAS made the most of the opportunity this year by providing 5200 hours of beam on-target to the research program. A record number of 60 experiments were completed and the {open_quotes}facility reliability{close_quotes} remained near the 90% level. Seven-day operation was made possible with the addition to the staff of two operator positions providing single-operator coverage during the weekend period. The normally scheduled coverage was augmented by an on-call list of system experts who respond to emergencies with phone-in advice and return to the Laboratory when necessary. This staffing approach continues but we rearranged our staffing patterns so that we now have one cryogenics engineer working a shift pattern which includes 8-hour daily coverage during the weekend. ATLAS provided a beam mix to users consisting of 26 different isotopic species, 23% of which were for A>100 in FY 1994. Approximately 60% of the beam time was provided by the Positive Ion Injector, slightly less than the usage rate of FY 1993. Experiments using uranium or lead beams accounted for 16.4% of the total beam time. The ECR ion source and high-voltage platform functioned well throughout the year. A new technique for solid material production in the source was developed which uses a sputtering process wherein the sample of material placed near the plasma chamber wall is biased negatively. Plasma ions are accelerated into the sample and material is sputtered from the surface into the plasma. This technique is now used routinely for many elements. Runs of calcium, germanium, nickel, lead, tellurium, and uranium were carried out with this technique.

  1. Measuring Cyber Operations Effectiveness

    Science.gov (United States)

    2014-11-01

    using network scanners and frameworks like the SANS Critical Security Controls. Finally, a network vulnerability penetration test can be performed to...effectiveness in network, defensive, and offensive operations is a difficult task. Measures may be static , automated, some combination of both or...by SANS identifies using port scanners as a way to verify the setup has been performed correctly and only needed ports and protocols are allowed

  2. Operation Unified Protector

    DEFF Research Database (Denmark)

    Buhl, Kenneth Øhlenschlæger

    2012-01-01

    Formålet med denne artikel er at se nærmere på erfaringerne fra den maritime kampagne under den militære indsats i konflikten i Libyen i 2011, som i NATO regi blev kendt som Operation Unified Protector (OUP). Dækningen i de danske medier fokuserede primært på luftkampagnen, hvilket må tilskrives,...

  3. Restructuring diversified telecom operators

    OpenAIRE

    Ulset, Svein

    2002-01-01

    The paper examines the divestiture trend among diversified major telecom operators using a combined agency and transaction cost economics approach. Our illustrative cases seem to support both the governance failure thesis of agency theory and the efficient governance theses of corporate finance and transaction cost economics. That is, manager-controlled companies tend to grow oversized and overdiversified before being transformed into more efficient scale and scope by actively intervening own...

  4. Education Payload Operation - Demonstrations

    Science.gov (United States)

    Keil, Matthew

    2009-01-01

    Education Payload Operation - Demonstrations (EPO-Demos) are recorded video education demonstrations performed on the International Space Station (ISS) by crewmembers using hardware already onboard the ISS. EPO-Demos are videotaped, edited, and used to enhance existing NASA education resources and programs for educators and students in grades K-12. EPO-Demos are designed to support the NASA mission to inspire the next generation of explorers.

  5. ALG-2, a multifunctional calcium binding protein?

    DEFF Research Database (Denmark)

    Tarabykina, Svetlana; Mollerup, Jens; Winding Gojkovic, P.;

    2004-01-01

    ALG-2 was originally discovered as a pro-apoptotic protein in a genetic screen. Due to its ability to bind calcium with high affinity it was postulated to provide a link between the known effect of calcium in programmed cell death and the molecular death execution machinery. This review article...

  6. Alkali binding in hydrated Portland cement paste

    NARCIS (Netherlands)

    Chen, W.; Brouwers, H.J.H.

    2010-01-01

    The alkali-binding capacity of C–S–H in hydrated Portland cement pastes is addressed in this study. The amount of bound alkalis in C–S–H is computed based on the alkali partition theories firstly proposed by Taylor (1987) and later further developed by Brouwers and Van Eijk (2003). Experimental data

  7. Information flow through calcium binding proteins

    Science.gov (United States)

    Bak, Ji Hyun; Bialek, William

    2013-03-01

    Calcium signaling is a ubiquitous mode of biological communication, which regulates a great variety of vital processes in living systems. Such a signal typically begins with an elementary event, in which calcium ions bind to a protein, inducing a change in the protein's structure. Information can only be lost, from what was conveyed through this initial event, as the signal is further transduced through the downstream networks. In the present work we analyze and optimize the information flow in the calcium binding process. We explicitly calculate the mutual information between the calcium concentration and the states of the protein, using a simple model for allosteric regulation in a dimeric protein. The optimal solution depends on the dynamic range of the input as well as on the timescale of signal integration. According to our result, the optimizing strategy involves allowing the calcium-binding protein to be ``activated'' by a partial occupation of its sites, and tuning independently the strengths of cooperative interactions in the binding and unbinding processes.

  8. Binding of flavonoids to staphylococcal enterotoxin B.

    Science.gov (United States)

    Benedik, Evgen; Skrt, Mihaela; Podlipnik, Crtomir; Ulrih, Nataša Poklar

    2014-12-01

    Staphylococcal enterotoxins are metabolic products of Staphylococcus aureus that are responsible for the second-most-commonly reported type of food poisoning. Polyphenols are known to interact with proteins to form complexes, the properties of which depend on the structures of both the polyphenols and the protein. In the present study, we investigated the binding of four flavonoid polyphenols to Staphylococcal enterotoxin B (SEB) at pH 7.5 and 25 °C: (-)-epigallocatechin-3-gallate (EGCG), (-)-epigallocatechin (EGC), kaempferol-3-glucoside (KAM-G) and kaempferol (KAM). Fluorescence emission spectrometry and molecular docking were applied to compare experimentally determined binding parameters with molecular modeling. EGCG showed an order of magnitude higher binding constant (1.4 × 10(5) M(-1)) than the other studied polyphenols. Our blind-docking results showed that EGCG and similar polyphenolic ligands is likely to bind to the channel at the surface of SEB that is responsible for the recognition of the T-cell beta chain fragment and influence the adhesion of SEB to T cells.

  9. Binding of cationic surfactants to humic substances

    NARCIS (Netherlands)

    Ishiguro, M.; Tan, W.; Koopal, L.K.

    2007-01-01

    Commercial surfactants are introduced into the environment either through waste products or site-specific contamination. The amphiphilic nature of both surfactants and humic substances (HS) leads to their mutual attraction especially when surfactant and HS are oppositely charged. Binding of the cati

  10. Oxytocin binding sites in bovine mammary tissue

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Xin.

    1989-01-01

    Oxytocin binding sites were identified and characterized in bovine mammary tissue. ({sup 3}H)-oxytocin binding reached equilibrium by 50 min at 20{degree}C and by 8 hr at 4{degree}C. The half-time of displacement at 20{degree}C was approximately 1 hr. Thyrotropin releasing hormone, adrenocorticotropin, angiotensin I, angiotensin II, pentagastrin, bradykinin, xenopsin and L-valyl-histidyl-L-leucyl-L-threonyl-L-prolyl-L-valyl-L-glutamyl-L-lysine were not competitive. In the presence of 10 nM LiCl, addition of oxytocin to dispersed bovine mammary cells, in which phosphatidylinositol was pre-labelled, caused a time and dose-dependent increase in radioactive inositiol monophosphate incorporation. The possibility that there are distinct vasopressin receptors in bovine mammary tissue was investigated. ({sup 3}H)-vasopressin binding reached equilibrium by 40 min at 20{degree}. The half-time of displacement at 20{degree}C was approximately 1 hr. The ability of the peptides to inhibit ({sup 3}H)-vasopressin binding was: (Thr{sup 4},Gly{sup 7})-oxytocin > Arg{sup 8}-vasopressin > (lys{sup 8})-vasopressin > (Deamino{sup 1},D-arg{sup 8})-vasopressin > oxytocin > d (CH{sub 2}){sub 5}Tyr(Me)AVP.

  11. Binding Hydrated Anions with Hydrophobic Pockets.

    Science.gov (United States)

    Sokkalingam, Punidha; Shraberg, Joshua; Rick, Steven W; Gibb, Bruce C

    2016-01-13

    Using a combination of isothermal titration calorimetry and quantum and molecular dynamics calculations, we demonstrate that relatively soft anions have an affinity for hydrophobic concavity. The results are consistent with the anions remaining partially hydrated upon binding, and suggest a novel strategy for anion recognition.

  12. Lipid binding proteins from parasitic platyhelminthes.

    Science.gov (United States)

    Alvite, Gabriela; Esteves, Adriana

    2012-01-01

    TWO MAIN FAMILIES OF LIPID BINDING PROTEINS HAVE BEEN IDENTIFIED IN PARASITIC PLATYHELMINTHES: hydrophobic ligand binding proteins (HLBPs) and fatty acid binding proteins (FABPs). Members of the former family of proteins are specific to the Cestoda class, while FABPs are conserved across a wide range of animal species. Because Platyhelminthes are unable to synthesize their own lipids, these lipid-binding proteins are important molecules in these organisms. HLBPs are a high molecular mass complex of proteins and lipids. They are composed of subunits of low molecular mass proteins and a wide array of lipid molecules ranging from CoA esters to cholesterol. These proteins are excretory-secretory molecules and are key serological tools for diagnosis of diseases caused by cestodes. FABPs are mainly intracellular proteins of low molecular weight. They are also vaccine candidates. Despite that the knowledge of their function is scarce, the differences in their molecular organization, ligand preferences, intra/extracellular localization, evolution, and phylogenetic distribution, suggest that platyhelminths HLBPs and FABPs should play different functions. FABPs might be involved in the removal of fatty acids from the inner surface of the cell membrane and in their subsequent targeting to specific cellular destinations. In contrast, HLBPs might be involved in fatty acid uptake from the host environment.

