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Sample records for bence jones proteins

  1. 21 CFR 866.5150 - Bence-Jones proteins immunological test system.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Bence-Jones proteins immunological test system....5150 Bence-Jones proteins immunological test system. (a) Identification. A Bence-Jones proteins... the Bence-Jones proteins in urine and plasma. Immunoglobulin molecules normally consist of pairs of...

  2. 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

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

    Directory of Open Access Journals (Sweden)

    M.J.B.A. Prado

    1997-07-01

    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

  4. Differential denaturation of a crystalline Bence-Jones type cryoprotein as monitored by fluorescence.

    Science.gov (United States)

    Finazzi Agrò, A; Crifò, C; Natali, P G; Chersi, A

    1978-01-01

    1) A Bence-Jones type protein (Cryo-Ver) showing the cold precipitation phenomenon has an extremely low intrinsic fluorescence when excited at 280-295 nm. 2) This fluorescence increases considerably upon denaturation of the molecule by heat or guanidine hydrochloride. Guanidine is about twice as effective as heat in terms of fluorescence yield. 3) The heat-denatured protein is still reactive with anti-cryoVer antibodies, at variance with the guanidine-treated samples. 4) Since the protein contains two tryptophans per mole, one in the constant portion of the molecule, the other in the variable region, it is proposed that heat treatment affects only the variable region, which seems involved in the cryoprecipitation phenomenon.

  5. Structure of a second crystal form of Bence-Jones protein Loc: Strikingly different domain associations in two crystal forms of a single protein

    International Nuclear Information System (INIS)

    Schiffer, M.; Ainsworth, C.; Xu, Z.B.; Carperos, W.; Olsen, K.; Solomon, A.; Stevens, F.J.; Chang, C.H.

    1989-01-01

    The authors have determined the structure of the immunoglobulin light-chain dimer Loc in a second crystal form that was grown from distilled water. The crystal structure was determined to 2.8-angstrom resolution; the R factor is 0.22. The two variable domains are related by local 2-fold axes and form an antigen binding pocket. The variable domain-variable domain interaction observed in this crystal form differs from the one exhibited by the protein when crystallized from ammonium sulfate in which the two variable domains formed a protrusion. The structure attained in the distilled water crystals is similar to, but not identical with, the one observed for the Mcg light-chain dimer in crystals grown from ammonium sulfate. Thus, two strikingly different structures were attained by this multisubunit protein in crystals grown under two different, commonly used, crystallization techniques. The quaternary interactions exhibited by the protein in the two crystal forms are sufficiently different to suggest fundamentally different interpretations of the structural basis for the function of this protein. This observation may have general implications regarding the use of single crystallographic determinations for detailed identification of structural and functional relationships. On the other hand, proteins whose structures can be altered by manipulation of crystallization conditions may provide useful systems for study of fundamental structural chemistry

  6. Comparison of the three-dimensional structures of a human Bence-Jones dimer crystallized on Earth and aboard US Space Shuttle Mission STS-95.

    Science.gov (United States)

    Terzyan, Simon S; Bourne, Christina R; Ramsland, Paul A; Bourne, Philip C; Edmundson, Allen B

    2003-01-01

    Crystals of a human (Sea) Bence-Jones dimer were produced in a capillary by vapor diffusion under microgravity conditions in the 9 day US Space Shuttle Mission STS-95. In comparison to ground-based experiments, nucleation was facile and spontaneous in space. Appearance of a very large (8 x 1.6 x 1.0 mm) crystal in a short time period is a strong endorsement for the use of microgravity to produce crystals sufficiently large for neutron diffraction studies. The Sea dimer crystallized in the orthorhombic space group P2(1)2(1)2(1), with a = 48.9 A, b = 85.2 A, and c = 114.0 A. The crystals grown in microgravity exhibited significantly lower mosaicities than those of ground-based crystals and the X-ray diffraction data had a lower overall B factor. Three-dimensional structures determined by X-ray analysis at two temperatures (100 and 293 K) were indistinguishable from those obtained from ground-based crystals. However, both the crystallographic R factor and the free R factor were slightly lower in the models derived from crystals produced in microgravity. The major difference between the two crystal growth systems is a lack of convection and sedimentation in a microgravity environment. This environment resulted in the growth of much larger, higher-quality crystals of the Sea Bence-Jones protein. Structurally, heretofore unrecognized grooves on the external surfaces of the Sea and other immunoglobulin-derived fragments are regular features and may offer supplementary binding regions for super antigens and other elongated ligands in the bloodstream and perivascular tissues. Copyright 2003 John Wiley & Sons, Ltd.

  7. Bence Jones proteinuria in smoldering multiple myeloma as a predictor marker of progression to symptomatic multiple myeloma.

    Science.gov (United States)

    González-Calle, V; Dávila, J; Escalante, F; de Coca, A G; Aguilera, C; López, R; Bárez, A; Alonso, J M; Hernández, R; Hernández, J M; de la Fuente, P; Puig, N; Ocio, E M; Gutiérrez, N C; García-Sanz, R; Mateos, M V

    2016-10-01

    The diagnosis of smoldering multiple myeloma (SMM) includes patients with a heterogeneous risk of progression to active multiple myeloma (MM): some patients will never progress, whereas others will have a high risk of progression within the first 2 years. Therefore, it is important to improve risk assessment at diagnosis. We conducted a retrospective study in a large cohort of SMM patients, in order to investigate the role of Bence Jones (BJ) proteinuria at diagnosis in the progression to active MM. We found that SMM patients presenting with BJ proteinuria had a significantly shorter median time to progression (TTP) to MM compared with patients without BJ proteinuria (22 vs 88 months, respectively; hazard ratio=2.3, 95% confidence interval=1.4-3.9, P=0.002). We also identified risk subgroups based on the amount of BJ proteinuria: ⩾500 mg/24 h, <500 mg/24 h and without it, with a significantly different median TTP (13, 37 and 88 months, P<0.001). Thus, BJ proteinuria at diagnosis is an independent variable of progression to MM that identifies a subgroup of high-risk SMM patients (51% risk of progression at 2 years) and ⩾500 mg of BJ proteinuria may allow, if validated in another series, to reclassify these patients to MM requiring therapy before the end-organ damage development.

  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

    AL-amyloidoses are generally described as a group of disorders in which N-terminal fragments of monoclonal immunoglobulin light chains are transferred into amyloid fibrils. We have, by amino acid sequence analyses and immunological methods, characterized the Bence-Jones protein and the correspond......AL-amyloidoses are generally described as a group of disorders in which N-terminal fragments of monoclonal immunoglobulin light chains are transferred into amyloid fibrils. We have, by amino acid sequence analyses and immunological methods, characterized the Bence-Jones protein...... 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......-Jones protein. Furthermore, both the Bence-Jones protein and the AL protein were glycosylated, with possibly a glycosylation in the constant part of the light chain....

  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......Daniel Jones (1881-1967) played a significant role in the emergence of phonetics as a fully developed academic discipline in the first half of the twentieth century. His views on the subject not only provided the foundations for the British tradition but also had a considerable, and often...... pioneering works, now out of print for many decades, are made easily accessible to scholars once again. Numerous articles encompassing a variety of phonetic/phonological topics, for example, phonemic analysis, juncture, models of pronunciation, and historiography, are also included (converted where necessary...

  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

    We study the propagation of solitons along the hydrogen bonds of an alpha helix. Modeling the hydrogen and peptide bonds with Lennard-Jones potentials, we show that the solitons can appear spontaneously and have long lifetimes. Remarkably, even if no explicit solution is known for the Lennard-Jon...

  11. 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

  12. B Stanly Jones Retnam

    Indian Academy of Sciences (India)

    Volume 33 Issue 5 October 2010 pp 525-528. Effect of nanoparticles on tensile, impact and fatigue properties of fibre reinforced plastics · R Nagalingam S ... Volume 37 Issue 5 August 2014 pp 1059-1064. Effects of fibre orientation on mechanical properties of hybrid bamboo/glass fibre polymer composites · B Stanly Jones ...

  13. 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...

  14. 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

  15. 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

  16. 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,…

  17. STS-98 Crew Interview: Tom Jones

    Science.gov (United States)

    2001-01-01

    The STS-98 Mission Specialist Tom Jones is seen being interviewed. He answers questions about his inspiration to become an astronaut, his career path, and his training. He gives details on the mission's goals and significance, and the payload and hardware it brings to the International Space Station (ISS). Mr. Jones discusses his role in the mission's spacewalks and activities.

  18. Immunonephelometric quantification of specific urinary proteins versus a simple electrophoretic method for characterizing proteinuria.

    Science.gov (United States)

    Wolff, Fleur; Willems, Dominique

    2008-04-01

    The quantification of urinary proteins presenting different molecular sizes is useful in characterizing a proteinuria. We assessed the performance of an electrophoretic system, the Hydragel Urine Profile, which allows firstly the identification of proteinuria and secondly a qualitative detection of monoclonal free light chains (FLC). Initially, the proteinuria was characterized on 127 pathological urines by quantifying albumin, a1microglobulin, immunoglobulins G by immunonephelometric quantification technique and the results were compared with the protein pattern obtained by the electrophoretic method. Secondly, we assessed the sensitivity and specificity of this electrophoretic test for the detection and characterization of Bence Jones proteins. FLC were analyzed quantitatively by an immunonephelometric assay and qualitatively by the electrophoretic test in 150 urines. The agreement between the two methods was good with a percentage of homology for characterizing the proteinuria of 89%. For detecting a monoclonal FLC, the electrophoretic method demonstrated a lesser sensitivity but a higher specificity compared to the immunoassay. The Urine Profile kit is a reliable assay that can be used as a screening test to differentiate the type of proteinuria.

  19. Bacterial Biofilms in Jones Tubes.

    Science.gov (United States)

    Ahn, Eric S; Hauck, Matthew J; Kirk Harris, Jonathan; Robertson, Charles E; Dailey, Roger A

    To investigate the presence and microbiology of bacterial biofilms on Jones tubes (JTs) by direct visualization with scanning electron microscopy and polymerase chain reaction (PCR) of representative JTs, and to correlate these findings with inflammation and/or infection related to the JT. In this study, prospective case series were performed. JTs were recovered from consecutive patients presenting to clinic for routine cleaning or recurrent irritation/infection. Four tubes were processed for scanning electron microscopy alone to visualize evidence of biofilms. Two tubes underwent PCR alone for bacterial quantification. One tube was divided in half and sent for scanning electron microscopy and PCR. Symptoms related to the JTs were recorded at the time of recovery. Seven tubes were obtained. Five underwent SEM, and 3 out of 5 showed evidence of biofilms (60%). Two of the 3 biofilms demonstrated cocci and the third revealed rods. Three tubes underwent PCR. The predominant bacteria identified were Pseudomonadales (39%), Pseudomonas (16%), and Staphylococcus (14%). Three of the 7 patients (43%) reported irritation and discharge at presentation. Two symptomatic patients, whose tubes were imaged only, revealed biofilms. The third symptomatic patient's tube underwent PCR only, showing predominantly Staphylococcus (56%) and Haemophilus (36%) species. Two of the 4 asymptomatic patients also showed biofilms. All symptomatic patients improved rapidly after tube exchange and steroid antibiotic drops. Bacterial biofilms were variably present on JTs, and did not always correlate with patients' symptoms. Nevertheless, routine JT cleaning is recommended to treat and possibly prevent inflammation caused by biofilms.

  20. The Cutoff Level for Urine Protein in Urine Immunofixation Electrophoresis.

    Science.gov (United States)

    Ellidag, Hamit Yasar; Curek, Gulten; Eren, Esin; Aydin, Ozgur; Yilmaz, Necat

    2015-01-01

    Immunofixation electrophoresis (IFE) maintains its importance in diagnosing monoclonal gammopathies. In particular, urine IFE detects free light chains (FLC) in urine samples even at low concentrations and offers higher sensitivity compared to serum electrophoresis and serum IFE. The aim of the present study was to determine the place and significance of quantitative urinary protein measurement before IFE in interpreting the results of subsequent IFE and to determine the most appropriate protein concentrations for the appearance of bands. The records of a total of 600 patients, who underwent screening for Bence Jones proteinuria using IFE on 24-hour urine, were retrospectively reviewed. Urine IFE was performed using Helena SAS-I and SAS-I devices. The total protein concentration in the urine was quantitatively determined by the Pyrogallol red method, and the urine albumin level was determined using the immunoturbidimetric method. These analyses were measured on an Olympus/Beckmann AU5800. The evaluation of IFE results revealed that 311 patients had normal results, 108 patients had monoclonal bands, five patients had biclonal bands, 28 had polyclonal bands, and 148 patients had various degrees of proteinuria. ROC curves were created in order to determine the most appropriate urinary protein and albumin levels to observe bands in IFE. Accordingly, urine baseline protein level (mg/dL) showed the highest AUC value (cutoff value: 19.4 mg/dL, sensitivity: 92%, specificity: 98.2%, AUC: 0.972). The present study showed that quantitative protein measurement before IFE eliminated the disadvantages associated with the IFE method and its interpretation.

  1. Review of "Cultures merging" by Eric Jones

    OpenAIRE

    Schlicht, Ekkehart

    2016-01-01

    This is an electronic reprint of a review of the book "Cultures Merging: A Historical and Economic Critique of Culture" by Eric L. Jones, Princeton: Princeton University Press that appeared in the Journal of Institutional and Theoretical Economics 2007, vol. 163, issue 3, pages 526-529, URL \\url{http://www.jstor.org/stable/40752660}.

  2. 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

    ... SECURITY Coast Guard 33 CFR Part 165 RIN 1625-AA00 Safety Zone; New York Air Show at Jones Beach State Park, Atlantic Ocean off of Jones Beach, Wantagh, NY AGENCY: Coast Guard, DHS. ACTION: Notice of proposed... Air Show at Jones Beach State Park in Wantagh, New York. This proposed safety zone is necessary to...

  3. Reduction U(VI) using jones reductor

    International Nuclear Information System (INIS)

    Simbolon, S.

    1996-01-01

    Reduction of dissolved oxide uranium in sulfuric acid use of reductor Jones Zn (Hg) was carried out. The reduced uranium sulfate solution was analyzed its U(IV) by measuring its absorbance on 652 nm and compared to oxidation U(IV) solution with KMnO 4 solution. It was found that the comparison was in a good agreement. However, measuring of absorbance of U(VI) solution on 429 nm result of oxidation U(IV) with KMnO 4 solution was not change. (author)

  4. Chemical Potential of a Lennard Jones Fluid

    Directory of Open Access Journals (Sweden)

    Celebonovic, V.

    2010-12-01

    Full Text Available The aim of this paper is to present results of analytical calculation of chemical potential of a Lennard Jones (LJ fluid performed in two ways: by using the thermodynamical formalism and the formalism of statistical mechanics. The integration range is divided into two regions. In the small distance region, which is $rleqsigma$ in the usual notation, the integration range had to be cut off in order to avoid the occurence of divergences. In the large distance region, the calculation is technically simpler. The calculation reported here will be useful in all kinds of studies concerning phase equilibrium in a LJ fluid. Interesting kinds of such systems are the giant planets and the icy satellites in various planetary systems, but also the (so far hypothetical quark stars.

  5. Chemical potential of a Lennard Jones fluid

    Directory of Open Access Journals (Sweden)

    Čelebonović V.

    2010-01-01

    Full Text Available The aim of this paper is to present results of analytical calculation of chemical potential of a Lennard Jones (LJ fluid performed in two ways: by using the thermodynamical formalism and the formalism of statistical mechanics. The integration range is divided into two regions. In the small distance region, which is r ≤ σ in the usual notation, the integration range had to be cut off in order to avoid the occurrence of divergences. In the large distance region, the calculation is technically simpler. The calculation reported here will be useful in all kinds of studies concerning phase equilibrium in a LJ fluid. Interesting kinds of such systems are the giant planets and the icy satellites in various planetary systems, but also the (so far hypothetical quark stars.

  6. Plutonium volumetric titration after reduction on a Jones' column

    International Nuclear Information System (INIS)

    Description of a plutonium analysis method, in hydrochloric or sulfuric solution, for plutonium content over 2 mg, by reduction from plutonium IV to plutonium III in a Jones' column. Volumetic titration by ceric sulfate with ferrous orthophenanthroline [fr

  7. 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"

  8. Mapping the magic numbers in binary Lennard-Jones clusters.

    Science.gov (United States)

    Doye, Jonathan P K; Meyer, Lars

    2005-08-05

    Using a global optimization approach that directly searches for the composition of greatest stability, we have been able to find the particularly stable structures for binary Lennard-Jones clusters with up to 100 atoms for a range of Lennard-Jones parameters. In particular, we have shown that just having atoms of different sizes leads to a remarkable stabilization of polytetrahedral structures, including both polyicosahedral clusters and at larger sizes structures with disclination lines.

  9. Jones phase microscopy of transparent and anisotropic samples.

    Science.gov (United States)

    Wang, Zhuo; Millet, Larry J; Gillette, Martha U; Popescu, Gabriel

    2008-06-01

    We developed an interferometric microscopy technique, referred to as Jones phase microscopy, capable of extracting the spatially resolved Jones polarization matrix associated with transparent and anisotropic samples. This is a generalization of quantitative phase imaging, which is recovered from one diagonal element of the measured matrix. The principle of the technique is demonstrated with measurements of a liquid crystal spatial light modulator and the potential for live cell imaging with experiments on live neurons in culture.

  10. 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

  11. Evaluation of the Jones jig appliance for distal molar movement.

    Science.gov (United States)

    Brickman, C D; Sinha, P K; Nanda, R S

    2000-11-01

    The purpose of this study was to determine the effects of the Jones jig appliance on distal movement of maxillary molars and reciprocal effects on premolars and maxillary incisors. Cephalometric radiographs before and after orthodontic treatment of 72 consecutively treated patients, 46 females and 26 males, were measured to define treatment changes attributed to the Jones jig. Comparative measurements were made on a matched sample of 35 patients (20 females and 15 males) treated with cervical headgear by the same clinician. Both series of patients were treated to correct an Angle Class II molar relationship. The molar correction in the Jones jig patients consisted primarily of molar distal movement. Dental, soft tissue, and skeletal changes were evaluated and compared for significant differences between techniques. The results from the Jones jig sample showed the mean maxillary first molar distal movement was 2.51 mm, with distal tipping of 7.53 degrees. The mean reciprocal mesial movement of the maxillary premolar was 2.0 mm, with mesial tipping of 4.76 degrees. The maxillary first molar extruded 0.14 mm; the maxillary premolar extruded 1.88 mm. The maxillary second molars were also moved distally 2.02 mm and tipped distally 7.89 degrees. The longitudinal assessment (initial to completion of orthodontic treatment) showed significant differences between the Jones jig sample and the cervical headgear sample for lower lip to E-line and SNA. The Jones jig sample showed a mean decrease in lower lip to E-line of 0.25 mm versus 1.20 mm (P jig sample versus 1.20 degrees (P jig sample and cervical headgear sample did not show significant differences of the final position in either linear or angular measurements of the maxillary first molars and corresponding premolar-incisor anchor units. The Jones jig appliance demonstrated treatment results comparable with those of the sample treated with cervical headgear. The Jones jig sample demonstrated effective distal molar

  12. 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.

  13. 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...

  14. 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...

  15. 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.

  16. 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.

  17. 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

  18. 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...

  19. Birefringence of Cellotape: Jones Representation and Experimental Analysis

    Science.gov (United States)

    Belendez, Augusto; Fernandez, Elena; Frances, Jorge; Neipp, Cristian

    2010-01-01

    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…

  20. Thermal conductivity of the Lennard-Jones chain fluid model.

    Science.gov (United States)

    Galliero, Guillaume; Boned, Christian

    2009-12-01

    Nonequilibrium molecular dynamics simulations have been performed to estimate, analyze, and correlate the thermal conductivity of a fluid composed of short Lennard-Jones chains (up to 16 segments) over a large range of thermodynamic conditions. It is shown that the dilute gas contribution to the thermal conductivity decreases when the chain length increases for a given temperature. In dense states, simulation results indicate that the residual thermal conductivity of the monomer increases strongly with density, but is weakly dependent on the temperature. Compared to the monomer value, it has been noted that the residual thermal conductivity of the chain was slightly decreasing with its length. Using these results, an empirical relation, including a contribution due to the critical enhancement, is proposed to provide an accurate estimation of the thermal conductivity of the Lennard-Jones chain fluid model (up to 16 segments) over the domain 0.8values of the Lennard-Jones chain fluid model merge on the same "universal" curve when plotted as a function of the excess entropy. Furthermore, it is shown that the reduced configurational thermal conductivity of the Lennard-Jones chain fluid model is approximately proportional to the reduced excess entropy for all fluid states and all chain lengths.

  1. 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 ...

  2. Comparative distalization effects of Jones jig and pendulum appliances.

    Science.gov (United States)

    Patel, Mayara Paim; Janson, Guilherme; Henriques, José Fernando Castanha; de Almeida, Renato Rodrigues; de Freitas, Marcos Roberto; Pinzan, Arnaldo; de Freitas, Karina Maria Salvatore

    2009-03-01

    In this study, we compared the dentoalveolar changes of Class II patients treated with Jones jig and pendulum appliances. The experimental group comprised 40 Class II malocclusion subjects, divided into 2 groups: group 1 consisted of 20 patients (11 boys, 9 girls) at a mean pretreatment age of 13.17 years, treated with the Jones jig appliance for 0.91 years; group 2 comprised 20 patients (8 boys, 12 girls) at a mean pretreatment age of 13.98 years, treated with the pendulum appliance for 1.18 years. Only active treatment time of molar distalization was evaluated in the predistalization and postdistalization lateral cephalograms. Molar, second premolar, and incisor angular and linear variables were obtained. The intergroup treatment changes in these variables were compared with independent t tests. The maxillary second premolars showed greater mesial tipping and extrusion in the Jones jig group, indicating more anchorage loss during molar distalization with this appliance. The amounts and the monthly rates of molar distalization were similar in both groups. The Jones jig group showed greater mesial tipping and extrusion of the maxillary second premolars. The mean amounts and the monthly rates of first molar distalization were similar in both groups.

  3. 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...

  4. C. Rick Jones Is IRPA Keynote Lecturer on Stakeholder Engagement

    International Nuclear Information System (INIS)

    Strom, Daniel J.

    2008-01-01

    At the recent IRPA 12 Conference in Buenos Aires, Argentina, C. Rick Jones gave the keynote lecture 'Stakeholder Engagement in Practice - Now Is the Time to Act' This was one of the very best talks at the conference, covering IRPA's draft 'Guiding Principles for Radiation Protection Professionals on Stakeholder Engagement'

  5. A note on Valeriana jatamansi Jones (Caprifoliaceae s.l.)

    NARCIS (Netherlands)

    Mabberley, D.J.; Noltie, H.J.

    2014-01-01

    The tangled arguments around the names of jatamansi drug plants are examined and the correct synonymies and typifications for Nardostachys jatamansi (D.Don) DC. and V. jatamansi Jones (both Caprifoliaceae s.l.) are provided. The conservation status of the former, and the need for further work on the

  6. 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

  7. Origin of line tension for a Lennard-Jones nanodroplet

    NARCIS (Netherlands)

    Weijs, Joost; Weijs, Joost H.; Marchand, Antonin; Andreotti, Bruno; Lohse, Detlef; Snoeijer, Jacobus Hendrikus

    2011-01-01

    The existence and origin of line tension has remained controversial in literature. To address this issue, we compute the shape of Lennard-Jones nanodrops using molecular dynamics and compare them to density functional theory in the approximation of the sharp kink interface. We show that the

  8. Shelley Jones: Helping Ugandan girls stay in school | IDRC ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    IDRC research awardee Shelley Jones travelled to Uganda to explore the obstacles the country's young women face in their efforts to pursue secondary education. Her research motivated young social entrepreneurs to launch a company that is keeping girls in school and providing them with jobs.

  9. Free energy of the Lennard-Jones solid

    NARCIS (Netherlands)

    van der Hoef, Martin Anton

    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

  10. Highlight: Dr David Butler-Jones on fighting pandemics | IDRC ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    2016-04-15

    Apr 15, 2016 ... In the context of developing countries, Butler-Jones drew attention to the importance of public healthcare teams of doctors and paramedics, data, and accreditation standards in identifying appropriate interventions. There is a need to explore the public-private nexus, traditional medicines, and public health ...

  11. Gas-solid coexistence of the Lennard-Jones system

    NARCIS (Netherlands)

    van der Hoef, Martin Anton

    2002-01-01

    Recently, the absolute free energies of the Lennard-Jones system at solid–liquid and solid–gas coexistence were computed from Monte Carlo simulations [J. Chem. Phys. 116, 7145 (2002)]. In this note, we show that the values along the sublimation line are in good agreement with the results from an

  12. Highlight: Dr David Butler-Jones on fighting pandemics | CRDI ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    15 avr. 2016 ... Dr David Butler-Jones, professor in the Faculty of Medicine at the University of Manitoba and former Chief Medical Health Officer of Canada, delivered a lecture on lessons learned from the 2009 flu pandemic in Canada. He also commented on India's draft National Health Policy 2015 at the India ...

  13. 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

  14. Jones matrix treatment for optical Fourier processors with structured polarization.

    Science.gov (United States)

    Moreno, Ignacio; Iemmi, Claudio; Campos, Juan; Yzuel, Maria J

    2011-02-28

    We present a Jones matrix method useful to analyze coherent optical Fourier processors employing structured polarization. The proposed method is a generalization of the standard classical optical Fourier transform processor, but considering vectorial spatial functions with two complex components corresponding to two orthogonal linear polarizations. As a result we derive a Jones matrix that describes the polarization output in terms of two vectorial functions defining respectively the structured polarization input and the generalized polarization impulse response. We apply the method to show and analyze an experiment in which a regular scalar diffraction grating is converted into equivalent polarization diffraction gratings by means of an appropriate polarization filtering. The technique is further demonstrated to generate arbitrary structured polarizations. Excellent experimental results are presented.

  15. 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.

  16. 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

  17. Solitons in a One-Dimensional Lennard-Jones Lattice

    OpenAIRE

    Yuji, ISHIMORI; Department of Applied Mathematics and Physics Kyoto University

    1982-01-01

    Nonlinear waves in a one-dimensional lattice with (2n, n) Lennard-Jones potential are studied in small-amplitude and long-wavelength approximations. Equations derived are classified into three types according to the value of the force-range parameter n. For n=2 and ≧4, we get the Benjamin-Ono equation and the Korteweg-de Vries equation, respectively.

  18. 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......", as often argued, and that the system has a single-peaked distribution of hopping-distances centered around the characteristic intermolecular distance....

  19. Early Experience with the StopLoss Jones Tube.

    Science.gov (United States)

    Bagdonaite, Laura; Pearson, Andrew R

    2015-06-01

    Extrusion is the most common reason for failure after Jones tube placement. The StopLoss Jones tube (SLJT) is a new innovation in Jones tubes that incorporates a flexible silicone internal flange to resist extrusion. We present our early experience of using this new tube and associated introducer system. We retrospectively analysed the case notes of a single surgeon consecutive series of patients having SLJT placement from November 2011 to November 2013. 29 SLJTs were placed in 25 eyes of 19 patients. Tube follow-up ranged from 1-25 months (mean 10 months) with a total of 291 tube-months. The indications for SLJT placement were: previous LJT complications (52%), failed canalicular-DCR surgery (31%), primary placement for inoperable canalicular occlusion (14%) and patent non-functioning DCR (3%). Tube length ranged from 10-16 mm. The tube introducer system was simple and effective and there were no intra-operative complications. The tube extrusion rate was 0%. Complications occurred in 5 tubes: 1 was too long, and 4 others (14%) developed conjunctival overgrowth/medial tube migration. Patient satisfaction with the tube was: 86% fully satisfied, 10% was moderately satisfied, 3% not satisfied. The overall final surgical success rate at last follow-up was 92%. In this short follow-up initial study the SLJT is simple to use and has a high rate of success and patient satisfaction. The addition of the internal silicone flange appears to prevent the previously common problem of extrusion.

  20. 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.

  1. A Biomechanical Comparison of Fifth Metatarsal Jones Fracture Fixation Methods.

    Science.gov (United States)

    Duplantier, Neil L; Mitchell, Ronald J; Zambrano, Steve; Stone, Aaron C; Delgado, Domenica A; Lambert, Bradley S; Moreno, Michael R; Harris, Joshua D; McCulloch, Patrick C; Lintner, David M; Varner, Kevin E

    2018-04-01

    Fifth metatarsal base fractures of the metaphyseal-diaphyseal watershed junction (Jones fracture) are commonly treated with surgical fixation in athletes. Intramedullary screw fixation remains the most utilized construct, although plantar-lateral plating is an alternative. Purpose/Hypothesis: The purpose was to compare the mechanical strength of fracture fixation between an intramedullary screw and plantar-lateral plating. The hypothesis was that plantar-lateral plate fixation would allow for more cycles and higher peak loads before failure, as well as less fracture gapping, than would an intramedullary screw in cadaveric foot specimens with simulated Jones fractures exposed to cantilever bending. Controlled laboratory study. Twelve pairs of male cadaver feet were separated into 2 groups (plate or screw) to conduct contralateral comparative testing of 2 devices with equally numbered right and left feet. For each fifth metatarsal, an osteotomy with a microsagittal saw was created to simulate a Jones fracture. The plate group underwent fixation with a 3.0-mm 4-hole low-profile titanium plate placed plantar-laterally with 3 locking screws and 1 nonlocking screw. The screw group underwent fixation with a 40- or 45-mm × 5.5-mm partially threaded solid titanium intramedullary screw. After fixation, the metatarsals were excised for biomechanical testing. Cyclic cantilever failure testing was conducted with a gradient-cycle method. Sinusoidal loading forces were applied, increasing by 5.0-pound-force increments per 10 cycles, until each specimen experienced mechanical failure of implant or bone. Failure mode, number of cycles to failure, peak failure load, gap width at the last mutual prefailure loading, and video data were recorded. Paired 2-tailed t test (α = 0.05) was used to compare groups ( P Plate fixation resulted in significantly higher mean ± SD values for cycles to failure (63.9 ± 27.0 vs 37.3 ± 36.9, P = .01) and peak failure load (159.2 ± 60.5 N vs 96.5

  2. Iridoids and sesquiterpenoids from the roots of Valeriana jatamansi Jones.

    Science.gov (United States)

    Dong, Fa-Wu; Liu Yang; Wu, Zhi-Kun; Wei-Gao; Zi, Chen-Ting; Dan Yang; Luo, Huai-Rong; Jun Zhou; Hu, Jiang-Miao

    2015-04-01

    Three new iridoids, jatamanvaltrates R-S (1-2) and jatamanin Q (3), as well as three new sesquiterpenoids, valeriananoids D-E (4, 5) and clovane-2β-isovaleroxy-9α-ol (6), together with nine known compounds were isolated from the roots of Valeriana jatamansi Jones. Compound 2 was the first reported iridoid with fatty acid esters in the Valerianaceae family. The structures of new compounds were established on the basis of extensive spectroscopic analysis. Moreover, all the isolates were evaluated for inhibitory activity on acetylcholinesterase (AChE). Copyright © 2015 Elsevier B.V. All rights reserved.

  3. Origin of line tension for a Lennard-Jones nanodroplet

    Science.gov (United States)

    Weijs, Joost H.; Marchand, Antonin; Andreotti, Bruno; Lohse, Detlef; Snoeijer, Jacco H.

    2011-02-01

    The existence and origin of line tension has remained controversial in literature. To address this issue, we compute the shape of Lennard-Jones nanodrops using molecular dynamics and compare them to density functional theory in the approximation of the sharp kink interface. We show that the deviation from Young's law is very small and would correspond to a typical line tension length scale (defined as line tension divided by surface tension) similar to the molecular size and decreasing with Young's angle. We propose an alternative interpretation based on the geometry of the interface at the molecular scale.

  4. Melting of 2D monatomic solids: Lennard-Jones system

    International Nuclear Information System (INIS)

    Yi, Y.M.; Guo, Z.C.

    1987-09-01

    The Lennard-Jones interaction has been introduced into the Collins mix lattice of 2D liquids. By means of rigorous calculation of the total potential and the free area, the Gibbs functions for 2D liquid and solid have been derived. The melting line obtained from the phase transition equation agrees quite well with the result of recent computer simulation experiments. The obtained reduced temperature of the triple point T* t =0.438 agrees with the data measured in experiments of some inert gas monolayers adsorbed on graphite as well as in computer simulation experiments. (author). 11 refs, 7 figs, 3 tabs

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    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...... 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...

  6. More on the melting of Lennard-Jones clusters

    International Nuclear Information System (INIS)

    Garzon, I.L.; Avalos-Borja, M.; Blaisten-Barojas, E.

    1989-01-01

    The melting of 13-atom clusters interacting via Lennard-Jones potentials has been revisited using molecular dynamics coupled to steepest descent quenches. A procedure was devised to account for the fraction of times the global and local minima of the potential energy surface are accessed during a long trajectory. This quantity presents a sigmoid shape. A phenomenological model of melting is given in terms of a correlated walk that maps the short time excursions among the global and local minima in configuration space. Comparison between the simulation results and the theoretical model shows that the melting transition is well described in terms of the temperature changes of the fraction of high energy minima accessed during the cluster trajectory. Cooperativity is clear from the S shape of this quantity, i.e., the access to a local minimum favours the access to other local minima. (orig.)

  7. Ralph Ellison, critique de LeRoi Jones

    OpenAIRE

    Parent, Emmanuel

    2007-01-01

    On se propose ici de revenir sur la polémique ayant opposé Ralph Ellison à LeRoi Jones à l’occasion de la publication du Peuple du blues (1963). En restituant leur théorie respective du blues et du jazz, on montre comment Ellison essaie de dépasser tant le parti pris nationaliste qu’une histoire du jazz positive et progressiste qui célèbre l’avènement au cours du xxe siècle d’un véritable jazz dégagé des contraintes du folklore et du divertissement. En articulant d’une manière originale la mu...

  8. When Ernest Jones First Arrived in Toronto, or Reappraising the Bruce Letter.

    Science.gov (United States)

    Kuhn, Philip

    2018-04-16

    In July 1962, Toronto-based surgeon, Herbert Bruce, wrote a private and confidential letter to social worker and historian Cyril Greenland with some memories and impressions of Sigmund Freud's lifelong friend and biographer, Ernest Jones, in Toronto (1908-1913). In the letter, Bruce described Jones as a 'sexual pervert'. Despite Bruce's condemnation of Jones, historians and biographers have largely ignored this controversial aspect of Jones' impression in Toronto. The article traces how scholars have handled the existence of the Bruce letter, and the consequences for how this history has been understood. In the latter half of the article, the author considers how the existence of this letter offers insights into how the Toronto medical establishment regarded Ernest Jones.

  9. Vere-Jones' self-similar branching model

    International Nuclear Information System (INIS)

    Saichev, A.; Sornette, D.

    2005-01-01

    Motivated by its potential application to earthquake statistics as well as for its intrinsic interest in the theory of branching processes, we study the exactly self-similar branching process introduced recently by Vere-Jones. This model extends the ETAS class of conditional self-excited branching point-processes of triggered seismicity by removing the problematic need for a minimum (as well as maximum) earthquake size. To make the theory convergent without the need for the usual ultraviolet and infrared cutoffs, the distribution of magnitudes m ' of daughters of first-generation of a mother of magnitude m has two branches m ' ' >m with exponent β+d, where β and d are two positive parameters. We investigate the condition and nature of the subcritical, critical, and supercritical regime in this and in an extended version interpolating smoothly between several models. We predict that the distribution of magnitudes of events triggered by a mother of magnitude m over all generations has also two branches m ' ' >m with exponent β+h, with h=d√(1-s), where s is the fraction of triggered events. This corresponds to a renormalization of the exponent d into h by the hierarchy of successive generations of triggered events. For a significant part of the parameter space, the distribution of magnitudes over a full catalog summed over an average steady flow of spontaneous sources (immigrants) reproduces the distribution of the spontaneous sources with a single branch and is blind to the exponents β,d of the distribution of triggered events. Since the distribution of earthquake magnitudes is usually obtained with catalogs including many sequences, we conclude that the two branches of the distribution of aftershocks are not directly observable and the model is compatible with real seismic catalogs. In summary, the exactly self-similar Vere-Jones model provides an attractive new approach to model triggered seismicity, which alleviates delicate questions on the role of

  10. El caso Marion Jones o el llanto de una reina

    Directory of Open Access Journals (Sweden)

    Juan A Martínez de Osaba y Goenega

    2008-03-01

    Full Text Available Con un somatotipo ideal esta atleta sobresalió en Sydney 2000. Se había propuesto obtener cinco medallas doradas en el hectómetro, los 200, relevos 4 por 100, 4 por 400 y salto largo. Tamaña proeza nunca la había logrado una mujer. Pero Marion llegó con el mundo a sus pies, preparada para la cima. Solo Jesse Owens, Carl Lewis y Fanny Blankers-Koen habían alcanzado cuatro. Otra cosa fue Paavo Nurmi en las carreras de resistencia, pues en París 1924 ganó cinco títulos, único hasta la fecha en el deporte rey.“Jones, Marion (1976. Considerada como la reina de los Juegos de la Olimpiada de Sydney 2000. Ganadora de cinco medallas durante esta lid; de ellas 3 de oro en: 200 (21,84 m y en 100 (10,75 m, y el relevo 4 x 400 metros planos, así como dos de bronce, en el relevo 4 x 100 metros planos y en el salto de longitud…”

  11. The Jones polynomial as a new invariant of topological fluid dynamics

    International Nuclear Information System (INIS)

    Ricca, Renzo L; Liu, Xin

    2014-01-01

    A new method based on the use of the Jones polynomial, a well-known topological invariant of knot theory, is introduced to tackle and quantify topological aspects of structural complexity of vortex tangles in ideal fluids. By re-writing the Jones polynomial in terms of helicity, the resulting polynomial becomes then function of knot topology and vortex circulation, providing thus a new invariant of topological fluid dynamics. Explicit computations of the Jones polynomial for some standard configurations, including the Whitehead link and the Borromean rings (whose linking numbers are zero), are presented for illustration. In the case of a homogeneous, isotropic tangle of vortex filaments with same circulation, the new Jones polynomial reduces to some simple algebraic expression, that can be easily computed by numerical methods. This shows that this technique may offer a new setting and a powerful tool to detect and compute topological complexity and to investigate relations with energy, by tackling fundamental aspects of turbulence research. (paper)

  12. Environmental Assessment Bank Stabilization along St. Jones River Dover Air Force Base, Delaware

    Science.gov (United States)

    2008-12-01

    considered the implementation of all hard technologies such as riprap and gabions along the impacted 3,000 linear feet of banking. However, cost and...that ranges from 70 feet below ground surface to within a few feet near the St. Jones River. The groundwater generally flows southwest toward the St...high water table. 3.3.2 Stormwater Management The St. Jones River flows along the western boundary of Dover AFB. Pipe Elm Creek of the Little

  13. Regulatory restrictions and energy: The impact of the Jones Act on spot gasoline prices

    International Nuclear Information System (INIS)

    Gius, Mark

    2013-01-01

    The purpose of the present study is to estimate the effects of the Jones Act on spot gasoline prices. Although the Jones Act pertains to the domestic shipment of all types of goods, the present study will only focus on gasoline. The present study will use data obtained from the Energy Information Administration in order to determine if the price of gasoline declined during Jones Act waiver periods. Looking at daily prices, the results regarding the effects of the Jones Act on spot gasoline prices are mixed. When using a t-test, the results indicated either that there was no significant difference or that prices were actually higher during the waiver periods. When using a first-order autoregressive model, it was found that prices were lower during the 2005 waiver period but higher during the 2012 waiver. Given these inconclusive results, it is not possible to conclude that the Jones Act restrictions contribute to higher gasoline prices. - Highlights: • I examine the effect of the Jones Act on spot gasoline prices. • I use daily price data over a seven year period. • I find that the results are mixed. • For the Hurricane Katrina waiver, prices fell, but for the Hurricane Sandy waiver, prices rose

  14. Biomechanical Comparison of Intramedullary Screw Versus Low-Profile Plate Fixation of a Jones Fracture.

    Science.gov (United States)

    Huh, Jeannie; Glisson, Richard R; Matsumoto, Takumi; Easley, Mark E

    2016-04-01

    Intramedullary screw fixation of fifth metatarsal Jones fractures often produces satisfactory results, however, nonunion and refracture rates are not negligible. The low-profile "hook" plate is an alternative fixation method that has been promoted to offer improved rotational control at the fracture site, but this remains to be proven. The purpose of this study was to document biomechanical performance differences between this type of plate and a contemporary solid, dual-pitch intramedullary screw in a cadaveric Jones fracture model. Simulated Jones fractures were created in 8 matched pairs of fresh-frozen cadaveric fifth metatarsals. One bone from each pair was stabilized using an intramedullary TriMed Jones Screw and the other using a TriMed Jones Fracture Plate (TriMed, Inc, Santa Clarita, CA). Controlled bending and torsional loads were applied. Bending stiffness and fracture site angulation, as well as torsional stiffness, peak torque, and fracture site rotation were quantified and compared. Intramedullary screw fixation demonstrated greater bending stiffness and less fracture site angulation than plate fixation during plantar-to-dorsal and lateral-to-medial bending. Torsional stiffness of screw-fixed metatarsals exceeded that of plate-fixed bones at initial loading; however, as rotation progressed, the plate resisted torque better than the screw. No difference in peak torque was demonstrable between fixation methods, but it was reached earlier in specimens fixed with screws and later in those fixed with plates as rotation progressed. In this cadaveric Jones fracture model, intramedullary screw fixation demonstrated bending stiffness and resistance to early torsional loading that was superior to that offered by plate fixation. Although low-profile "hook" plates offer an alternative for fixation of fifth metatarsal Jones fractures, intramedullary screw fixation may provide better resistance to bending and initiation of fracture site rotation. The influence of

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

    Science.gov (United States)

    You, Jie-Shu; Peng, Min; Shi, Jin-Li; Zheng, Hu-Zhan; Liu, Yong; Zhao, Bao-Sheng; Guo, Jian-You

    2012-11-21

    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. 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. Compound Valerianae Jatamansi Jones (2.4, 4.8 g/kg, p.o.) significantly increased entries (P0.05). In addition, compound Valerianae Jatamansi Jones treatment didn't affect the spontaneous activity in mice (P> 0.05). 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.

