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Sample records for bence jones proteins

  1. Four crystal forms of a Bence-Jones protein

    Energy Technology Data Exchange (ETDEWEB)

    Makino, Debora L.; Henschen-Edman, Agnes H.; McPherson, Alexander, E-mail: amcphers@uci.edu [Molecular Biology and Biochemistry, University of California, Irvine, 560 Steinhaus Hall, Irvine, CA 92697-3900 (United States)

    2005-01-01

    Four crystal forms have been grown and characterized by X-ray diffraction of a Bence-Jones protein collected from the urine of a multiple myeloma patient more than 40 y ago. The trigonal crystal form may shed some light on the formation of fibrils common to certain storage diseases. Four crystal forms have been grown and characterized by X-ray diffraction of a Bence-Jones protein collected from the urine of a multiple myeloma patient more than 40 years ago. Closely related tetragonal and orthorhombic forms belonging to space groups P4{sub 3}2{sub 1}2 and P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = b = 68.7, c = 182.1 and a = 67.7, b = 69.4, c = 87.3 Å, diffract to 1.5 and 1.9 Å, respectively. Two closely related trigonal forms, both belonging to space group P3{sub 1}21 with unit-cell parameters a = b = 154.3 Å but differing by a doubling of the c axis, one 46.9 Å and the other 94.0 Å, diffract to 2.9 and 2.6 Å resolution, respectively. The trigonal crystal of short c-axis length shows a positive indication of twinning. The trigonal crystal of longer c axis, which appeared only after eight months of incubation at room temperature, is likely to be composed of proteolytically degraded molecules and unlike the other crystal forms contains two entire Bence-Jones dimers in the asymmetric unit. This latter crystal form may shed some light on the formation of fibrils common to certain storage diseases.

  2. Bence Jones proteins: Powerful tool for fundamental study of protein chemistry and pathophysiology

    Energy Technology Data Exchange (ETDEWEB)

    Stevens, F.J.; Schiffer, M. [Argonne National Lab., IL (United States); Solomon, A. [University of Tennessee Medical Center, Knoxville, TN (United States)

    1991-12-31

    Bence Jones proteins are typically found in patients with monoclonal plasma cell or related B-cell immunoproliferative disorders. Because of their monoclonal origin and resulting chemical homogeneity much of the fundamental information on immunoglobulin structure came initially from their analysis. Amino acid analyses of these components revealed an N-terminal variable (V) and C-terminal constant (C) domain as well as the existence within the V domain of hypervariable segments that account for the specificity and diversity of antibodies. Over the past three decades, the primary structures of hundreds of light chains (complete and partial), from human and other sources, have been determined, aligned, and archived. Bence Jones proteins and V{sub L} dimers were the crystallizable homogeneous proteins which provided much of the early three-dimensional conformational data that helped explain the structural basis of antibody function. Remarkably, a single Bence Jones protein in two solvent systems (low and high ionic strength) exhibited significant differences in the interactions of the two monomeric subunits comprising the dimer, resulting in substantial variation in the structure of the antigen combining site under the two solution conditions. This observation led to a prediction that heterogeneity of domain interactions may contribute to antibody-antigen interactions. Experimental support for this hypothesis has come from comparisons of the detailed structures of antibody-antigen complexes. The interactions at the interface of the V{sub L} dimer are a function of primary structure and solution conditions. Study of these interactions has led to new information on the relationship between protein structure and function and, as discussed below, can account for specific pathophysiological properties associated with Bence Jones proteins.

  3. Nephrotoxicity of Bence-Jones proteins: correlation with endocytosis by BHK cells and intracellular movement

    Directory of Open Access Journals (Sweden)

    Ana Lucia Nicastri

    2001-06-01

    Full Text Available The aim of this investigation was to evaluate the endocytosis of two Bence-Jones proteins by renal cells in order to elucidate the interference of their physical and chemical characteristics on nephrotoxicity. Bence-Jones proteins (AK and GL were purified and isolated from the urine of two patients with multiple myeloma. The isotype of both proteins was characterised as being human monoclonal lambda light chain. The AK protein presented mainly an Ip>7.0, a high content of galactose and a low amount of sialic acid molecules. On the other hand, the GL protein presented a single band with an Ip of 4.3, a higher level of sialic acid and a reduced amount of galactose, in comparison with the AK protein. Baby Hamster Kidney (BHK cells were maintained in culture in bottles at 37ºC, using DMEM culture media supplemented with 10% of calf serum with a pH of 7.4. Once the monolayer was observed to be confluent, the BHK cells were incubated with the two proteins, dissolved in a serum-free medium for 1, 5, 15, 30, 60 minutes and 24 hours. Control cells were established omitting the incubation with Bence-Jones proteins, but maintaining all of the other conditions. After, this the cells were washed, trypsinised, centrifuged and fixed in a solution of 4% paraformaldehyde and 0.5% glutaraldehyde on a 0.1 M, pH 7.4 phosphate buffer. Cells were processed for immunocytochemical reactions by using protein A coupled with colloidal gold and further silver enhancement. Semi-thin sections of the pellets were obtained and submitted to the cytochemical reactions. Detection of labelling was made by using light microscopy. It was observed that GL protein tended to be directed towards a perinuclear position, whereas the AK protein tended to suffer lysosomal deviation, suggesting that there is a direct contribution of physical and chemical characteristics on intracellular direction taken by Bence-Jones proteins.O objetivo deste trabalho foi avaliar a endocitose de duas prote

  4. Human lambda light-chain constant region gene CMor lambda: the primary structure of lambda VI Bence Jones protein Mor.

    OpenAIRE

    Frangione, B.; Moloshok, T; Prelli, F; Solomon, A

    1985-01-01

    Serologic, structural, and genetic analyses have shown that the constant (C) region of human kappa light chains is encoded by a single gene, whereas that of lambda chains is encoded by multiple genes. We have determined the complete C region amino acid sequence of two monoclonal lambda VI light chains, Bence Jones proteins Sut and Mor. The C region of lambda chains Sut and Mor consists of 105 residues, as is characteristic for human lambda light chains, of which 102 are identical in sequence....

  5. The renal and hepatic distribution of Bence Jones proteins depends on glycosylation: a scintigraphic study in rats

    Directory of Open Access Journals (Sweden)

    Prado M.J.B.A.

    1997-01-01

    Full Text Available The aim of the present study was to evaluate renal and liver distribution of two monoclonal immunoglobulin light chains. The chains were purified individually from the urine of patients with multiple myeloma and characterized as lambda light chains with a molecular mass of 28 kDa. They were named BJg (high amount of galactose residues exposed and BJs (sialic acid residues exposed on the basis of carbohydrate content. A scintigraphic study was performed on male Wistar rats weighing 250 g for 60 min after iv administration of 1 mg of each protein (7.4 MBq, as the intact proteins and also after carbohydrate oxidation. Images were obtained with a Siemens gamma camera with a high-resolution collimator and processed with a MicroDelta system. Hepatic and renal distribution were established and are reported as percent of injected dose. Liver uptake of BJg was significantly higher than liver uptake of BJs (94.3 vs 81.4% (P<0.05. This contributed to its greater removal from the intravascular compartment, and consequently lower kidney accumulation of BJg in comparison to BJs (5.7 vs 18.6% (P<0.05. After carbohydrate oxidation, there was a decrease in hepatic accumulation of both proteins and consequently a higher renal overload. The tissue distribution of periodate-treated BJg was similar to that of native BJs: 82.7 vs 81.4% in the liver and 17.3 vs 18.6% in the kidneys. These observations indicate the important role of sugar residues of Bence Jones proteins for their recognition by specific membrane receptors, which leads to differential tissue accumulation and possible toxicity

  6. Feline lymphoplasmacytic stomatitis associated with monoclonal gammopathy and Bence-Jones proteinuria.

    Science.gov (United States)

    Lyon, K F

    1994-03-01

    Lymphoplasmacytic stomatitis and gingivitis was diagnosed in an 8-year old female domestic shorthair. The cat had evidence of severe generalized inflammation of the oral cavity. Biopsy samples were evaluated and displayed a lichenoid, interface stomatitis which was predominantly lymphoplasmacytic. Serum protein electrophoresis confirmed a monoclonal gammopathy. Urine protein electrophoresis confirmed Bence-Jones proteinuria. Protein electrophoresis was used to diagnose monoclonal gammopathy (the production of a monoclonal immunoglobulin, or paraprotein, which is associated with a characteristic "M" protein spike on serum electrophoresis). Diseases associated with monoclonal gammopathy are similar in the dog and cat. Alkylating agent chemotherapy is used to rapidly reduce paraprotein concentrations in multiple myeloma. Multiple myeloma is the most common disorder associated with monoclonal gammopathy. This condition is less common in the cat, compared to the dog. This report examines the diagnosis and treatment of multiple myeloma in a cat presenting with severe stomatitis.

  7. 21 CFR 866.5150 - Bence-Jones proteins immunological test system.

    Science.gov (United States)

    2010-04-01

    ... SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Immunological Test Systems § 866... bone marrow cells), leukemia (cancer of the blood-forming organs), and lymphoma (cancer of the...

  8. [Evaluation of the relations between serum proteins electrophoresis and other laboratory tests in monoclonal gammopathies (author's transl)].

    Science.gov (United States)

    Ramacciotti, P G; Lazzari, L; Minardi, P

    1976-03-01

    We have considered interesting to determine monoclonal gammopathies incidence, in 2191 serum proteins electrophoresis performed in our laboratory from January to December 1974. We have found 15 cases of monoclonal gammopathies, some cases combined with Mieloma (3 cases), some other with other with non specific diseases. We have considered the relations between type of gammopathy and other laboratory tests useful for any other diagnose: they are: immunochemical analysis, E.S.R., red and white count, total proteins, Bence Jones protein.

  9. Daniel Jones

    DEFF Research Database (Denmark)

    underrated, impact on the American structuralist school. This eight volume collection makes available the first editions of Jones' standard books, i.e. The Pronunciation of English (1909), An English Pronouncing Dictionary (1917) and An Outline of English Phonetics (1918). In addition, Jones' crucial...... Bridges, appears here for the first time. Also incorporated are extracts from his correspondence with prominent contemporary linguists such as David Abercrombie, Roger Kingdon, Harold Palmer and H. J. Uldall....

  10. Analytical tools for solitons and periodic waves corresponding to phonons on Lennard-Jones lattices in helical proteins

    DEFF Research Database (Denmark)

    D'ovidio, Francesco; Bohr, Henrik; Lindgård, Per-Anker

    2005-01-01

    -Jones potential, the solitons can be characterized analytically with a good quantitative agreement using formulas for a Toda potential with parameters fitted to the Lennard-Jones potential. We also discuss and show the robustness of the family of periodic solutions called cnoidal waves, corresponding to phonons....... The soliton phenomena described in the simulations of alpha helices may help to explain recent x-ray experiments on long alpha helices in Rhodopsin where a long lifetime of the vibrational modes has been observed....

  11. On the existence of Jones birefringence and Jones dichroism.

    Science.gov (United States)

    Arteaga, Oriol

    2010-05-01

    We claim that the so-called Jones birefringence and Jones dichroism effects, understood as new optical phenomena of difficult experimental observation, cannot be deduced from Jones publications and were proposed due to a misinterpretation of his original work.

  12. The Colored Jones Function

    Institute of Scientific and Technical Information of China (English)

    HAN You-fa; YAN Xin-ming; LV Li-li

    2012-01-01

    In this paper,we discuss the properties of the colored Jones function of knots.Particularly,we calculate the colored Jones function of some knots(31,41,51,52).Furthermore,one can compute the Kashaev's invariants and study some properties of the Kashaev's conjecture.

  13. Koltunud Indiana Jones / Kutt Kommel

    Index Scriptorium Estoniae

    Kommel, Kutt

    2008-01-01

    Steven Spielbergi neljas Indiana Jones'i film Harrison Fordiga nimiosas "Indiana Jones ja kristallpealuu kuningriik" ("Indiana Jones and the Kingdom of the Crystal Skull") : Ameerika Ühendriigid 2008

  14. Snorkeling and Jones tubes

    OpenAIRE

    Lam, Lewis Y. W.; Weatherhead, Robert G.

    2015-01-01

    We report a case of tympanic membrane rupture during snorkeling in a 17-year-old young man who had previously undergone bilateral Jones tubes placed for epiphora. To our knowledge, this phenomenon has not been previously reported.

  15. Snorkeling and Jones tubes.

    Science.gov (United States)

    Lam, Lewis Y W; Weatherhead, Robert G

    2015-01-01

    We report a case of tympanic membrane rupture during snorkeling in a 17-year-old young man who had previously undergone bilateral Jones tubes placed for epiphora. To our knowledge, this phenomenon has not been previously reported.

  16. Jones' instrument technology

    CERN Document Server

    Jones, Ernest Beachcroft; Kingham, Edward G; Radnai, Rudolf

    1985-01-01

    Jones' Instrument Technology, Volume 5: Automatic Instruments and Measuring Systems deals with general trends in automatic instruments and measuring systems. Specific examples are provided to illustrate the principles of such devices. A brief review of a considerable number of standards is undertaken, with emphasis on the IEC625 Interface System. Other relevant standards are reviewed, including the interface and backplane bus standards. This volume is comprised of seven chapters and begins with a short introduction to the principles of automatic measurements, classification of measuring system

  17. Tagging, Encoding, and Jones Optimality

    DEFF Research Database (Denmark)

    Danvy, Olivier; López, Pablo Ernesto Martínes

    2003-01-01

    A partial evaluator is said to be Jones-optimal if the result of specializing a self-interpreter with respect to a source program is textually identical to the source program, modulo renaming. Jones optimality has already been obtained if the self-interpreter is untyped. If the selfinterpreter is...

  18. Indiana Jones ja kristallpealuu kuningriik / Jaanus Noormets

    Index Scriptorium Estoniae

    Noormets, Jaanus

    2008-01-01

    Steven Spielbergi neljas Indiana Jones'i film Harrison Fordiga nimiosas "Indiana Jones ja kristallpealuu kuningriik" ("Indiana Jones and the Kingdom of the Crystal Skull") : Ameerika Ühendriigid 2008

  19. Tagging, Encoding, and Jones Optimality

    DEFF Research Database (Denmark)

    Danvy, Olivier; Lopez, Pablo E. Martinez

    2003-01-01

    A partial evaluator is said to be Jones-optimal if the result of specializing a self-interpreter with respect to a source program is textually identical to the source program, modulo renaming. Jones optimality has already been obtained if the self-interpreter is untyped. If the selfinterpreter...... is typed, however, residual programs are cluttered with type tags. To obtain the original source program, these tags must be removed. A number of sophisticated solutions have already been proposed. We observe, however, that with a simple representation shift, ordinary partial evaluation is already Jones-optimal...

  20. Stabiilne Ashley Jones / Svea Suvi

    Index Scriptorium Estoniae

    Suvi, Svea

    2006-01-01

    Ameerika teleseriaali "Vaprad ja ilusad" ("The Bold and the Beautiful") osatäitja Ashley Jones (Bridget Forrester). Sama artikkel pealkirjaga "Uus Bridget" : Nädal, 30. jan. 2006, nr. 4, lk. 12 : ill

  1. Magnetoelectric Jones Dichroism in Atoms

    CERN Document Server

    Budker, D

    2003-01-01

    The authors suggest that atomic experiments measuring the interference between magnetic-dipole and electric-field-induced electric-dipole transition amplitudes may provide a valuable system to study magnetoelectric Jones effects.

  2. No More Indiana Jones Warehouses

    Science.gov (United States)

    Pannapacker, William

    2012-01-01

    In "Raiders of the Lost Ark," Indiana Jones--perhaps the last heroic professor to appear in a major Hollywood film--survives a series of adventures involving spiders, snakes, treacherous colleagues, and countless Nazis who are determined to recover the ark of the covenant for their "Fuhrer." Apparently the ark has mystical powers. Ultimately,…

  3. Genesis: The Brynmor Jones Report

    Science.gov (United States)

    MacKenzie, Norman

    2005-01-01

    An account of the impetus given by the Brynmor Jones report ("Audio visual aids in Higher Education", 1965) to the development of educational technology in Britain. The author, who was closely involved in the developments, discusses the influence of the audio-visual movement in the United States and the emergence of a national organisation (NCET)…

  4. Conversations with...Hannah Jones

    Directory of Open Access Journals (Sweden)

    Amy Hinterberger

    2014-03-01

    Full Text Available Hannah Jones has conducted research on multiculture and multiculturalism, local government policy-making, community cohesion policy, migration policy, voluntary and community sector organising, regeneration and urban studies, and diversity and inequality. She is currently leading one of the first research projects funded by the ESRC Urgency Grants Mechanism, entitled '"Go Home": Mapping the unfolding controversy of Home Office Immigration Campaigns', working with colleagues at six other universities across the UK.

  5. 77 FR 19718 - Dow Jones & Company, Inc., Dow Jones Content Services Including On-Site Workers From Aerotek, Inc...

    Science.gov (United States)

    2012-04-02

    ... Employment and Training Administration Dow Jones & Company, Inc., Dow Jones Content Services Including On... at Dow Jones Corporation, Dow Jones Content Services Princeton, New Jersey. The workers are engaged... the Princeton, New Jersey location of Dow Jones & Company, Dow Jones Content Services, including...

  6. Chromosomal localization and molecular marker development of the lipopolysaccharide and beta-1,3-glucan binding protein gene in the Zhikong scallop Chlamys farreri (Jones et Preston (Pectinoida, Pectinidae

    Directory of Open Access Journals (Sweden)

    Pin Huan

    2010-01-01

    Full Text Available Zhikong scallop Chlamys farreri (Jones et Preston is an economically important species in China. Understanding its immune system would be of great help in controlling diseases. In the present study, an important immunity-related gene, the Lipopolysaccharide and Beta-1,3-glucan Binding Protein (LGBP gene, was located on C. farreri chromosomes by mapping several lgbp-containing BAC clones through fluorescence in situ hybridization (FISH. Through the localization of various BAC clones, it was shown that only one locus of this gene existed in the genome of C. farreri, and that this was located on the long arm of a pair of homologous chromosomes. Molecular markers, consisting of eight single nucleotide polymorphism (SNPs markers and one insertion-deletion (indel, were developed from the LGBP gene. Indel marker testing in an F1 family revealed slightly distorted segregation (p = 0.0472. These markers can be used to map the LGBP gene to the linkage map and assign the linkage group to the corresponding chromosome. Segregation distortion of the indel marker indicated genes with deleterious alleles might exist in the surrounding region of the LGBP gene.

  7. 77 FR 41807 - Dow Jones & Company, Inc., Dow Jones Content Services Division, Including On-Site Workers From...

    Science.gov (United States)

    2012-07-16

    ... Employment and Training Administration Dow Jones & Company, Inc., Dow Jones Content Services Division, Including On-Site Workers From Aerotek, Inc., Princeton, NJ; Generate, Inc., a Subsidiary of Dow Jones... January 26, 2011, applicable to workers of Dow Jones & Company, Inc., Dow Jones Content...

  8. Constant region of a kappa III immunoglobulin light chain as a major AL-amyloid protein

    DEFF Research Database (Denmark)

    Engvig, J P; Olsen, K E; Gislefoss, R E

    1998-01-01

    and the corresponding AL protein as a kappa III immunoglobulin light chain from material of a patient with systemic AL-amyloidosis presenting as a local inguinal tumour. The two proteins showed some unique features. The major part of the AL amyloid fibril protein consisted of C-terminal fragments of the Bence...

  9. Generalized Jones matrices for anisotropic media.

    Science.gov (United States)

    Ortega-Quijano, Noé; Arce-Diego, José Luis

    2013-03-25

    The interaction of arbitrary three-dimensional light beams with optical elements is described by the generalized Jones calculus, which has been formally proposed recently [Azzam, J. Opt. Soc. Am. A 28, 2279 (2011)]. In this work we obtain the parametric expression of the 3×3 differential generalized Jones matrix (dGJM) for arbitrary optical media assuming transverse light waves. The dGJM is intimately connected to the Gell-Mann matrices, and we show that it provides a versatile method for obtaining the macroscopic GJM of media with either sequential or simultaneous anisotropic effects. Explicit parametric expressions of the GJM for some relevant optical elements are provided.

  10. Dow Jones tugevdab oma koostist / Virge Lahe

    Index Scriptorium Estoniae

    Lahe, Virge

    2008-01-01

    USA tööstusettevõtteid koondav indeks Dow Jones vahetab nimekirjast välja kaks firmat ning lisab finants- ja kütusesektori osakaalu suurendamiseks Bank of America ja Chevroni. Vt. samas: Dow Jonesi tööstuskeskmisse lisandumine pole aktsiatele tiibu andnud; Dow Jonesi tööstuskeskmine

  11. Dow Jones News/Retrieval--An IndepthBxook.

    Science.gov (United States)

    Dempsey, Tim

    1984-01-01

    This introduction to the nonbibliographic databases offered by the Dow Jones News/Retrieval Service describes file content and search strategies in four groups: Dow Jones Business and Economic News; Dow Jones Quotes (market prices for stocks and other securities); Financial and Investment Services; General News and Information Services. Examples…

  12. 78 FR 49291 - Dow Jones & Company, Inc., Dow Jones Content Services Division, Including a Worker of Factiva...

    Science.gov (United States)

    2013-08-13

    ... Employment and Training Administration Dow Jones & Company, Inc., Dow Jones Content Services Division, Including a Worker of Factiva, Inc., A Subsidiary of Dow Jones Coporation and On-Site Leased Workers From... Assistance on January 26, 2012, applicable to workers of Aerotek, Inc., working on-site at Dow...

  13. Jones matrices of perfectly conducting metallic polarizers

    CERN Document Server

    Boyer, Philippe

    2014-01-01

    We deduce from Monomode Modal Method the analytical expressions of transmission and reflexion Jones matrices of an infinitely conducting metallic screen periodically pierced by subwavelength holes. The study is restricted to normal incidence and to the case of neglected evanescent fields (far-field) which covers many common cases. When only one non-degenerate mode propagates in cavities, they take identical forms to those of a polarizer, with Fabry-Perot-like spectral resonant factors depending on bigrating parameters. The isotropic or birefringent properties are then obtained when holes support two orthogonal polarization modes. This basic formalism is finally applied to design compact and efficient metallic half-wave plates.

  14. Robert T. Jones, One of a Kind

    Science.gov (United States)

    Vincenti, Walter G.

    2005-01-01

    His contemporaries saw R.T. Jones as one of the notably creative aerodynamicists of the twentieth century. This essay reviews his remarkable life and career, including his years as a farm-country boy, college dropout, and fledgling airplane designer in Missouri, his time as an elevator operator and self-directed student in Washington, D.C., and his long professional career as an aerodynamicist at the Langley and Ames Aeronautical Laboratories and Stanford University. The focus in his career is on his fundamental discovery of the benefits of sweepback for the wings of high-speed airplanes. This includes speculation about his highly intuitive thought processes in arriving at his creative ideas. I also give an account of his work on blood flow and the mechanical heart, his avocational accomplishments as a maker of telescopes and violins, and his philosophical interest in human affairs.

  15. Obituary: Frank Culver Jones, 1932-2007

    Science.gov (United States)

    Ormes, Johnathan F.; Streitmatter, Robert E.

    2007-12-01

    Frank C. Jones, an emeritus theoretical physicist at NASA, died May 2, 2007 at age 74 after a struggle with a rare form of cancer. He died at his home in Silver Spring, Maryland, surrounded by his family. Frank was born July 30, 1932 in Fort Worth, Texas, the oldest of three boys. His parents were Kenneth Hugh and Nancy Culver Jones. Frank's father was a lawyer, and his grandfather was a Methodist minister. Frank graduated from Rice University in 1954 and earned a master's degree in 1955 and a doctorate in 1961, both in physics, from the University of Chicago. He did his graduate work with Prof. John Simpson. Dr. Jones began his professional career as an instructor in physics at Princeton University before joining NASA's Goddard Space Flight Center in 1963 as a National Research Council associate. He subsequently became a member of the Theory Division and the Laboratory for High Energy Astrophysics. His area of expertise was the origin, transport, and electromagnetic interactions of cosmic rays. His particular focus was the stochastic physics related to the diffusion of particles in random fields, plasma turbulence, and the shock acceleration of charged particles in collisionless plasmas. From 1993 to 1995, Frank was head of Goddard's Theoretical High Energy Astrophysics Office and continued to serve as Head of the Theory group. In 2003 he served as Acting Chief of the Laboratory for High Energy Astrophysics. He retired in 2005 and continued his affiliation with NASA as an emeritus scientist at Goddard until his death. As a youngster, Frank showed the signs of curiosity and initiative that indicated he might become an experimentalist. At the memorial service for Frank, his brother related the stories of how Frank had rigged a hidden microphone to play through the family television as his brother courted a young woman on the front porch swing, and how one of Frank's early chemistry experiments caused all the family silverware to turn black. Although Frank started

  16. Accurate Jones Matrix of the Practical Faraday Rotator

    Institute of Scientific and Technical Information of China (English)

    王林斗; 祝昇翔; 李玉峰; 邢文烈; 魏景芝

    2003-01-01

    The Jones matrix of practical Faraday rotators is often used in the engineering calculation of non-reciprocal optical field. Nevertheless, only the approximate Jones matrix of practical Faraday rotators has been presented by now. Based on the theory of polarized light, this paper presents the accurate Jones matrix of practical Faraday rotators. In addition, an experiment has been carried out to verify the validity of the accurate Jones matrix. This matrix accurately describes the optical characteristics of practical Faraday rotators, including rotation, loss and depolarization of the polarized light. The accurate Jones matrix can be used to obtain the accurate results for the practical Faraday rotator to transform the polarized light, which paves the way for the accurate analysis and calculation of practical Faraday rotators in relevant engineering applications.

  17. La Bob Jones University : hier et aujourd’hui Bob Jones University : Past and Present

    Directory of Open Access Journals (Sweden)

    Mokhtar Ben Barka

    2009-11-01

    Full Text Available This article examines the separatist beliefs and practices at Bob Jones University. Firstly, it shows that despite the recent changes, this institution still represents the old face of fundamentalist higher education. Secondly, this essay focuses on the controversy around Republican candidate George W. Bush’s appearance at Bob Jones University.

  18. Triangular dissections, aperiodic tilings and Jones algebras

    CERN Document Server

    Coquereaux, Robert

    1994-01-01

    The Brattelli diagram associated with a given bicolored Dynkin-Coxeter graph of type A_n determines planar fractal sets obtained by infinite dissections of a given triangle. All triangles appearing in the dissection process have angles that are multiples of \\pi/ (n+1). There are usually several possible infinite dissections compatible with a given n but a given one makes use of n/2 triangle types if n is even. Jones algebra with index [ 4 \\ \\cos^2{\\pi \\over n+1}]^{-1} (values of the discrete range) act naturally on vector spaces associated with those fractal sets. Triangles of a given type are always congruent at each step of the dissection process. In the particular case n=4, there are isometric and the whole structure lead, after proper inflation, to aperiodic Penrose tilings. The other "tilings" associated with other values of the index are discussed and shown to be encoded by equivalence classes of infinite sequences (with appropriate constraints) using only n/2 digits (if n is even) and generalizing the ...

  19. Chuck Jones lahkus, tema kangelased elavad edasi / Neeme Korv

    Index Scriptorium Estoniae

    Korv, Neeme, 1974-

    2002-01-01

    Suri Chuck Jones (1912-2002), kuulus USA animafilmirežissöör, kelle animasari "Tom & Jerry" on praegugi Eestis väga populaarne. Ta on loonud enam kui 300 animafilmi, saanud 3 Oscarit ning 1996. aastal ka elutöö Oscari. Eesti lapsed nägid nõukogude ajal esmakordselt Chuck Jones'i loomingut Raivo Järvi lastesaadetes "Laupäeval koos isaga"

  20. Lyapunov instabilities of Lennard-Jones fluids.

    Science.gov (United States)

    Yang, Hong-liu; Radons, Günter

    2005-03-01

    Recent work on many-particle systems reveals the existence of regular collective perturbations corresponding to the smallest positive Lyapunov exponents (LEs), called hydrodynamic Lyapunov modes. Until now, however, these modes have been found only for hard-core systems. Here we report results on Lyapunov spectra and Lyapunov vectors (LVs) for Lennard-Jones fluids. By considering the Fourier transform of the coordinate fluctuation density u((alpha)) (x,t) , it is found that the LVs with lambda approximately equal to 0 are highly dominated by a few components with low wave numbers. These numerical results provide strong evidence that hydrodynamic Lyapunov modes do exist in soft-potential systems, although the collective Lyapunov modes are more vague than in hard-core systems. In studying the density and temperature dependence of these modes, it is found that, when the value of the Lyapunov exponent lambda((alpha)) is plotted as function of the dominant wave number k(max) of the corresponding LV, all data from simulations with different densities and temperatures collapse onto a single curve. This shows that the dispersion relation lambda((alpha)) vs k(max) for hydrodynamical Lyapunov modes appears to be universal for the low-density cases studied here. Despite the wavelike character of the LVs, no steplike structure exists in the Lyapunov spectrum of the systems studied here, in contrast to the hard-core case. Further numerical simulations show that the finite-time LEs fluctuate strongly. We have also investigated localization features of LVs and propose a length scale to characterize the Hamiltonian spatiotemporal chaotic states.

  1. Differential diagnosis of plasma cell dyscrasias in rheumatological practice

    Directory of Open Access Journals (Sweden)

    V I Vasilyev

    2010-01-01

    Conclusion. Many clinical and laboratory manifestations of primary PCD and RD are similar and only the absence of classical laboratory markers of autoimmune disease, as well as the presence of serum monoclonal immunoglobulins and urinary Bence Jones protein suggest the presence of PCD, both primary PCDs and those with RD.

  2. Bestemmelse af lette kæder i serum

    DEFF Research Database (Denmark)

    Hansen, Charlotte Toftmann; Nielsen, Lars; Münster, Anna-Marie Bloch

    2010-01-01

    Free light chains of the immunoglobulin are identical to the Bence Jones protein. In 2001, a commercially available assay for the measurement of free light chains in serum (sFLC) became available (FreeLite Free Kappa & Free Lambda assay). Evidence from the use of the sFLC analysis is rapidly...

  3. Differential diagnosis of plasma cell dyscrasias in rheumatological practice

    Directory of Open Access Journals (Sweden)

    V I Vasilyev

    2010-12-01

    Conclusion. Many clinical and laboratory manifestations of primary PCD and RD are similar and only the absence of classical laboratory markers of autoimmune disease, as well as the presence of serum monoclonal immunoglobulins and urinary Bence Jones protein suggest the presence of PCD, both primary PCDs and those with RD.

  4. NEWS: John Goronwy Jones (1920-1999)

    Science.gov (United States)

    Jennison, Brenda M.

    2000-05-01

    John Goronwy Jones Gron Jones, as he was known to all, was a champion of Physics Education and his death, shortly before his eightieth birthday, robbed physics teachers of a colleague who fought many battles on their behalf. He was not shy of taking issue with anyone in authority who might be putting forward policies which would harm his great love: Physics Education and Physics Teaching. His photograph shows a man with an impish grin, looking friend and foe alike straight in the eye, before delivering the death blow to an argument which was founded on less than common sense. At other times he would listen patiently to the woes of colleagues before offering them fatherly/grandfatherly advice so that whoever was on the receiving end would go away feeling better for the encounter. Gron was born in Swansea and educated at Lewis Boys Grammar School in Glamorgan before entering University College Cardiff first of all as a mathematician before graduating in Physics in 1941. After his war service in the RAF, working on signals and radar development, he returned to do an MSc in X-ray crystallography before completing a PGCE in Bristol. What then passed for teacher training in all institutions left him wary of returning to train teachers himself but after 14 years spent teaching physics in three schools he returned to Cardiff and began a 25 year career in teacher training. He and his two colleagues, Clifford Othen (chemistry) and Douglas Hillier (biology) built up the Cardiff Science Centre as a focus for initial and in-service science teacher training in South Wales. The triumvirate was well known and a power to be reckoned with. They created links between the University Science Departments and the Schools. Gron knew the local schools and their physics teachers intimately. Cardiff became a focus for science education both nationally and internationally. He was a frequent attender at both ICPE (International Commission for Physics Education) and GIREP (International Physics

  5. Flight into sanity. Jones's allegation of Ferenczi's mental deterioration reconsidered.

    Science.gov (United States)

    Bonomi, C

    1999-06-01

    In 'The Life and Work of Sigmund Freud', Volume III, Ernest Jones explained Ferenczi's final contributions as the product of a mental deterioration based on a progressive psychosis. Erich Fromm collected various testimonies by witnesses of Ferenczi's last years, all contrasting with Jones's assertions, and challenged Jones's manner of writing history. However, since Fromm was himself a dissident, and his witnesses were pupils, relatives or friends of Ferenczi's, they were discarded as 'partisans'. The present study aims at reconsidering the question of Ferenczi's insanity on the basis of many unpublished documents. The consulted documents do not support Jones's allegation of Ferenczi's insanity. At the same time, they show that Jones's allegation was not a one-man fabrication, but reflected a shared belief, eliciting many questions about the nature of this belief, the lack of scrutiny that characterised its spreading, and its possible function within the psychoanalytic community. It is suggested that Ferenczi's personality and teaching, especially his emphasis on the need to accept the patient's criticism, contrasted with the dominant conception of psychoanalysis, based on the analyst's infallibility.

  6. Cluster fusion algorithm: application to Lennard-Jones clusters

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter

    2008-01-01

    We present a new general theoretical framework for modelling the cluster structure and apply it to description of the Lennard-Jones clusters. Starting from the initial tetrahedral cluster configuration, adding new atoms to the system and absorbing its energy at each step, we find cluster growing...... paths up to the cluster size of 150 atoms. We demonstrate that in this way all known global minima structures of the Lennard-Jones clusters can be found. Our method provides an efficient tool for the calculation and analysis of atomic cluster structure. With its use we justify the magic number sequence...... for the clusters of noble gas atoms and compare it with experimental observations. We report the striking correspondence of the peaks in the dependence of the second derivative of the binding energy per atom on cluster size calculated for the chain of the Lennard-Jones clusters based on the icosahedral symmetry...

  7. Cluster fusion algorithm: application to Lennard-Jones clusters

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter

    2006-01-01

    We present a new general theoretical framework for modelling the cluster structure and apply it to description of the Lennard-Jones clusters. Starting from the initial tetrahedral cluster configuration, adding new atoms to the system and absorbing its energy at each step, we find cluster growing...... paths up to the cluster size of 150 atoms. We demonstrate that in this way all known global minima structures of the Lennard-Jones clusters can be found. Our method provides an efficient tool for the calculation and analysis of atomic cluster structure. With its use we justify the magic number sequence...... for the clusters of noble gas atoms and compare it with experimental observations. We report the striking correspondence of the peaks in the dependence of the second derivative of the binding energy per atom on cluster size calculated for the chain of the Lennard-Jones clusters based on the icosahedral symmetry...

  8. Guts of surfaces and the colored Jones polynomial

    CERN Document Server

    Futer, David; Purcell, Jessica

    2013-01-01

    This monograph derives direct and concrete relations between colored Jones polynomials and the topology of incompressible spanning surfaces in knot and link complements. Under mild diagrammatic hypotheses, we prove that the growth of the degree of the colored Jones polynomials is a boundary slope of an essential surface in the knot complement. We show that certain coefficients of the polynomial measure how far this surface is from being a fiber for the knot; in particular, the surface is a fiber if and only if a particular coefficient vanishes. We also relate hyperbolic volume to colored Jones polynomials. Our method is to generalize the checkerboard decompositions of alternating knots. Under mild diagrammatic hypotheses, we show that these surfaces are essential, and obtain an ideal polyhedral decomposition of their complement. We use normal surface theory to relate the pieces of the JSJ decomposition of the  complement to the combinatorics of certain surface spines (state graphs). Since state graphs have p...

  9. In-Office Jones tube exchange using the Seldinger technique.

    Science.gov (United States)

    Eloy, Jean Anderson; Choudhry, Osamah J; Shukla, Pratik A; Langer, Paul D

    2013-01-01

    Conjunctivodacryocystorhinostomy (CDCR) with Jones tube placement is usually performed as a primary procedure for severe stenosis or obstruction of both upper and lower canaliculi of the lacrimal drainage pathway, or occasionally, after unsuccessful dacryocystorhinostomy (DCR). Jones tube obstruction is quite common, and often requires removal of the obstructed tube and replacement or exchange of the tube in the operating room. This procedure is typically performed under general anesthesia, and is associated with the risks of general anesthesia, a significant investment of time, and the cost of the operating suite. Recently, there has been a movement toward in-office procedures in otolaryngology and ophthalmology due to greater patient satisfaction and savings in time and money for patients and physicians. In this report, we describe a novel in-office method to exchange an obstructed Jones tube that provides the aforementioned benefits while preserving patient comfort. No similar case has been previously reported in the literature.

  10. Guts of surfaces and the colored Jones polynomial

    CERN Document Server

    Futer, David; Purcell, Jessica S

    2011-01-01

    This work derives direct and concrete relations between colored Jones polynomials and the topology of incompressible spanning surfaces in knot and link complements. Under mild diagrammatic hypotheses that arise naturally in the study of knot polynomial invariants (A-adequacy), we prove that the growth of the degree of the colored Jones polynomials is a boundary slope of an essential surface in the knot complement. We show that certain coefficients of the polynomial measure how far this surface is from being a fiber in the knot complement; in particular, the surface is a fiber if and only if a particular coefficient vanishes. Our results also yield concrete relations between hyperbolic geometry and colored Jones polynomials: for certain families of links, coefficients of the polynomials determine the hyperbolic volume to within a factor of 4. Our approach is to generalize the checkerboard decompositions of alternating knots. Under mild diagrammatic hypotheses (A-adequacy), we show that the checkerboard knot su...

  11. Elisabeth Bennet y Bridget Jones: del protofeminismo al postfeminismo

    OpenAIRE

    Valero Valero, Dori

    2013-01-01

    XVIII Jornades de Foment de la Investigació de la Facultat de Ciències Humanes i Socials (Any 2013) Las teorías feministas se han introducido en la literatura de ficción facilitando modelos alternativos a las lectoras. Las heroínas llevan a cabo una tarea de «resistencia feminista», y tomaremos los siguientes ejemplos: Elizabeth Bennet, Orgullo y prejuicio (1813) y Bridget Jones, El diario de Bridget Jones (1999). Jane Austen construye protagonistas femeninas que responden a las est...

  12. Imaginando Palmares: a obra de Gayl Jones Imagining Palmares: the work of Gayl Jones

    Directory of Open Access Journals (Sweden)

    Stelamaris Coser

    2005-12-01

    Full Text Available O longo poema narrativo Song for Anninho (1981, da escritora negra Gayl Jones (Estados Unidos, interfere na narrativa da história colonial brasileira ao resgatar a figura feminina na República de Palmares, reescrever a saga de resistência dos palmaristas do ponto de vista imaginário de uma mulher negra do século XVII e, através dela, reinventar o cotidiano, os amores, as disputas e os sonhos das pessoas comuns que integravam o quilombo. O texto reflete sobre a verdade histórica, o aspecto construído de documentos, as seleções e exclusões da linguagem, e a importância do relato oral para o conhecimento de vivências e identidades à margem da história oficial. Nessa versão especial, o relato dramático do sonho, da luta e da destruição do mais famoso quilombo brasileiro usa a imaginação literária para expandir a memória e os arquivos de um dos fatos mais importantes da história das Américas, contribuindo para estimular o diálogo interamericano e iluminar a diáspora africana no Brasil e no continente.The long narrative poem Song for Anninho (1981, written by black U.S. writer Gayl Jones, interferes in the narrative of Brazilian colonial history as it highlights the female presence in the Republic of Palmares, rewrites the tale of resistance from the point of view of a black woman in the 17th Century, and, through her, reinvents the everyday lives, loves, disputes, and dreams of common people in the quilombo. The text reflects about historical truth, the constructed character of documents, selections and exclusions in language, and the importance of oral accounts to give visibility to experiences and identities marginalized by official history. In this special version, the dramatic report of the dreams, struggles, and destruction of the most famous Brazilian quilombo uses literary imagination to expand the memory and the archives of one of the most important facts in the history of the Americas, contributing to stimulate

  13. Free energy of the Lennard-Jones solid

    NARCIS (Netherlands)

    Hoef, van der Martin A.

    2000-01-01

    We have determined a simple expression for the absolute Helmholtz free energy of the fcc Lennard-Jones solid from molecular dynamics simulations. The pressure and energy data from these simulations have been fitted to a simple functional form (18 parameters) for densities ranging from around 0.94–1.

  14. Edward Burne-Jones' Heavenly Conception: A Biblical Cosmos

    Science.gov (United States)

    Cheney, L. D. G.

    2016-01-01

    Edward Burne-Jones was a Pre-Raphaelite artist and designer, who collaborated with William Morris on many decorative arts (stained glass windows, book illustrations, ceramic and tapestry designs). He was a founding partner in the firm Morris, Marshall, Faulkner & Company. Burne-Jones composed The Days of Creation between 1870 and 1876 for the Morris firm. These paintings were executed in gouache and gold paint, and cartoons were made for tile and in stained glass, for the Church of St. Editha at Tamworth in Staffordshire. Burne-Jones' creation was highly praised and elegantly described by Oscar Wilde: “The picture is divided into six compartments, each representing a day in the Creation of the World, under the symbol of an angel holding a crystal globe, within which is shown the work of a day.” This paper will examine how Burne-Jones visualized an unusual celestial creation where angels holding magical spheres unveil the divine manifestation for the creation of a terrestrial realm. He created a cosmic utopia of the natural world.

  15. Public lecture | "Science and society" by Bob Jones | 22 May

    CERN Multimedia

    2014-01-01

    Public lecture: "Science and society: the impact of computing at CERN on society" by Bob Jones 22 May at 7.30 p.m. Globe of Science and Innovation Lecture in English, translated in French. Entrance free. Limited number of seats. Reservation essential: +41 22 767 76 76 or cern.reception@cern.ch

  16. DREDGED MATERIAL RECLAMATION AT THE JONES ISLAND CONFINED DISPOSAL FACILITY - ITER

    Science.gov (United States)

    In this SITE demonstration, phytoremediation technology was applied to contaminated dredged materials from the Jones Island Confined Disposal Facility (CDF) located in Milwaukee Harbor, Wisconsin. The Jones Island CDF receives dredged materials from normal maintenance of Milwauke...

  17. 75 FR 20802 - Safety Zone; New York Air Show at Jones Beach State Park, Atlantic Ocean off of Jones Beach...

    Science.gov (United States)

    2010-04-21

    ..., Atlantic Ocean off of Jones Beach, Wantagh, NY AGENCY: Coast Guard, DHS. ACTION: Notice of proposed... an air show which consist of aircraft performing aerobatic maneuvers over the Atlantic Ocean off of..., which will then become highlighted in blue. In the ``Document Type'' drop down menu select...

  18. 75 FR 43563 - Dow Jones & Company, Sharon Pennsylvania Print Plant a Subsidiary of News Corporation, West...

    Science.gov (United States)

    2010-07-26

    ... Employment and Training Administration Dow Jones & Company, Sharon Pennsylvania Print Plant a Subsidiary of... the TAA petition filed on behalf of workers at Dow Jones & Company, Sharon Pennsylvania Print Plant, a... (Konica). Neither of those relationships exists between Dow Jones & Company, West Middlesex,...

  19. Indiana Jones on tagasi ja näitab, kuidas käituda / Kristiina Davidjants

    Index Scriptorium Estoniae

    Davidjants, Kristiina, 1974-

    2008-01-01

    22 mail esilinastub Steven Spielbergi järjekordne Indiana Jones'i film, kaasstsenaristiks ja produtsendiks George Lucas ja Harrison Fordiga nimiosas "Indiana Jones ja kristallpealuu kuningriik" ("Indiana Jones and the Kingdom of the Crystal Skull"). Saaga varasemast kolmest filmist

  20. Gauge-origin independent calculations of Jones birefringence

    Science.gov (United States)

    Shcherbin, Dmitry; Thorvaldsen, Andreas J.; Jonsson, Dan; Ruud, Kenneth

    2011-10-01

    We present the first gauge-origin independent formulation of Jones birefringence at the Hartree-Fock level of theory. Gauge-origin independence is achieved through the use of London atomic orbitals. The implementation is based on a recently proposed atomic orbital-based response theory formulation that allows for the use of both time- and perturbation-dependent basis sets [Thorvaldsen, Ruud, Kristensen, Jørgensen, and Coriani, J. Chem. Phys. 129, 214108 (2008)]. We present the detailed expressions for the response functions entering the Jones birefringence when London atomic orbitals are used. The implementation is tested on a set of polar and dipolar molecules at the Hartree-Fock level of theory. It is demonstrated that London orbitals lead to much improved basis-set convergence, and that the use of small, conventional basis sets may lead to the wrong sign for the calculated birefringence. For large basis sets, London orbitals and conventional basis sets converge to the same results.

  1. Birefringence of cellotape: Jones representation and experimental analysis

    Energy Technology Data Exchange (ETDEWEB)

    Belendez, Augusto; Frances, Jorge; Neipp, Cristian [Departamento de Fisica, Ingenieria de Sistemas y Teoria de la Senal, Universidad de Alicante, Apartado 99, E-03080 Alicante (Spain); Fernandez, Elena [Departamento de Optica, FarmacologIa y Anatomia, Universidad de Alicante, Apartado 99, E-03080 Alicante (Spain)], E-mail: a.belendez@ua.es

    2010-05-15

    In this paper, we analyse a simple experiment to study the effects of polarized light. A simple optical system composed of a polarizer, a retarder (cellotape) and an analyser is used to study the effect on the polarization state of the light which impinges on the setup. The optical system is characterized by means of a Jones matrix, and a simple procedure based on Jones vectors is used to obtain an expression for the intensity after the light passes through the optical system. The light intensity is measured by a photodetector and the expression obtained theoretically is experimentally validated. By fitting the experimental intensity data, the value of the retardation introduced by the retarder can also be obtained.

  2. Experimental approximation of the Jones polynomial with one quantum bit.

    Science.gov (United States)

    Passante, G; Moussa, O; Ryan, C A; Laflamme, R

    2009-12-18

    We present experimental results approximating the Jones polynomial using 4 qubits in a liquid state nuclear magnetic resonance quantum information processor. This is the first experimental implementation of a complete problem for the deterministic quantum computation with one quantum bit model of quantum computation, which uses a single qubit accompanied by a register of completely random states. The Jones polynomial is a knot invariant that is important not only to knot theory, but also to statistical mechanics and quantum field theory. The implemented algorithm is a modification of the algorithm developed by Shor and Jordan suitable for implementation in NMR. These experimental results show that for the restricted case of knots whose braid representations have four strands and exactly three crossings, identifying distinct knots is possible 91% of the time.

  3. Tubo de Lester-Jones: indicações e resultados Lester-Jones tube: indications and results

    Directory of Open Access Journals (Sweden)

    Walberto Passos Junior

    2004-12-01

    Full Text Available OBJETIVO: Avaliar as indicações, resultados e complicações advindas do seu uso. MÉTODOS: Avaliaram-se retrospectivamente 25 pacientes submetidos a 27 conjuntivorrinostomias com colocação de tubo de Lester-Jones. Foram estudados os dados do portador, a etiologia da afecção e as complicações que ocorreram no intra e no pós-operatório. Os dados foram avaliados segundo a freqüência de ocorrência. RESULTADOS: O tubo de Lester-Jones foi usado igualmente em ambos os sexos, mais em indivíduos abaixo dos 10 ou acima dos 50 anos de idade. As causas mais freqüentes para utilização foram a idiopática ou a agenesia congênita de pontos e canalículos. Houve melhora dos sintomas em 88% dos pacientes. Complicações ocorreram em 59,25% dos casos, dentre as quais: extrusão (40,74% e a migração (14,8% do tubo. CONCLUSÃO: Apesar das complicações observadas, o índice de cura com a utilização do tubo de Lester-Jones é alto, sendo boa opção para o tratamento das obstruções lacrimais altas.PURPOSE: To evaluate the results and the complications occurring with this procedure. METHODS: The authors retrospectively reviewed charts of 25 patients (27 lacrimal viers with upper lacrimal system obstruction who underwent conjunctivorhinostomy and Lester-Jones tube bypass. The patients were evaluated according to gender, causative factors and the com plications during and after surgery. The data were submitted to statistical analysis. RESULTS: The Lester-Jones bypass tube was used in both sexes and most frequently in patients under 10 or above 50 years. The most common obstructive factor was unknown and congenital agenesis. Eighty-eight per cent of the patients had no epiphora at the end of the treatment. Complications occurred in 59.25% of the patients, most of them related to tube extrusion (40.74% or migration (14.8%. The authors concluded that the Lester-Jones bypass tube is a good option to treat the upper lacrimal obstruction, in spite

  4. The Farrell-Jones Isomorphism Conjecture in K-Theory

    CERN Document Server

    Morteo, Marcelo Gomez

    2012-01-01

    We prove that the Farrell-Jones isomorphism conjecture for non connective K theory for a discrete group G and a coefficient ring R holds true if G belongs to the class of groups acting on trees under certain conditions on G and if R is either regular or hereditary, depending on the structure of G. It is known that these groups verify the isomorphism conjecture if finitely generated for any coefficient ring, but in this article G may not be finitely generated.

  5. Mueller-Jones Matrix measurement in material identification

    Science.gov (United States)

    Xu, Jiang; Qian, Weixian; Wang, Xiao

    2016-09-01

    The uniformity of lattice arrangement plays an important role in industrial processing, science and technology studies and environmental pollution detection. However, there are very little papers to study surface structure by depolarization characteristics. In order to improve the efficiency and accuracy of material identification system by polarization technology, we developed a new method to decompose the Mueller matrix, we studied the mechanism of the scattering of electromagnetic wave, and analyzed the relationship between the characteristics of depolarization and mechanism of scattering. We used the Jones Matrix and Mueller Matrix to set up the physical model, and decomposed the Mueller-Jones Matrix by the characteristics of polarization, then got the depolarization coefficients (ωd) of the surfaces of the samples. By using this theory, we deduced the relation formula of Mueller matrix, Mueller-Jones matrix and Isotropic-Depolarizer matrix. Based on the polarized characteristics of the samples, we analyzed design method of material identification system and gave the results of the experimental test. Finally, we applied the theory of Fresnel formulas to verify the theoretical model. From the results, we found that the depolarization coefficients of the samples' surfaces were related to the scattering, and in the whole measurement process, the depolarization coefficients of the samples were far different; the method could easily to distinguish the metal and nonmetal, and more quickly to analyze the surface roughness of the samples. Therefore, the depolarization technology had a great application value, and the paper had very important significance on the development of surface structure study.

  6. A Viola-Jones based hybrid face detection framework

    Science.gov (United States)

    Murphy, Thomas M.; Broussard, Randy; Schultz, Robert; Rakvic, Ryan; Ngo, Hau

    2013-12-01

    Improvements in face detection performance would benefit many applications. The OpenCV library implements a standard solution, the Viola-Jones detector, with a statistically boosted rejection cascade of binary classifiers. Empirical evidence has shown that Viola-Jones underdetects in some instances. This research shows that a truncated cascade augmented by a neural network could recover these undetected faces. A hybrid framework is constructed, with a truncated Viola-Jones cascade followed by an artificial neural network, used to refine the face decision. Optimally, a truncation stage that captured all faces and allowed the neural network to remove the false alarms is selected. A feedforward backpropagation network with one hidden layer is trained to discriminate faces based upon the thresholding (detection) values of intermediate stages of the full rejection cascade. A clustering algorithm is used as a precursor to the neural network, to group significant overlappings. Evaluated on the CMU/VASC Image Database, comparison with an unmodified OpenCV approach shows: (1) a 37% increase in detection rates if constrained by the requirement of no increase in false alarms, (2) a 48% increase in detection rates if some additional false alarms are tolerated, and (3) an 82% reduction in false alarms with no reduction in detection rates. These results demonstrate improved face detection and could address the need for such improvement in various applications.

  7. A Unified Model of All Generalizations from the Jones Polynomial

    Institute of Scientific and Technical Information of China (English)

    QIAN Shang-Wu; GU Zhi-Yu

    2001-01-01

    From the basic properties of skein systems, we build a generalized tangle algebra (GTA). The elements of GTA are four basic tangles. There are three operations, which are connection, splicing and scalar multiplication. From GTA we derive two generalized recursion formulae (GRF) and prove the existence of a generalized skein relation which satisfies GRF. The obtained generalized skein relation epitomizes all generalizations from the Jones polynomial and thus forms a unified model. Two important topological parameters, twisting measure and loop values, appear explicitly in the expressions of the unified model, and this fact greatly simplifies the operations.

  8. Transpose symmetry of the Jones matrix and topological phases.

    Science.gov (United States)

    Bhandari, Rajendra

    2008-04-15

    The transmission Jones matrix of an arbitrary stack of reciprocal plane-parallel plates that has been turned through 180 degrees about an axis in the plane of the stack is, in an appropriate basis, the transpose of the transmission matrix of the unturned slab with a change in the sign of the off-diagonal elements. We prove this convention-free result for the case where reflection at the interfaces can be ignored and use it to devise an experimental scheme to separate isotropic and topological phase changes in a reciprocal optical medium.

  9. The Kauffman bracket and the Jones polynomial in quantum gravity

    CERN Document Server

    Griego, J R

    1995-01-01

    An analysis of the action of the Hamiltonian constraint of quantum gravity on the Kauffman bracket and Jones knot polynomials is proposed. It is explicitely shown that the Kauffman bracket is a formal solution of the Hamiltonian constraint with cosmological constant (\\Lambda) to third order in \\Lambda. The calculation is performed in the extended loop representation of quantum gravity. The analysis makes use of the analytical expressions of the knot invariants in terms of the two and three point propagators of the Chern-Simons theory. Some particularities of the extended loop calculus are considered and the implications of the results to the case of the conventional loop representation are discussed.

  10. Accurate Critical Parameters for the Modified Lennard-Jones Model

    Science.gov (United States)

    Okamoto, Kazuma; Fuchizaki, Kazuhiro

    2017-03-01

    The critical parameters of the modified Lennard-Jones system were examined. The isothermal-isochoric ensemble was generated by conducting a molecular dynamics simulation for the system consisting of 6912, 8788, 10976, and 13500 particles. The equilibrium between the liquid and vapor phases was judged from the chemical potential of both phases upon establishing the coexistence envelope, from which the critical temperature and density were obtained invoking the renormalization group theory. The finite-size scaling enabled us to finally determine the critical temperature, pressure, and density as Tc = 1.0762(2), pc = 0.09394(17), and ρc = 0.331(3), respectively.

  11. Hopping in a supercooled binary Lennard-Jones liquid

    DEFF Research Database (Denmark)

    Schrøder, Thomas; Dyre, Jeppe

    1998-01-01

    A binary Lennard–Jones liquid has been investigated by molecular dynamics at equilibrium supercooled conditions. At the lowest temperature investigated, hopping is present in the system as indicated by a secondary peak in 4r2Gs(r,t), where Gs(r,t) is the van Hove self correlation function....... To examine the dynamics of the system, we consider transitions between the inherent structures (local minima in the potential energy) along the trajectory. We conclude that the plateau in the mean square displacement found at lower temperatures is indeed a result of particles being trapped in local "cages...

  12. Advanced Jones calculus for the classification of periodic metamaterials

    Science.gov (United States)

    Menzel, Christoph; Rockstuhl, Carsten; Lederer, Falk

    2010-11-01

    By relying on an advanced Jones calculus, we analyze the polarization properties of light upon propagation through metamaterial slabs in a comprehensive manner. Based on symmetry considerations, we show that all periodic metamaterials may be divided into five different classes only. It is shown that each class differently affects the polarization of the transmitted light and sustains different eigenmodes. We show how to deduce these five classes from symmetry considerations and provide a simple algorithm that can be applied to decide to which class a given metamaterial belongs by measuring only the transmitted intensities.

  13. Cytological diagnosis of solitary plasmacytoma of the skull: A rare case report

    Directory of Open Access Journals (Sweden)

    Mohamad Banyameen Iqbal

    2015-01-01

    Full Text Available Solitary plasmacytoma (SPC of the skull (SPS is rare, and only a few cases have been reported in the literature so far. Plasmacytoma of the skull has a wide spectrum of pathology, including a quite benign, SPC, and an extremely malignant, multiple myeloma at the two ends of the spectrum. SPC of bone including SPS is characterized by a radiologically solitary bone lesion, neoplastic plasma cells in the biopsy specimen, fewer than 5% plasma cells in bone marrow, <2.0 g/dl monoclonal protein in the serum when present and negative urine test for Bence Jones protein (monoclonal light chain. For diagnosing, a comprehensive examination and analysis, which includes radiological examination, immunoglobulin, biochemistry, test for Bence Jones protein in the urine and bone marrow is needed.