  13. Nucleic acids encoding a cellulose binding domain

    Energy Technology Data Exchange (ETDEWEB)

    Shoseyov, Oded (Karmey Yosef, IL); Shpiegl, Itai (Rehovot, IL); Goldstein, Marc A. (Davis, CA); Doi, Roy H. (Davis, CA)

    1996-01-01

    A cellulose binding domain (CBD) having a high affinity for crystalline cellulose and chitin is disclosed, along with methods for the molecular cloning and recombinant production thereof. Fusion products comprising the CBD and a second protein are likewise described. A wide range of applications are contemplated for both the CBD and the fusion products, including drug delivery, affinity separations, and diagnostic techniques.

  14. Development of a glucose binding protein biosensor

    Science.gov (United States)

    Dweik, M.; Milanick, M.; Grant, S.

    2007-09-01

    Glucose binding protein (GBP) is a monomeric periplasmic protein. It is synthesized in the cytoplasm of Escherichia coli which functions as a receptor for transport D-glucose. GBP binds glucose with high affinity. The binding mechanism is based on a hinge motion due to the protein conformational change. This change was utilized as an optical sensing mechanism by applying Fluorescence Resonance Energy Transfer (FRET). The wild-type GBP lacks cysteine in its structure, but by introducing a single cysteine at a specific site by site-directed mutagenesis, this ensured single-label attachment at specific sites with a fluorescent probe. The other sites were amino sites, which were labeled with second fluorophore. The near IR FRET pair, Alexa Fluor 680 (AF680) and Alexa Fluor 750(AF750), was utilized. The AF680 targeted the amine sites, which was the donor fluorophore, while the AF750 labeled the single cysteine site, which was the acceptor fluorophore. The sensing system strategy was based on the fluorescence changes of the probe as the protein undergoes a structural change upon binding. This biosensor had the ability to detect down to 10 uM concentrations of glucose. Next the probes were uploaded into red blood cells via hypo osmotic dialysis. The sensor responded to glucose while encapsulated with the red cells. These results showed the feasibility of an intracellular glucose biosensor.

  15. Tension-induced binding of semiflexible biopolymers

    CERN Document Server

    Benetatos, Panayotis; Zippelius, Annette

    2014-01-01

    We investigate theoretically the effect of polymer tension on the collective behavior of reversibly binding cross-links. For this purpose, we employ a model of two weakly bending wormlike chains aligned in parallel by a tensile force, with a sequence of inter-chain binding sites regularly spaced along the contours. Reversible cross-links attach and detach at the sites with an affinity controlled by a chemical potential. In a mean-field approach, we calculate the free energy of the system and find the emergence of a free-energy barrier which controls the reversible (un)binding. The tension affects the conformational entropy of the chains which competes with the binding energy of the cross-links. This competition gives rise to a sudden increase in the fraction of bound sites as the tension increases. We show that this transition is related to the cross-over between weak and strong localization of a directed polymer in a pinning potential. The cross-over to the strongly bound state can be interpreted as a mechan...

  16. Singular Value Decomposition and Ligand Binding Analysis

    Directory of Open Access Journals (Sweden)

    André Luiz Galo

    2013-01-01

    Full Text Available Singular values decomposition (SVD is one of the most important computations in linear algebra because of its vast application for data analysis. It is particularly useful for resolving problems involving least-squares minimization, the determination of matrix rank, and the solution of certain problems involving Euclidean norms. Such problems arise in the spectral analysis of ligand binding to macromolecule. Here, we present a spectral data analysis method using SVD (SVD analysis and nonlinear fitting to determine the binding characteristics of intercalating drugs to DNA. This methodology reduces noise and identifies distinct spectral species similar to traditional principal component analysis as well as fitting nonlinear binding parameters. We applied SVD analysis to investigate the interaction of actinomycin D and daunomycin with native DNA. This methodology does not require prior knowledge of ligand molar extinction coefficients (free and bound, which potentially limits binding analysis. Data are acquired simply by reconstructing the experimental data and by adjusting the product of deconvoluted matrices and the matrix of model coefficients determined by the Scatchard and McGee and von Hippel equation.

  17. Binding of cholera toxin to Giardia lamblia.

    OpenAIRE

    McCardell, B. A.; Madden, J M; Stanfield, J T; Tall, B D; Stephens, M. J.

    1987-01-01

    Binding of cholera toxin to Giardia lamblia was demonstrated by two slightly different methods: an immunofluorescence technique using antibody to cholera toxin and anti-rabbit immunoglobulin G conjugated to fluorescein isothiocyanate, and a one-step fluorescence method in which G. lamblia was incubated with the B subunit of cholera toxin conjugated to fluorescein isothiocyanate.

  18. The Double Bind: The next Generation

    Science.gov (United States)

    Malcom, Lindsey E.; Malcom, Shirley M.

    2011-01-01

    In this foreword, Shirley Malcom and Lindsey Malcom speak to the history and current status of women of color in science, technology, engineering, and mathematics (STEM) fields. As the author of the seminal report "The Double Bind: The Price of Being a Minority Woman in Science", Shirley Malcom is uniquely poised to give us an insightful…

  19. Factor VIIa binding and internalization in hepatocytes

    DEFF Research Database (Denmark)

    Hjortoe, G; Sorensen, B B; Petersen, L C

    2005-01-01

    The liver is believed to be the primary clearance organ for coagulation proteases, including factor VIIa (FVIIa). However, at present, clearance mechanisms for FVIIa in liver are unknown. To obtain information on the FVIIa clearance mechanism, we investigated the binding and internalization...

  20. Lipid Binding Proteins from Parasitic Platyhelmithes

    Directory of Open Access Journals (Sweden)

    Gabriela eAlvite

    2012-09-01

    Full Text Available Two main families of lipid binding proteins have been identified in parasitic Platyhelminthes: hydrophobic ligand binding proteins (HLBPs and fatty acid binding proteins (FABPs. Members of the former family of proteins are specific to the Cestoda class, while FABPs are conserved across a wide range of animal species. Because Platyhelminthes are unable to synthesise their own lipids, these lipid-binding proteins are important molecules in these organisms.HLBPs are a high molecular mass complex of proteins and lipids. They are composed of subunits of low molecular mass proteins and a wide array of lipid molecules ranging from CoA esters to cholesterol. These proteins are excretory-secretory molecules and are key serological tools for diagnosis of diseases caused by cestodes. FABPs are mainly intracellular proteins of low molecular weight. They are also vaccine candidates.Despite that the knowledge of their function is scarce, the differences in their molecular organisation, ligand preferences, intra/extracellular localisation, evolution, and phylogenetic distribution, suggest that platyhelminths HLBPs and FABPs should play different functions. FABPs might be involved in the removal of fatty acids from the inner surface of the cell membrane and in their subsequent targeting to specific cellular destinations. In contrast, HLBPs might be involved in fatty acid uptake from the host environment.

  1. ILC Operating Scenarios

    CERN Document Server

    Barklow, T; Fujii, K; Gao, J; List, J; Walker, N; Yokoya, K

    2015-01-01

    The ILC Technical Design Report documents the design for the construction of a linear collider which can be operated at energies up to 500 GeV. This report summarizes the outcome of a study of possible running scenarios, including a realistic estimate of the real time accumulation of integrated luminosity based on ramp-up and upgrade processes. The evolution of the physics outcomes is emphasized, including running initially at 500 GeV, then at 350 GeV and 250 GeV. The running scenarios have been chosen to optimize the Higgs precision measurements and top physics while searching for evidence for signals beyond the standard model, including dark matter. In addition to the certain precision physics on the Higgs and top that is the main focus of this study, there are scientific motivations that indicate the possibility for discoveries of new particles in the upcoming operations of the LHC or the early operation of the ILC. Follow-up studies of such discoveries could alter the plan for the centre-of-mass collision...

  2. Operational experience at ELBE

    Science.gov (United States)

    Michel, P.; Lehnert, U.; Seidel, W.

    2015-05-01

    The ELBE center for high power radiation sources is the largest user facility in the Helmholtz-Zentrum Dresden- Rossendorf. The facility is based on a 36 MeV superconducting RF Linac which can be operated up to 1.6 mA in cw mode. The electron beam is used to generate secondary radiation, such as infrared light (Free Electron Lasers), coherent THz radiation, MeV-Bremsstrahlung, fast neutrons and positrons for a wide range of basic research like semiconductor physics, nuclear astrophysics and radio biological investigations. Two high power laser systems (500 TW Ti:Sa laser, 2 PW diode pumped laser) are under construction for laser acceleration experiments and X-ray generation by Thomson scattering. The FELs are in operation since 2004 (mid-IR FEL, 4-22μm) and 2006 (far-IF FEL, 20-250μm). The fundamental features of the ELBE IR FELs, the FEL instrumentation and advanced beam diagnostics for the photon beam are described. During ten years of user operation experiences and statistical data were collected.

  3. Operational health physics training

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1992-06-01

    The initial four sections treat basic information concerning atomic structure and other useful physical quantities, natural radioactivity, the properties of {alpha}, {beta}, {gamma}, x rays and neutrons, and the concepts and units of radiation dosimetry (including SI units). Section 5 deals with biological effects and the risks associated with radiation exposure. Background radiation and man-made sources are discussed next. The basic recommendations of the ICRP concerning dose limitations: justification, optimization (ALARA concepts and applications) and dose limits are covered in Section seven. Section eight is an expanded version of shielding, and the internal dosimetry discussion has been extensively revised to reflect the concepts contained in the MIRD methodology and ICRP 30. The remaining sections discuss the operational health physics approach to monitoring radiation. Individual sections include radiation detection principles, instrument operation and counting statistics, health physics instruments and personnel monitoring devices. The last five sections deal with the nature of, operation principles of, health physics aspects of, and monitoring approaches to air sampling, reactors, nuclear safety, gloveboxes and hot cells, accelerators and x ray sources. Decontamination, waste disposal and transportation of radionuclides are added topics. Several appendices containing constants, symbols, selected mathematical topics, and the Chart of the Nuclides, and an index have been included.

