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Sample records for bloodusing simple protein

  1. Simple sequence proteins in prokaryotic proteomes

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    Ramachandran Srinivasan

    2006-06-01

    Full Text Available Abstract Background The structural and functional features associated with Simple Sequence Proteins (SSPs are non-globularity, disease states, signaling and post-translational modification. SSPs are also an important source of genetic and possibly phenotypic variation. Analysis of 249 prokaryotic proteomes offers a new opportunity to examine the genomic properties of SSPs. Results SSPs are a minority but they grow with proteome size. This relationship is exhibited across species varying in genomic GC, mutational bias, life style, and pathogenicity. Their proportion in each proteome is strongly influenced by genomic base compositional bias. In most species simple duplications is favoured, but in a few cases such as Mycobacteria, large families of duplications occur. Amino acid preference in SSPs exhibits a trend towards low cost of biosynthesis. In SSPs and in non-SSPs, Alanine, Glycine, Leucine, and Valine are abundant in species widely varying in genomic GC whereas Isoleucine and Lysine are rich only in organisms with low genomic GC. Arginine is abundant in SSPs of two species and in the non-SSPs of Xanthomonas oryzae. Asparagine is abundant only in SSPs of low GC species. Aspartic acid is abundant only in the non-SSPs of Halobacterium sp NRC1. The abundance of Serine in SSPs of 62 species extends over a broader range compared to that of non-SSPs. Threonine(T is abundant only in SSPs of a couple of species. SSPs exhibit preferential association with Cell surface, Cell membrane and Transport functions and a negative association with Metabolism. Mesophiles and Thermophiles display similar ranges in the content of SSPs. Conclusion Although SSPs are a minority, the genomic forces of base compositional bias and duplications influence their growth and pattern in each species. The preferences and abundance of amino acids are governed by low biosynthetic cost, evolutionary age and base composition of codons. Abundance of charged amino acids Arginine

  2. Simple models for charge and salt effects in protein crystallisation

    OpenAIRE

    Warren, Patrick B

    2002-01-01

    A simple extension of existing models for protein crystallisation is described, in which salt ions and charge neutrality are explicitly incorporated. This provides a straightforward explanation for the shape of protein crystallisation boundaries, the associated scaling properties seen for lysozyme, and can also explain much of the salt dependence of the second virial coefficient. The analysis has wider implications for the use of pair potentials to understand protein crystallisation.

  3. A Simple Algorithm for Maximum Clique and Matching Protein Structures

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    S. Balaji

    2010-09-01

    Full Text Available The maximum common subgraph (MCS problem has become increasingly important in matching protein structures of two proteins. Two proteins represented as graphs by simple contact map and product of these graphs was input to the proposed algorithm. A maximum clique in the product graph, found by the proposed algorithm, provides a measure of the structural similarity between the two proteins. The proposed algorithm produced optimal solution for most of the benchmark problem of the protein data bank and also for the public domain DIMACS benchmark problems of maximum clique. The computational results show that the prposed algorithm efficiently produces the common substructure of two proteins, used for protein structural analysis and protein classification.

  4. Promoting protein crystallization using a plate with simple geometry.

    Science.gov (United States)

    Chen, Rui-Qing; Yin, Da-Chuan; Liu, Yong-Ming; Lu, Qin-Qin; He, Jin; Liu, Yue

    2014-03-01

    Increasing the probability of obtaining protein crystals in crystallization screening is always an important goal for protein crystallography. In this paper, a new method called the cross-diffusion microbatch (CDM) method is presented, which aims to efficiently promote protein crystallization and increase the chance of obtaining protein crystals. In this method, a very simple crystallization plate was designed in which all crystallization droplets are in one sealed space, so that a variety of volatile components from one droplet can diffuse into any other droplet via vapour diffusion. Crystallization screening and reproducibility tests indicate that this method could be a potentially powerful technique in practical protein crystallization screening. It can help to obtain crystals with higher probability and at a lower cost, while using a simple and easy procedure.

  5. A simple stochastic model for the evolution of protein lengths

    OpenAIRE

    Destri C.; Miccio C.

    2007-01-01

    We analyze a simple discrete-time stochastic process for the theoretical modeling of the evolution of protein lengths. At every step of the process, a new protein is produced as a modi¿cation of one of the proteins already existing, and its length is assumed to be a random variable that depends only on the length of the originating protein. Thus a random recursive tree is produced over the natural numbers. If quasi scale invariance is assumed, the length distribution in a single history tends...

  6. A simple theory of motor protein kinetics and energetics. II.

    Science.gov (United States)

    Qian, H

    2000-01-10

    A three-state stochastic model of motor protein [Qian, Biophys. Chem. 67 (1997) pp. 263-267] is further developed to illustrate the relationship between the external load on an individual motor protein in aqueous solution with various ATP concentrations and its steady-state velocity. A wide variety of dynamic motor behavior are obtained from this simple model. For the particular case of free-load translocation being the most unfavorable step within the hydrolysis cycle, the load-velocity curve is quasi-linear, V/Vmax = (cF/Fmax-c)/(1-c), in contrast to the hyperbolic relationship proposed by A.V. Hill for macroscopic muscle. Significant deviation from the linearity is expected when the velocity is less than 10% of its maximal (free-load) value--a situation under which the processivity of motor diminishes and experimental observations are less certain. We then investigate the dependence of load-velocity curve on ATP (ADP) concentration. It is shown that the free load Vmax exhibits a Michaelis-Menten like behavior, and the isometric Fmax increases linearly with ln([ATP]/[ADP]). However, the quasi-linear region is independent of the ATP concentration, yielding an apparently ATP-independent maximal force below the true isometric force. Finally, the heat production as a function of ATP concentration and external load are calculated. In simple terms and solved with elementary algebra, the present model provides an integrated picture of biochemical kinetics and mechanical energetics of motor proteins. PMID:10631478

  7. Simple Protein Complex Purification and Identification Method Suitable for High- throughput Mapping of Protein Interaction Networks

    Energy Technology Data Exchange (ETDEWEB)

    Markillie, Lye Meng; Lin, Chiann Tso; Adkins, Joshua N.; Auberry, Deanna L.; Hill, Eric A.; Hooker, Brian S.; Moore, Priscilla A.; Moore, Ronald J.; Shi, Liang; Wiley, H. S.; Kery, Vladimir

    2005-04-11

    Most of the current methods for purification and identification of protein complexes use endogenous expression of affinity tagged bait, tandem affinity tag purification of protein complexes followed by specific elution of complexes from beads, gel separation, in-gel digestion and mass spectrometric analysis of protein interactors. We propose a single affinity tag in vitro pulldown assay with denaturing elution, trypsin digestion in organic solvent and LC ESI MS/MS protein identification using SEQUEST analysis. Our method is simple, easy to scale up and automate thus suitable for high throughput mapping of protein interaction networks and functional proteomics.

  8. A simple and fast heuristic for protein structure comparison

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    Moreno Vega Marcos

    2008-03-01

    Full Text Available Abstract Background Protein structure comparison is a key problem in bioinformatics. There exist several methods for doing protein comparison, being the solution of the Maximum Contact Map Overlap problem (MAX-CMO one of the alternatives available. Although this problem may be solved using exact algorithms, researchers require approximate algorithms that obtain good quality solutions using less computational resources than the formers. Results We propose a variable neighborhood search metaheuristic for solving MAX-CMO. We analyze this strategy in two aspects: 1 from an optimization point of view the strategy is tested on two different datasets, obtaining an error of 3.5%(over 2702 pairs and 1.7% (over 161 pairs with respect to optimal values; thus leading to high accurate solutions in a simpler and less expensive way than exact algorithms; 2 in terms of protein structure classification, we conduct experiments on three datasets and show that is feasible to detect structural similarities at SCOP's family and CATH's architecture levels using normalized overlap values. Some limitations and the role of normalization are outlined for doing classification at SCOP's fold level. Conclusion We designed, implemented and tested.a new tool for solving MAX-CMO, based on a well-known metaheuristic technique. The good balance between solution's quality and computational effort makes it a valuable tool. Moreover, to the best of our knowledge, this is the first time the MAX-CMO measure is tested at SCOP's fold and CATH's architecture levels with encouraging results. Software is available for download at http://modo.ugr.es/jrgonzalez/msvns4maxcmo.

  9. A simple immunoblotting method after separation of proteins in agarose gel

    DEFF Research Database (Denmark)

    Koch, C; Skjødt, K; Laursen, I

    1985-01-01

    A simple and sensitive method for immunoblotting of proteins after separation in agarose gels is described. It involves transfer of proteins onto nitrocellulose paper simply by diffusion through pressure, a transfer which only takes about 10 min. By this method we have demonstrated the existence ...

  10. Detection and characterization of protein interactions in vivo by a simple live-cell imaging method.

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    Oriol Gallego

    Full Text Available Over the last decades there has been an explosion of new methodologies to study protein complexes. However, most of the approaches currently used are based on in vitro assays (e.g. nuclear magnetic resonance, X-ray, electron microscopy, isothermal titration calorimetry etc. The accurate measurement of parameters that define protein complexes in a physiological context has been largely limited due to technical constrains. Here, we present PICT (Protein interactions from Imaging of Complexes after Translocation, a new method that provides a simple fluorescence microscopy readout for the study of protein complexes in living cells. We take advantage of the inducible dimerization of FK506-binding protein (FKBP and FKBP-rapamycin binding (FRB domain to translocate protein assemblies to membrane associated anchoring platforms in yeast. In this assay, GFP-tagged prey proteins interacting with the FRB-tagged bait will co-translocate to the FKBP-tagged anchor sites upon addition of rapamycin. The interactions are thus encoded into localization changes and can be detected by fluorescence live-cell imaging under different physiological conditions or upon perturbations. PICT can be automated for high-throughput studies and can be used to quantify dissociation rates of protein complexes in vivo. In this work we have used PICT to analyze protein-protein interactions from three biological pathways in the yeast Saccharomyces cerevisiae: Mitogen-activated protein kinase cascade (Ste5-Ste11-Ste50, exocytosis (exocyst complex and endocytosis (Ede1-Syp1.

  11. A Simple Model of Protein Domain Swapping in Crowded Cellular Environments.

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    Woodard, Jaie C; Dunatunga, Sachith; Shakhnovich, Eugene I

    2016-06-01

    Domain swapping in proteins is an important mechanism of functional and structural innovation. However, despite its ubiquity and importance, the physical mechanisms that lead to domain swapping are poorly understood. Here, we present a simple two-dimensional coarse-grained model of protein domain swapping in the cytoplasm. In our model, two-domain proteins partially unfold and diffuse in continuous space. Monte Carlo multiprotein simulations of the model reveal that domain swapping occurs at intermediate temperatures, whereas folded dimers and folded monomers prevail at low temperatures, and partially unfolded monomers predominate at high temperatures. We use a simplified amino acid alphabet consisting of four residue types, and find that the oligomeric state at a given temperature depends on the sequence of the protein. We also show that hinge strain between domains can promote domain swapping, consistent with experimental observations for real proteins. Domain swapping depends nonmonotonically on the protein concentration, with domain-swapped dimers occurring at intermediate concentrations and nonspecific interactions between partially unfolded proteins occurring at high concentrations. For folded proteins, we recover the result obtained in three-dimensional lattice simulations, i.e., that functional dimerization is most prevalent at intermediate temperatures and nonspecific interactions increase at low temperatures. PMID:27276255

  12. A rapid and simple assay for growth hormone-binding protein activity in human plasma

    International Nuclear Information System (INIS)

    The newly discovered circulating growth hormone binding proteins dictate a re-evaluation of the state of GH in plasma in health and disease as the binding proteins are known to affect GH metabolism and action. We describe a rapid and simple GH-binding assay that allows determination of free and complexed plasma GH, as well as GH-binding protein activity as an index of GH-binding protein levels, with relative ease. The method is based on incubation of plasma with 125I-GH and separation of bound from free GH on small DEAE-cellulose columns; it can be used on a large scale for routine determinations. The results obtained by this method are comparable to those obtained with the previously used slow and more cumbersome gel filtration technique. Initial data obtained in normal subject and certain disease states show that the bound fraction of plasma GH is similar in men, women and children, is unaffected by pregnancy or acute infection, but is marginally decreased in liver cirrhosis. In acromegaly, binding protein activity also appears normal when allowance is made for partial saturation of the binding proteins by the high prevailing GH levels. The technique we describe should facilitate investigations of normal and abnormal regulation of the GH binding proteins. (author)

  13. A Simple and Rapid Method for Preparing a Cell-Free Bacterial Lysate for Protein Synthesis

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    Kaduri, Maya; Shainsky-Roitman, Janna; Goldfeder, Mor; Ivanir, Eran; Benhar, Itai; Shoham, Yuval; Schroeder, Avi

    2016-01-01

    Cell-free protein synthesis (CFPS) systems are important laboratory tools that are used for various synthetic biology applications. Here, we present a simple and inexpensive laboratory-scale method for preparing a CFPS system from E. coli. The procedure uses basic lab equipment, a minimal set of reagents, and requires less than one hour to process the bacterial cell mass into a functional S30-T7 extract. BL21(DE3) and MRE600 E. coli strains were used to prepare the S30-T7 extract. The CFPS system was used to produce a set of fluorescent and therapeutic proteins of different molecular weights (up to 66 kDa). This system was able to produce 40–150 μg-protein/ml, with variations depending on the plasmid type, expressed protein and E. coli strain. Interestingly, the BL21-based CFPS exhibited stability and increased activity at 40 and 45°C. To the best of our knowledge, this is the most rapid and affordable lab-scale protocol for preparing a cell-free protein synthesis system, with high thermal stability and efficacy in producing therapeutic proteins. PMID:27768741

  14. A simple purification and activity assay of the coagulant protein from Moringa oleifera seed.

    Science.gov (United States)

    Ghebremichael, Kebreab A; Gunaratna, K R; Henriksson, Hongbin; Brumer, Harry; Dalhammar, Gunnel

    2005-06-01

    Use of extracts from Moringa oleifera (MO) is of great interest for low-cost water treatment. This paper discusses water and salt extraction of a coagulant protein from the seed, purification using ion exchange, its chemical characteristics, coagulation and antimicrobial properties. The coagulant from both extracts is a cationic protein with pI greater than 9.6 and molecular mass less than 6.5 kDa. Mass spectrometric analysis of the purified water extract indicated that it contained at least four homologous proteins, based on MS/MS peptide sequence data. The protein is thermoresistant and remained active after 5h heat treatment at 95 degrees C. The coagulant protein showed both flocculating and antibacterial effects of 1.1--4 log reduction. With samples of high turbidity, the MO extract showed similar coagulation activity as alum. Cecropin A and MO extract were found to have similar flocculation effects for clay and microorganisms. Simple methods for both the purification and assay of MO coagulating proteins are presented, which are necessary for large-scale water treatment applications. PMID:15921719

  15. [Binding of protein SCP to myelin, its identity with protein P2. A simple method of protein P2 isolation].

    Science.gov (United States)

    Terletskaia, Ia T; Syrovatskaia, L P; Khzuliná, E P; Ovander, M N; Belik, Ia V

    1980-01-01

    Protein SCP is found in myelin of spinal cord and spinal roots. It is shown that its amount accounts for 12% of the total protein content in myelin of spinal roots and only for 2% in myelin of spinal cord. Almost all the studied protein is extracted from myelin with 0.1 M NaCl (80-90%). The absolute identity of protens SCP and P2 is established using the cross reaction immunodiffusion with monospecific antisera. It is shown that- N-terminal amino acid in protein SCP, like in protein P2 is blocked. On the basis of the data obtained a conclusion is made that protein P2 is not an integral protein of myelin. However, myelin is capable under conditions of a nonionic medium of binding protein which then may be easily extracted by increasing the medium ionic strength. This gave reasons to propose a method for protein P2 isolation from myelin using 0.15 M NaCl with the subsequent purification by means of Sephadex G-50 gelfiltration. PMID:6167043

  16. Design and self-assembly of simple coat proteins for artificial viruses

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    Hernandez-Garcia, Armando; Kraft, Daniela J.; Janssen, Anne F. J.; Bomans, Paul H. H.; Sommerdijk, Nico A. J. M.; Thies-Weesie, Dominique M. E.; Favretto, Marco E.; Brock, Roland; de Wolf, Frits A.; Werten, Marc W. T.; van der Schoot, Paul; Stuart, Martien Cohen; de Vries, Renko

    2014-09-01

    Viruses are among the simplest biological systems and are highly effective vehicles for the delivery of genetic material into susceptible host cells. Artificial viruses can be used as model systems for providing insights into natural viruses and can be considered a testing ground for developing artificial life. Moreover, they are used in biomedical and biotechnological applications, such as targeted delivery of nucleic acids for gene therapy and as scaffolds in material science. In a natural setting, survival of viruses requires that a significant fraction of the replicated genomes be completely protected by coat proteins. Complete protection of the genome is ensured by a highly cooperative supramolecular process between the coat proteins and the nucleic acids, which is based on reversible, weak and allosteric interactions only. However, incorporating this type of supramolecular cooperativity into artificial viruses remains challenging. Here, we report a rational design for a self-assembling minimal viral coat protein based on simple polypeptide domains. Our coat protein features precise control over the cooperativity of its self-assembly with single DNA molecules to finally form rod-shaped virus-like particles. We confirm the validity of our design principles by showing that the kinetics of self-assembly of our virus-like particles follows a previous model developed for tobacco mosaic virus. We show that our virus-like particles protect DNA against enzymatic degradation and transfect cells with considerable efficiency, making them promising delivery vehicles.

  17. Simple horizontal magnetic tweezers for micromanipulation of single DNA molecules and DNA-protein complexes.

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    McAndrew, Christopher P; Tyson, Christopher; Zischkau, Joseph; Mehl, Patrick; Tuma, Pamela L; Pegg, Ian L; Sarkar, Abhijit

    2016-01-01

    We report the development of a simple-to-implement magnetic force transducer that can apply a wide range of piconewton (pN) scale forces on single DNA molecules and DNA-protein complexes in the horizontal plane. The resulting low-noise force-extension data enable very high-resolution detection of changes in the DNA tether's extension: ~0.05 pN in force and DNA in near equilibrium conditions through the wide range of forces by ramping the force from low to high and back again, and observing minimal hysteresis in the molecule's force response. Using a calibration technique based on Stokes' drag law, we have confirmed our force measurements from DNA force-extension experiments obtained using the fluctuation-dissipation theorem applied to transverse fluctuations of the magnetic microsphere. We present data on the force-distance characteristics of a DNA molecule complexed with histones. The results illustrate how the tweezers can be used to study DNA binding proteins at the single molecule level.

  18. A simple yeast-based strategy to identify host cellular processes targeted by bacterial effector proteins.

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    Eran Bosis

    Full Text Available Bacterial effector proteins, which are delivered into the host cell via the type III secretion system, play a key role in the pathogenicity of gram-negative bacteria by modulating various host cellular processes to the benefit of the pathogen. To identify cellular processes targeted by bacterial effectors, we developed a simple strategy that uses an array of yeast deletion strains fitted into a single 96-well plate. The array is unique in that it was optimized computationally such that despite the small number of deletion strains, it covers the majority of genes in the yeast synthetic lethal interaction network. The deletion strains in the array are screened for hypersensitivity to the expression of a bacterial effector of interest. The hypersensitive deletion strains are then analyzed for their synthetic lethal interactions to identify potential targets of the bacterial effector. We describe the identification, using this approach, of a cellular process targeted by the Xanthomonas campestris type III effector XopE2. Interestingly, we discover that XopE2 affects the yeast cell wall and the endoplasmic reticulum stress response. More generally, the use of a single 96-well plate makes the screening process accessible to any laboratory and facilitates the analysis of a large number of bacterial effectors in a short period of time. It therefore provides a promising platform for studying the functions and cellular targets of bacterial effectors and other virulence proteins.

  19. Development of a simple assay system for protein-stabilizing efficiency based on hemoglobin protection against denaturation and measurement of the cooperative effect of mixing protein stabilizers.

    Science.gov (United States)

    Chen, Siyu; Manabe, Yoshiyuki; Minamoto, Naoya; Saiki, Naoka; Fukase, Koichi

    2016-10-01

    We have elucidated the cooperative stabilization of proteins by sugars, amino acids, and other protein-stabilizing agents using a new and simple assay system. Our system determines the protein-stabilizing ability of various compounds by measuring their ability to protect hemoglobin from denaturation. Hemoglobin denaturation was readily measured by quantitative changes in its ultraviolet-visible absorption spectrum. The efficiency of our assay was confirmed using various sugars such as trehalose and sucrose that are known to be good protein stabilizers. We have also found that mixtures of two different types of protein stabilizers resulted in a cooperative stabilizing effect on protein. PMID:27253914

  20. Birth and death of protein domains: A simple model of evolution explains power law behavior

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    Berezovskaya Faina S

    2002-10-01

    Full Text Available Abstract Background Power distributions appear in numerous biological, physical and other contexts, which appear to be fundamentally different. In biology, power laws have been claimed to describe the distributions of the connections of enzymes and metabolites in metabolic networks, the number of interactions partners of a given protein, the number of members in paralogous families, and other quantities. In network analysis, power laws imply evolution of the network with preferential attachment, i.e. a greater likelihood of nodes being added to pre-existing hubs. Exploration of different types of evolutionary models in an attempt to determine which of them lead to power law distributions has the potential of revealing non-trivial aspects of genome evolution. Results A simple model of evolution of the domain composition of proteomes was developed, with the following elementary processes: i domain birth (duplication with divergence, ii death (inactivation and/or deletion, and iii innovation (emergence from non-coding or non-globular sequences or acquisition via horizontal gene transfer. This formalism can be described as a birth, death and innovation model (BDIM. The formulas for equilibrium frequencies of domain families of different size and the total number of families at equilibrium are derived for a general BDIM. All asymptotics of equilibrium frequencies of domain families possible for the given type of models are found and their appearance depending on model parameters is investigated. It is proved that the power law asymptotics appears if, and only if, the model is balanced, i.e. domain duplication and deletion rates are asymptotically equal up to the second order. It is further proved that any power asymptotic with the degree not equal to -1 can appear only if the hypothesis of independence of the duplication/deletion rates on the size of a domain family is rejected. Specific cases of BDIMs, namely simple, linear, polynomial and rational

  1. A Simple Spreadsheet Program to Simulate and Analyze the Far-UV Circular Dichroism Spectra of Proteins

    Science.gov (United States)

    Abriata, Luciano A.

    2011-01-01

    A simple algorithm was implemented in a spreadsheet program to simulate the circular dichroism spectra of proteins from their secondary structure content and to fit [alpha]-helix, [beta]-sheet, and random coil contents from experimental far-UV circular dichroism spectra. The physical basis of the method is briefly reviewed within the context of…

  2. Simple screening method for autoantigen proteins using the N-terminal biotinylated protein library produced by wheat cell-free synthesis.

    Science.gov (United States)

    Matsuoka, Kazuhiro; Komori, Hiroaki; Nose, Masato; Endo, Yaeta; Sawasaki, Tatsuya

    2010-08-01

    Autoimmune diseases are a heterogeneous group of diseases characterized by immune reactions against either a major or a limited number of the bodies own autoantigens, causing inflammation and damage to tissues and organs. Thus, identification of autoantigens is an important first step to understanding autoimmune diseases. Here we demonstrate a simple screening method for identification of autoantigens reacting with patient serum antibodies by combination of an N-terminal biotinylated protein library (BPL), produced using a wheat cell-free protein production system, and a commercially available luminescence system. Optimization studies using well-characterized autoantigens showed specific interactions between N-terminal biotinylated proteins and antibody that were sensitively detected under homogeneous reaction conditions. In this optimized assay, 1 microL of the translation mixture expressing the biotinylated proteins produced significant luminescence signal by addition of diluted serum between 1:500 and 1:10 000 in 25 microL of reaction volume. For the BPL construction, 214 mouse genes, consisting of 103 well-known autoantigens and 111 genes in the mouse autoimmune susceptibility loci, and the sera of MRL/lpr mouse were used as an autoimmune model. By this screening method, 25 well-known autoantigens and 71 proteins in the loci were identified as autoantigen proteins specifically reacting with sera antibodies. Cross-referencing with the Gene Ontology Database, 26 and 38 of autoantigen proteins were predicted to have nuclear localization and identified as membrane and/or extracellular proteins. The immune reaction of six randomly selected proteins was confirmed by immunoprecipitation and/or immunoblot analyses. Interestingly, three autoantigen proteins were recognized by immunoprecipitation but not by immunoblot analysis. These results suggest that the BPL-based method could provide a simple system for screening of autoantigen proteins and would help with

  3. Optimisation of a simple and reliable label-free methodology for the relative quantitation of raw pork meat proteins.

    Science.gov (United States)

    Gallego, Marta; Mora, Leticia; Aristoy, M Concepción; Toldrá, Fidel

    2015-09-01

    Recent advances in proteomics have become an indispensable tool for a fast, precise and sensitive analysis of proteins in complex biological samples at both, qualitative and quantitative level. In this study, a label-free quantitative proteomic methodology has been optimised for the relative quantitation of proteins extracted from raw pork meat. So, after the separation of proteins by one-dimensional gel electrophoresis and trypsin digestion, their identification and quantitation have been done using nanoliquid chromatography coupled to a quadrupole/time-of-flight (Q/ToF) mass spectrometer. Relative quantitation has been based on the measurement of mass spectral peak intensities, which have been described that are correlated with protein abundances. The results obtained regarding linearity, robustness, repeatability and accuracy show that this procedure could be used as a fast, simple, and reliable method to quantify changes in protein abundance in meat samples.

  4. A simple quantitative model of macromolecular crowding effects on protein folding: Application to the murine prion protein(121-231)

    Science.gov (United States)

    Bergasa-Caceres, Fernando; Rabitz, Herschel A.

    2013-06-01

    A model of protein folding kinetics is applied to study the effects of macromolecular crowding on protein folding rate and stability. Macromolecular crowding is found to promote a decrease of the entropic cost of folding of proteins that produces an increase of both the stability and the folding rate. The acceleration of the folding rate due to macromolecular crowding is shown to be a topology-dependent effect. The model is applied to the folding dynamics of the murine prion protein (121-231). The differential effect of macromolecular crowding as a function of protein topology suffices to make non-native configurations relatively more accessible.

  5. A simple detection method for low-affinity membrane protein interactions by baculoviral display.

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    Toshiko Sakihama

    Full Text Available BACKGROUND: Membrane protein interactions play an important role in cell-to-cell recognition in various biological activities such as in the immune or neural system. Nevertheless, there has remained the major obstacle of expression of the membrane proteins in their active form. Recently, we and other investigators found that functional membrane proteins express on baculovirus particles (budded virus, BV. In this study, we applied this BV display system to detect interaction between membrane proteins important for cell-to-cell interaction in immune system. METHODOLOGY/PRINCIPAL FINDINGS: We infected Sf9 cells with recombinant baculovirus encoding the T cell membrane protein CD2 or its ligand CD58 and recovered the BV. We detected specific interaction between CD2-displaying BV and CD58-displaying BV by an enzyme-linked immunosorbent assay (ELISA. Using this system, we also detected specific interaction between two other membrane receptor-ligand pairs, CD40-CD40 ligand (CD40L, and glucocorticoid-induced TNFR family-related protein (GITR-GITR ligand (GITRL. Furthermore, we observed specific binding of BV displaying CD58, CD40L, or GITRL to cells naturally expressing their respective receptors by flowcytometric analysis using anti-baculoviral gp64 antibody. Finally we isolated CD2 cDNA from a cDNA expression library by magnetic separation using CD58-displaying BV and anti-gp64 antibody. CONCLUSIONS: We found the BV display system worked effectively in the detection of the interaction of membrane proteins. Since various membrane proteins and their oligomeric complexes can be displayed on BV in the native form, this BV display system should prove highly useful in the search for natural ligands or to develop screening systems for therapeutic antibodies and/or compounds.

  6. Simple Method of Synthesizing Nickel-Nitrilotriacetic Acid Gold Nanoparticles with a Narrow Size Distribution for Protein Labeling

    Science.gov (United States)

    Kitai, Toshiyuki; Watanabe, Yuta; Toyoshima, Yoko Y.; Kobayashi, Takuya; Murayama, Takashi; Sakaue, Hiroyuki; Suzuki, Hitoshi; Takahagi, Takayuki

    2011-09-01

    We developed a simple method to synthesize nickel-nitrilotriacetic acid gold nanoparticles (Ni-NTA Au NPs) with a narrow size distribution for site-specific labeling in protein complexes. Au NPs were synthesized by the reduction of HAuCl4 using trisodium citrate and tannin acid. Then, the nanoparticle surfaces were modified with NTA and subsequent complexation with Ni2+. The mean diameter of the synthesized Ni-NTA Au NPs was 4.3 nm, and the coefficient of variation was 9%. The specific binding of the Ni-NTA Au NPs to polyhistidine-tagged (His-tagged) proteins was determined by transmission electron microscopy using kinesin and the p62 subunit of dynactin. Consequently, our method is useful for analyzing the substructures of protein complexes.

  7. A simple strategy for the purification of native recombinant full-length human RPL10 protein from inclusion bodies.

    Science.gov (United States)

    Pereira, Larissa M; Silva, Luana R; Alves, Joseane F; Marin, Nélida; Silva, Flavio Sousa; Morganti, Ligia; Silva, Ismael D C G; Affonso, Regina

    2014-09-01

    The L10 ribosomal protein (RPL10) plays a role in the binding of the 60 S and 40 S ribosomal subunits and in mRNA translation. The evidence indicates that RPL10 also has multiple extra-ribosomal functions, including tumor suppression. Recently, the presence of RPL10 in prostate and ovarian cancers was evaluated, and it was demonstrated to be associated with autistic disorders and premature ovarian failure. In the present work, we successfully cloned and expressed full-length human RPL10 (hRPL10) protein and isolated inclusion bodies containing this protein that had formed under mild growth conditions. The culture produced 376mg of hRPL10 protein per liter of induced bacterial culture, of which 102.4mg was present in the soluble fraction, and 25.6mg was recovered at approximately 94% purity. These results were obtained using a two-step process of non-denaturing protein extraction from pelleted inclusion bodies. We studied the characteristics of this protein using circular dichroism spectroscopy and by monitoring the changes induced by the presence or absence of zinc ions using fluorescence spectrometry. The results demonstrated that the protein obtained using these non-conventional methods retained its secondary and tertiary structure. The conformational changes induced by the incorporation of zinc suggested that this protein could interact with Jun or the SH3 domain of c-yes. The results suggested that the strategy used to obtain hRPL10 is simple and could be applied to obtaining other proteins that are susceptible to degradation.

  8. Simple Screening Method for Autoantigen Proteins Using the N-Terminal Biotinylated Protein Library Produced by Wheat Cell-Free Synthesis

    OpenAIRE

    Matsuoka, Kazuhiro; Komori, Hiroaki; Nose, Masato; Endo, Yaeta; Sawasaki, Tatsuya

    2010-01-01

    Autoimmune diseases are a heterogeneous group of diseases characterized by immune reactions against either a major or a limited number of the bodies own autoantigens, causing inflammation and damage to tissues and organs. Thus, identification of autoantigens is an important first step to understanding autoimmune diseases. Here we demonstrate a simple screening method for identification of autoantigens reacting with patient serum antibodies by combination of an N-terminal biotinylated protein ...

  9. Simple biophysics underpins collective conformations of the intrinsically disordered proteins of the Nuclear Pore Complex.

    Science.gov (United States)

    Vovk, Andrei; Gu, Chad; Opferman, Michael G; Kapinos, Larisa E; Lim, Roderick Yh; Coalson, Rob D; Jasnow, David; Zilman, Anton

    2016-01-01

    Nuclear Pore Complexes (NPCs) are key cellular transporter that control nucleocytoplasmic transport in eukaryotic cells, but its transport mechanism is still not understood. The centerpiece of NPC transport is the assembly of intrinsically disordered polypeptides, known as FG nucleoporins, lining its passageway. Their conformations and collective dynamics during transport are difficult to assess in vivo. In vitro investigations provide partially conflicting results, lending support to different models of transport, which invoke various conformational transitions of the FG nucleoporins induced by the cargo-carrying transport proteins. We show that the spatial organization of FG nucleoporin assemblies with the transport proteins can be understood within a first principles biophysical model with a minimal number of key physical variables, such as the average protein interaction strengths and spatial densities. These results address some of the outstanding controversies and suggest how molecularly divergent NPCs in different species can perform essentially the same function. PMID:27198189

  10. Simple Method To Prepare Oligonucleotide-Conjugated Antibodies and Its Application in Multiplex Protein Detection in Single Cells.

    Science.gov (United States)

    Gong, Haibiao; Holcomb, Ilona; Ooi, Aik; Wang, Xiaohui; Majonis, Daniel; Unger, Marc A; Ramakrishnan, Ramesh

    2016-01-20

    The diversity of nucleic acid sequences enables genomics studies in a highly multiplexed format. Since multiplex protein detection is still a challenge, it would be useful to use genomics tools for this purpose. This can be accomplished by conjugating specific oligonucleotides to antibodies. Upon binding of the oligonucleotide-conjugated antibodies to their targets, the protein levels can be converted to oligonucleotide levels. In this report we describe a simple method for preparing oligonucleotide-conjugated antibodies and discuss this method's application in oligonucleotide extension reaction (OER) for multiplex protein detection. Conjugation is based on strain-promoted alkyne-azide cycloaddition (the Cu-free click reaction), in which the antibody is activated with a dibenzocyclooctyne (DBCO) moiety and subsequently linked covalently with an azide-modified oligonucleotide. In the functional test, the reaction conditions and purification processes were optimized to achieve maximum yield and best performance. The OER assay employs a pair of antibody binders (two antibodies, each conjugated with its own oligonucleotide) developed for each protein target. The two oligonucleotides contain unique six-base complementary regions at their 3' prime ends to allow annealing and extension by DNA synthesis enzymes to form a DNA template. Following preamplification, the DNA template is detected by qPCR. Distinct oligonucleotide sequences are assigned to different antibody binders to enable multiplex protein detection. When tested using recombinant proteins, some antibody binders, such as those specific to CSTB, MET, EpCAM, and CASP3, had dynamic ranges of 5-6 logs. The antibody binders were also used in a multiplexed format in OER assays, and the binders successfully detected their protein targets in cell lysates, and in single cells in combination with the C1 system. This click reaction-based antibody conjugation procedure is cost-effective, needs minimal hands-on time, and

  11. Introducing Proteomics in the Undergraduate Curriculum: A Simple 2D Gel Electrophoresis Exercise with Serum Proteins

    Science.gov (United States)

    Kim, Thomas D.; Craig, Paul A.

    2010-01-01

    Two-dimensional gel electrophoresis (2DGE) remains an important tool in the study of biological systems by proteomics. While the use of 2DGE is commonplace in research publications, there are few instructional laboratories that address the use of 2DGE for analyzing complex protein samples. One reason for this lack is the fact that the preparation…

  12. Determination of olanzapine in whole blood using simple protein precipitation and liquid chromatography-tandem mass spectrometry

    DEFF Research Database (Denmark)

    Nielsen, Marie Katrine Klose; Johansen, Sys Stybe

    2009-01-01

    A simple, sensitive, and reproducible liquid chromatography-tandem mass spectrometry method has been developed and validated for the quantification of the antipsychotic drug olanzapine in whole blood using dibenzepine as internal standard (IS). After acidic methanol-induced protein precipitation...... of the whole blood samples, olanzapine and IS were chromatographed on a reversed-phase Zorbax Extend-C(18)-column at pH 9.0. Quantification was performed on a triple-quadrupole mass spectrometer employing electrospray ionization technique operating in multiple reaction monitoring and positive ion mode. Total...

  13. A Simple Method for Immunohistochemical Staining of Zebrafish Brain Sections for c-fos Protein Expression.

    Science.gov (United States)

    Chatterjee, Diptendu; Tran, Steven; Shams, Soaleha; Gerlai, Robert

    2015-12-01

    Immediate early genes (IEGs) are transcription factors whose own transcription is initiated rapidly, for example, in the brain in response to environmental stimuli. c-fos is an IEG often used as a marker of neuronal activation. c-fos mRNA expression has started to be quantified and localized in the zebrafish brain following environmental manipulations but analysis of the expression of c-fos protein in the zebrafish brain has rarely been attempted. Here, we describe an immunofluorescence staining method for quantifying c-fos protein expression in different regions of the zebrafish brain. In addition, we expose zebrafish to caffeine, a positive control for c-fos activation in the brain. To confirm cell nucleus specific binding of the c-fos antibody, we counterstained brain sections with the nuclear fluorescent stain DAPI. Furthermore, we describe a method for reducing background autofluorescence often observed in zebrafish brain tissue. Our analysis showed that exposure to caffeine increased the number of c-fos protein-positive cells in specific zebrafish brain regions detected by the immunofluorescence method. Our results demonstrate the feasibility of immunofluorescence-based methods in the analysis of neuronal activation in the zebrafish brain, and reinforce the utility of the zebrafish in behavioral neuroscience research.

  14. No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly

    Directory of Open Access Journals (Sweden)

    Koonin Eugene V

    2003-01-01

    Full Text Available Abstract Background It has been suggested that rates of protein evolution are influenced, to a great extent, by the proportion of amino acid residues that are directly involved in protein function. In agreement with this hypothesis, recent work has shown a negative correlation between evolutionary rates and the number of protein-protein interactions. However, the extent to which the number of protein-protein interactions influences evolutionary rates remains unclear. Here, we address this question at several different levels of evolutionary relatedness. Results Manually curated data on the number of protein-protein interactions among Saccharomyces cerevisiae proteins was examined for possible correlation with evolutionary rates between S. cerevisiae and Schizosaccharomyces pombe orthologs. Only a very weak negative correlation between the number of interactions and evolutionary rate of a protein was observed. Furthermore, no relationship was found between a more general measure of the evolutionary conservation of S. cerevisiae proteins, based on the taxonomic distribution of their homologs, and the number of protein-protein interactions. However, when the proteins from yeast were assorted into discrete bins according to the number of interactions, it turned out that 6.5% of the proteins with the greatest number of interactions evolved, on average, significantly slower than the rest of the proteins. Comparisons were also performed using protein-protein interaction data obtained with high-throughput analysis of Helicobacter pylori proteins. No convincing relationship between the number of protein-protein interactions and evolutionary rates was detected, either for comparisons of orthologs from two completely sequenced H. pylori strains or for comparisons of H. pylori and Campylobacter jejuni orthologs, even when the proteins were classified into bins by the number of interactions. Conclusion The currently available comparative-genomic data do not

  15. Calretinin: from a simple Ca2+ buffer to a multifunctional protein implicated in many biological processes

    Directory of Open Access Journals (Sweden)

    Beat eSchwaller

    2014-02-01

    Full Text Available The hexa-EF-hand Ca2+-binding protein calretinin (CR is predominantly expressed in specific neurons of the central and peripheral nervous system. However, CR expression is also observed in non-neuronal cells, e.g. during embryonic development and in mesothelioma cells. Of the 6 EF-hand domains, 5 are functional; the first 4 domains form 2 pairs showing high cooperativity within a pair that results in non-linear modulation of intracellular Ca2+ signals by CR. EF-hand domain 5 has a low affinity and represents the identified interaction site with CR-binding partners present in mouse cerebellar granule cells. CR binding to other targets including the pore-forming α1 subunit of the Ca2+ channel CaV2.1, as well as to huntingtin indicates additional Ca2+ sensor functions besides the well-known Ca2+-buffering functions. The absence of CR in cerebellar granule cells of CR-/- mice results in increased excitability and altered firing of Purkinje cells and promotes cerebellar 160-Hz oscillations impairing motor coordination. The putative role of CR in neuroprotection is still highly discussed. Altogether, CR emerges as a multi-functional protein also associated with development, i.e. cell proliferation, differentiation and cell death.

  16. Simple clinical means of documenting increased pulmonary endothelial permeability to protein

    Energy Technology Data Exchange (ETDEWEB)

    Mishkin, F.S.; Niden, A.; Kumar, A.; Thomas, A.; Reese, I.C.; Vasinrapee, P.

    1987-02-20

    The authors investigated a simple method that can be used at the bedside for documenting the net accumulation of albumin in the lung. The technique employs measurement with a computer-linked gamma camera of the activity ratio in an area of the right lung compared with the same-sized area in the heart at 20 minutes and three hours following intravenous injection of technetium Tc 99m albumin. They applied this measurement to three groups of patients: a control group and patients with roentgenographic evidence of edema classified according to clinically available criteria as either hydrostatic edema or permeability edema to see if they could document differences among these groups. In control patients this ratio did not increase by more than seven units between the 20-minute and three-hour measurements. Of 18 patients classified by other routine clinical means as having hydrostatic pulmonary edema, 89% showed no increase in lung albumin accumulation. In 29 patients with permeability edema associated with the so-called adult respiratory distress syndrome, 31% showed evidence of net pulmonary albumin accumulation. These findings suggest that some patients otherwise classified as having hydrostatic edema have concomitant permeability changes in the microvasculature and that permeability edema represents a spectrum of endothelial damage.

  17. A Simple Method for Discovering Druggable, Specific Glycosaminoglycan-Protein Systems. Elucidation of Key Principles from Heparin/Heparan Sulfate-Binding Proteins.

    Science.gov (United States)

    Sarkar, Aurijit; Desai, Umesh R

    2015-01-01

    Glycosaminoglycans (GAGs) affect human physiology and pathology by modulating more than 500 proteins. GAG-protein interactions are generally assumed to be ionic and nonspecific, but specific interactions do exist. Here, we present a simple method to identify the GAG-binding site (GBS) on proteins that in turn helps predict high specific GAG-protein systems. Contrary to contemporary thinking, we found that the electrostatic potential at basic arginine and lysine residues neither identifies the GBS consistently, nor its specificity. GBSs are better identified by considering the potential at neutral hydrogen bond donors such as asparagine or glutamine sidechains. Our studies also reveal that an unusual constellation of ionic and non-ionic residues in the binding site leads to specificity. Nature engineers the local environment of Asn45 of antithrombin, Gln255 of 3-O-sulfotransferase 3, Gln163 and Asn167 of 3-O-sulfotransferase 1 and Asn27 of basic fibroblast growth factor in the respective GBSs to induce specificity. Such residues are distinct from other uncharged residues on the same protein structure in possessing a significantly higher electrostatic potential, resultant from the local topology. In contrast, uncharged residues on nonspecific GBSs such as thrombin and serum albumin possess a diffuse spread of electrostatic potential. Our findings also contradict the paradigm that GAG-binding sites are simply a collection of contiguous Arg/Lys residues. Our work demonstrates the basis for discovering specifically interacting and druggable GAG-protein systems based on the structure of protein alone, without requiring access to any structure-function relationship data.

  18. A Simple Method for Discovering Druggable, Specific Glycosaminoglycan-Protein Systems. Elucidation of Key Principles from Heparin/Heparan Sulfate-Binding Proteins.

    Directory of Open Access Journals (Sweden)

    Aurijit Sarkar

    Full Text Available Glycosaminoglycans (GAGs affect human physiology and pathology by modulating more than 500 proteins. GAG-protein interactions are generally assumed to be ionic and nonspecific, but specific interactions do exist. Here, we present a simple method to identify the GAG-binding site (GBS on proteins that in turn helps predict high specific GAG-protein systems. Contrary to contemporary thinking, we found that the electrostatic potential at basic arginine and lysine residues neither identifies the GBS consistently, nor its specificity. GBSs are better identified by considering the potential at neutral hydrogen bond donors such as asparagine or glutamine sidechains. Our studies also reveal that an unusual constellation of ionic and non-ionic residues in the binding site leads to specificity. Nature engineers the local environment of Asn45 of antithrombin, Gln255 of 3-O-sulfotransferase 3, Gln163 and Asn167 of 3-O-sulfotransferase 1 and Asn27 of basic fibroblast growth factor in the respective GBSs to induce specificity. Such residues are distinct from other uncharged residues on the same protein structure in possessing a significantly higher electrostatic potential, resultant from the local topology. In contrast, uncharged residues on nonspecific GBSs such as thrombin and serum albumin possess a diffuse spread of electrostatic potential. Our findings also contradict the paradigm that GAG-binding sites are simply a collection of contiguous Arg/Lys residues. Our work demonstrates the basis for discovering specifically interacting and druggable GAG-protein systems based on the structure of protein alone, without requiring access to any structure-function relationship data.

  19. A Simple Protocol for High Efficiency Protein Isolation After RNA Isolation from Mouse Thyroid and Other Very Small Tissue Samples.

    Science.gov (United States)

    Ziros, Panos G; Chartoumpekis, Dionysios V; Sykiotis, Gerasimos P

    2016-01-01

    As a dedicated hormone-secreting organ, the thyroid gland possesses a complement of proteostatic systems, including antioxidant, unfolded protein, and autophagic responses. The vast majority of animal investigations of thyroid physiology and, more recently, proteostasis, have utilized as model the rat, rather than the mouse. This is due to the very small size of the thyroid gland in the latter, with a total weight of ~2 mg (~1 mg per thyroid lobe). However, this strategy has limited the utilization of genetic approaches, such as taking advantage of the various transgenic and knockout mouse models. Here, we describe a simple and highly efficient protocol for the simultaneous isolation of mRNA, micro-RNA and 150-200 μg of protein from as little as 1 mg of mouse thyroid tissue, the average weight of one of the two thyroid lobes, thus preserving the other lobe for immunohistochemical or other analyses. While our workflow is similar to other protocols published in the literature and/or proposed by commercial reagent providers, we have introduced a key modification that addresses efficiently the most challenging step of the protein isolation process: the solubilization of the protein pellet after RNA extraction and protein precipitation. We demonstrate the feasibility of our approach and its utility for downstream analyses (including Western blotting) that facilitate the comparative study of proteostatic pathways in the mouse thyroid. We have also successfully applied this protocol on samples from mouse liver, brown and white adipose tissue, as well as from rodent cell lines. PMID:27613051

  20. Analysis of disordered proteins using a simple apparatus for millisecond quench-flow H/D exchange.

    Science.gov (United States)

    Keppel, Theodore R; Weis, David D

    2013-05-21

    Measurement of amide H/D exchange on the ms time scale can provide valuable information about the dynamic behavior of the most flexible regions of proteins. We describe here a simple mixing apparatus, assembled solely from off-the-shelf components, that can be used for H/D exchange mass spectrometry to measure exchange on the 50-5000 ms time scale. Our apparatus utilizes flow-injection to minimize sample consumption. Although the mixer operates at low Reynolds numbers (less than 10(2)) where laminar flow is expected, H/D exchange kinetics were well-approximated using the assumption of plug-flow. We validated this approximation using fluorescence imaging of fluorescein-conjugated bovine serum albumin in the delay line and by demonstrating agreement between measured and calculated H/D exchange kinetics for a mixture of peptides. The performance of the apparatus was further validated by measuring rapid H/D exchange kinetics by an intrinsically disordered protein, murine CBP(2059-2117) (UniProt CBP_MOUSE). H/D exchange data from CBP, both free and in complex with human ACTR(1018-1088) (UniProt NCOA3_HUMAN), were consistent with previous biophysical studies of this protein.

  1. A simple two-state protein unfolds mechanically via multiple heterogeneous pathways at single-molecule resolution

    Science.gov (United States)

    Schönfelder, Jörg; Perez-Jimenez, Raul; Muñoz, Victor

    2016-06-01

    A major drive in protein folding has been to develop experimental technologies to resolve the myriads of microscopic pathways and complex mechanisms that purportedly underlie simple two-state folding behaviour. This is key for cross-validating predictions from theory and modern computer simulations. Detecting such complexity experimentally has remained elusive even using methods with improved time, structural or single-molecule resolution. Here, we investigate the mechanical unfolding of cold shock protein B (Csp), a showcase two-state folder, using single-molecule force-spectroscopy. Under controlled-moderate pulling forces, the unfolding of Csp emerges as highly heterogeneous with trajectories ranging from single sweeps to different combinations of multiple long-lived mechanical intermediates that also vary in order of appearance. Steered molecular dynamics simulations closely reproduce the experimental observations, thus matching unfolding patterns with structural events. Our results provide a direct glimpse at the nanoscale complexity underlying two-state folding, and postulate these combined methods as unique tools for dissecting the mechanical unfolding mechanisms of such proteins.

  2. Simple Machines Made Simple.

    Science.gov (United States)

    St. Andre, Ralph E.

    Simple machines have become a lost point of study in elementary schools as teachers continue to have more material to cover. This manual provides hands-on, cooperative learning activities for grades three through eight concerning the six simple machines: wheel and axle, inclined plane, screw, pulley, wedge, and lever. Most activities can be…

  3. Advanced oxidation protein products (AOPP) for monitoring oxidative stress in critically ill patients: a simple, fast and inexpensive automated technique.

    Science.gov (United States)

    Selmeci, László; Seres, Leila; Antal, Magda; Lukács, Júlia; Regöly-Mérei, Andrea; Acsády, György

    2005-01-01

    Oxidative stress is known to be involved in many human pathological processes. Although there are numerous methods available for the assessment of oxidative stress, most of them are still not easily applicable in a routine clinical laboratory due to the complex methodology and/or lack of automation. In research into human oxidative stress, the simplification and automation of techniques represent a key issue from a laboratory point of view at present. In 1996 a novel oxidative stress biomarker, referred to as advanced oxidation protein products (AOPP), was detected in the plasma of chronic uremic patients. Here we describe in detail an automated version of the originally published microplate-based technique that we adapted for a Cobas Mira Plus clinical chemistry analyzer. AOPP reference values were measured in plasma samples from 266 apparently healthy volunteers (university students; 81 male and 185 female subjects) with a mean age of 21.3 years (range 18-33). Over a period of 18 months we determined AOPP concentrations in more than 300 patients in our department. Our experiences appear to demonstrate that this technique is especially suitable for monitoring oxidative stress in critically ill patients (sepsis, reperfusion injury, heart failure) even at daily intervals, since AOPP exhibited rapid responses in both directions. We believe that the well-established relationship between AOPP response and induced damage makes this simple, fast and inexpensive automated technique applicable in daily routine laboratory practice for assessing and monitoring oxidative stress in critically ill or other patients.