  14. Freezing point depression in model Lennard-Jones solutions

    Science.gov (United States)

    Koschke, Konstantin; Jörg Limbach, Hans; Kremer, Kurt; Donadio, Davide

    2015-09-01

    Crystallisation of liquid solutions is of uttermost importance in a wide variety of processes in materials, atmospheric and food science. Depending on the type and concentration of solutes the freezing point shifts, thus allowing control on the thermodynamics of complex fluids. Here we investigate the basic principles of solute-induced freezing point depression by computing the melting temperature of a Lennard-Jones fluid with low concentrations of solutes, by means of equilibrium molecular dynamics simulations. The effect of solvophilic and weakly solvophobic solutes at low concentrations is analysed, scanning systematically the size and the concentration. We identify the range of parameters that produce deviations from the linear dependence of the freezing point on the molal concentration of solutes, expected for ideal solutions. Our simulations allow us also to link the shifts in coexistence temperature to the microscopic structure of the solutions.

  15. Nucleation for Lennard-Jones Fluid by Density Functional Theory

    Institute of Scientific and Technical Information of China (English)

    FU Dong

    2005-01-01

    @@ A non-mean field density functional theory is employed to investigate the vapour-liquid nucleation. The excess Helmholtz free energy functional is formulated in terms of a local density approximation for short ranged repulsion and a density-gradient expansion for long-ranged attractions. An analytical expression for the direct correlation function of a Lennard-Jones fluid is utilized to take into account the effect of long-ranged attractions on intermolecular correlations. With the predicted bulk properties and surface tension as input, the nucleation properties including density profile, work of formation and number of particles at the reduced temperatures T* = 0.694 and 0.741 are inuestigated. The obtained number of particles in the critical nucleus agrees well with the simulation data.

  16. Dow Jones Fund Opens Journalism Programs to White Students after Lawsuit

    Science.gov (United States)

    Scmidt, Peter

    2007-01-01

    This paper discusses a Lawsuit filed against Dow Jones Newspaper Fund and the legal settlement between the defendant and the plaintiff. The fund, a nonprofit organization affiliated with Dow Jones & Company had been operating more than 20 programs for minority high-school students to pursue careers in newspaper journalism. The organization…

  17. 107例多发性骨髓瘤M蛋白检测与免疫学分型分析%M Protein Detection and Immunology Typing Analysis of 107 Patients with Multiple Myeloma

    Institute of Scientific and Technical Information of China (English)

    刘玉梅; 赵有利; 石翀; 李光迪

    2011-01-01

    Objective To study the application of immunofixation electrophoresis (IFE) in typing M proteins. Methods Serum M proteins were detected in 107 patients by serum protein electrophoresis and IFE. Results Among 107 patients with MM,96 of them were affirmed to had M band with serum protein electrophoresis but M bands appeared in all of the MM patients with IFE. IFE manifest :there were IgG 63 cases (IgG κ 29 and IgG λ 34),IgA 25 cases (IgA κ 11 and IgA λ 14),IgM 3 cases (IgM κ 1 and IgM λ 2) and free light chain 15 cases (κ 2 and λ 13). Of 60 cases of MM,39 patients were detected to had Benee Jones proteins (12 κ and 27λ) in urine by IFE. The serum IFE had the highest sensitivity in identification M protein among the three methods. The second was serum protein electrophoresis and the lowest was the urine Bence Jones proteins (P < 0.01). Conclusion The technology of IFE, characterized by easy differentiation of electrophoretic bands,simple operation, high sensitivity and rapidity ,has great value in typing M proteins.%目的 探讨免疫固定电泳技术在鉴定M蛋白上的应用.方法 采用血清蛋白电泳技术、血清免疫固定技术(IFE)检测107例MM患者血清M蛋白.结果 107例MM患者中97例血清蛋白电泳检出M蛋白,107例免疫固定电泳均检出M蛋白.M蛋白IFE分型结果为IgG型63例,其中IgG κ型29例,IgG λ型34例;IgA型25例,其中IgA κ型11例,IgA λ型14例;IgM型3例,其中IgM κ型1例,IgM λ型2例;单纯轻链型15例,其中κ型2例,λ型13例.60例MM患者中有39例检出尿本-周氏蛋白,其中,12例为κ型,27例为λ型.三种方法中血清免疫固定电泳的检出率最高,血清蛋白电泳次之,尿液本周氏蛋白电泳检出率最低(P<0.01).结论 采用免疫固定电泳技术,操作简单、快速,灵敏度高,沉淀带容易识别,是鉴定各类型M蛋白的较准确、直观的有效方法.

  18. Update on diagnosis of acute rheumatic fever: 2015 Jones criteria.

    Science.gov (United States)

    Eroğlu, Ayşe Güler

    2016-03-01

    In the final Jones criteria, different diagnostic criteria were established for the diagnosis of acute rheumatic fever for low risk and moderate-high risk populations. Turkey was found to be compatible with moderate-high risk populations as a result of regional screenings performed in terms of acute rheumatic fever and rheumatic heart disease. The changes in the diagnostic criteria for low-risk populations include subclinical carditis found on echocardiogram as a major criterion in addition to carditis found clinically and a body temperature of 38.5°C and above as a minor criterion. In moderate-high risk populations including Turkey, subclinical carditis found on echocardiogram in addition to clinical carditis is used as a major criterion as a new amendment. In addition, aseptic monoarthritis and polyarthralgia are used as major criteria in addition to migratory arthritis and monoarhtralgia is used as a minor criterion among joint findings. However, differentiation of subclinical carditis from physiological valve regurgitation found in healthy individuals and exclusion of other diseases involving joints when aseptic monoarthritis and polyarthralgia are used as major criteria are very important. In addition, a body temperature of 38°C and above and an erythrocyte sedimentation rate of 30 mm/h and above have been accepted as minor criteria. The diagnostic criteria for the first attack have not been changed; three minor findings have been accepted in presence of previous sterptococcal infection in addition to the old cirteria for recurrent attacks. In the final Jones criteria, it has been recommended that patients who do not fully meet the diagnostic criteria of acute rheumatic fever should be treated as acute rheumatic fever if another diagnosis is not considered and should be followed up with benzathine penicilin prophylaxis for 12 months. It has been decided that these patients be evaluated 12 months later and a decision for continuation or discontinuation of

  19. Zeros of the Jones Polynomial for Torus Knots and 2-bridge Knots

    Institute of Scientific and Technical Information of China (English)

    HAN You-fa; ZHANG Rong-wei; WANG Lin-lin; MA Xiao-sha

    2014-01-01

    We study zeros of the Jones polynomial and their distributions for torus knots and 2-bridge knots. We prove that e(2m+1)πi/2 and e(2m+1)πi/4(m is a positive integer) can not be the zeros of Jones polynomial for torus knots Tp,q by the knowledge of the trigonometric function. We elicit the normal form of Jones polynomials of the 2-bridge knot C (−2, 2, · · · , (−1)r 2) by the recursive form and discuss the distribution of their zeros.

  20. Jones index, secret sharing and total quantum dimension

    Science.gov (United States)

    Fiedler, Leander; Naaijkens, Pieter; Osborne, Tobias J.

    2017-02-01

    We study the total quantum dimension in the thermodynamic limit of topologically ordered systems. In particular, using the anyons (or superselection sectors) of such models, we define a secret sharing scheme, storing information invisible to a malicious party, and argue that the total quantum dimension quantifies how well we can perform this task. We then argue that this can be made mathematically rigorous using the index theory of subfactors, originally due to Jones and later extended by Kosaki and Longo. This theory provides us with a ‘relative entropy’ of two von Neumann algebras and a quantum channel, and we argue how these can be used to quantify how much classical information two parties can hide form an adversary. We also review the total quantum dimension in finite systems, in particular how it relates to topological entanglement entropy. It is known that the latter also has an interpretation in terms of secret sharing schemes, although this is shown by completely different methods from ours. Our work provides a different and independent take on this, which at the same time is completely mathematically rigorous. This complementary point of view might be beneficial, for example, when studying the stability of the total quantum dimension when the system is perturbed.

  1. Magic Numbers for Classical Lennard-Jones Cluster Heat Capacities

    CERN Document Server

    Frantz, D D

    1994-01-01

    Heat capacity curves as functions of temperature for classical atomic clusters bound by pairwise Lennard-Jones potentials were calculated for aggregate sizes from 4 to 24 using Monte Carlo methods. J-walking (or jump-walking) was used to overcome convergence difficulties due to quasi-ergodicity in the solid-liquid transition region. The heat capacity curves were found to differ markedly and nonmonotonically as functions of cluster size. Curves for N = 4, 5 and 8 consisted of a smooth, featureless, monotonic increase throughout the transition region, while curves for N = 7 and 15-17 showed a distinct shoulder in this region; the remaining clusters had distinguishable transition heat capacity peaks. The size and location of these peaks exhibited "magic number" behavior, with the most pronounced peaks occurring for magic number sizes of N = 13, 19 and 23. A comparison of the heat capacities with other cluster properties in the solid-liquid transition region that have been reported in the literature indicates par...

  2. Contact angle of sessile drops in Lennard-Jones systems.

    Science.gov (United States)

    Becker, Stefan; Urbassek, Herbert M; Horsch, Martin; Hasse, Hans

    2014-11-18

    Molecular dynamics simulations are used for studying the contact angle of nanoscale sessile drops on a planar solid wall in a system interacting via the truncated and shifted Lennard-Jones potential. The entire range between total wetting and dewetting is investigated by varying the solid-fluid dispersive interaction energy. The temperature is varied between the triple point and the critical temperature. A correlation is obtained for the contact angle in dependence of the temperature and the dispersive interaction energy. Size effects are studied by varying the number of fluid particles at otherwise constant conditions, using up to 150,000 particles. For particle numbers below 10,000, a decrease of the contact angle is found. This is attributed to a dependence of the solid-liquid surface tension on the droplet size. A convergence to a constant contact angle is observed for larger system sizes. The influence of the wall model is studied by varying the density of the wall. The effective solid-fluid dispersive interaction energy at a contact angle of θ = 90° is found to be independent of temperature and to decrease linearly with the solid density. A correlation is developed that describes the contact angle as a function of the dispersive interaction, the temperature, and the solid density. The density profile of the sessile drop and the surrounding vapor phase is described by a correlation combining a sigmoidal function and an oscillation term.

  3. The Grande Dame of Afro-American Art: Lois Mailou Jones.

    Science.gov (United States)

    LaDuke, Betty

    1987-01-01

    Chronicles the personal and professional life of Lois Mailou Jones, a Black woman painter who blends Western and non-Western aesthetic traditions in her art. The influences of Haitian and African native traditions on her work are discussed. (BJV)

  4. Rogers-Ramanujan type identities and the head and tail of the colored Jones polynomial

    CERN Document Server

    Armond, Cody

    2011-01-01

    We study the head and tail of the colored Jones polynomial while focusing mainly on alternating links. Various ways to compute the colored Jones polynomial for a given link give rise to combinatorial identities for those power series. We further show that the head and tail functions only depend on the reduced checkerboard graphs of the knot diagram. Moreover the class of head and tail functions of prime alternating links forms a monoid.

  5. Viola-Jones based hybrid framework for real-time object detection in multispectral images

    Science.gov (United States)

    Kuznetsova, E.; Shvets, E.; Nikolaev, D.

    2015-12-01

    This paper describes a method for real-time object detection based on a hybrid of a Viola-Jones cascade with a convolutional neural network. This scheme allows flexible trade-offs between detection quality and computational performance. We also propose a generalization of this method to multispectral images that effectively and efficiently utilizes information from each spectral channel. The new scheme is experimentally compared to traditional Viola-Jones, showing improved detection quality with adjustable performance.

  6. Analysis of the Field of Public Management: A Response to Kelman, Thompson, Jones, and Schedler

    OpenAIRE

    Candreva, Philip J.

    2004-01-01

    This essay examines the field of public management as explicated in the dialogue between Kelman, Thompson, Jones and Schedler (2003) and others, from the perspective of the philosophy of science. While there may be wide consensus that a substantial body of information about public management exists, Kelman, Thompson, Jones and Schedler are consistent in their view that empirical generalizations and underlying principles do not exist. This assertion notwithstanding, this essay d...

  7. Scaling of the dynamics of flexible Lennard-Jones chains.

    Science.gov (United States)

    Veldhorst, Arno A; Dyre, Jeppe C; Schrøder, Thomas B

    2014-08-07

    The isomorph theory provides an explanation for the so-called power law density scaling which has been observed in many molecular and polymeric glass formers, both experimentally and in simulations. Power law density scaling (relaxation times and transport coefficients being functions of ρ(γ(S)), where ρ is density, T is temperature, and γ(S) is a material specific scaling exponent) is an approximation to a more general scaling predicted by the isomorph theory. Furthermore, the isomorph theory provides an explanation for Rosenfeld scaling (relaxation times and transport coefficients being functions of excess entropy) which has been observed in simulations of both molecular and polymeric systems. Doing molecular dynamics simulations of flexible Lennard-Jones chains (LJC) with rigid bonds, we here provide the first detailed test of the isomorph theory applied to flexible chain molecules. We confirm the existence of isomorphs, which are curves in the phase diagram along which the dynamics is invariant in the appropriate reduced units. This holds not only for the relaxation times but also for the full time dependence of the dynamics, including chain specific dynamics such as the end-to-end vector autocorrelation function and the relaxation of the Rouse modes. As predicted by the isomorph theory, jumps between different state points on the same isomorph happen instantaneously without any slow relaxation. Since the LJC is a simple coarse-grained model for alkanes and polymers, our results provide a possible explanation for why power-law density scaling is observed experimentally in alkanes and many polymeric systems. The theory provides an independent method of determining the scaling exponent, which is usually treated as an empirical scaling parameter.

  8. Evaluation of anxiolytic activity of compound Valeriana jatamansi Jones in mice

    Directory of Open Access Journals (Sweden)

    You Jie-Shu

    2012-11-01

    Full Text Available Abstract Background Compound Valeriana jatamansi Jones is a formula for treating anxiety-related diseases in the clinic, which is composed of Valeriana jatamansi Rhizoma et Radix, Ziziphi Spinosae Semen, Albiziae Cortex and Junci Medulla. The purpose of this study was to explore the anxiolytic properties of this compound in mice. Methods Male ICR mice were treated with compound Valerianae Jatamansi Jones (1.2 g/kg, 2.4 g/kg, 4.8 g/kg, saline, diazepam (2 mg/kg orally for 10 days and then exposed to elevated maze-plus (EPM and light–dark box (LDB. The effects of the compound on spontaneous activity were evaluated by locomotor activity test. We further investigated the mechanism of action underlying the anxiolytic-like effect of compound by pre-treating animals with antagonists of benzodiazepine (flumazenil, 3mg/kg prior to evaluation using EPM and LDB. Results Compound Valerianae Jatamansi Jones (2.4, 4.8 g/kg, p.o. significantly increased entries (PPPPP>0.05. In addition, compound Valerianae Jatamansi Jones treatment didn’t affect the spontaneous activity in mice (P> 0.05. Conclusions The present study supports the hypothesis that compound Valeriana jatamansi Jones exert anxiolytic action but no sedative effects in mice and that this effect might be mediated by benzodiazepine receptors.

  9. The Jones polynomial: quantum algorithms and applications in quantum complexity theory

    CERN Document Server

    Yard, J; Yard, Jon; Wocjan, Pawel

    2006-01-01

    We analyze relationships between the Jones polynomial and quantum computation. Our first result is a polynomial-time quantum algorithm which gives an additive approximation of the Jones polynomial, in the sense of Bordewich, Freedman, Lovasz and Welsh, of any link obtained from a certain general family of closures of braids, evaluated at any primitive root of unity. This family encompasses the well-known plat and trace closures, generalizing results recently obtained by Aharonov, Jones and Landau. We base our algorithm on a local qubit implementation of the unitary Jones-Wenzl representations of the braid group which makes the underlying representation theory apparent, allowing us to provide an algorithm for approximating the HOMFLYPT two-variable polynomial of the trace closure of a braid at certain pairs of values as well. Next, we provide a self-contained proof that any quantum computation can be replaced by an additive approximation of the Jones polynomial, evaluated at almost any primitive root of unity....

  10. LCD panel characterization by measuring full Jones matrix of individual pixels using polarization-sensitive digital holographic microscopy.

    Science.gov (United States)

    Park, Jongchan; Yu, Hyeonseung; Park, Jung-Hoon; Park, YongKeun

    2014-10-06

    We present measurements of the full Jones matrix of individual pixels in a liquid-crystal display (LCD) panel. Employing a polarization-sensitive digital holographic microscopy based on Mach-Zehnder interferometry, the complex amplitudes of the light passing through individual LCD pixels are precisely measured with respect to orthogonal bases of polarization states, from which the full Jones matrix components of individual pixels are obtained. We also measure the changes in the Jones matrix of individual LCD pixels with respect to an applied bias. In addition, the complex optical responses of a LCD panel with respect to arbitrary polarization states of incident light were characterized from the measured Jones matrix.

  11. Phase diagram of power law and Lennard-Jones systems: Crystal phases

    Energy Technology Data Exchange (ETDEWEB)

    Travesset, Alex [Ames Laboratory

    2014-10-28

    An extensive characterization of the low temperature phase diagram of particles interacting with power law or Lennard-Jones potentials is provided from Lattice Dynamical Theory. For power law systems, only two lattice structures are stable for certain values of the exponent (or softness) (A15, body centered cube (bcc)) and two more (face centered cubic (fcc), hexagonal close packed (hcp)) are always stable. Among them, only the fcc and bcc are equilibrium states. For Lennard-Jones systems, the equilibrium states are either hcp or fcc, with a coexistence curve in pressure and temperature that shows reentrant behavior. The hcp solid never coexists with the liquid. In all cases analyzed, for both power law and Lennard-Jones potentials, the fcc crystal has higher entropy than the hcp. The role of anharmonic terms is thoroughly analyzed and a general thermodynamic integration to account for them is proposed.

  12. The SL_3 Jones polynomial of the trefoil: a case study of $q$-holonomic recursions

    CERN Document Server

    Garoufalidis, Stavros

    2010-01-01

    The SL_3 colored Jones polynomial of the trefoil knot is a $q$-holonomic sequence of two variables with natural origin, namely quantum topology. The paper presents an explicit set of generators for the annihilator ideal of this $q$-holonomic sequence as a case study. On the one hand, our results are new and useful to quantum topology: this is the first example of a rank 2 Lie algebra computation concerning the colored Jones polynomial of a knot. On the other hand, this work illustrates the applicability and computational power of the employed computer algebra methods.

  13. Dynamic Loading Assessment at the Fifth Metatarsal in Elite Athletes with a history of Jones Fracture

    Science.gov (United States)

    Hunt, Kenneth; Goeb, Yannick

    2016-01-01

    Objectives: Fractures of the proximal metaphysis of the fifth metatarsal (i.e., Jones fractures) are common in the athletic population and frequently require surgical fixation to optimize healing rates and return to sport. Subtle hindfoot varus alignment, which likely results in greater forces at the fifth metatarsal, has been associated with increased risk of Jones fractures due to presumed increase in forces on the lateral foot. The goal of the present study was to dynamically assess plantar pressure loads at the fifth metatarsal in elite athletes with a history of Jones fracture. We hypothesize that athletes who have suffered Jones fractures will apply significantly higher loads at the fifth metatarsal base during athletic activities compared to matched uninjured athletes. Methods: Sixteen elite, competitive athletes were recruited to participate. Eight athletes had a history of Jones fracture and eight age, gender and position-matched athletes without a history of foot injury were recruited as controls. While wearing calibrated, wireless pressure mapping insoles, all athletes performed a standardized series of athletic movements including walking, running and cutting. Tests were repeated with the patient’s standard corrective insole. Peak pressure, mean pressure, maximum force, and force-time integral (i.e., impulse) were recorded for each activity. Comparison between groups was performed using a paired Wilcoxon Sign Rank test. Results: Athletes with a history of Jones fracture showed a significantly increased peak pressure (183 ±23 kPA vs. 138±7 kPA), mean pressure (124±14 kPA vs. 95±4 kPA), and maximum force (15±1.2%BW vs. 12±1.2%BW) at the fifth metatarsal base during walking and running compared to uninjured matched controls (all Pinsole did not significantly reduce peak or mean pressure, maximum force, or impulse at the fifth metatarsal base during running or cutting. Conclusion: Athletes with a history of Jones fracture exert significantly

  14. 1919: psychology and psychoanalysis, Cambridge and London - Myers, Jones and MacCurdy.

    Science.gov (United States)

    Forrester, John

    2008-01-01

    Viewing the reception of psychoanalysis in Britain from Cambridge, the paper examines the intertwining histories of the post-War British Psychological Society and the founding of the British Psycho-Analytical Society, following the initiatives of the two principal psychological entrepreneurs of the era, Charles Myers and Ernest Jones, Reforms in Cambridge in which psychoanalysis played a significant part are analysed, including the foundation of a Clinic for Nervous Diseases and the establishment of a separate Department of Experimental Psychology. The career of J. T. MacCurdy, Jones's student and Lecturer in Psychopathology at Cambridge, is discussed.

  15. Gingival Enlargement in a Case of Variant Jones Syndrome: a Case Report

    Directory of Open Access Journals (Sweden)

    Roopa DA

    2016-03-01

    Full Text Available Gingival enlargement can be caused by a variety of etiological factors like inflammation, drugs, and systemic diseases or can be presented as a part of a syndrome. One such syndrome is Jones Syndrome, which is associated with gingival enlargement and progressive hearing loss. We present here a case of fifteen-year-old boy with gingival enlargement, hearing loss, and generalized alveolar bone loss and diagnosed as Jones syndrome. The diagnosis was made based on history, clinical, radiographic, and histopathological findings. Gingival enlargement was surgically managed using gingivectomy and no recurrence was observed. The patient showed remarkable esthetical and functional improvement.

  16. Gingival Enlargement in a Case of Variant Jones Syndrome: a Case Report

    Science.gov (United States)

    DA, Roopa; Singh, Shinkhala; Gupta, Ira; Gopal, Saumiya

    2016-01-01

    Gingival enlargement can be caused by a variety of etiological factors like inflammation, drugs, and systemic diseases or can be presented as a part of a syndrome. One such syndrome is Jones Syndrome, which is associated with gingival enlargement and progressive hearing loss. We present here a case of fifteen-year-old boy with gingival enlargement, hearing loss, and generalized alveolar bone loss and diagnosed as Jones syndrome. The diagnosis was made based on history, clinical, radiographic, and histopathological findings. Gingival enlargement was surgically managed using gingivectomy and no recurrence was observed. The patient showed remarkable esthetical and functional improvement. PMID:26966711

  17. PHYTOREMEDIATION OF DREDGED SEDIMENTS: A CASE STUDY AT THE JONES ISLAND CDF

    Science.gov (United States)

    The Jones Island Confined Disposal Facility (CDF) is a 44 acre in-lake area that receives dredged material from Milwaukee Harbor and the surrounding waterways. Some of those materials are contaminated with industrial waste and urban run-off. The CDF is nearing the end of its desi...

  18. Enhancing Undergraduates' Capabilities through Team-Based Competitions: The Edward Jones Challenge

    Science.gov (United States)

    Umble, Elisabeth J.; Umble, Michael; Artz, Kendall

    2008-01-01

    The Edward Jones Company recently initiated financial sponsorship of team-based competitions in six undergraduate business core classes at Baylor University. The challenges were chosen to take place in an introductory freshman business class, Managerial Accounting, Principles of Marketing, Corporate Finance, Operations Management, and Strategic…

  19. Fusion process of Lennard-Jones clusters: global minima and magic numbers formation

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Solov'yov, Andrey V.; Greiner, Walter

    2004-01-01

    We present a new theoretical framework for modeling the fusion process of Lennard–Jones (LJ) clusters. Starting from the initial tetrahedral cluster configuration, adding new atoms to the system and absorbing its energy at each step, we find cluster growing paths up to the cluster size of 150 atoms...

  20. Thermodynamic Perturbation Theory for Solid-Liquid Phase Transition of Lennard-Jones Model

    Institute of Scientific and Technical Information of China (English)

    ZHOUShi-Qi; ZHANGXiao-Qi

    2004-01-01

    Both a free volume approach for Helmholtz free energy and a theoretically-based fitted formula for radial distribution function (rdf) of hard sphere solid are employed to describe the Helmholtz free energy of Lennard-Jones solid in the framework of the first order thermodynamic perturbation theory, which also is employed for the uniform Lennard Jones fluid. The dividing of the Lennard-Jones potential follows from the INCA prescription, but the specification of the equivalent hard sphere diameter is determined by a simple iteration procedure devised originally for liquid state, but extended to solid state in the present study. Two hundred shells are used in the rdf to get an accurate perturbation term.The present approach is very accurate for the description of excess Helmholtz free energy of LJ solid, but shows some deviation from the simulation for excess Helmholtz free energy of uniform LJ fluid when the reduced temperature kT/ε is higher then 5. The present approach is satisfactory for description of solid-liquid phase transition of the Lennard-Jones model.

  1. Thermodynamic Perturbation Theory for Solid-Liquid Phase Transition of Lennard-Jones Model

    Institute of Scientific and Technical Information of China (English)

    ZHOU Shi-Qi; ZHANG Xiao-Qi

    2004-01-01

    Both a free volume approach for Helmholtz free energy and a theoretically-based fitted formula for radial distribution function (rdf) of hard sphere solid are employed to describe the Helmholtz free energy of Lennard-Jones solid in the framework of the first order thermodynamic perturbation theory, which also is employed for the uniform LennardJones fluid. The dividing of the Lennard-Jones potential follows from the WCA prescription, but the specification of the equivalent hard sphere diameter is determined by a simple iteration procedure devised originally for liquid state, but extended to solid state in the present study. Two hundred sheiks are used in the rdf to get an accurate perturbation term.The present approach is very accurate for the description of excess Helmholtz free energy of LJ solid, but shows some deviation from the simulation for excess Helmholtz free energy of uniform LJ fluid when the reduced temperature kT/ε is higher then 5. The present approach is satisfactory for description of solid-liquid phase transition of the Lennard-Jones model.

  2. Käsitsi tegemise võlu / David Jones ; intervjueerinud Kai Lobjakas

    Index Scriptorium Estoniae

    Jones, David, 1953-

    2010-01-01

    10. Kohila keraamikasümpoosionil osalenud briti keraamik ja teoreetik David Jones endast, rakutehnikast, huvist põletamisega seonduvate teemade vastu, Kohila sümpoosioni raames tehtust, keraamika õpetamisest Inglismaal, käsitöö ja keraamika positsioonist praegu ja tulevikus jm.

  3. Freezing and melting equations for the n-6 Lennard-Jones systems

    Directory of Open Access Journals (Sweden)

    Sergey A. Khrapak

    2016-05-01

    Full Text Available We generalize previous approach of Khrapak and Morfill [J. Chem. Phys. 134, 094108 (2011] to construct simple and sufficiently accurate freezing and melting equations for the conventional Lennard-Jones (LJ system to n-6 LJ systems, using the accurate results for the triple points of these systems published by Sousa et al. [J. Chem. Phys. 136, 174502 (2012].

  4. Creative Imagination and Subjective Agency in Wynne-Jones' "The Maestro"

    Science.gov (United States)

    Cairns, Sue Ann

    2009-01-01

    The Canadian young adult novel "The Maestro" by Tim Wynne-Jones foregrounds the relationship between imagination and subjective agency. While Burl uses his imagination at the beginning to protect himself from his abusive father, his fantasies become dress rehearsals for small performances that allow him to try on new identities and exercise…

  5. Fairy tales? Marion Jones, C.J. Hunter and the framing of doping in American newspapers

    DEFF Research Database (Denmark)

    Pfister, Gertrud Ursula; Gems, Gerald

    2015-01-01

    under suspicion. At the same time, the 2000 Olympics can be considered a watershed in American anti-doping policy. The media portrayed Jones and Hunter as the Beauty and the Beast or Svengali and his victim, using a famous fairy tale and a well-known novel to capture attention, label the protagonists...

  6. "Armastuse retsepti" tippkokk Zeta Jones ei oska muna keeta / Triin Tael

    Index Scriptorium Estoniae

    Tael, Triin

    2007-01-01

    Scott Hicksi romantiline komöödiafilm "Armastuse retsept" ("No Reservations"), mille peaosas Walesist pärit näitlejanna Catherine Zeta Jones. Näitlejanna muljeid oma rolliks ettevalmistustest, mille hulka käis ka praktika pärisrestoranis

  7. The Representation of Latinos and the Use of Spanish: A Critical Content Analysis of "Skippyjon Jones"

    Science.gov (United States)

    Martínez-Roldan, Carmen M.

    2013-01-01

    This study illustrates the presence of Mock Spanish in some English-based picture books and the ways this usage misrepresents Latino people, language, and culture. The author conducted a critical content analysis of five Skippyjon Jones books. Her guiding question was, How is language used, particularly Spanish, in these English texts, and what…

  8. Malaria and the Decline of Ancient Greece: Revisiting the Jones Hypothesis in an Era of Interdisciplinarity

    Science.gov (United States)

    Baron, Christopher; Hamlin, Christopher

    2015-01-01

    Between 1906 and 1909 the biologist Ronald Ross and the classicist W.H.S. Jones pioneered interdisciplinary research in biology and history in advancing the claim that malaria had been crucial in the decline of golden-age Greece (fourth century BCE). The idea had originated with Ross, winner of the Nobel Prize for demonstrating the importance of…

  9. Machine News and Volatility: The Dow Jones Industrial Average and the TRNA Sentiment Series

    NARCIS (Netherlands)

    D.E. Allen (David); A.K. Singh (Abhay)

    2014-01-01

    markdownabstract__Abstract__ This paper features an analysis of the relationship between the volatility of the Dow Jones Industrial Average (DJIA) Index and a sentiment news series using daily data obtained from the Thomson Reuters News Analytics (TRNA) provided by SIRCA (The Securities Industry Re

  10. Can the Lennard-Jones solid be expected to be fcc?

    NARCIS (Netherlands)

    Waal, van de Benjamin W.

    1991-01-01

    The structure of the Lennard-Jones solid, obtained by molecular-dynamics simulation of crystallization in the supercooled liquid, may be fcc, although the hcp structure is energetically more favorable. This could derive from the cubic symmetry of the fcc lattice, allowing lattice defects that are no

  11. Widom line for the liquid-gas transition in Lennard-Jones system.

    Science.gov (United States)

    Brazhkin, V V; Fomin, Yu D; Lyapin, A G; Ryzhov, V N; Tsiok, E N

    2011-12-08

    The locus of extrema (ridges) for heat capacity, thermal expansion coefficient, compressibility, and density fluctuations for model particle systems with Lennard-Jones (LJ) potential in the supercritical region have been obtained. It was found that the ridges for different thermodynamic values virtually merge into a single Widom line at T Widom line for a liquid-gas transition.

  12. Long range correction for multi-site Lennard-Jones models and planar interfaces

    CERN Document Server

    Werth, Stephan; Horsch, Martin; Vrabec, Jadran; Hasse, Hans

    2015-01-01

    A slab based long range correction approach for multi-site Lennard-Jones models is presented for systems with a planar film geometry that is based on the work by Janecek, J. Phys. Chem. B 110: 6264 (2006). It is efficient because it relies on a center-of-mass cutoff scheme and scales in terms of numerics almost perfectly with the molecule number. For validation, a series of simulations with the two-center Lennard-Jones model fluid, carbon dioxide and cyclohexane is carried out. The results of the present approach, a site-based long range correction and simulations without any long range correction are compared with respect to the saturated liquid density and the surface tension. The present simulation results exhibit only a weak dependence on the cutoff radius, indicating a high accuracy of the implemented long range correction.

  13. Volatility Transmission between Dow Jones Stock Index and Emerging Bond Index

    Directory of Open Access Journals (Sweden)

    Amir Saadaoui

    2016-04-01

    Full Text Available In this paper, we use a bivariate GARCH model to estimate simultaneously of the mean and the conditional variance between the Dow Jones stock index and some emerging bond indices. We used the DCC-GARCH model to graphically demonstrate the peaks of the volatility transmission. We examined this transmission using daily returns between July, 30, 2009 and January, 18, 2011 extracted from Datastream. Our results demonstrate that there is a significant transmission of shocks and volatility between the Dow Jones stock index and bond indices of the emerging countries. The results also confirm the idea that the crisis was transmitted from the United States to the emerging countries due to foreign investment made in these countries.

  14. Curvature Dependence of Interfacial Properties for Associating Lennard-Jones Fluids: A Density Functional Study

    Institute of Scientific and Technical Information of China (English)

    SUN Zong-Li; KANG Yan-Shuang

    2011-01-01

    Classical density functional theory is used to study the associating Lennard Jones fluids in contact with spherical hard wall of different curvature radii. The interfacial properties including contact density and fluid-solid interfacial tension are investigated. The influences of associating energy, curvature of hard wall and the bulk density of Huids on these properties are analyzed in detail. The results may provide helpful clues to understand the interfacial properties of other complex fluids.%@@ Classical density functional theory is used to study the associating Lennard Jones fluids in contact with spherical hard wall of different curvature radii.The interfacial properties including contact density and fluid-solid intcrfacial tension are investigated.The influences of associating energy, curvature of hard wall and the hulk density of fluids on these properties are analyzed in detail.The results may provide helpful clues to understand the interfacial properties of other complex fluids.

  15. Is the third coefficient of the Jones knot polynomial a quantum state of gravity?

    CERN Document Server

    Griego, J R

    1996-01-01

    Some time ago it was conjectured that the coefficients of an expansion of the Jones polynomial in terms of the cosmological constant could provide an infinite string of knot invariants that are solutions of the vacuum Hamiltonian constraint of quantum gravity in the loop representation. Here we discuss the status of this conjecture at third order in the cosmological constant. The calculation is performed in the extended loop representation, a generalization of the loop representation. It is shown that the the Hamiltonian does not annihilate the third coefficient of the Jones polynomal (J_3) for general extended loops. For ordinary loops the result acquires an interesting geometrical meaning and new possibilities appear for J_3 to represent a quantum state of gravity.

  16. PENDETEKSIAN BAGIAN TUBUH MANUSIA UNTUK FILTER PORNOGRAFI DENGAN METODE VIOLA-JONES

    Directory of Open Access Journals (Sweden)

    Benny Senjaya

    2012-05-01

    application. First, several parts of the human body are chosen to be detected as the data training using the Viola-Jones method. Then, another set of images (similar body parts but different images are run through the application to be recognized. The result shows 86.25% of successful detection. The failures are identified and show that the inputted data are completely different with the data training.

  17. A Fractional Characteristic Study of Liquid and Vapor Interface in Lennard—Jones Fluids

    Institute of Scientific and Technical Information of China (English)

    LIUChao; ZENGDanling

    2002-01-01

    The molecular dynamic simulation results for the liquid-vapor interface of the pure Lennard-Jones fluid are presented.The thermodynamic properties,the surface tension and the effective thickness of interfacial layer are determined.The rough characteristic of the liquid-vapor interface is discussed with fractional Brownian motion theory.Thereupon the fractal dimension d of the liqud-vapor interface is obtained.

  18. A Lennard-Jones embedded-atom potential and its application to the study of melting

    Institute of Scientific and Technical Information of China (English)

    王暾; 周富信; 刘曰武

    2002-01-01

    The nearest-neighbour Lennard-Jones potential from the embedded-atom method is extended to a form thatincludes more than nearest neighbours. The model has been applied to study melting with molecular dynamics. Thecalculated melting point, fractional volume change on melting, heat of fusion and linear coefficients of thermal expansionare in good agreement with experimental data. We have found that the second and third neighbours influence the meltingpoint distinctly.

  19. Disrupted Expectations: Young/Old Protagonists in Diana Wynne Jones's Novels

    OpenAIRE

    Kaplan, Deborah

    2010-01-01

    The works of Diana Wynne Jones consistently break genre expectations regarding the age of the protagonists and a secondary characters. Some texts, such as Dark Lord of Derkholm with its cross-generational heroes, violate the genre's expected relationship between the age of the implied reader and that the protagonists. In other other texts, including Hexwood, the protagonist's true age is hidden from everyone, including the protagonist himself. These two texts aren't unusual in a body of work ...

  20. Shortcomings of the standard Lennard-Jones dispersion term in water models, studied with force matching

    OpenAIRE

    Nicolini, Paolo; Guàrdia Manuel, Elvira; Masia, Marco

    2013-01-01

    In this work, ab initio parametrization of water force field is used to get insights into the functional form of empirical potentials to properly model the physics underlying dispersion interactions. We exploited the force matching algorithm to fit the interaction forces obtained with dispersion corrected density functional theory based molecular dynamics simulations. We found that the standard Lennard-Jones interaction potentials poorly reproduce the attractive character of dispersion forces...

  1. Baby Boy Jones Interactive Case-Based Learning Activity: A Web-Delivered Teaching Strategy.

    Science.gov (United States)

    Cleveland, Lisa M; Carmona, Elenice Valentim; Paper, Bruce; Solis, Linda; Taylor, Bonnie

    2015-01-01

    Faced with limited resources, nurse educators are challenged with transforming nursing education while preparing enough qualified nurses to meet future demand; therefore, innovative approaches to teaching are needed. In this article, we describe the development of an innovative teaching activity. Baby Boy Jones is a Web-delivered, case-based learning activity focused on neonatal infection. It was created using e-learning authoring software and delivered through a learning management system.

  2. The path ahead for MD/PhD programs in Canada Commentary on Jones et al.

    Science.gov (United States)

    Rosenblum, Norman D

    2016-09-11

    The paper by Jones and colleagues, published in this edition of Clinical Investigative Medicine, contributes to our understanding of Canadian MD/PhD Programs. While there has been little published on this subject by the Canadian programs, themselves, this paper is the most recent in a series by leaders of the Clinical Investigator Trainee Association of Canada (CITAC). The authors are to be commended for their efforts and productivity.

  3. Can the Lennard-Jones solid be expected to be fcc?

    OpenAIRE

    Waal, de, SAJ Bas

    1991-01-01

    The structure of the Lennard-Jones solid, obtained by molecular-dynamics simulation of crystallization in the supercooled liquid, may be fcc, although the hcp structure is energetically more favorable. This could derive from the cubic symmetry of the fcc lattice, allowing lattice defects that are not possible in the hcp arrangement, but are essential to crystal growth in the simulated liquid. Two crossing stacking faults in a small fcc crystallite can produce nonvanishing, growth-promoting, b...

  4. Mutability and Deformity: Models of the Body and the Art of Edward Burne-Jones

    Directory of Open Access Journals (Sweden)

    Caroline Arscott

    2008-10-01

    Full Text Available This essay discusses the alternatives that emerged in the Victorian period to a perfect and regular neoclassical conception of the heroic male body. It charts the evolving fascination with mutable forms, whether heroic or monstrous, imagined first of all in the 1850s in terms of a body conceived of as bolted together or modified by the fusion of organic and inorganic substances. The early work of Burne-Jones is discussed in relation to investigations of cell structure and mechanical inventions in the Great Exhibition of 1851 such as the 'Expanding Model of a Man' invented by Count Dunin. Arscott also discusses the cybernetic implications of Burne-Jones's gouache, 'The Merciful Knight' (1863. Later works of Burne-Jones, in particular 'Perseus and the Graiae' (1878 and the reworked composition 'Love Among the Ruins' (1894, are discussed in terms of a turn towards a sense of the spread and mutation of organic being through and beyond the self. Arscott considers this alongside contemporary investigations of the role of bacilli in disease, looking at leprosy and the heroisation of the Leper Priest of Molokai, Father Damien in the 1880s and 1890s. In the late-Victorian period, Arscott concludes, monstrous distortion was imagined as the unpredictable and unruly proliferation of the organic by the organism in both its vital and morbid states.

  5. Mainekas teadlane soovitab Eestil enam väliskapitali ligi meelitada / Simon Jones ; interv. Aleksei Günter

    Index Scriptorium Estoniae

    Jones, Simon

    2005-01-01

    Pärnus telekommunikatsiooni- ja infofoorumil viibiv innovatsiooniekspert vastab küsimustele, mis puudutavad tema hinnangut Eesti teadus- ja arendustegevusele, tehnoloogia kasutamist sotsiaalprobleemide lahendamisel ning Eesti varustamist tasuta internetiühendusega. Lisa: Simon Jones

  6. Characterization, expression and function analysis of DAX1 gene of scallop ( Chlamys farreri jones and preston 1904) during its gametogenesis

    Science.gov (United States)

    Li, Hailong; Liu, Jianguo; Huang, Xiaoting; Wang, Dan; Zhang, Zhifeng

    2014-08-01

    DAX1, a member of nuclear receptor superfamily, has a function in the sex determination and gonadal differentiation of several vertebrate species. However, little information about DAX1 of invertebrates is available. Here we cloned a homolog of scallop ( Chlamys farreri Jones and Preston 1904) dax1, Cf-dax1, and determined its expression characteristics at mRNA and protein levels. The cDNA sequence of Cf-dax1 was 2093 bp in length, including 1404 bp open reading frame (ORF) encoding 467 amino acids. Unlike those of vertebrates, no conserved LXXLL-related motif was found in the putative DNA binding region of Cf-DAX1. Fluorescence in situ hybridization showed that Cf-dax1 located on the short arm of a pair of subtelocentric chromosomes. Tissue distribution analysis using semi-quantitative RT-PCR revealed that Cf-dax1 expressed widely in adult scallop tissues, with the highest expression level found in adductor muscle, moderate level in mantle, gill and testis, and low level in kidney, ovary and hepatopancreas. The result of quantitative real-time PCR indicated that the expression of Cf-dax1 was significantly higher ( Psex-dimorphic expression pattern. Furthermore, immunohistochemical detection found that Cf-DAX1 mainly located in spermatogonia and spermatocytes of testis and in oogonia and oocytes of ovary, implying that DAX1 may involve in gametogenesis of bivalves.

  7. Protein

    Science.gov (United States)

    ... Food Service Resources Additional Resources About FAQ Contact Protein Protein is found throughout the body—in muscle, ... the heart and respiratory system, and death. All Protein Isn’t Alike Protein is built from building ...

  8. A Hybrid LBFGS-DE Algorithm for Global Optimization of the Lennard-Jones Cluster Problem

    Directory of Open Access Journals (Sweden)

    Ernesto Padernal Adorio

    2004-12-01

    Full Text Available The Lennard-Jones cluster conformation problem is to determine a configuration of n atoms in three-dimensional space where the sum of the nonlinear pairwise potential function is at a minimum. In this formula, ri,j is the distance between atoms i and j. This optimization problem is a severe test for global optimization algorithms due to its computational complexity: the number of local minima grows exponentially large as the number of atoms in the cluster is increased. As a specific test case, a better cluster configuration than the previously published putative minimum for the 38-atom case was found in the mid-1990s.

  9. Numerical simulation of pool boiling of a Lennard-Jones liquid

    KAUST Repository

    Inaoka, Hajime

    2013-09-01

    We performed a numerical simulation of pool boiling by a molecular dynamics model. In the simulation, a liquid composed of Lennard-Jones particles in a uniform gravitational field is heated by a heat source at the bottom of the system. The model successfully reproduces the change in regimes of boiling from nucleate boiling to film boiling with the increase of the heat source temperature. We present the pool boiling curve by the model, whose general behavior is consistent with those observed in experiments of pool boiling. © 2013 Elsevier B.V. All rights reserved.

  10. "Smite this sleeping world awake": Edward Burne-Jones and "The legend of the briar rose".

    Science.gov (United States)

    Rager, Andrea Wolk

    2009-01-01

    Challenging entrenched preconceptions about the supposed escapism and conservatism of Edward Burne-Jones's art, this paper seeks to establish his monumental painted series, "The Legend of the Briar Rose," as a fundamentally radical and confrontational work. Critics have long viewed it as an endorsement of sleepy stasis, antithetical to the political activism espoused by his friend William Morris. By unraveling the intertwining themes of the series -- the transformative dream vision, artistic labor, the decorative mode, and social egalitarianism -- the "Briar Rose" series is revealed instead to be dramatization of the struggle for personal, social, artistic, and even environmental awakening.

  11. Comparing the density of states of binary Lennard-Jones glasses in bulk and film

    Science.gov (United States)

    Ghosh, Jayeeta; Faller, Roland

    2008-03-01

    We used Wang-Landau density of states Monte Carlo to study a binary Lennard-Jones glass-forming mixture in bulk and films between noninteracting walls. Thermodynamic properties are calculated using two different ensembles and film data are compared with the bulk. Bulk properties are in good agreement with previous simulations. We confirm the formation of a glass using various properties, e.g., energy, heat capacity, and pressure with temperature. We find a change in slope in the energy per particle and pressure as a function of temperature. We do not find any defined crystal structure. A higher glass transition temperature is found for the film.

  12. Cumulant expansion and analytic continuation in Monte Carlo simulation of classical Lennard-Jones clusters.

    Science.gov (United States)

    Kunikeev, Sharif D; Kim, Kwang S

    2012-11-01

    The Monte Carlo (MC) estimates of thermal averages are usually functions of system control parameters λ, such as temperature, volume, and interaction couplings. Given the MC average at a set of prescribed control parameters λ{0}, the problem of analytic continuation of the MC data to λ values in the neighborhood of λ{0} is considered in both classic and quantum domains. The key result is the theorem that links the differential properties of thermal averages to the higher order cumulants. The theorem and analytic continuation formulas expressed via higher order cumulants are numerically tested on the classical Lennard-Jones cluster system of N=13, 55, and 147 neon particles.

  13. Multivariate volatility models: an application to IBOVESPA and Dow Jones Industrial

    Directory of Open Access Journals (Sweden)

    Barossi-Filho Milton

    2012-09-01

    Full Text Available En este artículo se presenta una breve descripción de modelos GARCH multivariados y se realizan inferencias de la volatilidad de series de tiempo usando un enfoque Bayesiano, utilizando algoritmos de simulación de Monte Carlo (MCMC. Como una aplicación para ilustrar la metodología propuesta, se analizan los log-retornos de IBOVESPA y Dow Jones Industrial en una base semanal de 04/27/1993 para 11/03/2008.

  14. Monte Carlo study of the shear modulus at the surface of a Lennard-Jones crystal

    Science.gov (United States)

    Eerden, J. P. v. d.; Knops, H. J. F.; Roos, A.

    1992-01-01

    In this paper, we give a microscopic definition of local elastic constants. We apply this to the numerical evaluation of the shear modulus of an interface which is sharp as compared with the interaction range. The algorithm is applied to a study of the (001) face of a face-centered-cubic (fcc) Lennard-Jones crystal. The vanishing of the shear modulus gives an estimate of the melting temperature of the first layer which is well below the bulk triple point. Some theoretical aspects of surface melting are briefly discussed.

  15. A spin network generalization of the Jones Polynomial and Vassiliev invariants

    CERN Document Server

    Gambini, R; Pullin, J

    1998-01-01

    We apply the ideas of Alvarez and Labastida to the invariant of spin networks defined by Witten and Martin based on Chern-Simons theory. We show that it is possible to define ambient invariants of spin networks that (for the case of SU(2)) can be considered as extensions to spin networks of the Jones polynomial. Expansions of the coefficients of the polynomial yield primitive Vassiliev invariants. The resulting invariants are candidates for solutions of the Wheeler--DeWitt equations in the spin network representation of quantum gravity.

  16. Dynamical Temperature of a One- Dimensional Many-Body Systerm in the Lennard-Jones Model

    Institute of Scientific and Technical Information of China (English)

    刘觉平; 袁保仑

    2001-01-01

    A new way to derive the formula of the dynamical temperature by using the invariance of the Liouville measure and the ergodicity hypothesis is presented, based on the invariance of the functional under the transformation of the measure. The obtained dynamical temperature is intrinsic to the underlying dynamics of the system. A molecular dynamical simulation of a one-dimensional many-body system in the Lennard-Jones model has been performed. The temperature calculated from the Hamiltonian for the stationary state of the system coincides with that determined with the thermodynamical method.

  17. Idiopathic gingival fibromatosis associated with progressive hearing loss: A nonfamilial variant of Jones syndrome

    Directory of Open Access Journals (Sweden)

    Bagavad Gita

    2014-01-01

    Full Text Available Gingival fibromatosis is characterized by gingival tissue overgrowth of a firm and fibrotic nature. The growth is slow and progressive and is drug-induced, idiopathic, or hereditary in etiology. It occurs isolated or frequently as a component of various syndromes. Our patient presented with the complaint of gingival enlargement associated with progressive deafness, characteristic of Jones syndrome. This case report is important and unique since it is the first known one to have a Jones syndrome-like presentation without a family history. A male patient aged 14 years reported with the chief complaint of swelling of gums and progressive hearing loss in both ears for the past one year. There was no family history or history of drug intake. Enlargement was generalized, fibrotic and bulbous, involving the free and attached gingiva, extending up to the middle 1/3 rd of the crown. Investigations such as pure tone audiogram, impedance audiometry, and Tone decay test concluded that there was severe right and moderate left sensorineural hearing loss. The case was diagnosed to be idiopathic, generalized gingival fibromatosis with progressive hearing loss. The gingival overgrowth was managed by gingivectomy and periodic review. The patient was advised to use high occlusion computer generated hearing aids for his deafness as it was not treatable by medicines or surgery. This unique case report once again emphasizes the heterogeneity of gingival fibromatosis, which can present in an atypical manner.

  18. A geometric characterization of the upper bound for the span of the Jones polynomial

    CERN Document Server

    González-Meneses, J

    2009-01-01

    Let D be a link diagram with n crossings, s_A and s_B its extreme states and |s_AD| (resp. |s_BD|) the number of simple closed curves that appear when smoothing D according to s_A (resp. s_B). We give a general formula for the sum |s_AD|+|s_BD| for a k-almost alternating diagram D, for any k, characterising this sum as the number of faces in an appropriate triangulation of an appropriate surface with boundary. When D is dealternator connected, the triangulation is especially simple, obtaining that |s_AD|+|s_BD|=n+2-2k. This gives a simple geometric proof of the upper bound of the span of the Jones polynomial for dealternator connected diagrams, a result first obtained by Zhu in 1997. Another upper bound of the span of the Jones polynomial for dealternator connected and dealternator reduced diagrams, discovered historically first by Adams et al in 1992, is obtained as a corollary.

  19. A comparison of molecular dynamics and diffuse interface model predictions of Lennard-Jones fluid evaporation

    Energy Technology Data Exchange (ETDEWEB)

    Barbante, Paolo [Dipartimento di Matematica, Politecnico di Milano - Piazza Leonardo da Vinci 32 - 20133 Milano (Italy); Frezzotti, Aldo; Gibelli, Livio [Dipartimento di Scienze e Tecnologie Aerospaziali, Politecnico di Milano - Via La Masa 34 - 20156 Milano (Italy)

    2014-12-09

    The unsteady evaporation of a thin planar liquid film is studied by molecular dynamics simulations of Lennard-Jones fluid. The obtained results are compared with the predictions of a diffuse interface model in which capillary Korteweg contributions are added to hydrodynamic equations, in order to obtain a unified description of the liquid bulk, liquid-vapor interface and vapor region. Particular care has been taken in constructing a diffuse interface model matching the thermodynamic and transport properties of the Lennard-Jones fluid. The comparison of diffuse interface model and molecular dynamics results shows that, although good agreement is obtained in equilibrium conditions, remarkable deviations of diffuse interface model predictions from the reference molecular dynamics results are observed in the simulation of liquid film evaporation. It is also observed that molecular dynamics results are in good agreement with preliminary results obtained from a composite model which describes the liquid film by a standard hydrodynamic model and the vapor by the Boltzmann equation. The two mathematical model models are connected by kinetic boundary conditions assuming unit evaporation coefficient.

  20. A tumor-associated antigen specific for human kappa myeloma cells

    OpenAIRE

    1983-01-01

    A monoclonal antibody (K-1-21) raised against a kappa Bence Jones protein exhibits unique binding properties to malignant plasma cells. K- 1-21 is an IgG1 kappa antibody that reacts with human kappa light chains in free form, but shows no reactivity with heavy chain- associated kappa light chains. By immunofluorescence, K-1-21 binds to the surface of LICR LON/HMy2 (HMy2) kappa myeloma cells and to plasma cells from a majority (8/11) of patients with various types of kappa myeloma; it did not ...

  1. Gunfight at the NOT OK Corral: Reply to "High Noon for Microfinance" by Duvendack and Palmer-Jones (Uncut version).

    Science.gov (United States)

    Pitt, Mark M

    2012-01-01

    The paper "High Noon for Microfinance Impact Evaluations" by Duvendack and Palmer-Jones replicates the papers of Chemin (2008) and Pitt and Khandker (1998) that estimate the impact of microfinance in Bangladesh. My paper replicates the Duvendack and Palmer-Jones replication and finds so many serious errors in their code and misrepresentations of the methods described in their paper that I conclude that their results are spurious and provide no evidence about the validity of either the papers of Chemin or Pitt and Khandker or on the effectiveness of microfinance.

  2. Vectorial platform for manipulating the polarization mode train realized with Jones vectors in Mathematica

    Science.gov (United States)

    Kim, Tae Wan; Yun, Hee-Joong

    2016-09-01

    A fundamental concept in physics of polarization propagation of electromagnetic waves is newly understood as a cardinal keyword in quantum cryptography transport technology and cosmology. Recently, interactive visualization of the propagation mechanism of polarized electromagnetism in a medium with helicity has received attention from scientists in the age of information and communication. This study presents a new dynamic polarization platform that manipulates the polarization mode train of a transverse electromagnetic wave by using calculations with Jones vectors in the symbolic program Mathematica. The train of polarization modes is converted continuously through a desirable lineup of optical elements in the platform. The platform simulates a propagation process that satisfies Maxwell's two vector equations precisely with helicity in the vectorial nature of the electromagnetic wave.

  3. High Precision Calculations of the Lennard-Jones Lattice Constants for Five Lattices

    Science.gov (United States)

    Stein, Matthew

    2017-01-01

    The total potential energy of a crystal as described by the Lennard-Jones (L-J) potential depends in part upon the calculation of lattice constants. Knowing these constants to high precision is useful for prediction of the lattice type and simulation of crystals such as rare-gas solids or germanium detectors, but reaching higher precision is computationally costly and challenging. Presented here is the extension of the precision of the lattice constants, Lp, up to 32 decimal digits, and in some cases corrections from previous publication. The Lp terms are given for 4 cubic, face-centered cubic, body-centered cubic, hexagonal-close-pack, and diamond lattices. This precision was obtained through the use of careful parallelization technique, exploitation of the symmetries of each lattice, and the ``onionization'' of the simulated crystal. The results of this computation, along with the tools and algorithm strategies to make this computation possible, are explained in detail graphically.

  4. Energy transfer process in gas models of Lennard-Jones interactions

    CERN Document Server

    Yang, Jinghua; Wang, Jiao; Zhao, Hong

    2011-01-01

    We perform simulations to investigate how the energy carried by a molecule transfers to others in an equilibrium gas model. For this purpose we consider a microcanonical ensemble of equilibrium gas systems, each of them contains a tagged molecule located at the same position initially. The ensuing transfer process of the energy initially carried by the tagged molecule is then exposed in terms of the ensemble-averaged energy density distribution. In both a 2D and a 3D gas model with Lennard-Jones interactions at room temperature, it is found that the energy carried by a molecule propagates in the gas ballistically, in clear contrast with the Gaussian diffusion widely assumed in previous studies. A possible scheme of experimental study of this issue is also proposed

  5. Translation and cultural adaptation of the Jones Dependency Tool to Brazilian Portuguese

    Directory of Open Access Journals (Sweden)

    Karen Marchesan de Andrade

    2014-12-01

    Full Text Available Methodological study to translate and culturally adapt the Jones Dependency Tool (JDT to Portuguese. The translation and cultural adaptation method had four stages. First stage: translation of the original instrument from English to Portuguese. Second stage: content, cultural, semantic and conceptual equivalence in relation to the original instrument. Third stage: back-translation. Fourth stage: comparison of the translated and back-translated versions by a committee of specialists, resulting in the final version. In the Communication Domain, the original JDT measured pain using high, intermediate and low ranges, but the committee suggested replacing it with a visual analog scale. The translation and cultural adaptation of the JDT to Portuguese produced an instrument applicable to our reality. Studies need to be conducted to test the validity and reliability of the JDT in Brazilian Emergency Services. doi: 10.5216/ree.v16i4.22345.

