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Sample records for conformation avec modulation

  1. Classification of finite irreducible conformal modules over some Lie conformal algebras related to the Virasoro conformal algebra

    NASA Astrophysics Data System (ADS)

    Wu, Henan; Yuan, Lamei

    2017-04-01

    In this paper, we classify all finite irreducible conformal modules over a class of Lie conformal algebras W (b ) with b ∈ℂ related to the Virasoro conformal algebra. Explicitly, any finite irreducible conformal module over W (b ) is proved to be isomorphic to MΔ ,α ,β with Δ ≠0 or β ≠0 if b = 0, or MΔ ,α with Δ ≠0 if b ≠0 . As a byproduct, all finite irreducible conformal modules over the Heisenberg-Virasoro conformal algebra and the W(2, 2) Lie conformal algebra are classified. Finally, the same thing is done for the Schrödinger-Virasoro conformal algebra.

  2. Lipids modulate the conformational dynamics of a secondary multidrug transporter

    PubMed Central

    Martens, Chloé; Stein, Richard A; Masureel, Matthieu; Roth, Aurélie; Mishra, Smriti; Dawaliby, Rosie; Konijnenberg, Albert; Sobott, Frank; Govaerts, Cédric; Mchaourab, Hassane S

    2017-01-01

    Direct interactions with lipids have emerged as key determinants of the folding, structure and function of membrane proteins, but an understanding of how lipids modulate protein dynamics is still lacking. Here, we systematically explored the effects of lipids on the conformational dynamics of the proton-powered, multidrug transporter LmrP from Lactococcus lactis utilizing the pattern of distances between spin label pairs previously shown to fingerprint alternating access of the protein. We uncover at the molecular level how the lipid headgroups shape the conformational energy landscape of the transporter. The model emerging from our data hypothesizes a direct interaction between lipid headgroups and a conserved motif of charged residues that control the conformational equilibrium through an interplay of electrostatic interactions within the protein. Together, our data lay the foundation for a comprehensive model of secondary multidrug transport in lipid bilayers. PMID:27399258

  3. Halogen Bonding: A Powerful Tool for Modulation of Peptide Conformation.

    PubMed

    Danelius, Emma; Andersson, Hanna; Jarvoll, Patrik; Lood, Kajsa; Gräfenstein, Jürgen; Erdélyi, Máté

    2017-06-27

    Halogen bonding is a weak chemical force that has so far mostly found applications in crystal engineering. Despite its potential for use in drug discovery, as a new molecular tool in the direction of molecular recognition events, it has rarely been assessed in biopolymers. Motivated by this fact, we have developed a peptide model system that permits the quantitative evaluation of weak forces in a biologically relevant proteinlike environment and have applied it for the assessment of a halogen bond formed between two amino acid side chains. The influence of a single weak force is measured by detection of the extent to which it modulates the conformation of a cooperatively folding system. We have optimized the amino acid sequence of the model peptide on analogues with a hydrogen bond-forming site as a model for the intramolecular halogen bond to be studied, demonstrating the ability of the technique to provide information about any type of weak secondary interaction. A combined solution nuclear magnetic resonance spectroscopic and computational investigation demonstrates that an interstrand halogen bond is capable of conformational stabilization of a β-hairpin foldamer comparable to an analogous hydrogen bond. This is the first report of incorporation of a conformation-stabilizing halogen bond into a peptide/protein system, and the first quantification of a chlorine-centered halogen bond in a biologically relevant system in solution.

  4. Conformationally Selective RNA Aptamers Allosterically Modulate the β2-Adrenoceptor

    PubMed Central

    Kahsai, Alem W.; Wisler, James W.; Lee, Jungmin; Ahn, Seungkirl; Cahill, Thomas J.; Dennison, S. Moses; Staus, Dean P.; Thomsen, Alex R. B.; Anasti, Kara M.; Pani, Biswaranjan; Wingler, Laura M.; Desai, Hemant; Bompiani, Kristin M.; Strachan, Ryan T.; Qin, Xiaoxia; Alam, S. Munir; Sullenger, Bruce A.; Lefkowitz, Robert J.

    2016-01-01

    G-protein-coupled receptor (GPCR) ligands function by stabilizing multiple, functionally distinct receptor conformations. This property underlies how “biased agonists” activate specific subsets of a given receptor’s signaling profile. However, stabilization of distinct active GPCR conformations to enable structural characterization of mechanisms underlying GPCR activation remains difficult. These challenges have accentuated the need for receptor tools that allosterically stabilize and regulate receptor function via unique, previously unappreciated mechanisms. Here, utilizing a highly diverse RNA library combined with advanced selection strategies involving state-of-the-art next-generation sequencing and bioinformatics analyses, we identify RNA aptamers that bind a prototypical GPCR, β2-adrenoceptor (β2AR). Using biochemical, pharmacological, and biophysical approaches, we demonstrate that these aptamers bind with nanomolar affinity at defined surfaces of the receptor, allosterically stabilizing active, inactive, and ligand-specific receptor conformations. The discovery of RNA aptamers as allosteric GPCR modulators significantly expands the diversity of ligands available to study the structural and functional regulation of GPCRs. PMID:27398998

  5. Ca2+ and Mg2+ modulate conformational dynamics and stability of downstream regulatory element antagonist modulator

    PubMed Central

    Pham, Khoa; Dhulipala, Gangadhar; Gonzalez, Walter G; Gerstman, Bernard S; Regmi, Chola; Chapagain, Prem P; Miksovska, Jaroslava

    2015-01-01

    Downstream Regulatory Element Antagonist Modulator (DREAM) belongs to the family of neuronal calcium sensors (NCS) that transduce the intracellular changes in Ca2+ concentration into a variety of responses including gene expression, regulation of Kv channel activity, and calcium homeostasis. Despite the significant sequence and structural similarities with other NCS members, DREAM shows several features unique among NCS such as formation of a tetramer in the apo-state, and interactions with various intracellular biomacromolecules including DNA, presenilin, Kv channels, and calmodulin. Here we use spectroscopic techniques in combination with molecular dynamics simulation to study conformational changes induced by Ca2+/Mg2+ association to DREAM. Our data indicate a minor impact of Ca2+ association on the overall structure of the N- and C-terminal domains, although Ca2+ binding decreases the conformational heterogeneity as evident from the decrease in the fluorescence lifetime distribution in the Ca2+ bound forms of the protein. Time-resolved fluorescence data indicate that Ca2+binding triggers a conformational transition that is characterized by more efficient quenching of Trp residue. The unfolding of DREAM occurs through an partially unfolded intermediate that is stabilized by Ca2+ association to EF-hand 3 and EF-hand 4. The native state is stabilized with respect to the partially unfolded state only in the presence of both Ca2+ and Mg2+ suggesting that, under physiological conditions, Ca2+ free DREAM exhibits a high conformational flexibility that may facilitate its physiological functions. PMID:25627705

  6. Disorder transitions and conformational diversity cooperatively modulate biological function in proteins

    PubMed Central

    Zea, Diego Javier; Monzon, Alexander Miguel; Gonzalez, Claudia; Fornasari, María Silvina; Tosatto, Silvio C. E.

    2016-01-01

    Abstract Structural differences between conformers sustain protein biological function. Here, we studied in a large dataset of 745 intrinsically disordered proteins, how ordered‐disordered transitions modulate structural differences between conformers as derived from crystallographic data. We found that almost 50% of the proteins studied show no transitions and have low conformational diversity while the rest show transitions and a higher conformational diversity. In this last subset, 60% of the proteins become more ordered after ligand binding, while 40% more disordered. As protein conformational diversity is inherently connected with protein function our analysis suggests differences in structure‐function relationships related to order‐disorder transitions. PMID:27038125

  7. General Conformity Training Module 2.5: Proactive Role for Federal Agencies

    EPA Pesticide Factsheets

    Module 2.5 explains how taking a proactive role will allow a federal agency to more effectively participate in newly promulgated programs under the General Conformity Regulations, such as the emission reduction credits and the emission budgets programs.

  8. Osmolytes as modulators of conformational changes in serpins.

    PubMed

    Chow, M K; Devlin, G L; Bottomley, S P

    2001-11-01

    Protein misfolding and aggregation play an integral role in many diseases. The misfolding of the serpin (SERine Proteinase INhibitor) alpha1-antitrypsin results in the accumulation of insoluble polymers within hepatocytes and alpha1-antitrypsin deficiency in plasma, predisposing patients to liver cirrhosis and emphysema. We have examined the effect of three naturally occurring osmolytes, sarcosine, glycine betaine and trimethylamine N-oxide, on conformational changes in alpha1-antitrypsin. All three solutes protected native alpha1-antitrypsin against thermally induced polymerisation and inactivation in a concentration-dependent manner. Further spectroscopic analysis showed that sarcosine stabilises the native conformation of alpha1-antitrypsin, thus hindering its conversion to an intermediate state and subsequent polymerisation. On refolding in the presence of sarcosine, alpha1-antitrypsin formed a heterogeneous population, with increasing proportions of molecules adopting an inactive conformation in higher concentrations of the osmolyte. These data show that sarcosine can be used to prevent abnormal structural changes in native alpha1-antitrypsin, but is ineffective in facilitating the correct folding of the protein. The implications of these results in the context of conformational changes and states adopted by alpha1-antitrypsin are discussed.

  9. General Conformity Training Modules: Appendix A Sample Emissions Calculations

    EPA Pesticide Factsheets

    Appendix A of the training modules gives example calculations for external and internal combustion sources, construction, fuel storage and transfer, on-road vehicles, aircraft operations, storage piles, and paved roads.

  10. Engineering a hyper-catalytic enzyme by photo-activated conformation modulation

    SciTech Connect

    Agarwal, Pratul K

    2012-01-01

    Enzyme engineering for improved catalysis has wide implications. We describe a novel chemical modification of Candida antarctica lipase B that allows modulation of the enzyme conformation to promote catalysis. Computational modeling was used to identify dynamical enzyme regions that impact the catalytic mechanism. Surface loop regions located distal to active site but showing dynamical coupling to the reaction were connected by a chemical bridge between Lys136 and Pro192, containing a derivative of azobenzene. The conformational modulation of the enzyme was achieved using two sources of light that alternated the azobenzene moiety in cis and trans conformations. Computational model predicted that mechanical energy from the conformational fluctuations facilitate the reaction in the active-site. The results were consistent with predictions as the activity of the engineered enzyme was found to be enhanced with photoactivation. Preliminary estimations indicate that the engineered enzyme achieved 8-52 fold better catalytic activity than the unmodulated enzyme.

  11. Loop Electrostatics Asymmetry Modulates the Preexisting Conformational Equilibrium in Thrombin.

    PubMed

    Pozzi, Nicola; Zerbetto, Mirco; Acquasaliente, Laura; Tescari, Simone; Frezzato, Diego; Polimeno, Antonino; Gohara, David W; Di Cera, Enrico; De Filippis, Vincenzo

    2016-07-19

    Thrombin exists as an ensemble of active (E) and inactive (E*) conformations that differ in their accessibility to the active site. Here we show that redistribution of the E*-E equilibrium can be achieved by perturbing the electrostatic properties of the enzyme. Removal of the negative charge of the catalytic Asp102 or Asp189 in the primary specificity site destabilizes the E form and causes a shift in the 215-217 segment that compromises substrate entrance. Solution studies and existing structures of D102N document stabilization of the E* form. A new high-resolution structure of D189A also reveals the mutant in the collapsed E* form. These findings establish a new paradigm for the control of the E*-E equilibrium in the trypsin fold.

  12. Network-wide Screen Identifies Variation of Novel Precise On-module Targets Using Conformational Modudaoism.

    PubMed

    Li, Bing; Liu, Jun; Yu, Yanan; Wang, Pengqian; Zhang, Yingying; Ni, Xumin; Liu, Qiong; Zhang, Xiaoxu; Wang, Zhong; Wang, Yongyan

    2017-09-19

    Modular targeting is promising in drug research at network level, but it's challenging to quantificationally identify the precise On-modules. Based on a proposed Modudaoism (MD), we defined conserved MD (MDc) and varied MD (MDv) to quantitatively evaluate the conformational and energy variations of modules, and thereby identify the conserved and discrepant allosteric modules. Compared with the Zsummary , MDc/MDv got an optimized result of module preserved ratio and modular structure. In mice anti-ischemic networks, 3, 5, and 1 conserved allosteric modules as well as 4, 1, and 3 On-modules of baicalin (BA), jasminoidin (JA), and ursodeoxycholic acid (UA) were identified by MDc and MDv, 5 unique allosteric modules and their characteristic actions were revealed. Besides, Co-IP experiments validated the representative modular structure. MDc/MDv method can quantitatively define the conformational variations of modules and screen the precise On-modules at network-wide, which may provide a promising strategy for drug discovery. This article is protected by copyright. All rights reserved. © 2017 ASCPT.

  13. Conformational modulation of sequence recognition in synthetic macromolecules.

    PubMed

    Zhu, Zhixue; Cardin, Christine J; Gan, Yu; Murray, Claire A; White, Andrew J P; Williams, David J; Colquhoun, Howard M

    2011-12-07

    The different triplet sequences in high molecular weight aromatic copolyimides comprising pyromellitimide units ("I") flanked by either ether-ketone ("K") or ether-sulfone residues ("S") show different binding strengths for pyrene-based tweezer-molecules. Such molecules bind primarily to the diimide unit through complementary π-π-stacking and hydrogen bonding. However, as shown by the magnitudes of (1)H NMR complexation shifts and tweezer-polymer binding constants, the triplet "SIS" binds tweezer-molecules more strongly than "KIS" which in turn binds such molecules more strongly than "KIK". Computational models for tweezer-polymer binding, together with single-crystal X-ray analyses of tweezer-complexes with macrocyclic ether-imides, reveal that the variations in binding strength between the different triplet sequences arise from the different conformational preferences of aromatic rings at diarylketone and diarylsulfone linkages. These preferences determine whether or not chain-folding and secondary π-π-stacking occurs between the arms of the tweezer-molecule and the 4,4'-biphenylene units which flank the central diimide residue.

  14. Modulation of a pre-existing conformational equilibrium tunes adenylate kinase activity.

    PubMed

    Ådén, Jörgen; Verma, Abhinav; Schug, Alexander; Wolf-Watz, Magnus

    2012-10-10

    Structural plasticity is often required for distinct microscopic steps during enzymatic reaction cycles. Adenylate kinase from Escherichia coli (AK(eco)) populates two major conformations in solution; the open (inactive) and closed (active) state, and the overall turnover rate is inversely proportional to the lifetime of the active conformation. Therefore, structural plasticity is intimately coupled to enzymatic turnover in AK(eco). Here, we probe the open to closed conformational equilibrium in the absence of bound substrate with NMR spectroscopy and molecular dynamics simulations. The conformational equilibrium in absence of substrate and, in turn, the turnover number can be modulated with mutational- and osmolyte-driven perturbations. Removal of one hydrogen bond between the ATP and AMP binding subdomains results in a population shift toward the open conformation and a resulting increase of k(cat). Addition of the osmolyte TMAO to AK(eco) results in population shift toward the closed conformation and a significant reduction of k(cat). The Michaelis constants (K(M)) scale with the change in k(cat), which follows from the influence of the population of the closed conformation for substrate binding affinity. Hence, k(cat) and K(M) are mutually dependent, and in the case of AK(eco), any perturbation that modulates k(cat) is mirrored with a proportional response in K(M). Thus, our results demonstrate that the equilibrium constant of a pre-existing conformational equilibrium directly affects enzymatic catalysis. From an evolutionary perspective, our findings suggest that, for AK(eco), there exists ample flexibility to obtain a specificity constant (k(cat)/K(M)) that commensurate with the exerted cellular selective pressure.

  15. Pancreatic cancer planning: Complex conformal vs modulated therapies.

    PubMed

    Chapman, Katherine L; Witek, Matthew E; Chen, Hongyu; Showalter, Timothy N; Bar-Ad, Voichita; Harrison, Amy S

    2016-01-01

    To compare the roles of intensity-modulated radiation therapy (IMRT) and volumetric- modulated arc therapy (VMAT) therapy as compared to simple and complex 3-dimensional chemoradiotherpy (3DCRT) planning for resectable and borderline resectable pancreatic cancer. In all, 12 patients who received postoperative radiotherapy (8) or neoadjuvant concurrent chemoradiotherapy (4) were evaluated retrospectively. Radiotherapy planning was performed for 4 treatment techniques: simple 4-field box, complex 5-field 3DCRT, 5 to 6-field IMRT, and single-arc VMAT. All volumes were approved by a single observer in accordance with Radiation Therapy Oncology Group (RTOG) Pancreas Contouring Atlas. Plans included tumor/tumor bed and regional lymph nodes to 45Gy; with tumor/tumor bed boosted to 50.4Gy, at least 95% of planning target volume (PTV) received the prescription dose. Dose-volume histograms (DVH) for multiple end points, treatment planning, and delivery time were assessed. Complex 3DCRT, IMRT, and VMAT plans significantly (p < 0.05) decreased mean kidney dose, mean liver dose, liver (V30, V35), stomach (D10%), stomach (V45), mean right kidney dose, and right kidney (V15) as compared with the simple 4-field plans that are most commonly reported in the literature. IMRT plans resulted in decreased mean liver dose, liver (V35), and left kidney (V15, V18, V20). VMAT plans decreased small bowel (D10%, D15%), small bowel (V35, V45), stomach (D10%, D15%), stomach (V35, V45), mean liver dose, liver (V35), left kidney (V15, V18, V20), and right kidney (V18, V20). VMAT plans significantly decreased small bowel (D10%, D15%), left kidney (V20), and stomach (V45) as compared with IMRT plans. Treatment planning and delivery times were most efficient for simple 4-field box and VMAT. Excluding patient setup and imaging, average treatment delivery was within 10minutes for simple and complex 3DCRT, IMRT, and VMAT treatments. This article shows significant improvements in 3D plan performance

  16. Pancreatic cancer planning: Complex conformal vs modulated therapies

    SciTech Connect

    Chapman, Katherine L.; Witek, Matthew E.; Chen, Hongyu; Showalter, Timothy N.; Bar-Ad, Voichita; Harrison, Amy S.

    2016-07-01

    To compare the roles of intensity-modulated radiation therapy (IMRT) and volumetric- modulated arc therapy (VMAT) therapy as compared to simple and complex 3-dimensional chemoradiotherpy (3DCRT) planning for resectable and borderline resectable pancreatic cancer. In all, 12 patients who received postoperative radiotherapy (8) or neoadjuvant concurrent chemoradiotherapy (4) were evaluated retrospectively. Radiotherapy planning was performed for 4 treatment techniques: simple 4-field box, complex 5-field 3DCRT, 5 to 6-field IMRT, and single-arc VMAT. All volumes were approved by a single observer in accordance with Radiation Therapy Oncology Group (RTOG) Pancreas Contouring Atlas. Plans included tumor/tumor bed and regional lymph nodes to 45 Gy; with tumor/tumor bed boosted to 50.4 Gy, at least 95% of planning target volume (PTV) received the prescription dose. Dose-volume histograms (DVH) for multiple end points, treatment planning, and delivery time were assessed. Complex 3DCRT, IMRT, and VMAT plans significantly (p < 0.05) decreased mean kidney dose, mean liver dose, liver (V{sub 30}, V{sub 35}), stomach (D{sub 10}%), stomach (V{sub 45}), mean right kidney dose, and right kidney (V{sub 15}) as compared with the simple 4-field plans that are most commonly reported in the literature. IMRT plans resulted in decreased mean liver dose, liver (V{sub 35}), and left kidney (V{sub 15}, V{sub 18}, V{sub 20}). VMAT plans decreased small bowel (D{sub 10}%, D{sub 15}%), small bowel (V{sub 35}, V{sub 45}), stomach (D{sub 10}%, D{sub 15}%), stomach (V{sub 35}, V{sub 45}), mean liver dose, liver (V{sub 35}), left kidney (V{sub 15}, V{sub 18}, V{sub 20}), and right kidney (V{sub 18}, V{sub 20}). VMAT plans significantly decreased small bowel (D{sub 10}%, D{sub 15}%), left kidney (V{sub 20}), and stomach (V{sub 45}) as compared with IMRT plans. Treatment planning and delivery times were most efficient for simple 4-field box and VMAT. Excluding patient setup and imaging, average

  17. A nucleotide-controlled conformational switch modulates the activity of eukaryotic IMP dehydrogenases.

    PubMed

    Buey, Rubén M; Fernández-Justel, David; Marcos-Alcalde, Íñigo; Winter, Graeme; Gómez-Puertas, Paulino; de Pereda, José María; Luis Revuelta, José

    2017-06-01

    Inosine-5'-monophosphate dehydrogenase (IMPDH) is an essential enzyme for nucleotide metabolism and cell proliferation. Despite IMPDH is the target of drugs with antiviral, immunosuppressive and antitumor activities, its physiological mechanisms of regulation remain largely unknown. Using the enzyme from the industrial fungus Ashbya gossypii, we demonstrate that the binding of adenine and guanine nucleotides to the canonical nucleotide binding sites of the regulatory Bateman domain induces different enzyme conformations with significantly distinct catalytic activities. Thereby, the comparison of their high-resolution structures defines the mechanistic and structural details of a nucleotide-controlled conformational switch that allosterically modulates the catalytic activity of eukaryotic IMPDHs. Remarkably, retinopathy-associated mutations lie within the mechanical hinges of the conformational change, highlighting its physiological relevance. Our results expand the mechanistic repertoire of Bateman domains and pave the road to new approaches targeting IMPDHs.

  18. Functional modules and structural basis of conformational coupling in mitochondrial complex I.

    PubMed

    Hunte, Carola; Zickermann, Volker; Brandt, Ulrich

    2010-07-23

    Proton-pumping respiratory complex I is one of the largest and most complicated membrane protein complexes. Its function is critical for efficient energy supply in aerobic cells, and malfunctions are implicated in many neurodegenerative disorders. Here, we report an x-ray crystallographic analysis of mitochondrial complex I. The positions of all iron-sulfur clusters relative to the membrane arm were determined in the complete enzyme complex. The ubiquinone reduction site resides close to 30 angstroms above the membrane domain. The arrangement of functional modules suggests conformational coupling of redox chemistry with proton pumping and essentially excludes direct mechanisms. We suggest that a approximately 60-angstrom-long helical transmission element is critical for transducing conformational energy to proton-pumping elements in the distal module of the membrane arm.

  19. Energy transfer and concentration-dependent conformational modulation: a porphyrin-containing [3]rotaxane.

    PubMed

    Wang, Xiao-Ye; Han, Ji-Min; Pei, Jian

    2012-10-01

    A zinc porphyrin-containing [3]rotaxane A was synthesized through a copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction. Energy donors and acceptor porphyrin were introduced to dibenzo[24]crown-8 (DB24C8) and dibenzyl ammonium (DBA) units of [3]rotaxane A to understand the intramolecular energy transfer process. Investigations of the photophysical properties of [3]rotaxane A demonstrated that the intramolecular efficient energy transfer readily occurred from the donors on the wheels to the porphyrin center on the axis. The fluorescence of energy donors in the region of 400 to 450 nm was efficiently absorbed by the porphyrin acceptor under irradiation at 345 nm, and finally a red light emission at about 600 nm was achieved. Further investigation indicated that the conformation of [3]rotaxane A was self-modulated by changing its concentration in CH(2)Cl(2). The triazole groups on the wheel coordinated or uncoordinated to Zn(2+) through intramolecular self-coordination with the change in the concentration of [3]rotaxane A in CH(2)Cl(2). Therefore, this conformational change was reversible in a non-coordinating solvent such as CH(2)Cl(2) but inhibited in a coordinating solvent such as THF. Such interesting behaviors were rarely observed in porphyrin derivatives. This self-modulation feature opens up the possibility of controlling molecular conformation by varying concentration. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. Dynamic and Progressive Control of DNA Origami Conformation by Modulating DNA Helicity with Chemical Adducts.

    PubMed

    Chen, Haorong; Zhang, Hanyu; Pan, Jing; Cha, Tae-Gon; Li, Shiming; Andréasson, Joakim; Choi, Jong Hyun

    2016-05-24

    DNA origami has received enormous attention for its ability to program complex nanostructures with a few nanometer precision. Dynamic origami structures that change conformation in response to environmental cues or external signals hold great promises in sensing and actuation at the nanoscale. The reconfiguration mechanism of existing dynamic origami structures is mostly limited to single-stranded hinges and relies almost exclusively on DNA hybridization or strand displacement. Here, we show an alternative approach by demonstrating on-demand conformation changes with DNA-binding molecules, which intercalate between base pairs and unwind DNA double helices. The unwinding effect modulates the helicity mismatch in DNA origami, which significantly influences the internal stress and the global conformation of the origami structure. We demonstrate the switching of a polymerized origami nanoribbon between different twisting states and a well-constrained torsional deformation in a monomeric origami shaft. The structural transformation is shown to be reversible, and binding isotherms confirm the reconfiguration mechanism. This approach provides a rapid and reversible means to change DNA origami conformation, which can be used for dynamic and progressive control at the nanoscale.