  4. Direct, simple derivatization of disulfide bonds in proteins with organic mercury in alkaline medium without any chemical pre-reducing agents

    Energy Technology Data Exchange (ETDEWEB)

    Campanella, Beatrice; Onor, Massimo [National Research Council of Italy, C.N.R., Istituto di Chimica dei Composti Organo Metallici-ICCOM- UOS Pisa, Area di Ricerca, Via G. Moruzzi 1, 56124 Pisa (Italy); Ferrari, Carlo [National Research Council of Italy, C.N.R., Istituto Nazionale di Ottica, INO-UOS Pisa, Area di Ricerca, Via G. Moruzzi 1, 56124 Pisa (Italy); D’Ulivo, Alessandro [National Research Council of Italy, C.N.R., Istituto di Chimica dei Composti Organo Metallici-ICCOM- UOS Pisa, Area di Ricerca, Via G. Moruzzi 1, 56124 Pisa (Italy); Bramanti, Emilia, E-mail: bramanti@pi.iccom.cnr.it [National Research Council of Italy, C.N.R., Istituto di Chimica dei Composti Organo Metallici-ICCOM- UOS Pisa, Area di Ricerca, Via G. Moruzzi 1, 56124 Pisa (Italy)

    2014-09-16

    Highlights: • A simple procedure for the derivatization of proteins disulfide bonds. • Cysteine groups in several proteins derivatised with pHMB in alkaline media. • 75–100% labelling of cysteines in proteins with pHMB. - Abstract: In this work we have studied the derivatization of protein disulfide bonds with p-Hydroxymercurybenzoate (pHMB) in strong alkaline medium without any preliminary reduction. The reaction has been followed by the determination of the protein–pHMB complex using size exclusion chromatography coupled to a microwave/UV mercury oxidation system for the on-line oxidation of free and protein-complexed pHMB and atomic fluorescence spectrometry (SEC–CVG–AFS) detection. The reaction has been optimized by an experimental design using lysozyme as a model protein and applied to several thiolic proteins. The proposed method reports, for the first time, that it is possible to label 75–100% cysteines of proteins and, thus, to determine thiolic proteins without the need of any reducing step to obtain reduced -SH groups before mercury labelling. We obtained a detection limit of 100 nmol L{sup −1} based on a signal-to-noise ratio of 3 for unbound and complexed pHMB, corresponding to a detection limit of proteins ranged between 3 and 360 nmol L{sup −1}, depending on the number of cysteines in the protein sequence.

  5. The effect of time-dependent macromolecular crowding on the kinetics of protein aggregation: a simple model for the onset of age-related neurodegenerative disease

    Science.gov (United States)

    Minton, Allen

    2014-08-01

    A linear increase in the concentration of "inert" macromolecules with time is incorporated into simple excluded volume models for protein condensation or fibrillation. Such models predict a long latent period during which no significant amount of protein aggregates, followed by a steep increase in the total amount of aggregate. The elapsed time at which these models predict half-conversion of model protein to aggregate varies by less than a factor of two when the intrinsic rate constant for condensation or fibril growth of the protein is varied over many orders of magnitude. It is suggested that this concept can explain why the symptoms of neurodegenerative diseases associated with the aggregation of very different proteins and peptides appear at approximately the same advanced age in humans.

  6. A twist on folding: Predicting optimal sequences and optimal folds of simple protein models with the hidden-force algorithm

    CERN Document Server

    Kolossváry, István

    2012-01-01

    We propose a new way of looking at global optimization of off-lattice protein models. We present a dual optimization concept of predicting optimal sequences as well as optimal folds. We validate the utility of the recently introduced hidden-force Monte Carlo optimization algorithm by finding significantly lower energy folds for minimalist protein models than previously reported. Further, we also find the protein sequence that yields the lowest energy fold amongst all sequences for a given chain length and residue mixture. In particular, for protein models with a binary sequence, we show that the sequence-optimized folds form more compact cores than the lowest energy folds of the historically fixed, Fibonacci-series sequences of chain lengths of 13, 21, 34, 55, and 89. We emphasize that while the protein model we used is minimalist, the methodology is applicable to detailed protein models, and sequence optimization may yield novel folds and aid de novo protein design.

  7. Overcoming inefficient secretion of recombinant VEGF-C in baculovirus expression vector system by simple purification of the protein from cell lysate.

    Science.gov (United States)

    Klaus, Tomasz; Kulesza, Małgorzata; Bzowska, Monika; Wyroba, Barbara; Kilarski, Witold W; Bereta, Joanna

    2015-06-01

    The first reports about successfully expressed recombinant proteins with the use of a baculovirus vector were published over 30years ago. Despite the long time of refining this expression system, early problems with the production of baculovirus-derived secretory proteins are still not satisfactorily solved. The high expression level driven by baculoviral promoters often does not result in the desired yield of secreted recombinant proteins, which frequently accumulate inside insect cells and are only partially processed. During our attempts to produce vascular endothelial growth factor C (VEGF-C) with the use of a baculovirus vector we also faced an inefficient secretion of the recombinant protein to culture medium. We were not able to improve the outcome and obtain an acceptable concentration of VEGF-C in the medium by changing the culture conditions or utilizing different signal peptides. However, as a significant amount of native VEGF-C was detected inside the baculovirus-infected cells, we developed a simple method to purify recombinant, glycosylated VEGF-C from a lysate of the cells. The presented results indicate that the lack of a secretory protein in the insect cell culture medium after baculovirus infection does not necessarily signify failure in the production of the protein. As demonstrated by us and contrary to generally accepted views, the lysate of baculovirus-infected cells may constitute a valuable source of the biologically active, secretory protein.

  8. Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures

    Energy Technology Data Exchange (ETDEWEB)

    Berjanskii, Mark; Zhou Jianjun; Liang Yongjie; Lin Guohui; Wishart, David S., E-mail: david.wishart@ualberta.ca [University of Alberta, Department of Computing Science (Canada)

    2012-07-15

    In protein X-ray crystallography, resolution is often used as a good indicator of structural quality. Diffraction resolution of protein crystals correlates well with the number of X-ray observables that are used in structure generation and, therefore, with protein coordinate errors. In protein NMR, there is no parameter identical to X-ray resolution. Instead, resolution is often used as a synonym of NMR model quality. Resolution of NMR structures is often deduced from ensemble precision, torsion angle normality and number of distance restraints per residue. The lack of common techniques to assess the resolution of X-ray and NMR structures complicates the comparison of structures solved by these two methods. This problem is sometimes approached by calculating 'equivalent resolution' from structure quality metrics. However, existing protocols do not offer a comprehensive assessment of protein structure as they calculate equivalent resolution from a relatively small number (<5) of protein parameters. Here, we report a development of a protocol that calculates equivalent resolution from 25 measurable protein features. This new method offers better performance (correlation coefficient of 0.92, mean absolute error of 0.28 A) than existing predictors of equivalent resolution. Because the method uses coordinate data as a proxy for X-ray diffraction data, we call this measure 'Resolution-by-Proxy' or ResProx. We demonstrate that ResProx can be used to identify under-restrained, poorly refined or inaccurate NMR structures, and can discover structural defects that the other equivalent resolution methods cannot detect. The ResProx web server is available at http://www.resprox.cahttp://www.resprox.ca.

  9. Creating functional sophistication from simple protein building blocks, exemplified by factor H and the regulators of complement activation.

    Science.gov (United States)

    Makou, Elisavet; Herbert, Andrew P; Barlow, Paul N

    2015-10-01

    Complement control protein modules (CCPs) occur in numerous functionally diverse extracellular proteins. Also known as short consensus repeats (SCRs) or sushi domains each CCP contains approximately 60 amino acid residues, including four consensus cysteines participating in two disulfide bonds. Varying in length and sequence, CCPs adopt a β-sandwich type fold and have an overall prolate spheroidal shape with N- and C-termini lying close to opposite poles of the long axis. CCP-containing proteins are important as cytokine receptors and in neurotransmission, cell adhesion, blood clotting, extracellular matrix formation, haemoglobin metabolism and development, but CCPs are particularly well represented in the vertebrate complement system. For example, factor H (FH), a key soluble regulator of the alternative pathway of complement activation, is made up entirely from a chain of 20 CCPs joined by short linkers. Collectively, therefore, the 20 CCPs of FH must mediate all its functional capabilities. This is achieved via collaboration and division of labour among these modules. Structural studies have illuminated the dynamic architectures that allow FH and other CCP-rich proteins to perform their biological functions. These are largely the products of a highly varied set of intramolecular interactions between CCPs. The CCP can act as building block, spacer, highly versatile recognition site or dimerization mediator. Tandem CCPs may form composite binding sites or contribute to flexible, rigid or conformationally 'switchable' segments of the parent proteins. PMID:26517887

  10. The expression of a xylanase targeted to ER-protein bodies provides a simple strategy to produce active insoluble enzyme polymers in tobacco plants.

    Directory of Open Access Journals (Sweden)

    Immaculada Llop-Tous

    Full Text Available BACKGROUND: Xylanases deserve particular attention due to their potential application in the feed, pulp bleaching and paper industries. We have developed here an efficient system for the production of an active xylanase in tobacco plants fused to a proline-rich domain (Zera of the maize storage protein γ-zein. Zera is a self-assembling domain able to form protein aggregates in vivo packed in newly formed endoplasmic reticulum-derived organelles known as protein bodies (PBs. METHODOLOGY/PRINCIPAL FINDINGS: Tobacco leaves were transiently transformed with a binary vector containing the Zera-xylanase coding region, which was optimized for plant expression, under the control of the 35S CaMV promoter. The fusion protein was efficiently expressed and stored in dense PBs, resulting in yields of up to 9% of total protein. Zera-xylanase was post-translationally modified with high-mannose-type glycans. Xylanase fused to Zera was biologically active not only when solubilized from PBs but also in its insoluble form. The resistance of insoluble Zera-xylanase to trypsin digestion demonstrated that the correct folding of xylanase in PBs was not impaired by Zera oligomerization. The activity of insoluble Zera-xylanase was enhanced when substrate accessibility was facilitated by physical treatments such as ultrasound. Moreover, we found that the thermostability of the enzyme was improved when Zera was fused to the C-terminus of xylanase. CONCLUSION/SIGNIFICANCE: In the present work we have successfully produced an active insoluble aggregate of xylanase fused to Zera in plants. Zera-xylanase chimeric protein accumulates within ER-derived protein bodies as active aggregates that can easily be recovered by a simple density-based downstream process. The production of insoluble active Zera-xylanase protein in tobacco outlines the potential of Zera as a fusion partner for producing enzymes of biotechnological relevance. Zera-PBs could thus become efficient and low

  11. Saturation-Transfer Difference (STD) NMR: A Simple and Fast Method for Ligand Screening and Characterization of Protein Binding

    Science.gov (United States)

    Viegas, Aldino; Manso, Joao; Nobrega, Franklin L.; Cabrita, Eurico J.

    2011-01-01

    Saturation transfer difference (STD) NMR has emerged as one of the most popular ligand-based NMR techniques for the study of protein-ligand interactions. The success of this technique is a consequence of its robustness and the fact that it is focused on the signals of the ligand, without any need of processing NMR information about the receptor…

  12. Occurrence of antibodies against insect virus proteins in mammals: simple model to differentiate between passive exposure and active virus growth.

    Science.gov (United States)

    Moore, N F; McKnight, L; Tinsley, T W

    1981-02-01

    Antibodies against an "enterovirus-like" virus of insects, cricket paralysis virus, occur in the sera of domestic animals. When these antibodies were used in combination with the immunoprecipitation of radiolabeled virus proteins from infected Drosophila cells in culture, it could be demonstrated that the animals were exposed to preformed virus. PMID:6260677

  13. Occurrence of antibodies against insect virus proteins in mammals: simple model to differentiate between passive exposure and active virus growth.

    OpenAIRE

    Moore, N F; McKnight, L.; Tinsley, T. W.

    1981-01-01

    Antibodies against an "enterovirus-like" virus of insects, cricket paralysis virus, occur in the sera of domestic animals. When these antibodies were used in combination with the immunoprecipitation of radiolabeled virus proteins from infected Drosophila cells in culture, it could be demonstrated that the animals were exposed to preformed virus.

  14. Simple machines

    CERN Document Server

    Graybill, George

    2007-01-01

    Just how simple are simple machines? With our ready-to-use resource, they are simple to teach and easy to learn! Chocked full of information and activities, we begin with a look at force, motion and work, and examples of simple machines in daily life are given. With this background, we move on to different kinds of simple machines including: Levers, Inclined Planes, Wedges, Screws, Pulleys, and Wheels and Axles. An exploration of some compound machines follows, such as the can opener. Our resource is a real time-saver as all the reading passages, student activities are provided. Presented in s

  15. Simple immunoblot and immunohistochemical detection of Penaeus stylirostris densovirus using monoclonal antibodies to viral capsid protein expressed heterologously.

    Science.gov (United States)

    Sithigorngul, Paisarn; Hajimasalaeh, Warunee; Longyant, Siwaporn; Sridulyakul, Pattarin; Rukpratanporn, Sombat; Chaivisuthangkura, Parin

    2009-12-01

    Penaeus stylirostris densovirus (PstDNV), called formerly infectious hypodermal and hematopoietic necrosis virus (IHHNV), is an important shrimp pathogen which can cause mortality in the blue shrimp Penaeus (Litopenaeus) stylirostris and stunting in the whiteleg shrimp Penaeus (Litopenaeus) vannamei. Five monoclonal antibodies (MAbs) were produced against the 37kDa capsid protein 3 (CP3) of PstDNV expressed heterologously in the form of a fusion protein with glutathione-S-transferase called GST-CP3. All MAbs belonged to the IgG2b subclass and could bind to GST-CP3 at 300 pg/spot in immunodot-blot tests. They could detect CP3 in naturally infected shrimp extracts by Western blotting and dot blotting and in shrimp tissues by immunohistochemistry without cross-reactivity to extracts from uninfected shrimps or shrimps infected with several other viruses. Although dot blot assay sensitivity was approximately 1000 times lower than that of one step PCR for PstDNV, it easily detected PstDNV infections in field samples of Penaeus monodon and Penaeus vannamei. PMID:19654023

  16. A simple enzyme-substrate localized conjugation method to generate immobilized, functional glutathione S-transferase fusion protein columns for affinity enrichment.

    Science.gov (United States)

    Coughlin, John; Masci, Allyson; Gronke, Robert S; Bergelson, Svetlana; Co, Carl

    2016-07-15

    Immobilized protein receptors and enzymes are tools for isolating or enriching ligands and substrates based on affinity. For example, glutathione S-transferase (GST) is fused to proteins as a tag for binding to its substrate glutathione (GSH) linked to solid supports. One issue with this approach is that high-affinity interactions between receptors and ligands require harsh elution conditions such as low pH, which can result in leached receptor. Another issue is the inherent nonspecific chemical conjugation of reactive groups such as N-hydroxysuccinimide (NHS) that couple lysines to solid supports; the nonspecificity of NHS may result in residue modifications near the binding site(s) of the receptor that can affect ligand specificity. In this study, a simple conjugation procedure is presented that overcomes these limitations and results in immobilized GST fusion proteins that are functional and specific. Here, the affinity of GST for GSH was used to generate an enzyme-substrate site-specific cross-linking reaction; GSH-Sepharose was preactivated with 1-ethyl-3-(dimethylaminopropyl)carbodiimide (EDC) and then incubated Fc gamma receptor IIIa (FcγRIIIa)-GST. The immobilized FcγRIIIa-GST more specifically bound glycosylated immunoglobulin G1s (IgG1s) and was used to enrich nonfucosylated IgG1s from weaker binding species. This technique can be used when modifications of amino acids lead to changes in activity. PMID:27063248

  17. Simple high-cell density fed-batch technique for high-level recombinant protein production with Pichia pastoris: Application to intracellular production of Hepatitis B surface antigen

    Directory of Open Access Journals (Sweden)

    Ross Anton

    2009-02-01

    Full Text Available Abstract Background Hepatitis B is a serious global public health concern. Though a safe and efficacious recombinant vaccine is available, its use in several resource-poor countries is limited by cost. We have investigated the production of Hepatitis B virus surface antigen (HBsAg using the yeast Pichia pastoris GS115 by inserting the HBsAg gene into the alcohol oxidase 1 locus. Results Large-scale production was optimized by developing a simple fed-batch process leading to enhanced product titers. Cells were first grown rapidly to high-cell density in a batch process using a simple defined medium with low salt and high glycerol concentrations. Induction of recombinant product synthesis was carried out using rather drastic conditions, namely through the addition of methanol to a final concentration of 6 g L-1. This methanol concentration was kept constant for the remainder of the cultivation through continuous methanol feeding based on the on-line signal of a flame ionization detector employed as methanol analyzer in the off-gas stream. Using this robust feeding protocol, maximum concentrations of ~7 grams HBsAg per liter culture broth were obtained. The amount of soluble HBsAg, competent for assembly into characteristic virus-like particles (VLPs, an attribute critical to its immunogenicity and efficacy as a hepatitis B vaccine, reached 2.3 grams per liter of culture broth. Conclusion In comparison to the highest yields reported so far, our simple cultivation process resulted in an ~7 fold enhancement in total HBsAg production with more than 30% of soluble protein competent for assembly into VLPs. This work opens up the possibility of significantly reducing the cost of vaccine production with implications for expanding hepatitis B vaccination in resource-poor countries.

  18. Simple containers for simple hypergraphs

    OpenAIRE

    Saxton, David; Thomason, Andrew

    2014-01-01

    We give an easy method for constructing containers for simple hypergraphs. Some applications are given; in particular, a very transparent calculation is offered for the number of H-free hypergraphs, where H is some fixed uniform hypergraph.

  19. Simple synthesis of carbon-11-labeled chromen-4-one derivatives as new potential PET agents for imaging of DNA-dependent protein kinase (DNA-PK) in cancer

    International Nuclear Information System (INIS)

    Carbon-11-labeled chromen-4-one derivatives were synthesized as new potential PET agents for imaging of DNA repair enzyme DNA-dependent protein kinase (DNA-PK) in cancer. The target tracers, X-[11C]methoxy-2-morpholino-4H-chromen-4-ones (X=8, 7, 6, 5; [11C]4a–d), were prepared from their corresponding precursors, X-hydroxy-2-morpholino-4H-chromen-4-ones (X=8, 7, 6, 5; 5a–d), with [11C]CH3OTf through O-[11C]methylation and isolated by a simplified solid-phase extraction (SPE) method using a C-18 Sep-Pak Plus cartridge. The radiochemical yields decay corrected to end of bombardment (EOB), from [11C]CO2, were 40–60%. The specific activity at end of synthesis (EOS) was 185–370 GBq/μmol. - Highlights: ► New chromen-4-one derivatives were synthesized. ► New carbon-11-labeled chromen-4-one derivatives were synthesized. ► Simple solid-phase extraction (SPE) method was employed in radiosynthesis.

  20. A simple and visualized method to screen for effective siRNAs by using green fluorescence protein (GFP) as a reporter

    Institute of Scientific and Technical Information of China (English)

    Zhixin SHAN; Qiuxiong LIN; Yongheng FU; Chunyu DENG; Xiaohong LI; Xiyong YU

    2008-01-01

    To screen for effective small interference RNA (siRNA), a simple and visualized method was developed using the green fluorescence protein (GFP) as a reporter. Candidate siRNAs targeting macrophage migration inhibition factor genes (MIF) were identified. By using the pEGFP-N3 vector, the MIF-GFP expression plasmid, pEGFP-MIF, was constructed with the same Kozak con-sensus translation initiation site and start code ATG for the MIF-EGFP coding sequence. Based on the siRNA expression vector pSilencer-4,1,3 candidate MIF siRNA expression plasmids were constructed and co-transfected with the pEGFP-MIF into the H EK293 cells, respectively. The GFP expression in HEK293 cells could be viewed by fluorescence microscopy and the MIF mRNA expressions were determined by real-time quantitative PCR. The 3 candidate MIF siRNA expression plasmids were also co-transfected with the MIF expression plasmid into the HEK293 cells, respectively, and the MIF mRNA expres-sions were determined by real-time quantitative PCR. The results show that the down-regulated expression of the MIF mRNA was consistent with the GFP expression and the same effective MIF siRNAs were screened by using the pEGFP-MIF or MIF expression plasmid with the candidate MIF siRNAs expression plasmids. Therefore, by using the GFP as a reporter, a useful method was provided to screen for effective siRNAs tar-geting specific genes co-expressed with the GFP. This may be a good strategy for screening for effective siRNAs tar-geting different genes.

  1. Targeted toxicological screening for acidic, neutral and basic substances in postmortem and antemortem whole blood using simple protein precipitation and UPLC-HR-TOF-MS.

    Science.gov (United States)

    Telving, Rasmus; Hasselstrøm, Jørgen Bo; Andreasen, Mette Findal

    2016-09-01

    A broad targeted screening method based on broadband collision-induced dissociation (bbCID) ultra-performance liquid chromatography high-resolution time-of-flight mass spectrometry (UPLC-HR-TOF-MS) was developed and evaluated for toxicological screening of whole blood samples. The acidic, neutral and basic substances covered by the method were identified in postmortem and antemortem whole blood samples from forensic autopsy cases, clinical forensic cases and driving under the influence of drugs (DUID) cases by a reverse target database search. The screening method covered 467 substances. Validation was performed on spiked whole blood samples and authentic postmortem and antemortem whole blood samples. For most of the basic drugs, the established cut-off limits were very low, ranging from 0.25ng/g to 50ng/g. The established cut-off limits for most neutral and acidic drugs, were in the range from 50ng/g to 500ng/g. Sample preparation was performed using simple protein precipitation of 300μL of whole blood with acetonitrile and methanol. Ten microliters of the reconstituted extract were injected and separated within a 13.5min UPLC gradient reverse-phase run. Positive electrospray ionization (ESI) was used to generate the ions in the m/z range of 50-1000. Fragment ions were generated by bbCID. Identification was based on retention time, accurate mass, fragment ion(s) and isotopic pattern. A very sensitive broad toxicological screening method using positive electrospray ionization UPLC-HR-TOF-MS was achieved in one injection. This method covered basic substances, substances traditionally analyzed in negative ESI (e.g., salicylic acid), small highly polar substances such as beta- and gamma-hydroxybutyric acid (BHB and GHB, respectively) and highly non-polar substances such as amiodarone. The new method was shown to combine high sensitivity with a very broad scope that has not previously been reported in toxicological whole blood screening when using only one injection

  2. Simple Genetic Selection Protocol for Isolation of Overexpressed Genes That Enhance Accumulation of Membrane-Integrated Human G Protein-Coupled Receptors in Escherichia coli ▿

    OpenAIRE

    Skretas, Georgios; Georgiou, George

    2010-01-01

    The efficient production of membrane proteins in bacteria remains a major challenge. In this work, we sought to identify overexpressed genes that enhance the yields of recombinant membrane proteins in Escherichia coli. We developed a genetic selection system for bacterial membrane protein production, consisting of membrane protein fusions with the enzyme β-lactamase and facile selection of high-production strains on ampicillin-containing media. This system was used to screen the ASKA library,...

  3. Simple and Rapid Hollow Fiber Liquid Phase Microextraction Followed by High Performance Liquid Chromatography Method for Determination of Drug-protein Binding

    Institute of Scientific and Technical Information of China (English)

    XI Guo-chen; HU Shuang; BAI Xiao-hong

    2011-01-01

    A method was established using hollow fiber-liquid phase microextraction(HF-LPME) followed by high performance liquid chromatography(HPLC) to determine the concentration of the free(unbound) drug in the solution of the drug and protein.Measurements of drug-protein binding ratios and free drug concentrations were then analyzed with the Klotz equation to determine the equilibrium binding constant and number of binding sites for drug-protein interaction.The optimized method allows one to perform the efficient extraction and separation of free drug from protein-bound drug,protein,and other interfering substances.This approach was used to characterize the binding of the anticholinergic drugs atropine sulfate and scopolamine hydrobromide to proteins in human plasma and bovine serum albumin(BSA).The results demonstrate the utility of HF-LPME method for measuring free drug concentrations in protein-drug mixtures and determining the protein binding parameters of a pharmacologically important class of drugs.

  4. DOCLASP - Docking ligands to target proteins using spatial and electrostatic congruence extracted from a known holoenzyme and applying simple geometrical transformations

    Science.gov (United States)

    Chakraborty, Sandeep

    2016-01-01

    The ability to accurately and effectively predict the interaction between proteins and small drug-like compounds has long intrigued researchers for pedagogic, humanitarian and economic reasons. Protein docking methods (AutoDock, GOLD, DOCK, FlexX and Glide to name a few) rank a large number of possible conformations of protein-ligand complexes using fast algorithms. Previously, it has been shown that structural congruence leading to the same enzymatic function necessitates the congruence of electrostatic properties (CLASP). The current work presents a methodology for docking a ligand into a target protein, provided that there is at least one known holoenzyme with ligand bound - DOCLASP (Docking using CLASP). The contact points of the ligand in the holoenzyme defines a motif, which is used to query the target enzyme using CLASP. If there are significant matches, the holoenzyme and the target protein are superimposed based on congruent atoms. The same linear and rotational transformations are also applied to the ligand, thus creating a unified coordinate framework having the holoenzyme, the ligand and the target enzyme. In the current work, the dipeptidyl peptidase-IV inhibitor vildagliptin was docked to the PI-PLC structure complexed with myo-inositol using DOCLASP. Also, corroboration of the docking of phenylthiourea to the modelled structure of polyphenol oxidase (JrPPO1) from walnut is provided based on the subsequently solved structure of JrPPO1 (PDBid:5CE9). Analysis of the binding of the antitrypanosomial drug suramin to nine non-homologous proteins in the PDB database shows a diverse set of binding motifs, and multiple binding sites in the phospholipase A2-likeproteins from the Bothrops genus of pitvipers. The conformational changes in the suramin molecule on binding highlights the challenges in docking flexible ligands into an already ’plastic’ binding site. Thus, DOCLASP presents a method for ’soft docking’ ligands to proteins with low

  5. One simple step in the identification of the cofactors signals, one giant leap for the solution structure determination of multiheme proteins

    Energy Technology Data Exchange (ETDEWEB)

    Morgado, Leonor; Fernandes, Ana P. [Requimte-CQFB, Departamento de Quimica, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica (Portugal); Londer, Yuri Y. [Biosciences Division, Argonne National Laboratory, Argonne, IL 60439 (United States); Bruix, Marta [Departamento de Espectroscopia y Estructura Molecular, Instituto de Quimica-Fisica ' Rocasolano' , CSIC, Serrano 119, 28006 Madrid (Spain); Salgueiro, Carlos A., E-mail: csalgueiro@dq.fct.unl.pt [Requimte-CQFB, Departamento de Quimica, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, Campus Caparica, 2829-516 Caparica (Portugal)

    2010-03-12

    Multiheme proteins play major roles in various biological systems. Structural information on these systems in solution is crucial to understand their functional mechanisms. However, the presence of numerous proton-containing groups in the heme cofactors and the magnetic properties of the heme iron, in particular in the oxidised state, complicates significantly the assignment of the NMR signals. Consequently, the multiheme proteins superfamily is extremely under-represented in structural databases, which constitutes a severe bottleneck in the elucidation of their structural-functional relationships. In this work, we present a strategy that simplifies the assignment of the NMR signals in multiheme proteins and, concomitantly, their solution structure determination, using the triheme cytochrome PpcA from the bacterium Geobacter sulfurreducens as a model. Cost-effective isotopic labeling was used to double label ({sup 13}C/{sup 15}N) the protein in its polypeptide chain, with the correct folding and heme post-translational modifications. The combined analysis of {sup 1}H-{sup 13}C HSQC NMR spectra obtained for labeled and unlabeled samples of PpcA allowed a straight discrimination between the heme cofactors and the polypeptide chain signals and their confident assignment. The results presented here will be the foundations to assist solution structure determination of multiheme proteins, which are still very scarce in the literature.

  6. Optimising expression of the recombinant fusion protein biopesticide ω-hexatoxin-Hv1a/GNA in Pichia pastoris: sequence modifications and a simple method for the generation of multi-copy strains.

    Science.gov (United States)

    Pyati, Prashant; Fitches, Elaine; Gatehouse, John A

    2014-08-01

    Production of recombinant protein bio-insecticides on a commercial scale can only be cost effective if host strains with very high expression levels are available. A recombinant fusion protein containing an arthropod toxin, ω-hexatoxin-Hv1a, (from funnel web spider Hadronyche versuta) linked to snowdrop lectin (Galanthus nivalis agglutinin; GNA) is an effective oral insecticide and candidate biopesticide. However, the fusion protein was vulnerable to proteolysis during production in the yeast Pichia pastoris. To prevent proteolysis, the Hv1a/GNA fusion expression construct was modified by site-directed mutagenesis to remove a potential Kex2 cleavage site at the C-terminus of the Hv1a peptide. To obtain a high expressing clone of P. pastoris to produce recombinant Hv1a/GNA, a straightforward method was used to produce multi-copy expression plasmids, which does not require multiple integrations to give clones of P. pastoris containing high copy numbers of the introduced gene. Removal of the Kex2 site resulted in increased levels of intact fusion protein expressed in wild-type P. pastoris strains, improving levels of intact recombinant protein recoverable. Incorporation of a C-terminal (His)6 tag enabled single step purification of the fusion protein. These modifications did not affect the insecticidal activity of the recombinant toxin towards lepidopteran larvae. Introduction of multiple expression cassettes increased the amount of secreted recombinant fusion protein in a laboratory scale fermentation by almost tenfold on a per litre of culture basis. Simple modifications in the expression construct can be advantageous for the generation of high expressing P. pastoris strains for production of a recombinant protein, without altering its functional properties.

  7. Optimising expression of the recombinant fusion protein biopesticide ω-hexatoxin-Hv1a/GNA in Pichia pastoris: sequence modifications and a simple method for the generation of multi-copy strains.

    Science.gov (United States)

    Pyati, Prashant; Fitches, Elaine; Gatehouse, John A

    2014-08-01

    Production of recombinant protein bio-insecticides on a commercial scale can only be cost effective if host strains with very high expression levels are available. A recombinant fusion protein containing an arthropod toxin, ω-hexatoxin-Hv1a, (from funnel web spider Hadronyche versuta) linked to snowdrop lectin (Galanthus nivalis agglutinin; GNA) is an effective oral insecticide and candidate biopesticide. However, the fusion protein was vulnerable to proteolysis during production in the yeast Pichia pastoris. To prevent proteolysis, the Hv1a/GNA fusion expression construct was modified by site-directed mutagenesis to remove a potential Kex2 cleavage site at the C-terminus of the Hv1a peptide. To obtain a high expressing clone of P. pastoris to produce recombinant Hv1a/GNA, a straightforward method was used to produce multi-copy expression plasmids, which does not require multiple integrations to give clones of P. pastoris containing high copy numbers of the introduced gene. Removal of the Kex2 site resulted in increased levels of intact fusion protein expressed in wild-type P. pastoris strains, improving levels of intact recombinant protein recoverable. Incorporation of a C-terminal (His)6 tag enabled single step purification of the fusion protein. These modifications did not affect the insecticidal activity of the recombinant toxin towards lepidopteran larvae. Introduction of multiple expression cassettes increased the amount of secreted recombinant fusion protein in a laboratory scale fermentation by almost tenfold on a per litre of culture basis. Simple modifications in the expression construct can be advantageous for the generation of high expressing P. pastoris strains for production of a recombinant protein, without altering its functional properties. PMID:24898110

  8. Simple Epithelial Keratins.

    Science.gov (United States)

    Strnad, Pavel; Guldiken, Nurdan; Helenius, Terhi O; Misiorek, Julia O; Nyström, Joel H; Lähdeniemi, Iris A K; Silvander, Jonas S G; Kuscuoglu, Deniz; Toivola, Diana M

    2016-01-01

    Simple epithelial keratins (SEKs) are the cytoplasmic intermediate filament proteins of single-layered and glandular epithelial cells as found in the liver, pancreas, intestine, and lung. SEKs have broad cytoprotective functions, which are facilitated by dynamic posttranslational modifications and interaction with associated proteins. SEK filaments are composed of obligate heteropolymers of type II (K7, K8) and type I (K18-K20, K23) keratins. The multifaceted roles of SEKs are increasingly appreciated due to findings obtained from transgenic mouse models and human studies that identified SEK variants in several digestive diseases. Reorganization of the SEK network into aggregates called Mallory-Denk bodies (MDBs) is characteristic for specific liver disorders such as alcoholic and nonalcoholic steatohepatitis. To spur further research on SEKs, we here review the methods and potential caveats of their isolation as well as possibilities to study them in cell culture. The existing transgenic SEK mouse models, their advantages and potential drawbacks are discussed. The tools to induce MDBs, ways of their visualization and quantification, as well as the possibilities to detect SEK variants in humans are summarized.

  9. Idiopathic recurrent calcium urolithiasis (IRCU: variation of fasting urinary protein is a window to pathophysiology or simple consequence of renal stones in situ?

    Directory of Open Access Journals (Sweden)

    Schwille PO

    2009-09-01

    Full Text Available Abstract Background In IRCU it is uncertain whether variation of urinary protein, especially non-albumin protein (NAlb-P, is due to the presence of stones or reflects alteration of oxidative metabolism. Aims To validate in a tripartite cross-sectional study of 187 ambulatory male patients, undergoing a standardized laboratory programme, whether stones impact on N-Alb-P or the state of oxidative metabolism interferes with IRCU pathophysiology. Methods In part 1 the strata low and high of fasting urinary excretion rate per 2 h of N-Alb-P, malonedialdehyde, hypoxanthine, xanthine, pH and other urine components were compared, and association with renal stones in situ evaluated; in part 2 the co-variation of oxidatively modulated environment, fasting urinary pH, calcium (Ca salt crystallization risk and the number of patients with stones in situ was examined; in part 3, the nucleation of Ca oxalate and Ca phosphate was tested in undiluted postprandial urine of patients and related to the state of oxidative metabolism. Results In part 1, N-Alb-P excretion > 4.3 mg was associated with increase of blood pressure, excretion of total protein, hypoxanthine (a marker of tissue hypoxia, malonedialdehyde (a marker of lipid peroxidation, sodium, magnesium, citrate, uric acid, volume, pH, and increase of renal fractional excretion of both NAlb-P and uric acid; when stones were present, urinary pH was elevated but other parameters were unaffected. Significant predictors of N-Alb-P excretion were malonedialdehyde, fractional N-Alb-P and hypoxanthine. In part 2, urine pH > 6.14 was associated with unchanged blood pressure and plasma vasopressin, increase of blood pH, urinary volume, malonedialde hyde, fractional excretion of N-Alb-P, uric acid, Ca phosphate, but not Ca oxalate, supersaturation; this spectrum was accompanied by decrease of concentration of urinary total and free magnesium, total and complexed citrate, plasma uric acid (in humans the major

  10. A simple system for the identification of fluorescent dyes capable of reporting differences in secondary structure and hydrophobicity among amyloidogenic protein oligomers

    Science.gov (United States)

    Yates, Emma

    2012-02-01

    Thioflavin T and Congo Red are fluorescent dyes that are commonly used to identify the presence of amyloid structures, ordered protein aggregates. Despite the ubiquity of their use, little is known about their mechanism of interaction with amyloid fibrils, or whether other dyes, whose photophysics indicate that they may be more responsive to differences in macromolecular secondary structure and hydrophobicity, would be better suited to the identification of pathologically relevant oligomeric species in amyloid diseases. In order to systematically address this question, we have designed a strategy that discretely introduces differences in secondary structure and hydrophobicity amidst otherwise identical polyamino acids. This strategy will enable us to quantify and compare the affinities of Thioflavin T, Congo Red, and other, incompletely explored, fluorescent dyes for different secondary structural elements and hydrophobic motifs. With this information, we will identify dyes that give the most robust and quantitative information about structural differences among the complex population of oligomeric species present along an aggregation pathway between soluble monomers and amyloid fibrils, and correlate the resulting structural information with differential oligomeric toxicity.

  11. Simple fabrication of hydrophobic surface target for increased sensitivity and homogeneity in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis of peptides, phosphopeptides, carbohydrates and proteins.

    Science.gov (United States)

    Chen, Chao-Jung; Lai, Chien-Chen; Tseng, Mei-Chun; Liu, Yu-Ching; Lin, Shih-Yi; Tsai, Fuu-Jen

    2013-06-14

    To enhance sample signals and improve homogeneity in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) analysis, a simple, rapid, and efficient sample preparation method was developed in this study. Polydimethylsiloxane (PDMS) was coated on a stainless steel MALDI plate, forming a transparent, hydrophobic surface that enhanced sample signals without producing observable background signals. Compared to the use of an unmodified commercial metal MALDI plate, peptide signals were enhanced by ~7.1-11.0-fold due to the reduced sample spot area of the PDMS-coated plate, and showed improved peptide mass fingerprinting (PMF) and MS/MS peptide sequencing results. In the analysis of phosphopeptides and carbohydrates with a 2,5-dihydroxybenzoic acid (DHB) matrix, the PDMS-coated plate showed improved sample homogeneity and signal enhancements of ~5.2-8.2-fold and ~2.8-3.2-fold, respectively. Improved sensitivity in the observation of more unique fragment ions by MS/MS analysis, to successfully distinguish isomeric carbohydrates, was also illustrated. In protein analysis with a sinapinic acid (SA) matrix, a ~3.4-fold signal enhancement was observed. The PDMS film coating was easily removed and refabricated to avoid sample carryover, and was applicable to diverse commercial MALDI plates. The PDMS-coated approach is a simple, practical, and attractive method for enhancing analyte signals and homogeneity. PMID:23726097

  12. Simple Variance Swaps

    OpenAIRE

    Ian Martin

    2011-01-01

    The large asset price jumps that took place during 2008 and 2009 disrupted volatility derivatives markets and caused the single-name variance swap market to dry up completely. This paper defines and analyzes a simple variance swap, a relative of the variance swap that in several respects has more desirable properties. First, simple variance swaps are robust: they can be easily priced and hedged even if prices can jump. Second, simple variance swaps supply a more accurate measure of market-imp...

  13. Simple Machine Junk Cars

    Science.gov (United States)

    Herald, Christine

    2010-01-01

    During the month of May, the author's eighth-grade physical science students study the six simple machines through hands-on activities, reading assignments, videos, and notes. At the end of the month, they can easily identify the six types of simple machine: inclined plane, wheel and axle, pulley, screw, wedge, and lever. To conclude this unit,…

  14. A Simple Water Channel

    Science.gov (United States)

    White, A. S.

    1976-01-01

    Describes a simple water channel, for use with an overhead projector. It is run from a water tap and may be used for flow visualization experiments, including the effect of streamlining and elementary building aerodynamics. (MLH)

  15. The AGM Simple Pendulum

    OpenAIRE

    Villarino, Mark B.

    2012-01-01

    We present a self-contained development of Gauss' Arithmetic-Geometric Mean (AGM) and the work of A.E. Ingham who obtained rigorous error bounds for the AGM approximations to the period of a simple pendulum

  16. Strategy as simple rules.

    Science.gov (United States)

    Eisenhardt, K M; Sull, D N

    2001-01-01

    The success of Yahoo!, eBay, Enron, and other companies that have become adept at morphing to meet the demands of changing markets can't be explained using traditional thinking about competitive strategy. These companies have succeeded by pursuing constantly evolving strategies in market spaces that were considered unattractive according to traditional measures. In this article--the third in an HBR series by Kathleen Eisenhardt and Donald Sull on strategy in the new economy--the authors ask, what are the sources of competitive advantage in high-velocity markets? The secret, they say, is strategy as simple rules. The companies know that the greatest opportunities for competitive advantage lie in market confusion, but they recognize the need for a few crucial strategic processes and a few simple rules. In traditional strategy, advantage comes from exploiting resources or stable market positions. In strategy as simple rules, advantage comes from successfully seizing fleeting opportunities. Key strategic processes, such as product innovation, partnering, or spinout creation, place the company where the flow of opportunities is greatest. Simple rules then provide the guidelines within which managers can pursue such opportunities. Simple rules, which grow out of experience, fall into five broad categories: how- to rules, boundary conditions, priority rules, timing rules, and exit rules. Companies with simple-rules strategies must follow the rules religiously and avoid the temptation to change them too frequently. A consistent strategy helps managers sort through opportunities and gain short-term advantage by exploiting the attractive ones. In stable markets, managers rely on complicated strategies built on detailed predictions of the future. But when business is complicated, strategy should be simple. PMID:11189455

  17. Droids Made Simple

    CERN Document Server

    Mazo, Gary

    2011-01-01

    If you have a Droid series smartphone - Droid, Droid X, Droid 2, or Droid 2 Global - and are eager to get the most out of your device, Droids Made Simple is perfect for you. Authors Martin Trautschold, Gary Mazo and Marziah Karch guide you through all of the features, tips, and tricks using their proven combination of clear instructions and detailed visuals. With hundreds of annotated screenshots and step-by-step directions, Droids Made Simple will transform you into a Droid expert, improving your productivity, and most importantly, helping you take advantage of all of the cool features that c

  18. Simple guide to Skype

    CERN Document Server

    Winter, Rick

    2013-01-01

    Simple Guides give you Just the Facts Get up to speed with Skypefast! Simple Guides: get you started quickly. No extra clutter, no extra reading. Learn how to set up Skype, as well as how to add and set up all your friends, family, and other contacts. Find out about all the features of Skype, how to change views, set your status and conduct video and audio only calls. Learn about all the different things you can do to contact your friends and family on Skype for free, and start having fun!

  19. Excel 2010 Made Simple

    CERN Document Server

    Katz, Abbott

    2011-01-01

    Get the most out of Excel 2010 with Excel 2010 Made Simple - learn the key features, understand what's new, and utilize dozens of time-saving tips and tricks to get your job done. Over 500 screen visuals and clear-cut instructions guide you through the features of Excel 2010, from formulas and charts to navigating around a worksheet and understanding Visual Basic for Applications (VBA) and macros. Excel 2010 Made Simple takes a practical and highly effective approach to using Excel 2010, showing you the best way to complete your most common spreadsheet tasks. You'll learn how to input, format,

  20. Simple cryogenic infrared window

    NARCIS (Netherlands)

    Hartemink, M.; Godfried, H.P.

    1991-01-01

    A simple, cheap technique is reported that allows materials with both large and small thermal expansion coefficients to be mounted as windows in low temperature cryostats while at the same time avoiding thermal stresses. The construction may be thermally cycled many times with no change in its prope

  1. Simple Kidney Cysts

    Science.gov (United States)

    ... ended or closed at one end; some newer machines are designed to allow the person to lie in a more open space. Like CT scans, MRIs can show cysts and tumors. [ Top ] How are simple kidney cysts treated? Treatment is not needed for ...

  2. Entropy Is Simple, Qualitatively.

    Science.gov (United States)

    Lambert, Frank L.

    2002-01-01

    Suggests that qualitatively, entropy is simple. Entropy increase from a macro viewpoint is a measure of the dispersal of energy from localized to spread out at a temperature T. Fundamentally based on statistical and quantum mechanics, this approach is superior to the non-fundamental "disorder" as a descriptor of entropy change. (MM)

  3. Beyond Simple Headquarters Configurations

    DEFF Research Database (Denmark)

    Dellestrand, Henrik; Kappen, Philip; Nell, Phillip Christopher

    -divisional importance and embeddedness effects are contingent on the overall complexity of the innovation project as signified by the size of the development network. The results lend support for the notion that parenting in complex structures entails complex headquarters structures and that we need to go beyond simple...

  4. Working with Simple Machines

    Science.gov (United States)

    Norbury, John W.

    2006-01-01

    A set of examples is provided that illustrate the use of work as applied to simple machines. The ramp, pulley, lever and hydraulic press are common experiences in the life of a student, and their theoretical analysis therefore makes the abstract concept of work more real. The mechanical advantage of each of these systems is also discussed so that…

  5. A Simple Hydrogen Electrode

    Science.gov (United States)

    Eggen, Per-Odd

    2009-01-01

    This article describes the construction of an inexpensive, robust, and simple hydrogen electrode, as well as the use of this electrode to measure "standard" potentials. In the experiment described here the students can measure the reduction potentials of metal-metal ion pairs directly, without using a secondary reference electrode. Measurements…

  6. Central simple Poisson algebras

    Institute of Scientific and Technical Information of China (English)

    SU; Yucai; XU; Xiaoping

    2004-01-01

    Poisson algebras are fundamental algebraic structures in physics and symplectic geometry. However, the structure theory of Poisson algebras has not been well developed. In this paper, we determine the structure of the central simple Poisson algebras related to locally finite derivations, over an algebraically closed field of characteristic zero.The Lie algebra structures of these Poisson algebras are in general not finitely-graded.

  7. Information technology made simple

    CERN Document Server

    Carter, Roger

    1991-01-01

    Information Technology: Made Simple covers the full range of information technology topics, including more traditional subjects such as programming languages, data processing, and systems analysis. The book discusses information revolution, including topics about microchips, information processing operations, analog and digital systems, information processing system, and systems analysis. The text also describes computers, computer hardware, microprocessors, and microcomputers. The peripheral devices connected to the central processing unit; the main types of system software; application soft

  8. Simple Finite Jordan Pseudoalgebras

    Directory of Open Access Journals (Sweden)

    Pavel Kolesnikov

    2009-01-01

    Full Text Available We consider the structure of Jordan H-pseudoalgebras which are linearly finitely generated over a Hopf algebra H. There are two cases under consideration: H = U(h and H = U(h # C[Γ], where h is a finite-dimensional Lie algebra over C, Γ is an arbitrary group acting on U(h by automorphisms. We construct an analogue of the Tits-Kantor-Koecher construction for finite Jordan pseudoalgebras and describe all simple ones.

  9. Modern mathematics made simple

    CERN Document Server

    Murphy, Patrick

    1982-01-01

    Modern Mathematics: Made Simple presents topics in modern mathematics, from elementary mathematical logic and switching circuits to multibase arithmetic and finite systems. Sets and relations, vectors and matrices, tesselations, and linear programming are also discussed.Comprised of 12 chapters, this book begins with an introduction to sets and basic operations on sets, as well as solving problems with Venn diagrams. The discussion then turns to elementary mathematical logic, with emphasis on inductive and deductive reasoning; conjunctions and disjunctions; compound statements and conditional

  10. Working with simple machines

    Science.gov (United States)

    Norbury, John W.

    2006-11-01

    A set of examples is provided that illustrate the use of work as applied to simple machines. The ramp, pulley, lever and hydraulic press are common experiences in the life of a student, and their theoretical analysis therefore makes the abstract concept of work more real. The mechanical advantage of each of these systems is also discussed so that students can evaluate their usefulness as machines.

  11. Working with simple machines

    OpenAIRE

    Norbury, John W.

    2006-01-01

    A set of examples is provided that illustrate the use of work as applied to simple machines. The ramp, pulley, lever and hydraulic press are common experiences in the life of a student and their theoretical analysis therefore makes the abstract concept of work more real. The mechanical advantage of each of these systems is also discussed so that students can evaluate their usefulness as machines.

  12. Optimising expression of the recombinant fusion protein biopesticide ω-hexatoxin-Hv1a /GNA in Pichia pastoris : sequence modifications and a simple method for the generation of multi-copy strains.

    OpenAIRE

    Pyati, P; Fitches, E.; Gatehouse, J A

    2014-01-01

    Production of recombinant protein bio-insecticides on a commercial scale can only be cost effective if host strains with very high expression levels are available. A recombinant fusion protein containing an arthropod toxin, ω-hexatoxin-Hv1a, (from funnel web spider Hadronyche versuta) linked to snowdrop lectin (Galanthus nivalis agglutinin; GNA) is an effective oral insecticide and candidate biopesticide. However, the fusion protein was vulnerable to proteolysis during production in the yeast...

  13. Dimensional analysis made simple

    Science.gov (United States)

    Lira, Ignacio

    2013-11-01

    An inductive strategy is proposed for teaching dimensional analysis to second- or third-year students of physics, chemistry, or engineering. In this strategy, Buckingham's theorem is seen as a consequence and not as the starting point. In order to concentrate on the basics, the mathematics is kept as elementary as possible. Simple examples are suggested for classroom demonstrations of the power of the technique and others are put forward for homework or experimentation, but instructors are encouraged to produce examples of their own.

  14. Applied mathematics made simple

    CERN Document Server

    Murphy, Patrick

    1982-01-01

    Applied Mathematics: Made Simple provides an elementary study of the three main branches of classical applied mathematics: statics, hydrostatics, and dynamics. The book begins with discussion of the concepts of mechanics, parallel forces and rigid bodies, kinematics, motion with uniform acceleration in a straight line, and Newton's law of motion. Separate chapters cover vector algebra and coplanar motion, relative motion, projectiles, friction, and rigid bodies in equilibrium under the action of coplanar forces. The final chapters deal with machines and hydrostatics. The standard and conte

  15. Dimensional analysis made simple

    International Nuclear Information System (INIS)

    An inductive strategy is proposed for teaching dimensional analysis to second- or third-year students of physics, chemistry, or engineering. In this strategy, Buckingham's theorem is seen as a consequence and not as the starting point. In order to concentrate on the basics, the mathematics is kept as elementary as possible. Simple examples are suggested for classroom demonstrations of the power of the technique and others are put forward for homework or experimentation, but instructors are encouraged to produce examples of their own. (paper)

  16. Theory of simple liquids

    CERN Document Server

    Hansen, Jean-Pierre

    1986-01-01

    This book gives a comprehensive and up-to-date treatment of the theory of ""simple"" liquids. The new second edition has been rearranged and considerably expanded to give a balanced account both of basic theory and of the advances of the past decade. It presents the main ideas of modern liquid state theory in a way that is both pedagogical and self-contained. The book should be accessible to graduate students and research workers, both experimentalists and theorists, who have a good background in elementary mechanics.Key Features* Compares theoretical deductions with experimental r

  17. Simple Driving Techniques

    DEFF Research Database (Denmark)

    Rosendahl, Mads

    2002-01-01

    Driving was introduced as a program transformation technique by Valentin Turchin in some papers around 1980. It was intended for the programming language REFAL and used in metasystem transitions based on super compilation. In this paper we present one version of driving for a more conventional lisp......-like language. Our aim is to extract a simple notion of driving and show that even in this tamed form it has much of the power of more general notions of driving. Our driving technique may be used to simplify functional programs which use function composition and will often be able to remove intermediate data...

  18. A Simple Quintessence Model

    CERN Document Server

    Bento, M C; Santos, N M C

    2008-01-01

    A simple model of quintessential inflation with the modified exponential potential $e^{-\\alpha \\phi} [A+(\\phi-\\phi_0)^2]$ is analyzed in the braneworld context. Considering reheating via instant preheating, we conclude that the model exhibits transient acceleration at late times for $0.96 \\lesssim A \\alpha^2 \\lesssim 1.26$ and $271 \\lesssim \\phi_0 \\alpha \\lesssim 273$, while permanent acceleration is obtained for $2.3\\times10^{-8} \\lesssim A \\alpha^2 \\lesssim 0.98$ and $255 \\lesssim \\phi_0 \\alpha \\lesssim 273$. The steep parameter $\\alpha$ is constrained to be in the range $5.3 \\lesssim \\alpha \\lesssim 10.8$.