  6. A Jones matrix formalism for simulating 3D Polarised Light Imaging of brain tissue

    CERN Document Server

    Menzel, Miriam; De Raedt, Hans; Reckfort, Julia; Amunts, Katrin; Axer, Markus

    2015-01-01

    The neuroimaging technique 3D Polarised Light Imaging (3D-PLI) provides a high-resolution reconstruction of nerve fibres in human post-mortem brains. The orientations of the fibres are derived from birefringence measurements of histological brain sections assuming that the nerve fibres - consisting of an axon and a surrounding myelin sheath - are uniaxial birefringent and that the measured optic axis is oriented in direction of the nerve fibres (macroscopic model). Although experimental studies support this assumption, the molecular structure of the myelin sheath suggests that the birefringence of a nerve fibre can be described more precisely by multiple optic axes oriented radially around the fibre axis (microscopic model). In this paper, we compare the use of the macroscopic and the microscopic model for simulating 3D-PLI by means of the Jones matrix formalism. The simulations show that the macroscopic model ensures a reliable estimation of the fibre orientations as long as the polarimeter does not resolve ...

  7. Vapour-to-Liquid Nucleation in Associating Lennard-Jones Fluids with Multiple Association Sites

    Institute of Scientific and Technical Information of China (English)

    FU Dong; LIAO Tao

    2007-01-01

    The excess Helmholtz free energy functional for associating Lennard-Jones (LJ) fluid is formulated in terms of a weighted density approximation for short-ranged interactions and a Weeks Chandler-Andersen approximation for long-range attraction. Within the framework of density functional theory, phase equilibria, vapour-liquid surface tension and vapour-liquid nucleation properties including the density profile, work of formation, excess number of particles and critical supersaturation are investigated for associating LJ fluids with different numbers of association sites (M=1,2,3,4) per particle. The influences of association energy and association sites on phase equilibria, surface tension and vapour-liquid nucleation properties are discussed.

  8. Properties of the Lennard-Jones dimeric fluid in two dimensions: an integral equation study.

    Science.gov (United States)

    Urbic, Tomaz; Dias, Cristiano L

    2014-03-07

    The thermodynamic and structural properties of the planar soft-sites dumbbell fluid are examined by Monte Carlo simulations and integral equation theory. The dimers are built of two Lennard-Jones segments. Site-site integral equation theory in two dimensions is used to calculate the site-site radial distribution functions for a range of elongations and densities and the results are compared with Monte Carlo simulations. The critical parameters for selected types of dimers were also estimated. We analyze the influence of the bond length on critical point as well as tested correctness of site-site integral equation theory with different closures. The integral equations can be used to predict the phase diagram of dimers whose molecular parameters are known.

  9. On the establishment of thermal diffusion in binary Lennard-Jones liquids

    Science.gov (United States)

    Ferrario, M.; Bonella, S.; Ciccotti, G.

    2016-07-01

    The establishment of thermal diffusion in an Ar-Kr Lennard-Jones mixture is investigated via dynamical non equilibrium molecular dynamics [G. Ciccotti, G. Jacucci, Phys. Rev. Lett. 35, 789 (1975)]. We observe, in particular, the evolution of the density and temperature fields of the system following the onset of the thermal gradient. In stationary conditions, we also compute the Soret coefficient of the mixture. This study confirms that dynamical non equilibrium molecular dynamics is an effective tool to gather information on transient phenomena, even though the full evolution of the mass and energy fluxes associated to the temperature and density fields requires, in this case, a more substantial numerical effort than the one employed here.

  10. Shortcomings of the standard Lennard-Jones dispersion term in water models, studied with force matching

    Science.gov (United States)

    Nicolini, Paolo; Guàrdia, Elvira; Masia, Marco

    2013-11-01

    In this work, ab initio parametrization of water force field is used to get insights into the functional form of empirical potentials to properly model the physics underlying dispersion interactions. We exploited the force matching algorithm to fit the interaction forces obtained with dispersion corrected density functional theory based molecular dynamics simulations. We found that the standard Lennard-Jones interaction potentials poorly reproduce the attractive character of dispersion forces. This drawback can be resolved by accounting for the distinctive short range behavior of dispersion interactions, multiplying the r-6 term by a damping function. We propose two novel parametrizations of the force field using different damping functions. Structural and dynamical properties of the new models are computed and compared with the ones obtained from the non-damped force field, showing an improved agreement with reference first principle calculations.

  11. Phase diagram and universality of the Lennard-Jones gas-liquid system

    KAUST Repository

    Watanabe, Hiroshi

    2012-01-01

    The gas-liquid phase transition of the three-dimensional Lennard-Jones particles system is studied by molecular dynamics simulations. The gas and liquid densities in the coexisting state are determined with high accuracy. The critical point is determined by the block density analysis of the Binder parameter with the aid of the law of rectilinear diameter. From the critical behavior of the gas-liquid coexisting density, the critical exponent of the order parameter is estimated to be β = 0.3285(7). Surface tension is estimated from interface broadening behavior due to capillary waves. From the critical behavior of the surface tension, the critical exponent of the correlation length is estimated to be ν = 0.63(4). The obtained values of β and ν are consistent with those of the Ising universality class. © 2012 American Institute of Physics.

  12. Monte Carlo simulation of thermodynamic properties for two-dimensional Lennard-Jones fluids

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Canonical ensemble Monte Carlo simulations have been carried out to investigate the thermodynamic properties of two-dimensional fluids subjected to truncated Lennard-Jones 12-6 potential. The simulations of thermodynamic states sweep across liquid-vapor regime over a wide range of thermodynamic conditions. Simulated isotherms behave van der Waals loop-like characteristics in the liquid-vapor phase-transition region. It suggests a continuous isothermal phase transition in the case of micro system, in which the system size prohibits phase separation. Two-dimensional dimensionless van der Waals equation of states has been obtained from theoretical analysis. By fitting simulated data to this equation, temperature-dependent parameters in the equation have been determined.

  13. Mesoscopic Hamiltonian for the fluctuations of adsorbed Lennard-Jones liquid films.

    Science.gov (United States)

    Fernández, Eva M; Chacón, Enrique; MacDowell, Luis G; Tarazona, Pedro

    2015-06-01

    We use Monte Carlo simulations of a Lennard-Jones fluid adsorbed on a short-range planar wall substrate to study the fluctuations in the thickness of the wetting layer, and we get a quantitative and consistent characterization of their mesoscopic Hamiltonian, H[ξ]. We have observed important finite-size effects, which were hampering the analysis of previous results obtained with smaller systems. The results presented here support an appealing simple functional form for H[ξ], close but not exactly equal to the theoretical nonlocal proposal made on the basis a generic density-functional analysis by Parry and coworkers. We have analyzed systems under different wetting conditions, as a proof of principle for a method that provides a quantitative bridge between the molecular interactions and the phenomenology of wetting films at mesoscopic scales.

  14. Quantum Statistical Mechanics as an Exact Classical Expansion with Results for Lennard-Jones Helium

    CERN Document Server

    Attard, Phil

    2016-01-01

    The quantum states representing classical phase space are given, and these are used to formulate quantum statistical mechanics as a formally exact double perturbation expansion about classical statistical mechanics. One series of quantum contributions arises from the non-commutativity of the position and momentum operators. Although the formulation of the quantum states differs, the present results for separate averages of position operators and of momentum operators agree with Wigner (1932) and Kirkwood (1933). The second series arises from wave function symmetrization, and is given in terms of $l$-particle permutation loops in an infinite order re-summation. The series gives analytically the known exact result for the quantum ideal gas to all orders. The leading correction corrects a correction given by Kirkwood. The first four quantum corrections to the grand potential are calculated for a Lennard-Jones fluid using the hypernetted chain closure. For helium on liquid branch isotherms, the corrections range ...

  15. The Lion and the Lady Revisited: Another Look at the Firing of Mary L. Jones as Los Angeles Public Librarian in 1905.

    Science.gov (United States)

    Wiegand, Wayne A.

    1983-01-01

    Recounts events that led to the firing of Mary L. Jones, Director of Los Angeles Public Library (1905) and caught in public crossfire such figures as the mayor, city council, library board of directors, Charles Lummis (Jones's replacement), Susan B. Anthony, Anna Shaw, Herbert Putnam, and Melvil Dewey. (29 references) (EJS)

  16. Comment on Cross, Fine, Jones, and Walsh (2012): Good Therapeutic Services--Therapeutic Advocacy and Forensic Neutrality

    Science.gov (United States)

    Connell, Mary

    2012-01-01

    Cross, Fine, Jones, and Walsh (2012) provided a thoughtful review and critique of a book chapter describing the interview process at Child Advocacy Centers. They observed some of the ways that concerns raised in that chapter are being addressed and described revised guidelines that further clarify issues. Ongoing research and examination of the…

  17. An entropy based analysis of the relationship between the DOW JONES Index and the TRNA Sentiment series

    NARCIS (Netherlands)

    D.E. Allen (David); M.J. McAleer (Michael); A.K. Singh (Abhay)

    2016-01-01

    textabstractThis paper features an analysis of the relationship between the DOW JONES Industrial Average Index (DJIA) and a sentiment news series using daily data obtained from the Thomson Reuters News Analytics (TRNA)1 provided by SIRCA (The Securities Industry Research Centre of the Asia Pacic). T

  18. Polymerization of immunoglobulin domains: A model system for the development of facilitated macromolecular assembly

    Energy Technology Data Exchange (ETDEWEB)

    Stevens, F.J.; Myatt, E.A.

    1991-12-31

    We have recently determined that monoclonal immunoglobulin light chains (Bence Jones proteins) are capable of reversible polymerization at room temperature. This property, as exhibited by immunoglobulin light chains (normally a component of an intact antibody molecule), may have novel implications for the development of ``molecular nanotechnology.`` The polymerization capability of the immunoglobulin light chain is associated with the so-called variable domain of this molecule. The variable domain is a durable, compact beta-sheet structure of molecular weight approximately 12,000. Most of the primary sequence variation is limited to one portion of the molecule, that portion associated with the contribution of immunoglobulin light chains to the recognition and binding of thousand of different antigens by antibodies. As a consequence of these variations, different light chains polymerize with different degrees of avidity, from negligible to extensive. The polymerization process depends on solution parameters such as Ph. Thus, polymerization might be induced at one pH and suppressed or reversed at another. Combinations of molecules of appropriate specificities could assemble into structures of predetermined three-dimensional forms and properties. These features suggest that Bence Jones proteins represent a powerful model system within which to develop empirical rules relevant to a technology of protein-based ``construction``. Development of these rules will require the combined efforts of biophysical and crystallographic studies, protein engineering, and molecular modeling. 53 refs., 5 figs.

  19. Polymerization of immunoglobulin domains: A model system for the development of facilitated macromolecular assembly

    Energy Technology Data Exchange (ETDEWEB)

    Stevens, F.J.; Myatt, E.A.

    1991-01-01

    We have recently determined that monoclonal immunoglobulin light chains (Bence Jones proteins) are capable of reversible polymerization at room temperature. This property, as exhibited by immunoglobulin light chains (normally a component of an intact antibody molecule), may have novel implications for the development of molecular nanotechnology.'' The polymerization capability of the immunoglobulin light chain is associated with the so-called variable domain of this molecule. The variable domain is a durable, compact beta-sheet structure of molecular weight approximately 12,000. Most of the primary sequence variation is limited to one portion of the molecule, that portion associated with the contribution of immunoglobulin light chains to the recognition and binding of thousand of different antigens by antibodies. As a consequence of these variations, different light chains polymerize with different degrees of avidity, from negligible to extensive. The polymerization process depends on solution parameters such as Ph. Thus, polymerization might be induced at one pH and suppressed or reversed at another. Combinations of molecules of appropriate specificities could assemble into structures of predetermined three-dimensional forms and properties. These features suggest that Bence Jones proteins represent a powerful model system within which to develop empirical rules relevant to a technology of protein-based construction''. Development of these rules will require the combined efforts of biophysical and crystallographic studies, protein engineering, and molecular modeling. 53 refs., 5 figs.

  20. Identification of Insecticidal Constituents from the Essential Oil of Valeriana jatamansi Jones against Liposcelis bostrychophila Badonnel

    Directory of Open Access Journals (Sweden)

    Xin Chao Liu

    2013-01-01

    Full Text Available The aim of this research was to determine chemical composition and insecticidal activities of the essential oil of Valeriana jatamansi Jones roots against booklice, Liposcelis bostrychophila Badonnel, and to isolate insecticidal constituents from the oil. Essential oil of V. jatamansi was obtained by hydrodistillation and analyzed by GC-MS. A total of 27 components in the essential oil were identified. The major compounds were patchoulol (24.3%, α-bulnesene (13.8%, isovaleric acid (12.9%, α-guaiene (8.7%, and 3-methylvaleric acid (8.4%. Based on bioactivity-guided fractionation, isovaleric acid, 3-methylvaleric acid, and patchoulol were isolated and identified as the active constituents. The essential oil exhibited contact toxicity against L. bostrychophila with an LC50 value of 236.4 μg/cm2. Patchoulol (LC50 = 61.35 μg/cm2 exhibited stronger acute toxicity than 3-methylvaleric acid (LC50 = 210.69 μg/cm2 against the booklice. The essential oil also possessed fumigant toxicity against L. bostrychophila with an LC50 value of 6.0 mg/L, while 3-methylvaleric acid and isovaleric acid had LC50 values of 5.53 mg/L and 5.67 mg/L against the booklice, respectively. The results indicated that the essential oil and its constituent compounds have potential to develop into natural insecticides or fumigants for control of insects in stored grains.

  1. A multiscale transport model for binary Lennard Jones mixtures in slit nanopores

    Science.gov (United States)

    Bhadauria, Ravi; Aluru, N. R.

    2016-11-01

    We present a quasi-continuum multiscale hydrodynamic transport model for one dimensional isothermal, non-reacting binary mixture confined in slit shaped nanochannels. We focus on species transport equation that includes the viscous dissipation and interspecies diffusion term of the Maxwell-Stefan form. Partial viscosity variation is modeled by van der Waals one fluid approximation and the Local Average Density Method. We use friction boundary conditions where the wall-species friction parameter is computed using a novel species specific Generalized Langevin Equation model. The transport model accuracy is tested by predicting the velocity profiles of Lennard-Jones (LJ) methane-hydrogen and LJ methane-argon mixtures in graphene slit channels of different width. The resultant slip length from the continuum model is found to be invariant of channel width for a fixed mixture molar concentration. The mixtures considered are observed to behave as single species pseudo fluid, with the friction parameter displaying a linear dependence on the molar composition. The proposed model yields atomistic level accuracy with continuum scale efficiency.

  2. A Jones matrix formalism for simulating three-dimensional polarized light imaging of brain tissue.

    Science.gov (United States)

    Menzel, M; Michielsen, K; De Raedt, H; Reckfort, J; Amunts, K; Axer, M

    2015-10-06

    The neuroimaging technique three-dimensional polarized light imaging (3D-PLI) provides a high-resolution reconstruction of nerve fibres in human post-mortem brains. The orientations of the fibres are derived from birefringence measurements of histological brain sections assuming that the nerve fibres—consisting of an axon and a surrounding myelin sheath—are uniaxial birefringent and that the measured optic axis is oriented in the direction of the nerve fibres (macroscopic model). Although experimental studies support this assumption, the molecular structure of the myelin sheath suggests that the birefringence of a nerve fibre can be described more precisely by multiple optic axes oriented radially around the fibre axis (microscopic model). In this paper, we compare the use of the macroscopic and the microscopic model for simulating 3D-PLI by means of the Jones matrix formalism. The simulations show that the macroscopic model ensures a reliable estimation of the fibre orientations as long as the polarimeter does not resolve structures smaller than the diameter of single fibres. In the case of fibre bundles, polarimeters with even higher resolutions can be used without losing reliability. When taking the myelin density into account, the derived fibre orientations are considerably improved.

  3. Optimization of magneto-optical Kerr setup: analyzing experimental assemblies using Jones matrix formalism.

    Science.gov (United States)

    Polisetty, S; Scheffler, J; Sahoo, S; Wang, Yi; Mukherjee, T; He, Xi; Binek, Ch

    2008-05-01

    We present a comparative study on an experimental and theoretical optimization of magneto-optical Kerr setups based on photoelastic modulation and phase sensitive detector methodology. The first and second harmonics, I omega,2 omega, of the reflected light intensity are measured for a CoO/Co magnetic reference film. The magnetic field dependence of the optical off-diagonal Fresnel reflection coefficients rps and rsp follows the sample magnetization. Different Kerr setups provide various dependencies of I omega,2 omega on the reflection coefficients and, hence, on the Kerr ellipticity epsilon K and rotation theta K. Jones matrix formalism has been used to analyze the impact of a systematic variation of relative analyzer and polarizer orientations with respect to each other and with respect to the retardation axis of the modulator involved in longitudinal Kerr setups for incoming s-polarized light. We find one particular setup which maximizes I(omega) as well as I2 omega and maximizes the signal-to-noise ratio. Inefficient setups are characterized by I omega,2 omega intensities involving large nonmagnetic contributions of rp and rs.

  4. Spray flow-network flow transition of binary Lennard-Jones particle system

    KAUST Repository

    Inaoka, Hajime

    2010-07-01

    We simulate gas-liquid flows caused by rapid depressurization using a molecular dynamics model. The model consists of two types of Lennard-Jones particles, which we call liquid particles and gas particles. These two types of particles are distinguished by their mass and strength of interaction: a liquid particle has heavier mass and stronger interaction than a gas particle. By simulations with various initial number densities of these particles, we found that there is a transition from a spray flow to a network flow with an increase of the number density of the liquid particles. At the transition point, the size of the liquid droplets follows a power-law distribution, while it follows an exponential distribution when the number density of the liquid particles is lower than the critical value. The comparison between the transition of the model and that of models of percolation is discussed. The change of the average droplet size with the initial number density of the gas particles is also presented. © 2010 Elsevier B.V. All rights reserved.

  5. A comprehensive approach to an equation of state for hard spheres and Lennard-Jones fluids

    Institute of Scientific and Technical Information of China (English)

    S.B.Khasare

    2011-01-01

    We present a simple method of obtaining various equations of state for hard sphere fluid in a simple unifying way.We will guess equations of state by using suitable axiomatic functional forms(n =1,2,3,4,5)for surface tension Smnr,r≥d/2 with intermolecular separation r as a variable,where m is an arbitrary real number(pole).Among the equations of state obtained in this way are Percus-Yevick,scaled particle theory and Carnahan-Starling equations of state.In addition,we have found a simple equation of state for the hard sphere fluid in the region that represents the simulation data accurately.It is found that for both hard sphere fluids as well as Lennard-Jones fluids,with m =3/4 the derived equation of state(EOS)gives results which are in good agreement with computer simulation results.Furthermore,this equation of state gives the Percus-Yevick(pressure)EOS for the m = 0,the Carnahan-Starling EOS for m = 4/5,while for the value of m = 1 it corresponds to a scaled particle theory EOS.

  6. Magic number behavior for heat capacities of medium sized classical Lennard-Jones clusters

    CERN Document Server

    Frantz, D D

    2001-01-01

    Monte Carlo methods were used to calculate heat capacities as functions of temperature for classical atomic clusters of aggregate sizes $25 \\leq N \\leq 60$ that were bound by pairwise Lennard-Jones potentials. The parallel tempering method was used to overcome convergence difficulties due to quasiergodicity in the solid-liquid phase-change regions. All of the clusters studied had pronounced peaks in their heat capacity curves, most of which corresponded to their solid-liquid phase-change regions. The heat capacity peak height and location exhibited two general trends as functions of cluster size: for $N = 25$ to 36, the peak temperature slowly increased, while the peak height slowly decreased, disappearing by $N = 37$; for $N = 30$, a very small secondary peak at very low temperature emerged and quickly increased in size and temperature as $N$ increased, becoming the dominant peak by $N = 36$. Superimposed on these general trends were smaller fluctuations in the peak heights that corresponded to ``magic numbe...

  7. Face Detection and Recognition Using Viola-Jones with PCA-LDA and Square Euclidean Distance

    Directory of Open Access Journals (Sweden)

    Nawaf Hazim Barnouti

    2016-05-01

    Full Text Available In this paper, an automatic face recognition system is proposed based on appearance-based features that focus on the entire face image rather than local facial features. The first step in face recognition system is face detection. Viola-Jones face detection method that capable of processing images extremely while achieving high detection rates is used. This method has the most impact in the 2000’s and known as the first object detection framework to provide relevant object detection that can run in real time. Feature extraction and dimension reduction method will be applied after face detection. Principal Component Analysis (PCA method is widely used in pattern recognition. Linear Discriminant Analysis (LDA method that used to overcome drawback the PCA has been successfully applied to face recognition. It is achieved by projecting the image onto the Eigenface space by PCA after that implementing pure LDA over it. Square Euclidean Distance (SED is used. The distance between two images is a major concern in pattern recognition. The distance between the vectors of two images leads to image similarity. The proposed method is tested on three databases (MUCT, Face94, and Grimace. Different number of training and testing images are used to evaluate the system performance and it show that increasing the number of training images will increase the recognition rate.

  8. The Lennard-Jones Potential Minimization Problem for Prion AGAAAAGA Amyloid Fibril Molecular Modeling

    CERN Document Server

    Zhang, Jiapu

    2011-01-01

    The simplified Lennard-Jones (LJ) potential minimization problem is minimize f(x)=4\\sum_{i=1}^N \\sum_{j=1,j

  9. Spectral Analysis of Dow Jones Index and Comparison with Model Predicted Cycles During 1900-2005

    CERN Document Server

    Selvam, A M

    2006-01-01

    The day-to day fluctuations of Dow Jones Index exhibit fractal fluctuations, namely, a zigzag pattern of successive increases followed by decreases on all space-time scales. Self-similar fractal fluctuations are generic to dynamical systems in nature and imply long-range space-time correlations. The apparently unpredictable (chaotic) fluctuations of dynamical systems exhibit underlying order with the power spectra exhibiting inverse power law form, now identified as self-organized criticality. The physics of self-organized criticality is not yet identified. A general systems theory developed by the author shows that self-similar fractal fluctuations are signatures of quantum-like chaos in dynamical systems of all size scales ranging from the subatomic dynamics of quantum systems to macro-scale fluid flows. The model predicts the universal inverse power-law form of the statistical normal distribution for the power spectra of fractal space-time fluctuations of dynamical systems. In this paper it is shown that t...

  10. A Hybrid Vehicle Detection Method Based on Viola-Jones and HOG + SVM from UAV Images.

    Science.gov (United States)

    Xu, Yongzheng; Yu, Guizhen; Wang, Yunpeng; Wu, Xinkai; Ma, Yalong

    2016-08-19

    A new hybrid vehicle detection scheme which integrates the Viola-Jones (V-J) and linear SVM classifier with HOG feature (HOG + SVM) methods is proposed for vehicle detection from low-altitude unmanned aerial vehicle (UAV) images. As both V-J and HOG + SVM are sensitive to on-road vehicles' in-plane rotation, the proposed scheme first adopts a roadway orientation adjustment method, which rotates each UAV image to align the roads with the horizontal direction so the original V-J or HOG + SVM method can be directly applied to achieve fast detection and high accuracy. To address the issue of descending detection speed for V-J and HOG + SVM, the proposed scheme further develops an adaptive switching strategy which sophistically integrates V-J and HOG + SVM methods based on their different descending trends of detection speed to improve detection efficiency. A comprehensive evaluation shows that the switching strategy, combined with the road orientation adjustment method, can significantly improve the efficiency and effectiveness of the vehicle detection from UAV images. The results also show that the proposed vehicle detection method is competitive compared with other existing vehicle detection methods. Furthermore, since the proposed vehicle detection method can be performed on videos captured from moving UAV platforms without the need of image registration or additional road database, it has great potentials of field applications. Future research will be focusing on expanding the current method for detecting other transportation modes such as buses, trucks, motors, bicycles, and pedestrians.

  11. Factorizations for 3-rotations and polarization of the light in Mueller-Stokes an Jones formalisms

    CERN Document Server

    Red'kov, V M

    2008-01-01

    Formulas describing all 2-element and 3-element factorizations of arbitrary element of the groups SU(2) and SO(3,R) are derived. Six 2-element factorizations, $ (U_{2}U_{3}U'_{2}), (U_{3}U_{2}U'_{3}), (U_{3}U_{1}U'_{3}), (U_{1}U_{3}U'_{1}), (U_{1}U_{2}U'_{1}), (U_{2}U_{1}U'_{2})$, provide all possible way to define Euler type angles; and six 3-element ones, $ (U_{1}U_{2}U_{3}), (U_{1}U_{3}U'_{2}), (U_{2}U_{3}U_{1}), (U_{2}U_{1}U_{3}), (U_{3}U_{1}U_{2}), (U_{3}U_{2}U_{1})$ provide all possible ways to parameterize the unitary and orthogonal groups by three elementary angles. In thecontext the light polarization formalism of Stokes-Mueller vectors and Jones spinors, relations produced give a base to resolve arbitrary pure polarization rotators into all possible sets of elementary rotators of two or three constituents.

  12. Nucleation of liquid droplets and voids in a stretched Lennard-Jones fcc crystal.

    Science.gov (United States)

    Baidakov, Vladimir G; Tipeev, Azat O

    2015-09-28

    The method of molecular dynamics simulation has been used to investigate the phase decay of a metastable Lennard-Jones face-centered cubic crystal at positive and negative pressures. It is shown that at high degrees of metastability, crystal decay proceeds through the spontaneous formation and growth of new-phase nuclei. It has been found that there exists a certain boundary temperature. Below this temperature, the crystal phase disintegrates as the result of formation of voids, and above, as a result of formation of liquid droplets. The boundary temperature corresponds to the temperature of cessation of a crystal-liquid phase equilibrium when the melting line comes in contact with the spinodal of the stretched liquid. The results of the simulations are interpreted in the framework of classical nucleation theory. The thermodynamics of phase transitions in solids has been examined with allowance for the elastic energy of stresses arising owing to the difference in the densities of the initial and the forming phases. As a result of the action of elastic forces, at negative pressures, the boundary of the limiting superheating (stretching) of a crystal approaches the spinodal, on which the isothermal bulk modulus of dilatation becomes equal to zero. At the boundary of the limiting superheating (stretching), the shape of liquid droplets and voids is close to the spherical one.

  13. Single-site Lennard-Jones models via polynomial chaos surrogates of Monte Carlo molecular simulation

    KAUST Repository

    Kadoura, Ahmad Salim

    2016-06-01

    In this work, two Polynomial Chaos (PC) surrogates were generated to reproduce Monte Carlo (MC) molecular simulation results of the canonical (single-phase) and the NVT-Gibbs (two-phase) ensembles for a system of normalized structureless Lennard-Jones (LJ) particles. The main advantage of such surrogates, once generated, is the capability of accurately computing the needed thermodynamic quantities in a few seconds, thus efficiently replacing the computationally expensive MC molecular simulations. Benefiting from the tremendous computational time reduction, the PC surrogates were used to conduct large-scale optimization in order to propose single-site LJ models for several simple molecules. Experimental data, a set of supercritical isotherms, and part of the two-phase envelope, of several pure components were used for tuning the LJ parameters (ε, σ). Based on the conducted optimization, excellent fit was obtained for different noble gases (Ar, Kr, and Xe) and other small molecules (CH4, N2, and CO). On the other hand, due to the simplicity of the LJ model used, dramatic deviations between simulation and experimental data were observed, especially in the two-phase region, for more complex molecules such as CO2 and C2 H6.

  14. Efficient Implementations of Molecular Dynamics Simulations for Lennard-Jones Systems

    KAUST Repository

    Watanabe, H.

    2011-08-01

    Efficient implementations of the classical molecular dynamics (MD) method for Lennard-Jones particle systems are considered. Not only general algorithms but also techniques that are efficient for some specific CPU architectures are also explained. A simple spatialdecomposition-based strategy is adopted for parallelization. By utilizing the developed code, benchmark simulations are performed on a HITACHI SR16000/J2 system consisting of IBM POWER6 processors which are 4.7 GHz at the National Institute for Fusion Science (NIFS) and an SGI Altix ICE 8400EX system consisting of Intel Xeon processors which are 2.93 GHz at the Institute for Solid State Physics (ISSP), the University of Tokyo. The parallelization efficiency of the largest run, consisting of 4.1 billion particles with 8192 MPI processes, is about 73% relative to that of the smallest run with 128 MPI processes at NIFS, and it is about 66% relative to that of the smallest run with 4 MPI processes at ISSP. The factors causing the parallel overhead are investigated. It is found that fluctuations of the execution time of each process degrade the parallel efficiency. These fluctuations may be due to the interference of the operating system, which is known as OS Jitter.

  15. How long the singular value decomposed entropy predicts the stock market? - Evidence from the Dow Jones Industrial Average Index

    Science.gov (United States)

    Gu, Rongbao; Shao, Yanmin

    2016-07-01

    In this paper, a new concept of multi-scales singular value decomposition entropy based on DCCA cross correlation analysis is proposed and its predictive power for the Dow Jones Industrial Average Index is studied. Using Granger causality analysis with different time scales, it is found that, the singular value decomposition entropy has predictive power for the Dow Jones Industrial Average Index for period less than one month, but not for more than one month. This shows how long the singular value decomposition entropy predicts the stock market that extends Caraiani's result obtained in Caraiani (2014). On the other hand, the result also shows an essential characteristic of stock market as a chaotic dynamic system.

  16. Jones matrix analysis for a polarization-sensitive optical coherence tomography system using fiber-optic components

    OpenAIRE

    Park, B. H.; Pierce, M. C.; Cense, B.; De Boer, MR

    2004-01-01

    We present an analysis for polarization-sensitive optical coherence tomography that facilitates the unrestricted use of fiber and fiber-optic components throughout an interferometer and yields sample birefringence, diattenuation, and relative optic axis orientation. We use a novel Jones matrix approach that compares the polarization states of light reflected from the sample surface with those reflected from within a biological sample for pairs of depth scans. The incident polarization alterna...

  17. Book review: the Oxford handbook of creative industries edited by Candace Jones, Mark Lorenzen and Jonathan Sapsed

    OpenAIRE

    Pannini, Elisa

    2016-01-01

    The creative industries are on the rise across the globe and their economic importance is also increasing. Through their new book, The Oxford Handbook of Creative Industries, editors Candace Jones, Mark Lorenzen and Jonathan Sapsed offer a collection of scholarly articles reflecting on this growing sector through a number of disciplinary lenses, including economics, public policy, management and law. Elisa Pannini finds this a useful read not only for scholars researching the field, but also ...

  18. Structures and autocorrelation functions of liquid Al and Mg modelled via Lennard-Jones potential from molecular dynamics simulation

    Indian Academy of Sciences (India)

    G A Adebayo; O Akinlade; L A Hussain

    2005-02-01

    The structures and autocorrelation functions of Al and Mg in the liquid state are investigated through the pair distribution function (), the diffusion coefficients as well as the shear viscosity via the Green{Kubo and Einstein relations. From the structure and the Enskog relation we determined the frequency of collisions of atoms in the first shell of () in the systems. We also discovered that the packing fraction of Lennard-Jones liquids should be approximately half the reduced density value. This approximation is accurate to within 99%. The temperature dependence of the pair distribution function and the atomic mean square displacement are investigated by performing simulations at various experimental temperatures and corresponding densities. The structures of the systems are affected by temperature via movements of atoms in the first minimum of (). The Lennard-Jones model shows that density dependence of the shear viscosity is in agreement with what is expected of simple liquids in the range of investigated temperatures and densities. In the gas limit, the Stoke-Einstein relation = B/2 is grossly overestimated by Lennard-Jones model. This could not be attributed to defficiencies in the model, as other investigators using first principle method could not obtain the gas limit of the Stoke-Einstein relation.

  19. Riemannian geometry study of vapor-liquid phase equilibria and supercritical behavior of the Lennard-Jones fluid.

    Science.gov (United States)

    May, Helge-Otmar; Mausbach, Peter

    2012-03-01

    The behavior of thermodynamic response functions and the thermodynamic scalar curvature in the supercritical region have been studied for a Lennard-Jones fluid based on a revised modified Benedict-Webb-Rubin equation of state. Response function extrema are sometimes used to estimate the Widom line, which is characterized by the maxima of the correlation lengths. We calculated the Widom line for the Lennard-Jones fluid without using any response function extrema. Since the volume of the correlation length is proportional to the Riemannian thermodynamic scalar curvature, the locus of the Widom line follows the slope of maximum curvature. We show that the slope of the Widom line follows the slope of the isobaric heat capacity maximum only in the close vicinity of the critical point and that, therefore, the use of response function extrema in this context is problematic. Furthermore, we constructed the vapor-liquid coexistence line for the Lennard-Jones fluid using the fact that the correlation length, and therefore the thermodynamic scalar curvature, must be equal in the two coexisting phases. We compared the resulting phase envelope with those from simulation data where multiple histogram reweighting was used and found striking agreement between the two methods.

  20. A Hybrid Vehicle Detection Method Based on Viola-Jones and HOG + SVM from UAV Images

    Directory of Open Access Journals (Sweden)

    Yongzheng Xu

    2016-08-01

    Full Text Available A new hybrid vehicle detection scheme which integrates the Viola-Jones (V-J and linear SVM classifier with HOG feature (HOG + SVM methods is proposed for vehicle detection from low-altitude unmanned aerial vehicle (UAV images. As both V-J and HOG + SVM are sensitive to on-road vehicles’ in-plane rotation, the proposed scheme first adopts a roadway orientation adjustment method, which rotates each UAV image to align the roads with the horizontal direction so the original V-J or HOG + SVM method can be directly applied to achieve fast detection and high accuracy. To address the issue of descending detection speed for V-J and HOG + SVM, the proposed scheme further develops an adaptive switching strategy which sophistically integrates V-J and HOG + SVM methods based on their different descending trends of detection speed to improve detection efficiency. A comprehensive evaluation shows that the switching strategy, combined with the road orientation adjustment method, can significantly improve the efficiency and effectiveness of the vehicle detection from UAV images. The results also show that the proposed vehicle detection method is competitive compared with other existing vehicle detection methods. Furthermore, since the proposed vehicle detection method can be performed on videos captured from moving UAV platforms without the need of image registration or additional road database, it has great potentials of field applications. Future research will be focusing on expanding the current method for detecting other transportation modes such as buses, trucks, motors, bicycles, and pedestrians.

  1. The impact of surface area, volume, curvature, and Lennard-Jones potential to solvation modeling.

    Science.gov (United States)

    Nguyen, Duc D; Wei, Guo-Wei

    2017-01-05

    This article explores the impact of surface area, volume, curvature, and Lennard-Jones (LJ) potential on solvation free energy predictions. Rigidity surfaces are utilized to generate robust analytical expressions for maximum, minimum, mean, and Gaussian curvatures of solvent-solute interfaces, and define a generalized Poisson-Boltzmann (GPB) equation with a smooth dielectric profile. Extensive correlation analysis is performed to examine the linear dependence of surface area, surface enclosed volume, maximum curvature, minimum curvature, mean curvature, and Gaussian curvature for solvation modeling. It is found that surface area and surfaces enclosed volumes are highly correlated to each other's, and poorly correlated to various curvatures for six test sets of molecules. Different curvatures are weakly correlated to each other for six test sets of molecules, but are strongly correlated to each other within each test set of molecules. Based on correlation analysis, we construct twenty six nontrivial nonpolar solvation models. Our numerical results reveal that the LJ potential plays a vital role in nonpolar solvation modeling, especially for molecules involving strong van der Waals interactions. It is found that curvatures are at least as important as surface area or surface enclosed volume in nonpolar solvation modeling. In conjugation with the GPB model, various curvature-based nonpolar solvation models are shown to offer some of the best solvation free energy predictions for a wide range of test sets. For example, root mean square errors from a model constituting surface area, volume, mean curvature, and LJ potential are less than 0.42 kcal/mol for all test sets. © 2016 Wiley Periodicals, Inc.

  2. Detecting macroeconomic phases in the Dow Jones Industrial Average time series

    Science.gov (United States)

    Wong, Jian Cheng; Lian, Heng; Cheong, Siew Ann

    2009-11-01

    In this paper, we perform statistical segmentation and clustering analysis of the Dow Jones Industrial Average (DJI) time series between January 1997 and August 2008. Modeling the index movements and log-index movements as stationary Gaussian processes, we find a total of 116 and 119 statistically stationary segments respectively. These can then be grouped into between five and seven clusters, each representing a different macroeconomic phase. The macroeconomic phases are distinguished primarily by their volatilities. We find that the US economy, as measured by the DJI, spends most of its time in a low-volatility phase and a high-volatility phase. The former can be roughly associated with economic expansion, while the latter contains the economic contraction phase in the standard economic cycle. Both phases are interrupted by a moderate-volatility market correction phase, but extremely-high-volatility market crashes are found mostly within the high-volatility phase. From the temporal distribution of various phases, we see a high-volatility phase from mid-1998 to mid-2003, and another starting mid-2007 (the current global financial crisis). Transitions from the low-volatility phase to the high-volatility phase are preceded by a series of precursor shocks, whereas the transition from the high-volatility phase to the low-volatility phase is preceded by a series of inverted shocks. The time scale for both types of transitions is about a year. We also identify the July 1997 Asian Financial Crisis to be the trigger for the mid-1998 transition, and an unnamed May 2006 market event related to corrections in the Chinese markets to be the trigger for the mid-2007 transition.

  3. Renal failure in patients with multiple myeloma.

    Science.gov (United States)

    Almueilo, Samir H

    2015-01-01

    Renal dysfunction is encountered in 20-25% of patients with multiple myeloma (MM) at the time of diagnosis. There is often a precipitating event. Several biochemical and clinical correlations with renal failure in MM have been reported. Renal failure in MM is associated with worse outcome of the disease. We retrospectively analyzed the medical records of 64 patients with MM admitted to our institution during the period January 1992 to December 2012. Abnormal renal function was observed in 24 (37.5%) patients and 17 (26.6%) of them had renal failure; 14 of the 17 (82.4%) of patients with renal failure had Stage III MM. Urine Bence- Jones protein was positive in ten (58.8%) patients with renal failure versus ten (21.3%) patients without renal failure (P = 0.004). Potential precipitating factors of renal failure were determined in nine patients. Renal function normalized in 11 patients with simple measures, while six patients required hemodialysis; one remained dialysis dependent till time of death. Early mortality occurred in five (29.4%) patients with renal failure as compared with two (4.3%) patients in the group without renal failure (P = 0.005). In conclusion, renal failure is associated with a higher tumor burden and Bence-Jones proteinuria in patients with MM. It is reversible in the majority of patients; however, early mortality tends to be higher in patients with persistent renal failure.

  4. Liquid-liquid interfacial properties of a symmetrical Lennard-Jones binary mixture

    Energy Technology Data Exchange (ETDEWEB)

    Martínez-Ruiz, F. J.; Blas, F. J., E-mail: felipe@uhu.es [Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Física Aplicada, Universidad de Huelva, 21007 Huelva (Spain); Moreno-Ventas Bravo, A. I. [Laboratorio de Simulación Molecular y Química Computacional, CIQSO-Centro de Investigación en Química Sostenible and Departamento de Geología, Universidad de Huelva, 21007 Huelva (Spain)

    2015-09-14

    We determine the interfacial properties of a symmetrical binary mixture of equal-sized spherical Lennard-Jones molecules, σ{sub 11} = σ{sub 22}, with the same dispersive energy between like species, ϵ{sub 11} = ϵ{sub 22}, but different dispersive energies between unlike species low enough to induce phase separation. We use the extensions of the improved version of the inhomogeneous long-range corrections of Janecek [J. Phys. Chem. B 110, 6264 (2006)], presented recently by MacDowell and Blas [J. Chem. Phys. 131, 074705 (2009)] and Martínez-Ruiz et al. [J. Chem. Phys. 141, 184701 (2014)], to deal with the interaction energy and microscopic components of the pressure tensor. We perform Monte Carlo simulations in the canonical ensemble to obtain the interfacial properties of the symmetrical mixture with different cut-off distances r{sub c} and in combination with the inhomogeneous long-range corrections. The pressure tensor is obtained using the mechanical (virial) and thermodynamic route. The liquid-liquid interfacial tension is also evaluated using three different procedures, the Irving-Kirkwood method, the difference between the macroscopic components of the pressure tensor, and the test-area methodology. This allows to check the validity of the recent extensions presented to deal with the contributions due to long-range corrections for intermolecular energy and pressure tensor in the case of binary mixtures that exhibit liquid-liquid immiscibility. In addition to the pressure tensor and the surface tension, we also obtain density profiles and coexistence densities and compositions as functions of pressure, at a given temperature. According to our results, the main effect of increasing the cut-off distance r{sub c} is to sharpen the liquid-liquid interface and to increase the width of the biphasic coexistence region. Particularly interesting is the presence of a relative minimum in the total density profiles of the symmetrical mixture. This minimum is related

  5. The physical oceanography of Jones Bank: A mixing hotspot in the Celtic Sea

    Science.gov (United States)

    Palmer, Matthew R.; Inall, Mark E.; Sharples, Jonathan

    2013-10-01

    New measurements are presented of the currents and hydrography at Jones Bank in the Celtic Sea. These measurements, collected during the summer of 2008, identify a highly energetic internal wavefield generated by the local interaction of seasonally stratified flow with topography. Observations close to the bank crest reveal internal waves of up to 40 m amplitude; approaching 50% of the local water depth. These waves occur during spring periods and are predominantly associated with off-bank tidal flow. We provide evidence that these waves are the result of hydraulic control of the tidal currents which result in supercritical flow in the bottom mixed layer (bml) on the upper slopes of the bank. The waning tide produces a transition from super to subcritical flow, identifiable as a regular hydraulic jump on the bank slope. Microstructure measurements identify a turbulent 'bore' associated with such jumps that increases bml turbulence by several orders of magnitude and produces a regular burst of enhanced mixing at the base of the ever-present thermocline. Additional mixing in the surface mixed layer is provided during gale force conditions during the first of the two spring tides observed, occurring at the start of our three-week measurement period. The average thermocline mixing rate during stormy spring tide conditions is 1.9 (±1.0, 95%) × 10-3 m2 s-1, driven by both surface mixing and hydraulic jumps. During the later calm spring period the average thermocline mixing rate is 3.3 (±1.7) × 10-4 m2 s-1, dominated by jump associated events. By comparison, the intervening neap tide period produces no hydraulic jumps and is characterised by relatively calm weather. A strong shear layer is however maintained during this 'quiet' period sufficient to enhance thermocline turbulence by a factor 1000 above background levels. A short lived peak in thermocline turbulence during the neap period produces diapycnal mixing as high as 1.6 × 10-2 m2 s-1 however a more

  6. Certain Equilibrium Properties of Gases and Gas Mixtures an Steeper lennard-Jones and Stockmayer Type Potentials

    Directory of Open Access Journals (Sweden)

    S. C. Saxena

    1967-04-01

    Full Text Available The discussion on second virial and zero pressure Joule-Thomson coefficients of non polar gases and gas mixtures is given on the Lennard Jones Type Potentials with the choice of the repulsive index as 12 and 18. These studies are also extended to polar gases and gas mixtures by including the electric dipole-dipole moment term in the two potentials. The tabulations are given for the (18-6-3 potential to enable computations of second virial and Joule-Thomson coefficients.

  7. Test of classical nucleation theory and mean first-passage time formalism on crystallization in the Lennard-Jones liquid

    Science.gov (United States)

    Lundrigan, Sarah E. M.; Saika-Voivod, Ivan

    2009-09-01

    We perform molecular dynamics (MD) and Monte Carlo computer simulations to test the ability of the recently developed formalism of mean first-passage time (MFPT) [J. Wedekind, R. Strey, and D. Reguera, J. Chem. Phys. 126, 134103 (2007); J. Wedekind and D. Reguera, J. Phys. Chem. B 112, 11060 (2008)] to characterize crystal nucleation in the Lennard-Jones liquid. We find that the nucleation rate, critical embryo size, Zeldovich factor, attachment rate, and the nucleation barrier profile obtained from MFPT all compare very well to the same quantities calculated using other methods. Furthermore, we find that the nucleation rate obtained directly through MD closely matches the prediction of classical nucleation theory.

  8. Noise-immune complex correlation for vasculature imaging based on standard and Jones-matrix optical coherence tomography

    Science.gov (United States)

    Makita, Shuichi; Kurokawa, Kazuhiro; Hong, Young-Joo; Li, En; Miura, Masahiro; Yasuno, Yoshiaki

    2016-03-01

    A new optical coherence angiography (OCA) method, called correlation mapping OCA (cmOCA), is presented by using the SNR-corrected complex correlation. An SNR-correction theory for the complex correlation calculation is presented. The method also integrates a motion-artifact-removal method for the sample motion induced decorrelation artifact. The theory is further extended to compute more reliable correlation by using multi- channel OCT systems, such as Jones-matrix OCT. The high contrast vasculature imaging of in vivo human posterior eye has been obtained. Composite imaging of cmOCA and degree of polarization uniformity indicates abnormalities of vasculature and pigmented tissues simultaneously.

  9. Volatility Transmission Between Dow Jones Stock Index And Emerging Islamic Stock Index: Case Of Subprime Financial Crises

    Directory of Open Access Journals (Sweden)

    Amir Saadaoui

    2015-02-01

    Full Text Available In the course of the recent global crisis, the stock shocks are distributed and transmitted from their homes in the developed stock market to emerging stock markets. By supporting the development of emerging stock markets, this study aims to see the transmission of volatility between the Dow Jones stock index and the Dow Jones emerging Islamic stock indiex. In this study we have divided the period into three, periods, before, during and after this crisis to demonstrate the resilience of the Islamic market index in response to the global financial crisis. Another aim of this study is to provide a new guide line for investors in emerging stock market before making investment decisions. The data are daily, going from 02/01/2005 until 31/12/2012. To measure the transmission we used bivariate BEKK-GARCH and DCC-GARCH model. The result shows that there is a transmission mainly during the crisis period which means that the crisis affects all the financial assets whether Islamic or not. The same result also shows the preference to invest in both Islamic and classical stock indexes since they are less risky.

  10. Flory-Huggins parameter χ, from binary mixtures of Lennard-Jones particles to block copolymer melts

    Science.gov (United States)

    Chremos, Alexandros; Nikoubashman, Arash; Panagiotopoulos, Athanassios Z.

    2014-02-01

    In this contribution, we develop a coarse-graining methodology for mapping specific block copolymer systems to bead-spring particle-based models. We map the constituent Kuhn segments to Lennard-Jones particles, and establish a semi-empirical correlation between the experimentally determined Flory-Huggins parameter χ and the interaction of the model potential. For these purposes, we have performed an extensive set of isobaric-isothermal Monte Carlo simulations of binary mixtures of Lennard-Jones particles with the same size but with asymmetric energetic parameters. The phase behavior of these monomeric mixtures is then extended to chains with finite sizes through theoretical considerations. Such a top-down coarse-graining approach is important from a computational point of view, since many characteristic features of block copolymer systems are on time and length scales which are still inaccessible through fully atomistic simulations. We demonstrate the applicability of our method for generating parameters by reproducing the morphology diagram of a specific diblock copolymer, namely, poly(styrene-b-methyl methacrylate), which has been extensively studied in experiments.

  11. Local shear viscosity of strongly inhomogeneous dense fluids: from the hard-sphere to the Lennard-Jones fluids.

    Science.gov (United States)

    Hoang, Hai; Galliero, Guillaume

    2013-12-04

    This work aims at providing a tractable approach to model the local shear viscosity of strongly inhomogeneous dense fluids composed of spherical molecules, in which the density variations occur on molecular distance. The proposed scheme, which relies on the local density average model, has been applied to the quasi-hard-sphere, the Week-Chandler-Andersen and the Lennard-Jones fluids. A weight function has been developed to deal with the hard-sphere fluid given the specificities of momentum exchange. To extend the approach to the smoothly repulsive potential, we have taken into account that the non-local contributions to the viscosity due to the interactions of particles separated by a given distance are temperature dependent. Then, using a simple perturbation scheme, the approach is extended to the Lennard-Jones fluids. It is shown that the viscosity profiles of inhomogeneous dense fluids deduced from this approach are consistent with those directly computed by non-equilibrium molecular dynamics simulations.

  12. Comparison between Utsu's and Vere-Jones' aftershocks model by means of a computer simulation based on the acceptance-rejection sampling of von Neumann

    Science.gov (United States)

    Reyes, J.; Morales-Esteban, A.; González, E.; Martínez-Álvarez, F.

    2016-07-01

    In this research, a new algorithm for generating a stochastic earthquake catalog is presented. The algorithm is based on the acceptance-rejection sampling of von Neumann. The result is a computer simulation of earthquakes based on the calculated statistical properties of each zone. Vere-Jones states that an earthquake sequence can be modeled as a series of random events. This is the model used in the proposed simulation. Contrariwise, Utsu indicates that the mainshocks are special geophysical events. The algorithm has been applied to zones of Chile, China, Spain, Japan, and the USA. This allows classifying the zones according to Vere-Jones' or Utsu's model. The results have been quantified relating the mainshock with the largest aftershock within the next 5 days (which has been named as Bath event). The results show that some zones fit Utsu's model and others Vere-Jones'. Finally, the fraction of seismic events that satisfy certain properties of magnitude and occurrence is analyzed.

  13. The Emperor Jones de Louis Gruenberg : le long voyage au cœur/corps de l’Autre race Louis Gruenberg’s Emperor Jones: The Long Journey into the Heart of the Other Race

    Directory of Open Access Journals (Sweden)

    Benoît Depardieu

    2009-11-01

    Full Text Available On January 7, 1933, two years before Gershwin’s Porgy and Bess, The Emperor Jones, composed by Louis Gruenberg in 1931, had its world premiere at the Metropolitan Opera of New York. Although Gruenberg’s opera looks like a mere musical adaptation of O’Neill’s acclaimed play, first performed in 1920, some alterations made by the composer allow to question its ambivalent reception by the audience and the critics. Apart from the singular choice of O’Neill’s play and Gruenberg’s special interest in African American music and vocal traditions, this paper analyses the influence of the Harlem Renaissance period and the fantasmatics of race, present in both the play and the opera, albeit exacerbated in the latter through the scopic enjoyment of the body of the black Other.

  14. Unusual IgM-secreting multiple myeloma in a dog.

    Science.gov (United States)

    Lautzenhiser, Sarah J; Walker, Mark C; Goring, Robert L

    2003-09-01

    A 4-year-old castrated male dog was evaluated because of multiple-limb lameness. Signs of pain were elicited during palpation of the regions of the proximal tibial metaphyses and distal left radial diaphysis. Radiography revealed osteolytic lesions of the long bones. Blood analyses revealed hypercalcemia and transient cytopenias. Serum protein electrophoresis did not reveal a monoclonal gammopathy; however, urine protein electrophoresis revealed Bence Jones proteinuria. Serial diagnostic sampling of bone lesions, immunohistochemical staining methods, and serum and urine protein immunoelectrophoresis were required to establish a diagnosis of multiple myeloma. Two IgM components were identified via serum protein immunoelectrofixation. The dog improved clinically after initiation of chemotherapy with melphalan and prednisone; however, the dog ultimately was euthanatized because of pathologic fracture. The case was unique because there was lack of vertebral involvement, an unusual gammopathy, and difficulty in identifying myeloma cells via serial sampling.

  15. Jones matrix analysis for a polarization-sensitive optical coherence tomography system using fiber-optic components

    Science.gov (United States)

    Hyle Park, B.; Pierce, Mark C.; Cense, Barry; de Boer, Johannes F.

    2004-11-01

    We present an analysis for polarization-sensitive optical coherence tomography that facilitates the unrestricted use of fiber and fiber-optic components throughout an interferometer and yields sample birefringence, diattenuation, and relative optic axis orientation. We use a novel Jones matrix approach that compares the polarization states of light reflected from the sample surface with those reflected from within a biological sample for pairs of depth scans. The incident polarization alternated between two states that are perpendicular in a Poincaré sphere representation to ensure proper detection of tissue birefringence regardless of optical fiber contributions. The method was validated by comparing the calculated diattenuation of a polarizing sheet, chicken tendon, and muscle with that obtained by independent measurement. The relative importance of diattenuation versus birefringence to angular displacement of Stokes vectors on a Poincaré sphere was quantified.

  16. Effects of a slow harmonic displacement on an Atomic Force Microscope system under Lennard-Jones forces

    Directory of Open Access Journals (Sweden)

    Khadraoui Morad

    2016-01-01

    Full Text Available We focus in this paper on the modeling and dynamical analysis of a tapping mode atomic force microscopy (AFM. The microbeam is subjected to a low frequency harmonic displacement of its base and to the Lennard-Jones (LJ forces at its free end. Static and modal analysis are performed for various gaps between the tip of the microbeam and a sample. The Galerkin method is employed to reduce the equations of motion to a fast-slow dynamical system. We show that the dynamics of the AFM system is governed by the contact and the noncontact invariant slow manifolds. The tapping mode is triggered via two saddle-node bifurcations of these manifolds. Moreover, the contact time is computed and the effects of the base motion amplitude and the initial gap are discussed.

  17. Perturbation and variational approach for the equation of state for hard-sphere and Lennard-Jones fluids

    Institute of Scientific and Technical Information of China (English)

    S. B. Khasare

    2012-01-01

    The present work uses the concept of a scaled particle along with the perturbation and variation approach,to develop an equation of state (EOS) for a mixture of hard sphere (HS),Lennard-Jones (LJ) fluids.A suitable flexible functional form for the radial distribution function G(R) is assumed for the mixture,with R as a variable.The function G(R) has an arbitrary parameter m and a different equation of state can be obtained with a suitable choice of m.For m =0.75 and m =0.83 results are close to molecular dynamics (MD) result for pure HS and LJ fluid respectively.

  18. The extended Lennard-Jones potential energy function: A simpler model for direct-potential-fit analysis

    Science.gov (United States)

    Hajigeorgiou, Photos G.

    2016-12-01

    An analytical model for the diatomic potential energy function that was recently tested as a universal function (Hajigeorgiou, 2010) has been further modified and tested as a suitable model for direct-potential-fit analysis. Applications are presented for the ground electronic states of three diatomic molecules: oxygen, carbon monoxide, and hydrogen fluoride. The adjustable parameters of the extended Lennard-Jones potential model are determined through nonlinear regression by fits to calculated rovibrational energy term values or experimental spectroscopic line positions. The model is shown to lead to reliable, compact and simple representations for the potential energy functions of these systems and could therefore be classified as a suitable and attractive model for direct-potential-fit analysis.

  19. ANALYTIC EQUATION OF STATE FOR GENERALIZED LENNARD-JONES SOLID INCLUDING LOWEST-ORDER ANHARMONIC AND CORRELATION CORRECTIONS

    Institute of Scientific and Technical Information of China (English)

    Cheng Jian-zheng; Zhang De-jun; Lan Cong-qing; Ye Chao-hui

    2000-01-01

    Based on the cell model, the general formula for the free energy of solids is derived analytically with the lowest order anharmonic modification and correlation effect taken into account. Combining a method of summing over lattice sites, the analytic equation of state for generalized Lennard-Jones solid is derived. The calculations show that the agreement between theory and computer simulation is quite good and is significantly improved as compared with the numerical results in literature. The comparison of different effects shows the theory including all neighbors but only considering the lowest anharmonic and correlation effects may be a good and convenient approximation for practical solids. The approximation can be easily extended to the quantum case and other generalized potentials.

  20. Perturbation approach for equation of state for hard-sphere and Lennard–Jones pure fluids

    Indian Academy of Sciences (India)

    S B Khasare; M S Deshpande

    2011-06-01

    In this paper we have established the equation of state (EOS) for liquids. The EOS was established for hard-sphere (HS) fluid along with Lennard–Jones (LJ) fluid incorporating perturbation techniques. The calculations are based on suitable axiomatic functional forms for surface tension $S_m (r )$, $r ≥ d/2$ with intermolecular separation , as a variable, and is an arbitrary real number (pole). The results for /ρ from the present EOS thus obtained are compared with Percus-Yevick (PY), scaled particle theory (SPT), and Carnahan–Starling (CS). In addition, we have found a simple EOS for the HS fluid in the region which represents the simulation data accurately. It is observed that, this EOS for HS gives, PY (pressure) for = 0, CS for = 4/5, whereas for = 1 it corresponds to SPT.

  1. Immigration Reform: Implementation of Legalization Program. Statement of Arnold P. Jones, Senior Associate Director, General Government Division before the Subcommittee on Immigration and Refugee Affairs Committee.

    Science.gov (United States)

    Jones, Arnold P.

    This document presents the testimony of Arnold P. Jones, Senior Associate Director of the United States General Accounting Office, before the Senate Subcommittee on Immigration and Refugee Affairs, on the Immigration Reform and Control Act of 1986. The Act established a legalization program that permits undocumented aliens to become permanent…

  2. Reading Research on Core Values, Christian Ethos and School Transformation at England's Most Improved Academy: A Reply to Bragg, Allington, Simmons and Jones

    Science.gov (United States)

    Pike, Mark A.