  4. CH Packaging Operations Manual

    Energy Technology Data Exchange (ETDEWEB)

    None, None

    2009-05-27

    This document provides the user with instructions for assembling a payload. All the steps in Subsections 1.2, Preparing 55-Gallon Drum Payload Assembly; 1.3, Preparing "Short" 85-Gallon Drum Payload Assembly (TRUPACT-II and HalfPACT); 1.4, Preparing "Tall" 85-Gallon Drum Payload Assembly (HalfPACT only); 1.5, Preparing 100-Gallon Drum Payload Assembly; 1.6, Preparing Shielded Container Payload Assembly; 1.7, Preparing SWB Payload Assembly; and 1.8, Preparing TDOP Payload Assembly, must be completed, but may be performed in any order as long as radiological control steps are not bypassed. Transport trailer operations, package loading and unloading from transport trailers, hoisting and rigging activities such as ACGLF operations, equipment checkout and shutdown, and component inspection activities must be performed, but may be performed in any order and in parallel with other activities as long as radiological control steps are not bypassed. Steps involving OCA/ICV lid removal/installation and payload removal/loading may be performed in parallel if there are multiple operators working on the same packaging. Steps involving removal/installation of OCV/ICV upper and lower main O-rings must be performed in sequence, except as noted.

  5. CH Packaging Operations Manual

    Energy Technology Data Exchange (ETDEWEB)

    None, None

    2008-09-11

    This document provides the user with instructions for assembling a payload. All the steps in Subsections 1.2, Preparing 55-Gallon Drum Payload Assembly; 1.3, Preparing "Short" 85-Gallon Drum Payload Assembly (TRUPACT-II and HalfPACT); 1.4, Preparing "Tall" 85-gallon Drum Payload Assembly (HalfPACT only); 1.5, Preparing 100-Gallon Drum Payload Assembly; 1.6, Preparing SWB Payload Assembly; and 1.7, Preparing TDOP Payload Assembly, must be completed, but may be performed in any order as long as radiological control steps are not bypassed. Transport trailer operations, package loading and unloading from transport trailers, hoisting and rigging activities such as ACGLF operations, equipment checkout and shutdown, and component inspection activities must be performed, but may be performed in any order and in parallel with other activities as long as radiological control steps are not bypassed. Steps involving OCA/ICV lid removal/installation and payload removal/loading may be performed in parallel if there are multiple operators working on the same packaging. Steps involving removal/installation of OCV/ICV upper and lower main O-rings must be performed in sequence.

  6. Graphs of Hecke operators

    CERN Document Server

    Lorscheid, Oliver

    2010-01-01

    Let $X$ be a curve over $\\F_q$ with function field $F$. In this paper, we define a graph for each Hecke operator with fixed ramification. A priori, these graphs can be seen as a convenient language to organize formulas for the action of Hecke operators on automorphic forms. However, they will prove to be a powerful tool for explicit calculations and proofs of finite dimensionality results. We develop a structure theory for certain graphs $G_x$ of unramified Hecke operators, which is of a similar vein to Serre's theory of quotients of Bruhat Tits trees. To be precise, $G_x$ is locally a quotient of a Bruhat Tits tree and has finitely many components. An interpretation of $G_x$ in terms of rank 2 bundles on $X$ and methods from reduction theory show that $G_x$ is the union of finitely many cusps, which are infinite subgraphs of a simple nature, and a nucleus, which is a finite subgraph that depends heavily on the arithmetics of $F$. We describe how one recovers unramified automorphic forms as functions on the g...

  7. Integrating faces, houses, motion, and action: spontaneous binding across ventral and dorsal processing streams.

    Science.gov (United States)

    Keizer, André W; Colzato, Lorenza S; Hommel, Bernhard

    2008-01-01

    Perceiving an event requires the integration of its features across numerous brain maps and modules. Visual object perception is thought to be mediated by a ventral processing stream running from occipital to inferotemporal cortex, whereas most spatial processing and action control is attributed to the dorsal stream connecting occipital, parietal, and frontal cortex. Here we show that integration operates not only on ventral features and objects, such as faces and houses, but also across ventral and dorsal pathways, binding faces and houses to motion and manual action. Furthermore, these bindings seem to persist over time, as they influenced performance on future task-relevant visual stimuli. This is reflected by longer reaction times for repeating one, but alternating other features in a sequence, compared to complete repetition or alternation of features. Our findings are inconsistent with the notion that the dorsal stream is operating exclusively online and has no access to memory.

  8. CD36 binds oxidized low density lipoprotein (LDL) in a mechanism dependent upon fatty acid binding.

    Science.gov (United States)

    Jay, Anthony G; Chen, Alexander N; Paz, Miguel A; Hung, Justin P; Hamilton, James A

    2015-02-20

    The association of unesterified fatty acid (FA) with the scavenger receptor CD36 has been actively researched, with focuses on FA and oxidized low density lipoprotein (oxLDL) uptake. CD36 has been shown to bind FA, but this interaction has been poorly characterized to date. To gain new insights into the physiological relevance of binding of FA to CD36, we characterized FA binding to the ectodomain of CD36 by the biophysical method surface plasmon resonance. Five structurally distinct FAs (saturated, monounsaturated (cis and trans), polyunsaturated, and oxidized) were pulsed across surface plasmon resonance channels, generating association and dissociation binding curves. Except for the oxidized FA HODE, all FAs bound to CD36, with rapid association and dissociation kinetics similar to HSA. Next, to elucidate the role that each FA might play in CD36-mediated oxLDL uptake, we used a fluorescent oxLDL (Dii-oxLDL) live cell assay with confocal microscopy imaging. CD36-mediated uptake in serum-free medium was very low but greatly increased when serum was present. The addition of exogenous FA in serum-free medium increased oxLDL binding and uptake to levels found with serum and affected CD36 plasma membrane distribution. Binding/uptake of oxLDL was dependent upon the FA dose, except for docosahexaenoic acid, which exhibited binding to CD36 but did not activate the uptake of oxLDL. HODE also did not affect oxLDL uptake. High affinity FA binding to CD36 and the effects of each FA on oxLDL uptake have important implications for protein conformation, binding of other ligands, functional properties of CD36, and high plasma FA levels in obesity and type 2 diabetes.

  9. Retinoblastoma-binding protein 1 has an interdigitated double Tudor domain with DNA binding activity.

    Science.gov (United States)

    Gong, Weibin; Wang, Jinfeng; Perrett, Sarah; Feng, Yingang

    2014-02-21

    Retinoblastoma-binding protein 1 (RBBP1) is a tumor and leukemia suppressor that binds both methylated histone tails and DNA. Our previous studies indicated that RBBP1 possesses a Tudor domain, which cannot bind histone marks. In order to clarify the function of the Tudor domain, the solution structure of the RBBP1 Tudor domain was determined by NMR and is presented here. Although the proteins are unrelated, the RBBP1 Tudor domain forms an interdigitated double Tudor structure similar to the Tudor domain of JMJD2A, which is an epigenetic mark reader. This indicates the functional diversity of Tudor domains. The RBBP1 Tudor domain structure has a significant area of positively charged surface, which reveals a capability of the RBBP1 Tudor domain to bind nucleic acids. NMR titration and isothermal titration calorimetry experiments indicate that the RBBP1 Tudor domain binds both double- and single-stranded DNA with an affinity of 10-100 μM; no apparent DNA sequence specificity was detected. The DNA binding mode and key interaction residues were analyzed in detail based on a model structure of the Tudor domain-dsDNA complex, built by HADDOCK docking using the NMR data. Electrostatic interactions mediate the binding of the Tudor domain with DNA, which is consistent with NMR experiments performed at high salt concentration. The DNA-binding residues are conserved in Tudor domains of the RBBP1 protein family, resulting in conservation of the DNA-binding function in the RBBP1 Tudor domains. Our results provide further insights into the structure and function of RBBP1.

  10. Gestalt-binding of tropomyosin on actin during thin filament activation.

    Science.gov (United States)

    Lehman, William; Orzechowski, Marek; Li, Xiaochuan Edward; Fischer, Stefan; Raunser, Stefan

    2013-08-01

    Our thesis is that thin filament function can only be fully understood and muscle regulation then elucidated if atomic structures of the thin filament are available to reveal the positions of tropomyosin on actin in all physiological states. After all, it is tropomyosin influenced by troponin that regulates myosin-crossbridge cycling on actin and therefore controls contraction in all muscles. In addition, we maintain that a complete appreciation of thin filament activation also requires that the mechanical properties of tropomyosin itself are recognized and then related to the effect of myosin-association on actin. Taking the Gestalt-binding of tropomyosin into account, coupled with our electron microscopy structures and computational chemistry, we propose a comprehensive mechanism for tropomyosin regulatory movement over the actin filament surface that explains the cooperative muscle activation process. In fact, well-known point mutations of critical amino acids on the actin-tropomyosin binding interface disrupt Gestalt-binding and are associated with a number of inherited myopathies. Moreover, dysregulation of tropomyosin may also be a factor that interferes with the gatekeeping operation of non-muscle tropomyosin in the controlling interactions of a wide variety of cellular actin-binding proteins. The clinical relevance of Gestalt-binding is discussed in articles by the Marston and the Gunning groups in this special journal issue devoted to the impact of tropomyosin on biological systems.

  11. Cell adhesion-dependent membrane trafficking of a binding partner for the ebolavirus glycoprotein is a determinant of viral entry.