  19. Data processing made simple

    CERN Document Server

    Wooldridge, Susan

    2013-01-01

    Data Processing: Made Simple, Second Edition presents discussions of a number of trends and developments in the world of commercial data processing. The book covers the rapid growth of micro- and mini-computers for both home and office use; word processing and the 'automated office'; the advent of distributed data processing; and the continued growth of database-oriented systems. The text also discusses modern digital computers; fundamental computer concepts; information and data processing requirements of commercial organizations; and the historical perspective of the computer industry. The

  20. Electronics made simple

    CERN Document Server

    Olsen, George H

    1987-01-01

    Electronics: Made Simple covers the fundamental principles, basic devices, characteristics, and application of electronic equipment.This book is divided into 15 chapters and begins with reviews of the properties and behavior of resistors, capacitors, inductors, and semiconductor devices. Considerable chapters deal with how these devices can be assembled into useful fundamental circuits such as amplifiers, oscillators and power supplies. These topics are followed by discussions of the importance of integrated circuits and the use of digital equipment and photocells in control and computing appa

  1. ASP made simple

    CERN Document Server

    Deane, Sharon

    2003-01-01

    ASP Made Simple provides a brief introduction to ASP for the person who favours self teaching and/or does not have expensive computing facilities to learn on. The book will demonstrate how the principles of ASP can be learned with an ordinary PC running Personal Web Server, MS Access and a general text editor like Notepad.After working through the material readers should be able to:* Write ASP scripts that can display changing information on a web browser* Request records from a remote database or add records to it* Check user names & passwords and take this knowledge forward, either for their

  2. Program For Simple Algebra

    International Nuclear Information System (INIS)

    PFSA (Program For Simple Algebra) is designed to be helpful to people doing algebra and calculus with polynomial expressions. It is written entirely in Fortran and hence is portable and easily modified. It is much (approximately 90 times) faster than Macsyma. PFSA uses Fortran integer arithmetic to compute coefficients, and so the occurrence of an excessively large number in a numerator or denominator during a computation bombs the computation. The program was developed to enable a computation (of a canonical transformation for a Hamiltonian system) which was too big to be run in other systems available at the time. The intent in creating PFSA was to make a program which would do the Hamiltonian computation and similar computations easily and fast. The only language available (on the Cray) was Fortran. Example C in Section III is a very simple canonical transformation. In running the problem for which PFSA was written some intermediate expressions have more than 20,000 terms and some answers have more than 1000 terms

  3. Molecular genetics made simple

    Directory of Open Access Journals (Sweden)

    Heba Sh. Kassem

    2012-07-01

    Full Text Available Genetics have undoubtedly become an integral part of biomedical science and clinical practice, with important implications in deciphering disease pathogenesis and progression, identifying diagnostic and prognostic markers, as well as designing better targeted treatments. The exponential growth of our understanding of different genetic concepts is paralleled by a growing list of genetic terminology that can easily intimidate the unfamiliar reader. Rendering genetics incomprehensible to the clinician however, defeats the very essence of genetic research: its utilization for combating disease and improving quality of life. Herein we attempt to correct this notion by presenting the basic genetic concepts along with their usefulness in the cardiology clinic. Bringing genetics closer to the clinician will enable its harmonious incorporation into clinical care, thus not only restoring our perception of its simple and elegant nature, but importantly ensuring the maximal benefit for our patients.

  4. On Simple Noetherian Rings

    Institute of Scientific and Technical Information of China (English)

    Somyot Plubtieng

    2003-01-01

    A module M is called a CS-module (or extending module [5]) if every submodule of M is essential in a direct summand of M. It is shown that (i) a simple ring R is right noetherian if and only if every cyclic singular right R-module is either a CS-module or a noetherian module; (ii) for a prime ring R, if every proper cyclic right R-module is a direct sum of a quasi-injective module and a finitely cogenerated module, then R is either semisimple artinian or a right Ore domain; and (iii) a prime ring R is right noetherian if and only if every cyclic right R-module is a direct sum of a quasi-injective module and a noetherian module.

  5. SIMPLE LIFE AND RELIGION

    Directory of Open Access Journals (Sweden)

    Ahmet YILDIRIM

    2014-07-01

    Full Text Available Individuals in terms of the economy in which we live is one of the most important phenomenon of the century. This phenomenon present itself as the only determinant of people's lives by entering almost makes itself felt. The mo st obvious objective needs of the economy by triggering motive is to induce people to consume . Consumer culture pervades all aspects of the situation are people . Therefore, these people have the blessing of culture , beauty and value all in the name of w hatever is consumed. This is way out of the siege of moral and religious values we have is to go back again . Referred by local cultural and religious values, based on today increasingly come to the fore and the Muslim way of life appears to be close to th e plain / lean preferred by many people life has been a way of life. Even the simple life , a way of life in the Western world , a conception of life , a philosophy, a movement as it has become widely accepted. Here in determining the Muslim way of life Pr ophet. Prophet (sa lived the kind of life a very important model, sample, and determining which direction is known. Religious values, which is the carrier of the prophets, sent to the society they have always been examples and models. Because every aspect of human life, his life style and the surrounding area has a feature. We also value his life that he has unknowingly and without learning and skills and to understand it is not possible to live our religion . We also our presentation, we mainly of Islam o utlook on life and predicted life - style, including the Prophet of Islam 's (sa simple life to scrutinize and lifestyle issues related to reveal , in short Islam's how life has embraced and the Prophet. Prophet's will try to find answers to questions reg arding how to live.

  6. Complexity in `simple' metals

    Science.gov (United States)

    Rousseau, Bruno; Ashcroft, Neil W.

    2008-03-01

    In electronic and structural terms, the light alkalis have long been regarded as `simple systems', at least under ordinary conditions. However, when compressed they exhibit unforeseen complexity; the melting curve of sodium, for example, has a striking maximum, falling to near room temperature melting where a complex structure (CI16) is found, this being in the cubic class but with 16 atoms per unit cell [1,2]. The light alkalis have been extensively studied using ab initio methods with standard assumptions of transferability made for the key pseudopotential input information, largely atomic based. Lacking still, however, is a somewhat more intuitive and physical understanding of the developments in electronic structure with progressive increase in density. In the present work, the problem is treated with non-linear response theory and non-overlapping pseudopotentials, and the structural complexity traced to effective ion-ion interactions with features that both at short range and long display competing state dependence. [1] Gregoryanz et al., Phys. Rev. Lett. 94, 185502 (2005) [2] McMahon et al., Chem. Soc. Rev. 35, 943 (2006)

  7. Quasispecies made simple.

    Directory of Open Access Journals (Sweden)

    J J Bull

    2005-11-01

    Full Text Available Quasispecies are clouds of genotypes that appear in a population at mutation-selection balance. This concept has recently attracted the attention of virologists, because many RNA viruses appear to generate high levels of genetic variation that may enhance the evolution of drug resistance and immune escape. The literature on these important evolutionary processes is, however, quite challenging. Here we use simple models to link mutation-selection balance theory to the most novel property of quasispecies: the error threshold-a mutation rate below which populations equilibrate in a traditional mutation-selection balance and above which the population experiences an error catastrophe, that is, the loss of the favored genotype through frequent deleterious mutations. These models show that a single fitness landscape may contain multiple, hierarchically organized error thresholds and that an error threshold is affected by the extent of back mutation and redundancy in the genotype-to-phenotype map. Importantly, an error threshold is distinct from an extinction threshold, which is the complete loss of the population through lethal mutations. Based on this framework, we argue that the lethal mutagenesis of a viral infection by mutation-inducing drugs is not a true error catastophe, but is an extinction catastrophe.

  8. IVOA Simple Image Access

    CERN Document Server

    Dowler, Patrick; Bonnarel, François

    2016-01-01

    The Simple Image Access protocol (SIA) provides capabilities for the discovery, description, access, and retrieval of multi-dimensional image datasets, including 2-D images as well as datacubes of three or more dimensions. SIA data discovery is based on the ObsCore Data Model (ObsCoreDM), which primarily describes data products by the physical axes (spatial, spectral, time, and polarization). Image datasets with dimension greater than 2 are often referred to as datacubes, cube or image cube datasets and may be considered examples of hypercube or n-cube data. In this document the term "image" refers to general multi-dimensional datasets and is synonymous with these other terms unless the image dimensionality is otherwise specified. SIA provides capabilities for image discovery and access. Data discovery and metadata access (using ObsCoreDM) are defined here. The capabilities for drilling down to data files (and related resources) and services for remote access are defined elsewhere, but SIA also allows for dir...

  9. A Simple Accelerometer Calibrator

    Science.gov (United States)

    Salam, R. A.; Islamy, M. R. F.; Munir, M. M.; Latief, H.; Irsyam, M.; Khairurrijal

    2016-08-01

    High possibility of earthquake could lead to the high number of victims caused by it. It also can cause other hazards such as tsunami, landslide, etc. In that case it requires a system that can examine the earthquake occurrence. Some possible system to detect earthquake is by creating a vibration sensor system using accelerometer. However, the output of the system is usually put in the form of acceleration data. Therefore, a calibrator system for accelerometer to sense the vibration is needed. In this study, a simple accelerometer calibrator has been developed using 12 V DC motor, optocoupler, Liquid Crystal Display (LCD) and AVR 328 microcontroller as controller system. The system uses the Pulse Wave Modulation (PWM) form microcontroller to control the motor rotational speed as response to vibration frequency. The frequency of vibration was read by optocoupler and then those data was used as feedback to the system. The results show that the systems could control the rotational speed and the vibration frequencies in accordance with the defined PWM.

  10. The simple harmonic urn

    CERN Document Server

    Crane, Edward; Volkov, Stanislav; Wade, Andrew; Waters, Robert

    2009-01-01

    We study a generalized Polya urn model with two types of ball. If the drawn ball is red it is replaced together with a black ball, but if the drawn ball is black it is replaced and a red ball is thrown out of the urn. When only black balls remain, the roles of the colours are swapped and the process restarts. We prove that the resulting Markov chain is transient but that if we throw out a ball every time the colours swap, the process is positive-recurrent. We show that the embedded process obtained by observing the number of balls in the urn at the swapping times has a scaling limit that is essentially the square of a Bessel diffusion. We consider an oriented percolation model naturally associated with the urn process, and obtain detailed information about its structure, showing that the open subgraph is an infinite tree with a single end. We also study a natural continuous-time embedding of the urn process that demonstrates the relation to the simple harmonic oscillator; in this setting our transience result...

  11. Roughly Weighted Hierarchical Simple Games

    OpenAIRE

    Hameed, Ali; Slinko, Arkadii

    2012-01-01

    Hierarchical simple games - both disjunctive and conjunctive - are natural generalizations of simple majority games. They take their origin in the theory of secret sharing. Another important generalization of simple majority games with origin in economics and politics are weighted and roughly weighted majority games. In this paper we characterize roughly weighted hierarchical games identifying where the two approaches coincide.

  12. Amazon SimpleDB LITE

    CERN Document Server

    Chaganti, Prabhakar

    2011-01-01

    This focused book is an extracted LITE version of Packt's full: Amazon SimpleDB Developer Guide. It concentrates on getting a grounding in the value of SimpleDB, and shows how to set up an AWS account, enable a SimpleDB service for the account, and install and set up libraries for Java, PHP, and Python. If you are a developer wanting to get to grips with a primer into SimpleDB, then this book is for you. You do not need to know anything about SimpleDB to read and learn from this book, and no basic knowledge is strictly necessary.

  13. Simple high-cell density fed-batch technique for high-level recombinant protein production with Pichia pastoris: Application to intracellular production of Hepatitis B surface antigen

    OpenAIRE

    Ross Anton; Lünsdorf Heinrich; Gäbel Thomas; Adnan Ahmad; Gurramkonda Chandrasekhar; Nemani Satish; Swaminathan Sathyamangalam; Khanna Navin; Rinas Ursula

    2009-01-01

    Abstract Background Hepatitis B is a serious global public health concern. Though a safe and efficacious recombinant vaccine is available, its use in several resource-poor countries is limited by cost. We have investigated the production of Hepatitis B virus surface antigen (HBsAg) using the yeast Pichia pastoris GS115 by inserting the HBsAg gene into the alcohol oxidase 1 locus. Results Large-scale production was optimized by developing a simple fed-batch process leading to enhanced product ...

  14. Una historia muy simple

    Directory of Open Access Journals (Sweden)

    Miha Mazzini

    2009-12-01

    Full Text Available Voy a contarles una historia muy simple. Probablemente no les parecerá nada espe- cial y no quiero robarles tiempo, así que voy a tratar de hacerlo lo más rápido posible. Me inscribí en psicología porque eso hizo mi mejor amiga. Éramos compañeras desde jardín de infantes y siempre la seguí en todo. En tercer año de facultad conoció a su novio y continuó sus estudios en otro país; por primera vez no podía seguirla. Cuando rendí todos los exámenes, el profesor me preguntó si estaba interesada en hacer mi tesis sobre el perfil psicológico de los participantes de reality shows. Accedí para no tener que pensar en otro tema, aunque no veía mucho la televisión porque me pasaba las noches entre los libros de estudio. Enseguida me di cuenta de que, evidentemente, el profesor había firmado un contrato con la emisora: a él lo empleaban y y yo era la que iba a tener que trabajar, pero no me importaba. La tesis de licenciatura no es más que eso y hay que hacerla. Yo evaluaba los candidatos y elegía a los participantes que vivirían juntos duran- te algunos meses. Como hacían el programa con una licencia extranjera y ya sabían qué le interesaba a la audiencia, yo tenía preparados los rasgos de los perfiles psicológicos que en ese aislamiento colectivo no resultan bien. Tuve que elegir gente variada, pero dentro de la media; nunca nada verdaderamente especial. Cuando me gradué, tuve las noches libres: de pronto tenía mucho más tiempo y podía haber visto el programa, pero ya había terminado. Pero oí que había sido todo un éxito y que sobre todo a los chicos les había encantado el reality y los participantes elegidos.

  15. Simple Algebras of Invariant Operators

    Institute of Scientific and Technical Information of China (English)

    Xiaorong Shen; J.D.H. Smith

    2001-01-01

    Comtrans algebras were introduced in as algebras with two trilinear operators, a commutator [x, y, z] and a translator , which satisfy certain identities. Previously known simple comtrans algebras arise from rectangular matrices, simple Lie algebras, spaces equipped with a bilinear form having trivial radical, spaces of hermitian operators over a field with a minimum polynomial x2+1. This paper is about generalizing the hermitian case to the so-called invariant case. The main result of this paper shows that the vector space of n-dimensional invariant operators furnishes some comtrans algebra structures, which are simple provided that certain Jordan and Lie algebras are simple.

  16. On Simple-Injective Rings

    Institute of Scientific and Technical Information of China (English)

    W.K. Nicholson; Jae Keol Park; M.F. Yousif

    2002-01-01

    A ring R is called right simple-injective if every R-linear map from a right ideal of R to R with simple image can be extended to R. It is shown that a right simple-injective ring R is quasi-Frobenius if R is right Goldie with essential right socle, or R is left perfect and the right annihilator of k ∈ R is finitely generated whenever kR or Rk is simple. This extends a result of Bjork.

  17. Establishment of a simple cell-based ELISA for the direct detection of abnormal isoform of prion protein from prion-infected cells without cell lysis and proteinase K treatment.

    Science.gov (United States)

    Shan, Zhifu; Yamasaki, Takeshi; Suzuki, Akio; Hasebe, Rie; Horiuchi, Motohiro

    2016-07-01

    Prion-infected cells have been used for analyzing the effect of compounds on the formation of abnormal isoform of prion protein (PrP(Sc)). PrP(Sc) is usually detected using anti-prion protein (PrP) antibodies after the removal of the cellular isoform of prion protein (PrP(C)) by proteinase K (PK) treatment. However, it is expected that the PK-sensitive PrP(Sc) (PrP(Sc)-sen), which possesses higher infectivity and conversion activity than the PK-resistant PrP(Sc) (PrP(Sc)-res), is also digested through PK treatment. To overcome this problem, we established a novel cell-based ELISA in which PrP(Sc) can be directly detected from cells persistently infected with prions using anti-PrP monoclonal antibody (mAb) 132 that recognizes epitope consisting of mouse PrP amino acids 119-127. The novel cell-based ELISA could distinguish prion-infected cells from prion-uninfected cells without cell lysis and PK treatment. MAb 132 could detect both PrP(Sc)-sen and PrP(Sc)-res even if all PrP(Sc) molecules were not detected. The analytical dynamic range for PrP(Sc) detection was approximately 1 log. The coefficient of variation and signal-to-background ratio were 7%-11% and 2.5-3.3, respectively, demonstrating the reproducibility of this assay. The addition of a cytotoxicity assay immediately before PrP(Sc) detection did not affect the following PrP(Sc) detection. Thus, all the procedures including cell culture, cytotoxicity assay, and PrP(Sc) detection were completed in the same plate. The simplicity and non-requirement for cell lysis or PK treatment are advantages for the high throughput screening of anti-prion compounds. PMID:27565564

  18. Establishment of a simple cell-based ELISA for the direct detection of abnormal isoform of prion protein from prion-infected cells without cell lysis and proteinase K treatment.

    Science.gov (United States)

    Shan, Zhifu; Yamasaki, Takeshi; Suzuki, Akio; Hasebe, Rie; Horiuchi, Motohiro

    2016-07-01

    Prion-infected cells have been used for analyzing the effect of compounds on the formation of abnormal isoform of prion protein (PrP(Sc)). PrP(Sc) is usually detected using anti-prion protein (PrP) antibodies after the removal of the cellular isoform of prion protein (PrP(C)) by proteinase K (PK) treatment. However, it is expected that the PK-sensitive PrP(Sc) (PrP(Sc)-sen), which possesses higher infectivity and conversion activity than the PK-resistant PrP(Sc) (PrP(Sc)-res), is also digested through PK treatment. To overcome this problem, we established a novel cell-based ELISA in which PrP(Sc) can be directly detected from cells persistently infected with prions using anti-PrP monoclonal antibody (mAb) 132 that recognizes epitope consisting of mouse PrP amino acids 119-127. The novel cell-based ELISA could distinguish prion-infected cells from prion-uninfected cells without cell lysis and PK treatment. MAb 132 could detect both PrP(Sc)-sen and PrP(Sc)-res even if all PrP(Sc) molecules were not detected. The analytical dynamic range for PrP(Sc) detection was approximately 1 log. The coefficient of variation and signal-to-background ratio were 7%-11% and 2.5-3.3, respectively, demonstrating the reproducibility of this assay. The addition of a cytotoxicity assay immediately before PrP(Sc) detection did not affect the following PrP(Sc) detection. Thus, all the procedures including cell culture, cytotoxicity assay, and PrP(Sc) detection were completed in the same plate. The simplicity and non-requirement for cell lysis or PK treatment are advantages for the high throughput screening of anti-prion compounds.

  19. Simple Distillation and Fractional Distillation

    Institute of Scientific and Technical Information of China (English)

    张萍

    2004-01-01

    A pure solvent can be separated from a solution by simple distillation. Distillation is the process of boiling a liquid and condensing the vapor. For example, pure water can be obtained from salt solution by distillation. The figure below shows the apparatus used for simple distillation in the laboratory.

  20. Simple algebras of Weyl type

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Over a field F of arbitrary characteristic, we define the associative and the Lie algebras of Weyl type on the same vector space A[D]=A[D] from any pair of a commutative associative algebra A with an identity element and the polynomial algebra [D] of a commutative derivation subalgebra D of A. We prove that A[D], as a Lie algebra (modulo its center) or as an associative algebra, is simple if and only if A is D-simple and A[D] acts faithfully on A. Thus we obtain a lot of simple algebras.

  1. Simple ocean carbon cycle models

    Energy Technology Data Exchange (ETDEWEB)

    Caldeira, K. [Lawrence Livermore National Lab., CA (United States); Hoffert, M.I. [New York Univ., NY (United States). Dept. of Earth System Sciences; Siegenthaler, U. [Bern Univ. (Switzerland). Inst. fuer Physik

    1994-02-01

    Simple ocean carbon cycle models can be used to calculate the rate at which the oceans are likely to absorb CO{sub 2} from the atmosphere. For problems involving steady-state ocean circulation, well calibrated ocean models produce results that are very similar to results obtained using general circulation models. Hence, simple ocean carbon cycle models may be appropriate for use in studies in which the time or expense of running large scale general circulation models would be prohibitive. Simple ocean models have the advantage of being based on a small number of explicit assumptions. The simplicity of these ocean models facilitates the understanding of model results.

  2. Modeling Protein Domain Function

    Science.gov (United States)

    Baker, William P.; Jones, Carleton "Buck"; Hull, Elizabeth

    2007-01-01

    This simple but effective laboratory exercise helps students understand the concept of protein domain function. They use foam beads, Styrofoam craft balls, and pipe cleaners to explore how domains within protein active sites interact to form a functional protein. The activity allows students to gain content mastery and an understanding of the…

  3. Simple manipulator for rotating spheres

    International Nuclear Information System (INIS)

    We describe a simple device for rapidly rotating a small sphere to any orientation for inspection of the surface. The ball is held between two small, flat surfaces and rolls as the surfaces are moved differentially parallel to one another

  4. The Simple Publishing Interface (SPI)

    NARCIS (Netherlands)

    Ternier, Stefaan; Massart, David; Totschnig, Michael; Klerkx, Joris; Duval, Erik

    2010-01-01

    Ternier, S., Massart, D., Totschnig, M., Klerkx, J., & Duval, E. (2010). The Simple Publishing Interface (SPI). D-Lib Magazine, September/October 2010, Volume 16 Number 9/10, doi:10.1045/september2010-ternier

  5. Simple device measures solar radiation

    Science.gov (United States)

    Humphries, W. R.

    1977-01-01

    Simple inexpensive thermometer, insolated from surroundings by transparent glass or plastic encasement, measures intensities of solar radiation, or radiation from other sources such as furnaces or ovens. Unit can be further modified to accomplish readings from remote locations.

  6. On Conditional Simple Random Sample

    OpenAIRE

    Wywiał, Janusz L.

    2014-01-01

    Estimation of the population average in a finite and fixed population on the basis of the conditional simple random sampling design dependent on order statistics of the auxiliary variable is studied. The sampling scheme implementing the sampling design is proposed. The inclusion probabilities are derived. The well known Horvitz-Thompson statistic under the conditional simple random sampling designs is considered as the estimator of population mean. Moreover, it was shown that the Horvitz-Thom...

  7. Simple machines made simple a teacher resource manual

    CERN Document Server

    Andre, Ralph E St

    1993-01-01

    This book allows you to present scientific principles and simple mechanics through hands-on cooperative learning activities. Using inexpensive materials (e.g., tape, paper clips), students build simple machines-such as levers, pulleys, spring scales, gears, wheels and axles, windmills, and wedges-that demonstrate how things work. Activities have easy-to-locate materials lists, time requirements, and step-by-step directions (usually illustrated) on presentation. Ideas for bulletin boards, learning centers, and computer-assisted instruction are an added bonus.

  8. Complex Autocatalysis in Simple Chemistries.

    Science.gov (United States)

    Virgo, Nathaniel; Ikegami, Takashi; McGregor, Simon

    2016-01-01

    Life on Earth must originally have arisen from abiotic chemistry. Since the details of this chemistry are unknown, we wish to understand, in general, which types of chemistry can lead to complex, lifelike behavior. Here we show that even very simple chemistries in the thermodynamically reversible regime can self-organize to form complex autocatalytic cycles, with the catalytic effects emerging from the network structure. We demonstrate this with a very simple but thermodynamically reasonable artificial chemistry model. By suppressing the direct reaction from reactants to products, we obtain the simplest kind of autocatalytic cycle, resulting in exponential growth. When these simple first-order cycles are prevented from forming, the system achieves superexponential growth through more complex, higher-order autocatalytic cycles. This leads to nonlinear phenomena such as oscillations and bistability, the latter of which is of particular interest regarding the origins of life.

  9. Acupuncture Treatment of Simple Obesity

    Institute of Scientific and Technical Information of China (English)

    Wei Qunli; Liu Zhicheng

    2005-01-01

    In order to investigate the therapeutic effects of ear acupuncture, body acupuncture and the combined use of the two in the treatment of simple obesity, 195 cases of obesity were divided into three groups, in which different reinforcing and reducing methods were applied according to their symptoms and signs.The effects of body acupuncture and body plus ear acupuncture were obviously superior to that of ear acupuncture, and the combined use of ear acupuncture and body acupuncture was better than that of simple body acupuncture.

  10. The simple ethers of glycerin

    International Nuclear Information System (INIS)

    From glycerin derivatives the considerable interest is present simple ethers because many of them are biological active and found wide practical using as an effect drugs, inters for thin organic synthesis, vehicle for injections, regulators of plants growth, reagents, components for perfumery-cosmetic goods and etc

  11. Simple Machines Curriculum. [Teachers' Manual.

    Science.gov (United States)

    Anoka-Hennepin Independent School District No. 11, Coon Rapids, MN.

    This manual provides suggestions for investigating simple machines and the teaching of certain basic concepts which pertain to them. Many of the lessons are designed to be used with the commercially available LEGO kits, in an effort to teach concepts in a way in which students must translate pictures shown in two dimension into three-dimensional…

  12. Simple Machines in the Community

    Science.gov (United States)

    Bryan, Robert; Laroder, Aris; Tippins, Deborah; Emaz, Meliza; Fox, Ryan

    2008-01-01

    The community can be a powerful context and mini-laboratory for cultivating students' common understandings of science and mathematics. On the island of Panay in the Philippines, the community was the starting place for a group of fifth- and sixth-grade students to explore simple machines in their daily lives. What students learned in the process…

  13. Simple Games . . . or Are They?

    Science.gov (United States)

    Arn, Susan Kyle

    2006-01-01

    Students today begin using computers and playing video games as early as two years old. The technology behind these games is more complicated than most people can imagine. In this article, the author presents some simple number games which seem easy at the beginning, but as the games are repeated, mathematical content becomes more of the focus…

  14. A Simple Relativistic Bohr Atom

    Science.gov (United States)

    Terzis, Andreas F.

    2008-01-01

    A simple concise relativistic modification of the standard Bohr model for hydrogen-like atoms with circular orbits is presented. As the derivation requires basic knowledge of classical and relativistic mechanics, it can be taught in standard courses in modern physics and introductory quantum mechanics. In addition, it can be shown in a class that…

  15. Solving Simple Kinetics without Integrals

    Science.gov (United States)

    de la Pen~a, Lisandro Herna´ndez

    2016-01-01

    The solution of simple kinetic equations is analyzed without referencing any topic from differential equations or integral calculus. Guided by the physical meaning of the rate equation, a systematic procedure is used to generate an approximate solution that converges uniformly to the exact solution in the case of zero, first, and second order…

  16. Simple Indolizidine and Quinolizidine Alkaloids.

    Science.gov (United States)

    Michael, Joseph P

    2016-01-01

    This review of simple indolizidine and quinolizidine alkaloids (i.e., those in which the parent bicyclic systems are in general not embedded in polycyclic arrays) is an update of the previous coverage in Volume 55 of this series (2001). The present survey covers the literature from mid-1999 to the end of 2013; and in addition to aspects of the isolation, characterization, and biological activity of the alkaloids, much emphasis is placed on their total synthesis. A brief introduction to the topic is followed by an overview of relevant alkaloids from fungal and microbial sources, among them slaframine, cyclizidine, Steptomyces metabolites, and the pantocins. The important iminosugar alkaloids lentiginosine, steviamine, swainsonine, castanospermine, and related hydroxyindolizidines are dealt with in the subsequent section. The fourth and fifth sections cover metabolites from terrestrial plants. Pertinent plant alkaloids bearing alkyl, functionalized alkyl or alkenyl substituents include dendroprimine, anibamine, simple alkaloids belonging to the genera Prosopis, Elaeocarpus, Lycopodium, and Poranthera, and bicyclic alkaloids of the lupin family. Plant alkaloids bearing aryl or heteroaryl substituents include ipalbidine and analogs, secophenanthroindolizidine and secophenanthroquinolizidine alkaloids (among them septicine, julandine, and analogs), ficuseptine, lasubines, and other simple quinolizidines of the Lythraceae, the simple furyl-substituted Nuphar alkaloids, and a mixed quinolizidine-quinazoline alkaloid. The penultimate section of the review deals with the sizable group of simple indolizidine and quinolizidine alkaloids isolated from, or detected in, ants, mites, and terrestrial amphibians, and includes an overview of the "dietary hypothesis" for the origin of the amphibian metabolites. The final section surveys relevant alkaloids from marine sources, and includes clathryimines and analogs, stellettamides, the clavepictines and pictamine, and bis

  17. Simple fixed functional space maintainer.

    Science.gov (United States)

    Goenka, Puneet; Sarawgi, Aditi; Marwah, Nikhil; Gumber, Parvind; Dutta, Samir

    2014-01-01

    Premature loss of a primary tooth is one of the most common etiology for malocclusion. Space maintainers are employed to prevent this complication. In anterior region, esthetics is an important concern along with function and space management. Fiber-reinforced composite (FRC) retained space maintainer solves all these purposes ef ficiently and ef fectively. In addition, the technique is simple and the appliance is very comfortable inside the oral cavity. Here is a case of premature loss of anterior primary tooth which was replaced by FRC retained esthetic functional space maintainer. The appliance was found to be functioning satisfactorily inside the oral cavity till the last visit (1 Year). How to cite this article: Goenka P, Sarawgi A, Marwah N, Gumber P, Dutta S. Simple Fixed Functional Space Maintainer. Int J Clin Pediatr Dent 2014;7(3):225-228.

  18. Webcam classification using simple features

    Science.gov (United States)

    Pramoun, Thitiporn; Choe, Jeehyun; Li, He; Chen, Qingshuang; Amornraksa, Thumrongrat; Lu, Yung-Hsiang; Delp, Edward J.

    2015-03-01

    Thousands of sensors are connected to the Internet and many of these sensors are cameras. The "Internet of Things" will contain many "things" that are image sensors. This vast network of distributed cameras (i.e. web cams) will continue to exponentially grow. In this paper we examine simple methods to classify an image from a web cam as "indoor/outdoor" and having "people/no people" based on simple features. We use four types of image features to classify an image as indoor/outdoor: color, edge, line, and text. To classify an image as having people/no people we use HOG and texture features. The features are weighted based on their significance and combined. A support vector machine is used for classification. Our system with feature weighting and feature combination yields 95.5% accuracy.

  19. Simple model of hydrophobic hydration.

    Science.gov (United States)

    Lukšič, Miha; Urbic, Tomaz; Hribar-Lee, Barbara; Dill, Ken A

    2012-05-31

    Water is an unusual liquid in its solvation properties. Here, we model the process of transferring a nonpolar solute into water. Our goal was to capture the physical balance between water's hydrogen bonding and van der Waals interactions in a model that is simple enough to be nearly analytical and not heavily computational. We develop a 2-dimensional Mercedes-Benz-like model of water with which we compute the free energy, enthalpy, entropy, and the heat capacity of transfer as a function of temperature, pressure, and solute size. As validation, we find that this model gives the same trends as Monte Carlo simulations of the underlying 2D model and gives qualitative agreement with experiments. The advantages of this model are that it gives simple insights and that computational time is negligible. It may provide a useful starting point for developing more efficient and more realistic 3D models of aqueous solvation. PMID:22564051

  20. Simple Fixed Functional Space Maintainer

    OpenAIRE

    Goenka, Puneet; Sarawgi, Aditi; Marwah, Nikhil; Gumber, Parvind; Dutta, Samir

    2015-01-01

    ABSTRACT% Premature loss of a primary tooth is one of the most common etiology for malocclusion. Space maintainers are employed to prevent this complication. In anterior region, esthetics is an important concern along with function and space management. Fiber-reinforced composite (FRC) retained space maintainer solves all these purposes ef ficiently and ef fectively. In addition, the technique is simple and the appliance is very comfortable inside the oral cavity. Here is a case of premature ...

  1. SIMPLE INNOVATION OF FINANCIAL ASSET

    Institute of Scientific and Technical Information of China (English)

    ZHANG Shunming

    2001-01-01

    This paper presents a simple two-period model of the innovationof financial asset by commission-revenue maximization exchange. The economic agents with meanvariance preferences take transaction costs in the process of trading the financial asset, the buying per-unit commission of the futures contract and the selling per-unit commission of the financial asset. The commission-revenue maximization exchange innovates financial asset.

  2. Classification of simple current invariants

    CERN Document Server

    Gato-Rivera, Beatriz

    1992-01-01

    We summarize recent work on the classification of modular invariant partition functions that can be obtained with simple currents in theories with a center (Z_p)^k with p prime. New empirical results for other centers are also presented. Our observation that the total number of invariants is monodromy-independent for (Z_p)^k appears to be true in general as well. (Talk presented in the parallel session on string theory of the Lepton-Photon/EPS Conference, Geneva, 1991.)

  3. Classification of Simple Current Invariants

    CERN Document Server

    Gato-Rivera, Beatriz

    1991-01-01

    We summarize recent work on the classification of modular invariant partition functions that can be obtained with simple currents in theories with a center (Z_p)^k with p prime. New empirical results for other centers are also presented. Our observation that the total number of invariants is monodromy-independent for (Z_p)^k appears to be true in general as well. (Talk presented in the parallel session on string theory of the Lepton-Photon/EPS Conference, Geneva, 1991.)

  4. Simple algebras of Weyl type

    Institute of Scientific and Technical Information of China (English)

    SU; Yucai(

    2001-01-01

    [1] Kawamoto, N., Generalizations of Witt algebras over a field of characteristic zero, Hiroshima Math. J., 1986, 16: 417.[2] Osborn, J. M., New simple infinite-dimensional Lie algebras of characteristic 0, J. Alg., 1996, 185: 820.[3] Dokovic, D. Z., Zhao, K., Derivations, isomorphisms, and second cohomology of generalized Witt algebras, Trans. of Amer. Math. Soc., 1998, 350(2): 643.[4] Dokovic, D. Z., Zhao, K., Generalized Cartan type W Lie algebras in characteristic zero, J. Alg., 1997, 195: 170.[5] Osborn, J. M., Zhao, K., Generalized Poisson bracket and Lie algebras of type H in characteristic 0, Math. Z., 1999, 230: 107.[6] Osborn, J. M., Zhao, K., Generalized Cartan type K Lie algebras in characteristic 0, Comm. Alg., 1997, 25: 3325.[7] Zhao, K., Isomorphisms between generalized Cartan type W Lie algebras in characteristic zero, Canadian J. Math., 1998, 50: 210.[8] Passman, D. P., Simple Lie algebras of Witt type, J. Algebra, 1998, 206: 682.[9] Jordan, D. A., On the simplicity of Lie algebras of derivations of commutative algebras, J. Alg., 2000, 206: 682.[10] Xu, X., New generalized simple Lie algebras of Cartan type over a field with characteristic 0, J. Alg., 2000, 244: 23.[11] Su, Y., Xu, X., Zhang, H., Derivation-simple algebras and the structures of Lie algebras of generalized Witt type, J. Alg., 2000, 233: 642.[12] Dixmer, J., Enveloping Algebras, Amsterdam: North Holland, 1977.

  5. SIMPLE THOUGHTS IN ECONOMIC LIFE

    Directory of Open Access Journals (Sweden)

    Ahmet YILDIRIM

    2015-07-01

    Full Text Available One of the most important realities of our life is econ omy. This reality is such a thing that determines alone all over the life of the human being. The most crucial aims of economy is directing people to spent mony by triggering the instinct of individuals’ need. The culture of consumption not only embraces a ll the life of individuals but does it couses of the crises of the society. Although it depends on the time, surroundings and characters of individual, the understanding of simple life represents an idea that people shlould consume more than they need. It is well known that most of the problems in the world arouses from the bad usages of the natural sources of the world. The sources of the world is limited and is decreasing time by time. Becuase of this reality people need to use natural sorcers very caref ully. In order to control the sources, responsible institutions, governments and people must advise and suggest to individuals to be carefull in using the money and the sources. They should teach the people to live in a simple life without spending sources too much. In this study, at the beginning, consumption which couses the economical and financial crises will be handled, secondly the characteristics of simple life will be discussed and lastly the relationships between simple life and economy will be exa mined. At the end, the way in which the solutions might take place will be shown and some suggestions will be directed to the people.

  6. Simple and Realistic Data Generation

    DEFF Research Database (Denmark)

    Pedersen, Kenneth Houkjær; Torp, Kristian; Wind, Rico

    2006-01-01

    This paper presents a generic, DBMS independent, and highly extensible relational data generation tool. The tool can efficiently generate realistic test data for OLTP, OLAP, and data streaming applications. The tool uses a graph model to direct the data generation. This model makes it very simple...... to generate data even for large database schemas with complex inter- and intra table relationships. The model also makes it possible to generate data with very accurate characteristics....

  7. Comparing Simple Quasar Demographics Models

    CERN Document Server

    Veale, Melanie; Conroy, Charlie

    2014-01-01

    This paper explores several simple model variations for the connections among quasars, galaxies, and dark matter halos for redshifts 1 < z < 6. A key component of these models is that we enforce a self-consistent black hole (BH) history by tracking both BH mass and BH growth rate at all redshifts. We connect objects across redshift with a simple constant-number-density procedure, and choose a fiducial model with a relationship between BH and galaxy growth rates that is linear and evolves in a simple way with redshift. Within this fiducial model, we find the quasar luminosity function (QLF) by calculating an "intrinsic" luminosity based on either the BH mass or BH growth rate, and then choosing a model of quasar variability with either a lognormal or truncated power-law distribution of instantaneous luminosities. This gives four model variations, which we fit to the observed QLF at each redshift. With the best-fit models in hand, we undertake a detailed comparison of the four fiducial models, and explore...

  8. Acute otitis media: a simple diagnosis, a simple treatment.

    Science.gov (United States)

    Chhetri, S S

    2014-09-01

    To assess the symptoms and signs of acute otitis media and efficiency of simple antibiotics like amoxicillin in its treatment in the primary health care setup. This is a prospective longitudinal study including 204 patients from different institutions. Patients were diagnosed as suffering from acute otitis media when presented with earache, fever, fullness and or otorrhea. Patients were divided into two equal groups on basis of the treatment they received, Group A received only symptomatic treatment while Group B were given Amoxicillin (40 mg/kg/day) for 7 days. Acute otitis media was common in children under 15 years (64.7%). Patients presented with earache (100%), aural fullness (90.68%), fever (76.47%) associated with recent onset of upper respiratory tract infections (88.23%). In group A, improvement was noticed in 28.43% in 3 days while 35.29% in 7 days. In group B, improvement was noticed in 48.03% in day 3 while 86.27% in day 7. In countries where medical care is scarce, patients lost to follow up, it is wise to treat with simple antibiotics like amoxicillin in adequate dose than to treat only symptomatically. It prevents chronicity, early hearing impairments and reduces antibiotic resistance.

  9. What Is a Simple Liquid?

    Science.gov (United States)

    Ingebrigtsen, Trond S.; Schrøder, Thomas B.; Dyre, Jeppe C.

    2012-01-01

    This paper is an attempt to identify the real essence of simplicity of liquids in John Locke’s understanding of the term. Simple liquids are traditionally defined as many-body systems of classical particles interacting via radially symmetric pair potentials. We suggest that a simple liquid should be defined instead by the property of having strong correlations between virial and potential-energy equilibrium fluctuations in the NVT ensemble. There is considerable overlap between the two definitions, but also some notable differences. For instance, in the new definition simplicity is not a direct property of the intermolecular potential because a liquid is usually only strongly correlating in part of its phase diagram. Moreover, not all simple liquids are atomic (i.e., with radially symmetric pair potentials) and not all atomic liquids are simple. The main part of the paper motivates the new definition of liquid simplicity by presenting evidence that a liquid is strongly correlating if and only if its intermolecular interactions may be ignored beyond the first coordination shell (FCS). This is demonstrated by NVT simulations of the structure and dynamics of several atomic and three molecular model liquids with a shifted-forces cutoff placed at the first minimum of the radial distribution function. The liquids studied are inverse power-law systems (r-n pair potentials with n=18,6,4), Lennard-Jones (LJ) models (the standard LJ model, two generalized Kob-Andersen binary LJ mixtures, and the Wahnstrom binary LJ mixture), the Buckingham model, the Dzugutov model, the LJ Gaussian model, the Gaussian core model, the Hansen-McDonald molten salt model, the Lewis-Wahnstrom ortho-terphenyl model, the asymmetric dumbbell model, and the single-point charge water model. The final part of the paper summarizes properties of strongly correlating liquids, emphasizing that these are simpler than liquids in general. Simple liquids, as defined here, may be characterized in three quite

  10. A simple Cavendish experimental apparatus

    Science.gov (United States)

    Kossler, W. J.; Klein, Susann; Morrow, Dominick; Juliao, Andre

    2016-03-01

    A simple Cavendish apparatus is described that allows measurement of the gravitational constant G and makes observable the gravitational attraction between commonplace objects. The apparatus consists of a torsion balance constructed from readily available materials, including lead bricks and fishing weights ("sinkers"). A computer program is used to determine the gravitational field at the location of the small mass due to a nearby lead brick, which allows students to gain experience with numerical methods. Experimental results obtained are compatible with the accepted value of G.

  11. A Simple Model of Conflict

    OpenAIRE

    Ille, Sebastian

    2013-01-01

    This paper develops a simple dynamic, non-symmetric game between two player populations that can be generalised to a large variety of conflicts. One population attempts to re-write a current (social) contract in its favour, whereas the other prefers to maintain the status quo. In the model's initial set up, the free-rider problem obstructs the occurrence of a conflict, leading to a low probability of a successful turn-over. The normative and conventional framework, in which players interact, ...

  12. Computer electronics made simple computerbooks

    CERN Document Server

    Bourdillon, J F B

    2014-01-01

    Computer Electronics: Made Simple Computerbooks presents the basics of computer electronics and explains how a microprocessor works. Various types of PROMs, static RAMs, dynamic RAMs, floppy disks, and hard disks are considered, along with microprocessor support devices made by Intel, Motorola and Zilog. Bit slice logic and some AMD bit slice products are also described.Comprised of 14 chapters, this book begins with an introduction to the fundamentals of hardware design, followed by a discussion on the basic building blocks of hardware (NAND, NOR, AND, OR, NOT, XOR); tools and equipment that

  13. Windows Phone 7 Made Simple

    CERN Document Server

    Trautschold, Martin

    2011-01-01

    With Windows Phone 7, Microsoft has created a completely new smartphone operating system that focuses on allowing users to be productive with their smartphone in new ways, while offering seamless integration and use of Microsoft Office Mobile as well as other productivity apps available in the Microsoft App Store. Windows Phone 7 Made Simple offers a clear, visual, step-by-step approach to using your Windows Phone 7 smartphone, no matter what the manufacturer. Author Jon Westfall is an expert in mobile devices, recognized by Microsoft as a "Most Valuable Professional" with experience

  14. Systems analysis made simple computerbooks

    CERN Document Server

    Antill, Lyn

    1980-01-01

    Systems Analysis: Made Simple Computerbooks introduces the essential elements of information systems analysis and design and teaches basic technical skills required for the tasks involved. The book covers the aspects to the design of an information system; information systems and the organization, including the types of information processing activity and computer-based information systems; the role of the systems analyst; and the human activity system. The text also discusses information modeling, socio-technical design, man-machine interface, and the database design. Software specification

  15. Identifying Protein-Protein Interaction Sites Using Covering Algorithm

    OpenAIRE

    Jie Song; Jiaxing Cheng; Xiuquan Du

    2009-01-01

    Identification of protein-protein interface residues is crucial for structural biology. This paper proposes a covering algorithm for predicting protein-protein interface residues with features including protein sequence profile and residue accessible area. This method adequately utilizes the characters of a covering algorithm which have simple, lower complexity and high accuracy for high dimension data. The covering algorithm can achieve a comparable performance (69.62%, Complete dataset; 60....

  16. Simple approximations for condensational growth

    Energy Technology Data Exchange (ETDEWEB)

    Kostinski, A B [Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931-1200 (United States)], E-mail: alex.kostinski@mtu.edu

    2009-01-15

    A simple geometric argument relating to the liquid water content of clouds is given. The phase relaxation time and the nature of the quasi-steady approximation for the diffusional growth of cloud drops are elucidated directly in terms of water vapor concentration. Spatial gradients of vapor concentration, inherent in the notion of quasi-steady growth, are discussed and we argue for an occasional reversal of the traditional point of view: rather than a drop growing in response to a given supersaturation, the observed values of the supersaturation in clouds are the result of a vapor field adjusting to droplet growth. Our perspective is illustrated by comparing the exponential decay of condensation trails with a quasi-steady regime of cirrus clouds. The role of aerosol loading in decreasing relaxation times and increasing the rate of growth of the liquid water content is also discussed.

  17. Supernova Feedback Keeps Galaxies Simple

    CERN Document Server

    Chakraborti, Sayan

    2011-01-01

    Galaxies evolve continuously under the influence of self-gravity, rotation, accretion, mergers and feedback. The currently favored cold dark matter cosmological framework, suggests a hierarchical process of galaxy formation, wherein the present properties of galaxies are decided by their individual histories of being assembled from smaller pieces. However, recent studies have uncovered surprising correlations among the properties of galaxies, to the extent of forming a one-parameter set lying on a single fundamental line. It has been argued in the literature that such simplicity is hard to explain within the paradigm of hierarchical galaxy mergers. One of the puzzling results, is the simple linear correlation between the neutral hydrogen mass and the surface area, implying that widely different galaxies share very similar neutral hydrogen surface densities. In this work we show that self-regulated star formation, driven by the competition between gravitational instabilities and mechanical feedback from supern...

  18. Simple Models of Superconformal Flavor

    CERN Document Server

    Craig, Nathaniel

    2010-01-01

    The observed hierarchy of fermion masses and mixings may be generated by renormalization group flow if the Standard Model is coupled to a near-conformal sector at high energies. If the conformal sector is supersymmetric, these effects are rendered calculable by a combination of superconformal symmetry and a-maximization. The viability of such models depends on whether they generate the observed fermion mass hierarchy before the Standard Model gauge couplings hit a Landau pole. Here we construct a variety of simple vector-like models of superconformal flavor, including both ten-centered and democratic variations. We discuss in detail the subtleties of applying the a-maximization procedure to determine anomalous dimensions of Standard Model fields. We find that a wide range of models based on SU(N) or Sp(2N) SQCD with fundamental and adjoint matter are viable theories of superconformal flavor.

  19. Simple Algorithm Portfolio for SAT

    CERN Document Server

    Nikolic, Mladen; Janicic, Predrag

    2011-01-01

    The importance of algorithm portfolio techniques for SAT has long been noted, and a number of very successful systems have been devised, including the most successful one --- SATzilla. However, all these systems are quite complex (to understand, reimplement, or modify). In this paper we propose a new algorithm portfolio for SAT that is extremely simple, but in the same time so efficient that it outperforms SATzilla. For a new SAT instance to be solved, our portfolio finds its k-nearest neighbors from the training set and invokes a solver that performs the best at those instances. The main distinguishing feature of our algorithm portfolio is the locality of the selection procedure --- the selection of a SAT solver is based only on few instances similar to the input one.

  20. A simple ice nucleation spectrometer.

    Science.gov (United States)

    Wharton, David A; Mutch, Jodi S; Wilson, Peter W; Marshall, Craig J; Lim, Miang

    2004-01-01

    The construction of a simple ice nucleation spectrometer is described. It uses 10 microliter droplets loaded into glass capillary tubes which are then inserted into an aluminium holder. Each holder takes six capillary tubes surrounding a central thermocouple. Four holders are placed into a cooling block, cooled by fluid from a programmable refrigerated circulator, and the thermocouples interfaced to a computer to record temperatures. Freezing of each sample is detected by an exotherm on the temperature recording, with 24 samples recorded per run. The spectrometer was tested using deionized water, an extract from a New Zealand alpine cockroach and an extract of lawn grass. The cockroach extract is estimated to contain about 10(3) more nucleators, active at -5 degrees C, than the grass extract. PMID:15618985

  1. iPad Made Simple

    CERN Document Server

    Trautschold, Martin; Learning, MSL Made Simple

    2010-01-01

    The new iPad is sleek, powerful, and most importantly, it's much more than just a big iPhone. Your iPad is can be used for reading, surfing the web, emailing, watching TV/Movies, getting work done, and much more. And with the upcoming wave of iPad apps, the possibilities are endless. iPad X Made Simple clarifies all of the key features on the iPad, introduces what's new, and also reveals dozens of time-saving shortcuts and techniques. The book has over 1,000 screen shots that are carefully annotated with step-by-step instructions. * Clear instructions on how to set up and use the iPad * Illust

  2. Methadone radioimmunoassay: two simple methods

    International Nuclear Information System (INIS)

    Two simple and economical radioimmunoassays for methadone in blood or urine are described. Haemolysis, decomposition, common anticoagulants and sodium fluoride do not affect the results. One assay used commercially-available [1-3H](-)-methadone hydrobromide as the label, while the other uses a radioiodinated conjugate of 4-dimethylamino-2,2-diphenylpentanoic acid and L-tyrosine methyl ester. A commercially-available antiserum is used in both assays. Normethadone and α-methadol cross-react to a small extent with the antiserum while methadone metabolites, dextropropoxyphene, dipipanone and phenadoxone have negligible cross-reactivities. The 'cut-offs' of the two assays as described are 30 and 33 ng ml-1 for blood, and 24 and 21 ng ml-1 for urine. The assay using the radioiodinated conjugate can be made more sensitive if required by increasing the specific activity of the label. (author)

  3. Methadone radioimmunoassay: two simple methods

    Energy Technology Data Exchange (ETDEWEB)

    Robinson, K.; Smith, R.N. (Metropolitan Police Forensic Science Laboratory, London (UK))

    1983-09-01

    Two simple and economical radioimmunoassays for methadone in blood or urine are described. Haemolysis, decomposition, common anticoagulants and sodium fluoride do not affect the results. One assay used commercially-available (1-/sup 3/H)(-)-methadone hydrobromide as the label, while the other uses a radioiodinated conjugate of 4-dimethylamino-2,2-diphenylpentanoic acid and L-tyrosine methyl ester. A commercially-available antiserum is used in both assays. Normethadone and ..cap alpha..-methadol cross-react to a small extent with the antiserum while methadone metabolites, dextropropoxyphene, dipipanone and phenadoxone have negligible cross-reactivities. The 'cut-offs' of the two assays as described are 30 and 33 ng ml/sup -1/ for blood, and 24 and 21 ng ml/sup -1/ for urine. The assay using the radioiodinated conjugate can be made more sensitive if required by increasing the specific activity of the label.

  4. Two Simple Models for Fracking

    Science.gov (United States)

    Norris, Jaren Quinn

    Recent developments in fracking have enable the recovery of oil and gas from tight shale reservoirs. These developments have also made fracking one of the most controversial environmental issues in the United States. Despite the growing controversy surrounding fracking, there is relatively little publicly available research. This dissertation introduces two simple models for fracking that were developed using techniques from non-linear and statistical physics. The first model assumes that the volume of induced fractures must be equal to the volume of injected fluid. For simplicity, these fractures are assumed to form a spherically symmetric damage region around the borehole. The predicted volumes of water necessary to create a damage region with a given radius are in good agreement with reported values. The second model is a modification of invasion percolation which was previously introduced to model water flooding. The reservoir rock is represented by a regular lattice of local traps that contain oil and/or gas separated by rock barriers. The barriers are assumed to be highly heterogeneous and are assigned random strengths. Fluid is injected from a central site and the weakest rock barrier breaks allowing fluid to flow into the adjacent site. The process repeats with the weakest barrier breaking and fluid flowing to an adjacent site each time step. Extensive numerical simulations were carried out to obtain statistical properties of the growing fracture network. The network was found to be fractal with fractal dimensions differing slightly from the accepted values for traditional percolation. Additionally, the network follows Horton-Strahler and Tokunaga branching statistics which have been used to characterize river networks. As with other percolation models, the growth of the network occurs in bursts. These bursts follow a power-law size distribution similar to observed microseismic events. Reservoir stress anisotropy is incorporated into the model by assigning

  5. Simple Solutions for Treating Dry Mouth

    Science.gov (United States)

    Patient Education Sheet Simple Solutions for Treating Dry Mouth Clinicians: Please make as many copies of this ... Philadelphia, for authoring “Simple Solutions for Treating Dry Mouth.” Ask your family doctor to discontinue or provide ...