    2011-01-01

    This article presents the author's reply to the comments of Bragg, Allington, Simmons and Jones to his article "Transaction and transformation at Trinity" (Pike, 2010) wherein he reported a case study of Trinity Academy, which serves a former mining community and social priority area near Doncaster in South Yorkshire. In 2008, just…

  3. Comment on Cross, Fine, Jones, and Walsh (2012): Do Mental Health Professionals Who Serve on/with Child Advocacy Centers Experience Role Conflict?

    Science.gov (United States)

    Friend, Colleen

    2012-01-01

    Cross, Fine, Jones, and Walsh's (2012) article "Mental Health Professionals in Children's Advocacy Centers: Is There Role Conflict?" challenges two recent publications' criticisms that child advocacy centers create role conflict for mental health professionals and explains how child advocacy centers actually work, describing the different roles…

  4. Sex Differences in Left-Handedness Are Also Evident in Scandinavia and in Twins: Comment on Papadatou-Pastou, Martin, Munafo, and Jones (2008)

    Science.gov (United States)

    Vuoksimaa, Eero; Kaprio, Jaakko

    2010-01-01

    The lack of sex difference in left-handedness in Scandinavian countries reported by Papadatou-Pastou, Martin, Munafo, and Jones (2008) is questioned. We investigated the sex difference in left-handedness in two Finnish, one Norwegian, and one Swedish population-based sample not included in the Papadatou-Pastou et al. (2008) meta-analysis. The…

  5. A Case Report of Tracheal Extramedullary Plasmacytoma

    Institute of Scientific and Technical Information of China (English)

    Kun Wang; Yunchao Huang; Anning Chen

    2008-01-01

    @@ Introduction Extramedullary plasmacytoma (EMP) is an uncommon tumor that often develops outside the bone and arises from clonal proliferation of atypical plasma cells before EMP is diagnosed. Multiple myeloma(MM) must be excluded by performing laboratory tests such as serum protein electrophoresis, bone marrow biopsy and skeletal imaging ex-aminations. A bone marrow biopsy should show no evidence of mul-tiple myeloma, and less than 3% of plasma cells. Monoclonal bands of serum protein and Bence-Jones protein in the urine can sometimes be detected. EMP can involve any extraosseous organs, but it pre-dominantly affects the head and neck areas. Any extra-osseous organ may also be involved[1,2]. Tracheal involvement is a rare finding. Only a few cases of primary tracheal extramedullary plasmcytoma have been reported[2-4], Here we present a rare case of truly localized tra-cheal extram edullary plasmacytoma without evidence of myelomaelsewhere.

  6. Commercial Instrumentation Technology Associates Inc. Biomedical Experiments Payload (CIBX-2)

    Science.gov (United States)

    Morrison, Dennis; Edmundson, Allen; Robinson, Keith (Technical Monitor)

    2002-01-01

    Experiments to find solutions for a range of biomedical issues are being hosted by the Commercial Instrumentation Technology Associates Inc. (ITA) Biomedical Experiments (CIBX-2) payload. This research encompasses more than 20 separate experiments including cancer research, commercial experiments and hands-on student experiments from 10 schools as part of ITA's ongoing University Among the Stars program. Protein crystal growth experiments will address the structure of urokinase - a protein that has been identified as a key enzyme in the spread of brain, lung, colon, prostate and breast cancers. Crystals of Bence Jones, a protein associated with bone cancer, will also be grown. Understanding their structures may help scientists develop treatments. In a related area, the Microencapsulation of Drugs (MEPS) is an anti-cancer drug delivery system, based on a 10-year partnership with NASA's Johnson Space Center. On this mission, the co-encapsulation of antibodies and immune stimulants will be made in submicron microcapsules to target pulmonary and bacterial infections.

  7. A Strategy for Synthesis of Pathogenic Human Immunoglobulin Free Light Chains in E. coli

    Science.gov (United States)

    Rognoni, Paola; Lavatelli, Francesca; Casarini, Simona; Palladini, Giovanni; Verga, Laura; Pedrazzoli, Paolo; Valentini, Giovanna; Merlini, Giampaolo; Perfetti, Vittorio

    2013-01-01

    Monoclonal immunoglobulin light chains are normally synthesized in excess compared to the heavy chain partners and can be detected in serum and urine (“free” LC). Occasionally free LC are per se cause of organ toxicity, as in free LC-related disorders. In AL amyloidosis, the most common of these conditions, free LC with peculiar biophysical properties related to their primary structure damage target organs and organize in amyloid fibrils. Unlimited availability of well-characterized free LC is instrumental to investigate the toxic effect of these proteins and to study their interactions with targets. We present a straightforward strategy to obtain recombinant monoclonal free LC by using a bacterial system. These proteins, expressed as inclusion bodies, were subjected to solubilization and refolding procedures to recover them in native form. To minimize differences from the circulating natural LC, full-length recombinant LC were expressed, i.e. complete of variable and constant regions, with the original amino acid sequence along the entire protein, and with no purification tags. The strategy was exploited to generate free LC from three AL amyloidosis patients. After purification, recombinant proteins were biochemically characterized and compared to the natural Bence Jones protein isolated from one of the patients. Results showed that the recombinant free LC were properly folded and formed homodimers in solution, similar to the natural Bence Jones protein used for comparison. Furthermore, as proof of pathogenicity, recombinant proteins formed amyloid fibrils in vitro. We believe that the present strategy represents a valuable tool to speed research in free LC-related disorders. PMID:24086679

  8. A strategy for synthesis of pathogenic human immunoglobulin free light chains in E. coli.

    Directory of Open Access Journals (Sweden)

    Paola Rognoni

    Full Text Available Monoclonal immunoglobulin light chains are normally synthesized in excess compared to the heavy chain partners and can be detected in serum and urine ("free" LC. Occasionally free LC are per se cause of organ toxicity, as in free LC-related disorders. In AL amyloidosis, the most common of these conditions, free LC with peculiar biophysical properties related to their primary structure damage target organs and organize in amyloid fibrils. Unlimited availability of well-characterized free LC is instrumental to investigate the toxic effect of these proteins and to study their interactions with targets. We present a straightforward strategy to obtain recombinant monoclonal free LC by using a bacterial system. These proteins, expressed as inclusion bodies, were subjected to solubilization and refolding procedures to recover them in native form. To minimize differences from the circulating natural LC, full-length recombinant LC were expressed, i.e. complete of variable and constant regions, with the original amino acid sequence along the entire protein, and with no purification tags. The strategy was exploited to generate free LC from three AL amyloidosis patients. After purification, recombinant proteins were biochemically characterized and compared to the natural Bence Jones protein isolated from one of the patients. Results showed that the recombinant free LC were properly folded and formed homodimers in solution, similar to the natural Bence Jones protein used for comparison. Furthermore, as proof of pathogenicity, recombinant proteins formed amyloid fibrils in vitro. We believe that the present strategy represents a valuable tool to speed research in free LC-related disorders.

  9. Ouincy Jones / Quincy Jones ; intervjueerinud Emil Wilbekin

    Index Scriptorium Estoniae

    Jones, Quincy, 1933-

    2009-01-01

    Endise jazzartisti ja preaguse muusikaärimehe, produtsendi Quincy Jonesi mõtteid tööst viieosalise dokumentaalfilmiga "Say it Loud: Black Music in America" , tööst Michael Jacksoniga ja muusikast

  10. A case of plasmacytoma of scalp in pediatric thalassemia human immunodeficiency virus positive child

    Directory of Open Access Journals (Sweden)

    Swapan Kumar Mallick

    2013-01-01

    Full Text Available A 9-year-old female child, known case of beta thalassemia major and human immunodeficiency virus seropositive, presented with two slowly growing masses in the temporoparietal region of the skull on both sides. Irregular bony erosion at left parietal area with underlying scalp hematoma with similar change at the right side to a lesser degree were found. Fine needle aspiration cytology from masses showed abundant plasmacytoid cells some of which are binucleated along with free erythroblasts. Cytological features were suggestive of plasmacytoma. Serum protein electrophoresis showed no M-band. Urine was negative for Bence-Jones protein. Bone marrow biopsy showed no plasma cell neoplasm. Diagnosed as first reported case of primary multiple solitary plasmacyomas affecting bilateral temporoparietal bones in a pediatric patient, the child was treated with external beam radiation therapy to scalp lesions showing excellent results and on further follow-up showed no evidence of progressive disease.

  11. Effect of gold nanoparticles on structure and dynamics of binary Lennard-Jones liquid: Wave-vector space analysis

    Science.gov (United States)

    Separdar, L.; Davatolhagh, S.

    2016-12-01

    Molecular dynamics simulations at constant (N , V , T) are used to study the mutual effects of gold nanoparticles on the structure and dynamics of Kob-Andersen binary Lennard-Jones (BLJ) liquid within the framework of mode coupling theory of dynamic glass transition in the reciprocal space. The results show the 'softening' effect of the gold nanoparticles on the liquid dynamics in terms of (i) reducing the mode coupling crossover temperature Tc with respect to that of the bulk BLJ (i.e. BLJ without nanoparticles), (ii) decreasing the time interval of β-relaxation, and (iii) decreasing the exponent γ characterizing the power-law behavior of the α-relaxation time. This softening effect is explained in terms of the van der Waals attraction between the gold atoms comprising the nanoparticle and the BLJ host atoms, such that adsorption of host atoms onto the nanoparticle surface creates more space or free-volume for the other atoms to diffuse. By the same token interactions of purely excluded-volume-type are expected to result in the opposite effect. It is also noted that, much unlike BLJ host particles, the dynamics of gold nanoparticles is much less dependent on the wave-vector and that it exhibits a nearly exponential behavior in the α-relaxation regime.

  12. Molecular dynamics simulation of polymerlike thin films irradiated by fast ions: A comparison between FENE and Lennard-Jones potentials

    Science.gov (United States)

    Lima, N. W.; Gutierres, L. I.; Gonzalez, R. I.; Müller, S.; Thomaz, R. S.; Bringa, E. M.; Papaléo, R. M.

    2016-11-01

    In this paper, the surface effects of individual heavy ions impacting thin polymerlike films were investigated, using molecular dynamics simulations with the finite extensible nonlinear elastic (FENE) potential to describe the molecular chains. The perturbation introduced by the ions in the lattice was modeled assuming that the initial excitation energy in the ion track is converted into an effective temperature, as in a thermal spike. The track was heated only within the film thickness h , leaving a nonexcited substrate below. The effect of decreasing thickness on cratering and sputtering was evaluated. The results were compared to experimental data of thin polymer films bombarded by MeV-GeV ions and to simulations performed with the Lennard-Jones potential. While several qualitative results observed in the experiments were also seen in the simulations, irrespective of the potential used, there are important differences observed on FENE films. Crater dimensions, rim volume, and sputtering yields are substantially reduced, and a threshold thickness for molecular ejection appears in FENE simulations. This is attributed to the additional restrictions on mass transport out of the excited track region imposed by interchain interactions (entanglements) and by the low mobility of the molten phase induced by the spike.

  13. Mapping the phase diagram for neon to a quantum Lennard-Jones fluid using Gibbs ensemble simulations.

    Science.gov (United States)

    Georgescu, Ionuţ; Brown, Sandra E; Mandelshtam, Vladimir A

    2013-04-01

    In order to address the issue of whether neon liquid in coexistence with its gas phase can be mapped to a quantum Lennard-Jones (LJ) fluid, we perform a series of simulations using Gibbs ensemble Monte Carlo for a range of de Boer quantum parameters Λ=ℏ/(σ√(mε)). The quantum effects are incorporated by implementing the variational gaussian wavepacket method, which provides an efficient numerical framework for estimating the quantum density at thermal equilibrium. The computed data for the LJ liquid is used to produce its phase diagram as a function of the quantum parameter, 0.065 ≤ Λ ≤ 0.11. These data are then used to fit the experimental phase diagram for neon liquid. The resulting parameters, ε = 35.68 ± 0.03 K and σ = 2.7616 ± 0.0005 Å (Λ = 0.0940), of the LJ pair potential are optimized to best represent liquid neon in coexistence with its gas phase for a range of physically relevant temperatures. This multi-temperature approach towards fitting and assessing a pair-potential is much more consistent than merely fitting a single data point, such as a melting temperature or a second virial coefficient.

  14. The role of fcc tetrahedral subunits in the phase behavior of medium sized Lennard-Jones clusters.

    Science.gov (United States)

    Saika-Voivod, Ivan; Poon, Louis; Bowles, Richard K

    2010-08-21

    The free energy of a 600-atom Lennard-Jones cluster is calculated as a function of surface and bulk crystallinity in order to study the structural transformations that occur in the core of medium sized clusters. Within the order parameter range studied, we find the existence of two free energy minima at temperatures near freezing. One minimum, at low values of both bulk and surface order, belongs to the liquid phase. The second minimum exhibits a highly ordered core with a disordered surface and is related to structures containing a single fcc-tetrahedral subunit, with an edge length of seven atoms (l=7), located in the particle core. At lower temperatures, a third minimum appears at intermediate values of the bulk order parameter which is shown to be related to the formation of multiple l=6 tetrahedra in the core of the cluster. We also use molecular dynamics simulations to follow a series of nucleation events and find that the clusters freeze to structures containing l=5, 6, 7, and 8 sized tetrahedra as well as those containing no tetrahedral units. The structural correlations between bulk and surface order with the size of the tetrahedral units in the cluster core are examined. Finally, the relationships between the formation of fcc tetrahedral subunits in the core, the phase behavior of medium sized clusters and the nucleation of noncrystalline global structures such as icosahedra and decahedra are discussed.

  15. "No interest in human anatomy as such": Frederic Wood Jones dissects anatomical investigation in the United States in the 1920s.

    Science.gov (United States)

    Jones, Ross L

    2014-03-01

    In 1926, Frederic Wood Jones, professor of Anatomy at the University of Adelaide and a leading figure in the British anatomical world, took a Rockefeller Foundation funded trip to the United States in order to inspect anatomy programmes and medical museums and to meet leading figures in the anatomical and anthropological world. His later reflections paint a picture of a discipline in transition. Physical anthropology and gross anatomy were coming to a crisis point in the United States, increasingly displaced by research in histology, embryology and radiological anatomy. Meanwhile, in Britain and its colonial outposts, anatomists such as Wood Jones were attempting to re-invigorate the discipline in the field, studying biological specimens as functional and active agents in their particular milieus, but with human dissection at the core. Thus, an examination of this trip allows us to see how the interaction between two traditions in anatomy informed the process of the development of human biology in this critical period.

  16. Fibrillary glomerulonephritis combined with chronic inflammatory demyelinating polyneuropathy

    Directory of Open Access Journals (Sweden)

    Woo Kyung Sung

    2015-06-01

    Full Text Available A 58-yr-old man presented with leg edema and subacute weakness of his bilateral lower extremities. Urinary and serum immunoelectrophoresis revealed the presence of lambda-type Bence Jones proteins. He was ultimately diagnosed with monoclonal gammopathy of undetermined significance (MGUS. A renal biopsy specimen showed fibrillary glomerulonephritis (FGN, which was randomly arranged as 12–20 m nonbranching fibrils in the basement membranes. Immunofluorescence studies were negative for immunoglobulin (IgG, IgM, IgA, C3, and kappa light chains in the capillary walls and mesangial areas. A Congo red stain for amyloid was negative. Electromyography and nerve conduction velocity examinations results were compatible with the presence of demyelinating polyneuropathy. This case showed a rare combination of FGN, without Ig deposition, and MGUS combined with chronic inflammatory demyelinating polyneuropathy (CIDP.

  17. Prozone effect of serum IgE levels in a case of plasma cell leukemia

    Directory of Open Access Journals (Sweden)

    Talamo Giampaolo

    2010-09-01

    Full Text Available Abstract We describe a case of multiple myeloma (MM and secondary plasma cell leukemia (PCL secreting IgE-kappa immunoglobulin. To our knowledge, only 2 cases of IgE-producing secondary PCL have been reported in the medical literature. In our patient, the only tumor marker available for monitoring the therapeutic response to chemotherapy and allogeneic stem cell transplantation was the quantitative M component at serum protein electrophoresis (SPEP, because serum free light chains were in the normal range, Bence-Jones proteinuria was absent, and quantitative serum IgE levels provided inaccurate and erratic results, due to the prozone effect. This is a laboratory phenomenon that occurs when antigen excess interferes with antibody-based methods requiring immune complex formation for detection. It is important to recognize the presence of a prozone effect, because it can produce falsely normal results, and therefore it could lead clinicians to incorrect assessment of the response to therapy.

  18. Scaling relation and regime map of explosive gas–liquid flow of binary Lennard-Jones particle system

    KAUST Repository

    Inaoka, Hajime

    2012-02-01

    We study explosive gasliquid flows caused by rapid depressurization using a molecular dynamics model of Lennard-Jones particle systems. A unique feature of our model is that it consists of two types of particles: liquid particles, which tend to form liquid droplets, and gas particles, which remain supercritical gaseous states under the depressurization realized by simulations. The system has a pipe-like structure similar to the model of a shock tube. We observed physical quantities and flow regimes in systems with various combinations of initial particle number densities and initial temperatures. It is observed that a physical quantity Q, such as pressure, at position z measured along a pipe-like system at time t follows a scaling relation Q(z,t)=Q(zt) with a scaling function Q(ζ). A similar scaling relation holds for time evolution of flow regimes in a system. These scaling relations lead to a regime map of explosive flows in parameter spaces of local physical quantities. The validity of the scaling relations of physical quantities means that physics of equilibrium systems, such as an equation of state, is applicable to explosive flows in our simulations, though the explosive flows involve highly nonequilibrium processes. In other words, if the breaking of the scaling relations is observed, it means that the explosive flows cannot be fully described by physics of equilibrium systems. We show the possibility of breaking of the scaling relations and discuss its implications in the last section. © 2011 Elsevier B.V. All rights reserved.

  19. Immunological evidence of monoclonal gammopathy in North India: a hospital based study

    Directory of Open Access Journals (Sweden)

    Kalpana Singh

    2010-08-01

    Full Text Available Kalpana Singh1, Bhawna Singh2, Sarika Arora2, Alpana Saxena11Department of Biochemistry, Maulana Azad Medical College and LN Hospital, New Delhi, India; 2Department of Biochemistry, GB Pant Hospital, New Delhi, IndiaBackground: Monoclonal gammopathy of unknown significance (MGUS is a condition in which a paraprotein is found in the blood during standard laboratory tests. It is age-related and characterized by accumulation of bone marrow plasma cells derived from a single abnormal clone. The aim of this study was to investigate the pattern of MGUS in North Indian urban population.Methods: Serum and urine samples were collected from 320 suspected cases of gammopathy, were analyzed by sensitive immunological technique based protein electrophoresis followed by immunofixation for detection and type of monoclonal/polyclonal gammopathies. Twenty-five healthy subjects were included as controls.Results: Gammopathies were observed in 38 (11.88% patients. Out of these 7.5% were ¬monoclonal and 4.3% were polyclonal. Overall age of presentation of these monoclonal ¬gammopathies in both sexes was between 21 and 76 years. Gender-related ratio (men:women for these gammopathies was 1:1.18. Predominant heavy chain isotype was IgG (62.5% followed by IgA (37.5%. Among light chains, kappa (κ and lambda (λ chains appeared in 91.6% and 8.4% gammopathies respectively. Paraprotein fractions obtained were IgGκ (58.3%, IgGλ (4.16%, IgAκ (33.3%, and IgAλ (4.16% with 25% samples being positive for Bence Jones proteinuria.Conclusions: Clinical laboratories play an important role in confirming the immunological diagnosis of gammopathies. Determination of nature of paraproteinemia and its associated diseases calls for more extensive studies in India.Keywords: monoclonal gammopathy, immunoelectrophoresis, multiple myeloma, bence jones protein, immunoglobulins

  20. FLOODPLAIN, JONES COUNTY, USA

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — The Floodplain Mapping/Redelineation study deliverables depict and quantify the flood risks for the study area. The primary risk classifications used are the...

  1. HYDRAULICS, Jones County, Iowa

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Survey data includes spatial datasets and data tables necessary to digitally represent data collected in the survey phase of the study. (Source: FEMA Guidelines and...

  2. HYDROLOGY, JONES COUNTY, USA

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Hydrology data include spatial datasets and data tables necessary for documenting the hydrologic procedures for estimating flood discharges for a flood insurance...

  3. Lennard-Jones parameters for small diameter carbon nanotubes and water for molecular mechanics simulations from van der Waals density functional calculations.

    Science.gov (United States)

    Kaukonen, M; Gulans, A; Havu, P; Kauppinen, E

    2012-03-05

    Lennard-Jones (LJ) parameters are derived for classical nonpolarizable force fields for carbon nanotubes (CNTs) and for CNT-water interaction from van der Waals (vdW) enhanced density functional calculations. The new LJ parameters for carbon-carbon interactions are of the same order as those previously used in the literature but differ significantly for CNT-water interactions. This may partially originate from the fact that in addition to pure vdW interactions the polarization and other quantum mechanics effects are embedded into the LJ-potential.

  4. La Chartreuse de Parme,Tom Jones et Vanity Fair : la représentation autoconsciente dans trois stades de développement

    OpenAIRE

    Vågslid, Gudfrid

    2007-01-01

    En résumé INTRODUCTION Pour ce mémoire j ai choisi trois uvres réalistes, notamment The History of Tom Jones, a Foundling publié par Henry Fielding en 1749, La Chartreuse de Parme de Stendhal (1839) et Vanity Fair, a novel without a hero de William Makepeace Thackeray qui est paru en feuilleton en 1847-48. Je me concentrerai sur la Chartreuse et me servirai d exemples des deux autres uvres pour mettre en relief celle de Stendhal. Stendhal et Fielding partageaient « le m...

  5. Solitons on H bonds in proteins

    DEFF Research Database (Denmark)

    d'Ovidio, F.; Bohr, H.G.; Lindgård, Per-Anker

    2003-01-01

    system shows that the solitons are spontaneously created and are stable and moving along the helix axis. A perturbation on one of the three H-bond lines forms solitons on the other H bonds as well. The robust solitary wave may explain very long-lived modes in the frequency range of 100 cm(-1) which...... are found in recent x-ray laser experiments. The dynamics parameters of the Toda lattice are in accordance with the usual Lennard-Jones parameters used for realistic H-bond potentials in proteins....

  6. Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent.

    Science.gov (United States)

    Li, Pengfei; Roberts, Benjamin P; Chakravorty, Dhruva K; Merz, Kenneth M

    2013-06-11

    Metal ions play significant roles in biological systems. Accurate molecular dynamics (MD) simulations on these systems require a validated set of parameters. Although there are more detailed ways to model metal ions, the nonbonded model, which employs a 12-6 Lennard-Jones (LJ) term plus an electrostatic potential is still widely used in MD simulations today due to its simple form. However, LJ parameters have limited transferability due to different combining rules, various water models and diverse simulation methods. Recently, simulations employing a Particle Mesh Ewald (PME) treatment for long-range electrostatics have become more and more popular owing to their speed and accuracy. In the present work we have systematically designed LJ parameters for 24 +2 metal (M(II)) cations to reproduce different experimental properties appropriate for the Lorentz-Berthelot combining rules and PME simulations. We began by testing the transferability of currently available M(II) ion LJ parameters. The results showed that there are differences between simulations employing Ewald summation with other simulation methods and that it was necessary to design new parameters specific for PME based simulations. Employing the thermodynamic integration (TI) method and performing periodic boundary MD simulations employing PME, allowed for the systematic investigation of the LJ parameter space. Hydration free energies (HFEs), the ion-oxygen distance in the first solvation shell (IOD) and coordination numbers (CNs) were obtained for various combinations of the parameters of the LJ potential for four widely used water models (TIP3P, SPC/E, TIP4P and TIP4PEW). Results showed that the three simulated properties were highly correlated. Meanwhile, M(II) ions with the same parameters in different water models produce remarkably different HFEs but similar structural properties. It is difficult to reproduce various experimental values simultaneously because the nonbonded model underestimates the

  7. Application of the density functional method to study phase transitions in an associating Lennard-Jones fluid adsorbed in energetically heterogeneous slit-like pores

    Science.gov (United States)

    Huerta, Adrian; Pizio, Orest; Bryk, Pawel; Sokolowski, Stefan

    A density functional approach is used to study the adsorption of the four-bonding-site model associating Lennard-Jones fluid in slit-like pores with energetically heterogeneous walls. The fluid-wall potential is qualitatively similar to that invoked by Röcken, P., Somoza, A., Tarazona, P., and Findenegg, G. H., 1999, J. chem. Phys., 108, 8089, i.e. it consists of a homogeneous part that varies in the direction perpendicular to the wall and a periodic part, varying also in one direction parallel to the wall. Both parts are modelled by Lennard-Jones 9,3-type functions. The structure of the adsorbed film is characterized by the local densities of all particles and the densities of the monomers. The phase diagrams are evaluated for several systems characterized by different corrugation of the adsorbing potential. The adsorbing field is strong enough to allow for the layering transition. As well as the formation of the so-called bridge phase that fills the pore space over the most energetic parts of the wall and of capillary condensation, the layering transition is observed within the first layer adjacent to the pore walls. If the adsorbing potential due to each pore wall is shifted in phase by pi/2, the bridge phase is not formed.

  8. 改良Pendulum与改良Jones远移磨牙的对比分析%A comparative analysis on molar distalization with modified pendulum appliance and modified Jones

    Institute of Scientific and Technical Information of China (English)

    张琳林; 吴杨; 邹林洪; 张定铭; 李欣; 戴红卫

    2011-01-01

    目的:探讨改良Pendulum矫治器、改良Jones装置推磨牙向远中的疗效.方法:选择22例轻中度前牙拥挤的安氏Ⅱ类错(牙合)病例,介于拔牙和不拔牙矫治的边缘,所有病例被平均随机分配在2个组,分别采用2种装置推磨牙向远中,在治疗前后进行X线头影测量和模型测量分析,采用SPSS软件对数据进行分析.结果:2组远中移动效果均比较明显,但在移动速度、磨牙中央窝宽度差、前牙覆胎差、上颌第二前磨牙以及第一磨牙的倾斜度的统计分析上差异有统计学意义.结论:改良Pendulum矫治器、Jones装置均可有效地推上颌磨牙向远中移动,但改良Jones组磨牙向远中更少发生倾斜移动,矫治时间短,移动速度更快,对前牙支抗消耗相对较低.%Objective: To investigate the clinical effects of modified pendulum appliance and modified Jones on distalization of maxillary first molars. Methods: Twenty-two moderate anterior crowding of class Ⅱ malocclusion patients , between extraction and non-extraction treatment were chosen. The 22 patients were divided into two equal groups randomly. This study measured the changes in distance, velocity and position of maxillary first molars. The effects were evaluated by cephalometric radiographs and dental models analysis before and after distalization treatment. SPSS was used to determine if there were any significant differences. Results: Two effects of distal movement were obvious. However, there were significant differences between group A and group B in the travel speed, molar central fossa width , overbite , the inclination of maxillary second premolar and first molar. Conclusion: The results indicate that both modified pendulum appliance and modified Jones candistalize maxillary molars effectively. But the molars of Modified Jones Group have less distal tilting, and with short treatment time, faster movement, and consume lower anterior teeth anchorage.

  9. Sand on the move: Post Hurricane Sandy analysis of the coastal sediment budget and bedform migration at Jones Inlet, Long Island, NY

    Science.gov (United States)

    Bales, M. K.; Goff, J. A.; Austin, J. A.; Flood, R. D.; Christensen, B. A.; Browne, C. M.; Saustrup, S.

    2013-12-01

    Hurricane Sandy struck the Northeast coast of the United States on October 29, 2012. Although sustained winds were downgraded to ~70 kts upon landfall, the vast area of the storm along with the direction of impact resulted in major storm-surge flooding and damage, as well as significant changes to the morphology of the coast-line, altering the characteristics of major barrier islands, inlets, and estuaries. A January 2013 post-storm survey aboard the R/V Pritchard, conducted by the University of Texas Institute for Geophysics, Stony Brook University, and Adelphi University, sought to investigate the impact of this post-tropical cyclone on the southwestern coast of Long Island, NY which sustained storm surges of up to 4 m above normal sea level. The objective of this project is to gain insight on the sedimentological volume changes and bathymetrical alterations made on the seafloor within Jones Inlet and the immediate estuaries behind Jones Beach and Long Beach Island. By studying these changes we hope to gain a better understanding of how large cyclonic storms alter sediment volumes and seafloor topography within major inlets and estuarine systems. These modifications can be observed in post-storm multibeam swath bathymetry and backscatter when compared to similar pre-storm data collected in 2010 by Stony Brook University. Post-storm CHIRP seismic reflection data were also collected, in order to define stratigraphic geometries, as well as grab samples to determine grain size distributions and ground truth for the backscatter data. The acoustic reflections imaged in the CHIRP data allow basal reflectors and dominate horizons to be traced throughout the inlet and estuaries. Our analysis focuses on (1) defining and quantifying areas of deposition and erosion from before-and-after bathymetry data; (2) comparing bedform patterns and grain size distributions from before-and-after backscatter and grab sample analysis; and (3) defining stratal geometries of the shallow

  10. Equation of state and some structural and dynamical properties of the confined Lennard-Jones fluid into carbon nanotube: A molecular dynamics study

    Science.gov (United States)

    Abbaspour, Mohsen; Akbarzadeh, Hamed; Salemi, Sirous; Abroodi, Mousarreza

    2016-11-01

    By considering the anisotropic pressure tensor, two separate equations of state (EoS) as functions of the density, temperature, and carbon nanotube (CNT) diameter have been proposed for the radial and axial directions for the confined Lennard-Jones (LJ) fluid into (11,11), (12,10), and (19,0) CNTs from 120 to 600 K using molecular dynamics (MD) simulations. We have also investigated the effects of the pore size, pore loading, chirality, and temperature on some of the structural and dynamical properties of the confined LJ fluid into (11,11), (12,10), (19,0), and (19,19) CNTs such as the radial density profile and self-diffusion coefficient. We have also determined the EoS for the confined LJ fluid into double and triple walled CNTs.

  11. Thermodynamic, Structural and Transport Properties of Lennard-Jones Liquid Systems. A Molecular Dynamics Simulations of Liquid Helium, Neon, Methane and Nitrogen

    Directory of Open Access Journals (Sweden)

    F. Ould Kadour

    2003-12-01

    Full Text Available Abstract: Molecular dynamics calculations are carried out in order to find the properties of Lennard Jones liquids in different state points of their phase diagram. The spherical shape and the stability of the helium, neon, methane and nitrogen make the liquids easily accessible to numerical simulation. Thermodynamic, structural, and transport properties are studied and compared with both experimental data and recent theoretical investigations. In the present work, up to 22 state points are covered, some of which are near or at the triple point. It will be shown that the classical approach leads to data that are in very good agreement with experiments and other types of calculations. At high temperatures and low densities, we observe a decrease in the uncertainties in the stress autocorrelation function by increasing the number of iterations.

  12. The Effectively Used Expressionistic Devices in The Emperor Jones%表现主义手法在《琼斯皇》中的应用

    Institute of Scientific and Technical Information of China (English)

    和伟

    2004-01-01

    本文从表现主义手法的角度对奥尼尔的进行了研究,着重探讨了表现主义手法在揭示剧中人物内心灵魂,挖掘人物的精神世界,展示其深刻的内心体验,及畸形心理形为中的体现.%This article inquires into how O' Neill uses expressionistic techniques to express Jones'inner world. The author points out the function of revealing the character's spirit, excavating the character's spiritual world, the character's profound experience and complicated abnormal psychology when O' Neill applies the symbology.

  13. Accurate Monte Carlo simulations on FCC and HCP Lennard-Jones solids at very low temperatures and high reduced densities up to 1.30.

    Science.gov (United States)

    Adidharma, Hertanto; Tan, Sugata P

    2016-07-07

    Canonical Monte Carlo simulations on face-centered cubic (FCC) and hexagonal closed packed (HCP) Lennard-Jones (LJ) solids are conducted at very low temperatures (0.10 ≤ T(∗) ≤ 1.20) and high densities (0.96 ≤ ρ(∗) ≤ 1.30). A simple and robust method is introduced to determine whether or not the cutoff distance used in the simulation is large enough to provide accurate thermodynamic properties, which enables us to distinguish the properties of FCC from that of HCP LJ solids with confidence, despite their close similarities. Free-energy expressions derived from the simulation results are also proposed, not only to describe the properties of those individual structures but also the FCC-liquid, FCC-vapor, and FCC-HCP solid phase equilibria.

  14. Moore’s Law: The Life of Gordon Moore, Silicon Valley’s Quiet Revolutionary Arnold Thackray, David C. Brock, and Rachel Jones

    Energy Technology Data Exchange (ETDEWEB)

    Devanathan, Ram

    2016-05-01

    Five decades ago, Gordon Moore, who would go on to co-found Intel Corporation, made a prescient observation about the exponential advance of semiconductor technology with a corresponding decrease in device cost. His prediction about the pace of doubling of the number of transistors in an integrated circuit came to be known eponymously as Moore’s law and has held true for 50 years. He also foresaw, way back in 1965, the development of home computers, electronic controls in automobiles, portable communications systems, and electronic wrist watches. Moore’s fascinating life, characterized by relentless innovation, charity and breathtaking humility, is the subject of this comprehensive authorized biography. The enthralling narrative is the product of collaboration between an academic (Thackray), a technology historian (Brock) and a journalist (Jones), and draws its material from numerous interviews, Moore’s meticulously maintained notes and professional records, personal papers, industry data, published volumes, and news accounts.

  15. Phase Equilibria and Plate-fluid Interfacial Tensions for Four-site Associating Lennard-Jones Fluids Confined in Slit Pores

    Institute of Scientific and Technical Information of China (English)

    FU Dong; YAN Shu-Mei; WANG Xue-Min

    2008-01-01

    The excess Helmholtz free energy functional for four-site associating Lennard-Jones(LJ)fluid was formulated in terms of a modified fundamental measure theory for short-ranged interactions and a first-order mean-spherical approximation theory for long-ranged attraction.Within the framework of density functional theory,the thermodynamic properties including the average density isotherms,density profiles and fractions of not bonded monomers characterizing the coexistences between gas-like and liquid-like phases for capillary condensation,phase equilibria and equilibrium plate-fluid interfacial tensions were investigated.The influences of association energy,fluid-solid interaction and pore width on the inhomogeneous behavior of four-site associating LJ fluids confined in slit pores were discussed.

  16. Evidence for a size-dependent transition between noncrystalline structures and crystalline structures with defects in frozen Lennard-Jones clusters.

    Science.gov (United States)

    Polak, W

    2008-03-01

    Liquid Lennard-Jones clusters of 14 different sizes from N=55-923 atoms were cooled down in Monte Carlo simulations (40 runs for each size) to the reduced temperature T* = 0.05 . Structural analysis and visualization were applied for classification of the internal structure of all 560 final clusters. Small clusters revealed the presence of the multishell icosahedra or regular polyicosahedra. In larger clusters, beginning from N=309 , the noncrystalline atom ordering is often replaced by the formation of defected crystalline clusters in the form of layered face-centered cubic-hexagonal close-packed (fcc-hcp) clusters or defected layered clusters with some additional nonparallel hcp overlayers. The presence of regular polyicosahedral clusters, relatively numerous even at the largest analyzed sizes, is attributed to kinetic effects in structure formation.

  17. Avaliação radiográfica dos efeitos do aparelho Jones Jig nas distalizações intra-bucais: um estudo piloto Radiographic evaluation of the effects of Jones Jig appliance in intrabuccal distalizations: a pilot study

    Directory of Open Access Journals (Sweden)

    Juliana Maria Monteiro de Oliveira

    2004-10-01

    Full Text Available Na Classe II dentária, aparelhos extra ou intra-bucais são utilizados na distalização dos molares superiores, sendo que o dispositivo extra-bucal, apesar de ser eficiente, apresenta uma série de inconvenientes, destacando-se entre eles, a necessidade de cooperação do paciente. Em virtude da total dependência da colaboração e aceitação do paciente, aparelhos alternativos intra-bucais foram sendo criados, promovendo assim, um maior controle do tratamento por parte do profissional. Dentre esses aparelhos, destaca-se o Jones Jig. Foram selecionados para a pesquisa seis pacientes, com idades compreendidas entre 12 a 18 anos, que apresentavam um padrão esquelético de Classe I ou Classe II suave, vertical normal e má oclusão de Classe II dentária. Esses pacientes utilizaram o Jones Jig numa primeira fase do tratamento ortodôntico. Radiografias laterais cefalométricas foram obtidas antes e após o tratamento com o Jones Jig e a partir delas, traçados cefalométricos foram feitos para obter medidas de tecidos moles, esqueléticas e dentárias. Os resultados encontrados foram determinados, comparando-se as medidas do pré e do pós-tratamento. A fim de avaliar a significância estatística desses resultados, utilizou-se o teste de Wilcoxon. A ocorrência de uma inclinação distal dos primeiros e segundos molares superiores foi a única alteração estatisticamente significante encontrada.In dental Class II relationship, extra or intrabuccal appliances are used during the upper molars distalization. The extrabuccal appliance, although to be efficient, present many inconveniences, such as the patient compliance. For these reasons, alternative intrabuccal appliances were created in order to get more control during the treatment of no compliances patients. One of these appliances is the Jones Jig. Six patients, as standard as possible, were selected for this research, with the age ranged from 12 to 18 years old. These patients shown a

  18. Avaliação cefalométrica das alterações dentoesqueléticas de jovens com má oclusão de Classe II dentária tratados com distalizadores Jones jig Cephalometric evaluation of dentoskeletal changes in Class II young patients treated with Jones jig appliances

    Directory of Open Access Journals (Sweden)

    Mayara Paim Patel

    2009-06-01

    Full Text Available OBJETIVO: esta pesquisa objetivou avaliar cefalometricamente as alterações dentoesqueléticas de jovens com Classe II dentária tratados com o distalizador Jones jig. METODOLOGIA: foram avaliados 30 pacientes, sendo 15 de cada gênero, com média de idades iniciais de 13,63 anos; brasileiros, naturais da cidade de Bauru/SP, caracterizados por má oclusão de Classe II, 1ª e 2ª divisões de Angle sem comprometimento esquelético. Os jovens foram tratados com aparelho Jones jig a fim de distalizar os molares superiores a uma relação molar de "super Classe I"; sendo que esse dispositivo permaneceu, em média, por 0,55 anos. Ao final da sobrecorreção, os molares distalizados receberam um botão de Nance e, como ancoragem extrabucal, o aparelho extrabucal (AEB com tração média-alta, com o intuito de verticalizar e corrigir a angulação radicular dos molares distalizados. Foram realizadas telerradiografias em normal lateral inicial (T1 e pós-distalização (T2. As medidas cefalométricas foram submetidas ao teste t dependente de Student para avaliar as alterações de T1 para T2. RESULTADOS: com base nos resultados obtidos e a partir da metodologia empregada, observou-se alterações dentárias significativas, como a movimentação distal linear e angular, assim como a intrusão dos segundos e primeiros molares superiores no sentido vertical. Também se confirmou efeitos indesejáveis, como a perda de ancoragem refletida em mesialização, extrusão e angulação mesial dos segundos pré-molares, a protrusão dos incisivos superiores e o aumento do trespasse vertical e horizontal. Pode-se confirmar que certas movimentações dentárias promovem significativas alterações esqueléticas de estruturas localizadas à distância, ou seja, observou-se extrusão significativa dos segundos pré-molares superiores, o que resultou em rotação mandibular, aumento significativo da altura facial anteroinferior e protrusão do lábio inferior

  19. A pressure consistent bridge correction of Kovalenko-Hirata closure in Ornstein-Zernike theory for Lennard-Jones fluids by apparently adjusting sigma parameter

    Science.gov (United States)

    Ebato, Yuki; Miyata, Tatsuhiko

    2016-05-01

    Ornstein-Zernike (OZ) integral equation theory is known to overestimate the excess internal energy, Uex, pressure through the virial route, Pv, and excess chemical potential, μex, for one-component Lennard-Jones (LJ) fluids under hypernetted chain (HNC) and Kovalenko-Hirata (KH) approximatons. As one of the bridge correction methods to improve the precision of these thermodynamic quantities, it was shown in our previous paper that the method to apparently adjust σ parameter in the LJ potential is effective [T. Miyata and Y. Ebato, J. Molec. Liquids. 217, 75 (2016)]. In our previous paper, we evaluated the actual variation in the σ parameter by using a fitting procedure to molecular dynamics (MD) results. In this article, we propose an alternative method to determine the actual variation in the σ parameter. The proposed method utilizes a condition that the virial and compressibility pressures coincide with each other. This method can correct OZ theory without a fitting procedure to MD results, and possesses characteristics of keeping a form of HNC and/or KH closure. We calculate the radial distribution function, pressure, excess internal energy, and excess chemical potential for one-component LJ fluids to check the performance of our proposed bridge function. We discuss the precision of these thermodynamic quantities by comparing with MD results. In addition, we also calculate a corrected gas-liquid coexistence curve based on a corrected KH-type closure and compare it with MD results.

  20. Impactos do Índice Dow Jones, Commodities e Câmbio sobre o Ibovespa: uma Análise do Efeito Contágio

    Directory of Open Access Journals (Sweden)

    Pedro Raffy Vartanian

    2012-07-01

    Full Text Available The purpose of this research is to evaluate the existence of contagion effects of the Dow Jones index, commodity prices and exchange rate on the trajectory of the Bovespa index in the period 1999-2010, and analyze the longterm relationships between the variables. The theoretical framework is based on contagion effect, which occurs in the spread of market disturbances from one country to another country as discussed by Dornbusch, Park and Claessens (2000, Pericoli and Sbracia (2003, and Forbes and Rigobon (2002, as well as in empirical studies such as Lamounier and Nogueira (2007, Tabak e Lima (2003, Groppo (2006 and Pimenta (2004, among others, complete with research of the impact on commodity prices in the stock market, as can be seen in Barr and Kantor (2002. For this purpose, a cointegration test from the procedure suggested by Johansen (1991 was applied, and a vector autoregression model (VAR, initially proposed by Sims (1980 and Sims (1986, with the causality/exogeneity Granger test, was utilized. The results of Johansen cointegration test did not indicate the existence of long-term relationships between the variables. As to short-term effects, the impulse response functions showed that the Brazilian stock market index reacts positively to shocks in commodity prices and the U.S. stock market, and it demonstrates a positive reaction to currency depreciation, which suggests presence of the contagion effect.

  1. A pressure consistent bridge correction of Kovalenko-Hirata closure in Ornstein-Zernike theory for Lennard-Jones fluids by apparently adjusting sigma parameter

    Directory of Open Access Journals (Sweden)

    Yuki Ebato

    2016-05-01

    Full Text Available Ornstein-Zernike (OZ integral equation theory is known to overestimate the excess internal energy, Uex, pressure through the virial route, Pv, and excess chemical potential, μex, for one-component Lennard-Jones (LJ fluids under hypernetted chain (HNC and Kovalenko-Hirata (KH approximatons. As one of the bridge correction methods to improve the precision of these thermodynamic quantities, it was shown in our previous paper that the method to apparently adjust σ parameter in the LJ potential is effective [T. Miyata and Y. Ebato, J. Molec. Liquids. 217, 75 (2016]. In our previous paper, we evaluated the actual variation in the σ parameter by using a fitting procedure to molecular dynamics (MD results. In this article, we propose an alternative method to determine the actual variation in the σ parameter. The proposed method utilizes a condition that the virial and compressibility pressures coincide with each other. This method can correct OZ theory without a fitting procedure to MD results, and possesses characteristics of keeping a form of HNC and/or KH closure. We calculate the radial distribution function, pressure, excess internal energy, and excess chemical potential for one-component LJ fluids to check the performance of our proposed bridge function. We discuss the precision of these thermodynamic quantities by comparing with MD results. In addition, we also calculate a corrected gas-liquid coexistence curve based on a corrected KH-type closure and compare it with MD results.

  2. Power-law correlations in finance-related Google searches, and their cross-correlations with volatility and traded volume: Evidence from the Dow Jones Industrial components

    Science.gov (United States)

    Kristoufek, Ladislav

    2015-06-01

    We study power-law correlations properties of the Google search queries for Dow Jones Industrial Average (DJIA) component stocks. Examining the daily data of the searched terms with a combination of the rescaled range and rescaled variance tests together with the detrended fluctuation analysis, we show that the searches are in fact power-law correlated with Hurst exponents between 0.8 and 1.1. The general interest in the DJIA stocks is thus strongly persistent. We further reinvestigate the cross-correlation structure between the searches, traded volume and volatility of the component stocks using the detrended cross-correlation and detrending moving-average cross-correlation coefficients. Contrary to the universal power-law correlations structure of the related Google searches, the results suggest that there is no universal relationship between the online search queries and the analyzed financial measures. Even though we confirm positive correlation for a majority of pairs, there are several pairs with insignificant or even negative correlations. In addition, the correlations vary quite strongly across scales.

  3. A Study of Features of Fielding's Novel Tom Jones%《汤姆· 琼斯》创作特点研究

    Institute of Scientific and Technical Information of China (English)

    郑佩伟; 张景玲

    2016-01-01

    Henry Fielding is the most important realistic novelist both in England and even in Europe in the 18th century.In the developing course of English novels and the establishing of all the forms of modern no -vels, his importance as a novelist is incomparable , so he is regarded as "the Father of English Fiction". While he values the ideological content of the novel , Fielding pays more attention to formal elements of the no-vel.His masterpiece Tom Jones has its salient artistic features in terms of structure , dramatic elements, edu-cational function and language style .%亨利· 菲尔丁是18世纪英国乃至欧洲最重要的现实主义小说家,在英国小说的发展过程和确立现代小说的形式方面,他的重要性是无与伦比的,有着"英国小说之父"的称号. 菲尔丁在注重小说思想性的同时,也格外关注小说形式方面的问题,其代表作《汤姆· 琼斯》在框架结构、戏剧成分、教育功能和语言风格等方面都有其鲜明的创作特点.

  4. Use of Multiple Methods to Estimate Walrus (Odobenus rosmarus rosmarus Abundance in the Penny Strait-Lancaster Sound and West Jones Sound Stocks, Canada

    Directory of Open Access Journals (Sweden)

    Robert EA Stewart

    2014-12-01

    Full Text Available Surveys to estimate walrus abundance at terrestrial haulout sites in the Penny Strait-Lancaster Sound (PS-LS and West Jones Sound (WJS stocks were conducted in 1977 and 1998-2009. The Minimum Counted Population (MCP was similar in 1977 (565 to recent years (557 for the PS-LS stock. The MCP for the WJS stock was higher in recent surveys (404 than in 1977 (290. Regression analysis of MCP and density (number of walrus divided by number of haulouts surveyed showed no significant trends over time. We also calculated bounded count estimates for comparison. Finally, we used broad-scale behavioural data to estimate the proportion of the total stock that could be considered countable, to produce two adjusted estimates. We selected recent surveys with good coverage and ignored adjusted estimates that were lower than MCP. For the PS-LS stock, the adjusted MCP (with 95% CL was 672 (575-768 and 727 (623-831 walrus in 2007 and 2009, respectively. For WJS, the best estimates were the adjusted MCP of 503 (473-534 in 2008 and the adjusted bounded count of 470 (297-1732 in 2009. While both stocks appear to have remained stable over three decades, differences in survey coverage and possible differences in walrus distribution make precise population estimation difficult.

  5. Examination of Electric Utility CEO Compensation 2000-2011 and its significance to Company Earnings, Company Revenue, Company Stock and the Dow Jones Utility Average

    Science.gov (United States)

    Labovitch, Andrew

    This dissertation examined electric utility CEO compensation during the years 2000 through 2011 for United States owned and operated companies. To determine the extent to which agency theory may apply to electric utility CEO compensation, this examination segmented the industry by four types of company financial metrics: revenue, earnings, stock price and the Dow Jones Utility Average; by five categories of CEO compensation: base salary, bonus, stock grants, all other compensation and total compensation; and by four categories of company size as measured by revenue: large, medium, small and the industry as a whole. Electric utility CEO compensation data was analyzed with the financial metrics to determine correlations. No type of compensation was highly correlated to any of the financial metrics for any size industry segment indicating that there was little agency. CEO compensation in large electric utility companies was higher than compensation in medium and smaller companies even though the CEOs at larger companies earned less per dollar of revenue and per dollar of earnings than their counterparts in smaller companies.

  6. Self-consistent phonons revisited. I. The role of thermal versus quantum fluctuations on structural transitions in large Lennard-Jones clusters.

    Science.gov (United States)

    Georgescu, Ionuţ; Mandelshtam, Vladimir A

    2012-10-14

    The theory of self-consistent phonons (SCP) was originally developed to address the anharmonic effects in condensed matter systems. The method seeks a harmonic, temperature-dependent Hamiltonian that provides the "best fit" for the physical Hamiltonian, the "best fit" being defined as the one that optimizes the Helmholtz free energy at a fixed temperature. The present developments provide a scalable O(N) unified framework that accounts for anharmonic effects in a many-body system, when it is probed by either thermal (ℏ → 0) or quantum fluctuations (T → 0). In these important limits, the solution of the nonlinear SCP equations can be reached in a manner that requires only the multiplication of 3N × 3N matrices, with no need of diagonalization. For short range potentials, such as Lennard-Jones, the Hessian, and other related matrices are highly sparse, so that the scaling of the matrix multiplications can be reduced from O(N(3)) to ~O(N). We investigate the role of quantum effects by continuously varying the de-Boer quantum delocalization parameter Λ and report the N-Λ (T = 0), and also the classical N-T (Λ = 0) phase diagrams for sizes up to N ~ 10(4). Our results demonstrate that the harmonic approximation becomes inadequate already for such weakly quantum systems as neon clusters, or for classical systems much below the melting temperatures.

  7. Development of molecular closures for the reference interaction site model theory with application to square-well and Lennard-Jones homonuclear diatomics

    Science.gov (United States)

    Munaò, Gianmarco; Costa, Dino; Caccamo, Carlo

    2016-10-01

    Inspired by significant improvements obtained for the performances of the polymer reference interaction site model (PRISM) theory of the fluid phase when coupled with ‘molecular closures’ (Schweizer and Yethiraj 1993 J. Chem. Phys. 98 9053), we exploit a matrix generalization of this concept, suitable for the more general RISM framework. We report a preliminary test of the formalism, as applied to prototype square-well homonuclear diatomics. As for the structure, comparison with Monte Carlo shows that molecular closures are slightly more predictive than their ‘atomic’ counterparts, and thermodynamic properties are equally accurate. We also devise an application of molecular closures to models interacting via continuous, soft-core potentials, by using well established prescriptions in liquid state perturbation theories. In the case of Lennard-Jones dimers, our scheme definitely improves over the atomic one, providing semi-quantitative structural results, and quite good estimates of internal energy, pressure and phase coexistence. Our finding paves the way to a systematic employment of molecular closures within the RISM framework to be applied to more complex systems, such as molecules constituted by several non-equivalent interaction sites.

  8. Density-functional and electron correlated study of five linear birefringences--Kerr, Cotton-Mouton, Buckingham, Jones, and magnetoelectric--in gaseous benzene.

    Science.gov (United States)

    Rizzo, Antonio; Cappelli, Chiara; Jansík, Branislav; Jonsson, Dan; Sałek, Paweł; Coriani, Sonia; Agren, Hans

    2004-11-08

    We present the results of an extended study of five birefringences--Kerr, Cotton-Mouton, Buckingham, Jones, and Magnetoelectric--on benzene in the gas phase. The relevant molecular quantities--first-order properties, linear, quadratic, and cubic response functions--are computed employing the density-functional theory (DFT) response theory, with a choice of functionals. In some cases, different functionals are employed for the wave-function computational step and for the subsequent analytical response calculation to determine the combination yielding at the same time the optimal energy and energy derivative results. Augmented correlation consistent basis sets of double and triple zeta quality are used. The DFT results are compared to those obtained at the Hartree-Fock level and in some cases within a coupled cluster singles and doubles electronic structure model. The study tries to assess the ability of the DFT response theory to describe a wide range of properties in a system of rather large size and high complexity. The relative strength of the five birefringences for plausible experimental conditions is determined and, when possible, comparison is made with the results of the measurements.

  9. Critical anomaly and finite size scaling of the self-diffusion coefficient for Lennard-Jones fluids by non-equilibrium molecular dynamic simulation

    Institute of Scientific and Technical Information of China (English)

    Ahmed Asad; Wu Jiang-Tao

    2011-01-01

    We use non-equilibrium molecular dynamics simulations to calculate the self-diffusion coefficient,D,of a Lennard Jones fluid over a wide density and temperature range.The change in self-diffusion coefficient with temperature decreases by increasing density.For density p* =pσ3 =0.84 we observe a peak at the value of the self-diffusion coefficient and the critical temperature T* =kT/ε =1.25.The value of the self-diffusion coefficient strongly depends on system size.The data of the self-diffusion coefficient are fitted to a simple analytic relation based on hydrodynamic arguments.This correction scales as N-α,where α is an adjustable parameter and N is the number of particles.It is observed that the values of α < 1 provide quite a good correction to the simulation data.The system size dependence is very strong for lower densities,but it is not as strong for higher densities.The self-diffusion coefficient calculated with non-equilibrium molecular dynamic simulations at different temperatures and densities is in good agreement with other calculations from the literature.

  10. Psychology, not educational neuroscience, is the way forward for improving educational outcomes for all children: Reply to Gabrieli (2016) and Howard-Jones et al. (2016).

    Science.gov (United States)

    Bowers, Jeffrey S

    2016-10-01

    In Bowers (2016), I argued that there are (a) practical problems with educational neuroscience (EN) that explain why there are no examples of EN improving teaching and (b) principled problems with the logic motivating EN that explain why it is likely that there never will be. In the following article, I consider the main responses raised by both Gabrieli (2016) and Howard-Jones et al. (2016) and find them all unconvincing. Following this exchange, there are still no examples of EN providing new insights to teaching in the classroom, there are still no examples of EN providing new insights to remedial instructions for individuals, and, as I detail in this article, there is no evidence that EN is useful for the diagnosis of learning difficulties. The authors have also failed to address the reasons why EN is unlikely to benefit educational outcomes in the future. Psychology, by contrast, can (and has) made important discoveries that can (and should) be used to improve teaching and diagnostic tests for learning difficulties. This is not a debate about whether science is relevant to education, rather it is about what sort of science is relevant. (PsycINFO Database Record

  11. 免疫固定电泳对多发性骨髓瘤的临床应用价值%Clinical Value of Immunofixation Electrophoresis on The Diagnosis of Multiple Myeloma

    Institute of Scientific and Technical Information of China (English)

    姚红; 吴亚楠

    2014-01-01

    Objective To study the clinical value immunofixation electrophoresis on the diagnosis of multiple myeloma ( MM) .Methods Serum protein electrophoresis and immunofixation electrophoresis of 32 patients diagnosed with multiple mye-loma was measured by France Sebia HYDRASYS automatic electrophoresis .2States Beckman Immage 800 specific protein analy-zer was used to detect serum immunoglobulins ,light chain determination of urine and blood .Bence-Jones protein of urine was de-tected by handmade nitric acid method .Results There were 14 IgG (43.75%),9 IgA (28.13%),1 IgM (3.13%),and 2 light chain (6.25%).There were 13 Kappa chain (40.63%),11 lambda chain (34.38%) and 18 Bence-Jones protein positive patients (56.25%).2Immunofixation electrophoresis showed that M protein positive rate was 96.9%.Conclusion IgG、IgA ac-count for the largest proportion in the immunoglobulin types ,kappa chain is slightly more than lambda chain ,and the positive rate of Bence-Jones protein of urine is higher than the negative rate .Immunofixation electrophoresis has important clinical value on the diagnosis and classification of MM .%目的:探讨免疫固定电泳对多发性骨髓瘤( MM)的临床诊断价值。方法应用法国Sebia HYDRASYS全自动电泳仪,对32例MM患者进行血清蛋白电泳测定和免疫固定电泳测定。应用美国Beckman Immage 800特定蛋白分析仪进行血清免疫球蛋白和血、尿轻链测定。采用手工硝酸法进行尿本周氏蛋白测定。结果32例多发性骨髓瘤中IgG型14例(43.75%),IgA型9例(28.13%),IgM型1例(3.13%),轻链型2例(6.25%)。所有类型中κ链13例(40.63%),λ链11例(34.38%),尿本周氏蛋白阳性18例(56.25%)。免疫固定电泳检测M蛋白阳性率为96.9%。结论 MM患者以IgG型、IgA型比例最高,轻链类型中κ链比例稍高于λ链,尿本周氏蛋白阳性者多于尿本周氏蛋白阴性患者,免疫固定电

  12. 空心螺钉内固定术治疗Jones骨折32例分析%The analyses of 32 Jones fracture by using hollow screw internal fixation

    Institute of Scientific and Technical Information of China (English)

    唐兵; 秦定扬

    2010-01-01

    目的 观察空心螺钉内固定术治疗Jones骨折的临床疗效.方法 回顾性分析采用切开复位空心螺钉内固定术治疗Jones骨折32例患者的临床资料.结果 32例患者均治愈出院,平均随访18个月,根据Maryland足部评分系统评分:优25例,良6例,差1例,优良率96.9%.结论 空心螺钉内固定术治疗Jones骨折,操作简单,术后不用外固定,功能恢复快,并发症少,疗效满意.%Objective To analyze the therapy method and the therapeutic effect of Jones fracture by using hollow screw internal fixation.Methods All the Jones fractures were treated by open reduction hollow screw internal fixation and the plaster external fixation were not used after operation.Results The 32 cases with Jones fractures got excellent 25 cases,good 6cases and poor 1 case which used by Maryland foot score system to appraisal.All the cases were followed up for 6 months to 30 months and the average follow-up time is 18 months.Conclusion The treatment of hollow screw internal fixation was a satisfactory method to cure Jones fracture,which had get advantages of simple operation,small wound,short operation time,not external fixation,quick recovery and few complications.