  16. Cephalometric effects of the Jones Jig appliance followed by fixed appliances in Class II malocclusion treatment.

    Science.gov (United States)

    Patel, Mayara Paim; Henriques, José Fernando Castanha; Freitas, Karina Maria Salvatore; Grec, Roberto Henrique da Costa

    2014-01-01

    The aim of this study was to cephalometrically assess the skeletal and dentoalveolar effects of Class II malocclusion treatment performed with the Jones Jig appliance followed by fixed appliances. The sample comprised 25 patients with Class II malocclusion treated with the Jones Jig appliance followed by fixed appliances, at a mean initial age of 12.90 years old. The mean time of the entire orthodontic treatment was 3.89 years. The distalization phase lasted for 0.85 years, after which the fixed appliance was used for 3.04 years. Cephalograms were used at initial (T1), post-distalization (T2) and final phases of treatment (T3). For intragroup comparison of the three phases evaluated, dependent ANOVA and Tukey tests were used. Jones Jig appliance did not interfere in the maxillary and mandibular component and did not change maxillomandibular relationship. Jones Jig appliance promoted distalization of first molars with anchorage loss, mesialization and significant extrusion of first and second premolars, as well as a significant increase in anterior face height at the end of treatment. The majority of adverse effects that occur during intraoral distalization are subsequently corrected during corrective mechanics. Buccal inclination and protrusion of mandibular incisors were identified. By the end of treatment, correction of overjet and overbite was observed. Jones Jig appliance promoted distalization of first molars with anchorage loss represented by significant mesial movement and extrusion of first and second premolars, in addition to a significant increase in anterior face height.

  17. Cephalometric effects of the Jones Jig appliance followed by fixed appliances in Class II malocclusion treatment

    Science.gov (United States)

    Patel, Mayara Paim; Henriques, José Fernando Castanha; de Freitas, Karina Maria Salvatore; Grec, Roberto Henrique da Costa

    2014-01-01

    Objective The aim of this study was to cephalometrically assess the skeletal and dentoalveolar effects of Class II malocclusion treatment performed with the Jones Jig appliance followed by fixed appliances. Methods The sample comprised 25 patients with Class II malocclusion treated with the Jones Jig appliance followed by fixed appliances, at a mean initial age of 12.90 years old. The mean time of the entire orthodontic treatment was 3.89 years. The distalization phase lasted for 0.85 years, after which the fixed appliance was used for 3.04 years. Cephalograms were used at initial (T1), post-distalization (T2) and final phases of treatment (T3). For intragroup comparison of the three phases evaluated, dependent ANOVA and Tukey tests were used. Results Jones Jig appliance did not interfere in the maxillary and mandibular component and did not change maxillomandibular relationship. Jones Jig appliance promoted distalization of first molars with anchorage loss, mesialization and significant extrusion of first and second premolars, as well as a significant increase in anterior face height at the end of treatment. The majority of adverse effects that occur during intraoral distalization are subsequently corrected during corrective mechanics. Buccal inclination and protrusion of mandibular incisors were identified. By the end of treatment, correction of overjet and overbite was observed. Conclusions Jones Jig appliance promoted distalization of first molars with anchorage loss represented by significant mesial movement and extrusion of first and second premolars, in addition to a significant increase in anterior face height. PMID:25162565

  18. 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.

  19. System of multifunctional Jones matrix tomography of phase anisotropy in diagnostics of endometriosis

    Science.gov (United States)

    Ushenko, V. O.; Koval, G. D.; Ushenko, Yu. O.; Pidkamin, L. Y.; Sidor, M. I.; Vanchuliak, O.; Motrich, A. V.; Gorsky, M. P.; Meglinskiy, I.

    2017-09-01

    The paper presents the results of Jones-matrix mapping of uterine wall histological sections with second-degree and third-degree endometriosis. The technique of experimental measurement of coordinate distributions of the modulus and phase values of Jones matrix elements is suggested. Within the statistical and cross-correlation approaches the modulus and phase maps of Jones matrix images of optically thin biological layers of polycrystalline films of plasma and cerebrospinal fluid are analyzed. A set of objective parameters (statistical and generalized correlation moments), which are the most sensitive to changes in the phase of anisotropy, associated with the features of polycrystalline structure of uterine wall histological sections with second-degree and third-degree endometriosis are determined.

  20. Observation of Two-Dimensional Localized Jones-Roberts Solitons in Bose-Einstein Condensates

    Science.gov (United States)

    Meyer, Nadine; Proud, Harry; Perea-Ortiz, Marisa; O'Neale, Charlotte; Baumert, Mathis; Holynski, Michael; Kronjäger, Jochen; Barontini, Giovanni; Bongs, Kai

    2017-10-01

    Jones-Roberts solitons are the only known class of stable dark solitonic solutions of the nonlinear Schrödinger equation in two and three dimensions. They feature a distinctive elongated elliptical shape that allows them to travel without change of form. By imprinting a triangular phase pattern, we experimentally generate two-dimensional Jones-Roberts solitons in a three-dimensional atomic Bose-Einstein condensate. We monitor their dynamics, observing that this kind of soliton is indeed not affected by dynamic (snaking) or thermodynamic instabilities, that instead make other classes of dark solitons unstable in dimensions higher than one. Our results confirm the prediction that Jones-Roberts solitons are stable solutions of the nonlinear Schrödinger equation and promote them for applications beyond matter wave physics, like energy and information transport in noisy and inhomogeneous environments.

  1. Return to Play and Performance After Jones Fracture in National Basketball Association Athletes

    Science.gov (United States)

    Begly, John P.; Guss, Michael; Ramme, Austin J.; Karia, Raj; Meislin, Robert J.

    2015-01-01

    Background: Basketball players are at risk for foot injuries, including Jones fractures. It is unknown how this injury affects the future play and performance of athletes. Hypothesis: National Basketball Association (NBA) players who sustain Jones fractures of the base of the fifth metatarsal have high rates of return to play and do not experience a decrease in performance on return to competition when compared with preinjury and with control-matched peers. Study Design: Retrospective cohort study. Level of Evidence: Level 5. Methods: Data on 26 elite basketball players with Jones fractures over 19 NBA seasons (1994-1995 to 2012-2013) were obtained from injury reports, press releases, player profiles, and online public databases. Variables included age, body mass index (BMI), player position, experience, and surgical treatment. Individual season statistics pre- and postinjury were collected. Twenty-six controls were identified by matched player position, age, and performance statistics. Results: The mean age at the time of injury was 24.8 years, mean BMI was 24.7 kg/m2, and the mean experience prior to injury was 4.1 NBA seasons. Return to previous level of competition was achieved by 85% of athletes. There was no change in player efficiency rating (PER) when pre- and postinjury performance was compared. When compared with controls, no decline in PER measured performance was identified. Conclusion: The majority of NBA players sustaining a Jones fracture return to their preinjury level of competition. These elite athletes demonstrate no decrease in performance on their return to play. Clinical Relevance: Jones fractures are well-studied injuries in terms of etiology, diagnosis, and management. However, the effect of these injuries on future performance of athletes is unknown. Using the findings of our study, orthopaedic surgeons may be better prepared to counsel and educate elite athletes who sustain a Jones fracture. PMID:26627111

  2. Upper removable appliance or Jones Jig for distalizing first molars? A randomized clinical trial.

    Science.gov (United States)

    Paul, L D; O'Brien, K D; Mandall, N A

    2002-11-01

    To compare the effectiveness of two intra-oral methods of distalizing upper first permanent molars: an upper removable appliance (URA) and a Jones Jig. Twelve patients were randomly allocated to URA treatment and 11 patients to a Jones Jig. Upper study models were collected at the start of treatment and after 6 months of appliance wear. The amount of distal movement, tipping and rotation of the upper first permanent molars and mesial movement of the upper first permanent premolars was measured using a reflex metrograph. There were no statistically significant differences between the two treatment methods for any of the outcome measures (P Jig as a non-compliance appliance.

  3. Occurrence of pathotypes of Ascochyta pinodes (Jones in the Olsztyn district

    Directory of Open Access Journals (Sweden)

    Helena Furgał-Węgrzycka

    2013-12-01

    Full Text Available The causal agent of leaf and pods spot-pot of peas and field peas in the Olsztyn district was the fungus Ascochyta pinodes (Jones. Investigated isolates of A. pinoides different by macroscopic and microscopic features. From diseased leaves and pods of peas and field peas saprophytic fungi were also obtained. Among them Alternaria alternata, Cladosporium cladosporioides, Epicoccum purpurascens, Stemphylium botryosum, Sordaria fimicola and mycelia sterilia were dominant. In the study on the identification and distribution of pathotypes of A. pinodes (Jones six pathotypes were identified among which pathotypes 3 dominated. The identified pathotypes differed by macroscopic and microscopic features.

  4. Polarization-interference Jones-matrix mapping of biological crystal networks

    Science.gov (United States)

    Ushenko, O. G.; Dubolazov, O. V.; Pidkamin, L. Y.; Sidor, M. I.; Pavlyukovich, N.; Pavlyukovich, O.

    2018-01-01

    The paper consists of two parts. The first part presents short theoretical basics of the method of Jones-matrix mapping with the help of reference wave. It was provided experimentally measured coordinate distributions of modulus of Jones-matrix elements of polycrystalline film of bile. It was defined the values and ranges of changing of statistic moments, which characterize such distributions. The second part presents the data of statistic analysis of the distributions of matrix elements of polycrystalline film of urine of donors and patients with albuminuria. It was defined the objective criteria of differentiation of albuminuria.

  5. Algorithm for optimization of Viola–Jones object detection framework parameters

    Science.gov (United States)

    Egorov, A. D.

    2018-01-01

    The Viola-Jones algorithm is one of the most popular algorithms for objects recognition in an image. This research paper deals with the possibilities of parametric optimization of the Viola-Jones algorithm to achieve maximum efficiency of the algorithm in specific environmental conditions. It is shown that with the use of additional modifications it is possible to increase the speed of the algorithm in a particular image by 2-5 times with the loss of accuracy and completeness of work by not more than 3-5%.

  6. Non-equilibrium surface tension of the vapour-liquid interface of active Lennard-Jones particles

    NARCIS (Netherlands)

    Paliwal, Siddharth; Prymidis, Vasileios; Filion, Laura; Dijkstra, Marjolein

    2017-01-01

    We study a three-dimensional system of self-propelled Brownian particles interacting via the Lennard-Jones potential. Using Brownian dynamics simulations in an elongated simulation box, we investigate the steady states of vapour-liquid phase coexistence of active Lennard-Jones particles with planar

  7. Class II malocclusion treatment effects with Jones Jig and Distal Jet followed by fixed appliances.

    Science.gov (United States)

    Vilanova, Lorena; Henriques, José Fernando Castanha; Janson, Guilherme; Patel, Mayara Paim; Reis, Rachelle Simões; Aliaga-Del Castillo, Aron

    2018-01-01

    To compare the skeletal, dentoalveolar, and soft tissue changes in Class II malocclusion patients treated with Jones Jig and Distal Jet distalizers followed by fixed appliances. The experimental groups comprised 45 Class II malocclusion subjects divided into two groups. Group 1 consisted of 25 patients treated with the Jones Jig, and group 2 consisted of 20 patients treated with the Distal Jet. Group 3 comprised 19 untreated Class II subjects. Cephalograms were analyzed before and after orthodontic treatment. For intergroup comparisons, one-way analysis of variance and post hoc Tukey tests were performed. During treatment, the experimental groups exhibited significant increases in occlusal plane inclination and maxillary second molar mesial tipping. Additionally, the molar relationship improved and overjet decreased significantly in the experimental groups. The Jones Jig group showed greater mandibular incisor proclination and greater overbite reduction than the control group. No significant intergroup differences in nasolabial angle changes were found. Treatment protocols using the Jones Jig and Distal Jet followed by fixed appliances were effective in correcting Class II malocclusion by means of dentoalveolar changes without significant skeletal and soft tissue changes. The experimental groups showed occlusal plane clockwise rotation and greater mesial tipping of maxillary second molars when compared to the untreated group.

  8. Flexible equation of state for a hard sphere and Lennard–Jones fluid ...

    Indian Academy of Sciences (India)

    Equation of state; Lennard–Jones potential; hard-sphere potential; liquid mixture; computer simulation. ... deviation than Barker–Henderson BH2 for LJ fluids, and results are much closer to molecular dynamics (MD) simulations than expectations and reproduce the existing simulation data and present EoS for LJ potential, ...

  9. "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

  10. The Game TV Plays: Or, Why an English Teacher Came to Hate Barnaby Jones.

    Science.gov (United States)

    Shaw, Patrick W.

    The message of current popular television shows in which the hero is, or appears to be, a dumb clod (e.g., Archie Bunker, Fred Sanford, Columbo, and Barnaby Jones), apparently is that corruption may be equated with articulation, wealth, and education, while virtue may be equated with poverty and, often, illiteracy. Unfortunately, the effect of…

  11. 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.

  12. 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…

  13. 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

  14. 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…

  15. 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.

  16. Collision kernels in the eikonal approximation for Lennard-Jones interaction potential

    International Nuclear Information System (INIS)

    Zielinska, S.

    1985-03-01

    The velocity changing collisions are conveniently described by collisional kernels. These kernels depend on an interaction potential and there is a necessity for evaluating them for realistic interatomic potentials. Using the collision kernels, we are able to investigate the redistribution of atomic population's caused by the laser light and velocity changing collisions. In this paper we present the method of evaluating the collision kernels in the eikonal approximation. We discuss the influence of the potential parameters Rsub(o)sup(i), epsilonsub(o)sup(i) on kernel width for a given atomic state. It turns out that unlike the collision kernel for the hard sphere model of scattering the Lennard-Jones kernel is not so sensitive to changes of Rsub(o)sup(i) as the previous one. Contrary to the general tendency of approximating collisional kernels by the Gaussian curve, kernels for the Lennard-Jones potential do not exhibit such a behaviour. (author)

  17. Jones-matrix tomography of biological tissues phase anisotropy in the diagnosis of uterus wall prolapse

    Science.gov (United States)

    Trifonyuk, L.; Baranovsky, V.; Dubolazov, O. V.; Ushenko, V. O.; Ushenko, O. G.; Zhytaryuk, V. G.; Prydiy, O. G.; Vanchulyak, O.

    2018-01-01

    The work consists of two parts. In the first part - we mapped a distribution of optical activity and birefringence in polycrystalline networks of biological tissues. The Jones-matrix formalism is used for accessible quantitative description of these types of optical anisotropy. We demonstrate that differentiation of polycrystalline networks of biological tissues can be performed based on the statistical analysis of distribution of rotation angles and phase shifts associated with the optical activity and birefringence, respectively. In the second part we defined - practical operational characteristics, such as sensitivity, specificity and accuracy of Jones-matrix reconstruction of optical anisotropy were identified with the special emphasis on biomedical application, specifically for differentiation of two types of pathology: prolapse and albuminuria.

  18. Mapping of polycrystalline films of biological fluids utilizing the Jones-matrix formalism

    Science.gov (United States)

    Ushenko, Vladimir A.; Dubolazov, Alexander V.; Pidkamin, Leonid Y.; Sakchnovsky, Michael Yu; Bodnar, Anna B.; Ushenko, Yuriy A.; Ushenko, Alexander G.; Bykov, Alexander; Meglinski, Igor

    2018-02-01

    Utilizing a polarized light approach, we reconstruct the spatial distribution of birefringence and optical activity in polycrystalline films of biological fluids. The Jones-matrix formalism is used for an accessible quantitative description of these types of optical anisotropy. We demonstrate that differentiation of polycrystalline films of biological fluids can be performed based on a statistical analysis of the distribution of rotation angles and phase shifts associated with the optical activity and birefringence, respectively. Finally, practical operational characteristics, such as sensitivity, specificity and accuracy of the Jones-matrix reconstruction of optical anisotropy, were identified with special emphasis on biomedical application, specifically for differentiation of bile films taken from healthy donors and from patients with cholelithiasis.

  19. Effect of Energy Polydispersity on the Nature of Lennard-Jones Liquids

    OpenAIRE

    Ingebrigtsen, Trond S.; Tanaka, Hajime

    2016-01-01

    In the companion paper [T. S. Ingebrigtsen and H. Tanaka, J. Phys. Chem. B 119, 11052 (2015)] the effect of size polydispersity on the nature of Lennard-Jones (LJ) liquids, which represent most molecular liquids without hydrogen bonds, was studied. More specifically, it was shown that even highly size polydisperse LJ liquids are Roskilde-simple (RS) liquids. RS liquids are liquids with strong correlation between constant volume equilibrium fluctuations of virial and potential energy and are s...

  20. Fluctuations and thermodynamic response functions in a Lennard-Jones solid

    International Nuclear Information System (INIS)

    Li, M.; Johnson, W.L.

    1992-01-01

    Thermodynamic response functions of a nearest-neighbor Lennard-Jones solid--heat capacity, thermal-expansion coefficient, compressibility, and elastic constants--are calculated directly from fluctuations using molecular-dynamics simulations. The algorithm used is the earlier Parrinello-Rahman molecular dynamics modified to take into account symmetry and rotation invariance of the system under investigation. The convergence is very fast and results are in good agreement with existing Monte Carlo and molecular-dynamics results

  1. Melting in Two-Dimensional Lennard-Jones Systems: Observation of a Metastable Hexatic Phase

    International Nuclear Information System (INIS)

    Chen, K.; Kaplan, T.; Mostoller, M.

    1995-01-01

    Large scale molecular dynamics simulations of two-dimensional melting have been carried out using a recently revised Parrinello-Rahman scheme on massively parallel supercomputers. A metastable state is observed between the solid and liquid phases in Lennard-Jones systems of 36 864 and 102 400 atoms. This intermediate state shows the characteristics of the hexatic phase predicted by the theory of Kosterlitz, Thouless, Halperin, Nelson, and Young

  2. Screw fixation diameter for fifth metatarsal jones fracture: a cadaveric study.

    Science.gov (United States)

    Scott, Ryan T; Hyer, Christopher F; DeMill, Shyler L

    2015-01-01

    The fifth metatarsal Jones fracture is a well-documented injury occurring at the proximal diaphyseal-metaphyseal junction. Conservative versus surgical intervention has been discussed in published studies for the management of Jones fractures. Solid intramedullary fixation relies on accurate matching of the screw diameter to the intraosseous diameter. The purpose of the present cadaveric study was to determine the average intraosseous diameter of the proximal fifth metatarsal as it relates to screw size selection for Jones fracture stabilization. Twenty fresh-frozen cadaver legs were used for examination. The fifth metatarsal was completely dissected. A transverse osteotomy was performed from laterally to medially along the midline of the metatarsal. A digital caliper was used to measure the diameter of the medullary canal of the fifth metatarsal. The measurement was taken at the narrowest portion of the medullary canal just distal to the proximal metaphysis. The mean dorsal to plantar diameter of the fifth metatarsal was 6.475 ± 1.54 (range 4 to 12) mm and the mean medial to lateral diameter was 4.6 ± 0.85 (range 3 to 6) mm. Intramedullary screw fixation has shown beneficial results in the treatment protocol of fifth metatarsal Jones fractures. Our study has demonstrated that a 4.5-mm cannulated screw is the narrowest diameter screw that can be used in the average fifth metatarsal and still obtain adequate intraosseous purchase. When selecting the appropriate screw, the surgeon must be comfortable selecting the largest screw that will achieve the maximal interface with the dense cortical bone in both the medial to lateral and dorsal to plantar plane. Copyright © 2015 American College of Foot and Ankle Surgeons. Published by Elsevier Inc. All rights reserved.

  3. Optimal Fixation of Jones Fractures Sacrifices the Peroneal Brevis Tendon Insertion andthe Plantar Fascia

    OpenAIRE

    van Dijk, Pim A.d.; Breuking, Sofie; Vopat, Bryan G.; Guss, Daniel; Johnson, Anne H.; Hosseini, Ali; DiGiovanni, Christopher

    2017-01-01

    Objectives: Patients with Jones fractures (JF) frequently undergo operative management with intramedullary screw fixation. Screw insertion through the base of the fifth metatarsal potentially compromises attachment points of the plantar fascia (PF) and peroneal brevis tendon (PB), and appropriate screw length and diameter remains controversial. The aim of this study was to define the anatomy of the fifth metatarsal bone using CT modeling in order to provide better guidance regarding optimized...

  4. Metastability, spectrum, and eigencurrents of the Lennard-Jones-38 network

    International Nuclear Information System (INIS)

    Cameron, Maria K.

    2014-01-01

    We develop computational tools for spectral analysis of stochastic networks representing energy landscapes of atomic and molecular clusters. Physical meaning and some properties of eigenvalues, left and right eigenvectors, and eigencurrents are discussed. We propose an approach to compute a collection of eigenpairs and corresponding eigencurrents describing the most important relaxation processes taking place in the system on its way to the equilibrium. It is suitable for large and complex stochastic networks where pairwise transition rates, given by the Arrhenius law, vary by orders of magnitude. The proposed methodology is applied to the network representing the Lennard-Jones-38 cluster created by Wales's group. Its energy landscape has a double funnel structure with a deep and narrow face-centered cubic funnel and a shallower and wider icosahedral funnel. However, the complete spectrum of the generator matrix of the Lennard-Jones-38 network has no appreciable spectral gap separating the eigenvalue corresponding to the escape from the icosahedral funnel. We provide a detailed description of the escape process from the icosahedral funnel using the eigencurrent and demonstrate a superexponential growth of the corresponding eigenvalue. The proposed spectral approach is compared to the methodology of the Transition Path Theory. Finally, we discuss whether the Lennard-Jones-38 cluster is metastable from the points of view of a mathematician and a chemical physicist, and make a connection with experimental works

  5. 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.

  6. Pendeteksian Bagian Tubuh Manusia untuk Filter Pornografi dengan Metode Viola-Jones

    Directory of Open Access Journals (Sweden)

    Benny Senjaya

    2012-06-01

    Full Text Available Information Technology does help people to get information promptly anytime and anywhere. Unfortunately, the information gathered from the Internet does not always come out positive. Some information can be destructive, such as porn images. To mitigate this problem, the study aims to create a desktop application that could detect parts of human body which can be expanded in the future to become an image filter application for pornography. The detection methodology in this study is Viola-Jones method which provides a complete framework for extracting and recognizing image features. A combination of Viola-Jones method with Haar-like features, integral image, boosting algorithm, and cascade classifier provide a robust detector for the 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.

  7. 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

  8. Strategic Analysis and Associated Management Products Supporting the Reengineering of Bayne-Jones Army Community Hospital: Consultative Products and Findings

    National Research Council Canada - National Science Library

    Fulton, Larry

    1998-01-01

    .... ̂Product 2 - "Bayne-Jones Army Community Hospital Web Site," a strategic Internet web site for marketing health and wellness, the TRICARE medical network, the Joint Readiness Training Center Surgeon's...

  9. Studies on the regulation of lipid metabolism and its mechanism of the iridoids rich fraction in Valeriana jatamansi Jones.

    Science.gov (United States)

    Zhu, Jiali; Xu, Keke; Zhang, Xuemei; Cao, Jiahong; Jia, Zhanrong; Yang, Ruocong; Ma, Chaoying; Chen, Chang; Zhang, Tiane; Yan, Zhiyong

    2016-12-01

    Valeriana jatamansi Jones, a plant with heart-shaped leaves in the Valeriana genus of Valerianaceae, is widely used in Chinese folk medicine. Iridoid is an important constituent of V. jatamansi that contributes to the pharmacological efficacy of the herb. This study aims to investigate the regulation of lipid metabolism and its mechanism of the iridoids rich fraction in V. jatamansi (IRFV). A high fat diet was used to establish the hyperlipidemia rat model, with 2mg/kg/d of simvastatin as a positive control, fed with 7.5, 15, and 30mg/kg/d of IRFV for 20days to investigate the lipid regulation activity and mechanism of IRFV. Body weight, liver index, total cholesterol (TC), triglyceride (TG), low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol (HDL-C) in both serum and liver, as well as total bile acid (TBA), aspartate aminotransferase (AST), and alanine aminotransferase (ALT) in serum were measured. The lipoprotein lipase (LPL) and hepatic lipase (HL) activities and the apoprotein A5 (ApoA5), peroxisome proliferator-activated receptor α (PPAR-α), sterol regulatory element-binding proteins (SREBP-1c), and liver X receptor α (LXR-α) protein expressions were observed. Liver pathology was described through hematoxylin-eosin (HE) staining. Compared with the model group, three different IRFV dosages can slow down the weight gain of rats, reduce the contents of TG, and increase the contents of HDL-C in serum. Low IRFV dosage can significantly reduce the AST and ALT contents in serum, liver index, and the TG contents in liver, enhance LPL activity. Medium IRFV dosage can significantly decrease the TG and LDL-C contents in liver. High IRFV dosage can significantly reduce LDL-C, TBA, AST, and ALT contents in serum, and enhance HL activity. Three different IRFV dosages can significantly increase the ApoA5 and PPAR-α protein expression and decrease the SREBP-1c protein expression. Furthermore, the LXR-α protein expression decreased in

  10. Staging Henry Fielding: The Author-Narrator in Tom Jones On Screen

    Directory of Open Access Journals (Sweden)

    Eli Løfaldli

    2017-06-01

    Full Text Available As recent adaptation theory has shown, classic-novel adaptation typically sets issues connected to authorship and literal and figurative ownership into play. This key feature of such adaptations is also central to the screen versions of Henry Fielding’s Tom Jones (1749. In much of Fielding’s fiction, the narrator, typically understood as an embodiment of Fielding himself, is a particularly prominent presence. The author-narrator in Tom Jones is no exception: not only is his presence strongly felt throughout the novel, but through a variety of means, ‘The History of Tom Jones, A Foundling’ is also distinctly marked as being under his control and ownership. The two adaptations of Fielding’s novel, a 1963 film and a 1997 television series, both retain the figure of the author-narrator, but differ greatly in their handling of this device and its consequent thematic ramifications. Although the 1963 film de-emphasises Henry Fielding’s status as proprietor of the story, the author-narrator as represented in the film’s voiceover commentary is a figure of authority and authorial control. In contrast, the 1997 adaptation emphasises Fielding’s ownership of the narrative and even includes the author-narrator as a character in the series, but this ownership is undermined by the irreverent treatment to which he is consistently subjected. The representations of Henry Fielding in the form of the author-narrator in both adaptations are not only indicative of shifting conceptions of authorship, but also of the important interplay between authorship, ownership and adaptation more generally.

  11. Formation of global energy minimim structures in the growth process of Lennard-Jones clusters

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Koshelev, Andrey; Shutovich, Andrey

    2003-01-01

    that in this way all known global minimum structures of the Lennard-Jones (LJ) 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 numbers sequence for the clusters of noble gases atoms and compare...... for the clusters of noble gases atoms. Our method serves an efficient alternative to the global optimization techniques based on the Monte-Carlo simulations and it can be applied for the solution of a broad variety of problems in which atomic cluster structure is important....

  12. Evidence of hexatic phase formation in two-dimensional Lennard-Jones binary arrays

    International Nuclear Information System (INIS)

    Li, M.; Johnson, W.L.; Goddard, W.A. III

    1996-01-01

    We report evidence of the hexatic phase formation in Lennard-Jones binary substitutional random arrays from isothermal-isobaric molecular-dynamics simulations. The hexatic phase is analogous to those predicted in Kosterlitz-Thouless theory of melting that is characterized by short-range translational order and quasi-long-range orientational order. At the crystal to hexatic phase transition, dislocation pairs are observed to unbind into isolated dislocations. Further disordering of the hexatic phase, however, does not lead to dissociation of dislocations into disclinations. Instead, the dislocations become clustered and form dislocation networks which results in formation of amorphous phases. copyright 1996 The American Physical Society

  13. Replica exchange molecular simulation of Lennard-Jones particles in a two-dimensional confined system

    Science.gov (United States)

    Doi, Hideo; Yasuoka, Kenji

    2017-05-01

    Confined systems exhibit interesting properties that are applied to the fields of lubrication, adhesion and nanotechnology. The replica exchange molecular simulation method was applied to calculate the phase equilibrium points of Lennard-Jones particles in a two-dimensional confined system. The liquid-solid phase equilibrium points and the solid structure with a dependency of the slit width were determined and the order parameter of the solid structure was analyzed. Such confined systems are shown to be favorable for manipulation of the phase equilibrium points.

  14. Replica exchange molecular simulation of Lennard–Jones particles in a two-dimensional confined system

    Directory of Open Access Journals (Sweden)

    Hideo Doi

    2017-05-01

    Full Text Available Confined systems exhibit interesting properties that are applied to the fields of lubrication, adhesion and nanotechnology. The replica exchange molecular simulation method was applied to calculate the phase equilibrium points of Lennard–Jones particles in a two-dimensional confined system. The liquid–solid phase equilibrium points and the solid structure with a dependency of the slit width were determined and the order parameter of the solid structure was analyzed. Such confined systems are shown to be favorable for manipulation of the phase equilibrium points.

  15. 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.

  16. 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

    convicted of doping. The material consists of sport reports about the 2000 Olympic Games in three American newspapers. These Games proved controversial due to the allegations and inquiries of the media (both national and international) regarding doping issues and the prominence of the American athletes...... 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...

  17. Nonlinear transport processes and fluid dynamics: Cylindrical Couette flow of Lennard-Jones fluids

    International Nuclear Information System (INIS)

    Khayat, R.E.; Eu, B.C.

    1988-01-01

    In this paper we report on calculations of flow profiles for cylindrical Couette flow of a Lennard-Jones fluid. The flow is subjected to a temperature gradient and thermoviscous effects are taken into consideration. We apply the generalized fluid dynamic equations which are provided by the modified moment method for the Boltzmann equation reported previously. The results of calculations are in good agreement with the Monte Carlo direct simulation method by K. Nanbu [Phys. Fluids 27, 2632 (1984)] for most of Knudsen numbers for which the simulation data are available

  18. Self-diffusion coefficients of the metastable Lennard-Jones vapor

    Energy Technology Data Exchange (ETDEWEB)

    Nie Chu; Zhou Youhua [School of Physics and Information Engineering, Jianghan University, Wuhan 430056 (China); Marlow, W H; Hassan, Y A [Department of Nuclear Engineering, Texas A and M University, College Station, TX 77843 (United States)], E-mail: yhzhou@jhun.edu.cn

    2008-10-15

    Self-diffusion coefficients of a metastable Lennard-Jones vapor were obtained using the memory function formalism and the frequency moments of the velocity autocorrelation function at reduced temperatures from 0.75 to 1.0. The radial density distribution functions used to evaluate the second, fourth and sixth frequency moments of the velocity autocorrelation function were obtained from the restricted canonical ensemble Monte Carlo simulation (Corti and Debenedetti 1994 Chem. Eng. Sci. 49 2717). The self-diffusion coefficients at reduced temperature 0.75 do not vary monotonically as the density increases, and for the other three temperatures the self-diffusion coefficients vary normally.

  19. Stability limits for the supercooled liquid and superheated crystal of Lennard-Jones particles.

    Science.gov (United States)

    Loscar, Ernesto S; Martin, Daniel A; Grigera, Tomás S

    2017-07-21

    We have studied the limits of stability in the first order liquid-solid phase transition in a Lennard-Jones system by means of the short-time relaxation method and using the bond-orientational order parameter Q 6 . These limits are compared with the melting line. We have paid special attention to the supercooled liquid, comparing our results with the point where the free energy cost of forming a nucleating droplet goes to zero. We also indirectly estimate the dimension associated to the critical nucleus at the spinodal, expected to be fractal according to mean field theories of nucleation.

  20. A quantitative test of Jones NTC beaming theory using CLUSTER constellation

    Directory of Open Access Journals (Sweden)

    S. Grimald

    2007-03-01

    Full Text Available Non-thermal continuum (NTC radiation is, with auroral kilometric radiation (AKR, one of the two electromagnetic emissions generated within the Earth's magnetosphere and radiated into space. The location of the source of NTC has been sought for several decades, with only limited success. The constellation formed by the four CLUSTER spacecraft provides the possibility of triangulation in the vicinity of the source, thus allowing progress in source localisation, while simultaneously revealing the beaming properties of NTC radio sources.

    We present a case event showing two beams localised on opposite sides of the magnetic equator. At any selected frequency, triangulation points to a single region source of small size. Its position is compatible with the range of possible loci of sources predicted by the radio window theory of Jones (1982 in a frame of constraints relaxed from the simple sketch proposed in early works. The analysis of similar observations from the Dynamics Explorer 1 by Jones et al. (1987 enabled the authors to claim validation of the radio window theory. CLUSTER observations, however, reveal a large beaming cone angle projected onto the ecliptic plane, a feature unobservable by Dynamics Explorer which had a different spin axis orientation. According to the radio window theory, such a large observed cone angle can only be formed by a series of point sources, each beaming in a narrow cone angle. This study demonstrates the difficulty of validating NTC linear generation mechanisms using global beaming properties alone.

  1. Safe aftercare following foot ankle surgery: Doing less is more: The Jones dressing cast, part 2.

    Science.gov (United States)

    Gottlieb, Tonio; Klaue, Kaj

    2018-04-01

    There is no universal approach to surgery aftercare among foot and ankle surgeons. Although infections following foot and ankle surgery are rare, soft tissue healing can be jeopardized after extensive and multiple approaches. We defined a precise fixation technique of the foot and ankle in the immediate post-operative phase using what we call "the Jones dressing cast". This technique is a modification of the Jones dressing bandage. In a previous study we compared two groups of patients (N=20/23) who underwent similar reconstructive surgery with the application of the described cast for one week and without. At the two-month follow-up we observed that the group treated with the cast required less pain relief, spent less time in hospital and achieved faster autonomy using crutches (Gottlieb and Klaue, 2013). In this study we considered a group of 45 patients who underwent similar reconstructive procedures to those in the first study and who were treated with the cast for two weeks post-operatively. There was no visual check of the soft tissues before removal of the cast. Unlike the earlier study, the results from this second study were more significant. Revision surgery occurred far less frequently in the group wearing the cast for two weeks. The reduced strain to the soft tissue around the foot due to the cast and less manipulation of the wound dressing decrease complications in the post-operative period. Copyright © 2017 European Foot and Ankle Society. Published by Elsevier Ltd. All rights reserved.

  2. Glass transitions in one-, two-, three-, and four-dimensional binary Lennard-Jones systems

    Energy Technology Data Exchange (ETDEWEB)

    Bruening, Ralf; St-Onge, Denis A; Patterson, Steve [Physics Department, Mount Allison University, Sackville, NB, E4L 1E6 (Canada); Kob, Walter [Laboratoire des Colloides, Verres et Nanomateriaux, UMR5587, Universite Montpellier II and CNRS, 34095 Montpellier Cedex (France)], E-mail: rbruening@mta.ca

    2009-01-21

    We investigate the calorimetric liquid-glass transition by performing simulations of a binary Lennard-Jones mixture in one through four dimensions. Starting at a high temperature, the systems are cooled to T = 0 and heated back to the ergodic liquid state at constant rates. Glass transitions are observed in two, three and four dimensions as a hysteresis between the cooling and heating curves. This hysteresis appears in the energy and pressure diagrams, and the scanning rate dependence of the area and height of the hysteresis can be described using power laws. The one-dimensional system does not experience a glass transition but its specific heat curve resembles the shape of the D{>=}2 results in the supercooled liquid regime above the glass transition. As D increases, the radial distribution functions reflect reduced geometric constraints. Nearest neighbor distances become smaller with increasing D due to interactions between nearest and next-nearest neighbors. Simulation data for the glasses are compared with crystal and melting data obtained with a Lennard-Jones system with only one type of particle and we find that with increasing D crystallization becomes increasingly more difficult.

  3. 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.

  4. Phase Diagram of Kob-Andersen-Type Binary Lennard-Jones Mixtures

    Science.gov (United States)

    Pedersen, Ulf R.; Schrøder, Thomas B.; Dyre, Jeppe C.

    2018-04-01

    The binary Kob-Andersen (KA) Lennard-Jones mixture is the standard model for computational studies of viscous liquids and the glass transition. For very long simulations, the viscous KA system crystallizes, however, by phase separating into a pure A particle phase forming a fcc crystal. We present the thermodynamic phase diagram for KA-type mixtures consisting of up to 50% small (B ) particles showing, in particular, that the melting temperature of the standard KA system at liquid density 1.2 is 1.028(3) in A particle Lennard-Jones units. At large B particle concentrations, the system crystallizes into the CsCl crystal structure. The eutectic corresponding to the fcc and CsCl structures is cutoff in a narrow interval of B particle concentrations around 26% at which the bipyramidal orthorhombic PuBr3 structure is the thermodynamically stable phase. The melting temperature's variation with B particle concentration at two constant pressures, as well as at the constant density 1.2, is estimated from simulations at pressure 10.19 using isomorph theory. Our data demonstrate approximate identity between the melting temperature and the onset temperature below which viscous dynamics appears. Finally, the nature of the solid-liquid interface is briefly discussed.

  5. 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.

  6. The fish and fisheries of Jones Bank and the wider Celtic Sea

    Science.gov (United States)

    Martinez, I.; Ellis, J. R.; Scott, B.; Tidd, A.

    2013-10-01

    The Celtic Sea is a diverse fishing ground that supports important commercial fisheries for a range of demersal fish, large and small-bodied pelagic fish and a variety of cephalopods and other shellfish. A regional overview of the main commercial fish stocks of the Celtic Sea and of the fish that occur in the vicinity of Jones Bank are provided through analyses of landings data from English and Welsh vessels, and from scientific trawl surveys. Dedicated smaller scale sampling via trawl surveys combined with baited cameras on and around the Jones Bank were also analysed to investigate the importance of sandbank habitats with attention paid to the differences in the species occurring on the top of the bank in comparison to adjacent off-bank habitats. Official landing statistics for UK (English and Welsh) vessels indicated that the predominant commercial demersal species in ICES Divisions VIIg,h (in terms of quantities landed) were anglerfish, megrim, pollack and skates (Rajidae). There were, however, regional differences in the distribution of fish and fisheries, and the area surrounding Jones Bank (ICES Rectangles 28E1 and 28E2) supports fisheries for megrim, anglerfish, skates, hake, ling and turbot, with otter trawl, gillnet and beam trawl the main gears used. Recent survey data collected with GOV (Grande Ouverture Verticale) trawl from the Celtic Sea (ICES Divisions VIIe-h, 2007-2010) were used to highlight the broad scale distribution of the main fish assemblages in the Celtic Sea. Analyses of the fish and cephalopod catches from these surveys indicated that there were four broad assemblages in the area, including (i) a region around the Cornwall (which will also be partly influenced by the necessity to use rockhopper ground gear on these rough grounds), (ii) the shallower regions of the north-western Celtic Sea (including parts of the Bristol Channel), (iii) the deeper parts of the outer shelf and (iv) the central Celtic Sea. These data also provided

  7. Localized fluidity modes and the topology of the constant-potential-energy hypersurfaces of Lennard-Jones matter

    DEFF Research Database (Denmark)

    Cotterill, Rodney M J; Madsen, J.