  6. The Nature of Simple Random Sampling

    OpenAIRE

    Mitra, S. K.; P.K. Pathak

    1984-01-01

    As an estimator of the population mean, the sample mean based only on the distinct units possesses a remarkable invariance property. Under three forms of simple random sampling, viz. simple random sampling without replacement (SRSWOR), simple random sampling with replacement (SRSWR), and fixed cost simple random sampling (SRSFC), it is admissible and unbiased; and asymptotically normally distributed if and only if the Erdos-Renyi-Hajek condition is satisfied. An important implication of this ...

  7. Squid – a simple bioinformatics grid

    Directory of Open Access Journals (Sweden)

    de Miranda Antonio B

    2005-08-01

    Full Text Available Abstract Background BLAST is a widely used genetic research tool for analysis of similarity between nucleotide and protein sequences. This paper presents a software application entitled "Squid" that makes use of grid technology. The current version, as an example, is configured for BLAST applications, but adaptation for other computing intensive repetitive tasks can be easily accomplished in the open source version. This enables the allocation of remote resources to perform distributed computing, making large BLAST queries viable without the need of high-end computers. Results Most distributed computing / grid solutions have complex installation procedures requiring a computer specialist, or have limitations regarding operating systems. Squid is a multi-platform, open-source program designed to "keep things simple" while offering high-end computing power for large scale applications. Squid also has an efficient fault tolerance and crash recovery system against data loss, being able to re-route jobs upon node failure and recover even if the master machine fails. Our results show that a Squid application, working with N nodes and proper network resources, can process BLAST queries almost N times faster than if working with only one computer. Conclusion Squid offers high-end computing, even for the non-specialist, and is freely available at the project web site. Its open-source and binary Windows distributions contain detailed instructions and a "plug-n-play" instalation containing a pre-configured example.

  8. Simple Treat.i Sensivity Analysis

    OpenAIRE

    Sneekes, A.C.; Wal, van der, M.F.

    2009-01-01

    The topic of this report is a sensitivity analysis of the SimpleTreat.i model. SimpleTreat.i (Van der Wal 2008) is a slightly modified version of the SimpleTreat model for evaluating municipal waste water treatment plants (WWTPs). The original SimpleTreat model is described in Struijs (1996). The modifications are intended to make SimpleTreat.i more easily applicable in an industrial setting. Both the initial modifications and the sensitivity analyses haven been performed under contracts from...

  9. Efficacy comparison between simple mixed-dilution and simple mid-dilution on-line hemodiafiltration techniques: a crossover study.

    Science.gov (United States)

    Susantitaphong, Paweena; Tiranathanagul, Khajohn; Katavetin, Pisut; Hanwiwatwong, Orawadee; Wittayalertpanya, Supeecha; Praditpornsilpa, Kearkiat; Tungsanga, Kriang; Eiam-Ong, Somchai

    2012-12-01

    Mid-dilution and mixed-dilution on-line hemodiafiltration (OL-HDF) techniques are innovated to overcome the limitations of two standard techniques including predilution and postdilution. Unfortunately, the head-to-head comparisons between these two novel techniques in the same study are still limited. Moreover, the original mid-dilution and mixed-dilution OL-HDF need special dialyzers and special machines. In the present study, simple mid-dilution and simple mixed-dilution OL-HDF were settled with the aim for clinical use in general hemodialysis (HD) centers. The efficacies of uremic toxins removal between both modalities were measured and compared. This prospective randomized crossover study was conducted on 12 stable HD patients undergoing simple mixed-dilution and simple mid-dilution OL-HDF techniques. HD prescriptions were similar in both techniques. The dialysis efficacies were determined by calculating small- (urea, creatinine, and phosphate) and middle-molecule (beta-2 microglobulin [β2M]) removal. Moreover, potential complications such as high transmembrane pressure (TMP) and protein loss were also observed. Simple mixed-dilution OL-HDF provided significantly greater clearances of urea, creatinine, and β2M when compared with the simple mid-dilution OL-HDF techniques. Phosphate clearances in both techniques were comparable. In addition, TMP and dialysate albumin loss were not different. There were no intradialytic complications in both techniques. Simple mixed-dilution OL-HDF could provide greater efficacy for small- and middle-molecule clearances and acceptable potential risks, while phosphate removal is comparable.

  10. A Simple Measure of Economic Complexity

    OpenAIRE

    Inoua, Sabiou

    2016-01-01

    We show from a simple model that a country's technological development can be measured by the logarithm of the number of products it makes. We show that much of the income gaps among countries are due to differences in technology, as measured by this simple metric. Finally, we show that the so-called Economic Complexity Index (ECI), a recently proposed measure of collective knowhow, is in fact an estimate of this simple metric (with correlation above 0.9).

  11. Simple model systems: a challenge for Alzheimer's disease

    Directory of Open Access Journals (Sweden)

    Di Carlo Marta

    2012-04-01

    Full Text Available Abstract The success of biomedical researches has led to improvement in human health and increased life expectancy. An unexpected consequence has been an increase of age-related diseases and, in particular, neurodegenerative diseases. These disorders are generally late onset and exhibit complex pathologies including memory loss, cognitive defects, movement disorders and death. Here, it is described as the use of simple animal models such as worms, fishes, flies, Ascidians and sea urchins, have facilitated the understanding of several biochemical mechanisms underlying Alzheimer's disease (AD, one of the most diffuse neurodegenerative pathologies. The discovery of specific genes and proteins associated with AD, and the development of new technologies for the production of transgenic animals, has helped researchers to overcome the lack of natural models. Moreover, simple model systems of AD have been utilized to obtain key information for evaluating potential therapeutic interventions and for testing efficacy of putative neuroprotective compounds.

  12. Protein Thin Film Machines

    OpenAIRE

    Federici, Stefania; Oliviero, Giulio; Hamad-Schifferli, Kimberly; Bergese, Paolo

    2010-01-01

    We report the first example of microcantilever beams that are reversibly driven by protein thin film machines fuelled by cycling the salt concentration of the surrounding solution. We also show that upon the same salinity stimulus the drive can be completely reversed in its direction by introducing a surface coating ligand. Experimental results are throughout discussed within a general yet simple thermodynamic model.

  13. Simple utility functions with Giffen demand

    DEFF Research Database (Denmark)

    Sørensen, Peter Norman

    2007-01-01

    Simple utility functions with the Giffen property are presented: locally, the demand curve for a good is upward sloping. The utility functions represent continuous, monotone, convex preferences......Simple utility functions with the Giffen property are presented: locally, the demand curve for a good is upward sloping. The utility functions represent continuous, monotone, convex preferences...

  14. Sunspots and Their Simple Harmonic Motion

    Science.gov (United States)

    Ribeiro, C. I.

    2013-01-01

    In this paper an example of a simple harmonic motion, the apparent motion of sunspots due to the Sun's rotation, is described, which can be used to teach this subject to high-school students. Using real images of the Sun, students can calculate the star's rotation period with the simple harmonic motion mathematical expression.

  15. A simple approach to nonlinear oscillators

    Science.gov (United States)

    Ren, Zhong-Fu; He, Ji-Huan

    2009-10-01

    A very simple and effective approach to nonlinear oscillators is suggested. Anyone with basic knowledge of advanced calculus can apply the method to finding approximately the amplitude-frequency relationship of a nonlinear oscillator. Some examples are given to illustrate its extremely simple solution procedure and an acceptable accuracy of the obtained solutions.

  16. Stochastic Programming with Simple Integer Recourse

    NARCIS (Netherlands)

    Louveaux, François V.; van der Vlerk, Maarten H.

    1993-01-01

    Stochastic integer programs are notoriously difficult. Very few properties are known and solution algorithms are very scarce. In this paper, we introduce the class of stochastic programs with simple integer recourse, a natural extension of the simple recourse case extensively studied in stochastic c

  17. The Fluid Foil: The Seventh Simple Machine

    Science.gov (United States)

    Mitts, Charles R.

    2012-01-01

    A simple machine does one of two things: create a mechanical advantage (lever) or change the direction of an applied force (pulley). Fluid foils are unique among simple machines because they not only change the direction of an applied force (wheel and axle); they convert fluid energy into mechanical energy (wind and Kaplan turbines) or vice versa,…

  18. Protein Foods

    Science.gov (United States)

    ... Text Size: A A A Listen En Español Protein Foods Foods high in protein such as fish, ... the vegetarian proteins, whether they have carbohydrate. Best Protein Choices The best choices are: Plant-based proteins ...

  19. Simple and rapid determination of myristicin in human serum.

    Science.gov (United States)

    Dawidowicz, Andrzej L; Dybowski, Michal P

    2013-01-01

    Myristicin (5-allyl-1-methoxy-2,3-methylenodioxybenzene) is the main component of nutmeg (Myristica fragrans Houtt.) essential oil. The increasing use of myristicin as a cheap hallucinogenic intoxicant, frequently causing fatal cases of myristicin poisoning, requires new methods for determination of this compound in blood. This report describes the rapid, simple, and useful procedure for myristicin analysis in human serum, involving myristicin-protein complex degradation before chromatographic analysis. The developed method is characterized by a high recovery (above 99 %), a low detection limit (6.0 ng/g) and good repeatability (average RDS of 2.01 %). PMID:23440626

  20. Changes of acylation stimulating protein,adiponectin level in simple obese children and their clinical significance%单纯性肥胖症儿童促酰化蛋白和脂联素水平变化的临床意义

    Institute of Scientific and Technical Information of China (English)

    龚雪萍; 廖均梅

    2015-01-01

    Objective To explore the relationship between acylation stimulating protein(ASP),adiponectin(ADPN)and the inci-dence of childhood obesity and the significance of them in diagnoses and therapy of children's obesity. Methods 200 children including 62 obese children,73 overweight children and 65 healthy control children were recruited. Fasting plasma glucose (FPG),fasting insulin (FINS),total cholesterol(TC),triglyeerides (TG),low density lipoprotein-cholesterol (LDL-C),and HDL-C (high density lipoprotein-cholesterol)were determined by automatic blood analyses machine. Serum ASP and ADPN levels were determined by enzyme linked immu-nosorbent assay(ELISA). Results Compared with healthy children group,FPG,FINS,LDL-C,TC,TG,insulin resistance index(IRI), ASP of obese and overweight children groups were significantly higher(P < 0. 05),while the level of HDL-C,ADPN and insulin sensitivity index(ISI)were significantly lower(P < 0. 05). And there was significant difference in the levels of FPG,FINS,LDL-C,TC,TG and IRI between obese and overweight children groups(P < 0. 05). ASP was negatively connected with ADPN in neonates with HIE. Conclusion In simple obesity children,there was a significant change in serum ASP and ADPN. And ASP and ADPN were involved in the disorder of lipid metabolism in obese children. Serum ASP and ADPN levels can be used as a new indicator to evaluate the risk of childhood obesity trends and future evaluation of diabetes and cardiovascular diseases.%目的:探讨单纯性肥胖症儿童促酰化蛋白(ASP)和脂联素(ADPN)水平变化的临床意义。方法选取2014年1月至2014年12月惠州市第一妇幼保健院儿科内分泌门诊就诊及健康体检的200例儿童作为研究对象,其中单纯性肥胖组62例,超重组73例和健康对照组65例。根据患者的身高和体质量计算出体质量指数(BMI)。测定空腹血糖(FPG)、空腹胰岛素(FINS)、总胆固醇( TC)、三酰甘油(TG)、低

  1. Multiplex PCR Assay for Direct Identification of Group B Streptococcal Alpha-Protein-Like Protein Genes

    OpenAIRE

    Creti, Roberta; Fabretti, Francesca; Orefici, Graziella; von Hunolstein, Christina

    2004-01-01

    We developed a group B streptococcus multiplex PCR assay which allows, by direct analysis of the amplicon size, determination of the surface protein antigen genes of alpha-C protein, epsilon protein, Rib, Alp2, Alp3, and Alp4. The multiplex PCR assay offers a rapid and simple method of subtyping Streptococcus agalactiae based on surface protein genes.

  2. Simple and Clear Proofs of Stirling's Formula

    Science.gov (United States)

    Niizeki, Shozo; Araki, Makoto

    2010-01-01

    The purpose of our article is to show two simpler and clearer methods of proving Stirling's formula than the traditional and conventional ones. The distinction of our method is to use the simple trapezoidal formula.

  3. Classification rule with simple select SQL statement

    CERN Document Server

    H, Spits Warnars H L

    2010-01-01

    A simple sql statement can be used to search learning or rule in relational database for data mining purposes particularly for classification rule. With just only one simple sql statement, characteristic and classification rule can be created simultaneously. Collaboration sql statement with any other application software will increase the ability for creating t-weight as measurement the typicality of each record in the characteristic rule and d-weight as measurement the discriminating behavior of the learned classification/discriminant rule, specifically for further generalization in characteristic rule. Handling concept hierarchy into tables based on concept tree will influence for the successful simple sql statement and by knowing the right standard knowledge to transform each of concept tree in concept hierarchy into one table as to transform concept hierarchy into table, the simple sql statement can be run properly.

  4. A Simple Preparation Method for Diphosphoimidazole

    DEFF Research Database (Denmark)

    Rosenberg, T.

    1964-01-01

    A simple method for the preparation of diphosphoimidazole is presented that involves direct phosphorylation of imidazole by phosphorus oxychloride in alkaline aqueous solution. Details are given on the use of diphosphoimidazole in preparing sodium phosphoramidate and certain phosphorylated amino...

  5. A simple method for medial canthal reconstruction

    NARCIS (Netherlands)

    Wittkampf, ARM; Mourits, MP

    2001-01-01

    A simple method for medical canthal wiring reconstruction with the help of a homolaterally fixed osteosynthesis plate and a metal wire is presented. This avoids transnasal wiring and gives superior control when correcting the position of the lacerated Omedial canthus.

  6. The Invention Convention: Mind Meets Simple Machines.

    Science.gov (United States)

    Hadi-Tabassum, Samina

    1997-01-01

    Describes an Earth Day celebration where students had to design an invention made of simple machines that could crush an empty aluminum can through 10 rapid mechanical movements using materials foraged from the students' homes. (JRH)

  7. Simple shear of deformable square objects

    Science.gov (United States)

    Treagus, Susan H.; Lan, Labao

    2003-12-01

    Finite element models of square objects in a contrasting matrix in simple shear show that the objects deform to a variety of shapes. For a range of viscosity contrasts, we catalogue the changing shapes and orientations of objects in progressive simple shear. At moderate simple shear ( γ=1.5), the shapes are virtually indistinguishable from those in equivalent pure shear models with the same bulk strain ( RS=4), examined in a previous study. In theory, differences would be expected, especially for very stiff objects or at very large strain. In all our simple shear models, relatively competent square objects become asymmetric barrel shapes with concave shortened edges, similar to some types of boudin. Incompetent objects develop shapes surprisingly similar to mica fish described in mylonites.

  8. Simple Signal Source based Micro Controller

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Using micro controller, DAC and Multi-periods syn-thesis, we can buildup a very simple signal source with precisefrequency, amplitude and waveform. Wave parameters can beprogrammed in advance. The circuit can satisfy some special re-quirements.

  9. Generalized Inflations of Completely Simple Semigroups

    Institute of Scientific and Technical Information of China (English)

    Qiang Wang; Shelly L. Wismath

    2007-01-01

    Clarke and Monzo defined a construction called a generalized inflation of a semigroup, and proved that for unions of groups, all null extensions are generalized inflations. We characterize when a groupoid containing a completely simple semigroup B is an as\tsociative generalized inflation of B, and thus provide a way to construct all associative generalized inflations (null extensions) of a given completely simple semigroup.This answers a question posed by Clarke and Monzo.

  10. Introducing ASK, A Simple Knowledgeable System

    OpenAIRE

    Thompson, Bozena H.; Thompson, Frederick B.

    1982-01-01

    ASK, A Simple Knowledgeable System, is a total system for the structuring, manipulation and communication of information. It is a simple system in the sense that its development concentrated on clean engineering solutions to what could be done now with good response times. The user interface is a limited dialect of English. In contrast to expert systems, in which experts build the knowledge base and users make use of this expert knowledge, ASK is aimed at the user who wishes to create, tes...

  11. Signed Young Modules and Simple Specht Modules

    OpenAIRE

    Danz, Susanne; Lim, Kay Jin

    2015-01-01

    By a result of Hemmer, every simple Specht module of a finite symmetric group over a field of odd characteristic is a signed Young module. While Specht modules are parametrized by partitions, indecomposable signed Young modules are parametrized by certain pairs of partitions. The main result of this article establishes the signed Young module labels of simple Specht modules. Along the way we prove a number of results concerning indecomposable signed Young modules that are of independent inter...

  12. Force, motion & simple machines big book

    CERN Document Server

    Graybill, George

    2007-01-01

    Our Combined resource includes all the required fundamentals for teaching Force, Motion & Simple Machines. Give your students a kick start on learning with our resource that has simplified language and vocabulary. We begin with a look at force, motion and work, with examples of simple machines in daily life. Discover what a force is, and different kinds of forces that work on contact and at a distance.

  13. Robotic-Assisted Simple Prostatectomy: An Overview.

    Science.gov (United States)

    Holden, Marc; Parsons, J Kellogg

    2016-08-01

    Despite widespread use of medical therapy for benign prostatic hyperplasia, a need remains for robust surgical therapy in select patients. Robotic-assisted simple prostatectomy (RASP) is an efficacious and safe therapy for patients with bladder outlet obstruction owing to large volume prostates. Data from 13 published cohorts suggest functional outcomes equivalent to open simple prostatectomy with substantially decreased length of hospital stay and risk of transfusion. However, there are few longer term data.

  14. Prediction of potential drug targets based on simple sequence properties

    Directory of Open Access Journals (Sweden)

    Lai Luhua

    2007-09-01

    Full Text Available Abstract Background During the past decades, research and development in drug discovery have attracted much attention and efforts. However, only 324 drug targets are known for clinical drugs up to now. Identifying potential drug targets is the first step in the process of modern drug discovery for developing novel therapeutic agents. Therefore, the identification and validation of new and effective drug targets are of great value for drug discovery in both academia and pharmaceutical industry. If a protein can be predicted in advance for its potential application as a drug target, the drug discovery process targeting this protein will be greatly speeded up. In the current study, based on the properties of known drug targets, we have developed a sequence-based drug target prediction method for fast identification of novel drug targets. Results Based on simple physicochemical properties extracted from protein sequences of known drug targets, several support vector machine models have been constructed in this study. The best model can distinguish currently known drug targets from non drug targets at an accuracy of 84%. Using this model, potential protein drug targets of human origin from Swiss-Prot were predicted, some of which have already attracted much attention as potential drug targets in pharmaceutical research. Conclusion We have developed a drug target prediction method based solely on protein sequence information without the knowledge of family/domain annotation, or the protein 3D structure. This method can be applied in novel drug target identification and validation, as well as genome scale drug target predictions.

  15. Acanthamoeba castellanii STAT protein.

    Directory of Open Access Journals (Sweden)

    Anna Kicinska

    Full Text Available STAT (signal transducers and activators of transcription proteins are one of the important mediators of phosphotyrosine-regulated signaling in metazoan cells. We described the presence of STAT protein in a unicellular, free-living amoebae with a simple life cycle, Acanthamoeba castellanii. A. castellanii is the only, studied to date, Amoebozoan that does not belong to Mycetozoa but possesses STATs. A sequence of the A. castellanii STAT protein includes domains similar to those of the Dictyostelium STAT proteins: a coiled coil (characteristic for Dictyostelium STAT coiled coil, a STAT DNA-binding domain and a Src-homology domain. The search for protein sequences homologous to A. castellanii STAT revealed 17 additional sequences from lower eukaryotes. Interestingly, all of these sequences come from Amoebozoa organisms that belong to either Mycetozoa (slime molds or Centramoebida. We showed that there are four separated clades within the slime mold STAT proteins. The A. castellanii STAT protein branches next to a group of STATc proteins from Mycetozoa. We also demonstrate that Amoebozoa form a distinct monophyletic lineage within the STAT protein world that is well separated from the other groups.

  16. Acanthamoeba castellanii STAT protein.

    Science.gov (United States)

    Kicinska, Anna; Leluk, Jacek; Jarmuszkiewicz, Wieslawa

    2014-01-01

    STAT (signal transducers and activators of transcription) proteins are one of the important mediators of phosphotyrosine-regulated signaling in metazoan cells. We described the presence of STAT protein in a unicellular, free-living amoebae with a simple life cycle, Acanthamoeba castellanii. A. castellanii is the only, studied to date, Amoebozoan that does not belong to Mycetozoa but possesses STATs. A sequence of the A. castellanii STAT protein includes domains similar to those of the Dictyostelium STAT proteins: a coiled coil (characteristic for Dictyostelium STAT coiled coil), a STAT DNA-binding domain and a Src-homology domain. The search for protein sequences homologous to A. castellanii STAT revealed 17 additional sequences from lower eukaryotes. Interestingly, all of these sequences come from Amoebozoa organisms that belong to either Mycetozoa (slime molds) or Centramoebida. We showed that there are four separated clades within the slime mold STAT proteins. The A. castellanii STAT protein branches next to a group of STATc proteins from Mycetozoa. We also demonstrate that Amoebozoa form a distinct monophyletic lineage within the STAT protein world that is well separated from the other groups. PMID:25338074

  17. Protein-protein interactions

    DEFF Research Database (Denmark)

    Byron, Olwyn; Vestergaard, Bente

    2015-01-01

    . The biophysical and structural investigations of PPIs consequently demand hybrid approaches, implementing orthogonal methods and strategies for global data analysis. Currently, impressive developments in hardware and software within several methodologies define a new era for the biostructural community. Data can......Responsive formation of protein:protein interaction (PPI) upon diverse stimuli is a fundament of cellular function. As a consequence, PPIs are complex, adaptive entities, and exist in structurally heterogeneous interplays defined by the energetic states of the free and complexed protomers...

  18. The Design of SimpleITK.

    Science.gov (United States)

    Lowekamp, Bradley C; Chen, David T; Ibáñez, Luis; Blezek, Daniel

    2013-01-01

    SimpleITK is a new interface to the Insight Segmentation and Registration Toolkit (ITK) designed to facilitate rapid prototyping, education and scientific activities via high level programming languages. ITK is a templated C++ library of image processing algorithms and frameworks for biomedical and other applications, and it was designed to be generic, flexible and extensible. Initially, ITK provided a direct wrapping interface to languages such as Python and Tcl through the WrapITK system. Unlike WrapITK, which exposed ITK's complex templated interface, SimpleITK was designed to provide an easy to use and simplified interface to ITK's algorithms. It includes procedural methods, hides ITK's demand driven pipeline, and provides a template-less layer. Also SimpleITK provides practical conveniences such as binary distribution packages and overloaded operators. Our user-friendly design goals dictated a departure from the direct interface wrapping approach of WrapITK, toward a new facade class structure that only exposes the required functionality, hiding ITK's extensive template use. Internally SimpleITK utilizes a manual description of each filter with code-generation and advanced C++ meta-programming to provide the higher-level interface, bringing the capabilities of ITK to a wider audience. SimpleITK is licensed as open source software library under the Apache License Version 2.0 and more information about downloading it can be found at http://www.simpleitk.org.

  19. The Design of SimpleITK

    Directory of Open Access Journals (Sweden)

    Bradley Christopher Lowekamp

    2013-12-01

    Full Text Available SimpleITK is a new interface to the Insight Segmentation andRegistration Toolkit (ITK designed to facilitate rapid prototyping, educationand scientific activities, via high level programminglanguages. ITK is a templated C++ library of image processingalgorithms and frameworks for biomedical and other applications, andit was designed to be generic, flexible and extensible. Initially, ITKprovided a direct wrapping interface to languages such as Python andTcl through the WrapITK system. Unlike WrapITK, which exposed ITK'scomplex templated interface, SimpleITK was designed to provide an easyto use and simplified interface to ITK's algorithms. It includesprocedural methods, hides ITK's demand driven pipeline, and provides atemplate-less layer. Also SimpleITK provides practical conveniencessuch as binary distribution packages and overloaded operators. Ouruser-friendly design goals dictated a departure from the directinterface wrapping approach of WrapITK, towards a new facadeclass structure that only exposes the required functionality, hidingITK's extensive template use. Internally SimpleITK utilizes a manualdescription of each filter with code-generation and advanced C++meta-programming to provide the higher-level interface, bringing thecapabilities of ITK to a wider audience. SimpleITK is licensed asopen source software under the Apache License Version 2.0 and more informationabout downloading it can be found at http://www.simpleitk.org.

  20. Gaussian peaks decomposing of simple liquids’ RDF

    Institute of Scientific and Technical Information of China (English)

    王伟民; 边秀房; 秦敬玉; 张林; 叶以富

    1999-01-01

    According to feasibility of Gaussian peaks decomposing distribution function (DF) 4πrρ(r), radial distribution function (RDF) 4πr~2ρ(r) of simple liquids also is possibly decomposed into Gaussian peaks with r in the size of several atoms. Experimental structure parameters of pure liquid Al and Si were obtained by θ-θ X-ray diffraction measurements and following data processing. Based on Gaussian decomposing liquid aluminun’s DF 4πrρ(r), liquid aluminum and silicon’s radial distribution function (RDF) 4πr~2ρ(r), it is shown that RDF of simple liquids is able to be decomposed in Gaussian function, compared with decomposing of DF, supplying more physical meaning and better indicating the short range order of liquids, whicb draws a clearer structure picture of simple liquids.

  1. Maximal temperature in a simple thermodynamical system

    Science.gov (United States)

    Dai, De-Chang; Stojkovic, Dejan

    2016-06-01

    Temperature in a simple thermodynamical system is not limited from above. It is also widely believed that it does not make sense talking about temperatures higher than the Planck temperature in the absence of the full theory of quantum gravity. Here, we demonstrate that there exist a maximal achievable temperature in a system where particles obey the laws of quantum mechanics and classical gravity before we reach the realm of quantum gravity. Namely, if two particles with a given center of mass energy come at the distance shorter than the Schwarzschild diameter apart, according to classical gravity they will form a black hole. It is possible to calculate that a simple thermodynamical system will be dominated by black holes at a critical temperature which is about three times lower than the Planck temperature. That represents the maximal achievable temperature in a simple thermodynamical system.

  2. TRSkit: A Simple Digital Library Toolkit

    Science.gov (United States)

    Nelson, Michael L.; Esler, Sandra L.

    1997-01-01

    This paper introduces TRSkit, a simple and effective toolkit for building digital libraries on the World Wide Web. The toolkit was developed for the creation of the Langley Technical Report Server and the NASA Technical Report Server, but is applicable to most simple distribution paradigms. TRSkit contains a handful of freely available software components designed to be run under the UNIX operating system and served via the World Wide Web. The intended customer is the person that must continuously and synchronously distribute anywhere from 100 - 100,000's of information units and does not have extensive resources to devote to the problem.

  3. Simple approach to study biomolecule adsorption in polymeric microfluidic channels

    Energy Technology Data Exchange (ETDEWEB)

    Gubala, Vladimir, E-mail: V.Gubala@kent.ac.uk [Biomedical Diagnostics Institute (BDI), National Centre for Sensor Research (NCSR), Dublin City University, Dublin 9 (Ireland); Medway School of Pharmacy, University of Kent, Central Avenue, Anson 120, Chatham Maritime, Kent ME4 4TB (United Kingdom); Siegrist, Jonathan; Monaghan, Ruairi; O' Reilly, Brian; Gandhiraman, Ram Prasad [Biomedical Diagnostics Institute (BDI), National Centre for Sensor Research (NCSR), Dublin City University, Dublin 9 (Ireland); Daniels, Stephen [Biomedical Diagnostics Institute (BDI), National Centre for Sensor Research (NCSR), Dublin City University, Dublin 9 (Ireland); National Centre for Plasma Science and Technology (NCPST), Dublin City University, Dublin 9 (Ireland); Williams, David E. [Biomedical Diagnostics Institute (BDI), National Centre for Sensor Research (NCSR), Dublin City University, Dublin 9 (Ireland); MacDiarmid Institute for Advanced Materials and Nanotechnology, School of Chemical Sciences, University of Auckland, Auckland 1142 (New Zealand); Ducree, Jens [Biomedical Diagnostics Institute (BDI), National Centre for Sensor Research (NCSR), Dublin City University, Dublin 9 (Ireland)

    2013-01-14

    Highlights: Black-Right-Pointing-Pointer A simple tool to assess biomolecule adsorption onto the surfaces of microchannels. Black-Right-Pointing-Pointer Development for dilution by surface-adsorption based depletion of protein samples. Black-Right-Pointing-Pointer It can easily be done using a readily available apparatus like a spin-coater. Black-Right-Pointing-Pointer The assessment tool is facile and quantitative. Black-Right-Pointing-Pointer Straightforward comparison of different surface chemistries. - Abstract: Herein a simple analytical method is presented for the characterization of biomolecule adsorption on cyclo olefin polymer (COP, trade name: Zeonor{sup Registered-Sign }) substrates which are widely used in microfluidic lab-on-a-chip devices. These Zeonor{sup Registered-Sign} substrates do not possess native functional groups for specific reactions with biomolecules. Therefore, depending on the application, such substrates must be functionalized by surface chemistry methods to either enhance or suppress biomolecular adsorption. This work demonstrates a microfluidic method for evaluating the adsorption of antibodies and oligonucleotides surfaces. The method uses centrifugal microfluidic flow-through chips and can easily be implemented using common equipment such as a spin coater. The working principle is very simple. The user adds 40 L of the solution containing the sample to the starting side of a microfluidic channel, where it is moved through by centrifugal force. Some molecules are adsorbed in the channel. The sample is then collected at the other end in a small reservoir and the biomolecule concentration is measured. As a pilot application, we characterized the adsorption of goat anti-human IgG and a 20-mer DNA on Zeonor{sup Registered-Sign }, and on three types of functionalized Zeonor: 3-aminopropyltriethoxysilane (APTES) modified surface with mainly positive charge, negatively charged surface with immobilized bovine serum albumin (BSA), and

  4. Flowering Buds of Globular Proteins: Transpiring Simplicity of Protein Organization

    Science.gov (United States)

    Berezovsky, Igor N.

    2002-01-01

    Structural and functional complexity of proteins is dramatically reduced to a simple linear picture when the laws of polymer physics are considered. A basic unit of the protein structure is a nearly standard closed loop of 25–35 amino acid residues, and every globular protein is built of consecutively connected closed loops. The physical necessity of the closed loops had been apparently imposed on the early stages of protein evolution. Indeed, the most frequent prototype sequence motifs in prokaryotic proteins have the same sequence size, and their high match representatives are found as closed loops in crystallized proteins. Thus, the linear organization of the closed loop elements is a quintessence of protein evolution, structure and folding. PMID:18629251

  5. Simple graphical display program for physics

    International Nuclear Information System (INIS)

    A simple subroutine based on the Tektronix Plot-10/Advanced Graphing II package to be used with a Tektronix CRT terminal is presented. It is specifically designed for the needs of a physicist, but contains enough options to allow for a wider use. 1 figure

  6. SLURM: Simple Linux Utility for Resource Management

    Energy Technology Data Exchange (ETDEWEB)

    Jette, M; Grondona, M

    2002-12-19

    Simple Linux Utility for Resource Management (SLURM) is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for Linux clusters of thousands of nodes. Components include machine status, partition management, job management, scheduling and stream copy modules. This paper presents an overview of the SLURM architecture and functionality.

  7. A novel and simple atrial retractor.

    Science.gov (United States)

    Kofidis, Theo; Lee, Chuen Neng

    2011-05-01

    Minimally invasive cardiac operations require specialized equipment. Atrial retractors are a frequently used tool to expose heart valves for minimally invasive and open procedures. The models currently available in the market are efficient; however, they may be complex, bulky, or expensive. We introduce a novel, very simple atrial retractor we designed using ubiquitously available materials. PMID:21524488

  8. Simple autonomic seizures and ictal enuresis

    DEFF Research Database (Denmark)

    Rosenzweig, Ivana; Varga, Edina T; Akeson, Per;

    2011-01-01

    manifestation of the de novo post-traumatic simple autonomic seizures. Source analysis of the ictal epileptiform discharges showed activation of the cortical areas surrounding the right inferior frontal sulcus, adjacent to the lesional zone. The case depicted here further endorses recent neuroimaging studies...

  9. Strong Bisimilarity of Simple Process Algebras

    DEFF Research Database (Denmark)

    Srba, Jirí

    2003-01-01

    We study bisimilarity and regularity problems of simple process algebras. In particular, we show PSPACE-hardness of the following problems: (i) strong bisimilarity of Basic Parallel Processes (BPP), (ii) strong bisimilarity of Basic Process Algebra (BPA), (iii) strong regularity of BPP, and (iv) ...

  10. A Simple Homemade Polarised Sunglasses Test Card

    Science.gov (United States)

    Bamdad, Farzad

    2016-01-01

    In this article construction of a simple and inexpensive test card which can be used to demonstrate the polarisation ability of sunglasses is described. The card was fabricated simply by using a piece of polariser sheet with one to three layers of cellophane tape fixed on it.

  11. Simple matrix elements with dynamical fermions

    International Nuclear Information System (INIS)

    We report on studies of simple matrix elements from simulations with two flavors of sea quarks, both staggered and Wilson. We show the decay constants of vector and pseudoscalar mesons. The effects of sea quarks are small. These simulations are done at relatively large lattice spacing compared to most quenched studies. (orig.)

  12. Geometric classification of simple graph algebras

    DEFF Research Database (Denmark)

    Sørensen, Adam Peder Wie

    2013-01-01

    Inspired by Franks’ classification of irreducible shifts of finite type, we provide a short list of allowed moves on graphs that preserve the stable isomorphism class of the associated C ∗ -algebras. We show that if two graphs have stably isomorphic and simple unital algebras then we can use these...

  13. Simple Analysis of Historical Lime Mortars

    Science.gov (United States)

    Pires, Joa~o

    2015-01-01

    A laboratory experiment is described in which a simple characterization of a historical lime mortar is made by the determination of its approximate composition by a gravimetric method. Fourier transform infrared (FTIR) spectroscopy and X-ray diffraction (XRD) are also used for the qualitative characterization of the lime mortar components. These…

  14. Jacks--A Study of Simple Machines.

    Science.gov (United States)

    Parsons, Ralph

    This vocational physics individualized student instructional module on jacks (simple machines used to lift heavy objects) contains student prerequisites and objectives, an introduction, and sections on the ratchet bumper jack, the hydraulic jack, the screw jack, and load limitations. Designed with a laboratory orientation, each section consists of…

  15. Simple Lie groups without the approximation property

    DEFF Research Database (Denmark)

    Haagerup, Uffe; de Laat, Tim

    2013-01-01

    on the space M0A(G). Recently, Lafforgue and de la Salle proved that SL(3,R) does not have the AP, implying the first example of an exact discrete group without it, namely, SL(3,Z). In this paper we prove that Sp(2,R) does not have the AP. It follows that all connected simple Lie groups with finite center...

  16. Simple wave interaction of an elastic string

    NARCIS (Netherlands)

    Broer, L.J.F.; Groesen, van E.W.C.

    1977-01-01

    The equations for the two-dimensional motion of a completely flexible elastic string can be derived from a Lagrangian. The equations of motion possess four characteristic velocities, to which the following four simple wave solutions correspond: leftward and rightward propagating longitudinal and tra

  17. Simple classical approach to spin resonance phenomena

    DEFF Research Database (Denmark)

    Gordon, R A

    1977-01-01

    A simple classical method of describing spin resonance in terms of the average power absorbed by a spin system is discussed. The method has several advantages over more conventional treatments, and a number of important spin resonance phenomena, not normally considered at the introductory level...

  18. Correcting the SIMPLE Model of Free Recall

    Science.gov (United States)

    Lee, Michael D.; Pooley, James P.

    2013-01-01

    The scale-invariant memory, perception, and learning (SIMPLE) model developed by Brown, Neath, and Chater (2007) formalizes the theoretical idea that scale invariance is an important organizing principle across numerous cognitive domains and has made an influential contribution to the literature dealing with modeling human memory. In the context…

  19. A Simple and Efficient Kinetic Spanner

    DEFF Research Database (Denmark)

    Abam, Mohammad; de Berg, Mark; Gudmundsson, Joachim

    2008-01-01

    We present a new and simple (1+ε)-spanner of size O(nε2) for a set of n points in the plane, which can be maintained efficiently as the points move. Assuming the trajectories of the points can be described by polynomials whose degrees are at most s, the number of topological changes to the spanner...

  20. Building Simple Hidden Markov Models. Classroom Notes

    Science.gov (United States)

    Ching, Wai-Ki; Ng, Michael K.

    2004-01-01

    Hidden Markov models (HMMs) are widely used in bioinformatics, speech recognition and many other areas. This note presents HMMs via the framework of classical Markov chain models. A simple example is given to illustrate the model. An estimation method for the transition probabilities of the hidden states is also discussed.

  1. Simple Cloud Chambers Using Gel Ice Packs

    Science.gov (United States)

    Kamata, Masahiro; Kubota, Miki

    2012-01-01

    Although cloud chambers are highly regarded as teaching aids for radiation education, school teachers have difficulty in using cloud chambers because they have to prepare dry ice or liquid nitrogen before the experiment. We developed a very simple and inexpensive cloud chamber that uses the contents of gel ice packs which can substitute for dry…

  2. Hooked… make it simple and easy

    Directory of Open Access Journals (Sweden)

    Sheetal Potnis

    2014-01-01

    Full Text Available Temporary anchorage devices (TADs have solved a lot of orthodontic treatment dilemmas. Attachment of elastomers to these TADs is sometimes difficult, especially with embedded microimplants like in the infrazygomatic area. Here, a simple modification has been made in the attachment of elastomeric chain to ligature wire for ease of replacing the elastomeric chain.

  3. Studying the Greenhouse Effect: A Simple Demonstration.

    Science.gov (United States)

    Papageorgiou, G.; Ouzounis, K.

    2000-01-01

    Studies the parameters involved in a presentation of the greenhouse effect and describes a simple demonstration of this effect. Required equipment includes a 100-120 watt lamp, a 250mL beaker, and a thermometer capable of recording 0-750 degrees Celsius together with a small amount of chloroform. (Author/SAH)

  4. A Simple Acronym for Doing Calculus: CAL

    Science.gov (United States)

    Hathaway, Richard J.

    2008-01-01

    An acronym is presented that provides students a potentially useful, unifying view of the major topics covered in an elementary calculus sequence. The acronym (CAL) is based on viewing the calculus procedure for solving a calculus problem P* in three steps: (1) recognizing that the problem cannot be solved using simple (non-calculus) techniques;…

  5. Microwave Radiometer Linearity Measured by Simple Means

    DEFF Research Database (Denmark)

    Skou, Niels

    2002-01-01

    Modern spaceborne radiometer systems feature an almost perfect on-board calibration, hence the primary calibration task to be carried out before launch is a check of radiometer linearity. This paper describes two ways of measuring linearity of microwave radiometers only requiring relatively simple...

  6. SIMPLE LATTICE BOLTZMANN MODEL FOR TRAFFIC FLOWS

    Institute of Scientific and Technical Information of China (English)

    Yan Guangwu; Hu Shouxin

    2000-01-01

    A lattice Boltzmann model with 5-bit lattice for traffic flows is proposed.Using the Chapman-Enskog expansion and multi-scale technique,we obtain the higher-order moments of equilibrium distribution function.A simple traffic light problem is simulated by using the present lattice Boltzmann model,and the result agrees well with analytical solution.

  7. Learning in a Simple Motor System

    Science.gov (United States)

    Broussard, Dianne M.; Kassardjian, Charles D.

    2004-01-01

    Motor learning is a very basic, essential form of learning that appears to share common mechanisms across different motor systems. We evaluate and compare a few conceptual models for learning in a relatively simple neural system, the vestibulo-ocular reflex (VOR) of vertebrates. We also compare the different animal models that have been used to…

  8. A Simple Condition for Bounded Displacement

    CERN Document Server

    Solomon, Yaar

    2011-01-01

    We study separated nets that correspond to substitution tilings of the Euclidean space. We give a simple condition, in terms of the eigenvalues and eigenspaces of the substitution matrix, to know whether the separated net is a bounded displacement of the integer lattice or not.

  9. Nature versus Nurture: The Simple Contrast

    Science.gov (United States)

    Davidoff, Jules; Goldstein, Julie; Roberson, Debi

    2009-01-01

    We respond to the commentary of Franklin, Wright, and Davies ("Journal of Experimental Child Psychology, 102", 239-245 [2009]) by returning to the simple contrast between nature and nurture. We find no evidence from the toddler data that makes us revise our ideas that color categories are learned and never innate. (Contains 1 figure.)

  10. Charge operators in simple Lie groups

    Science.gov (United States)

    Taormina, A.

    1984-03-01

    Charge operators for representations of dimension less than or equal to 16 are computed in all simple Lie groups. The representations for which the charge operator reproduces the charge spectrum of leptons and quarks of one family are analyzed from a GUT point of view.

  11. Long, polymorphic microsatellites in simple organisms.

    Science.gov (United States)

    Field, D; Wills, C

    1996-02-22

    We have examined the phylogenetic distribution of the longest, perfect microsatellites in GenBank. Despite the large contributions of model higher-eukaryotic organisms to GenBank, the selective cloning of long microsatellites from these organisms as genetic markers, and the relative lack of concentration on the microsatellites in lower eukaryotes and prokaryotes, we found that simple organisms, defined here as slime molds, fungi, protists, prokaryotes, viruses, organelles and plasmids, contributed 78 of the 375 examined sequences. These 78 simple-organism microsatellites are characterized predominantly by trinucleotide repeats, nearly half of which lie in exons, and in general show a bias towards A+T rich motifs. Simple-organism microsatellites represented more than once in GenBank displayed length polymorphisms when independent clones were compared. These facts collectively raise speculation as to the role of these 'junk' sequences in such highly economical genomes, especially when precise changes in long microsatellites are known to regulate critical virulence factors in several prokaryotes. Regardless of their biological significance, simple-organism microsatellites may provide a general source of molecular markers to track disease outbreaks and the evolution of microorganisms in unprecedented detail. PMID:8728984

  12. Nature versus nurture: The simple contrast

    OpenAIRE

    Davidoff, Jules B.; Goldstein, Julie; Roberson, Debi

    2009-01-01

    We respond to the commentary of Franklin, Wright, and Davies (Journal of Experimental Child Psychology, 102, 239-245 [2009]) by returning to the simple contrast between nature and nurture. We find no evidence from the toddler data that makes us revise our ideas that color categories are learned and never innate.

  13. Current-induced forces: a simple derivation

    DEFF Research Database (Denmark)

    Todorov, Tchavdar N.; Dundas, Daniel; Lü, Jing-Tao;

    2014-01-01

    We revisit the problem of forces on atoms under current in nanoscale conductors. We derive and discuss the five principal kinds of force under steady-state conditions from a simple standpoint that-with the help of background literature-should be accessible to physics undergraduates. The discussio...

  14. Automorphism groups of finite dimensional simple algebras

    OpenAIRE

    Gordeev, Nikolai L.; Popov, Vladimir L.

    2004-01-01

    We show that if a field k contains sufficiently many elements(for instance, if k is infinite), and K is an algebraically closed field containing k, then every linear algebraic k-group over K is k-isomorphic to Aut(A\\otimes_kK), where A is a finite dimensional simple algebra over k.

  15. Using Simple Machines to Leverage Learning

    Science.gov (United States)

    Dotger, Sharon

    2008-01-01

    What would your students say if you told them they could lift you off the ground using a block and a board? Using a simple machine, they'll find out they can, and they'll learn about work, energy, and motion in the process! In addition, this integrated lesson gives students the opportunity to investigate variables while practicing measurement…

  16. A Simple Method for Collecting Airborne Pollen

    Science.gov (United States)

    Kevan, Peter G.; DiGiovanni, Franco; Ho, Rong H.; Taki, Hisatomo; Ferguson, Kristyn A.; Pawlowski, Agata K.

    2006-01-01

    Pollination is a broad area of study within biology. For many plants, pollen carried by wind is required for successful seed set. Airborne pollen also affects human health. To foster studies of airborne pollen, we introduce a simple device--the "megastigma"--for collecting pollen from the air. This device is flexible, yielding easily obtained data…

  17. Testing theory in practice: a simple experiment

    NARCIS (Netherlands)

    Terpstra, R.; Ferreira Pires, L.; Heerink, A.W.; Tretmans, G.J.; Brezocnik, Z.; Kapus, T.

    1996-01-01

    In this paper we discuss the experiences gained in conducting a simple testing experiment. The goal of this experiment is to apply the abstract, formal testing framework [8] in a practical setting, and to indicate the critical aspects in its application to realistic testing situations. For that purp

  18. A Simple Technique for High Resistance Measurement

    Science.gov (United States)

    Aguilar, Horacio Munguia; Landin, Ramon Ochoa

    2012-01-01

    A simple electronic system for the measurement of high values of resistance is shown. This system allows the measurement of resistance in the range of a few megohm up to 10[superscript 9] [omega]. We have used this system for the evaluation of CdS thin film resistance, but other practical uses in the basic physics laboratory are presented.…

  19. Fractal surfaces from simple arithmetic operations

    Science.gov (United States)

    García-Morales, Vladimir

    2016-04-01

    Fractal surfaces ('patchwork quilts') are shown to arise under most general circumstances involving simple bitwise operations between real numbers. A theory is presented for all deterministic bitwise operations on a finite alphabet. It is shown that these models give rise to a roughness exponent H that shapes the resulting spatial patterns, larger values of the exponent leading to coarser surfaces.

  20. Simple Obstacle Avoidance Algorithm for Rehabilitation Robots

    NARCIS (Netherlands)

    Stuyt, F.H.A.; Römer, G.R.B.; Stuyt, H.J.A.

    2007-01-01

    The efficiency of a rehabilitation robot is improved by offering record-and-replay to operate the robot. While automatically moving to a stored target (replay) collisions of the robot with obstacles in its work space must be avoided. A simple, though effective, generic and deterministic algorithm fo

  1. Population Monotonic Path Schemes for Simple Games

    NARCIS (Netherlands)

    Ciftci, B.B.; Borm, P.E.M.; Hamers, H.J.M.

    2006-01-01

    A path scheme for a simple game is composed of a path, i.e., a sequence of coalitions that is formed during the coalition formation process and a scheme, i.e., a payoff vector for each coalition in the path.A path scheme is called population monotonic if a player's payoff does not decrease as the pa

  2. Simple Activity Demonstrates Wind Energy Principles

    Science.gov (United States)

    Roman, Harry T.

    2012-01-01

    Wind energy is an exciting and clean energy option often described as the fastest-growing energy system on the planet. With some simple materials, teachers can easily demonstrate its key principles in their classroom. (Contains 1 figure and 2 tables.)

  3. A Simple ELISA Exercise for Undergraduate Biology.

    Science.gov (United States)

    Baker, William P.; Moore, Cathy R.

    Understanding of immunological techniques such as the Enzyme Linked Immuno Sorbent Assay (ELISA) is an important part of instructional units in human health, developmental biology, microbiology, and biotechnology. This paper describes a simple ELISA exercise for undergraduate biology that effectively simulates the technique using a paper model.…

  4. Simulated Holograms: A Simple Introduction to Holography.

    Science.gov (United States)

    Dittmann, H.; Schneider, W. B.

    1992-01-01

    Describes a project that uses a computer and a dot matrix printer to simulate the holographic recording process of simple object structures. The process' four steps are (1) superposition of waves; (2) representing the superposition of a plane reference wave on the monitor screen; (3) photographic reduction of the images; and (4) reconstruction of…

  5. Simple high-temperature thermal diffusivity apparatus

    Science.gov (United States)

    Wood, C.; Zoltan, A.

    1984-01-01

    A simple and inexpensive thermal diffusivity apparatus is described for measurement up to 1600 K. The novel features of apparatus include a light pipe, a long furnace, and a differential thermocouple. A low heat-load sample holder for clamping the sample in a vertical position is also described. The results of measurements on AXM-5Q graphite are reported.

  6. Simple Harmonic Motion in Harmonic Plane Waves.

    Science.gov (United States)

    Benumof, Reuben

    1980-01-01

    Discusses the distribution of kinetic and potential energy in transverse and longitudinal waves and examines the transmission of power and momentum. This discussion is intended to aid in understanding the simple harmonic motion of a particle involved in the propagation of a harmonic mechanical plane wave. (HM)

  7. A novel and simple atrial retractor.

    Science.gov (United States)

    Kofidis, Theo; Lee, Chuen Neng

    2011-05-01

    Minimally invasive cardiac operations require specialized equipment. Atrial retractors are a frequently used tool to expose heart valves for minimally invasive and open procedures. The models currently available in the market are efficient; however, they may be complex, bulky, or expensive. We introduce a novel, very simple atrial retractor we designed using ubiquitously available materials.

  8. Simple adaptive tracking control for mobile robots

    Science.gov (United States)

    Bobtsov, Alexey; Faronov, Maxim; Kolyubin, Sergey; Pyrkin, Anton

    2014-12-01

    The problem of simple adaptive and robust control is studied for the case of parametric and dynamic dimension uncertainties: only the maximum possible relative degree of the plant model is known. The control approach "consecutive compensator" is investigated. To illustrate the efficiency of proposed approach an example with the mobile robot motion control using computer vision system is considered.

  9. EVALUATION OF SURGERY IN SIMPLE OVARIAN CYSTS

    Institute of Scientific and Technical Information of China (English)

    丁晓曼; 冷金花; 郎景和; 李华军

    2003-01-01

    Objective. To evaluate the surgery in simple ovarian cysts.Methods. From Jan. 1994 to Dec. 1999, 221 women with simple ovarian cysts were admitted into ourhospital. The diameter of cysts was <5 cm in 76 cases, and was≥5 cm in 145 cases ultrasonically.One hundred and eighty-four patients underwent laparosocopy, and thirty-seven underwent laparotomy.Results. Histological findings showed no malignancy in this series. Simple cysts, paraovarian cystsand corpus luteum were found histologically in 90.8% of cases with cysts <5 cm, and 60% of those withcysts >7 cm respectively, their difference was significant (X2=-37.13, P<0.001). The simple cysts, paraovar-ian cysts and corpus luteum cysts were found in 81.5% of postmenopausal women and 84.0% of pre-menopausal women. Conclusion. Patients with cysts >7 cm are indicated for surgical procedures, while a period of fol-lowup is acceptable for patients with cysts <7 cm, and surgery is advisable if the cyst is persistent dur-ing followup. Postmenopausal women with cysts should have operations.

  10. Simple random sampling with over-replacement

    OpenAIRE

    Antal, Erika; Tillé, Yves

    2016-01-01

    There are several ways to select units with replacement and an equal inclusion expectation. We present a new sampling design called simple random sampling with over-replacement. Its interest lies in the high variance produced for the Horvitz–Thompson estimator. This characteristic could be useful for resampling methods.