  13. Thermal motion in proteins: Large effects on the time-averaged interaction energies

    Directory of Open Access Journals (Sweden)

    Martin Goethe

    2016-03-01

    Full Text Available As a consequence of thermal motion, inter-atomic distances in proteins fluctuate strongly around their average values, and hence, also interaction energies (i.e. the pair-potentials evaluated at the fluctuating distances are not constant in time but exhibit pronounced fluctuations. These fluctuations cause that time-averaged interaction energies do generally not coincide with the energy values obtained by evaluating the pair-potentials at the average distances. More precisely, time-averaged interaction energies behave typically smoother in terms of the average distance than the corresponding pair-potentials. This averaging effect is referred to as the thermal smoothing effect. Here, we estimate the strength of the thermal smoothing effect on the Lennard-Jones pair-potential for globular proteins at ambient conditions using x-ray diffraction and simulation data of a representative set of proteins. For specific atom species, we find a significant smoothing effect where the time-averaged interaction energy of a single atom pair can differ by various tens of cal/mol from the Lennard-Jones potential at the average distance. Importantly, we observe a dependency of the effect on the local environment of the involved atoms. The effect is typically weaker for bulky backbone atoms in beta sheets than for side-chain atoms belonging to other secondary structure on the surface of the protein. The results of this work have important practical implications for protein software relying on free energy expressions. We show that the accuracy of free energy expressions can largely be increased by introducing environment specific Lennard-Jones parameters accounting for the fact that the typical thermal motion of protein atoms depends strongly on their local environment.

  14. Thermal motion in proteins: Large effects on the time-averaged interaction energies

    Science.gov (United States)

    Goethe, Martin; Fita, Ignacio; Rubi, J. Miguel

    2016-03-01

    As a consequence of thermal motion, inter-atomic distances in proteins fluctuate strongly around their average values, and hence, also interaction energies (i.e. the pair-potentials evaluated at the fluctuating distances) are not constant in time but exhibit pronounced fluctuations. These fluctuations cause that time-averaged interaction energies do generally not coincide with the energy values obtained by evaluating the pair-potentials at the average distances. More precisely, time-averaged interaction energies behave typically smoother in terms of the average distance than the corresponding pair-potentials. This averaging effect is referred to as the thermal smoothing effect. Here, we estimate the strength of the thermal smoothing effect on the Lennard-Jones pair-potential for globular proteins at ambient conditions using x-ray diffraction and simulation data of a representative set of proteins. For specific atom species, we find a significant smoothing effect where the time-averaged interaction energy of a single atom pair can differ by various tens of cal/mol from the Lennard-Jones potential at the average distance. Importantly, we observe a dependency of the effect on the local environment of the involved atoms. The effect is typically weaker for bulky backbone atoms in beta sheets than for side-chain atoms belonging to other secondary structure on the surface of the protein. The results of this work have important practical implications for protein software relying on free energy expressions. We show that the accuracy of free energy expressions can largely be increased by introducing environment specific Lennard-Jones parameters accounting for the fact that the typical thermal motion of protein atoms depends strongly on their local environment.

  15. A reference-modified density functional theory: An application to solvation free-energy calculations for a Lennard-Jones solution.

    Science.gov (United States)

    Sumi, Tomonari; Maruyama, Yutaka; Mitsutake, Ayori; Koga, Kenichiro

    2016-06-14

    In the conventional classical density functional theory (DFT) for simple fluids, an ideal gas is usually chosen as the reference system because there is a one-to-one correspondence between the external field and the density distribution function, and the exact intrinsic free-energy functional is available for the ideal gas. In this case, the second-order density functional Taylor series expansion of the excess intrinsic free-energy functional provides the hypernetted-chain (HNC) approximation. Recently, it has been shown that the HNC approximation significantly overestimates the solvation free energy (SFE) for an infinitely dilute Lennard-Jones (LJ) solution, especially when the solute particles are several times larger than the solvent particles [T. Miyata and J. Thapa, Chem. Phys. Lett. 604, 122 (2014)]. In the present study, we propose a reference-modified density functional theory as a systematic approach to improve the SFE functional as well as the pair distribution functions. The second-order density functional Taylor series expansion for the excess part of the intrinsic free-energy functional in which a hard-sphere fluid is introduced as the reference system instead of an ideal gas is applied to the LJ pure and infinitely dilute solution systems and is proved to remarkably improve the drawbacks of the HNC approximation. Furthermore, the third-order density functional expansion approximation in which a factorization approximation is applied to the triplet direct correlation function is examined for the LJ systems. We also show that the third-order contribution can yield further refinements for both the pair distribution function and the excess chemical potential for the pure LJ liquids.

  16. Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field.

    Science.gov (United States)

    Baker, Christopher M; Lopes, Pedro E M; Zhu, Xiao; Roux, Benoît; Mackerell, Alexander D

    2010-03-01

    Lennard-Jones (LJ) parameters for a variety of model compounds have previously been optimized within the CHARMM Drude polarizable force field to reproduce accurately pure liquid phase thermodynamic properties as well as additional target data. While the polarizable force field resulting from this optimization procedure has been shown to satisfactorily reproduce a wide range of experimental reference data across numerous series of small molecules, a slight but systematic overestimate of the hydration free energies has also been noted. Here, the reproduction of experimental hydration free energies is greatly improved by the introduction of pair-specific LJ parameters between solute heavy atoms and water oxygen atoms that override the standard LJ parameters obtained from combining rules. The changes are small and a systematic protocol is developed for the optimization of pair-specific LJ parameters and applied to the development of pair-specific LJ parameters for alkanes, alcohols and ethers. The resulting parameters not only yield hydration free energies in good agreement with experimental values, but also provide a framework upon which other pair-specific LJ parameters can be added as new compounds are parametrized within the CHARMM Drude polarizable force field. Detailed analysis of the contributions to the hydration free energies reveals that the dispersion interaction is the main source of the systematic errors in the hydration free energies. This information suggests that the systematic error may result from problems with the LJ combining rules and is combined with analysis of the pair-specific LJ parameters obtained in this work to identify a preliminary improved combining rule.

  17. Local pressure components and interfacial tension at a liquid-solid interface obtained by the perturbative method in the Lennard-Jones system.

    Science.gov (United States)

    Fujiwara, K; Shibahara, M

    2014-07-21

    A classical molecular dynamics simulation was conducted for a system composed of fluid molecules between two planar solid surfaces, and whose interactions are described by the 12-6 Lennard-Jones form. This paper presents a general description of the pressure components and interfacial tension at a fluid-solid interface obtained by the perturbative method on the basis of statistical thermodynamics, proposes a method to consider the pressure components tangential to an interface which are affected by interactions with solid atoms, and applies this method to the calculation system. The description of the perturbative method is extended to subsystems, and the local pressure components and interfacial tension at a liquid-solid interface are obtained and examined in one- and two-dimensions. The results are compared with those obtained by two alternative methods: (a) an evaluation of the intermolecular force acting on a plane, and (b) the conventional method based on the virial expression. The accuracy of the numerical results is examined through the comparison of the results obtained by each method. The calculated local pressure components and interfacial tension of the fluid at a liquid-solid interface agreed well with the results of the two alternative methods at each local position in one dimension. In two dimensions, the results showed a characteristic profile of the tangential pressure component which depended on the direction tangential to the liquid-solid interface, which agreed with that obtained by the evaluation of the intermolecular force acting on a plane in the present study. Such good agreement suggests that the perturbative method on the basis of statistical thermodynamics used in this study is valid to obtain the local pressure components and interfacial tension at a liquid-solid interface.

  18. Local pressure components and interfacial tension at a liquid-solid interface obtained by the perturbative method in the Lennard-Jones system

    Energy Technology Data Exchange (ETDEWEB)

    Fujiwara, K., E-mail: ku.fujiwara@screen.co.jp [R and D Group, R and D Center, Dainippon Screen Mfg. Co., Ltd., 322 Furukawa-cho, Hazukashi, Fushimi-ku, Kyoto, Kyoto 612-8486 (Japan); Department of Mechanical Engineering, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 (Japan); Shibahara, M., E-mail: siba@mech.eng.osaka-u.ac.jp [Department of Mechanical Engineering, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871 (Japan)

    2014-07-21

    A classical molecular dynamics simulation was conducted for a system composed of fluid molecules between two planar solid surfaces, and whose interactions are described by the 12-6 Lennard-Jones form. This paper presents a general description of the pressure components and interfacial tension at a fluid-solid interface obtained by the perturbative method on the basis of statistical thermodynamics, proposes a method to consider the pressure components tangential to an interface which are affected by interactions with solid atoms, and applies this method to the calculation system. The description of the perturbative method is extended to subsystems, and the local pressure components and interfacial tension at a liquid-solid interface are obtained and examined in one- and two-dimensions. The results are compared with those obtained by two alternative methods: (a) an evaluation of the intermolecular force acting on a plane, and (b) the conventional method based on the virial expression. The accuracy of the numerical results is examined through the comparison of the results obtained by each method. The calculated local pressure components and interfacial tension of the fluid at a liquid-solid interface agreed well with the results of the two alternative methods at each local position in one dimension. In two dimensions, the results showed a characteristic profile of the tangential pressure component which depended on the direction tangential to the liquid-solid interface, which agreed with that obtained by the evaluation of the intermolecular force acting on a plane in the present study. Such good agreement suggests that the perturbative method on the basis of statistical thermodynamics used in this study is valid to obtain the local pressure components and interfacial tension at a liquid-solid interface.

  19. HYDRAULICS, JONES COUNTY, IA - PMR

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — Recent developments in digital terrain and geospatial database management technology make it possible to protect this investment for existing and future projects to...

  20. Effect of dispersive long-range corrections to the pressure tensor: The vapour-liquid interfacial properties of the Lennard-Jones system revisited

    Energy Technology Data Exchange (ETDEWEB)

    Martínez-Ruiz, F. J.; Blas, F. J., E-mail: felipe@uhu.es [Departamento de Física Aplicada, Universidad de Huelva, 21071 Huelva (Spain); Centro de Investigación de Física Teórica y Matemática, Universidad de Huelva, 21071 Huelva (Spain); Mendiboure, B. [Laboratoire des Fluides Complexes et leurs Réservoirs, UMR5150, Université de Pau et des Pays de l’Adour, B. P. 1155, Pau Cedex 64014 (France); Moreno-Ventas Bravo, A. I. [Centro de Investigación de Física Teórica y Matemática, Universidad de Huelva, 21071 Huelva (Spain); Departamento de Geología, Facultad de Ciencias Experimentales, Universidad de Huelva, 21071 Huelva (Spain)

    2014-11-14

    We propose an extension of the improved version of the inhomogeneous long-range corrections of Janeček [J. Phys. Chem. B 110, 6264–6269 (2006)], presented recently by MacDowell and Blas [J. Chem. Phys. 131, 074705 (2009)] to account for the intermolecular potential energy of spherical, rigid, and flexible molecular systems, to deal with the contributions to the microscopic components of the pressure tensor due to the dispersive long-range corrections. We have performed Monte Carlo simulations in the canonical ensemble to obtain the interfacial properties of spherical Lennard-Jones molecules with different cutoff distances, r{sub c} = 2.5, 3, 4, and 5σ. In addition, we have also considered cutoff distances r{sub c} = 2.5 and 3σ in combination with the inhomogeneous long-range corrections proposed in this work. The normal and tangential microscopic components of the pressure tensor are obtained using the mechanical or virial route in combination with the recipe of Irving and Kirkwood, while the macroscopic components are calculated using the Volume Perturbation thermodynamic route proposed by de Miguel and Jackson [J. Chem. Phys. 125, 164109 (2006)]. The vapour-liquid interfacial tension is evaluated using three different procedures, the Irving-Kirkwood method, the difference between the macroscopic components of the pressure tensor, and the Test-Area methodology. In addition to the pressure tensor and the surface tension, we also obtain density profiles, coexistence densities, vapour pressure, critical temperature and density, and interfacial thickness as functions of temperature, paying particular attention to the effect of the cutoff distance and the long-range corrections on these properties. According to our results, the main effect of increasing the cutoff distance (at fixed temperature) is to sharpen the vapour-liquid interface, to decrease the vapour pressure, and to increase the width of the biphasic coexistence region. As a result, the interfacial

  1. Ocorrência do fungo entomopatogênico Isaria javanica (Frieder. & Bally Samson & Hywell-Jones (Fungi, Sordariomycetes em lagartas de Lonomia obliqua Walker (Lepidoptera, Saturniidae, Hemileucinae Occurrence of the entomopathogenic fungus Isaria javanica (Frieder. & Bally Samson & Hywell-Jones (Fungi, Sordariomycetes infecting Lonomia obliqua Walker (Lepidoptera, Saturniidae, Hemileucinae caterpillars

    Directory of Open Access Journals (Sweden)

    Alexandre Specht

    2009-01-01

    Full Text Available Este fungo foi isolado pela primeira vez de lagartas de L. obliqua de uma agregação em plátano (Platanus acerifolia (Aiton Wild - Platanaceae, em Bento Gonçalves, RS, Brasil. Após isolamento, purificação e caracterização, realizou-se um teste de patogenicidade com lagartas sadias de L. obliqua para corroborar, sua infectividade pelo postulado de Koch. Constatou-se correspondência morfológica e molecular entre o inóculo e o reisolado, comprovando sua patogenicidade a L. obliqua.It is recorded for the first time the occurrence of the entomopathogenic fungus Isaria javanica (Frieder. & Bally Samson & Hywell-Jones (Fungi: Sordariomycetes infecting Lonomia obliqua Walker (Lepidoptera: Saturniidae: Hemileucinae caterpillars. This fungus was isolated from L. obliqua individuals collected from Platanus acerifolia (Aiton Wild- Platanaceae in Rio Grande do Sul state, Brazil. After isolation, purification and characterization, fungal conidia were inoculated on healthy L. obliqua caterpillars and from dead caterpillars the fungal isolates were again obtained. New isolates and the original isolate did not differ when compared by morphological and molecular tests.

  2. Energy world governance. Review of the conference which was held at IFRI, 26 March 2009, with Tatsuo Masuda, Andre Mernier et Richard H. Jones; La gouvernance mondiale de l'Energie - Resume de la conference qui a eu lieu a l'Ifri le 26 Mar 2009 autour de Tatsuo Masuda, Andre Mernier et Richard H. Jones

    Energy Technology Data Exchange (ETDEWEB)

    Schulke, Ch.

    2009-07-01

    The conference was related with some of the major questions concerning global energy governance today, the role of the different international organizations dealing with energy, the rules of the game between market and state players, the efforts to deal with climate change, and the integration of emerging countries in global energy governance, the roles of the different international organizations dealing with energy (will we see further fragmentation or more cooperation between them?). Tatsuo Masuda in his contribution discussed global energy governance from an oil perspective. Andre Mernier noted the particular nature of the Energy Charter, which, as it is founded upon an international treaty, is unlike other organizations in being legally binding. The legal basis of the organization means that agreements are especially powerful. Then Richard H. Jones underlined that last summer's volatility in oil markets, the ensuing financial and economic crisis, the major disruption in gas supplies to European markets this winter and the upcoming climate change negotiations have led to increasing calls for a stronger global dialogue on energy issues. This dialogue should deal with prices and investment, energy security and climate change

  3. Study on Antimicrobial and Antioxidant Activities of Essential Oils from Valeriana officinalis L. and Valeriana jatamansi Jones.%缬草与蜘蛛香挥发油的抗菌抗氧化活性研究

    Institute of Scientific and Technical Information of China (English)

    赵兵; 郝萍; 高昂; 巩江; 陈千良; 倪士峰

    2013-01-01

    通过对缬草和蜘蛛香挥发油抗菌抗氧化活性的研究,为开发天然高效的抗菌抗氧化药物提供新的选择.采用纸片扩散法和试管稀释法对缬草和蜘蛛香挥发油进行抑菌圈大小及最小抑菌浓度的测定;用DPPH法对其抗氧化能力进行研究.结果表明:缬草和蜘蛛香挥发油均具有一定的抗菌作用,细菌试验中对金黄色葡萄球菌的作用最强,二者对其最小抑菌浓度分别为3.125 mg/mL和6.25 mg/mL;对真菌的抑制作用相对较弱,其中蜘蛛香挥发油作用强于缬草挥发油.两者挥发油不同浓度对DPPH自由基有较好的清除能力,实验浓度范围内,最高清除率分别达65.35%和71.75%,均强于阳性对照品BHT.%In this study,the antibacterial and antioxidant activities of essential oil from Valeriana offcinalis L.and Valeriana jatamansi Jones.were investigated.Disc diffusion method and tube dilution method were applied to measure the antibacterial circle diameter and the Minimum Inhibitory Concentration (MIC) of the essential oils of V.officinalis L.and V.jatamansi Jones..The DPPH radical scavenging activity was detected by UV-Vis spectrophotometry.The results showed that the essential oils of V.officinalis L.and V.jatamansi Jones.had antibacterial effects and the strongest effect was against Staphylococcus aureu,the MICs of V.officinalis L.and V.jatamansi Jones.were 3.125 mg/mL and 6.25 mg/mL,respectively.In addition,different concentrations of the two vohtile oils possessed good scavenging activity on DPPH free radical.The highest scavenging rates reached to 65.35%,71.75%,respectively and were both stronger than the positive control BHT.

  4. Protein-protein interactions

    DEFF Research Database (Denmark)

    Byron, Olwyn; Vestergaard, Bente

    2015-01-01

    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......, are reported. The aim is to depict how the elucidation of the interplay of structures requires the interplay of methods....

  5. IMMUNOMETRIC ASSAY TO DETERMINE FREE LIGHT CHAIN CONCENTRATIONS OF HUMAN IMMUNOGLOBULINS

    Directory of Open Access Journals (Sweden)

    M. P. Samoylovich

    2016-01-01

    Full Text Available Detection of total free light chains (FLC of immunoglobulins and their ratio (kappa/lambda quotient are used in diagnostics and monitoring of multiple myeloma and other gammapathies, primary amyloidosis and multiple sclerosis. Previously described immunoassays with monoclonal antibodies (Mabs against cryptic and constantly exposed epitopes of FLC failed to recognize rare variants of lambda Bence-Jones proteins and a significant proportion of lambda chains excreted with urine. Aiming to improve this approach, a novel murine Mab (IgG2b coded as 1C8 was employed, which specifically binds free lambda chains but doesn’t interact with native IgA, IgG, and IgM. The novel Mab recognized an epitope exposed at free lambda chains in peripheral blood of healthy donors and patients with multiple myeloma. It is not destroyed or masked upon renal filtration.The aim of this study was to determine basic features of improved assay system, and to estimate its potential in diagnostics of monoclonal gammapathies. The mixtures of three Bence-Jones proteins of either kappa- or lambda- types purified from the urine of multiple myeloma patients were used as calibrator samples.Improved immunometric assay is able to detect free kappa and lambda chains in serum and urine at a scale of 1 to 100 ng/ml, thus being three orders more sensitive than, e.g., detection levels of Freelite method based on polyclonal antibodies.A novel assay allows to detect free kappa and lambda chains at comparable levels in serum or urine, and to deduce kappa/lambda ratio. The proposed assay is able to detect FLC in 10,000-fold excess of whole IgG molecules. The calibrating plots for both antigens are linear on log-log scales, with very similar slopes. Detection thresholds for kappa or lambda chains proved to be 5 and 3 ng/ml, respectively. Mean concentrations of free kappa chains in sera of healthy donors were 6.7±2.1, in urine, 4.2±3.8 mcg/ml. Mean concentrations of free lambda chains were 4

  6. Smoldering Multiple Myeloma

    Directory of Open Access Journals (Sweden)

    Minjie Gao

    2015-01-01

    Full Text Available Smoldering multiple myeloma (SMM is an asymptomatic precursor stage of multiple myeloma (MM characterized by clonal bone marrow plasma cells (BMPC ≥ 10% and/or M protein level ≥ 30 g/L in the absence of end organ damage. It represents an intermediate stage between monoclonal gammopathy of undetermined significance (MGUS and symptomatic MM. The risk of progression to symptomatic MM is not uniform, and several parameters have been reported to predict the risk of progression. These include the level of M protein and the percentage of BMPC, the proportion of immunophenotypically aberrant plasma cells, and the presence of immunoparesis, free light-chain (FLC ratio, peripheral blood plasma cells (PBPC, pattern of serum M protein evolution, abnormal magnetic resonance imaging (MRI, cytogenetic abnormalities, IgA isotype, and Bence Jones proteinuria. So far treatment is still not recommended for SMM, because several trials suggested that patients with SMM do not benefit from early treatment. However, the Mateos et al. trial showed a survival benefit after early treatment with lenalidomide plus dexamethasone in patients with high-risk SMM. This trial has prompted a reevaluation of early treatment in an asymptomatic patient population.

  7. High incidence of intact or fragmented immunoglobulin in urine of patients with multiple myeloma.

    Science.gov (United States)

    Kraj, Maria; Kruk, Barbara; Lech-Marańda, Ewa; Warzocha, Krzysztof; Prochorec-Sobieszek, Monika

    2015-01-01

    In this prospective study we determined the incidence of intact/fragmented immunoglobulin and Bence Jones protein in urine immunofixation using Sebia reagents and HydrasysTM 2 apparatus and compared the results to concentrations of serum free light chains (FLC) assessed using Siemens BNTM II nephelometer and the immunoassay Freelite (Binding Site) in 289 patients with multiple myeloma at diagnosis. It was found that in one third of IgG, IgA and IgD myeloma patients, intact/fragmented immunoglobulin can be detected in urine and is connected with impaired renal function and reduced survival. Urine immunofixation detects monoclonal protein (FLC and intact/fragmented immunoglobulin) in 66-79% of IgG and IgA myeloma patients while serum FLC immunoassay detect it in 82-94% of IgG and IgA myeloma patients. However, the latter method is inadequate for detection of intact/fragmented immunoglobulin in urine. Serum FLC immunoassay and urine immunofixation are complementary methods in diagnosing and monitoring monoclonal protein in patients with myeloma.

  8. Protein Condensation

    Science.gov (United States)

    Gunton, James D.; Shiryayev, Andrey; Pagan, Daniel L.

    2014-07-01

    Preface; 1. Introduction; 2. Globular protein structure; 3. Experimental methods; 4. Thermodynamics and statistical mechanics; 5. Protein-protein interactions; 6. Theoretical studies of equilibrium; 7. Nucleation theory; 8. Experimental studies of nucleation; 9. Lysozyme; 10. Some other globular proteins; 11. Membrane proteins; 12. Crystallins and cataracts; 13. Sickle hemoglobin and sickle cell anemia; 14, Alzheimer's disease; Index.

  9. Archive of Digitized Analog Boomer Seismic Reflection Data Collected from the Mississippi-Alabama-Florida Shelf During Cruises Onboard the R/V Kit Jones, June 1990 and July 1991

    Science.gov (United States)

    Sanford, Jordan M.; Harrison, Arnell S.; Wiese, Dana S.; Flocks, James G.

    2009-01-01

    In June of 1990 and July of 1991, the U.S. Geological Survey (USGS) conducted geophysical surveys to investigate the shallow geologic framework of the Mississippi-Alabama-Florida shelf in the northern Gulf of Mexico, from Mississippi Sound to the Florida Panhandle. Work was done onboard the Mississippi Mineral Resources Institute R/V Kit Jones as part of a project to study coastal erosion and offshore sand resources. This report is part of a series to digitally archive the legacy analog data collected from the Mississippi-Alabama SHelf (MASH). The MASH data rescue project is a cooperative effort by the USGS and the Minerals Management Service (MMS). This report serves as an archive of high-resolution scanned Tagged Image File Format (TIFF) and Graphics Interchange Format (GIF) images of the original boomer paper records, navigation files, trackline maps, Geographic Information System (GIS) files, cruise logs, and formal Federal Geographic Data Committee (FGDC) metadata.

  10. Enhanced sampling and applications in protein folding in explicit solvent

    CERN Document Server

    Zhang, Cheng

    2010-01-01

    We report a single-copy tempering method for enhancing sampling in simulating large complex systems. A continuous temperature space random walk is achieved by a Langevin equation, which is guided by a runtime estimate of the thermal average energy through a novel integral identity. We first validated the method in a two-dimensional Ising model and a Lennard-Jones liquid system. Then the method was applied to folding of three small proteins, trpzip2, trp-cage, and villin headpiece in explicit solvent. Within 0.5~1 microsecond, all three systems were folded into atomic accuracy: the alpha carbon root mean square deviation of the best folded conformations from the native states are 0.2 A, 0.4 A, and 0.4 A, for trpzip2, trp-cage, and villin headpiece, respectively.

  11. 5 June 2013 - European Union Ambassador to Switzerland and the Principality of Liechtenstein R. Jones in the ATLAS cavern with ATLAS Collaboration Deputy Spokesperson T. Wengler, in the LHC tunnel at Point 1 with Technology Department Head F. Bordry and signing the guest book with Director-General R. Heuer. Head of the EU Projects Office S. Stavrev present.

    CERN Multimedia

    Jean-Claude Gadmer

    2013-01-01

    5 June 2013 - European Union Ambassador to Switzerland and the Principality of Liechtenstein R. Jones in the ATLAS cavern with ATLAS Collaboration Deputy Spokesperson T. Wengler, in the LHC tunnel at Point 1 with Technology Department Head F. Bordry and signing the guest book with Director-General R. Heuer. Head of the EU Projects Office S. Stavrev present.

  12. CLINICAL MANIFESTATIONS OF VASCULITIS AT THE ONSET OF MULTIPLE MYELOMA

    Directory of Open Access Journals (Sweden)

    V I Vasil'ev

    2010-01-01

    Full Text Available The paper describes two patients (a 50-year woman and a 72-year man in whom the clinical manifestations of ulceronecrotic vasculitis had long preceded before the diagnosis of multiple myeloma was made. In the former, monoclonal cryoglobulinemia type I induced ulcerative lesions with the development of dry toe gangrene and paraproteinemic renal lesion. In the latter, ulceronecrotic vasculitis with the development of dry toe gangrene was a manifestation of monoclonal paraproteinemia without signs of cryoglobulinemia. Both patients were found to have monoclonal blood secretion (РIgGλ и РIgGκ and urine Bence Jones protein (BJλ+BJκ, BJκ in the absence of immunological markers of vasculitis developing in patients with rheumatic diseases. Immunochemical study of serum/urine and, when monoclonal secretion of PIg+BJ is detected, further examination for plasma cell dyscrasia should be performed in all cases of vascular disorders (cold allergy, Raynaud's syndrome, purpura, ulcers of cruses, and gangrene of distal phalanxes of the hands/feet in patients with atypical vasculitis. The timely immunochemical study of blood and urine will make it possible to diagnose plasma cell dyscrasia (different types of myelomic disease, Waldenstrцm macroglobulinemia, primary amyloidosis at the early stage of the disease and to rule out unjustifiably diagnosed vasculitis in patients with atypical vascular lesions.

  13. Nasal septum extramedullary plasmacytoma

    Directory of Open Access Journals (Sweden)

    Belić Branislav

    2013-01-01

    Full Text Available Introduction. Plasmacytomas are malignant tumors characterized by abnormal monoclonal proliferation of plasma cells. They originate in either bone - solitary osseous plasmacytoma, or in soft tissue - extramedullary plasmacytoma (EMP. EMP represents less than 1% of all head and neck malignancies. Case report. We presented a case of EMP of the nasal septum in a 44-year-old male who had progressive difficulty in breathing through the nose and frequent heavy epistaxis on the right side. Nasal endoscopy showed dark red, soft, polypoid tumor in the last third of the right nasal cavity arising from the nasal septum. The biopsy showed that it was plasmacytoma. Bence Jones protein in the urine, serum electrophoresis, bone marrow biopsy, skeletal survey and other screening tests failed to detect multiple myeloma. This confirmed the diagnosis of EMP. The mass was completely removed via an endoscopic approach, and then, 4 week later, radiotherapy was conducted with a radiation dose of 50 Gray. No recurrence was noted in a 3-year follow- up period. Conclusion. EMP of the nasal cavity, being rare and having long natural history, represents a diagnostic and therapeutic challenge for any ear, nose and throat surgeon. Depending on the resectability of the lesion, a combined therapy is the accepted treatment.

  14. 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 ...

  15. 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…

  16. Prediction of Protein-DNA binding by Monte Carlo method

    Science.gov (United States)

    Deng, Yuefan; Eisenberg, Moises; Korobka, Alex

    1997-08-01

    We present an analysis and prediction of protein-DNA binding specificity based on the hydrogen bonding between DNA, protein, and auxillary clusters of water molecules. Zif268, glucocorticoid receptor, λ-repressor mutant, HIN-recombinase, and tramtrack protein-DNA complexes are studied. Hydrogen bonds are approximated by the Lennard-Jones potential with a cutoff distance between the hydrogen and the acceptor atoms set to 3.2 Åand an angular component based on a dipole-dipole interaction. We use a three-stage docking algorithm: geometric hashing that matches pairs of hydrogen bonding sites; (2) least-squares minimization of pairwise distances to filter out insignificant matches; and (3) Monte Carlo stochastic search to minimize the energy of the system. More information can be obtained from our first paper on this subject [Y.Deng et all, J.Computational Chemistry (1995)]. Results show that the biologically correct base pair is selected preferentially when there are two or more strong hydrogen bonds (with LJ potential lower than -0.20) that bind it to the protein. Predicted sequences are less stable in the case of weaker bonding sites. In general the inclusion of water bridges does increase the number of base pairs for which correct specificity is predicted.

  17. Models for the Binary Complex of Bacteriophage T4 Gp59 Helicase Loading Protein. GP32 Single-Stranded DNA-Binding Protein and Ternary Complex with Pseudo-Y Junction DNA

    Energy Technology Data Exchange (ETDEWEB)

    Hinerman, Jennifer M. [Univ. of Toledo, OH (United States); Dignam, J. David [Univ. of Toledo, OH (United States); Mueser, Timothy C. [Univ. of Toledo, OH (United States)

    2012-04-05

    The bacteriophage T4 gp59 helicase assembly protein (gp59) is required for loading of gp41 replicative helicase onto DNA protected by gp32 single-stranded DNA-binding protein. The gp59 protein recognizes branched DNA structures found at replication and recombination sites. Binding of gp32 protein (full-length and deletion constructs) to gp59 protein measured by isothermal titration calorimetry demonstrates that the gp32 protein C-terminal A-domain is essential for protein-protein interaction in the absence of DNA. Sedimentation velocity experiments with gp59 protein and gp32ΔB protein (an N-terminal B-domain deletion) show that these proteins are monomers but form a 1:1 complex with a dissociation constant comparable with that determined by isothermal titration calorimetry. Small angle x-ray scattering (SAXS) studies indicate that the gp59 protein is a prolate monomer, consistent with the crystal structure and hydrodynamic properties determined from sedimentation velocity experiments. SAXS experiments also demonstrate that gp32ΔB protein is a prolate monomer with an elongated A-domain protruding from the core. Moreover, fitting structures of gp59 protein and the gp32 core into the SAXS-derived molecular envelope supports a model for the gp59 protein-gp32ΔB protein complex. Our earlier work demonstrated that gp59 protein attracts full-length gp32 protein to pseudo-Y junctions. A model of the gp59 protein-DNA complex, modified to accommodate new SAXS data for the binary complex together with mutational analysis of gp59 protein, is presented in the accompanying article (Dolezal, D., Jones, C. E., Lai, X., Brister, J. R., Mueser, T. C., Nossal, N. G., and Hinton, D. M. (2012) J. Biol. Chem. 287, 18596–18607).

  18. Thermodynamic Properties and Phase Equilibrium Study of Lennard-Jones Model and Application to Real Molecules%LJ模型的热力学特性、相平衡及用于真实分子的研究

    Institute of Scientific and Technical Information of China (English)

    周世琦

    2005-01-01

    Both a free volume approach for Helmholtz free energy and a theoretically-based fitted formula for radial distribution function (rdf) of hard sphere solid were employed to describe the Helmholtz free energy of Lennard-Jones (LJ) solid in the framework of first order thermodynamic perturbation theory. Dividing the LJ potential follows from a modified WCA prescription, the specification of equivalent hard sphere diameter was determined by a simple iteration procedure devised originally for liquid state, but extended to solid state in the present study. Two hundred shells were used in the rdf to get an accurate perturbation term. Bulk fluid thermodynamic property of the LJ model is from a recently proposed equation of state. The present approach is very accurate for the description of excess Helmholtz free energy and equation of state of LJ solid, but shows some deviation from the simulation for excess Helmholtz free energy of uniform LJ fluid when the reduced temperature is lower than 0.75. The present approach is satisfactory for description of phase equilibrium of the LJ model. By choosing the appropriate LJ potential parameter, the present approach can describe the melting curve of real molecules accurately.%结合描述硬球固体Helmholtz自由能的自由体积方法与描述硬球固体径向分布函数的拟合的分析表达式与一阶热力学摄动理论,用于描述Lennard-Jones(LJ)固体的Helmholtz自由能.按照一个修正的WCA方法将LJ势分为短程排斥部分与长程吸引部分,将文献中一个用于求取液相的等价的硬球直径的简单的迭代法扩展到固相,用于求取固相的等价的硬球直径.在固体Helmholtz自由能的计算中,使用200壳层,以便获得精确的结果.体相LJ液体的热力学特性由一个最近提出的状态方程求取.该方法很好地描述了LJ固体的过量Helmholtz自由能与状态方程,满意地描述了Lennard-Jones模型的相平衡;通过选取合适的LJ势参数,能很

  19. A Comparative Study of the Dramatic Devices in The Emperor Jones and Macbeth%《麦克白》与《琼斯皇》戏剧手法比较探讨

    Institute of Scientific and Technical Information of China (English)

    姚小娟

    2010-01-01

    是威廉·莎士比亚四大悲剧中最精彩的一出.是尤金·奥尼尔的第一部表现主义戏剧.两部戏剧中,莎士比亚和奥尼尔都采用声音效果来营造可怕气氛并外显主人翁的内心恐惧,借助类似的象征如黒或黑暗、皇袍以及海来刻画人物,并通过独白来提露人物思考以及无意识情感.%Macbeth is the most tremendous of the Shakespeare tragedies. The Emperor Jones is Eugene O'Neill's first expressionistic play. In both plays, Shakespeare and O'Neill adopt aural effect to create the frightful atmosphere and externalize the internal fear of our heroes. And both plays resort to similar symbols such as blackness or darkness, the royal robe and sea to depict the characters. Besides, through soliloquies, both plays tend to reveal the character's conscious thought and unconscious emotions.

  20. 菲尔丁《汤姆·琼斯》典故网中的文化“肴馔”%The “Feast” of Culture in the Networks of Allusion in Henry Fielding's Tom Jones

    Institute of Scientific and Technical Information of China (English)

    张杨莉

    2013-01-01

    研究亨利·菲尔丁《汤姆·琼斯》典故网中的文化主题,分析菲尔丁如何网状般地构造其笑、打、美、醉、怒典故网及其在文化主题中所起到的多种作用。典故网的叙述方式间接地表达了小说家的思想与观点,表现了其叙述的艺术特征,唤起了读者的想象力,为读者带来了愉悦的文化“肴馔”享受。%This article studies the cultural theme in the networks of allusion used in Henry Fielding's Tom Jones, and analyzes how Fielding constructs the networks of allusion concerning smile, whipping,beauty, drunkenness and fury, which achieve various cultural functions. The narrative method of the networks of allusion indirectly expresses the novelist's ideas and views, illustrates the artistic features of the narration, evokes the reader's imagination and offers the reader the pleasure of appreciating the“feast” of culture.

  1. Use of polydispersity index as control parameter to study melting/freezing of Lennard-Jones system: Comparison among predictions of bifurcation theory with Lindemann criterion, inherent structure analysis and Hansen-Verlet rule

    Indian Academy of Sciences (India)

    Sarmistha Sarkar; Rajib Biswas; Partha Pratim Ray; Biman Bagchi

    2015-10-01

    Using polydispersity index as an additional order parameter we investigate freezing/melting transition of Lennard-Jones polydisperse systems (with Gaussian polydispersity in size), especially to gain insight into the origin of the terminal polydispersity. The average inherent structure (IS) energy and root mean square displacement (RMSD) of the solid before melting both exhibit quite similar polydispersity dependence including a discontinuity at solid-liquid transition point. Lindemann ratio, obtained from RMSD, is found to be dependent on temperature. At a given number density, there exists a value of polydispersity index (P) above which no crystalline solid is stable. This transition value of polydispersity (termed as transition polydispersity, P) is found to depend strongly on temperature, a feature missed in hard sphere model systems. Additionally, for a particular temperature when number density is increased, P shifts to higher values. This temperature and number density dependent value of P saturates surprisingly to a value which is found to be nearly the same for all temperatures, known as terminal polydispersity (TP). This value (TP ∼ 0.11) is in excellent agreement with the experimental value of 0.12, but differs from hard sphere transition where this limiting value is only 0.048. Terminal polydispersity (TP) thus has a quasiuniversal character. Interestingly, the bifurcation diagram obtained from non-linear integral equation theories of freezing seems to provide an explanation of the existence of unique terminal polydispersity in polydisperse systems. Global bond orientational order parameter is calculated to obtain further insights into mechanism for melting.

  2. Comment on "A praxis-oriented perspective of streamflow inference from stage observations – the method of Dottori et al. (2009 and the alternative of the Jones Formula, with the kinematic wave celerity computed on the looped rating curve" by Koussis (2009

    Directory of Open Access Journals (Sweden)

    A. D. Koussis

    2010-06-01

    Full Text Available The estimation of transient streamflow from stage measurements is indeed important and the study of Dottori, Martina and Todini (2009 (henceforth DMT is useful, however, DMT seem to miss certain of its practical aspects. The goal is to infer the discharge from measurements of the stage conveniently and with accuracy adequate for practical work. This comment addresses issues of the applicability of the DMT method in the field. DMT also advocate their method as a replacement of the widely used Jones Formula. The Jones Formula was modified by Thomas (Henderson, 1966 to include the temporal derivative of the depth, instead of the spatial one, to specifically allow discharge estimation from at-a-section stage observations. The outcome of the comparison is not surprising in view of this approximation. However, this discussion intends to show that, properly evaluated, the praxis-oriented Jones Formula, which did well in the tests, can perform better than DMT imply. It will be also documented that the DMT methodology relates to a known method for computing flood depth profiles.

  3. Total nitrogen vs. amino-acid profile as indicator of protein content of beef.

    Science.gov (United States)

    Hall, Nicolette G; Schönfeldt, Hettie C

    2013-10-01

    In most cited food composition studies and tables, the proximate system measures protein as total nitrogen (N) (determined by Kjeldahl or Dumas method) multiplied by a specific factor. A factor of 6.25 is used for determining total protein from total N (Jones, Munsey, & Walker, 1942). Although more expensive, it is considered more accurate to base protein content of foods on amino acid data (Greenfield & Southgate, 2003). A study on the nutrient composition of beef analysed the full amino-acid profile of fifteen retail cuts from three age groups and six fat codes, as well as determined total nitrogen content to determine proximate protein composition. For all cuts, the correlation coefficient of total amino acids to protein (N×6.25) was 0.635. This indicates a poor correlation for predicting actual protein content (as determined by total amino acid count), based on the nitrogen factor of 6.25. On average, the sum of amino acids per cut amounted to 91% of total determined protein (N×6.25) for the same cut.

  4. Whey Protein

    Science.gov (United States)

    ... Fraction de Lactosérum, Fraction de Petit-Lait, Goat Milk Whey, Goat Whey, Isolat de Protéine de Lactosérum, Isolat ... Lactosérum de Lait de Chèvre, MBP, Milk Protein, Milk Protein Isolate, Mineral Whey Concentrate, Proteínas del Suero de la Leche, Protéine ...

  5. 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...

  6. 改良Watson-Jones入路与改良Hardinge 入路全髋关节置换术的疗效比较%Modified Watson-Jones approach versus modified Hardinge approach for total hip arthroplasty

    Institute of Scientific and Technical Information of China (English)

    吴若; 徐耀增; 耿德春; 李荣群; 黄立新

    2011-01-01

    目的 比较改良Watson-Jones入路与改良Hardinge入路全髋关节置换术(THA)的疗效.方法 对2005年1月至2008年2月行THA治疗且获得随访的90例患者资料进行回顾性研究,其中采用改良Watson-Jones入路行微创THA(A组)44例,男20例,女24例;平均年龄(68.2±8.0)岁.病因:股骨颈骨折23例,股骨头坏死9例等.采用改良Hardinge入路行THA(B组)46例,男21例,女25例;平均年龄(69.1±9.2)岁.病因:股骨颈骨折21例,股骨头坏死6例等.手术均由同一组医生完成.临床评估包括术后3个月和末次随访时Harris髋关节功能评分及Barthel指数等,放射学评估包括髋臼外展角,记录并发症的发生情况.结果 所有患者术后获平均(50.9±10.1)个月随访.A组患者切口长度较B组短,失血量较B组少,术后3d内下床例数较B组多,两组比较差异均有统计学意义(p<0.05).两组患者髋臼外展角差异无统计学意义(P> 0.05).术后3个月A组患者Harris评分[(82.4±3.3)分]及Barthel指数(85.4±3.8)均高于B组患者[(72.3±3.7)分、77.2±5.4],差异均有统计学意义(P<0.05).但末次随访时两组患者的Harris评分及Barthel指数比较差异均无统计学意义(P>0.05).两组患者均末出现伤口感染、假体松动、髋关节脱位、血管神经损伤或深静脉血栓形成等并发症.结论 改良Watson-Jones入路与改良Hardinge入路均能满意应用于THA,但改良Watson-Jones入路微创THA术后前3个月内功能恢复更佳.%Objective To compare clinical results of modified Watson-Jones minimally invasive approach and modified Hardinge approach in total hip arthroplasty(THA).Methods This study reviewed 90 patients who had undergone THA from January 2005 through February 2008.The modified Watson-Jones approach was used in 44 patients(group A),20 men and 24 women,with an average age of 68.2 ±8.0 years; the modified Hardinge approach was used in 46 patients(group B),21 men and 25 women,with an average age of

  7. 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......Years of meticulous curation of scientific literature and increasingly reliable computational predictions have resulted in creation of vast databases of protein interaction data. Over the years, these repositories have become a basic framework in which experiments are analyzed and new directions...

  8. Indiana Jones Punalipulises Põhjamere laevastikus / Jaan Ruus

    Index Scriptorium Estoniae

    Ruus, Jaan, 1938-2017

    2002-01-01

    USA mängufilm nõukogude allveelaevaga 1991.a. toimunud avariist "K-19 : The Widowmaker" (režissöör Kathryn Bigelow) esilinastus Venemaal Peterburi Mariinski teatris. Osalesid ka avarii läbiteinud veteranid. Ka nende ja vene kriitikute hinnanguid

  9. Matthew Jones House: Recommendations for Treatment

    Science.gov (United States)

    2016-04-01

    important to wear shoes with slip-resistant soles and to use safety ropes . necessary, to keep the ladder from crushing the gutter. Use a garden hose...of law , no person shall be subject to any penalty for failing to comply with a collection of information if it does not display a currently valid OMB

  10. 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.

  11. A Single Mutation at the Sheet Switch Region Results in Conformational Changes Favoring 6 Light-Chain Fibrillogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Hernández-Santoyo, A.; Del Pozo Yauner, L; Fuentes-Silva, D; Ortiz, E; Rudiño-Piñera, E; Sánchez-López, R; Horjales, E; Becerril, B; Rodríguez-Romero, A

    2010-01-01

    Systemic amyloid light-chain (LC) amyloidosis is a disease process characterized by the pathological deposition of monoclonal LCs in tissue. All LC subtypes are capable of fibril formation although {lambda} chains, particularly those belonging to the {lambda}6 type, are overrepresented. Here, we report the thermodynamic and in vitro fibrillogenic properties of several mutants of the {lambda}6 protein 6aJL2 in which Pro7 and/or His8 was substituted by Ser or Pro. The H8P and H8S mutants were almost as stable as the wild-type protein and were poorly fibrillogenic. In contrast, the P7S mutation decreased the thermodynamic stability of 6aJL2 and greatly enhanced its capacity to form amyloid-like fibrils in vitro. The crystal structure of the P7S mutant showed that the substitution induced both local and long-distance effects, such as the rearrangement of the VL (variable region of the light chain)-VL interface. This mutant crystallized in two orthorhombic polymorphs, P2{sub 1}2{sub 1}2{sub 1} and C222{sub 1}. In the latter, a monomer that was not arranged in the typical Bence-Jones dimer was observed for the first time. Crystal-packing analysis of the C222{sub 1} lattice showed the establishment of intermolecular {beta}-{beta} interactions that involved the N-terminus and {beta}-strand B and that these could be relevant in the mechanism of LC fibril formation. Our results strongly suggest that Pro7 is a key residue in the conformation of the N-terminal sheet switch motif and, through long-distance interactions, is also critically involved in the contacts that stabilized the VL interface in {lambda}6 LCs.

  12. Non-exposed variant of bisphosphonate-related osteonecrosis of the jaw (BRONJ with a plasmacytoma: A rare case report

    Directory of Open Access Journals (Sweden)

    Arvind Muthukrishnan

    2015-01-01

    Full Text Available Bisphoshonate-related osteonecrosis of the jaw (BRONJ is an avascular osteo-chemonecrosis of the jaw which results after administration of the group of drugs called as bisphosphonates. Bisphosphonates are given to prevent bone resorption in osteolytic diseases such as Paget′s, osteoporosis, osteogenic carcinoma, and other carcinomas where there could be metastasis and bone resorption. Incidence of BRONJ is reported to be high in western literature and is found to be more after intravenous route compared to oral route of administration. There are various clinical stages of BRONJ as per the American Association of Oral and Maxillofacial Surgeons (AAOMS. Here, we present a rare case of a 60-year-old lady who presented with a complaint of a painless swelling in the alveolus and gingiva in the left maxillary posterior region. This patient was on intravenous Zolendronate for more than 4 years. Thorough examination with detailed investigations revealed BRONJ along with a coexisting second primary tumor, plasmacytoma. Metastasis to distant site is a common feature of malignancy. A metastatic lesion usually occurs within 6 months to 1 year after treatment of a primary lesion. Any fresh neoplasm beyond 1 or 2 years after detection of a primary can be regarded as a second primary tumor. Solitary bone plasmacytoma is a localized form of plasma cell tumor. Diagnosis is based on the presence of the following: Malignant proliferation of plasma cells in biopsy, absence of osteolytic bone lesion, absence of Bence Jones proteins, low concentration of monoclonal proteins, elevated IgG and gamma globulin levels.

  13. Testicular extramedullary plasmacytoma

    Directory of Open Access Journals (Sweden)

    M Samet

    2006-04-01

    Full Text Available Extramedullary plasmacytomas are plasma cell tumors that arise outside the bone marrow. They are most often located in the head and neck. Extramedullary plasmacytomas account for approximately 3 percent of plasma cell malignancies. The diagnosis of an extramedullary plasmacytoma depends upon the demonstration of a monoclonal plasma cell tumor at an extramedullary site with no evidence of multiple myeloma based upon bone marrow examination and roentgenographic studies, absence of an M-protein in serum and/ or urine, and no related organ or tissue impairment. These tumors are highly responsive to local radiation therapy and rarely progress or recur. A 77 year old man referred for gradual enlargement of scrotum in April, 2004. He had no fever, weight loss or loss of appetite during the period. No tenderness, warmth or erythem of scrotum was observed on physical examination. No lymphadenopathy was detected. Later he had temporary relief because of antibiotic therapy . 7 months later, he referred again following the aggravation of his symptom. Ultrasonography of his scrotum was done and enlargement in the left testis was reported. Lab data including CBC,diff,ESR,AFP were normal but βHCG titer was reported higher than normal . He underwent radical orchiectomy and the specimen was sent for pathological study. Spermatocytic seminoma and plasmacytoma were suspected, but plasmacytoma was reported after the IHC . In order to rule out multiple myeloma, whole body bone scanning with sestamibi and urine Bence Jones protein were examined, all of which were negative. In bone marrow aspiration, the cellularity was normal and no pathologic lesion was reported. Considering clinical and paraclinical evidences, the diagnosis was extramedullary plasmacytoma.

  14. Protein inference: A protein quantification perspective.

    Science.gov (United States)

    He, Zengyou; Huang, Ting; Liu, Xiaoqing; Zhu, Peijun; Teng, Ben; Deng, Shengchun

    2016-08-01

    In mass spectrometry-based shotgun proteomics, protein quantification and protein identification are two major computational problems. To quantify the protein abundance, a list of proteins must be firstly inferred from the raw data. Then the relative or absolute protein abundance is estimated with quantification methods, such as spectral counting. Until now, most researchers have been dealing with these two processes separately. In fact, the protein inference problem can be regarded as a special protein quantification problem in the sense that truly present proteins are those proteins whose abundance values are not zero. Some recent published papers have conceptually discussed this possibility. However, there is still a lack of rigorous experimental studies to test this hypothesis. In this paper, we investigate the feasibility of using protein quantification methods to solve the protein inference problem. Protein inference methods aim to determine whether each candidate protein is present in the sample or not. Protein quantification methods estimate the abundance value of each inferred protein. Naturally, the abundance value of an absent protein should be zero. Thus, we argue that the protein inference problem can be viewed as a special protein quantification problem in which one protein is considered to be present if its abundance is not zero. Based on this idea, our paper tries to use three simple protein quantification methods to solve the protein inference problem effectively. The experimental results on six data sets show that these three methods are competitive with previous protein inference algorithms. This demonstrates that it is plausible to model the protein inference problem as a special protein quantification task, which opens the door of devising more effective protein inference algorithms from a quantification perspective. The source codes of our methods are available at: http://code.google.com/p/protein-inference/.

  15. Probabilistic sampling of protein conformations: new hope for brute force?

    Science.gov (United States)

    Feldman, Howard J; Hogue, Christopher W V

    2002-01-01

    Protein structure prediction from sequence alone by "brute force" random methods is a computationally expensive problem. Estimates have suggested that it could take all the computers in the world longer than the age of the universe to compute the structure of a single 200-residue protein. Here we investigate the use of a faster version of our FOLDTRAJ probabilistic all-atom protein-structure-sampling algorithm. We have improved the method so that it is now over twenty times faster than originally reported, and capable of rapidly sampling conformational space without lattices. It uses geometrical constraints and a Leonard-Jones type potential for self-avoidance. We have also implemented a novel method to add secondary structure-prediction information to make protein-like amounts of secondary structure in sampled structures. In a set of 100,000 probabilistic conformers of 1VII, 1ENH, and 1PMC generated, the structures with smallest Calpha RMSD from native are 3.95, 5.12, and 5.95A, respectively. Expanding this test to a set of 17 distinct protein folds, we find that all-helical structures are "hit" by brute force more frequently than beta or mixed structures. For small helical proteins or very small non-helical ones, this approach should have a "hit" close enough to detect with a good scoring function in a pool of several million conformers. By fitting the distribution of RMSDs from the native state of each of the 17 sets of conformers to the extreme value distribution, we are able to estimate the size of conformational space for each. With a 0.5A RMSD cutoff, the number of conformers is roughly 2N where N is the number of residues in the protein. This is smaller than previous estimates, indicating an average of only two possible conformations per residue when sterics are accounted for. Our method reduces the effective number of conformations available at each residue by probabilistic bias, without requiring any particular discretization of residue conformational

  16. Grafting of protein-protein binding sites

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    A strategy for grafting protein-protein binding sites is described. Firstly, key interaction residues at the interface of ligand protein to be grafted are identified and suitable positions in scaffold protein for grafting these key residues are sought. Secondly, the scaffold proteins are superposed onto the ligand protein based on the corresponding Ca and Cb atoms. The complementarity between the scaffold protein and the receptor protein is evaluated and only matches with high score are accepted. The relative position between scaffold and receptor proteins is adjusted so that the interface has a reasonable packing density. Then the scaffold protein is mutated to corresponding residues in ligand protein at each candidate position. And the residues having bad steric contacts with the receptor proteins, or buried charged residues not involved in the formation of any salt bridge are mutated. Finally, the mutated scaffold protein in complex with receptor protein is co-minimized by Charmm. In addition, we deduce a scoring function to evaluate the affinity between mutated scaffold protein and receptor protein by statistical analysis of rigid binding data sets.

  17. Multiple myeloma in Nigeria: a multi-centre epidemiological and biomedical study

    Science.gov (United States)

    Nnonyelum, Odunukwe Nkiruka; Anazoeze, Madu Jude; Eunice, Nnodu Obigeli; Emmanuel, Okocha Onyichide; Stella, Akingbola Titilola; Marcus, Asuquo Inyama; Taiwo, Balogun Modupe; Olufela, Kalejaiye Olufunto; Chinawaeze, Aneke John; Orkuma, Joseph Aondowase; Dalhat, Gwarzo Gwarzo; Otobo, Ujah Innocent

    2015-01-01

    Introduction Myelomatosis is a malignant proliferation of plasma cells in the bone marrow, with relatively high prevalence in African populations. Variation in genetic mutations has been observed in individual patients and may be responsible for differences in disease pattern and treatment outcomes. This study described the presentations and treatment outcomes of multiple myeloma in nigerian. Methods The data was obtained retrospectively from the case notes of 135 patients diagnosed with multiple myeloma from eight tertiary health institutions across the six geopolitical zones of Nigeria from 2005 to 2014. Data analysis was carried out using SPSS 17.0. Results The predominant presentations were bone pain in 97 (74%), nephropathy in 47 (35.9%) and pathological fractures in 58 (44.3%). Sixty-seven percent (67%) of the patients were less than 60 years, and 35% had Bence Jones proteinuria. The overall survival beyond 6 months was 91.3%, mean duration of survival rate was 7.4 months. Majority (66.2%) were on Melphalan alone or on melphalan-containing combinations. A higher packed cell volume (PCV) and total serum protein levels at presentation were associated with increased survival, p=0.033 and 0.036, respectively. Conclusion This study portrayed the importance of detail investigation on the causes of bone pain and anaemia in person's aged 40 years and above. There is a high prevalence of nephropathy in this cohort of patients which needs to be further investigated. Majority of the patients, though < 65 years of age were placed on melphalan-containing combinations, which foreclosed chances of future autologous bone marrow transplantation. PMID:26966488

  18. New patterns of relapse in multiple myeloma: a case of "light chain escape" in which FLC predicted relapse earlier than urine and serum immunofixation.

    Science.gov (United States)

    Caldini, Anna; Nozzoli, Chiara; Terreni, Alessandro; Staderini, Michela; Berardi, Margherita; Biagioli, Tiziana; Brogi, Marco; Bosi, Alberto

    2016-06-01

    Multiple myeloma (MM) is characterized, in about 80% of cases, by the production of monoclonal intact immunoglobulin and more than 95% of them have elevated concentrations of involved (i.e. of the same class of intact immunoglobulin) free light chain (FLC). The introduction of novel therapeutic strategies has changed the natural history of the disease, leading to new manifestations of relapse. Light chain escape (LCE) is a pattern of relapse in which the FLC increase is not accompanied by a concomitant raise of the original monoclonal component (MC). Here we present a case of a 55-year-old man with an IgG kappa MM stage III diagnosed in September 2007. At presentation an IgG kappa MC and urine Bence Jones protein (BJP) kappa were present. Bone marrow biopsy (BMB) showed the presence of 80% monotypic kappa plasma cells (PCs). The patient received bortezomib, thalidomide, dexamethasone before undergoing a double autologous stem cell transplantation (ASCT) in October 2008 and April 2009. In May 2011 he relapsed showing the same pattern of presentation and treatment with lenalidomide and dexamethasone was started. ln May 2013 serum and urine immunofixation and FLC became negative. In September 2014, an increase of kappa FLC was observed, while serum and urine immunofixations remained negative until January 2015, when urine immunofixation became positive. Eventually, in February 2015, serum immunofixation revealed the presence of a free kappa MC. After a new BMB showing 80% of monotypic kappa PCs, a LCE relapse was diagnosed and the patient started the treatment with bendamustine, bortezomib and dexamethasone. In the present case, the increase of kappa FLC has indicated relapse 4 and 5 months earlier than urine and serum IFE, respectively. Our observation confirms that it is advisable to routinely perform FLC or BJP during follow up of MM patients undergoing ASCT and/or treatment with biological drugs to ensure that LCE is not missed.