    Science.gov (United States)

    Dube, Derek; Schornberg, Kathryn L; Shoemaker, Charles J; Delos, Sue E; Stantchev, Tzanko S; Clouse, Kathleen A; Broder, Christopher C; White, Judith M

    2010-09-21

    Ebolavirus is a hemorrhagic fever virus associated with high mortality. Although much has been learned about the viral lifecycle and pathogenesis, many questions remain about virus entry. We recently showed that binding of the receptor binding region (RBR) of the ebolavirus glycoprotein (GP) and infection by GP pseudovirions increase on cell adhesion independently of mRNA or protein synthesis. One model to explain these observations is that, on cell adhesion, an RBR binding partner translocates from an intracellular vesicle to the cell surface. Here, we provide evidence for this model by showing that suspension 293F cells contain an RBR binding site within a membrane-bound compartment associated with the trans-Golgi network and microtubule-organizing center. Consistently, trafficking of the RBR binding partner to the cell surface depends on microtubules, and the RBR binding partner is internalized when adherent cells are placed in suspension. Based on these observations, we reexamined the claim that lymphocytes, which are critical for ebolavirus pathogenesis, are refractory to infection because they lack an RBR binding partner. We found that both cultured and primary human lymphocytes (in suspension) contain an intracellular pool of an RBR binding partner. Moreover, we identified two adherent primate lymphocytic cell lines that bind RBR at their surface and strikingly, support GP-mediated entry and infection. In summary, our results reveal a mode of determining viral entry by a membrane-trafficking event that translocates an RBR binding partner to the cell surface, and they suggest that this process may be operative in cells important for ebolavirus pathogenesis (e.g., lymphocytes and macrophages).

  12. Chromate Binding and Removal by the Molybdate-Binding Protein ModA.

    Science.gov (United States)

    Karpus, Jason; Bosscher, Michael; Ajiboye, Ifedayo; Zhang, Liang; He, Chuan

    2017-04-04

    Effective and cheap methods and techniques for the safe removal of hexavalent chromate from the environment are in increasingly high demand. High concentrations of hexavalent chromate have been shown to have numerous harmful effects on human biology. We show that the E. coli molybdate-binding protein ModA is a genetically encoded tool capable of removing chromate from aqueous solutions. Although previously reported to not bind chromate, we show that ModA binds chromate tightly and is capable of removing chromate to levels well below current US federal standards. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. STARD4 Membrane Interactions and Sterol Binding.

    Science.gov (United States)

    Iaea, David B; Dikiy, Igor; Kiburu, Irene; Eliezer, David; Maxfield, Frederick R

    2015-08-01

    The steroidogenic acute regulatory protein-related lipid transfer (START) domain family is defined by a conserved 210-amino acid sequence that folds into an α/β helix-grip structure. Members of this protein family bind a variety of ligands, including cholesterol, phospholipids, sphingolipids, and bile acids, with putative roles in nonvesicular lipid transport, metabolism, and cell signaling. Among the soluble START proteins, STARD4 is expressed in most tissues and has previously been shown to transfer sterol, but the molecular mechanisms of membrane interaction and sterol binding remain unclear. In this work, we use biochemical techniques to characterize regions of STARD4 and determine their role in membrane interaction and sterol binding. Our results show that STARD4 interacts with anionic membranes through a surface-exposed basic patch and that introducing a mutation (L124D) into the Omega-1 (Ω1) loop, which covers the sterol binding pocket, attenuates sterol transfer activity. To gain insight into the attenuating mechanism of the L124D mutation, we conducted structural and biophysical studies of wild-type and L124D STARD4. These studies show that the L124D mutation reduces the conformational flexibility of the protein, resulting in a diminished level of membrane interaction and sterol transfer. These studies also reveal that the C-terminal α-helix, and not the Ω1 loop, partitions into the membrane bilayer. On the basis of these observations, we propose a model of STARD4 membrane interaction and sterol binding and release that requires dynamic movement of both the Ω1 loop and membrane insertion of the C-terminal α-helix.

  14. A genome-wide signature of glucocorticoid receptor binding in neuronal PC12 cells

    Directory of Open Access Journals (Sweden)

    Polman J Annelies E

    2012-10-01

    Full Text Available Abstract Background Glucocorticoids, secreted by the adrenals in response to stress, profoundly affect structure and plasticity of neurons. Glucocorticoid action in neurons is mediated by glucocorticoid receptors (GR that operate as transcription factors in the regulation of gene expression and either bind directly to genomic glucocorticoid response elements (GREs or indirectly to the genome via interactions with bound transcription factors. These two modes of action, respectively called transactivation and transrepression, result in the regulation of a wide variety of genes important for neuronal function. The objective of the present study was to identify genome-wide glucocorticoid receptor binding sites in neuronal PC12 cells using Chromatin ImmunoPrecipitation combined with next generation sequencing (ChIP-Seq. Results In total we identified 1183 genomic binding sites of GR, the majority of which were novel and not identified in other ChIP-Seq studies on GR binding. More than half (58% of the binding sites contained a GRE. The remaining 42% of the GBS did not harbour a GRE and therefore likely bind GR via an intermediate transcription factor tethering GR to the DNA. While the GRE-containing binding sites were more often located nearby genes involved in general cell functions and processes such as apoptosis, cell motion, protein dimerization activity and vasculature development, the binding sites without a GRE were located nearby genes with a clear role in neuronal processes such as neuron projection morphogenesis, neuron projection regeneration, synaptic transmission and catecholamine biosynthetic process. A closer look at the sequence of the GR binding sites revealed the presence of several motifs for transcription factors that are highly divergent from those previously linked to GR-signaling, including Gabpa, Prrx2, Zfp281, Gata1 and Zbtb3. These transcription factors may represent novel crosstalk partners of GR in a neuronal context

  15. Structure and operation of bacterial tripartite pumps.

    Science.gov (United States)

    Hinchliffe, Philip; Symmons, Martyn F; Hughes, Colin; Koronakis, Vassilis

    2013-01-01

    In bacteria such as Pseudomonas aeruginosa and Escherichia coli, tripartite membrane machineries, or pumps, determine the efflux of small noxious molecules, such as detergents, heavy metals, and antibiotics, and the export of large proteins including toxins. They are therefore influential in bacterial survival, particularly during infections caused by multidrug-resistant pathogens. In these tripartite pumps an inner membrane transporter, typically an ATPase or proton antiporter, binds and translocates export or efflux substrates. In cooperation with a periplasmic adaptor protein it recruits and opens a TolC family cell exit duct, which is anchored in the outer membrane and projects across the periplasmic space between inner and outer membranes. Assembled tripartite pumps thus span the entire bacterial cell envelope. We review the atomic structures of each of the three pump components and discuss how these have allowed high-resolution views of tripartite pump assembly, operation, and possible inhibition.

  16. On Bosonic Magnetic Flux Operator and Bosonic Faraday Operator Formula

    Institute of Scientific and Technical Information of China (English)

    FAN Hong-Yi; WANG Tong-Tong; WANG Ji-Suo

    2007-01-01

    In the literature about mesoscopic Josephson devices the magnetic flux is considered as an operator, the fundamental commutative relation between the magnetic flux operator and the Cooper-pair charge operator is usually preengaged. In this paper we show that such a relation can be deduced from the basic Bose operators' commutative relation through the entangled state representation. The Faraday formula in bosonic form is then equivalent to the second Josephson equation. The current operator equation for LC mesoscopic circuit is also derived.

  17. Automatic Binding Time Analysis for a Typed Lambda-Calculus

    DEFF Research Database (Denmark)

    Nielson, Hanne Riis; Nielson, Flemming

    1988-01-01

    A binding time analysis imposes a distinction between the computations to be performed early (e.g. at compile-time) and those to be performed late (e.g. at run-time). For the lambda-calculus this distinction is formalized by a two-level lambda-calculus. The authors present an algorithm for static...... analysis of the binding times of a typed lambda-calculus with products, sums, lists and general recursive types. Given partial information about the binding times of some of the subexpressions it will complete that information such that (i) early bindings may be turned into late bindings but not vice versa......, (ii) the resulting two-level lambda-expression reflects our intuition about binding times, e.g. that early bindings are performed before late bindings, and (iii) as few changes as possible have been made compared with the initial binding information. The results can be applied in the implementation...

  18. Potentiometric sensors doped with biomolecules as a new approach to small molecule/biomolecule binding kinetics analysis.

    Science.gov (United States)

    Daems, D; De Wael, K; Vissenberg, K; Van Camp, G; Nagels, L

    2014-04-15

    The most successful binding kinetics analysis systems at this moment include surface plasmon resonance (SPR), quartz microcrystal balance (QMB) and surface acoustic wave (SAW). Although these are powerful methods, they generally are complex, expensive and require the use of monolayers. Here, we report on potentiometric sensors as an inexpensive and simple alternative to do binding kinetics analysis between small molecules in solution and biomolecules (covalently) attached in a biopolymer sensor coating layer. As an example, dopamine and an anti-dopamine aptamer were used as the small molecule and the biomolecule respectively. Binding between both follows a Langmuir adsorption type model and creates a surface potential. The system operates in Flow Injection Analysis mode (FIA). Besides being an interesting new binding kinetics tool, the approach allows systematic design of potentiometric biosensors (in the present study a dopamine sensor), and gives new insights into the functioning of ion-selective electrodes (ISE's).