  1. Modulation of Cell Proliferation and Differentiation through Substrate-dependent Changes in Fibronectin Conformation

    PubMed Central

    García, Andrés J.; Vega, María D.; Boettiger, David

    1999-01-01

    Integrin-mediated cell adhesion to extracellular matrices provides signals essential for cell cycle progression and differentiation. We demonstrate that substrate-dependent changes in the conformation of adsorbed fibronectin (Fn) modulated integrin binding and controlled switching between proliferation and differentiation. Adsorption of Fn onto bacterial polystyrene (B), tissue culture polystyrene (T), and collagen (C) resulted in differences in Fn conformation as indicated by antibody binding. Using a biochemical method to quantify bound integrins in cultured cells, we found that differences in Fn conformation altered the quantity of bound α5 and β1 integrin subunits but not αv or β3. C2C12 myoblasts grown on these Fn-coated substrates proliferated to different levels (B > T > C). Immunostaining for muscle-specific myosin revealed minimal differentiation on B, significant levels on T, and extensive differentiation on C. Differentiation required binding to the RGD cell binding site in Fn and was blocked by antibodies specific for this site. Switching between proliferation and differentiation was controlled by the levels of α5β1 integrin bound to Fn, and differentiation was inhibited by anti-α5, but not anti-αv, antibodies, suggesting distinct integrin-mediated signaling pathways. Control of cell proliferation and differentiation through conformational changes in extracellular matrix proteins represents a versatile mechanism to elicit specific cellular responses for biological and biotechnological applications. PMID:10069818

  2. CEF1/CDC5 alleles modulate transitions between catalytic conformations of the spliceosome

    PubMed Central

    Query, Charles C.; Konarska, Maria M.

    2012-01-01

    Conformational change within the spliceosome is required between the first and second catalytic steps of pre-mRNA splicing. A prior genetic screen for suppressors of an intron mutant that stalls between the two steps yielded both prp8 and non-prp8 alleles that suppressed second-step splicing defects. We have now identified the strongest non-prp8 suppressors as alleles of the NTC (Prp19 complex) component, CEF1. These cef1 alleles generally suppress second-step defects caused by a variety of intron mutations, mutations in U6 snRNA, or deletion of the second-step protein factor Prp17, and they can activate alternative 3′ splice sites. Genetic and functional interactions between cef1 and prp8 alleles suggest that they modulate the same event(s) in the first-to-second-step transition, most likely by stabilization of the second-step spliceosome; in contrast, alleles of U6 snRNA that also alter this transition modulate a distinct event, most likely by stabilization of the first-step spliceosome. These results implicate a myb-like domain of Cef1/CDC5 in interactions that modulate conformational states of the spliceosome and suggest that alteration of these events affects splice site use, resulting in alternative splicing-like patterns in yeast. PMID:22408182

  3. Retrospective evaluation of dosimetric quality for prostate carcinomas treated with 3D conformal, intensity modulated and volumetric modulated arc radiotherapy

    PubMed Central

    Crowe, Scott B; Kairn, Tanya; Middlebrook, Nigel; Hill, Brendan; Christie, David R H; Knight, Richard T; Kenny, John; Langton, Christian M; Trapp, Jamie V

    2013-01-01

    Introduction This study examines and compares the dosimetric quality of radiotherapy treatment plans for prostate carcinoma across a cohort of 163 patients treated across five centres: 83 treated with three-dimensional conformal radiotherapy (3DCRT), 33 treated with intensity modulated radiotherapy (IMRT) and 47 treated with volumetric modulated arc therapy (VMAT). Methods Treatment plan quality was evaluated in terms of target dose homogeneity and organs at risk (OAR), through the use of a set of dose metrics. These included the mean, maximum and minimum doses; the homogeneity and conformity indices for the target volumes; and a selection of dose coverage values that were relevant to each OAR. Statistical significance was evaluated using two-tailed Welch's T-tests. The Monte Carlo DICOM ToolKit software was adapted to permit the evaluation of dose metrics from DICOM data exported from a commercial radiotherapy treatment planning system. Results The 3DCRT treatment plans offered greater planning target volume dose homogeneity than the other two treatment modalities. The IMRT and VMAT plans offered greater dose reduction in the OAR: with increased compliance with recommended OAR dose constraints, compared to conventional 3DCRT treatments. When compared to each other, IMRT and VMAT did not provide significantly different treatment plan quality for like-sized tumour volumes. Conclusions This study indicates that IMRT and VMAT have provided similar dosimetric quality, which is superior to the dosimetric quality achieved with 3DCRT. PMID:26229621

  4. Retrospective evaluation of dosimetric quality for prostate carcinomas treated with 3D conformal, intensity modulated and volumetric modulated arc radiotherapy

    SciTech Connect

    Crowe, Scott B; Kairn, Tanya; Middlebrook, Nigel; Hill, Brendan; Christie, David R H; Knight, Richard T; Kenny, John; Langton, Christian M; Trapp, Jamie V

    2013-12-15

    This study examines and compares the dosimetric quality of radiotherapy treatment plans for prostate carcinoma across a cohort of 163 patients treated across five centres: 83 treated with three-dimensional conformal radiotherapy (3DCRT), 33 treated with intensity modulated radiotherapy (IMRT) and 47 treated with volumetric modulated arc therapy (VMAT). Treatment plan quality was evaluated in terms of target dose homogeneity and organs at risk (OAR), through the use of a set of dose metrics. These included the mean, maximum and minimum doses; the homogeneity and conformity indices for the target volumes; and a selection of dose coverage values that were relevant to each OAR. Statistical significance was evaluated using two-tailed Welch's T-tests. The Monte Carlo DICOM ToolKit software was adapted to permit the evaluation of dose metrics from DICOM data exported from a commercial radiotherapy treatment planning system. The 3DCRT treatment plans offered greater planning target volume dose homogeneity than the other two treatment modalities. The IMRT and VMAT plans offered greater dose reduction in the OAR: with increased compliance with recommended OAR dose constraints, compared to conventional 3DCRT treatments. When compared to each other, IMRT and VMAT did not provide significantly different treatment plan quality for like-sized tumour volumes. This study indicates that IMRT and VMAT have provided similar dosimetric quality, which is superior to the dosimetric quality achieved with 3DCRT.

  5. Integrable perturbations of conformal field theories and Yetter-Drinfeld modules

    SciTech Connect

    Bücher, David; Runkel, Ingo

    2014-11-15

    In this paper we relate a problem in representation theory — the study of Yetter-Drinfeld modules over certain braided Hopf algebras — to a problem in two-dimensional quantum field theory, namely, the identification of integrable perturbations of a conformal field theory. A prescription that parallels Lusztig's construction allows one to read off the quantum group governing the integrable symmetry. As an example, we illustrate how the quantum group for the loop algebra of sl(2) appears in the integrable structure of the perturbed uncompactified and compactified free boson.

  6. Four types of (super)conformal mechanics: D-module reps and invariant actions

    NASA Astrophysics Data System (ADS)

    Holanda, N. L.; Toppan, F.

    2014-06-01

    (Super)conformal mechanics in one dimension is induced by parabolic or hyperbolic/trigonometric transformations, either homogeneous (for a scaling dimension λ) or inhomogeneous (at λ = 0, with ρ an inhomogeneity parameter). Four types of (super)conformal actions are thus obtained. With the exclusion of the homogeneous parabolic case, dimensional constants are present. Both the inhomogeneity and the insertion of λ generalize the construction of Papadopoulos [Class. Quant. Grav. 30, 075018 (2013); e-print arXiv:1210.1719]. Inhomogeneous D-module reps are presented for the d = 1 superconformal algebras osp(1|2), sl(2|1), B(1, 1), and A(1, 1). For centerless superVirasoro algebras, D-module reps are presented (in the homogeneous case for N=1,2,3,4; in the inhomogeneous case for N=1,2,3). The four types of d = 1 superconformal actions are derived for N=1,2,4 systems. When N=4, the homogeneously induced actions are D(2, 1; α)-invariant (α is critically linked to λ); the inhomogeneously induced actions are A(1, 1)-invariant.

  7. Elucidating Ligand-Modulated Conformational Landscape of GPCRs Using Cloud-Computing Approaches.

    PubMed

    Shukla, Diwakar; Lawrenz, Morgan; Pande, Vijay S

    2015-01-01

    G-protein-coupled receptors (GPCRs) are a versatile family of membrane-bound signaling proteins. Despite the recent successes in obtaining crystal structures of GPCRs, much needs to be learned about the conformational changes associated with their activation. Furthermore, the mechanism by which ligands modulate the activation of GPCRs has remained elusive. Molecular simulations provide a way of obtaining detailed an atomistic description of GPCR activation dynamics. However, simulating GPCR activation is challenging due to the long timescales involved and the associated challenge of gaining insights from the "Big" simulation datasets. Here, we demonstrate how cloud-computing approaches have been used to tackle these challenges and obtain insights into the activation mechanism of GPCRs. In particular, we review the use of Markov state model (MSM)-based sampling algorithms for sampling milliseconds of dynamics of a major drug target, the G-protein-coupled receptor β2-AR. MSMs of agonist and inverse agonist-bound β2-AR reveal multiple activation pathways and how ligands function via modulation of the ensemble of activation pathways. We target this ensemble of conformations with computer-aided drug design approaches, with the goal of designing drugs that interact more closely with diverse receptor states, for overall increased efficacy and specificity. We conclude by discussing how cloud-based approaches present a powerful and broadly available tool for studying the complex biological systems routinely.

  8. Conformational-Modulated Enzyme Catalysis: Generalized Michaelis-Menten Equation and Single Molecule Measurements

    NASA Astrophysics Data System (ADS)

    Cao, Jianshu

    2012-02-01

    The Michaelis-Menten (MM) equation is a basic rate equation to describe the substrate-dependence of enzymatic reactions; therefore, it is important to establish the validity of the MM-equation for complex enzymatic reactions and derive the correction terms when the MM equation fails. Indeed, single molecule experiments reveal complex catalytic behaviors induced by conformational dynamics and possible deviations from the MM rate equation. To model such complex catalytic reactions, we construct a generic kinetic network model characterized by multiple intermediates and multiple conformational sub-states and, by solving for the turnover rate of this network, we extend the MM equation into a general form. The generalized MM equation predicts that (i) the MM equation holds under detailed balance and (ii) the correction to the MM expression depends on the unbalanced conformational currents. Using these predictions, we can establish a relationship between the substrate-dependence of the turnover rate and the connectivity of the enzymatic network. To confirm these predictions, we propose several single molecule indicators to test the violations of detailed balance. However, these single molecule indicators may be difficult to resolve from noisy single molecule data. To address these issues, we propose information theory based data analysis methods to process single molecule time series, and apply the Baysian technique to analyze a single protein fluctuation experiment. [4pt] [1] Jianlan Wu and Jianshu Cao, ``Generalized Michaelis-Menten equation for conformation modulated monomeric enzymes,'' in Adv. Chem. Phys. (2011) [0pt] [2] Jianshu Cao, ``Michaelis-Menten Equation and Detailed Balance in Enzymatic Networks,'' JPC B, P5493 (2001) [0pt] [3] Jianshu Cao and Rob Silbey, ``Generic models of single molecule kinetics: self-consistent solutions,'' JPC B, 112, p12876 (2008) feature article [0pt] [4] Jim Witkoskie and Jianshu Cao, ``Analysis of the entire sequence of a single

  9. Smooth muscle myosin light chain kinase, supramolecular organization, modulation of activity, and related conformational changes.

    PubMed Central

    Filenko, A M; Danilova, V M; Sobieszek, A

    1997-01-01

    It has recently been suggested that activation of smooth muscle myosin light chain kinase (MLCK) can be modulated by formation of supramolecular structures (Sobieszek, A. 1991. Regulation of smooth muscle myosin light chain kinase. Allosteric effects and co-operative activation by CaM. J. Mol. Biol. 220:947-957). The present light scattering data demonstrate that the inactive (calmodulin-free) MLCK apoenzyme exists in solution as a mixture of oligomeric (2% by weight), dimeric (53%), and monomeric (45%) species at physiological ionic strength (160 mM salt). These long-living assemblies, the lifetime of which was measured by minutes, were in equilibrium with each other. The most likely form of the oligomer was a spiral-like hexamer, the dimensions of which fit very well the helical structure of self-assembled myosin filaments (Sobieszek, A. 1972. Cross-bridges on self-assembled smooth muscle myosin filaments. J. Mol. Biol. 70:741-744). After activation of the kinase by calmodulin (CaM) we could not detect any appreciable changes in the distribution of the kinase species either when the kinase was saturated with CaM or when its molar concentration exceeded that of CaM. Our fluorescent measurements suggest that the earlier observed inhibition of kinase at substoichiometric amounts of CaM (Sobieszek, A., A. Strobl, B. Ortner, and E. Babiychuk. 1993. Ca2+-calmodulin-dependent modification of smooth-muscle myosin light chain kinase leading to its co-operative activation by calmodulin. Biochem. J. 295:405-411) is associated with slow conformational change(s) of the activated (CaM-bound) kinase molecules. Such conformational rearrangements also took place with equimolar kinase to CaM; however, in this case there was no decrease in MLCK activity. The nature of these conformational changes, which are accompanied by reduction of the kinase for CaM affinity, is discussed. PMID:9284326

  10. Postprandial apoE Isoform and Conformational Changes Associated with VLDL Lipolysis Products Modulate Monocyte Inflammation

    PubMed Central

    den Hartigh, Laura J.; Altman, Robin; Hutchinson, Romobia; Petrlova, Jitka; Budamagunta, Madhu S.; Tetali, Sarada D.; Lagerstedt, Jens O.; Voss, John C.; Rutledge, John C.

    2012-01-01

    Objective Postprandial hyperlipemia, characterized by increased circulating very low-density lipoproteins (VLDL) and circulating lipopolysaccharide (LPS), has been proposed as a mechanism of vascular injury. Our goal was to examine the interactions between postprandial lipoproteins, LPS, and apoE3 and apoE4 on monocyte activation. Methods and Results We showed that apoE3 complexed to phospholipid vesicles attenuates LPS-induced THP-1 monocyte cytokine expression, while apoE4 increases expression. ELISA revealed that apoE3 binds to LPS with higher affinity than apoE4. Electron paramagnetic resonance (EPR) spectroscopy of site-directed spin labels placed on specific amino acids of apoE3 showed that LPS interferes with conformational changes normally associated with lipid binding. Specifically, compared to apoE4, apoE bearing the E3-like R112→Ser mutation displays increased self association when exposed to LPS, consistent with a stronger apoE3-LPS interaction. Additionally, lipolysis of fasting VLDL from normal human donors attenuated LPS-induced TNFα secretion from monocytes to a greater extent than postprandial VLDL, an effect partially reversed by blocking apoE. This effect was reproduced using fasting VLDL lipolysis products from e3/e3 donors, but not from e4/e4 subjects, suggesting that apoE3 on fasting VLDL prevents LPS-induced inflammation more readily than apoE4. Conclusion Postprandial apoE isoform and conformational changes associated with VLDL dramatically modulate vascular inflammation. PMID:23209766

  11. Integral dose in three-dimensional conformal radiotherapy, intensity-modulated radiotherapy and helical tomotherapy.

    PubMed

    Yang, R; Xu, S; Jiang, W; Xie, C; Wang, J

    2009-11-01

    To evaluate the integral dose to organs at risk (OARs), normal tissue and the whole body in three-dimensional conformal radiotherapy (3DCRT), intensity-modulated radiotherapy (IMRT) and helical tomotherapy for whole pelvic radiotherapy (WPRT) in postoperative endometrial cancer patients. We selected 10 patients with endometrial cancer undergoing postoperative WPRT. Plans of 6MV-3DCRT, 18MV-3DCRT, 6MV-IMRT, 18MV-IMRT and helical tomotherapy were developed for each patient. The integral doses to OARs, normal tissue and the whole body were compared. Compared with 3DCRT, both IMRT and helical tomotherapy significantly improved dose conformity and the integral doses to OARs (8.8-29.9%, P<0.05). Compared with 6MV-3DCRT, IMRT resulted in 13.2 and 11.0% lower integral doses to normal tissue and the whole body, respectively (P=0.00), whereas no significant difference was found with helical tomotherapy. Compared directly with IMRT, helical tomotherapy reduced the integral doses to the rectum and bladder. However, the integral doses to normal tissue were 13.9 and 17.1% higher than 6MV-IMRT and 18MV-IMRT plans, respectively (P=0.00); the integral doses to pelvic bones also slightly increased with helical tomotherapy. The use of 18MV resulted in 5.8 and 2.7% lower integral doses to normal tissue and 4.8 and 2.1% lower integral doses to the whole body in the 3DCRT and IMRT plans, respectively (P=0.00). Results show that IMRT and helical tomotherapy offer better conformity and lower integral doses to OARs for postoperative WPRT of endometrial cancers compared with 3DCRT. The integral doses to normal tissue and the whole body were significantly lower with IMRT, whereas no significant difference was found with helical tomotherapy compared with 6MV-3DCRT. Compared directly with IMRT, helical tomotherapy further reduced the integral doses to the rectum and bladder, at the expense of a slightly higher integral dose to pelvic bones and normal tissue. The use of 18MV improved the

  12. Intensity-Modulated vs. Conformal Radiotherapy of Parotid Gland Tumors: Potential Impact on Hearing Loss

    SciTech Connect

    Lamers-Kuijper, E. Schwarz, M.; Rasch, C.; Mijnheer, B.

    2007-01-01

    In 3-dimensional (3D) conformal radiotherapy of parotid gland tumors, little effort is made to avoid the auditory system or the oral cavity. Damage may occur when the ear is located inside the treatment field. The purpose of this study was to design and evaluate an intensity-modulation radiotherapy (IMRT) class solution, and to compare this technique to a 3D conformal approach with respect to hearing loss. Twenty patients with parotid gland cancer were retrospectively planned with 2 different techniques using the original planning target volume (PTV). First, a conventional technique using a wedged beam pair was applied, yielding a dose distribution conformal to the shape of the PTV. Next, an IMRT technique using a fluence map optimization with predefined constraints was designed. A dose of 66 Gy in the PTV was given at the International Commission on Radiation Units and Measures (ICRU) dose prescription point. Dose-volume histograms of the PTV and organs at risk (OARs), such as auditory system, oral cavity, and spinal cord, were compared. The dose in the OARs was lower in the IMRT plans. The mean volume of the middle ear receiving a dose higher than 50 Gy decreased from 66.5% to 33.4%. The mean dose in the oral cavity decreased from 19.4 Gy to 16.6 Gy. The auditory system can be spared if the distance between the inner ear and the PTV is 0.6 cm or larger, and if the overlap between the middle ear and the PTV is smaller than 10%. The maximum dose in the spinal cord was below 40 Gy in all treatment plans. The mean volume of the PTV receiving less than 95% of the prescribed dose increased in the IMRT plan slightly from 3.3% to 4.3 % (p = 0.01). The mean volume receiving more than 107% increased from 0.9% to 2.5% (p = 0.02). It can be concluded that the auditory system, as well as the oral cavity, can be spared with IMRT, but at the cost of a slightly larger dose inhomogeneity in the PTV. The IMRT technique can therefore, in most cases, be recommended as the treatment

  13. Comparison of intensity-modulated tomotherapy with stereotactically guided conformal radiotherapy for brain tumors.

    PubMed

    Khoo, V S; Oldham, M; Adams, E J; Bedford, J L; Webb, S; Brada, M

    1999-09-01

    Intensity-modulated radiotherapy (IMRT) offers the potential to more closely conform dose distributions to the target, and spare organs at risk (OAR). Its clinical value is still being defined. The present study aims to compare IMRT with stereotactically guided conformal radiotherapy (SCRT) for patients with medium size convex-shaped brain tumors. Five patients planned with SCRT were replanned with the IMRT-tomotherapy method using the Peacock system (Nomos Corporation). The planning target volume (PTV) and relevant OAR were assessed, and compared relative to SCRT plans using dose statistics, dose-volume histograms (DVH), and the Radiation Therapy Oncology Group (RTOG) stereotactic radiosurgery criteria. The median and mean PTV were 78 cm3 and 85 cm3 respectively (range 62-119 cm3). The differences in PTV doses for the whole group (Peacock-SCRT +/-1 SD) were 2%+/-1.8 (minimum PTV), and 0.1%+/-1.9 (maximum PTV). The PTV homogeneity achieved by Peacock was 12.1%+/-1.7 compared to 13.9%+/-1.3 with SCRT. Using RTOG guidelines, Peacock plans provided acceptable PTV coverage for all 5/5 plans compared to minor coverage deviations in 4/5 SCRT plans; acceptable homogeneity index for both plans (Peacock = 1.1 vs. SCRT = 1.2); and comparable conformity index (1.4 each). As a consequence of the transaxial method of arc delivery, the optic nerves received mean and maximum doses that were 11.1 to 11.6%, and 10.3 to 15.2% higher respectively with Peacock plan. The maximum optic lens, and brainstem dose were 3.1 to 4.8% higher, and 0.6% lower respectively with Peacock plan. However, all doses remained below the tolerance threshold (5 Gy for lens, and 50 Gy for optic nerves) and were clinically acceptable. The Peacock method provided improved PTV coverage, albeit small, in this group of convex tumors. Although the OAR doses were higher using the Peacock plans, all doses remained within the clinically defined threshold and were clinically acceptable. Further improvements may be

  14. Dosimetric effect of Elekta Beam modulator micromultileaf in three-dimensional conformal radiotherapy and intensity-modulated radiotherapy for prostate cancer.

    PubMed

    Carosi, Alessandra; Ingrosso, Gianluca; Ponti, Elisabetta; Tolu, Barbara; Murgia, Alessandra; di Cristino, Daniela; Santoni, Riccardo

    2014-01-01

    The purpose of this study is to analyze the dosimetric effect of Elekta Beam Modulator in 3-dimensional conformal radiation therapy (3DCRT) and in intensity-modulated radiation therapy (IMRT) for localized prostate cancer. We compared treatment plans developed with 2 different Elekta multileaf collimators (MLC): Beam Modulator micro-MLC (mMLC) (4-mm leaf width at the isocenter) and standard MLC (10-mm leaf width at the isocenter). The comparison was performed for 15 patients with localized prostate cancer in 3DCRT and IMRT delivery; a total of 60 treatment plans were processed. The dose-volume histograms were used to provide the quantitative comparison between plans. In particular, we analyzed differences between rectum and bladder sparing in terms of a set of appropriate Vx (percentage of organ at risk [OAR] volume receiving the x dose) and differences between target conformity and coverage in terms of coverage factor and conformation number. Our analysis demonstrates that in 3DCRT there is an advantage in the use of Elekta Beam Modulator mMLC in terms of organ sparing; in particular, a significant decrease in rectal V60 and V50 (p = 0.001) and in bladder V70 and V65 (p = 0.007 and 0.002, respectively) was found. Moreover, a better target dose conformity was obtained (p = 0.002). IMRT plans comparison demonstrated no significant differences between the use of the 4 or 10-mm MLCs. Our analysis shows that in 3DCRT the use of the Elekta Beam Modulator mMLC gives a gain in target conformity and in OARs dose sparing whereas in IMRT plans there is no advantage.

  15. Dosimetric effect of Elekta Beam Modulator micromultileaf in three-dimensional conformal radiotherapy and intensity-modulated radiotherapy for prostate cancer

    SciTech Connect

    Carosi, Alessandra Ingrosso, Gianluca; Ponti, Elisabetta; Tolu, Barbara; Murgia, Alessandra; Cristino, Daniela di; Santoni, Riccardo

    2014-07-01

    The purpose of this study is to analyze the dosimetric effect of Elekta Beam Modulator in 3-dimensional conformal radiation therapy (3DCRT) and in intensity-modulated radiation therapy (IMRT) for localized prostate cancer. We compared treatment plans developed with 2 different Elekta multileaf collimators (MLC): Beam Modulator micro-MLC (mMLC) (4-mm leaf width at the isocenter) and standard MLC (10-mm leaf width at the isocenter). The comparison was performed for 15 patients with localized prostate cancer in 3DCRT and IMRT delivery; a total of 60 treatment plans were processed. The dose-volume histograms were used to provide the quantitative comparison between plans. In particular, we analyzed differences between rectum and bladder sparing in terms of a set of appropriate Vx (percentage of organ at risk [OAR] volume receiving the x dose) and differences between target conformity and coverage in terms of coverage factor and conformation number. Our analysis demonstrates that in 3DCRT there is an advantage in the use of Elekta Beam Modulator mMLC in terms of organ sparing; in particular, a significant decrease in rectal V{sub 60} and V{sub 50} (p = 0.001) and in bladder V{sub 70} and V{sub 65} (p = 0.007 and 0.002, respectively) was found. Moreover, a better target dose conformity was obtained (p = 0.002). IMRT plans comparison demonstrated no significant differences between the use of the 4 or 10-mm MLCs. Our analysis shows that in 3DCRT the use of the Elekta Beam Modulator mMLC gives a gain in target conformity and in OARs dose sparing whereas in IMRT plans there is no advantage.