  19. EDITORIAL: Precision proteins Precision proteins

    Science.gov (United States)

    Demming, Anna

    2010-06-01

    Since the birth of modern day medicine, during the times of Hippocrates in ancient Greece, the profession has developed from the rudimentary classification of disease into a rigorous science with an inspiring capability to treat and cure. Scientific methodology has distilled clinical diagnostic tools from the early arts of prognosis, which used to rely as much on revelation and prophecy, as intuition and judgement [1]. Over the past decade, research into the interactions between proteins and nanosystems has provided some ingenious and apt techniques for delving into the intricacies of anatomical systems. In vivo biosensing has emerged as a vibrant field of research, as much of medical diagnosis relies on the detection of substances or an imbalance in the chemicals in the body. The inherent properties of nanoscale structures, such as cantilevers, make them well suited to biosensing applications that demand the detection of molecules at very low concentrations. Measurable deflections in cantilevers functionalised with antibodies provide quantitative indicators of the presence of specific antigens when the two react. Such developments have roused mounting interest in the interactions of proteins with nanostructures, such as carbon nanotubes [3], which have demonstrated great potential as generic biomarkers. Plasmonic properties are also being exploited in sensing applications, such as the molecular sentinel recently devised by researchers in the US. The device uses the plasmonic properties of a silver nanoparticle linked to a Raman labelled hairpin DNA probe to signal changes in the probe geometry resulting from interactions with substances in the environment. Success stories so far include the detection of two specific genes associated with breast cancer [4]. A greater understanding of how RNA interference regulates gene expression has highlighted the potential of using this natural process as another agent for combating disease in personalized medicine. However, the

  20. Scaffolds for blocking protein-protein interactions.

    Science.gov (United States)

    Hershberger, Stefan J; Lee, Song-Gil; Chmielewski, Jean

    2007-01-01

    Due to the pivotal roles that protein-protein interactions play in a plethora of biological processes, the design of therapeutic agents targeting these interactions has become an attractive and important area of research. The development of such agents is faced with a variety of challenges. Nevertheless, considerable progress has been made in the design of proteomimetics capable of disrupting protein-protein interactions. Those inhibitors based on molecular scaffold designs hold considerable interest because of the ease of variation in regard to their displayed functionality. In particular, protein surface mimetics, alpha-helical mimetics, beta-sheet/beta-strand mimetics, as well as beta-turn mimetics have successfully modulated protein-protein interactions involved in such diseases as cancer and HIV. In this review, current progress in the development of molecular scaffolds designed for the disruption of protein-protein interactions will be discussed with an emphasis on those active against biological targets.

  1. Fusion-protein-assisted protein crystallization.

    Science.gov (United States)

    Kobe, Bostjan; Ve, Thomas; Williams, Simon J

    2015-07-01

    Fusion proteins can be used directly in protein crystallization to assist crystallization in at least two different ways. In one approach, the `heterologous fusion-protein approach', the fusion partner can provide additional surface area to promote crystal contact formation. In another approach, the `fusion of interacting proteins approach', protein assemblies can be stabilized by covalently linking the interacting partners. The linker connecting the proteins plays different roles in the two applications: in the first approach a rigid linker is required to reduce conformational heterogeneity; in the second, conversely, a flexible linker is required that allows the native interaction between the fused proteins. The two approaches can also be combined. The recent applications of fusion-protein technology in protein crystallization from the work of our own and other laboratories are briefly reviewed.

  2. Fractura mandibular patológica por plasmocitoma intraóseo Pathological mandibular fracture due to intraosseous plasmacytoma

    Directory of Open Access Journals (Sweden)

    D. Antunes Freitas

    2012-06-01

    duct and rarely in the oral cavity. The search for a systemic disease is important in cases where the diagnosis is made. A case of a patient, a man of 73 years of age, residing in the rural village of Great Mogol, Minas Gerais (Brazil, Computed tomography showed irregular osteolytic hypodensity and resorption at the base of the left mandibular alveolar ridge. The lesion measuring 38.0 mm × 19.0 mm × 15.0 mm. On CT clearly shows the presence of pathological fracture of the left side. Needle aspiration was performed, where blood was obtained. Incisional biopsy was performed. The presumptive diagnosis was ameloblastoma. The biopsy specimen was sent for analysis anatomohistopatológica. Microscopy showed tumor cells composed of monomorphic cells with oval nuclei, large peripheral and eccentric, prominent nucleoli and basophilic cytoplasm, surrounded by scant stroma and infiltration of cancellous bone. The urine test was conducted specifically for the Bence-Jones protein, which was negative. The skull and chest radiographs were performed and showed no changes. He then completed a diagnosis of solitary plasmacytoma of the jaw. The patient is undergoing radiotherapy at the Oncology Department of Santa Casa de Misericordia. The patient had severe mucositis and changes in facial color as a result of radiotherapy.

  3. Protein docking prediction using predicted protein-protein interface

    Directory of Open Access Journals (Sweden)

    Li Bin

    2012-01-01

    Full Text Available Abstract Background Many important cellular processes are carried out by protein complexes. To provide physical pictures of interacting proteins, many computational protein-protein prediction methods have been developed in the past. However, it is still difficult to identify the correct docking complex structure within top ranks among alternative conformations. Results We present a novel protein docking algorithm that utilizes imperfect protein-protein binding interface prediction for guiding protein docking. Since the accuracy of protein binding site prediction varies depending on cases, the challenge is to develop a method which does not deteriorate but improves docking results by using a binding site prediction which may not be 100% accurate. The algorithm, named PI-LZerD (using Predicted Interface with Local 3D Zernike descriptor-based Docking algorithm, is based on a pair wise protein docking prediction algorithm, LZerD, which we have developed earlier. PI-LZerD starts from performing docking prediction using the provided protein-protein binding interface prediction as constraints, which is followed by the second round of docking with updated docking interface information to further improve docking conformation. Benchmark results on bound and unbound cases show that PI-LZerD consistently improves the docking prediction accuracy as compared with docking without using binding site prediction or using the binding site prediction as post-filtering. Conclusion We have developed PI-LZerD, a pairwise docking algorithm, which uses imperfect protein-protein binding interface prediction to improve docking accuracy. PI-LZerD consistently showed better prediction accuracy over alternative methods in the series of benchmark experiments including docking using actual docking interface site predictions as well as unbound docking cases.

  4. Short-term clinical effects of modified Watson-Jones total hip arthroplasty versus modified Gibson approach%以改良Watson-Jones入路微创行全髋关节置换与改良Gibson后侧入路全髋关节置换的近期疗效比较

    Institute of Scientific and Technical Information of China (English)

    韦庆军; 赵劲民; 陆荣斌; 李晓峰; 陆定贵

    2011-01-01

    BACKGROUND: Recently, modified Watson-Jones total hip arthroplasty (THA) has been widely used in the world.OBJECTIVE: To compare short-term clinical effects between minimally invasive modified Watson-Jones THA and modifiedGibson THA.METHODS: Twenty-two patients accepted modified Watson-Jones method and 30 patients underwent modified Gibsonapproach.RESULTS AND CONCLUSION: The follow-up time was 18 months in 49 cases, 1 case lost to follow-up in modified Watson-Jonesgroup and 2 cases in modified Gibson group. The significant differences between two groups were observed in decreases ofindicators such as length of incision, volume of blood loss perioperative period, volume of blood transfusion, days at hospitalpostoperatively and ti me of operation (P < 0.05). Volume of postoperative blood loss, position of prosthesis, and hip functionalevaluation system (Harris) were not significantly different between two groups. Complications including infection, dislocation,neurovascular injury, deep vein embolism were not observed in all cases. The general results of modified Watson-Jones group arebetter than modified Gibson group according to the short term follow-up data. Minimal invasive method leads to decreases ofcomplications, loss of blood and time at hospital, good results in hip function, and early exercise is available.%背景:采用改良Watson-Jones入路的微创全髋关节置换近年来在国内外得到广泛的应用.目的:比较改良Watson-Jones入路微创全髋关节置换与改良Gibson 后侧入路全髋关节置换的近期疗效.方法:52例接受单侧髋关节置换患者,根据入院日期单双号,随机分为2组,实验组22例接受改良Watson-Jones入路微创人工全髋关节置换;对照组30例接受改良Gibson后侧入路人工全髋关节置换.结果与结论:两组患者完整随访至置换后18个月49例,实验组失访1例,对照组失访2例.实验组手术时间多于对照组(P < 0.05),实验组切口长度、术中出血量、

  5. Protein Crystal Based Nanomaterials

    Science.gov (United States)

    Bell, Jeffrey A.; VanRoey, Patrick

    2001-01-01

    This is the final report on a NASA Grant. It concerns a description of work done, which includes: (1) Protein crystals cross-linked to form fibers; (2) Engineering of protein to favor crystallization; (3) Better knowledge-based potentials for protein-protein contacts; (4) Simulation of protein crystallization.

  6. Shotgun protein sequencing.

    Energy Technology Data Exchange (ETDEWEB)

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  7. 表现主义戏剧的经典范型——奥尼尔《琼斯皇》论析%Classic Paradigm of Expressionist Drama——Analysis of The Emperor Jones by Eugene O'Neill

    Institute of Scientific and Technical Information of China (English)

    李勇强; 宁辰

    2011-01-01

    The Expressionist drama The Emperor Jones by American playwright Eugene O'Neill,not only shows rational psychology of images,such as thinking and will,but also explores irrational personal unconscious and collective unconscious.The protagonist Jones is an image full of diversified perception and multiple personality.In this sense,O'Neill's Expressionist plays better develop Expressionist drama owing to his image-building techniques of integrating real soul into an individual and therefore reflecting the complexity and diversity of humanity instead of following the patterns of typical and abstract characters.%美国戏剧家奥尼尔的表现主义戏剧《琼斯皇》不仅展现了形象主体的思想、意志等理性心理,而且深入到个人无意识及集体无意识等非理性深层。主人公琼斯是一个充盈感性丰富性的、具有多层次内在心理的形象。从这个意义上讲,奥尼尔的表现主义剧作挣脱了"类型化"、抽象式人物的窠臼,使灵魂的各个层面完整地融汇于某个个体,形象的心理内涵变得极为复杂、深刻,将表现主义戏剧的形象塑造提升到更加完善的高度,同时也深化并发展了表现主义戏剧艺术。

  8. Protein folding, protein homeostasis, and cancer

    Institute of Scientific and Technical Information of China (English)

    John H. Van Drie

    2011-01-01

    Proteins fold into their functional 3-dimensional structures from a linear amino acid sequence. In vitro this process is spontaneous; while in vivo it is orchestrated by a specialized set of proteins, called chaperones. Protein folding is an ongoing cellular process, as cellular proteins constantly undergo synthesis and degradation. Here emerging links between this process and cancer are reviewed. This perspective both yields insights into the current struggle to develop novel cancer chemotherapeutics and has implications for future chemotherapy discovery.

  9. Oligomeric protein structure networks: insights into protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Brinda KV

    2005-12-01

    Full Text Available Abstract Background Protein-protein association is essential for a variety of cellular processes and hence a large number of investigations are being carried out to understand the principles of protein-protein interactions. In this study, oligomeric protein structures are viewed from a network perspective to obtain new insights into protein association. Structure graphs of proteins have been constructed from a non-redundant set of protein oligomer crystal structures by considering amino acid residues as nodes and the edges are based on the strength of the non-covalent interactions between the residues. The analysis of such networks has been carried out in terms of amino acid clusters and hubs (highly connected residues with special emphasis to protein interfaces. Results A variety of interactions such as hydrogen bond, salt bridges, aromatic and hydrophobic interactions, which occur at the interfaces are identified in a consolidated manner as amino acid clusters at the interface, from this study. Moreover, the characterization of the highly connected hub-forming residues at the interfaces and their comparison with the hubs from the non-interface regions and the non-hubs in the interface regions show that there is a predominance of charged interactions at the interfaces. Further, strong and weak interfaces are identified on the basis of the interaction strength between amino acid residues and the sizes of the interface clusters, which also show that many protein interfaces are stronger than their monomeric protein cores. The interface strengths evaluated based on the interface clusters and hubs also correlate well with experimentally determined dissociation constants for known complexes. Finally, the interface hubs identified using the present method correlate very well with experimentally determined hotspots in the interfaces of protein complexes obtained from the Alanine Scanning Energetics database (ASEdb. A few predictions of interface hot

  10. Protein-losing enteropathy

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/007338.htm Protein-losing enteropathy To use the sharing features on this page, please enable JavaScript. Protein-losing enteropathy is an abnormal loss of protein ...

  11. Efficient Parameter Estimation of Generalizable Coarse-Grained Protein Force Fields Using Contrastive Divergence: A Maximum Likelihood Approach.

    Science.gov (United States)

    Várnai, Csilla; Burkoff, Nikolas S; Wild, David L

    2013-12-10

    Maximum Likelihood (ML) optimization schemes are widely used for parameter inference. They maximize the likelihood of some experimentally observed data, with respect to the model parameters iteratively, following the gradient of the logarithm of the likelihood. Here, we employ a ML inference scheme to infer a generalizable, physics-based coarse-grained protein model (which includes Go̅-like biasing terms to stabilize secondary structure elements in room-temperature simulations), using native conformations of a training set of proteins as the observed data. Contrastive divergence, a novel statistical machine learning technique, is used to efficiently approximate the direction of the gradient ascent, which enables the use of a large training set of proteins. Unlike previous work, the generalizability of the protein model allows the folding of peptides and a protein (protein G) which are not part of the training set. We compare the same force field with different van der Waals (vdW) potential forms: a hard cutoff model, and a Lennard-Jones (LJ) potential with vdW parameters inferred or adopted from the CHARMM or AMBER force fields. Simulations of peptides and protein G show that the LJ model with inferred parameters outperforms the hard cutoff potential, which is consistent with previous observations. Simulations using the LJ potential with inferred vdW parameters also outperforms the protein models with adopted vdW parameter values, demonstrating that model parameters generally cannot be used with force fields with different energy functions. The software is available at https://sites.google.com/site/crankite/.

  12. Conductometric monitoring of protein-protein interactions.

    Science.gov (United States)

    Spera, Rosanna; Festa, Fernanda; Bragazzi, Nicola L; Pechkova, Eugenia; LaBaer, Joshua; Nicolini, Claudio

    2013-12-06

    Conductometric monitoring of protein-protein and protein-sterol interactions is here proved feasible by coupling quartz crystal microbalance with dissipation monitoring (QCM_D) to nucleic acid programmable protein arrays (NAPPA). The conductance curves measured in NAPPA microarrays printed on quartz surface allowed the identification of binding events between the immobilized proteins and the query. NAPPA allows the immobilization on the quartz surface of a wide range of proteins and can be easily adapted to generate innumerous types of biosensors. Indeed multiple proteins on the same quartz crystal have been tested and envisaged proving the possibility of analyzing the same array for several distinct interactions. Two examples of NAPPA-based conductometer applications with clinical relevance are presented herein, the interaction between the transcription factors Jun and ATF2 and the interaction between Cytochrome P540scc and cholesterol.

  13. Protein sequence comparison and protein evolution

    Energy Technology Data Exchange (ETDEWEB)

    Pearson, W.R. [Univ. of Virginia, Charlottesville, VA (United States). Dept. of Biochemistry

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. This tutorial examines how the information conserved during the evolution of a protein molecule can be used to infer reliably homology, and thus a shared proteinfold and possibly a shared active site or function. The authors start by reviewing a geological/evolutionary time scale. Next they look at the evolution of several protein families. During the tutorial, these families will be used to demonstrate that homologous protein ancestry can be inferred with confidence. They also examine different modes of protein evolution and consider some hypotheses that have been presented to explain the very earliest events in protein evolution. The next part of the tutorial will examine the technical aspects of protein sequence comparison. Both optimal and heuristic algorithms and their associated parameters that are used to characterize protein sequence similarities are discussed. Perhaps more importantly, they survey the statistics of local similarity scores, and how these statistics can both be used to improve the selectivity of a search and to evaluate the significance of a match. They them examine distantly related members of three protein families, the serine proteases, the glutathione transferases, and the G-protein-coupled receptors (GCRs). Finally, the discuss how sequence similarity can be used to examine internal repeated or mosaic structures in proteins.

  14. Prediction of Protein-Protein Interactions Using Protein Signature Profiling

    Institute of Scientific and Technical Information of China (English)

    Mahmood A. Mahdavi; Yen-Han Lin

    2007-01-01

    Protein domains are conserved and functionally independent structures that play an important role in interactions among related proteins. Domain-domain inter- actions have been recently used to predict protein-protein interactions (PPI). In general, the interaction probability of a pair of domains is scored using a trained scoring function. Satisfying a threshold, the protein pairs carrying those domains are regarded as "interacting". In this study, the signature contents of proteins were utilized to predict PPI pairs in Saccharomyces cerevisiae, Caenorhabditis ele- gans, and Homo sapiens. Similarity between protein signature patterns was scored and PPI predictions were drawn based on the binary similarity scoring function. Results show that the true positive rate of prediction by the proposed approach is approximately 32% higher than that using the maximum likelihood estimation method when compared with a test set, resulting in 22% increase in the area un- der the receiver operating characteristic (ROC) curve. When proteins containing one or two signatures were removed, the sensitivity of the predicted PPI pairs in- creased significantly. The predicted PPI pairs are on average 11 times more likely to interact than the random selection at a confidence level of 0.95, and on aver- age 4 times better than those predicted by either phylogenetic profiling or gene expression profiling.

  15. Inferring Protein Associations Using Protein Pulldown Assays

    Energy Technology Data Exchange (ETDEWEB)

    Sharp, Julia L.; Anderson, Kevin K.; Daly, Don S.; Auberry, Deanna L.; Borkowski, John J.; Cannon, William R.

    2007-02-01

    Background: One method to infer protein-protein associations is through a “bait-prey pulldown” assay using a protein affinity agent and an LC-MS (liquid chromatography-mass spectrometry)-based protein identification method. False positive and negative protein identifications are not uncommon, however, leading to incorrect inferences. Methods: A pulldown experiment generates a protein association matrix wherein each column represents a sample from one bait protein, each row represents one prey protein and each cell contains a presence/absence association indicator. Our method evaluates the presence/absence pattern across a prey protein (row) with a Likelihood Ratio Test (LRT), computing its p-value with simulated LRT test statistic distributions after a check with simulated binomial random variates disqualified the large sample 2 test. A pulldown experiment often involves hundreds of tests so we apply the false discovery rate method to control the false positive rate. Based on the p-value, each prey protein is assigned a category (specific association, non-specific association, or not associated) and appraised with respect to the pulldown experiment’s goal and design. The method is illustrated using a pulldown experiment investigating the protein complexes of Shewanella oneidensis MR-1. Results: The Monte Carlo simulated LRT p-values objectively reveal specific and ubiquitous prey, as well as potential systematic errors. The example analysis shows the results to be biologically sensible and more realistic than the ad hoc screening methods previously utilized. Conclusions: The method presented appears to be informative for screening for protein-protein associations.

  16. Polymer Directed Protein Assemblies

    NARCIS (Netherlands)

    van Rijn, Patrick

    2013-01-01

    Protein aggregation and protein self-assembly is an important occurrence in natural systems, and is in some form or other dictated by biopolymers. Very obvious influences of biopolymers on protein assemblies are, e. g., virus particles. Viruses are a multi-protein assembly of which the morphology is

  17. Mirror image proteins.

    Science.gov (United States)

    Zhao, Le; Lu, Wuyuan

    2014-10-01

    Proteins composed entirely of unnatural d-amino acids and the achiral amino acid glycine are mirror image forms of their native l-protein counterparts. Recent advances in chemical protein synthesis afford unique and facile synthetic access to domain-sized mirror image d-proteins, enabling protein research to be conducted through 'the looking glass' and in a way previously unattainable. d-Proteins can facilitate structure determination of their native l-forms that are difficult to crystallize (racemic X-ray crystallography); d-proteins can serve as the bait for library screening to ultimately yield pharmacologically superior d-peptide/d-protein therapeutics (mirror-image phage display); d-proteins can also be used as a powerful mechanistic tool for probing molecular events in biology. This review examines recent progress in the application of mirror image proteins to structural biology, drug discovery, and immunology.

  18. Protein- protein interaction detection system using fluorescent protein microdomains

    Science.gov (United States)

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2010-02-23

    The invention provides a protein labeling and interaction detection system based on engineered fragments of fluorescent and chromophoric proteins that require fused interacting polypeptides to drive the association of the fragments, and further are soluble and stable, and do not change the solubility of polypeptides to which they are fused. In one embodiment, a test protein X is fused to a sixteen amino acid fragment of GFP (.beta.-strand 10, amino acids 198-214), engineered to not perturb fusion protein solubility. A second test protein Y is fused to a sixteen amino acid fragment of GFP (.beta.-strand 11, amino acids 215-230), engineered to not perturb fusion protein solubility. When X and Y interact, they bring the GFP strands into proximity, and are detected by complementation with a third GFP fragment consisting of GFP amino acids 1-198 (strands 1-9). When GFP strands 10 and 11 are held together by interaction of protein X and Y, they spontaneous association with GFP strands 1-9, resulting in structural complementation, folding, and concomitant GFP fluorescence.

  19. Urine Protein and Urine Protein to Creatinine Ratio

    Science.gov (United States)

    ... limited. Home Visit Global Sites Search Help? Urine Protein and Urine Protein to Creatinine Ratio Share this page: Was this page helpful? Also known as: 24-Hour Urine Protein; Urine Total Protein; Urine Protein to Creatinine Ratio; ...

  20. IGSF9 Family Proteins

    DEFF Research Database (Denmark)

    Hansen, Maria; Walmod, Peter Schledermann

    2013-01-01

    The Drosophila protein Turtle and the vertebrate proteins immunoglobulin superfamily (IgSF), member 9 (IGSF9/Dasm1) and IGSF9B are members of an evolutionarily ancient protein family. A bioinformatics analysis of the protein family revealed that invertebrates contain only a single IGSF9 family gene......, the longest isoforms of the proteins have the same general organization as the neural cell adhesion molecule family of cell adhesion molecule proteins, and like this family of proteins, IGSF9 family members are expressed in the nervous system. A review of the literature revealed that Drosophila Turtle...... facilitates homophilic cell adhesion. Moreover, IGSF9 family proteins have been implicated in the outgrowth and branching of neurites, axon guidance, synapse maturation, self-avoidance, and tiling. However, despite the few published studies on IGSF9 family proteins, reports on the functions of both Turtle...

  1. Reconciling the understanding of ‘hydrophobicity’ with physics-based models of proteins

    Science.gov (United States)

    Harris, Robert C.; Montgomery Pettitt, B.

    2016-03-01

    The idea that a ‘hydrophobic energy’ drives protein folding, aggregation, and binding by favoring the sequestration of bulky residues from water into the protein interior is widespread. The solvation free energies (Δ {{G}\\text{solv}} ) of small nonpolar solutes increase with surface area (A), and the free energies of creating macroscopic cavities in water increase linearly with A. These observations seem to imply that there is a hydrophobic component (Δ {{G}\\text{hyd}} ) of Δ {{G}\\text{solv}} that increases linearly with A, and this assumption is widely used in implicit solvent models. However, some explicit-solvent molecular dynamics studies appear to contradict these ideas. For example, one definition (Δ {{G}\\text{LJ}} ) of Δ {{G}\\text{hyd}} is that it is the free energy of turning on the Lennard-Jones (LJ) interactions between the solute and solvent. However, Δ {{G}\\text{LJ}} decreases with A for alanine and glycine peptides. Here we argue that these apparent contradictions can be reconciled by defining Δ {{G}\\text{hyd}} to be a near hard core insertion energy (Δ {{G}\\text{rep}} ), as in the partitioning proposed by Weeks, Chandler, and Andersen. However, recent results have shown that Δ {{G}\\text{rep}} is not a simple function of geometric properties of the molecule, such as A and the molecular volume, and that the free energy of turning on the attractive part of the LJ potential cannot be computed from first-order perturbation theory for proteins. The theories that have been developed from these assumptions to predict Δ {{G}\\text{hyd}} are therefore inadequate for proteins.

  2. Physics of protein motility and motor proteins

    Science.gov (United States)

    Kolomeisky, Anatoly B.

    2013-09-01

    Motor proteins are enzymatic molecules that transform chemical energy into mechanical motion and work. They are critically important for supporting various cellular activities and functions. In the last 15 years significant progress in understanding the functioning of motor proteins has been achieved due to revolutionary breakthroughs in single-molecule experimental techniques and strong advances in theoretical modelling. However, microscopic mechanisms of protein motility are still not well explained, and the collective efforts of many scientists are needed in order to solve these complex problems. In this special section the reader will find the latest advances on the difficult road to mapping motor proteins dynamics in various systems. Recent experimental developments have allowed researchers to monitor and to influence the activity of single motor proteins with a high spatial and temporal resolution. It has stimulated significant theoretical efforts to understand the non-equilibrium nature of protein motility phenomena. The latest results from all these advances are presented and discussed in this special section. We would like to thank the scientists from all over the world who have reported their latest research results for this special section. We are also grateful to the staff and editors of Journal of Physics: Condensed Matter for their invaluable help in handling all the administrative and refereeing activities. The field of motor proteins and protein motility is fast moving, and we hope that this collection of articles will be a useful source of information in this highly interdisciplinary area. Physics of protein motility and motor proteins contents Physics of protein motility and motor proteinsAnatoly B Kolomeisky Identification of unique interactions between the flexible linker and the RecA-like domains of DEAD-box helicase Mss116 Yuan Zhang, Mirkó Palla, Andrew Sun and Jung-Chi Liao The load dependence of the physical properties of a molecular motor

  3. Polymer Directed Protein Assemblies

    Directory of Open Access Journals (Sweden)

    Patrick van Rijn

    2013-05-01

    Full Text Available Protein aggregation and protein self-assembly is an important occurrence in natural systems, and is in some form or other dictated by biopolymers. Very obvious influences of biopolymers on protein assemblies are, e.g., virus particles. Viruses are a multi-protein assembly of which the morphology is dictated by poly-nucleotides namely RNA or DNA. This “biopolymer” directs the proteins and imposes limitations on the structure like the length or diameter of the particle. Not only do these bionanoparticles use polymer-directed self-assembly, also processes like amyloid formation are in a way a result of directed protein assembly by partial unfolded/misfolded biopolymers namely, polypeptides. The combination of proteins and synthetic polymers, inspired by the natural processes, are therefore regarded as a highly promising area of research. Directed protein assembly is versatile with respect to the possible interactions which brings together the protein and polymer, e.g., electrostatic, v.d. Waals forces or covalent conjugation, and possible combinations are numerous due to the large amounts of different polymers and proteins available. The protein-polymer interacting behavior and overall morphology is envisioned to aid in clarifying protein-protein interactions and are thought to entail some interesting new functions and properties which will ultimately lead to novel bio-hybrid materials.

  4. Protein and protein hydrolysates in sports nutrition.

    Science.gov (United States)

    van Loon, Luc J C; Kies, Arie K; Saris, Wim H M

    2007-08-01

    With the increasing knowledge about the role of nutrition in increasing exercise performance, it has become clear over the last 2 decades that amino acids, protein, and protein hydrolysates can play an important role. Most of the attention has been focused on their effects at a muscular level. As these nutrients are ingested, however, it also means that gastrointestinal digestibility and absorption can modulate their efficacy significantly. Therefore, discussing the role of amino acids, protein, and protein hydrolysates in sports nutrition entails holding a discussion on all levels of the metabolic route. On May 28-29, 2007, a small group of researchers active in the field of exercise science and protein metabolism presented an overview of the different aspects of the application of protein and protein hydrolysates in sports nutrition. In addition, they were asked to share their opinions on the future progress in their fields of research. In this overview, an introduction to the workshop and a short summary of its outcome is provided.

  5. Protein electrophoresis - serum

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/003540.htm Protein electrophoresis - serum To use the sharing features on ... JavaScript. This lab test measures the types of protein in the fluid (serum) part of a blood ...

  6. Protein Data Bank (PDB)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and...

  7. Abnormal protein aggregationand neurodegenerativediseases

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Abnormal protein aggregation or amyloid is the major cause ofmany neurodegenerative disorders. The present review focuses on the correlation between sequence and structure features of proteins related to the diseases and abnormal protein aggregation. Recent progress has improved our knowledge on understand-ing the mechanism of amyloid formation. We suggest a nucleation model for ordered protein aggregation, which can also explain pathogenesis mechanisms of these neurodegenerative diseases in vivo.

  8. CSF total protein

    Science.gov (United States)

    CSF total protein is a test to determine the amount of protein in your spinal fluid, also called cerebrospinal fluid (CSF). ... The normal protein range varies from lab to lab, but is typically about 15 to 60 milligrams per deciliter (mg/dL) ...

  9. Protein domain prediction

    NARCIS (Netherlands)

    Ingolfsson, Helgi; Yona, Golan

    2008-01-01

    Domains are considered to be the building blocks of protein structures. A protein can contain a single domain or multiple domains, each one typically associated with a specific function. The combination of domains determines the function of the protein, its subcellular localization and the interacti

  10. Destabilized bioluminescent proteins

    Science.gov (United States)

    Allen, Michael S.; Rakesh, Gupta; Gary, Sayler S.

    2007-07-31

    Purified nucleic acids, vectors and cells containing a gene cassette encoding at least one modified bioluminescent protein, wherein the modification includes the addition of a peptide sequence. The duration of bioluminescence emitted by the modified bioluminescent protein is shorter than the duration of bioluminescence emitted by an unmodified form of the bioluminescent protein.

  11. Protein Frustratometer 2

    DEFF Research Database (Denmark)

    Gonzalo Parra, R.; Schafer, Nicholas P.; Radusky, Leandro G.

    2016-01-01

    The protein frustratometer is an energy landscape theory-inspired algorithm that aims at localizing and quantifying the energetic frustration present in protein molecules. Frustration is a useful concept for analyzing proteins' biological behavior. It compares the energy distributions of the nati...... a user-friendly interface. The webserver is freely available at URL: http://frustratometer.qb.fcen.uba.ar....

  12. Protopia: a protein-protein interaction tool

    Science.gov (United States)

    Real-Chicharro, Alejandro; Ruiz-Mostazo, Iván; Navas-Delgado, Ismael; Kerzazi, Amine; Chniber, Othmane; Sánchez-Jiménez, Francisca; Medina, Miguel Ángel; Aldana-Montes, José F

    2009-01-01

    Background Protein-protein interactions can be considered the basic skeleton for living organism self-organization and homeostasis. Impressive quantities of experimental data are being obtained and computational tools are essential to integrate and to organize this information. This paper presents Protopia, a biological tool that offers a way of searching for proteins and their interactions in different Protein Interaction Web Databases, as a part of a multidisciplinary initiative of our institution for the integration of biological data . Results The tool accesses the different Databases (at present, the free version of Transfac, DIP, Hprd, Int-Act and iHop), and results are expressed with biological protein names or databases codes and can be depicted as a vector or a matrix. They can be represented and handled interactively as an organic graph. Comparison among databases is carried out using the Uniprot codes annotated for each protein. Conclusion The tool locates and integrates the current information stored in the aforementioned databases, and redundancies among them are detected. Results are compatible with the most important network analysers, so that they can be compared and analysed by other world-wide known tools and platforms. The visualization possibilities help to attain this goal and they are especially interesting for handling multiple-step or complex networks. PMID:19828077

  13. Protein crystallization with paper

    Science.gov (United States)

    Matsuoka, Miki; Kakinouchi, Keisuke; Adachi, Hiroaki; Maruyama, Mihoko; Sugiyama, Shigeru; Sano, Satoshi; Yoshikawa, Hiroshi Y.; Takahashi, Yoshinori; Yoshimura, Masashi; Matsumura, Hiroyoshi; Murakami, Satoshi; Inoue, Tsuyoshi; Mori, Yusuke; Takano, Kazufumi

    2016-05-01

    We developed a new protein crystallization method that incorporates paper. A small piece of paper, such as facial tissue or KimWipes, was added to a drop of protein solution in the traditional sitting drop vapor diffusion technique, and protein crystals grew by incorporating paper. By this method, we achieved the growth of protein crystals with reducing osmotic shock. Because the technique is very simple and the materials are easy to obtain, this method will come into wide use for protein crystallization. In the future, it could be applied to nanoliter-scale crystallization screening on a paper sheet such as in inkjet printing.

  14. Highly thermostable fluorescent proteins

    Science.gov (United States)

    Bradbury, Andrew M.; Waldo, Geoffrey S.; Kiss, Csaba

    2011-03-22

    Thermostable fluorescent proteins (TSFPs), methods for generating these and other stability-enhanced proteins, polynucleotides encoding such proteins, and assays and method for using the TSFPs and TSFP-encoding nucleic acid molecules are provided. The TSFPs of the invention show extremely enhanced levels of stability and thermotolerance. In one case, for example, a TSFP of the invention is so stable it can be heated to 99.degree. C. for short periods of time without denaturing, and retains 85% of its fluorescence when heated to 80.degree. C. for several minutes. The invention also provides a method for generating stability-enhanced variants of a protein, including but not limited to fluorescent proteins.

  15. Protein oxidation and peroxidation

    DEFF Research Database (Denmark)

    Davies, Michael Jonathan

    2016-01-01

    and chain reactions with alcohols and carbonyls as major products; the latter are commonly used markers of protein damage. Direct oxidation of cysteine (and less commonly) methionine residues is a major reaction; this is typically faster than with H2O2, and results in altered protein activity and function....... Unlike H2O2, which is rapidly removed by protective enzymes, protein peroxides are only slowly removed, and catabolism is a major fate. Although turnover of modified proteins by proteasomal and lysosomal enzymes, and other proteases (e.g. mitochondrial Lon), can be efficient, protein hydroperoxides...

  16. Protein aggregate myopathies

    Directory of Open Access Journals (Sweden)

    Sharma M

    2005-01-01

    Full Text Available Protein aggregate myopathies (PAM are an emerging group of muscle diseases characterized by structural abnormalities. Protein aggregate myopathies are marked by the aggregation of intrinsic proteins within muscle fibers and fall into four major groups or conditions: (1 desmin-related myopathies (DRM that include desminopathies, a-B crystallinopathies, selenoproteinopathies caused by mutations in the, a-B crystallin and selenoprotein N1 genes, (2 hereditary inclusion body myopathies, several of which have been linked to different chromosomal gene loci, but with as yet unidentified protein product, (3 actinopathies marked by mutations in the sarcomeric ACTA1 gene, and (4 myosinopathy marked by a mutation in the MYH-7 gene. While PAM forms 1 and 2 are probably based on impaired extralysosomal protein degradation, resulting in the accumulation of numerous and diverse proteins (in familial types in addition to respective mutant proteins, PAM forms 3 and 4 may represent anabolic or developmental defects because of preservation of sarcomeres outside of the actin and myosin aggregates and dearth or absence of other proteins in these actin or myosin aggregates, respectively. The pathogenetic principles governing protein aggregation within muscle fibers and subsequent structural sarcomeres are still largely unknown in both the putative catabolic and anabolic forms of PAM. Presence of inclusions and their protein composition in other congenital myopathies such as reducing bodies, cylindrical spirals, tubular aggregates and others await clarification. The hitherto described PAMs were first identified by immunohistochemistry of proteins and subsequently by molecular analysis of their genes.

  17. Racemic protein crystallography.

    Science.gov (United States)

    Yeates, Todd O; Kent, Stephen B H

    2012-01-01

    Although natural proteins are chiral and are all of one "handedness," their mirror image forms can be prepared by chemical synthesis. This opens up new opportunities for protein crystallography. A racemic mixture of the enantiomeric forms of a protein molecule can crystallize in ways that natural proteins cannot. Recent experimental data support a theoretical prediction that this should make racemic protein mixtures highly amenable to crystallization. Crystals obtained from racemic mixtures also offer advantages in structure determination strategies. The relevance of these potential advantages is heightened by advances in synthetic methods, which are extending the size limit for proteins that can be prepared by chemical synthesis. Recent ideas and results in the area of racemic protein crystallography are reviewed.

  18. Probing possible downhill folding: native contact topology likely places a significant constraint on the folding cooperativity of proteins with approximately 40 residues.

    Science.gov (United States)

    Badasyan, Artem; Liu, Zhirong; Chan, Hue Sun

    2008-12-12

    Experiments point to appreciable variations in folding cooperativity among natural proteins with approximately 40 residues, indicating that the behaviors of these proteins are valuable for delineating the contributing factors to cooperative folding. To explore the role of native topology in a protein's propensity to fold cooperatively and how native topology might constrain the degree of cooperativity achievable by a given set of physical interactions, we compared folding/unfolding kinetics simulated using three classes of native-centric C(alpha) chain models with different interaction schemes. The approach was applied to two homologous 45-residue fragments from the peripheral subunit-binding domain family and a 39-residue fragment of the N-terminal domain of ribosomal protein L9. Free-energy profiles as functions of native contact number were computed to assess the heights of thermodynamic barriers to folding. In addition, chevron plots of folding/unfolding rates were constructed as functions of native stability to facilitate comparison with available experimental data. Although common Gō-like models with pairwise Lennard-Jones-type interactions generally fold less cooperatively than real proteins, the rank ordering of cooperativity predicted by these models is consistent with experiment for the proteins investigated, showing increasing folding cooperativity with increasing nonlocality of a protein's native contacts. Models that account for water-expulsion (desolvation) barriers and models with many-body (nonadditive) interactions generally entail higher degrees of folding cooperativity indicated by more linear model chevron plots, but the rank ordering of cooperativity remains unchanged. A robust, experimentally valid rank ordering of model folding cooperativity independent of the multiple native-centric interaction schemes tested here argues that native topology places significant constraints on how cooperatively a protein can fold.

  19. Toxic proteins in plants.

    Science.gov (United States)

    Dang, Liuyi; Van Damme, Els J M

    2015-09-01

    Plants have evolved to synthesize a variety of noxious compounds to cope with unfavorable circumstances, among which a large group of toxic proteins that play a critical role in plant defense against predators and microbes. Up to now, a wide range of harmful proteins have been discovered in different plants, including lectins, ribosome-inactivating proteins, protease inhibitors, ureases, arcelins, antimicrobial peptides and pore-forming toxins. To fulfill their role in plant defense, these proteins exhibit various degrees of toxicity towards animals, insects, bacteria or fungi. Numerous studies have been carried out to investigate the toxic effects and mode of action of these plant proteins in order to explore their possible applications. Indeed, because of their biological activities, toxic plant proteins are also considered as potentially useful tools in crop protection and in biomedical applications, such as cancer treatment. Genes encoding toxic plant proteins have been introduced into crop genomes using genetic engineering technology in order to increase the plant's resistance against pathogens and diseases. Despite the availability of ample information on toxic plant proteins, very few publications have attempted to summarize the research progress made during the last decades. This review focuses on the diversity of toxic plant proteins in view of their toxicity as well as their mode of action. Furthermore, an outlook towards the biological role(s) of these proteins and their potential applications is discussed.

  20. PROTEIN - WHICH IS BEST?

    Directory of Open Access Journals (Sweden)

    Michael J. Falvo

    2004-09-01

    Full Text Available Protein intake that exceeds the recommended daily allowance is widely accepted for both endurance and power athletes. However, considering the variety of proteins that are available much less is known concerning the benefits of consuming one protein versus another. The purpose of this paper is to identify and analyze key factors in order to make responsible recommendations to both the general and athletic populations. Evaluation of a protein is fundamental in determining its appropriateness in the human diet. Proteins that are of inferior content and digestibility are important to recognize and restrict or limit in the diet. Similarly, such knowledge will provide an ability to identify proteins that provide the greatest benefit and should be consumed. The various techniques utilized to rate protein will be discussed. Traditionally, sources of dietary protein are seen as either being of animal or vegetable origin. Animal sources provide a complete source of protein (i.e. containing all essential amino acids, whereas vegetable sources generally lack one or more of the essential amino acids. Animal sources of dietary protein, despite providing a complete protein and numerous vitamins and minerals, have some health professionals concerned about the amount of saturated fat common in these foods compared to vegetable sources. The advent of processing techniques has shifted some of this attention and ignited the sports supplement marketplace with derivative products such as whey, casein and soy. Individually, these products vary in quality and applicability to certain populations. The benefits that these particular proteins possess are discussed. In addition, the impact that elevated protein consumption has on health and safety issues (i.e. bone health, renal function are also reviewed

  1. Protein kinesis: The dynamics of protein trafficking and stability

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-12-31

    The purpose of this conference is to provide a multidisciplinary forum for exchange of state-of-the-art information on protein kinesis. This volume contains abstracts of papers in the following areas: protein folding and modification in the endoplasmic reticulum; protein trafficking; protein translocation and folding; protein degradation; polarity; nuclear trafficking; membrane dynamics; and protein import into organelles.

  2. Protein Electrophoresis/Immunofixation Electrophoresis

    Science.gov (United States)

    ... be limited. Home Visit Global Sites Search Help? Protein Electrophoresis Immunofixation Electrophoresis Share this page: Was this page helpful? Also known as: Serum Protein Electrophoresis; Protein ELP; SPE; SPEP; Urine Protein Electrophoresis; ...

  3. Protein: FEA4 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FEA4 Proteins in gibberellin signaling GID2 F-box protein GID2 Gibberellin-insensitive dwarf protein 2, Prot...ein GIBBERELLIN INSENSITIVE DWARF2 39947 Oryza sativa subsp. japonica Q7XAK4 ...

  4. NMR of unfolded proteins

    Indian Academy of Sciences (India)

    Amarnath Chtterjee; Ashutosh Kumar; Jeetender Chugh; Sudha Srivastava; Neel S Bhavesh; Ramakrishna V Hosur

    2005-01-01

    In the post-genomic era, as more and more genome sequences are becoming known and hectic efforts are underway to decode the information content in them, it is becoming increasingly evident that flexibility in proteins plays a crucial role in many of the biological functions. Many proteins have intrinsic disorder either wholly or in specific regions. It appears that this disorder may be important for regulatory functions of the proteins, on the one hand, and may help in directing the folding process to reach the compact native state, on the other. Nuclear magnetic resonance (NMR) has over the last two decades emerged as the sole, most powerful technique to help characterize these disordered protein systems. In this review, we first discuss the significance of disorder in proteins and then describe the recent developments in NMR methods for their characterization. A brief description of the results obtained on several disordered proteins is presented at the end.

  5. Computational Protein Design

    DEFF Research Database (Denmark)

    Johansson, Kristoffer Enøe

    Proteins are the major functional group of molecules in biology. The impact of protein science on medicine and chemical productions is rapidly increasing. However, the greatest potential remains to be realized. The fi eld of protein design has advanced computational modeling from a tool of support...... to a central method that enables new developments. For example, novel enzymes with functions not found in natural proteins have been de novo designed to give enough activity for experimental optimization. This thesis presents the current state-of-the-art within computational design methods together...... with a novel method based on probability theory. With the aim of assembling a complete pipeline for protein design, this work touches upon several aspects of protein design. The presented work is the computational half of a design project where the other half is dedicated to the experimental part...

  6. Protein Models Comparator

    CERN Document Server

    Widera, Paweł

    2011-01-01

    The process of comparison of computer generated protein structural models is an important element of protein structure prediction. It has many uses including model quality evaluation, selection of the final models from a large set of candidates or optimisation of parameters of energy functions used in template free modelling and refinement. Although many protein comparison methods are available online on numerous web servers, their ability to handle a large scale model comparison is often very limited. Most of the servers offer only a single pairwise structural comparison, and they usually do not provide a model-specific comparison with a fixed alignment between the models. To bridge the gap between the protein and model structure comparison we have developed the Protein Models Comparator (pm-cmp). To be able to deliver the scalability on demand and handle large comparison experiments the pm-cmp was implemented "in the cloud". Protein Models Comparator is a scalable web application for a fast distributed comp...

  7. Mayaro virus proteins.

    Science.gov (United States)

    Mezencio, J M; Rebello, M A

    1993-01-01

    Mayaro virus was grown in BHK-21 cells and purified by centrifugation in a potassium-tartrate gradient (5-50%). The electron microscopy analyses of the purified virus showed an homogeneous population of enveloped particles with 69 +/- 2.3 nm in diameter. Three structural virus proteins were identified and designated p1, p2 and p3. Their average molecular weight were p1, 54 KDa; p2, 50 KDa and p3, 34 KDa. In Mayaro virus infected Aedes albopictus cells and in BHK-21 infected cells we detected six viral proteins, in which three of them are the structural virus proteins and the other three were products from processing of precursors of viral proteins, whose molecular weights are 62 KDa, 64 KDa and 110 KDa. The 34 KDa protein was the first viral protein synthesized at 5 hours post-infection in both cell lines studied.

  8. Mayaro virus proteins

    Directory of Open Access Journals (Sweden)

    J. M. S. Mezencio

    1993-06-01

    Full Text Available Mayaro virus was grown in BHK-21 cells and purified by centrifugation in a potassium-tartrate gradient (5-50%. The electron microscopy analyses of the purified virus showed an homogeneous population of enveloped particles with 69 ñ 2.3 nm in diameter. Three structural virus proteins were identified and designated pl, p2 and p3. Their average molecular weight were p1, 54 KDa; p2, 50 KDa and p3, 34 KDa. In Mayaro virus infected. Aedes albopictus cells and in BHK-21 infected cells we detected six viral proteins, in wich three of them are the structural virus proteins and the other three were products from processing of precursors of viral proteins, whose molecular weights are 62 KDa, 64 KDa and 110 KDa. The 34 KDa protein was the first viral protein sinthesized at 5 hours post-infection in both cell lines studied.

  9. Proteins: Form and function

    OpenAIRE

    Roy D Sleator

    2012-01-01

    An overwhelming array of structural variants has evolved from a comparatively small number of protein structural domains; which has in turn facilitated an expanse of functional derivatives. Herein, I review the primary mechanisms which have contributed to the vastness of our existing, and expanding, protein repertoires. Protein function prediction strategies, both sequence and structure based, are also discussed and their associated strengths and weaknesses assessed.

  10. Pressure cryocooling protein crystals

    Science.gov (United States)

    Kim, Chae Un; Gruner, Sol M.

    2011-10-04

    Preparation of cryocooled protein crystal is provided by use of helium pressurizing and cryocooling to obtain cryocooled protein crystal allowing collection of high resolution data and by heavier noble gas (krypton or xenon) binding followed by helium pressurizing and cryocooling to obtain cryocooled protein crystal for collection of high resolution data and SAD phasing simultaneously. The helium pressurizing is carried out on crystal coated to prevent dehydration or on crystal grown in aqueous solution in a capillary.

  11. Acanthamoeba castellanii STAT Protein

    OpenAIRE

    Anna Kicinska; Jacek Leluk; Wieslawa Jarmuszkiewicz

    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 Dictyos...

  12. Moonlighting proteins in cancer.

    Science.gov (United States)

    Min, Kyung-Won; Lee, Seong-Ho; Baek, Seung Joon

    2016-01-01

    Since the 1980s, growing evidence suggested that the cellular localization of proteins determined their activity and biological functions. In a classical view, a protein is characterized by the single cellular compartment where it primarily resides and functions. It is now believed that when proteins appear in different subcellular locations, the cells surpass the expected activity of proteins given the same genomic information to fulfill complex biological behavior. Many proteins are recognized for having the potential to exist in multiple locations in cells. Dysregulation of translocation may cause cancer or contribute to poorer cancer prognosis. Thus, quantitative and comprehensive assessment of dynamic proteins and associated protein movements could be a promising indicator in determining cancer prognosis and efficiency of cancer treatment and therapy. This review will summarize these so-called moonlighting proteins, in terms of a coupled intracellular cancer signaling pathway. Determination of the detailed biological intracellular and extracellular transit and regulatory activity of moonlighting proteins permits a better understanding of cancer and identification of potential means of molecular intervention.

  13. Self assembling proteins

    Science.gov (United States)

    Yeates, Todd O.; Padilla, Jennifer; Colovos, Chris

    2004-06-29

    Novel fusion proteins capable of self-assembling into regular structures, as well as nucleic acids encoding the same, are provided. The subject fusion proteins comprise at least two oligomerization domains rigidly linked together, e.g. through an alpha helical linking group. Also provided are regular structures comprising a plurality of self-assembled fusion proteins of the subject invention, and methods for producing the same. The subject fusion proteins find use in the preparation of a variety of nanostructures, where such structures include: cages, shells, double-layer rings, two-dimensional layers, three-dimensional crystals, filaments, and tubes.

  14. 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.

  15. 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.

  16. PIC: Protein Interactions Calculator.

    Science.gov (United States)

    Tina, K G; Bhadra, R; Srinivasan, N

    2007-07-01

    Interactions within a protein structure and interactions between proteins in an assembly are essential considerations in understanding molecular basis of stability and functions of proteins and their complexes. There are several weak and strong interactions that render stability to a protein structure or an assembly. Protein Interactions Calculator (PIC) is a server which, given the coordinate set of 3D structure of a protein or an assembly, computes various interactions such as disulphide bonds, interactions between hydrophobic residues, ionic interactions, hydrogen bonds, aromatic-aromatic interactions, aromatic-sulphur interactions and cation-pi interactions within a protein or between proteins in a complex. Interactions are calculated on the basis of standard, published criteria. The identified interactions between residues can be visualized using a RasMol and Jmol interface. The advantage with PIC server is the easy availability of inter-residue interaction calculations in a single site. It also determines the accessible surface area and residue-depth, which is the distance of a residue from the surface of the protein. User can also recognize specific kind of interactions, such as apolar-apolar residue interactions or ionic interactions, that are formed between buried or exposed residues or near the surface or deep inside.

  17. Characterization of Metal Proteins

    Science.gov (United States)

    Unno, Masaki; Ikeda-Saito, Masao

    Some metals are essential for life. Most of these metals are associated with biological macromolecule like DNA (deoxyribonucleic acid), RNA (ribonucleic acid), and more often with proteins: metals bind or interact with them. A number of protein molecules intrinsically contain metals in their structure. Some of these proteins catalyze unique chemical reactions and perform specific physiological functions. In this chapter, we will shed light on the several metalcontaining proteins, termed metalloproteins, and other proteins interacting metals. We will also introduce several key techniques which have been used to characterize these proteins. Characterizing these proteins and to understand the relationships between their structures and functions shall continue to be one of the major avenues to solve the mysteries of life. At first, we introduce what are the protein structures and how these proteins interact with metals. In the next section, we discuss the physiological roles of some representative metals. Next, we show two examples of special metal cofactors those help the biological macromolecules to carry out their functions. Then we describe some functions of metalloproteins. Finally, we introduce some physical methods to characterize metalloproteins.

  18. Dietary proteins and angiogenesis.

    Science.gov (United States)

    Medina, Miguel Ángel; Quesada, Ana R

    2014-01-17

    Both defective and persistent angiogenesis are linked to pathological situations in the adult. Compounds able to modulate angiogenesis have a potential value for the treatment of such pathologies. Several small molecules present in the diet have been shown to have modulatory effects on angiogenesis. This review presents the current state of knowledge on the potential modulatory roles of dietary proteins on angiogenesis. There is currently limited available information on the topic. Milk contains at least three proteins for which modulatory effects on angiogenesis have been previously demonstrated. On the other hand, there is some scarce information on the potential of dietary lectins, edible plant proteins and high protein diets to modulate angiogenesis.

  19. [Alternative scaffold proteins].

    Science.gov (United States)

    Petrovskaia, L E; Shingarova, L N; Dolgikh, D A; Kirpichnikov, M P

    2011-01-01

    Review is devoted to the challenging direction in modem molecular biology and bioengineering - the properties of alternative scaffold proteins (ASP) and methods for obtaining ASP binding molecules. ASP molecules incorporate conservative protein core and hypervariable regions, providing for the binding function. Structural classification of ASP includes several types which differ also in their molecular targets and potential applications. Construction of artificial binding proteins on the ASP basis implies a combinatorial library design with subsequent selection of specific binders with the use of phage display or the modem cell-free systems. Alternative binding proteins on non-immunoglobulin scaffolds find broad applications in different fields ofbiotechnology and molecular medicine.

  20. Ultrafiltration of pegylated proteins

    Science.gov (United States)

    Molek, Jessica R.

    There is considerable clinical interest in the use of "second-generation" therapeutics produced by conjugation of a native protein with various polymers including polyethylene glycol (PEG). PEG--protein conjugates, so-called PEGylated proteins, can exhibit enhanced stability, half-life, and bioavailability. One of the challenges in the commercial production of PEGylated proteins is the purification required to remove unreacted polymer, native protein, and in many cases PEGylated proteins with nonoptimal degrees of conjugation. The overall objective of this thesis was to examine the use of ultrafiltration for the purification of PEGylated proteins. This included: (1) analysis of size-based separation of PEGylated proteins using conventional ultrafiltration membranes, (2) use of electrically-charged membranes to exploit differences in electrostatic interactions, and (3) examination of the effects of PEGylation on protein fouling. The experimental results were analyzed using appropriate theoretical models, with the underlying physical properties of the PEGylated proteins evaluated using size exclusion chromatography, capillary electrophoresis, dynamic light scattering, and reverse phase chromatography. PEGylated proteins were produced by covalent attachment of activated PEG to a protein via primary amines on the lysine residues. A simple model was developed for the reaction kinetics, which was used to explore the effect of reaction conditions and mode of operation on the distribution of PEGylated products. The effective size of the PEGylated proteins was evaluated using size exclusion chromatography, with appropriate correlations developed for the size in terms of the molecular weight of the native protein and attached PEG. The electrophoretic mobility of the PEGylated proteins were evaluated by capillary electrophoresis with the data in good agreement with a simple model accounting for the increase in protein size and the reduction in the number of protonated amine

  1. Protein oxidation in aquatic foods

    DEFF Research Database (Denmark)

    Baron, Caroline P.

    2014-01-01

    The chapter discusses general considerations about protein oxidation and reviews the mechanisms involved in protein oxidation and consequences of protein oxidation on fish proteins. It presents two case studies, the first deals with protein and lipid oxidation in frozen rainbow trout, and the sec......The chapter discusses general considerations about protein oxidation and reviews the mechanisms involved in protein oxidation and consequences of protein oxidation on fish proteins. It presents two case studies, the first deals with protein and lipid oxidation in frozen rainbow trout...... oxidation. The protein carbonyl group measurement is the widely used method for estimating protein oxidation in foods and has been used in fish muscle. The chapter also talks about the impact of protein oxidation on protein functionality, fish muscle texture, and food nutritional value. Protein oxidation...... may not only induce quality losses but may be desirable in some type of foods, such as salted herring....