    1986-01-01

    Sections of configuration space for Lennard-Jones matter were obtained by probing all the normal-mode energy profiles, following diagonalization of the dynamical matrix for a 240-particle system. For the crystal and sufficiently cold glass, these are single welled, whereas increasing numbers...... of double wells occur as the glass is warmed toward the fluid. This indicates that there might be a fundamental difference between the topologies of the constant-potential-energy hypersurfaces of crystalline and noncrystalline Lennard-Jones matter....

  8. An equation of state for two-center Lennard-Jones fluids

    Science.gov (United States)

    Mecke, M.; Müller, A.; Winkelmann, J.; Fischer, J.

    1997-05-01

    A new equation of state (EOS) is proposed for the Helmholzt energy F of two-center Lennard-Jones fluids. The EOS is written in the form of a generalized van der Waals equation, F=F H + F A , where F H accounts for the hard-body interaction and F A for the attractive dispersion forces. The equation is constructed on the basis of previously published data sets and results from new extensive computer simulation studies. It correlates pressures and internal energies over a wide fluid range for two-center model fluids with elongations up to 0.67 in reduced units with a high accuracy and shows an excellent description of the vapor-liquid coexistence properties. Comparisons of results from the new EOS with other data sets and recently published VLE from the NpT plus test particle method show very good agreement.

  9. 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.

  10. Insight into induced charges at metal surfaces and biointerfaces using a polarizable Lennard-Jones potential.

    Science.gov (United States)

    Geada, Isidro Lorenzo; Ramezani-Dakhel, Hadi; Jamil, Tariq; Sulpizi, Marialore; Heinz, Hendrik

    2018-02-19

    Metallic nanostructures have become popular for applications in therapeutics, catalysts, imaging, and gene delivery. Molecular dynamics simulations are gaining influence to predict nanostructure assembly and performance; however, instantaneous polarization effects due to induced charges in the free electron gas are not routinely included. Here we present a simple, compatible, and accurate polarizable potential for gold that consists of a Lennard-Jones potential and a harmonically coupled core-shell charge pair for every metal atom. The model reproduces the classical image potential of adsorbed ions as well as surface, bulk, and aqueous interfacial properties in excellent agreement with experiment. Induced charges affect the adsorption of ions onto gold surfaces in the gas phase at a strength similar to chemical bonds while ions and charged peptides in solution are influenced at a strength similar to intermolecular bonds. The proposed model can be applied to complex gold interfaces, electrode processes, and extended to other metals.

  11. Viscoelastic crack propagation and closing with Lennard-Jones surface forces

    International Nuclear Information System (INIS)

    Greenwood, J A

    2007-01-01

    An analysis of the opening and closing of a crack in a viscoelastic solid has been made assuming a Lennard-Jones law of force acting between the crack faces. The results are compared with those of an earlier analysis in which a simple Dugdale model of the surface forces was assumed. The approximate 'reciprocal rule' between the apparent surface energies for opening and closing cracks is confirmed. At low speeds a linear relation between the apparent surface energy and the crack speed is found. The lengths of the process zone for opening and closing cracks are found to be very similar and so presumably are not responsible for the very different values of the apparent surface energy

  12. Viscoelastic crack propagation and closing with Lennard-Jones surface forces

    Energy Technology Data Exchange (ETDEWEB)

    Greenwood, J A [Department of Engineering, Trumpington Street, Cambridge, CB2 1PZ (United Kingdom)

    2007-03-21

    An analysis of the opening and closing of a crack in a viscoelastic solid has been made assuming a Lennard-Jones law of force acting between the crack faces. The results are compared with those of an earlier analysis in which a simple Dugdale model of the surface forces was assumed. The approximate 'reciprocal rule' between the apparent surface energies for opening and closing cracks is confirmed. At low speeds a linear relation between the apparent surface energy and the crack speed is found. The lengths of the process zone for opening and closing cracks are found to be very similar and so presumably are not responsible for the very different values of the apparent surface energy.

  13. The Value of Multivariate Model Sophistication: An Application to pricing Dow Jones Industrial Average options

    DEFF Research Database (Denmark)

    Rombouts, Jeroen V.K.; Stentoft, Lars; Violante, Francesco

    innovation for a Laplace innovation assumption improves the pricing in a smaller way. Apart from investigating directly the value of model sophistication in terms of dollar losses, we also use the model condence set approach to statistically infer the set of models that delivers the best pricing performance.......We assess the predictive accuracy of a large number of multivariate volatility models in terms of pricing options on the Dow Jones Industrial Average. We measure the value of model sophistication in terms of dollar losses by considering a set 248 multivariate models that differer...... in their specification of the conditional variance, conditional correlation, and innovation distribution. All models belong to the dynamic conditional correlation class which is particularly suited because it allows to consistently estimate the risk neutral dynamics with a manageable computational effort in relatively...

  14. Platform for Manipulating Polarization Modes Realized with Jones Vectors in MATHEMATICA

    Directory of Open Access Journals (Sweden)

    Yong-Dae Choi

    2015-06-01

    Full Text Available The fundamental conception in physics of the propagation of the electromagnetic wave polarization in matter is newly understood as the cardinal keyword in free-space quantum communication technology and cosmology in astrophysics. Interactive visualization of the propagation mechanism of polarized electromagnetism in a medium with its helicity has accordingly received attention from scientists exploiting the protocol of quantum key distribution (QKD to guarantee unconditional security in cryptography communication. We have provided a dynamic polarization platform for presenting the polarization modes of a transverse electromagnetic wave, converting the state of polarization through the arrangement of optical elements, using Jones vectors calculations in Methematica. The platform graphically simulates the mechanism of production and propagation of the polarized waves in a medium while satisfying Maxwell's equations.

  15. John Paul Jones: An Overlooked Autopsy Finding that May Explain His Terminal Illness.

    Science.gov (United States)

    Hamrell, Burt B

    2016-03-01

    A finding in the autopsy of John Paul Jones, the American Revolutionary War naval hero, may explain his terminal illness. During his last 2 years, he had a persistent productive cough and dyspnea. Ten days before death, he developed rapidly progressive dependent edema and ascites. He died in France in 1792. His body, preserved in alcohol in a lead coffin, was, in 1905, removed to the United States. Glomerulonephritis was noted on an autopsy, performed in France, but there was no comment then or since about ventricular wall thickness being the same in both ventricles at 5-6 mm. Hypertrophy and dilatation with biventricular failure followed by tissue shrinkage during 113 years in alcohol could have resulted in these ventricular wall findings. Systemic hypertension and left ventricular failure are consistent with his respiratory symptoms complicated perhaps by pulmonary emboli, right ventricular failure with tricuspid regurgitation, peripheral congestion, and jaundice. © 2015 American Academy of Forensic Sciences.

  16. Sufism in Writings: Mysticism and Spirituality in the Love Poems of Salleh Ben Joned

    Directory of Open Access Journals (Sweden)

    Nadiah Abdol Ghani

    2013-07-01

    Full Text Available Salleh Ben Joned is seen as a notorious figure in the Malaysian literary scene as a result of his use of profanities and vulgarities, interlacing them into ideas or texts that are seen to be sacred by the society. He is most infamously known for his vivid descriptions of carnal images and sex and its vicissitudes in his poems, thus earning the accusations of being an apostate and his works to be blasphemous. This essay is an attempt at reappraising his love poetry, by explicating the poems using the doctrine of Sufism and its central theme of love and the Beloved/Divine. My view is that his poems are not just describing the ‘profane’ act of sexual copulation, but rather would be more apt in describing a devotee’s spiritual journey towards finding his Beloved or the Divine.

  17. 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

    measured for the clusters of noble gas atoms. Our method serves as an efficient alternative to the global optimization techniques based on the Monte-Carlo simulations and it can be applied for the solutions of a broad variety of problems in which atomic cluster structure is important.......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....... We demonstrate that in this way all known global minima structures of the (LJ)-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...

  18. Dynamics of vacancies in two-dimensional Lennard-Jones crystals

    Science.gov (United States)

    Yao, Zhenwei; Olvera de La Cruz, Monica

    2015-03-01

    Vacancies represent an important class of crystallographic defects, and their behaviors can be strongly coupled with relevant material properties. We report the rich dynamics of vacancies in two-dimensional Lennard-Jones crystals in several thermodynamic states. Specifically, we numerically observe significantly faster diffusion of the 2-point vacancy with two missing particles in comparison with other types of vacancies; it opens the possibility of doping 2-point vacancies into atomic materials to enhance atomic migration. In addition, the resulting dislocations in the healing of a long vacancy suggest the intimate connection between vacancies and topological defects that may provide an extra dimension in the engineering of defects in extensive crystalline materials for desired properties. We thank the financial support from the U.S. Department of Commerce, National Institute of Standards and Technology, the Office of the Director of Defense Research and Engineering (DDR&E) and the Air Force Office of Scientific Research.

  19. 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...... building, and the analysis is a potentially powerful supplement to the diagnostic tools already used in the diagnosis and monitoring of patients with monoclonal plasma cell disorders. However, there are several unsolved aspects for the use of this analysis which must be considered before sFLC can be used...

  20. Viscous Growth in Spinodal Decomposition of the Two-component Lennard-Jones Model in Two Dimensions

    DEFF Research Database (Denmark)

    Laradji, M.; Toxvaerd, S.; Mouritsen, Ole G.

    1997-01-01

    The dynamics of phase separation of a two-component Lennard-Jones model in three dimensions is investigated by means of large scale molecular dynamics simulation. A systematic study over a wide range of quench temperatures within the coexistence region shows that the binary system reaches...

  1. 77 FR 17530 - Order Granting an Application of Edward Jones & Co. LLP Exemption From Exchange Act Section 11(d...

    Science.gov (United States)

    2012-03-26

    ...'') requested that the Securities and Exchange Commission (``Commission'') issue to Edward Jones an exemption... subject to the conditions contained in this order, is exempt from the new issue lending restriction of... SECURITIES AND EXCHANGE COMMISSION [Release No. 34-66624] Order Granting an Application of Edward...

  2. 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).

  3. Life on the edge in eastern Alaska: Basal Ordovician(Tremadocian), platform-margin faunas of the Jones Ridge Formation

    Science.gov (United States)

    Taylor, J. F.; Allen, T. J.; Repetski, John E.; Strauss, J. V.; Irwin, S. J.

    2015-01-01

    As the most fossiliferous and least deformed succession of unequivocally Laurentian lower Paleozoic strata in Alaska, the Jones Ridge Limestone has provided critical data for numerous stratigraphic studies (e. g. Palmer 1968; Harris et al. 1995; Dumoulin et al. 2002; Dumoulin and Harris 2012) focused on the Cambrian and Ordovician of northwestern North America/northeastern Laurentia (Figure 1). The Jones Ridge faunas are also significant in having provided the type material for some of the widespread and biostratigraphically useful latest Furongian and (perhaps) earliest Tremadocian species described by Kobayashi (1936) and Palmer (1968). Unfortunately, some of those taxa were based on very limited material for which, in the earlier study in particular, no detailed information regarding locality or stratigraphic horizon was provided. The limited amount of information and material available for study from Jones Ridge results largely from its remote location on the Yukon-Alaska boundary approximately 25km north of Eagle, Alaska, which renders it accessible only by helicopter. Parts of three field seasons (2010, 2011, and 2014) were invested in re-description and intensive sampling of the type section of the Jones Ridge Formation in order to produce an integrated and greatly refined set of biostratigraphic, chemostratigraphic, and sedimentological data. The new data support the interpretation offered by Palmer (1968) of the Jones Ridge strata as the product of deposition in outermost platform to upper slope environments offered by Palmer (1968) on the basis of taxonomic content of the faunas and close proximity of deep water units of equivalent age a very short distance to the southwest.

  4. Diagnostic accuracy of modified kenneth jones scoring criteria (mkjsc) in confirmed cases of tuberculosis in children

    International Nuclear Information System (INIS)

    Farid, A.; Iqbal, S.M.J.; Hanif, A.

    2013-01-01

    Background: Tuberculosis (TB) is a granulomatous disease caused by Mycobacterium tuberculosis. The gold standard for the diagnosis of tuberculosis is detection of Mycobacterium tubercle bacilli. However, clinical scoring systems are most widely used for the diagnosis of TB in children. Objective: To determine the diagnostic accuracy of modified Kenneth Jones scoring criteria (MKJSC) in conformed cases of tuberculosis. Methodology: This cross-sectional comparative study was conducted in the department of Paediatrics, King Edward Medical University / Mayo Hospital, Lahore from January to June 2007. One hundred children below 15 years of age were enrolled. They were diagnosed as suspected cases of TB on the basis of fever and cough for more than 15 days. MKJSC was applied and each child was subjected to confirmatory test for TB. Results: There was an overall male preponderance of 54%. The mean age of study population was 1.8 +- 0.7 years. Out of 100 children, 66% were diagnosed as TB cases (23 with confirmatory tests and 43 with MKJSC of 5 or more). Sensitivity, specificity, positive and negative predictive value of MKJSC was 73.91%, 44.16%, 28.33%, and 85% respectively. Diagnostic accuracy of MKJSC was 51%. Conclusion: Present study does not support the hypothesis that MKJSC is a good alternative to confirmatory tests to diagnose tuberculosis in children. However, MKJSC is a simple tool, which can be applied to improve the case detection rate in the absence of sophisticated tests. (author)

  5. 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.

  6. Chemical diversity in the essential oil of Indian valerian (Valeriana jatamansi Jones).

    Science.gov (United States)

    Verma, Ram S; Verma, Rajesh K; Padalia, Rajendra C; Chauhan, Amit; Singh, Anand; Singh, Hemendra P

    2011-10-01

    To explore the diversity in the essential oil yield and composition of Valeriana jatamansi Jones (syn. V. wallichii DC) growing wild in Uttarakhand (Western Himalaya), 17 populations were collected from different locations and grown under similar conditions. Comparative results showed considerable variations in the essential oil yield and composition. The essential oil yield varied from 0.21 to 0.46% in the fresh roots and rhizomes of different populations of V. jatamansi. Analysis of the essential oils by GC (RI) and GC/MS and the subsequent classification by principal component analysis (PCA) resulted in six clusters with significant variations in their terpenoid composition. Major components in the essential oils of the different populations were patchouli alcohol (1; 13.4-66.7%), α-bulnesene (3; <0.05-23.5%), α-guaiene (4; 0.2-13.3%), guaiol (5; <0.05-12.2%), seychellene (6; 0.2-9.9%) viridiflorol (<0.05-7.3%), and β-gurjunene (7; 0.0-7.1%). V. jatamansi populations with contents of 1 higher than 60% may be utilized commercially in perfumery. Copyright © 2011 Verlag Helvetica Chimica Acta AG, Zürich.

  7. Essential Oil Composition of Valeriana Jatamansi Jones from Himalayan Regions of India

    Science.gov (United States)

    Raina, Archana P.; Negi, K. S.

    2015-01-01

    Valeriana jatamansi Jones germplasm collected from sub-temperate Himalayan region of Uttarakhand and North-East state of Meghalaya, India was evaluated under identical conditions at National Bureau of Plant Genetic Resources, Bhowali, India, to study germplasm diversity based on essential oil composition. Twenty one compounds were identified in V. jatamansi root oil by GC and GC-MS. The major compounds identified were patchouli alcohol (0.4-63.7%), maaliol (2.9-53.8%), seychellene (4.1-27.4%), calarene/ß-gurjunene (3.0-20.8%), α-santalene (0.6-12.0%). Other compounds present were bornyl acetate (0.6-1.5%), α-guaiene (0.7-2.3%), α-bulnesene/δ-guaiene (0.7-6.3%), 7-epi-α-selinene (0.4-1.4%), kessane (2.1-3.3%), spathulenol (0.7-3.4%), viridiflorol (0.9-7.1%), α-patchoulene (0.8-6.6%), ß-patchoulene (0.4-0.8%). Two superior chemotypes identified in V. jatamansi oil from Uttarakhand were: patchouli alcohol rich (IC573221, 63.7%) and maaliol rich (IC573222, 53.8%; IC589096, 51.7%), while accession from north-east was patchouli alcohol rich chemotype (IC574522, 57.2%). These superior chemotypes with higher amounts of patchouli alcohol and maaliol could be used for promoting cultivation as well as for meeting need of pharmaceutical industries. PMID:26009656

  8. Monological Drama to Reshape the Northern Irish Identity: A Night in November by Marie Jones

    Directory of Open Access Journals (Sweden)

    Virginie Privas

    2010-03-01

    Full Text Available In this contemporary one-man theatre play, Marie Jones’s character, Kenneth McCallister, is prompted to break free from the prejudices in and against Northern Ireland. Indeed, the playwright aims at finding new ways to deconstruct the preconceived idea that there are two different identities in Northern Ireland closely linked to the division between two religious communities. Instead, she seeks connections, even with the Irish who migrated (the diasporic dimension, though, is not to be discussed within this paper. The author explores this possibility through the psychological evolution of a Northern Irish Protestant who comes to lack references in terms of identity. On stage, he recalls the events that launched him on a quest to redefine his identity, an identity in which his religious denomination is taken into account but is not the only community marker. Marie Jones eventually offers an insight into what being and feeling Irish means for someone who has always lived as a Protestant in Northern Ireland. Monologue and the notion of “frontiers” (be they social, political, geographical, historical or theatrical that emerge only to be destroyed, are some of the theatrical devices she resorts to in order to voice her aim in  this experimental play which ultimately proposes to reshape the contours of Northern Irish drama about the Troubles.

  9. A multifractal detrended fluctuation analysis of financial market efficiency: Comparison using Dow Jones sector ETF indices

    Science.gov (United States)

    Tiwari, Aviral Kumar; Albulescu, Claudiu Tiberiu; Yoon, Seong-Min

    2017-10-01

    This study challenges the efficient market hypothesis, relying on the Dow Jones sector Exchange-Traded Fund (ETF) indices. For this purpose, we use the generalized Hurst exponent and multifractal detrended fluctuation analysis (MF-DFA) methods, using daily data over the timespan from 2000 to 2015. We compare the sector ETF indices in terms of market efficiency between short- and long-run horizons, small and large fluctuations, and before and after the global financial crisis (GFC). Our findings can be summarized as follows. First, there is clear evidence that the sector ETF markets are multifractal in nature. We also find a crossover in the multifractality of sector ETF market dynamics. Second, the utilities and consumer goods sector ETF markets are more efficient compared with the financial and telecommunications sector ETF markets, in terms of price prediction. Third, there are noteworthy discrepancies in terms of market efficiency, between the short- and long-term horizons. Fourth, the ETF market efficiency is considerably diminished after the global financial crisis.

  10. 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.

  11. Enhancement of the droplet nucleation in a dense supersaturated Lennard-Jones vapor

    Energy Technology Data Exchange (ETDEWEB)

    Zhukhovitskii, D. I., E-mail: dmr@ihed.ras.ru [Joint Institute of High Temperatures, Russian Academy of Sciences, Izhorskaya 13, Bd. 2, 125412 Moscow (Russian Federation)

    2016-05-14

    The vapor–liquid nucleation in a dense Lennard-Jones system is studied analytically and numerically. A solution of the nucleation kinetic equations, which includes the elementary processes of condensation/evaporation involving the lightest clusters, is obtained, and the nucleation rate is calculated. Based on the equation of state for the cluster vapor, the pre-exponential factor is obtained. The latter diverges as a spinodal is reached, which results in the nucleation enhancement. The work of critical cluster formation is calculated using the previously developed two-parameter model (TPM) of small clusters. A simple expression for the nucleation rate is deduced and it is shown that the work of cluster formation is reduced for a dense vapor. This results in the nucleation enhancement as well. To verify the TPM, a simulation is performed that mimics a steady-state nucleation experiments in the thermal diffusion cloud chamber. The nucleating vapor with and without a carrier gas is simulated using two different thermostats for the monomers and clusters. The TPM proves to match the simulation results of this work and of other studies.

  12. Generation and optimization of superpixels as image processing kernels for Jones matrix optical coherence tomography.

    Science.gov (United States)

    Miyazawa, Arata; Hong, Young-Joo; Makita, Shuichi; Kasaragod, Deepa; Yasuno, Yoshiaki

    2017-10-01

    Jones matrix-based polarization sensitive optical coherence tomography (JM-OCT) simultaneously measures optical intensity, birefringence, degree of polarization uniformity, and OCT angiography. The statistics of the optical features in a local region, such as the local mean of the OCT intensity, are frequently used for image processing and the quantitative analysis of JM-OCT. Conventionally, local statistics have been computed with fixed-size rectangular kernels. However, this results in a trade-off between image sharpness and statistical accuracy. We introduce a superpixel method to JM-OCT for generating the flexible kernels of local statistics. A superpixel is a cluster of image pixels that is formed by the pixels' spatial and signal value proximities. An algorithm for superpixel generation specialized for JM-OCT and its optimization methods are presented in this paper. The spatial proximity is in two-dimensional cross-sectional space and the signal values are the four optical features. Hence, the superpixel method is a six-dimensional clustering technique for JM-OCT pixels. The performance of the JM-OCT superpixels and its optimization methods are evaluated in detail using JM-OCT datasets of posterior eyes. The superpixels were found to well preserve tissue structures, such as layer structures, sclera, vessels, and retinal pigment epithelium. And hence, they are more suitable for local statistics kernels than conventional uniform rectangular kernels.

  13. A Closer Look at the Halloween Effect: The Case of the Dow Jones Industrial Average

    Directory of Open Access Journals (Sweden)

    Peter Arendas

    2018-04-01

    Full Text Available The Halloween effect is one of the most famous calendar anomalies. It is based on the observation that stock returns tend to perform much better over the winter half of the year (November–April than over the summer half of the year (May–October. The vast majority of studies that investigated the Halloween effect over the recent decades focused only on stock indices. This means that they evaluated whether a stock index follows the Halloween effect pattern, but they omitted digging a little deeper and analyze the Halloween effect on the individual stocks level. This paper investigates to what extent the blue-chips stocks included in the Dow Jones Industrial Average are affected by the Halloween effect and whether the Halloween effect is widespread or the behavior of the whole index is driven by only a handful of stocks that are strongly affected by the Halloween effect. The results show that, although the strength of the Halloween effect varies quite rapidly from stock to stock, the vast majority of analyzed stocks experienced a notably higher average winter period than summer period returns over the 1980–2017 period. Moreover, in 18 out of 35 cases, the Halloween effect was statistically significant.

  14. 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.

  15. 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.

  16. Smart imaging for power-efficient extraction of Viola-Jones local descriptors

    Science.gov (United States)

    Fernández-Berni, J.; Carmona-Galán, R. A.; del Río, R.; Leñero-Bardallo, Juan A.; Suárez-Cambre, M.; Rodríguez-Vázquez, Á.

    2014-03-01

    In computer vision, local descriptors permit to summarize relevant visual cues through feature vectors. These vectors constitute inputs for trained classifiers which in turn enable different high-level vision tasks. While local descriptors certainly alleviate the computation load of subsequent processing stages by preventing them from handling raw images, they still have to deal with individual pixels. Feature vector extraction can thus become a major limitation for conventional embedded vision hardware. In this paper, we present a power-efficient sensing processing array conceived to provide the computation of integral images at different scales. These images are intermediate representations that speed up feature extraction. In particular, the mixed-signal array operation is tailored for extraction of Haar-like features. These features feed the cascade of classifiers at the core of the Viola-Jones framework. The processing lattice has been designed for the standard UMC 0.18μm 1P6M CMOS process. In addition to integral image computation, the array can be reprogrammed to deliver other early vision tasks: concurrent rectangular area sum, block-wise HDR imaging, Gaussian pyramids and image pre-warping for subsequent reduced kernel filtering.

  17. 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.

  18. Thermodynamic equivalence between the Lennard-Jones and hard-core attractive Yukawa systems

    International Nuclear Information System (INIS)

    Kadiri, Y.; Albaki, R.; Bretonnet, J.L.

    2008-01-01

    The investigation of the thermodynamic properties of the Lennard-Jones (LJ) fluid is made by means of a system of particles interacting with a potential of hard-core plus attractive Yukawa tail (HCY). Due to the similarity between the LJ potential and the HCY potential in its overall form, it is worthwhile seeking to approximate the LJ potential in much the same way that the hard-sphere reference potential has been so used. The study consists in describing the thermodynamics of the LJ fluid in terms of the equivalent HCY system, whose the properties are known accurately, by means of mapping the thermodynamic quantities for the HCY potential parameters. The method is feasible owing to a convenient analytical expression of the Helmholtz free energy from the mean-spherical approximation expanded in power of the inverse temperature. Two different procedures are used to determine the parameters of the HCY potential as a function of the thermodynamic states: one is based on the simultaneous fits of pressure and internal energy of the LJ system and the other uses the concept of collision frequency. The reasonable homogeneity of the results in both procedures of mapping makes that the HCY potential is a very good reference system, whose the proposed theoretical expressions can be used confidently to predict the thermodynamic properties of more realistic potentials

  19. Modified Benedict-Webb-Rubin Equation of State for the Modified Lennard-Jones Fluid

    Science.gov (United States)

    Asano, Yuta; Fuchizaki, Kazuhiro

    2014-03-01

    We have proposed a modified Lennard-Jones (mLJ) potential to deal with problems, such as the accurate determination of the melting condition, in which an attractive interaction plays an essential role, but its range need not necessarily extend to infinity. An accurate phase diagram, including the triple and the critical points of the system characterized by the mLJ potential, has been investigated using mainly thermodynamic integration. To predict the thermodynamic behavior of the system, it is further desired to construct the equation of state (EOS) as accurately as possible. The modified Benedict-Webb-Rubin EOS was employed to this end. The 33 parameters involved in the equation were carefully determined in order for the EOS to be compatible with the temperature dependences of the virial coefficients as well as with an extremely large set of thermodynamic data obtained from our own molecular dynamics simulation performed over a wide fluid region. The resultant EOS was found to be not only sufficiently accurate at temperatures up to twenty times as high as the critical-point temperature but also effective in practical use.

  20. Comprehensive representation of the Lennard-Jones equation of state based on molecular dynamics simulation data

    Science.gov (United States)

    Pieprzyk, S.; Brańka, A. C.; Maćkowiak, Sz.; Heyes, D. M.

    2018-03-01

    The equation of state (EoS) of the Lennard-Jones fluid is calculated using a new set of molecular dynamics data which extends to higher temperature than in previous studies. The modified Benedict-Webb-Rubin (MBWR) equation, which goes up to ca. T ˜ 6, is reparametrized with new simulation data. A new analytic form for the EoS, which breaks the fluid range into two regions with different analytic forms and goes up to ca. T ≃ 35, is also proposed. The accuracy of the new formulas is at least as good as the MBWR fit and goes to much higher temperature allowing it to now encompass the Amagat line. The fitted formula extends into the high temperature range where the system can be well represented by inverse power potential scaling, which means that our specification of the equation of state covers the entire (ρ, T) plane. Accurate analytic fit formulas for the Boyle, Amagat, and inversion curves are presented. Parametrizations of the extrema loci of the isochoric, CV, and isobaric, CP, heat capacities are given. As found by others, a line maxima of CP terminates in the critical point region, and a line of minima of CP terminates on the freezing line. The line of maxima of CV terminates close to or at the critical point, and a line of minima of CV terminates to the right of the critical point. No evidence for a divergence in CV in the critical region is found.

  1. Non-equilibrium surface tension of the vapour-liquid interface of active Lennard-Jones particles

    Science.gov (United States)

    Paliwal, Siddharth; Prymidis, Vasileios; Filion, Laura; Dijkstra, Marjolein

    2017-08-01

    We study a three-dimensional system of self-propelled Brownian particles interacting via the Lennard-Jones potential. Using Brownian dynamics simulations in an elongated simulation box, we investigate the steady states of vapour-liquid phase coexistence of active Lennard-Jones particles with planar interfaces. We measure the normal and tangential components of the pressure tensor along the direction perpendicular to the interface and verify mechanical equilibrium of the two coexisting phases. In addition, we determine the non-equilibrium interfacial tension by integrating the difference of the normal and tangential components of the pressure tensor and show that the surface tension as a function of strength of particle attractions is well fitted by simple power laws. Finally, we measure the interfacial stiffness using capillary wave theory and the equipartition theorem and find a simple linear relation between surface tension and interfacial stiffness with a proportionality constant characterized by an effective temperature.

  2. The roofs of Wren and Jones: a seventeenth-century migration of technical knowledge from Italy to England

    OpenAIRE

    Simona Valeriani

    2006-01-01

    Seventeenth-century English architecture saw the introduction of a new style, influenced by continental Europe, and driven, to a large extent, by the work of Inigo Jones and Christopher Wren. But along with the aesthetic novelty came novel building techniques; construction methods embedded within the stylistic changes showing that the continental influence was felt as much within the structures of the buildings as it was upon their façades. Focussing here on the methods used to construct wood...

  3. Ab initio study of the atomic motion in liquid metal surfaces: comparison with Lennard-Jones systems

    International Nuclear Information System (INIS)

    Gonzalez, Luis E; Gonzalez, David J

    2006-01-01

    It is established that liquid metals exhibit surface layering at the liquid-vapour interface, while dielectric simple systems, like those interacting through Lennard-Jones potentials, show a monotonic decay from the liquid density to that of the vapour. First principles molecular dynamics simulations of the free liquid surface of several liquid metals (Li, Na, K, Rb, Cs, Mg, Ba, Al, Tl and Si), and the Na 3 K 7 alloy near their triple points have been performed in order to study the atomic motion at the interface, mainly at the outer layer. Comparison with the results of classical molecular dynamics simulations of a Lennard-Jones system shows interesting differences and similarities. The probability distribution function of the time of residence in a layer shows a peak at very short times and a long-lasting tail. The mean residence time in a layer increases when approaching the interfacial region, slightly in the Lennard-Jones system but strongly in the metallic systems. The motion within the layers, parallel to the interface, can be described as diffusion enhanced (strongly in the case of the outermost layer) with respect to the bulk, for both types of systems, despite its reduced dimensionality in metals

  4. Comparative cephalometric study of Class II malocclusion treatment with Pendulum and Jones jig appliances followed by fixed corrective orthodontics.

    Science.gov (United States)

    Patel, Mayara Paim; Henriques, José Fernando Castanha; de Almeida, Renato Rodrigues; Pinzan, Arnaldo; Janson, Guilherme; de Freitas, Marcos Roberto

    2013-01-01

    The purpose of this study was to cephalometrically compare the skeletal and dentoalveolar effects in the treatment of Class II malocclusion with Pendulum and Jones jig appliances, followed by fixed corrective orthodontics, and to compare such effects to a control group. The sample was divided into three groups. Group 1: 18 patients treated with Pendulum, Group 2: 25 patients treated with Jones jig, and Group 3: 19 young subjects with untreated Class II malocclusions and initial mean age of 12.88 years. The chi-square test was applied to assess severity and gender distribution. Groups 1 and 2 were compared to the control group by means of the one-way ANOVA and Tukey tests in order to differentiate treatment changes from those occurred by craniofacial growth. There were no significant changes among the three groups with regard to the components of the maxilla and the mandible, maxillomandibular relationship, cephalometric and tegumental pattern. Buccal tipping of mandibular incisors was significantly greater in the experimental groups and increased mesial angulation of the maxillary second molars was found in the Jones jig group. In the experimental groups, dental relationship, overbite and overjet were corrected. It can be stated that the distalization achieved its purpose of correcting the Class II.

  5. Comparison of the Pendulum appliance and the Jones Jig: A prospective comparative study.

    Science.gov (United States)

    Shetty, Sushruth; Maurya, Rajkumar; Raj, H V Pruthvi; Patil, Anand

    2017-01-01

    To compare two molar distalization devices, the Pendulum appliance (PA) and the Jones Jig (JJ) in dental Class II patients. Pretreatment and postdistalization lateral cephalograms and study models of 20 subjects (6 males, 14 females) Class II malocclusion subjects were examined. PA and JJ group both consisted of 10 patients each with a mean pretreatment age of 12 years 1 month for females and 12 years 5 months for males. The PA and the JJ appliance were activated once in a month until Class II molar relationship was corrected to a super Class I molar relationship in both groups. Initial and final measurements and treatment changes were compared by means of Paired t -test. Maxillary first molar distalized an average of 3.85 mm in the PA and 2.75 mm in the JJ between T1 and T2; rate of molar distalization was 1.59 mm/month for PA, and the JJ appliance averaged 0.88 mm/month, distal molar tipping was greater in PA (6.2°) than in the JJ (3.9°). Average mesial movement of the premolars was 2.2 mm with PA and JJ both. JJ showed a greater rotation of first molars after distalization as compared to PA. The increase in vertical facial height was also greater for JJ as compared to PA. Both the appliances were effective in molar distalization with PA requiring less distalization time (16 days less than JJ). Some adverse effects were noted with both which one should strive to control.

  6. Drying and wetting transitions of a Lennard-Jones fluid: Simulations and density functional theory

    Science.gov (United States)

    Evans, Robert; Stewart, Maria C.; Wilding, Nigel B.

    2017-07-01

    We report a theoretical and simulation study of the drying and wetting phase transitions of a truncated Lennard-Jones fluid at a flat structureless wall. Binding potential calculations predict that the nature of these transitions depends on whether the wall-fluid attraction has a long ranged (LR) power law decay or is instead truncated, rendering it short ranged (SR). Using grand canonical Monte Carlo simulation and classical density functional theory, we examine both cases in detail. We find that for the LR case wetting is first order, while drying is continuous (critical) and occurs exactly at zero attractive wall strength, i.e., in the limit of a hard wall. In the SR case, drying is also critical but the order of the wetting transition depends on the truncation range of the wall-fluid potential. We characterize the approach to critical drying and wetting in terms of the density and local compressibility profiles and via the finite-size scaling properties of the probability distribution of the overall density. For the LR case, where the drying point is known exactly, this analysis allows us to estimate the exponent ν∥, which controls the parallel correlation length, i.e., the extent of vapor bubbles at the wall. Surprisingly, the value we obtain is over twice that predicted by mean field and renormalization group calculations, despite the fact that our three dimensional system is at the upper critical dimension where mean field theory for critical exponents is expected to hold. Possible reasons for this discrepancy are discussed in the light of fresh insights into the nature of near critical finite-size effects.

  7. Chemical potential and solid-solid equilibrium of near-spherical Lennard-Jones dumbbell crystal

    International Nuclear Information System (INIS)

    Lee, Sangwon; Kim, Minkyu; Chang, Jaeeon

    2016-01-01

    We studied the orientational order-disorder transition of crystals made up of near-spherical Lennard-Jones dumbbells, of which reduced bond lengths are 0.225, 0.250 and 0.275. Various techniques of Monte Carlo (MC) simulations are used to calculate the chemical potentials of ordered and disordered crystals, and thereby to predict order disorder phase transition. First, we performed NPT MC simulations to determine crystal structure, equilibrium positions and orientations of the molecules. We then calculated the free energies of the crystals using the expanded ensemble MC simulations combined with the Einstein-molecule method and the thermodynamic integration method. The solid-solid phase equilibrium is determined from the free energy profiles of the individual phases by equating the chemical potential. The predictions of phase transition obtained from the conventional NPT MC simulation and the free energy simulation were in excellent agreement with each other, which confirms the validity of the present method of calculating the chemical potential of crystal. In addition, the Gibbs-Duhem integration was performed to obtain a complete coexistence curve between the two crystal phases. Orientational probability distributions of molecular axes were analyzed to find the characteristic behavior of rotational motion of molecule in the crystal. At sufficiently low temperature, flipping rotation of molecule in the ordered crystal is suppressed. In contrast, the flipping rotation occurs at higher temperature close to the transition while orientationally ordered structure is still maintained. In the free energy calculation, such a unique rotational behavior requires to use a suitable form of external rotational potential with proper symmetry number. The present study demonstrates how one can judiciously choose a correct simulation scheme for the calculation of chemical potentials of molecular crystals.

  8. Drying and wetting transitions of a Lennard-Jones fluid: Simulations and density functional theory.

    Science.gov (United States)

    Evans, Robert; Stewart, Maria C; Wilding, Nigel B

    2017-07-28

    We report a theoretical and simulation study of the drying and wetting phase transitions of a truncated Lennard-Jones fluid at a flat structureless wall. Binding potential calculations predict that the nature of these transitions depends on whether the wall-fluid attraction has a long ranged (LR) power law decay or is instead truncated, rendering it short ranged (SR). Using grand canonical Monte Carlo simulation and classical density functional theory, we examine both cases in detail. We find that for the LR case wetting is first order, while drying is continuous (critical) and occurs exactly at zero attractive wall strength, i.e., in the limit of a hard wall. In the SR case, drying is also critical but the order of the wetting transition depends on the truncation range of the wall-fluid potential. We characterize the approach to critical drying and wetting in terms of the density and local compressibility profiles and via the finite-size scaling properties of the probability distribution of the overall density. For the LR case, where the drying point is known exactly, this analysis allows us to estimate the exponent ν ∥ , which controls the parallel correlation length, i.e., the extent of vapor bubbles at the wall. Surprisingly, the value we obtain is over twice that predicted by mean field and renormalization group calculations, despite the fact that our three dimensional system is at the upper critical dimension where mean field theory for critical exponents is expected to hold. Possible reasons for this discrepancy are discussed in the light of fresh insights into the nature of near critical finite-size effects.

  9. 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

  10. Size-effects on the surface tension near the critical point: Monte Carlo simulations of the Lennard-Jones fluid

    Science.gov (United States)

    Goujon, Florent; Ghoufi, Aziz; Malfreyt, Patrice

    2018-02-01

    We report Monte Carlo (MC) simulations of the Lennard-Jones (LJ) fluid at the liquid-vapor interface in the critical region. A slab-based tail method is associated with the MC simulations to approach as close as possible the critical point (T∗ = 0.98 TC∗) . We investigate then the impact of system-sizes on the surface tension and coexisting densities by considering very large box dimensions for which the surface tension is independent of system-sizes at low temperatures.

  11. The self-referential method for linear rigid bodies: application to hard and Lennard-Jones dumbbells.

    Science.gov (United States)

    Sweatman, Martin B; Atamas, Alexander; Leyssale, Jean-Marc

    2009-01-14

    The self-referential (SR) method incorporating thermodynamic integration (TI) [Sweatman et al., J. Chem. Phys. 128, 064102 (2008)] is extended to treat systems of rigid linear bodies. The method is then applied to obtain the canonical ensemble Helmholtz free energy of the alpha-N(2) and plastic face centered cubic phases of systems of hard and Lennard-Jones dumbbells using Monte Carlo simulations. Generally good agreement with reference literature data is obtained, which indicates that the SR-TI method is potentially very general and robust.

  12. 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.

  13. Percutaneous internal fixation of proximal fifth metatarsal jones fractures (Zones II and III) with Charlotte Carolina screw and bone marrow aspirate concentrate: an outcome study in athletes.

    Science.gov (United States)

    Murawski, Christopher D; Kennedy, John G

    2011-06-01

    Internal fixation is a popular first-line treatment method for proximal fifth metatarsal Jones fractures in athletes; however, nonunions and screw breakage can occur, in part because of nonspecific fixation hardware and poor blood supply. To report the results from 26 patients who underwent percutaneous internal fixation with a specialized screw system of a proximal fifth metatarsal Jones fracture (zones II and III) and bone marrow aspirate concentrate. Case series; Level of evidence, 4. Percutaneous internal fixation for a proximal fifth metatarsal Jones fracture (zones II and III) was performed on 26 athletic patients (mean age, 27.47 years; range, 18-47). All patients were competing at some level of sport and were assessed preoperatively and postoperatively using the Foot and Ankle Outcome Score and SF-12 outcome scores. The mean follow-up time was 20.62 months (range, 12-28). Of the 26 fractures, 17 were traditional zone II Jones fractures, and the remaining 9 were zone III proximal diaphyseal fractures. The mean Foot and Ankle Outcome Score significantly increased, from 51.15 points preoperatively (range, 14-69) to 90.91 at final follow-up (range, 71-100; P fixation of proximal fifth metatarsal Jones fractures, with a Charlotte Carolina screw and bone marrow aspirate concentrate, provides more predictable results while permitting athletes a return to sport at their previous levels of competition, with few complications.