  11. A simple thermodynamic test to discriminate between two-state and downhill folding.

    Science.gov (United States)

    Oliva, Fabiana Y; Muñoz, Victor

    2004-07-21

    The recent discovery of one-state folding, in which proteins unfold by progressive structural disorganizations (i.e., downhill folding), has emphasized the need for simple thermodynamic tests to discriminate between this behavior and classical two-state folding. On the basis of theoretical results from elementary statistical mechanical models, we propose such a test. The test involves monitoring the equilibrium unfolding transition induced by a combination of temperature and chemical denaturants with a probe that is sensitive to the average protein backbone conformation. The rationale is that the coupling between two different denaturation procedures can reveal subtle changes in protein conformational ensembles even when using bulk measurements. We demonstrate the applicability of the test by studying the unfolding process of the protein BBL, which has been previously characterized as a downhill folding protein. This test should be very useful for high-throughput design strategies and for the analysis of mutational effects in small proteins. PMID:15250680

  12. Cuentos Faciles. Habia una vez.... (Simple Stories. There was a Time....) (Presenting Simple Stories in Spanish.)

    Science.gov (United States)

    Arroyo, Nancy; And Others

    For Spanish-speaking children, simple stories in Spanish, told in a natural language suitable for their age, are not only entertaining, but a means of developing vocabulary and concepts. Non-Spanish-speaking children, too, need exposure to more language than they can understand word for word. However, the simple stories for the Spanish speaker…

  13. Simple solutions for reduced fish farm hazards.

    Science.gov (United States)

    Myers, Melvin L; Cole, Henry P

    2009-01-01

    Aquaculture poses emerging challenges for agricultural safety and health. Fish farming has many of the same hazards as other types of farming, but it also poses additional hazards associated with water impoundments and night-time work. In a multidisciplinary approach, researchers from four universities are identifying occupational hazards in fish farming and identifying no-cost or low-cost "simple solutions" to reduce or eliminate them. Simple solutions are discovered through farm visits so as to understand the countermeasures that individual stakeholders have taken to protect their workforce, and these countermeasures are documented and photographed to inform other farmers of these solutions. Equipping tractors with rollover protective structures is a standard practice to protect operators from serious injury in the event of an overturn. Other solutions identified include eliminating the need to climb feed bins to open and close the hatch for feed delivery by using a pull-cable at ground level. This simple technology eliminates the exposure to falling from an elevation, a risk that accounts for at least one reported death of a worker on a fish farm. Another solution is to replace metal paddles on a hatchery trough with plastic paddles that if and when entangled in a worker's hair or clothing slip on the rotating drive shaft and thus reduce laceration and entanglement injuries. Another simple solution to prevent entanglements in large pond aerators, used to mechanically dissolve oxygen into the water, that are operated by farm tractor power take-off shafts is to use electrically powered aerators. Bubble-type aerators are safer than electrically powered paddle aerators because workers are shielded from moving parts. Many additional simple solutions have been identified for a range of tasks in this environment. PMID:19437271

  14. A simple assay for measurement of ovotransferrin - a marker of inflammation and infection in birds

    NARCIS (Netherlands)

    Horrocks, Nicholas P. C.; Tieleman, B. Irene; Matson, Kevin D.

    2011-01-01

    1. Ovotransferrin is an acute-phase protein with iron-binding and immunomodulatory functions. In poultry, ovotransferrin levels increase in response to inflammation or infection, but little is known about responses in wild bird species. 2. We present a simple assay for the determination of ovotransf

  15. Mathematical methods for protein science

    Energy Technology Data Exchange (ETDEWEB)

    Hart, W.; Istrail, S.; Atkins, J. [Sandia National Labs., Albuquerque, NM (United States)

    1997-12-31

    Understanding the structure and function of proteins is a fundamental endeavor in molecular biology. Currently, over 100,000 protein sequences have been determined by experimental methods. The three dimensional structure of the protein determines its function, but there are currently less than 4,000 structures known to atomic resolution. Accordingly, techniques to predict protein structure from sequence have an important role in aiding the understanding of the Genome and the effects of mutations in genetic disease. The authors describe current efforts at Sandia to better understand the structure of proteins through rigorous mathematical analyses of simple lattice models. The efforts have focused on two aspects of protein science: mathematical structure prediction, and inverse protein folding.

  16. Biomedical sensors for disease detection made simple

    DEFF Research Database (Denmark)

    Veldhuis, Djuke

    2015-01-01

    Researchers in Korea have succeeded in making a new protein detection platform, using low-cost plastic and paper substrates. Their work could help reduce the cost and improve the accuracy of infectious disease diagnosis....

  17. Power spectra of a constrained totally asymmetric simple exclusion process

    Science.gov (United States)

    Cook, L. Jonathan; Zia, R. K. P.

    2010-07-01

    In nature, all biological systems function in a far-from-equilibrium state. Here, we study the process of translation in protein synthesis, using the totally asymmetric simple exclusion process (TASEP) as a model. In particular, we explore the effects of a finite supply of particles for the TASEP, as in a living cell with a finite pool of ribosomes. Specifically, we investigate the power spectrum associated with total occupancy, utilizing both Monte Carlo simulations and theoretical analysis. New features arise, such as large suppressions at low frequencies, due to the added constraint. A theory is formulated based on a Langevin approach with discrete space and time. With good agreement between the simulation and theory, we gain some insights into the effects of finite resources on the TASEP.

  18. SWITCHING CONTROL:FROM SIMPLE RULES TO COMPLEX CHAOTIC SYSTEMS

    Institute of Scientific and Technical Information of China (English)

    L(U) Jinhu

    2003-01-01

    This paper reviews and introduces some simple switching piecewise-linear controllers, which can generate complex chaotic behaviors from simple switching systems. The mechanism of simple switching rules creating complex chaotic behaviors is further investigated.

  19. A simple fibril and lectin model for cyst walls of Entamoeba and perhaps Giardia.

    Science.gov (United States)

    Samuelson, John; Robbins, Phillips

    2011-01-01

    Cyst walls of Entamoeba and Giardia protect them from environmental insults, stomach acids, and intestinal proteases. Each cyst wall contains a sugar homopolymer: chitin in Entamoeba and a unique N-acetylgalactosamine (GalNAc) homopolymer in Giardia. Entamoeba cyst wall proteins include Jacob lectins (carbohydrate-binding proteins) that crosslink chitin, chitinases that degrade chitin, and Jessie lectins that make walls impermeable. Giardia cyst wall proteins are also lectins that bind fibrils of the GalNAc homopolymer. Although many of the details remain to be determined for the cyst wall of Giardia, current data suggest a relatively simple fibril and lectin model for the Entamoeba cyst wall.

  20. BASIC: A Simple and Accurate Modular DNA Assembly Method.

    Science.gov (United States)

    Storch, Marko; Casini, Arturo; Mackrow, Ben; Ellis, Tom; Baldwin, Geoff S

    2017-01-01

    Biopart Assembly Standard for Idempotent Cloning (BASIC) is a simple, accurate, and robust DNA assembly method. The method is based on linker-mediated DNA assembly and provides highly accurate DNA assembly with 99 % correct assemblies for four parts and 90 % correct assemblies for seven parts [1]. The BASIC standard defines a single entry vector for all parts flanked by the same prefix and suffix sequences and its idempotent nature means that the assembled construct is returned in the same format. Once a part has been adapted into the BASIC format it can be placed at any position within a BASIC assembly without the need for reformatting. This allows laboratories to grow comprehensive and universal part libraries and to share them efficiently. The modularity within the BASIC framework is further extended by the possibility of encoding ribosomal binding sites (RBS) and peptide linker sequences directly on the linkers used for assembly. This makes BASIC a highly versatile library construction method for combinatorial part assembly including the construction of promoter, RBS, gene variant, and protein-tag libraries. In comparison with other DNA assembly standards and methods, BASIC offers a simple robust protocol; it relies on a single entry vector, provides for easy hierarchical assembly, and is highly accurate for up to seven parts per assembly round [2].

  1. A simple method suitable to study de novo root organogenesis

    Directory of Open Access Journals (Sweden)

    Xiaodong eChen

    2014-05-01

    Full Text Available De novo root organogenesis is the process in which adventitious roots regenerate from detached or wounded plant tissues or organs. In tissue culture, appropriate types and concentrations of plant hormones in the medium are critical for inducing adventitious roots. However, in natural conditions, regeneration from detached organs is likely to rely on endogenous hormones. To investigate the actions of endogenous hormones and the molecular mechanisms guiding de novo root organogenesis, we developed a simple method to imitate natural conditions for adventitious root formation by culturing Arabidopsis thaliana leaf explants on B5 medium without additive hormones. Here we show that the ability of the leaf explants to regenerate roots depends on the age of the leaf and on certain nutrients in the medium. Based on these observations, we provide examples of how this method can be used in different situations, and how it can be optimized. This simple method could be used to investigate the effects of various physiological and molecular changes on the regeneration of adventitious roots. It is also useful for tracing cell lineage during the regeneration process by differential interference contrast observation of -glucuronidase staining, and by live imaging of proteins labeled with fluorescent tags.

  2. Is the world simple or complicated

    CERN Document Server

    Barrow, John D

    1998-01-01

    Stop some particle physicists in the street and they will soon be trying to persuade you that the world is altogether simple and symmetrical. But stop a biologist, an economist, or a social scientist and they will tell you quite the opposite: the world is a higgledy-piggledy collection of complexities that owes little to symmetry and displays precious little simplicity. So who is right : is the world really complicated or is it simple ? We shall look at the reasoning that leads to these different conclusions, show why we got different answers to our question, and look at some of the recent developments that have taken place in the study of systems from sand-piles to music on the border between order and chaos. We shall also look at some of the connections between our aesthetic sensibilities and the structure of scientific theories.

  3. On Nichols algebras associated to simple racks

    CERN Document Server

    Andruskiewitsch, N; Garcia, G A; Vendramin, L

    2010-01-01

    This is a report on the present state of the problem of determining the dimension of the Nichols algebra associated to a rack and a cocycle. This is relevant for the classification of finite-dimensional complex pointed Hopf algebras whose group of group-likes is non-abelian. We deal mainly with simple racks. We recall the notion of rack of type D, collect the known lists of simple racks of type D and include preliminary results for the open cases. This notion is important because the Nichols algebra associated to a rack of type D and any cocycle has infinite dimension. For those racks not of type D, the computation of the cohomology groups is needed. We discuss some techniques for this problem and compute explicitly the cohomology groups corresponding to some conjugacy classes in symmetric or alternating groups of low order.

  4. Simple educational tool for digital speckle shearography

    International Nuclear Information System (INIS)

    In this study, an educational tool has been prepared for obtaining short-term and more economic training on digital speckle shearography (DSS). Shearography non-destructive testing (NDT) has gained wide acceptance over the last decade, providing a number of important and exciting inspection solutions in aerospace, electronics and medical device manufacturing. For exploring these motivations, it is important to develop didactic tools to understand the potential of digital shearography through training and didactic courses in the field of NDT. In this paper we describe a simple tool for making one familiar with the potential of DSS in the area of education and training. The system is realized with a simple and economic optical setup and a virtual instrument based on the LabVIEW™ and DAQ. (paper)

  5. Simple chloride sensors for continuous groundwater monitoring

    DEFF Research Database (Denmark)

    Thorn, Paul; Mortensen, John

    2012-01-01

    The development of chloride sensors which can be used for continuous, on-line monitoring of groundwater could be very valuable in the management of our coastal water resources. However, sensor stability, drift, and durability all need to be addressed in order for the sensors to be used...... in continuous application. This study looks at the development of a simple, inexpensive chloride electrode, and evaluates its performance under continuous use, both in the laboratory and in a field test in a monitoring well. The results from the study showed a consistent response to changing chloride...... sensor remained responsive even at low chloride concentrations, where the conductivity electrode was no longer responding to changing chloride levels. With the results, it is believed that the simple chloride sensor could be used for continuous monitoring of groundwater quality....

  6. Simple model of stacking-fault energies

    DEFF Research Database (Denmark)

    Stokbro, Kurt; Jacobsen, Lærke Wedel

    1993-01-01

    -density calculations of stacking-fault energies, and gives a simple way of understanding the calculated energy contributions from the different atomic layers in the stacking-fault region. The two parameters in the model describe the relative energy contributions of the s and d electrons in the noble and transition......A simple model for the energetics of stacking faults in fcc metals is constructed. The model contains third-nearest-neighbor pairwise interactions and a term involving the fourth moment of the electronic density of states. The model is in excellent agreement with recently published local...... metals, and thereby explain the pronounced differences in energetics in these two classes of metals. The model is discussed in the framework of the effective-medium theory where it is possible to find a functional form for the pair potential and relate the contribution associated with the fourth moment...

  7. The SIMPLE Phase II Dark Matter Search

    CERN Document Server

    Felizardo, M; Morlat, T; Fernandes, A C; Ramos, A R; Marques, J G; Kling, A; Puibasset, J; Auguste, M; Boyer, D; Cavaillou, A; Poupeney, J; Sudre, C; Carvalho, F P; Prudencio, M I; Marques, R

    2014-01-01

    Phase II of SIMPLE (Superheated Instrument for Massive ParticLe Experiments) searched for astroparticle dark matter using superheated liquid C$_{2}$ClF$_{5}$ droplet detectors. Each droplet generally requires an energy deposition with linear energy transfer (LET) $\\gtrsim$ 150 keV/$\\mu$m for a liquid-to-gas phase transition, providing an intrinsic rejection against minimum ionizing particles of order 10$^{-10}$, and reducing the backgrounds to primarily $\\alpha$ and neutron-induced recoil events. The droplet phase transition generates a millimetric-sized gas bubble which is recorded by acoustic means. We describe the SIMPLE detectors, their acoustic instrumentation, and the characterizations, signal analysis and data selection which yield a particle-induced, "true nucleation" event detection efficiency of better than 97% at a 95% C.L. The recoil-$\\alpha$ event discrimination, determined using detectors first irradiated with neutrons and then doped with alpha emitters, provides a recoil identification of bette...

  8. Molecular implementation of simple logic programs

    Science.gov (United States)

    Ran, Tom; Kaplan, Shai; Shapiro, Ehud

    2009-11-01

    Autonomous programmable computing devices made of biomolecules could interact with a biological environment and be used in future biological and medical applications. Biomolecular implementations of finite automata and logic gates have already been developed. Here, we report an autonomous programmable molecular system based on the manipulation of DNA strands that is capable of performing simple logical deductions. Using molecular representations of facts such as Man(Socrates) and rules such as Mortal(X) system can answer molecular queries such as Mortal(Socrates)? (Is Socrates Mortal?) and Mortal(X)? (Who is Mortal?). This biomolecular computing system compares favourably with previous approaches in terms of expressive power, performance and precision. A compiler translates facts, rules and queries into their molecular representations and subsequently operates a robotic system that assembles the logical deductions and delivers the result. This prototype is the first simple programming language with a molecular-scale implementation.

  9. Magnetic monopole interactions in simple atoms

    International Nuclear Information System (INIS)

    The excitation of simple atoms by slow moving massive monopoles is discussed. Previously presented results for a monopole of Dirac strength on hydrogen and helium are reviewed, and current efforts to refine the helium result are described. Helium proportional counters currently in operation which exploit this effect are briefly discussed. It is concluded that such counters are reliable and effective detectors for monopoles of arbitrary strength, and for negatively charged ions. (author)

  10. Insurance and Redistribution with Simple Tax Instruments

    OpenAIRE

    Sachs, Dominik; Findeisen, Sebastian

    2015-01-01

    We study optimal nonlinear taxation of labor income and linear taxation of capital income in a life-cycle framework with private information and idiosyncratic risk. We focus on simple history-independent tax instruments. We first analyze the welfare losses from this simplification as compared to optimal history-dependent policies. We find very small losses from restricting the complexity of savings wedges. Eliminating history dependence of labor wedges leads to larger welfare losses: moving f...

  11. The simple persistent unique digital store (SPUDS)

    OpenAIRE

    Gibson, Hilton

    2010-01-01

    This paper introduces the concept of the simple persistent unique digital store which is an attempt to provide a means of digital object storage that will survive one hundred years into the future using open standards , technologies and formats. In addition it will attempt to make the digital object store independent of the software used to ingest, store, manage and disseminate the objects. Doing this greatly eliminates the risk of the present interdependence of the digital object store with ...

  12. A simple model of quantum trajectories

    OpenAIRE

    Brun, Todd A.

    2001-01-01

    Quantum trajectory theory, developed largely in the quantum optics community to describe open quantum systems subjected to continuous monitoring, has applications in many areas of quantum physics. In this paper I present a simple model, using two-level quantum systems (q-bits), to illustrate the essential physics of quantum trajectories and how different monitoring schemes correspond to different ``unravelings'' of a mixed state master equation. I also comment briefly on the relationship of t...

  13. A simple model of aggregate pension expenditure

    OpenAIRE

    Fuente, Ángel de la

    2011-01-01

    This paper develops a simple model that can be used to analyze the long-term sustainability of the contributive pension system and the steady-state response of pension expenditure to changes in some key demographic and economic variables, in the characteristics of the average pensioner an d in the parameters that describe how pensions are calculated in Spain as a function of workers’ Social Security contribution histories.

  14. Simple 2-representations and Classification of Categorifications

    DEFF Research Database (Denmark)

    Agerholm, Troels

    We consider selfadjoint functors defined on categories of modules over finite dimensional algebras and classify those that satisfy some simple relations. In particular we classify self- adjoint idempotents and selfadjoint squareroots of a multiple of the identity functor. This is related to the t...... to the theory of algebraic categorification which we review with the viewpoint that a genuine categorification is a 2-representation of a 2-category....

  15. SLURM: Simple Linux Utility for Resource Management

    Energy Technology Data Exchange (ETDEWEB)

    Jette, M; Dunlap, C; Garlick, J; Grondona, M

    2002-07-08

    Simple Linux Utility for Resource Management (SLURM) is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for Linux clusters of thousands of nodes. Components include machine status, partition management, job management, scheduling and stream copy modules. The design also includes a scalable, general-purpose communication infrastructure. This paper presents a overview of the SLURM architecture and functionality.

  16. A simple Cartesian scheme for compressible multimaterials

    CERN Document Server

    Gorsse, Yannick; Milcent, Thomas; TELIB, Haysam

    2014-01-01

    We present a simple numerical method to simulate the interaction of two non-miscible compressible materials separated by an interface. The media considered may have significantly different physical properties and constitutive laws, describing for example fluids or hyperelastic solids. The model is fully Eulerian and the scheme is the same for all materials. We show stiff numerical illustrations in case of gas--gas, gas--water, gas--elastic solid interactions in the large deformation regime.

  17. Simple models of evolution and extinction

    CERN Document Server

    Newman, M E J

    1999-01-01

    This article gives a brief introduction to the mathematical modeling of large-scale biological evolution and extinction. We give three examples of simple models in this field: the coevolutionary avalanche model of Bak and Sneppen, the environmental stress model of Newman, and the increasing fitness model of Sibani, Schmidt, and Alstrom. We describe the features of real evolution which these models are intended to explain and compare the results of simulations against data drawn from the fossil record.

  18. Simple models of evolution and extinction

    OpenAIRE

    Newman, M. E. J.

    1999-01-01

    This article gives a brief introduction to the mathematical modeling of large-scale biological evolution and extinction. We give three examples of simple models in this field: the coevolutionary avalanche model of Bak and Sneppen, the environmental stress model of Newman, and the increasing fitness model of Sibani, Schmidt, and Alstrom. We describe the features of real evolution which these models are intended to explain and compare the results of simulations against data drawn from the fossi...

  19. Multiphase flow in geometrically simple fracture intersections

    Science.gov (United States)

    Basagaoglu, H.; Meakin, P.; Green, C.T.; Mathew, M.

    2006-01-01

    A two-dimensional lattice Boltzmann (LB) model with fluid-fluid and solid-fluid interaction potentials was used to study gravity-driven flow in geometrically simple fracture intersections. Simulated scenarios included fluid dripping from a fracture aperture, two-phase flow through intersecting fractures and thin-film flow on smooth and undulating solid surfaces. Qualitative comparisons with recently published experimental findings indicate that for these scenarios the LB model captured the underlying physics reasonably well.

  20. SWiM: A Simple Window Mover

    OpenAIRE

    Chang, Tony; Cook, Damon; Su, Ramona

    2005-01-01

    As computers become more ubiquitous, traditional two-dimensional interfaces must be replaced with interfaces based on a three-dimensional metaphor. However, these interfaces must still be as simple and functional as their two-dimensional predecessors. This paper introduces SWiM, a new interface for moving application windows between various screens, such as wall displays, laptop monitors, and desktop displays, in a three-dimensional physical environment. SWiM was designed based on the results...

  1. A simple proof of Sarkozy's theorem

    CERN Document Server

    Lyall, Neil

    2011-01-01

    It is a striking and elegant fact (proved independently by Furstenberg and Sarkozy) that in any subset of the natural numbers of positive upper density there necessarily exist two distinct elements whose difference is given by a perfect square. In this article we present a new and simple proof of this result by adapting an argument originally developed by Croot and Sisask to give a new proof of Roth's theorem.

  2. Multiphase Flow in Geometrically Simple Fracture Intersections

    Energy Technology Data Exchange (ETDEWEB)

    Hakan Basagaoglu; Paul Meakin; Sauro Succi; Timothy R. Ginn

    2006-03-01

    A two-dimensional lattice Boltzmann (LB) model with fluid-fluid and solid-fluid interaction potentials was used to Study gravity-driven flow in geometrically simple fracture intersections. simulated scenarios included fluid dripping from a fracture aperture, two-phase flow through intersecting fractures and thin-filin flow oil smooth and undulating solid surfaces. Qualitative comparisons with recently published experimental findings indicate that for these scenarios the LB model captured the underlying physics reasonably well.

  3. Simple model of resource exploitation”

    OpenAIRE

    Reis, A. Heitor

    2010-01-01

    Here we present a simple model of finite resource exploitation that is parameterized by initial cost ratio, a technologic and management index m accounting for the rise of the exploitation cost with decrease of resource amount, plus another index  accounting for the avidity of the market to the resource. The analysis showed that the model captures essential features of finite resource exploitation, namely those concerning to oil exploitation. Scenarios for future oil exploitat...

  4. Radioluminescence : A simple model for fluorescent layers

    OpenAIRE

    Lindström, Jan

    2011-01-01

    The aim of this thesis is to present a simple model for the radiation to light conversion processes in fluorescent layers as an aid in future developments and applications. Optimisation between sensitivity and spatial resolution for fluorescent layers in digital radiology is a delicate task where the extrinsic efficiency for various phosphors needs to be established for varying parameters. The extrinsic efficiency of a fluorescent layer can be expressed as the ratio of the light energy per un...

  5. Liouville Extensions of Artinian Simple Module Algebras

    OpenAIRE

    Amano, Katsutoshi

    2006-01-01

    In a previous article (Amano and Masuoka, 2005), the author and Masuoka developed a Picard-Vessiot theory for module algebras over a cocommutative pointed smooth Hopf algebra D. By using the notion of Artinian simple (AS)D-module algebras, it generalizes and unifies the standard Picard-Vessiot theories for linear differential and difference equations. The purpose of this article is to define the notion of Liouville extensions of AS D-module algebras and to characterize the corresponding Picar...

  6. Two simple models of classical heat pumps

    OpenAIRE

    Marathe, Rahul; Jayannavar, A. M.; Dhar, Abhishek

    2006-01-01

    Motivated by recent studies on models of particle and heat quantum pumps, we study similar simple classical models and examine the possibility of heat pumping. Unlike many of the usual ratchet models of molecular engines, the models we study do not have particle transport. We consider a two-spin system and a coupled oscillator system which exchange heat with multiple heat reservoirs and which are acted upon by periodic forces. The simplicity of our models allows accurate numerical and exact s...

  7. A Simple Experiment for Visualizing Diffusion

    Science.gov (United States)

    Helseth, L. E.

    2011-01-01

    We propose a simple and fascinating experiment for studying diffusion in gels using a pH-sensitive dye. By doping agar with methyl red, we obtain a gel which rapidly reacts to changes in pH by changing its absorption spectrum. The pH gradients can be followed using a digital camera, and we demonstrate here that the pH-sensitive colour changes can…

  8. A simple model of dimensional collapse

    CERN Document Server

    Correia, J D

    1996-01-01

    We consider a simple model of d families of scalar field interacting with geometry in two dimensions. The geometry is locally flat and has only global degrees of freedom. When d0 it collapses to a one dimensional manifold. The model has some, but not all, of the characteristics believed to be features of the full theory of conformal matter interacting with quantum gravity which has local geometric degrees of freedom.

  9. A Simple Analysis on Business English Translation

    Institute of Scientific and Technical Information of China (English)

    Jiang Yue

    2016-01-01

    With the development of economic globalization, foreign business activities have penetrated into all aspects of the society. Meanwhile business English translation plays an indispensable role in foreign business communication as a bridge. This paper carries out a simple analysis about business English translation based on three aspects: linguistic features of business English, translation methods of business English, criteria in business English translation. Based on the analysis, some feasible suggestions have been proposed for business English translators.

  10. Simple Benchmark Specifications for Space Radiation Protection

    Science.gov (United States)

    Singleterry, Robert C. Jr.; Aghara, Sukesh K.

    2013-01-01

    This report defines space radiation benchmark specifications. This specification starts with simple, monoenergetic, mono-directional particles on slabs and progresses to human models in spacecraft. This report specifies the models and sources needed to what the team performing the benchmark needs to produce in a report. Also included are brief descriptions of how OLTARIS, the NASA Langley website for space radiation analysis, performs its analysis.

  11. Badlands: too complex to be simple?

    Science.gov (United States)

    Kuhn, Nikolaus J.

    2016-04-01

    Badlands are an intensively dissected barren landscape, devoid of soil cover, with a sparse or absent vegetation. The very high drainage densities, V-shaped valleys and steep slopes, have often led to believe that badlands represent a landscape where the frequency and magnitude of overland flow and erosion processes are very high, resulting in rapid landscape evolution and a close connection between form and process. This perceived proximity between form and process is the main reason why badlands have sometimes been regarded as "ideal field laboratories" for testing landscape evolution hypothesis. Recent research has shed a critical light on the "simple landscape" perspective. Two key issues support this change in persprective. First, the erosion rates and sediment yields observed badland areas vary widely. As a consequence, only weak relationships were found between average annual rainfall and average erosion rates for annual rainfalls in the wide range of 80-1250 mm. Both the spatial variability and the limited relationship to annual rainfall present a serious barrier for the extrapolation of erosion rates from the hill slope to catchment scales and certainly to landscape evolution over longer geological time scales under changing climatic conditions. A second reason contradicting the simple landscape assessment is the mismatch observed between current erosion rates and the long-term denudation rates, indicating a hiatus between a potentially short period of badland formation and the overall age of the landform. As a consequence, the actual meaning of badland has been questioned, ranging from a description for features to a more complex meaning including current erosion and complex interaction of processes, such as pipe and tunnel erosion. In the light of this critical assessment, the idea of badlands as a "natural and simple laboratory" for landscape development can be questioned because badlands are too complex to be simple. However, one could also wonder

  12. Einstein solvmanifolds with a simple Einstein derivation

    OpenAIRE

    Nikolayevsky, Y.

    2007-01-01

    The structure of a solvable Lie groups admitting an Einstein left-invariant metric is, in a sense, completely determined by the nilradical of its Lie algebra. We give an easy-to-check necessary and sufficient condition for a nilpotent algebra to be an Einstein nilradical whose Einstein derivation has simple eigenvalues. As an application, we classify filiform Einstein nilradicals (modulo known classification results on filiform graded Lie algebras).

  13. Simple Euclidean arrangements with one (>=5)-gon

    CERN Document Server

    Leaños, Jesus; Rivera-Martinez, Luis Manuel

    2010-01-01

    Let L be a simple Euclidean arrangement of n pseudolines. It is shown that if L has exactly one (>=5)=gon P, and k is the number of edges of P that are adjacent to an unbounded cell of the subarrangement of L induced by the pseudolines in P, then L has exactly n-k triangles and k+n(n-5)/2 quadrilaterals. We also prove that if each pseudoline of L is adjacent to P then L is stretchable.

  14. Nonanonymity and sensitivity of computable simple games

    OpenAIRE

    H. Reiju Mihara

    2003-01-01

    This paper investigates algorithmic computability of simple games (voting games). It shows that (i) games with a finite carrier are computable, (ii) computable games have both finite winning coalitions and cofinite losing coalitions, and (iii) computable games violate any conceivable notion of anonymity, including finite anonymity and measurebased anonymity. The paper argues that computable games are excluded from the intuitive class of gnice h infinite games, employing the notion of ginsensi...

  15. Behaviour of Polariton in a Simple Model

    Institute of Scientific and Technical Information of China (English)

    WAN Shao-Long; MA Shuang-Ge; WANG Ke-Lin

    2003-01-01

    Behaviour of a simple model polariton system is restudied. The distribution of phonons in polariton never is sub-Poisson given by computation of the thermal counterpart of the Q parameter and the matrix m'3\\ The polariton complex as a whole shows non-classical behaviour below a threshold temperature, which depends on the photon-phonon coupling strength, when the distribution of phonons is always classical at any temperature.

  16. APPLYING SIMPLE TECHNOLOGY ACCOMPLISHES VISUAL INSPECTION CHALLENGES

    Energy Technology Data Exchange (ETDEWEB)

    Robinson, C

    2007-07-21

    This paper discusses the successful implementation of simple video technologies at the Savannah River Site (SRS) to perform complex visual inspection, monitoring, and surveillance tasks. Because SRS facilities are similar to those of an industrial plant, the environmental and accessibility considerations for remote viewing are the primary determining factors in the selection of technology. The constraints and challenges associated with remote viewing are discussed, and examples of applications are given.

  17. The Monash University Interactive Simple Climate Model

    Science.gov (United States)

    Dommenget, D.

    2013-12-01

    The Monash university interactive simple climate model is a web-based interface that allows students and the general public to explore the physical simulation of the climate system with a real global climate model. It is based on the Globally Resolved Energy Balance (GREB) model, which is a climate model published by Dommenget and Floeter [2011] in the international peer review science journal Climate Dynamics. The model simulates most of the main physical processes in the climate system in a very simplistic way and therefore allows very fast and simple climate model simulations on a normal PC computer. Despite its simplicity the model simulates the climate response to external forcings, such as doubling of the CO2 concentrations very realistically (similar to state of the art climate models). The Monash simple climate model web-interface allows you to study the results of more than a 2000 different model experiments in an interactive way and it allows you to study a number of tutorials on the interactions of physical processes in the climate system and solve some puzzles. By switching OFF/ON physical processes you can deconstruct the climate and learn how all the different processes interact to generate the observed climate and how the processes interact to generate the IPCC predicted climate change for anthropogenic CO2 increase. The presentation will illustrate how this web-base tool works and what are the possibilities in teaching students with this tool are.

  18. A Simple Model for Quasar Demographics

    CERN Document Server

    Conroy, Charlie

    2012-01-01

    We present a simple model for the relationship between quasars, galaxies, and dark matter halos from 0simple "scattered" light bulb model for quasars is adopted, wherein BHs shine at a fixed fraction of the Eddington luminosity during accretion episodes, and Eddington ratios are drawn from a lognormal distribution that is redshift-independent. This model has two free, physically meaningful parameters at each redshift, the normalization of the M_BH-M_gal relation and the quasar duty cycle; these parameters are fit to the observed quasar luminosity function (LF) over the interval 0.5simple model provides an excellent fit to the LF at all epochs, and also successfully predicts the observed projected two-point correlation of quasars from 0.5

  19. Modeling reproductive decisions with simple heuristics

    Directory of Open Access Journals (Sweden)

    Peter Todd

    2013-10-01

    Full Text Available BACKGROUND Many of the reproductive decisions that humans make happen without much planning or forethought, arising instead through the use of simple choice rules or heuristics that involve relatively little information and processing. Nonetheless, these heuristic-guided decisions are typically beneficial, owing to humans' ecological rationality - the evolved fit between our constrained decision mechanisms and the adaptive problems we face. OBJECTIVE This paper reviews research on the ecological rationality of human decision making in the domain of reproduction, showing how fertility-related decisions are commonly made using various simple heuristics matched to the structure of the environment in which they are applied, rather than being made with information-hungry mechanisms based on optimization or rational economic choice. METHODS First, heuristics for sequential mate search are covered; these heuristics determine when to stop the process of mate search by deciding that a good-enough mate who is also mutually interested has been found, using a process of aspiration-level setting and assessing. These models are tested via computer simulation and comparison to demographic age-at-first-marriage data. Next, a heuristic process of feature-based mate comparison and choice is discussed, in which mate choices are determined by a simple process of feature-matching with relaxing standards over time. Parental investment heuristics used to divide resources among offspring are summarized. Finally, methods for testing the use of such mate choice heuristics in a specific population over time are then described.

  20. Prevalence of Simple Renal Cysts in Acromegaly.

    Science.gov (United States)

    Yamamoto, Masaaki; Matsumoto, Ryusaku; Fukuoka, Hidenori; Iguchi, Genzo; Takahashi, Michiko; Nishizawa, Hitoshi; Suda, Kentaro; Bando, Hironori; Takahashi, Yutaka

    2016-01-01

    Objective Various organs are known to be affected by the comorbidities of acromegaly. However, the involvement of renal structural comorbidities, such as cysts, has so far remained largely unknown. In this single-center study, we aimed to determine the prevalence and factors associated with simple renal cysts in Japanese patients with acromegaly. Methods A total of 71 consecutive patients with acromegaly were analyzed, who all underwent abdominal ultrasonography at diagnosis between 1986 and 2012 at Kobe University Hospital. Results Of these 71 patients, 23 (32.4%) exhibited simple renal cysts. Acromegalic patients with renal cysts tended to be significantly older, had a higher prevalence of smoking- and higher nadir growth hormone (GH) levels during the oral glucose tolerance test (OGTT) than did those without renal cysts. A multivariate logistic regression analysis showed age, smoking, and nadir GH to be independent factors associated with renal cysts. Interestingly, the number of renal cysts positively correlated with both the basal GH levels and nadir GH levels during OGTT (r=0.66, pacromegaly. Elevated nadir GH levels during OGTT were found to be associated with an increased risk of simple renal cysts. Therefore, an excessive secretion of GH may be related to the development of renal cysts. PMID:27374666

  1. A NASA Recipe for Protein Crystallography. Educational Brief.

    Science.gov (United States)

    National Aeronautics and Space Administration, Washington, DC.

    This brief discusses growing protein crystals. Protein crystals can be very difficult to grow. This activity for grades 9-12 provides a simple recipe for growing protein crystals from Brazil nuts. Included are a history of protein crystals, a discussion of microgravity effects on growth, connections to academic standards, and lab sheets. (MVL)

  2. IVOA Recommendation: SimpleDALRegExt: Describing Simple Data Access Services

    CERN Document Server

    Plante, Raymond; Harrison, Paul; Tody, Doug

    2014-01-01

    An application that queries or consumes descriptions of VO resources must be able to recognize a resource's support for standard IVOA protocols. This specification describes how to describe a service that supports any of the four fundamental data access protocols -- Simple Cone Search (SCS), Simple Image Access (SIA), Simple Spectral Access (SSA), Simple Line Access (SLA) -- using the VOResource XML encoding standard. A key part of this specification is the set of VOResource XML extension schemas that define new metadata that are specific to those protocols. This document describes in particular rules for describing such services within the context of IVOA Registries and data discovery as well as the VO Standard Interface (VOSI) and service self-description. In particular, this document spells out the essential markup needed to identify support for a standard protocol and the base URL required to access the interface that supports that protocol.

  3. Simple method for purification of enterotoxigenic Escherichia coli fimbriae.

    Science.gov (United States)

    Curtis, Brittany; Grassel, Christen; Laufer, Rachel S; Sears, Khandra T; Pasetti, Marcela F; Barry, Eileen M; Simon, Raphael

    2016-03-01

    Enterotoxigenic Escherichia coli (ETEC) are endemic pathogens in the developing world. They frequently cause illness in travelers, and are among the most prevalent causes of diarrheal disease in children. Pathogenic ETEC strains employ fimbriae as adhesion factors to bind the luminal surface of the intestinal epithelium and establish infection. Accordingly, there is marked interest in immunoprophylactic strategies targeting fimbriae to protect against ETEC infections. Multiple strategies have been reported for purification of ETEC fimbriae, however none is ideal. Purification has typically involved the use of highly virulent wild-type strains. We report here a simple and improved method to purify ETEC fimbriae, which was applied to obtain two different Class 5 fimbriae types of clinical relevance (CFA/I and CS4) expressed recombinantly in E. coli production strains. Following removal from cells by shearing, fimbriae proteins were purified by orthogonal purification steps employing ultracentrifugation, precipitation, and ion-exchange membrane chromatography. Purified fimbriae demonstrated the anticipated size and morphology by electron microscopy analysis, contained negligible levels of residual host cell proteins, nucleic acid, and endotoxin, and were recognized by convalescent human anti-sera.

  4. A 'simple' hybrid model for power derivatives

    International Nuclear Information System (INIS)

    This paper presents a method for valuing power derivatives using a supply-demand approach. Our method extends work in the field by incorporating randomness into the base load portion of the supply stack function and equating it with a noisy demand process. We obtain closed form solutions for European option prices written on average spot prices considering two different supply models: a mean-reverting model and a Markov chain model. The results are extensions of the classic Black-Scholes equation. The model provides a relatively simple approach to describe the complicated price behaviour observed in electricity spot markets and also allows for computationally efficient derivatives pricing. (author)

  5. Theory of high pressure hydrogen, made simple

    CERN Document Server

    Magdau, Ioan B; Ackland, Graeme J

    2015-01-01

    Phase I of hydrogen has several peculiarities. Despite having a close-packed crystal structure, it is less dense than either the low temperature Phase II or the liquid phase. At high pressure, it transforms into either phase III or IV, depending on the temperature. Moreover, spectroscopy suggests that the quantum rotor behaviour disappears with pressurisation, without any apparent phase transition. Here we present a simple thermodynamic model for this behaviour based on packing atoms and molecules and discuss the thermodynamics of the phase boundaries. We also report first principles molecular dynamics calculations for a more detailed look at the same phase transitions.

  6. Neutrosophic Correlation and Simple Linear Regression

    Directory of Open Access Journals (Sweden)

    A. A. Salama

    2014-09-01

    Full Text Available Since the world is full of indeterminacy, the neutrosophics found their place into contemporary research. The fundamental concepts of neutrosophic set, introduced by Smarandache. Recently, Salama et al., introduced the concept of correlation coefficient of neutrosophic data. In this paper, we introduce and study the concepts of correlation and correlation coefficient of neutrosophic data in probability spaces and study some of their properties. Also, we introduce and study the neutrosophic simple linear regression model. Possible applications to data processing are touched upon.

  7. A Simple Class of Measures of Skewness

    OpenAIRE

    ALTINAY, Galip

    2016-01-01

    In this paper, a simple class of measures for detecting skewness in samples is introduced. The new class of measures is based on a new definition of skewness that takes midrange into consideration. The proposed coefficients of skewness can be computed easily with only three of the summary statistics, i.e., the minimum value, the maximum value and the median (or the mode, or the mean). Another advantage of the new statistics is that they are bounded by -1 and +1, hence, the coefficients of ske...

  8. A simple ear splint for microtia patients

    Directory of Open Access Journals (Sweden)

    C J Venkata Krishnan

    2015-01-01

    Full Text Available Microtia is a congenital anomaly of the ear can occur as an isolated birth defect or as part of a spectrum of anomalies or as a syndrome. Microtia is often associated with impaired hearing and or total loss of hearing. Such patients typically require treatment for surgical ear reconstruction and for hearing impairment. Maintenance of ear projection and post auricular sulcus in staged ear reconstruction in microtia is a trying problem. So also is the maintenance of the patency of the external auditory meatus following recanalization and meatoplasty.This case report describes a simple effective way of fabrication of ear splint prosthesis.

  9. Semi-simple rings and commutativity

    OpenAIRE

    Giri, R. D.; Bujade, V. G.

    1992-01-01

    Sia R un anello semisemplice. Si prova che se per ogni coppia di elementi x, y in R esistono interi positivi m=m(x, y) ed n=(x, y) tali che $\\left[\\left[\\left(yxy\\right)^{m},\\left(x,y\\right)^{n}+\\left(y,x\\right)^{n}\\right],\\left(yxy\\right)\\right]=0$ allora R è commutativo. Let R be a semi-simple ring. We prove that if for any pair of elements x, y in R there exist positive integers m=m(x, y) and n=(x, y) such that $\\left[\\left[\\left(yxy\\right)^{m},\\left(x,y\\right)^{n}+\\left(...

  10. Simple Approach to Superamphiphobic Overhanging Silicon Nanostructures

    DEFF Research Database (Denmark)

    Kumar, Rajendra; Mogensen, Klaus Bo; Bøggild, Peter

    2010-01-01

    Superhydrophobic silicon nanostructures were fabricated by anisotropic etching of silicon coated with a thin hydrophobic layer. At certain etch parameters, overhanging nanostructures form at the apexes of the rod-shaped tips, This leads to superoleophobic behavior for several oily liquids...... with contact angles up to 152 degrees and roll-off angle down to 8 degrees. Such nonlithographic nanoscale overhanging Structures can also be added to silicon nanograss by deposition of a thin SiO2 layer, which equips the silicon rods with 100-300 nm sized overhanging Structures. This is a simple, fast...

  11. A Simple Fuzzy Time Series Forecasting Model

    DEFF Research Database (Denmark)

    Ortiz-Arroyo, Daniel

    2016-01-01

    In this paper we describe a new first order fuzzy time series forecasting model. We show that our automatic fuzzy partitioning method provides an accurate approximation to the time series that when combined with rule forecasting and an OWA operator improves forecasting accuracy. Our model does...... not attempt to provide the best results in comparison with other forecasting methods but to show how to improve first order models using simple techniques. However, we show that our first order model is still capable of outperforming some more complex higher order fuzzy time series models....

  12. Simple MCA supports a variety of applications

    International Nuclear Information System (INIS)

    A greatly enhanced version of the Violinist I, Simple Multichannel analyzer has been developed at Los Alamos. The new instrument includes a more powerful microprocessor, more memory, and a sophisticated set of I/O devices. The combination of these features allow the same basic electronics package to function in a variety of smart sophisticated monitoring instruments. Only the packaging, detector, and software need be changed to change the instrument from a field survey instrument for Pu contamination to a continuous air monitor to a neutron dosimeter. This instrument should spawn a new generation of user-friendly, highly effective instrumentation

  13. Understanding the tsunami with a simple model

    CERN Document Server

    Helene, O

    2006-01-01

    In this paper, we use the approximation of shallow water waves (Margaritondo G 2005 Eur. J. Phys. 26 401) to understand the behaviour of a tsunami in a variable depth. We deduce the shallow water wave equation and the continuity equation that must be satisfied when a wave encounters a discontinuity in the sea depth. A short explanation about how the tsunami hit the west coast of India is given based on the refraction phenomenon. Our procedure also includes a simple numerical calculation suitable for undergraduate students in physics and engineering.

  14. Chaos from simple models to complex systems

    CERN Document Server

    Cencini, Massimo; Vulpiani, Angelo

    2010-01-01

    Chaos: from simple models to complex systems aims to guide science and engineering students through chaos and nonlinear dynamics from classical examples to the most recent fields of research. The first part, intended for undergraduate and graduate students, is a gentle and self-contained introduction to the concepts and main tools for the characterization of deterministic chaotic systems, with emphasis to statistical approaches. The second part can be used as a reference by researchers as it focuses on more advanced topics including the characterization of chaos with tools of information theor

  15. Algorithms for the Simple Equal Flow Problem

    OpenAIRE

    Ahuja, Ravindra K.; Orlin, James B.; Sechi, Giovanni M.; Paola Zuddas

    1999-01-01

    The minimum cost flow problem is to determine a least cost shipment of a commodity through a network G = (N, A) in order to satisfy demands at certain nodes from available supplies at other nodes. In this paper, we study a variant of the minimum cost flow problem where we are given a set R \\subseteq A of arcs and require that each arc in R must carry the same amount of flow. This problem, which we call the simple equal flow problem, arose while modeling a water resource system management in S...

  16. Crawling on Simple Models of Web Graphs

    OpenAIRE

    Cooper, Colin; Frieze, Alan

    2003-01-01

    We consider the problem of searching a randomly growing graph by a random walk. In particular we consider two simple models of "web-graphs." Thus at each time step a new vertex is added and it is connected to the current graph by randomly chosen edges. At the same time a "spider" S makes a number of steps of a random walk on the current graph. The parameter we consider is the expected proportion of vertices that have been visited by S up to time t.

  17. Backward Bifurcation in Simple SIS Model

    Institute of Scientific and Technical Information of China (English)

    Zhan-wei Wang

    2009-01-01

    We describe and analyze a simple SIS model with treatment.In particular,we give a completely qualitative analysis by means of the theory of asymptotically autonomous system.It is found that a backward bifurcation occurs if the adequate contact rate or the capacity is small.It is also found that there exists bistable endemic equilibria.In the case of disease-induced death,it is shown that the backward bifurcation also occurs.Moreover,there is no limit cycle under some conditions,and the subcritical Hopf bifurcation occurs under another conditions.

  18. A simple experiment for visualizing diffusion

    Energy Technology Data Exchange (ETDEWEB)

    Helseth, L E, E-mail: Lars.Helseth@ift.uib.no [Department of Physics and Technology, University of Bergen, Allegaten 55, N-5007 Bergen (Norway)

    2011-09-15

    We propose a simple and fascinating experiment for studying diffusion in gels using a pH-sensitive dye. By doping agar with methyl red, we obtain a gel which rapidly reacts to changes in pH by changing its absorption spectrum. The pH gradients can be followed using a digital camera, and we demonstrate here that the pH-sensitive colour changes can be used to print colour patterns in the gel which due to diffusion of ions may disappear entirely.

  19. Understanding Social Preferences with Simple Tests

    OpenAIRE

    Charness, Gary; Rabin, Matthew

    2003-01-01

    Departures from self-interest in economic experiments have recently inspired models of “social preferences†. We design a range of simple experimental games that test these theories more directly than existing experiments. Our experiments show that subjects are more concerned with increasing social welfare—sacrificing to increase the payoffs for all recipients, especially low-payoff recipients—than with reducing differences in payoffs (as supposed in recent models). Subjects are also m...

  20. Simple multifunction discriminator for multichannel triggers

    International Nuclear Information System (INIS)

    A simple version of a multifunction timing discriminator using only two integrated circuits is presented. It can be configured as a leading edge, a constant fraction, a zero cross or a dual threshold timing discriminator. Since so few parts are used, it is well suited for building multichannel timing discriminators. Two versions of this circuit are described: a quadruple multifunction discriminator and an octal constant fraction trigger. The different compromises made in these units are discussed. Results for walk and jitter obtained with these are presented and possible improvements are disussed

  1. A simple multifunction discriminator for multichannel triggers

    International Nuclear Information System (INIS)

    A simple version of a multifunction timing discriminator using only two integrated circuits is presented. It can be configured as a leading edge, a constant fraction, a zero cross or a dual threshold timing discriminator. Since so few parts are used, it is well suited for building multichannel timing discriminators. Two versions of this circuit are described: a quadruple multifunction discriminator and an octal constant fraction trigger. The different compromises made in these units are discussed. Results for walk and jitter obtained with these are presented and possible improvements are discussed

  2. A simple model of direct gauge mediation

    International Nuclear Information System (INIS)

    In the context of direct gauge mediation Wess-Zumino models are very attractive in supersymmetry model building. Besides the spontaneous supersymmetry and R-symmetry breaking, the problems of small gaugino mass as well as μ and Bμ terms should be solved so as to achieve a viable model. In this Letter, we propose a simple model as an existence proof, in which all these subjects are realized simultaneously, with no need of fine tuning. This completion also implies that much of parameter space for direct gauge mediation can be directly explored at LHC.

  3. Which finite simple groups are unit groups?

    DEFF Research Database (Denmark)

    Davis, Christopher James; Occhipinti, Tommy

    2014-01-01

    We prove that if G is a finite simple group which is the unit group of a ring, then G is isomorphic to either (a) a cyclic group of order 2; (b) a cyclic group of prime order 2^k −1 for some k; or (c) a projective special linear group PSLn(F2) for some n ≥ 3. Moreover, these groups do all occur as...... unit groups. We deduce this classification from a more general result, which holds for groups G with no non-trivial normal 2-subgroup....

  4. Thermoeconomic Analysis of Simple Trigeneration Systems

    Directory of Open Access Journals (Sweden)

    Luis M. Serra

    2009-09-01

    Full Text Available

    Trigeneration is the combined production of heating, cooling and power from the same source of energy. In this paper, the operation of a simple trigeneration system is analyzed. The system is interconnected to the electric utility grid, both to receive electricity and to deliver surplus electricity. For any given demand required by the users, a great number of operating conditions are possible. The operational mode with the lowest variable cost is obtained through a linear programming model. Three different approaches to determine the costs of internal flows and final products of the simple trigeneration systems are presented: marginal costs corresponding to optimal operation, costs obtained when production costs are distributed to the final products according to their market prices, and internal costs corresponding to a thermoeconomic analysis of the operation mode of the system. As expected, the costs obtained with the approaches mentioned are different and it can be concluded that there are no general rules to decide which approach is best: it depends on the issue under investigation.

    • This paper is an updated version of a paper published in the ECOS'08 proceedings. 

  5. Understanding target delineation using simple probabilistic modelling

    Science.gov (United States)

    Willis, Chris J.

    2015-10-01

    Performance assessment is carried out for a simple target delineation process based on thresholding and shape fitting. The method uses the information contained in Receiver Operating Characteristic curves together with basic observations regarding target sizes and shapes. Performance is gauged by considering the delineations that might result from having particular arrangements of detected pixels within the vicinity of a hypothesized target. In particular, the method considers the qualities of delineations generated when having various combinations of detected pixels at a number of locations around the inner and outer boundaries of the underlying object. Three distinct types of arrangement for pixels on the inner target boundary are considered. Each has the potential to lead to a good quality delineation in a thresholding and shape fitting scheme. The deleterious effect of false alarms within the surrounding local region is also taken into account. The resulting ensembles of detected pixels are treated using familiar rules for combination to form probabilities for the delineations as a whole. Example results are produced for simple target prototypes in cluttered SAR imagery.

  6. Simple replica micromolding of biocompatible styrenic elastomers.

    Science.gov (United States)

    Borysiak, Mark D; Bielawski, Kevin S; Sniadecki, Nathan J; Jenkel, Colin F; Vogt, Bryan D; Posner, Jonathan D

    2013-07-21

    In this work, we introduce a simple solvent-assisted micromolding technique for the fabrication of high-fidelity styrene-ethylene/butylene-styrene (SEBS) microfluidic devices with high polystyrene (PS) content (42 wt% PS, SEBS42). SEBS triblock copolymers are styrenic thermoplastic elastomers that exhibit both glassy thermoplastic and elastomeric properties resulting from their respective hard PS and rubbery ethylene/butylene segments. The PS fraction gives SEBS microdevices many of the appealing properties of pure PS devices, while the elastomeric properties simplify fabrication of the devices, similar to PDMS. SEBS42 devices have wettable, stable surfaces (both contact angle and zeta potential) that support cell attachment and proliferation consistent with tissue culture dish substrates, do not adsorb hydrophobic molecules, and have high bond strength to wide range of substrates (glass, PS, SEBS). Furthermore, SEBS42 devices are mechanically robust, thermally stable, as well as exhibit low auto-fluorescence and high transmissivity. We characterize SEBS42 surface properties by contact angle measurements, cell culture studies, zeta potential measurements, and the adsorption of hydrophobic molecules. The PS surface composition of SEBS microdevices cast on different substrates is determined by time-of-flight secondary ion mass spectrometry (ToF-SIMS). The attractive SEBS42 material properties, coupled with the simple fabrication method, make SEBS42 a quality substrate for microfluidic applications where the properties of PS are desired but the ease of PDMS micromolding is favoured. PMID:23670166

  7. Simple Deterministically Constructed Recurrent Neural Networks

    Science.gov (United States)

    Rodan, Ali; Tiňo, Peter

    A large number of models for time series processing, forecasting or modeling follows a state-space formulation. Models in the specific class of state-space approaches, referred to as Reservoir Computing, fix their state-transition function. The state space with the associated state transition structure forms a reservoir, which is supposed to be sufficiently complex so as to capture a large number of features of the input stream that can be potentially exploited by the reservoir-to-output readout mapping. The largely "black box" character of reservoirs prevents us from performing a deeper theoretical investigation of the dynamical properties of successful reservoirs. Reservoir construction is largely driven by a series of (more-or-less) ad-hoc randomized model building stages, with both the researchers and practitioners having to rely on a series of trials and errors. We show that a very simple deterministically constructed reservoir with simple cycle topology gives performances comparable to those of the Echo State Network (ESN) on a number of time series benchmarks. Moreover, we argue that the memory capacity of such a model can be made arbitrarily close to the proved theoretical limit.