  2. Clinical pathologic observation of the solitary plasmacytoma of bone%6例骨的孤立性浆细胞瘤临床病理观察

    Institute of Scientific and Technical Information of China (English)

    阳桂丽; 钟先荣; 胡碧清

    2011-01-01

    目的 探讨骨的孤立性浆细胞瘤的临床病理特征及诊断方法.方法 收集和复习本院1996年1月至2009年12月病理确诊为骨的孤立性浆细胞瘤6例临床资料,通过对其临床特征、影像学表现、血尿检测、病理常规HE染色及免疫组化染色等进行分析,并复习相关文献.结果 6例骨的孤立性浆细胞瘤均为单一区域骨骼破坏,好发于红髓丰富的部位,分别为肋骨2例、颅骨2例、胸椎1例、股骨干1例;男性比女性常见,男女之比为2∶1.临床表现为单骨部位疼痛,无贫血、高钙血症和肾功能损害,尿Bence-Jones蛋白阴性;免疫组化表达CD38和/或CD138,单克隆表达轻链球蛋白Kappa 2例、Lambda 4例.结论 骨的孤立性浆细胞瘤较为罕见,确诊需综合多方面情况,且首先应排除骨多发性骨髓瘤.%Objective To investigate the clinical pathologic feature and the diagnosis method about the solitary plasmacytoma of bone. Methods We collected and reviewed the clinical information of 6 cases of the final pathologic diagnosis solitary plasmacyoma of bone who were treated in our hospital from January, 1966 to December, 2009 , through the clinical feature, imageologic appearance, the detection of blood and urine, pathologic routine HE staining and immunohistochemical staining to analyze, and reviewed pertinent literature. Results All the 6 cases with the solitary plasmacytoma of bone were skeletal destruction of single region,especially frequent in the location of abundance splenic pulp,2 lesions involved the costal bone,2 leisons cranium,l leison thoracic vertebra and 1 leison involved shaft of femur,respectively,and more common in male than that in female(the ratio of male to female was 2 : 1). The clinical situations were the pain of single bone location, no anaemia, hypercalcinemia and the damage of renal function, negative urine Bence-Jones proteins. Immunohistochemical expressions were CD38 and(or)CD138 ,and monoclonal

  3. Influences of 11-ethoxyviburtinal of Valeriana jatamansi Jones on the ex-pression of enterochromaffin cells and mast cells in rats with irritable bowel syndrome%蜘蛛香成分11-ethoxyviburtinal对肠易激综合征大鼠肠嗜铬细胞及肥大细胞表达的影响∗

    Institute of Scientific and Technical Information of China (English)

    肖丛瑞; 陶丝雨; 闫兴丽; 高增平; 史瑞瑞; 王娟; 王晶

    2016-01-01

    Objective To investigate the effects of 11-ethoxyviburtinal of Valeriana jatamansi Jones on the expression of enterochromaffin cells ( EC) and mast cells ( MC) in rats with irritable bowel syndrome ( IBS) . Methods The IBS rat model was induced by chronic unpredictable stress with isolation. Male SD rats were randomly divided into six groups:control group,model group, pinaverium group at the dose of 25 mg/kg,and high-, mid-and low-dose of 11-ethoxyviburtinal group at dose of 1. 2, 0. 6, and 0. 3 mg/kg respectively. The number of 5-HT positive immunoreactive colonic EC was detected by the method of immunohistochemistry and that of colonic MC was measured with toluidine blue staining. Results Compared with control group, the number of 5-HT positive immunoreactive colonic EC and MC increased significantly in model group ( P <0 . 05 ) . The high dose of 11-ethoxyviburtinal could significantly de-crease the number of colonic EC and MC ( P<0 . 05 ) . Conclusion The 11-ethoxyviburtinal of Valeri-ana jatamansi Jones could significantly reduce the number of 5-HT positive immunoreactive 5-HT positive immunoreactive EC and MC in colon tissue of rats with IBS.%目的:探讨蜘蛛香成分11-ethoxyviburtinal对肠易激综合征( IBS)大鼠肠嗜铬细胞( EC)及肥大细胞(MC)表达的影响。方法 SD 雄性大鼠随机分为空白对照组、模型组、匹维溴铵(25 mg/kg)组和蜘蛛香成分11-ethoxyviburtinal大、中、小剂量(1.2、0.6、0.3 mg/kg)组。采用孤养复合慢性不可预见性应激法建立IBS 大鼠模型,免疫组化法检测大鼠结肠5-羟色胺(5-HT)免疫反应阳性细胞EC数量的变化,甲苯胺蓝染色法检测大鼠结肠MC数量的变化。结果孤养复合慢性不可预见性应激可造成大鼠结肠5-HT 免疫反应阳性细胞EC数量显著增加( P<0.01),结肠MC数量显著增多( P<0.05)。蜘蛛香成分11-ethoxyviburtinal大剂量可显著减少结肠5-HT免疫反应阳性细胞EC和MC数量( P<0.05)

  4. Protein and Heart Health

    Science.gov (United States)

    ... of food? Drink an 8-ounce glass of milk, and you’ll log 8 grams of protein. Add a cup of yogurt for another 11 ... low-fat options, such as lean meats, skim milk or other foods with high levels of protein. Legumes, for example, can pack about 16 grams ...

  5. Brushes and proteins

    NARCIS (Netherlands)

    Bosker, W.T.E.

    2011-01-01

      Brushes and Proteins   Wouter T. E. Bosker         Protein adsorption at solid surfaces can be prevented by applying a polymer brush at the surface. A polymer brush consists of polymer chains end-grafted to the surface at such a grafting density that th

  6. Poxviral Ankyrin Proteins

    Directory of Open Access Journals (Sweden)

    Michael H. Herbert

    2015-02-01

    Full Text Available Multiple repeats of the ankyrin motif (ANK are ubiquitous throughout the kingdoms of life but are absent from most viruses. The main exception to this is the poxvirus family, and specifically the chordopoxviruses, with ANK repeat proteins present in all but three species from separate genera. The poxviral ANK repeat proteins belong to distinct orthologue groups spread over different species, and align well with the phylogeny of their genera. This distribution throughout the chordopoxviruses indicates these proteins were present in an ancestral vertebrate poxvirus, and have since undergone numerous duplication events. Most poxviral ANK repeat proteins contain an unusual topology of multiple ANK motifs starting at the N-terminus with a C-terminal poxviral homologue of the cellular F-box enabling interaction with the cellular SCF ubiquitin ligase complex. The subtle variations between ANK repeat proteins of individual poxviruses suggest an array of different substrates may be bound by these protein-protein interaction domains and, via the F-box, potentially directed to cellular ubiquitination pathways and possible degradation. Known interaction partners of several of these proteins indicate that the NF-κB coordinated anti-viral response is a key target, whilst some poxviral ANK repeat domains also have an F-box independent affect on viral host-range.

  7. Learning about Proteins

    Science.gov (United States)

    ... Emergency Room? What Happens in the Operating Room? Learning About Proteins KidsHealth > For Kids > Learning About Proteins A A A What's in this ... Nutrition & Fitness Center Minerals Vitamins Eating for Sports Learning About Fats MyPlate Food Guide Word! Nutrition Contact ...

  8. Protein Attachment on Nanodiamonds.

    Science.gov (United States)

    Lin, Chung-Lun; Lin, Cheng-Huang; Chang, Huan-Cheng; Su, Meng-Chih

    2015-07-16

    A recent advance in nanotechnology is the scale-up production of small and nonaggregated diamond nanoparticles suitable for biological applications. Using detonation nanodiamonds (NDs) with an average diameter of ∼4 nm as the adsorbents, we have studied the static attachment of three proteins (myoglobin, bovine serum albumin, and insulin) onto the nanoparticles by optical spectroscopy, mass spectrometry, and dynamic light scattering, and electrophoretic zeta potential measurements. Results show that the protein surface coverage is predominantly determined by the competition between protein-protein and protein-ND interactions, giving each protein a unique and characteristic structural configuration in its own complex. Specifically, both myoglobin and bovine serum albumin show a Langmuir-type adsorption behavior, forming 1:1 complexes at saturation, whereas insulin folds into a tightly bound multimer before adsorption. The markedly different adsorption patterns appear to be independent of the protein concentration and are closely related to the affinity of the individual proteins for the NDs. The present study provides a fundamental understanding for the use of NDs as a platform for nanomedical drug delivery.

  9. Engineered Protein Polymers

    Science.gov (United States)

    2010-05-31

    of each pure polymer, we plan to combine the various polymer solutions in different ratios to tune the composition and physico-chemical properties...protein materials as vehicles for storage and delivery of small molecules. Each protein polymer under concentrations for particle formation ( vida

  10. Sensitizing properties of proteins

    DEFF Research Database (Denmark)

    Poulsen, Lars K.; Ladics, Gregory S; McClain, Scott;

    2014-01-01

    The scope of allergy risk is diverse considering the myriad ways in which protein allergenicity is affected by physiochemical characteristics of proteins. The complexity created by the matrices of foods and the variability of the human immune system add additional challenges to understanding...... the relationship between sensitization potential and allergy disease. To address these and other issues, an April 2012 international symposium was held in Prague, Czech Republic, to review and discuss the state-of-the-science of sensitizing properties of protein allergens. The symposium, organized by the Protein...... Allergenicity Technical Committee of the International Life Sciences Institute's Health and Environmental Sciences Institute, featured presentations on current methods, test systems, research trends, and unanswered questions in the field of protein sensitization. A diverse group of over 70 interdisciplinary...

  11. Unconventional protein secretion.

    Science.gov (United States)

    Ding, Yu; Wang, Juan; Wang, Junqi; Stierhof, York-Dieter; Robinson, David G; Jiang, Liwen

    2012-10-01

    It is generally believed that protein secretion or exocytosis is achieved via a conventional ER (endoplasmic reticulum)-Golgi-TGN (trans-Golgi network)-PM (plasma membrane) pathway in the plant endomembrane system. However, such signal peptide (SP)-dependent protein secretion cannot explain the increasing number of SP-lacking proteins which are found outside of the PM in plant cells. The process by which such leaderless secretory proteins (LSPs) gain access to the cell exterior is termed unconventional protein secretion (UPS) and has been well-studied in animal and yeast cells, but largely ignored by the plant community. Here, we review the evidence for UPS in plants especially in regard to the recently discovered EXPO (exocyst-positive-organelle).

  12. Protein Unfolding and Alzheimer's

    Science.gov (United States)

    Cheng, Kelvin

    2012-10-01

    Early interaction events of beta-amyloid (Aβ) proteins with neurons have been associated with the pathogenesis of Alzheimer's disease. Knowledge pertaining to the role of lipid molecules, particularly cholesterol, in modulating the single Aβ interactions with neurons at the atomic length and picosecond time resolutions, remains unclear. In our research, we have used atomistic molecular dynamics simulations to explore early molecular events including protein insertion kinetics, protein unfolding, and protein-induced membrane disruption of Aβ in lipid domains that mimic the nanoscopic raft and non-raft regions of the neural membrane. In this talk, I will summarize our current work on investigating the role of cholesterol in regulating the Aβ interaction events with membranes at the molecular level. I will also explain how our results will provide new insights into understanding the pathogenesis of Alzheimer's disease associated with the Aβ proteins.

  13. Manipulating and Visualizing Proteins

    Energy Technology Data Exchange (ETDEWEB)

    Simon, Horst D.

    2003-12-05

    ProteinShop Gives Researchers a Hands-On Tool for Manipulating, Visualizing Protein Structures. The Human Genome Project and other biological research efforts are creating an avalanche of new data about the chemical makeup and genetic codes of living organisms. But in order to make sense of this raw data, researchers need software tools which let them explore and model data in a more intuitive fashion. With this in mind, researchers at Lawrence Berkeley National Laboratory and the University of California, Davis, have developed ProteinShop, a visualization and modeling program which allows researchers to manipulate protein structures with pinpoint control, guided in large part by their own biological and experimental instincts. Biologists have spent the last half century trying to unravel the ''protein folding problem,'' which refers to the way chains of amino acids physically fold themselves into three-dimensional proteins. This final shape, which resembles a crumpled ribbon or piece of origami, is what determines how the protein functions and translates genetic information. Understanding and modeling this geometrically complex formation is no easy matter. ProteinShop takes a given sequence of amino acids and uses visualization guides to help generate predictions about the secondary structures, identifying alpha helices and flat beta strands, and the coil regions that bind them. Once secondary structures are in place, researchers can twist and turn these pre-configurations until they come up with a number of possible tertiary structure conformations. In turn, these are fed into a computationally intensive optimization procedure that tries to find the final, three-dimensional protein structure. Most importantly, ProteinShop allows users to add human knowledge and intuition to the protein structure prediction process, thus bypassing bad configurations that would otherwise be fruitless for optimization. This saves compute cycles and accelerates

  14. Transdermal delivery of proteins.

    Science.gov (United States)

    Kalluri, Haripriya; Banga, Ajay K

    2011-03-01

    Transdermal delivery of peptides and proteins avoids the disadvantages associated with the invasive parenteral route of administration and other alternative routes such as the pulmonary and nasal routes. Since proteins have a large size and are hydrophilic in nature, they cannot permeate passively across the skin due to the stratum corneum which allows the transport of only small lipophilic drug molecules. Enhancement techniques such as chemical enhancers, iontophoresis, microneedles, electroporation, sonophoresis, thermal ablation, laser ablation, radiofrequency ablation and noninvasive jet injectors aid in the delivery of proteins by overcoming the skin barrier in different ways. In this review, these enhancement techniques that can enable the transdermal delivery of proteins are discussed, including a discussion of mechanisms, sterility requirements, and commercial development of products. Combination of enhancement techniques may result in a synergistic effect allowing increased protein delivery and these are also discussed.

  15. Modified Watson-Jones approach with locking compression paediatric hip plate for femoral neck fractures in children%改良Watson-Jones入路联合小儿髋部锁定加压接骨板治疗股骨颈骨折

    Institute of Scientific and Technical Information of China (English)

    王波; 楼跃; 唐凯; 张志群; 林刚; 孙祥水; 刘飞; 倪磊; 鞠黎

    2016-01-01

    Objective To evaluate the methods and curative effect of modified Watson-Jones approach with locking compression paediatric hip plate(LCP-PHP) for femoral neck fractures in children.Methods From January 2012 to August 2014,11 children including 6 male and 5 female with femoral neck fractures(5 lefts,6 rights) underwent operation of modified Watson-Jones approach with LCP-PHP in Nanjing Children's Hospital Affiliated to Nanjing Medical University.The average age at injury was 7.8 years old.All the children received preoperative X-ray and postoperative X-ray regularly.Neck stem angles of preoperative health side,neck stem angles of the sick side 3 days after surgery and the last follow-up were measured,and the loss of neck stem angles,delayed union,nonunion,osteonecrosis,premature physeal closure were evaluated by using X-ray.Meanwhile,hip function of the last follow-up was evaluated by Harris score.Results All the patients were postoperatively followed up for 13-44 months with an average of 26 months.The neck stem angles of preoperative health side 134.70° ± 3.58°,postoperative sick side in 3 days 134.60°±3.46° and the last follow-up 133.50°±3.25°,and there was no statistical difference (F=3.63,P>0.05).The loss of neck stem angles,delayed union,nonunion,and premature physeal closure did not occur.Osteonecrosis(Ratliff type Ⅰ) occurred in 1 child.Harris score was very good in 9 cases(82.0%) and good in 2 cases (18.0%).Conclusions The modified Watson-Jones approach with LCP-PHP for unsuccessful closed reduction femur neck fractures in children can clearly show the fracture,with internal fixation stability and less complications.%目的 探讨改良Watson-Jones入路联合小儿髋部锁定加压接骨板(LCP-PHP)治疗股骨颈骨折的方法及疗效.方法 2012年1月至2014年8月南京医科大学附属南京儿童医院采用改良Watson-Jones入路联合LCP-PHP治疗11例闭合复位失败的股骨颈骨折患儿,其中男6例,女5

  16. Coarse-grain modelling of protein-protein interactions

    NARCIS (Netherlands)

    Baaden, Marc; Marrink, Siewert J.

    2013-01-01

    Here, we review recent advances towards the modelling of protein-protein interactions (PPI) at the coarse-grained (CG) level, a technique that is now widely used to understand protein affinity, aggregation and self-assembly behaviour. PPI models of soluble proteins and membrane proteins are separate

  17. Protein Binding Pocket Dynamics.

    Science.gov (United States)

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

    2016-05-17

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

  18. Anchored design of protein-protein interfaces.

    Directory of Open Access Journals (Sweden)

    Steven M Lewis

    Full Text Available BACKGROUND: Few existing protein-protein interface design methods allow for extensive backbone rearrangements during the design process. There is also a dichotomy between redesign methods, which take advantage of the native interface, and de novo methods, which produce novel binders. METHODOLOGY: Here, we propose a new method for designing novel protein reagents that combines advantages of redesign and de novo methods and allows for extensive backbone motion. This method requires a bound structure of a target and one of its natural binding partners. A key interaction in this interface, the anchor, is computationally grafted out of the partner and into a surface loop on the design scaffold. The design scaffold's surface is then redesigned with backbone flexibility to create a new binding partner for the target. Careful choice of a scaffold will bring experimentally desirable characteristics into the new complex. The use of an anchor both expedites the design process and ensures that binding proceeds against a known location on the target. The use of surface loops on the scaffold allows for flexible-backbone redesign to properly search conformational space. CONCLUSIONS AND SIGNIFICANCE: This protocol was implemented within the Rosetta3 software suite. To demonstrate and evaluate this protocol, we have developed a benchmarking set of structures from the PDB with loop-mediated interfaces. This protocol can recover the correct loop-mediated interface in 15 out of 16 tested structures, using only a single residue as an anchor.

  19. PSC: protein surface classification.

    Science.gov (United States)

    Tseng, Yan Yuan; Li, Wen-Hsiung

    2012-07-01

    We recently proposed to classify proteins by their functional surfaces. Using the structural attributes of functional surfaces, we inferred the pairwise relationships of proteins and constructed an expandable database of protein surface classification (PSC). As the functional surface(s) of a protein is the local region where the protein performs its function, our classification may reflect the functional relationships among proteins. Currently, PSC contains a library of 1974 surface types that include 25,857 functional surfaces identified from 24,170 bound structures. The search tool in PSC empowers users to explore related surfaces that share similar local structures and core functions. Each functional surface is characterized by structural attributes, which are geometric, physicochemical or evolutionary features. The attributes have been normalized as descriptors and integrated to produce a profile for each functional surface in PSC. In addition, binding ligands are recorded for comparisons among homologs. PSC allows users to exploit related binding surfaces to reveal the changes in functionally important residues on homologs that have led to functional divergence during evolution. The substitutions at the key residues of a spatial pattern may determine the functional evolution of a protein. In PSC (http://pocket.uchicago.edu/psc/), a pool of changes in residues on similar functional surfaces is provided.

  20. Bacterial Ice Crystal Controlling Proteins

    Directory of Open Access Journals (Sweden)

    Janet S. H. Lorv

    2014-01-01

    Full Text Available Across the world, many ice active bacteria utilize ice crystal controlling proteins for aid in freezing tolerance at subzero temperatures. Ice crystal controlling proteins include both antifreeze and ice nucleation proteins. Antifreeze proteins minimize freezing damage by inhibiting growth of large ice crystals, while ice nucleation proteins induce formation of embryonic ice crystals. Although both protein classes have differing functions, these proteins use the same ice binding mechanisms. Rather than direct binding, it is probable that these protein classes create an ice surface prior to ice crystal surface adsorption. Function is differentiated by molecular size of the protein. This paper reviews the similar and different aspects of bacterial antifreeze and ice nucleation proteins, the role of these proteins in freezing tolerance, prevalence of these proteins in psychrophiles, and current mechanisms of protein-ice interactions.

  1. Alpha Shapes and Proteins

    DEFF Research Database (Denmark)

    Winter, Pawel; Sterner, Henrik; Sterner, Peter

    2009-01-01

    We provide a unified description of (weighted) alpha shapes, beta shapes and the corresponding simplicialcomplexes. We discuss their applicability to various protein-related problems. We also discuss filtrations of alpha shapes and touch upon related persistence issues.We claim that the full...... potential of alpha-shapes and related geometrical constructs in protein-related problems yet remains to be realized and verified. We suggest parallel algorithms for (weighted) alpha shapes, and we argue that future use of filtrations and kinetic variants for larger proteins will need such implementation....

  2. Protein oxidation and ageing

    DEFF Research Database (Denmark)

    Linton, S; Davies, Michael Jonathan; Dean, R T

    2001-01-01

    of redox-active metal ions that could catalyse oxidant formation. As a result of this decrease in antioxidant defences, and increased rate of ROS formation, it is possible that the impact of ROS increases with age. ROS are known to oxidise biological macromolecules, with proteins an important target....... If the argument that the impact of ROS increases with age is true, then proteins would be expected to accumulate oxidised materials with age, and the rate of such accumulation should increase with time, reflecting impaired inefficiency of homeostasis. Here we review the evidence for the accumulation of oxidised......, or modified, extra- and intra-cellular proteins in vivo....

  3. Piezoelectric allostery of protein

    Science.gov (United States)

    Ohnuki, Jun; Sato, Takato; Takano, Mitsunori

    2016-07-01

    Allostery is indispensable for a protein to work, where a locally applied stimulus is transmitted to a distant part of the molecule. While the allostery due to chemical stimuli such as ligand binding has long been studied, the growing interest in mechanobiology prompts the study of the mechanically stimulated allostery, the physical mechanism of which has not been established. By molecular dynamics simulation of a motor protein myosin, we found that a locally applied mechanical stimulus induces electrostatic potential change at distant regions, just like the piezoelectricity. This novel allosteric mechanism, "piezoelectric allostery", should be of particularly high value for mechanosensor/transducer proteins.

  4. Protein crystallography prescreen kit

    Science.gov (United States)

    Segelke, Brent W.; Krupka, Heike I.; Rupp, Bernhard

    2005-07-12

    A kit for prescreening protein concentration for crystallization includes a multiplicity of vials, a multiplicity of pre-selected reagents, and a multiplicity of sample plates. The reagents and a corresponding multiplicity of samples of the protein in solutions of varying concentrations are placed on sample plates. The sample plates containing the reagents and samples are incubated. After incubation the sample plates are examined to determine which of the sample concentrations are too low and which the sample concentrations are too high. The sample concentrations that are optimal for protein crystallization are selected and used.

  5. Protein: MPA6 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available in 30 kDa adipocyte complement-related protein, Adipocyte complement-related 30 kDa protein, Adipocyte, C1q ...and collagen domain-containing protein, Adipose most abundant gene transcript 1 protein, Gelatin-binding protein 9606 Homo sapiens Q15848 9370 9370 Q15848 18054335, 19646806 ...

  6. Protein: FEB6 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FEB6 Photoresponse regulatory proteins HD1 SE1 Zinc finger protein HD1 Protein CONSTANS-like, Prot...ein HEADING DATE 1, Protein PHOTOPERIOD SENSITIVITY 1 39947 Oryza sativa subsp. japonica 4340746 Q9FDX8 21952207, 19246394 #shimamoto ...

  7. New approach for predicting protein-protein interactions

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    @@ Protein-protein interactions (PPIs) are of vital importance for virtually all processes of a living cell. The study of these associations of protein molecules could improve people's understanding of diseases and provide basis for therapeutic approaches.

  8. Analysis of correlations between protein complex and protein-protein interaction and mRNA expression

    Institute of Scientific and Technical Information of China (English)

    CAI Lun; XUE Hong; LU Hongchao; ZHAO Yi; ZHU Xiaopeng; BU Dongbo; LING Lunjiang; CHEN Runsheng

    2003-01-01

    Protein-protein interaction is a physical interaction of two proteins in living cells. In budding yeast Saccharomyces cerevisiae, large-scale protein-protein interaction data have been obtained through high-throughput yeast two-hybrid systems (Y2H) and protein complex purification techniques based on mass-spectrometry. Here, we collect 11855 interactions between total 2617 proteins. Through seriate genome-wide mRNA expression data, similarity between two genes could be measured. Protein complex data can also be obtained publicly and can be translated to pair relationship that any two proteins can only exist in the same complex or not. Analysis of protein complex data, protein-protein interaction data and mRNA expression data can elucidate correlations between them. The results show that proteins that have interactions or similar expression patterns have a higher possibility to be in the same protein complex than randomized selected proteins, and proteins which have interactions and similar expression patterns are even more possible to exist in the same protein complex. The work indicates that comprehensive integration and analysis of public large-scale bioinformatical data, such as protein complex data, protein-protein interaction data and mRNA expression data, may help to uncover their relationships and common biological information underlying these data. The strategies described here may help to integrate and analyze other functional genomic and proteomic data, such as gene expression profiling, protein-localization mapping and large-scale phenotypic data, both in yeast and in other organisms.

  9. A Bayesian Estimator of Protein-Protein Association Probabilities

    Energy Technology Data Exchange (ETDEWEB)

    Gilmore, Jason M.; Auberry, Deanna L.; Sharp, Julia L.; White, Amanda M.; Anderson, Kevin K.; Daly, Don S.

    2008-07-01

    The Bayesian Estimator of Protein-Protein Association Probabilities (BEPro3) is a software tool for estimating probabilities of protein-protein association between bait and prey protein pairs using data from multiple-bait, multiple-replicate, protein pull-down LC-MS assay experiments. BEPro3 is open source software that runs on both Windows XP and Mac OS 10.4 or newer versions, and is freely available from http://www.pnl.gov/statistics/BEPro3.

  10. Protein in diet

    Science.gov (United States)

    ... Dietary Reference Intakes for Energy, Carbohydrate, Fiber, Fat, Fatty Acids, Cholesterol, Protein, and Amino Acids . National Academy Press. Washington, DC, 2005. US Department of Health and Human Services and US Department of Agriculture. ...

  11. Protein Colloidal Aggregation Project

    Science.gov (United States)

    Oliva-Buisson, Yvette J. (Compiler)

    2014-01-01

    To investigate the pathways and kinetics of protein aggregation to allow accurate predictive modeling of the process and evaluation of potential inhibitors to prevalent diseases including cataract formation, chronic traumatic encephalopathy, Alzheimer's Disease, Parkinson's Disease and others.

  12. Protein Model Database

    Energy Technology Data Exchange (ETDEWEB)

    Fidelis, K; Adzhubej, A; Kryshtafovych, A; Daniluk, P

    2005-02-23

    The phenomenal success of the genome sequencing projects reveals the power of completeness in revolutionizing biological science. Currently it is possible to sequence entire organisms at a time, allowing for a systemic rather than fractional view of their organization and the various genome-encoded functions. There is an international plan to move towards a similar goal in the area of protein structure. This will not be achieved by experiment alone, but rather by a combination of efforts in crystallography, NMR spectroscopy, and computational modeling. Only a small fraction of structures are expected to be identified experimentally, the remainder to be modeled. Presently there is no organized infrastructure to critically evaluate and present these data to the biological community. The goal of the Protein Model Database project is to create such infrastructure, including (1) public database of theoretically derived protein structures; (2) reliable annotation of protein model quality, (3) novel structure analysis tools, and (4) access to the highest quality modeling techniques available.

  13. Plant protein glycosylation

    Science.gov (United States)

    Strasser, Richard

    2016-01-01

    Protein glycosylation is an essential co- and post-translational modification of secretory and membrane proteins in all eukaryotes. The initial steps of N-glycosylation and N-glycan processing are highly conserved between plants, mammals and yeast. In contrast, late N-glycan maturation steps in the Golgi differ significantly in plants giving rise to complex N-glycans with β1,2-linked xylose, core α1,3-linked fucose and Lewis A-type structures. While the essential role of N-glycan modifications on distinct mammalian glycoproteins is already well documented, we have only begun to decipher the biological function of this ubiquitous protein modification in different plant species. In this review, I focus on the biosynthesis and function of different protein N-linked glycans in plants. Special emphasis is given on glycan-mediated quality control processes in the ER and on the biological role of characteristic complex N-glycan structures. PMID:26911286

  14. Interactive protein manipulation

    Energy Technology Data Exchange (ETDEWEB)

    SNCrivelli@lbl.gov

    2003-07-01

    We describe an interactive visualization and modeling program for the creation of protein structures ''from scratch''. The input to our program is an amino acid sequence -decoded from a gene- and a sequence of predicted secondary structure types for each amino acid-provided by external structure prediction programs. Our program can be used in the set-up phase of a protein structure prediction process; the structures created with it serve as input for a subsequent global internal energy minimization, or another method of protein structure prediction. Our program supports basic visualization methods for protein structures, interactive manipulation based on inverse kinematics, and visualization guides to aid a user in creating ''good'' initial structures.

  15. MicroProteins

    DEFF Research Database (Denmark)

    Eguen, Teinai Ebimienere; Straub, Daniel; Graeff, Moritz;

    2015-01-01

    MicroProteins (miPs) are short, usually single-domain proteins that, in analogy to miRNAs, heterodimerize with their targets and exert a dominant-negative effect. Recent bioinformatic attempts to identify miPs have resulted in a list of potential miPs, many of which lack the defining...... characteristics of a miP. In this opinion article, we clearly state the characteristics of a miP as evidenced by known proteins that fit the definition; we explain why modulatory proteins misrepresented as miPs do not qualify as true miPs. We also discuss the evolutionary history of miPs, and how the miP concept...

  16. Polymers for Protein Conjugation

    Directory of Open Access Journals (Sweden)

    Gianfranco Pasut

    2014-01-01

    Full Text Available Polyethylene glycol (PEG at the moment is considered the leading polymer for protein conjugation in view of its unique properties, as well as to its low toxicity in humans, qualities which have been confirmed by its extensive use in clinical practice. Other polymers that are safe, biodegradable and custom-designed have, nevertheless, also been investigated as potential candidates for protein conjugation. This review will focus on natural polymers and synthetic linear polymers that have been used for protein delivery and the results associated with their use. Genetic fusion approaches for the preparation of protein-polypeptide conjugates will be also reviewed and compared with the best known chemical conjugation ones.

  17. Electron transfer in proteins

    DEFF Research Database (Denmark)

    Farver, O; Pecht, I

    1991-01-01

    Electron migration between and within proteins is one of the most prevalent forms of biological energy conversion processes. Electron transfer reactions take place between active centers such as transition metal ions or organic cofactors over considerable distances at fast rates and with remarkable...... specificity. The electron transfer is attained through weak electronic interaction between the active sites, so that considerable research efforts are centered on resolving the factors that control the rates of long-distance electron transfer reactions in proteins. These factors include (in addition......-containing proteins. These proteins serve almost exclusively in electron transfer reactions, and as it turns out, their metal coordination sites are endowed with properties uniquely optimized for their function....

  18. Recombinant Collagenlike Proteins

    Science.gov (United States)

    Fertala, Andzej

    2007-01-01

    A group of collagenlike recombinant proteins containing high densities of biologically active sites has been invented. The method used to express these proteins is similar to a method of expressing recombinant procollagens and collagens described in U. S. Patent 5,593,859, "Synthesis of human procollagens and collagens in recombinant DNA systems." Customized collagenous proteins are needed for biomedical applications. In particular, fibrillar collagens are attractive for production of matrices needed for tissue engineering and drug delivery. Prior to this invention, there was no way of producing customized collagenous proteins for these and other applications. Heretofore, collagenous proteins have been produced by use of such biological systems as yeasts, bacteria, and transgenic animals and plants. These products are normal collagens that can also be extracted from such sources as tendons, bones, and hides. These products cannot be made to consist only of biologically active, specific amino acid sequences that may be needed for specific applications. Prior to this invention, it had been established that fibrillar collagens consist of domains that are responsible for such processes as interaction with cells, binding of growth factors, and interaction with a number of structural proteins present in the extracellular matrix. A normal collagen consists of a sequence of domains that can be represented by a corresponding sequence of labels, e.g., D1D2D3D4. A collagenlike protein of the present invention contains regions of collagen II that contain multiples of a single domain (e.g., D1D1D1D1 or D4D4D4D4) chosen for its specific biological activity. By virtue of the multiplicity of the chosen domain, the density of sites having that specific biological activity is greater than it is in a normal collagen. A collagenlike protein according to this invention can thus be made to have properties that are necessary for tissue engineering.

  19. Occupational protein contact dermatitis.

    Science.gov (United States)

    Barbaud, Annick; Poreaux, Claire; Penven, Emmanuelle; Waton, Julie

    2015-01-01

    Occupational contact dermatitis is generally caused by haptens but can also be induced by proteins causing mainly immunological contact urticaria (ICU); chronic hand eczema in the context of protein contact dermatitis (PCD). In a monocentric retrospective study, from our database, only 31 (0.41%) of patients with contact dermatitis had positive skin tests with proteins: 22 had occupational PCD, 3 had non-occupational PCD, 5 occupational ICU and 1 cook had a neutrophilic fixed food eruption (NFFE) due to fish. From these results and analysis of literature, the characteristics of PCD can be summarized as follows. It is a chronic eczematous dermatitis, possibly exacerbated by work, suggestive if associated with inflammatory perionyxix and immediate erythema with pruritis, to be investigated when the patient resumes work after a period of interruption. Prick tests with the suspected protein-containing material are essential, as patch tests have negative results. In case of multisensitisation revealed by prick tests, it is advisable to analyse IgE against recombinant allergens. A history of atopy, found in 56 to 68% of the patients, has to be checked for. Most of the cases are observed among food-handlers but PCD can also be due to non-edible plants, latex, hydrolysed proteins or animal proteins. Occupational exposure to proteins can thus lead to the development of ICU. Reflecting hypersensitivity to very low concentrations of allergens, investigating ICU therefore requires caution and prick tests should be performed with a diluted form of the causative protein-containing product. Causes are food, especially fruit peel, non-edible plants, cosmetic products, latex, animals.

  20. Colorimetric protein assay techniques.

    Science.gov (United States)

    Sapan, C V; Lundblad, R L; Price, N C

    1999-04-01

    There has been an increase in the number of colorimetric assay techniques for the determination of protein concentration over the past 20 years. This has resulted in a perceived increase in sensitivity and accuracy with the advent of new techniques. The present review considers these advances with emphasis on the potential use of such technologies in the assay of biopharmaceuticals. The techniques reviewed include Coomassie Blue G-250 dye binding (the Bradford assay), the Lowry assay, the bicinchoninic acid assay and the biuret assay. It is shown that each assay has advantages and disadvantages relative to sensitivity, ease of performance, acceptance in the literature, accuracy and reproducibility/coefficient of variation/laboratory-to-laboratory variation. A comparison of the use of several assays with the same sample population is presented. It is suggested that the most critical issue in the use of a chromogenic protein assay for the characterization of a biopharmaceutical is the selection of a standard for the calibration of the assay; it is crucial that the standard be representative of the sample. If it is not possible to match the standard with the sample from the perspective of protein composition, then it is preferable to use an assay that is not sensitive to the composition of the protein such as a micro-Kjeldahl technique, quantitative amino acid analysis or the biuret assay. In a complex mixture it might be inappropriate to focus on a general method of protein determination and much more informative to use specific methods relating to the protein(s) of particular interest, using either specific assays or antibody-based methods. The key point is that whatever method is adopted as the 'gold standard' for a given protein, this method needs to be used routinely for calibration.

  1. Protein Nitrogen Determination

    Science.gov (United States)

    Nielsen, S. Suzanne

    The protein content of foods can be determined by numerous methods. The Kjeldahl method and the nitrogen combustion (Dumas) method for protein analysis are based on nitrogen determination. Both methods are official for the purposes of nutrition labeling of foods. While the Kjeldahl method has been used widely for over a hundred years, the recent availability of automated instrumentation for the Dumas method in many cases is replacing use of the Kjeldahl method.

  2. Transdermal Delivery of Proteins

    OpenAIRE

    Kalluri, Haripriya; Banga, Ajay K.

    2011-01-01

    Transdermal delivery of peptides and proteins avoids the disadvantages associated with the invasive parenteral route of administration and other alternative routes such as the pulmonary and nasal routes. Since proteins have a large size and are hydrophilic in nature, they cannot permeate passively across the skin due to the stratum corneum which allows the transport of only small lipophilic drug molecules. Enhancement techniques such as chemical enhancers, iontophoresis, microneedles, electro...

  3. Development of a highly-sensitive multi-plex assay using monoclonal antibodies for the simultaneous measurement of kappa and lambda immunoglobulin free light chains in serum and urine.

    Science.gov (United States)

    Campbell, John P; Cobbold, Mark; Wang, Yanyun; Goodall, Margaret; Bonney, Sarah L; Chamba, Anita; Birtwistle, Jane; Plant, Timothy; Afzal, Zaheer; Jefferis, Roy; Drayson, Mark T

    2013-05-31

    Monoclonal κ and λ immunoglobulin free light chain (FLC) paraproteins in serum and urine are important markers in the diagnosis and monitoring of B cell dyscrasias. Current nephelometric and turbidimetric methods that use sheep polyclonal antisera to quantify serum FLC have a number of well-observed limitations. In this report, we describe an improved method using specific mouse anti-human FLC monoclonal antibodies (mAbs). Anti-κ and anti-λ FLC mAbs were, separately, covalently coupled to polystyrene Xmap® beads and assayed, simultaneously, in a multi-plex format by Luminex® (mAb assay). The mAbs displayed no cross-reactivity to bound LC, the alternate LC type, or other human proteins and had improved sensitivity and specificity over immunofixation electrophoresis (IFE) and Freelite™. The assay gives good linearity and sensitivity (<1 mg/L), and the competitive inhibition format gave a broad calibration curve up to 437.5 mg/L and prevented anomalous results for samples in antigen excess i.e. high FLC levels. The mAbs displayed good concordance with Freelite™ for the quantitation of normal polyclonal FLC in plasma from healthy donors (n=249). The mAb assay identified all monoclonal FLC in serum from consecutive patient samples (n=1000; 50.1% with monoclonal paraprotein by serum IFE), and all FLC in a large cohort of urine samples tested for Bence Jones proteins (n=13090; 22.8% with monoclonal κ, 9.0% with monoclonal λ, and 0.8% with poly LC detected by urine IFE). Importantly this shows that the mAbs are at least close to the ideal of detecting FLC from all patients and neoplastic plasma cell clones. Given the overall effectiveness of the anti-FLC mAbs, further clinical validation is now warranted on serial samples from a range of patients with B cell disorders. Use of these mAbs on other assay platforms should also be investigated.

  4. Nahm sums, stability and the colored Jones polynomial

    CERN Document Server

    Garoufalidis, Stavros

    2011-01-01

    Nahm sums are $q$-series of a special hypergeometric type that appear in character formulas in Conformal Field Theory, and give rise to elements ot the Bloch group, and have interesting modularity properties. In our paper, we show how Nahm sums arise natural in Quantum Knot Theory, namely we prove the stability of the coefficients of an alternating link and present a Nahm sum formula for the resulting power series, defined in terms of a reduced, downward diagram of an alternating link. The Nahm sum formula comes with a computer implementation, illustrated in numerous examples of proven or conjectural identities among $q$-series.

  5. Matthew Jones House: Historic Maintenance and Repair Manual

    Science.gov (United States)

    2014-08-01

    Web . “General Masonry Inspection.” Online resource (n.d.) available at: http://www.oldhouseweb.com/how-to-advice/general-masonry-inspection.shtml. 14...with accurate door types (Figure 110), and • the wood is scraped , primed, and repainted, and/or • any broken elements are repaired or replaced as...repainting of wood includes: cleaning of surfaces; light scraping to remove loose and scaling paint; feather of edges; priming of bare wood; and

  6. Külaline kunstiilma tipust / Mark Jones ; intervjueerinud Tanel Veenre

    Index Scriptorium Estoniae

    Jones, Mark

    2010-01-01

    Kumu Kunstimuuseumis on 23. jaanuarini 2011 avatud näitus "John Constable. Victoria & Alberti muuseumi kogudest". Tallinnas viibinud muuseumi direktori söör Mark Jonesiga John Costable'i loomingust, Tallinna näitusest, Constable'i kollektsioonist Victoria & Alberti muuseumis, Victoria & Alberti muuseumist ja selle näitustest

  7. Max Jones E时代的新闻神童

    Institute of Scientific and Technical Information of China (English)

    雨宫萤

    2010-01-01

    “我有两只狗和一只猫。我在奥兰多的Lake Highland预科学校念书,最喜欢蓝色。我在一个管弦乐团拉大提琴。我的家乡在加拿大多伦多,爸妈离婚了。每年夏天我都会回加拿大,我还是‘对抗饥饿’组织的支持者。”

  8. Two Lectures On The Jones Polynomial And Khovanov Homology

    CERN Document Server

    Witten, Edward

    2014-01-01

    In the first of these two lectures, I describe a gauge theory approach to understanding quantum knot invariants as Laurent polynomials in a complex variable q. The two main steps are to reinterpret three-dimensional Chern-Simons gauge theory in four dimensional terms and then to apply electric-magnetic duality. The variable q is associated to instanton number in the dual description in four dimensions. In the second lecture, I describe how Khovanov homology can emerge upon adding a fifth dimension. (Based on lectures presented at the Clay Research Conference at Oxford University, and also at the Galileo Galilei Institute in Florence, the University of Milan, Harvard University, and the University of Pennsylvania.)

  9. DIGITAL FLOOD INSURANCE RATE MAP DATABASE, JONES COUNTY, GEORGIA, USA

    Data.gov (United States)

    Federal Emergency Management Agency, Department of Homeland Security — The Digital Flood Insurance Rate Map (DFIRM) Database depicts flood risk Information And supporting data used to develop the risk data. The primary risk;...

  10. Marine geophysics. By E.J.W. Jones

    Digital Repository Service at National Institute of Oceanography (India)

    Rao, D.G.

    recommend this book as valuable addition to all libraries more particularly to the educational and research institutions. D. Gopala Rao National Institute of Oceanography, Dona Paula, Goa-403004, India Ž.PII: S0012-8252 01 00027-1 Environmental change...

  11. 直击现场:Edward Jones

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Edward Jones先生曾在马德里Complutense大学学习法律,并获得了西班牙商会国际贸易文凭。1982年,Edward Jones加入阿特拉斯·科普柯(西班牙)公司供应部工作;1985年调往墨西哥,担任重点客户关系经理;

  12. Scaling of the dynamics of flexible Lennard-Jones chains

    DEFF Research Database (Denmark)

    Veldhorst, Arno; Dyre, J. C.; Schrøder, Thomas

    2014-01-01

    The isomorph theory provides an explanation for the so-called power law density scaling which has been observed in many molecular and polymeric glass formers, both experimentally and in simulations. Power law density scaling (relaxation times and transport coefficients being functions of ργ......S/T , where ρ is density, T is temperature, and γ S is a material specific scaling exponent) is an approximation to a more general scaling predicted by the isomorph theory. Furthermore, the isomorph theory provides an explanation for Rosenfeld scaling (relaxation times and transport coefficients being...... provide a possible explanation for why power-law density scaling is observed experimentally in alkanes and many polymeric systems. The theory provides an independent method of determining the scaling exponent, which is usually treated as an empirical scaling parameter....

  13. Sy Montgomery: Part Indiana Jones and Part Emily Dickinson

    Science.gov (United States)

    Young, Terrell A.

    2008-01-01

    As important as accuracy may be to nonfiction writers, few have taken such risks as Sy Montgomery in gathering information for her articles, books, and films. In this profile article, Young recounts many of the risks and adventures Montgomery has taken for the sake of accurate and impassioned writing. Montgomery says, "I consider my books love…

  14. The Road Inventory of Jones Hole National Fish Hatchery

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — To determine the relative needs of the U.S. Fish and Wildlife Service, the Federal Highway Administration (FHWA) was asked to inventory all public access and...

  15. Geodetic Control Points, Published in 2004, Jones County GIS.

    Data.gov (United States)

    NSGIC GIS Inventory (aka Ramona) — This Geodetic Control Points dataset, was produced all or in part from Field Survey/GPS information as of 2004. Data by this publisher are often provided in State...

  16. Bridget Jones Meets Mr. Darcy: Challenges of Contemporary Fiction

    Science.gov (United States)

    Alsop, Justine

    2007-01-01

    This exploratory study seeks to investigate the collection practices of English Literature librarians with regard to contemporary fiction, including popular genres such as detective fiction and "chick lit". Results of an online survey suggest literature librarians are increasingly receptive to the acquisition of popular genres and identify the…

  17. Protein phosphorylation and photorespiration.

    Science.gov (United States)

    Hodges, M; Jossier, M; Boex-Fontvieille, E; Tcherkez, G

    2013-07-01

    Photorespiration allows the recycling of carbon atoms of 2-phosphoglycolate produced by ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) oxygenase activity, as well as the removal of potentially toxic metabolites. The photorespiratory pathway takes place in the light, encompasses four cellular compartments and interacts with several other metabolic pathways and functions. Therefore, the regulation of this cycle is probably of paramount importance to plant metabolism, however, our current knowledge is poor. To rapidly respond to changing conditions, proteins undergo a number of different post-translational modifications that include acetylation, methylation and ubiquitylation, but protein phosphorylation is probably the most common. The reversible covalent addition of a phosphate group to a specific amino acid residue allows the modulation of protein function, such as activity, subcellular localisation, capacity to interact with other proteins and stability. Recent data indicate that many photorespiratory enzymes can be phosphorylated, and thus it seems that the photorespiratory cycle is, in part, regulated by protein phosphorylation. In this review, the known phosphorylation sites of each Arabidopsis thaliana photorespiratory enzyme and several photorespiratory-associated proteins are described and discussed. A brief account of phosphoproteomic protocols is also given since the published data compiled in this review are the fruit of this approach.

  18. Hepatitis C virus proteins

    Institute of Scientific and Technical Information of China (English)

    Jean Dubuisson

    2007-01-01

    Hepatitis C virus (HCV) encodes a single polyprotein,which is processed by cellular and viral proteases to generate 10 polypeptides. The HCV genome also contains an overlapping +1 reading frame that may lead to the synthesis of an additional protein. Until recently,studies of HCV have been hampered by the lack of a productive cell culture system. Since the identification of HCV genome approximately 17 years ago, structural,biochemical and biological information on HCV proteins has mainly been obtained with proteins produced by heterologous expression systems. In addition, some functional studies have also been confirmed with replicon systems or with retroviral particles pseudotyped with HCV envelope glycoproteins. The data that have accumulated on HCV proteins begin to provide a framework for understanding the molecular mechanisms involved in the major steps of HCV life cycle. Moreover,the knowledge accumulated on HCV proteins is also leading to the development of antiviral drugs among which some are showing promising results in early-phase clinical trials. This review summarizes the current knowledge on the functions and biochemical features of HCV proteins.

  19. Cardiolipin Interactions with Proteins.

    Science.gov (United States)

    Planas-Iglesias, Joan; Dwarakanath, Himal; Mohammadyani, Dariush; Yanamala, Naveena; Kagan, Valerian E; Klein-Seetharaman, Judith

    2015-09-15

    Cardiolipins (CL) represent unique phospholipids of bacteria and eukaryotic mitochondria with four acyl chains and two phosphate groups that have been implicated in numerous functions from energy metabolism to apoptosis. Many proteins are known to interact with CL, and several cocrystal structures of protein-CL complexes exist. In this work, we describe the collection of the first systematic and, to the best of our knowledge, the comprehensive gold standard data set of all known CL-binding proteins. There are 62 proteins in this data set, 21 of which have nonredundant crystal structures with bound CL molecules available. Using binding patch analysis of amino acid frequencies, secondary structures and loop supersecondary structures considering phosphate and acyl chain binding regions together and separately, we gained a detailed understanding of the general structural and dynamic features involved in CL binding to proteins. Exhaustive docking of CL to all known structures of proteins experimentally shown to interact with CL demonstrated the validity of the docking approach, and provides a rich source of information for experimentalists who may wish to validate predictions.

  20. Disease specific protein corona

    Science.gov (United States)

    Rahman, M.; Mahmoudi, M.

    2015-03-01

    It is now well accepted that upon their entrance into the biological environments, the surface of nanomaterials would be covered by various biomacromolecules (e.g., proteins and lipids). The absorption of these biomolecules, so called `protein corona', onto the surface of (nano)biomaterials confers them a new `biological identity'. Although the formation of protein coronas on the surface of nanoparticles has been widely investigated, there are few reports on the effect of various diseases on the biological identity of nanoparticles. As the type of diseases may tremendously changes the composition of the protein source (e.g., human plasma/serum), one can expect that amount and composition of associated proteins in the corona composition may be varied, in disease type manner. Here, we show that corona coated silica and polystyrene nanoparticles (after interaction with in the plasma of the healthy individuals) could induce unfolding of fibrinogen, which promotes release of the inflammatory cytokines. However, no considerable releases of inflammatory cytokines were observed for corona coated graphene sheets. In contrast, the obtained corona coated silica and polystyrene nanoparticles from the hypofibrinogenemia patients could not induce inflammatory cytokine release where graphene sheets do. Therefore, one can expect that disease-specific protein coronas can provide a novel approach for applying nanomedicine to personalized medicine, improving diagnosis and treatment of different diseases tailored to the specific conditions and circumstances.

  1. The effect of protein-protein and protein-membrane interactions on membrane fouling in ultrafiltration

    NARCIS (Netherlands)

    Huisman, I.H.; Prádanos, P.; Hernández, A.

    2000-01-01

    It was studied how protein-protein and protein-membrane interactions influence the filtration performance during the ultrafiltration of protein solutions over polymeric membranes. This was done by measuring flux, streaming potential, and protein transmission during filtration of bovine serum albumin

  2. Similarity measures for protein ensembles

    DEFF Research Database (Denmark)

    Lindorff-Larsen, Kresten; Ferkinghoff-Borg, Jesper

    2009-01-01

    Analyses of similarities and changes in protein conformation can provide important information regarding protein function and evolution. Many scores, including the commonly used root mean square deviation, have therefore been developed to quantify the similarities of different protein conformatio...

  3. Controllability in protein interaction networks.

    Science.gov (United States)

    Wuchty, Stefan

    2014-05-13

    Recently, the focus of network research shifted to network controllability, prompting us to determine proteins that are important for the control of the underlying interaction webs. In particular, we determined minimum dominating sets of proteins (MDSets) in human and yeast protein interaction networks. Such groups of proteins were defined as optimized subsets where each non-MDSet protein can be reached by an interaction from an MDSet protein. Notably, we found that MDSet proteins were enriched with essential, cancer-related, and virus-targeted genes. Their central position allowed MDSet proteins to connect protein complexes and to have a higher impact on network resilience than hub proteins. As for their involvement in regulatory functions, MDSet proteins were enriched with transcription factors and protein kinases and were significantly involved in bottleneck interactions, regulatory links, phosphorylation events, and genetic interactions.

  4. A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny

    Directory of Open Access Journals (Sweden)

    Li Karen

    2008-12-01

    Full Text Available Abstract Background Widely used substitution models for proteins, such as the Jones-Taylor-Thornton (JTT or Whelan and Goldman (WAG models, are based on empirical amino acid interchange matrices estimated from databases of protein alignments that incorporate the average amino acid frequencies of the data set under examination (e.g JTT + F. Variation in the evolutionary process between sites is typically modelled by a rates-across-sites distribution such as the gamma (Γ distribution. However, sites in proteins also vary in the kinds of amino acid interchanges that are favoured, a feature that is ignored by standard empirical substitution matrices. Here we examine the degree to which the pattern of evolution at sites differs from that expected based on empirical amino acid substitution models and evaluate the impact of these deviations on phylogenetic estimation. Results We analyzed 21 large protein alignments with two statistical tests designed to detect deviation of site-specific amino acid distributions from data simulated under the standard empirical substitution model: JTT+ F + Γ. We found that the number of states at a given site is, on average, smaller and the frequencies of these states are less uniform than expected based on a JTT + F + Γ substitution model. With a four-taxon example, we show that phylogenetic estimation under the JTT + F + Γ model is seriously biased by a long-branch attraction artefact if the data are simulated under a model utilizing the observed site-specific amino acid frequencies from an alignment. Principal components analyses indicate the existence of at least four major site-specific frequency classes in these 21 protein alignments. Using a mixture model with these four separate classes of site-specific state frequencies plus a fifth class of global frequencies (the JTT + cF + Γ model, significant improvements in model fit for real data sets can be achieved. This simple mixture model also reduces the long

  5. Protein hydrolysates in sports nutrition

    Directory of Open Access Journals (Sweden)

    Manninen Anssi H

    2009-09-01

    Full Text Available Abstract It has been suggested that protein hydrolysates providing mainly di- and tripeptides are superior to intact (whole proteins and free amino acids in terms of skeletal muscle protein anabolism. This review provides a critical examination of protein hydrolysate studies conducted in healthy humans with special reference to sports nutrition. The effects of protein hydrolysate ingestion on blood amino acid levels, muscle protein anabolism, body composition, exercise performance and muscle glycogen resynthesis are discussed.

  6. Protein Functionality in Food Systems

    Institute of Scientific and Technical Information of China (English)

    WANG Panpan

    2010-01-01

    The structure,shape,color,smell and taste of food were decided by protein functionality.The utilization of protein will improve by changing the protein functionality.Protein functionality is also advantage to maintain and utilize the nutrition of food.This paper summarized the nature,classification,factors and prospect of protein functionality.It ccn provide a theoretical basis for application of protein in food industry.

  7. The cullin protein family.

    Science.gov (United States)

    Sarikas, Antonio; Hartmann, Thomas; Pan, Zhen-Qiang

    2011-01-01

    Cullin proteins are molecular scaffolds that have crucial roles in the post-translational modification of cellular proteins involving ubiquitin. The mammalian cullin protein family comprises eight members (CUL1 to CUL7 and PARC), which are characterized by a cullin homology domain. CUL1 to CUL7 assemble multi-subunit Cullin-RING E3 ubiquitin ligase (CRL) complexes, the largest family of E3 ligases with more than 200 members. Although CUL7 and PARC are present only in chordates, other members of the cullin protein family are found in Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana and yeast. A cullin protein tethers both a substrate-targeting unit, often through an adaptor protein, and the RING finger component in a CRL. The cullin-organized CRL thus positions a substrate close to the RING-bound E2 ubiquitin-conjugating enzyme, which catalyzes the transfer of ubiquitin to the substrate. In addition, conjugation of cullins with the ubiquitin-like molecule Nedd8 modulates activation of the corresponding CRL complex, probably through conformational regulation of the interactions between cullin's carboxy-terminal tail and CRL's RING subunit. Genetic studies in several model organisms have helped to unravel a multitude of physiological functions associated with cullin proteins and their respective CRLs. CRLs target numerous substrates and thus have an impact on a range of biological processes, including cell growth, development, signal transduction, transcriptional control, genomic integrity and tumor suppression. Moreover, mutations in CUL7 and CUL4B genes have been linked to hereditary human diseases.

  8. PROTEIN SYNTHESIS GAME

    Directory of Open Access Journals (Sweden)

    J.C.Q. Carvalho

    2004-05-01

    Full Text Available The theoretical explanation of biological concepts, associated with the use of teaching games andmodels, intensify the comprehension and increase students interest, stimulating them to participateactively on the teaching-learning process. The sta of dissemination from Centro de BiotecnologiaMolecular Estrutural (CBME, in partnership with the Centro de Divulgac~ao Cientca e Cultural(CDCC, presents, in this work, a new educational resource denoted: Protein Synthesis Game. Theapproach of the game involves the cytological aspects of protein synthesis, directed to high schoolstudents. Students are presented to day-by-day facts related to the function of a given protein in thehuman body. Such task leads players to the goal of solving out a problem through synthesizing aspecied protein. The game comprises: (1 a board illustrated with the transversal section of animalcell, with its main structures and organelles and sequences of hypothetical genes; (2 cards with thedescription of steps and other structures required for protein synthesis in eukaryotic cells; (3 piecesrepresenting nucleotides, polynucleotides, ribosome, amino acids, and polypeptide chains. In order toplay the game, students take cards that sequentially permit them to acquire the necessary pieces forproduction of the protein described in each objective. Players must move the pieces on the board andsimulate the steps of protein synthesis. The dynamic of the game allows students to easily comprehendprocesses of transcription and translation. This game was presented to dierent groups of high schoolteachers and students. Their judgments have been heard and indicated points to be improved, whichhelped us with the game development. Furthermore, the opinions colleted were always favorable forthe application of this game as a teaching resource in classrooms.

  9. Bioinformatics and moonlighting proteins

    Directory of Open Access Journals (Sweden)

    Sergio eHernández

    2015-06-01

    Full Text Available Multitasking or moonlighting is the capability of some proteins to execute two or more biochemical functions. Usually, moonlighting proteins are experimentally revealed by serendipity. For this reason, it would be helpful that Bioinformatics could predict this multifunctionality, especially because of the large amounts of sequences from genome projects. In the present work, we analyse and describe several approaches that use sequences, structures, interactomics and current bioinformatics algorithms and programs to try to overcome this problem. Among these approaches are: a remote homology searches using Psi-Blast, b detection of functional motifs and domains, c analysis of data from protein-protein interaction databases (PPIs, d match the query protein sequence to 3D databases (i.e., algorithms as PISITE, e mutation correlation analysis between amino acids by algorithms as MISTIC. Programs designed to identify functional motif/domains detect mainly the canonical function but usually fail in the detection of the moonlighting one, Pfam and ProDom being the best methods. Remote homology search by Psi-Blast combined with data from interactomics databases (PPIs have the best performance. Structural information and mutation correlation analysis can help us to map the functional sites. Mutation correlation analysis can only be used in very specific situations –it requires the existence of multialigned family protein sequences - but can suggest how the evolutionary process of second function acquisition took place. The multitasking protein database MultitaskProtDB (http://wallace.uab.es/multitask/, previously published by our group, has been used as a benchmark for the all of the analyses.