  16. Detection of Mutant Huntingtin Aggregation Conformers and Modulation of SDS-Soluble Fibrillar Oligomers by Small Molecules

    PubMed Central

    Sontag, Emily Mitchell; Lotz, Gregor P.; Yang, Guocheng; Sontag, Christopher J.; Cummings, Brian J.; Glabe, Charles G.; Muchowski, Paul J.; Thompson, Leslie Michels

    2012-01-01

    The Huntington’s disease (HD) mutation leads to a complex process of Huntingtin (Htt) aggregation into multimeric species that eventually form visible inclusions in cytoplasm, nuclei and neuronal processes. One hypothesis is that smaller, soluble forms of amyloid proteins confer toxic effects and contribute to early cell dysfunction. However, analysis of mutant Htt aggregation intermediates to identify conformers that may represent toxic forms of the protein and represent potential drug targets remains difficult. We performed a detailed analysis of aggregation conformers in multiple in vitro, cell and ex vivo models of HD. Conformation-specific antibodies were used to identify and characterize aggregation species, allowing assessment of multiple conformers present during the aggregation process. Using a series of assays together with these antibodies, several forms could be identified. Fibrillar oligomers, defined as having a β-sheet rich conformation, are observed in vitro using recombinant protein and in protein extracts from cells in culture or mouse brain and shown to be globular, soluble and non-sedimentable structures. Compounds previously described to modulate visible inclusion body formation and reduce toxicity in HD models were also tested and consistently found to alter the formation of fibrillar oligomers. Interestingly, these compounds did not alter the rate of visible inclusion formation, indicating that fibrillar oligomers are not necessarily the rate limiting step of inclusion body formation. Taken together, we provide insights into the structure and formation of mutant Htt fibrillar oligomers that are modulated by small molecules with protective potential in HD models. PMID:24086178

  17. Leaf position error during conformal dynamic arc and intensity modulated arc treatments.

    PubMed

    Ramsey, C R; Spencer, K M; Alhakeem, R; Oliver, A L

    2001-01-01

    Conformal dynamic arc (CD-ARC) and intensity modulated arc treatments (IMAT) are both treatment modalities where the multileaf collimator (MLC) can change leaf position dynamically during gantry rotation. These treatment techniques can be used to generate complex isodose distributions, similar to those used in fix-gantry intensity modulation. However, a beam-hold delay cannot be used during CD-ARC or IMAT treatments to reduce spatial error. Consequently, a certain amount of leaf position error will have to be accepted in order to make the treatment deliverable. Measurements of leaf position accuracy were taken with leaf velocities ranging from 0.3 to 3.0 cm/s. The average and maximum leaf position errors were measured, and a least-squares linear regression analysis was performed on the measured data to determine the MLC velocity error coefficient. The average position errors range from 0.03 to 0.21 cm, with the largest deviations occurring at the maximum achievable leaf velocity (3.0 cm/s). The measured MLC velocity error coefficient was 0.0674 s for a collimator rotation of 0 degrees and 0.0681 s for a collimator rotation of 90 degrees. The distribution in leaf position error between the 0 degrees and 90 degrees collimator rotations was within statistical uncertainty. A simple formula was developed based on these results for estimating the velocity-dependent dosimetric error. Using this technique, a dosimetric error index for plan evaluation can be calculated from the treatment time and the dynamic MLC leaf controller file.

  18. Estimating the costs of intensity-modulated and 3-dimensional conformal radiotherapy in Ontario.

    PubMed

    Yong, J H E; McGowan, T; Redmond-Misner, R; Beca, J; Warde, P; Gutierrez, E; Hoch, J S

    2016-06-01

    Radiotherapy is a common treatment for many cancers, but up-to-date estimates of the costs of radiotherapy are lacking. In the present study, we estimated the unit costs of intensity-modulated radiotherapy (imrt) and 3-dimensional conformal radiotherapy (3D-crt) in Ontario. An activity-based costing model was developed to estimate the costs of imrt and 3D-crt in prostate cancer. It included the costs of equipment, staff, and supporting infrastructure. The framework was subsequently adapted to estimate the costs of radiotherapy in breast cancer and head-and-neck cancer. We also tested various scenarios by varying the program maturity and the use of volumetric modulated arc therapy (vmat) alongside imrt. From the perspective of the health care system, treating prostate cancer with imrt and 3D-crt respectively cost $12,834 and $12,453 per patient. The cost of radiotherapy ranged from $5,270 to $14,155 and was sensitive to analytic perspective, radiation technique, and disease site. Cases of head-and-neck cancer were the most costly, being driven by treatment complexity and fractions per treatment. Although imrt was more costly than 3D-crt, its cost will likely decline over time as programs mature and vmat is incorporated. Our costing model can be modified to estimate the costs of 3D-crt and imrt for various disease sites and settings. The results demonstrate the important role of capital costs in studies of radiotherapy cost from a health system perspective, which our model can accommodate. In addition, our study established the need for future analyses of imrt cost to consider how vmat affects time consumption.

  19. Estimating the costs of intensity-modulated and 3-dimensional conformal radiotherapy in Ontario

    PubMed Central

    Yong, J.H.E.; McGowan, T.; Redmond-Misner, R.; Beca, J.; Warde, P.; Gutierrez, E.; Hoch, J.S.

    2016-01-01

    Background Radiotherapy is a common treatment for many cancers, but up-to-date estimates of the costs of radiotherapy are lacking. In the present study, we estimated the unit costs of intensity-modulated radiotherapy (imrt) and 3-dimensional conformal radiotherapy (3D-crt) in Ontario. Methods An activity-based costing model was developed to estimate the costs of imrt and 3D-crt in prostate cancer. It included the costs of equipment, staff, and supporting infrastructure. The framework was subsequently adapted to estimate the costs of radiotherapy in breast cancer and head-and-neck cancer. We also tested various scenarios by varying the program maturity and the use of volumetric modulated arc therapy (vmat) alongside imrt. Results From the perspective of the health care system, treating prostate cancer with imrt and 3D-crt respectively cost $12,834 and $12,453 per patient. The cost of radiotherapy ranged from $5,270 to $14,155 and was sensitive to analytic perspective, radiation technique, and disease site. Cases of head-and-neck cancer were the most costly, being driven by treatment complexity and fractions per treatment. Although imrt was more costly than 3D-crt, its cost will likely decline over time as programs mature and vmat is incorporated. Conclusions Our costing model can be modified to estimate the costs of 3D-crt and imrt for various disease sites and settings. The results demonstrate the important role of capital costs in studies of radiotherapy cost from a health system perspective, which our model can accommodate. In addition, our study established the need for future analyses of imrt cost to consider how vmat affects time consumption. PMID:27330359

  20. Carcinoma of the anal canal: Intensity modulated radiation therapy (IMRT) versus three-dimensional conformal radiation therapy (3DCRT)

    SciTech Connect

    Sale, Charlotte; Moloney, Phillip; Mathlum, Maitham

    2013-12-15

    Patients with anal canal carcinoma treated with standard conformal radiotherapy frequently experience severe acute and late toxicity reactions to the treatment area. Roohipour et al. (Dis Colon Rectum 2008; 51: 147–53) stated a patient's tolerance of chemoradiation to be an important prediction of treatment success. A new intensity modulated radiation therapy (IMRT) technique for anal carcinoma cases has been developed at the Andrew Love Cancer Centre aimed at reducing radiation to surrounding healthy tissue. A same-subject repeated measures design was used for this study, where five anal carcinoma cases at the Andrew Love Cancer Centre were selected. Conformal and IMRT plans were generated and dosimetric evaluations were performed. Each plan was prescribed a total of 54 Gray (Gy) over a course of 30 fractions to the primary site. The IMRT plans resulted in improved dosimetry to the planning target volume (PTV) and reduction in radiation to the critical structures (bladder, external genitalia and femoral heads). Statistically there was no difference between the IMRT and conformal plans in the dose to the small and large bowel; however, the bowel IMRT dose–volume histogram (DVH) doses were consistently lower. The IMRT plans were superior to the conformal plans with improved dose conformity and reduced radiation to the surrounding healthy tissue. Anecdotally it was found that patients tolerated the IMRT treatment better than the three-dimensional (3D) conformal radiation therapy. This study describes and compares the planning techniques.

  1. Carcinoma of the anal canal: Intensity modulated radiation therapy (IMRT) versus three-dimensional conformal radiation therapy (3DCRT)

    PubMed Central

    Sale, Charlotte; Moloney, Phillip; Mathlum, Maitham

    2013-01-01

    Introduction Patients with anal canal carcinoma treated with standard conformal radiotherapy frequently experience severe acute and late toxicity reactions to the treatment area. Roohipour et al. (Dis Colon Rectum 2008; 51: 147–53) stated a patient's tolerance of chemoradiation to be an important prediction of treatment success. A new intensity modulated radiation therapy (IMRT) technique for anal carcinoma cases has been developed at the Andrew Love Cancer Centre aimed at reducing radiation to surrounding healthy tissue. Methods A same-subject repeated measures design was used for this study, where five anal carcinoma cases at the Andrew Love Cancer Centre were selected. Conformal and IMRT plans were generated and dosimetric evaluations were performed. Each plan was prescribed a total of 54 Gray (Gy) over a course of 30 fractions to the primary site. Results The IMRT plans resulted in improved dosimetry to the planning target volume (PTV) and reduction in radiation to the critical structures (bladder, external genitalia and femoral heads). Statistically there was no difference between the IMRT and conformal plans in the dose to the small and large bowel; however, the bowel IMRT dose–volume histogram (DVH) doses were consistently lower. Conclusion The IMRT plans were superior to the conformal plans with improved dose conformity and reduced radiation to the surrounding healthy tissue. Anecdotally it was found that patients tolerated the IMRT treatment better than the three-dimensional (3D) conformal radiation therapy. This study describes and compares the planning techniques. PMID:26229623

  2. Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles

    NASA Astrophysics Data System (ADS)

    Park, So-Jung; Kufareva, Irina; Abagyan, Ruben

    2010-05-01

    Nuclear receptors (NRs) are ligand dependent transcriptional factors and play a key role in reproduction, development, and homeostasis of organism. NRs are potential targets for treatment of cancer and other diseases such as inflammatory diseases, and diabetes. In this study, we present a comprehensive library of pocket conformational ensembles of thirteen human nuclear receptors (NRs), and test the ability of these ensembles to recognize their ligands in virtual screening, as well as predict their binding geometry, functional type, and relative binding affinity. 157 known NR modulators and 66 structures were used as a benchmark. Our pocket ensemble library correctly predicted the ligand binding poses in 94% of the cases. The models were also highly selective for the active ligands in virtual screening, with the areas under the ROC curves ranging from 82 to a remarkable 99%. Using the computationally determined receptor-specific binding energy offsets, we showed that the ensembles can be used for predicting selectivity profiles of NR ligands. Our results evaluate and demonstrate the advantages of using receptor ensembles for compound docking, screening, and profiling.

  3. Compact multileaf collimator for conformal and intensity modulated fast neutron therapy: Electromechanical design and validation

    SciTech Connect

    Farr, J. B.; Maughan, R. L.; Yudelev, M.; Blosser, E.; Brandon, J.; Horste, T.; Forman, J. D.

    2006-09-15

    The electromechanical properties of a 120-leaf, high-resolution, computer-controlled, fast neutron multileaf collimator (MLC) are presented. The MLC replaces an aging, manually operated multirod collimator. The MLC leaves project 5 mm in the isocentric plane perpendicular to the beam axis. A taper is included on the leaves matching beam divergence along one axis. The 5-mm leaf projection width is chosen to give high-resolution conformality across the entire field. The maximum field size provided is 30x30 cm{sup 2}. To reduce the interleaf transmission a 0.254-mm blocking step is included. End-leaf steps totaling 0.762 mm are also provided allowing opposing leaves to close off within the primary radiation beam. The neutron MLC also includes individual 45 deg. and 60 deg. automated universal tungsten wedges. The automated high-resolution neutron collimation provides an increase in patient throughput capacity, enables a new modality, intensity modulated neutron therapy, and limits occupational radiation exposure by providing remote operation from a shielded console area.

  4. Compact multileaf collimator for conformal and intensity modulated fast neutron therapy: electromechanical design and validation.

    PubMed

    Farr, J B; Maughan, R L; Yudelev, M; Blosser, E; Brandon, J; Horste, T; Forman, J D

    2006-09-01

    The electromechanical properties of a 120-leaf, high-resolution, computer-controlled, fast neutron multileaf collimator (MLC) are presented. The MLC replaces an aging, manually operated multirod collimator. The MLC leaves project 5 mm in the isocentric plane perpendicular to the beam axis. A taper is included on the leaves matching beam divergence along one axis. The 5-mm leaf projection width is chosen to give high-resolution conformality across the entire field. The maximum field size provided is 30 x 30 cm2. To reduce the interleaf transmission a 0.254-mm blocking step is included. End-leaf steps totaling 0.762 mm are also provided allowing opposing leaves to close off within the primary radiation beam. The neutron MLC also includes individual 45 degrees and 60 degrees automated universal tungsten wedges. The automated high-resolution neutron collimation provides an increase in patient throughput capacity, enables a new modality, intensity modulated neutron therapy, and limits occupational radiation exposure by providing remote operation from a shielded console area.

  5. Disease Control After Reduced Volume Conformal and Intensity Modulated Radiation Therapy for Childhood Craniopharyngioma

    SciTech Connect

    Merchant, Thomas E.; Kun, Larry E.; Hua, Chia-Ho; Wu, Shengjie; Xiong, Xiaoping; Sanford, Robert A.; Boop, Frederick A.

    2013-03-15

    Purpose: To estimate the rate of disease control after conformal radiation therapy using reduced clinical target volume (CTV) margins and to determine factors that predict for tumor progression. Methods and Materials: Eighty-eight children (median age, 8.5 years; range, 3.2-17.6 years) received conformal or intensity modulated radiation therapy between 1998 and 2009. The study group included those prospectively treated from 1998 to 2003, using a 10-mm CTV, defined as the margin surrounding the solid and cystic tumor targeted to receive the prescription dose of 54 Gy. The CTV margin was subsequently reduced after 2003, yielding 2 groups of patients: those treated with a CTV margin greater than 5 mm (n=26) and those treated with a CTV margin less than or equal to 5 mm (n=62). Disease progression was estimated on the basis of additional variables including sex, race, extent of resection, tumor interventions, target volume margins, and frequency of weekly surveillance magnetic resonance (MR) imaging during radiation therapy. Median follow-up was 5 years. Results: There was no difference between progression-free survival rates based on CTV margins (>5 mm vs ≤5 mm) at 5 years (88.1% ± 6.3% vs 96.2% ± 4.4% [P=.6386]). There were no differences based on planning target volume (PTV) margins (or combined CTV plus PTV margins). The PTV was systematically reduced from 5 to 3 mm during the time period of the study. Factors predictive of superior progression-free survival included Caucasian race (P=.0175), no requirement for cerebrospinal fluid shunting (P=.0066), and number of surveillance imaging studies during treatment (P=.0216). Patients whose treatment protocol included a higher number of weekly surveillance MR imaging evaluations had a lower rate of tumor progression. Conclusions: These results suggest that targeted volume reductions for radiation therapy using smaller margins are feasible and safe but require careful monitoring. We are currently investigating

  6. Outcomes After Intensity-Modulated Versus Conformal Radiotherapy in Older Men With Nonmetastatic Prostate Cancer

    SciTech Connect

    Bekelman, Justin E.; Mitra, Nandita; Efstathiou, Jason; Liao Kaijun; Sunderland, Robert; Yeboa, Deborah N.; Armstrong, Katrina

    2011-11-15

    Purpose: There is little evidence comparing complications after intensity-modulated (IMRT) vs. three-dimensional conformal radiotherapy (CRT) for prostate cancer. The study objective was to test the hypothesis that IMRT, compared with CRT, is associated with a reduction in bowel, urinary, and erectile complications in elderly men with nonmetastatic prostate cancer. Methods and Materials: We undertook an observational cohort study using registry and administrative claims data from the SEER-Medicare database. We identified men aged 65 years or older diagnosed with nonmetastatic prostate cancer in the United States between 2002 and 2004 who received IMRT (n = 5,845) or CRT (n = 6,753). The primary outcome was a composite measure of bowel complications. Secondary outcomes were composite measures of urinary and erectile complications. We also examined specific subsets of bowel (proctitis/hemorrhage) and urinary (cystitis/hematuria) events within the composite complication measures. Results: IMRT was associated with reductions in composite bowel complications (24-month cumulative incidence 18.8% vs. 22.5%; hazard ratio [HR] 0.86; 95% confidence interval [CI], 0.79-0.93) and proctitis/hemorrhage (HR 0.78; 95% CI, 0.64-0.95). IMRT was not associated with rates of composite urinary complications (HR 0.93; 95% CI, 0.83-1.04) or cystitis/hematuria (HR 0.94; 95% CI, 0.83-1.07). The incidence of erectile complications involving invasive procedures was low and did not differ significantly between groups, although IMRT was associated with an increase in new diagnoses of impotence (HR 1.27, 95% CI, 1.14-1.42). Conclusion: IMRT is associated with a small reduction in composite bowel complications and proctitis/hemorrhage compared with CRT in elderly men with nonmetastatic prostate cancer.

  7. Radiation therapy of anal canal cancer: from conformal therapy to volumetric modulated arc therapy.

    PubMed

    Tozzi, Angelo; Cozzi, Luca; Iftode, Cristina; Ascolese, Annamaria; Campisi, Maria Concetta; Clerici, Elena; Comito, Tiziana; De Rose, Fiorenza; Fogliata, Antonella; Franzese, Ciro; Mancosu, Pietro; Navarria, Piera; Tomatis, Stefano; Villa, Elisa; Scorsetti, Marta

    2014-11-18

    To appraise the role of volumetric modulated arc (RapidArc, RA) in the treatment of anal canal carcinoma (ACC). A retrospective analysis has been conducted on 36 patients treated with RA since 2009 comparing outcome against a group of 28 patients treated with conformal therapy (CRT). RA treatments were prescribed with SIB technique with 59.4 Gy to the primary tumor and nodes and 49.5 Gy to the elective nodes. CRT was sequentially delivered with 45 Gy to the pelvic target and a boost of 14.4 Gy to the primary tumor. Median age of patients was 65 yrs for RA (59 yrs for CRT); 90% had Stage II-III (93% in the CRT group). No statistically significant differences were observed concerning survival or control. 5 yrs disease specific survival was 85.7% and 81.2%, loco-regional control was of 78.1% and 82.1% for RA and CRT respectively. RA treatments lead to lower incidence of higher grade of toxicity events (all retrospectively retrieved from charts as worse events). Grade 2-3 toxicity, compared to CRT, reduced from 89% to 68% for GI, from 39% to 33% for GU and from 82% to 75% for the skin. Late toxicity was as follows: 5/36 (14%) and 3/36 (8%) patients had G1 or G2 GI toxicity in the RA group (1/28 (4%) and 4/28 (14%) in the CRT group). GU late toxicity was observed only in 4/28 (14%) patients of the CRT group: 3/28 (11%) had G2 and 1/28 (4%) had G1. RA treatments of ACC patients proved to be equally effective than CRT but it was associated to a reduction of toxicity.

  8. Ligand-modulated conformational switching in a fully synthetic membrane-bound receptor

    NASA Astrophysics Data System (ADS)

    Lister, Francis G. A.; Le Bailly, Bryden A. F.; Webb, Simon J.; Clayden, Jonathan

    2017-05-01

    Signal transduction through G-protein-coupled receptors (GPCRs) involves binding to signalling molecules at the cell surface, which leads to global changes in molecular conformation that are communicated through the membrane. Artificial mechanisms for communication involving ligand binding and global conformational switching have been demonstrated so far only in the solution phase. Here, we report a membrane-bound synthetic receptor that responds to binding of a ligand by undergoing a conformational change that is propagated over several nanometres, deep into the phospholipid bilayer. Our design uses a helical foldamer core, with structural features borrowed from a class of membrane-active fungal antibiotics, ligated to a water-compatible, metal-centred binding site and a conformationally responsive fluorophore. Using the fluorophore as a remote reporter of conformational change, we find that binding of specific carboxylate ligands to a Cu(II) cofactor at the binding site perturbs the foldamer's global conformation, mimicking the conformational response of a GPCR to ligand binding.

  9. Delivery confirmation of bolus electron conformal therapy combined with intensity modulated x-ray therapy

    SciTech Connect

    Kavanaugh, James A.; Hogstrom, Kenneth R.; Fontenot, Jonas P.; Henkelmann, Gregory; Chu, Connel; Carver, Robert A.

    2013-02-15

    Purpose: The purpose of this study was to demonstrate that a bolus electron conformal therapy (ECT) dose plan and a mixed beam plan, composed of an intensity modulated x-ray therapy (IMXT) dose plan optimized on top of the bolus ECT plan, can be accurately delivered. Methods: Calculated dose distributions were compared with measured dose distributions for parotid and chest wall (CW) bolus ECT and mixed beam plans, each simulated in a cylindrical polystyrene phantom that allowed film dose measurements. Bolus ECT plans were created for both parotid and CW PTVs (planning target volumes) using 20 and 16 MeV beams, respectively, whose 90% dose surface conformed to the PTV. Mixed beam plans consisted of an IMXT dose plan optimized on top of the bolus ECT dose plan. The bolus ECT, IMXT, and mixed beam dose distributions were measured using radiographic films in five transverse and one sagittal planes for a total of 36 measurement conditions. Corrections for film dose response, effects of edge-on photon irradiation, and effects of irregular phantom optical properties on the Cerenkov component of the film signal resulted in high precision measurements. Data set consistency was verified by agreement of depth dose at the intersections of the sagittal plane with the five measured transverse planes. For these same depth doses, results for the mixed beam plan agreed with the sum of the individual depth doses for the bolus ECT and IMXT plans. The six mean measured planar dose distributions were compared with those calculated by the treatment planning system for all modalities. Dose agreement was assessed using the 4% dose difference and 0.2 cm distance to agreement. Results: For the combined high-dose region and low-dose region, pass rates for the parotid and CW plans were 98.7% and 96.2%, respectively, for the bolus ECT plans and 97.9% and 97.4%, respectively, for the mixed beam plans. For the high-dose gradient region, pass rates for the parotid and CW plans were 93.1% and 94

  10. Comparison of Three-Dimensional (3D) Conformal Proton Radiotherapy (RT), 3D Conformal Photon RT, and Intensity-Modulated RT for Retroperitoneal and Intra-Abdominal Sarcomas

    SciTech Connect

    Swanson, Erika L.; Indelicato, Daniel J.; Louis, Debbie; Flampouri, Stella; Li, Zuofeng; Morris, Christopher G.; Paryani, Nitesh; Slopsema, Roelf

    2012-08-01

    Purpose: To compare three-dimensional conformal proton radiotherapy (3DCPT), intensity-modulated photon radiotherapy (IMRT), and 3D conformal photon radiotherapy (3DCRT) to predict the optimal RT technique for retroperitoneal sarcomas. Methods and Materials: 3DCRT, IMRT, and 3DCPT plans were created for treating eight patients with retroperitoneal or intra-abdominal sarcomas. The clinical target volume (CTV) included the gross tumor plus a 2-cm margin, limited by bone and intact fascial planes. For photon plans, the planning target volume (PTV) included a uniform expansion of 5 mm. For the proton plans, the PTV was nonuniform and beam-specific. The prescription dose was 50.4 Gy/Cobalt gray equivalent CGE. Plans were normalized so that >95% of the CTV received 100% of the dose. Results: The CTV was covered adequately by all techniques. The median conformity index was 0.69 for 3DCPT, 0.75 for IMRT, and 0.51 for 3DCRT. The median inhomogeneity coefficient was 0.062 for 3DCPT, 0.066 for IMRT, and 0.073 for 3DCRT. The bowel median volume receiving 15 Gy (V15) was 16.4% for 3DCPT, 52.2% for IMRT, and 66.1% for 3DCRT. The bowel median V45 was 6.3% for 3DCPT, 4.7% for IMRT, and 15.6% for 3DCRT. The median ipsilateral mean kidney dose was 22.5 CGE for 3DCPT, 34.1 Gy for IMRT, and 37.8 Gy for 3DCRT. The median contralateral mean kidney dose was 0 CGE for 3DCPT, 6.4 Gy for IMRT, and 11 Gy for 3DCRT. The median contralateral kidney V5 was 0% for 3DCPT, 49.9% for IMRT, and 99.7% for 3DCRT. Regardless of technique, the median mean liver dose was <30 Gy, and the median cord V50 was 0%. The median integral dose was 126 J for 3DCPT, 400 J for IMRT, and 432 J for 3DCRT. Conclusions: IMRT and 3DCPT result in plans that are more conformal and homogenous than 3DCRT. Based on Quantitative Analysis of Normal Tissue Effects in Clinic benchmarks, the dosimetric advantage of proton therapy may be less gastrointestinal and genitourinary toxicity.