  8. A simple aid to digoxin prescribing.

    Science.gov (United States)

    Taggart, A J; McDevitt, D G; Johnston, G D

    1987-01-01

    We have designed a simple nomogram for predicting digoxin dosage and have tested it prospectively in two consecutive studies. These were both conducted in hospital inpatients who were not already taking digoxin but who required drug therapy for atrial tachyarrhythmias and/or cardiac failure. Study I. Sixty-seven patients received digoxin according to the nomogram and 50 completed the ten day course of the study. Forty-one of these patients were eligible for the final analysis. On the tenth day of treatment, 28 patients were within the therapeutic range for plasma digoxin (0.8 to 2.0 ng.ml-1), 12 were subtherapeutic (less than 0.8 ng.ml) and one was potentially toxic (greater than 2.0 ng.ml-1). Study II. Thirty patients completed the second study. Digoxin was prescribed according to the nomogram with the addition of a dosage correction based on the plasma digoxin level on Day 3. On the tenth day of treatment, 24 patients were within the therapeutic range, one in the subtherapeutic and 5 in the potentially toxic. This simple digoxin nomogram, with or without the Day 3 dosage correction, should prove to be a useful aid to prescribing in patients who do not require rapid digitalisation. It is particularly relevant to elderly inpatients with atrial tachyarrhythmias and/or cardiac failure. PMID:3428337

  9. Uniones adhesivas de traslape simple de compuestos

    Directory of Open Access Journals (Sweden)

    Peter Alvarado Prieto

    2013-09-01

    Full Text Available El siguiente artículo muestra un estudio de uniones de traslape simple de materiales compuestos, con y sin modificación. La falla de este tipo de uniones es causada por el alto esfuerzo de despegue en dirección perpendicular a la aplicación de la fuerza presentado en la singularidad geométrica. Se muestra que la resistencia de la unión es afectada por factores como la preparación de la superficie, el proceso de curado del adhesivo, y la limpieza. Ambas configuraciones, con y sin modificación, son comparadas. Se muestra que la unión de traslape simple modificada, tiene una mayor resistencia que sin modificación cuando se remueve el exceso de adhesivo en la singularidad geométrica. Sin embargo, el bajo incremento en la resistencia de la unión y la complejidad para manufactura, deja a consideración del fabricante la decisión respecto a qué tipo de unión usar.

  10. Simulated Evolution of Protein-Protein Interaction Networks with Realistic Topology

    OpenAIRE

    G Jack Peterson; Steve Pressé; Peterson, Kristin S.; Dill, Ken A.

    2012-01-01

    We model the evolution of eukaryotic protein-protein interaction (PPI) networks. In our model, PPI networks evolve by two known biological mechanisms: (1) Gene duplication, which is followed by rapid diversification of duplicate interactions. (2) Neofunctionalization, in which a mutation leads to a new interaction with some other protein. Since many interactions are due to simple surface compatibility, we hypothesize there is an increased likelihood of interacting with other proteins in the t...

  11. Protein-protein interaction based on pairwise similarity

    Directory of Open Access Journals (Sweden)

    Zaki Nazar

    2009-05-01

    Full Text Available Abstract Background Protein-protein interaction (PPI is essential to most biological processes. Abnormal interactions may have implications in a number of neurological syndromes. Given that the association and dissociation of protein molecules is crucial, computational tools capable of effectively identifying PPI are desirable. In this paper, we propose a simple yet effective method to detect PPI based on pairwise similarity and using only the primary structure of the protein. The PPI based on Pairwise Similarity (PPI-PS method consists of a representation of each protein sequence by a vector of pairwise similarities against large subsequences of amino acids created by a shifting window which passes over concatenated protein training sequences. Each coordinate of this vector is typically the E-value of the Smith-Waterman score. These vectors are then used to compute the kernel matrix which will be exploited in conjunction with support vector machines. Results To assess the ability of the proposed method to recognize the difference between "interacted" and "non-interacted" proteins pairs, we applied it on different datasets from the available yeast saccharomyces cerevisiae protein interaction. The proposed method achieved reasonable improvement over the existing state-of-the-art methods for PPI prediction. Conclusion Pairwise similarity score provides a relevant measure of similarity between protein sequences. This similarity incorporates biological knowledge about proteins and it is extremely powerful when combined with support vector machine to predict PPI.

  12. Total protein

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/003483.htm Total protein To use the sharing features on this page, please enable JavaScript. The total protein test measures the total amount of two classes ...

  13. Simple and Sensitive Detection of HBsAg by Using a Quantum Dots Nanobeads Based Dot-Blot Immunoassay

    OpenAIRE

    Zhang, Pengfei; Lu, Huiqi; Chen, Jia; HAN, HUANXING; MA, Wei

    2014-01-01

    Simple and sensitive detection of infectious disease at an affordable cost is urgently needed in developing nations. In this regard, the dot blot immunoassay has been used as a common protein detection method for detection of disease markers. However, the traditional signal reporting systems, such as those using enzymes or gold nanoparticles lack sensitivity and thus restrict the application of these methods for disease detection. In this study, we report a simple and sensitive detection meth...

  14. A SIMPLE EXPERIMENTAL MODEL OF HEAT SHOCK RESPONSE IN RATS

    Directory of Open Access Journals (Sweden)

    Tufi Neder Meyer

    1998-10-01

    Full Text Available Objective: To obtain a simple model for the elicitation of the heat shock response in rats. Design: Laboratory study. Setting: University research laboratories. Sample: Seventy-nine adult male albino rats (weight range 200 g to 570 g. Procedures: Exposure to heat stress by heating animals in a warm bath for 5 min after their rectal temperatures reached 107.60 F (420 C. Liver and lung samples were collected for heat-shock protein 70 (HSP70 detection (Western analysis. Results: Western analysis was positive for HSP70 in the liver and in the lungs of heated animals. There was a temporal correlation between heating and HSP70 detection: it was strongest 1 day after heating and reduced afterwards. No heated animals died. Conclusion: These data show that heating rats in a warm (45o C bath, according to parameters set in this model, elicits efficiently the heat shock response.OBJETIVO: Obter um modelo simples para tentar esclarecer a resposta ao choque térmico em ratos. LOCAL: Laboratório de pesquisa da Universidade. MÉTODO: Amostra: 79 ratos albinos, adultos, entre 200g a 570g. Procedimentos: Exposição ao calor, em banho quente, por 5 minutos, após a temperatura retal chegar a 42 graus centigrados. Biópsias de fígado e pulmão foram obtidas para detectar a proteina 70 (HSP 70, pelo "Western blot". RESULTADOS: As análises foram positivas nos animais aquecidos, com uma correlação entre aquecimento e constatação da HSP 70. Foi mais elevada no primeiro dia e não houve óbitos nos animais aquecidos. CONCLUSÃO: Os ratos aquecidos a 45 graus centígrados respondem eficientemente ao choque térmico.

  15. A simple physical model predicts small exon length variations.

    Directory of Open Access Journals (Sweden)

    2006-04-01

    Full Text Available One of the most common splice variations are small exon length variations caused by the use of alternative donor or acceptor splice sites that are in very close proximity on the pre-mRNA. Among these, three-nucleotide variations at so-called NAGNAG tandem acceptor sites have recently attracted considerable attention, and it has been suggested that these variations are regulated and serve to fine-tune protein forms by the addition or removal of a single amino acid. In this paper we first show that in-frame exon length variations are generally overrepresented and that this overrepresentation can be quantitatively explained by the effect of nonsense-mediated decay. Our analysis allows us to estimate that about 50% of frame-shifted coding transcripts are targeted by nonsense-mediated decay. Second, we show that a simple physical model that assumes that the splicing machinery stochastically binds to nearby splice sites in proportion to the affinities of the sites correctly predicts the relative abundances of different small length variations at both boundaries. Finally, using the same simple physical model, we show that for NAGNAG sites, the difference in affinities of the neighboring sites for the splicing machinery accurately predicts whether splicing will occur only at the first site, splicing will occur only at the second site, or three-nucleotide splice variants are likely to occur. Our analysis thus suggests that small exon length variations are the result of stochastic binding of the spliceosome at neighboring splice sites. Small exon length variations occur when there are nearby alternative splice sites that have similar affinity for the splicing machinery.

  16. Versatile microrobotics using simple modular subunits

    Science.gov (United States)

    Cheang, U. Kei; Meshkati, Farshad; Kim, Hoyeon; Lee, Kyoungwoo; Fu, Henry Chien; Kim, Min Jun

    2016-07-01

    The realization of reconfigurable modular microrobots could aid drug delivery and microsurgery by allowing a single system to navigate diverse environments and perform multiple tasks. So far, microrobotic systems are limited by insufficient versatility; for instance, helical shapes commonly used for magnetic swimmers cannot effectively assemble and disassemble into different size and shapes. Here by using microswimmers with simple geometries constructed of spherical particles, we show how magnetohydrodynamics can be used to assemble and disassemble modular microrobots with different physical characteristics. We develop a mechanistic physical model that we use to improve assembly strategies. Furthermore, we experimentally demonstrate the feasibility of dynamically changing the physical properties of microswimmers through assembly and disassembly in a controlled fluidic environment. Finally, we show that different configurations have different swimming properties by examining swimming speed dependence on configuration size.

  17. Simple nonlinear models suggest variable star universality

    CERN Document Server

    Lindner, John F; Kia, Behnam; Hippke, Michael; Learned, John G; Ditto, William L

    2015-01-01

    Dramatically improved data from observatories like the CoRoT and Kepler spacecraft have recently facilitated nonlinear time series analysis and phenomenological modeling of variable stars, including the search for strange (aka fractal) or chaotic dynamics. We recently argued [Lindner et al., Phys. Rev. Lett. 114 (2015) 054101] that the Kepler data includes "golden" stars, whose luminosities vary quasiperiodically with two frequencies nearly in the golden ratio, and whose secondary frequencies exhibit power-law scaling with exponent near -1.5, suggesting strange nonchaotic dynamics and singular spectra. Here we use a series of phenomenological models to make plausible the connection between golden stars and fractal spectra. We thereby suggest that at least some features of variable star dynamics reflect universal nonlinear phenomena common to even simple systems.

  18. A Simple HCCI Engine Model for Control

    Energy Technology Data Exchange (ETDEWEB)

    Killingsworth, N; Aceves, S; Flowers, D; Krstic, M

    2006-06-29

    The homogeneous charge compression ignition (HCCI) engine is an attractive technology because of its high efficiency and low emissions. However, HCCI lacks a direct combustion trigger making control of combustion timing challenging, especially during transients. To aid in HCCI engine control we present a simple model of the HCCI combustion process valid over a range of intake pressures, intake temperatures, equivalence ratios, and engine speeds. The model provides an estimate of the combustion timing on a cycle-by-cycle basis. An ignition threshold, which is a function of the in-cylinder motored temperature and pressure is used to predict start of combustion. This model allows the synthesis of nonlinear control laws, which can be utilized for control of an HCCI engine during transients.

  19. Simple noninvasive measurement of skin autofluorescence.

    Science.gov (United States)

    Meerwaldt, Robbert; Links, Thera; Graaff, Reindert; Thorpe, Suzannne R; Baynes, John W; Hartog, Jasper; Gans, Reinold; Smit, Andries

    2005-06-01

    Accumulation of advanced glycation end products (AGEs) is thought to play a role in the pathogenesis of chronic complications of diabetes mellitus and renal failure. Several studies indicate that AGE accumulation in tissue may reflect the cumulative effect of hyperglycemia and oxidative stress over many years. Simple quantitation of AGE accumulation in tissue could provide a tool for assessing the risk of long-term complications. Because several AGEs exhibit autofluorescence, we developed a noninvasive autofluorescence reader (AFR). Skin autofluorescence measured with the AFR correlates with collagen-linked fluorescence and specific skin AGE levels from skin biopsy samples. Furthermore, skin autofluorescence correlates with long-term glycemic control and renal function, and preliminary results show correlations with the presence of long-term complications in diabetes. The AFR may be useful as a clinical tool for rapid assessment of risk for AGE-related long-term complications in diabetes and in other conditions associated with AGE accumulation.

  20. Genealogies in simple models of evolution

    International Nuclear Information System (INIS)

    We review the statistical properties of the genealogies of a few models of evolution. In the asexual case, selection leads to coalescence times which grow logarithmically with the size of the population, in contrast with the linear growth of the neutral case. Moreover for a whole class of models, the statistics of the genealogies are those of the Bolthausen–Sznitman coalescent rather than the Kingman coalescent in the neutral case. For sexual reproduction in the neutral case, the time to reach the first common ancestors for the whole population and the time for all individuals to have all their ancestors in common are also logarithmic in the population size, as predicted by Chang in 1999. We discuss how these times are modified by introducing selection in a simple way. (paper)

  1. A simple framework for complex system improvement.

    Science.gov (United States)

    Kraft, Sally; Carayon, Pascale; Weiss, Jennifer; Pandhi, Nancy

    2015-05-01

    The need to rapidly improve health care value is unquestioned, but the means to accomplish this task is unknown. Improving performance at the level of the health care organization frequently involves multiple interventions, which must be coordinated and sequenced to fit the specific context. Those responsible for achieving large-scale improvements are challenged by the lack of a framework to describe and organize improvement strategies. Drawing from the fields of health services, industrial engineering, and organizational behavior, a simple framework was developed and has been used to guide and evaluate improvement initiatives at an academic health center. The authors anticipate that this framework will be helpful for health system leaders responsible for improving health care quality. PMID:24723664

  2. SLURM: Simple Linux Utility for Resource Management

    Energy Technology Data Exchange (ETDEWEB)

    Jette, M; Dunlap, C; Garlick, J; Grondona, M

    2002-04-24

    Simple Linux Utility for Resource Management (SLURM) is an open source, fault-tolerant, and highly scalable cluster management and job scheduling system for Linux clusters of thousands of nodes. Components include machine status, partition management, job management, and scheduling modules. The design also includes a scalable, general-purpose communication infrastructure. Development will take place in four phases: Phase I results in a solid infrastructure; Phase II produces a functional but limited interactive job initiation capability without use of the interconnect/switch; Phase III provides switch support and documentation; Phase IV provides job status, fault-tolerance, and job queuing and control through Livermore's Distributed Production Control System (DPCS), a meta-batch and resource management system.

  3. Dynamics of a Simple Evolutionary Process

    Science.gov (United States)

    Stauffer, Dietrich; Newman, M. E. J.

    We study the simple evolutionary process in which we repeatedly find the least fit agent in a population of agents and give it a new fitness, which is chosen independently at random from a specified distribution. We show that many of the average properties of this process can be calculated exactly using analytic methods. In particular, we find the distribution of fitnesses at arbitrary time, and the distribution of the lengths of runs of hits on the same agent, the latter being found to follow a power law with exponent -1, similar to the distribution of times between evolutionary events in the Bak-Sneppen model and models based on the so-called record dynamics. We confirm our analytic results with extensive numerical simulations.

  4. Simple noninvasive measurement of skin autofluorescence.

    Science.gov (United States)

    Meerwaldt, Robbert; Links, Thera; Graaff, Reindert; Thorpe, Suzannne R; Baynes, John W; Hartog, Jasper; Gans, Reinold; Smit, Andries

    2005-06-01

    Accumulation of advanced glycation end products (AGEs) is thought to play a role in the pathogenesis of chronic complications of diabetes mellitus and renal failure. Several studies indicate that AGE accumulation in tissue may reflect the cumulative effect of hyperglycemia and oxidative stress over many years. Simple quantitation of AGE accumulation in tissue could provide a tool for assessing the risk of long-term complications. Because several AGEs exhibit autofluorescence, we developed a noninvasive autofluorescence reader (AFR). Skin autofluorescence measured with the AFR correlates with collagen-linked fluorescence and specific skin AGE levels from skin biopsy samples. Furthermore, skin autofluorescence correlates with long-term glycemic control and renal function, and preliminary results show correlations with the presence of long-term complications in diabetes. The AFR may be useful as a clinical tool for rapid assessment of risk for AGE-related long-term complications in diabetes and in other conditions associated with AGE accumulation. PMID:16037251

  5. A simple EHF hemispheric coverage antenna

    Science.gov (United States)

    Lee, J. C.

    1994-08-01

    A circulary polarized, axially symmetric, wide-beam radiator is required in many applications, including TT&C for UAV's and satellites. This report discusses some existing wide-beam antenna designs including divergent lenses and reflectors and introduces a new antenna design. Using a simple dielectric ring in conjunction with a dielectric loaded circular waveguide opening, a near ideal, axially symmetric, hemispheric coverage antenna with circular polarization of good axial ratio and wide-band impedance match is realized. Mechanically, the antenna is small, lightweight, and low cost. The dielectric used is the common Rexolite. Since no lossy materials or resonant scatterers are used, the antenna performance is inherently broadband and low loss. A K sub a-band prototype as well as compact designs for both Q- and K-bands are described.

  6. Spontaneous oscillations in simple fluid networks

    CERN Document Server

    Karst, Nathaniel J; Geddes, John B

    2013-01-01

    Nonlinear phenomena including multiple equilibria and spontaneous oscillations are common in fluid networks containing either multiple phases or constituent flows. In many systems, such behavior might be attributed to the complicated geometry of the network, the complex rheology of the constituent fluids, or, in the case of microvascular blood flow, biological control. In this paper we investigate two examples of a simple three-node fluid network containing two miscible Newtonian fluids of differing viscosities, the first modeling microvascular blood flow and the second modeling stratified laminar flow. We use a combination of analytic and numerical techniques to identify and track saddle-node and Hopf bifurcations through the large parameter space. In both models, we document sustained spontaneous oscillations and, for an experimentally relevant example of parameter analysis, investigate the sensitivity of these oscillations to changes in the viscosity contrast between the constituent fluids and the inlet fl...

  7. Simple operated multipurpose temperature control cryostat

    Institute of Scientific and Technical Information of China (English)

    ABBAS T.A.; OMAR M.S.

    2007-01-01

    A suitable simple optical cryostat for optical, magneto-optical, electrical and thermo-electrical measurements was designed. It is suitable for use in a magnetic pool gap as narrow as less than 1 cm. Throughout a long period of time, the heat diffusion process of the cryostat can be easily operated at slow increase in sample temperature in a range 1.25 K/min at 200 K that will be reduced gradually to 0.66 K at room temperature. Liquid nitrogen was used to cool down the temperature. During the operation, the change in the measured energy gap of a semiconductor sample and other physical parameters resulting from the change of temperature can be corrected through the temperature coefficient of that parameter at the corresponding temperature.The cryostat was successfully used for all experiments mentioned above to measure the properties of a single crystal of GaP (Gallium Phosphate) semiconductor.

  8. Hierarchical Simple Games: Representations and Weightedness

    CERN Document Server

    Gvozdeva, Tatiana; Slinko, Arkadii

    2011-01-01

    In many situations, both in human and artificial societies, cooperating agents have different status with respect to the activity and it is not uncommon that certain actions are only allowed to coalitions that satisfy certain criteria, e.g., to sufficiently large coalitions or coalitions which involve players of sufficient seniority. Simmons (1988) formalized this idea in the context of secret sharing schemes by defining the concept of a (disjunctive) hierarchical access structure. Tassa (2007) introduced their conjunctive counterpart. From the game theory perspective access structures in secret sharing schemes are simple games. In this paper we prove the duality between disjunctive and conjunctive hierarchical games. We introduce a canonical representation theorem for both types of hierarchical games and characterize disjunctive ones as complete games with a unique shift-maximal losing coalition. We give a short combinatorial proof of the Beimel-Tassa-Weinreb (2008) characterization of weighted disjunctive h...

  9. A Small Deformation of a Simple Theory

    CERN Document Server

    Buican, Matthew

    2016-01-01

    We study an interesting relevant deformation of the simplest interacting N=2 SCFT---the original Argyres-Douglas (AD) theory. We argue that, although this deformation is not strictly speaking Banks-Zaks like (certain operator dimensions change macroscopically), there are senses in which it constitutes a mild deformation of the parent AD theory: the exact change in the "a" anomaly is small and is essentially saturated at one loop. Moreover, contributions from IR operators that have a simple description in the UV theory reproduce a particular limit of the IR index to a remarkably high order. These results lead us to conclude that the IR theory is an N=1 SCFT with the smallest-known "a" and "c" central charges for an interacting SCFT in four dimensions.

  10. iPad 2 Made Simple

    CERN Document Server

    Mazo, Gary; Ritchie, Rene

    2011-01-01

    The iPad 2 is thinner, more powerful, intuitive and very fun for users of all ages. Your iPad can be used for reading, surfing the web, emailing, watching TV and movies, getting work done and much more. And with over 65,000 apps just for the iPad, as well as the ability to run over 30,000 iPhone apps, the possibilities are endless. iPad 2 Made Simple clarifies all of the key features on the iPad, introduces what's new, and also reveals dozens of time-saving shortcuts and techniques. The book has over 1,000 screen shots that are carefully annotated with step-by-step instructions. * Clear instru

  11. A simple Proof of Stolarsky's Invariance Principle

    CERN Document Server

    Brauchart, Johann S

    2011-01-01

    Stolarsky [Proc. Amer. Math. Soc. 41 (1973), 575--582] showed a beautiful relation that balances the sums of distances of points on the unit sphere and their spherical cap $\\mathbb{L}_2$-discrepancy to give the distance integral of the uniform measure on the sphere a potential-theoretical quantity (Bj{\\"o}rck [Ark. Mat. 3 (1956), 255--269]). Read differently it expresses the worst-case numerical integration error for functions from the unit ball in a certain Hilbert space setting in terms of the $\\mathbb{L}_2$-discrepancy and vice versa (first author and Womersley [Preprint]). In this note we give a simple proof of the invariance principle using reproducing kernel Hilbert spaces.

  12. Recursion vs. Replication in Simple Cryptographic Protocols

    DEFF Research Database (Denmark)

    Huttel, Hans; Srba, Jiri

    2005-01-01

    We use some recent techniques from process algebra to draw several conclusions about the well studied class of ping-pong protocols introduced by Dolev and Yao. In particular we show that all nontrivial properties, including reachability and equivalence checking wrt. the whole van Glabbeek......'s spectrum, become undecidable for a very simple recursive extension of the protocol. The result holds even if no nondeterministic choice operator is allowed. We also show that the extended calculus is capable of an implicit description of the active intruder, including full analysis and synthesis of...... messages in the sense of Amadio, Lugiez and Vanackere. We conclude by showing that reachability analysis for a replicative variant of the protocol becomes decidable....

  13. A simple model of bank bankruptcies

    Science.gov (United States)

    Aleksiejuk, Agata; Hołyst, Janusz A.

    2001-10-01

    Interbank deposits (loans and credits) are quite common in banking system all over the world. Such interbank co-operation is profitable for banks but it can also lead to collective financial failures. In this paper, we introduce a new model of directed percolation as a simple representation for contagion process and mass bankruptcies in banking systems. Directed connections that are randomly distributed between junctions of bank lattice simulate flows of money in our model. Critical values of a mean density of interbank connections as well as static and dynamic scaling laws for the statistics of avalanche bankruptcies are found. Results of computer simulations for the universal profile of bankruptcies spreading are in a qualitative agreement with the third wave of bank suspensions during The Great Depression in USA.

  14. Centralizers in simple locally finite groups

    Directory of Open Access Journals (Sweden)

    Mahmut Kuzucuoğlu

    2013-03-01

    Full Text Available This is a survey article on centralizers of finitesubgroups in locally finite, simple groups or LFS-groups as wewill call them. We mention some of the open problems aboutcentralizers of subgroups in LFS-groups and applications of theknown information about the centralizers of subgroups to thestructure of the locally finite group. We also prove thefollowing: Let $G$ be a countably infinite non-linear LFS-groupwith a Kegel sequence $mathcal{K}={(G_i,N_i | iinmathbf{N} }$. If there exists an upper bound for ${ |N_i| |iin mathbf{N} }$, then for any finite semisimplesubgroup $F$ in $G$ the subgroup $C_G(F$ has elements oforder $p_i$ for infinitely many distinct prime $p_i$. Inparticular $C_G(F$ is an infinite group. This answers Hartley'squestion provided that there exists a bound on ${ |N_i| | iin mathbf{N}$.

  15. Versatile microrobotics using simple modular subunits.

    Science.gov (United States)

    Cheang, U Kei; Meshkati, Farshad; Kim, Hoyeon; Lee, Kyoungwoo; Fu, Henry Chien; Kim, Min Jun

    2016-01-01

    The realization of reconfigurable modular microrobots could aid drug delivery and microsurgery by allowing a single system to navigate diverse environments and perform multiple tasks. So far, microrobotic systems are limited by insufficient versatility; for instance, helical shapes commonly used for magnetic swimmers cannot effectively assemble and disassemble into different size and shapes. Here by using microswimmers with simple geometries constructed of spherical particles, we show how magnetohydrodynamics can be used to assemble and disassemble modular microrobots with different physical characteristics. We develop a mechanistic physical model that we use to improve assembly strategies. Furthermore, we experimentally demonstrate the feasibility of dynamically changing the physical properties of microswimmers through assembly and disassembly in a controlled fluidic environment. Finally, we show that different configurations have different swimming properties by examining swimming speed dependence on configuration size. PMID:27464852

  16. Swarming behavior of simple model squirmers

    Energy Technology Data Exchange (ETDEWEB)

    Thutupalli, Shashi; Seemann, Ralf; Herminghaus, Stephan, E-mail: shashi.thutupalli@ds.mpg.de, E-mail: stephan.herminghaus@ds.mpg.de [Max Planck Institute for Dynamics and Self-Organization, Bunsenstrasse 10, 37073 Goettingen (Germany)

    2011-07-15

    We have studied experimentally the collective behavior of self-propelling liquid droplets, which closely mimic the locomotion of some protozoal organisms, the so-called squirmers. For the sake of simplicity, we concentrate on quasi-two-dimensional (2D) settings, although our swimmers provide a fully 3D propulsion scheme. At an areal density of 0.46, we find strong polar correlation of the locomotion velocities of neighboring droplets, which decays over less than one droplet diameter. When the areal density is increased to 0.78, distinct peaks show up in the angular correlation function, which point to the formation of ordered rafts. This shows that pronounced textures, beyond what has been seen in simulations so far, may show up in crowds of simple model squirmers, despite the simplicity of their (purely physical) mutual interaction.

  17. Lensing and Dynamics in Two Simple Steps

    CERN Document Server

    Agnello, A; Evans, N W

    2012-01-01

    We present a ready-to-use method to constrain the density distribution in early-type galaxy lenses. Assuming a power-law density profile, then joint use of the virial theorem and the lens equation yields simple formulae for the power-law index (or logarithmic density gradient). Any dependence on orbital anisotropy can be tightly constrained or even erased completely. Our results rely just on surface brightnesses and line-of-sight kinematics, making deprojection unnecessary. We revisit three systems that have already been examined in the literature (the Cosmic Horseshoe, the Jackpot and B1608+656) and provide our estimates. Finally, we show that the method yields a good approximation for the density profile even when the true profile is a broken power-law, albeit with a mild bias towards isothermality.

  18. Wobbling geometry in simple triaxial rotor

    CERN Document Server

    Shi, W X

    2014-01-01

    The spectroscopy properties and angular momentum geometry for the wobbling motion of a simple triaxial rotor are investigated within the triaxial rotor model up to spin $I=40\\hbar$. The obtained exact solutions of energy spectra and reduced quadrupole transition probabilities are compared to the approximate analytic solutions by harmonic approximation formula and Holstein-Primakoff formula. It is found that the low lying wobbling bands can be well described by the analytic formulas. The evolution of the angular momentum geometry as well as the $K$-distribution with respect to the rotation and the wobbling phonon excitation are studied in detail. It is demonstrated that with the increasing of wobbling phonon number, the triaxial rotor changes its wobbling motions along the axis with the largest moment of inertia to the axis with the smallest moment of inertia. In this process, a specific evolutionary track that can be used to depict the motion of a triaxial rotating nuclei is proposed.

  19. A Simple Weighing Method for Spherical Cells.

    Science.gov (United States)

    Zhao, Qili; Shirinzadeh, Bijan; Cui, Maosheng; Sun, Mingzhu; Zhao, Xin

    2015-08-01

    This article presents a simple weighing method for spherical cells to avoid the high cost of correlated devices in traditional cell-weighing methods. In this method, the constant falling speeds of the spherical objects in liquid are derived to estimate their masses online. Using this method, the detected density of one type of microbead is highly in accordance with the known value. This method is proved to be capable of detecting tiny variations of the cell mass (at least within 1% of the cell mass). Finally, the proposed method is applied in nuclear transplantation operations, and, for the first time, the proper amount of the removed cytoplasm in porcine enucleation is estimated. The proposed method is able to weigh cells with a success rate of 92% at an average speed of 22 s/cell, and it can be performed on traditional microoperation systems, which makes it easily applicable in biological applications. PMID:25911396

  20. Star clusters as simple stellar populations

    CERN Document Server

    Bruzual, A Gustavo

    2009-01-01

    In this paper, I review to what extent we can understand the photometric properties of star clusters, and of low-mass, unresolved galaxies, in terms of population synthesis models designed to describe `simple stellar populations' (SSPs), i.e., groups of stars born at the same time, in the same volume of space, and from a gas cloud of homogeneous chemical composition. The photometric properties predicted by these models do not readily match the observations of most star clusters, unless we properly take into account the expected variation in the number of stars occupying sparsely populated evolutionary stages, due to stochastic fluctuations in the stellar initial mass function. In this case, population synthesis models reproduce remarkably well the full ranges of observed integrated colours and absolute magnitudes of star clusters of various ages and metallicities. The disagreement between the model predictions and observations of cluster colours and magnitudes may indicate problems with or deficiencies in the...

  1. The Structure of gr-simple Rings

    Institute of Scientific and Technical Information of China (English)

    朱彬

    2003-01-01

    A characterization of gr-simple rings is given by using the notion of componentwise-dense subrings of a full matrix ring over a division ring. As a conse-quence, any G-graded full matrix ring over a division ring is isomorphic to a dense subring of a full matrix ring with a good G-grading. Some conditions for a grading of a full matrix ring to be isomorphic to a good one are given, which generalize some results in: Dáscáscu, S., Lon, B., Niǎstǎsescu, C. and Montes, J. R., Group gradingson full matrix rings, J. Algebra, 220(1999), 709-728.

  2. A Simple Holographic Model of Nonlinear Conductivity

    CERN Document Server

    Horowitz, Gary T; Santos, Jorge E

    2013-01-01

    We present a simple analytic gravitational solution which describes the holographic dual of a 2+1-dimensional conductor which goes beyond the usual linear response. In particular it includes Joule heating. We find that the nonlinear frequency-dependent conductivity is a constant. Surprisingly, the pressure remains isotropic. We also apply an electric field to a holographic insulator and show that there is a maximum electric field below which it can remain an insulator. Above this critical value, we argue that it becomes a conductor due to pair creation of charged particles. Finally, we study 1+1 and 3+1 dimensional conductors at the nonlinear level; here exact solutions are not available and a perturbative analysis shows that the current becomes time dependent, but in a way that is captured by a time-dependent effective temperature.

  3. Simple expressions for the long walk distance

    CERN Document Server

    Chebotarev, Pavel; Balaji, R

    2011-01-01

    The walk distances in graphs are defined as the result of appropriate transformations of the $\\sum_{k=0}^\\infty(tA)^k$ proximity measures, where $A$ is the weighted adjacency matrix of a connected weighted graph and $t$ is a sufficiently small positive parameter. The walk distances are graph-geodetic, moreover, they converge to the shortest path distance and to the so-called long walk distance as the parameter $t$ approaches its limiting values. In this paper, simple expressions for the long walk distance are obtained. They involve the generalized inverse, minors, and inverses of submatrices of the symmetric irreducible singular M-matrix ${\\cal L}=\\rho I-A,$ where $\\rho$ is the Perron root of $A.$

  4. SIMPLE QUALITY ASSESSMENT FOR BINARY IMAGES

    Institute of Scientific and Technical Information of China (English)

    Zhang Chun'e; Qiu Zhengding

    2007-01-01

    Usually image assessment methods could be classified into two categories: subjective assessments and objective ones. The latter are judged by the correlation coefficient with subjective quality measurement MOS (Mean Opinion Score). This paper presents an objective quality assessment algorithm special for binary images. In the algorithm, noise energy is measured by Euclidean distance between noises and signals and the structural effects caused by noise are described by Euler number change. The assessment on image quality is calculated quantitatively in terms of PSNR (Peak Signal to Noise Ratio). Our experiments show that the results of the algorithm are highly correlative with subjective MOS and the algorithm is more simple and computational saving than traditional objective assessment methods.

  5. Simple device for treating prolapsing loop colostomy.

    Science.gov (United States)

    Hsieh, Ming-Yu; Liu, Chinsu; Ho, Shin-Huei; Wung, Shin-Huev; Chin, Taiwai; Wei, Choufu

    2006-03-01

    Stoma prolapse is a common complication of intestinal stoma. Although various surgical methods yield satisfactory results, nonsurgical treatment may be better for a temporary stoma. We report a case of a patient with a distal limb prolapse of a right transverse colostomy who received nonsurgical treatment with satisfactory results. For the treatment of a temporary transverse loop colostomy with distal limb prolapse, we designed a simple device consisting of a pediatric plastic medicine cup, which was rolled into a towel to shape the bottom of the cup into a compressor. The towel was put on the stoma outside of the colostomy bag with the compressor above the prolapsing limb of the colostomy. An abdominal binder was applied to fix the towel. PMID:16599021

  6. Gauge invariance in simple mechanical systems

    International Nuclear Information System (INIS)

    This article discusses and explains the Hamiltonian formulation for a class of simple gauge invariant mechanical systems consisting of point masses and idealized rods. The study of these models may be helpful to advanced undergraduate or graduate students in theoretical physics to understand, in a familiar context, some concepts relevant to the study of classical and quantum field theories. We use a geometric approach to derive the Hamiltonian formulation for the model considered in the paper: four equal masses connected by six ideal rods. We obtain and discuss the meaning of several important elements, in particular, the constraints and the Hamiltonian vector fields that define the dynamics of the system, the constraint manifold, gauge symmetries, gauge orbits, gauge fixing, and the reduced phase space. (papers)

  7. [A simple method for counting Rickettsia cells].

    Science.gov (United States)

    Emel'ianov, V V

    1990-01-01

    A simple modification of the method for counting Rickettsiae is described. The Escherichia coli cells (ECC) which served as reference particles were stained in suspension with methylene blue mixed with Rickettsia prowazekii (RP) and quickly sprayed over the glass slide. After fixation the samples were stained according to the technique of Gimenez and examined in the light microscope under oil immersion. Through a grid in the eye-piece it was not so difficult to count red-coloured RP and dark-blue ECC against a background formed by impurities. To calculate RP concentration, the reference particles' concentration was multiplied by the dilution factor of RP suspension by the ratio of RP to ECC enumerated. The statistical approach has shown that the wash of the slides during staining procedure does not change this ratio. Differential staining of Rickettsiae with fuchsin is the main clue of this new method to count them even in the crude preparations of infected yolk sacs. PMID:1693751

  8. A simple model of a swing

    Science.gov (United States)

    Mayer, V. V.; Varaksina, E. I.

    2016-07-01

    The paper presents a simple model of a swing meant for undergraduates’ educational experiments. The purpose of these experiments is the experimental study of physical principles of self-oscillations, free, forced and parametric oscillations. The model contains a pendulum. A coil with a movable steel core serves as its load. A neodymium magnet is placed at the lower end of the core. A magnetically operated sealed switch is stationed under the magnet at the equilibrium position of the pendulum. The switch is connected in series with the coil and a battery. If we displace the pendulum from the equilibrium position, the pendulum makes undamped oscillations. The system receives energy every time the core is drawn into the coil at the lower position of the pendulum.

  9. Multiple equilibria in a simple elastocapillary system

    KAUST Repository

    Taroni, Michele

    2012-09-28

    We consider the elastocapillary interaction of a liquid drop placed between two elastic beams, which are both clamped at one end to a rigid substrate. This is a simple model system relevant to the problem of surface-tension-induced collapse of flexible micro-channels that has been observed in the manufacture of microelectromechanical systems (MEMS). We determine the conditions under which the beams remain separated, touch at a point, or stick along a portion of their length. Surprisingly, we show that in many circumstances multiple equilibrium states are possible. We develop a lubrication-type model for the flow of liquid out of equilibrium and thereby investigate the stability of the multiple equilibria. We demonstrate that for given material properties two stable equilibria may exist, and show via numerical solutions of the dynamic model that it is the initial state of the system that determines which stable equilibrium is ultimately reached. © 2012 Cambridge University Press.

  10. Simple emission metrics for climate impacts

    Directory of Open Access Journals (Sweden)

    B. Aamaas

    2013-06-01

    Full Text Available In the context of climate change, emissions of different species (e.g., carbon dioxide and methane are not directly comparable since they have different radiative efficiencies and lifetimes. Since comparisons via detailed climate models are computationally expensive and complex, emission metrics were developed to allow a simple and straightforward comparison of the estimated climate impacts of emissions of different species. Emission metrics are not unique and variety of different emission metrics has been proposed, with key choices being the climate impacts and time horizon to use for comparisons. In this paper, we present analytical expressions and describe how to calculate common emission metrics for different species. We include the climate metrics radiative forcing, integrated radiative forcing, temperature change and integrated temperature change in both absolute form and normalised to a reference gas. We consider pulse emissions, sustained emissions and emission scenarios. The species are separated into three types: CO2 which has a complex decay over time, species with a simple exponential decay, and ozone precursors (NOx, CO, VOC which indirectly effect climate via various chemical interactions. We also discuss deriving Impulse Response Functions, radiative efficiency, regional dependencies, consistency within and between metrics and uncertainties. We perform various applications to highlight key applications of emission metrics, which show that emissions of CO2 are important regardless of what metric and time horizon is used, but that the importance of short lived climate forcers varies greatly depending on the metric choices made. Further, the ranking of countries by emissions changes very little with different metrics despite large differences in metric values, except for the shortest time horizons (GWP20.

  11. Protein Structure

    Science.gov (United States)

    Asmus, Elaine Garbarino

    2007-01-01

    Individual students model specific amino acids and then, through dehydration synthesis, a class of students models a protein. The students clearly learn amino acid structure, primary, secondary, tertiary, and quaternary structure in proteins and the nature of the bonds maintaining a protein's shape. This activity is fun, concrete, inexpensive and…

  12. Proteins aggregation and human diseases

    Science.gov (United States)

    Hu, Chin-Kun

    2015-04-01

    Many human diseases and the death of most supercentenarians are related to protein aggregation. Neurodegenerative diseases include Alzheimer's disease (AD), Huntington's disease (HD), Parkinson's disease (PD), frontotemporallobar degeneration, etc. Such diseases are due to progressive loss of structure or function of neurons caused by protein aggregation. For example, AD is considered to be related to aggregation of Aβ40 (peptide with 40 amino acids) and Aβ42 (peptide with 42 amino acids) and HD is considered to be related to aggregation of polyQ (polyglutamine) peptides. In this paper, we briefly review our recent discovery of key factors for protein aggregation. We used a lattice model to study the aggregation rates of proteins and found that the probability for a protein sequence to appear in the conformation of the aggregated state can be used to determine the temperature at which proteins can aggregate most quickly. We used molecular dynamics and simple models of polymer chains to study relaxation and aggregation of proteins under various conditions and found that when the bending-angle dependent and torsion-angle dependent interactions are zero or very small, then protein chains tend to aggregate at lower temperatures. All atom models were used to identify a key peptide chain for the aggregation of insulin chains and to find that two polyQ chains prefer anti-parallel conformation. It is pointed out that in many cases, protein aggregation does not result from protein mis-folding. A potential drug from Chinese medicine was found for Alzheimer's disease.

  13. Protein science research in China

    Institute of Scientific and Technical Information of China (English)

    Ming Sun; Rui-Ming Xu

    2010-01-01

    @@ Proteins are major executors of life processes, carrying out essential and nonessential functions inside and outside of the cell, in species ranging from simple unicellular organisms to mammals. Thus, not surpris-ingly, studies of structure and function of proteins span the entire spectrum of molecular biology and modern biomedical sciences in general. Due to historical rea-sons, protein science research in China was isolated and limited in scope until late 1970s. In the last two decades,China has seen an outburst of research activities,government initiatives, and aggregation of human talents in protein science research. This article provides an overview of major initiatives in research funding, invest-ment in infrastructures, and research forces for protein science research in China.

  14. Silver staining of proteins in polyacrylamide gels

    OpenAIRE

    Chevallet, Mireille; Luche, Sylvie; Rabilloud, Thierry

    2006-01-01

    International audience Silver staining is used to detect proteins after electrophoretic separation on polyacrylamide gels. It combines excellent sensitivity (in the low nanogram range) with the use of very simple and cheap equipment and chemicals. It is compatible with downstream processing, such as mass spectrometry analysis after protein digestion. The sequential phases of silver staining are protein fixation, then sensitization, then silver impregnation and finally image development. Se...

  15. Novel Technology for Protein-Protein Interaction-based Targeted Drug Discovery

    Directory of Open Access Journals (Sweden)

    Jung Me Hwang

    2011-12-01

    Full Text Available We have developed a simple but highly efficient in-cell protein-protein interaction (PPI discovery system based on the translocation properties of protein kinase C- and its C1a domain in live cells. This system allows the visual detection of trimeric and dimeric protein interactions including cytosolic, nuclear, and/or membrane proteins with their cognate ligands. In addition, this system can be used to identify pharmacological small compounds that inhibit specific PPIs. These properties make this PPI system an attractive tool for screening drug candidates and mapping the protein interactome.

  16. A simple histone code opens many paths to epigenetics.

    Science.gov (United States)

    Sneppen, Kim; Dodd, Ian B

    2012-01-01

    Nucleosomes can be covalently modified by addition of various chemical groups on several of their exposed histone amino acids. These modifications are added and removed by enzymes (writers) and can be recognized by nucleosome-binding proteins (readers). Linking a reader domain and a writer domain that recognize and create the same modification state should allow nucleosomes in a particular modification state to recruit enzymes that create that modification state on nearby nucleosomes. This positive feedback has the potential to provide the alternative stable and heritable states required for epigenetic memory. However, analysis of simple histone codes involving interconversions between only two or three types of modified nucleosomes has revealed only a few circuit designs that allow heritable bistability. Here we show by computer simulations that a histone code involving alternative modifications at two histone positions, producing four modification states, combined with reader-writer proteins able to distinguish these states, allows for hundreds of different circuits capable of heritable bistability. These expanded possibilities result from multiple ways of generating two-step cooperativity in the positive feedback--through alternative pathways and an additional, novel cooperativity motif. Our analysis reveals other properties of such epigenetic circuits. They are most robust when the dominant nucleosome types are different at both modification positions and are not the type inserted after DNA replication. The dominant nucleosome types often recruit enzymes that create their own type or destroy the opposing type, but never catalyze their own destruction. The circuits appear to be evolutionary accessible; most circuits can be changed stepwise into almost any other circuit without losing heritable bistability. Thus, our analysis indicates that systems that utilize an expanded histone code have huge potential for generating stable and heritable nucleosome

  17. A simple histone code opens many paths to epigenetics.

    Directory of Open Access Journals (Sweden)

    Kim Sneppen

    Full Text Available Nucleosomes can be covalently modified by addition of various chemical groups on several of their exposed histone amino acids. These modifications are added and removed by enzymes (writers and can be recognized by nucleosome-binding proteins (readers. Linking a reader domain and a writer domain that recognize and create the same modification state should allow nucleosomes in a particular modification state to recruit enzymes that create that modification state on nearby nucleosomes. This positive feedback has the potential to provide the alternative stable and heritable states required for epigenetic memory. However, analysis of simple histone codes involving interconversions between only two or three types of modified nucleosomes has revealed only a few circuit designs that allow heritable bistability. Here we show by computer simulations that a histone code involving alternative modifications at two histone positions, producing four modification states, combined with reader-writer proteins able to distinguish these states, allows for hundreds of different circuits capable of heritable bistability. These expanded possibilities result from multiple ways of generating two-step cooperativity in the positive feedback--through alternative pathways and an additional, novel cooperativity motif. Our analysis reveals other properties of such epigenetic circuits. They are most robust when the dominant nucleosome types are different at both modification positions and are not the type inserted after DNA replication. The dominant nucleosome types often recruit enzymes that create their own type or destroy the opposing type, but never catalyze their own destruction. The circuits appear to be evolutionary accessible; most circuits can be changed stepwise into almost any other circuit without losing heritable bistability. Thus, our analysis indicates that systems that utilize an expanded histone code have huge potential for generating stable and heritable

  18. Exploring the repeat protein universe through computational protein design.

    Science.gov (United States)

    Brunette, T J; Parmeggiani, Fabio; Huang, Po-Ssu; Bhabha, Gira; Ekiert, Damian C; Tsutakawa, Susan E; Hura, Greg L; Tainer, John A; Baker, David

    2015-12-24

    A central question in protein evolution is the extent to which naturally occurring proteins sample the space of folded structures accessible to the polypeptide chain. Repeat proteins composed of multiple tandem copies of a modular structure unit are widespread in nature and have critical roles in molecular recognition, signalling, and other essential biological processes. Naturally occurring repeat proteins have been re-engineered for molecular recognition and modular scaffolding applications. Here we use computational protein design to investigate the space of folded structures that can be generated by tandem repeating a simple helix-loop-helix-loop structural motif. Eighty-three designs with sequences unrelated to known repeat proteins were experimentally characterized. Of these, 53 are monomeric and stable at 95 °C, and 43 have solution X-ray scattering spectra consistent with the design models. Crystal structures of 15 designs spanning a broad range of curvatures are in close agreement with the design models with root mean square deviations ranging from 0.7 to 2.5 Å. Our results show that existing repeat proteins occupy only a small fraction of the possible repeat protein sequence and structure space and that it is possible to design novel repeat proteins with precisely specified geometries, opening up a wide array of new possibilities for biomolecular engineering.

  19. An assay for measurement of protein adsorption to glass vials.

    Science.gov (United States)

    Varmette, Elizabeth; Strony, Brianne; Haines, Daniel; Redkar, Rajendra

    2010-01-01

    Protein adsorption to primary packaging is one of the problems faced by biopharmaceutical drug companies. An assay was developed to quantify loss of proteins to glass vial surfaces. The assay involves the labeling of protein with a fluorescent dye, incubation of the labeled protein with the vial surface, elution of the adsorbed protein using a stripping buffer, and determination of fluorescence of the adsorbed protein using a fluorometer. The assay is simple to set up, accurate, sensitive, and flexible. The assay can be modified for indirect measurement of protein adsorption and offers an attractive alternative for researchers to quantify protein adsorption to glass vials and syringes. PMID:21502031

  20. Simple queueing approach to segregation dynamics in Schelling model

    OpenAIRE

    Sobkowicz, Pawel

    2007-01-01

    A simple queueing approach for segregation of agents in modified one dimensional Schelling segregation model is presented. The goal is to arrive at simple formula for the number of unhappy agents remaining after the segregation.

  1. Creating Simple Admin Tools Using Info*Engine and Java

    Science.gov (United States)

    Jones, Corey; Kapatos, Dennis; Skradski, Cory; Felkins, J. D.

    2012-01-01

    PTC has provided a simple way to dynamically interact with Windchill using Info*Engine. This presentation will describe how to create a simple Info*Engine Tasks capable of saving Windchill 10.0 administration of tedious work.

  2. Simple Broadband Circular Polarizer in Oversized Waveguide

    Science.gov (United States)

    Stange, Torsten

    2016-02-01

    In this paper, a possibility is shown to realize a simple waveguide polarizer producing nearly the same circular polarization over a broad frequency range up to an octave. It is based upon the combination of two smoothly squeezed oversized waveguides with different diameters. The principle is similar to an achromatic lens in optics, where two counteracting lenses with differently sloped wavelength dependencies of the refractive index are combined to compensate the dispersion in the desired wavelength range. Consequently, two different wavelengths of light are brought into focus at the same plane. A waveguide for the transmission of microwaves has a similar frequency dependence of the refractive index resulting in a frequency-dependent phase shift between two propagating waves polarized along the symmetry axes of a waveguide with an elliptical cross section. For this reason, an incident wave with a linear polarization between the axes of symmetry can be only converted into a circularly polarized wave over a limited frequency range. However, the diameter and the shape along two counteracting squeezed waveguides can be adjusted in such a way that the frequency dependence of the resultant phase shift is finally canceled out.

  3. A simple model for biased divertors

    Energy Technology Data Exchange (ETDEWEB)

    Lachambre, J.-L.; Quirion, B.; Gunn, J.; Boucher, C.; Stansfield, B.; Gauvreau, J.-L. [Centre canadien de fusion magnetique, 1804, boulevard Lionel-Boulet, Varennes, Quebec, J3X 1S1 (Canada)

    1997-12-01

    Ionization near the target plate is shown to play an important role in biasing experiments. Our previous SOL model, which calculates the induced radial electric field, is found to be inadequate to treat the new divertor geometry of TdeV. When recycling is included via the measured D{sub {alpha}} emission near the plate, the upgraded model correctly reproduces all the observed electric currents and fields during biasing in the new divertor configuration. A simple divertor model using this calculated field has been developed to simulate the evolution of the divertor ion and neutral parameters under the action of neutralization plate biasing. Using a 1D adiabatic fluid model for the divertor ions, a 1D convective representation for the SOL neutrals and a 0D calculation for the plenum pressure, this divertor model satisfactorily simulates most of the TdeV biasing experiments at all biasing voltages and all toroidal field directions at low line-averaged densities. The weaker agreement at high densities is largely a consequence of the crudeness of the general divertor physics rather than of the deficiency of the biasing physics implemented in the model. The model is finally used to explain the polarity asymmetries observed in divertor efficiencies during biasing, and to demonstrate that no mechanism other than plate current saturation is required to interpret the saturation of toroidal rotation observed in the SOL at large biasing voltages of either polarity. (author)

  4. A simple deduction of the Lindblad equation

    CERN Document Server

    Brasil, Carlos Alexandre; Napolitano, Reginaldo de Jesus

    2011-01-01

    We present a deduction of the Lindblad equation that is accessible to students with a basic background on quantum mechanics. We consider a specific case, corresponding to a very simple situation, where a primary system interacts with a bath of harmonic oscillators at zero temperature, with an interaction Hamiltonian that resembles the Jaynes-Cummings format. We start with the Born-Markov equation and, tracing out the bath degrees of freedom, we obtain an equation in the Lindblad form. The speci?c situation is very instructive, for it makes it easy to realize that the Lindblads represent the e?ect on the main system caused by the interaction with the bath, and that the Markov approximation is a fundamental condition for the emergence of the Lindbladian operator. The formal derivation of the Lindblad equation for a more general case requires broader considerations regarding the environment, the temperature, and the use of quantum dynamical semi-groups than we have considered in the particular case treated here.