  14. 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.

  15. 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.

  16. Density-scaling exponents and virial potential-energy correlation coefficients for the (2n, n) Lennard-Jones system

    DEFF Research Database (Denmark)

    Friisberg, Ida Marie; Costigliola, Lorenzo; Dyre, Jeppe C.

    2017-01-01

    This paper investigates the relation between the density-scaling exponent γ and the virial potentialenergy coefficient R at several thermodynamic state points in three dimensions for the generalized (2n, n) Lennard-Jones (LJ) system for n = 4, 9, 12, 18, as well as for the standard n = 6 LJ system...... in two, three, and four dimensions. The state points studied include many low-density states at which the virial potentialenergy correlations are not strong. For these state points we find the roughly linear relation γ ∼= 3n R/d in d dimensions. This result is discussed in light of the approximate...... → 1, a limit that is approached at high densities and/or high temperatures at which the repulsive r−2n term dominates the physics....

  17. Noise-immune complex correlation for optical coherence angiography based on standard and Jones matrix optical coherence tomography.

    Science.gov (United States)

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

    2016-04-01

    This paper describes a complex correlation mapping algorithm for optical coherence angiography (cmOCA). The proposed algorithm avoids the signal-to-noise ratio dependence and exhibits low noise in vasculature imaging. The complex correlation coefficient of the signals, rather than that of the measured data are estimated, and two-step averaging is introduced. Algorithms of motion artifact removal based on non perfusing tissue detection using correlation are developed. The algorithms are implemented with Jones-matrix OCT. Simultaneous imaging of pigmented tissue and vasculature is also achieved using degree of polarization uniformity imaging with cmOCA. An application of cmOCA to in vivo posterior human eyes is presented to demonstrate that high-contrast images of patients' eyes can be obtained.

  18. Premelting, solid-fluid equilibria, and thermodynamic properties in the high density region based on the Lennard-Jones potential

    Science.gov (United States)

    Köster, Andreas; Mausbach, Peter; Vrabec, Jadran

    2017-10-01

    The Lennard-Jones potential is used to study the high density fluid and face centered cubic solid state region, including solid-fluid equilibria. Numerous thermodynamic properties are considered, elucidating the behavior of matter in this poorly studied region. The present molecular simulation results are extensively compared to the latest and most accurate equation of state models for fluid and solid phases. It is shown that current models do not cover the thermodynamics of the system adequately near the solid-fluid phase transition. Furthermore, thermodynamic stability is analyzed, indicating that published solid-fluid coexistence data may not be correct at high temperatures. Particular attention is paid to the premelting zone, a range of states close to the melting line, which is characterized by strong variations of several thermodynamic properties. Because the underlying microscopic mechanisms are not yet fully understood, it is hoped that these data may contribute to the development of a theoretical framework for describing premelting effects.

  19. Effect of surface tension on the behavior of adhesive contact based on Lennard-Jones potential law

    Science.gov (United States)

    Zhu, Xinyao; Xu, Wei

    2018-02-01

    The present study explores the effect of surface tension on adhesive contact behavior where the adhesion is interpreted by long-range intermolecular forces. The adhesive contact is analyzed using the equivalent system of a rigid sphere and an elastic half space covered by a membrane with surface tension. The long-range intermolecular forces are modeled with the Lennard‒Jones (L‒J) potential law. The current adhesive contact issue can be represented by a nonlinear integral equation, which can be solved by Newton‒Raphson method. In contrast to previous studies which consider intermolecular forces as short-range, the present study reveals more details of the features of adhesive contact with surface tension, in terms of jump instabilities, pull-off forces, pressure distribution within the contact area, etc. The transition of the pull-off force is not only consistent with previous studies, but also presents some new interesting characteristics in the current situation.

  20. Selection and Validation of Charge and Lennard-Jones Parameters for QM/MM Simulations of Hydrocarbon Interactions with Zeolites.

    Science.gov (United States)

    Zimmerman, Paul M; Head-Gordon, Martin; Bell, Alexis T

    2011-06-14

    Quantum mechanics/molecular mechanics (QM/MM) models are an appealing method for performing zeolite simulations. In QM/MM, a small cluster chosen to encompass the active center is described by QM, while the rest of the zeolite is described by MM. In the present study, we demonstrate that the charges and Lennard-Jones parameters on Si and O must be chosen properly for QM/MM calculations of adsorption energies and activation energies to agree closely with full QM calculations. The selection of parameters for Si and O is based on using the ωB97X-D functional for DFT calculations of the QM region, which is effective in capturing the effects of van der Waals interactions. A comparison of the heats of adsorption for a variety of adsorbates and activation energies for the cracking of propane and butane reveals that energies derived from QM/MM calculation carried out with appropriately selected MM parameters agree to within an rms error of ∼1.5 kcal/mol with QM calculations. To avoid reparametrization for new substrates, Lennard-Jones zeolite parameters are chosen to be compatible with existing CHARMM parameters. Transferability of these parameters is demonstrated by tests utilizing the B3LYP density functional and simulations of MFI and FAU zeolites. Moreover, the computational time for QM/MM calculations is considerably lower than that for QM calculations, and the ratio of computational times decreases rapidly with increasing size of the cluster used to represent the zeolite.

  1. 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

  2. A QM/MM and QM/QM/MM study of Kerr, Cotton-Mouton and Jones linear birefringences in liquid acetonitrile

    DEFF Research Database (Denmark)

    Fahleson, Tobias; Olsen, Jógvan Magnus Haugaard; Norman, Patrick

    2018-01-01

    QM/MM and QM/QM/MM protocols are applied to the ab initio study of the three linear birefringences Kerr, Cotton-Mouton, and Jones, as shown by acetonitrile in the gas and pure liquid phases. The relevant first-order properties as well as linear, quadratic, and cubic frequency-dependent response...

  3. The white-margined penstemon (Penstemon albomarginatus Jones), a rare Mohave Desert species, and the Hualapai Mountains land exchange in Mohave County, Arizona

    Science.gov (United States)

    John L. Anderson

    2001-01-01

    The white-margined penstemon (Penstemon albomarginatus Jones) is a rare Mohave Desert species with an unusual tripartite distribution with disjunct localities in Arizona, California, and Nevada. The Arizona population is the largest single population occurring with a range of 15 miles by 5 miles in Dutch Flat near Yucca, Arizona in Mohave County. The land ownership...

  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. Revision of the Jones Criteria for the diagnosis of acute rheumatic fever in the era of Doppler echocardiography: a scientific statement from the American Heart Association.

    Science.gov (United States)

    Gewitz, Michael H; Baltimore, Robert S; Tani, Lloyd Y; Sable, Craig A; Shulman, Stanford T; Carapetis, Jonathan; Remenyi, Bo; Taubert, Kathryn A; Bolger, Ann F; Beerman, Lee; Mayosi, Bongani M; Beaton, Andrea; Pandian, Natesa G; Kaplan, Edward L

    2015-05-19

    Acute rheumatic fever remains a serious healthcare concern for the majority of the world's population despite its decline in incidence in Europe and North America. The goal of this statement was to review the historic Jones criteria used to diagnose acute rheumatic fever in the context of the current epidemiology of the disease and to update those criteria to also take into account recent evidence supporting the use of Doppler echocardiography in the diagnosis of carditis as a major manifestation of acute rheumatic fever. To achieve this goal, the American Heart Association's Council on Cardiovascular Disease in the Young and its Rheumatic Fever, Endocarditis, and Kawasaki Disease Committee organized a writing group to comprehensively review and evaluate the impact of population-specific differences in acute rheumatic fever presentation and changes in presentation that can result from the now worldwide availability of nonsteroidal anti-inflammatory drugs. In addition, a methodological assessment of the numerous published studies that support the use of Doppler echocardiography as a means to diagnose cardiac involvement in acute rheumatic fever, even when overt clinical findings are not apparent, was undertaken to determine the evidence basis for defining subclinical carditis and including it as a major criterion of the Jones criteria. This effort has resulted in the first substantial revision to the Jones criteria by the American Heart Association since 1992 and the first application of the Classification of Recommendations and Levels of Evidence categories developed by the American College of Cardiology/American Heart Association to the Jones criteria. This revision of the Jones criteria now brings them into closer alignment with other international guidelines for the diagnosis of acute rheumatic fever by defining high-risk populations, recognizing variability in clinical presentation in these high-risk populations, and including Doppler echocardiography as a tool

  6. Analysis of compression forces between varying sizes of cannulated screws versus rail external fixation for treatment of Jones type fifth metatarsal fracture.

    Science.gov (United States)

    Freschi, Scot A; Vardaxis, Vassilios; Dodson, Nic

    2008-01-01

    This study compared peak compression load in Newtons and stiffness in Newtons/millimeter for varying interfragmental screw sizes versus mini rail external fixation for the surgical treatment of Jones fifth metatarsal fractures. Four groups were included into this study: (1) Jones fracture with external fixation (Orthofix, Inc., McKinney, TX); (2) Jones fracture with 4.5-mm interfragmental cannulated screw; (3) Jones fracture with 5.5-mm interfragmental cannulated screw; and (4) Jones fracture with 6.5-mm interfragmental cannulated screw. There was no statistically significant difference between the peak compression achieved with the different groups of interfragmental cannulated screws: 4.5-mm interfragmental cannulated screw = 30.56 (+/- 9.40) N; 5.5-mm interfragmental cannulated screw = 30.69 (+/- 10.75) N; and 6.5-mm interfragmental cannulated screw = 32.84 (+/- 9.65) N. When comparing the compression achieved with the different groups of interfragmental cannulated screws to that achieved with the small rail external fixator (69.70 [+/- 14.69] N), a statistically significant difference was noted. There was no statistically significant difference in regard to stiffness (Newtons/millimeter) noted between the intramedullary cannulated screw groups: 4.5 cannulated screw 5.25 (+/- 1.96), 5.5 cannulated screw 5.50 (+/- 2.01), and 6.5 cannulated screw 6.75 (+/- 2.60). A statistically significant difference was noted when the stiffness (Newtons/millimeter) of the rail external fixator (12.69 (+/- 4.52) was compared to the stiffness achieved with the different interfragmental screws. The results indicated that the small rail external fixation device provided increased compression and an increased ability to resist bending when compared to the different intramedullary cannulated screws.

  7. Multiple Myeloma Presenting as Acute Renal Failure in the Absence of Other Characteristic Features.

    Science.gov (United States)

    Gastelum, Zachary N; Biggs, Diana M; Scott, Aaron

    2017-09-20

    This case report describes a 54-year-old, asymptomatic man who presented with hyperkalemia on routine lab testing who was later found to have acute renal failure, unresponsive to fluid resuscitation, with minimal improvement after hemodialysis. After a comprehensive evaluation ruled out common causes of acute renal failure, the patient underwent testing with a bone survey, urine protein electrophoresis (UPEP), serum protein electrophoresis (SPEP), and immunoelectrophoresis for suspected plasma cell dyscrasia and received plasmapheresis for hyperviscosity syndrome and nephrotoxicity, which resulted in improved renal function. Lab results showed monoclonal gammopathy, elevated serum free light chains, and Bence Jones protein in the urine with a follow-up bone marrow biopsy indicating plasma cell dyscrasia. The patient received a diagnosis of multiple myeloma (MM) and was started on chemotherapy and immunosuppression. In patients presenting with acute renal failure with an evaluation ruling out prerenal and postrenal causes, multiple myeloma should be considered.

  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. 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.

  10. Icosahedron-fcc transition size by molecular dynamics simulation of Lennard-Jones clusters at a finite temperature.

    Science.gov (United States)

    Ikeshoji, T; Torchet, G; de Feraudy, M F; Koga, K

    2001-03-01

    We studied finite-temperature ensembles of solid clusters produced by cooling liquid droplets either by evaporation or by a thermostat through a molecular dynamics calculation using the Lennard-Jones potential. The ensembles consist of either single or binary component clusters with 25% of the atoms 8% smaller in diameter than the other 75%. These clusters (380 clusters in total) exhibit various structures in the size range of n=160-2200, where n is the number of atoms in a cluster. For increasing size, the clusters show a gradual transition from icosahedral to a variety of structures: decahedral, face centered cubic, a small amount of hexagonal, and some icosahedral structures. They are asymmetrical or faulted. Electron diffraction patterns calculated with average structure factors of clusters after grouping them into several size regions are very similar to those experimentally observed. The size transition is around n=450 for single component clusters whatever the cooling process, evaporation or thermostat. This size is smaller than the experimental transition size estimated for argon clusters formed in a supersonic expansion. The transition size for binary component clusters is around n=600 for evaporative cooling, and larger for thermostatic cooling. The larger transition size found for the binary component clusters is consistent with the large icosahedral Au-Fe and Au-Cu alloy clusters observed experimentally.

  11. Equation of state and Helmholtz free energy for the atomic system of the repulsive Lennard-Jones particles.

    Science.gov (United States)

    Mirzaeinia, Ali; Feyzi, Farzaneh; Hashemianzadeh, Seyed Majid

    2017-12-07

    Simple and accurate expressions are presented for the equation of state (EOS) and absolute Helmholtz free energy of a system composed of simple atomic particles interacting through the repulsive Lennard-Jones potential model in the fluid and solid phases. The introduced EOS has 17 and 22 coefficients for fluid and solid phases, respectively, which are regressed to the Monte Carlo (MC) simulation data over the reduced temperature range of 0.6≤T * ≤6.0 and the packing fraction range of 0.1 ≤ η ≤ 0.72. The average absolute relative percent deviation in fitting the EOS parameters to the MC data is 0.06 and 0.14 for the fluid and solid phases, respectively. The thermodynamic integration method is used to calculate the free energy using the MC simulation results. The Helmholtz free energy of the ideal gas is employed as the reference state for the fluid phase. For the solid phase, the values of the free energy at the reduced density equivalent to the close-packed of a hard sphere are used as the reference state. To check the validity of the predicted values of the Helmholtz free energy, the Widom particle insertion method and the Einstein crystal technique of Frenkel and Ladd are employed. The results obtained from the MC simulation approaches are well agreed to the EOS results, which show that the proposed model can reliably be utilized in the framework of thermodynamic theories.

  12. Phenotypic and Genetic Characterization of Erwiniua carotovora spp. carotovora (JOnes Bergey et al. Isolates from Grafted Tomato in Sardinia, Italy

    Directory of Open Access Journals (Sweden)

    M. Fiori

    2005-04-01

    Full Text Available A disease symptomatically similar to that caused by Erwinia carotovora occurred on “Cuore di Bue” and “Cencara” tomato plants grafted on “Beaufort” and “He-Man”, or ungrafted, in greenhouses in Sardinia (Italy. Symptoms were: dark brown/black longitudinal stem lesions, soft stem rot, pith breakdown of the stems, hollow stems, vascular tissue discoloration, wilting and collapse of the plants. Numerous bacterial colonies from stem tissues were isolated on yeast extract salts (YS medium. Seven isolates (DPP As-1, DPP As-2, DPP As-3, DPP As-14, DPP Pu6, DPP Pu7 e DPP Pu8 were selected on the basis of their ability to cause rot on potato pieces and a hypersensitivity reaction in “White burley” tobacco leaves. Pathogenicity tests revealed that five of these isolates infected artichoke, basil, dwarf bean, fennel, marrow, melon, pepper, eggplant, grafted and ungrafted tomato, and white cabbage. Of the remaining two isolates, one (DPP As-1 did not infect white cabbage, and the other (DPP Pu8 did not infect basil, marrow or white cabbage. Phenotypic properties and ELISA, also performed on naturally infected tissues, revealed that all the isolates were E. c. ssp. carotovora (Jones Bergey et al. PCR-RFLP analysis placed two (DPP As-2 and DPP As-3 of the seven isolates in RFLP group 8. Five isolates belonged to a hitherto unknown RFLP group. Prevention and control measures for this disease are suggested.

  13. Influence of DC electric field on the Lennard-Jones potential and phonon vibrations of carbon nanotube on catalyst

    International Nuclear Information System (INIS)

    Saeidi, Mohammadreza; Vaezzadeh, Majid; Badakhshan, Farzaneh

    2011-01-01

    Influence of DC electric field on carbon nanotube (CNT) growth in chemical vapor deposition is studied. Investigation of electric field effect in van der Waals interaction shows that increase in DC electric field raises the magnitude of attractive term of the Lennard-Jones potential. By using a theoretical model based on phonon vibrations of CNT on catalyst, it is shown that there is an optimum field for growth. Also it is observed that CNT under optimum electric field is longer than CNT in the absence of field. Finally, the relation between optimum DC electric field and type of catalyst is investigated and for some intervals of electric field, the best catalyst is introduced, which is very useful for experimental researches. -- Research highlights: → Influence of DC electric field on CNT growth in CVD. → Effect of electric field on van der Waals interaction between CNT and its catalyst. → Applying DC electric field increases attractive term of Lennard-Jonespotential. → There is an optimum DC field for CNT growth. → For catalyst with stronger van der Waals interaction, optimum field is smaller.

  14. Novel method for localization of common carotid artery transverse section in ultrasound images using modified Viola-Jones detector.

    Science.gov (United States)

    Ríha, Kamil; Mašek, Jan; Burget, Radim; Beneš, Radek; Závodná, Eva

    2013-10-01

    This article describes a novel method for highly accurate and effective localization of the transverse section of the carotis comunis artery in ultrasound images. The method has a high success rate, approximately 97%. Unlike analytical methods based on geometric descriptions of the object sought, the method proposed here can cover a large area of shape variation of the artery under study, which normally occurs during examinations as a result of the pressure on the examined tissue, tilt of the probe, setup of the sonographic device, and other factors. This method shows great promise in automating the process of determining circulatory system parameters in the non-invasive clinical diagnostics of cardiovascular diseases. The method employs a Viola-Jones detector that has been specially adapted for efficient detection of transverse sections of the carotid artery. This algorithm is trained on a set of labeled images using the AdaBoost algorithm, Haar-like features and the Matthews coefficient. The training algorithm of the artery detector was modified using evolutionary algorithms. The method for training a cascade of classifiers achieves on a small number of positive and negative training data samples (about 500 images) a high success rate in a computational time that allows implementation of the detector in real time. Testing was performed on images of different patients for whom different ultrasonic instruments were used under different conditions (settings) so that the algorithm developed is applicable in general radiologic practice. 2013 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved

  15. Numerical computations of the Lennard-Jones resonances and ''relative displacements'' of the scattered atomic beams from the system He/LiF(001)

    International Nuclear Information System (INIS)

    Garcia, N.

    1976-01-01

    This paper considers the effect of the attractive part of the interaction potential on the scattering of He atoms from a LiF(001) surface. We calculate, in particular, the Lennard-Jones resonances on the intensities and the phases of the scattered amplitudes, using a square well in the front of a hard corrugated surface model. We show that the amplitudes for incident energies smaller than the depth of the well are dominated by the resonances

  16. Method and system of Jones-matrix mapping of blood plasma films with "fuzzy" analysis in differentiation of breast pathology changes

    Science.gov (United States)

    Zabolotna, Natalia I.; Radchenko, Kostiantyn O.; Karas, Oleksandr V.

    2018-01-01

    A fibroadenoma diagnosing of breast using statistical analysis (determination and analysis of statistical moments of the 1st-4th order) of the obtained polarization images of Jones matrix imaginary elements of the optically thin (attenuation coefficient τ fibroadenoma" of breast was 82.7% by the method of linear discriminant analysis, and by the "fuzzy" logic method is 95.3%. The obtained results allow to confirm the potentially high level of reliability of the method of differentiation by "fuzzy" analysis.

  17. [Differential diagnosis of proteinuria].

    Science.gov (United States)

    Rupprecht, H D

    2004-10-21

    Normally, protein secretion in the urine is less than 150 mg/day or less than 100 mg/g creatinine. Orthostatic proteinuria, proteinuria in the presence of fever, and effort proteinuria are benign forms. In cases of persistent proteinuria, prerenal or overflow proteinuria are distinguished from renal and post-renal proteinuria. Renal forms can be differentiated into glomerular and tubular as well as mixed forms. The urine dipstick is of only low sensitivity, and is therefore unsuitable as a screening test for diabetic microalbuminuria. In addition, it cannot detect immunoglobulin light chains in Bence Jones proteinuria. For the differentiation between glomerular and tubular forms of proteinuria, the determination of marker proteins in the urine, for example, alpha1 microglobulin, albumin and IgG, has proven utility.

  18. Holocene environmental and parasequence development of the St. Jones Estuary, Delaware (USA): Foraminiferal proxies of natural climatic and anthropogenic change

    Science.gov (United States)

    Leorri, E.; Martin, R.; McLaughlin, P.

    2006-01-01

    The benthic foraminiferal record of marshes located along western Delaware Bay (St. Jones Estuary, USA) reflects the response of estuaries to sea-level and paleoclimate change during the Holocene. System tracts are recognized and within them parasequences based on sedimentological and foraminiferal assemblages identification. The parasequences defined by foraminiferal assemblages appear correlative with rapid Holocene climate changes that are of worldwide significance: 6000-5000, 4200-3800, 3500-2500, 1200-1000, and 600??cal years BP. Following postglacial sea-level rise, modern subestuaries and marshes in the region began to develop between 6000 and 4000??years BP, depending on their proximity to the mouth of Delaware Bay and coastal geomorphology. Initial sediments were fluvial in origin, with freshwater marshes established around 4000??years BP. The subsequent sea-level transgression occurred sufficiently slowly that freshwater marshes alternated with salt marshes at the same sites to around 3000??years BP. Locally another two transgressions are identified at 1800 and 1000??years BP respectively. Marine influence increased in the estuaries until 600??years BP (Little Ice Age), when regression occurred. Sea-level began to rise again during the mid-19th Century at the end of the Little Ice Age, when marshes became established. The presence of a sand lens in the upper and middle estuary and the reduction in the number of tests in the top samples in cores from the same area also suggest an anthropogenic influence. The estuary infill resulted in a sharp transgressive sequence, represented by salt marsh foraminiferal assemblages in the upper part of the cores. The increase in marsh foraminifera in both areas suggests an increase in marine influence that might be due to the transgression beginning at the end of the Little Ice Age about 150-180??years ago coupled with anthropogenic straightening of the channel in 1913. ?? 2006 Elsevier B.V. All rights reserved.

  19. 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.

  20. Research

    African Journals Online (AJOL)

    ebutamanya

    2015-11-24

    Nov 24, 2015 ... 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 ...

  1. Vapour-liquid equilibria of two-centre Lennard-Jones fluids from the NpT plus test particle method

    Science.gov (United States)

    Kriebel, Christian; Müller, Andreas; Winkelmann, Jochen; Fischer, Johann

    Vapour-liquid phase equilibria (VLE) are determined from the NpT plus test particle method for two-centre Lennard-Jones fluids of elongations L* = 0·22, 0·3292, 0·505, and 0·67. The resulting vapour pressures as well as the saturated vapour and liquid densities are correlated by simple equations. The thermodynamic consistency of the VLE data is confirmed on the basis of the Clausius-Clapeyron equation. Comparison is made with results from previous simulations, and from perturbation theory.

  2. 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...

  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. Copyright © 2012 Wiley Periodicals, Inc.

  4. 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....

  5. "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. Copyright © 2013 Elsevier Ltd. All rights reserved.

  6. Jones matrix description of Fabry-Perot interference in a single axis photo-elastic modulator and the consequences for the magneto-optical measurement method

    Science.gov (United States)

    Talukder, Md. Abdul Ahad; Geerts, Wilhelmus J.

    2017-08-01

    When using a Photo-elastic modulator (PEM) in combination with a coherent light source, in addition to the modulation of the phase, Fabry-Perot interference in the PEM's optical head induces large offsets in the 1ω and 2ω detector signals. A Jones matrix which describes both effects simultaneously, was derived for a single axis PEM and used to find an expression for the detector signal for two different MO Kerr setups. The effect of the PEM tilt angle, polarizer angle, analyzer angle, and retardation, on the detector signal offsets show that offsets can be zeroed by adjusting PEM tilt angle, polarizer angle, and retardation. This strategy will allow one to avoid large offset drifts due to the small retardation, intensity, and beam direction fluctuations caused by lab temperature fluctuations. In addition, it will enable one to measure in the most sensitive range of the lock-in amplifiers further improving the signal to noise ratio of the setup.

  7. 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.

  8. Inside the Literature: An Interview with Sally G. Hoskins, 2017 Recipient of the Elizabeth W. Jones Award for Excellence in Education.

    Science.gov (United States)

    Hoskins, Sally G

    2017-12-01

    The Genetics Society of America's Elizabeth W. Jones Award for Excellence in Education recognizes significant and sustained impact on genetics education. The 2017 recipient is Sally G. Hoskins, in recognition of her role in developing and promoting the transformative science education method CREATE (Consider, Read, Elucidate hypotheses, Analyze and interpret data, and Think of the next Experiment). This innovative approach uses primary literature to engage students, allowing them to experience for themselves the creativity and challenge of study design, analysis, interpretation, collaboration, and debate. Comprehensive evaluation of CREATE has consistently found that students improve in difficult-to-teach skills like critical thinking and experimental design, while showing improved attitudes and beliefs about science.This is an abridged version of the interview. The full interview is available on the Genes to Genomes blog, at genestogenomes.org/hoskins/. Copyright © 2017 by the Genetics Society of America.

  9. Monte Carlo simulation of some thermophysical properties of two-centre Lennard-Jones fluids along the vapour-liquid equilibrium curve

    Science.gov (United States)

    Kronome, Gergely; Liszi, Janos; Szalai, Istvan

    The vapour pressures, saturated liquid and vapour densities, enthalpies of vaporization, isobaric, and saturation heat capacities are calculated for ethane and ethylene along their vapour-liquid equilibrium (VLE) curves from Monte Carlo simulations using the extended NpT plus test particle (XNpT + TP) method (Boda, D., Liszi, J., and Szalai, I., 1995, Chem. Phys. Lett. , 235, 140). The substances are modelled by two-centre Lennard-Jones molecules of elongations L * = 0.67 for ethane and L * = 0.74 for ethylene. Simulation results are compared with correlated experimental data. In the case of ethylene new values are required for the model parameters to obtain a good agreement with experimental data along the VLE curve. Our results show that the XNpT + TP method is appropriate for the simulation of caloric properties of molecular fluids along the VLE curve.

  10. 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

  11. 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

  12. Jones matrix description of Fabry-Perot interference in a single axis photo-elastic modulator and the consequences for the magneto-optical measurement method

    Directory of Open Access Journals (Sweden)

    Md. Abdul Ahad Talukder

    2017-08-01

    Full Text Available When using a Photo-elastic modulator (PEM in combination with a coherent light source, in addition to the modulation of the phase, Fabry-Perot interference in the PEM’s optical head induces large offsets in the 1ω and 2ω detector signals. A Jones matrix which describes both effects simultaneously, was derived for a single axis PEM and used to find an expression for the detector signal for two different MO Kerr setups. The effect of the PEM tilt angle, polarizer angle, analyzer angle, and retardation, on the detector signal offsets show that offsets can be zeroed by adjusting PEM tilt angle, polarizer angle, and retardation. This strategy will allow one to avoid large offset drifts due to the small retardation, intensity, and beam direction fluctuations caused by lab temperature fluctuations. In addition, it will enable one to measure in the most sensitive range of the lock-in amplifiers further improving the signal to noise ratio of the setup.

  13. 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 (c) 2016 APA, all rights reserved).

  14. Optimization Concentration of Sulfuric Acid on the Reduction U(VI) UsingJones Reductor to U(IV) with UV-VIS Spectrophotometry Method

    International Nuclear Information System (INIS)

    Simbolon, Sahat

    2000-01-01

    Reduction of U(VI) solution in sulfuric acid media with reductor Jones invarying concentration of sulfuric acid from 0.05 M - 1.5 M had been done.Compound of U 3 O 8 was used as a standard, it was dissolved in varying ofsulfuric acid from 0.05 M to 1.5 M, the amount of U(IV) was determined bytitration with KMnO 4 solution. The amount of U(VI) in solution was based onthe concentration U(IV) and the U 3 O 8 formula. Each concentration ofsulfuric acid 0.05 M to 1.5 M were used to dissolve U 3 O 8 and it was used tocalibrate the amount of U(IV) in solution after reduction with Jonesreductor. Analysis varian was used to determine the difference the absorbanceof uranyl sulfate. It was found that optimum concentration of sulfuric acidmedia for reduction U(VI) solution to U(IV) was 0.5 M. (author)

  15. A 10-Year Follow-Up of Two-Incision and Modified Watson-Jones Total Hip Arthroplasty in Patients with Osteonecrosis of the Femoral Head.

    Science.gov (United States)

    Lin, Shih-Jie; Huang, Tsan-Wen; Lin, Po-Chun; Kuo, Feng-Chih; Peng, Kuo-Ti; Huang, Kuo-Chin; Lee, Mel S

    2017-01-01

    Long-term data and information indicating whether minimally invasive surgery (MIS) approaches are safe and effective with total hip arthroplasty (THA) are lacking. Between 2004 and 2006, 75 patients with alcohol-related osteonecrosis of the femoral head (ONFH) who underwent 75 THAs with the two-incision approach were studied. The medical records, radiographic parameters, and functional outcomes were collected prospectively. All data were compared with those for matched patients who underwent a modified Watson-Jones (WJ) approach. THA using the two-incision approach was associated with longer operation time, more blood loss, more lateral femoral cutaneous nerve injury, and more periprosthetic femoral fractures ( p < 0.05 for all four) than the modified WJ approach. The Harris Hip Score (HHS) and Western Ontario and McMaster University Osteoarthritis Index (WOMAC) increased significantly from the period preoperatively to 6 weeks postoperatively and thereafter up to the last follow-up in both groups. However, there were no significant differences in terms of radiographic parameters and functional outcomes between the two groups throughout the study period. Both the two-incision and the modified WJ approach provided satisfactory results and survival rates at a mean follow-up of 10.8 years. A prospective, randomized, large-scale cohort study is still warranted for evidence-based recommendations.

  16. V.L. Ginzburg's elliptic screw polarization modes in an optical medium with linear birefringence and twist: Determination of their parameters by the method of Jones matrices

    Science.gov (United States)

    Malykin, G. B.; Pozdnyakova, V. I.

    2017-01-01

    Using the method of Jones matrices, we have calculated parameters of elliptic screw polarization modes (ESPMs). ESPM formalism has been proposed by V.L. Ginzburg for an optical medium with unperturbed linear birefringence and circular birefringence induced by twisting of the medium. The evolution of the polarization state of radiation (PSR) in relation to the length of the examined optical medium has been considered, which is important for twisted single-mode optical fibers and cholesteric liquid crystals. We have shown that the problem can be substantially simplified if the evolution of ESPMs is considered in a screw coordinate system comoving with the twist of the optical medium. In particular, we have shown that a curve on the Poincaré sphere mapping the evolution of the PSR for natural (normal) waves of the examined optical medium in the screw coordinate system degenerates into a point. For comparison, we have found natural waves of this medium in a fixed (laboratory) coordinate system and considered the evolution of their PSR, which is represented by a complex curve on the Poincaré sphere. Also, the evolution of the PSR of improper waves passed through the examined optical medium has been studied in both the fixed and the screw coordinate systems.

  17. 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.

  18. Energy world governance. Review of the conference which was held at IFRI, 26 March 2009, with Tatsuo Masuda, Andre Mernier et Richard H. Jones

    International Nuclear Information System (INIS)

    Schulke, Ch.

    2009-01-01

    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

  19. İstanbul Menkul Kıymetler Borsası ve “Dow Jones Industrial” Arasındaki İlişki: Eşbütünleşme Analizi( The Relation Between The Istanbul Stock Exchange And The Dow Jones Industrial: The Cointegration Analysis

    Directory of Open Access Journals (Sweden)

    Şahin BULUT

    2012-01-01

    Full Text Available In this study, the relationship between the İstanbul Stock Exchange and the Dow Jones Industrial is analyzed by taking into consideration the closing prices for weekly in the period between 05.01.2001-30.12.2010. The causal relationship between the series is analyzed through the Granger test, long-short term and cointegration analysis; the Johansen and VEC methods. Research findings points out that the DJI causes the Granger of the ISE for three-lags. According to the results of the cointegration analysis, the series act together in the long term, that is, they are cointegrated. In the short term, the error correction term works and for three terms the DJI significantly affects the ISE.

  20. Protein Foods

    Science.gov (United States)

    ... Text Size: A A A Listen En Español Protein Foods Foods high in protein such as fish, ... for the vegetarian proteins, whether they have carbohydrate. Protein Choices Plant-Based Proteins Plant-based protein foods ...

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

    Energy Technology Data Exchange (ETDEWEB)

    Goethe, Martin, E-mail: martingoethe@ub.edu; Rubi, J. Miguel [Departament de Física Fonamental, Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona (Spain); Fita, Ignacio [Institut de Biologia Molecular de Barcelona, Baldiri Reixac 10, 08028 Barcelona (Spain)

    2016-03-15

    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.

  2. Evaluation of safety of iridoids rich fraction from Valeriana jatamansi Jones: Acute and sub-chronic toxicity study in mice and rats.

    Science.gov (United States)

    Xu, Keke; Lin, Yu; Zhang, Ruitong; Lan, Ming; Chen, Chaoyong; Li, Shaohua; Zuo, Changying; Chen, Chang; Zhang, Tiane; Yan, Zhiyong

    2015-08-22

    Valeriana jatamansi Jones named Zhizhuxiang in China is one of the most popular traditional medicine for varied ailments related to malaise, abdominal distention, insomnia, and rheumatism. Evaluate the safety of iridoids rich fraction from V. jatamansi Jones (IRFV) and to provide data for clinical application. The acute and sub-chronic toxicity of IRFV were investigated by employing established methods. The acute toxicity study was conducted through oral administration of a single dose (3,200 mg/kg body weight) of IRFV to adult mice. The vehicle used for dilution of the IRFV was a mixture of 0.5% CMC-Na and 99.5% water. The weight, diet, toxic reaction, and death after 14 days were observed. In the sub-chronic toxicity study, low doses (240 mg/kg bw), middle doses (960 mg/kg bw), and high doses (1,200 mg/kg bw) of IRFV were administered daily to adult rats for 6 days a week (except Sunday) for 3 months. The general behavior of the rats was observed and recorded daily. The weight and food consumption of rats were tested weekly. The effect on organs, the hematological and blood biochemical parameters, and the histopathology were assessed after 1.5 months (five males and five females) and after 3 months (10 males and 10 females).The remaining 10 rats (five males and five females) in each group were fed for 2 weeks to observe reversible and delayed toxicity after the medicine was administered. In the acute toxicity study, no significant difference was found in the body weight of the mice in the control group and those in the drug group (p>0.05). The maximum tolerated dose of IRFV on mice was 3,200 mg/kg, which is 2666 times of the clinical adult daily dose. In the sub-chronic toxicity study on rats, the daily single oral doses of the IRFV did not result in death nor affected the general behavior, including appearance, activities, discharge, and waste at all tested doses. Moreover, no significant difference was found (p>0.05) between the body weights of the rats from

  3. Phase separation of a Lennard-Jones fluid interacting with a long, condensed polymer chain: implications for the nuclear body formation near chromosomes.

    Science.gov (United States)

    Oh, Inrok; Choi, Saehyun; Jung, YounJoon; Kim, Jun Soo

    2015-08-28

    Phase separation in a biological cell nucleus occurs in a heterogeneous environment filled with a high density of chromatins and thus it is inevitably influenced by interactions with chromatins. As a model system of nuclear body formation in a cell nucleus filled with chromatins, we simulate the phase separation of a low-density Lennard-Jones (LJ) fluid interacting with a long, condensed polymer chain. The influence of the density variation of LJ particles above and below the phase boundary and the role of attractive interactions between LJ particles and polymer segments are investigated at a fixed value of strong self-interaction between LJ particles. For a density of LJ particles above the phase boundary, phase separation occurs and a dense domain of LJ particles forms irrespective of interactions with the condensed polymer chain whereas its localization relative to the polymer chain is determined by the LJ-polymer attraction strength. Especially, in the case of moderately weak attractions, the domain forms separately from the polymer chain and subsequently associates with the polymer chain. When the density is below the phase boundary, however, the formation of a dense domain is possible only when the LJ-polymer attraction is strong enough, for which the domain grows in direct contact with the interacting polymer chain. In this work, different growth behaviors of LJ particles result from the differences in the density of LJ particles and in the LJ-polymer interaction, and this work suggests that the distinct formation of activity-dependent and activity-independent nuclear bodies (NBs) in a cell nucleus may originate from the differences in the concentrations of body-specific NB components and in their interaction with chromatins.

  4. Delayed Union of a Jones Fracture in a Patient With Rothmund-Thomson Syndrome: A Case Report and Review of the Literature.

    Science.gov (United States)

    Barisonek, Kirsten L; Protzman, Nicole M; Wobst, Garrett M; Brigido, Stephen A

    2016-01-01

    Rothmund-Thomson syndrome is a rare autosomal recessive genodermatosis, characterized by poikiloderma, small stature, juvenile cataracts, sparse hair, skeletal abnormalities, and a predisposition to osteogenic sarcomas and skin cancers. Although numerous skeletal abnormalities have been described in patients with Rothmund-Thomson syndrome, to our knowledge, only 1 study has shown evidence of delayed fracture healing in a patient with Rothmund-Thomson syndrome. We present the case of a 13-year-old female diagnosed with Rothmund-Thomson syndrome who demonstrated delayed union of her fifth metatarsal after a Jones fracture. She was treated conservatively for 6 weeks with non-weightbearing cast immobilization and was then transitioned to a controlled ankle motion walker for an additional 4 weeks. Two months later, however, she continued to experience pain, and, on radiographic examination, the fracture remained unchanged. Therefore, with her guardian's consent, the patient elected to undergo open reduction and internal fixation of the fifth metatarsal fracture. At 8 weeks postoperatively, the patient reported a subsidence of symptoms and had returned to normal activity. With our report, we hope to increase practitioner awareness that delayed bone healing could be a possibility in patients with Rothmund-Thomson syndrome and encourage consideration of routine imaging and supplementation with calcium and vitamin D. Additionally, the present findings suggest that patients with Rothmund-Thomson syndrome could benefit from early surgical intervention, given their poor bone healing capacity and high likelihood of nonunion. Although the association between impaired bone healing and Rothmund-Thomson syndrome is rational, additional studies are needed to determine the prevalence of chronic nonunion in this patient population. Copyright © 2016 American College of Foot and Ankle Surgeons. Published by Elsevier Inc. All rights reserved.

  5. Explicit expressions of self-diffusion coefficient, shear viscosity, and the Stokes-Einstein relation for binary mixtures of Lennard-Jones liquids

    International Nuclear Information System (INIS)

    Ohtori, Norikazu; Ishii, Yoshiki

    2015-01-01

    Explicit expressions of the self-diffusion coefficient, D i , and shear viscosity, η sv , are presented for Lennard-Jones (LJ) binary mixtures in the liquid states along the saturated vapor line. The variables necessary for the expressions were derived from dimensional analysis of the properties: atomic mass, number density, packing fraction, temperature, and the size and energy parameters used in the LJ potential. The unknown dependence of the properties on each variable was determined by molecular dynamics (MD) calculations for an equimolar mixture of Ar and Kr at the temperature of 140 K and density of 1676 kg m −3 . The scaling equations obtained by multiplying all the single-variable dependences can well express D i and η sv evaluated by the MD simulation for a whole range of compositions and temperatures without any significant coupling between the variables. The equation for D i can also explain the dual atomic-mass dependence, i.e., the average-mass and the individual-mass dependence; the latter accounts for the “isotope effect” on D i . The Stokes-Einstein (SE) relation obtained from these equations is fully consistent with the SE relation for pure LJ liquids and that for infinitely dilute solutions. The main differences from the original SE relation are the presence of dependence on the individual mass and on the individual energy parameter. In addition, the packing-fraction dependence turned out to bridge another gap between the present and original SE relations as well as unifying the SE relation between pure liquids and infinitely dilute solutions

  6. 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.