  11. Ligand-Dependent Modulation of G Protein Conformation Alters Drug Efficacy.

    PubMed

    Furness, Sebastian George Barton; Liang, Yi-Lynn; Nowell, Cameron James; Halls, Michelle Louise; Wookey, Peter John; Dal Maso, Emma; Inoue, Asuka; Christopoulos, Arthur; Wootten, Denise; Sexton, Patrick Michael

    2016-10-20

    G protein-coupled receptor (GPCR) signaling, mediated by hetero-trimeric G proteins, can be differentially controlled by agonists. At a molecular level, this is thought to occur principally via stabilization of distinct receptor conformations by individual ligands. These distinct conformations control subsequent recruitment of transducer and effector proteins. Here, we report that ligand efficacy at the calcitonin GPCR (CTR) is also correlated with ligand-dependent alterations to G protein conformation. We observe ligand-dependent differences in the sensitivity of the G protein ternary complex to disruption by GTP, due to conformational differences in the receptor-bound G protein hetero-trimer. This results in divergent agonist-dependent receptor-residency times for the hetero-trimeric G protein and different accumulation rates for downstream second messengers. This study demonstrates that factors influencing efficacy extend beyond receptor conformation(s) and expands understanding of the molecular basis for how G proteins control/influence efficacy. This has important implications for the mechanisms that underlie ligand-mediated biased agonism. VIDEO ABSTRACT.

  12. Molecular Environment Modulates Conformational Differences between Crystal and Solution States of Human β-Defensin 2.

    PubMed

    Li, Jianguo; Hu, Zhongqiao; Beuerman, Roger; Verma, Chandra

    2017-04-06

    Human β-defensin 2 is a cysteine-rich antimicrobial peptide. In the crystal state, the N-terminal segment (residues 1-11) exhibits a helical conformation. However, a truncated form, with four amino acids removed from the N-terminus, adopts nonhelical conformations in solution, as shown by NMR. To explore the molecular origins of these different conformations, we performed Hamiltonian replica exchange molecular dynamics simulations of the peptide in solution and in the crystal state. It is found that backbone hydration and specific protein-protein interactions are key parameters that determine the peptide conformation. The helical conformation in the crystal state mainly arises from reduced hydration as well as a salt bridge between the peptide and a symmetry-related neighboring monomer in the crystal. When the extent of hydration is reduced and the salt bridge is reintroduced artificially, the peptide is successfully folded back to the helical conformation in solution. The findings not only shed light on the development of accurate force field parameters for protein molecules but also provide practical guidance in the design of functional proteins and peptides.

  13. Remote position substituents as modulators of conformational and reactive properties of quinones. Relevance of the pi/pi intramolecular interaction.

    PubMed

    Roura-Pérez, Guillermo; Quiróz, Beatriz; Aguilar-Martínez, Martha; Frontana, Carlos; Solano, Alejandro; Gonzalez, Ignacio; Bautista-Martínez, José Antonio; Jiménez-Barbero, Jesús; Cuevas, Gabriel

    2007-03-16

    Several studies have described that quinoid rings with electron-rich olefins at remote position experience changes in their redox potential. Since the original description of these changes, different approaches have been developed to describe the properties of the binding sites of ubiquinones. The origin of this phenomenon has been attributed to lateral chain flexibility and its effect on the recognition between proteins and substrates associated with their important biological activity. The use of electrochemical-electron spin resonance (EC-ESR) assays and theoretical calculations at MP2/6-31G(d,p) and MP2/6-31++G(d,p)//MP2/6-31G(d,p) levels of several conformers of perezone [(2-(1,5-dimethyl-4-hexenyl)-3-hydroxy-5-methyl-1,4-benzoquinone] established that a weak pi-pi interaction controls not only the molecular conformation but also its diffusion coefficient and electrochemical properties. An analogous interaction can be suggested as the origin of similar properties of ubiquinone Q10. The use of nuclear magnetic resonance rendered, for the first time, direct evidence of the participation of different perezone conformers in solution and explained the cycloaddition process observed when the aforementioned quinone is heated to form pipitzols, sesquiterpenes with a cedrene skeleton. The fact that biological systems can modulate the redox potential of this type of quinones depending on the conformer recognized by an enzyme during a biological transformation is of great relevance.

  14. Media effects in modulating the conformational equilibrium of a model compound for tumor necrosis factor converting enzyme inhibition

    NASA Astrophysics Data System (ADS)

    Banchelli, Martina; Guardiani, Carlo; Sandberg, Robert B.; Menichetti, Stefano; Procacci, Piero; Caminati, Gabriella

    2015-07-01

    Small-molecule inhibitors of Tumor Necrosis Factor α Converting Enzyme (TACE) are a promising therapeutic tool for Rheumatoid Arthritis, Multiple Sclerosis and other autoimmune diseases. Here we report on an extensive chemical-physical analysis of the media effects in modulating the conformational landscape of MBET306, the common scaffold and a synthetic precursor of a family of recently discovered tartrate-based TACE inhibitors. The structural features of this molecule with potential pharmaceutical applications have been disclosed by interpreting extensive photophysical measurements in various solvents with the aid of enhanced sampling molecular dynamics simulations and time dependent density functional calculations. Using a combination of experimental and computational techniques, the paper provides a general protocol for studying the structure in solution of molecular systems characterized by the existence of conformational metastable states.

  15. Small Molecules Detected by Second-Harmonic Generation Modulate the Conformation of Monomeric α-Synuclein and Reduce Its Aggregation in Cells*

    PubMed Central

    Moree, Ben; Yin, Guowei; Lázaro, Diana F.; Munari, Francesca; Strohäker, Timo; Giller, Karin; Becker, Stefan; Outeiro, Tiago F.; Zweckstetter, Markus; Salafsky, Joshua

    2015-01-01

    Proteins are structurally dynamic molecules that perform specialized functions through unique conformational changes accessible in physiological environments. An ability to specifically and selectively control protein function via conformational modulation is an important goal for development of novel therapeutics and studies of protein mechanism in biological networks and disease. Here we applied a second-harmonic generation-based technique for studying protein conformation in solution and in real time to the intrinsically disordered, Parkinson disease related protein α-synuclein. From a fragment library, we identified small molecule modulators that bind to monomeric α-synuclein in vitro and significantly reduce α-synuclein aggregation in a neuronal cell culture model. Our results indicate that the conformation of α-synuclein is linked to the aggregation of protein in cells. They also provide support for a therapeutic strategy of targeting specific conformations of the protein to suppress or control its aggregation. PMID:26396193

  16. Intensity-modulated radiotherapy, not 3D conformal, is the preferred technique for treating locally advanced lung cancer

    PubMed Central

    Chang, Joe Y.

    2015-01-01

    When used to treat lung cancer, intensity-modulated radiotherapy (IMRT) can deliver higher dose to the targets and spare more critical organs in lung cancer than can 3D conformal radiotherapy (3DCRT). However, tumor-motion management and optimized radiotherapy planning based on four-dimensional computed tomography (4D CT) scanning are crucial to maximize the benefit of IMRT and to eliminate or minimize potential uncertainties. This article summarizes these strategies and reviews published findings supporting the safety and efficacy of IMRT for lung cancer. PMID:25771415

  17. A novel conformity index for intensity modulated radiation therapy plan evaluation

    SciTech Connect

    Cheung, Fion W. K.; Law, Maria Y. Y.

    2012-09-15

    Purpose: Intensity modulated radiation therapy (IMRT) has gained popularity in the treatment of cancers. Manual evaluation of IMRT plans for head-and-neck cancers has been especially challenging necessitating efficient and objective assessment tools. In this work, the authors address this issue by developing a personalized conformity index (CI) for comparison of IMRT plans for head-and-neck cancers and evaluating its plan quality discerning power in comparison with other widely used CIs. Methods: A two-dimensional CI with dose and distance incorporated (CI{sub DD}) was developed using the MATLAB program language, to quantify the planning target volume (PTV) coverage. Valuable information contained in the digital imaging and communication in medicine (DICOM) RT objects were harvested for computation of each of the CI{sub DD} components. Apart from the dose penalty factor, a distance-based exponential function was employed by varying the penalty weight associated with the location of cold spots within the PTV. With the goal of deriving a customized penalty factor, the distances between individual pixel and its nearest PTV boundary was found. Using the exponential function, the impact of distance penalty was substantially larger for cold spots closer to the PTV centroid but petered out quickly wherever they were situated in the vicinity of PTV border. In order to evaluate the CI{sub DD} scoring system, three CT image data sets of nasopharyngeal carcinoma (NPC) patients were collected. Ten IMRT plans with degrading qualities were generated from each dataset and were ranked based on CI{sub DD} and other existing indices. The coefficient of variance was calculated for each dataset to compare the degree of variation. Results: The CI{sub DD} scoring system that considered spatial importance of each voxel within the PTV was successfully developed. The results demonstrated that the CI{sub DD} including four discrete factors could provide accurate rankings of plan quality by

  18. Regulation of ES cell differentiation by functional and conformational modulation of p53.

    PubMed Central

    Sabapathy, K; Klemm, M; Jaenisch, R; Wagner, E F

    1997-01-01

    Embryonic stem (ES) cell lines were used to examine the role of p53 during in vitro differentiation. Undifferentiated ES cells express high levels of p53 exclusively in the wild-type conformation, immunoprecipitable by monoclonal antibody PAb246, and p53 was found to be functionally active as determined by its ability to bind DNA specifically and to activate transcription of target genes. Differentiation in vitro resulted in a decrease in the levels of p53 and in a shift in its conformational status to the mutant form, detectable by monoclonal antibody PAb240, with a concomitant loss of functional activity. The presence of functional p53 in the undifferentiated ES cells renders them hypersensitive to UV irradiation, whereas the differentiated cells were resistant to UV treatment. ES cells lacking p53 exhibit enhanced proliferation in both the undifferentiated and differentiated state, and apoptosis accompanying differentiation was found to be reduced. Furthermore, wild-type ES cells undergoing apoptosis expressed functional p53. Expression of the temperature-sensitive p53val135 mutant in wild-type ES cells resulted in a reduction of apoptosis accompanying differentiation when it adopted a mutant conformation at 39 degrees C. These data demonstrate that functional inactivation of p53 allows differentiating cells to escape from apoptosis, and suggest that the conformational switch could regulate the inactivation process. PMID:9321401

  19. A J-modulated protonless NMR experiment characterizes the conformational ensemble of the intrinsically disordered protein WIP.

    PubMed

    Rozentur-Shkop, Eva; Goobes, Gil; Chill, Jordan H

    2016-12-01

    Intrinsically disordered proteins (IDPs) are multi-conformational polypeptides that lack a single stable three-dimensional structure. It has become increasingly clear that the versatile IDPs play key roles in a multitude of biological processes, and, given their flexible nature, NMR is a leading method to investigate IDP behavior on the molecular level. Here we present an IDP-tailored J-modulated experiment designed to monitor changes in the conformational ensemble characteristic of IDPs by accurately measuring backbone one- and two-bond J((15)N,(13)Cα) couplings. This concept was realized using a unidirectional (H)NCO (13)C-detected experiment suitable for poor spectral dispersion and optimized for maximum coverage of amino acid types. To demonstrate the utility of this approach we applied it to the disordered actin-binding N-terminal domain of WASp interacting protein (WIP), a ubiquitous key modulator of cytoskeletal changes in a range of biological systems. One- and two-bond J((15)N,(13)Cα) couplings were acquired for WIP residues 2-65 at various temperatures, and in denaturing and crowding environments. Under native conditions fitted J-couplings identified in the WIP conformational ensemble a propensity for extended conformation at residues 16-23 and 45-60, and a helical tendency at residues 28-42. These findings are consistent with a previous study of the based upon chemical shift and RDC data and confirm that the WIP(2-65) conformational ensemble is biased towards the structure assumed by this fragment in its actin-bound form. The effects of environmental changes upon this ensemble were readily apparent in the J-coupling data, which reflected a significant decrease in structural propensity at higher temperatures, in the presence of 8 M urea, and under the influence of a bacterial cell lysate. The latter suggests that crowding can cause protein unfolding through protein-protein interactions that stabilize the unfolded state. We conclude that J-couplings are

  20. Three-dimensional conformal intensity-modulated radiation therapy of left femur foci does not damage the sciatic nerve

    PubMed Central

    Xu, Wanlong; Zhao, Xibin; Wang, Qing; Sun, Jungang; Xu, Jiangbo; Zhou, Wenzheng; Wang, Hao; Yan, Shigui; Yuan, Hong

    2014-01-01

    During radiotherapy to kill femoral hydatid tapeworms, the sciatic nerve surrounding the focus can be easily damaged by the treatment. Thus, it is very important to evaluate the effects of radiotherapy on the surrounding nervous tissue. In the present study, we used three-dimensional, conformal, intensity-modulated radiation therapy to treat bilateral femoral hydatid disease in Meriones meridiani. The focus of the hydatid disease on the left femur was subjected to radiotherapy (40 Gy) for 14 days, and the right femur received sham irradiation. Hematoxylin-eosin staining, electron microscopy, and terminal deoxynucleotidyl transferase-dUTP nick end labeling assays on the left femurs showed that the left sciatic nerve cell structure was normal, with no obvious apoptosis after radiation. Trypan blue staining demonstrated that the overall protoscolex structure in bone parasitized with Echinococcus granulosus disappeared in the left femur of the animals after treatment. The mortality of the protoscolex was higher in the left side than in the right side. The succinate dehydrogenase activity in the protoscolex in bone parasitized with Echinococcus granulosus was lower in the left femur than in the right femur. These results suggest that three-dimensional conformal intensity-modulated radiation therapy achieves good therapeutic effects on the secondary bone in hydatid disease in Meriones meridiani without damaging the morphology or function of the sciatic nerve. PMID:25422645

  1. Mutational landscape of antibody variable domains reveals a switch modulating the interdomain conformational dynamics and antigen binding

    PubMed Central

    Koenig, Patrick; Lee, Chingwei V.; Walters, Benjamin T.; Janakiraman, Vasantharajan; Stinson, Jeremy; Patapoff, Thomas W.; Fuh, Germaine

    2017-01-01

    Somatic mutations within the antibody variable domains are critical to the immense capacity of the immune repertoire. Here, via a deep mutational scan, we dissect how mutations at all positions of the variable domains of a high-affinity anti-VEGF antibody G6.31 impact its antigen-binding function. The resulting mutational landscape demonstrates that large portions of antibody variable domain positions are open to mutation, and that beneficial mutations can be found throughout the variable domains. We determine the role of one antigen-distal light chain position 83, demonstrating that mutation at this site optimizes both antigen affinity and thermostability by modulating the interdomain conformational dynamics of the antigen-binding fragment. Furthermore, by analyzing a large number of human antibody sequences and structures, we demonstrate that somatic mutations occur frequently at position 83, with corresponding domain conformations observed for G6.31. Therefore, the modulation of interdomain dynamics represents an important mechanism during antibody maturation in vivo. PMID:28057863

  2. Limited Advantages of Intensity-Modulated Radiotherapy Over 3D Conformal Radiation Therapy in the Adjuvant Management of Gastric Cancer

    SciTech Connect

    Alani, Shlomo; Soyfer, Viacheslav; Strauss, Natan; Schifter, Dan; Corn, Benjamin W.

    2009-06-01

    Purpose: Although chemoradiotherapy was considered the standard adjuvant treatment for gastric cancer, a recent Phase III trial (Medical Research Council Adjuvant Gastric Infusional Chemotherapy [MAGIC]) did not include radiotherapy in the randomization scheme because it was considered expendable. Given radiotherapy's potential, efforts needed to be made to optimize its use for treating gastric cancer. We assessed whether intensity-modulated radiotherapy (IMRT) could improve upon our published results in patients treated with three-dimensional (3D) conformal therapy. Methods and Materials: Fourteen patients with adenocarcinoma of the stomach were treated with adjuvant chemoradiotherapy using a noncoplanar four-field arrangement. Subsequently, a nine-field IMRT plan was designed using a CMS Xio IMRT version 4.3.3 module. Two IMRT beam arrangements were evaluated: beam arrangement 1 consisted of gantry angles of 0 deg., 53 deg., 107 deg., 158 deg., 204 deg., 255 deg., and 306 deg.. Beam arrangement 2 consisted of gantry angles of 30 deg., 90 deg., 315 deg., and 345 deg.; a gantry angle of 320 deg./couch, 30 deg.; and a gantry angle of 35{sup o}/couch, 312{sup o}. Both the target volume coverage and the dose deposition in adjacent critical organs were assessed in the plans. Dose-volume histograms were generated for the clinical target volume, kidneys, spine, and liver. Results: Comparison of the clinical target volumes revealed satisfactory coverage by the 95% isodose envelope using either IMRT or 3D conformal therapy. However, IMRT was only marginally better than 3D conformal therapy at protecting the spine and kidneys from radiation. Conclusions: IMRT confers only a marginal benefit in the adjuvant treatment of gastric cancer and should be used only in the small subset of patients with risk factors for kidney disease or those with a preexisting nephropathy.

  3. Modulation of the Disordered Conformational Ensembles of the p53 Transactivation Domain by Cancer-Associated Mutations

    PubMed Central

    Ganguly, Debabani; Chen, Jianhan

    2015-01-01

    Intrinsically disordered proteins (IDPs) are frequently associated with human diseases such as cancers, and about one-fourth of disease-associated missense mutations have been mapped into predicted disordered regions. Understanding how these mutations affect the structure-function relationship of IDPs is a formidable task that requires detailed characterization of the disordered conformational ensembles. Implicit solvent coupled with enhanced sampling has been proposed to provide a balance between accuracy and efficiency necessary for systematic and comparative assessments of the effects of mutations as well as post-translational modifications on IDP structure and interaction. Here, we utilize a recently developed replica exchange with guided annealing enhanced sampling technique to calculate well-converged atomistic conformational ensembles of the intrinsically disordered transactivation domain (TAD) of tumor suppressor p53 and several cancer-associated mutants in implicit solvent. The simulations are critically assessed by quantitative comparisons with several types of experimental data that provide structural information on both secondary and tertiary levels. The results show that the calculated ensembles reproduce local structural features of wild-type p53-TAD and the effects of K24N mutation quantitatively. On the tertiary level, the simulated ensembles are overly compact, even though they appear to recapitulate the overall features of transient long-range contacts qualitatively. A key finding is that, while p53-TAD and its cancer mutants sample a similar set of conformational states, cancer mutants could introduce both local and long-range structural modulations to potentially perturb the balance of p53 binding to various regulatory proteins and further alter how this balance is regulated by multisite phosphorylation of p53-TAD. The current study clearly demonstrates the promise of atomistic simulations for detailed characterization of IDP conformations, and

  4. Modulation of the disordered conformational ensembles of the p53 transactivation domain by cancer-associated mutations.

    PubMed

    Ganguly, Debabani; Chen, Jianhan

    2015-04-01

    Intrinsically disordered proteins (IDPs) are frequently associated with human diseases such as cancers, and about one-fourth of disease-associated missense mutations have been mapped into predicted disordered regions. Understanding how these mutations affect the structure-function relationship of IDPs is a formidable task that requires detailed characterization of the disordered conformational ensembles. Implicit solvent coupled with enhanced sampling has been proposed to provide a balance between accuracy and efficiency necessary for systematic and comparative assessments of the effects of mutations as well as post-translational modifications on IDP structure and interaction. Here, we utilize a recently developed replica exchange with guided annealing enhanced sampling technique to calculate well-converged atomistic conformational ensembles of the intrinsically disordered transactivation domain (TAD) of tumor suppressor p53 and several cancer-associated mutants in implicit solvent. The simulations are critically assessed by quantitative comparisons with several types of experimental data that provide structural information on both secondary and tertiary levels. The results show that the calculated ensembles reproduce local structural features of wild-type p53-TAD and the effects of K24N mutation quantitatively. On the tertiary level, the simulated ensembles are overly compact, even though they appear to recapitulate the overall features of transient long-range contacts qualitatively. A key finding is that, while p53-TAD and its cancer mutants sample a similar set of conformational states, cancer mutants could introduce both local and long-range structural modulations to potentially perturb the balance of p53 binding to various regulatory proteins and further alter how this balance is regulated by multisite phosphorylation of p53-TAD. The current study clearly demonstrates the promise of atomistic simulations for detailed characterization of IDP conformations, and

  5. Single mutations in tau modulate the populations of fibril conformers through seed selection.

    PubMed

    Meyer, Virginia; Dinkel, Paul D; Luo, Yin; Yu, Xiang; Wei, Guanghong; Zheng, Jie; Eaton, Gareth R; Ma, Buyong; Nussinov, Ruth; Eaton, Sandra S; Margittai, Martin

    2014-02-03

    Seeded conversion of tau monomers into fibrils is a central step in the progression of tau pathology in Alzheimer's disease and other neurodegenerative disorders. Self-assembly is mediated by the microtubule binding repeats in tau. There are either three or four repeats present depending on the protein isoform. Here, double electron-electron resonance spectroscopy was used to investigate the conformational ensemble of four-repeat tau fibrils. Single point mutations at key positions in the protein (ΔK280, P301S, P312I, D314I) markedly change the distribution of fibril conformers after template-assisted growth, whereas other mutations in the protein (I308M, S320F, G323I, G326I, Q336R) do not. These findings provide unprecedented insights into the seed selection of tau disease mutants and establish conformational compatibility as an important driving force in tau fibril propagation. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. A neglected modulator of insulin-degrading enzyme activity and conformation: The pH.

    PubMed

    Grasso, Giuseppe; Satriano, Cristina; Milardi, Danilo

    2015-01-01

    Insulin-degrading enzyme (IDE), a ubiquitously expressed zinc metalloprotease, has multiple activities in addition to insulin degradation and its malfunction is believed to connect type 2 diabetes with Alzheimer's disease. IDE has been found in many different cellular compartments, where it may experience significant physio-pathological pH variations. However, the exact role of pH variations on the interplay between enzyme conformations, stability, oligomerization state and catalysis is not understood. Here, we use ESI mass spectrometry, atomic force microscopy, surface plasmon resonance and circular dichroism to investigate the structure-activity relationship of IDE at different pH values. We show that acidic pH affects the ability of the enzyme to bind the substrate and decrease the stability of the protein by inducing an α-helical bundle conformation with a concomitant dissociation of multi-subunit IDE assemblies into monomeric units and loss of activity. These effects suggest a major role played by electrostatic forces in regulating multi-subunit enzyme assembly and function. Our results clearly indicate a pH dependent coupling among enzyme conformation, assembly and stability and suggest that cellular acidosis can have a large effect on IDE oligomerization state, inducing an enzyme inactivation and an altered insulin degradation that could have an impact on insulin signaling. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. The clinical potential of high energy, intensity and energy modulated electron beams optimized by simulated annealing for conformal radiation therapy

    NASA Astrophysics Data System (ADS)

    Salter, Bill Jean, Jr.

    Purpose. The advent of new, so called IVth Generation, external beam radiation therapy treatment machines (e.g. Scanditronix' MM50 Racetrack Microtron) has raised the question of how the capabilities of these new machines might be exploited to produce extremely conformal dose distributions. Such machines possess the ability to produce electron energies as high as 50 MeV and, due to their scanned beam delivery of electron treatments, to modulate intensity and even energy, within a broad field. Materials and methods. Two patients with 'challenging' tumor geometries were selected from the patient archives of the Cancer Therapy and Research Center (CTRC), in San Antonio Texas. The treatment scheme that was tested allowed for twelve, energy and intensity modulated beams, equi-spaced about the patient-only intensity was modulated for the photon treatment. The elementary beams, incident from any of the twelve allowed directions, were assumed parallel, and the elementary electron beams were modeled by elementary beam data. The optimal arrangement of elementary beam energies and/or intensities was optimized by Szu-Hartley Fast Simulated Annealing Optimization. Optimized treatment plans were determined for each patient using both the high energy, intensity and energy modulated electron (HIEME) modality, and the 6 MV photon modality. The 'quality' of rival plans were scored using three different, popular objective functions which included Root Mean Square (RMS), Maximize Dose Subject to Dose and Volume Limitations (MDVL - Morrill et. al.), and Probability of Uncomplicated Tumor Control (PUTC) methods. The scores of the two optimized treatments (i.e. HIEME and intensity modulated photons) were compared to the score of the conventional plan with which the patient was actually treated. Results. The first patient evaluated presented a deeply located target volume, partially surrounding the spinal cord. A healthy right kidney was immediately adjacent to the tumor volume, separated

  8. Anion concentration modulates the conformation and stability of the molten globule of cytochrome c.

    PubMed

    Sinibaldi, Federica; Howes, Barry D; Smulevich, Giulietta; Ciaccio, Chiara; Coletta, Massimo; Santucci, Roberto

    2003-07-01

    Anions induce collapse of acid-denatured cytochrome c into a compact state, the A-state, showing molten globule character. Since structural information on partially folded forms of proteins is important for a deeper understanding of folding mechanisms and of the factors affecting protein stabilization, in this paper we have investigated in detail the effects of anions on the tertiary conformation of the A-state. We have found that the salt-induced collapse of acid-denatured cytochrome c leads to a number of equilibria between high-spin and low-spin heme states and between two types of low-spin states. The two latter states are characterized by conformations leading to a native-like Met-Fe-His axial coordination and a bis-His configuration. The equilibrium between these two A-states is dependent on the concentration and/or size of the anions (i.e. the bigger the anion, the greater its effect). Further, on the basis of fast kinetic data, a kinetic model of the folding process from the acid-unfolded protein to the A-state (at low and high anion concentration) is described.