  5. Simple, parallel virtual machines for extreme computations

    Science.gov (United States)

    Chokoufe Nejad, Bijan; Ohl, Thorsten; Reuter, Jürgen

    2015-11-01

    We introduce a virtual machine (VM) written in a numerically fast language like Fortran or C for evaluating very large expressions. We discuss the general concept of how to perform computations in terms of a VM and present specifically a VM that is able to compute tree-level cross sections for any number of external legs, given the corresponding byte-code from the optimal matrix element generator, O'MEGA. Furthermore, this approach allows to formulate the parallel computation of a single phase space point in a simple and obvious way. We analyze hereby the scaling behavior with multiple threads as well as the benefits and drawbacks that are introduced with this method. Our implementation of a VM can run faster than the corresponding native, compiled code for certain processes and compilers, especially for very high multiplicities, and has in general runtimes in the same order of magnitude. By avoiding the tedious compile and link steps, which may fail for source code files of gigabyte sizes, new processes or complex higher order corrections that are currently out of reach could be evaluated with a VM given enough computing power.

  6. Simple fabrication of gold nanobelts and patterns.

    Directory of Open Access Journals (Sweden)

    Renyun Zhang

    Full Text Available Gold nanobelts are of interest in several areas; however, there are only few methods available to produce these belts. We report here on a simple evaporation induced self-assembly (EISA method to produce porous gold nanobelts with dimensions that scale across nanometer (thickness ∼80 nm and micrometer (width ∼20 µm, to decimeter (length ∼0.15 m. The gold nanobelts are well packed on the beaker wall and can be easily made to float on the surface of the solution for depositing onto other substrates. Microscopy showed that gold nanobelts had a different structure on the two sides of the belt; the density of gold nanowires on one side was greater than on the other side. Electrical measurements showed that these nanobelts were sensitive to compressive or tensile forces, indicating a potential use as a strain sensor. The patterned nanobelts were further used as a template to grow ZnO nanowires for potential use in applications such as piezo-electronics.

  7. Comparing Simple Flood Reservoir Operation Rules

    Directory of Open Access Journals (Sweden)

    James Connaughton

    2014-09-01

    Full Text Available The effectiveness of three simple flood operating rules in reducing the peak flow is compared for four simplified hydrograph shapes. The Minimize Flood Peak rule uses available flood storage capacity to store peak flows from an accurate hydrograph forecast. The less demanding Minimize Flooding Frequency operating rule releases water at or below channel capacity until the flood storage pool is filled and outflows are forced to exceed the channel capacity. The Short Forecast Peak Minimization rule minimizes flood peak over a short foreseeable future with existing flood storage capacity. Four simplified hydrograph shapes (triangular, abrupt wave, flood pulse and broad peak were used. The Minimize Flood Peak rule reduces peak flows better than alternatives, but is often impractical. The Short Forecast Peak Minimization rule reduces peak flows for a wide range of conditions. The Minimize Flood Frequency rule may be more relevant where damages occur abruptly, as in many leveed systems. All rules reduce peak outflow more efficiently for more steeply rising hydrographs. The approach suggests some general insights for flood operations of reservoirs.

  8. Toward the Verification of a Simple Hypervisor

    CERN Document Server

    Dahlin, Mike; Krug, Robert Bellarmine; McCoyd, Michael; Young, William; 10.4204/EPTCS.70.3

    2011-01-01

    Virtualization promises significant benefits in security, efficiency, dependability, and cost. Achieving these benefits depends upon the reliability of the underlying virtual machine monitors (hypervisors). This paper describes an ongoing project to develop and verify MinVisor, a simple but functional Type-I x86 hypervisor, proving protection properties at the assembly level using ACL2. Originally based on an existing research hypervisor, MinVisor provides protection of its own memory from a malicious guest. Our long-term goal is to fully verify MinVisor, providing a vehicle to investigate the modeling and verification of hypervisors at the implementation level, and also a basis for further systems research. Functional segments of the MinVisor C code base are translated into Y86 assembly, and verified with respect to the Y86 model. The inductive assertions (also known as "compositional cutpoints") methodology is used to prove the correctness of the code. The proof of the code that sets up the nested page tabl...

  9. Scenarios selection for a simple concept landfill

    International Nuclear Information System (INIS)

    Scenarios are used to deal with uncertainty on the evolution of complex systems. The scenario selection methodologies also have to provide a basis for reflexion and traceability of the reasoning. A scenario selection method has been developed for the case of disposal of uranium mill tailings in a landfill site. In the case of a simple concept landfill, a methodology that fulfils these requirements has been developed. It distinguishes on the one hand the landfill evolution, and on the other hand, the human behavior evolution. It is based on three steps: (i) characterization of the landfill itself, in order to define situations leading to releases of radionuclides, (ii) characterization of the human behavior in order to define situations leading to intrusions, and (iii) characterization of the interfaces between the two subsystems, in order to identify situations which could lead to a radiological risk for man. The method, applied to performance assessment for landfill of uranium mill tailings, has led to one reference scenario, and five altered scenarios taking into account specific landfill evolutions such as loss of covering or loss of integrity of the dike, and human intrusions such as housing on the site of landfill or excavation of the site. Copyright (2001) Material Research Society

  10. Two simple tools for industrial OR

    Directory of Open Access Journals (Sweden)

    K. Sandrock

    2003-12-01

    Full Text Available At the 1985 Annual Congress of the South African Production & Inventory Control Society it was pointed out that the productivity growth rate for South Africa is completely out of kilter with that for the western industrialised nations. The latter all display positive rates (some as high as that of Japan whereas the rate for South Africa is - NEGATIVE. Partly as a result of this situation, more and more attention is being given to quality control and reliability engineering by our industrialists in their attempts to improve productivity. This is going hand in hand with the introduction of better techniques and better use of the latest technology. We should also give attention to analytical tools that may be used in a simple inexpensive way to improve our methods of analysing industrial data, and in this way to improve our performance at little or no additional cost. To this end two tools are discussed. They are by means new. But it does seem as though they could be more widely applied in the industrial milieu.

  11. Simple mathematical law benchmarks human confrontations

    Science.gov (United States)

    Johnson, Neil F.; Medina, Pablo; Zhao, Guannan; Messinger, Daniel S.; Horgan, John; Gill, Paul; Bohorquez, Juan Camilo; Mattson, Whitney; Gangi, Devon; Qi, Hong; Manrique, Pedro; Velasquez, Nicolas; Morgenstern, Ana; Restrepo, Elvira; Johnson, Nicholas; Spagat, Michael; Zarama, Roberto

    2013-12-01

    Many high-profile societal problems involve an individual or group repeatedly attacking another - from child-parent disputes, sexual violence against women, civil unrest, violent conflicts and acts of terror, to current cyber-attacks on national infrastructure and ultrafast cyber-trades attacking stockholders. There is an urgent need to quantify the likely severity and timing of such future acts, shed light on likely perpetrators, and identify intervention strategies. Here we present a combined analysis of multiple datasets across all these domains which account for >100,000 events, and show that a simple mathematical law can benchmark them all. We derive this benchmark and interpret it, using a minimal mechanistic model grounded by state-of-the-art fieldwork. Our findings provide quantitative predictions concerning future attacks; a tool to help detect common perpetrators and abnormal behaviors; insight into the trajectory of a `lone wolf' identification of a critical threshold for spreading a message or idea among perpetrators; an intervention strategy to erode the most lethal clusters; and more broadly, a quantitative starting point for cross-disciplinary theorizing about human aggression at the individual and group level, in both real and online worlds.

  12. A simple model of the slingshot effect

    CERN Document Server

    Fiore, Gaetano

    2015-01-01

    We present a detailed quantitative description of the recently proposed "slingshot effect" [Fiore, Fedele, De angelis 2014]. Namely, we determine a broad range of conditions under which the impact of a very short and intense laser pulse normally onto a plasma (or matter to be locally completely ionized into a plasma by the pulse) causes the expulsion of a bunch of surface electrons in the direction opposite to the one of propagation of the pulse, and the detailed, ready-for-experiments features of the expelled electrons (energy spectrum, collimation, etc). The effect is due to the combined actions of the ponderomotive force and the huge longitudinal field arising from charge separation. Our predictions are based on estimating 3D corrections to a simple, yet powerful plane magnetofluidodynamic model where the equations to be solved are reduced to a system of Hamilton equations in one dimension (or a collection of) which become autonomous after the pulse has overcome the electrons. Experimental tests seem to be...

  13. Simple models of the hydrofracture process

    KAUST Repository

    Marder, M.

    2015-12-29

    Hydrofracturing to recover natural gas and oil relies on the creation of a fracture network with pressurized water. We analyze the creation of the network in two ways. First, we assemble a collection of analytical estimates for pressure-driven crack motion in simple geometries, including crack speed as a function of length, energy dissipated by fluid viscosity and used to break rock, and the conditions under which a second crack will initiate while a first is running. We develop a pseudo-three-dimensional numerical model that couples fluid motion with solid mechanics and can generate branching crack structures not specified in advance. One of our main conclusions is that the typical spacing between fractures must be on the order of a meter, and this conclusion arises in two separate ways. First, it arises from analysis of gas production rates, given the diffusion constants for gas in the rock. Second, it arises from the number of fractures that should be generated given the scale of the affected region and the amounts of water pumped into the rock.

  14. Simple light gas guns for hypervelocity studies

    International Nuclear Information System (INIS)

    Two-stage light guns are used extensively in hypervelocity research. The applications of this technology include impact studies and special materials development. Oak Ridge National Laboratory (ORNL) has developed two-stage guns that accelerate small projectiles (4-mm nominal diameter) to velocities of up to ∼5 km/s. These guns are relatively small and simple (thus, easy to operate), allowing a significant number of test shots to be carried out and data accumulated in a short time. Materials that have been used for projectiles include plastics, frozen isotopes of hydrogen, and lithium hydride. One gun has been used to demonstrate repetitive operation at a rate of 0.7 Hz; and, with a few design improvements, it appears capable of performing at firing frequencies of 1--2 Hz. A schematic of ORNL two-stage device is shown below. Unlike most such devices, no rupture disks are used. Instead, a fast valve (high-flow type) initiates the acceleration process in the first stage. Projectiles can be loaded into the gun breech via the slide mechanism; this action has been automated which allows repetitive firing. Alternatively, the device is equipped with ''pipe gun'' apparatus in which gas can be frozen in situ in the gun barrel to form the projectile. This equipment operates with high reliability and is well suited for small-scale testing at high velocity. 17 refs., 6 figs., 2 tabs

  15. A SIMPLE LAW OF STAR FORMATION

    International Nuclear Information System (INIS)

    We show that supersonic MHD turbulence yields a star formation rate (SFR) as low as observed in molecular clouds, for characteristic values of the free-fall time divided by the dynamical time, tff/tdyn, the Alfvénic Mach number, Ma, and the sonic Mach number, Ms. Using a very large set of deep adaptive-mesh-refinement simulations, we quantify the dependence of the SFR per free-fall time, εff, on the above parameters. Our main results are (1) that εff decreases exponentially with increasing tff/tdyn, but is insensitive to changes in Ms, for constant values of tff/tdyn and Ma. (2) Decreasing values of Ma (stronger magnetic fields) reduce εff, but only to a point, beyond which εff increases with a further decrease of Ma. (3) For values of Ma characteristic of star-forming regions, εff varies with Ma by less than a factor of two. We propose a simple star formation law, based on the empirical fit to the minimum εff, and depending only on tff/tdyn: εff ≈ εwindexp (– 1.6 tff/tdyn). Because it only depends on the mean gas density and rms velocity, this law is straightforward to implement in simulations and analytical models of galaxy formation and evolution.

  16. Simple UV spectrophotometric assay of Mefenamic acid

    Directory of Open Access Journals (Sweden)

    Dr. Safila Naveed

    2014-07-01

    Full Text Available Mefenamic acid belongs to non-steroidal antiinflammatory drugs (NSAID.. It is being used widely for the treatment of analgesia. It is also used as antirheumatic and antipyretic drug. Our aim of study is to develop a efficient least time consuming and simple spectrophotometric method for the assay of mefenamic acid. Comparision of assay of three different brands of mefenamic acid (mefnac,ponstan,dolar available in public medical store of Karachi, Pakistan has also been done. The assay is based on the ultraviolet UV absorbance maxima at about 288nm wavelength of mefenamic acid, water is used as solvent. A sample of drug was dissolved in water to produce a solution containing mefenamic acid. Similarly, a sample of ground tablets of different brand were dissolved in water and various dilutions were made. The absorbance of sample preparation was measured at 288nm against the solvent blank and the assay was determined by comparing with the absorbance of available brand. Our results reveals that among all the three brands of mefenamic acid (mefnac,ponstan,dolar rosulin and rovista shows highest percentage assay 107.5%. xplended and rosubar shows percent assay of 106.25% and 103.75% while rovactor shows lowest value for percentage assay 98.75%.

  17. Simple benchmark for complex dose finding studies.

    Science.gov (United States)

    Cheung, Ying Kuen

    2014-06-01

    While a general goal of early phase clinical studies is to identify an acceptable dose for further investigation, modern dose finding studies and designs are highly specific to individual clinical settings. In addition, as outcome-adaptive dose finding methods often involve complex algorithms, it is crucial to have diagnostic tools to evaluate the plausibility of a method's simulated performance and the adequacy of the algorithm. In this article, we propose a simple technique that provides an upper limit, or a benchmark, of accuracy for dose finding methods for a given design objective. The proposed benchmark is nonparametric optimal in the sense of O'Quigley et al. (2002, Biostatistics 3, 51-56), and is demonstrated by examples to be a practical accuracy upper bound for model-based dose finding methods. We illustrate the implementation of the technique in the context of phase I trials that consider multiple toxicities and phase I/II trials where dosing decisions are based on both toxicity and efficacy, and apply the benchmark to several clinical examples considered in the literature. By comparing the operating characteristics of a dose finding method to that of the benchmark, we can form quick initial assessments of whether the method is adequately calibrated and evaluate its sensitivity to the dose-outcome relationships.

  18. ZeroMQ: Messaging Made Simple

    CERN Document Server

    CERN. Geneva

    2013-01-01

    Since its inception in 2007, ZeroMQ has defined a new product category of thin, fast, open source message transports. This little library has now grown into a large, vibrant community of projects tied together with standard protocols and APIs. Applications, written in any language, talk to each other over TCP, multicast, or inproc transports, using a single socket-based API, and a set of "patterns" (pub-sub, request-reply, dealer-router, pipeline). ZeroMQ handles message framing, batching, and I/O, but ignores aspects like serialization and persistence. By focussing on the essentials, and acting as a toolkit rather than a pre-packaged solution, ZeroMQ turns the complex problem of distributed computing into a relatively simple recipe. About the speaker Pieter Hintjens is a writer, programmer, and public speaker who has spent decades building large software systems, organizations, and businesses. He designed the Advanced Message Queuing Protocol (AMQP) in 2006 for JPMorganChase and left ...

  19. A simple theory of Rijke tube oscillation

    Institute of Scientific and Technical Information of China (English)

    Maa Dah-You

    2002-01-01

    A simple theory of Rijke tube oscillation is presented based on mathematical realization of Rayleigh's qualitative explanation of the mechanism of Rijke tube. This is done by assuming a single point of high temperature in an otherwise uniform tube and the sound source produced when cold air flows passing this point. The wave equation thus obtained is then rigorously solved. It is found that the Rijke tube oscillation is a feedback system. There is no feedback nor oscillation when the hot spot is at a node or antinode in the tube. The mean flow is necessary for the oscillation, the particle velocity of which is proportional to the mean velocity, and the ratio is proportional to the gauze temperature when the later is low and the feedback does not affect much the magnitude of the particle velocity. When the temperature is high, the feedback increases rapidly and the particle velocity might grow to several or even tens of times of the mean velocity, and almost indefinitely when the heater temperature is high enough. Otherwise the growth is rather slow, when the mean flow or high temperature is first applied. The oscillations stop immediately when the mean flow is stopped. If the mean flow is controlled by a valve or a paddle at one end of the tube, an interesting sound is produced.

  20. Laparoscopic Pyloromyotomy: A Modified Simple Technique

    Directory of Open Access Journals (Sweden)

    Mohammed Omer Anwar

    2016-01-01

    Full Text Available Background: A modified laparoscopic pyloromyotomy (LP technique may provide an alternative to treating infantile hypertrophic pyloric stenosis (IHPS by improving operative timing with reduction of postoperative complication rates, compared with a three-port trocar system.Methods: Thirty-three infants were treated with IHPS at a single-centre between January 2002 and December 2011. The local surgical incision to the pylorus was performed according to Ramstedt’s pyloromyotomy; but with a two-port trocar system (umbilical and right lower abdominal crease ports, following a controlled stab wound into the epigastric region and a 3mm incision to allow introduction of ophthalmic knife. With the aid of atraumatic forceps and camera guidance, the ophthalmic knife was used to carefully incise the seromuscular layer, which allows improved manual tactile sensation compared to ergonomic laparoscopic spreaders. A Benson pyloric spreader was then used to further separate the pyloric muscle layer to complete the procedure.Results: In all 33 infants treated, LP was safely performed with no evidence of duodenal or mucosal perforation with complete pyloromyotomy achieved in each case. The postoperative course was rather uneventful apart from an umbilical wound infection.Conclusion: This modified approach is simple, safe and allows improved operative timing, whilst increasing surgeon’s confidence by tactile sensation.

  1. Simple goiter in children and juveniles

    Energy Technology Data Exchange (ETDEWEB)

    Wiebel, J.

    1983-10-31

    Non-toxic, simple goiter is the most common cause of thyroid enlargement in adolescents and children. Although initially there are hardly any complaints it should be treated with l-thyroxine to prevent further enlargement, degenerative alterations, development of nodules, possible hyper- or hypothyroidism occurring with increasing age. Anamnesis and clinical features are as important for establishing the diagnosis as laboratory parameters, which are not always necessary. Thyroid nodules in children or adolescents are more likely to be malignant than in later life; their nature has to be clarified by sonography, scintigraphy, fine needle biopsy or even operation. After l-thyroxine therapy has normalized thyroid size (60-90%), goiter prophylaxis with iodine supplementation can be tried, since iodine deficiency exists throughout Germany. If the goiter reappears continuous l-thyroxine treatment is recommended. Following the general introduction of iodine prophylaxis using iodinized salt there has been a significant reduction in goiter incidence in Switzerland, Austria and other areas with iodine deficiency. New legislation in the FRG now allows for the general use of e.g., Bad Reichenhaller Jodsalz, Duera Vollsalz or Bayerisches Vollsalz to prevent the development of the majority of goiters in children and adolescents.

  2. Mental chronometry with simple linear regression.

    Science.gov (United States)

    Chen, J Y

    1997-10-01

    Typically, mental chronometry is performed by means of introducing an independent variable postulated to affect selectively some stage of a presumed multistage process. However, the effect could be a global one that spreads proportionally over all stages of the process. Currently, there is no method to test this possibility although simple linear regression might serve the purpose. In the present study, the regression approach was tested with tasks (memory scanning and mental rotation) that involved a selective effect and with a task (word superiority effect) that involved a global effect, by the dominant theories. The results indicate (1) the manipulation of the size of a memory set or of angular disparity affects the intercept of the regression function that relates the times for memory scanning with different set sizes or for mental rotation with different angular disparities and (2) the manipulation of context affects the slope of the regression function that relates the times for detecting a target character under word and nonword conditions. These ratify the regression approach as a useful method for doing mental chronometry. PMID:9347535

  3. Simple models of the hydrofracture process.

    Science.gov (United States)

    Marder, M; Chen, Chih-Hung; Patzek, T

    2015-12-01

    Hydrofracturing to recover natural gas and oil relies on the creation of a fracture network with pressurized water. We analyze the creation of the network in two ways. First, we assemble a collection of analytical estimates for pressure-driven crack motion in simple geometries, including crack speed as a function of length, energy dissipated by fluid viscosity and used to break rock, and the conditions under which a second crack will initiate while a first is running. We develop a pseudo-three-dimensional numerical model that couples fluid motion with solid mechanics and can generate branching crack structures not specified in advance. One of our main conclusions is that the typical spacing between fractures must be on the order of a meter, and this conclusion arises in two separate ways. First, it arises from analysis of gas production rates, given the diffusion constants for gas in the rock. Second, it arises from the number of fractures that should be generated given the scale of the affected region and the amounts of water pumped into the rock. PMID:26764704

  4. Simple models of assortment through environmental feedback.

    Science.gov (United States)

    Pepper, John W

    2007-01-01

    Social evolution depends critically on assortment, or segregation versus even mixing, between cooperators and noncooperators. Altruistic traits, which reduce the absolute fitness of their bearers, cannot evolve without positive assortment (excess segregation). The question of how positive assortment can arise has been controversial, but most evolutionary biologists believe that common descent is the only effective general mechanism. Here I investigate another recently proposed mechanism for generating nonrandom assortment, termed environmental feedback. This requires only that two forms of a trait affect the quality of the local environment differently in such a way that all individuals are more likely to leave low-quality locales. Experiments with simple computational models confirm that environmental feedback generates significant levels of genetic similarity among non-kin within locales. The mechanism is fairly general, and can under some conditions produce levels of genetic similarity comparable to those resulting from close genealogical relationship. Environmental feedback can also generate the negative assortment necessary for the evolution of spiteful traits. Environmental feedback is expected to create positive frequency-dependent selection, which thus favor any social trait that becomes common in the population. Results from this stylized model suggest that environmental feedback could be important in the evolution of both cooperation and spite, within as well as between species.

  5. A simple law of star formation

    DEFF Research Database (Denmark)

    Padoan, Paolo; Haugbølle, Troels; Nordlund, Åke

    2012-01-01

    We show that supersonic MHD turbulence yields a star formation rate (SFR) as low as observed in molecular clouds, for characteristic values of the free-fall time divided by the dynamical time, t ff/t dyn, the Alfvénic Mach number, {\\cal M}_a, and the sonic Mach number, {\\cal M}_s. Using a very...... values of t ff/t dyn and {\\cal M}_a. (2) Decreasing values of {\\cal M}_a (stronger magnetic fields) reduce epsilonff, but only to a point, beyond which epsilonff increases with a further decrease of {\\cal M}_a. (3) For values of {\\cal M}_a characteristic of star-forming regions, epsilonff varies...... with {\\cal M}_a by less than a factor of two. We propose a simple star formation law, based on the empirical fit to the minimum epsilonff, and depending only on t ff/t dyn: epsilonff ˜ epsilonwindexp (– 1.6 t ff/t dyn). Because it only depends on the mean gas density and rms velocity, this law...

  6. A scalable and operationally simple radical trifluoromethylation.

    Science.gov (United States)

    Beatty, Joel W; Douglas, James J; Cole, Kevin P; Stephenson, Corey R J

    2015-01-01

    The large number of reagents that have been developed for the synthesis of trifluoromethylated compounds is a testament to the importance of the CF3 group as well as the associated synthetic challenge. Current state-of-the-art reagents for appending the CF3 functionality directly are highly effective; however, their use on preparative scale has minimal precedent because they require multistep synthesis for their preparation, and/or are prohibitively expensive for large-scale application. For a scalable trifluoromethylation methodology, trifluoroacetic acid and its anhydride represent an attractive solution in terms of cost and availability; however, because of the exceedingly high oxidation potential of trifluoroacetate, previous endeavours to use this material as a CF3 source have required the use of highly forcing conditions. Here we report a strategy for the use of trifluoroacetic anhydride for a scalable and operationally simple trifluoromethylation reaction using pyridine N-oxide and photoredox catalysis to affect a facile decarboxylation to the CF3 radical. PMID:26258541

  7. Simple Low-Frequency Beam Pickup

    Energy Technology Data Exchange (ETDEWEB)

    Novokhatski, A.; Heifets, S.; /SLAC; Aleksandrov, A.; /Oak Ridge

    2011-10-12

    Detection of the field induced by a beam outside of the beam pipe can be used as a beam diagnostic. Wires placed in longitudinal slots in the outside wall of the beam pipe can be used as a beam pickup. This has a very small beam-coupling impedance and avoids complications of having a feedthrough. The signal can be reasonably high at low frequencies. We present a field waveform at the outer side of a beam pipe, obtained as a result of calculations and measurements. We calculate the beam-coupling impedance due to a long longitudinal slot in the resistive wall and the signal induced in a wire placed in such a slot and shielded by a thin screen from the beam. These results should be relevant for impedance calculations of the slot in an antechamber and for slots in the PEP-II distributed ion pump screens. The design of the low-frequency beam position monitor is very simple. It can be used in storage rings, synchrotron light sources, and free electron lasers, like LINAC coherent light source.

  8. A Simple Technique for Shoulder Arthrography

    International Nuclear Information System (INIS)

    Purpose: To present a systematic approach to teaching a technique for arthrography of the shoulder. Using an adhesive marker-plate with radiopaque coordinates, precise sites for puncture can be identified and the need for fluoroscopic guidance obviated. Material and Methods: Forty-six glenohumeral arthrograms were performed in 45 patients; in 1 case involving examination of both shoulders. The stages of the technique are described in detail, as are the fundamental aspects of achieving an effective glenohumeral injection. Pain intensity was measured in all patients using a verbal description scale. Results: Shoulder arthrography was successful in all cases. Average time taken for the procedure was 7 min, with no difference in the respective times required by an experienced radiologist and a resident. The procedure was well tolerated by most patients, with slight discomfort being observed in a very few cases. Conclusion: The arthrographic technique used in this study is simple, safe, rapid, and reproducible, and has the advantage of precise localization of the site for puncture without need for fluoroscopic guidance. The procedure described in this study can be of help in teaching residents and can reduce the learning curve for radiologists with no experience in arthrographic methods. It also reduces the time of exposure to fluoroscopy Keywords: Arthrography, joint, shoulder

  9. Evolutionary dynamics in a simple model of self-assembly

    Science.gov (United States)

    Johnston, Iain G.; Ahnert, Sebastian E.; Doye, Jonathan P. K.; Louis, Ard A.

    2011-06-01

    We investigate the evolutionary dynamics of an idealized model for the robust self-assembly of two-dimensional structures called polyominoes. The model includes rules that encode interactions between sets of square tiles that drive the self-assembly process. The relationship between the model’s rule set and its resulting self-assembled structure can be viewed as a genotype-phenotype map and incorporated into a genetic algorithm. The rule sets evolve under selection for specified target structures. The corresponding complex fitness landscape generates rich evolutionary dynamics as a function of parameters such as the population size, search space size, mutation rate, and method of recombination. Furthermore, these systems are simple enough that in some cases the associated model genome space can be completely characterized, shedding light on how the evolutionary dynamics depends on the detailed structure of the fitness landscape. Finally, we apply the model to study the emergence of the preference for dihedral over cyclic symmetry observed for homomeric protein tetramers.

  10. A simple and efficient DNA isolation method for Salvia officinalis.

    Science.gov (United States)

    Aleksić, Jelena M; Stojanović, Danilo; Banović, Bojana; Jančić, Radiša

    2012-12-01

    We report an efficient, simple, and cost-effective protocol for the isolation of genomic DNA from an aromatic medicinal plant, common sage (Salvia officinalis L.). Our modification of the standard CTAB protocol includes two polyphenol adsorbents (PVP 10 and activated charcoal), high NaCl concentrations (4 M) for removing polysaccharides, and repeated Sevag treatment to remove proteins and other carbohydrate contaminants. The mean DNA yield obtained with our Protocol 2 was 330.6 μg DNA g(-1) of dry leaf tissue, and the absorbance ratios 260/280 and 260/230 nm averaged 1.909 and 1.894, respectively, revealing lack of contamination. PCR amplifications of one nuclear (26S rDNA) and one chloroplast (rps16-trnK) locus indicated that our DNA isolation protocol may be used in common sage and other aromatic and medicinal plants containing essential oil for molecular biologic and biotechnological studies and for population genetics, phylogeographic, and conservation surveys in which nuclear or chloroplast genomes would be studied in large numbers of individuals.

  11. A novel and simple method for construction of recombinant adenoviruses.

    Science.gov (United States)

    Tan, Rong; Li, Chunhua; Jiang, Sijing; Ma, Lixin

    2006-07-19

    Recombinant adenoviruses have been widely used for various applications, including protein expression and gene therapy. We herein report a new and simple cloning approach to an efficient and robust construction of recombinant adenoviral genomes based on the mating-assisted genetically integrated cloning (MAGIC) strategy. The production of recombinant adenovirus serotype 5-based vectors was greatly facilitated by the use of the MAGIC procedure and the development of the Adeasy adenoviral vector system. The recombinant adenoviral plasmid can be generated by a direct and seamless substitution, which replaces the stuff fragment in a full-length adenoviral genome with the gene of interest in a small plasmid in Escherichia coli. Recombinant adenoviral plasmids can be rapidly constructed in vivo by using the new method, without manipulations of the large adenoviral genome. In contrast to other traditional systems, it reduces the need for multiple in vitro manipulations, such as endonuclease cleavage, ligation and transformation, thus achieving a higher efficiency with negligible background. This strategy has been proven to be suitable for constructing an adenoviral cDNA expression library. In summary, the new method is highly efficient, technically less demanding and less labor-intensive for constructing recombinant adenoviruses, which will be beneficial for functional genomic and proteomic researches in mammalian cells.

  12. Parvoviruses: Small Does Not Mean Simple.

    Science.gov (United States)

    Cotmore, Susan F; Tattersall, Peter

    2014-11-01

    Parvoviruses are small, rugged, nonenveloped protein particles containing a linear, nonpermuted, single-stranded DNA genome of ∼5 kb. Their limited coding potential requires optimal adaptation to the environment of particular host cells, where entry is mediated by a variable program of capsid dynamics, ultimately leading to genome ejection from intact particles within the host nucleus. Genomes are amplified by a continuous unidirectional strand-displacement mechanism, a linear adaptation of rolling circle replication that relies on the repeated folding and unfolding of small hairpin telomeres to reorient the advancing fork. Progeny genomes are propelled by the viral helicase into the preformed capsid via a pore at one of its icosahedral fivefold axes. Here we explore how the fine-tuning of this unique replication system and the mechanics that regulate opening and closing of the capsid fivefold portals have evolved in different viral lineages to create a remarkably complex spectrum of phenotypes.

  13. Design, properties, and applications of protein micro- and nanoparticles

    NARCIS (Netherlands)

    Saglam, Dilek; Venema, Paul; van der Linden, Erik; de Vries, Renko

    2014-01-01

    The design of protein particles with tailored properties has received an increased attention recently. Several approaches, from simple heat treatment in dilute systems to the combination of heat and mechanical treatments in concentrated protein solutions, have been used to obtain protein particles w

  14. SIMPL enhancement of tumor necrosis factor-α dependent p65-MED1 complex formation is required for mammalian hematopoietic stem and progenitor cell function.

    Directory of Open Access Journals (Sweden)

    Weina Zhao

    Full Text Available Significant insight into the signaling pathways leading to activation of the Rel transcription factor family, collectively termed NF-κB, has been gained. Less well understood is how subsets of NF-κB-dependent genes are regulated in a signal specific manner. The SIMPL protein (signaling molecule that interacts with mouse pelle-like kinase is required for full Tumor Necrosis Factor-α (TNFα induced NF-κB activity. We show that SIMPL is required for steady-state hematopoiesis and the expression of a subset of TNFα induced genes whose products regulate hematopoietic cell activity. To gain insight into the mechanism through which SIMPL modulates gene expression we focused on the Tnf gene, an immune response regulator required for steady-state hematopoiesis. In response to TNFα SIMPL localizes to the Tnf gene promoter where it modulates the initiation of Tnf gene transcription. SIMPL binding partners identified by mass spectrometry include proteins involved in transcription and the interaction between SIMPL and MED1 was characterized in more detail. In response to TNFα, SIMPL is found in p65-MED1 complexes where SIMPL enhances p65/MED1/SIMPL complex formation. Together our results indicate that SIMPL functions as a TNFα-dependent p65 co-activator by facilitating the recruitment of MED1 to p65 containing transcriptional complexes to control the expression of a subset of TNFα-induced genes.

  15. Heat Shock Proteins (HSPs: a Review

    Directory of Open Access Journals (Sweden)

    Jana Tkáčová

    2012-05-01

    Full Text Available Heat shock proteins (HSPs are a large class of proteins that have been conserved throughout evolution and exist by prokaryote and eukaryote organisms. Heat shock proteins play an important role in protein homeostasis. They can found in all major cellular compartments. The HSP90 family are important in the formation of the steroid receptor complex. The HSP70 family is necessary for protein synthesis, translocation, and folding. HSP60 family is important in protein stability. Many factors, e. g. heavy metals and organic toxic substances, elevated temperature in all cells responsive to the formation of proteins called stress proteins. This is happening with a simple bacterium and with complex of neurons too. The concentration of HSPs in muscle in young and adults birds is increasing rapidly in the cellular stress. Increasing HSPs leads to significant changes in gene expression, which lead to reconstruction of skeletal muscle.

  16. An Arduino Investigation of Simple Harmonic Motion

    Science.gov (United States)

    Galeriu, Calin; Edwards, Scott; Esper, Geoffrey

    2014-03-01

    We cannot hope for a new generation of scientists and engineers if we don't let our young students take ownership of their scientific and engineering explorations, if we don't let them enjoy the hands-on cycle of design and production, and if we don't let them implant their creativity into a technologically friendly environment. With this educational philosophy in mind, Massimo Banzi and his team have developed and popularized the open source Arduino microcontroller board. The Arduino board has helped countless people in their science, electronics, robotics, or engineering projects, allowing them to build things that we have not even dreamed of. Physics instructors have also realized the advantages of using Arduino boards for lab experiments. The schools are saving money because the homemade experimental equipment is much cheaper than the commercial alternatives. The students are thankful for an educational experience that is more interesting, more loaded with STEM content, and more fun. As further proof of this new trend in physics education, Vernier5 is now documenting the use of their probes with Arduino boards. This is why we have developed an Arduino-based physics investigation of the simple harmonic motion (SHM) of a mass on a spring. The experimental data are collected with the help of an ultrasonic distance sensor and an Arduino Uno board. The data are then graphed and analyzed using Origin 9. This rich cross-curricular STEM activity integrates electronics, computer programming, physics, and mathematics in a way that is both experimentally exciting and intellectually rewarding.

  17. A SIMPLE LAW OF STAR FORMATION

    Energy Technology Data Exchange (ETDEWEB)

    Padoan, Paolo [ICREA and ICC, University of Barcelona, Marti i Franques 1, E-08028 Barcelona (Spain); Haugbolle, Troels [Centre for Star and Planet Formation, University of Copenhagen, Oestervoldgade 5-7., DK-1350, Copenhagen (Denmark); Nordlund, Ake, E-mail: ppadoan@icc.ub.edu, E-mail: haugboel@nbi.dk, E-mail: aake@nbi.dk [Centre for Star and Planet Formation and Niels Bohr Institute, University of Copenhagen, Juliane Maries Vej 30, DK-2100, Copenhagen (Denmark)

    2012-11-10

    We show that supersonic MHD turbulence yields a star formation rate (SFR) as low as observed in molecular clouds, for characteristic values of the free-fall time divided by the dynamical time, t{sub ff}/t{sub dyn}, the Alfvenic Mach number, M{sub a}, and the sonic Mach number, M{sub s}. Using a very large set of deep adaptive-mesh-refinement simulations, we quantify the dependence of the SFR per free-fall time, {epsilon}{sub ff}, on the above parameters. Our main results are (1) that {epsilon}{sub ff} decreases exponentially with increasing t{sub ff}/t{sub dyn}, but is insensitive to changes in M{sub s}, for constant values of t{sub ff}/t{sub dyn} and M{sub a}. (2) Decreasing values of M{sub a} (stronger magnetic fields) reduce {epsilon}{sub ff}, but only to a point, beyond which {epsilon}{sub ff} increases with a further decrease of M{sub a}. (3) For values of M{sub a} characteristic of star-forming regions, {epsilon}{sub ff} varies with M{sub a} by less than a factor of two. We propose a simple star formation law, based on the empirical fit to the minimum {epsilon}{sub ff}, and depending only on t{sub ff}/t{sub dyn}: {epsilon}{sub ff} Almost-Equal-To {epsilon}{sub wind}exp (- 1.6 t{sub ff}/t{sub dyn}). Because it only depends on the mean gas density and rms velocity, this law is straightforward to implement in simulations and analytical models of galaxy formation and evolution.

  18. A simple procedure for estimating soil porosity

    Science.gov (United States)

    Emmet-Booth, Jeremy; Forristal, Dermot; Fenton, Owen; Holden, Nick

    2016-04-01

    Soil degradation from mismanagement is of international concern. Simple, accessible tools for rapidly assessing impacts of soil management are required. Soil structure is a key component of soil quality and porosity is a useful indicator of structure. We outline a version of a procedure described by Piwowarczyk et al. (2011) used to estimate porosity of samples taken during a soil quality survey of 38 sites across Ireland as part of the Government funded SQUARE (Soil Quality Assessment Research) project. This required intact core (r = 2.5 cm, H = 5cm) samples taken at 5-10 cm and 10-20 cm depth, to be covered with muslin cloth at one end and secured with a jubilee clip. Samples were saturated in sealable water tanks for ≈ 64 hours, then allowed to drain by gravity for 24 hours, at which point Field Capacity (F.C.) was assumed to have been reached, followed by oven drying with weight determined at each stage. This allowed the calculation of bulk density and the estimation of water content at saturation and following gravitational drainage, thus total and functional porosity. The assumption that F.C. was reached following 24 hours of gravitational drainage was based on the Soil Moisture Deficit model used in Ireland to predict when soils are potentially vulnerable to structural damage and used nationally as a management tool. Preliminary results indicate moderately strong, negative correlations between estimated total porosity at 5-10 cm and 10-20 cm depth (rs = -0.7, P risk of damage owing to grazing animals? Soil Use and Management, 27, 255-263.

  19. A simple method for defining malaria seasonality

    Directory of Open Access Journals (Sweden)

    Smith Lucy

    2009-12-01

    Full Text Available Abstract Background There is currently no standard way of defining malaria seasonality, resulting in a wide range of definitions reported in the literature. Malaria cases show seasonal peaks in most endemic settings, and the choice and timing for optimal malaria control may vary by seasonality. A simple approach is presented to describe the seasonality of malaria, to aid localized policymaking and targeting of interventions. Methods A series of systematic literature reviews were undertaken to identify studies reporting on monthly data for full calendar years on clinical malaria, hospital admission with malaria and entomological inoculation rates (EIR. Sites were defined as having 'marked seasonality' if 75% or more of all episodes occurred in six or less months of the year. A 'concentrated period of malaria' was defined as the six consecutive months with the highest cumulative proportion of cases. A sensitivity analysis was performed based on a variety of cut-offs. Results Monthly data for full calendar years on clinical malaria, all hospital admissions with malaria, and entomological inoculation rates were available for 13, 18, and 11 sites respectively. Most sites showed year-round transmission with seasonal peaks for both clinical malaria and hospital admissions with malaria, with a few sites fitting the definition of 'marked seasonality'. For these sites, consistent results were observed when more than one outcome or more than one calendar year was available from the same site. The use of monthly EIR data was found to be of limited value when looking at seasonal variations of malaria transmission, particularly at low and medium intensity levels. Conclusion The proposed definition discriminated well between studies with 'marked seasonality' and those with less seasonality. However, a poor fit was observed in sites with two seasonal peaks. Further work is needed to explore the applicability of this definition on a wide-scale, using routine

  20. Simple sequence repeats in mycobacterial genomes

    Indian Academy of Sciences (India)

    Vattipally B Sreenu; Pankaj Kumar; Javaregowda Nagaraju; Hampapathalu A Nagarajaram

    2007-01-01

    Simple sequence repeats (SSRs) or microsatellites are the repetitive nucleotide sequences of motifs of length 1–6 bp. They are scattered throughout the genomes of all the known organisms ranging from viruses to eukaryotes. Microsatellites undergo mutations in the form of insertions and deletions (INDELS) of their repeat units with some bias towards insertions that lead to microsatellite tract expansion. Although prokaryotic genomes derive some plasticity due to microsatellite mutations they have in-built mechanisms to arrest undue expansions of microsatellites and one such mechanism is constituted by post-replicative DNA repair enzymes MutL, MutH and MutS. The mycobacterial genomes lack these enzymes and as a null hypothesis one could expect these genomes to harbour many long tracts. It is therefore interesting to analyse the mycobacterial genomes for distribution and abundance of microsatellites tracts and to look for potentially polymorphic microsatellites. Available mycobacterial genomes, Mycobacterium avium, M. leprae, M. bovis and the two strains of M. tuberculosis (CDC1551 and H37Rv) were analysed for frequencies and abundance of SSRs. Our analysis revealed that the SSRs are distributed throughout the mycobacterial genomes at an average of 220–230 SSR tracts per kb. All the mycobacterial genomes contain few regions that are conspicuously denser or poorer in microsatellites compared to their expected genome averages. The genomes distinctly show scarcity of long microsatellites despite the absence of a post-replicative DNA repair system. Such severe scarcity of long microsatellites could arise as a result of strong selection pressures operating against long and unstable sequences although influence of GC-content and role of point mutations in arresting microsatellite expansions can not be ruled out. Nonetheless, the long tracts occasionally found in coding as well as non-coding regions may account for limited genome plasticity in these genomes.

  1. A simple procedure for estimating soil porosity

    Science.gov (United States)

    Emmet-Booth, Jeremy; Forristal, Dermot; Fenton, Owen; Holden, Nick

    2016-04-01

    Soil degradation from mismanagement is of international concern. Simple, accessible tools for rapidly assessing impacts of soil management are required. Soil structure is a key component of soil quality and porosity is a useful indicator of structure. We outline a version of a procedure described by Piwowarczyk et al. (2011) used to estimate porosity of samples taken during a soil quality survey of 38 sites across Ireland as part of the Government funded SQUARE (Soil Quality Assessment Research) project. This required intact core (r = 2.5 cm, H = 5cm) samples taken at 5-10 cm and 10-20 cm depth, to be covered with muslin cloth at one end and secured with a jubilee clip. Samples were saturated in sealable water tanks for ≈ 64 hours, then allowed to drain by gravity for 24 hours, at which point Field Capacity (F.C.) was assumed to have been reached, followed by oven drying with weight determined at each stage. This allowed the calculation of bulk density and the estimation of water content at saturation and following gravitational drainage, thus total and functional porosity. The assumption that F.C. was reached following 24 hours of gravitational drainage was based on the Soil Moisture Deficit model used in Ireland to predict when soils are potentially vulnerable to structural damage and used nationally as a management tool. Preliminary results indicate moderately strong, negative correlations between estimated total porosity at 5-10 cm and 10-20 cm depth (rs = -0.7, P Holden, N.M. 2011. Can soil moisture deficit be used to forecast when soils are at high risk of damage owing to grazing animals? Soil Use and Management, 27, 255-263.

  2. Controlling exposure to chemicals: a simple guide.

    Science.gov (United States)

    Hay, Alastair

    2006-09-01

    Controlling exposure to chemicals in the workplace has been made easier by the use of a guide published by the U.K. Health and Safety Executive (HSE). Known as COSHH (Control of Substances Hazardous to Health Regulations) Essentials, the guide is a simple five-step procedure to devise appropriate control strategies to reduce exposures to various substances under different conditions. U.K. health and safety law requires risk assessments prior to use of hazardous substances and installation of appropriate control strategies before work commences. A 1996 survey of 1500 safety managers and trade union safety representatives revealed that the majority had little understanding of occupational safety limits for chemicals. Small- and medium-sized companies had little understanding of limits, and most could not develop control strategies. A new approach was required. COSHH Essentials is it. Developed over 3 years by a working group of hygienists and toxicologists representing HSE, industry, trade unions, and independent experts, the guide is now available in both paper-based and internet versions. It applies a hazard banding approach validated by data for 111 substances that have well-founded U.K. occupational exposure limits. New users select an appropriate hazard band for chemicals based on risk phrases. Details about dustiness for powders or volatility for liquids are inserted, and the guide allocates substances to one of four exposure bands linked, in turn, to specific control strategies. Now accessible through the HSE web site, COSHH Essentials will offer control strategies for both single chemicals and whole processes. To date over 300,000 risk assessments have been carried out using the internet version of COSHH Essentials. PMID:17119256

  3. Emergent biosynthetic capacity in simple microbial communities.

    Directory of Open Access Journals (Sweden)

    Hsuan-Chao Chiu

    2014-07-01

    Full Text Available Microbes have an astonishing capacity to transform their environments. Yet, the metabolic capacity of a single species is limited and the vast majority of microorganisms form complex communities and join forces to exhibit capabilities far exceeding those achieved by any single species. Such enhanced metabolic capacities represent a promising route to many medical, environmental, and industrial applications and call for the development of a predictive, systems-level understanding of synergistic microbial capacity. Here we present a comprehensive computational framework, integrating high-quality metabolic models of multiple species, temporal dynamics, and flux variability analysis, to study the metabolic capacity and dynamics of simple two-species microbial ecosystems. We specifically focus on detecting emergent biosynthetic capacity--instances in which a community growing on some medium produces and secretes metabolites that are not secreted by any member species when growing in isolation on that same medium. Using this framework to model a large collection of two-species communities on multiple media, we demonstrate that emergent biosynthetic capacity is highly prevalent. We identify commonly observed emergent metabolites and metabolic reprogramming patterns, characterizing typical mechanisms of emergent capacity. We further find that emergent secretion tends to occur in two waves, the first as soon as the two organisms are introduced, and the second when the medium is depleted and nutrients become limited. Finally, aiming to identify global community determinants of emergent capacity, we find a marked association between the level of emergent biosynthetic capacity and the functional/phylogenetic distance between community members. Specifically, we demonstrate a "Goldilocks" principle, where high levels of emergent capacity are observed when the species comprising the community are functionally neither too close, nor too distant. Taken together

  4. Simple Ligand–Receptor Interaction Descriptor (SILIRID for alignment-free binding site comparison

    Directory of Open Access Journals (Sweden)

    Vladimir Chupakhin

    2014-06-01

    Full Text Available We describe SILIRID (Simple Ligand–Receptor Interaction Descriptor, a novel fixed size descriptor characterizing protein–ligand interactions. SILIRID can be obtained from the binary interaction fingerprints (IFPs by summing up the bits corresponding to identical amino acids. This results in a vector of 168 integer numbers corresponding to the product of the number of entries (20 amino acids and one cofactor and 8 interaction types per amino acid (hydrophobic, aromatic face to face, aromatic edge to face, H-bond donated by the protein, H-bond donated by the ligand, ionic bond with protein cation and protein anion, and interaction with metal ion. Efficiency of SILIRID to distinguish different protein binding sites has been examined in similarity search in sc-PDB database, a druggable portion of the Protein Data Bank, using various protein–ligand complexes as queries. The performance of retrieval of structurally and evolutionary related classes of proteins was comparable to that of state-of-the-art approaches (ROC AUC ≈ 0.91. SILIRID can efficiently be used to visualize chemogenomic space covered by sc-PDB using Generative Topographic Mapping (GTM: sc-PDB SILIRID data form clusters corresponding to different protein types.

  5. The protein-water phase diagram and the growth of protein crystals from aqueous solution

    NARCIS (Netherlands)

    Haas, C; Drenth, J

    1998-01-01

    The phase diagram of a protein-water system is described with a simple model with parameters for the interaction between protein molecules in the liquid and in the solid phase. The model reproduces essential features of the phase diagram, such as the (metastable) liquid-liquid immiscibility region a

  6. Thermal Forces in Simple and Complex Fluids

    Science.gov (United States)

    Piazza, Roberto; Giglio, Marzio

    2004-11-01

    This topical issue of The European Physical Journal E deals with mass transport effects driven by thermal gradients, or, as we shall call them, with “thermal forces”. In simple fluid mixtures, coupling of heat and mass diffusion is due to the Ludwig-Soret effect, also known as thermal diffusion. The Soret effect dramatically lowers the thermal convection threshold, since concentration gradients relax much more slowly than temperature gradients, due to the disparate values of the mass diffusion coefficient and of the thermal diffusivity. Therefore, thermal diffusion plays an important role in naturally occurring processes like thermohaline convection (“salt fingering”) in oceans, crystal growth, component segregation in metallic alloys, volcanic lava and the Earth crust. More recently, its has been shown that thermal diffusion is a very convenient process in the generation of giant non-equilibrium fluctuations in fluid mixtures. Thermophoresis is a closely akin process that takes place both in aerosols and in liquid suspensions, consisting in the drift of dispersed particles induced by thermal inhomogeneities. Thermophoresis of airborne particles has an important role in atmospheric physics and ambient pollution, and can seriously affect semiconductor manufacturing. In macromolecular solutions and colloidal suspensions, these “thermal forces” are generally much stronger than in simple mixtures or in gases: for instance, recent experiments on DNA solutions have shown that thermophoresis may concur with thermal convection in leading to patterns where the local macromolecular concentration is amplified up to a thousandfold. Although known since a long time and clearly framed in terms of non-equilibrium thermodynamics concepts, both the Soret effect and particle thermophoresis in liquids still lack a general microscopic picture. For instance, in most cases the denser component of a binary mixture drifts to the cold, but examples of reverse behaviour are

  7. Principles of protein-protein interactions.

    OpenAIRE

    Jones, S; Thornton, J. M.

    1996-01-01

    This review examines protein complexes in the Brookhaven Protein Databank to gain a better understanding of the principles governing the interactions involved in protein-protein recognition. The factors that influence the formation of protein-protein complexes are explored in four different types of protein-protein complexes--homodimeric proteins, heterodimeric proteins, enzyme-inhibitor complexes, and antibody-protein complexes. The comparison between the complexes highlights differences tha...

  8. Tau protein

    DEFF Research Database (Denmark)

    Frederiksen, Jette Lautrup Battistini; Kristensen, Kim; Bahl, Jmc;

    2011-01-01

    Background: Tau protein has been proposed as biomarker of axonal damage leading to irreversible neurological impairment in MS. CSF concentrations may be useful when determining risk of progression from ON to MS. Objective: To investigate the association between tau protein concentration and 14......-3-3 protein in the cerebrospinal fluid (CSF) of patients with monosymptomatic optic neuritis (ON) versus patients with monosymptomatic onset who progressed to multiple sclerosis (MS). To evaluate results against data found in a complete literature review. Methods: A total of 66 patients with MS and/or ON from...... the Department of Neurology of Glostrup Hospital, University of Copenhagen, Denmark, were included. CSF samples were analysed for tau protein and 14-3-3 protein, and clinical and paraclinical information was obtained from medical records. Results: The study shows a significantly increased concentration of tau...