  19. Isothermal titration calorimetry: general formalism using binding polynomials.

    Science.gov (United States)

    Freire, Ernesto; Schön, Arne; Velazquez-Campoy, Adrian

    2009-01-01

    The theory of the binding polynomial constitutes a very powerful formalism by which many experimental biological systems involving ligand binding can be analyzed under a unified framework. The analysis of isothermal titration calorimetry (ITC) data for systems possessing more than one binding site has been cumbersome because it required the user to develop a binding model to fit the data. Furthermore, in many instances, different binding models give rise to identical binding isotherms, making it impossible to discriminate binding mechanisms using binding data alone. One of the main advantages of the binding polynomials is that experimental data can be analyzed by employing a general model-free methodology that provides essential information about the system behavior (e.g., whether there exists binding cooperativity, whether the cooperativity is positive or negative, and the magnitude of the cooperative energy). Data analysis utilizing binding polynomials yields a set of binding association constants and enthalpy values that conserve their validity after the correct model has been determined. In fact, once the correct model is validated, the binding polynomial parameters can be immediately translated into the model specific constants. In this chapter, we describe the general binding polynomial formalism and provide specific theoretical and experimental examples of its application to isothermal titration calorimetry.

  20. Operational Maneuver: Function or Fiction?

    Science.gov (United States)

    2007-11-02

    the premise that this would never happen, so why plan for it. That is just the point. Operational art planning should not leave any stone unturned . The... unturned during operational art planning and execution. The maneuver apex theory can be applied to the Air Force operating environment, however, operational

  1. Tractor Operation and Daily Care.

    Science.gov (United States)

    Fore, J. M.; And Others

    Written for the tractor operator, the manual describes, with the aid of colored illustrations and diagrams, the tasks involved in the proper operation and daily maintenance of tractors. It offers explanations for the desirability of the various servicing and adjustment operations, as well as guidelines for tractor operation and safety. The…

  2. Adams Operations on Matrix Factorizations

    OpenAIRE

    Brown, Michael K.; Miller, Claudia; Thompson, Peder; Walker, Mark E.

    2016-01-01

    We define Adams operations on matrix factorizations, and we show these operations enjoy analogues of several key properties of the Adams operations on perfect complexes with support developed by Gillet-Soul\\'e in their paper "Intersection Theory Using Adams Operations". As an application, we give a proof of a conjecture of Dao-Kurano concerning the vanishing of Hochster's theta invariant.

  3. ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors.

    Science.gov (United States)

    Chu, Wen-Yi; Huang, Yu-Feng; Huang, Chun-Chin; Cheng, Yi-Sheng; Huang, Chien-Kang; Oyang, Yen-Jen

    2009-07-01

    This article presents the design of a sequence-based predictor named ProteDNA for identifying the sequence-specific binding residues in a transcription factor (TF). Concerning protein-DNA interactions, there are two types of binding mechanisms involved, namely sequence-specific binding and nonspecific binding. Sequence-specific bindings occur between protein sidechains and nucleotide bases and correspond to sequence-specific recognition of genes. Therefore, sequence-specific bindings are essential for correct gene regulation. In this respect, ProteDNA is distinctive since it has been designed to identify sequence-specific binding residues. In order to accommodate users with different application needs, ProteDNA has been designed to operate under two modes, namely, the high-precision mode and the balanced mode. According to the experiments reported in this article, under the high-precision mode, ProteDNA has been able to deliver precision of 82.3%, specificity of 99.3%, sensitivity of 49.8% and accuracy of 96.5%. Meanwhile, under the balanced mode, ProteDNA has been able to deliver precision of 60.8%, specificity of 97.6%, sensitivity of 60.7% and accuracy of 95.4%. ProteDNA is available at the following websites: http://protedna.csbb.ntu.edu.tw/, http://protedna.csie.ntu.edu.tw/, http://bio222.esoe.ntu.edu.tw/ProteDNA/.

  4. Protein-binding RNA aptamers affect molecular interactions distantly from their binding sites

    DEFF Research Database (Denmark)

    Dupont, Daniel M; Thuesen, Cathrine K; Bøtkjær, Kenneth A;

    2015-01-01

    Nucleic acid aptamer selection is a powerful strategy for the development of regulatory agents for molecular intervention. Accordingly, aptamers have proven their diligence in the intervention with serine protease activities, which play important roles in physiology and pathophysiology. Nonetheless...... potential, both binding to the serine protease urokinase-type plasminogen activator (uPA). We determine the subsequent impact of aptamer binding on the well-established molecular interactions (plasmin, PAI-1, uPAR, and LRP-1A) controlling uPA activities. One of the aptamers (upanap-126) binds to the area...... around the C-terminal α-helix in pro-uPA, while the other aptamer (upanap-12) binds to both the β-hairpin of the growth factor domain and the kringle domain of uPA. Based on the mapping studies, combined with data from small-angle X-ray scattering analysis, we construct a model for the upanap-12:pro...

  5. The inhibition of anti-DNA binding to DNA by nucleic acid binding polymers.

    Directory of Open Access Journals (Sweden)

    Nancy A Stearns

    Full Text Available Antibodies to DNA (anti-DNA are the serological hallmark of systemic lupus erythematosus (SLE and can mediate disease pathogenesis by the formation of immune complexes. Since blocking immune complex formation can attenuate disease manifestations, the effects of nucleic acid binding polymers (NABPs on anti-DNA binding in vitro were investigated. The compounds tested included polyamidoamine dendrimer, 1,4-diaminobutane core, generation 3.0 (PAMAM-G3, hexadimethrine bromide, and a β-cylodextrin-containing polycation. As shown with plasma from patients with SLE, NABPs can inhibit anti-DNA antibody binding in ELISA assays. The inhibition was specific since the NABPs did not affect binding to tetanus toxoid or the Sm protein, another lupus autoantigen. Furthermore, the polymers could displace antibody from preformed complexes. Together, these results indicate that NABPs can inhibit the formation of immune complexes and may represent a new approach to treatment.

  6. A new zinc binding fold underlines the versatility of zinc binding modules in protein evolution.

    Science.gov (United States)

    Sharpe, Belinda K; Matthews, Jacqueline M; Kwan, Ann H Y; Newton, Anthea; Gell, David A; Crossley, Merlin; Mackay, Joel P

    2002-05-01

    Many different zinc binding modules have been identified. Their abundance and variety suggests that the formation of zinc binding folds might be relatively common. We have determined the structure of CH1(1), a 27-residue peptide derived from the first cysteine/histidine-rich region (CH1) of CREB binding protein (CBP). This peptide forms a highly ordered zinc-dependent fold that is distinct from known folds. The structure differs from a subsequently determined structure of a larger region from the CH3 region of CBP, and the CH1(1) fold probably represents a nonphysiologically active form. Despite this, the fold is thermostable and tolerant to both multiple alanine mutations and changes in the zinc-ligand spacing. Our data support the idea that zinc binding domains may arise frequently. Additionally, such structures may prove useful as scaffolds for protein design, given their stability and robustness.

  7. Equipment Operational Requirements

    Energy Technology Data Exchange (ETDEWEB)

    Greenwalt, B; Henderer, B; Hibbard, W; Mercer, M

    2009-06-11

    The Iraq Department of Border Enforcement is rich in personnel, but poor in equipment. An effective border control system must include detection, discrimination, decision, tracking and interdiction, capture, identification, and disposition. An equipment solution that addresses only a part of this will not succeed, likewise equipment by itself is not the answer without considering the personnel and how they would employ the equipment. The solution should take advantage of the existing in-place system and address all of the critical functions. The solutions are envisioned as being implemented in a phased manner, where Solution 1 is followed by Solution 2 and eventually by Solution 3. This allows adequate time for training and gaining operational experience for successively more complex equipment. Detailed descriptions of the components follow the solution descriptions. Solution 1 - This solution is based on changes to CONOPs, and does not have a technology component. It consists of observers at the forts and annexes, forward patrols along the swamp edge, in depth patrols approximately 10 kilometers inland from the swamp, and checkpoints on major roads. Solution 2 - This solution adds a ground sensor array to the Solution 1 system. Solution 3 - This solution is based around installing a radar/video camera system on each fort. It employs the CONOPS from Solution 1, but uses minimal ground sensors deployed only in areas with poor radar/video camera coverage (such as canals and streams shielded by vegetation), or by roads covered by radar but outside the range of the radar associated cameras. This document provides broad operational requirements for major equipment components along with sufficient operational details to allow the technical community to identify potential hardware candidates. Continuing analysis will develop quantities required and more detailed tactics, techniques, and procedures.

  8. Operation and development 1999

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2001-07-01

    This issue of the Technical Report on the Accelerators describes the operations for physics experiments and beam tests, various technical improvements and ongoing projects during the year 1999. As usual, the first chapter reports on the standard operation of GANIL with stable ions, with analysis of the beam time distribution and statistics, including failures. A major project was the production and subsequent acceleration, over a long period of time, of an intense {sub 58}Ni{sup 11+} beam produced using the MIVOC method, which contributed strongly to the discovery of the doubly-magic {sub 48}Ni element. The renovation and development program (Chapter 2), including methods for producing metallic ion beams, gathered speed thanks to the completion of SPIRAL. A large share of these projects were high-intensity oriented. This trend also obviously applies to projects directly linked to the THI operation. In a special test, a 1.3 x 10{sup 13} pps {sub 13}C beam (later raised to 2 x 10{sup 13} pps for several hours) was accelerated and extracted from SSC2 at an energy of 75 MeV/n. Simultaneously, comparisons were made between simulations and beam test results for a clearer understanding of space charge effects on accelerator transmission efficiency. Chapter 3 covers the THI related projects. The final chapter deals with IRRSUD. This project, which is funded and on the way to completion, uses low energy beams delivered by the two injector cyclotrons for industrial applications and research, such as nano-technologies and simulation of defects in solids. (author)

  9. Relating the shape of protein binding sites to binding affinity profiles: is there an association?

    Directory of Open Access Journals (Sweden)