  9. A Highly Conserved gp120 Inner Domain Residue Modulates Env Conformation and Trimer Stability

    PubMed Central

    Ding, Shilei; Tolbert, William D.; Prévost, Jérémie; Pacheco, Beatriz; Coutu, Mathieu; Debbeche, Olfa; Xiang, Shi-Hua

    2016-01-01

    ABSTRACT Previous studies have shown that highly conserved residues in the inner domain of gp120 are required for HIV-1 envelope glycoprotein (Env) transitions to the CD4-bound conformation (A. Finzi, S. H. Xiang, B. Pacheco, L. Wang, J. Haight, et al., Mol Cell 37:656–667, 2010, http://dx.doi.org/10.1016/j.molcel.2010.02.012; A. Desormeaux, M. Coutu, H. Medjahed, B. Pacheco, A. Herschhorn, et al., J Virol 87:2549–2562, 2013, http://dx.doi.org/10.1128/JVI.03104-12). Moreover, W69, a highly conserved residue located at the interface between layer 1 and layer 2 of the inner domain, was recently shown to be important for efficient Env recognition by CD4-induced (CD4i) antibodies capable of potent antibody-dependent cellular cytotoxicity (W. D. Tolbert, N. Gohain, M. Veillette, J. P. Chapleau, C. Orlandi, et al., 2016, Structure 24:697–709, http://dx.doi.org/10.1016/j.str.2016.03.005; S. Ding, M. Veillette, M. Coutu, J. Prevost, L. Scharf, et al., 2016, J Virol 90:2127–2134, http://dx.doi.org/10.1128/JVI.02779-15). We evaluated the contribution of the hydrophobicity of W69 to conformational changes of Env by replacing it with a series of residues with aliphatic or aromatic side chains of decreasing chain length. We have found that the hydrophobicity of residue 69 is important for Env processing, CD4 binding, and its transition to the CD4-bound conformation. The most deleterious effect was observed when W69 was replaced with alanine or glycine residues. However, the functions lost due to W69 mutations could be progressively restored with amino acids of increasing aliphatic chain length and fully recovered with residues bearing an aromatic ring. Interestingly, poor CD4 binding of W69A could be fully restored by introducing a compensatory mutation within layer 2 (S115W). Structural studies of HIV-1 gp120 coree W69A/S115W mutant bound to the CD4 peptide mimetic M48U1 and Fab of anti-cluster A antibody N60-i3 revealed no perturbations to the overall structure of the

  10. Balancing between affinity and speed in target DNA search by zinc-finger proteins via modulation of dynamic conformational ensemble

    PubMed Central

    Zandarashvili, Levani; Esadze, Alexandre; Vuzman, Dana; Kemme, Catherine A.; Levy, Yaakov; Iwahara, Junji

    2015-01-01

    Although engineering of transcription factors and DNA-modifying enzymes has drawn substantial attention for artificial gene regulation and genome editing, most efforts focus on affinity and specificity of the DNA-binding proteins, typically overlooking the kinetic properties of these proteins. However, a simplistic pursuit of high affinity can lead to kinetically deficient proteins that spend too much time at nonspecific sites before reaching their targets on DNA. We demonstrate that structural dynamic knowledge of the DNA-scanning process allows for kinetically and thermodynamically balanced engineering of DNA-binding proteins. Our current study of the zinc-finger protein Egr-1 (also known as Zif268) and its nuclease derivatives reveals kinetic and thermodynamic roles of the dynamic conformational equilibrium between two modes during the DNA-scanning process: one mode suitable for search and the other for recognition. By mutagenesis, we were able to shift this equilibrium, as confirmed by NMR spectroscopy. Using fluorescence and biochemical assays as well as computational simulations, we analyzed how the shifts of the conformational equilibrium influence binding affinity, target search kinetics, and efficiency in displacing other proteins from the target sites. A shift toward the recognition mode caused an increase in affinity for DNA and a decrease in search efficiency. In contrast, a shift toward the search mode caused a decrease in affinity and an increase in search efficiency. This accelerated site-specific DNA cleavage by the zinc-finger nuclease, without enhancing off-target cleavage. Our study shows that appropriate modulation of the dynamic conformational ensemble can greatly improve zinc-finger technology, which has used Egr-1 (Zif268) as a major scaffold for engineering. PMID:26324943

  11. Post-transcriptional modifications modulate conformational dynamics in human U2-U6 snRNA complex.

    PubMed

    Karunatilaka, Krishanthi S; Rueda, David

    2014-01-01

    The spliceosome catalyzes precursor-mRNA splicing in all eukaryotes. It consists of over 100 proteins and five small nuclear RNAs (snRNAs), including U2 and U6 snRNAs, which are essential for catalysis. Human and yeast snRNAs share structural similarities despite the fact that human snRNAs contain numerous post-transcriptional modifications. Although functions for these modifications have been proposed, their exact roles are still not well understood. To help elucidate these roles in pre-mRNA splicing, we have used single-molecule fluorescence to characterize the effect of several post-transcriptional modifications in U2 snRNA on the conformation and dynamics of the U2-U6 complex in vitro. Consistent with yeast, the human U2-U6 complex reveals the presence of a magnesium-dependent dynamic equilibrium among three conformations. Interestingly, our data show that modifications in human U2 stem I modulate the dynamic equilibrium of the U2-U6 complex by stabilizing the four-helix structure. However, the small magnitude of this effect suggests that post-transcriptional modifications in human snRNAs may have a primary role in the mediation of specific RNA-protein interactions in vivo.

  12. Post-transcriptional modifications modulate conformational dynamics in human U2–U6 snRNA complex

    PubMed Central

    Karunatilaka, Krishanthi S.; Rueda, David

    2014-01-01

    The spliceosome catalyzes precursor-mRNA splicing in all eukaryotes. It consists of over 100 proteins and five small nuclear RNAs (snRNAs), including U2 and U6 snRNAs, which are essential for catalysis. Human and yeast snRNAs share structural similarities despite the fact that human snRNAs contain numerous post-transcriptional modifications. Although functions for these modifications have been proposed, their exact roles are still not well understood. To help elucidate these roles in pre-mRNA splicing, we have used single-molecule fluorescence to characterize the effect of several post-transcriptional modifications in U2 snRNA on the conformation and dynamics of the U2–U6 complex in vitro. Consistent with yeast, the human U2–U6 complex reveals the presence of a magnesium-dependent dynamic equilibrium among three conformations. Interestingly, our data show that modifications in human U2 stem I modulate the dynamic equilibrium of the U2–U6 complex by stabilizing the four-helix structure. However, the small magnitude of this effect suggests that post-transcriptional modifications in human snRNAs may have a primary role in the mediation of specific RNA–protein interactions in vivo. PMID:24243115

  13. Effect of MLC tracking latency on conformal volumetric modulated arc therapy (VMAT) plans in 4D stereotactic lung treatment

    PubMed Central

    Bedford, James L.; Fast, Martin F.; Nill, Simeon; McDonald, Fiona M.A.; Ahmed, Merina; Hansen, Vibeke N.; Oelfke, Uwe

    2015-01-01

    Background and purpose The latency of a multileaf collimator (MLC) tracking system used to overcome respiratory motion causes misalignment of the treatment beam with respect to the gross tumour volume, which may result in reduced target coverage. This study investigates the magnitude of this effect. Material and methods Simulated superior–inferior breathing motion was used to construct histograms of isocentre offset with respect to the gross tumour volume (GTV) for a variety of tracking latencies. Dose distributions for conformal volumetric modulated arc therapy (VMAT) arcs were then calculated at a range of offsets and summed according to these displacement histograms. The results were verified by delivering the plans to a Delta4 phantom on a motion platform. Results In the absence of an internal target margin, a tracking latency of 150 ms reduces the GTV D95% by approximately 2%. With a margin of 2 mm, the same drop in dose occurs for a tracking latency of 450 ms. Lung V13Gy is unaffected by a range of latencies. These results are supported by the phantom measurements. Conclusions Assuming that internal motion can be modelled by a rigid translation of the patient, MLC tracking of conformal VMAT can be effectively accomplished in the absence of an internal target margin for substantial breathing motion (4 s period and 20 mm peak–peak amplitude) so long as the system latency is less than 150 ms. PMID:26277856

  14. Modulation of in:out and out:out conformations in [X.X'.X''] phosphatranes by Lewis acids.

    PubMed

    Sánchez-Sanz, Goar; Trujillo, Cristina; Alkorta, Ibon; Elguero, José

    2017-08-09

    A theoretical study of [X.X'.X'']phosphatrane:Lewis acid complexes has been carried out in order to analyze how the in:out and out:out conformations can be modulated by the interaction with Lewis acids (LA). It has been found that in:out structures are more stable in larger systems i.e. in [4.4.3]:LA and [4.4.4]:LA than in [3.3.3]:LA and [4.3.3]:LA. The results obtained for the relative energies in conjunction with electron density properties showed that upon complexation, in:out conformers become more stable with the increasing acidity of the corresponding Lewis acid. In fact, the binding energies found for in:out complexes are larger than those obtained for out:out complexes. The complexes with the largest relative energy favoring the in:out structure correspond to those with charged Lewis acids, followed by the complexes with ClF. In all cases, the complexes are cooperative, reaching a maximum value of 168.5 kJ mol(-1) for the [4.3.3]:F(+) complex.

  15. Mapping light-driven conformational changes within the photosensory module of plant phytochrome B

    PubMed Central

    von Horsten, Silke; Straß, Simon; Hellwig, Nils; Gruth, Verena; Klasen, Ramona; Mielcarek, Andreas; Linne, Uwe; Morgner, Nina; Essen, Lars-Oliver

    2016-01-01

    Organisms developed different photoreceptors to be able to adapt to changing environmental light conditions. Phytochromes are red/far-red (r/fr) photochromic photoreceptors that belong to the classical photoreceptors along with cryptochromes and phototropins. They convert absorbed light into a biological signal by switching between two states in a light-dependent manner therefore enabling the light control downstream signalling. Their Pfr conformation is the biological active form in plants, but until now only a structure of the ground state (Pr) was solved. Here, the authors provide information about structural changes occurring during photoconversion within phytochrome B and identify possible interaction sites for its N-terminal extension (NTE) utilising hydrogen/deuterium exchange rate analyses of its amide backbone. Especially, the newly identified light-dependency of two regions in the NTE are of particular interest for understanding the involvement of the phytochrome’s NTE in the regulation of its downstream signalling. PMID:27694986

  16. Terminal Interface Conformations Modulate Dimer Stability Prior to Amino Terminal Autoprocessing of HIV-1 Protease

    SciTech Connect

    Agniswamy, Johnson; Sayer, Jane M.; Weber, Irene T.; Louis, John M.

    2012-04-17

    The HIV-1 protease (PR) mediates its own release (autoprocessing) from the polyprotein precursor, Gag-Pol, flanked by the transframe region (TFR) and reverse transcriptase at its N- and C-termini, respectively. Autoprocessing at the N-terminus of PR mediates stable dimer formation essential for catalytic activity, leading to the formation of infectious virus. An antiparallel {beta}-sheet interface formed by the four N- and C-terminal residues of each subunit is important for dimer stability. Here, we present the first high-resolution crystal structures of model protease precursor-clinical inhibitor (PI darunavir or saquinavir) complexes, revealing varying conformations of the N-terminal flanking (S{sup -4}FNF{sup -1}) and interface residues (P{sup 1}QIT{sup 4}). A 180{sup o} rotation of the T{sup 4}-L{sup 5} peptide bond is accompanied by a new Q{sup 2}-L{sup 5} hydrogen bond and complete disengagement of PQIT from the {beta}-sheet dimer interface, which may be a feature for intramolecular autoprocessing. This result is consistent with drastically lower thermal stability by 14-20 C of PI complexes of precursors and the mature PR lacking its PQIT residues (by 18.3 C). Similar to the TFR-PR precursor, this deletion also results in a darunavir dissociation constant (2 x 10{sup 4})-fold higher and a markedly increased dimer dissociation constant relative to the mature PR. The terminal {beta}-sheet perturbations of the dimeric structure likely account for the drastically poorer inhibition of autoprocessing of TFR-PR relative to the mature PR, even though significant differences in active site-PI interactions in these structures were not observed. The novel conformations of the dimer interface may be exploited to target selectively the protease precursor prior to its N-terminal cleavage.

  17. Optimization of 3D conformal electron beam therapy in inhomogeneous media by concomitant fluence and energy modulation

    NASA Astrophysics Data System (ADS)

    Åsell, Mats; Hyödynmaa, Simo; Gustafsson, Anders; Brahme, Anders

    1997-11-01

    The possibilities of using simultaneous fluence and energy modulation techniques in electron beam therapy to shape the dose distribution and almost eliminate the influences of tissue inhomogeneities have been investigated. By using a radiobiologically based optimization algorithm the radiobiological properties of the tissues can be taken into account when trying to find the best possible dose delivery. First water phantoms with differently shaped surfaces were used to study the effect of surface irregularities. We also studied water phantoms with internal inhomogeneities consisting of air or cortical bone. It was possible to improve substantially the dose distribution by fluence modulation in these cases. In addition to the fluence modulation the most suitable single electron energy in each case was also determined. Finally, the simultaneous use of several preselected electron beam energies was also tested, each with an individually optimized fluence profile. One to six electron energies were used, resulting in a slow improvement in complication-free cure with increasing number of beam energies. To apply these techniques to a more clinically relevant situation a post-operative breast cancer patient was studied. For simplicity this patient was treated with only one anterior beam portal to clearly illustrate the effect of inhomogeneities like bone and lung on the dose distribution. It is shown that by using fluence modulation the influence of dose inhomogeneities can be significantly reduced. When two or more electron beam energies with individually optimized fluence profiles are used the dose conformality to the internal target volume is further increased, particularly for targets with complex shapes.

  18. Optimization of 3D conformal electron beam therapy in inhomogeneous media by concomitant fluence and energy modulation.

    PubMed

    Asell, M; Hyödynmaa, S; Gustafsson, A; Brahme, A

    1997-11-01

    The possibilities of using simultaneous fluence and energy modulation techniques in electron beam therapy to shape the dose distribution and almost eliminate the influences of tissue inhomogeneities have been investigated. By using a radiobiologically based optimization algorithm the radiobiological properties of the tissues can be taken into account when trying to find the best possible dose delivery. First water phantoms with differently shaped surfaces were used to study the effect of surface irregularities. We also studied water phantoms with internal inhomogeneities consisting of air or cortical bone. It was possible to improve substantially the dose distribution by fluence modulation in these cases. In addition to the fluence modulation the most suitable single electron energy in each case was also determined. Finally, the simultaneous use of several preselected electron beam energies was also tested, each with an individually optimized fluence profile. One to six electron energies were used, resulting in a slow improvement in complication-free cure with increasing number of beam energies. To apply these techniques to a more clinically relevant situation a post-operative breast cancer patient was studied. For simplicity this patient was treated with only one anterior beam portal to clearly illustrate the effect of inhomogeneities like bone and lung on the dose distribution. It is shown that by using fluence modulation the influence of dose inhomogeneities can be significantly reduced. When two or more electron beam energies with individually optimized fluence profiles are used the dose conformality to the internal target volume is further increased, particularly for targets with complex shapes.

  19. Protein conformational modulation by photons: a mechanism for laser treatment effects.

    PubMed

    Liebert, Ann D; Bicknell, Brian T; Adams, Roger D

    2014-03-01

    Responsiveness to low-level laser treatment (LLTT) at a wavelength of 450-910 nm has established it as an effective treatment of medical, veterinary and dental chronic pain, chronic inflammation conditions (arthritis and macular degeneration), wound repair, and lymphoedema, yet the mechanisms underlying the effectiveness of LLLT remain unclear. However, there is now sufficient evidence from recent research to propose an integrated model of LLLT action. The hypothesis presented in this paper is that external applications of photons (through laser at an appropriate dose) modulates the nervous system through an integrated mechanism. This stimulated mechanism involves protein-to-protein interaction, where two or more proteins bind together to facilitate molecular processes, including modification of proteins by members of SUMO (small ubiquitin-related modifier proteins) and also protein phosphorylation and tyrosination. SUMO has been shown to have a role in multiple nuclear and perinuclear targets, including ion channels, and in the maintenance of telomeres and the post-translational modification of genes. The consequence of laser application in treatment, therefore, can be seen as influencing the transmission of neural information via an integrated and rapid modulation of ion channels, achieved through both direct action on photo-acceptors (such as cytochrome c-oxidase) and through indirect modulation via enzymes, including tyrosine hydroxylase (TH), tyrosine kinases and tyrosine kinase receptors. This exogenous action then facilitates an existing photonic biomodulation mechanism within the body, and initiates ion channel modulation both in the periphery and the central nervous system (CNS). Evidence indicates that the ion channel modulation functions predominately through the potassium channels, including two pore leak channels (K2P), which act as signal integrators from the periphery to the cortex. Photonic action also transforms SUMOylation processes at the cell

  20. Volumetric-modulated arc radiotherapy for pancreatic malignancies: Dosimetric comparison with sliding-window intensity-modulated radiotherapy and 3-dimensional conformal radiotherapy

    SciTech Connect

    Nabavizadeh, Nima Simeonova, Anna O.; Waller, Joseph G.; Romer, Jeanna L.; Monaco, Debra L.; Elliott, David A.; Tanyi, James A.; Fuss, Martin; Thomas, Charles R.; Holland, John M.

    2014-10-01

    Volumetric-modulated arc radiotherapy (VMAT) is an iteration of intensity-modulated radiotherapy (IMRT), both of which deliver highly conformal dose distributions. Studies have shown the superiority of VMAT and IMRT in comparison with 3-dimensional conformal radiotherapy (3D-CRT) in planning target volume (PTV) coverage and organs-at-risk (OARs) sparing. This is the first study examining the benefits of VMAT in pancreatic cancer for doses more than 55.8 Gy. A planning study comparing 3D-CRT, IMRT, and VMAT was performed in 20 patients with pancreatic cancer. Treatments were planned for a 25-fraction delivery of 45 Gy to a large field followed by a reduced-volume 8-fraction external beam boost to 59.4 Gy in total. OARs and PTV doses, conformality index (CI) deviations from 1.0, monitor units (MUs) delivered, and isodose volumes were compared. IMRT and VMAT CI deviations from 1.0 for the large-field and the boost plans were equivalent (large field: 0.032 and 0.046, respectively; boost: 0.042 and 0.037, respectively; p > 0.05 for all comparisons). Both IMRT and VMAT CI deviations from 1.0 were statistically superior to 3D-CRT (large field: 0.217, boost: 0.177; p < 0.05 for all comparisons). VMAT showed reduction of the mean dose to the boost PTV (VMAT: 61.4 Gy, IMRT: 62.4 Gy, and 3D-CRT: 62.3 Gy; p < 0.05). The mean number of MUs per fraction was significantly lower for VMAT for both the large-field and the boost plans. VMAT delivery time was less than 3 minutes compared with 8 minutes for IMRT. Although no statistically significant dose reduction to the OARs was identified when comparing VMAT with IMRT, VMAT showed a reduction in the volumes of the 100% isodose line for the large-field plans. Dose escalation to 59.4 Gy in pancreatic cancer is dosimetrically feasible with shorter treatment times, fewer MUs delivered, and comparable CIs for VMAT when compared with IMRT.

  1. Chest wall desmoid tumours treated with definitive radiotherapy: a plan comparison of 3D conformal radiotherapy, intensity-modulated radiotherapy and volumetric-modulated arc radiotherapy.

    PubMed

    Liu, Jia; Ng, Diana; Lee, James; Stalley, Paul; Hong, Angela

    2016-03-02

    Definitive radiotherapy is often used for chest wall desmoid tumours due to size or anatomical location. The delivery of radiotherapy is challenging due to the large size and constraints of normal surrounding structures. We compared the dosimetry of 3D conformal radiotherapy (3DCRT), intensity-modulated radiotherapy (IMRT) and volumetric-modulated arc radiotherapy (VMAT) to evaluate the best treatment option. Ten consecutive patients with inoperable chest wall desmoid tumours (PTV range 416-4549 cm(3)) were selected. For each patient, 3DCRT, IMRT and VMAT plans were generated and the Conformity Index (CI), organ at risk (OAR) doses and monitor unit (MU) were evaluated. The Wilcoxon signed-rank test was used to compare dose delivered to both target and OARs. The mean number of fields for 3DCRT and IMRT were 6.3 ± 2.1, 7.2 ± 1.8. The mean number of arcs for VMAT was 3.7 ± 1.1. The mean conformity index of VMAT (0.98 ± 0.14) was similar to that of IMRT (1.03 ± 0.13), both of which were significantly better than 3DCRT (1.35 ± 0.20; p = 0.005). The mean dose to lung was significantly higher for 3DCRT (11.9Gy ± 7.9) compared to IMRT (9.4Gy ± 5.4, p = 0.014) and VMAT (8.9Gy ± 4.5, p = 0.017). For the 3 females, the low dose regions in the ipsilateral breast for VMAT were generally less with VMAT. IMRT plans required 1427 ± 532 MU per fraction which was almost 4-fold higher than 3DCRT (313 ± 112, P = 0.005). Compared to IMRT, VMAT plans required 60 % less MU (570 ± 285, P = 0.005). For inoperable chest wall desmoid tumours, VMAT delivered equivalent target coverage when compared to IMRT but required 60 % less MU. Both VMAT and IMRT were superior to 3DCRT in terms of better PTV coverage and sparing of lung tissue.

  2. Multiple disulfide bridges modulate conformational stability and flexibility in hyperthermophilic archaeal purine nucleoside phosphorylase.

    PubMed

    Bagarolo, Maria Libera; Porcelli, Marina; Martino, Elisa; Feller, Georges; Cacciapuoti, Giovanna

    2015-10-01

    5'-Deoxy-5'-methylthioadenosine phosphorylase from Sulfolobus solfataricus is a hexameric hyperthermophilic protein containing in each subunit two pairs of disulfide bridges, a CXC motif, and one free cysteine. The contribution of each disulfide bridge to the protein conformational stability and flexibility has been assessed by comparing the thermal unfolding and the limited proteolysis of the wild-type enzyme and its variants obtained by site-directed mutagenesis of the seven cysteine residues. All variants catalyzed efficiently MTA cleavage with specific activity similar to the wild-type enzyme. The elimination of all cysteine residues caused a substantial decrease of ΔHcal (850 kcal/mol) and Tmax (39°C) with respect to the wild-type indicating that all cysteine pairs and especially the CXC motif significantly contribute to the enzyme thermal stability. Disulfide bond Cys200-Cys262 and the CXC motif weakly affected protein flexibility while the elimination of the disulfide bond Cys138-Cys205 lead to an increased protease susceptibility. Experimental evidence from limited proteolysis, differential scanning calorimetry, and sodium dodecyl sulfate-polyacrylamide gel electrophoresis under reducing and nonreducing conditions also allowed to propose a stabilizing role for the free Cys164. Copyright © 2015 Elsevier B.V. All rights reserved.

  3. A Slow Conformational Switch in the BMAL1 Transactivation Domain Modulates Circadian Rhythms.

    PubMed

    Gustafson, Chelsea L; Parsley, Nicole C; Asimgil, Hande; Lee, Hsiau-Wei; Ahlbach, Christopher; Michael, Alicia K; Xu, Haiyan; Williams, Owen L; Davis, Tara L; Liu, Andrew C; Partch, Carrie L

    2017-05-18

    The C-terminal transactivation domain (TAD) of BMAL1 (brain and muscle ARNT-like 1) is a regulatory hub for transcriptional coactivators and repressors that compete for binding and, consequently, contributes to period determination of the mammalian circadian clock. Here, we report the discovery of two distinct conformational states that slowly exchange within the dynamic TAD to control timing. This binary switch results from cis/trans isomerization about a highly conserved Trp-Pro imide bond in a region of the TAD that is required for normal circadian timekeeping. Both cis and trans isomers interact with transcriptional regulators, suggesting that isomerization could serve a role in assembling regulatory complexes in vivo. Toward this end, we show that locking the switch into the trans isomer leads to shortened circadian periods. Furthermore, isomerization is regulated by the cyclophilin family of peptidyl-prolyl isomerases, highlighting the potential for regulation of BMAL1 protein dynamics in period determination. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. The nicotinic acetylcholine receptor and its prokaryotic homologues: Structure, conformational transitions & allosteric modulation.