  7. Explicit expressions of self-diffusion coefficient, shear viscosity, and the Stokes-Einstein relation for binary mixtures of Lennard-Jones liquids

    Energy Technology Data Exchange (ETDEWEB)

    Ohtori, Norikazu, E-mail: ohtori@chem.sc.niigata-u.ac.jp [Department of Chemistry, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181 (Japan); Ishii, Yoshiki [Graduate School of Science and Technology, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata 950-2181 (Japan)

    2015-10-28

    Explicit expressions of the self-diffusion coefficient, D{sub i}, and shear viscosity, η{sub sv}, are presented for Lennard-Jones (LJ) binary mixtures in the liquid states along the saturated vapor line. The variables necessary for the expressions were derived from dimensional analysis of the properties: atomic mass, number density, packing fraction, temperature, and the size and energy parameters used in the LJ potential. The unknown dependence of the properties on each variable was determined by molecular dynamics (MD) calculations for an equimolar mixture of Ar and Kr at the temperature of 140 K and density of 1676 kg m{sup −3}. The scaling equations obtained by multiplying all the single-variable dependences can well express D{sub i} and η{sub sv} evaluated by the MD simulation for a whole range of compositions and temperatures without any significant coupling between the variables. The equation for D{sub i} can also explain the dual atomic-mass dependence, i.e., the average-mass and the individual-mass dependence; the latter accounts for the “isotope effect” on D{sub i}. The Stokes-Einstein (SE) relation obtained from these equations is fully consistent with the SE relation for pure LJ liquids and that for infinitely dilute solutions. The main differences from the original SE relation are the presence of dependence on the individual mass and on the individual energy parameter. In addition, the packing-fraction dependence turned out to bridge another gap between the present and original SE relations as well as unifying the SE relation between pure liquids and infinitely dilute solutions.

  8. Directional Jones and Stokes Vectors

    National Research Council Canada - National Science Library

    Luneburg, E

    2005-01-01

    .... The conventional Forward Scattering Alignment (FSA) convention for setting up a coordinate system for the description of the polarization characteristics of these waves has to be replaced by the Back Scattering Alignment (BSA...

  9. 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

  10. 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....

  11. Formerly utilized MED/AEC sites Remedial Action Program. Report of the decontamination of Jones Chemical Laboratory, Ryerson Physical Laboratory, and Eckhart Hall, the University of Chicago, Chicago, Illinois

    Energy Technology Data Exchange (ETDEWEB)

    Wynuveen, R.A.; Smith, W.H.; Sholeen, C.M.; Flynn, K.F.

    1984-08-01

    The US Department of Energy (DOE) has implemented a program to decontaminate radioactively contaminated sites that were formerly utilized by the Manhattan Engineer District (MED) and/or the Atomic Energy Commission (AEC) for activities that included handling of radioactive material. This program is referred to as the ''Formerly Utilized Sites Remedial Action Program'' (FUSRAP). Among these sites are Jones Chemical Laboratory, Ryerson Physical Laboratory, Kent Chemical Laboratory, and Eckhart Hall of The University of Chicago, Chicago, Illinois. Since 1977, the University of Chicago decontaminated Kent Chemical Laboratory as part of a facilities renovation program. All areas of Eckhart Hall, Ryerson Physical Laboratory, and Jones Chemical Laboratory that had been identified as contaminated in excess of current guidelines in the 1976-1977 surveys were decontaminated to levels where no contamination could be detected relative to natural backgrounds. All areas that required defacing to achieve this goal were restored to their original condition. The radiological evaluation of the sewer system, based primarily on the radiochemical analyses of sludge and water samples, indicated that the entire sewer system is potentially contaminated. While this evaluation was defined as part of this project, the decontamination of the sewer system was not included in the purview of this effort. The documentation included in this report substantiates the judgment that all contaminated areas identified in the earlier reports in the three structures included in the decontamination effort (Eckhart Hall, Ryerson Physical Laboratory, and Jones Chemical Laboratory) were cleaned to levels commensurate with release for unrestricted use.

  12. Formerly Utilized MED/AEC Sites Remedial Action Program. Project management plan for the decontamination of Jones Laboratory, Ryerson Physical Laboratory, and Eckhart Hall, the University of Chicago, Chicago, Illinois

    International Nuclear Information System (INIS)

    Flynn, K.F.; Smith, W.H.; Wynveen, R.A.

    1984-01-01

    The Department of Energy (DOE) has in place a plan for the decontamination and decommissioning of contaminated sites that had been formerly utilized by the Manhattan Engineering District (MED) and/or the Atomic Energy Commission. This plan is referred to as the Formerly Utilized Sites Remedial Action Program (FUSRAP). Among these sites are Jones Laboratory, Ryerson Physical Laboratory and Eckhart Hall of The University of Chicago at Chicago, Illinois. This document represents the Project Management Plan for the decontamination of these facilities. 13 references, 3 figures, 1 table

  13. Formerly Utilized MED/AEC Sites Remedial Action Program. Project management plan for the decontamination of Jones Laboratory, Ryerson Physical Laboratory, and Eckhart Hall, the University of Chicago, Chicago, Illinois

    Energy Technology Data Exchange (ETDEWEB)

    Flynn, K.F.; Smith, W.H.; Wynveen, R.A.

    1984-01-01

    The Department of Energy (DOE) has in place a plan for the decontamination and decommissioning of contaminated sites that had been formerly utilized by the Manhattan Engineering District (MED) and/or the Atomic Energy Commission. This plan is referred to as the Formerly Utilized Sites Remedial Action Program (FUSRAP). Among these sites are Jones Laboratory, Ryerson Physical Laboratory and Eckhart Hall of The University of Chicago at Chicago, Illinois. This document represents the Project Management Plan for the decontamination of these facilities. 13 references, 3 figures, 1 table.

  14. Serum protein changes in immune and nonimmune pigeons infected with various strains of Trichomonas gallinae.

    Science.gov (United States)

    Kocan, R M; Herman, C M

    1970-01-01

    Serum protein changes were studied in immune and nonimmune pigeons infected with three different strains of Trichomonas gallinae. Strain I (nonvirulent) produced no change in the relative concentration of serum components. Strains II (oral canker) and III (Jones' Barn) produced decreases in albumin and alpha globulins, and increases in beta and gamma globulins between the 7th and 20th days post infection. Birds infected with strain II began to return to normal by the 20th day, while all those infected with strain III were dead between 10 and 14 days post infection. Two serum protein patterns resulted from infection of immune birds with the Jones' Barn strain. One showed no change in relative protein concentrations and no tissue invasion by the parasite while the other was similar to that seen in nonimmune birds infected with a strain producing oral canker. These also showed evidence of tissue invasion by the parasite. It was concluded that tissue invasion was necessary to evoke a quantitative change in serum protein concentrations.

  15. [Clinical courses and risk factors for progression of smoldering multiple myeloma: a nationwide cohort study in Japan].

    Science.gov (United States)

    Takamatsu, Yasushi; Muta, Tsuyoshi

    2015-08-01

    We carried out a cohort study of smoldering multiple myeloma (SMM) in Japan. The clinical data of 207 patients with SMM, median age 69 years (range: 27-90), were collected from 63 institutions. The subtype of myeloma was IgG type in 168, IgA type in 30, and Bence Jones type in 9 patients. At a median follow-up of 39 months, 53% of the patients had progressed to symptomatic MM (within 5 years of the initial diagnosis). As previously described, a serum free light chain ratio>8 or <0.125, along with the number of bone marrow plasma cells being 10% or more and the serum M-protein level being at least 3 g/dl, was a significant predictor of rapid progression. We found that the rate of increase in serum M-protein levels correlated negatively with the risk of progression. The probability of progression within 5 years was 100% in patients whose rate of serum M-protein level increase was 2 mg/dl/day or higher. This indicates that the serum M-protein level increase rate might be a useful predictor of disease progression in SMM.

  16. Primary systemic amyloidosis associated with multiple myeloma Amiloidose sistêmica primária associada ao mieloma múltiplo

    Directory of Open Access Journals (Sweden)

    Ederson Valei Lopes de Oliveira

    2012-02-01

    Full Text Available This case report is about a 48-year-old female patient with systemic amyloidosis and multiple myeloma simultaneously. Amyloid cutaneous infiltrative lesions like papules, nodules, or plaques with a serous-hemorrhagic aspect were found in the eyelids, neck and retroauricular region, among others. She had presented intermittent papular lesions on the upper eyelids one year before, which worsened following local trauma. A local skin biopsy showed amorphous and eosinophilic substance in the dermis. Congo red staining confirmed the amyloid deposits. Abnormal exams: proteinuria (570mg/24h, Bence-Jones proteinuria and clonal plasma cells (70% found in myelogram. Following the diagnosis of multiple myeloma based on amyloid skin lesions, the patient was referred to the Hematology service and died 5 months after the diagnosis.Relatamos um caso de uma paciente de 48 anos com amiloidose sistêmica associada a mieloma múltiplo. Lesões infiltrativas cutâneas como pápulas, nódulos ou placas com aspecto sero-hemorrágico podem ser localizados nas pálpebras, pescoço, região retroauricular dentre outras. No presente caso, as pálpebras foram acometidas por pápulas, há 1 ano, de caráter intermitente e piora após trauma local. Biópsia local evidenciou material amorfo e eosinofílico na derme. A coloração vermelho do Congo confirmou presença de substância amiloide. Exames anormais: proteinúria de 570mg/24 horas, proteinúria de Bence-Jones positiva e mielograma com 70% de plasmócitos atípicos. Assim, realizou-se o diagnóstico de mieloma múltiplo a partir de manifestações cutâneas de amiloidose. Paciente encaminhada ao serviço de hematologia e foi a óbito em 5 meses.

  17. 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.

  18. Energetic frustrations in protein folding at residue resolution: a homologous simulation study of Im9 proteins.

    Directory of Open Access Journals (Sweden)

    Yunxiang Sun

    Full Text Available Energetic frustration is becoming an important topic for understanding the mechanisms of protein folding, which is a long-standing big biological problem usually investigated by the free energy landscape theory. Despite the significant advances in probing the effects of folding frustrations on the overall features of protein folding pathways and folding intermediates, detailed characterizations of folding frustrations at an atomic or residue level are still lacking. In addition, how and to what extent folding frustrations interact with protein topology in determining folding mechanisms remains unclear. In this paper, we tried to understand energetic frustrations in the context of protein topology structures or native-contact networks by comparing the energetic frustrations of five homologous Im9 alpha-helix proteins that share very similar topology structures but have a single hydrophilic-to-hydrophobic mutual mutation. The folding simulations were performed using a coarse-grained Gō-like model, while non-native hydrophobic interactions were introduced as energetic frustrations using a Lennard-Jones potential function. Energetic frustrations were then examined at residue level based on φ-value analyses of the transition state ensemble structures and mapped back to native-contact networks. Our calculations show that energetic frustrations have highly heterogeneous influences on the folding of the four helices of the examined structures depending on the local environment of the frustration centers. Also, the closer the introduced frustration is to the center of the native-contact network, the larger the changes in the protein folding. Our findings add a new dimension to the understanding of protein folding the topology determination in that energetic frustrations works closely with native-contact networks to affect the protein folding.

  19. Interfacial Protein-Protein Associations

    OpenAIRE

    Langdon, Blake B.; Kastantin, Mark; Walder, Robert; Schwartz, Daniel K.

    2013-01-01

    While traditional models of protein adsorption focus primarily on direct protein-surface interactions, recent findings suggest that protein-protein interactions may play a central role. Using high-throughput intermolecular resonance energy transfer (RET) tracking, we directly observed dynamic, protein-protein associations of bovine serum albumin on poly(ethylene glycol) modified surfaces. The associations were heterogeneous and reversible, and associating molecules resided on the surface for ...

  20. Cutaneous plasmacytosis: A rare entity with unique presentation

    Directory of Open Access Journals (Sweden)

    Subhra Dhar

    2017-01-01

    Full Text Available Primary cutaneous plasmacytosis is a rare cutaneous disorder with extensive cutaneous plaques/papules mainly on the trunk and face. Cases have mostly been documented from Japan. We present here a rare case of cutaneous plasmacytosis from India of Mongolian descent. This 50-year-old female from Mizoram had extensive maculo-papular violaceous plaques distributed on the face, axillae, trunk and lower extremities. Initial and repeat skin biopsy revealed dense perivascular and periadnexal mature plasma cells. She also had lymphadenopathy. Serum protein electrophoresis did not reveal any M band and the Bence Jones protein was negative in urine. The patient had multiple superficial lymph nodes and a biopsy from the cervical lymph node showed effacement of normal nodal architecture by sheets of plasma cells. Immuno histochemistry was done from both skin and lymph node biopsies. The kappa and lambda tight chains were not restricted; there by proving the polyclonal nature of the plasma cells. The novelty of the case lies in its classical clinical presentation with histopathological documentation.

  1. 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.

  2. Random matrices, amalgamated free products and subfactors of the von Neumann algebra of a free group et sous-facteurs de L(F$_{\\infty}$) ayant l'indice dans la partie discrète de la série de Jones (version francaise abrégée)

    CERN Document Server

    Radulescu, F G

    1991-01-01

    Random matrices, amalgamated free products and subfactors of the von Neumann algebra of a free group et sous-facteurs de L(F$_{\\infty}$) ayant l'indice dans la partie discrète de la série de Jones (version francaise abrégée)

  3. Proteins engineering

    International Nuclear Information System (INIS)

    2000-01-01

    At the - Departement d'Ingenierie et d'etudes de proteines (Deip) of the CEA more than seventy researchers are working hard to understand the function of proteins. For that they use the molecular labelling technique (F.M.)

  4. 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 ...

  5. Cisplatin-Induced Nephrotoxicity and HIV Associated Nephropathy: Mimickers of Myeloma-Like Cast Nephropathy

    Directory of Open Access Journals (Sweden)

    Muhammad Siddique Khurram

    2017-01-01

    Full Text Available Myeloma cast nephropathy is an obstructing disorder of renal tubules, caused by precipitation of Bence Jones proteins. Myeloma-like cast nephropathy (MLCN has been reported in the literature to occur in various primary renal and nonrenal diseases. We present a series of three rare cases of cast nephropathy, two of which are HIV patients, and the third patient is receiving cisplatin-based chemotherapy. However, in all three patients plasma cell dyscrasia has been ruled out. A 30-year-old male was admitted to the hospital with facial cellulitis. The second patient is a 31-year-old male who presented with Pneumocystis jiroveci pneumonia. The third patient was treated with cisplatin-based chemotherapy for carcinoma. First two cases revealed foci of diffuse tubular dilatation containing hyaline casts and interstitial inflammatory infiltrate, in addition to globally sclerotic glomeruli with ultrastructural foot process fusion and mesangium expansion. The third case showed acute tubular injury and cast formation of irregular casts composed of amorphous or granular material of low density admixed with scattered high electron-dense globules. Myeloma-like cast nephropathy and true myeloma cast nephropathy pose similar destructive effects on renal parenchyma. This new pattern of HIV-related nephropathy should be considered in HIV patients with MLCN, once monoclonal gammopathy is ruled out.

  6. 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.

  7. 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.

  8. Fanconi syndrome and CKD in a patient with paroxysmal nocturnal hemoglobinuria and hemosiderosis.

    Science.gov (United States)

    Hsiao, Po-Jen; Wang, Shou-Chieh; Wen, Mei-Chin; Diang, Liang-Kuang; Lin, Shih-Hua

    2010-01-01

    Fanconi syndrome and chronic kidney disease associated with paroxysmal nocturnal hemoglobinuria is rarely reported. We describe a 51-year-old woman with glomerular filtration rate decrease and hypokalemia, glucosuria, and proteinuria during a 4-year period. Paroxysmal nocturnal hemoglobinuria was diagnosed 17 years earlier, and she has received multiple blood transfusions because of hemolytic episodes during the last 5 years. Deteriorating kidney function and persistent Fanconi syndrome were accompanied by a progressive increase in serum ferritin levels. Laboratory studies showed proximal renal tubular acidosis, hypophosphotemic hyperphosphaturia, normoglycemic glucosuria, and aminoaciduria. Serologic testing, tumor markers, Bence-Jones protein, and heavy-metal screening results were negative. Abdominal magnetic resonance imaging showed characteristic features of iron deposition in the bilateral renal cortices. Kidney biopsy showed chronic interstitial nephritis with prominent hemosiderin deposition in the proximal tubules. With potassium citrate, calcitriol, and deferoxamine therapy, Fanconi syndrome persisted, but kidney function was stable. Renal hemosiderosis secondary to both chronic repetitive hemolytic episodes and transfusion-related iron overload in patients with paroxysmal nocturnal hemoglobinuria can lead to Fanconi syndrome and chronic kidney disease. Copyright 2009 National Kidney Foundation, Inc. Published by Elsevier Inc. All rights reserved.

  9. Protein Extractability

    African Journals Online (AJOL)

    Results showed that protein extractability was dependent on pH, type of salt, salt concentrations and extraction time. Salts extracted more proteins from the moringa seed flour than water. Maximum extraction of protein was. 85.06% and 84.72% with 0.5 M CaCl and 0.75 M NaCl respectively. On varying the pH, maximum ...

  10. Protein politics

    NARCIS (Netherlands)

    Vijver, Marike

    2005-01-01

    This study is part of the program of the interdisciplinary research group Profetas (protein foods, environment, technology and society). Profetas consists of technological, environmental and socio-economic research projects on protein food systems which result in the development of scenarios and

  11. Whey Protein

    Science.gov (United States)

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

  12. Protein adhesives

    Science.gov (United States)

    Charles R. Frihart; Linda F. Lorenz

    2018-01-01

    Nature uses a wide variety of chemicals for providing adhesion internally (e.g., cell to cell) and externally (e.g., mussels to ships and piers). This adhesive bonding is chemically and mechanically complex, involving a variety of proteins, carbohydrates, and other compounds.Consequently,the effect of protein structures on adhesive properties is only partially...

  13. 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...

  14. Protein-Protein Interaction Databases

    DEFF Research Database (Denmark)

    Szklarczyk, Damian; Jensen, Lars Juhl

    2015-01-01

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

  15. Protein deamidation

    OpenAIRE

    Robinson, Noah E.

    2002-01-01

    A completely automatic computerized technique for the quantitative estimation of the deamidation rates of any protein for which the three-dimensional structure is known has been developed. Calculations of the specific deamidation rates of 170,014 asparaginyl residues in 13,335 proteins have been carried out. The calculated values have good quantitative reliability when compared with experimental measurements. These rates demonstrate that deamidation may be a biologically ...

  16. Formerly utilized MED/AEC sites remedial action program. Radiological survey of The George Herbert Jones Chemical Laboratory, The University of Chicago, Chicago, Illinois, June 13-17, 1977

    International Nuclear Information System (INIS)

    Wynveen, R.A.; Smith, W.H.; Mayes, C.B.; Justus, A.L.

    1982-05-01

    A comprehensive radiological survey was conducted at George Herbert Jones Chemical Laboratory at the University of Chicago, Chicago, Illinois. Radiochemistry for the MED/AEC project was performed in this building in the 1940s. The building is now used as laboratories, offices, and classrooms. The survey was undertaken to determine the location and quantities of any radioactive materials remaining from the MED/AEC operations. Forty-three spots of contamination possibly resulting from MED/AEC occupancy in 17 rooms exceeded the allowable limits as given in the ANSI Standard N13.12. Under current use conditions, the potential for radiation exposure to occupants of this building from these sources of contamination is remote. Concentrations of radon daughters in the air of the building, as measured with grab-sampling techniques, were below the limit of 0.01 WL above background as given in the Surgeon General's Guidelines. No long-lived radionuclides were detected in any air sample. Concentrations of radionuclides in soil samples from near the laboratory generally indicated background levels. In order to reduce the potential for radiation exposure, remedial measures such as stabilization of the contamination in place would be applicable as a short-term measure. In order to reduce the risk in the event that building modifications take place in the future, health physics procedures and coverage are recommended. The long-term solution would involve decontamination by removal of the radioactive residues from the 17 rooms or areas where contamination possibly resulting from MED/AEC activities was detected

  17. Russia steps up Baltic incursions / Bruce Jones

    Index Scriptorium Estoniae

    Jones, Bruce

    2017-01-01

    Peale Leedu presidendi 31. juuli avaldust, et Leetu Šiauliai õhuväebaasi tuuakse NATO hävituslennukeid juurde, on Balti õhuruumis märgatud järjest rohkem registreerimata ja sisselülitamata transponderitega Venemaa lennukeid. Selle üheks põhjuseks peetakse lähenevat Venemaa sõjalist suurõppust Zapad 2017

  18. Lennard-Jones fluids in a nanochannel

    NARCIS (Netherlands)

    Hartkamp, Remco; Luding, Stefan; Nuernberg Messe GmbH,

    2010-01-01

    During the past few decades molecular dynamics has been a widely applied tool to simulate fluid confined in micro/nano geometries. What makes interfacial fluids fundamentally different from the bulk fluid is the fact that their density varies considerably over microscopic distances. A class of such

  19. Management of treatment resistant schizophrenia | Jones | African ...

    African Journals Online (AJOL)

    Whilst gains have been made in recent years in the pharmacological treatment of schizophrenia, a number of patients still have residual symptoms and disabilities, or simply do not show response to antipsychotic medications. For such 'treatment resistant' patients, there is little by way of randomised controlled data to ...

  20. Management of treatment resistant schizophrenia | Jones | African ...

    African Journals Online (AJOL)

    African Journal of Psychiatry. Journal Home · ABOUT THIS JOURNAL · Advanced Search · Current Issue · Archives · Journal Home > Vol 9, No 1 (2006) >. Log in or Register to get access to full text downloads. Username, Password, Remember me, or Register · Download this PDF file. The PDF file you selected should load ...

  1. Matthew Jones House: Recommendations for Treatment

    Science.gov (United States)

    2016-04-01

    cosmetic purposes to reduce frequency (Fig 9). When cleaning, use the gentlest means possible; start with natural bristle brushes and water and only add... algae , or mildew. Use plain water and a soft natural or nylon bristle brush. Unless thoroughly researched and tested beforehand on a discreet area of...Backing Materials Mildew/ Algae Growth Damaged Interior Finshes Efflorescence See TN 23 Series www.gobrick.com | Brick Industry

  2. Influenza: prevention, prophylaxis and treatment | Jones | South ...

    African Journals Online (AJOL)

    Influenza spreads rapidly to affect 515% of the global population on an annual basis. It is estimated that influenza causes between three and five million cases of severe illness and between a quarter and half a million deaths every year. In South Africa during the period from 1997 to 2001, influenza and pneumonia ...

  3. Management of treatment resistant schizophrenia | Jones | African ...

    African Journals Online (AJOL)

    This article selectively reviews the literature treatment resistance in schizophrenia, and emphasises the importance of an holistic approach to individual patients. Keywords: schizophrenia, treatment resistance, antipsychotics, augmentation, psychosocial treatments. South African Psychiatry Review Vol. 9(1) 2006: 17-23 ...

  4. 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

  5. Protein Crystallizability.

    Science.gov (United States)

    Smialowski, Pawel; Wong, Philip

    2016-01-01

    Obtaining diffracting quality crystals remains a major challenge in protein structure research. We summarize and compare methods for selecting the best protein targets for crystallization, construct optimization and crystallization condition design. Target selection methods are divided into algorithms predicting the chance of successful progression through all stages of structural determination (from cloning to solving the structure) and those focusing only on the crystallization step. We tried to highlight pros and cons of different approaches examining the following aspects: data size, redundancy and representativeness, overfitting during model construction, and results evaluation. In summary, although in recent years progress was made and several sequence properties were reported to be relevant for crystallization, the successful prediction of protein crystallization behavior and selection of corresponding crystallization conditions continue to challenge structural researchers.

  6. Computation of methodology-independent single-ion solvation properties from molecular simulations. IV. Optimized Lennard-Jones interaction parameter sets for the alkali and halide ions in water

    Science.gov (United States)

    Reif, Maria M.; Hünenberger, Philippe H.

    2011-04-01

    The raw single-ion solvation free energies computed from atomistic (explicit-solvent) simulations are extremely sensitive to the boundary conditions and treatment of electrostatic interactions used during these simulations. However, as shown recently [M. A. Kastenholz and P. H. Hünenberger, J. Chem. Phys. 124, 224501 (2006), 10.1529/biophysj.106.083667; M. M. Reif and P. H. Hünenberger, J. Chem. Phys. 134, 144103 (2010)], the application of appropriate correction terms permits to obtain methodology-independent results. The corrected values are then exclusively characteristic of the underlying molecular model including in particular the ion-solvent van der Waals interaction parameters, determining the effective ion size and the magnitude of its dispersion interactions. In the present study, the comparison of calculated (corrected) hydration free energies with experimental data (along with the consideration of ionic polarizabilities) is used to calibrate new sets of ion-solvent van der Waals (Lennard-Jones) interaction parameters for the alkali (Li+, Na+, K+, Rb+, Cs+) and halide (F-, Cl-, Br-, I-) ions along with either the SPC or the SPC/E water models. The experimental dataset is defined by conventional single-ion hydration free energies [Tissandier et al., J. Phys. Chem. A 102, 7787 (1998), 10.1021/jp982638r; Fawcett, J. Phys. Chem. B 103, 11181] along with three plausible choices for the (experimentally elusive) value of the absolute (intrinsic) hydration free energy of the proton, namely, Δ G_hyd^{ominus }[H+] = -1100, -1075 or -1050 kJ mol-1, resulting in three sets L, M, and H for the SPC water model and three sets LE, ME, and HE for the SPC/E water model (alternative sets can easily be interpolated to intermediate Δ G_hyd^{ominus }[H+] values). The residual sensitivity of the calculated (corrected) hydration free energies on the volume-pressure boundary conditions and on the effective ionic radius entering into the calculation of the correction terms is

  7. Protein nanoparticles for therapeutic protein delivery.

    Science.gov (United States)

    Herrera Estrada, L P; Champion, J A

    2015-06-01

    Therapeutic proteins can face substantial challenges to their activity, requiring protein modification or use of a delivery vehicle. Nanoparticles can significantly enhance delivery of encapsulated cargo, but traditional small molecule carriers have some limitations in their use for protein delivery. Nanoparticles made from protein have been proposed as alternative carriers and have benefits specific to therapeutic protein delivery. This review describes protein nanoparticles made by self-assembly, including protein cages, protein polymers, and charged or amphipathic peptides, and by desolvation. It presents particle fabrication and delivery characterization for a variety of therapeutic and model proteins, as well as comparison of the features of different protein nanoparticles.

  8. Recombinant protein production technology

    Science.gov (United States)

    Recombinant protein production is an important technology for antibody production, biochemical activity study, and structural determination during the post-genomic era. Limiting factors in recombinant protein production include low-level protein expression, protein precipitation, and loss of protein...

  9. Stridor: unusual presentation of multiple myeloma.

    Science.gov (United States)

    Sinclair, David; Resouly, Adel; Spedding, Anne

    2003-10-01

    We present a patient with multiple myeloma whose only presenting symptom was stridor caused by a subglottic stenosis. Biopsy suggested the presence of amyloid which prompted immunological investigations that showed hypogammaglobulinaemia and the presence of Bence Jones proteinuria at 0.93 g/24 hours. Further investigation demonstrated a 15 per cent plasma cell infiltrate into the bone marrow and a lytic lesion in the mid-shaft of the right femur. Chemotherapy and localized radiotherapy were commenced. This is a most unusual presentation of multiple myeloma and shows that immunoglobulin profiles should be properly investigated in such cases.

  10. Aquaporin Protein-Protein Interactions

    Directory of Open Access Journals (Sweden)

    Jennifer Virginia Roche

    2017-10-01

    Full Text Available Aquaporins are tetrameric membrane-bound channels that facilitate transport of water and other small solutes across cell membranes. In eukaryotes, they are frequently regulated by gating or trafficking, allowing for the cell to control membrane permeability in a specific manner. Protein–protein interactions play crucial roles in both regulatory processes and also mediate alternative functions such as cell adhesion. In this review, we summarize recent knowledge about aquaporin protein–protein interactions; dividing the interactions into three types: (1 interactions between aquaporin tetramers; (2 interactions between aquaporin monomers within a tetramer (hetero-tetramerization; and (3 transient interactions with regulatory proteins. We particularly focus on the structural aspects of the interactions, discussing the small differences within a conserved overall fold that allow for aquaporins to be differentially regulated in an organism-, tissue- and trigger-specific manner. A deep knowledge about these differences is needed to fully understand aquaporin function and regulation in many physiological processes, and may enable design of compounds targeting specific aquaporins for treatment of human disease.

  11. Protein immobilization strategies for protein biochips

    NARCIS (Netherlands)

    Rusmini, F.; Rusmini, Federica; Zhong, Zhiyuan; Feijen, Jan

    2007-01-01

    In the past few years, protein biochips have emerged as promising proteomic and diagnostic tools for obtaining information about protein functions and interactions. Important technological innovations have been made. However, considerable development is still required, especially regarding protein

  12. Learning about Proteins

    Science.gov (United States)

    ... Videos for Educators Search English Español Learning About Proteins KidsHealth / For Kids / Learning About Proteins What's in ... from the foods you eat. Different Kinds of Protein Protein from animal sources, such as meat and ...

  13. 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.

  14. 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.

  15. Membrane bending by protein-protein crowding.

    Science.gov (United States)

    Stachowiak, Jeanne C; Schmid, Eva M; Ryan, Christopher J; Ann, Hyoung Sook; Sasaki, Darryl Y; Sherman, Michael B; Geissler, Phillip L; Fletcher, Daniel A; Hayden, Carl C

    2012-09-01

    Curved membranes are an essential feature of dynamic cellular structures, including endocytic pits, filopodia protrusions and most organelles. It has been proposed that specialized proteins induce curvature by binding to membranes through two primary mechanisms: membrane scaffolding by curved proteins or complexes; and insertion of wedge-like amphipathic helices into the membrane. Recent computational studies have raised questions about the efficiency of the helix-insertion mechanism, predicting that proteins must cover nearly 100% of the membrane surface to generate high curvature, an improbable physiological situation. Thus, at present, we lack a sufficient physical explanation of how protein attachment bends membranes efficiently. On the basis of studies of epsin1 and AP180, proteins involved in clathrin-mediated endocytosis, we propose a third general mechanism for bending fluid cellular membranes: protein-protein crowding. By correlating membrane tubulation with measurements of protein densities on membrane surfaces, we demonstrate that lateral pressure generated by collisions between bound proteins drives bending. Whether proteins attach by inserting a helix or by binding lipid heads with an engineered tag, protein coverage above ~20% is sufficient to bend membranes. Consistent with this crowding mechanism, we find that even proteins unrelated to membrane curvature, such as green fluorescent protein (GFP), can bend membranes when sufficiently concentrated. These findings demonstrate a highly efficient mechanism by which the crowded protein environment on the surface of cellular membranes can contribute to membrane shape change.

  16. 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

  17. 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.

  18. 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.

  19. Our interests in protein-protein interactions

    Indian Academy of Sciences (India)

    protein interactions. Evolution of P-P partnerships. Evolution of P-P structures. Evolutionary dynamics of P-P interactions. Dynamics of P-P interaction network. Host-pathogen interactions. CryoEM mapping of gigantic protein assemblies.

  20. Evolution of protein-protein interactions

    Indian Academy of Sciences (India)

    Evolution of protein-protein interactions · Our interests in protein-protein interactions · Slide 3 · Slide 4 · Slide 5 · Slide 6 · Slide 7 · Slide 8 · Slide 9 · Slide 10 · Slide 11 · Slide 12 · Slide 13 · Slide 14 · Slide 15 · Slide 16 · Slide 17 · Slide 18 · Slide 19 · Slide 20.

  1. Ontological visualization of protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Hill David P

    2005-02-01

    Full Text Available Abstract Background Cellular processes require the interaction of many proteins across several cellular compartments. Determining the collective network of such interactions is an important aspect of understanding the role and regulation of individual proteins. The Gene Ontology (GO is used by model organism databases and other bioinformatics resources to provide functional annotation of proteins. The annotation process provides a mechanism to document the binding of one protein with another. We have constructed protein interaction networks for mouse proteins utilizing the information encoded in the GO annotations. The work reported here presents a methodology for integrating and visualizing information on protein-protein interactions. Results GO annotation at Mouse Genome Informatics (MGI captures 1318 curated, documented interactions. These include 129 binary interactions and 125 interaction involving three or more gene products. Three networks involve over 30 partners, the largest involving 109 proteins. Several tools are available at MGI to visualize and analyze these data. Conclusions Curators at the MGI database annotate protein-protein interaction data from experimental reports from the literature. Integration of these data with the other types of data curated at MGI places protein binding data into the larger context of mouse biology and facilitates the generation of new biological hypotheses based on physical interactions among gene products.

  2. 24-hour urine protein

    Science.gov (United States)

    Urine protein - 24 hour; Chronic kidney disease - urine protein; Kidney failure - urine protein ... Heart failure High blood pressure during pregnancy ( preeclampsia ) Kidney disease caused by diabetes, high blood pressure, autoimmune disorders, ...

  3. 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 ...

  4. Protein in diet

    Science.gov (United States)

    Diet - protein ... Protein foods are broken down into parts called amino acids during digestion. The human body needs a ... to eat animal products to get all the protein you need in your diet. Amino acids are ...

  5. 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

  6. Protein surface shielding agents in protein crystallization

    International Nuclear Information System (INIS)

    Hašek, J.

    2011-01-01

    The crystallization process can be controlled by protein surface shielding agents blocking undesirable competitive adhesion modes during non-equilibrium processes of deposition of protein molecules on the surface of growing crystalline blocks. The hypothesis is based on a number of experimental proofs from diffraction experiments and also retrieved from the Protein Data Bank. The molecules adhering temporarily on the surface of protein molecules change the propensity of protein molecules to deposit on the crystal surface in a definite position and orientation. The concepts of competitive adhesion modes and protein surface shielding agents acting on the surface of molecules in a non-equilibrium process of protein crystallization provide a useful platform for the control of crystallization. The desirable goal, i.e. a transient preference of a single dominating adhesion mode between protein molecules during crystallization, leads to uniform deposition of proteins in a crystal. This condition is the most important factor for diffraction quality and thus also for the accuracy of protein structure determination. The presented hypothesis is a generalization of the experimentally well proven behaviour of hydrophilic polymers on the surface of protein molecules of other compounds

  7. Nanotechnologies in protein microarrays.

    Science.gov (United States)

    Krizkova, Sona; Heger, Zbynek; Zalewska, Marta; Moulick, Amitava; Adam, Vojtech; Kizek, Rene

    2015-01-01

    Protein microarray technology became an important research tool for study and detection of proteins, protein-protein interactions and a number of other applications. The utilization of nanoparticle-based materials and nanotechnology-based techniques for immobilization allows us not only to extend the surface for biomolecule immobilization resulting in enhanced substrate binding properties, decreased background signals and enhanced reporter systems for more sensitive assays. Generally in contemporarily developed microarray systems, multiple nanotechnology-based techniques are combined. In this review, applications of nanoparticles and nanotechnologies in creating protein microarrays, proteins immobilization and detection are summarized. We anticipate that advanced nanotechnologies can be exploited to expand promising fields of proteins identification, monitoring of protein-protein or drug-protein interactions, or proteins structures.

  8. 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.

  9. Protein digestion in ruminants

    African Journals Online (AJOL)

    digestibility, or the contribution of endogenous protein to the indigestible feed .... endogenous protein fractions. Alternatively, Stern & Satter (1984) suggested a method whereby the increased protein outflow to the small intestine, resulting from the incremental addition of ..... definition of the various protein fractions. Finally ...

  10. The Protein Model Portal

    OpenAIRE

    Arnold, Konstantin; Kiefer, Florian; Kopp, J?rgen; Battey, James N. D.; Podvinec, Michael; Westbrook, John D.; Berman, Helen M.; Bordoli, Lorenza; Schwede, Torsten

    2008-01-01

    Structural Genomics has been successful in determining the structures of many unique proteins in a high throughput manner. Still, the number of known protein sequences is much larger than the number of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. Thereby, experimental structure determination efforts and homology modeling complement each other in the exploratio...

  11. Photoswitchable cyan fluorescent protein for protein tracking.

    Science.gov (United States)

    Chudakov, Dmitriy M; Verkhusha, Vladislav V; Staroverov, Dmitry B; Souslova, Ekaterina A; Lukyanov, Sergey; Lukyanov, Konstantin A

    2004-11-01

    In recent years diverse photolabeling techniques using green fluorescent protein (GFP)-like proteins have been reported, including photoactivatable PA-GFP, photoactivatable protein Kaede, the DsRed 'greening' technique and kindling fluorescent proteins. So far, only PA-GFP, which is monomeric and gives 100-fold fluorescence contrast, could be applied for protein tracking. Here we describe a dual-color monomeric protein, photoswitchable cyan fluorescent protein (PS-CFP). PS-CFP is capable of efficient photoconversion from cyan to green, changing both its excitation and emission spectra in response to 405-nm light irradiation. Complete photoactivation of PS-CFP results in a 1,500-fold increase in the green-to-cyan fluorescence ratio, making it the highest-contrast monomeric photoactivatable fluorescent protein described to date. We used PS-CFP as a photoswitchable tag to study trafficking of human dopamine transporter in living cells. At moderate excitation intensities, PS-CFP can be used as a pH-stable cyan label for protein tagging and fluorescence resonance energy transfer applications.

  12. 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.

  13. Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins.

    Science.gov (United States)

    Gaines, J C; Acebes, S; Virrueta, A; Butler, M; Regan, L; O'Hern, C S

    2018-05-01

    We compare side chain prediction and packing of core and non-core regions of soluble proteins, protein-protein interfaces, and transmembrane proteins. We first identified or created comparable databases of high-resolution crystal structures of these 3 protein classes. We show that the solvent-inaccessible cores of the 3 classes of proteins are equally densely packed. As a result, the side chains of core residues at protein-protein interfaces and in the membrane-exposed regions of transmembrane proteins can be predicted by the hard-sphere plus stereochemical constraint model with the same high prediction accuracies (>90%) as core residues in soluble proteins. We also find that for all 3 classes of proteins, as one moves away from the solvent-inaccessible core, the packing fraction decreases as the solvent accessibility increases. However, the side chain predictability remains high (80% within 30°) up to a relative solvent accessibility, rSASA≲0.3, for all 3 protein classes. Our results show that ≈40% of the interface regions in protein complexes are "core", that is, densely packed with side chain conformations that can be accurately predicted using the hard-sphere model. We propose packing fraction as a metric that can be used to distinguish real protein-protein interactions from designed, non-binding, decoys. Our results also show that cores of membrane proteins are the same as cores of soluble proteins. Thus, the computational methods we are developing for the analysis of the effect of hydrophobic core mutations in soluble proteins will be equally applicable to analyses of mutations in membrane proteins. © 2018 Wiley Periodicals, Inc.

  14. 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......, whereas vertebrates contain two to four genes. In cnidarians, the gene appears to encode a secreted protein, but transmembrane isoforms of the protein have also evolved, and in many species, alternative splicing facilitates the expression of both transmembrane and secreted isoforms. In most species......, 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...

  15. Prediction of Protein-Protein Interactions Related to Protein Complexes Based on Protein Interaction Networks

    Directory of Open Access Journals (Sweden)

    Peng Liu

    2015-01-01

    Full Text Available A method for predicting protein-protein interactions based on detected protein complexes is proposed to repair deficient interactions derived from high-throughput biological experiments. Protein complexes are pruned and decomposed into small parts based on the adaptive k-cores method to predict protein-protein interactions associated with the complexes. The proposed method is adaptive to protein complexes with different structure, number, and size of nodes in a protein-protein interaction network. Based on different complex sets detected by various algorithms, we can obtain different prediction sets of protein-protein interactions. The reliability of the predicted interaction sets is proved by using estimations with statistical tests and direct confirmation of the biological data. In comparison with the approaches which predict the interactions based on the cliques, the overlap of the predictions is small. Similarly, the overlaps among the predicted sets of interactions derived from various complex sets are also small. Thus, every predicted set of interactions may complement and improve the quality of the original network data. Meanwhile, the predictions from the proposed method replenish protein-protein interactions associated with protein complexes using only the network topology.

  16. Personalizing Protein Nourishment

    Science.gov (United States)

    DALLAS, DAVID C.; SANCTUARY, MEGAN R.; QU, YUNYAO; KHAJAVI, SHABNAM HAGHIGHAT; VAN ZANDT, ALEXANDRIA E.; DYANDRA, MELISSA; FRESE, STEVEN A.; BARILE, DANIELA; GERMAN, J. BRUCE

    2016-01-01

    Proteins are not equally digestible—their proteolytic susceptibility varies by their source and processing method. Incomplete digestion increases colonic microbial protein fermentation (putrefaction), which produces toxic metabolites that can induce inflammation in vitro and have been associated with inflammation in vivo. Individual humans differ in protein digestive capacity based on phenotypes, particularly disease states. To avoid putrefaction-induced intestinal inflammation, protein sources and processing methods must be tailored to the consumer’s digestive capacity. This review explores how food processing techniques alter protein digestibility and examines how physiological conditions alter digestive capacity. Possible solutions to improving digestive function or matching low digestive capacity with more digestible protein sources are explored. Beyond the ileal digestibility measurements of protein digestibility, less invasive, quicker and cheaper techniques for monitoring the extent of protein digestion and fermentation are needed to personalize protein nourishment. Biomarkers of protein digestive capacity and efficiency can be identified with the toolsets of peptidomics, metabolomics, microbial sequencing and multiplexed protein analysis of fecal and urine samples. By monitoring individual protein digestive function, the protein component of diets can be tailored via protein source and processing selection to match individual needs to minimize colonic putrefaction and, thus, optimize gut health. PMID:26713355

  17. Development of the knowledge-based and empirical combined scoring algorithm (KECSA) to score protein-ligand interactions.