    Bitter István

    2010-10-01

    Full Text Available Abstract Background Various pattern-based methods exist that use in vitro or in silico affinity profiles for classification and functional examination of proteins. Nevertheless, the connection between the protein affinity profiles and the structural characteristics of the binding sites is still unclear. Our aim was to investigate the association between virtual drug screening results (calculated binding free energy values and the geometry of protein binding sites. Molecular Affinity Fingerprints (MAFs were determined for 154 proteins based on their molecular docking energy results for 1,255 FDA-approved drugs. Protein binding site geometries were characterized by 420 PocketPicker descriptors. The basic underlying component structure of MAFs and binding site geometries, respectively, were examined by principal component analysis; association between principal components extracted from these two sets of variables was then investigated by canonical correlation and redundancy analyses. Results PCA analysis of the MAF variables provided 30 factors which explained 71.4% of the total variance of the energy values while 13 factors were obtained from the PocketPicker descriptors which cumulatively explained 94.1% of the total variance. Canonical correlation analysis resulted in 3 statistically significant canonical factor pairs with correlation values of 0.87, 0.84 and 0.77, respectively. Redundancy analysis indicated that PocketPicker descriptor factors explain 6.9% of the variance of the MAF factor set while MAF factors explain 15.9% of the total variance of PocketPicker descriptor factors. Based on the salient structures of the factor pairs, we identified a clear-cut association between the shape and bulkiness of the drug molecules and the protein binding site descriptors. Conclusions This is the first study to investigate complex multivariate associations between affinity profiles and the geometric properties of protein binding sites. We found that

  10. What an Operation

    Institute of Scientific and Technical Information of China (English)

    LISA; CARDUCCI

    2006-01-01

    Every year I take a PAP test, or a CTC as it is called in China. Last August, I was diagnosed with a uterine polypus. A "tumor?" Though a polypus is seldom cancerous, doctors insisted I have a biopsy. Were they concerned because I'm a foreigner or did they want to make money out of me? I preferred having the tumor removed rather than only a biopsy. They agreed. Before I knew it I was on the operation table after an electrocardiogram and a simple blood test.

  11. Continuity of Translation Operators

    CERN Document Server

    Athreya, Krishna B

    2010-01-01

    For a Radon measure $\\mu$ on $\\bbR,$ we show that $L^{\\infty}(\\mu)$ is invariant under the group of translation operators $T_t(f)(x) = {$f(x-t)$}\\ (t \\in \\bbR)$ if and only if $\\mu$ is equivalent to Lebesgue measure $m$. We also give necessary and sufficient conditions for $L^p(\\mu),\\1 \\leq p < \\infty,$ to be invariant under the group $\\{T_t\\}$ in terms of the Radon-Nikodym derivative w.r.t. $m$.

  12. ALMA science operations

    Science.gov (United States)

    Nyman, Lars-Åke; Andreani, Paola; Hibbard, John; Okumura, Sachiko K.

    2010-07-01

    The ALMA (Atacama Large Millimeter/submillimeter Array) project is an international collaboration between Europe, East Asia and North America in cooperation with the Republic of Chile. The ALMA Array Operations Site (AOS) is located at Chajnantor, a plateau at an altitude of 5000 m in the Atacama desert in Chile, and the ALMA Operations Support Facility (OSF) is located near the AOS at an altitude of 2900 m. ALMA will consist of an array of 66 antennas, with baselines up to 16 km and state-of-the-art receivers that cover all the atmospheric windows up to 1 THz. An important component of ALMA is the compact array of twelwe 7-m and four 12-m antennas (the Atacama Compact Array, ACA), which will greatly enhance ALMA's ability to image extended sources. Construction of ALMA started in 2003 and will be completed in 2013. Commissioning started in January 2010 and Early Science Operations is expected to start during the second half of 2011. ALMA science operations is provided by the Joint ALMA Observatory (JAO) in Chile, and the three ALMA Regional Centers (ARCs) located in each ALMA region - Europe, North America and East Asia. ALMA observations will take place 24h per day, interrupted by maintenance periods, and will be done in service observing mode with flexible (dynamic) scheduling. The observations are executed in the form of scheduling blocks (SBs), each of which contains all information necessary to schedule and execute the observations. The default output to the astronomer will be pipeline-reduced images calibrated according to the calibration plan. The JAO is responsible for the data product quality. All science and calibration raw data are captured and archived in the ALMA archive, a distributed system with nodes at the OSF, the Santiago central office and the ARCs. Observation preparation will follow a Phase 1/Phase 2 process. During Phase 1, observation proposals will be created using software tools provided by the JAO and submitted for scientific and

  13. Revamping Spacecraft Operational Intelligence

    Science.gov (United States)

    Hwang, Victor

    2012-01-01

    The EPOXI flight mission has been testing a new commercial system, Splunk, which employs data mining techniques to organize and present spacecraft telemetry data in a high-level manner. By abstracting away data-source specific details, Splunk unifies arbitrary data formats into one uniform system. This not only reduces the time and effort for retrieving relevant data, but it also increases operational visibility by allowing a spacecraft team to correlate data across many different sources. Splunk's scalable architecture coupled with its graphing modules also provide a solid toolset for generating data visualizations and building real-time applications such as browser-based telemetry displays.

  14. Information Operations Primer

    Science.gov (United States)

    2011-11-01

    creation of two new cybersecurity organizations. At the operational level, the Cyber Defence Management Authority ( CDMA ) was established in Brussels...information contact Mr. James McNeive at 703-784-5826 ( DSN : 273) or email at jmcneive@mcia.osis.gov. Updated: October 2011 82 Back to Table of...contact JC2IOS- IO@jfsc.ndu.edu or at 757-443-6336/6333 ( DSN : 646). Web Site: http://www.jfsc.ndu.edu/ Reviewed: October 2011 151 Back to Table

  15. A science of operations

    CERN Document Server

    Priestley, Mark

    2011-01-01

    Today, computers fulfil a dazzling array of roles, a flexibility resulting from the great range of programs that can be run on them. A Science of Operations examines the history of what we now call programming, defined not simply as computer programming, but more broadly as the definition of the steps involved in computations and other information-processing activities. This unique perspective highlights how the history of programming is distinct from the history of the computer, despite the close relationship between the two in the 20th century. The book also discusses how the development of

  16. Playing in Operations Management

    Directory of Open Access Journals (Sweden)

    Laura Guitart-Tarrés

    2017-06-01

    Full Text Available The current model of competency-based learning requires new tools that allow students to develop these competencies and become active subjects of their learning (rather than passive receivers of a contents. Gamification or ludification is becoming an innovative trend in many areas, also in higher education. Games can provide a useful environment for students to acquire professional skills, a fact that is much more difficult to acquire through traditional learning methods. In that sense, this paper presents the experience of designing a game for Operations Management students.

  17. Operational Research and Networks

    CERN Document Server

    Finke, Gerd

    2008-01-01

    This book presents the principal concepts of operations research (OR) as tools for the planning, support, and management of various types of networks, including both physical and logical networks. It analyzes real problems, and offers a collection of models for many application areas, together with the corresponding solution techniques. Following this, important application areas are addressed, such as project scheduling, distribution networks, telecommunication networks, and planning of satellite imaging. Anyone involved in the theory or practice in this field will find this a vital resource.

  18. GMRES and integral operators

    Energy Technology Data Exchange (ETDEWEB)

    Kelley, C.T.; Xue, Z.Q. [North Carolina State Univ., Raleigh, NC (United States)

    1994-12-31

    Many discretizations of integral equations and compact fixed point problems are collectively compact and strongly convergent in spaces of continuous functions. These properties not only lead to stable and convergent approximations but also can be used in the construction of fast multilevel algorithms. Recently the GMRES algorithm has become a standard coarse mesh solver. The purpose of this paper is to show how the special properties of integral operators and their approximations are reflected in the performance of the GMRES iteration and how these properties can be used to strengthen the norm in which convergence takes place. The authors illustrate these ideas with composite Gauss rules for integral equations on the unit interval.

  19. CMS Tracker operational experience

    CERN Document Server

    Fiori, Francesco

    2016-01-01

    The CMS Tracker was repaired, recalibrated and commissioned successfully for the second run of Large Hadron Collider. In 2015 the Tracker performed well with improved hit efficiency and spatial resolution compared to Run I. Operations successfully transitioned to lower temperatures after commissioning environmental control and monitoring. This year the detector is expected to withstand luminosities that are beyond its design limits and will need a combined effort of both online and offline team to yield the high quality data that is required to reach our physics goals. We present the experience gained during the second run of the LHC and show the latest performance results of the CMS Tracker.

  20. Studies on the biotin-binding site of avidin. Minimized fragments that bind biotin.

    OpenAIRE

    Hiller, Y; Bayer, E A; Wilchek, M

    1991-01-01

    The object of this study was to define minimized biotin-binding fragments, or 'prorecognition sites', of either the egg-white glycoprotein avidin or its bacterial analogue streptavidin. Because of the extreme stability to enzymic hydrolysis, fragments of avidin were prepared by chemical means and examined for their individual biotin-binding capacity. Treatment of avidin with hydroxylamine was shown to result in new cleavage sites in addition to the known Asn-Gly cleavage site (position 88-89 ...

  1. Hausdorff operators on Euclidean spaces

    Institute of Scientific and Technical Information of China (English)

    CHEN Jie-cheng; FAN Da-shan; WANG Si-lei

    2013-01-01

    Hausdorff operator is an important operator raised from the dilation on Euclidean space and rooted in the classical summability of number series and Fourier series. It is also connected to many well known operators in real and complex analysis. This article is a survey of some recent developments and extensions on the Hausdorff operator. Particularly, various boundedness properties of the Hausdorff operators, studied recently by our research group, are addressed.

  2. Finite Operator-Valued Frames

    OpenAIRE

    Meng, Bin

    2010-01-01

    Operator-valued frames are natural generalization of frames that have been used in quantum computing, packets encoding, etc. In this paper, we focus on developing the theory about operator-valued frames for finite Hilbert spaces. Some results concerning dilation, alternate dual, and existence of operator-valued frames are given. Then we characterize the optimal operator-valued frames under the case which one packet of data is lost in transmission. At last we construct the operator-valued fram...