  10. Modeling Mercury in Proteins

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Jeremy C [ORNL; Parks, Jerry M [ORNL

    2016-01-01

    Mercury (Hg) is a naturally occurring element that is released into the biosphere both by natural processes and anthropogenic activities. Although its reduced, elemental form Hg(0) is relatively non-toxic, other forms such as Hg2+ and, in particular, its methylated form, methylmercury, are toxic, with deleterious effects on both ecosystems and humans. Microorganisms play important roles in the transformation of mercury in the environment. Inorganic Hg2+ can be methylated by certain bacteria and archaea to form methylmercury. Conversely, bacteria also demethylate methylmercury and reduce Hg2+ to relatively inert Hg(0). Transformations and toxicity occur as a result of mercury interacting with various proteins. Clearly, then, understanding the toxic effects of mercury and its cycling in the environment requires characterization of these interactions. Computational approaches are ideally suited to studies of mercury in proteins because they can provide a detailed picture and circumvent issues associated with toxicity. Here we describe computational methods for investigating and characterizing how mercury binds to proteins, how inter- and intra-protein transfer of mercury is orchestrated in biological systems, and how chemical reactions in proteins transform the metal. We describe quantum chemical analyses of aqueous Hg(II), which reveal critical factors that determine ligand binding propensities. We then provide a perspective on how we used chemical reasoning to discover how microorganisms methylate mercury. We also highlight our combined computational and experimental studies of the proteins and enzymes of the mer operon, a suite of genes that confers mercury resistance in many bacteria. Lastly, we place work on mercury in proteins in the context of what is needed for a comprehensive multi-scale model of environmental mercury cycling.

  11. A Novel Approach for Protein-Named Entity Recognition and Protein-Protein Interaction Extraction

    OpenAIRE

    Meijing Li; Tsendsuren Munkhdalai; Xiuming Yu; Keun Ho Ryu

    2015-01-01

    Many researchers focus on developing protein-named entity recognition (Protein-NER) or PPI extraction systems. However, the studies about these two topics cannot be merged well; then existing PPI extraction systems’ Protein-NER still needs to improve. In this paper, we developed the protein-protein interaction extraction system named PPIMiner based on Support Vector Machine (SVM) and parsing tree. PPIMiner consists of three main models: natural language processing (NLP) model, Protein-NER mod...

  12. ADSORPTION OF PROTEIN ON NANOPARTICLES

    Institute of Scientific and Technical Information of China (English)

    WU Qi

    1994-01-01

    The adsorption of protein on nanoparticles was studied by using dynamic light scattering to measure the hydrodynamic size of both pure protein and nanoparticles adsorbed with different amounts of protein. The thickness of the adsorbed protein layer increases as protein concentration, but decreases as the initial size of nanoparticles. After properly scaling the thickness with the initial diameter, we are able to fit all experimental data with a single master curve. Our experimental results suggest that the adsorbed proteins form a monolayeron the nanoparticle surface and the adsorbed protein molecules are attached to the particle surface at many points through a possible hydrogen-bonding. Our results also indicate that as protein concentration increases, the overall shape of the adsorbed protein molecule continuously changes from a flat layer on the particle surface to a stretched coil extended into water. During the change, the hydrodynamic volume of the adsorbed protein increases linearly with protein concentration.

  13. Benchtop Detection of Proteins

    Science.gov (United States)

    Scardelletti, Maximilian C.; Varaljay, Vanessa

    2007-01-01

    A process, and a benchtop-scale apparatus for implementing the process, have been developed to detect proteins associated with specific microbes in water. The process and apparatus may also be useful for detection of proteins in other, more complex liquids. There may be numerous potential applications, including monitoring lakes and streams for contamination, testing of blood and other bodily fluids in medical laboratories, and testing for microbial contamination of liquids in restaurants and industrial food-processing facilities. A sample can be prepared and analyzed by use of this process and apparatus within minutes, whereas an equivalent analysis performed by use of other processes and equipment can often take hours to days. The process begins with the conjugation of near-infrared-fluorescent dyes to antibodies that are specific to a particular protein. Initially, the research has focused on using near-infrared dyes to detect antigens or associated proteins in solution, which has proven successful vs. microbial cells, and streamlining the technique in use for surface protein detection on microbes would theoretically render similar results. However, it is noted that additional work is needed to transition protein-based techniques to microbial cell detection. Consequently, multiple such dye/antibody pairs could be prepared to enable detection of multiple selected microbial species, using a different dye for each species. When excited by near-infrared light of a suitable wavelength, each dye fluoresces at a unique longer wavelength that differs from those of the other dyes, enabling discrimination among the various species. In initial tests, the dye/antibody pairs are mixed into a solution suspected of containing the selected proteins, causing the binding of the dye/antibody pairs to such suspect proteins that may be present. The solution is then run through a microcentrifuge that includes a membrane that acts as a filter in that it retains the dye/antibody/protein

  14. Purine inhibitors of protein kinases, G proteins and polymerases

    Energy Technology Data Exchange (ETDEWEB)

    Gray, Nathanael S. (Berkeley, CA); Schultz, Peter (Oakland, CA); Kim, Sung-Hou (Moraga, CA); Meijer, Laurent (Roscoff, FR)

    2001-07-03

    The present invention relates to purine analogs that inhibit, inter alia, protein kinases, G-proteins and polymerases. In addition, the present invention relates to methods of using such purine analogs to inhibit protein kinases, G-proteins, polymerases and other cellular processes and to treat cellular proliferative diseases.

  15. Integral UBL domain proteins: a family of proteasome interacting proteins

    DEFF Research Database (Denmark)

    Hartmann-Petersen, Rasmus; Gordon, Colin

    2004-01-01

    The family of ubiquitin-like (UBL) domain proteins (UDPs) comprises a conserved group of proteins involved in a multitude of different cellular activities. However, recent studies on UBL-domain proteins indicate that these proteins appear to share a common property in their ability to interact wi...

  16. Electrochemical nanomoulding through proteins

    Science.gov (United States)

    Allred, Daniel B.

    The continued improvements in performance of modern electronic devices are directly related to the manufacturing of smaller, denser features on surfaces. Electrochemical fabrication has played a large role in continuing this trend due to its low cost and ease of scaleability toward ever smaller dimensions. This work introduces the concept of using proteins, essentially monodisperse complex polymers whose three-dimensional structures are fixed by their encoded amino acid sequences, as "moulds" around which nanostructures can be built by electrochemical fabrication. Bacterial cell-surface layer proteins, or "S-layer" proteins, from two organisms---Deinococcus radiodurans and Sporosarcina ureae---were used as the "moulds" for electrochemical fabrication. The proteins are easily purified as micron-sized sheets of periodic molecular complexes with 18-nm hexagonal and 13-nm square unit cell lattices, respectively. Direct imaging by transmission electron microscopy on ultrathin noble metal films without sample preparation eliminates potential artifacts to the high surface energy substrates necessary for high nucleation densities. Characterization involved imaging, electron diffraction, spectroscopy, and three-dimensional reconstruction. The S-layer protein of D. radiodurans was further subjected to an atomic force microscope based assay to determine the integrity of its structure and long-range order and was found to be useful for fabrication from around pH 3 to 12.

  17. Protein Dynamics in Enzymology

    Science.gov (United States)

    Brooks, , III

    2001-03-01

    Enzymes carry-out the chemical activity essential for living processes by providing particular structural arrangements of chemically functional moieties through the structure of their constituent proteins. They are suggested to be optimized through evolution to specifically bind the transition state for the chemical processes they participate in, thereby enhancing the rate of these chemical events by 6-12 orders of magnitude. However, proteins are malleable and fluctuating many-body systems and may also utilize coupling between motional processes with catalysis to regulate or promote these processes. Our studies are aimed at exploring the hypothesis that motions of the protein couple distant regions of the molecule to assist catalytic processes. We demonstrate, through the use of molecular simulations, that strongly coupled motions occur in regions of protein molecules distant in sequence and space from each other, and the enzyme’s active site, when the protein is in a reactant state. Further, we find that the presence of this coupling disappears in complexes no longer reactive-competent, i.e., for product configurations and mutant sequences. The implications of these findings and aspects of evolutionary relationships and mutational studies which support the coupling hypothesis will be discussed in the context of our work on dihydrofolate reductase.

  18. Heat Capacity in Proteins

    Science.gov (United States)

    Prabhu, Ninad V.; Sharp, Kim A.

    2005-05-01

    Heat capacity (Cp) is one of several major thermodynamic quantities commonly measured in proteins. With more than half a dozen definitions, it is the hardest of these quantities to understand in physical terms, but the richest in insight. There are many ramifications of observed Cp changes: The sign distinguishes apolar from polar solvation. It imparts a temperature (T) dependence to entropy and enthalpy that may change their signs and which of them dominate. Protein unfolding usually has a positive ΔCp, producing a maximum in stability and sometimes cold denaturation. There are two heat capacity contributions, from hydration and protein-protein interactions; which dominates in folding and binding is an open question. Theoretical work to date has dealt mostly with the hydration term and can account, at least semiquantitatively, for the major Cp-related features: the positive and negative Cp of hydration for apolar and polar groups, respectively; the convergence of apolar group hydration entropy at T ≈ 112°C; the decrease in apolar hydration Cp with increasing T; and the T-maximum in protein stability and cold denaturation.

  19. Protein Crystal Serum Albumin

    Science.gov (United States)

    1998-01-01

    As the most abundant protein in the circulatory system albumin contributes 80% to colloid osmotic blood pressure. Albumin is also chiefly responsible for the maintenance of blood pH. It is located in every tissue and bodily secretion, with extracellular protein comprising 60% of total albumin. Perhaps the most outstanding property of albumin is its ability to bind reversibly to an incredible variety of ligands. It is widely accepted in the pharmaceutical industry that the overall distribution, metabolism, and efficiency of many drugs are rendered ineffective because of their unusually high affinity for this abundant protein. An understanding of the chemistry of the various classes of pharmaceutical interactions with albumin can suggest new approaches to drug therapy and design. Principal Investigator: Dan Carter/New Century Pharmaceuticals

  20. Polarizable protein packing

    KAUST Repository

    Ng, Albert H.

    2011-01-24

    To incorporate protein polarization effects within a protein combinatorial optimization framework, we decompose the polarizable force field AMOEBA into low order terms. Including terms up to the third-order provides a fair approximation to the full energy while maintaining tractability. We represent the polarizable packing problem for protein G as a hypergraph and solve for optimal rotamers with the FASTER combinatorial optimization algorithm. These approximate energy models can be improved to high accuracy [root mean square deviation (rmsd) < 1 kJ mol -1] via ridge regression. The resulting trained approximations are used to efficiently identify new, low-energy solutions. The approach is general and should allow combinatorial optimization of other many-body problems. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011 Copyright © 2011 Wiley Periodicals, Inc.

  1. Discovery of binding proteins for a protein target using protein-protein docking-based virtual screening.

    Science.gov (United States)

    Zhang, Changsheng; Tang, Bo; Wang, Qian; Lai, Luhua

    2014-10-01

    Target structure-based virtual screening, which employs protein-small molecule docking to identify potential ligands, has been widely used in small-molecule drug discovery. In the present study, we used a protein-protein docking program to identify proteins that bind to a specific target protein. In the testing phase, an all-to-all protein-protein docking run on a large dataset was performed. The three-dimensional rigid docking program SDOCK was used to examine protein-protein docking on all protein pairs in the dataset. Both the binding affinity and features of the binding energy landscape were considered in the scoring function in order to distinguish positive binding pairs from negative binding pairs. Thus, the lowest docking score, the average Z-score, and convergency of the low-score solutions were incorporated in the analysis. The hybrid scoring function was optimized in the all-to-all docking test. The docking method and the hybrid scoring function were then used to screen for proteins that bind to tumor necrosis factor-α (TNFα), which is a well-known therapeutic target for rheumatoid arthritis and other autoimmune diseases. A protein library containing 677 proteins was used for the screen. Proteins with scores among the top 20% were further examined. Sixteen proteins from the top-ranking 67 proteins were selected for experimental study. Two of these proteins showed significant binding to TNFα in an in vitro binding study. The results of the present study demonstrate the power and potential application of protein-protein docking for the discovery of novel binding proteins for specific protein targets.

  2. The representation of protein complexes in the Protein Ontology (PRO

    Directory of Open Access Journals (Sweden)

    Smith Barry

    2011-09-01

    Full Text Available Abstract Background Representing species-specific proteins and protein complexes in ontologies that are both human- and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. Description We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. Conclusion PRO is a unique database resource for species-specific protein complexes. PRO facilitates robust annotation of variations in composition and function contexts for protein complexes within and between species.

  3. Stress proteins in CNS inflammation

    NARCIS (Netherlands)

    Noort, J.M. van

    2008-01-01

    Stress proteins or heat shock proteins (HSPs) are ubiquitous cellular components that have long been known to act as molecular chaperones. By assisting proper folding and transport of proteins, and by assisting in the degradation of aberrant proteins, they play key roles in cellular metabolism. The

  4. Protein: FBA3 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FBA3 Atg1 kinase complex ATG1 APG1, AUT3, CVT10 Serine/threonine-protein kinase ATG1 Autophagy prot...ein 3, Autophagy-related protein 1, Cytoplasm to vacuole targeting protein 10 559292 Sacchar

  5. Protein: FEA3 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FEA3 AREB pathway: Signaling proteins SRK2E OST1, SNRK2.6 Serine/threonine-protein kinase SRK2E Prot...ein OPEN STOMATA 1, SNF1-related kinase 2.6, Serine/threonine-protein kinase OST1 3702 Arabidopsis thaliana 829541 Q940H6 3UC4, 3ZUT, 3ZUU, 3UDB 19805022 ...

  6. Protein: FEA3 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FEA3 AREB pathway: Signaling proteins AZF1 OZAKGYO, ZF1 At5g67450, Cys2/His2-type zinc finger prot...ein 1, Zinc finger protein OZAKGYO, Zinc-finger protein 1 3702 Arabidopsis thaliana 836881 Q9SSW1 21852415 ...

  7. Ubiquitin domain proteins in disease

    DEFF Research Database (Denmark)

    Klausen, Louise Kjær; Schulze, Andrea; Seeger, Michael;

    2007-01-01

    The human genome encodes several ubiquitin-like (UBL) domain proteins (UDPs). Members of this protein family are involved in a variety of cellular functions and many are connected to the ubiquitin proteasome system, an essential pathway for protein degradation in eukaryotic cells. Despite...... and cancer. Publication history: Republished from Current BioData's Targeted Proteins database (TPdb; http://www.targetedproteinsdb.com)....

  8. The Formation of Protein Structure

    DEFF Research Database (Denmark)

    Bohr, Jakob; Bohr, Henrik; Brunak, Søren

    1996-01-01

    Dynamically induced curvature owing to long-range excitations along the backbones of protein molecules with non-linear elastic properties may control the folding of proteins.......Dynamically induced curvature owing to long-range excitations along the backbones of protein molecules with non-linear elastic properties may control the folding of proteins....

  9. Protein: FBB5 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FBB5 RNA silencing TNRC6A CAGH26, KIAA1460, TNRC6 TNRC6A Trinucleotide repeat-containing gene 6A protein... CAG repeat protein 26, EMSY interactor protein, GW182 autoantigen, Glycine-tryptophan protein of 182 kDa 9606 Homo sapiens Q8NDV7 27327 27327 19398495 ...

  10. Cold gelation of globular proteins

    NARCIS (Netherlands)

    Alting, A.C.

    2003-01-01

    Keywords : globular proteins, whey protein, ovalbumin, cold gelation, disulfide bonds, texture, gel hardnessProtein gelation in food products is important to obtain desirable sensory and textural properties. Cold gelation is a novel method to produce protein-based gels. It is a two step process in w

  11. Protein: FBA7 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FBA7 claudin-zona occluden TJP3 ZO3 TJP3 Tight junction protein ZO-3 Tight junction protein 3, Zona occlude...ns protein 3, Zonula occludens protein 3 9606 Homo sapiens O95049 27134 3KFV 27134 O95049 ...

  12. Protein: FBA7 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FBA7 claudin-zona occluden TJP2 X104, ZO2 TJP2 Tight junction protein ZO-2 Tight ju...nction protein 2, Zona occludens protein 2, Zonula occludens protein 2 9606 Homo sapiens Q9UDY2 9414 3E17, 2OSG 9414 ...

  13. Protein: FBA7 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FBA7 claudin-zona occluden Tjp1 Zo1 Tight junction protein ZO-1 Tight junction protein 1, Zona occlude...ns protein 1, Zonula occludens protein 1 10090 Mus musculus 21872 P39447 2RRM P39447 21431884 ...

  14. PSPP: A Protein Structure Prediction Pipeline for Computing Clusters

    Science.gov (United States)

    2009-07-01

    Clusters 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT NUMBER 5e. TASK NUMBER 5f. WORK UNIT NUMBER 7...Fold recognition/threading [34] [60] PSIPRED Jones Secondary structure prediction [21] [61] Rosetta Baker Ab initio folder [41] [62] SCOP/ ASTRAL Chothia...the folds of the models that result from the Rosetta code, the structures of the top few models are compared against ASTRAL PDB-style coordinates of

  15. A simple dependence between protein evolution rate and the number of protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Hirsh Aaron E

    2003-05-01

    Full Text Available Abstract Background It has been shown for an evolutionarily distant genomic comparison that the number of protein-protein interactions a protein has correlates negatively with their rates of evolution. However, the generality of this observation has recently been challenged. Here we examine the problem using protein-protein interaction data from the yeast Saccharomyces cerevisiae and genome sequences from two other yeast species. Results In contrast to a previous study that used an incomplete set of protein-protein interactions, we observed a highly significant correlation between number of interactions and evolutionary distance to either Candida albicans or Schizosaccharomyces pombe. This study differs from the previous one in that it includes all known protein interactions from S. cerevisiae, and a larger set of protein evolutionary rates. In both evolutionary comparisons, a simple monotonic relationship was found across the entire range of the number of protein-protein interactions. In agreement with our earlier findings, this relationship cannot be explained by the fact that proteins with many interactions tend to be important to yeast. The generality of these correlations in other kingdoms of life unfortunately cannot be addressed at this time, due to the incompleteness of protein-protein interaction data from organisms other than S. cerevisiae. Conclusions Protein-protein interactions tend to slow the rate at which proteins evolve. This may be due to structural constraints that must be met to maintain interactions, but more work is needed to definitively establish the mechanism(s behind the correlations we have observed.

  16. The Development and Characterization of Protein-Based Stationary Phases for Studying Drug-Protein and Protein-Protein Interactions

    OpenAIRE

    Sanghvi, Mitesh; Moaddel, Ruin; Wainer, Irving W.

    2011-01-01

    Protein-based liquid chromatography stationary phases are used in bioaffinity chromatography for studying drug-protein interactions, the determination of binding affinities, competitive and allosteric interactions, as well as for studying protein-protein interactions. This review addresses the development and characterization of protein-based stationary phase, and the application of these phases using frontal and zonal chromatography techniques. The approach will be illustrated using immobili...

  17. Sound of proteins

    DEFF Research Database (Denmark)

    2007-01-01

    and statistical analysis of the resulting molecular trajectories (as everybody else!). However, recently I started assigning a particular sound frequency to each amino acid in the protein, and by setting the amplitude of each frequency according to the movement amplitude we can "hear" whenever two aminoacids...

  18. Protein Requirements during Aging

    Directory of Open Access Journals (Sweden)

    Glenda Courtney-Martin

    2016-08-01

    Full Text Available Protein recommendations for elderly, both men and women, are based on nitrogen balance studies. They are set at 0.66 and 0.8 g/kg/day as the estimated average requirement (EAR and recommended dietary allowance (RDA, respectively, similar to young adults. This recommendation is based on single linear regression of available nitrogen balance data obtained at test protein intakes close to or below zero balance. Using the indicator amino acid oxidation (IAAO method, we estimated the protein requirement in young adults and in both elderly men and women to be 0.9 and 1.2 g/kg/day as the EAR and RDA, respectively. This suggests that there is no difference in requirement on a gender basis or on a per kg body weight basis between younger and older adults. The requirement estimates however are ~40% higher than the current protein recommendations on a body weight basis. They are also 40% higher than our estimates in young men when calculated on the basis of fat free mass. Thus, current recommendations may need to be re-assessed. Potential rationale for this difference includes a decreased sensitivity to dietary amino acids and increased insulin resistance in the elderly compared with younger individuals.

  19. Markers of protein oxidation

    DEFF Research Database (Denmark)

    Headlam, Henrietta A; Davies, Michael Jonathan

    2004-01-01

    Exposure of proteins to radicals in the presence of O2 gives both side-chain oxidation and backbone fragmentation. These processes can be interrelated, with initial side-chain oxidation giving rise to backbone damage via transfer reactions. We have shown previously that alkoxyl radicals formed on...

  20. Protein oxidation and peroxidation

    DEFF Research Database (Denmark)

    Davies, Michael Jonathan

    2016-01-01

    to the residues targeted and their spatial location. Modification can result in increased side-chain hydrophilicity, side-chain and backbone fragmentation, aggregation via covalent cross-linking or hydrophobic interactions, protein unfolding and altered conformation, altered interactions with biological partners...

  1. Cellulose binding domain proteins

    Science.gov (United States)

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

    1998-01-01

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

  2. Tuber storage proteins.

    Science.gov (United States)

    Shewry, Peter R

    2003-06-01

    A wide range of plants are grown for their edible tubers, but five species together account for almost 90 % of the total world production. These are potato (Solanum tuberosum), cassava (Manihot esculenta), sweet potato (Ipomoea batatus), yams (Dioscorea spp.) and taro (Colocasia, Cyrtosperma and Xanthosoma spp.). All of these, except cassava, contain groups of storage proteins, but these differ in the biological properties and evolutionary relationships. Thus, patatin from potato exhibits activity as an acylhydrolase and esterase, sporamin from sweet potato is an inhibitor of trypsin, and dioscorin from yam is a carbonic anhydrase. Both sporamin and dioscorin also exhibit antioxidant and radical scavenging activity. Taro differs from the other three crops in that it contains two major types of storage protein: a trypsin inhibitor related to sporamin and a mannose-binding lectin. These characteristics indicate that tuber storage proteins have evolved independently in different species, which contrasts with the highly conserved families of storage proteins present in seeds. Furthermore, all exhibit biological activities which could contribute to resistance to pests, pathogens or abiotic stresses, indicating that they may have dual roles in the tubers.

  3. Kidney failure as an unusual initial presentation of biclonal gammopathy (IgD multiple myeloma associated with light chain disease: A case report

    Directory of Open Access Journals (Sweden)

    Rabrenović Violeta

    2015-01-01

    Full Text Available Introduction. Immunoglobulin D (IgD myeloma is a rare disease, about 2% of all myelomas, even rarer when accompanied with another multiple myeloma in biclonal gammopathy. We presented a case of biclonal gammopathy - associated manifestation of IgD myeloma and light chain disease in a patient who initially had renal failure. Case report. 37-year-old male approximately one month before hospitalization began to feel malaise and fatigue along with decreased urination. Laboratory analysis revealed azotemia. A dialysis catheter was placed and hemodialysis started. The patient was then admitted to our hospital for further tests and during admission, objective examination revealed pronounced paleness with hepatosplenomegaly and hypertension (170/95 mmHg. Laboratory analysis showed erythrocyte sedimentation rate 122 mm/h, expressed anemic syndrome (Hb 71 g/L and renal failure dialysis rank: creatinine 1,408 μmol/L, urea31.7 mmol/L. There was two M components in serum protein electrophoresis: IgD lambda and free light chain lambda. Proteinuria was nephrotic rank (5.4 g/24 h, whose electrophoresis revealed 2 M components - massive in α 2 fraction of 71%; 7% in the discrete β fraction, beta 2M /serum 110 mg/L, in urine 1.8 mg/L - extremely high; IgL kappa / lambda index 1 : 13 (reference value ratio 2 : 1. The findings pointed to double myeloma disease: IgD myeloma and Bence Jones lambda myeloma. Bone biopsy confirmed IgD myeloma lambda 100% infiltration medulla predominantly plasmablasts. The treatment continued with hemodialysis 3 times per week with chemotherapy protocol bortezomib, doxorubicin, dexamethasone. After 4 cycles of chemotherapy, there was a decrease of IgD, λ - light chains, reduction in proteinuria (1.03 g/24 h, so hemodialysis was reduced to once per week. Six months after treatment initiation the patient underwent autologous bone marrow transplantation. In a 2-year follow-up period double myeloma disease showed complete remission

  4. Predicting where small molecules bind at protein-protein interfaces.

    Directory of Open Access Journals (Sweden)

    Peter Walter

    Full Text Available Small molecules that bind at protein-protein interfaces may either block or stabilize protein-protein interactions in cells. Thus, some of these binding interfaces may turn into prospective targets for drug design. Here, we collected 175 pairs of protein-protein (PP complexes and protein-ligand (PL complexes with known three-dimensional structures for which (1 one protein from the PP complex shares at least 40% sequence identity with the protein from the PL complex, and (2 the interface regions of these proteins overlap at least partially with each other. We found that those residues of the interfaces that may bind the other protein as well as the small molecule are evolutionary more conserved on average, have a higher tendency of being located in pockets and expose a smaller fraction of their surface area to the solvent than the remaining protein-protein interface region. Based on these findings we derived a statistical classifier that predicts patches at binding interfaces that have a higher tendency to bind small molecules. We applied this new prediction method to more than 10,000 interfaces from the protein data bank. For several complexes related to apoptosis the predicted binding patches were in direct contact to co-crystallized small molecules.

  5. Interaction between plate make and protein in protein crystallisation screening.

    Directory of Open Access Journals (Sweden)

    Gordon J King

    Full Text Available BACKGROUND: Protein crystallisation screening involves the parallel testing of large numbers of candidate conditions with the aim of identifying conditions suitable as a starting point for the production of diffraction quality crystals. Generally, condition screening is performed in 96-well plates. While previous studies have examined the effects of protein construct, protein purity, or crystallisation condition ingredients on protein crystallisation, few have examined the effect of the crystallisation plate. METHODOLOGY/PRINCIPAL FINDINGS: We performed a statistically rigorous examination of protein crystallisation, and evaluated interactions between crystallisation success and plate row/column, different plates of same make, different plate makes and different proteins. From our analysis of protein crystallisation, we found a significant interaction between plate make and the specific protein being crystallised. CONCLUSIONS/SIGNIFICANCE: Protein crystal structure determination is the principal method for determining protein structure but is limited by the need to produce crystals of the protein under study. Many important proteins are difficult to crystallize, so that identification of factors that assist crystallisation could open up the structure determination of these more challenging targets. Our findings suggest that protein crystallisation success may be improved by matching a protein with its optimal plate make.

  6. An evaluation of in vitro protein-protein interaction techniques: assessing contaminating background proteins.

    Science.gov (United States)

    Howell, Jenika M; Winstone, Tara L; Coorssen, Jens R; Turner, Raymond J

    2006-04-01

    Determination of protein-protein interactions is an important component in assigning function and discerning the biological relevance of proteins within a broader cellular context. In vitro protein-protein interaction methodologies, including affinity chromatography, coimmunoprecipitation, and newer approaches such as protein chip arrays, hold much promise in the detection of protein interactions, particularly in well-characterized organisms with sequenced genomes. However, each of these approaches attracts certain background proteins that can thwart detection and identification of true interactors. In addition, recombinant proteins expressed in Escherichia coli are also extensively used to assess protein-protein interactions, and background proteins in these isolates can thus contaminate interaction studies. Rigorous validation of a true interaction thus requires not only that an interaction be found by alternate techniques, but more importantly that researchers be aware of and control for matrix/support dependence. Here, we evaluate these methods for proteins interacting with DmsD (an E. coli redox enzyme maturation protein chaperone), in vitro, using E. coli subcellular fractions as prey sources. We compare and contrast the various in vitro interaction methods to identify some of the background proteins and protein profiles that are inherent to each of the methods in an E. coli system.

  7. Exploring NMR ensembles of calcium binding proteins: Perspectives to design inhibitors of protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Craescu Constantin T

    2011-05-01

    Full Text Available Abstract Background Disrupting protein-protein interactions by small organic molecules is nowadays a promising strategy employed to block protein targets involved in different pathologies. However, structural changes occurring at the binding interfaces make difficult drug discovery processes using structure-based drug design/virtual screening approaches. Here we focused on two homologous calcium binding proteins, calmodulin and human centrin 2, involved in different cellular functions via protein-protein interactions, and known to undergo important conformational changes upon ligand binding. Results In order to find suitable protein conformations of calmodulin and centrin for further structure-based drug design/virtual screening, we performed in silico structural/energetic analysis and molecular docking of terphenyl (a mimicking alpha-helical molecule known to inhibit protein-protein interactions of calmodulin into X-ray and NMR ensembles of calmodulin and centrin. We employed several scoring methods in order to find the best protein conformations. Our results show that docking on NMR structures of calmodulin and centrin can be very helpful to take into account conformational changes occurring at protein-protein interfaces. Conclusions NMR structures of protein-protein complexes nowadays available could efficiently be exploited for further structure-based drug design/virtual screening processes employed to design small molecule inhibitors of protein-protein interactions.

  8. Bayesian Estimator of Protein-Protein Association Probabilities

    Energy Technology Data Exchange (ETDEWEB)

    2008-05-28

    The Bayesian Estimator of Protein-Protein Association Probabilities (BEPro3) is a software tool for estimating probabilities of protein-protein association between bait and prey protein pairs using data from multiple-bait, multiple-replicate, protein LC-MS/MS affinity isolation experiments. BEPro3 is public domain software, has been tested on Windows XP and version 10.4 or newer of the Mac OS 10.4, and is freely available. A user guide, example dataset with analysis and additional documentation are included with the BEPro3 download.

  9. High quality protein microarray using in situ protein purification

    Directory of Open Access Journals (Sweden)

    Fleischmann Robert D

    2009-08-01

    Full Text Available Abstract Background In the postgenomic era, high throughput protein expression and protein microarray technologies have progressed markedly permitting screening of therapeutic reagents and discovery of novel protein functions. Hexa-histidine is one of the most commonly used fusion tags for protein expression due to its small size and convenient purification via immobilized metal ion affinity chromatography (IMAC. This purification process has been adapted to the protein microarray format, but the quality of in situ His-tagged protein purification on slides has not been systematically evaluated. We established methods to determine the level of purification of such proteins on metal chelate-modified slide surfaces. Optimized in situ purification of His-tagged recombinant proteins has the potential to become the new gold standard for cost-effective generation of high-quality and high-density protein microarrays. Results Two slide surfaces were examined, chelated Cu2+ slides suspended on a polyethylene glycol (PEG coating and chelated Ni2+ slides immobilized on a support without PEG coating. Using PEG-coated chelated Cu2+ slides, consistently higher purities of recombinant proteins were measured. An optimized wash buffer (PBST composed of 10 mM phosphate buffer, 2.7 mM KCl, 140 mM NaCl and 0.05% Tween 20, pH 7.4, further improved protein purity levels. Using Escherichia coli cell lysates expressing 90 recombinant Streptococcus pneumoniae proteins, 73 proteins were successfully immobilized, and 66 proteins were in situ purified with greater than 90% purity. We identified several antigens among the in situ-purified proteins via assays with anti-S. pneumoniae rabbit antibodies and a human patient antiserum, as a demonstration project of large scale microarray-based immunoproteomics profiling. The methodology is compatible with higher throughput formats of in vivo protein expression, eliminates the need for resin-based purification and circumvents

  10. Metabolism of minor isoforms of prion proteins: Cytosolic prion protein and transmembrane prion protein

    OpenAIRE

    Song, Zhiqi; Zhao, Deming; Yang, Lifeng

    2013-01-01

    Transmissible spongiform encephalopathy or prion disease is triggered by the conversion from cellular prion protein to pathogenic prion protein. Growing evidence has concentrated on prion protein configuration changes and their correlation with prion disease transmissibility and pathogenicity. In vivo and in vitro studies have shown that several cytosolic forms of prion protein with specific topological structure can destroy intracellular stability and contribute to prion protein pathogenicit...

  11. Dairy Proteins and Energy Balance

    DEFF Research Database (Denmark)

    Bendtsen, Line Quist

    High protein diets affect energy balance beneficially through decreased hunger, enhanced satiety and increased energy expenditure. Dairy products are a major source of protein. Dairy proteins are comprised of two classes, casein (80%) and whey proteins (20%), which are both of high quality......, but casein is absorbed slowly and whey is absorbed rapidly. The present PhD study investigated the effects of total dairy proteins, whey, and casein, on energy balance and the mechanisms behind any differences in the effects of the specific proteins. The results do not support the hypothesis that dairy...... proteins, whey or casein are more beneficial than other protein sources in the regulation of energy balance, and suggest that dairy proteins, whey or casein seem to play only a minor role, if any, in the prevention and treatment of obesity....

  12. The quality of microparticulated protein.

    Science.gov (United States)

    Erdman, J W

    1990-08-01

    The purpose of this paper is to describe the effects of microparticulation upon the quality of microparticulated protein products and to confirm that microparticulation does not result in changes in protein structure or quality different from those that occur with cooking. Two products were tested: microparticulated egg white and skim milk proteins and microparticulated whey protein concentrate. Three approaches were used to monitor for changes in amino acid and protein value: amino acid analysis, protein efficiency ratio (PER) bioassay, and both one- and two-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis. Evaluation of the results of these tests indicates that no significant differences were found when comparing the premix before and after microparticulation. Significant differences also did not occur when the premix was cooked using conventional methods. Collectively, the data provide strong evidence that the protein microparticulation process used to prepare microparticulated protein products (e.g., Simplesse) does not alter the quality or nutritional value of protein in the final products.

  13. Coevolution study of mitochondria respiratory chain proteins:Toward the understanding of protein-protein interaction

    Institute of Scientific and Technical Information of China (English)

    Ming Yang; Yan Ge; Jiayan Wu; Jingfa Xiao; Jun Yu

    2011-01-01

    Coevolution can be seen as the interdependency between evolutionary histories. In the context of protein evolution, functional correlation proteins are ever-present coordinated evolutionary characters without disruption of organismal integrity. As to complex system, there are two forms of protein-protein interactions in vivo, which refer to inter-complex interaction and intra-complex interaction. In this paper, we studied the difference of coevolution characters between inter-complex interaction and intra-complex interaction using "Mirror tree" method on the respiratory chain (RC) proteins. We divided the correlation coefficients of every pairwise RC proteins into two groups corresponding to the binary protein-protein interaction in intra-complex and the binary protein-protein interaction in inter-complex, respectively. A dramatical discrepancy is detected between the coevolution characters of the two sets of protein interactions (Wilcoxon test, p-value = 4.4 x 10-6). Our finding reveals some critical information on coevolutionary study and assists the mechanical investigation of protein-protein interaction.Furthermore, the results also provide some unique clue for supramolecular organization of protein complexes in the mitochondrial inner membrane. More detailed binding sites map and genome information of nuclear encoded RC proteins will be extraordinary valuable for the further mitochondria dynamics study.

  14. Mapping the human protein interactome

    Institute of Scientific and Technical Information of China (English)

    Daniel Figeys

    2008-01-01

    Interactions are the essence of all biomolecules because they cannot fulfill their roles without interacting with other molecules. Hence, mapping the interactions of biomolecules can be useful for understanding their roles and functions. Furthermore, the development of molecular based systems biology requires an understanding of the biomolecular interactions. In recent years, the mapping of protein-protein interactions in different species has been reported, but few reports have focused on the large-scale mapping of protein-protein interactions in human. Here, we review the developments in protein interaction mapping and we discuss issues and strategies for the mapping of the human protein interactome.

  15. Hydrogels Constructed from Engineered Proteins.

    Science.gov (United States)

    Li, Hongbin; Kong, Na; Laver, Bryce; Liu, Junqiu

    2016-02-24

    Due to their various potential biomedical applications, hydrogels based on engineered proteins have attracted considerable interest. Benefitting from significant progress in recombinant DNA technology and protein engineering/design techniques, the field of protein hydrogels has made amazing progress. The latest progress of hydrogels constructed from engineered recombinant proteins are presented, mainly focused on biorecognition-driven physical hydrogels as well as chemically crosslinked hydrogels. The various bio-recognition based physical crosslinking strategies are discussed, as well as chemical crosslinking chemistries used to engineer protein hydrogels, and protein hydrogels' various biomedical applications. The future perspectives of this fast evolving field of biomaterials are also discussed.

  16. Competitive Protein Adsorption - Multilayer Adsorption and Surface Induced Protein Aggregation

    DEFF Research Database (Denmark)

    Holmberg, Maria; Hou, Xiaolin

    2009-01-01

    In this study, competitive adsorption of albumin and IgG (immunoglobulin G) from human serum solutions and protein mixtures onto polymer surfaces is studied by means of radioactive labeling. By using two different radiolabels (125I and 131I), albumin and IgG adsorption to polymer surfaces...... is monitored simultaneously and the influence from the presence of other human serum proteins on albumin and IgG adsorption, as well as their mutual influence during adsorption processes, is investigated. Exploring protein adsorption by combining analysis of competitive adsorption from complex solutions...... of high concentration with investigation of single protein adsorption and interdependent adsorption between two specific proteins enables us to map protein adsorption sequences during competitive protein adsorption. Our study shows that proteins can adsorb in a multilayer fashion onto the polymer surfaces...

  17. Inferring protein-protein interaction complexes from immunoprecipitation data

    NARCIS (Netherlands)

    Kutzera, J.; Hoefsloot, H.C.J.; Malovannaya, A.; Smit, A.B.; Van Mechelen, I.; Smilde, A.K.

    2013-01-01

    BACKGROUND: Protein inverted question markprotein interactions in cells are widely explored using small inverted question markscale experiments. However, the search for protein complexes and their interactions in data from high throughput experiments such as immunoprecipitation is still a challenge.

  18. Cow's Milk Protein Allergy.

    Science.gov (United States)

    Mousan, Grace; Kamat, Deepak

    2016-10-01

    Cow's milk protein allergy (CMPA) is a common condition encountered in children with incidence estimated as 2% to 7.5% in the first year of life. Formula and breast-fed babies can present with symptoms of CMPA. It is important to accurately diagnose CMPA to avoid the consequences of either under- or overdiagnosis. CMPA is classically categorized into immunoglobulin E (IgE)- or non-IgE-mediated reaction that vary in clinical manifestations, diagnostic evaluation, and prognosis. The most commonly involved systems in patients with CMPA are gastrointestinal, skin, and respiratory. Evaluation of CMPA starts with good data gathering followed by testing if indicated. Treatment is simply by avoidance of cow's milk protein (CMP) in the child's or mother's diet, if exclusively breast-feeding. This article reviews the definition, epidemiology, risk factors, pathogenesis, clinical presentation, evaluation, management, and prognosis of CMPA and provides an overview of different options for formulas and their indication in the treatment of CMPA.

  19. Water-transporting proteins

    DEFF Research Database (Denmark)

    Zeuthen, Thomas

    2010-01-01

    . 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......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...... 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...

  20. Protein Functionalized Nanodiamond Arrays

    Directory of Open Access Journals (Sweden)

    Liu YL

    2010-01-01

    Full Text Available Abstract Various nanoscale elements are currently being explored for bio-applications, such as in bio-images, bio-detection, and bio-sensors. Among them, nanodiamonds possess remarkable features such as low bio-cytotoxicity, good optical property in fluorescent and Raman spectra, and good photostability for bio-applications. In this work, we devise techniques to position functionalized nanodiamonds on self-assembled monolayer (SAMs arrays adsorbed on silicon and ITO substrates surface using electron beam lithography techniques. The nanodiamond arrays were functionalized with lysozyme to target a certain biomolecule or protein specifically. The optical properties of the nanodiamond-protein complex arrays were characterized by a high throughput confocal microscope. The synthesized nanodiamond-lysozyme complex arrays were found to still retain their functionality in interacting with E. coli.

  1. Neurocognitive derivation of protein surface property from protein aggregate parameters

    OpenAIRE

    Mishra, Hrishikesh; Lahiri, Tapobrata

    2011-01-01

    Current work targeted to predicate parametric relationship between aggregate and individual property of a protein. In this approach, we considered individual property of a protein as its Surface Roughness Index (SRI) which was shown to have potential to classify SCOP protein families. The bulk property was however considered as Intensity Level based Multi-fractal Dimension (ILMFD) of ordinary microscopic images of heat denatured protein aggregates which was known to have potential to serve as...

  2. Purine inhibitors of protein kinases, G proteins and polymerases

    Energy Technology Data Exchange (ETDEWEB)

    Gray, Nathanael S.; Schultz, Peter; Kim, Sung-Hou; Meijer, Laurent

    2004-10-12

    The present invention relates to 2-N-substituted 6-(4-methoxybenzylamino)-9-isopropylpurines that inhibit, inter alia, protein kinases, G-proteins and polymerases. In addition, the present invention relates to methods of using such 2-N-substituted 6-(4-methoxybenzylamino)-9-isopropylpurines to inhibit protein kinases, G-proteins, polymerases and other cellular processes and to treat cellular proliferative diseases.

  3. Protein-protein fusion catalyzed by sortase A.

    Science.gov (United States)

    Levary, David A; Parthasarathy, Ranganath; Boder, Eric T; Ackerman, Margaret E

    2011-04-06

    Chimeric proteins boast widespread use in areas ranging from cell biology to drug delivery. Post-translational protein fusion using the bacterial transpeptidase sortase A provides an attractive alternative when traditional gene fusion fails. We describe use of this enzyme for in vitro protein ligation and report the successful fusion of 10 pairs of protein domains with preserved functionality--demonstrating the robust and facile nature of this reaction.

  4. Protein-protein fusion catalyzed by sortase A.

    Directory of Open Access Journals (Sweden)

    David A Levary

    Full Text Available Chimeric proteins boast widespread use in areas ranging from cell biology to drug delivery. Post-translational protein fusion using the bacterial transpeptidase sortase A provides an attractive alternative when traditional gene fusion fails. We describe use of this enzyme for in vitro protein ligation and report the successful fusion of 10 pairs of protein domains with preserved functionality--demonstrating the robust and facile nature of this reaction.

  5. Quality protein maize: QPM

    Directory of Open Access Journals (Sweden)

    Ignjatović-Micić Dragana

    2008-01-01

    Full Text Available Quality protein maize (QPM contains the opaque-2 gene along with numerous modifiers for kernel hardness. Therefore, QPM is maize with high nutritive value of endosperm protein, with substantially higher content of two essential amino acids - lysine and tryptophan, and with good agronomical performances. Although QPM was developed primarily for utilization in the regions where, because of poverty, maize is the main staple food, it has many advantages for production and consumption in other parts of the world, too. QPM can be used for production of conventional and new animal feed, as well as for human nurture. As the rate of animal weight gain is doubled with QPM and portion viability is better, a part of normal maize production could be available for other purposes, such as, for example, ethanol production. Thus, breeding QPM is set as a challenge to produce high quality protein maize with high yield and other important agronomical traits, especially with today's food and feed demands and significance of energy crisis.

  6. Process for protein PEGylation.

    Science.gov (United States)

    Pfister, David; Morbidelli, Massimo

    2014-04-28

    PEGylation is a versatile drug delivery technique that presents a particularly wide range of conjugation chemistry and polymer structure. The conjugated protein can be tuned to specifically meet the needs of the desired application. In the area of drug delivery this typically means to increase the persistency in the human body without affecting the activity profile of the original protein. On the other hand, because of the high costs associated with the production of therapeutic proteins, subsequent operations imposed by PEGylation must be optimized to minimize the costs inherent to the additional steps. The closest attention has to be given to the PEGylation reaction engineering and to the subsequent purification processes. This review article focuses on these two aspects and critically reviews the current state of the art with a clear focus on the development of industrial scale processes which can meet the market requirements in terms of quality and costs. The possibility of using continuous processes, with integration between the reaction and the separation steps is also illustrated.

  7. Hydrolyzed Proteins in Allergy.

    Science.gov (United States)

    Salvatore, Silvia; Vandenplas, Yvan

    2016-01-01

    Hydrolyzed proteins are used worldwide in the therapeutic management of infants with allergic manifestations and have long been proposed as a dietetic measure to prevent allergy in at risk infants. The degree and method of hydrolysis, protein source and non-nitrogen components characterize different hydrolyzed formulas (HFs) and may determine clinical efficacy, tolerance and nutritional effects. Cow's milk (CM)-based HFs are classified as extensively (eHF) or partially HF (pHF) based on the percentage of small peptides. One whey pHF has been shown to reduce atopic dermatitis in high-risk infants who are not exclusively breastfed. More studies are needed to determine the benefit of these formulas in the prevention of CM allergy (CMA) and in the general population. eHFs represent up to now the treatment of choice for most infants with CMA. However, new developments, such as an extensively hydrolyzed rice protein-based formula, could become alternative options if safety and nutritional and therapeutic efficacy are confirmed as this type of formula is less expensive. In some countries, an extensive soy hydrolysate is available.

  8. Neutron protein crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Niimura, Nobuo [Japan Atomic Energy Research Inst., Tokai, Ibaraki (Japan). Tokai Research Establishment

    1998-10-01

    X-ray diffraction of single crystal has enriched the knowledge of various biological molecules such as proteins, DNA, t-RNA, viruses, etc. It is difficult to make structural analysis of hydrogen atoms in a protein using X-ray crystallography, whereas neutron diffraction seems usable to directly determine the location of those hydrogen atoms. Here, neutron diffraction method was applied to structural analysis of hen egg-white lysozyme. Since the crystal size of a protein to analyze is generally small (5 mm{sup 3} at most), the neutron beam at the sample position in monochromator system was set to less than 5 x 5 mm{sup 2} and beam divergence to 0.4 degree or less. Neutron imaging plate with {sup 6}Li or Gd mixed with photostimulated luminescence material was used and about 2500 Bragg reflections were recorded in one crystal setting. A total of 38278 reflections for 2.0 A resolution were collected in less than 10 days. Thus, stereo views of Trp-111 omit map around the indol ring of Trp-111 was presented and the three-dimensional arrangement of 696H and 264D atoms in the lysozyme molecules was determined using the omit map. (M.N.)

  9. A Bayesian Framework for Combining Protein and Network Topology Information for Predicting Protein-Protein Interactions.

    Science.gov (United States)

    Birlutiu, Adriana; d'Alché-Buc, Florence; Heskes, Tom

    2015-01-01

    Computational methods for predicting protein-protein interactions are important tools that can complement high-throughput technologies and guide biologists in designing new laboratory experiments. The proteins and the interactions between them can be described by a network which is characterized by several topological properties. Information about proteins and interactions between them, in combination with knowledge about topological properties of the network, can be used for developing computational methods that can accurately predict unknown protein-protein interactions. This paper presents a supervised learning framework based on Bayesian inference for combining two types of information: i) network topology information, and ii) information related to proteins and the interactions between them. The motivation of our model is that by combining these two types of information one can achieve a better accuracy in predicting protein-protein interactions, than by using models constructed from these two types of information independently.

  10. Metabolism of minor isoforms of prion proteins Cytosolic prion protein and transmembrane prion protein*

    Institute of Scientific and Technical Information of China (English)

    Zhiqi Song; Deming Zhao; Lifeng Yang

    2013-01-01

    Transmissible spongiform encephalopathy or prion disease is triggered by the conversion from cellular prion protein to pathogenic prion protein. Growing evidence has concentrated on prion protein configuration changes and their correlation with prion disease transmissibility and pathoge-nicity. In vivo and in vitro studies have shown that several cytosolic forms of prion protein with spe-cific topological structure can destroy intracellular stability and contribute to prion protein pathoge-nicity. In this study, the latest molecular chaperone system associated with endoplasmic reticu-lum-associated protein degradation, the endoplasmic reticulum resident protein quality-control system and the ubiquitination proteasome system, is outlined. The molecular chaperone system directly correlates with the prion protein degradation pathway. Understanding the molecular me-chanisms wil help provide a fascinating avenue for further investigations on prion disease treatment and prion protein-induced neurodegenerative diseases.

  11. Predicting disease-related proteins based on clique backbone in protein-protein interaction network.

    Science.gov (United States)

    Yang, Lei; Zhao, Xudong; Tang, Xianglong

    2014-01-01

    Network biology integrates different kinds of data, including physical or functional networks and disease gene sets, to interpret human disease. A clique (maximal complete subgraph) in a protein-protein interaction network is a topological module and possesses inherently biological significance. A disease-related clique possibly associates with complex diseases. Fully identifying disease components in a clique is conductive to uncovering disease mechanisms. This paper proposes an approach of predicting disease proteins based on cliques in a protein-protein interaction network. To tolerate false positive and negative interactions in protein networks, extending cliques and scoring predicted disease proteins with gene ontology terms are introduced to the clique-based method. Precisions of predicted disease proteins are verified by disease phenotypes and steadily keep to more than 95%. The predicted disease proteins associated with cliques can partly complement mapping between genotype and phenotype, and provide clues for understanding the pathogenesis of serious diseases.

  12. 中美股市的联动性分析--基于沪深300与道琼斯工业平均指数的实证研究%Analysis of the Co-Movement between China’s and U.S.Stock Markets:Based on the CSI 3 0 0 and the Dow Jones Industrial Average Index

    Institute of Scientific and Technical Information of China (English)

    罗雪玲

    2014-01-01

    随着世界经济一体化的推进和金融全球化的发展,国际资本市场间的联系愈发紧密,而研究最具成熟资本市场标志的美国股市与作为新兴市场代表的中国股市之间的联动关系具有重大意义。可以沪深300股指和道琼斯工业平均指数作为考察对象,利用协整检验考察中美两国股市的长期均衡关系,并运用Granger因果关系检验和DCC-GARCH 模型分析两股市在短期的收益均值和波动率溢出效应,进一步地,再用分位数回归分析研究极端情形下的股市联动性。研究结果表明,中美股市不存在长期均衡关系;在短期,美国股市对中国股市存在显著的均值溢出和波动溢出,且在极端情形下影响更为显著。%With the development of world economic integration and financial globalization,the relationship between the international capital markets are more and more closely.So the research on the Co-movement between China’s and U.S.stock markets,which as a representative of the mature market and the emerging market respectively,is of great significance.Based on the CSI 300 and the Dow Jones industrial average index,the paper uses the co-integration test to examine long-term equilibrium relationship between two markets,and uses the Granger causality test and DCC-GARCH model to analyze the mean and volatility spillover effects of the stock markets in the short term.Further,by using the quantile regression to research the stock markets’co-movement on extreme circumstances.The empirical results indicate that there is no long-term equilibrium relationship between stock market of China and the U.S.,while in the short term,there is significant mean spillover and volatility spillover from U.S.to China’s stock market ,and the effect is stronger on extreme circumstances.

  13. Protein engineering techniques gateways to synthetic protein universe

    CERN Document Server

    Poluri, Krishna Mohan

    2017-01-01

    This brief provides a broad overview of protein-engineering research, offering a glimpse of the most common experimental methods. It also presents various computational programs with applications that are widely used in directed evolution, computational and de novo protein design. Further, it sheds light on the advantages and pitfalls of existing methodologies and future perspectives of protein engineering techniques.

  14. Ontology integration to identify protein complex in protein interaction networks

    Directory of Open Access Journals (Sweden)

    Yang Zhihao

    2011-10-01

    Full Text Available Abstract Background Protein complexes can be identified from the protein interaction networks derived from experimental data sets. However, these analyses are challenging because of the presence of unreliable interactions and the complex connectivity of the network. The integration of protein-protein interactions with the data from other sources can be leveraged for improving the effectiveness of protein complexes detection algorithms. Methods We have developed novel semantic similarity method, which use Gene Ontology (GO annotations to measure the reliability of protein-protein interactions. The protein interaction networks can be converted into a weighted graph representation by assigning the reliability values to each interaction as a weight. Following the approach of that of the previously proposed clustering algorithm IPCA which expands clusters starting from seeded vertices, we present a clustering algorithm OIIP based on the new weighted Protein-Protein interaction networks for identifying protein complexes. Results The algorithm OIIP is applied to the protein interaction network of Sacchromyces cerevisiae and identifies many well known complexes. Experimental results show that the algorithm OIIP has higher F-measure and accuracy compared to other competing approaches.

  15. Buffers more than buffering agent: introducing a new class of stabilizers for the protein BSA.

    Science.gov (United States)

    Gupta, Bhupender S; Taha, Mohamed; Lee, Ming-Jer

    2015-01-14

    In this study, we have analyzed the influence of four biological buffers on the thermal stability of bovine serum albumin (BSA) using dynamic light scattering (DLS). The investigated buffers include 4-(2-hydroxyethyl)piperazine-1-ethanesulfonic acid (HEPES), 4-(2-hydroxyethyl)-1-piperazine-propanesulfonic acid (EPPS), 4-(2-hydroxyethyl)piperazine-1-ethanesulfonic acid sodium salt (HEPES-Na), and 4-morpholinepropanesulfonic acid sodium salt (MOPS-Na). These buffers behave as a potential stabilizer for the native structure of BSA against thermal denaturation. The stabilization tendency follows the order of MOPS-Na > HEPES-Na > HEPES ≫ EPPS. To obtain an insight into the role of hydration layers and peptide backbone in the stabilization of BSA by these buffers, we have also explored the phase transition of a thermoresponsive polymer, poly(N-isopropylacrylamide (PNIPAM)), a model compound for protein, in aqueous solutions of HEPES, EPPS, HEPES-Na, and MOPS-Na buffers at different concentrations. It was found that the lower critical solution temperatures (LCST) of PNIPAM in the aqueous buffer solutions substantially decrease with increase in buffer concentration. The mechanism of interactions between these buffers and protein BSA was probed by various techniques, including UV-visible, fluorescence, and FTIR. The results of this series of studies reveal that the interactions are mainly governed by the influence of the buffers on the hydration layers surrounding the protein. We have also explored the possible binding sites of BSA with these buffers using a molecular docking technique. Moreover, the activities of an industrially important enzyme α-chymotrypsin (α-CT) in 0.05 M, 0.5 M, and 1.0 M of HEPES, EPPS, HEPES-Na, and MOPS-Na buffer solutions were analyzed at pH = 8.0 and T = 25 °C. Interestingly, the activities of α-CT were found to be enhanced in the aqueous solutions of these investigated buffers. Based upon the Jones-Dole viscosity parameters, the

  16. Multiscale modeling of proteins.

    Science.gov (United States)

    Tozzini, Valentina

    2010-02-16

    The activity within a living cell is based on a complex network of interactions among biomolecules, exchanging information and energy through biochemical processes. These events occur on different scales, from the nano- to the macroscale, spanning about 10 orders of magnitude in the space domain and 15 orders of magnitude in the time domain. Consequently, many different modeling techniques, each proper for a particular time or space scale, are commonly used. In addition, a single process often spans more than a single time or space scale. Thus, the necessity arises for combining the modeling techniques in multiscale approaches. In this Account, I first review the different modeling methods for bio-systems, from quantum mechanics to the coarse-grained and continuum-like descriptions, passing through the atomistic force field simulations. Special attention is devoted to their combination in different possible multiscale approaches and to the questions and problems related to their coherent matching in the space and time domains. These aspects are often considered secondary, but in fact, they have primary relevance when the aim is the coherent and complete description of bioprocesses. Subsequently, applications are illustrated by means of two paradigmatic examples: (i) the green fluorescent protein (GFP) family and (ii) the proteins involved in the human immunodeficiency virus (HIV) replication cycle. The GFPs are currently one of the most frequently used markers for monitoring protein trafficking within living cells; nanobiotechnology and cell biology strongly rely on their use in fluorescence microscopy techniques. A detailed knowledge of the actions of the virus-specific enzymes of HIV (specifically HIV protease and integrase) is necessary to study novel therapeutic strategies against this disease. Thus, the insight accumulated over years of intense study is an excellent framework for this Account. The foremost relevance of these two biomolecular systems was

  17. Chemical Protein Modification through Cysteine.

    Science.gov (United States)

    Gunnoo, Smita B; Madder, Annemieke

    2016-04-01

    The modification of proteins with non-protein entities is important for a wealth of applications, and methods for chemically modifying proteins attract considerable attention. Generally, modification is desired at a single site to maintain homogeneity and to minimise loss of function. Though protein modification can be achieved by targeting some natural amino acid side chains, this often leads to ill-defined and randomly modified proteins. Amongst the natural amino acids, cysteine combines advantageous properties contributing to its suitability for site-selective modification, including a unique nucleophilicity, and a low natural abundance--both allowing chemo- and regioselectivity. Native cysteine residues can be targeted, or Cys can be introduced at a desired site in a protein by means of reliable genetic engineering techniques. This review on chemical protein modification through cysteine should appeal to those interested in modifying proteins for a range of applications.

  18. Protein Linked to Atopic Dermatitis

    Science.gov (United States)

    ... Research Matters NIH Research Matters January 14, 2013 Protein Linked to Atopic Dermatitis Normal skin from a ... in mice suggests that lack of a certain protein may trigger atopic dermatitis, the most common type ...

  19. Protein: MPA1 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available feron stimulator, Mediator of IRF3 activation, Stimulator of interferon genes protein 9606 Homo sapiens Q86WV6 340061 ... ...MPA1 TLR signaling molecules TMEM173 ERIS, MITA, STING Transmembrane protein 173 Endoplasmic reticulum inter

  20. Protein: FBA3 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FBA3 Atg1 kinase complex TOR1 DRR1 Serine/threonine-protein kinase TOR1 Dominant rapamycin... resistance protein 1, Phosphatidylinositol kinase homolog TOR1, Target of rapamycin kinase 1 559292