    Science.gov (United States)

    Zheng, Zheng; Merz, Kenneth M

    2013-05-24

    We describe a novel knowledge-based protein-ligand scoring function that employs a new definition for the reference state, allowing us to relate a statistical potential to a Lennard-Jones (LJ) potential. In this way, the LJ potential parameters were generated from protein-ligand complex structural data contained in the Protein Databank (PDB). Forty-nine (49) types of atomic pairwise interactions were derived using this method, which we call the knowledge-based and empirical combined scoring algorithm (KECSA). Two validation benchmarks were introduced to test the performance of KECSA. The first validation benchmark included two test sets that address the training set and enthalpy/entropy of KECSA. The second validation benchmark suite included two large-scale and five small-scale test sets, to compare the reproducibility of KECSA, with respect to two empirical score functions previously developed in our laboratory (LISA and LISA+), as well as to other well-known scoring methods. Validation results illustrate that KECSA shows improved performance in all test sets when compared with other scoring methods, especially in its ability to minimize the root mean square error (RMSE). LISA and LISA+ displayed similar performance using the correlation coefficient and Kendall τ as the metric of quality for some of the small test sets. Further pathways for improvement are discussed for which would allow KECSA to be more sensitive to subtle changes in ligand structure.

  18. 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.

  19. 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...

  20. Protein electrophoresis - urine

    Science.gov (United States)

    ... medlineplus.gov/ency/article/003589.htm Urine protein electrophoresis test To use the sharing features on this page, please enable JavaScript. The urine protein electrophoresis (UPEP) test is used to estimate how much ...

  1. 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 ...

  2. 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) ...

  3. Protein sequence databases.

    Science.gov (United States)

    Apweiler, Rolf; Bairoch, Amos; Wu, Cathy H

    2004-02-01

    A variety of protein sequence databases exist, ranging from simple sequence repositories, which store data with little or no manual intervention in the creation of the records, to expertly curated universal databases that cover all species and in which the original sequence data are enhanced by the manual addition of further information in each sequence record. As the focus of researchers moves from the genome to the proteins encoded by it, these databases will play an even more important role as central comprehensive resources of protein information. Several the leading protein sequence databases are discussed here, with special emphasis on the databases now provided by the Universal Protein Knowledgebase (UniProt) consortium.

  4. Protein hydration and dynamics

    International Nuclear Information System (INIS)

    Nakagawa, Hiroshi; Kataoka, Mikio

    2015-01-01

    Inelastic neutron scattering can measure the protein thermal fluctuations under the physiological aqueous environment, especially it is powerful to observe the low-energy protein dynamics in THz region, which are revealed theoretically to be coupled with solvations. Neutron enables the selective observation of protein and hydration water by deuteration. The complementary analysis with molecular dynamics simulation is also effective for the study of protein hydration. Some examples of the application toward the understanding of molecular basis of protein functions will be introduced. (author)

  5. Highly thermostable fluorescent proteins

    Science.gov (United States)

    Bradbury, Andrew M [Santa Fe, NM; Waldo, Geoffrey S [Santa Fe, NM; Kiss, Csaba [Los Alamos, NM

    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.

  6. Targeting proteins for degradation.

    Science.gov (United States)

    Schrader, Erin K; Harstad, Kristine G; Matouschek, Andreas

    2009-11-01

    Protein degradation plays a central role in many cellular functions. Misfolded and damaged proteins are removed from the cell to avoid toxicity. The concentrations of regulatory proteins are adjusted by degradation at the appropriate time. Both foreign and native proteins are digested into small peptides as part of the adaptive immune response. In eukaryotic cells, an ATP-dependent protease called the proteasome is responsible for much of this proteolysis. Proteins are targeted for proteasomal degradation by a two-part degron, which consists of a proteasome binding signal and a degradation initiation site. Here we describe how both components contribute to the specificity of degradation.

  7. Protein supplementation with aging.

    Science.gov (United States)

    Bauer, Juergen M; Diekmann, Rebecca

    2015-01-01

    To highlight the recent evicence for optimal protein intake and protein supplementation in older adults. A special focus has been placed on the effects on muscle protein synthesis, strength and overall performance in this population. Although for older adults, some additional evidence on the benefits of a higher protein intake than 0.8 g/kg body weight per day has been provided, the results of studies focusing on the timing of protein intake over the day have been contradictory. Supplementation with so-called 'fast' proteins, which are also rich in leucine, for example whey protein, proved superior with regard to muscle protein synthesis. First studies in frail older persons showed increased strength after supplementation with milk protein, whereas the combination with physical exercise increased muscle mass without additional benefit for strength or functionality. Recent evidence suggests positive effects of protein supplementation on muscle protein synthesis, muscle mass and muscle strength. However, as most studies included only small numbers of participants for short treatment periods, larger studies with longer duration are necessary to support the clinical relevance of these observations.

  8. 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.

  9. Intracellular protein breakdown. 8

    International Nuclear Information System (INIS)

    Bohley, P.; Kirschke, H.; Langner, J.; Wiederanders, B.; Ansorge, S.

    1976-01-01

    Double-labelled proteins from rat liver cytosol ( 14 C in long-lived, 3 H in short-lived proteins after in-vivo-labelling) are used as substrates for unlabelled proteinases in vitro. Differences in the degradation rates of short-lived and long-lived proteins in vitro by different proteinases and after addition of different effectors allow conclusions concerning their importance for the in-vivo-turnover of substrate proteins. The main activity (>90%) of soluble lysosomal proteinases at pH 6.1 and pH 6.9 is caused by thiolproteinases, which degrade preferentially short-lived cytosol proteins. These proteinases are inhibited by leupeptin. Autolysis of double-labelled cell fractions shows a remarkably faster breakdown of short-lived substrate proteins only in the soluble part of lysosomes. Microsomal fractions degrade in vitro preferentially long-lived substrate proteins. (author)

  10. Protein solubility modeling

    Science.gov (United States)

    Agena, S. M.; Pusey, M. L.; Bogle, I. D.

    1999-01-01

    A thermodynamic framework (UNIQUAC model with temperature dependent parameters) is applied to model the salt-induced protein crystallization equilibrium, i.e., protein solubility. The framework introduces a term for the solubility product describing protein transfer between the liquid and solid phase and a term for the solution behavior describing deviation from ideal solution. Protein solubility is modeled as a function of salt concentration and temperature for a four-component system consisting of a protein, pseudo solvent (water and buffer), cation, and anion (salt). Two different systems, lysozyme with sodium chloride and concanavalin A with ammonium sulfate, are investigated. Comparison of the modeled and experimental protein solubility data results in an average root mean square deviation of 5.8%, demonstrating that the model closely follows the experimental behavior. Model calculations and model parameters are reviewed to examine the model and protein crystallization process. Copyright 1999 John Wiley & Sons, Inc.

  11. 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.

  12. 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

  13. Protein oxidation and peroxidation

    DEFF Research Database (Denmark)

    Davies, Michael Jonathan

    2016-01-01

    Proteins are major targets for radicals and two-electron oxidants in biological systems due to their abundance and high rate constants for reaction. With highly reactive radicals damage occurs at multiple side-chain and backbone sites. Less reactive species show greater selectivity with regard...... and modified turnover. In the presence of O2, high yields of peroxyl radicals and peroxides (protein peroxidation) are formed; the latter account for up to 70% of the initial oxidant flux. Protein peroxides can oxidize both proteins and other targets. One-electron reduction results in additional radicals...... 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...

  14. Protein Misfolding Diseases.

    Science.gov (United States)

    Hartl, F Ulrich

    2017-06-20

    The majority of protein molecules must fold into defined three-dimensional structures to acquire functional activity. However, protein chains can adopt a multitude of conformational states, and their biologically active conformation is often only marginally stable. Metastable proteins tend to populate misfolded species that are prone to forming toxic aggregates, including soluble oligomers and fibrillar amyloid deposits, which are linked with neurodegeneration in Alzheimer and Parkinson disease, and many other pathologies. To prevent or regulate protein aggregation, all cells contain an extensive protein homeostasis (or proteostasis) network comprising molecular chaperones and other factors. These defense systems tend to decline during aging, facilitating the manifestation of aggregate deposition diseases. This volume of the Annual Review of Biochemistry contains a set of three articles addressing our current understanding of the structures of pathological protein aggregates and their associated disease mechanisms. These articles also discuss recent insights into the strategies cells have evolved to neutralize toxic aggregates by sequestering them in specific cellular locations.

  15. Computational Protein Design

    DEFF Research Database (Denmark)

    Johansson, Kristoffer Enøe

    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......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...

  16. 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...

  17. Specificity and affinity quantification of protein-protein interactions.

    Science.gov (United States)

    Yan, Zhiqiang; Guo, Liyong; Hu, Liang; Wang, Jin

    2013-05-01

    Most biological processes are mediated by the protein-protein interactions. Determination of the protein-protein structures and insight into their interactions are vital to understand the mechanisms of protein functions. Currently, compared with the isolated protein structures, only a small fraction of protein-protein structures are experimentally solved. Therefore, the computational docking methods play an increasing role in predicting the structures and interactions of protein-protein complexes. The scoring function of protein-protein interactions is the key responsible for the accuracy of the computational docking. Previous scoring functions were mostly developed by optimizing the binding affinity which determines the stability of the protein-protein complex, but they are often lack of the consideration of specificity which determines the discrimination of native protein-protein complex against competitive ones. We developed a scoring function (named as SPA-PP, specificity and affinity of the protein-protein interactions) by incorporating both the specificity and affinity into the optimization strategy. The testing results and comparisons with other scoring functions show that SPA-PP performs remarkably on both predictions of binding pose and binding affinity. Thus, SPA-PP is a promising quantification of protein-protein interactions, which can be implemented into the protein docking tools and applied for the predictions of protein-protein structure and affinity. The algorithm is implemented in C language, and the code can be downloaded from http://dl.dropbox.com/u/1865642/Optimization.cpp.

  18. Successful Protein Production

    OpenAIRE

    Culp, J.

    2011-01-01

    Successful production of functional proteins is more than an immunoreactive band on a Western blot. Availability of multiple expression vectors make accessible a variety of expression systems and parallel expression approaches can speed results and increase chance of success. The next hurdle is isolation of the protein target in sufficient amounts and with sufficient purity to support subsequent experimental work. Occasionally, protein refolding is the only method available to achieve the des...

  19. Pressure cryocooling protein crystals

    Science.gov (United States)

    Kim, Chae Un [Ithaca, NY; Gruner, Sol M [Ithaca, NY

    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.

  20. Protein intakes in India.

    Science.gov (United States)

    Swaminathan, Sumathi; Vaz, Mario; Kurpad, Anura V

    2012-08-01

    Indian diets derive almost 60 % of their protein from cereals with relatively low digestibility and quality. There have been several surveys of diets and protein intakes in India by the National Nutrition Monitoring Board (NNMB) over the last 25 years, in urban and rural, as well as in slum dwellers and tribal populations. Data of disadvantaged populations from slums, tribals and sedentary rural Indian populations show that the protein intake (mainly from cereals) is about 1 gm/kg/day. However, the protein intake looks less promising in terms of the protein digestibility corrected amino acid score (PDCAAS), using lysine as the first limiting amino acid, where all populations, particularly rural and tribal, appear to have an inadequate quality to their protein intake. The protein: energy (PE) ratio is a measure of dietary quality, and has been used in the 2007 WHO/FAO/UNU report to define reference requirement values with which the adequacy of diets can be evaluated in terms of a protein quality corrected PE ratio. It is likely that about one third of this sedentary rural population is at risk of not meeting their requirements. These levels of risk of deficiency are in a population with relatively low BMI populations, whose diets are also inadequate in fruits and vegetables. Therefore, while the burden of enhancing the quality of protein intake in rural India exists, the quality of the diet, in general, represents a challenge that must be met.

  1. Protein carbonylation in plants

    DEFF Research Database (Denmark)

    Møller, Ian Max; Havelund, Jesper; Rogowska-Wrzesinska, Adelina

    2017-01-01

    This chapter provides an overview of the current knowledge on protein carbonylation in plants and its role in plant physiology. It starts with a brief outline of the turnover and production sites of reactive oxygen species (ROS) in plants and the causes of protein carbonylation. This is followed...... by a description of the methods used to study protein carbonylation in plants, which is also very brief as the methods are similar to those used in studies on animals. The chapter also focuses on protein carbonylation in plants in general and in mitochondria and in seeds in particular, as case stories where...

  2. 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 characterist......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...

  3. 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.

  4. 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.

  5. What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae?

    OpenAIRE

    Ekman, Diana; Light, Sara; Bj?rklund, ?sa K; Elofsson, Arne

    2006-01-01

    Background Most proteins interact with only a few other proteins while a small number of proteins (hubs) have many interaction partners. Hub proteins and non-hub proteins differ in several respects; however, understanding is not complete about what properties characterize the hubs and set them apart from proteins of low connectivity. Therefore, we have investigated what differentiates hubs from non-hubs and static hubs (party hubs) from dynamic hubs (date hubs) in the protein-protein interact...

  6. Comparisons of the M1 genome segments and encoded μ2 proteins of different reovirus isolates

    Directory of Open Access Journals (Sweden)

    Arnold Michelle M

    2004-09-01

    Full Text Available Abstract Background The reovirus M1 genome segment encodes the μ2 protein, a structurally minor component of the viral core, which has been identified as a transcriptase cofactor, nucleoside and RNA triphosphatase, and microtubule-binding protein. The μ2 protein is the most poorly understood of the reovirus structural proteins. Genome segment sequences have been reported for 9 of the 10 genome segments for the 3 prototypic reoviruses type 1 Lang (T1L, type 2 Jones (T2J, and type 3 Dearing (T3D, but the M1 genome segment sequences for only T1L and T3D have been previously reported. For this study, we determined the M1 nucleotide and deduced μ2 amino acid sequences for T2J, nine other reovirus field isolates, and various T3D plaque-isolated clones from different laboratories. Results Determination of the T2J M1 sequence completes the analysis of all ten genome segments of that prototype. The T2J M1 sequence contained a 1 base pair deletion in the 3' non-translated region, compared to the T1L and T3D M1 sequences. The T2J M1 gene showed ~80% nucleotide homology, and the encoded μ2 protein showed ~71% amino acid identity, with the T1L and T3D M1 and μ2 sequences, respectively, making the T2J M1 gene and μ2 proteins amongst the most divergent of all reovirus genes and proteins. Comparisons of these newly determined M1 and μ2 sequences with newly determined M1 and μ2 sequences from nine additional field isolates and a variety of laboratory T3D clones identified conserved features and/or regions that provide clues about μ2 structure and function. Conclusions The findings suggest a model for the domain organization of μ2 and provide further evidence for a role of μ2 in viral RNA synthesis. The new sequences were also used to explore the basis for M1/μ2-determined differences in the morphology of viral factories in infected cells. The findings confirm the key role of Ser/Pro208 as a prevalent determinant of differences in factory morphology

  7. Allosteric Regulation of Proteins

    Indian Academy of Sciences (India)

    For example, the structural changes that allowed for allosteric regulation of haemoglobin were re- vealed through structural elucidation of the protein in free and oxygen-bound forms by X-ray crystallography. Following this,. X-ray crystallography has been utilized to study a variety of al- losteric proteins including ATCase. 2.

  8. Modular protein domains

    National Research Council Canada - National Science Library

    Cesareni, Giovanni

    2005-01-01

    ... encodes not only sequence, but somehow explicitly specifies folding, structure, and biological function as well. How, then, can one learn to read this 'language of proteins'? One of the most powerful approaches to 'cracking the protein code' has involved sequence comparisons between and within species, a task now greatly simplified by the ever...

  9. Amino acids and proteins

    NARCIS (Netherlands)

    van Goudoever, Johannes B.; Vlaardingerbroek, Hester; van den Akker, Chris H.; de Groof, Femke; van der Schoor, Sophie R. D.

    2014-01-01

    Amino acids and protein are key factors for growth. The neonatal period requires the highest intake in life to meet the demands. Those demands include amino acids for growth, but proteins and amino acids also function as signalling molecules and function as neurotransmitters. Often the nutritional

  10. MODELS OF PROTEIN FOLDING

    Directory of Open Access Journals (Sweden)

    Unnati Ahluwalia

    2012-12-01

    Full Text Available In an attempt to explore the understanding of protein folding mechanism, various models have been proposed in the literature. Advances in recent experimental and computational techniques rationalized our understanding on some of the fundamental features of the protein folding pathways. The goal of this review is to revisit the various models and outline the essential aspects of the folding reaction.

  11. Green fluorescent protein.

    Science.gov (United States)

    Chalfie, M

    1995-10-01

    Several bioluminescent coelenterates use a secondary fluorescent protein, the green fluorescent protein (GFP), in an energy transfer reaction to produce green light. The most studied of these proteins have been the GFPs from the jellyfish Aequorea victoria and the sea pansy Renilla reniformis. Although the proteins from these organisms are not identical, they are thought to have the same chromophore, which is derived from the primary amino acid sequence of GFP. The differences are thought to be due to changes in the protein environment of the chromophore. Recent interest in these molecules has arisen from the cloning of the Aequorea gfp cDNA and the demonstration that its expression in the absence of other Aequorea proteins results in a fluorescent product. This demonstration indicated that GFP could be used as a marker of gene expression and protein localization in living and fixed tissues. Bacterial, plant and animal (including mammalian) cells all express GFP. The heterologous expression of the gfp cDNA has also meant that it could be mutated to produce proteins with different fluorescent properties. Variants with more intense fluorescence or alterations in the excitation and emission spectra have been produced.

  12. Proteins at surfaces

    NARCIS (Netherlands)

    Efimova, Y.M.

    2006-01-01

    Understanding protein adsorption is of vital importance in many fields of medicine and industry that can be divided into two categories: those in which it is desired to minimize adsorption, and those in which protein adsorption is desired. The first category covers materials for kidney dialysis

  13. 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.

  14. 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.

  15. Advances in Protein Precipitation

    NARCIS (Netherlands)

    Golubovic, M.

    2009-01-01

    Proteins are biological macromolecules, which are among the key components of all living organisms. Proteins are nowadays present in all fields of biotech industry, such as food and feed, synthetic and pharmaceutical industry. They are isolated from their natural sources or produced in different

  16. NMR of unfolded proteins

    Indian Academy of Sciences (India)

    Unknown

    2005-01-03

    Jan 3, 2005 ... emerged as the sole, most powerful technique to help characterize these disordered protein systems. In ... tion of a protein is related to its significant and ...... This is likely to allow a number of both charged and hydrophobic groups to be presented to fibronectin for highly spe- cific binding.76. 5.3 Lysozyme.

  17. NMR of unfolded proteins

    Indian Academy of Sciences (India)

    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 ...

  18. 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

  19. Artificially Engineered Protein Polymers.

    Science.gov (United States)

    Yang, Yun Jung; Holmberg, Angela L; Olsen, Bradley D

    2017-06-07

    Modern polymer science increasingly requires precise control over macromolecular structure and properties for engineering advanced materials and biomedical systems. The application of biological processes to design and synthesize artificial protein polymers offers a means for furthering macromolecular tunability, enabling polymers with dispersities of ∼1.0 and monomer-level sequence control. Taking inspiration from materials evolved in nature, scientists have created modular building blocks with simplified monomer sequences that replicate the function of natural systems. The corresponding protein engineering toolbox has enabled the systematic development of complex functional polymeric materials across areas as diverse as adhesives, responsive polymers, and medical materials. This review discusses the natural proteins that have inspired the development of key building blocks for protein polymer engineering and the function of these elements in material design. The prospects and progress for scalable commercialization of protein polymers are reviewed, discussing both technology needs and opportunities.

  20. Protein restriction and cancer.

    Science.gov (United States)

    Yin, Jie; Ren, Wenkai; Huang, Xingguo; Li, Tiejun; Yin, Yulong

    2018-03-26

    Protein restriction without malnutrition is currently an effective nutritional intervention known to prevent diseases and promote health span from yeast to human. Recently, low protein diets are reported to be associated with lowered cancer incidence and mortality risk of cancers in human. In murine models, protein restriction inhibits tumor growth via mTOR signaling pathway. IGF-1, amino acid metabolic programing, FGF21, and autophagy may also serve as potential mechanisms of protein restriction mediated cancer prevention. Together, dietary intervention aimed at reducing protein intake can be beneficial and has the potential to be widely adopted and effective in preventing and treating cancers. Copyright © 2018 Elsevier B.V. All rights reserved.

  1. 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...

  2. The Protein Model Portal.

    Science.gov (United States)

    Arnold, Konstantin; Kiefer, Florian; Kopp, Jürgen; Battey, James N D; Podvinec, Michael; Westbrook, John D; Berman, Helen M; Bordoli, Lorenza; Schwede, Torsten

    2009-03-01

    Structural Genomics has been successful in determining the structures of many unique proteins in a high throughput manner. Still, the number of known protein sequences is much larger than the number of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. Thereby, experimental structure determination efforts and homology modeling complement each other in the exploration of the protein structure space. One of the challenges in using model information effectively has been to access all models available for a specific protein in heterogeneous formats at different sites using various incompatible accession code systems. Often, structure models for hundreds of proteins can be derived from a given experimentally determined structure, using a variety of established methods. This has been done by all of the PSI centers, and by various independent modeling groups. The goal of the Protein Model Portal (PMP) is to provide a single portal which gives access to the various models that can be leveraged from PSI targets and other experimental protein structures. A single interface allows all existing pre-computed models across these various sites to be queried simultaneously, and provides links to interactive services for template selection, target-template alignment, model building, and quality assessment. The current release of the portal consists of 7.6 million model structures provided by different partner resources (CSMP, JCSG, MCSG, NESG, NYSGXRC, JCMM, ModBase, SWISS-MODEL Repository). The PMP is available at http://www.proteinmodelportal.org and from the PSI Structural Genomics Knowledgebase.

  3. Protein trapping of nanoparticles

    International Nuclear Information System (INIS)

    Ang, Joo C.; Lin, Jack M.; Yaron, Peter N.; White, John W.

    2009-01-01

    Full text: We have observed the formation of protein-nanoparticle complexes at the air-water interfaces from three different methods of presenting the nanoparticles to proteins. The structures formed resemble the 'protein-nanoparticle corona' proposed by Lynch et al. [1-3) in relation to a possible route for nanoparticle entry into living cells. To do this, the methods of x-ray and neutron reflectivity (with isotopic contrast variation between the protein and nanoparticles) have been used to study the structures formed at the air-water interface of l 3 - casein presented to silica nanoparticle dispersions. Whilst the silica dispersions showed no observable reflectivity, strong signals appear in the reflectivity when protein is present. Drop-wise spreading of a small amount of protein at the air-silica sol interface and presentation of the silica sol to an isolated monomolecular protein film (made by the 'flow-trough' method [4]) gave an immediate signal. Mixing the components in solution only produces a slow response but in all cases a similar structure is formed. The different responses are interpreted in structural and stoichiometric ways.

  4. Anchored design of protein-protein interfaces.

    Directory of Open Access Journals (Sweden)

    Steven M Lewis

    Full Text Available 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.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.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.

  5. Intercellular protein-protein interactions at synapses.

    Science.gov (United States)

    Yang, Xiaofei; Hou, Dongmei; Jiang, Wei; Zhang, Chen

    2014-06-01

    Chemical synapses are asymmetric intercellular junctions through which neurons send nerve impulses to communicate with other neurons or excitable cells. The appropriate formation of synapses, both spatially and temporally, is essential for brain function and depends on the intercellular protein-protein interactions of cell adhesion molecules (CAMs) at synaptic clefts. The CAM proteins link pre- and post-synaptic sites, and play essential roles in promoting synapse formation and maturation, maintaining synapse number and type, accumulating neurotransmitter receptors and ion channels, controlling neuronal differentiation, and even regulating synaptic plasticity directly. Alteration of the interactions of CAMs leads to structural and functional impairments, which results in many neurological disorders, such as autism, Alzheimer's disease and schizophrenia. Therefore, it is crucial to understand the functions of CAMs during development and in the mature neural system, as well as in the pathogenesis of some neurological disorders. Here, we review the function of the major classes of CAMs, and how dysfunction of CAMs relates to several neurological disorders.

  6. 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 second with oxidation in salted herring. The mechanisms responsible for initiation of protein oxidation are unclear, but it is generally accepted that free radical species initiating lipid oxidation can also initiate protein oxidation. The chapter focuses on interaction between protein and lipid...... 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...

  7. Microbial Physiology of the Conversion of Residual Oil to Methane: A Protein Prospective

    Science.gov (United States)

    Morris, Brandon E. L.; Bastida-Lopez, Felipe; von Bergen, Martin; Richnow, Hans-Hermann; Suflita, Joseph M.

    2010-05-01

    Traditional petroleum recovery techniques are unable to extract the majority of oil in most petroliferous deposits. The recovery of even a fraction of residual hydrocarbon in conventional reserves could represent a substantive energy supply. To this end, the microbial conversion of residual oil to methane has gained increasing relevance in recent years [1,2]. Worldwide demand for methane is expected to increase through 2030 [3], as it is a cleaner-burning alternative to traditional fuels [4]. To investigate the microbial physiology of hydrocarbon-decomposition and ultimate methanogenesis, we initiated a two-pronged approach. First, a model alkane-degrading sulfate-reducing bacterium, Desulfoglaeba alkanexedens, was used to interrogate the predominant metabolic pathway(s) differentially expressed during growth on either n-decane or butyrate. A total of 81 proteins were differentially expressed during bacterial growth on butyrate, while 100 proteins were unique to the alkane-grown condition. Proteins related to alkylsuccinate synthase, or the homologous 1-methyl alkylsuccinate synthase, were identified only in the presence of the hydrocarbon. Secondly, we used a newly developed stable isotope probing technique [5] targeted towards proteins to monitor the flux of carbon through a residual oil-degrading bacterial consortium enriched from a gas-condensate contaminated aquifer [1]. Combined carbon and hydrogen stable isotope fractionation identified acetoclastic methanogenesis as the dominant process in this system. Such findings agree with the previous clone library characterization of the consortium. Furthermore, hydrocarbon activation was determined to be the rate-limiting process during the net conversion of residual oil to methane. References 1. Gieg, L.M., K.E. Duncan, and J.M. Suflita, Bioenegy production via microbial conversion of residual oil to natural gas. Appl Environ Micro, 2008. 74(10): p. 3022-3029. 2. Jones, D.M., et al., Crude-oil biodegradation via

  8. 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....

  9. 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.

  10. Sound of proteins

    DEFF Research Database (Denmark)

    2007-01-01

    In my group we work with Molecular Dynamics to model several different proteins and protein systems. We submit our modelled molecules to changes in temperature, changes in solvent composition and even external pulling forces. To analyze our simulation results we have so far used visual inspection...... 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...

  11. 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....

  12. Protein Crystal Malic Enzyme

    Science.gov (United States)

    1992-01-01

    Malic Enzyme is a target protein for drug design because it is a key protein in the life cycle of intestinal parasites. After 2 years of effort on Earth, investigators were unable to produce any crystals that were of high enough quality and for this reason the structure of this important protein could not be determined. Crystals obtained from one STS-50 were of superior quality allowing the structure to be determined. This is just one example why access to space is so vital for these studies. Principal Investigator is Larry DeLucas.

  13. Designing microcapsules based on protein fibrils and protein - polysaccharide complexes

    NARCIS (Netherlands)

    Hua, K.N.P.

    2012-01-01

    Keywords: encapsulation, microcapsule, protein, fibril, protein-polysaccharide complex, controlled release, interfacial rheology, lysozyme, ovalbumin This thesis describes the design of encapsulation systems using mesostructures from proteins and polysaccharides. The approach was to first

  14. Designing microcapsules based on protein fibrils and protein - polysaccharide complexes

    NARCIS (Netherlands)

    Hua, K.N.P.

    2012-01-01

    Keywords: encapsulation, microcapsule, protein, fibril, protein-polysaccharide complex, controlled release, interfacial rheology, lysozyme, ovalbumin

    This thesis describes the design of encapsulation systems using mesostructures from proteins and polysaccharides. The approach

  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......-domain proteins catalyse the formation of ubiquitin-protein conjugates, whereas others appear to target ubiquitinated proteins for degradation and interact with chaperones. Hence, by binding to the 26S proteasome the UBL-domain proteins seem to tailor and direct the basic proteolytic functions of the particle...

  16. 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.

  17. Retinoblastoma protein partners.

    Science.gov (United States)

    Morris, E J; Dyson, N J

    2001-01-01

    Studies of the retinoblastoma gene (Rb) have shown that its protein product (pRb) acts to restrict cell proliferation, inhibit apoptosis, and promote cell differentiation. The frequent mutation of the Rb gene, and the functional inactivation of pRb in tumor cells, have spurred interest in the mechanism of pRb action. Recently, much attention has focused on pRb's role in the regulation of the E2F transcription factor. However, biochemical studies have suggested that E2F is only one of many pRb-targets and, to date, at least 110 cellular proteins have been reported to associate with pRb. The plethora of pRb-binding proteins raises several important questions. How many functions does pRb possess, which of these functions are important for development, and which contribute to tumor suppression? The goal of this review is to summarize the current literature of pRb-associated proteins.

  18. Interactive protein manipulation

    International Nuclear Information System (INIS)

    2003-01-01

    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

  19. The Pentapeptide Repeat Proteins

    Energy Technology Data Exchange (ETDEWEB)

    Vetting,M.; Hegde, S.; Fajardo, J.; Fiser, A.; Roderick, S.; Takiff, H.; Blanchard, J.

    2006-01-01

    The Pentapeptide Repeat Protein (PRP) family has over 500 members in the prokaryotic and eukaryotic kingdoms. These proteins are composed of, or contain domains composed of, tandemly repeated amino acid sequences with a consensus sequence of [S, T,A, V][D, N][L, F]-[S, T,R][G]. The biochemical function of the vast majority of PRP family members is unknown. The three-dimensional structure of the first member of the PRP family was determined for the fluoroquinolone resistance protein (MfpA) from Mycobacterium tuberculosis. The structure revealed that the pentapeptide repeats encode the folding of a novel right-handed quadrilateral {beta}-helix. MfpA binds to DNA gyrase and inhibits its activity. The rod-shaped, dimeric protein exhibits remarkable size, shape and electrostatic similarity to DNA.

  20. 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.

  1. The protein protocols handbook

    National Research Council Canada - National Science Library

    Walker, John M

    2002-01-01

    .... The new chapters cover with many rapidly developing areas, particularly the application of mass spectrometry in protein characterization, as well as the now well-established 2-D PAGE technique in proteomics...

  2. 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.

  3. 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.

  4. Protein targeting protocols

    National Research Council Canada - National Science Library

    Clegg, Roger A

    1998-01-01

    ... of intracellular environment. Because the concept of protein targeting is intuitive rather than explicitly defined, it has been variously used by different groups of researchers in cell biology, biochemistry, and molecular biology. For those working in the field of intracellular signaling, an influential introduction to the topic was the seminal article by Hubbard & Cohen (TIBS [1993] 18, 172- 177), which was based on the work of Cohen's laboratory on protein phosphatases. Subsequently, the ideas that t...

  5. Protein conducting nanopores

    International Nuclear Information System (INIS)

    Harsman, Anke; Krueger, Vivien; Bartsch, Philipp; Honigmann, Alf; Wagner, Richard; Schmidt, Oliver; Rao, Sanjana; Meisinger, Christof

    2010-01-01

    About 50% of the cellular proteins have to be transported into or across cellular membranes. This transport is an essential step in the protein biosynthesis. In eukaryotic cells secretory proteins are transported into the endoplasmic reticulum before they are transported in vesicles to the plasma membrane. Almost all proteins of the endosymbiotic organelles chloroplasts and mitochondria are synthesized on cytosolic ribosomes and posttranslationally imported. Genetic, biochemical and biophysical approaches led to rather detailed knowledge on the composition of the translocon-complexes which catalyze the membrane transport of the preproteins. Comprehensive concepts on the targeting and membrane transport of polypeptides emerged, however little detail on the molecular nature and mechanisms of the protein translocation channels comprising nanopores has been achieved. In this paper we will highlight recent developments of the diverse protein translocation systems and focus particularly on the common biophysical properties and functions of the protein conducting nanopores. We also provide a first analysis of the interaction between the genuine protein conducting nanopore Tom40 SC as well as a mutant Tom40 SC (S 54 →E) containing an additional negative charge at the channel vestibule and one of its native substrates, CoxIV, a mitochondrial targeting peptide. The polypeptide induced a voltage-dependent increase in the frequency of channel closure of Tom40 SC corresponding to a voltage-dependent association rate, which was even more pronounced for the Tom40 SC S54E mutant. The corresponding dwelltime reflecting association/transport of the peptide could be determined with t-bar off ≅1.1 ms for the wildtype, whereas the mutant Tom40 SC S54E displayed a biphasic dwelltime distribution ( t-bar off 1 ≅0.4 ms; t-bar off 2 ≅4.6 ms).

  6. 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

  7. 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...

  8. 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 conformations...

  9. Protein: MPA1 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available MPA1 TLR signaling molecules RSAD2 CIG5 Radical S-adenosyl methionine domain-containing protein 2 Cytomegalo...virus-induced gene 5 protein, Viperin, Virus inhibitory protein, endoplasmic reticu

  10. More protein in cereals?

    International Nuclear Information System (INIS)

    1969-01-01

    Ways in which the protein content of plant crops may be raised by the use of nuclear radiation are to be discussed at a symposium in Vienna in June next year, organized by the joint Food and Agriculture Organization/Agency Division of Atomic Energy in Food and Agriculture. Plant crops - especially cereal grains - are the basic food and protein source of most of the world's population, particularly in less-developed countries. But their natural protein content is low; increasing the quantity and nutritional quality of plant protein is potentially the most feasible way to combat widespread protein malnutrition. This improvement in seed stock can be achieved by plant breeding methods in which nuclear irradiation techniques are used to induce mutations in grain, and other isotopic techniques can be used to select only those mutants which have the desired properties. The scientists who attend the symposium will have an opportunity to review what mutation plant breeders have achieved, the application of nuclear techniques to screening for protein and amino-acid content and nutritional value, and isotopic methods which contribute to research in plant nutrition and physiology. (author)

  11. 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.

  12. Electrophoretic transfer protein zymography.

    Science.gov (United States)

    Pan, Daniel; Hill, Adam P; Kashou, Anthony; Wilson, Karl A; Tan-Wilson, Anna

    2011-04-15

    Zymography detects and characterizes proteolytic enzymes by electrophoresis of protease-containing samples into a nonreducing sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) gel containing a copolymerized protein substrate. The usefulness of zymography for molecular weight determination and proteomic analysis is hampered by the fact that some proteases exhibit slower migration through a gel that contains substrate protein. This article introduces electrophoretic transfer protein zymography as one solution to this problem. In this technique, samples containing proteolytic enzymes are first resolved in nonreducing SDS-PAGE on a gel without protein substrate. The proteins in the resolving gel are then electrophoretically transferred to a receiving gel previously prepared with a copolymerized protein substrate. The receiving gel is then developed as a zymogram to visualize clear or lightly stained bands in a dark background. Band intensities are linearly related to the amount of protease, extending the usefulness of the technique so long as conditions for transfer and development of the zymogram are kept constant. Conditions of transfer, such as the pore sizes of resolving and receiving gels and the transfer time relative to the molecular weight of the protease, are explored. Copyright © 2011 Elsevier Inc. All rights reserved.

  13. 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…

  14. Levels of PAHs in shrimps, Penaeus monodon from Jones Creek ...

    African Journals Online (AJOL)

    High concentrations were recorded during the rainy season and during the first quarter of the year. The investigated samples were classified as minimally contaminated when compared with FDA levels of PAHs in shrimp samples. Distribution patterns showed that PAHs with 3 and 4 rings dominated confirming the pyrogenic ...

  15. Comparison of Jones jig molar distalization appliance with extraoral traction.

    Science.gov (United States)

    Haydar, S; Uner, O

    2000-01-01

    In this study, 20 patients were evaluated. Ten were treated with intraoral distalization followed by fixed appliance therapy, and 10 were treated with extra oral traction followed by fixed appliance therapy. Molar relationship correction was achieved in 2.5 months with intraoral distalization and in 10.7 months with extraoral distalization. A significant anterior movement of the anchorage unit (P <.001) was observed with the intraoral distalization and a significant distal drift of premolars was observed in the headgear group (P <.05). Palatal plane was found to tip downward significantly in the headgear group (P <.05). Total outcome of the 2 methods were discussed evaluating the advantages and disadvantages of the 2 distalization methods.

  16. Sustentabilidade empresarial: o caso Dow Jones Sutainability Index

    OpenAIRE

    Zago, Ana Paula Pinheiro

    2007-01-01

    A escolha de uma empresa para fazer parte da listagem do DJSI gera uma série de expectativas quanto aos benefícios advindos desta conquista. Espera-se que o investimento no desenvolvimento sustentável e a conseqüente inclusão da empresa neste seleto grupo, além de facilitar o acesso às fontes de recursos e melhorar a imagem da empresa, traga benefícios econômicos e estratégicos refletidos na valorização da empresa no mercado. Entretanto, a relação entre desempenho sócio-ambient...

  17. Iridoids from the roots of Valeriana jatamansi Jones.

    Science.gov (United States)

    Wang, Ru-Jing; Chen, Hai-Mei; Yang, Fan; Deng, Yun; Ao, Hui; Xie, Xiao-Fang; Li, Hong-Xiang; Zhang, Hai; Cao, Zhi-Xing; Zhu, Li-Xia; Chen, Yin; Peng, Cheng; Tan, Yu-Zhu

    2017-09-01

    Five iridoids, named as chlorovaltrate P-T, together with six known analogues, (4β,8β)-8-methoxy-3-methoxy-10-methylene-2,9-dioxatricyclo[4.3.1.0 3,7 ]decan-4-ol, chlorovaltrate A, (1R,3R,5R,7S,8R,9S)-3,8-epoxy-1-O-ethyl-5-hydroxyvalechlorine, 8-methoxy-4-acetoxy-3-chlormethyl-10-methylen-2,9-dioxa-tricyclo[4.3.1.0 3,7 ]decan, (1S,3R,5R,7S,8R,9S)-3,8-epoxy-1-O-ethyl-5-hydroxyvalechlorine, (1R,3R,5R,7S,8R,9S)-3,8-epoxy-1-O-methyl-5-hydroxyvalechlorine were isolated from the roots of Valeriana jatamansi (syn. Valeriana wallichii). Their structures were elucidated by extensive analysis of 1D, 2D NMR and HRESIMS spectroscopic. The absolute configuration of chlorovaltrate P-T were established by comparing their experimental and calculated electronic circular dichroism (ECD) spectra. 3,8-epoxy iridoids exhibited weak cytotoxicity against the lung adenocarcinoma (A 549) and gastric carcinoma cells (SGC 7901). Some also showed moderate neuroprotective effects against CoCl 2 -induced neuronal cell death in PC12 cells. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Terrestrial heat flow and global warming | Jones | Zimbabwe ...

    African Journals Online (AJOL)

    The variation of temperature with depth and the amount of heat escaping from the interior of the Earth through its surface are easily measured and give useful information on the ventilation requirements of deep mines, the deep structure of the Earth's crust and on global warming. This paper presents some ...

  19. Shelley Jones — Aider les jeunes Ougandaises à poursuivre leurs ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    18 nov. 2014 ... En Afrique, ajoute-t-elle, il est crucial que les adolescentes puissent se faire entendre et échangent sur leurs expériences et leurs impressions, car elles font face à des problèmes complexes et sont en situation de grande vulnérabilité, notamment en ce qui a trait au mariage et aux grossesses précoces, ...