  3. Cobalamin and its binding protein in rat milk

    DEFF Research Database (Denmark)

    Raaberg, Lasse; Nexø, Ebba; Poulsen, Steen Seier

    1989-01-01

    Cobalamin and its binding protein, haptocorrin, are present in rat milk throughout the lactation period. The concentration of cobalamin is approximately 0.3-times the concentration of the unsaturated binding protein. The concentration of the unsaturated cobalamin-binding protein varies between 18...... nmol l-1 and 16 nmol l-1. The binding protein has a Stokes radius of 2.49 nm when saturated with cobalamin and 2.61 nm when unsaturated. It binds cobalamin over a broad range of pH and is able to bind cobinamide also. With immunohistochemistry, we find haptocorrin immunoreactivity in the mammary glands...

  4. Is there a link between selectivity and binding thermodynamics profiles?

    Science.gov (United States)

    Tarcsay, Ákos; Keserű, György M

    2015-01-01

    Thermodynamics of ligand binding is influenced by the interplay between enthalpy and entropy contributions of the binding event. The impact of these binding free energy components, however, is not limited to the primary target only. Here, we investigate the relationship between binding thermodynamics and selectivity profiles by combining publicly available data from broad off-target assay profiling and the corresponding thermodynamics measurements. Our analysis indicates that compounds binding their primary targets with higher entropy contributions tend to hit more off-targets compared with those ligands that demonstrated enthalpy-driven binding.

  5. CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins.

    Science.gov (United States)

    Khorshid, Mohsen; Rodak, Christoph; Zavolan, Mihaela

    2011-01-01

    The stability, localization and translation rate of mRNAs are regulated by a multitude of RNA-binding proteins (RBPs) that find their targets directly or with the help of guide RNAs. Among the experimental methods for mapping RBP binding sites, cross-linking and immunoprecipitation (CLIP) coupled with deep sequencing provides transcriptome-wide coverage as well as high resolution. However, partly due to their vast volume, the data that were so far generated in CLIP experiments have not been put in a form that enables fast and interactive exploration of binding sites. To address this need, we have developed the CLIPZ database and analysis environment. Binding site data for RBPs such as Argonaute 1-4, Insulin-like growth factor II mRNA-binding protein 1-3, TNRC6 proteins A-C, Pumilio 2, Quaking and Polypyrimidine tract binding protein can be visualized at the level of the genome and of individual transcripts. Individual users can upload their own sequence data sets while being able to limit the access to these data to specific users, and analyses of the public and private data sets can be performed interactively. CLIPZ, available at http://www.clipz.unibas.ch, aims to provide an open access repository of information for post-transcriptional regulatory elements.

  6. Sugar-Binding Profiles of Chitin-Binding Lectins from the Hevein Family: A Comprehensive Study

    Directory of Open Access Journals (Sweden)

    Yoko Itakura

    2017-05-01

    Full Text Available Chitin-binding lectins form the hevein family in plants, which are defined by the presence of single or multiple structurally conserved GlcNAc (N-acetylglucosamine-binding domains. Although they have been used as probes for chito-oligosaccharides, their detailed specificities remain to be investigated. In this study, we analyzed six chitin-binding lectins, DSA, LEL, PWM, STL, UDA, and WGA, by quantitative frontal affinity chromatography. Some novel features were evident: WGA showed almost comparable affinity for pyridylaminated chitotriose and chitotetraose, while LEL and UDA showed much weaker affinity, and DSA, PWM, and STL had no substantial affinity for the former. WGA showed selective affinity for hybrid-type N-glycans harboring a bisecting GlcNAc residue. UDA showed extensive binding to high-mannose type N-glycans, with affinity increasing with the number of Man residues. DSA showed the highest affinity for highly branched N-glycans consisting of type II LacNAc (N-acetyllactosamine. Further, multivalent features of these lectins were investigated by using glycoconjugate and lectin microarrays. The lectins showed substantial binding to immobilized LacNAc as well as chito-oligosaccharides, although the extents to which they bound varied among them. WGA showed strong binding to heavily sialylated glycoproteins. The above observations will help interpret lectin-glycoprotein interactions in histochemical studies and glyco-biomarker investigations.

  7. Ligand Binding and Conformational Changes in the Purine-Binding Riboswitch Aptamer Domains

    Science.gov (United States)

    Noeske, Jonas; Buck, Janina; Wöhnert, Jens; Schwalbe, Harald

    Riboswitches are highly structured mRNA elements that regulate gene expression upon specific binding of small metabolite molecules. The purine-binding riboswitches bind different purine ligands by forming both canonical Watson—Crick and non-canonical intermolecular base pairs, involving a variety of hydrogen bonds between the riboswitch aptamer domain and the purine ligand. Here, we summarize work on the ligand binding modes of both purine-binding aptamer domains, their con-formational characteristics in the free and ligand-bound forms, and their ligand-induced folding. The adenine- and guanine-binding riboswitch aptamer domains display different conformations in their free forms, despite nearly identical nucleotide loop sequences that form a loop—loop interaction in the ligand-bound forms. Interestingly, the stability of helix II is crucial for the formation of the loop—loop interaction in the free form. A more stable helix II in the guanine riboswitch leads to a preformed loop—loop interaction in its free form. In contrast, a less stable helix II in the adenine riboswitch results in a lack of this loop—loop interaction in the absence of ligand and divalent cations.

  8. Fucosyl neoglycoprotein binds to mouse epididymal spermatozoa and inhibits sperm binding to the egg zona pellucida.

    Science.gov (United States)

    Oh, Y S; Ahn, H S; Gye, M C

    2013-12-01

    Glycan epitopes of cellular glycoconjugates act as versatile biochemical signals, and this sugar coding plays an important role in cell-to-cell recognition processes. In this study, our aims were to determine the distribution of sperm receptors with activity for fucosyl- and galactosyl glycans and to address whether monosugar neoglycoproteins functionally mimic the binding between zona pellucida (ZP) glycoproteins and spermatozoa. In mouse epididymal spermatozoa with intact acrosomes, fucopyranosyl bovine serum albumin (BSA-Fuc) bound to the segment of the acrosome, the equatorial segment, and the postacrosome region of the sperm head. Galactosyl BSA (BSA-Gal) binding activity was similar to that of BSA-Fuc, but was weaker. In acrosome-reacted spermatozoa treated with the Ca(2+) ionophore A23187, BSA-zuc binding was lost in the apical segment of the acrosome but remained in the equatorial segment and postacrosome regions. BSA-Gal binding to the equatorial region was increased. In the presence of 2.5 μg ml(-1) BSA-Fuc, in vitro sperm-ZP binding was significantly decreased, indicating that fucosyl BSA functionally mimics ZP glycoproteins during sperm-egg ZP interactions. At the same concentration, BSA-Gal was not effective. Fucosyl BSA that efficiently inhibited the sperm-ZP binding can mimic the ZP glycoconjugate and has potential for use as a sperm fertility control agent in mouse.

  9. Being a binding site: characterizing residue composition of binding sites on proteins.

    Science.gov (United States)

    Iván, Gábor; Szabadka, Zoltán; Grolmusz, Vince

    2007-12-30

    The Protein Data Bank contains the description of more than 45,000 three-dimensional protein and nucleic-acid structures today. Started to exist as the computer-readable depository of crystallographic data complementing printed articles, the proper interpretation of the content of the individual files in the PDB still frequently needs the detailed information found in the citing publication. This fact implies that the fully automatic processing of the whole PDB is a very hard task. We first cleaned and re-structured the PDB data, then analyzed the residue composition of the binding sites in the whole PDB for frequency and for hidden association rules. Main results of the paper: (i) the cleaning and repairing algorithm (ii) redundancy elimination from the data (iii) application of association rule mining to the cleaned non-redundant data set. We have found numerous significant relations of the residue-composition of the ligand binding sites on protein surfaces, summarized in two figures. One of the classical data-mining methods for exploring implication-rules, the association-rule mining, is capable to find previously unknown residue-set preferences of bind ligands on protein surfaces. Since protein-ligand binding is a key step in enzymatic mechanisms and in drug discovery, these uncovered preferences in the study of more than 19,500 binding sites may help in identifying new binding protein-ligand pairs.

  10. Operations dashboard: comparative study

    Science.gov (United States)

    Ramly, Noor Nashriq; Ismail, Ahmad Zuhairi; Aziz, Mohd Haris; Ahmad, Nurul Haszeli

    2011-10-01

    In this present days and age, there are increasing needs for companies to monitor application and infrastructure health. Apart from having proactive measures to secure their application and infrastructure, many see monitoring dashboards as crucial investment in disaster preparedness. As companies struggle to find the best solution to cater for their needs and interest for monitoring their application and infrastructure's health, this paper summarizes the studies made on several known off-the-shelf operations dashboard and in-house developed dashboard. A few criteria of good dashboard are collected from previous studies carried out by several researchers and rank them according to importance and business needs. The finalized criteria that will be discussed in later sections are data visualization, performance indicator, dashboard personalization, audit capability and alert/ notification. Comparative studies between several popular dashboards were then carried out to determine whether they met these criteria that we derived from the first exercise. The findings hopefully can be used to educate and provide an overview of selecting the best IT application and infrastructure operations dashboard that suit business needs, thus become the main contribution of this paper.

  11. ATLAS solenoid operates underground

    CERN Document Server

    2006-01-01

    A new phase for the ATLAS collaboration started with the first operation of a completed sub-system: the Central Solenoid. Teams monitoring the cooling and powering of the ATLAS solenoid in the control room. The solenoid was cooled down to 4.5 K from 17 to 23 May. The first current was established the same evening that the solenoid became cold and superconductive. 'This makes the ATLAS Central Solenoid the very first cold and superconducting magnet to be operated in the LHC underground areas!', said Takahiko Kondo, professor at KEK. Though the current was limited to 1 kA, the cool-down and powering of the solenoid was a major milestone for all of the control, cryogenic, power and vacuum systems-a milestone reached by the hard work and many long evenings invested by various teams from ATLAS, all of CERN's departments and several large and small companies. Since the Central Solenoid and the barrel liquid argon (LAr) calorimeter share the same cryostat vacuum vessel, this achievement was only possible in perfe...