    PubMed

    Cecchini, Marco; Changeux, Jean-Pierre

    2015-09-01

    Pentameric ligand-gated ion channels (pLGICs) play a central role in intercellular communications in the nervous system by converting the binding of a chemical messenger - a neurotransmitter - into an ion flux through the postsynaptic membrane. Here, we present an overview of the most recent advances on the signal transduction mechanism boosted by X-ray crystallography of both prokaryotic and eukaryotic homologues of the nicotinic acetylcholine receptor (nAChR) in conjunction with time-resolved analyses based on single-channel electrophysiology and Molecular Dynamics simulations. The available data consistently point to a global mechanism of gating that involves a large reorganization of the receptor mediated by two distinct quaternary transitions: a global twisting and a radial expansion/contraction of the extracellular domain. These transitions profoundly modify the organization of the interface between subunits, which host several sites for orthosteric and allosteric modulatory ligands. The same mechanism may thus mediate both positive and negative allosteric modulations of pLGICs ligand binding at topographically distinct sites. The emerging picture of signal transduction is expected to pave the way to new pharmacological strategies for the development of allosteric modulators of nAChR and pLGICs in general. This article is part of the Special Issue entitled 'The Nicotinic Acetylcholine Receptor: From Molecular Biology to Cognition'. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Conformation-dependent QSAR approach for the prediction of inhibitory activity of bromodomain modulators.

    PubMed

    García-Jacas, C R; Martinez-Mayorga, K; Marrero-Ponce, Y; Medina-Franco, J L

    2017-01-01

    Epigenetic drug discovery is a promising research field with growing interest in the scientific community, as evidenced by the number of publications and the large amount of structure-epigenetic activity information currently available in the public domain. Computational methods are valuable tools to analyse and understand the activity of large compound collections from their structural information. In this manuscript, QSAR models to predict the inhibitory activity of a diverse and heterogeneous set of 88 organic molecules against the bromodomains BRD2, BRD3 and BRD4 are presented. A conformation-dependent representation of the chemical structures was established using the RDKit software and a training and test set division was performed. Several two-linear and three-linear QuBiLS-MIDAS molecular descriptors ( www.tomocomd.com ) were computed to extract the geometric structural features of the compounds studied. QuBiLS-MIDAS-based features sets, to be used in the modelling, were selected using dimensionality reduction strategies. The multiple linear regression procedure coupled with a genetic algorithm were employed to build the predictive models. Regression models containing between 6 to 9 variables were developed and assessed according to several internal and external validation methods. Analyses of outlier compounds and the applicability domain for each model were performed. As a result, the models against BRD2 and BRD3 with 8 variables and the model with 9 variables against BRD4 were those with the best overall performance according to the criteria accounted for. The results obtained suggest that the models proposed will be a good tool for studying the inhibitory activities of drug candidates against the bromodomains considered during epigenetic drug discovery.

  6. Clinical applications of image guided-intensity modulated radiation therapy (IG-IMRT) for conformal avoidance of normal tissue

    NASA Astrophysics Data System (ADS)

    Gutierrez, Alonso Navar

    2007-12-01

    Recent improvements in imaging technology and radiation delivery have led to the development of advanced treatment techniques in radiotherapy which have opened the door for novel therapeutic approaches to improve the efficacy of radiation cancer treatments. Among these advances is image-guided, intensity modulated radiation therapy (IG-IMRT), in which imaging is incorporated to aid in inter-/intra-fractional target localization and to ensure accurate delivery of precise and highly conformal dose distributions. In principle, clinical implementation of IG-IMRT should improve normal tissue sparing and permit effective biological dose escalation thus widening the radiation therapeutic window and lead to increases in survival through improved local control of primary neoplastic diseases. Details of the development of three clinical applications made possible solely with IG-IMRT radiation delivery techniques are presented: (1) Laparoscopically implanted tissue expander radiotherapy (LITE-RT) has been developed to enhance conformal avoidance of normal tissue during the treatment of intra-abdominopelvic cancers. LITE-RT functions by geometrically displacing surrounding normal tissue and isolating the target volume through the interfractional inflation of a custom-shaped tissue expander throughout the course of treatment. (2) The unique delivery geometry of helical tomotherapy, a novel form of IG-IMRT, enables the delivery of composite treatment plan m which whole brain radiotherapy (WBRT) with hippocampal avoidance, hypothesized to reduce the risk of memory function decline and improve the patient's quality of life, and simultaneously integrated boost to multiple brain metastases to improve intracranial tumor control is achieved. (3) Escalation of biological dose to targets through integrated, selective subvolume boosts have been shown to efficiently increase tumor dose without significantly increasing normal tissue dose. Helical tomotherapy was used to investigate the

  7. Complex interactions between cis-regulatory modules in native conformation are critical for Drosophila snail expression

    PubMed Central

    Dunipace, Leslie; Ozdemir, Anil; Stathopoulos, Angelike

    2011-01-01

    It has been shown in several organisms that multiple cis-regulatory modules (CRMs) of a gene locus can be active concurrently to support similar spatiotemporal expression. To understand the functional importance of such seemingly redundant CRMs, we examined two CRMs from the Drosophila snail gene locus, which are both active in the ventral region of pre-gastrulation embryos. By performing a deletion series in a ∼25 kb DNA rescue construct using BAC recombineering and site-directed transgenesis, we demonstrate that the two CRMs are not redundant. The distal CRM is absolutely required for viability, whereas the proximal CRM is required only under extreme conditions such as high temperature. Consistent with their distinct requirements, the CRMs support distinct expression patterns: the proximal CRM exhibits an expanded expression domain relative to endogenous snail, whereas the distal CRM exhibits almost complete overlap with snail except at the anterior-most pole. We further show that the distal CRM normally limits the increased expression domain of the proximal CRM and that the proximal CRM serves as a `damper' for the expression levels driven by the distal CRM. Thus, the two CRMs interact in cis in a non-additive fashion and these interactions may be important for fine-tuning the domains and levels of gene expression. PMID:21813571

  8. Calcium-modulated conformational affinity chromatography. Application to the purification of calmodulin and S100 proteins.

    PubMed

    Fleminger, G; Neufeld, T; Star-Weinstock, M; Litvak, M; Solomon, B

    1992-04-24

    The purification of proteins by affinity chromatography is based on their highly specific interaction with an immobilized ligand followed by elution under conditions where their affinity towards the ligand is markedly reduced. Thus, a high-degree purification by a single chromatographic step is achieved. However, when several proteins in the crude mixture share affinity to a common immobilized ligand, they may not be resolved by affinity chromatography and subsequent "real" chromatographic purification steps may be required. It is shown that by using properly selected gradient elution conditions, the affinities of the various proteins towards the immobilized ligand may be gradually modulated and their separation may be achieved. This is exemplified by the isolation and separation of a group of Ca(2+)-activated proteins, Calmodulin, S100a and S100b, from bovine brain extract, using a melittin-Eupergit C affinity column which is developed with Ca(2+)-chelator gradients. As expected, separation of the three proteins into individual peaks, eluted in order of increasing affinity to the matrix, was obtained. Sigmoid selectivity curves calculated from the elution volumes under different elution conditions for each of the proteins were obtained, illustrating the chromatographic behaviour of the gradient affinity separation system.

  9. Comparison of Rapid Arc and Intensity-modulated Radiotherapy Plans Using Unified Dosimetry Index and the Impact of Conformity Index on Unified Dosimetry Index Evaluation.

    PubMed

    Krishnan, Jayapalan; Shetty, Jayarama; Rao, Suresh; Hegde, Sanath; Shambhavi, C

    2017-01-01

    The aim of this study was to evaluate the impact of conformity index in the unified dosimetry index (UDI) score for two different planning techniques namely intensity-modulated radiotherapy (IMRT) and Rapid Arc. Rapid Arc and IMRT plans of 57 patients were evaluated and compared using UDI score which incorporates four indices. To determine the impact of conformity index on the IMRT and Rapid Arc plans, UDI at conformity index one of all plan (UDIunit_CI) score was calculated by assuming conformity index is equal to one. Mean and standard deviations of all indices were calculated. Rapid Arc technique plans of different treatment sites of all patients scored lesser UDI than IMRT plans, and the conformity index of Rapid Arc plan was significantly better than IMRT plan. The average dose gradient, homogeneity, coverage, and conformity index of all sites with Rapid Arc plans were 0.212 ± 0.05, 1.123 ± 0.03, 0.959 ± 0.03, and 1.056 ± 0.09; with IMRT plans were 0.190 ± 0.05, 1.113 ± 0.04, 0.950 ± 0.04, and 1.172 ± 0.16, respectively. UDI score value with actual conformity index of Rapid Arc and IMRT plans differed significantly (P < 0.001). However, UDIunit_CI score values with assumed conformity index equal to one did not differ significantly (P = 0.528). In the comparison of IMRT and Rapid Arc plans using the UDI score, the impact of conformity index was significant.

  10. Comparison of Rapid Arc and Intensity-modulated Radiotherapy Plans Using Unified Dosimetry Index and the Impact of Conformity Index on Unified Dosimetry Index Evaluation

    PubMed Central

    Krishnan, Jayapalan; Shetty, Jayarama; Rao, Suresh; Hegde, Sanath; Shambhavi, C

    2017-01-01

    The aim of this study was to evaluate the impact of conformity index in the unified dosimetry index (UDI) score for two different planning techniques namely intensity-modulated radiotherapy (IMRT) and Rapid Arc. Rapid Arc and IMRT plans of 57 patients were evaluated and compared using UDI score which incorporates four indices. To determine the impact of conformity index on the IMRT and Rapid Arc plans, UDI at conformity index one of all plan (UDIunit_CI) score was calculated by assuming conformity index is equal to one. Mean and standard deviations of all indices were calculated. Rapid Arc technique plans of different treatment sites of all patients scored lesser UDI than IMRT plans, and the conformity index of Rapid Arc plan was significantly better than IMRT plan. The average dose gradient, homogeneity, coverage, and conformity index of all sites with Rapid Arc plans were 0.212 ± 0.05, 1.123 ± 0.03, 0.959 ± 0.03, and 1.056 ± 0.09; with IMRT plans were 0.190 ± 0.05, 1.113 ± 0.04, 0.950 ± 0.04, and 1.172 ± 0.16, respectively. UDI score value with actual conformity index of Rapid Arc and IMRT plans differed significantly (P < 0.001). However, UDIunit_CI score values with assumed conformity index equal to one did not differ significantly (P = 0.528). In the comparison of IMRT and Rapid Arc plans using the UDI score, the impact of conformity index was significant. PMID:28405103

  11. Mutation in the β-hairpin of the Bordetella pertussis adenylate cyclase toxin modulates N-lobe conformation in calmodulin

    SciTech Connect

    Springer, Tzvia I.; Goebel, Erich; Hariraju, Dinesh; Finley, Natosha L.

    2014-10-10

    Highlights: • Bordetella pertussis adenylate cyclase toxin modulates bi-lobal structure of CaM. • The structure and stability of the complex rely on intermolecular associations. • A novel mode of CaM-dependent activation of the adenylate cyclase toxin is proposed. - Abstract: Bordetella pertussis, causative agent of whooping cough, produces an adenylate cyclase toxin (CyaA) that is an important virulence factor. In the host cell, the adenylate cyclase domain of CyaA (CyaA-ACD) is activated upon association with calmodulin (CaM), an EF-hand protein comprised of N- and C-lobes (N-CaM and C-CaM, respectively) connected by a flexible tether. Maximal CyaA-ACD activation is achieved through its binding to both lobes of intact CaM, but the structural mechanisms remain unclear. No high-resolution structure of the intact CaM/CyaA-ACD complex is available, but crystal structures of isolated C-CaM bound to CyaA-ACD shed light on the molecular mechanism by which this lobe activates the toxin. Previous studies using molecular modeling, biochemical, and biophysical experiments demonstrate that CyaA-ACD’s β-hairpin participates in site-specific interactions with N-CaM. In this study, we utilize nuclear magnetic resonance (NMR) spectroscopy to probe the molecular association between intact CaM and CyaA-ACD. Our results indicate binding of CyaA-ACD to CaM induces large conformational perturbations mapping to C-CaM, while substantially smaller structural changes are localized primarily to helices I, II, and IV, and the metal-binding sites in N-CaM. Site-specific mutations in CyaA-ACD’s β-hairpin structurally modulate N-CaM, resulting in conformational perturbations in metal binding sites I and II, while no significant structural modifications are observed in C-CaM. Moreover, dynamic light scattering (DLS) analysis reveals that mutation of the β-hairpin results in a decreased hydrodynamic radius (R{sub h}) and reduced thermal stability in the mutant complex. Taken

  12. Dosimetric impact of different CT datasets for stereotactic treatment planning using 3D conformal radiotherapy or volumetric modulated arc therapy.

    PubMed

    Oechsner, Markus; Odersky, Leonhard; Berndt, Johannes; Combs, Stephanie Elisabeth; Wilkens, Jan Jakob; Duma, Marciana Nona

    2015-12-01

    The purpose of this study was to assess the impact on dose to the planning target volume (PTV) and organs at risk (OAR) by using four differently generated CT datasets for dose calculation in stereotactic body radiotherapy (SBRT) of lung and liver tumors. Additionally, dose differences between 3D conformal radiotherapy and volumetric modulated arc therapy (VMAT) plans calculated on these CT datasets were determined. Twenty SBRT patients, ten lung cases and ten liver cases, were retrospectively selected for this study. Treatment plans were optimized on average intensity projection (AIP) CTs using 3D conformal radiotherapy (3D-CRT) and volumetric modulated arc therapy (VMAT). Afterwards, the plans were copied to the planning CTs (PCT), maximum intensity projection (MIP) and mid-ventilation (MidV) CT datasets and dose was recalculated keeping all beam parameters and monitor units unchanged. Ipsilateral lung and liver volumes and dosimetric parameters for PTV (Dmean, D2, D98, D95), ipsilateral lung and liver (Dmean, V30, V20, V10) were determined and statistically analysed using Wilcoxon test. Significant but small mean differences were found for PTV dose between the CTs (lung SBRT: ≤2.5 %; liver SBRT: ≤1.6 %). MIPs achieved the smallest lung and the largest liver volumes. OAR mean doses in MIP plans were distinctly smaller than in the other CT datasets. Furthermore, overlapping of tumors with the diaphragm results in underestimated ipsilateral lung dose in MIP plans. Best agreement was found between AIP and MidV (lung SBRT). Overall, differences in liver SBRT were smaller than in lung SBRT and VMAT plans achieved slightly smaller differences than 3D-CRT plans. Only small differences were found for PTV parameters between the four CT datasets. Larger differences occurred for the doses to organs at risk (ipsilateral lung, liver) especially for MIP plans. No relevant differences were observed between 3D-CRT or VMAT plans. MIP CTs are not appropriate for OAR dose

  13. SU-E-T-62: Cardiac Toxicity in Dynamic Conformal Arc Therapy, Intensity-Modulated Radiation Therapy and Volumetric Modulated Arc Therapy of Lung Cancers

    SciTech Connect

    Ming, X; Zhang, Y; Feng, Y; Zhou, L; Deng, J

    2014-06-01

    Purpose: The cardiac toxicity for lung cancer patients, each treated with dynamic conformal arc therapy (DAT), intensity-modulated radiation therapy (IMRT), or volumetric modulated arc therapy (VMAT) is investigated. Methods: 120 lung patients were selected for this study: 25 treated with DAT, 50 with IMRT and 45 with VMAT. For comparison, all plans were generated in the same treatment planning system, normalized such that the 100% isodose lines encompassed 95% of planning target volume. The plan quality was evaluated in terms of homogeneity index (HI) and 95% conformity index (%95 CI) for target dose coverage and mean dose, maximum dose, V{sub 30} Gy as well as V{sub 5} Gy for cardiac toxicity analysis. Results: When all the plans were analyzed, the VMAT plans offered the best target coverage with 95% CI = 0.992 and HI = 1.23. The DAT plans provided the best heart sparing with mean heart dose = 2.3Gy and maximum dose = 11.6Gy, as compared to 5.7 Gy and 31.1 Gy by IMRT as well as 4.6 Gy and 30.9 Gy by VMAT. The mean V30Gy and V5Gy of the heart in the DAT plans were up to 11.7% lower in comparison to the IMRT and VMAT plans. When the tumor volume was considered, the VMAT plans spared up to 70.9% more doses to the heart when the equivalent diameter of the tumor was larger than 4cm. Yet the maximum dose to the heart was reduced the most in the DAT plans with up to 139.8% less than that of the other two plans. Conclusion: Overall, the VMAT plans achieved the best target coverage among the three treatment modalities, and would spare the heart the most for the larger tumors. The DAT plans appeared advantageous in delivering the least maximum dose to the heart as compared to the IMRT and VMAT plans.

  14. Dosimetric Comparison of Three-Dimensional Conformal Proton Radiotherapy, Intensity-Modulated Proton Therapy, and Intensity-Modulated Radiotherapy for Treatment of Pediatric Craniopharyngiomas

    SciTech Connect

    Boehling, Nicholas S.; Grosshans, David R.; Bluett, Jaques B.; Palmer, Matthew T.; Song, Xiaofei; Amos, Richard A.; Sahoo, Narayan; Meyer, Jeffrey J.; Mahajan, Anita; Woo, Shiao Y.

    2012-02-01

    Purpose: Cranial irradiation in pediatric patients is associated with serious long-term adverse effects. We sought to determine whether both three-dimensional conformal proton radiotherapy (3D-PRT) and intensity-modulated proton therapy (IMPT) compared with intensity-modulated radiotherapy (IMRT) decrease integral dose to brain areas known to harbor neuronal stem cells, major blood vessels, and other normal brain structures for pediatric patients with craniopharyngiomas. Methods and Materials: IMRT, forward planned, passive scattering proton, and IMPT plans were generated and optimized for 10 pediatric patients. The dose was 50.4 Gy (or cobalt Gy equivalent) delivered in 28 fractions with the requirement for planning target volume (PTV) coverage of 95% or better. Integral dose data were calculated from differential dose-volume histograms. Results: The PTV target coverage was adequate for all modalities. IMRT and IMPT yielded the most conformal plans in comparison to 3D-PRT. Compared with IMRT, 3D-PRT and IMPT plans had a relative reduction of integral dose to the hippocampus (3D-PRT, 20.4; IMPT, 51.3%{sup Asterisk-Operator }), dentate gyrus (27.3, 75.0%{sup Asterisk-Operator }), and subventricular zone (4.5, 57.8%{sup Asterisk-Operator }). Vascular organs at risk also had reduced integral dose with the use of proton therapy (anterior cerebral arteries, 33.3{sup Asterisk-Operator }, 100.0%{sup Asterisk-Operator }; middle cerebral arteries, 25.9%{sup Asterisk-Operator }, 100%{sup Asterisk-Operator }; anterior communicating arteries, 30.8{sup Asterisk-Operator }, 41.7%{sup Asterisk-Operator }; and carotid arteries, 51.5{sup Asterisk-Operator }, 77.6{sup Asterisk-Operator }). Relative reduction of integral dose to the infratentorial brain (190.7{sup Asterisk-Operator }, 109.7%{sup Asterisk-Operator }), supratentorial brain without PTV (9.6, 26.8%{sup Asterisk-Operator }), brainstem (45.6, 22.4%{sup Asterisk-Operator }), and whole brain without PTV (19.4{sup Asterisk

  15. Conventional, conformal, and intensity-modulated radiation therapy treatment planning of external beam radiotherapy for cervical cancer: The impact of tumor regression.

    PubMed

    van de Bunt, Linda; van der Heide, Uulke A; Ketelaars, Martijn; de Kort, Gerard A P; Jürgenliemk-Schulz, Ina M

    2006-01-01

    Investigating the impact of tumor regression on the dose within cervical tumors and surrounding organs, comparing conventional, conformal, and intensity-modulated radiotherapy (IMRT) and the need for repeated treatment planning during irradiation. Fourteen patients with cervical cancer underwent magnetic resonance (MR) imaging before treatment and once during treatment, after about 30 Gy. Target volumes and critical organs were delineated. First conventional, conformal, and IMRT plans were generated. To evaluate the impact of tumor regression, we calculated dose-volume histograms for these plans, using the delineations of the intratreatment MR images. Second conformal and IMRT plans were made based on the delineations of the intratreatment MR images. First and second plans were compared. The average volume receiving 95% of the prescribed dose (43 Gy) by the conventional, conformal, and IMRT plans was, respectively, for the bowel 626 cc, 427 cc, and 232 cc; for the rectum 101 cc, 90 cc, and 60 cc; and for the bladder 89 cc, 70 cc, and 58 cc. The volumes of critical organs at this dose level were significantly reduced using IMRT compared with conventional and conformal planning (p < 0.02 in all cases). After having delivered about 30 Gy external beam radiation therapy, the primary gross tumor volumes decreased on average by 46% (range, 6.1-100%). The target volumes on the intratreatment MR images remained sufficiently covered by the 95% isodose. Second IMRT plans significantly diminished the treated bowel volume, if the primary gross tumor volumes decreased >30 cc. Intensity-modulated radiation therapy is superior in sparing of critical organs compared with conventional and conformal treatment, with adequate coverage of the target volumes. Intensity-modulated radiation therapy remains superior after 30 Gy external beam radiation therapy, despite tumor regression and internal organ motion. Repeated IMRT planning can improve the sparing of the bowel and rectum in

  16. Comparison of volumetric-modulated arc therapy and dynamic conformal arc treatment planning for cranial stereotactic radiosurgery.

    PubMed

    Molinier, Jessica; Kerr, Christine; Simeon, Sebastien; Ailleres, Norbert; Charissoux, Marie; Azria, David; Fenoglietto, Pascal

    2016-01-08

    The aim was to analyze arc therapy techniques according to the number and position of the brain lesions reported by comparing dynamic noncoplanar conformal arcs (DCA), two coplanar full arcs (RAC) with volumetric-modulated arc therapy (VMAT), multiple noncoplanar partial arcs with VMAT (RANC), and two full arcs with VMAT and 10° table rotation (RAT). Patients with a single lesion (n= 10), multiple lesions (n = 10) or a single lesion close to organs at risk (n = 5) and previously treated with DCA were selected. For each patient, the DCA treatment was replanned with all VMAT techniques. All DCA plans were compared with VMAT plans and evaluated in regard to the different quality indices and dosimetric parameters. For single lesion, homogeneity index (HI) better results were found for the RANC technique (0.17 ± 0.05) compared with DCA procedure (0.27± 0.05). Concerning conformity index (CI), the RAT technique gave higher and better values (0.85 ± 0.04) compared with those obtained with the DCA technique (0.77 ± 0.05). DCA improved healthy brain protection (8.35 ± 5.61 cc vs. 10.52 ± 6.40 cc for RANC) and reduced monitor unit numbers (3046 ± 374 MU vs. 4651 ± 736 for RANC), even if global room occupation was higher. For multiple lesions, VMAT techniques provided better HI (0.16) than DCA (0.24 ± 0.07). The CI was improved with RAT (0.8 ± 0.08 for RAT vs. 0.71 ± 0.08 for DCA). The V10Gy healthy brain was better protected with DCA (9.27 ± 4.57 cc). Regarding the MU numbers: RANC < RAT< RAC < DCA. For a single lesion close to OAR, RAT achieved high degrees of homogeneity (0.27 ± 0.03 vs. 0.53 ± 0.2 for DCA) and conformity (0.72± 0.06vs. 0.56 ± 0.13 for DCA) while sparing organs at risk (Dmax = 12.36 ± 1.05Gyvs. 14.12 ± 0.59 Gy for DCA, and Dmean = 3.96 ± 3.57Gyvs. 4.72 ± 3.28Gy for DCA). On the other hand, MU numbers were lower with DCA (2254 ± 190 MUvs. 3438 ± 457 MU for RANC) even if overall time was inferior with RAC. For a single lesion, DCA

  17. Dosimetric Evaluation of Intensity Modulated Radiotherapy and 4-Field 3-D Conformal Radiotherapy in Prostate Cancer Treatment

    PubMed Central

    Uysal, Bora; Beyzadeoğlu, Murat; Sager, Ömer; Dinçoğlan, Ferrat; Demiral, Selçuk; Gamsız, Hakan; Sürenkök, Serdar; Oysul, Kaan

    2013-01-01

    Objective: The purpose of this dosimetric study is the targeted dose homogeneity and critical organ dose comparison of 7-field Intensity Modulated Radiotherapy (IMRT) and 3-D 4-field conformal radiotherapy. Study Design: Cross sectional study. Material and Methods: Twenty patients with low and moderate risk prostate cancer treated at Gülhane Military Medical School Radiation Oncology Department between January 2009 and December 2009 are included in this study. Two seperate dosimetric plans both for 7-field IMRT and 3D-CRT have been generated for each patient to comparatively evaluate the dosimetric status of both techniques and all the patients received 7-field IMRT. Results: Dose-comparative evaluation of two techniques revealed the superiority of IMRT technique with statistically significantly lower femoral head doses along with reduced critical organ dose-volume parameters of bladder V60 (the volume receiving 60 Gy) and rectal V40 (the volume receiving 40 Gy) and V60. Conclusion: It can be concluded that IMRT is an effective definitive management tool for prostate cancer with improved critical organ sparing and excellent dose homogenization in target organs of prostate and seminal vesicles. PMID:25207069

  18. Comparison of intensity-modulated radiotherapy with three-dimensional conformal radiation therapy planning for glioblastoma multiforme

    SciTech Connect

    Chan, Maria F.; Schupak, Karen; Burman, Chandra; Chui, C.-S.; Ling, C. Clifton

    2003-12-31

    This study was designed to assess the feasibility and potential benefit of using intensity-modulated radiotherapy (IMRT) planning for patients newly diagnosed with glioblastoma multiforme (GBM). Five consecutive patients with confirmed histopathologically GBM were entered into the study. These patients were planned and treated with 3-dimensional conformal radiation therapy (3DCRT) using our standard plan of 3 noncoplanar wedged fields. They were then replanned with the IMRT method that included a simultaneous boost to the gross tumor volume (GTV). The dose distributions and dose-volume histograms (DHVs) for the planning treatment volume (PTV), GTV, and the relevant critical structures, as obtained with 3DCRT and IMRT, respectively, were compared. In both the 3DCRT and IMRT plans, 59.4 Gy was delivered to the GTV plus a margin of 2.5 cm, with doses to critical structures below the tolerance threshold. However, with the simultaneous boost in IMRT, a higher tumor dose of {approx}70 Gy could be delivered to the GTV, while still maintaining the uninvolved brain at dose levels of the 3DCRT technique. In addition, our experience indicated that IMRT planning is less labor intensive and time consuming than 3DCRT planning. Our study shows that IMRT planning is feasible and efficient for radiotherapy of GBM. In particular, IMRT can deliver a simultaneous boost to the GTV while better sparing the normal brain and other critical structures.