  20. Matthew Jones House: Historic Maintenance and Repair Manual

    Science.gov (United States)

    2014-08-01

    space versus the closed-off drywalled space. This issue needs to be investigated; one suggestion would be to have two separate HVAC systems—one per...specialized space—to control the appropriate amount of humidity. Drywall has mold retention capabilities, therefore, some of it might have to be re...separates this room from the stair pas- sage. The ceiling joists have been covered with drywall . This room is cur- rently used as a viewing room for the

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

    Digital Repository Service at National Institute of Oceanography (India)

    Rao, D.G.

    briefly in Chapter 1. Under its eight sub-heads, the varied seabed morphologies from con- tinent to deep-oceans of converging and diverging plates boundaries, and fan-shaped rises have been outlined. The earnest interest of the author is explic- itly... of sediments and probable lithologies. The development of sedimentary reflectors stratal pattern in relation to the boundaries of the deposi- tional sequences, fault controlled to flexure con- trolled subsidence have been presented. Classic ex- amples...

  2. The function and content of amusement | Jones | South African ...

    African Journals Online (AJOL)

    Once we establish that the fundamental subject matter of the study of humour is a mental state – which I will call finding funny – then it immediately follows that we need to find the content and function of this mental state. The main contender for the content of finding funny is the incongruous (the incongruity thesis); the main ...

  3. Training for human security | Jones | Journal of Social Development ...

    African Journals Online (AJOL)

    The focus in this article is on the trainers, trainees, and training methods of human security. Case examples are drawn from different regions around the globe, with particular though not exclusive, emphasis on Africa. The aim is to explore the scope of training, national and regional approaches, the choice of training methods ...

  4. Sexual risk reduction among Zambian couples | Jones | SAHARA-J ...

    African Journals Online (AJOL)

    Zambia has over 1 million HIV infections nationwide and an urban prevalence rate of 23%. This study compared the impact of male involvement in multiple and single session risk reduction interventions among inconsistent condom users in Zambia and the role of serostatus among HIV-seropositive and serodiscordant ...

  5. Equilibrium fluctuations of the Lennard-Jones cluster surface

    Science.gov (United States)

    Zhukhovitskii, D. I.

    2008-11-01

    Spectra of the cluster surface equilibrium fluctuations are treated by decomposition into the bulk and net capillary ones. The bulk fluctuations without capillary ones are simulated by the surface of a cluster truncated by a sphere. The bulk fluctuation spectrum is shown to be generated primarily by the discontinuity in the spatial distribution of cluster internal particles. The net capillary fluctuation slice spectrum is obtained in molecular dynamics simulation by subtraction of the bulk fluctuation spectrum from the total one. This net spectrum is in the best agreement with a theoretical estimation if we assume the intrinsic surface tension to be independent of the wave number. The wave number cutoff is brought in balance with the intrinsic surface tension and excess surface area induced by the capillary fluctuations. It is shown that the ratio of the ordinary surface tension to the intrinsic one can be considered as a universal constant independent of the temperature and cluster size.

  6. Modelling of proteins in membranes

    DEFF Research Database (Denmark)

    Sperotto, Maria Maddalena; May, S.; Baumgaertner, A.

    2006-01-01

    This review describes some recent theories and simulations of mesoscopic and microscopic models of lipid membranes with embedded or attached proteins. We summarize results supporting our understanding of phenomena for which the activities of proteins in membranes are expected to be significantly...... oppositely charged lipid membranes, lipid-induced tilting of proteins embedded in lipid bilayers, protein-induced bilayer deformations, protein insertion and assembly, and lipid-controlled functioning of membrane proteins....

  7. Peptide Signals Encode Protein Localization▿

    OpenAIRE

    Russell, Jay H.; Keiler, Kenneth C.

    2007-01-01

    Many bacterial proteins are localized to precise intracellular locations, but in most cases the mechanism for encoding localization information is not known. Screening libraries of peptides fused to green fluorescent protein identified sequences that directed the protein to helical structures or to midcell. These peptides indicate that protein localization can be encoded in 20-amino-acid peptides instead of complex protein-protein interactions and raise the possibility that the location of a ...

  8. 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.

  9. An Extremely Rare Manifestation of Multiple Myeloma: An Immunoglobulin D Secreting Testicular Plasmacytoma.

    Science.gov (United States)

    Sharma, Ashish; Binazir, Tina; Sintow, Alexandre; Lee, Chi Chan; Shaharyar, Sameer; Tache, Jason

    2017-06-27

    Multiple myelomas (MM) of the immunoglobulin D (IgD) subtype is rare amongst plasma cell malignancies. It can present a diagnostic challenge because of the low amount of immunoglobulin in the serum. The amount of monoclonal (M)-protein is often undetectable on electrophoresis. Historically, survival in these patients was typically shorter compared to the immunoglobulin A (IgA) and immunoglobulin G (IgG) subtypes due to advanced disease upon presentation. With the advent of better diagnostic techniques, the prognosis of this disease is changing. We describe a case of an extramedullary testicular plasmacytoma (EMP) of the IgD subtype as the primary feature of MM, which responded well to novel therapy. A 72-year-old White male presented to the emergency room with a right testicular mass for three months. He subsequently underwent right radical orchiectomy. Pathology of the specimen revealed plasmacytoid cells positive for cluster of differentiation (CD79a), lambda free light chain, IgD, and BCL-1 (Cyclin D1) on immunochemical stains. Urine and serum immunofixation were positive for monoclonal IgD with lambda light chain specificity and Bence Jones proteinuria. Bone marrow biopsy showed large sheets of plasma cells with greater than 90% cellularity. Flow cytometry displayed atypical plasma cells expressing cluster of differentiation (CD38, CD20, and CD56) with cytoplasm and lambda light chain, approximately 20%, consistent with a plasma cell dyscrasia. Stage 3 IgD lambda multiple myeloma was diagnosed. He received novel treatment with Bortezomib and dexamethasone for three months, followed by Lenalidomide. His performance status and lab data improved significantly. He had progression-free survival (PFS) of approximately three years and remained in complete remission low-dose dose of Lenalidomide daily. IgD myeloma was considered a diagnostic challenge due to undetectable M-protein levels on serum protein electrophoresis (SPEP). With the advent of serum free light chain

  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. Protein quality control and cancerogenesis.

    Science.gov (United States)

    Trcka, F; Vojtesek, B; Muller, P

    2012-01-01

    Both nascent and mature proteins are prone to damaging changes induced by either external or internal stimuli. Dysfunctional or misfolded proteins cause direct physiological risk in crowded cellular environment and must be readily and efficiently eliminated. To ensure protein homeostasis, eukaryotic cells have evolved several protein quality control machineries. Protein quality control plays a special role in cancer cells. Genetic instability causing increased production of damaged and/or deregulated proteins is a hallmark of cancer cells. Therefore, intrinsic genetic instability together with hostile tumour microenvironment represents a demanding task for protein quality control machineries in tumours. Regulation of general protein turnover as well as degradation of tumour-promoting/suppressing proteins by protein quality control machineries thus represent an important processes involved in cancer development and progression. The review focuses on the description of three major protein quality control pathways and their roles in cancer.

  12. Purine inhibitors of protein kinases, G proteins and polymerases

    Science.gov (United States)

    Gray, Nathanael S.; Schultz, Peter; Kim, Sung-Hou; Meijer, Laurent

    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.

  13. Measuring protein breakdown rate in individual proteins in vivo

    DEFF Research Database (Denmark)

    Holm, Lars; Kjaer, Michael

    2010-01-01

    To outline different approaches of how protein breakdown can be quantified and to present a new approach to determine the fractional breakdown rate of individual slow turnover proteins in vivo.......To outline different approaches of how protein breakdown can be quantified and to present a new approach to determine the fractional breakdown rate of individual slow turnover proteins in vivo....

  14. 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...

  15. Protein Correlation Profiles Identify Lipid Droplet Proteins with High Confidence*

    Science.gov (United States)

    Krahmer, Natalie; Hilger, Maximiliane; Kory, Nora; Wilfling, Florian; Stoehr, Gabriele; Mann, Matthias; Farese, Robert V.; Walther, Tobias C.

    2013-01-01

    Lipid droplets (LDs) are important organelles in energy metabolism and lipid storage. Their cores are composed of neutral lipids that form a hydrophobic phase and are surrounded by a phospholipid monolayer that harbors specific proteins. Most well-established LD proteins perform important functions, particularly in cellular lipid metabolism. Morphological studies show LDs in close proximity to and interacting with membrane-bound cellular organelles, including the endoplasmic reticulum, mitochondria, peroxisomes, and endosomes. Because of these close associations, it is difficult to purify LDs to homogeneity. Consequently, the confident identification of bona fide LD proteins via proteomics has been challenging. Here, we report a methodology for LD protein identification based on mass spectrometry and protein correlation profiles. Using LD purification and quantitative, high-resolution mass spectrometry, we identified LD proteins by correlating their purification profiles to those of known LD proteins. Application of the protein correlation profile strategy to LDs isolated from Drosophila S2 cells led to the identification of 111 LD proteins in a cellular LD fraction in which 1481 proteins were detected. LD localization was confirmed in a subset of identified proteins via microscopy of the expressed proteins, thereby validating the approach. Among the identified LD proteins were both well-characterized LD proteins and proteins not previously known to be localized to LDs. Our method provides a high-confidence LD proteome of Drosophila cells and a novel approach that can be applied to identify LD proteins of other cell types and tissues. PMID:23319140

  16. Utilization of soya protein as an alternative protein source in ...

    African Journals Online (AJOL)

    The effect of replacing fish protein with soya protein in tilapia (Oreochromis niloticus) diets was examined. Three isoproteic (35%) diets containing 0% (FD); 50% (MD) and 100% (SD) fish protein substituted by soya protein were formulated. Fish (initial weight = 11.56 ± 4.22 g) was fed with experimental diets for 180 days.

  17. Changes in protein composition and protein phosphorylation during ...

    African Journals Online (AJOL)

    Changes in protein profiles and protein phosphorylation were studied in various stages of germinating somatic and zygotic embryos. Many proteins, which were expressed in cotyledonary stage somatic embryos, were also present in the zygotic embryos obtained from mature dry seed. The intensity of 22 kDa protein was ...

  18. A Stevedore's protein knot.

    Directory of Open Access Journals (Sweden)

    Daniel Bölinger

    2010-04-01

    Full Text Available Protein knots, mostly regarded as intriguing oddities, are gradually being recognized as significant structural motifs. Seven distinctly knotted folds have already been identified. It is by and large unclear how these exceptional structures actually fold, and only recently, experiments and simulations have begun to shed some light on this issue. In checking the new protein structures submitted to the Protein Data Bank, we encountered the most complex and the smallest knots to date: A recently uncovered alpha-haloacid dehalogenase structure contains a knot with six crossings, a so-called Stevedore knot, in a projection onto a plane. The smallest protein knot is present in an as yet unclassified protein fragment that consists of only 92 amino acids. The topological complexity of the Stevedore knot presents a puzzle as to how it could possibly fold. To unravel this enigma, we performed folding simulations with a structure-based coarse-grained model and uncovered a possible mechanism by which the knot forms in a single loop flip.

  19. Thermal hysteresis proteins.

    Science.gov (United States)

    Barrett, J

    2001-02-01

    Extreme environments present a wealth of biochemical adaptations. Thermal hysteresis proteins (THPs) have been found in vertebrates, invertebrates, plants, bacteria and fungi and are able to depress the freezing point of water (in the presence of ice crystals) in a non-colligative manner by binding to the surface of nascent ice crystals. The THPs comprise a disparate group of proteins with a variety of tertiary structures and often no common sequence similarities or structural motifs. Different THPs bind to different faces of the ice crystal, and no single mechanism has been proposed to account for THP ice binding affinity and specificity. Experimentally THPs have been used in the cryopreservation of tissues and cells and to induce cold tolerance in freeze susceptible organisms. THPs represent a remarkable example of parallel and convergent evolution with different proteins being adapted for an anti-freeze role.

  20. Protein Polymers and Amyloids

    DEFF Research Database (Denmark)

    Risør, Michael Wulff

    2014-01-01

    Several human disorders are caused by a common general disease mechanism arising from abnormal folding and aggregation of the underlying protein. These include the prevalent dementias like Alzheimer’s and Parkinson’s, where accumulation of protein fibrillar structures, known as amyloid fibrils...... that inhibits its target protease through a large conformational change but mutations compromise this function and cause premature structural collapse into hyperstable polymers. Understanding the conformational disorders at a molecular level is not only important for our general knowledge on protein folding......, underlining the importance of understanding this relationship. The monomeric C-36 peptide was investigated by liquid-state NMR spectroscopy and found to be intrinsically disordered with minor propensities towards β-sheet structure. The plasticity of such a peptide makes it suitable for a whole range...

  1. 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.

  2. Trisulfides in Proteins

    DEFF Research Database (Denmark)

    Nielsen, Rasmus W.; Tachibana, Christine; Hansen, Niels Erik

    2011-01-01

    Trisulfides and other oligosulfides are widely distributed in the biological world. In plants, e.g., garlic, trisulfides are associated with potentially beneficial properties. However, an extra neutral sulfur atom covalently bound between the two sulfur atoms of a pair of cysteines is not a commo...... post-translational modification, and the number of proteins in which a trisulfide has been unambiguously identified is small. Nevertheless, we believe that its prevalence may be underestimated, particularly with the increasing evidence for significant pools of sulfides in living tissues...... and their possible roles in cellular metabolism. This review focuses on examples of proteins that are known to contain a trisulfide bridge, and gives an overview of the chemistry of trisulfide formation, and the methods by which it is detected in proteins....

  3. Accessory Proteins at ERES

    DEFF Research Database (Denmark)

    Klinkenberg, Rafael David

    proteins. Together these components co‐operate in cargo‐selection as well as forming, loading and releasing budding vesicles from specific regions on the membrane surface of the ER. Coat components furthermore convey vesicle targeting towards the Golgi. However, not much is known about the mechanisms...... that regulate the COPII assembly at the vesicle bud site. This thesis provides the first regulatory mechanism of COPII assembly in relation to ER‐membrane lipid‐signal recognition by the accessory protein p125A (Sec23IP). The aim of the project was to characterize p125A function by dissecting two main domains...... in the protein; a putative lipid‐associating domain termed the DDHD domain that is defined by the four amino acid motif that gives the domain its name; and a ubiquitously found domain termed Sterile α‐motif (SAM), which is mostly associated with oligomerization and polymerization. We first show, that the DDHD...

  4. Vibrational spectroscopy of proteins

    International Nuclear Information System (INIS)

    Schwaighofer, A.

    2013-01-01

    Two important steps for the development of a biosensor are the immobilization of the biological component (e.g. protein) on a surface and the enhancement of the signal to improve the sensitivity of detection. To address these subjects, the present work describes Fourier transform infrared (FTIR) investigations of several proteins bound to the surface of an attenuated total reflection (ATR) crystal. Furthermore, new nanostructured surfaces for signal enhancement were developed for use in FTIR microscopy. The mitochondrial redox-protein cytochrome c oxidase (CcO) was incorporated into a protein-tethered bilayer lipid membrane (ptBLM) on an ATR crystal featuring a roughened two-layer gold surface for signal enhancement. Electrochemical excitation by periodic potential pulses at different modulation frequencies was followed by time-resolved FTIR spectroscopy. Phase sensitive detection was used for deconvolution of the IR spectra into vibrational components. A model based on protonation-dependent chemical reaction kinetics could be fitted to the time evolution of IR bands attributed to several different redox centers of the CcO. Further investigations involved the odorant binding protein 14 (OBP14) of the honey bee (Apis mellifera), which was studied using ATR-FTIR spectroscopy and circular dichroism. OBP14 was found to be thermally stable up to 45 °C, thus permitting the potential application of this protein for the fabrication of biosensors. Thermal denaturation measurements showed that odorant binding increases the thermal stability of the OBP-odorant complex. In another project, plasmonic nanostructures were fabricated that enhance the absorbance in FTIR microscopy measurements. The nanostructures are composed of an array of round-shaped insulator and gold discs on top of a continuous gold layer. Enhancement factors of up to ⁓125 could be observed with self-assembled monolayers of dodecanethiol molecules immobilized on the gold surface (author) [de

  5. Can infrared spectroscopy provide information on protein-protein interactions?

    Science.gov (United States)

    Haris, Parvez I

    2010-08-01

    For most biophysical techniques, characterization of protein-protein interactions is challenging; this is especially true with methods that rely on a physical phenomenon that is common to both of the interacting proteins. Thus, for example, in IR spectroscopy, the carbonyl vibration (1600-1700 cm(-1)) associated with the amide bonds from both of the interacting proteins will overlap extensively, making the interpretation of spectral changes very complicated. Isotope-edited infrared spectroscopy, where one of the interacting proteins is uniformly labelled with (13)C or (13)C,(15)N has been introduced as a solution to this problem, enabling the study of protein-protein interactions using IR spectroscopy. The large shift of the amide I band (approx. 45 cm(-1) towards lower frequency) upon (13)C labelling of one of the proteins reveals the amide I band of the unlabelled protein, enabling it to be used as a probe for monitoring conformational changes. With site-specific isotopic labelling, structural resolution at the level of individual amino acid residues can be achieved. Furthermore, the ability to record IR spectra of proteins in diverse environments means that isotope-edited IR spectroscopy can be used to structurally characterize difficult systems such as protein-protein complexes bound to membranes or large insoluble peptide/protein aggregates. In the present article, examples of application of isotope-edited IR spectroscopy for studying protein-protein interactions are provided.

  6. Protein: FBA7 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FBA7 claudin-zona occluden TJP1 ZO1 TJP1 Tight junction protein ZO-1 Tight junction pro...tein 1, Zona occludens protein 1, Zonula occludens protein 1 9606 Homo sapiens Q07157 7082 2H2C, 2H2B, 3

  7. 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 occludens pr...otein 1, Zonula occludens protein 1 10090 Mus musculus 21872 P39447 2RRM P39447 21431884 ...

  8. Protein: FEA3 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FEA3 AREB pathway: Signaling proteins At4g11890/T26M18_100 At4g11890, Protein kinase family pr...otein, Putative uncharacterized protein At4g11890/T26M18_100 3702 Arabidopsis thaliana 826796 Q8GY82 22225700 ...

  9. 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)....

  10. Protein–protein interactions

    OpenAIRE

    Janin, J.; Bonvin, A.M.J.J.

    2013-01-01

    We are proud to present the first edition of the Protein–protein interactions Section of Current Opinion in Structural Biology. The Section is new, but the topic has been present in the journal from the very start. Volume 1, Issue 1, dated February 1991, had a review by Janin entitled Protein–protein interactions and assembly, and others by Bode and Huber on Proteinase–inhibitor interaction, and by Chothia on Antigen recognition. The Editorial Overview, signed by TE Creighton and PS Kim, note...

  11. Heme Sensor Proteins*

    Science.gov (United States)

    Girvan, Hazel M.; Munro, Andrew W.

    2013-01-01

    Heme is a prosthetic group best known for roles in oxygen transport, oxidative catalysis, and respiratory electron transport. Recent years have seen the roles of heme extended to sensors of gases such as O2 and NO and cell redox state, and as mediators of cellular responses to changes in intracellular levels of these gases. The importance of heme is further evident from identification of proteins that bind heme reversibly, using it as a signal, e.g. to regulate gene expression in circadian rhythm pathways and control heme synthesis itself. In this minireview, we explore the current knowledge of the diverse roles of heme sensor proteins. PMID:23539616

  12. Protein production and purification.

    Science.gov (United States)

    Gräslund, Susanne; Nordlund, Pär; Weigelt, Johan; Hallberg, B Martin; Bray, James; Gileadi, Opher; Knapp, Stefan; Oppermann, Udo; Arrowsmith, Cheryl; Hui, Raymond; Ming, Jinrong; dhe-Paganon, Sirano; Park, Hee-won; Savchenko, Alexei; Yee, Adelinda; Edwards, Aled; Vincentelli, Renaud; Cambillau, Christian; Kim, Rosalind; Kim, Sung-Hou; Rao, Zihe; Shi, Yunyu; Terwilliger, Thomas C; Kim, Chang-Yub; Hung, Li-Wei; Waldo, Geoffrey S; Peleg, Yoav; Albeck, Shira; Unger, Tamar; Dym, Orly; Prilusky, Jaime; Sussman, Joel L; Stevens, Ray C; Lesley, Scott A; Wilson, Ian A; Joachimiak, Andrzej; Collart, Frank; Dementieva, Irina; Donnelly, Mark I; Eschenfeldt, William H; Kim, Youngchang; Stols, Lucy; Wu, Ruying; Zhou, Min; Burley, Stephen K; Emtage, J Spencer; Sauder, J Michael; Thompson, Devon; Bain, Kevin; Luz, John; Gheyi, Tarun; Zhang, Fred; Atwell, Shane; Almo, Steven C; Bonanno, Jeffrey B; Fiser, Andras; Swaminathan, Sivasubramanian; Studier, F William; Chance, Mark R; Sali, Andrej; Acton, Thomas B; Xiao, Rong; Zhao, Li; Ma, Li Chung; Hunt, John F; Tong, Liang; Cunningham, Kellie; Inouye, Masayori; Anderson, Stephen; Janjua, Heleema; Shastry, Ritu; Ho, Chi Kent; Wang, Dongyan; Wang, Huang; Jiang, Mei; Montelione, Gaetano T; Stuart, David I; Owens, Raymond J; Daenke, Susan; Schütz, Anja; Heinemann, Udo; Yokoyama, Shigeyuki; Büssow, Konrad; Gunsalus, Kristin C

    2008-02-01

    In selecting a method to produce a recombinant protein, a researcher is faced with a bewildering array of choices as to where to start. To facilitate decision-making, we describe a consensus 'what to try first' strategy based on our collective analysis of the expression and purification of over 10,000 different proteins. This review presents methods that could be applied at the outset of any project, a prioritized list of alternate strategies and a list of pitfalls that trip many new investigators.

  13. Protein energy malnutrition.

    Science.gov (United States)

    Grover, Zubin; Ee, Looi C

    2009-10-01

    Protein energy malnutrition (PEM) is a common problem worldwide and occurs in both developing and industrialized nations. In the developing world, it is frequently a result of socioeconomic, political, or environmental factors. In contrast, protein energy malnutrition in the developed world usually occurs in the context of chronic disease. There remains much variation in the criteria used to define malnutrition, with each method having its own limitations. Early recognition, prompt management, and robust follow up are critical for best outcomes in preventing and treating PEM.

  14. Stability of Hyperthermophilic Proteins

    DEFF Research Database (Denmark)

    Stiefler-Jensen, Daniel

    to life at high temperatures so are their enzymes, as a result the high stability is accompanied by low activity at moderate temperatures. Thus, much effort had been put into decoding the mechanisms behind the high stability of the thermophilic enzymes. The hope is to enable scientist to design enzymes...... in the high stability of hyperthermophilic enzymes. The thesis starts with an introduction to the field of protein and enzyme stability with special focus on the thermophilic and hyperthermophilic enzymes and proteins. After the introduction three original research manuscripts present the experimental data...

  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. Transport of Proteins through Nanopores

    Science.gov (United States)

    Luan, Binquan

    In biological cells, a malfunctioned protein (such as misfolded or damaged) is degraded by a protease in which an unfoldase actively drags the protein into a nanopore-like structure and then a peptidase cuts the linearized protein into small fragments (i.e. a recycling process). Mimicking this biological process, many experimental studies have focused on the transport of proteins through a biological protein pore or a synthetic solid-state nanopore. Potentially, the nanopore-based sensors can provide a platform for interrogating proteins that might be disease-related or be targeted by a new drug molecule. The single-profile of a protein chain inside an extremely small nanopore might even permit the sequencing of the protein. Here, through all-atom molecular dynamics simulations, I will show various types of protein transport through a nanopore and reveal the nanoscale mechanics/energetics that plays an important role governing the protein transport.

  17. Truly Absorbed Microbial Protein Synthesis, Rumen Bypass Protein, Endogenous Protein, and Total Metabolizable Protein from Starchy and Protein-Rich Raw Materials

    NARCIS (Netherlands)

    Parand, Ehsan; Vakili, Alireza; Mesgaran, Mohsen Danesh; Duinkerken, Van Gert; Yu, Peiqiang

    2015-01-01

    This study was carried out to measure truly absorbed microbial protein synthesis, rumen bypass protein, and endogenous protein loss, as well as total metabolizable protein, from starchy and protein-rich raw feed materials with model comparisons. Predictions by the DVE2010 system as a more

  18. Acute gouty arthritis and rapidly progressive renal failure as manifestation of multiple myeloma: clinical case description

    Directory of Open Access Journals (Sweden)

    O.V. Gudym

    2017-08-01

    Full Text Available The article describes a clinical case of multiple myeloma in 78-year-old man, its clinical onset was as an acute attack of gout. The patient was admitted to hospital due to the development of the first acute attack of gout. The attack was characterized by polyarthricular joint lesion of the upper and lower extremities, pronounced inflammatory reaction, insufficient response to the use of non-steroidal anti-inflammatory drugs, and a high level of hyperuricemia. The serum uric acid concentration ranged from 636 to 712 μmol/l. The study of the synovial fluid of the inflamed knee joint made it possible to reveal uric acid crystals and to confirm the diagnosis of acute gouty arthritis. Simultaneously, the patient had significant renal impairment: creatinine was 574 μmol/l, urea — 39.9 mmol/l, glomerular filtration rate according to CKD-EPI — 8 ml/min. The daily proteinuria was 1.8 g. A retrospective assessment of laboratory parameters allowed to reveal completely normal indicators of renal function 6 months ago. Considering the development of acute gouty arthritis, its polyarticular nature, persistent course, rapid involvement of new joints, high uric acid levels during an acute attack exceeding 600 μmol/l (10 mg/dL, rapid development of renal failure within 6 months until the terminal stage, it was suggested the secondary nature of gout on the background of kidney damage by another pathological process. Further clinical, laboratory and instrumental studies allowed verifying multiple myeloma with renal damage. Bence Jones protein in the urine was not detected, there was also no evidence of hyperproteinemia. However, pain in the spine, ribs and chest was the basis for carrying out an X-ray study of the bones of the skeleton. Changes in the skeleton typical for multiple myeloma have been identified. Myelogram showed a high content of plasma cells (21.1 %, electrophoresis of blood proteins showed a high M-gradient (30.42 %, and a cytochemical

  19. Accessory proteins for heterotrimeric G-proteins in the kidney.

    Science.gov (United States)

    Park, Frank

    2015-01-01

    Heterotrimeric G-proteins play a fundamentally important role in regulating signal transduction pathways in the kidney. Accessory proteins are being identified as direct binding partners for heterotrimeric G-protein α or βγ subunits to promote more diverse mechanisms by which G-protein signaling is controlled. In some instances, accessory proteins can modulate the signaling magnitude, localization, and duration following the activation of cell membrane-associated receptors. Alternatively, accessory proteins complexed with their G-protein α or βγ subunits can promote non-canonical models of signaling activity within the cell. In this review, we will highlight the expression profile, localization and functional importance of these newly identified accessory proteins to control the function of select G-protein subunits under normal and various disease conditions observed in the kidney.

  20. Complementarity of structure ensembles in protein-protein binding.

    Science.gov (United States)

    Grünberg, Raik; Leckner, Johan; Nilges, Michael

    2004-12-01

    Protein-protein association is often accompanied by changes in receptor and ligand structure. This interplay between protein flexibility and protein-protein recognition is currently the largest obstacle both to our understanding of and to the reliable prediction of protein complexes. We performed two sets of molecular dynamics simulations for the unbound receptor and ligand structures of 17 protein complexes and applied shape-driven rigid body docking to all combinations of representative snapshots. The crossdocking of structure ensembles increased the likelihood of finding near-native solutions. The free ensembles appeared to contain multiple complementary conformations. These were in general not related to the bound structure. We suggest that protein-protein binding follows a three-step mechanism of diffusion, free conformer selection, and refolding. This model combines previously conflicting ideas and is in better agreement with the current data on interaction forces, time scales, and kinetics.

  1. 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.

  2. Fragments of protein A eluted during protein A affinity chromatography.

    Science.gov (United States)

    Carter-Franklin, Jayme N; Victa, Corazon; McDonald, Paul; Fahrner, Robert

    2007-09-07

    Protein A affinity chromatography is a common method for process scale purification of monoclonal antibodies. During protein A affinity chromatography, protein A ligand co-elutes with the antibody (commonly called leaching), which is a potential disadvantage since the leached protein A may need to be cleared for pharmaceutical antibodies. To determine the mechanism of protein A leaching and characterize the leached protein A, we fluorescently labeled the protein A ligand in situ on protein A affinity chromatography media. We found that intact protein A leaches when loading either purified antibody or unpurified antibody in harvested cell culture fluid (HCCF), and that additionally fragments of protein A leach when loading HCCF. The leaching of protein A fragments can be reduced by EDTA, suggesting that proteinases contribute to the generation of protein A fragments. We found that protein A fragments larger than about 6000 Da can be measured by enzyme linked immunosorbent assay, and that they can be more difficult to clear than whole protein A by cation-exchange chromatography.

  3. Mobility of photosynthetic proteins

    Czech Academy of Sciences Publication Activity Database

    Kaňa, Radek

    2013-01-01

    Roč. 116, 2-3 (2013), s. 465-479 ISSN 0166-8595 R&D Projects: GA ČR GAP501/12/0304; GA MŠk(CZ) ED2.1.00/03.0110 Institutional support: RVO:61388971 Keywords : Photosynthesis * Protein mobility * FRAP Subject RIV: EE - Microbiology, Virology Impact factor: 3.185, year: 2013

  4. Combinable protein crop production

    OpenAIRE

    Wright, Isobel

    2008-01-01

    This research topic review aims to summarise research knowledge and observational experience of combinable protein crop production in organic farming systems for the UK. European research on peas, faba beans and lupins is included; considering their role in the rotation, nitrogen fixation, varieties, establishment, weed control, yields, problems experienced and intercropping with cereals.

  5. Antifreeze Proteins of Bacteria

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 12; Issue 12. Antifreeze Proteins of Bacteria. M K Chattopadhyay. General Article Volume 12 Issue 12 December 2007 pp 25-30. Fulltext. Click here to view fulltext PDF. Permanent link: https://www.ias.ac.in/article/fulltext/reso/012/12/0025-0030 ...

  6. 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...

  7. Protein thin film machines.

    Science.gov (United States)

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

    2010-12-01

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

  8. Tuber Storage Proteins

    Science.gov (United States)

    SHEWRY, PETER R.

    2003-01-01

    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. PMID:12730067

  9. 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...

  10. Antifreeze Proteins of Bacteria

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 12; Issue 12. Antifreeze Proteins of Bacteria. M K Chattopadhyay. General Article Volume 12 Issue 12 December 2007 pp 25-30. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/012/12/0025-0030. Keywords.

  11. NMR of unfolded proteins

    Indian Academy of Sciences (India)

    Unknown

    2005-01-03

    Jan 3, 2005 ... out' response to environmental changes with structural complexity ... of 3D structure at atomic resolution of folded proteins ...... 5.14 HIV-1 protease. NMR identification of local structural preferences in. HIV-1 protease in the 'unfolded state' at 6 M gua- nidine hydrochloride has been reported.49 Analyses.

  12. Thermodynamics of meat proteins

    NARCIS (Netherlands)

    Sman, van der R.G.M.

    2012-01-01

    We describe the water activity of meat, being a mixture of proteins, salts and water, by the Free-Volume-Flory–Huggins (FVFH) theory augmented with the equation. Earlier, the FVFH theory is successfully applied to describe the thermodynamics to glucose homopolymers like starch, dextrans and

  13. and heat shock proteins

    African Journals Online (AJOL)

    concentrations of Cu and tributylin in zebra mussels in the laboratory. The time period of sampling appears to have had no signifi- cant relationship with enzyme activity, protein quantity and metal concentration in this study. Metal bioaccumulation and bioconcentration values were different in the pectoral muscles.

  14. 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.

  15. Allosteric Regulation of Proteins

    Indian Academy of Sciences (India)

    triguingly, the substrate or the product of the inhibited enzyme can be structurally different from the inhibitor. ... ulation of proteins in this fashion as 'allosteric' in the year 1961. [9]. The word allostery originated from the ..... flux occurs via the conformational selec- tion pathway at low concentrations of the ligand, while the trend.

  16. Allosteric Regulation of Proteins

    Indian Academy of Sciences (India)

    ... Lecture Workshops · Refresher Courses · Symposia · Live Streaming. Home; Journals; Resonance – Journal of Science Education; Volume 22; Issue 1. Allosteric Regulation of Proteins: A Historical Perspective on the Development of Concepts and Techniques. General Article Volume 22 Issue 1 January 2017 pp 37-50 ...

  17. Protein Sorting Prediction

    DEFF Research Database (Denmark)

    Nielsen, Henrik

    2017-01-01

    Many computational methods are available for predicting protein sorting in bacteria. When comparing them, it is important to know that they can be grouped into three fundamentally different approaches: signal-based, global-property-based and homology-based prediction. In this chapter, the strengths...

  18. Regulators of G-protein-signaling proteins: negative modulators of G-protein-coupled receptor signaling.

    Science.gov (United States)

    Woodard, Geoffrey E; Jardín, Isaac; Berna-Erro, A; Salido, Gines M; Rosado, Juan A

    2015-01-01

    Regulators of G-protein-signaling (RGS) proteins are a category of intracellular proteins that have an inhibitory effect on the intracellular signaling produced by G-protein-coupled receptors (GPCRs). RGS along with RGS-like proteins switch on through direct contact G-alpha subunits providing a variety of intracellular functions through intracellular signaling. RGS proteins have a common RGS domain that binds to G alpha. RGS proteins accelerate GTPase and thus enhance guanosine triphosphate hydrolysis through the alpha subunit of heterotrimeric G proteins. As a result, they inactivate the G protein and quickly turn off GPCR signaling thus terminating the resulting downstream signals. Activity and subcellular localization of RGS proteins can be changed through covalent molecular changes to the enzyme, differential gene splicing, and processing of the protein. Other roles of RGS proteins have shown them to not be solely committed to being inhibitors but behave more as modulators and integrators of signaling. RGS proteins modulate the duration and kinetics of slow calcium oscillations and rapid phototransduction and ion signaling events. In other cases, RGS proteins integrate G proteins with signaling pathways linked to such diverse cellular responses as cell growth and differentiation, cell motility, and intracellular trafficking. Human and animal studies have revealed that RGS proteins play a vital role in physiology and can be ideal targets for diseases such as those related to addiction where receptor signaling seems continuously switched on. Copyright © 2015 Elsevier Inc. All rights reserved.

  19. Protein Molecular Structures, Protein SubFractions, and Protein Availability Affected by Heat Processing: A Review

    International Nuclear Information System (INIS)

    Yu, P.

    2007-01-01

    The utilization and availability of protein depended on the types of protein and their specific susceptibility to enzymatic hydrolysis (inhibitory activities) in the gastrointestine and was highly associated with protein molecular structures. Studying internal protein structure and protein subfraction profiles leaded to an understanding of the components that make up a whole protein. An understanding of the molecular structure of the whole protein was often vital to understanding its digestive behavior and nutritive value in animals. In this review, recently obtained information on protein molecular structural effects of heat processing was reviewed, in relation to protein characteristics affecting digestive behavior and nutrient utilization and availability. The emphasis of this review was on (1) using the newly advanced synchrotron technology (S-FTIR) as a novel approach to reveal protein molecular chemistry affected by heat processing within intact plant tissues; (2) revealing the effects of heat processing on the profile changes of protein subfractions associated with digestive behaviors and kinetics manipulated by heat processing; (3) prediction of the changes of protein availability and supply after heat processing, using the advanced DVE/OEB and NRC-2001 models, and (4) obtaining information on optimal processing conditions of protein as intestinal protein source to achieve target values for potential high net absorbable protein in the small intestine. The information described in this article may give better insight in the mechanisms involved and the intrinsic protein molecular structural changes occurring upon processing.

  20. Iodine-based contrast media, multiple myeloma and monoclonal gammopathies: literature review and ESUR Contrast Media Safety Committee guidelines.

    Science.gov (United States)

    Stacul, Fulvio; Bertolotto, Michele; Thomsen, Henrik S; Pozzato, Gabriele; Ugolini, Donatella; Bellin, Marie-France; Bongartz, Georg; Clement, Olivier; Heinz-Peer, Gertraud; van der Molen, Aart; Reimer, Peter; Webb, Judith A W

    2018-02-01

    Many radiologists and clinicians still consider multiple myeloma (MM) and monoclonal gammopathies (MG) a contraindication for using iodine-based contrast media. The ESUR Contrast Media Safety Committee performed a systematic review of the incidence of post-contrast acute kidney injury (PC-AKI) in these patients. A systematic search in Medline and Scopus databases was performed for renal function deterioration studies in patients with MM or MG following administration of iodine-based contrast media. Data collection and analysis were performed according to the PRISMA statement 2009. Eligibility criteria and methods of analysis were specified in advance. Cohort and case-control studies reporting changes in renal function were included. Thirteen studies were selected that reported 824 iodine-based contrast medium administrations in 642 patients with MM or MG, in which 12 unconfounded cases of PC-AKI were found (1.6 %). The majority of patients had intravenous urography with high osmolality ionic contrast media after preparatory dehydration and purgation. MM and MG alone are not risk factors for PC-AKI. However, the risk of PC-AKI may become significant in dehydrated patients with impaired renal function. Hypercalcaemia may increase the risk of kidney damage, and should be corrected before contrast medium administration. Assessment for Bence-Jones proteinuria is not necessary. • Monoclonal gammopathies including multiple myeloma are a large spectrum of disorders. • In monoclonal gammopathy with normal renal function, PC-AKI risk is not increased. • Renal function is often reduced in myeloma, increasing the risk of PC-AKI. • Correction of hypercalcaemia is necessary in myeloma before iodine-based contrast medium administration. • Bence-Jones proteinuria assessment in myeloma is unnecessary before iodine-based contrast medium administration.

  1. Inferring protein function by domain context similarities in protein-protein interaction networks

    Directory of Open Access Journals (Sweden)

    Sun Zhirong

    2009-12-01

    Full Text Available Abstract Background Genome sequencing projects generate massive amounts of sequence data but there are still many proteins whose functions remain unknown. The availability of large scale protein-protein interaction data sets makes it possible to develop new function prediction methods based on protein-protein interaction (PPI networks. Although several existing methods combine multiple information resources, there is no study that integrates protein domain information and PPI networks to predict protein functions. Results The domain context similarity can be a useful index to predict protein function similarity. The prediction accuracy of our method in yeast is between 63%-67%, which outperforms the other methods in terms of ROC curves. Conclusion This paper presents a novel protein function prediction method that combines protein domain composition information and PPI networks. Performance evaluations show that this method outperforms existing methods.

  2. In Situ Protein Binding Assay Using Fc-Fusion Proteins.

    Science.gov (United States)

    Padmanabhan, Nirmala; Siddiqui, Tabrez J

    2017-01-01

    This protocol describes an in situ protein-protein interaction assay between tagged recombinant proteins and cell-surface expressed synaptic proteins. The assay is arguably more sensitive than other traditional protein binding assays such as co-immunoprecipitation and pull-downs and provides a visual readout for binding. This assay has been widely used to determine the dissociation constant of binding of trans-synaptic adhesion proteins. The step-wise description in the protocol should facilitate the adoption of this method in other laboratories.

  3. 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

  4. 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....

  5. Regulation of protein turnover by heat shock proteins.

    Science.gov (United States)

    Bozaykut, Perinur; Ozer, Nesrin Kartal; Karademir, Betul

    2014-12-01

    Protein turnover reflects the balance between synthesis and degradation of proteins, and it is a crucial process for the maintenance of the cellular protein pool. The folding of proteins, refolding of misfolded proteins, and also degradation of misfolded and damaged proteins are involved in the protein quality control (PQC) system. Correct protein folding and degradation are controlled by many different factors, one of the most important of which is the heat shock protein family. Heat shock proteins (HSPs) are in the class of molecular chaperones, which may prevent the inappropriate interaction of proteins and induce correct folding. On the other hand, these proteins play significant roles in the degradation pathways, including endoplasmic reticulum-associated degradation (ERAD), the ubiquitin-proteasome system, and autophagy. This review focuses on the emerging role of HSPs in the regulation of protein turnover; the effects of HSPs on the degradation machineries ERAD, autophagy, and proteasome; as well as the role of posttranslational modifications in the PQC system. Copyright © 2014 Elsevier Inc. All rights reserved.