  12. South African Airborne Operations

    Directory of Open Access Journals (Sweden)

    McGill Alexander

    2012-02-01

    Full Text Available Airborne operations entail the delivery of ground troops and their equipment by air to their area of operations. They can also include the subsequent support of these troops and their equipment by air. Historically, and by definition, this would encompass delivery by fixed-wing powered aircraft, by glider, by parachute or by helicopter. Almost any troops can be delivered by most of these means. However, the technical expertise and physical as well as psychological demands required by parachuting have resulted in specialist troops being selected and trained for this role. Some of the material advantages of using parachute troops, or paratroops, are: the enormous strategic reach provided by the long-distance transport aircraft used to convey them; the considerable payload which these aircraft are capable of carrying; the speed with which the parachute force can deploy; and the fact that no infrastructure such as airfields are required for their arrival. Perhaps most attractively to cash-strapped governments, the light equipment scales of parachute units’ makes them economical to establish and maintain. There are also less tangible advantages: the soldiers selected are invariably volunteers with a willingness or even desire to tackle challenges; their selection and training produces tough, confident and aggressive troops, psychologically geared to face superior odds and to function independently from other units; and their initiative and self-reliance combined with a high level of physical fitness makes them suitable for a number of different and demanding roles.

  13. Plasticity-related binding of GABA and muscarinic receptor sites in piriform cortex of rat: An autoradiographic study

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, A.P.; Westrum, L.E. (Univ. of Washington, Seattle (USA))

    1989-09-01

    This study has used the recently developed in vitro quantitative autoradiographic technique to examine the effects of olfactory bulb (OB) removal on receptor-binding sites in the deafferented piriform cortex (PC) of the rat. The gamma-aminobutyric acid-benzodiazepine receptor (GABA-BZR)- and muscarinic cholinergic receptor (MChR)-binding sites in layer I of PC were localized using (3H)flunitrazepam and (3H)quinuclidinyl benzilate as ligands, respectively. From the resultant autoradiograms the optical densities were measured using a Drexel-DUMAS image analysis system. The densities of BZR and MChR-binding sites were markedly increased in the PC ipsilateral to the lesion as compared to the contralateral side in those subjects that were operated in adulthood (Postnatal Day 100, PN 100). Comparisons between the unoperated and PN 100 operated animals also showed significant increases in the deafferented PC. In the animals operated on the day of birth (PN 0) no significant differences were seen between the operated and the contralateral PC. The difference between the PN 0 deafferented PC and the unoperated controls shows a slight decrease in BZR density in the former group; however, in case of the MChR there is a slight increase on the side of the lesion. These results demonstrate that deafferentation of PC by OB removal appears to modulate both the BZR-binding sites that are coupled with the GABA-A receptor complex and the MChR-binding sites. The results also suggest that possibility of a role for these neurotransmitter receptor-binding sites in plasticity following deafferentation.

  14. Essential mechanisms in the triton binding

    Energy Technology Data Exchange (ETDEWEB)

    Brandenburg, R.A.; Chulick, G.S.; Machleidt, R.; Picklesimer, A.; Thaler, R.M.

    1988-03-01

    The recent successful prediction of the triton binding energy, E/sub t/, with the static Bonn potential is examined. Modified versions of the potential are introduced to isolate separately the effects of the deuteron D-state admixture and the /sup 1/S/sub 0/ scattering length on E/sub t/. Within this model study we find a monotonic relation between E/sub t/ and the /sup 1/S/sub 0/ scattering length and a strict linear dependence of E/sub t/ on the D-state admixture, in accordance with general well-known trends and earlier separable-potential model studies. The mechanism through which the weaker tensor force (lower D-state admixture) leads to a stronger binding of the triton is investigated by the introduction and study of effective energy-dependent central potentials

  15. Autologous antibodies that bind neuroblastoma cells.

    Science.gov (United States)

    Sun, Yujing; Sholler, Giselle S; Shukla, Girja S; Pero, Stephanie C; Carman, Chelsea L; Zhao, Ping; Krag, David N

    2015-11-01

    Antibody therapy of neuroblastoma is promising and our goal is to derive antibodies from patients with neuroblastoma for developing new therapeutic antibodies. The feasibility of using residual bone marrow obtained for clinical indications as a source of tumor cells and a source of antibodies was assessed. From marrow samples, neuroblastoma cells were recovered, grown in cell culture and also implanted into mice to create xenografts. Mononuclear cells from the marrow were used as a source to generate phage display antibody libraries and also hybridomas. Growth of neuroblastoma patient cells was possible both in vitro and as xenografts. Antibodies from the phage libraries and from the monoclonal hybridomas bound autologous neuroblastoma cells with some selectivity. It appears feasible to recover neuroblastoma cells from residual marrow specimens and to generate human antibodies that bind autologous neuroblastoma cells. Expansion of this approach is underway to collect more specimens, optimize methods to generate antibodies, and to evaluate the bioactivity of neuroblastoma-binding antibodies.

  16. Lectin binding in normal donkey eyeball

    Directory of Open Access Journals (Sweden)

    Khaled Aly

    2013-10-01

    Full Text Available In the present study, the distribution of various sugar residues in the eyeball tissues of sexually mature donkey was examined by employing fluorescein isothiocyanate-conjugated lectins. Our results revealed the presence of mannose (labeled by lectins ConA, galactose (labeled by PNA, GSAI, ECA, GalNAc (labeled by SBA, VVA, and GlcNAc (labeled by WGA residues in the donkey ocular tissues. The epithelium and stroma of the ocular tissues were labeled with mannose (ConA and GlcNAc (WGA binding lectins. Binding sites for WGA and PNA to the rod and cone cells of the retina were evident. The lectins Con A, WGA and GSAI are bound strongly to the endothelium of blood vessels and to smooth muscle cells of the iris. In conclusion, the findings of the present study clearly indicate that the donkey eyeball contains a wide range of glycoconjugates (bearing mannosyl, galactosyl and glucosly residues, and it lacks fucosyl residues.

  17. K- nuclear states: Binding energies and widths

    Science.gov (United States)

    Hrtánková, J.; Mareš, J.

    2017-07-01

    K- optical potentials relevant to calculations of K- nuclear quasibound states were developed within several chiral meson-baryon coupled-channels interaction models. The applied models yield quite different K- binding energies and widths. Then the K- multinucleon interactions were incorporated by a phenomenological optical potential fitted recently to kaonic atom data. Though the applied K- interaction models differ significantly in the K-N subthreshold region, our self-consistent calculations of kaonic nuclei across the periodic table lead to conclusions valid quite generally. Due to K- multinucleon absorption in the nuclear medium, the calculated widths of K- nuclear states are sizable, ΓK-≥90 MeV, and exceed substantially their binding energies in all considered nuclei.

  18. Comparison of Transcription Factor Binding Site Models

    KAUST Repository

    Bhuyan, Sharifulislam

    2012-05-01

    Modeling of transcription factor binding sites (TFBSs) and TFBS prediction on genomic sequences are important steps to elucidate transcription regulatory mechanism. Dependency of transcription regulation on a great number of factors such as chemical specificity, molecular structure, genomic and epigenetic characteristics, long distance interaction, makes this a challenging problem. Different experimental procedures generate evidence that DNA-binding domains of transcription factors show considerable DNA sequence specificity. Probabilistic modeling of TFBSs has been moderately successful in identifying patterns from a family of sequences. In this study, we compare performances of different probabilistic models and try to estimate their efficacy over experimental TFBSs data. We build a pipeline to calculate sensitivity and specificity from aligned TFBS sequences for several probabilistic models, such as Markov chains, hidden Markov models, Bayesian networks. Our work, containing relevant statistics and evaluation for the models, can help researchers to choose the most appropriate model for the problem at hand.

  19. Quantifying drug-protein binding in vivo.

    Energy Technology Data Exchange (ETDEWEB)

    Buchholz, B; Bench, G; Keating III, G; Palmblad, M; Vogel, J; Grant, P G; Hillegonds, D

    2004-02-17

    Accelerator mass spectrometry (AMS) provides precise quantitation of isotope labeled compounds that are bound to biological macromolecules such as DNA or proteins. The sensitivity is high enough to allow for sub-pharmacological (''micro-'') dosing to determine macromolecular targets without inducing toxicities or altering the system under study, whether it is healthy or diseased. We demonstrated an application of AMS in quantifying the physiologic effects of one dosed chemical compound upon the binding level of another compound in vivo at sub-toxic doses [4].We are using tissues left from this study to develop protocols for quantifying specific binding to isolated and identified proteins. We also developed a new technique to quantify nanogram to milligram amounts of isolated protein at precisions that are comparable to those for quantifying the bound compound by AMS.

  20. Causal binding of actions to their effects.

    Science.gov (United States)

    Buehner, Marc J; Humphreys, Gruffydd R

    2009-10-01

    According to widely held views in cognitive science harking back to David Hume, causality cannot be perceived directly, but instead is inferred from patterns of sensory experience, and the quality of these inferences is determined by perceivable quantities such as contingency and contiguity. We report results that suggest a reversal of Hume's conjecture: People's sense of time is warped by the experience of causality. In a stimulus-anticipation task, participants' response behavior reflected a shortened experience of time in the case of target stimuli participants themselves had generated, relative to equidistant, equally predictable stimuli they had not caused. These findings suggest that causality in the mind leads to temporal binding of cause and effect, and extend and generalize beyond earlier claims of intentional binding between action and outcome.