  19. A Comparison of Helical Intensity-Modulated Radiotherapy, Intensity-Modulated Radiotherapy, and 3D-Conformal Radiation Therapy for Pancreatic Cancer

    SciTech Connect

    Poppe, Matthew M.; Narra, Venkat; Yue, Ning J.; Zhou Jinghao; Nelson, Carl; Jabbour, Salma K.

    2011-01-01

    We assessed dosimetric differences in pancreatic cancer radiotherapy via helical intensity-modulated radiotherapy (HIMRT), linac-based IMRT, and 3D-conformal radiation therapy (3D-CRT) with regard to successful plan acceptance and dose to critical organs. Dosimetric analysis was performed in 16 pancreatic cases that were planned to 54 Gy; both post-pancreaticoduodenectomy (n = 8) and unresected (n = 8) cases were compared. Without volume modification, plans met constraints 75% of the time with HIMRT and IMRT and 13% with 3D-CRT. There was no statistically significantly improvement with HIMRT over conventional IMRT in reducing liver V35, stomach V45, or bowel V45. HIMRT offers improved planning target volume (PTV) dose homogeneity compared with IMRT, averaging a lower maximum dose and higher volume receiving the prescription dose (D100). HIMRT showed an increased mean dose over IMRT to bowel and liver. Both HIMRT and IMRT offer a statistically significant improvement over 3D-CRT in lowering dose to liver, stomach, and bowel. The results were similar for both unresected and resected patients. In pancreatic cancer, HIMRT offers improved dose homogeneity over conventional IMRT and several significant benefits to 3D-CRT. Factors to consider before incorporating IMRT into pancreatic cancer therapy are respiratory motion, dose inhomogeneity, and mean dose.

  20. Involved-Site Image-Guided Intensity Modulated Versus 3D Conformal Radiation Therapy in Early Stage Supradiaphragmatic Hodgkin Lymphoma

    SciTech Connect

    Filippi, Andrea Riccardo; Ciammella, Patrizia; Piva, Cristina; Ragona, Riccardo; Botto, Barbara; Gavarotti, Paolo; Merli, Francesco; Vitolo, Umberto; Iotti, Cinzia; Ricardi, Umberto

    2014-06-01

    Purpose: Image-guided intensity modulated radiation therapy (IG-IMRT) allows for margin reduction and highly conformal dose distribution, with consistent advantages in sparing of normal tissues. The purpose of this retrospective study was to compare involved-site IG-IMRT with involved-site 3D conformal RT (3D-CRT) in the treatment of early stage Hodgkin lymphoma (HL) involving the mediastinum, with efficacy and toxicity as primary clinical endpoints. Methods and Materials: We analyzed 90 stage IIA HL patients treated with either involved-site 3D-CRT or IG-IMRT between 2005 and 2012 in 2 different institutions. Inclusion criteria were favorable or unfavorable disease (according to European Organization for Research and Treatment of Cancer criteria), complete response after 3 to 4 cycles of an adriamycin- bleomycin-vinblastine-dacarbazine (ABVD) regimen plus 30 Gy as total radiation dose. Exclusion criteria were chemotherapy other than ABVD, partial response after ABVD, total radiation dose other than 30 Gy. Clinical endpoints were relapse-free survival (RFS) and acute toxicity. Results: Forty-nine patients were treated with 3D-CRT (54.4%) and 41 with IG-IMRT (45.6%). Median follow-up time was 54.2 months for 3D-CRT and 24.1 months for IG-IMRT. No differences in RFS were observed between the 2 groups, with 1 relapse each. Three-year RFS was 98.7% for 3D-CRT and 100% for IG-IMRT. Grade 2 toxicity events, mainly mucositis, were recorded in 32.7% of 3D-CRT patients (16 of 49) and in 9.8% of IG-IMRT patients (4 of 41). IG-IMRT was significantly associated with a lower incidence of grade 2 acute toxicity (P=.043). Conclusions: RFS rates at 3 years were extremely high in both groups, albeit the median follow-up time is different. Acute tolerance profiles were better for IG-IMRT than for 3D-CRT. Our preliminary results support the clinical safety and efficacy of advanced RT planning and delivery techniques in patients affected with early stage HL, achieving complete

  1. Patient-Reported Outcomes After 3-Dimensional Conformal, Intensity-Modulated, or Proton Beam Radiotherapy for Localized Prostate Cancer

    PubMed Central

    Gray, Phillip J.; Paly, Jonathan J.; Yeap, Beow Y.; Sanda, Martin G.; Sandler, Howard. M.; Michalski, Jeff M.; Talcott, James A.; Coen, John J.; Hamstra, Daniel A.; Shipley, William U.; Hahn, Stephen M.; Zietman, Anthony L.; Bekelman, Justin E.; Efstathiou, Jason A.

    2013-01-01

    BACKGROUND Recent studies have suggested differing toxicity patterns for patients with prostate cancer who receive treatment with 3-dimensional conformal radiotherapy (3DCRT), intensity-modulated radiotherapy (IMRT), or proton beam therapy (PBT). METHODS The authors reviewed patient-reported outcomes data collected prospectively using validated instruments that assessed bowel and urinary quality of life (QOL) for patients with localized prostate cancer who received 3DCRT (n = 123), IMRT (n = 153) or PBT (n = 95). Clinically meaningful differences in mean QOL scores were defined as those exceeding half the standard deviation of the baseline mean value. Changes from baseline were compared within groups at the first post-treatment follow-up (2–3 months from the start of treatment) and at 12 months and 24 months. RESULTS At the first post-treatment follow-up, patients who received 3DCRT and IMRT, but not those who received PBT, reported a clinically meaningful decrement in bowel QOL. At 12 months and 24 months, all 3 cohorts reported clinically meaningful decrements in bowel QOL. Patients who received IMRT reported clinically meaningful decrements in the domains of urinary irritation/obstruction and incontinence at the first post-treatment follow-up. At 12 months, patients who received PBT, but not those who received IMRT or 3DCRT, reported a clinically meaningful decrement in the urinary irritation/ obstruction domain. At 24 months, none of the 3 cohorts reported clinically meaningful changes in urinary QOL. CONCLUSIONS Patients who received 3DCRT, IMRT, or PBT reported distinct patterns of treatment-related QOL. Although the timing of toxicity varied between the cohorts, patients reported similar modest QOL decrements in the bowel domain and minimal QOL decrements in the urinary domains at 24 months. Prospective randomized trials are needed to further examine these differences. PMID:23436283

  2. Cost-Effectiveness Analysis of Intensity Modulated Radiation Therapy Versus 3-Dimensional Conformal Radiation Therapy for Anal Cancer

    SciTech Connect

    Hodges, Joseph C.; Beg, Muhammad S.; Das, Prajnan; Meyer, Jeffrey

    2014-07-15

    Purpose: To compare the cost-effectiveness of intensity modulated radiation therapy (IMRT) and 3-dimensional conformal radiation therapy (3D-CRT) for anal cancer and determine disease, patient, and treatment parameters that influence the result. Methods and Materials: A Markov decision model was designed with the various disease states for the base case of a 65-year-old patient with anal cancer treated with either IMRT or 3D-CRT and concurrent chemotherapy. Health states accounting for rates of local failure, colostomy failure, treatment breaks, patient prognosis, acute and late toxicities, and the utility of toxicities were informed by existing literature and analyzed with deterministic and probabilistic sensitivity analysis. Results: In the base case, mean costs and quality-adjusted life expectancy in years (QALY) for IMRT and 3D-CRT were $32,291 (4.81) and $28,444 (4.78), respectively, resulting in an incremental cost-effectiveness ratio of $128,233/QALY for IMRT compared with 3D-CRT. Probabilistic sensitivity analysis found that IMRT was cost-effective in 22%, 47%, and 65% of iterations at willingness-to-pay thresholds of $50,000, $100,000, and $150,000 per QALY, respectively. Conclusions: In our base model, IMRT was a cost-ineffective strategy despite the reduced acute treatment toxicities and their associated costs of management. The model outcome was sensitive to variations in local and colostomy failure rates, as well as patient-reported utilities relating to acute toxicities.

  3. Modulation of arginine decarboxylase activity from Mycobacterium smegmatis. Evidence for pyridoxal-5'-phosphate-mediated conformational changes in the enzyme.

    PubMed

    Balasundaram, D; Tyagi, A K

    1989-08-01

    Arginine decarboxylase (arginine carboxy-lyase, EC 4.1.1.19) from Mycobacterium smegmatis, TMC 1546 has been purified to homogeneity. The enzyme has a molecular mass of 232 kDa and a subunit mass of 58.9 kDa. The enzyme from mycobacteria is totally dependent on pyridoxal 5'-phosphate for its activity at its optimal pH and, unlike that from Escherichia coli, Mg2+ does not play an active role in the enzyme conformation. The enzyme is specific for arginine (Km = 1.6 mM). The holoenzyme is completely resolved in dialysis against hydroxylamine. Reconstitution of the apoenzyme with pyridoxal 5'-phosphate shows sigmoidal binding characteristics at pH 8.4 with a Hill coefficient of 2.77, whereas at pH 6.2 the binding is hyperbolic in nature. The kinetics of reconstitution at pH 8.4 are apparently sigmoidal, indicating the occurrence of two binding types of differing strengths. A low-affinity (Kd = 22.5 microM) binding to apoenzyme at high pyridoxal 5'-phosphate concentrations and a high-affinity (Kd = 3.0 microM) binding to apoenzyme at high pyridoxal 5'-phosphate concentrations. The restoration of full activity occurred in parallel with the tight binding (high affinity) of pyridoxal 5'-phosphate to the apoenzyme. Along with these characteristics, spectral analyses of holoenzyme and apoenzyme at pH 8.4 and pH 6.2 indicate a pH-dependent modulation of coenzyme function. Based on the pH-dependent changes in the polarity of the active-site environment, pyridoxal 5'-phosphate forms different Schiff-base tautomers at pH 8.4 and pH 6.2 with absorption maxima at 415 nm and 333 nm, respectively. These separate forms of Schiff-base confer different catalytic efficiencies to the enzyme.

  4. Treatment Planning Study to Determine Potential Benefit of Intensity-Modulated Radiotherapy Versus Conformal Radiotherapy for Unresectable Hepatic Malignancies

    SciTech Connect

    Eccles, Cynthia L.; Bissonnette, Jean-Pierre; Craig, Tim; Taremi, Mojgan; Wu Xia; Dawson, Laura A.

    2008-10-01

    Purpose: To compare intensity-modulated radiotherapy (IMRT) with conformal RT (CRT) for hypofractionated isotoxicity liver RT and explore dose escalation using IMRT for the same/improved nominal risk of liver toxicity in a treatment planning study. Methods and Materials: A total of 26 CRT plans were evaluated. Prescription doses (24-54 Gy within six fractions) were individualized on the basis of the effective liver volume irradiated maintaining {<=}5% risk of radiation-induced liver disease. The dose constraints included bowel (0.5 cm{sup 3}) and stomach (0.5 cm{sup 3}) to {<=}30 Gy, spinal cord to {<=}25 Gy, and planning target volume (PTV) to {<=}140% of the prescribed dose. Two groups were evaluated: (1) PTV overlapping or directly adjacent to serial functioning normal tissues (n = 14), and (2) the liver as the dose-limiting normal tissue (n = 12). IMRT plans using direct machine parameter optimization maintained the CRT plan beam arrangements, an estimated radiation-induced liver disease risk of 5%, and underwent dose escalation, if all normal tissue constraints were maintained. Results: IMRT improved PTV coverage in 19 of 26 plans (73%). Dose escalation was feasible in 9 cases by an average of 3.8 Gy (range, 0.6-13.2) in six fractions. Three of seven plans without improved PTV coverage had small gross tumor volumes ({<=}105 cm{sup 3}) already receiving 54 Gy, the maximal prescription dose allowed. In the remaining cases, the PTV range was 9.6-689 cm{sup 3}; two had overlapped organs at risk; and one had four targets. IMRT did not improve these plans owing to poor target coverage (n = 2) and nonliver (n = 2) dose limits. Conclusion: Direct machine parameter optimization IMRT improved PTV coverage while maintaining normal tissue tolerances in most CRT liver plans. Dose escalation was possible in a minority of patients.

  5. Indirect readout of DNA sequence by p22 repressor: roles of DNA and protein functional groups in modulating DNA conformation.

    PubMed

    Harris, Lydia-Ann; Watkins, Derrick; Williams, Loren Dean; Koudelka, Gerald B

    2013-01-09

    The repressor of bacteriophage P22 (P22R) discriminates between its various DNA binding sites by sensing the identity of non-contacted base pairs at the center of its binding site. The "indirect readout" of these non-contacted bases is apparently based on DNA's sequence-dependent conformational preferences. The structures of P22R-DNA complexes indicate that the non-contacted base pairs at the center of the binding site are in the B' state. This finding suggests that indirect readout and therefore binding site discrimination depend on P22R's ability to either sense and/or impose the B' state on the non-contacted bases of its binding sites. We show here that the affinity of binding sites for P22R depends on the tendency of the central bases to assume the B'-DNA state. Furthermore, we identify functional groups in the minor groove of the non-contacted bases as the essential modulators of indirect readout by P22R. In P22R-DNA complexes, the negatively charged E44 and E48 residues are provocatively positioned near the negatively charged DNA phosphates of the non-contacted nucleotides. The close proximity of the negatively charged groups on protein and DNA suggests that electrostatics may play a key role in the indirect readout process. Changing either of two negatively charged residues to uncharged residues eliminates the ability of P22R to impose structural changes on DNA and to recognize non-contacted base sequence. These findings suggest that these negatively charged amino acids function to force the P22R-bound DNA into the B' state and therefore play a key role in indirect readout by P22R.

  6. Assessment and Comparison of Homogeneity and Conformity Indexes in Step-and-Shoot and Compensator-Based Intensity Modulated Radiation Therapy (IMRT) and Three-Dimensional Conformal Radiation Therapy (3D CRT) in Prostate Cancer

    PubMed Central

    Salimi, Marzieh; Abi, Kaveh Shirani Tak; Nedaie, Hassan Ali; Hassani, Hossein; Gharaati, Hussain; Samei, Mahmood; Shahi, Rezgar; Zarei, Hamed

    2017-01-01

    Intensity modulated radiation therapy (IMRT) and three-dimensional conformal radiation therapy (3D CRT) are two treatment modalities in prostate cancer, which provide acceptable dose distribution in tumor region with sparing the surrounding normal tissues. IMRT is based on inverse planning optimization; in which, intensity of beams is modified by using multileaf collimators and also compensators with optimum shapes in step and shoot (SAS) and compensator-based method, respectively. In the recent study, some important parameters were compared in two IMRT and 3D CRT methods. Prescribed dose was 80 Gy for both IMRT procedures and 70 Gy for 3D CRT. Treatment plans of 15 prostate cancer candidates were compared to target the minimum dose, maximum dose, V 76 Gy (for IMRT plans) V 66.5 Gy (for 3D CRT), mean dose, conformity index (CI), and homogeneity index (HI). Dose conformity in compensators-based IMRT was better than SAS and 3D CRT. The same outcome was also achieved for homogeneity index. The target coverage was achieved 95% of prescribed dose to 95% of planning target volume (PTV) in 3D CRT and 95% of prescribed dose to 98% of PTV in IMRT methods. IMRT increases maximum dose of tumor region, improves CI and HI of target volume, and also reduces dose of organs at risks. PMID:28553583

  7. Intensity modulated radiotherapy in early stage Hodgkin lymphoma patients: Is it better than three dimensional conformal radiotherapy?

    PubMed Central

    2012-01-01

    Background Cure rate of early Hodgkin Lymphoma are high and avoidance of late toxicities is of paramount importance. This comparative study aims to assess the normal tissue sparing capability of intensity-modulated radiation therapy (IMRT) versus standard three-dimensional conformal radiotherapy (3D-CRT) in terms of dose-volume parameters and normal tissue complication probability (NTCP) for different organs at risk in supradiaphragmatic Hodgkin Lymphoma (HL) patients. Methods Ten HL patients were actually treated with 3D-CRT and all treatments were then re-planned with IMRT. Dose-volume parameters for thyroid, oesophagus, heart, coronary arteries, lung, spinal cord and breast were evaluated. Dose-volume histograms generated by TPS were analyzed to predict the NTCP for the considered organs at risk, according to different endpoints. Results Regarding dose-volume parameters no statistically significant differences were recorded for heart and origin of coronary arteries. We recorded statistically significant lower V30 with IMRT for oesophagus (6.42 vs 0.33, p = 0.02) and lungs (4.7 vs 0.1 p = 0.014 for the left lung and 2.59 vs 0.1 p = 0.017 for the right lung) and lower V20 for spinal cord (17.8 vs 7.2 p = 0.02). Moreover the maximum dose to the spinal cord was lower with IMRT (30.2 vs 19.9, p <0.001). Higher V10 with IMRT for thyroid (64.8 vs 95, p = 0.0019) and V5 for lungs (30.3 vs 44.8, p = 0.03, for right lung and 28.9 vs 48.1, p = 0.001 for left lung) were found, respectively. Higher V5 and V10 for breasts were found with IMRT (V5: 4.14 vs 20.6, p = 0.018 for left breast and 3.3 vs 17, p = 0.059 for right breast; V10: 2.5 vs 13.6 p = 0.035 for left breast and 1.7 vs 11, p = 0.07 for the right breast.) As for the NTCP, our data point out that IMRT is not always likely to significantly increase the NTCP to OARs. Conclusions In HL male patients IMRT seems feasible and accurate while for women HL patients IMRT should be

  8. The conserved disulfide bond of human tear lipocalin modulates conformation and lipid binding in a ligand selective manner

    PubMed Central

    Gasymov, Oktay K.; Abduragimov, Adil R.; Glasgow, Ben J.

    2011-01-01

    The primary aim of this study is the elucidation of the mechanism of disulfide induced alteration of ligand binding in human tear lipocalin (TL). Disulfide bonds may act as dynamic scaffolds to regulate conformational changes that alter protein function including receptor-ligand interactions. A single disulfide bond, (Cys61-Cys153), exists in TL that is highly conserved in the lipocalin superfamily. Circular dichroism and fluorescence spectroscopies were applied to investigate the mechanism by which disulfide bond removal effects protein stability, dynamics and ligand binding properties. Although the secondary structure is not altered by disulfide elimination, TL shows decreased stability against urea denaturation. Free energy change (ΔG0) decreases from 4.9± 0.2 to 2.1± 0.3 kcal/mol with removal of the disulfide bond. Furthermore, ligand binding properties of TL without the disulfide vary according to the type of ligand. The binding of a bulky ligand, NBD-cholesterol, has a decreased time constant (from 11.8± 0.2 to 3.3 s). In contrast, the NBD-labeled phospholipid shows a moderate decrease in the time constant for binding, from 33.2± 0.2 to 22.2± 0.4 s. FRET experiments indicate that the hairpin CD is directly involved in modulation of both ligand binding and flexibility of TL. In TL complexed with palmitc acid (PA-TL), the distance between the residues 62 of strand D and 81 of loop EF is decreased by disulfide bond reduction. Consequently, removal of the disulfide bond boosts flexibility of the protein to reach a CD-EF loop distance (24.3 Å, between residues 62 and 81), which is not accessible for the protein with an intact disulfide bond (26.2 Å). The results suggest that enhanced flexibility of the protein promotes a faster accommodation of the ligand inside the cavity and energetically favorable ligand-protein complex. PMID:21466861

  9. High-dose radiotherapy in inoperable nonsmall cell lung cancer: Comparison of volumetric modulated arc therapy, dynamic IMRT and 3D conformal radiotherapy

    SciTech Connect

    Bree, Ingrid de; Hinsberg, Marieelle G.E. van; Veelen, Lieneke R. van

    2012-01-01

    Conformal 3D radiotherapy (3D-CRT) combined with chemotherapy for inoperable non-small cell lung cancer (NSCLC) to the preferable high dose is often not achievable because of dose-limiting organs. This reduces the probability of regional tumor control. Therefore, the surplus value of using intensity-modulated radiation therapy (IMRT) techniques, specifically volumetric modulated arc therapy (RapidArc [RA]) and dynamic IMRT (d-IMRT) has been investigated. RA and d-IMRT plans were compared with 3D-CRT treatment plans for 20 patients eligible for concurrent high-dose chemoradiotherapy, in whom a dose of 60 Gy was not achievable. Comparison of dose delivery in the target volume and organs at risk was carried out by evaluating 3D dose distributions and dose-volume histograms. Quality of the dose distribution was assessed using the inhomogeneity and conformity index. For most patients, a higher dose to the target volume can be delivered using RA or d-IMRT; in 15% of the patients a dose {>=}60 Gy was possible. Both IMRT techniques result in a better conformity of the dose (p < 0.001). There are no significant differences in homogeneity of dose in the target volume. IMRT techniques for NSCLC patients allow higher dose to the target volume, thus improving regional tumor control.

  10. Three-dimensional conformal versus intensity-modulated radiotherapy dose planning in stereotactic radiotherapy: Application of standard quality parameters for plan evaluation

    SciTech Connect

    Grzadziel, Aleksandra; Grosu, Anca-Ligia . E-mail: anca-ligia.grosu@lrz.tum.de; Kneschaurek, Peter

    2006-11-15

    Purpose: The implementation of intensity-modulated radiotherapy (IMRT) technique into clinical practice is becoming routine, but still lacks a generally accepted method for plan evaluation. We present a comparison of the dose distribution of conformal three-dimensional radiotherapy plans with IMRT plans for cranial lesions in stereotactic radiotherapy. The primary aim of this study was to judge the quality of the treatment plans. The next purpose was to assess the usefulness of several quality factors for plan evaluation. Methods and Materials: Five patients, who were treated in our department, were analyzed. Four had meningioma and one had pituitary adenoma. For each case, 10 different plans were created and analyzed: 2 conventional conformal three-dimensional plans and 8 IMRT plans, using the 'step and shoot' delivery method. The first conventional plan was an individually designed beam arrangement and was used for patient treatment. The second plan was a standard plan with the same beam arrangement for all patients. Beam arrangements from the conformal plans were the base for the inversely planned IMRT. To evaluate the plans, the following factors were investigated: minimal and maximal dose to the planning target volume, homogeneity index, coverage index, conformity index, and tumor control probabilities and normal tissue complication probabilities. These quantities were incorporated into scoring factors and assigned to each plan. Results: The greatest homogeneity was reached in the conformal plans and IMRT plans with high planning target volume priority in the optimization process. This consequently led to a better probability of tumor control. Better protection of organs at risk and thereby lower normal tissue complication probabilities were achieved in the IMRT plans with increased weighting of the organs at risk. Conclusion: These results show the efficiency, as well as some limitations, of the IMRT techniques. The use of different quality factors allowed us

  11. Nucleotide binding triggers a conformational change of the CBS module of the magnesium transporter CNNM2 from a twisted towards a flat structure.

    PubMed

    Corral-Rodríguez, María Ángeles; Stuiver, Marchel; Abascal-Palacios, Guillermo; Diercks, Tammo; Oyenarte, Iker; Ereño-Orbea, June; de Opakua, Alain Ibáñez; Blanco, Francisco J; Encinar, José Antonio; Spiwok, Vojtêch; Terashima, Hiroyuki; Accardi, Alessio; Müller, Dominik; Martínez-Cruz, Luis Alfonso

    2014-11-15

    Recent studies suggest CNNM2 (cyclin M2) to be part of the long-sought basolateral Mg2+ extruder at the renal distal convoluted tubule, or its regulator. In the present study, we explore structural features and ligand-binding capacities of the Bateman module of CNNM2 (residues 429-584), an intracellular domain structurally equivalent to the region involved in Mg2+ handling by the bacterial Mg2+ transporter MgtE, and AMP binding by the Mg2+ efflux protein CorC. Additionally, we studied the structural impact of the pathogenic mutation T568I located in this region. Our crystal structures reveal that nucleotides such as AMP, ADP or ATP bind at only one of the two cavities present in CNNM2429-584. Mg2+ favours ATP binding by alleviating the otherwise negative charge repulsion existing between acidic residues and the polyphosphate group of ATP. In crystals CNNM2429-584 forms parallel dimers, commonly referred to as CBS (cystathionine β-synthase) modules. Interestingly, nucleotide binding triggers a conformational change in the CBS module from a twisted towards a flat disc-like structure that mostly affects the structural elements connecting the Bateman module with the transmembrane region. We furthermore show that the T568I mutation, which causes dominant hypomagnesaemia, mimics the structural effect induced by nucleotide binding. The results of the present study suggest that the T568I mutation exerts its pathogenic effect in humans by constraining the conformational equilibrium of the CBS module of CNNM2, which becomes 'locked' in its flat form.