  9. Conformations of Proteins in Equilibrium

    Energy Technology Data Exchange (ETDEWEB)

    Micheletti, Cristian; Banavar, Jayanth R.; Maritan, Amos

    2001-08-20

    We introduce a simple theoretical approach for an equilibrium study of proteins with known native-state structures. We test our approach with results on well-studied globular proteins, chymotrypsin inhibitor (2ci2), barnase, and the alpha spectrin SH3 domain, and present evidence for a hierarchical onset of order on lowering the temperature with significant organization at the local level even at high temperatures. A further application to the folding process of HIV-1 protease shows that the model can be reliably used to identify key folding sites that are responsible for the development of drug resistance.

  10. Simple and Reproducible Sample Preparation for Single-Shot Phosphoproteomics with High Sensitivity

    DEFF Research Database (Denmark)

    Jersie-Christensen, Rosa R.; Sultan, Abida; Olsen, Jesper V

    2016-01-01

    The traditional sample preparation workflow for mass spectrometry (MS)-based phosphoproteomics is time consuming and usually requires multiple steps, e.g., lysis, protein precipitation, reduction, alkylation, digestion, fractionation, and phosphopeptide enrichment. Each step can introduce chemical......, and alkylation are performed in a single step, thus reducing sample loss and increasing reproducibility. Moreover, unlike standard cell lysis procedures the cell harvesting is performed at high temperatures (99 °C) and without detergents and subsequent need for protein precipitation. Phosphopeptides are enriched...... artifacts, in vitro protein and peptide modifications, and contaminations. Those often result in sample loss and affect the sensitivity, dynamic range and accuracy of the mass spectrometric analysis. Here we describe a simple and reproducible phosphoproteomics protocol, where lysis, denaturation, reduction...

  11. Was ist Really Simple Syndication - RSS? / What is Really Simple Syndication - RSS?

    Directory of Open Access Journals (Sweden)

    Obst, Oliver

    2006-09-01

    Full Text Available The new magic word for efficient information exchange is RSS - Really Simple Syndication. Within a short time, RSS experienced a rapid spreading to become the fourth exchange form for information in the Internet - beside E-Mail, HTML, and PDF. RSS is based on XML and - according to Wikipedia - comes first at the area of the semantic Web. With RSS the reversal and control of the information flow are possible. Numerous libraries and scientist make usage of Weblogs or RSS feeds for communication with their customers and colleagues.

  12. Measuring protein-protein and protein-nucleic Acid interactions by biolayer interferometry.

    Science.gov (United States)

    Sultana, Azmiri; Lee, Jeffrey E

    2015-01-01

    Biolayer interferometry (BLI) is a simple, optical dip-and-read system useful for measuring interactions between proteins, peptides, nucleic acids, small molecules, and/or lipids in real time. In BLI, a biomolecular bait is immobilized on a matrix at the tip of a fiber-optic sensor. The binding between the immobilized ligand and another molecule in an analyte solution produces a change in optical thickness at the tip and results in a wavelength shift proportional to binding. BLI provides direct binding affinities and rates of association and dissociation. This unit describes an efficient approach using streptavidin-based BLI to analyze DNA-protein and protein-protein interactions. A quantitative set of equilibrium binding affinities (K(d)) and rates of association and dissociation (k(a)/k(d)) can be measured in minutes using nanomole quantities of sample.

  13. Biogas Digester with Simple Solar Heater

    Directory of Open Access Journals (Sweden)

    Kh S Karimov

    2012-10-01

    Full Text Available ABSTRACT: In this research work, the design, fabrication and investigation of a biogas digester with simple solar heater are presented. For the solar heater, a built-in reverse absorber type heater was used. The maximum temperature (50°C inside the methane tank was taken as a main parameter for the design of the digester. Then, the energy balance equation for the case of a static mass of fluid being heated was used to model the process. The parameters of thermal insulation of the methane tank were also included in the calculations. The biogas digester consisted of a methane tank with built-in solar reverse absorber heater to harness the radiant solar energy for heating the slurry comprising of different organic wastes (dung, sewage, food wastes etc.. The methane tank was initially filled to 70% of its volume with organic wastes from the GIK institute’s sewage. The remaining volume was filled with sewage and cow dung from other sources. During a three month period (October-December, 2009 and another two month period (February-March, 2010, the digester was investigated. The effects of solar radiation on the absorber, the slurry’s temperature, and the ambient temperature were all measured during these investigations. It was found that using sewage only and sewage with cow dung in the slurry resulted in retention times of four and two weeks, respectively. The corresponding biogas produced was 0.4 m3 and 8.0 m3, respectively. Finally, this paper also elaborates on the upgradation of biogas through the removal of carbon dioxide, hydrogen sulphide and water vapour, and also the process of conversion of biogas energy into electric powerABSTRAK: Kajian ini membentangkan rekabentuk, fabrikasi dan penyelidikan tentang pencerna biogas dengan pemanas solar ringkas. Sebagai pemanas solar, ia dilengkapkan dengan penyerap pemanas beralik. Suhu maksimum(50oC di dalam tangki metana telah diambil sebagai parameter utama rekabentuk pencerna. Dengan menggunakan

  14. Protein-Protein Interaction Databases

    DEFF Research Database (Denmark)

    Szklarczyk, Damian; Jensen, Lars Juhl

    2015-01-01

    of research are explored. Here we present an overview of the most widely used protein-protein interaction databases and the methods they employ to gather, combine, and predict interactions. We also point out the trade-off between comprehensiveness and accuracy and the main pitfall scientists have to be aware...

  15. Physical Microscopic Model of Proteins Under Force

    OpenAIRE

    Dokholyan, Nikolay V.

    2012-01-01

    Nature has evolved proteins to counter-act forces applied on living cells, and designed proteins that can sense forces. One can appreciate Nature’s ingenuity in evolving these proteins to be highly sensitive to force and to have a high dynamic force range at which they operate. To achieve this level of sensitivity, many of these proteins are comprised of multiple domains and linking peptides connecting these domain, each of them have their own force response regimes. Here, using a simple mode...

  16. Development of a simple estimation tool for LMFBR construction cost

    Energy Technology Data Exchange (ETDEWEB)

    Yoshida, Kazuo; Kinoshita, Izumi [Central Research Inst. of Electric Power Industry, Komae, Tokyo (Japan). Komae Research Lab

    1999-05-01

    A simple tool for estimating the construction costs of liquid-metal-cooled fast breeder reactors (LMFBRs), 'Simple Cost' was developed in this study. Simple Cost is based on a new estimation formula that can reduce the amount of design data required to estimate construction costs. Consequently, Simple cost can be used to estimate the construction costs of innovative LMFBR concepts for which detailed design has not been carried out. The results of test calculation show that Simple Cost provides cost estimations equivalent to those obtained with conventional methods within the range of plant power from 325 to 1500 MWe. Sensitivity analyses for typical design parameters were conducted using Simple Cost. The effects of four major parameters - reactor vessel diameter, core outlet temperature, sodium handling area and number of secondary loops - on the construction costs of LMFBRs were evaluated quantitatively. The results show that the reduction of sodium handling area is particularly effective in reducing construction costs. (author)

  17. Analysis of protein folds using protein contact networks

    Indian Academy of Sciences (India)

    Pankaj Barah; Somdatta Sinha

    2008-08-01

    Proteins are important biomolecules, which perform diverse structural and functional roles in living systems. Starting from a linear chain of amino acids, proteins fold to different secondary structures, which then fold through short- and long-range interactions to give rise to the final three-dimensional shapes useful to carry out the biophysical and biochemical functions. Proteins are defined as having a common `fold' if they have major secondary structural elements with same topological connections. It is known that folding mechanisms are largely determined by a protein's topology rather than its interatomic interactions. The native state protein structures can, thus, be modelled, using a graph-theoretical approach, as coarse-grained networks of amino acid residues as `nodes' and the inter-residue interactions/contacts as `links'. Using the network representation of protein structures and their 2D contact maps, we have identified the conserved contact patterns (groups of contacts) representing two typical folds – the EF-hand and the ubiquitin-like folds. Our results suggest that this direct and computationally simple methodology can be used to infer about the presence of specific folds from the protein's contact map alone.

  18. A Simple Hydraulic Analog Model of Oxidative Phosphorylation.

    Science.gov (United States)

    Willis, Wayne T; Jackman, Matthew R; Messer, Jeffrey I; Kuzmiak-Glancy, Sarah; Glancy, Brian

    2016-06-01

    Mitochondrial oxidative phosphorylation is the primary source of cellular energy transduction in mammals. This energy conversion involves dozens of enzymatic reactions, energetic intermediates, and the dynamic interactions among them. With the goal of providing greater insight into the complex thermodynamics and kinetics ("thermokinetics") of mitochondrial energy transduction, a simple hydraulic analog model of oxidative phosphorylation is presented. In the hydraulic model, water tanks represent the forward and back "pressures" exerted by thermodynamic driving forces: the matrix redox potential (ΔGredox), the electrochemical potential for protons across the mitochondrial inner membrane (ΔGH), and the free energy of adenosine 5'-triphosphate (ATP) (ΔGATP). Net water flow proceeds from tanks with higher water pressure to tanks with lower pressure through "enzyme pipes" whose diameters represent the conductances (effective activities) of the proteins that catalyze the energy transfer. These enzyme pipes include the reactions of dehydrogenase enzymes, the electron transport chain (ETC), and the combined action of ATP synthase plus the ATP-adenosine 5'-diphosphate exchanger that spans the inner membrane. In addition, reactive oxygen species production is included in the model as a leak that is driven out of the ETC pipe by high pressure (high ΔGredox) and a proton leak dependent on the ΔGH for both its driving force and the conductance of the leak pathway. Model water pressures and flows are shown to simulate thermodynamic forces and metabolic fluxes that have been experimentally observed in mammalian skeletal muscle in response to acute exercise, chronic endurance training, and reduced substrate availability, as well as account for the thermokinetic behavior of mitochondria from fast- and slow-twitch skeletal muscle and the metabolic capacitance of the creatine kinase reaction.

  19. A Simple Hydraulic Analog Model of Oxidative Phosphorylation.

    Science.gov (United States)

    Willis, Wayne T; Jackman, Matthew R; Messer, Jeffrey I; Kuzmiak-Glancy, Sarah; Glancy, Brian

    2016-06-01

    Mitochondrial oxidative phosphorylation is the primary source of cellular energy transduction in mammals. This energy conversion involves dozens of enzymatic reactions, energetic intermediates, and the dynamic interactions among them. With the goal of providing greater insight into the complex thermodynamics and kinetics ("thermokinetics") of mitochondrial energy transduction, a simple hydraulic analog model of oxidative phosphorylation is presented. In the hydraulic model, water tanks represent the forward and back "pressures" exerted by thermodynamic driving forces: the matrix redox potential (ΔGredox), the electrochemical potential for protons across the mitochondrial inner membrane (ΔGH), and the free energy of adenosine 5'-triphosphate (ATP) (ΔGATP). Net water flow proceeds from tanks with higher water pressure to tanks with lower pressure through "enzyme pipes" whose diameters represent the conductances (effective activities) of the proteins that catalyze the energy transfer. These enzyme pipes include the reactions of dehydrogenase enzymes, the electron transport chain (ETC), and the combined action of ATP synthase plus the ATP-adenosine 5'-diphosphate exchanger that spans the inner membrane. In addition, reactive oxygen species production is included in the model as a leak that is driven out of the ETC pipe by high pressure (high ΔGredox) and a proton leak dependent on the ΔGH for both its driving force and the conductance of the leak pathway. Model water pressures and flows are shown to simulate thermodynamic forces and metabolic fluxes that have been experimentally observed in mammalian skeletal muscle in response to acute exercise, chronic endurance training, and reduced substrate availability, as well as account for the thermokinetic behavior of mitochondria from fast- and slow-twitch skeletal muscle and the metabolic capacitance of the creatine kinase reaction. PMID:26807634

  20. Black Holes Have Simple Feeding Habits

    Science.gov (United States)

    2008-06-01

    The biggest black holes may feed just like the smallest ones, according to data from NASA’s Chandra X-ray Observatory and ground-based telescopes. This discovery supports the implication of Einstein's relativity theory that black holes of all sizes have similar properties, and will be useful for predicting the properties of a conjectured new class of black holes. The conclusion comes from a large observing campaign of the spiral galaxy M81, which is about 12 million light years from Earth. In the center of M81 is a black hole that is about 70 million times more massive than the Sun, and generates energy and radiation as it pulls gas in the central region of the galaxy inwards at high speed. In contrast, so-called stellar mass black holes, which have about 10 times more mass than the Sun, have a different source of food. These smaller black holes acquire new material by pulling gas from an orbiting companion star. Because the bigger and smaller black holes are found in different environments with different sources of material to feed from, a question has remained about whether they feed in the same way. Using these new observations and a detailed theoretical model, a research team compared the properties of M81's black hole with those of stellar mass black holes. The results show that either big or little, black holes indeed appear to eat similarly to each other, and produce a similar distribution of X-rays, optical and radio light. AnimationMulti-wavelength Images of M81 One of the implications of Einstein's theory of General Relativity is that black holes are simple objects and only their masses and spins determine their effect on space-time. The latest research indicates that this simplicity manifests itself in spite of complicated environmental effects. "This confirms that the feeding patterns for black holes of different sizes can be very similar," said Sera Markoff of the Astronomical Institute, University of Amsterdam in the Netherlands, who led the study

  1. Simple Type Theory as Framework for Combining Logics

    CERN Document Server

    Benzmueller, Christoph

    2010-01-01

    Simple type theory is suited as framework for combining classical and non-classical logics. This claim is based on the observation that various prominent logics, including (quantified) multimodal logics and intuitionistic logics, can be elegantly embedded in simple type theory. Furthermore, simple type theory is sufficiently expressive to model combinations of embedded logics and it has a well understood semantics. Off-the-shelf reasoning systems for simple type theory exist that can be uniformly employed for reasoning within and about combinations of logics.

  2. [True place of simple sugars in the cause of caries].

    Science.gov (United States)

    Julien, M G

    1991-02-01

    A recent leaflet published for dental patients by the Canadian Association of Confectioners promotes the consumption of sweets, considering them on an equal basis, in regard to caries, as any other foods containing simple sugars, such as: fruits, vegetables, bread or pasta. This article intends to demistify such inference. While it is true that most foods containing simple sugars can lower plaque pH when considered alone, in the context of a total diet, the relationship between simple sugars and caries is much more complex. Also, in regard to total health, one can not equate all simple sugars since they differ considerably in terms of nutritional value. PMID:1869698

  3. The New Enhanced Simple Authenticated Key Agreement Algorithm

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Simple authenticated key agreement algorithm is one of the Diffie-Hellman key agreement variations. It prevents man-inthe-middle attack with only two more packets required to agree on the secret session key, but it has some weaknesses. In this paper, a new enhanced simple authenticated key agreement algorithm is proposed to overcome these weaknesses on the basis of analyzing the weaknesses of the related protocols. The new enhanced simple authenticated key agreement algorithm can get over replay attack and password guessing attack, provide perfect forward secrecy, and hold the merits of the simple authenticated key agreement algorithm.

  4. Infinitary Term Graph Rewriting is Simple, Sound and Complete

    DEFF Research Database (Denmark)

    Bahr, Patrick

    2012-01-01

    Based on a simple metric and a simple partial order on term graphs, we develop two infinitary calculi of term graph rewriting. We show that, similarly to infinitary term rewriting, the partial order formalisation yields a conservative extension of the metric formalisation of the calculus. By show......Based on a simple metric and a simple partial order on term graphs, we develop two infinitary calculi of term graph rewriting. We show that, similarly to infinitary term rewriting, the partial order formalisation yields a conservative extension of the metric formalisation of the calculus...

  5. Design and self-assembly of simple coat proteins for artificial viruses

    NARCIS (Netherlands)

    Hernandez-Garcia, Armando; Kraft, Daniela J.; Janssen, Anne F. J.; Bomans, Paul H. H.; Sommerdijk, Nico A. J. M.; Thies-Weesie, Dominique M. E.; Favretto, Marco E.; Brock, Roland; de Wolf, Frits A.; Werten, Marc W. T.; van der Schoot, Paul; Stuart, Martien Cohen; de Vries, Renko

    2014-01-01

    Viruses are among the simplest biological systems and are highly effective vehicles for the delivery of genetic material into susceptible host cells(1). Artificial viruses can be used as model systems for providing insights into natural viruses and can be considered a testing ground for developing a

  6. Design and self-assembly of simple coat proteins for artificial viruses

    NARCIS (Netherlands)

    Hernandez-Garcia, Armando; Kraft, Daniela J.; Janssen, Anne F J; Bomans, Paul H H; Sommerdijk, Nico A J M; Thies - Weesie, Dominique; Favretto, Marco E.; Brock, Roland; de Wolf, Frits A.; Werten, Marc W T; van der Schoot, Paul; Stuart, Martien Cohen; de Vries, Renko; Thies - Weesie, Dominique

    2014-01-01

    Viruses are among the simplest biological systems and are highly effective vehicles for the delivery of genetic material into susceptible host cells. Artificial viruses can be used as model systems for providing insights into natural viruses and can be considered a testing ground for developing arti

  7. Design and self-assembly of simple coat proteins for artificial viruses

    NARCIS (Netherlands)

    Hernandez Garcia, A.; Kraft, D.J.; Janssen, A.F.J.; Bomans, P.H.H.; Sommerdijk, N.A.J.M.; Thies-Weesie, D.M.E.; Favretto, M.E.; Brock, R.; Wolf, de F.A.; Werten, M.W.T.; Schoot, van der P.; Cohen Stuart, M.A.; Vries, de R.J.

    2014-01-01

    Viruses are among the simplest biological systems and are highly effective vehicles for the delivery of genetic material into susceptible host cells1. Artificial viruses can be used as model systems for providing insights into natural viruses and can be considered a testing ground for developing art

  8. Catalytic mechanism in successive two-step protein-film voltammetry—Theoretical study in square-wave voltammetry

    OpenAIRE

    Gulaboski, Rubin; Mihajlov, Ljupco

    2011-01-01

    Protein-film voltammetry is established as an effective tool that provides insight to the redox features of various lipophilic proteins by using a simple methodology. Although the protein-film experimental set up is relatively simple, the redox mechanisms of many proteins are quite complicated, and very often they cannot be resolved without having support from adequate mathematical models. In this work we continue our contribution to modeling relevant redox mechanisms in protein-f...

  9. Computational model for protein unfolding simulation

    Science.gov (United States)

    Tian, Xu-Hong; Zheng, Ye-Han; Jiao, Xiong; Liu, Cai-Xing; Chang, Shan

    2011-06-01

    The protein folding problem is one of the fundamental and important questions in molecular biology. However, the all-atom molecular dynamics studies of protein folding and unfolding are still computationally expensive and severely limited by the time scale of simulation. In this paper, a simple and fast protein unfolding method is proposed based on the conformational stability analyses and structure modeling. In this method, two structure-based conditions are considered to identify the unstable regions of proteins during the unfolding processes. The protein unfolding trajectories are mimicked through iterative structure modeling according to conformational stability analyses. Two proteins, chymotrypsin inhibitor 2 (CI2) and α -spectrin SH3 domain (SH3) were simulated by this method. Their unfolding pathways are consistent with the previous molecular dynamics simulations. Furthermore, the transition states of the two proteins were identified in unfolding processes and the theoretical Φ values of these transition states showed significant correlations with the experimental data (the correlation coefficients are >0.8). The results indicate that this method is effective in studying protein unfolding. Moreover, we analyzed and discussed the influence of parameters on the unfolding simulation. This simple coarse-grained model may provide a general and fast approach for the mechanism studies of protein folding.

  10. On an Inverse Semi-Group which is Simple but Not Completely Simple

    Directory of Open Access Journals (Sweden)

    Lawrence N. EZEAKO

    2007-08-01

    Full Text Available W. D. Munn, (1966 has shown that if E is a semilattice, then the Munn semigroup TE of E is an inverse semigroup whose semilattice of idempotents is isomorphic to E. If E is a uniform semillatice, then TE is a bisimple inverse semigroup. J. M. Howie, (1976 proved that up to isomorphism, the only fundamental bisimple semigroup S, having E = CW = { e0, e1, e2,………………} with e0> e1> e2Is the Bisyclic semigroup. In this paper is highlighted the structure of the Bicyclic semigroup and prove that every simple semigroup which has idempotent, none of which is primitive, must necessarily be a web of bicyclic semigroups.

  11. Rational disruption of the oligomerization of the mini-ferritin E. coli DPS through protein-protein interface mutation

    OpenAIRE

    Zhang, Yu; Fu, Jing; Chee, Sze Y; Ang, Emmiline X W; Orner, Brendan P.

    2011-01-01

    DNA-binding protein from starved cells (DPS), a mini-ferritin capable of self-assembling into a 12-meric nano-cage, was chosen as the basis for an alanine-shaving mutagenesis study to investigate the importance of key amino acid residues, located at symmetry-related protein-protein interfaces, in controlling protein stability and self-assembly. Nine mutants were designed through simple inspection, synthesized, and subjected to transmission electron microscopy, circular dichroism, size exclusi...

  12. A simple method of catalase purification for the undergraduate experimental course.

    Science.gov (United States)

    Chen, Qian; Cheng, Meng; Wang, Yinnan; Yao, Ming; Chen, Yongchun; Gao, Yuan; Ding, Wenyuan

    2015-02-01

    Catalase is a characteristic enzyme of peroxisomes, of which it is the most abundant protein. This enzyme serves as a typical example of a peroxisomal enzyme and is important in the teaching of biochemistry and molecular biology. Although there is substantial information regarding catalase purification, purifying catalase for the junior‑grade undergraduate experimental course face challenges in obtaining materials and increasingly expensive purification equipment. This study presents a simple method for the purification of mouse liver catalase using ethanol‑chloroform treatment, sodium sulfate fractionation, dialysis and Sephadex G‑200 gel filtration chromatography. Catalase was purified 31.8‑fold with an 18.3% yield. The advantages of this method were its low operating environment requirements, simple procedure and reduced cost. Furthermore, the method was designed to improve students' comprehensive ability and manipulative ability and to introduce a sense of innovation in the fields of biochemistry and molecular biology during their junior year.

  13. Secondary School Students' Misconceptions about Simple Electric Circuits

    Science.gov (United States)

    Küçüközer, Hüseyin; Kocakülah, Sabri

    2007-01-01

    The aim of this study is to reveal secondary school students' misconceptions about simple electric circuits and to define whether specific misconceptions peculiar to Turkish students exist within those identified. Data were obtained with a conceptual understanding test for simple electric circuits and semi-structured interviews. Conceptual…

  14. Validating SimpleBox-Computed Steady-State Concentration Ratios

    NARCIS (Netherlands)

    Bakker J; Brandes LJ; Hollander HA den; Meent D van de; Struijs J; SEC; IMP; LER

    2004-01-01

    The validity of the multi-media model SimpleBox version 2.0 with respect to its specific use in the procedure of testing the coherence of independently derived environmental quality objectives is evaluated. The SimpleBox procedure for testing the coherence of environmental quality objectives has bee

  15. Fully Consistent SIMPLE-Like Algorithms on Collocated Grids

    DEFF Research Database (Denmark)

    Kolmogorov, Dmitry; Shen, Wen Zhong; Sørensen, Niels N.;

    2015-01-01

    To increase the convergence rate of SIMPLE-like algorithms on collocated grids, a compatibility condition between mass flux interpolation methods and SIMPLE-like algorithms is presented. Results of unsteady flow computations show that the SIMPLEC algorithm, when obeying the compatibility conditio...

  16. Early Prediction of Reading Comprehension within the Simple View Framework

    Science.gov (United States)

    Catts, Hugh W.; Herrera, Sarah; Nielsen, Diane Corcoran; Bridges, Mindy Sittner

    2015-01-01

    The simple view of reading proposes that reading comprehension is the product of word reading and language comprehension. In this study, we used the simple view framework to examine the early prediction of reading comprehension abilities. Using multiple measures for all constructs, we assessed word reading precursors (i.e., letter knowledge,…

  17. Energy and linear and angular momenta in simple electromagnetic systems

    CERN Document Server

    Mansuripur, Masud

    2015-01-01

    We present examples of simple electromagnetic systems in which energy, linear momentum, and angular momentum exhibit interesting behavior. The systems are sufficiently simple to allow exact solutions of Maxwell's equations in conjunction with the electrodynamic laws of force, torque, energy, and momentum. In all the cases examined, conservation of energy and momentum is confirmed.

  18. A simple way of introducing stochastic differential equations

    Science.gov (United States)

    Basharov, A. M.

    2016-05-01

    The notion of the Ito increment and the stochastic differential equation of the non-Wiener type were introduced using the simple “natural” property of counting process. The properties of the stochastic differential and integral were demonstrated and clarified in a simple and original way.

  19. Solving Simple Stochastic Games with Few Random Vertices

    NARCIS (Netherlands)

    Gimbert, H.; Horn, F.

    2009-01-01

    Simple stochastic games are two-player zero-sum stochastic games with turn-based moves, perfect information, and reachability winning conditions. We present two new algorithms computing the values of simple stochastic games. Both of them rely on the existence of optimal permutation strategies, a cla

  20. Haptics-Augmented Simple-Machine Educational Tools.

    Science.gov (United States)

    Williams, Robert L., II; Chen, Meng-Yun; Seaton, Jeffrey M.

    2003-01-01

    Describes a unique project using commercial haptic interfaces to augment the teaching of simple machines in elementary school. Suggests that the use of haptics in virtual simple-machine simulations has the potential for deeper, more engaging learning. (Contains 13 references.) (Author/YDS)

  1. 10 CFR 436.23 - Estimated simple payback time.

    Science.gov (United States)

    2010-01-01

    ... 10 Energy 3 2010-01-01 2010-01-01 false Estimated simple payback time. 436.23 Section 436.23 Energy DEPARTMENT OF ENERGY ENERGY CONSERVATION FEDERAL ENERGY MANAGEMENT AND PLANNING PROGRAMS Methodology and Procedures for Life Cycle Cost Analyses § 436.23 Estimated simple payback time. The...

  2. Using "Tracker" to Prove the Simple Harmonic Motion Equation

    Science.gov (United States)

    Kinchin, John

    2016-01-01

    Simple harmonic motion (SHM) is a common topic for many students to study. Using the free, though versatile, motion tracking software; "Tracker", we can extend the students experience and show that the general equation for SHM does lead to the correct period of a simple pendulum.

  3. Using Tracker to prove the simple harmonic motion equation

    Science.gov (United States)

    Kinchin, John

    2016-09-01

    Simple harmonic motion (SHM) is a common topic for many students to study. Using the free, though versatile, motion tracking software; Tracker, we can extend the students experience and show that the general equation for SHM does lead to the correct period of a simple pendulum.

  4. Learn about Physical Science: Simple Machines. [CD-ROM].

    Science.gov (United States)

    2000

    This CD-ROM, designed for students in grades K-2, explores the world of simple machines. It allows students to delve into the mechanical world and learn the ways in which simple machines make work easier. Animated demonstrations are provided of the lever, pulley, wheel, screw, wedge, and inclined plane. Activities include practical matching and…

  5. Solving Simple Stochastic Games with Few Coin Toss Positions

    DEFF Research Database (Denmark)

    Ibsen-Jensen, Rasmus; Miltersen, Peter Bro

    2012-01-01

    Gimbert and Horn gave an algorithm for solving simple stochastic games with running time O(r! n) where n is the number of positions of the simple stochastic game and r is the number of its coin toss positions. Chatterjee et al. pointed out that a variant of strategy iteration can be implemented...

  6. Simple cubic function fields and class number computations

    CERN Document Server

    Rozenhart, Pieter

    2011-01-01

    In this paper, we study simple cubic fields in the function field setting, and also generalize the notion of a set exceptional units to cubic function fields, namely the notion of $k$-exceptional units. We give a simple proof that the Galois simple cubic function fields are the immediate analog of Shanks simplest cubic number fields. In addition to computing the invariants, including a formula for the regulator, we compute the class numbers of the Galois simple cubic function fields over $\\mathbb{F}_{5}$ and $\\mathbb{F}_{7}$ using truncated Euler products. Finally, as an additional application, we determine all Galois simple cubic function fields with class number one, subject to a mild restriction.

  7. Protein Crystallization

    Science.gov (United States)

    Chernov, Alexander A.

    2005-01-01

    Nucleation, growth and perfection of protein crystals will be overviewed along with crystal mechanical properties. The knowledge is based on experiments using optical and force crystals behave similar to inorganic crystals, though with a difference in orders of magnitude in growing parameters. For example, the low incorporation rate of large biomolecules requires up to 100 times larger supersaturation to grow protein, rather than inorganic crystals. Nucleation is often poorly reproducible, partly because of turbulence accompanying the mixing of precipitant with protein solution. Light scattering reveals fluctuations of molecular cluster size, its growth, surface energies and increased clustering as protein ages. Growth most often occurs layer-by-layer resulting in faceted crystals. New molecular layer on crystal face is terminated by a step where molecular incorporation occurs. Quantitative data on the incorporation rate will be discussed. Rounded crystals with molecularly disordered interfaces will be explained. Defects in crystals compromise the x-ray diffraction resolution crucially needed to find the 3D atomic structure of biomolecules. The defects are immobile so that birth defects stay forever. All lattice defects known for inorganics are revealed in protein crystals. Contribution of molecular conformations to lattice disorder is important, but not studied. This contribution may be enhanced by stress field from other defects. Homologous impurities (e.g., dimers, acetylated molecules) are trapped more willingly by a growing crystal than foreign protein impurities. The trapped impurities induce internal stress eliminated in crystals exceeding a critical size (part of mni for ferritin, lysozyme). Lesser impurities are trapped from stagnant, as compared to the flowing, solution. Freezing may induce much more defects unless quickly amorphysizing intracrystalline water.

  8. Stochastic single-molecule dynamics of synaptic membrane protein domains

    CERN Document Server

    Kahraman, Osman; Haselwandter, Christoph A

    2016-01-01

    Motivated by single-molecule experiments on synaptic membrane protein domains, we use a stochastic lattice model to study protein reaction and diffusion processes in crowded membranes. We find that the stochastic reaction-diffusion dynamics of synaptic proteins provide a simple physical mechanism for collective fluctuations in synaptic domains, the molecular turnover observed at synaptic domains, key features of the single-molecule trajectories observed for synaptic proteins, and spatially inhomogeneous protein lifetimes at the cell membrane. Our results suggest that central aspects of the single-molecule and collective dynamics observed for membrane protein domains can be understood in terms of stochastic reaction-diffusion processes at the cell membrane.

  9. Cellufine sulfate column chromatography as a simple, rapid, and effective method to purify dengue virus.

    Science.gov (United States)

    Kanlaya, Rattiyaporn; Thongboonkerd, Visith

    2016-08-01

    Conventional method to purify/concentrate dengue virus (DENV) is time-consuming with low virus recovery yield. Herein, we applied cellufine sulfate column chromatography to purify/concentrate DENV based on the mimicry between heparan sulfate and DENV envelope protein. Comparative analysis demonstrated that this new method offered higher purity (as determined by less contamination of bovine serum albumin) and recovery yield (as determined by greater infectivity). Moreover, overall duration used for cellufine sulfate column chromatography to purify/concentrate DENV was approximately 1/20 of that of conventional method. Therefore, cellufine sulfate column chromatography serves as a simple, rapid, and effective alternative method for DENV purification/concentration.

  10. Cellufine sulfate column chromatography as a simple, rapid, and effective method to purify dengue virus.

    Science.gov (United States)

    Kanlaya, Rattiyaporn; Thongboonkerd, Visith

    2016-08-01

    Conventional method to purify/concentrate dengue virus (DENV) is time-consuming with low virus recovery yield. Herein, we applied cellufine sulfate column chromatography to purify/concentrate DENV based on the mimicry between heparan sulfate and DENV envelope protein. Comparative analysis demonstrated that this new method offered higher purity (as determined by less contamination of bovine serum albumin) and recovery yield (as determined by greater infectivity). Moreover, overall duration used for cellufine sulfate column chromatography to purify/concentrate DENV was approximately 1/20 of that of conventional method. Therefore, cellufine sulfate column chromatography serves as a simple, rapid, and effective alternative method for DENV purification/concentration. PMID:27155240

  11. Power Spectra of a Totally Asymmetric Simple Exclusion Process with Finite Resources

    Science.gov (United States)

    Cook, L. Jonathan; Zia, Royce K. P.

    2010-03-01

    In a cell, a mRNA has only a finite number of ribosomes to use during protein synthesis. We take this constraint into account in the modeling of translation by a totally asymmetric simple exclusion process (TASEP). Through Monte Carlo simulations and analytical methods, we study the power spectrum of the total particle occupancy of the TASEP. New features are found, such as a severe suppression at low frequencies. We formulate a theory based on a linearized Langevin equation with discrete space and time. With good agreement between the theoretical approach and the simulations, we gain some insight in how finite resources affect a TASEP.

  12. Concentration Dependent Ion-Protein Interaction Patterns Underlying Protein Oligomerization Behaviours

    Science.gov (United States)

    Batoulis, Helena; Schmidt, Thomas H.; Weber, Pascal; Schloetel, Jan-Gero; Kandt, Christian; Lang, Thorsten

    2016-01-01

    Salts and proteins comprise two of the basic molecular components of biological materials. Kosmotropic/chaotropic co-solvation and matching ion water affinities explain basic ionic effects on protein aggregation observed in simple solutions. However, it is unclear how these theories apply to proteins in complex biological environments and what the underlying ionic binding patterns are. Using the positive ion Ca2+ and the negatively charged membrane protein SNAP25, we studied ion effects on protein oligomerization in solution, in native membranes and in molecular dynamics (MD) simulations. We find that concentration-dependent ion-induced protein oligomerization is a fundamental chemico-physical principle applying not only to soluble but also to membrane-anchored proteins in their native environment. Oligomerization is driven by the interaction of Ca2+ ions with the carboxylate groups of aspartate and glutamate. From low up to middle concentrations, salt bridges between Ca2+ ions and two or more protein residues lead to increasingly larger oligomers, while at high concentrations oligomers disperse due to overcharging effects. The insights provide a conceptual framework at the interface of physics, chemistry and biology to explain binding of ions to charged protein surfaces on an atomistic scale, as occurring during protein solubilisation, aggregation and oligomerization both in simple solutions and membrane systems. PMID:27052788

  13. Topological relations between directed lines and simple geometries

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Directed lines are fundamental geometric elements to represent directed linear en-tities. The representations of their topological relations are so different from those of simple lines that they cannot be solved exactly with normal methods. In this paper,a new model based on point-set topology is defined to represent the topo-logical relations between directed lines and simple geometries. Through the inter-sections between the start-points,end-points,and interiors of the directed lines and the interiors,boundaries,and exteriors of the simple geometries,this model identifies 5 cases of topological relations between directed lines and points,39 cases of simple lines,and 26 cases of simple polygons. Another 4 cases of simple lines and one case of simple polygons are distinguished if considering the exteri-ors of the directed lines. All possible cases are furthermore grouped into an exclu-sive and complete set containing 11 named predicts. And the conceptual neigh-borhood graph is set up to illustrate their relationship and similarity. This model can provide a basis for natural language description and spatial query language to present the dynamic semantics of directed lines relative to the background fea-tures.

  14. Structural hot spots for the solubility of globular proteins.

    Science.gov (United States)

    Ganesan, Ashok; Siekierska, Aleksandra; Beerten, Jacinte; Brams, Marijke; Van Durme, Joost; De Baets, Greet; Van der Kant, Rob; Gallardo, Rodrigo; Ramakers, Meine; Langenberg, Tobias; Wilkinson, Hannah; De Smet, Frederik; Ulens, Chris; Rousseau, Frederic; Schymkowitz, Joost

    2016-01-01

    Natural selection shapes protein solubility to physiological requirements and recombinant applications that require higher protein concentrations are often problematic. This raises the question whether the solubility of natural protein sequences can be improved. We here show an anti-correlation between the number of aggregation prone regions (APRs) in a protein sequence and its solubility, suggesting that mutational suppression of APRs provides a simple strategy to increase protein solubility. We show that mutations at specific positions within a protein structure can act as APR suppressors without affecting protein stability. These hot spots for protein solubility are both structure and sequence dependent but can be computationally predicted. We demonstrate this by reducing the aggregation of human α-galactosidase and protective antigen of Bacillus anthracis through mutation. Our results indicate that many proteins possess hot spots allowing to adapt protein solubility independently of structure and function. PMID:26905391

  15. Simple bone cyst of the mandible: Report of two cases

    International Nuclear Information System (INIS)

    Despite their names, simple bone cysts are no longer categorized as cysts since they lack an epithelial lining. However, their nature remains controversial. The internal structure is totally radiolucent, sometimes showing multilocular appearance, although the lesion does not contain true septa and the ridges of bone is produced by the scalloping effect. We presented two cases of histopathologically confirmed simple bone cyst. Radiographic features such as multilocular appearance and significant buccal and lingual expansion are not usual findings for simple bone cyst, whereas evident in our presented cases.

  16. Generalized Lotka—Volterra systems connected with simple Lie algebras

    Science.gov (United States)

    Charalambides, Stelios A.; Damianou, Pantelis A.; Evripidou, Charalambos A.

    2015-06-01

    We devise a new method for producing Hamiltonian systems by constructing the corresponding Lax pairs. This is achieved by considering a larger subset of the positive roots than the simple roots of the root system of a simple Lie algebra. We classify all subsets of the positive roots of the root system of type An for which the corresponding Hamiltonian systems are transformed, via a simple change of variables, to Lotka-Volterra systems. For some special cases of subsets of the positive roots of the root system of type An, we produce new integrable Hamiltonian systems.

  17. Recursion relations and branching rules for simple Lie algebras

    CERN Document Server

    Lyakhovsky, V D

    1995-01-01

    The branching rules between simple Lie algebras and its regular (maximal) simple subalgebras are studied. Two types of recursion relations for anomalous relative multiplicities are obtained. One of them is proved to be the factorized version of the other. The factorization property is based on the existence of the set of weights \\Gamma specific for each injection. The structure of \\Gamma is easily deduced from the correspondence between the root systems of algebra and subalgebra. The recursion relations thus obtained give rise to simple and effective algorithm for branching rules. The details are exposed by performing the explicit decomposition procedure for A_{3} \\oplus u(1) \\rightarrow B_{4} injection.

  18. A simple derivation of mean field limits for quantum systems

    CERN Document Server

    Pickl, Peter

    2009-01-01

    We shall present a new strategy for handling mean field limits of quantum mechanical systems. The new method is simple and effective. It is simple, because it translates the idea behind the mean field description of a many particle quantum system directly into a mathematical algorithm. It is effective because the strategy yields with lesser effort better results than previously achieved. As an instructional example we treat a simple model for the time dependent Hartree equation which we derive under more general conditions than what has been considered so far. Other mean field scalings leading e.g. to the Gross-Pitaevskii equation can also be treated.

  19. Computational Study for Protein-Protein Docking Using Global Optimization and Empirical Potentials

    Directory of Open Access Journals (Sweden)

    Kyoungrim Lee

    2008-01-01

    Full Text Available Protein-protein interactions are important for biochemical processes in biological systems. The 3D structure of the macromolecular complex resulting from the protein-protein association is a very useful source to understand its specific functions. This work focuses on computational study for protein-protein docking, where the individually crystallized structures of interacting proteins are treated as rigid, and the conformational space generated by the two interacting proteins is explored extensively. The energy function consists of intermolecular electrostatic potential, desolvation free energy represented by empirical contact potential, and simple repulsive energy terms. The conformational space is six dimensional, represented by translational vectors and rotational angles formed between two interacting proteins. The conformational sampling is carried out by the search algorithms such as simulated annealing (SA, conformational space annealing (CSA, and CSA combined with SA simulations (combined CSA/SA. Benchmark tests are performed on a set of 18 protein-protein complexes selected from various protein families to examine feasibility of these search methods coupled with the energy function above for protein docking study.

  20. Water-transporting proteins.

    Science.gov (United States)

    Zeuthen, Thomas

    2010-04-01

    Transport through lipids and aquaporins is osmotic and entirely driven by the difference in osmotic pressure. Water transport in cotransporters and uniporters is different: Water can be cotransported, energized by coupling to the substrate flux by a mechanism closely associated with protein. In the K(+)/Cl(-) and the Na(+)/K(+)/2Cl(-) cotransporters, water is entirely cotransported, while water transport in glucose uniporters and Na(+)-coupled transporters of nutrients and neurotransmitters takes place by both osmosis and cotransport. The molecular mechanism behind cotransport of water is not clear. It is associated with the substrate movements in aqueous pathways within the protein; a conventional unstirred layer mechanism can be ruled out, due to high rates of diffusion in the cytoplasm. The physiological roles of the various modes of water transport are reviewed in relation to epithelial transport. Epithelial water transport is energized by the movements of ions, but how the coupling takes place is uncertain. All epithelia can transport water uphill against an osmotic gradient, which is hard to explain by simple osmosis. Furthermore, genetic removal of aquaporins has not given support to osmosis as the exclusive mode of transport. Water cotransport can explain the coupling between ion and water transport, a major fraction of transepithelial water transport and uphill water transport. Aquaporins enhance water transport by utilizing osmotic gradients and cause the osmolarity of the transportate to approach isotonicity. PMID:20091162

  1. SERUM ZINC LEVEL IN PATIENTS WITH SIMPLE FEBRILE SEIZURE

    Directory of Open Access Journals (Sweden)

    Farhad HEYDARIAN

    2010-10-01

    Full Text Available ObjectiveTo evaluate the serum zinc level of the patients with simple febrile seizure and compare them with febrile children without seizure.Materials & MethodsThis prospective case - control study was performed on 60 patients aged 6 months to 6 years from Apr. 2009 to Jan.2010 in Ghaem, Imam Reza and Dr. Sheikh Hospitals in Mashhad. The serum zinc level was assessed and compared between the cases (30 individuals who suffered from simple febrile seizure and the controls (30 individuals who had fever without seizure.ResultsMean serum zinc level was 663.7 µg /l and 758.33  µg /l in the case group and the control group, respectively (PConclusionIt was revealed that the serum level of zinc was significantly lower in children with simple febrile seizure in comparison with febrile children without seizure.Keywords: Simple febrile seizure, children, zinc, CSF (cerebrospinal fluid

  2. Simple circuit functions as frequency discriminator for PFM signals

    Science.gov (United States)

    Billingsley, J.

    1965-01-01

    Simple circuit monitors the frequency of PFM /Pulse Frequency Modulated/ telemetry signals. This discriminator can be used as a constant current integrator in such circuits as linear sweep and time delay.

  3. A simple and efficient route for synthesis of 2-alkylbenzothiazoles

    Directory of Open Access Journals (Sweden)

    Wijitra Waengdongbung

    2016-05-01

    Full Text Available The condensation of 2-aminothiophenol with aliphatic aldehydes in the presence of 4Å molecular sieves, followed by oxidation with silica gel supported pyridinium chlorochromate offers a simple and efficient route to 2-alkylbenzothiazoles.

  4. A simple convex optimization problem with many applications

    DEFF Research Database (Denmark)

    Vidal, Rene Victor Valqui

    1994-01-01

    This paper presents an algorithm for the solution of a simple convex optimization problem. This problem is a generalization of several other optimization problems which have applications to resource allocation, optimal capacity expansion, and vehicle scheduling. The algorithm is based...

  5. Two simple amine hydrochlorides from the soft coral Lobophytum strictum

    Digital Repository Service at National Institute of Oceanography (India)

    Parameswaran, P.S.; Naik, C.G.; Das, B.; Kamat, S.Y.

    Two simple amine hydrochlorides, viz., 1-amino-1, 1-dimethyl-3-oxo-butane hydrochloride (1) (Diacetonamine) and 2, 2, 6, 6-tetramethylpiperidone hydrochloride (2) have been isolated from the fraction of the methanolic extract of the soft coral...

  6. Effectiveness of Simple Individual Psychoeducation for Bipolar II Disorder.

    Science.gov (United States)

    Saito-Tanji, Yuka; Tsujimoto, Emi; Taketani, Reiko; Yamamoto, Ami; Ono, Hisae

    2016-01-01

    Several studies have proven the effectiveness of psychoeducation in bipolar II disorder patients; however, simpler psychoeducation is needed in daily medical practice. Therefore, we devised a simple individual psychoeducation program, which involved 20-minute sessions spent reading a textbook aloud in the waiting time before examination. Here, we report a successful case of simple individual psychoeducation with a patient with bipolar II disorder, a 64-year-old woman who had misconceptions surrounding her mood due to 24 years of treatment for depression. Her perception of mood state, particularly mixed state, was dramatically changed, and her quality of life was improved after the simple individual psychoeducation. This case suggests that the simple individual psychoeducation could be effective for bipolar II disorder by improving understanding of the disease and by meeting different individual needs. PMID:27559486

  7. [A simple peritoneovenous shunt in the treatment of chronic ascites].

    Science.gov (United States)

    Pafko, P; Hladík, P

    2001-02-01

    The authors describe their own initial experience with a peritoneo-venous shunt in otherwise incurable ascites. It is a simple procedure which is more satisfactory than the formerly used technique of implantation of Le Veen's system. PMID:12881921

  8. Measured and Modeled Morphometry of Simple Impact Craters

    Science.gov (United States)

    Watters, W. A.; Collins, G. S.

    2015-09-01

    We discuss the measured diameter dependence of well-preserved simple crater morphometry on Mars and compare with iSALE simulations. We also describe future work to fully characterize the dependence on impactor velocity and mass, and target properties.

  9. Educational Materials Development in Primary Science: Simple Machines

    Science.gov (United States)

    Franks, Frank L.; Butterfield, Lawrence H., Jr.

    1977-01-01

    Evaluated was the ability of 27 legally blind elementary students to identify and manipulate the parts of the following adapted simple machines: lever, inclined plane, wheel and axle, and pulley. (SBH)

  10. Simple elbow dislocations: a systematic review of the literature

    NARCIS (Netherlands)

    J. de Haan (Jeroen); N.W.L. Schep (Niels); P. Patka (Peter); D. den Hartog (Dennis)

    2009-01-01

    textabstractObjective: To identify if functional treatment is the best available treatment for simple elbow dislocations. Search strategy: Electronic databases MEDLINE, EMBASE, LILACS, and the Cochrane Central Register of Controlled Trials. Selection criteria: Studies were eligible for inclusion if

  11. A Simple Parallel Photochemical Reactor for Photodecomposition Studies

    Science.gov (United States)

    Xiaobo Chen; Halasz, Sarah M.; Giles, Eric C.; Mankus, Jessica V.; Johnson, Joseph C.; Burda, Clemens

    2006-01-01

    A simple and useful parallel photochemical reactor intended to study the photodecomposition of dyes using semiconductor photocatalysis is presented. The photochemical reactions are followed through time-dependent changes in the ground-state absorption spectra of the dyes.

  12. Publishing on the WWW : part 6 : simple graphic manipulation

    OpenAIRE

    Grech, Victor E.

    2001-01-01

    Modern graphic manipulation software is quick and simple to use, and allows medical quality graphics to be produced for online publication. This article demonstrates, step by step, how submitted images are processed by the journal in preparation for publication.

  13. Simple, Micro-Miniature Total Organic Carbon Analyzer Project

    Data.gov (United States)

    National Aeronautics and Space Administration — Development of a simple method for on-orbit or advanced mission Total Organic Carbon (TOC) monitoring has been a goal for many years. This proposal seeks to develop...

  14. Simple self-reduction method for anterior shoulder dislocation

    Directory of Open Access Journals (Sweden)

    Reiner Wirbel

    2014-01-01

    Conclusion: The presented Boss-Holzach-Matter method for reduction of anterior shoulder dislocation is a simple method without the need of anaesthesia, but cooperation from patients is crucial. The successful rate is comparable with other established methods.

  15. Relation between Tolman length and isothermal compressibility for simple liquids

    Institute of Scientific and Technical Information of China (English)

    Wang Xiao-Song; Zhu Ru-Zeng

    2013-01-01

    The Tolman length δ0 of a liquid with a plane surface has attracted increasing theoretical attention in recent years,but the expression of Tolman length in terms of observable quantities is still not very clear.In 2001,Bartell gave a simple expression of Tolman length δ0 in terms of isothermal compressibility.However,this expression predicts that Tolman length is always negative,which is contrary to the results of molecular dynamics simulations (MDS) for simple liquids.In this paper,this contradiction is analyzed and the reason for the discrepancy in the sign is found.In addition,we introduce a new expression of Tolman length in terms of isothermal compressibility for simple fluids not near the critical points under some weak restrictions.The Tolman length of simple liquids calculated by using this formula is consistent with that obtained using MDS regarding the sign.

  16. Simple Experiments on the Use of Solar Energy

    Science.gov (United States)

    Vella, G. J.; Goldsmid, H. J.

    1976-01-01

    Describes 5 solar energy experiments that can be used in secondary school: flat-plate collector, solar thermoelectric generator, simple concentrators, solar cell, and natural storage of solar energy. (MLH)

  17. Fistulotomy and marsupialisation for simple fistula-in-ano.

    Science.gov (United States)

    Yang, C Y

    1992-06-01

    Nineteen consecutive cases of simple fistula-in-ano treated with fistulotomy and marsupialisation were retrospectively reviewed. Fourteen cases were simple intersphincteric and the remaining 5 cases were uncomplicated transphincteric fistulae. The cases were followed up for between 3 to 10 months (mean 6.9 months). There were no reports of bowel incontinence or recurrence of fistula. The advantages of this 'tissue conserving' procedure are discussed in the paper. PMID:1631585

  18. Simple dependent pairs of exponential and uniform random variables

    OpenAIRE

    A. J. Lawrance; Lewis, Peter Adrian Walter

    1982-01-01

    A random-coefficient linear function of two independent exponential variables yielding a third exponential variable is used in the construction of simple, dependent pairs of exponential variables. By employing antithetic exponential variables, the constructions are developed to encompass negative dependency. By employing negative exponentiation, the constructions yield simple multiplicative-based models for dependent uniform pairs. The ranges of dependency allowable in the models are assessed...

  19. A simple approximation of productivity scores of fuzzy production plans

    DEFF Research Database (Denmark)

    Hougaard, Jens Leth

    2005-01-01

    This paper suggests a simple approximation procedure for the assessment of productivity scores with respect to fuzzy production plans. The procedure has a clear economic interpretation and all the necessary calculations can be performed in a spreadsheet making it highly operational......This paper suggests a simple approximation procedure for the assessment of productivity scores with respect to fuzzy production plans. The procedure has a clear economic interpretation and all the necessary calculations can be performed in a spreadsheet making it highly operational...

  20. A Simple Complexity Measurement for Software Verification and Software Testing

    OpenAIRE

    Cheng, Zheng; Monahan, Rosemary; Power, James F.

    2012-01-01

    In this paper, we used a simple metric (i.e. Lines of Code) to measure the complexity involved in software verification and software testing. The goal is then, to argue for software verification over software testing, and motivate a discussion of how to reduce the complexity involved in software verification. We propose to reduce this complexity by translating the software to a simple intermediate representation which can be verified using an efficient verifier, such as Boog...