  6. Circular dichroism spectroscopy of fluorescent proteins

    NARCIS (Netherlands)

    Visser, N.V.; Hink, M.A.; Borst, J.W.; Krogt, van der G.N.M.; Visser, A.J.W.G.

    2002-01-01

    Circular dichroism (CD) spectra have been obtained from several variants of green fluorescent protein: blue fluorescent protein (BFP), enhanced cyan fluorescent protein (CFP), enhanced green fluorescent protein (GFP), enhanced yellow fluorescent protein (YFP), all from Aequorea victoria, and the red

  7. 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 the C-3 carbons of Ala, Val, Leu, and Asp residues undergo beta-scission to give backbone alpha-carbon radicals, with the release of the side- chain as a carbonyl compound. We now show that this is a general mechanism that occurs with a wide range of oxidants. The quantitative significance...... of this process depends on the extent of oxidation at C-3 compared with other sites. HO*, generated by gamma radiolysis, gave the highest total carbonyl yield, with protein-bound carbonyls predominating over released. In contrast, metal ion/H2O2 systems, gave more released than bound carbonyls, with this ratio...

  8. Problems in Protein Biosynthesis

    Science.gov (United States)

    Lengyel, Peter

    1966-01-01

    Outline of the steps in protein synthesis. Nature of the genetic code. The use of synthetic oligo- and polynucleotides in deciphering the code. Structure of the code: relatedness of synonym codons. The wobble hypothesis. Chain initiation and N-formyl-methionine. Chain termination and nonsense codons. Mistakes in translation: ambiguity in vitro. Suppressor mutations resulting in ambiguity. Limitations in the universality of the code. Attempts to determine the particular codons used by a species. Mechanisms of suppression, caused by (a) abnormal aminoacyl-tRNA, (b) ribosomal malfunction. Effect of streptomycin. The problem of "reading" a nucleic acid template. Different ribosomal mutants and DNA polymerase mutants might cause different mistakes. The possibility of involvement of allosteric proteins in template reading. PMID:5338560

  9. Immunostimulatory mouse granuloma protein.

    Science.gov (United States)

    Fontan, E; Fauve, R M; Hevin, B; Jusforgues, H

    1983-10-01

    Earlier studies have shown that from subcutaneous talc-induced granuloma in mice, a fraction could be extracted that fully protected mice against Listeria monocytogenes. Using standard biochemical procedures--i.e., ammonium sulfate fractionation, preparative electrophoresis, gel filtration chromatography, isoelectric focusing, and preparative polyacrylamide gel electrophoresis--we have now purified an active factor to homogeneity. A single band was obtained in NaDodSO4/polyacrylamide gel with an apparent Mr of 55,000. It migrated with alpha 1-globulins and the isoelectric point was 5 +/- 0.1. The biological activity was destroyed with Pronase but not with trypsin and a monospecific polyclonal rabbit antiserum was obtained. The intravenous injection of 5 micrograms of this "mouse granuloma protein" fully protects mice against a lethal inoculum of L. monocytogenes. Moreover, after their incubation with 10 nM mouse granuloma protein, mouse peritoneal cells became cytostatic against Lewis carcinoma cells.

  10. 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.

  11. PDBTM: Protein Data Bank of transmembrane proteins after 8 years

    OpenAIRE

    Kozma, D?niel; Simon, Istv?n; Tusn?dy, G?bor E.

    2012-01-01

    The PDBTM database (available at http://pdbtm.enzim.hu), the first comprehensive and up-to-date transmembrane protein selection of the Protein Data Bank, was launched in 2004. The database was created and has been continuously updated by the TMDET algorithm that is able to distinguish between transmembrane and non-transmembrane proteins using their 3D atomic coordinates only. The TMDET algorithm can locate the spatial positions of transmembrane proteins in lipid bilayer as well. During the la...

  12. A Mesoscopic Model for Protein-Protein Interactions in Solution

    OpenAIRE

    Lund, Mikael; Jönsson, Bo

    2003-01-01

    Protein self-association may be detrimental in biological systems, but can be utilized in a controlled fashion for protein crystallization. It is hence of considerable interest to understand how factors like solution conditions prevent or promote aggregation. Here we present a computational model describing interactions between protein molecules in solution. The calculations are based on a molecular description capturing the detailed structure of the protein molecule using x-ray or nuclear ma...

  13. Mapping Protein-Protein Interactions by Quantitative Proteomics

    DEFF Research Database (Denmark)

    Dengjel, Joern; Kratchmarova, Irina; Blagoev, Blagoy

    2010-01-01

    Proteins exert their function inside a cell generally in multiprotein complexes. These complexes are highly dynamic structures changing their composition over time and cell state. The same protein may thereby fulfill different functions depending on its binding partners. Quantitative mass...... to characterize protein interaction networks. In this chapter we describe in detail the use of stable isotope labeling by amino acids in cell culture (SILAC) for the quantitative analysis of stimulus-dependent dynamic protein interactions....

  14. Prion Protein and Aging

    Directory of Open Access Journals (Sweden)

    Lisa eGasperini

    2014-08-01

    Full Text Available The cellular prion protein (PrPC has been widely investigated ever since its conformational isoform, the prion (or PrPSc, was identified as the etiological agent of prion disorders. The high homology shared by the PrPC-encoding gene among mammals, its high turnover rate and expression in every tissue strongly suggest that PrPC may possess key physiological functions. Therefore, defining PrPC roles, properties and fate in the physiology of mammalian cells would be fundamental to understand its pathological involvement in prion diseases. Since the incidence of these neurodegenerative disorders is enhanced in aging, understanding PrPC functions in this life phase may be of crucial importance. Indeed, a large body of evidence suggests that PrPC plays a neuroprotective and antioxidant role. Moreover, it has been suggested that PrPC is involved in Alzheimer disease, another neurodegenerative pathology that develops predominantly in the aging population. In prion diseases, PrPC function is likely lost upon protein aggregation occurring in the course of the disease. Additionally, the aging process may alter PrPC biochemical properties, thus influencing its propensity to convert into PrPSc. Both phenomena may contribute to the disease development and progression. In Alzheimer disease, PrPC has a controversial role because its presence seems to mediate β-amyloid toxicity, while its down-regulation correlates with neuronal death. The role of PrPC in aging has been investigated from different perspectives, often leading to contrasting results. The putative protein functions in aging have been studied in relation to memory, behavior and myelin maintenance. In aging mice, PrPC changes in subcellular localization and post-translational modifications have been explored in an attempt to relate them to different protein roles and propensity to convert into PrPSc. Here we provide an overview of the most relevant studies attempting to delineate PrPC functions and

  15. Urinary Protein Biomarker Analysis

    Science.gov (United States)

    2017-10-01

    associated protein biomarkers were identified by transcriptomic comparison of cancer cells vs. normal luminal cells; cancer-associated stromal cells vs...analysis; (C) correction with PSA, P = 0.012); (D) ROC curve analysis. 4-1. Use of PSA levels for marker level normalization Other organs along the...Copyright: Shi et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY 3.0), which

  16. Redox meets protein trafficking.

    Science.gov (United States)

    Bölter, Bettina; Soll, Jürgen; Schwenkert, Serena

    2015-09-01

    After the engulfment of two prokaryotic organisms, the thus emerged eukaryotic cell needed to establish means of communication and signaling to properly integrate the acquired organelles into its metabolism. Regulatory mechanisms had to evolve to ensure that chloroplasts and mitochondria smoothly function in accordance with all other cellular processes. One essential process is the post-translational import of nuclear encoded organellar proteins, which needs to be adapted according to the requirements of the plant. The demand for protein import is constantly changing depending on varying environmental conditions, as well as external and internal stimuli or different developmental stages. Apart from long-term regulatory mechanisms such as transcriptional/translation control, possibilities for short-term acclimation are mandatory. To this end, protein import is integrated into the cellular redox network, utilizing the recognition of signals from within the organelles and modifying the efficiency of the translocon complexes. Thereby, cellular requirements can be communicated throughout the whole organism. This article is part of a Special Issue entitled: Chloroplast Biogenesis. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. 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.)

  18. 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.

  19. Analysis of protein folds using protein contact networks

    Indian Academy of Sciences (India)

    Proteins are important biomolecules, which perform diverse structural and functional roles in living systems. Starting from a .... even be extended up to the level of protein secondary structural elements, as seen in protein topology cartoons [13]. Even though ... chemical interactions [8]. This distance map is a 2D symmetric, ...

  20. Recent excitements in protein NMR: Large proteins and biologically ...

    Indian Academy of Sciences (India)

    The advent of Transverse Relaxation Optimized SpectroscopY (TROSY) and perdeuteration allowed biomolecularNMR spectroscopists to overcome the size limitation barrier (~20 kDa) in de novo structure determination of proteins.The utility of these techniques was immediately demonstrated on large proteins and protein ...

  1. 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.

  2. Protein-ECE MEtallopincer Hybrids

    NARCIS (Netherlands)

    Kruithof, C.A.

    2007-01-01

    Modification of proteins with metal complexes is a promising and a relatively new field which conceals many challenges and potential applications. The field is a balance of contributions from the biological (protein engineering, bioconjugation) and chemical sciences (organic, inorganic and

  3. Protein: FEA3 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FEA3 AREB pathway: AREB transcription factors ABF2 AREB1, BZIP36 ABSCISIC ACID-INSENSITIVE 5-like pro...tein 5 ABA-responsive element-binding protein 1, Abscisic acid responsive elements-binding

  4. Protein folding and wring resonances

    DEFF Research Database (Denmark)

    Bohr, Jakob; Bohr, Henrik; Brunak, Søren

    1997-01-01

    The polypeptide chain of a protein is shown to obey topological contraints which enable long range excitations in the form of wring modes of the protein backbone. Wring modes of proteins of specific lengths can therefore resonate with molecular modes present in the cell. It is suggested that prot......The polypeptide chain of a protein is shown to obey topological contraints which enable long range excitations in the form of wring modes of the protein backbone. Wring modes of proteins of specific lengths can therefore resonate with molecular modes present in the cell. It is suggested...... that protein folding takes place when the amplitude of a wring excitation becomes so large that it is energetically favorable to bend the protein backbone. The condition under which such structural transformations can occur is found, and it is shown that both cold and hot denaturation (the unfolding...

  5. 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. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Protein Precipitation Using Ammonium Sulfate

    OpenAIRE

    Wingfield, Paul T.

    2001-01-01

    The basic theory of protein precipitation by addition of ammonium sulfate is presented and the most common applications are listed, Tables are provided for calculating the appropriate amount of ammonium sulfate to add to a particular protein solution.

  7. 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 ...

  8. Functional aspects of protein flexibility

    DEFF Research Database (Denmark)

    Teilum, Kaare; Olsen, Johan G; Kragelund, Birthe B

    2009-01-01

    . The thermodynamics involved are reviewed, and examples of structure-function studies involving experimentally determined flexibility descriptions are presented. While much remains to be understood about protein flexibility, it is clear that it is encoded within their amino acid sequence and should be viewed......Proteins are dynamic entities, and they possess an inherent flexibility that allows them to function through molecular interactions within the cell, among cells and even between organisms. Appreciation of the non-static nature of proteins is emerging, but to describe and incorporate...... this into an intuitive perception of protein function is challenging. Flexibility is of overwhelming importance for protein function, and the changes in protein structure during interactions with binding partners can be dramatic. The present review addresses protein flexibility, focusing on protein-ligand interactions...

  9. Protein kinase substrate identification on functional protein arrays

    Directory of Open Access Journals (Sweden)

    Zhou Fang

    2008-02-01

    Full Text Available Abstract Background Over the last decade, kinases have emerged as attractive therapeutic targets for a number of different diseases, and numerous high throughput screening efforts in the pharmaceutical community are directed towards discovery of compounds that regulate kinase function. The emerging utility of systems biology approaches has necessitated the development of multiplex tools suitable for proteomic-scale experiments to replace lower throughput technologies such as mass spectroscopy for the study of protein phosphorylation. Recently, a new approach for identifying substrates of protein kinases has applied the miniaturized format of functional protein arrays to characterize phosphorylation for thousands of candidate protein substrates in a single experiment. This method involves the addition of protein kinases in solution to arrays of immobilized proteins to identify substrates using highly sensitive radioactive detection and hit identification algorithms. Results To date, the factors required for optimal performance of protein array-based kinase substrate identification have not been described. In the current study, we have carried out a detailed characterization of the protein array-based method for kinase substrate identification, including an examination of the effects of time, buffer compositions, and protein concentration on the results. The protein array approach was compared to standard solution-based assays for assessing substrate phosphorylation, and a correlation of greater than 80% was observed. The results presented here demonstrate how novel substrates for protein kinases can be quickly identified from arrays containing thousands of human proteins to provide new clues to protein kinase function. In addition, a pooling-deconvolution strategy was developed and applied that enhances characterization of specific kinase-substrate relationships and decreases reagent consumption. Conclusion Functional protein microarrays are an

  10. A Novel Approach for Protein-Named Entity Recognition and Protein-Protein Interaction Extraction

    Directory of Open Access Journals (Sweden)

    Meijing Li

    2015-01-01

    Full Text Available 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 model, and PPI discovery model. The Protein-NER model, which is named ProNER, identifies the protein names based on two methods: dictionary-based method and machine learning-based method. ProNER is capable of identifying more proteins than dictionary-based Protein-NER model in other existing systems. The final discovered PPIs extracted via PPI discovery model are represented in detail because we showed the protein interaction types and the occurrence frequency through two different methods. In the experiments, the result shows that the performances achieved by our ProNER and PPI discovery model are better than other existing tools. PPIMiner applied this protein-named entity recognition approach and parsing tree based PPI extraction method to improve the performance of PPI extraction. We also provide an easy-to-use interface to access PPIs database and an online system for PPIs extraction and Protein-NER.

  11. Proteins: Chemistry, Characterization, and Quality

    NARCIS (Netherlands)

    Sforza, S.; Tedeschi, T.; Wierenga, P.A.

    2016-01-01

    Proteins are one of the major macronutrients in food, and several traditional food commodities are good sources of proteins (meat, egg, milk and dairy products, fish, and soya). Proteins are polymers made by 20 different amino acids. They might undergo desired or undesired chemical or enzymatic

  12. Protein: FBA6 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FBA6 vesicular transport ARFGAP2 ZNF289 ADP-ribosylation factor GTPase-activating pro...tein 2 GTPase-activating protein ZNF289, Zinc finger protein 289 9606 Homo sapiens Q8N6H7 84364 2P57 ...

  13. Transient interactions between photosynthetic proteins

    NARCIS (Netherlands)

    Hulsker, Rinske

    2008-01-01

    The biological processes that are the basis of all life forms are mediated largely by protein-protein interactions. The protein complexes involved in these interactions can be categorised by their affinity, which results in a range from static to transient complexes. Electron transfer complexes,

  14. Protein: FBA8 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FBA8 LUBAC (linear ubiquitin chain-assembly complex) RNF31 ZIBRA RNF31 RING finger pr...otein 31 HOIL-1-interacting protein, Zinc in-between-RING-finger ubiquitin-associated domain protein 9606 Homo sapiens Q96EP0 55072 2CT7 55072 Q96EP0 ...

  15. Protein: MPA1 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available MPA1 TLR signaling molecules MAVS IPS1, KIAA1271, VISA VISA_(gene) Mitochondrial antiviral-signaling pr...otein CARD adapter inducing interferon beta, Interferon beta promoter stimulator protein... 1, Putative NF-kappa-B-activating protein 031N, Virus-induced-signaling adapter 9606 Homo sapiens Q7Z434 57506 2VGQ 57506 ...

  16. Protein: FBA3 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available FBA3 Ubiquitination CBLB RNF56 CBLB E3 ubiquitin-protein ligase CBL-B Casitas B-lineage lymphoma pr...oto-oncogene b, RING finger protein 56, SH3-binding protein CBL-B, Signal transduction prote

  17. Protein: MPB2 [TP Atlas

    Lifescience Database Archive (English)

    Full Text Available MPB2 Ubiquitin ligases WWP1 WWP1 NEDD4-like E3 ubiquitin-protein ligase WWP1 Atrophin-1-interacting pr...otein 5, WW domain-containing protein 1 9606 Homo sapiens Q9H0M0 11059 2OP7, 1ND7 11059 ...

  18. Functional Foods Containing Whey Proteins

    Science.gov (United States)

    Whey proteins, modified whey proteins, and whey components are useful as nutrients or supplements for health maintenance. Extrusion modified whey proteins can easily fit into new products such as beverages, confectionery items (e.g., candies), convenience foods, desserts, baked goods, sauces, and in...

  19. Protein Supplements: Pros and Cons.

    Science.gov (United States)

    Samal, Jay Rabindra Kumar; Samal, Indira R

    2018-05-04

    To provide a comprehensive analysis of the literature examining the pros and cons of protein supplementation, various articles on protein supplementation were obtained from Google Scholar, PubMed, and National Center for Biotechnology Information. Over the past few years, protein supplementation has become commonplace for gym-goers as well as for the public. A large segment of the general population relies on protein supplementation for meal replacement, weight reduction, and purported health benefits. These protein supplements have varying pros and cons associated with them, which are often overlooked by the public. This review aims to assimilate existing studies and form a consensus regarding the benefits and disadvantages of protein supplementation. The purported health benefits of protein supplementation have led to overuse by both adults and adolescents. Although the pros and cons of protein supplementation is a widely debated topic, not many studies have been conducted regarding the same. The few studies that exist either provide insufficient evidence or have not employed proper conditions for the conduct of the tests. It should be considered that protein supplements are processed materials and often do not contain other essential nutrients required for the sustenance of a healthy lifestyle. It is suggested that the required protein intake should be obtained from natural food sources and protein supplementation should be resorted to only if sufficient protein is not available in the normal diet.

  20. Protein Misfolding and Human Disease

    DEFF Research Database (Denmark)

    Gregersen, Niels; Bross, Peter Gerd; Vang, Søren

    2006-01-01

    Protein misfolding is a common event in living cells. In young and healthy cells, the misfolded protein load is disposed of by protein quality control (PQC) systems. In aging cells and in cells from certain individuals with genetic diseases, the load may overwhelm the PQC capacity, resulting in a...

  1. Modeling complexes of modeled proteins.

    Science.gov (United States)

    Anishchenko, Ivan; Kundrotas, Petras J; Vakser, Ilya A

    2017-03-01

    Structural characterization of proteins is essential for understanding life processes at the molecular level. However, only a fraction of known proteins have experimentally determined structures. This fraction is even smaller for protein-protein complexes. Thus, structural modeling of protein-protein interactions (docking) primarily has to rely on modeled structures of the individual proteins, which typically are less accurate than the experimentally determined ones. Such "double" modeling is the Grand Challenge of structural reconstruction of the interactome. Yet it remains so far largely untested in a systematic way. We present a comprehensive validation of template-based and free docking on a set of 165 complexes, where each protein model has six levels of structural accuracy, from 1 to 6 Å C α RMSD. Many template-based docking predictions fall into acceptable quality category, according to the CAPRI criteria, even for highly inaccurate proteins (5-6 Å RMSD), although the number of such models (and, consequently, the docking success rate) drops significantly for models with RMSD > 4 Å. The results show that the existing docking methodologies can be successfully applied to protein models with a broad range of structural accuracy, and the template-based docking is much less sensitive to inaccuracies of protein models than the free docking. Proteins 2017; 85:470-478. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  2. Protein-protein interactions and cancer: targeting the central dogma.

    Science.gov (United States)

    Garner, Amanda L; Janda, Kim D

    2011-01-01

    Between 40,000 and 200,000 protein-protein interactions have been predicted to exist within the human interactome. As these interactions are of a critical nature in many important cellular functions and their dysregulation is causal of disease, the modulation of these binding events has emerged as a leading, yet difficult therapeutic arena. In particular, the targeting of protein-protein interactions relevant to cancer is of fundamental importance as the tumor-promoting function of several aberrantly expressed proteins in the cancerous state is directly resultant of its ability to interact with a protein-binding partner. Of significance, these protein complexes play a crucial role in each of the steps of the central dogma of molecular biology, the fundamental processes of genetic transmission. With the many important discoveries being made regarding the mechanisms of these genetic process, the identification of new chemical probes are needed to better understand and validate the druggability of protein-protein interactions related to the central dogma. In this review, we provide an overview of current small molecule-based protein-protein interaction inhibitors for each stage of the central dogma: transcription, mRNA splicing and translation. Importantly, through our analysis we have uncovered a lack of necessary probes targeting mRNA splicing and translation, thus, opening up the possibility for expansion of these fields.

  3. The Proteins API: accessing key integrated protein and genome information.

    Science.gov (United States)

    Nightingale, Andrew; Antunes, Ricardo; Alpi, Emanuele; Bursteinas, Borisas; Gonzales, Leonardo; Liu, Wudong; Luo, Jie; Qi, Guoying; Turner, Edd; Martin, Maria

    2017-07-03

    The Proteins API provides searching and programmatic access to protein and associated genomics data such as curated protein sequence positional annotations from UniProtKB, as well as mapped variation and proteomics data from large scale data sources (LSS). Using the coordinates service, researchers are able to retrieve the genomic sequence coordinates for proteins in UniProtKB. This, the LSS genomics and proteomics data for UniProt proteins is programmatically only available through this service. A Swagger UI has been implemented to provide documentation, an interface for users, with little or no programming experience, to 'talk' to the services to quickly and easily formulate queries with the services and obtain dynamically generated source code for popular programming languages, such as Java, Perl, Python and Ruby. Search results are returned as standard JSON, XML or GFF data objects. The Proteins API is a scalable, reliable, fast, easy to use RESTful services that provides a broad protein information resource for users to ask questions based upon their field of expertise and allowing them to gain an integrated overview of protein annotations available to aid their knowledge gain on proteins in biological processes. The Proteins API is available at (http://www.ebi.ac.uk/proteins/api/doc). © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  4. Biophysics of protein evolution and evolutionary protein biophysics

    Science.gov (United States)

    Sikosek, Tobias; Chan, Hue Sun

    2014-01-01

    The study of molecular evolution at the level of protein-coding genes often entails comparing large datasets of sequences to infer their evolutionary relationships. Despite the importance of a protein's structure and conformational dynamics to its function and thus its fitness, common phylogenetic methods embody minimal biophysical knowledge of proteins. To underscore the biophysical constraints on natural selection, we survey effects of protein mutations, highlighting the physical basis for marginal stability of natural globular proteins and how requirement for kinetic stability and avoidance of misfolding and misinteractions might have affected protein evolution. The biophysical underpinnings of these effects have been addressed by models with an explicit coarse-grained spatial representation of the polypeptide chain. Sequence–structure mappings based on such models are powerful conceptual tools that rationalize mutational robustness, evolvability, epistasis, promiscuous function performed by ‘hidden’ conformational states, resolution of adaptive conflicts and conformational switches in the evolution from one protein fold to another. Recently, protein biophysics has been applied to derive more accurate evolutionary accounts of sequence data. Methods have also been developed to exploit sequence-based evolutionary information to predict biophysical behaviours of proteins. The success of these approaches demonstrates a deep synergy between the fields of protein biophysics and protein evolution. PMID:25165599

  5. The Proteins API: accessing key integrated protein and genome information

    Science.gov (United States)

    Antunes, Ricardo; Alpi, Emanuele; Gonzales, Leonardo; Liu, Wudong; Luo, Jie; Qi, Guoying; Turner, Edd

    2017-01-01

    Abstract The Proteins API provides searching and programmatic access to protein and associated genomics data such as curated protein sequence positional annotations from UniProtKB, as well as mapped variation and proteomics data from large scale data sources (LSS). Using the coordinates service, researchers are able to retrieve the genomic sequence coordinates for proteins in UniProtKB. This, the LSS genomics and proteomics data for UniProt proteins is programmatically only available through this service. A Swagger UI has been implemented to provide documentation, an interface for users, with little or no programming experience, to ‘talk’ to the services to quickly and easily formulate queries with the services and obtain dynamically generated source code for popular programming languages, such as Java, Perl, Python and Ruby. Search results are returned as standard JSON, XML or GFF data objects. The Proteins API is a scalable, reliable, fast, easy to use RESTful services that provides a broad protein information resource for users to ask questions based upon their field of expertise and allowing them to gain an integrated overview of protein annotations available to aid their knowledge gain on proteins in biological processes. The Proteins API is available at (http://www.ebi.ac.uk/proteins/api/doc). PMID:28383659

  6. Recombinant protein hydrazides: application to site-specific protein PEGylation.

    Science.gov (United States)

    Thom, Jennifer; Anderson, David; McGregor, Joanne; Cotton, Graham

    2011-06-15

    Here, we describe a novel method for the site-specific C-terminal PEGylation of recombinant proteins. This general approach exploits chemical cleavage of precursor intein-fusion proteins with hydrazine to directly produce recombinant protein hydrazides. This unique functionality within the protein sequence then facilitates site-specific C-terminal modification by hydrazone-forming ligation reactions. This approach was used to generate folded, site-specifically C-terminal PEGylated IFNalpha2b and IFNbeta1b, which retained excellent antiviral activity, demonstrating the utility of this technology in the PEGylation of therapeutic proteins. As this methodology is straightforward to perform, is compatible with disulfide bonds, and is exclusively selective for the protein C-terminus, it shows great potential as general technology for the site-specific engineering and labeling of recombinant proteins.

  7. Protein subcellular localization assays using split fluorescent proteins

    Science.gov (United States)

    Waldo, Geoffrey S [Santa Fe, NM; Cabantous, Stephanie [Los Alamos, NM

    2009-09-08

    The invention provides protein subcellular localization assays using split fluorescent protein systems. The assays are conducted in living cells, do not require fixation and washing steps inherent in existing immunostaining and related techniques, and permit rapid, non-invasive, direct visualization of protein localization in living cells. The split fluorescent protein systems used in the practice of the invention generally comprise two or more self-complementing fragments of a fluorescent protein, such as GFP, wherein one or more of the fragments correspond to one or more beta-strand microdomains and are used to "tag" proteins of interest, and a complementary "assay" fragment of the fluorescent protein. Either or both of the fragments may be functionalized with a subcellular targeting sequence enabling it to be expressed in or directed to a particular subcellular compartment (i.e., the nucleus).

  8. Diffusion of Integral Membrane Proteins in Protein-Rich Membranes

    DEFF Research Database (Denmark)

    Javanainen, Matti; Martinez-Seara, Hector; Metzler, Ralf

    2017-01-01

    -like dependence D ∝ 1/R. We propose that this 1/R law mainly arises due to geometrical factors: smaller proteins are able to avoid confinement effects much better than their larger counterparts. The results highlight that the lateral dynamics in the crowded setting found in native membranes is radically different......The lateral diffusion of embedded proteins along lipid membranes in protein-poor conditions has been successfully described in terms of the Saffman-Delbrück (SD) model, which predicts that the protein diffusion coefficient D is weakly dependent on its radius R as D ∝ ln(1/R). However, instead...... of being protein-poor, native cell membranes are extremely crowded with proteins. On the basis of extensive molecular simulations, we here demonstrate that protein crowding of the membrane at physiological levels leads to deviations from the SD relation and to the emergence of a stronger Stokes...

  9. Protein homeostasis and aging: role of ubiquitin protein ligases.

    Science.gov (United States)

    Jana, Nihar Ranjan

    2012-04-01

    Protein homeostasis is fundamental in normal cellular function and cell survival. The ubiquitin-proteasome system (UPS) plays a central role in maintaining the protein homeostasis network through selective elimination of misfolded and damaged proteins. Impaired function of UPS is implicated in normal aging process and also in several age-related neurodegenerative disorders that are characterized by increased accumulation oxidatively modified proteins and protein aggregates. Growing literature also indicate the potential role of various ubiquitin protein ligases in the regulation of aging process by enhancing the degradation of either central lifespan regulators or abnormally folded and damaged proteins. This review mainly focuses on our current understanding of the importance of UPS function in the regulation of normal aging process. Copyright © 2012 Elsevier Ltd. All rights reserved.

  10. Exploiting amino acid composition for predicting protein-protein interactions.

    Directory of Open Access Journals (Sweden)

    Sushmita Roy

    2009-11-01

    Full Text Available Computational prediction of protein interactions typically use protein domains as classifier features because they capture conserved information of interaction surfaces. However, approaches relying on domains as features cannot be applied to proteins without any domain information. In this paper, we explore the contribution of pure amino acid composition (AAC for protein interaction prediction. This simple feature, which is based on normalized counts of single or pairs of amino acids, is applicable to proteins from any sequenced organism and can be used to compensate for the lack of domain information.AAC performed at par with protein interaction prediction based on domains on three yeast protein interaction datasets. Similar behavior was obtained using different classifiers, indicating that our results are a function of features and not of classifiers. In addition to yeast datasets, AAC performed comparably on worm and fly datasets. Prediction of interactions for the entire yeast proteome identified a large number of novel interactions, the majority of which co-localized or participated in the same processes. Our high confidence interaction network included both well-studied and uncharacterized proteins. Proteins with known function were involved in actin assembly and cell budding. Uncharacterized proteins interacted with proteins involved in reproduction and cell budding, thus providing putative biological roles for the uncharacterized proteins.AAC is a simple, yet powerful feature for predicting protein interactions, and can be used alone or in conjunction with protein domains to predict new and validate existing interactions. More importantly, AAC alone performs at par with existing, but more complex, features indicating the presence of sequence-level information that is predictive of interaction, but which is not necessarily restricted to domains.

  11. NMR Studies of Protein Hydration and Protein-Ligand Interactions

    Science.gov (United States)

    Chong, Yuan

    Water on the surface of a protein is called hydration water. Hydration water is known to play a crucial role in a variety of biological processes including protein folding, enzymatic activation, and drug binding. Although the significance of hydration water has been recognized, the underlying mechanism remains far from being understood. This dissertation employs a unique in-situ nuclear magnetic resonance (NMR) technique to study the mechanism of protein hydration and the role of hydration in alcohol-protein interactions. Water isotherms in proteins are measured at different temperatures via the in-situ NMR technique. Water is found to interact differently with hydrophilic and hydrophobic groups on the protein. Water adsorption on hydrophilic groups is hardly affected by the temperature, while water adsorption on hydrophobic groups strongly depends on the temperature around 10 C, below which the adsorption is substantially reduced. This effect is induced by the dramatic decrease in the protein flexibility below 10 C. Furthermore, nanosecond to microsecond protein dynamics and the free energy, enthalpy, and entropy of protein hydration are studied as a function of hydration level and temperature. A crossover at 10 C in protein dynamics and thermodynamics is revealed. The effect of water at hydrophilic groups on protein dynamics and thermodynamics shows little temperature dependence, whereas water at hydrophobic groups has stronger effect above 10 C. In addition, I investigate the role of water in alcohol binding to the protein using the in-situ NMR detection. The isotherms of alcohols are first measured on dry proteins, then on proteins with a series of controlled hydration levels. The free energy, enthalpy, and entropy of alcohol binding are also determined. Two distinct types of alcohol binding are identified. On the one hand, alcohols can directly bind to a few specific sites on the protein. This type of binding is independent of temperature and can be

  12. Essential Protein Detection by Random Walk on Weighted Protein-Protein Interaction Networks.

    Science.gov (United States)

    Xu, Bin; Guan, Jihong; Wang, Yang; Wang, Zewei

    2017-05-12

    Essential proteins are critical to the development and survival of cells. Identification of essential proteins is helpful for understanding the minimal set of required genes in a living cell and for designing new drugs. To detect essential proteins, various computational methods have been proposed based on protein-protein interaction (PPI) networks. However, protein interaction data obtained by highthroughput experiments usually contain high false positives, which negatively impacts the accuracy of essential protein detection. Moreover, most existing studies focused on the local information of proteins in PPI networks, while ignoring the influence of indirect protein interactions on essentiality. In this paper, we propose a novel method, called Essentiality Ranking (EssRank in short), to boost the accuracy of essential protein detection. To deal with the inaccuracy of PPI data, confidence scores of interactions are evaluated by integrating various biological information. Weighted edge clustering coefficient (WECC), considering both interaction confidence scores and network topology, is proposed to calculate edge weights in PPI networks. The weight of each node is evaluated by the sum of WECC values of its linking edges. A random walk method, making use of both direct and indirect protein interactions, is then employed to calculate protein essentiality iteratively. Experimental results on the yeast PPI network show that EssRank outperforms most existing methods, including the most commonly-used centrality measures (SC, DC, BC, CC, IC, EC), topology based methods (DMNC and NC) and the data integrating method IEW.

  13. Detection of protein complex from protein-protein interaction network using Markov clustering

    International Nuclear Information System (INIS)

    Ochieng, P J; Kusuma, W A; Haryanto, T

    2017-01-01

    Detection of complexes, or groups of functionally related proteins, is an important challenge while analysing biological networks. However, existing algorithms to identify protein complexes are insufficient when applied to dense networks of experimentally derived interaction data. Therefore, we introduced a graph clustering method based on Markov clustering algorithm to identify protein complex within highly interconnected protein-protein interaction networks. Protein-protein interaction network was first constructed to develop geometrical network, the network was then partitioned using Markov clustering to detect protein complexes. The interest of the proposed method was illustrated by its application to Human Proteins associated to type II diabetes mellitus. Flow simulation of MCL algorithm was initially performed and topological properties of the resultant network were analysed for detection of the protein complex. The results indicated the proposed method successfully detect an overall of 34 complexes with 11 complexes consisting of overlapping modules and 20 non-overlapping modules. The major complex consisted of 102 proteins and 521 interactions with cluster modularity and density of 0.745 and 0.101 respectively. The comparison analysis revealed MCL out perform AP, MCODE and SCPS algorithms with high clustering coefficient (0.751) network density and modularity index (0.630). This demonstrated MCL was the most reliable and efficient graph clustering algorithm for detection of protein complexes from PPI networks. (paper)

  14. Protein-protein interaction network-based detection of functionally similar proteins within species.

    Science.gov (United States)

    Song, Baoxing; Wang, Fen; Guo, Yang; Sang, Qing; Liu, Min; Li, Dengyun; Fang, Wei; Zhang, Deli

    2012-07-01

    Although functionally similar proteins across species have been widely studied, functionally similar proteins within species showing low sequence similarity have not been examined in detail. Identification of these proteins is of significant importance for understanding biological functions, evolution of protein families, progression of co-evolution, and convergent evolution and others which cannot be obtained by detection of functionally similar proteins across species. Here, we explored a method of detecting functionally similar proteins within species based on graph theory. After denoting protein-protein interaction networks using graphs, we split the graphs into subgraphs using the 1-hop method. Proteins with functional similarities in a species were detected using a method of modified shortest path to compare these subgraphs and to find the eligible optimal results. Using seven protein-protein interaction networks and this method, some functionally similar proteins with low sequence similarity that cannot detected by sequence alignment were identified. By analyzing the results, we found that, sometimes, it is difficult to separate homologous from convergent evolution. Evaluation of the performance of our method by gene ontology term overlap showed that the precision of our method was excellent. Copyright © 2012 Wiley Periodicals, Inc.

  15. Human cancer protein-protein interaction network: a structural perspective.

    Directory of Open Access Journals (Sweden)

    Gozde Kar

    2009-12-01

    Full Text Available Protein-protein interaction networks provide a global picture of cellular function and biological processes. Some proteins act as hub proteins, highly connected to others, whereas some others have few interactions. The dysfunction of some interactions causes many diseases, including cancer. Proteins interact through their interfaces. Therefore, studying the interface properties of cancer-related proteins will help explain their role in the interaction networks. Similar or overlapping binding sites should be used repeatedly in single interface hub proteins, making them promiscuous. Alternatively, multi-interface hub proteins make use of several distinct binding sites to bind to different partners. We propose a methodology to integrate protein interfaces into cancer interaction networks (ciSPIN, cancer structural protein interface network. The interactions in the human protein interaction network are replaced by interfaces, coming from either known or predicted complexes. We provide a detailed analysis of cancer related human protein-protein interfaces and the topological properties of the cancer network. The results reveal that cancer-related proteins have smaller, more planar, more charged and less hydrophobic binding sites than non-cancer proteins, which may indicate low affinity and high specificity of the cancer-related interactions. We also classified the genes in ciSPIN according to phenotypes. Within phenotypes, for breast cancer, colorectal cancer and leukemia, interface properties were found to be discriminating from non-cancer interfaces with an accuracy of 71%, 67%, 61%, respectively. In addition, cancer-related proteins tend to interact with their partners through distinct interfaces, corresponding mostly to multi-interface hubs, which comprise 56% of cancer-related proteins, and constituting the nodes with higher essentiality in the network (76%. We illustrate the interface related affinity properties of two cancer-related hub

  16. Protein folding and wring resonances

    DEFF Research Database (Denmark)

    Bohr, Jakob; Bohr, Henrik; Brunak, Søren

    1997-01-01

    The polypeptide chain of a protein is shown to obey topological contraints which enable long range excitations in the form of wring modes of the protein backbone. Wring modes of proteins of specific lengths can therefore resonate with molecular modes present in the cell. It is suggested...... that protein folding takes place when the amplitude of a wring excitation becomes so large that it is energetically favorable to bend the protein backbone. The condition under which such structural transformations can occur is found, and it is shown that both cold and hot denaturation (the unfolding...... of proteins) are natural consequences of the suggested wring mode model. Native (folded) proteins are found to possess an intrinsic standing wring mode....

  17. Metagenomics and the protein universe

    Science.gov (United States)

    Godzik, Adam

    2011-01-01

    Metagenomics sequencing projects have dramatically increased our knowledge of the protein universe and provided over one-half of currently known protein sequences; they have also introduced a much broader phylogenetic diversity into the protein databases. The full analysis of metagenomic datasets is only beginning, but it has already led to the discovery of thousands of new protein families, likely representing novel functions specific to given environments. At the same time, a deeper analysis of such novel families, including experimental structure determination of some representatives, suggests that most of them represent distant homologs of already characterized protein families, and thus most of the protein diversity present in the new environments are due to functional divergence of the known protein families rather than the emergence of new ones. PMID:21497084

  18. Protein Adsorption in Three Dimensions

    Science.gov (United States)

    Vogler, Erwin A.

    2011-01-01

    Recent experimental and theoretical work clarifying the physical chemistry of blood-protein adsorption from aqueous-buffer solution to various kinds of surfaces is reviewed and interpreted within the context of biomaterial applications, especially toward development of cardiovascular biomaterials. The importance of this subject in biomaterials surface science is emphasized by reducing the “protein-adsorption problem” to three core questions that require quantitative answer. An overview of the protein-adsorption literature identifies some of the sources of inconsistency among many investigators participating in more than five decades of focused research. A tutorial on the fundamental biophysical chemistry of protein adsorption sets the stage for a detailed discussion of the kinetics and thermodynamics of protein adsorption, including adsorption competition between two proteins for the same adsorbent immersed in a binary-protein mixture. Both kinetics and steady-state adsorption can be rationalized using a single interpretive paradigm asserting that protein molecules partition from solution into a three-dimensional (3D) interphase separating bulk solution from the physical-adsorbent surface. Adsorbed protein collects in one-or-more adsorbed layers, depending on protein size, solution concentration, and adsorbent surface energy (water wettability). The adsorption process begins with the hydration of an adsorbent surface brought into contact with an aqueous-protein solution. Surface hydration reactions instantaneously form a thin, pseudo-2D interface between the adsorbent and protein solution. Protein molecules rapidly diffuse into this newly-formed interface, creating a truly 3D interphase that inflates with arriving proteins and fills to capacity within milliseconds at mg/mL bulk-solution concentrations CB. This inflated interphase subsequently undergoes time-dependent (minutes-to-hours) decrease in volume VI by expulsion of either-or-both interphase water and

  19. Protein stability, flexibility and function

    DEFF Research Database (Denmark)

    Teilum, Kaare; Olsen, Johan G; Kragelund, Birthe B

    2011-01-01

    Proteins rely on flexibility to respond to environmental changes, ligand binding and chemical modifications. Potentially, a perturbation that changes the flexibility of a protein may interfere with its function. Millions of mutations have been performed on thousands of proteins in quests...... for a delineation of the molecular details of their function. Several of these mutations interfered with the binding of a specific ligand with a concomitant effect on the stability of the protein scaffold. It has been ambiguous and not straightforward to recognize if any relationships exist between the stability...... of a protein and the affinity for its ligand. In this review, we present examples of proteins where changes in stability results in changes in affinity and of proteins where stability and affinity are uncorrelated. We discuss the possibility for a relationship between stability and binding. From the data...

  20. Protein-protein interaction based on pairwise similarity

    Directory of Open Access Journals (Sweden)

    Zaki Nazar

    2009-05-01

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