  12. Telemetre Laser a Onde Entretenue a 10.6 micrometers avec Postdetection non Lineaire: Etude d’un Systeme a un Laser (A 10.6 micrometer Amplitude Modulated Telemeter Laser with Nonlinear Postdetection: Study of a Single Laser System),

    DTIC Science & Technology

    1981-04-01

    polarisation ’Is" (lames X/2 et CaF 2enlev~es). Deux lentilles L 1et L2(Ge, f = 20 cm) permettent d’injecter le faisceau laser (w =2.5 mm) dans le cristal...CLASSIFIE 9 Le faisceau modul6 est envoy6 sur la cible qui le retourne au d~tecteur a travers une lentille L 3 (ZnSe, f = 12.5 cm,, diam. = 5 cm) ou L 4 (Ge...modulateur, mesur~e a X = 10.6 u~m, est la suivante: Ttotale )j.3 TX4 = .8 o1 085, T CdTe .5 sans lentilles ). 4.3 Systame de d6tection et de

  13. Radiobiologic comparison of helical tomotherapy, intensity modulated radiotherapy, and conformal radiotherapy in treating lung cancer accounting for secondary malignancy risks

    SciTech Connect

    Komisopoulos, Georgios; Mavroidis, Panayiotis; Rodriguez, Salvador; Stathakis, Sotirios; Papanikolaou, Nikos; Nikiforidis, Georgios C.; Sakellaropoulos, Georgios C.

    2014-01-01

    The aim of the present study is to examine the importance of using measures to predict the risk of inducing secondary malignancies in association with the clinical effectiveness of treatment plans in terms of tumor control and normal tissue complication probabilities. This is achieved by using radiobiologic parameters and measures, which may provide a closer association between clinical outcome and treatment delivery. Overall, 4 patients having been treated for lung cancer were examined. For each of them, 3 treatment plans were developed based on the helical tomotherapy (HT), multileaf collimator-based intensity modulated radiation therapy (IMRT), and 3-dimensional conformal radiation therapy (CRT) modalities. The different plans were evaluated using the complication-free tumor control probability (p{sub +}), the overall probability of injury (p{sub I}), the overall probability of control/benefit (p{sub B}), and the biologically effective uniform dose (D{sup ¯¯}). These radiobiologic measures were used to develop dose-response curves (p-D{sup ¯¯} diagram), which can help to evaluate different treatment plans when used in conjunction with standard dosimetric criteria. The risks for secondary malignancies in the heart and the contralateral lung were calculated for the 3 radiation modalities based on the corresponding dose-volume histograms (DVHs) of each patient. Regarding the overall evaluation of the different radiation modalities based on the p{sub +} index, the average values of the HT, IMRT, and CRT are 67.3%, 61.2%, and 68.2%, respectively. The corresponding average values of p{sub B} are 75.6%, 70.5%, and 71.0%, respectively, whereas the average values of p{sub I} are 8.3%, 9.3%, and 2.8%, respectively. Among the organs at risk (OARs), lungs show the highest probabilities for complications, which are 7.1%, 8.0%, and 1.3% for the HT, IMRT, and CRT modalities, respectively. Similarly, the biologically effective prescription doses (D{sub B}{sup ¯¯}) for the

  14. Radiobiologic comparison of helical tomotherapy, intensity modulated radiotherapy, and conformal radiotherapy in treating lung cancer accounting for secondary malignancy risks.

    PubMed

    Komisopoulos, Georgios; Mavroidis, Panayiotis; Rodriguez, Salvador; Stathakis, Sotirios; Papanikolaou, Nikos; Nikiforidis, Georgios C; Sakellaropoulos, Georgios C

    2014-01-01

    The aim of the present study is to examine the importance of using measures to predict the risk of inducing secondary malignancies in association with the clinical effectiveness of treatment plans in terms of tumor control and normal tissue complication probabilities. This is achieved by using radiobiologic parameters and measures, which may provide a closer association between clinical outcome and treatment delivery. Overall, 4 patients having been treated for lung cancer were examined. For each of them, 3 treatment plans were developed based on the helical tomotherapy (HT), multileaf collimator-based intensity modulated radiation therapy (IMRT), and 3-dimensional conformal radiation therapy (CRT) modalities. The different plans were evaluated using the complication-free tumor control probability (p+), the overall probability of injury (pI), the overall probability of control/benefit (pB), and the biologically effective uniform dose (D¯¯). These radiobiologic measures were used to develop dose-response curves (p-D¯¯ diagram), which can help to evaluate different treatment plans when used in conjunction with standard dosimetric criteria. The risks for secondary malignancies in the heart and the contralateral lung were calculated for the 3 radiation modalities based on the corresponding dose-volume histograms (DVHs) of each patient. Regarding the overall evaluation of the different radiation modalities based on the p+ index, the average values of the HT, IMRT, and CRT are 67.3%, 61.2%, and 68.2%, respectively. The corresponding average values of pB are 75.6%, 70.5%, and 71.0%, respectively, whereas the average values of pI are 8.3%, 9.3%, and 2.8%, respectively. Among the organs at risk (OARs), lungs show the highest probabilities for complications, which are 7.1%, 8.0%, and 1.3% for the HT, IMRT, and CRT modalities, respectively. Similarly, the biologically effective prescription doses (DB¯¯) for the HT, IMRT, and CRT modalities are 64.0, 60.9, and 60.8Gy

  15. Comparison of heart and coronary artery doses associated with intensity-modulated radiotherapy versus three-dimensional conformal radiotherapy for distal esophageal cancer.

    PubMed

    Kole, Thomas P; Aghayere, Osarhieme; Kwah, Jason; Yorke, Ellen D; Goodman, Karyn A

    2012-08-01

    To compare heart and coronary artery radiation exposure using intensity-modulated radiotherapy (IMRT) vs. four-field three-dimensional conformal radiotherapy (3D-CRT) treatment plans for patients with distal esophageal cancer undergoing chemoradiation. Nineteen patients with distal esophageal cancers treated with IMRT from March 2007 to May 2008 were identified. All patients were treated to 50.4 Gy with five-field IMRT plans. Theoretical 3D-CRT plans with four-field beam arrangements were generated. Dose-volume histograms of the planning target volume, heart, right coronary artery, left coronary artery, and other critical normal tissues were compared between the IMRT and 3D-CRT plans, and selected parameters were statistically evaluated using the Wilcoxon rank-sum test. Intensity-modulated radiotherapy treatment planning showed significant reduction (p < 0.05) in heart dose over 3D-CRT as assessed by average mean dose (22.9 vs. 28.2 Gy) and V30 (24.8% vs. 61.0%). There was also significant sparing of the right coronary artery (average mean dose, 23.8 Gy vs. 35.5 Gy), whereas the left coronary artery showed no significant improvement (mean dose, 11.2 Gy vs. 9.2 Gy), p = 0.11. There was no significant difference in percentage of total lung volume receiving at least 10, 15, or 20 Gy or in the mean lung dose between the planning methods. There were also no significant differences observed for the kidneys, liver, stomach, or spinal cord. Intensity-modulated radiotherapy achieved a significant improvement in target conformity as measured by the conformality index (ratio of total volume receiving 95% of prescription dose to planning target volume receiving 95% of prescription dose), with the mean conformality index reduced from 1.56 to 1.30 using IMRT. Treatment of patients with distal esophageal cancer using IMRT significantly decreases the exposure of the heart and right coronary artery when compared with 3D-CRT. Long-term studies are necessary to determine how this

  16. Comparison of Heart and Coronary Artery Doses Associated With Intensity-Modulated Radiotherapy Versus Three-Dimensional Conformal Radiotherapy for Distal Esophageal Cancer

    SciTech Connect

    Kole, Thomas P.; Aghayere, Osarhieme; Kwah, Jason; Yorke, Ellen D.; Goodman, Karyn A.

    2012-08-01

    Purpose: To compare heart and coronary artery radiation exposure using intensity-modulated radiotherapy (IMRT) vs. four-field three-dimensional conformal radiotherapy (3D-CRT) treatment plans for patients with distal esophageal cancer undergoing chemoradiation. Methods and Materials: Nineteen patients with distal esophageal cancers treated with IMRT from March 2007 to May 2008 were identified. All patients were treated to 50.4 Gy with five-field IMRT plans. Theoretical 3D-CRT plans with four-field beam arrangements were generated. Dose-volume histograms of the planning target volume, heart, right coronary artery, left coronary artery, and other critical normal tissues were compared between the IMRT and 3D-CRT plans, and selected parameters were statistically evaluated using the Wilcoxon rank-sum test. Results: Intensity-modulated radiotherapy treatment planning showed significant reduction (p < 0.05) in heart dose over 3D-CRT as assessed by average mean dose (22.9 vs. 28.2 Gy) and V30 (24.8% vs. 61.0%). There was also significant sparing of the right coronary artery (average mean dose, 23.8 Gy vs. 35.5 Gy), whereas the left coronary artery showed no significant improvement (mean dose, 11.2 Gy vs. 9.2 Gy), p = 0.11. There was no significant difference in percentage of total lung volume receiving at least 10, 15, or 20 Gy or in the mean lung dose between the planning methods. There were also no significant differences observed for the kidneys, liver, stomach, or spinal cord. Intensity-modulated radiotherapy achieved a significant improvement in target conformity as measured by the conformality index (ratio of total volume receiving 95% of prescription dose to planning target volume receiving 95% of prescription dose), with the mean conformality index reduced from 1.56 to 1.30 using IMRT. Conclusions: Treatment of patients with distal esophageal cancer using IMRT significantly decreases the exposure of the heart and right coronary artery when compared with 3D

  17. Epac and the high affinity rolipram binding conformer of PDE4 modulate neurite outgrowth and myelination using an in vitro spinal cord injury model

    PubMed Central

    Boomkamp, S D; McGrath, M A; Houslay, M D; Barnett, S C

    2014-01-01

    Background and Purpose cAMP and pharmacological inhibition of PDE4, which degrades it, are promising therapeutic targets for the treatment of spinal cord injury (SCI). Using our previously described in vitro SCI model, we studied the mechanisms by which cAMP modulators promote neurite outgrowth and myelination using enantiomers of the PDE4-specific inhibitor rolipram and other modulators of downstream signalling effectors. Experimental Approach Rat mixed neural cell myelinating cultures were cut with a scalpel and treated with enantiomers of the PDE4-specific inhibitor rolipram, Epac agonists and PKA antagonists. Neurite outgrowth, density and myelination were assessed by immunocytochemistry and cytokine levels analysed by qPCR. Key Results Inhibition of the high-affinity rolipram-binding state (HARBS), rather than the low-affinity rolipram binding state (LARBS) PDE4 conformer promoted neurite outgrowth and myelination. These effects were mediated through the activation of Epac and not through PKA. Expression of the chemokine CXCL10, known to inhibit myelination, was markedly elevated in astrocytes after Rho inhibition and this was blocked by inhibition of Rho kinase or PDE4. Conclusions and Implications PDE4 inhibitors targeted at the HARBS conformer or Epac agonists may provide promising novel targets for the treatment of SCI. Our study demonstrates the differential mechanisms of action of these compounds, as well as the benefit of a combined pharmacological approach and highlighting potential promising targets for the treatment of SCI. These findings need to be confirmed in vivo. PMID:24467222

  18. Whole breast and excision cavity radiotherapy plan comparison: Conformal radiotherapy with sequential boost versus intensity-modulated radiation therapy with a simultaneously integrated boost

    SciTech Connect

    Small, Katherine; Kelly, Chris; Beldham-Collins, Rachael; Gebski, Val

    2013-03-15

    A comparative study was conducted comparing the difference between (1) conformal radiotherapy (CRT) to the whole breast with sequential boost excision cavity plans and (2) intensity-modulated radiation therapy (IMRT) to the whole breast with simultaneously integrated boost to the excision cavity. The computed tomography (CT) data sets of 25 breast cancer patients were used and the results analysed to determine if either planning method produced superior plans. CT data sets from 25 past breast cancer patients were planned using (1) CRT prescribed to 50 Gy in 25 fractions (Fx) to the whole-breast planning target volume (PTV) and 10 Gy in 5Fx to the excision cavity and (2) IMRT prescribed to 60 Gy in 25Fx, with 60 Gy delivered to the excision cavity PTV and 50 Gy delivered to the whole-breast PTV, treated simultaneously. In total, 50 plans were created, with each plan evaluated by PTV coverage using conformity indices, plan maximum dose, lung dose, and heart maximum dose for patients with left-side lesions. CRT plans delivered the lowest plan maximum doses in 56% of cases (average CRT = 6314.34 cGy, IMRT = 6371.52 cGy). They also delivered the lowest mean lung dose in 68% of cases (average CRT = 1206.64 cGy, IMRT = 1288.37 cGy) and V20 in 88% of cases (average CRT = 20.03%, IMRT = 21.73%) and V30 doses in 92% of cases (average CRT = 16.82%, IMRT = 17.97%). IMRT created more conformal plans, using both conformity index and conformation number, in every instance, and lower heart maximum doses in 78.6% of cases (average CRT = 5295.26 cGy, IMRT = 5209.87 cGy). IMRT plans produced superior dose conformity and shorter treatment duration, but a slightly higher planning maximum and increased lung doses. IMRT plans are also faster to treat on a daily basis, with shorter fractionation.

  19. Modulation of the conformational state of the SV2A protein by an allosteric mechanism as evidenced by ligand binding assays

    PubMed Central

    Daniels, V; Wood, M; Leclercq, K; Kaminski, R M; Gillard, M

    2013-01-01

    Background and Purpose Synaptic vesicle protein 2A (SV2A) is the specific binding site of the anti-epileptic drug levetiracetam (LEV) and its higher affinity analogue UCB30889. Moreover, the protein has been well validated as a target for anticonvulsant therapy. Here, we report the identification of UCB1244283 acting as a SV2A positive allosteric modulator of UCB30889. Experimental Approach UCB1244283 was characterized in vitro using radioligand binding assays with [3H]UCB30889 on recombinant SV2A expressed in HEK cells and on rat cortex. In vivo, the compound was tested in sound-sensitive mice. Key Results Saturation binding experiments in the presence of UCB1244283 demonstrated a fivefold increase in the affinity of [3H]UCB30889 for human recombinant SV2A, combined with a twofold increase of the total number of binding sites. Similar results were obtained on rat cortex. In competition binding experiments, UCB1244283 potentiated the affinity of UCB30889 while the affinity of LEV remained unchanged. UCB1244283 significantly slowed down both the association and dissociation kinetics of [3H]UCB30889. Following i.c.v. administration in sound-sensitive mice, UCB1244283 showed a clear protective effect against both tonic and clonic convulsions. Conclusions and Implications These results indicate that UCB1244283 can modulate the conformation of SV2A, thereby inducing a higher affinity state for UCB30889. Our results also suggest that the conformation of SV2A per se might be an important determinant of its functioning, especially during epileptic seizures. Therefore, agents that act on the conformation of SV2A might hold great potential in the search for new SV2A-based anticonvulsant therapies. PMID:23530581

  20. Sorting of LPXTG peptides by archetypal sortase A: role of invariant substrate residues in modulating the enzyme dynamics and conformational signature of a productive substrate.

    PubMed

    Biswas, Tora; Pawale, Vijaykumar S; Choudhury, Devapriya; Roy, Rajendra P

    2014-04-22

    Transpeptidase sortase catalyzes the covalent anchoring of surface proteins to the cell wall in Gram-positive bacteria. Sortase A (SrtA) of Staphylococcus aureus is a prototype enzyme and considered a bona fide drug target because several substrate proteins are virulence-related and implicated in pathogenesis. Besides, SrtA also works as a versatile tool in protein engineering. Surface proteins destined for cell wall anchoring contain a LPXTG sequence located in their C-terminus which serves as a substrate recognition motif for SrtA. Recent studies have implicated substrate-induced conformational dynamics in SrtA. In the present work, we have explored the roles of invariant Leu and Pro residues of the substrate in modulating the enzyme dynamics with a view to understand the selection process of a catalytically competent substrate. Overall results of molecular dynamics simulations and experiments carried out with noncanonical substrates and site-directed mutagenesis reveal that the kinked conformation due to Pro in LPXTG is obligatory for productive binding but does not per se control the enzyme dynamics. The Leu residue of the substrate appears to play the crucial role of an anchor to the beta6-beta7 loop directing the conformational transition of the enzyme from an "open" to a "closed" state subsequent to which the Pro residue facilitates the consummation of binding through predominant engagement of the loop and catalytic motif residues in hydrophobic interactions. Collectively, our study provides insights about specificity, tolerance, and conformational sorting of substrate by SrtA. These results have important implications in designing newer substrates and inhibitors for this multifaceted enzyme.

  1. Influence of multi-leaf collimator leaf width in radiosurgery via volumetric modulated arc therapy and 3D dynamic conformal arc therapy.

    PubMed

    Serna, Alfredo; Puchades, Vicente; Mata, Fernando; Ramos, David; Alcaraz, Miguel

    2015-05-01

    To study the influence of Multileaf Collimator (MLC) leaf width in radiosurgery treatment planning for Volumetric Modulated Arc Therapy (VMAT) and 3D Dynamic Conformal Arc Therapy (3D-DCA). 16 patients with solitary brain metastases treated with radiosurgery via the non-coplanar VMAT were replanned for the 3D-DCA. For each planning technique two MLC leaf width sizes were utilized, i.e. 5 mm and 2.5 mm. These treatment plans were compared using dosimetric indices (conformity, gradient and mean dose for brain tissue) and the normal tissue complication probability (NTCP). An improvement in planning quality for VMAT was observed versus 3D-DCA for any MLC leaf width, mainly with regards to dose conformity and to a lesser extent regards dose gradient. No significant difference was observed for any of both techniques using smaller leaf width. However, dose gradient was improved in favor of the 2.5 mm MLC for either of both techniques (15% VMAT and 10% 3D-DCA); being noticeable for lesions smaller than 10cm(3). Nonetheless, the NTCP index was not significantly affected by variations in the dose gradient index. This, our present study, suggests that the use of an MLC leaf width of 2.5 mm via the noncoplanar VMAT and 3D-DCA techniques provides improvement in terms of dose gradient for small volumes, over those results obtained with an MLC leaf width of 5 mm. The 3D-DCA does also benefit from MLC leaf widths of a smaller size, mainly in terms of conformity. Copyright © 2015 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  2. Dosimetric comparison of postoperative whole pelvic radiotherapy for endometrial cancer using three-dimensional conformal radiotherapy, intensity-modulated radiotherapy, and helical tomotherapy.

    PubMed

    Yang, Ruijie; Xu, Shouping; Jiang, Weijuan; Wang, Junjie; Xie, Chuanbin

    2010-01-01

    The use of Intensity-modulated radiotherapy (IMRT) and Helical tomotherapy (HT) is increasing in gynecological cancer patients. No published studies have performed a dosimetric evaluation of whole pelvic radiotherapy (WPRT) using HT for postoperative endometrial cancer. The purpose of this study was to perform a direct dosimetric comparison of three-dimensional conformal radiotherapy (3D-CRT), IMRT and HT plans for WPRT in postoperative endometrial cancer patients, and to evaluate the integral dose to organs at risk (OARs) and normal tissue. We selected ten patients with endometrial cancer undergoing postoperative WPRT. Plans for 3D-CRT, IMRT and HT were developed for each patient. All plans were normalized to deliver 50 Gy to 95% of the PTV. The dosimetry and integral dose to OARs and normal tissue were compared. The significance of differences was tested using a paired two-tailed Student t-test. IMRT were superior to 3D-CRT in dose conformity (conformity index: 0.87 vs. 0.61, p = 0.00) and integral dose to OARs and normal tissue, although a greater volume of normal tissue receiving dose below 10 Gy was observed. The results were similar in HT except that the integral dose to normal tissue increased slightly. Compared directly with IMRT, HT showed better dose homogeneity and lower integral dose to rectum and bladder, but the integral dose to pelvic bones and normal tissue slightly increased. In postoperative WPRT of endometrial cancer, IMRT and HT result in better conformity and lower integral dose to OARs compared with 3D-CRT. The integral dose to normal tissue did not increase significantly in IMRT, although a greater volume of normal tissue is irradiated to the dose below 10 Gy. HT further improves the dose homogeneity and integral dose to rectum and bladder, at the expense of a slightly higher integral dose to pelvic bones and normal tissue.

  3. A comprehensive dosimetric study of pancreatic cancer treatment using three-dimensional conformal radiation therapy (3DCRT), intensity-modulated radiation therapy (IMRT), volumetric-modulated radiation therapy (VMAT), and passive-scattering and modulated-scanning proton therapy (PT).

    PubMed

    Ding, Xuanfeng; Dionisi, Francesco; Tang, Shikui; Ingram, Mark; Hung, Chun-Yu; Prionas, Evangelos; Lichtenwalner, Phil; Butterwick, Ian; Zhai, Huifang; Yin, Lingshu; Lin, Haibo; Kassaee, Alireza; Avery, Stephen

    2014-01-01

    With traditional photon therapy to treat large postoperative pancreatic target volume, it often leads to poor tolerance of the therapy delivered and may contribute to interrupted treatment course. This study was performed to evaluate the potential advantage of using passive-scattering (PS) and modulated-scanning (MS) proton therapy (PT) to reduce normal tissue exposure in postoperative pancreatic cancer treatment. A total of 11 patients with postoperative pancreatic cancer who had been previously treated with PS PT in University of Pennsylvania Roberts Proton Therapy Center from 2010 to 2013 were identified. The clinical target volume (CTV) includes the pancreatic tumor bed as well as the adjacent high-risk nodal areas. Internal (iCTV) was generated from 4-dimensional (4D) computed tomography (CT), taking into account target motion from breathing cycle. Three-field and 4-field 3D conformal radiation therapy (3DCRT), 5-field intensity-modulated radiation therapy, 2-arc volumetric-modulated radiation therapy, and 2-field PS and MS PT were created on the patients' average CT. All the plans delivered 50.4Gy to the planning target volume (PTV). Overall, 98% of PTV was covered by 95% of the prescription dose and 99% of iCTV received 98% prescription dose. The results show that all the proton plans offer significant lower doses to the left kidney (mean and V18Gy), stomach (mean and V20Gy), and cord (maximum dose) compared with all the photon plans, except 3-field 3DCRT in cord maximum dose. In addition, MS PT also provides lower doses to the right kidney (mean and V18Gy), liver (mean dose), total bowel (V20Gy and mean dose), and small bowel (V15Gy absolute volume ratio) compared with all the photon plans and PS PT. The dosimetric advantage of PT points to the possibility of treating tumor bed and comprehensive nodal areas while providing a more tolerable treatment course that could be used for dose escalation and combining with radiosensitizing chemotherapy. Published by

  4. A comprehensive dosimetric study of pancreatic cancer treatment using three-dimensional conformal radiation therapy (3DCRT), intensity-modulated radiation therapy (IMRT), volumetric-modulated radiation therapy (VMAT), and passive-scattering and modulated-scanning proton therapy (PT)

    SciTech Connect

    Ding, Xuanfeng; Dionisi, Francesco; Tang, Shikui; Ingram, Mark; Hung, Chun-Yu; Prionas, Evangelos; Lichtenwalner, Phil; Butterwick, Ian; Zhai, Huifang; Yin, Lingshu; Lin, Haibo; Kassaee, Alireza; Avery, Stephen

    2014-07-01

    With traditional photon therapy to treat large postoperative pancreatic target volume, it often leads to poor tolerance of the therapy delivered and may contribute to interrupted treatment course. This study was performed to evaluate the potential advantage of using passive-scattering (PS) and modulated-scanning (MS) proton therapy (PT) to reduce normal tissue exposure in postoperative pancreatic cancer treatment. A total of 11 patients with postoperative pancreatic cancer who had been previously treated with PS PT in University of Pennsylvania Roberts Proton Therapy Center from 2010 to 2013 were identified. The clinical target volume (CTV) includes the pancreatic tumor bed as well as the adjacent high-risk nodal areas. Internal (iCTV) was generated from 4-dimensional (4D) computed tomography (CT), taking into account target motion from breathing cycle. Three-field and 4-field 3D conformal radiation therapy (3DCRT), 5-field intensity-modulated radiation therapy, 2-arc volumetric-modulated radiation therapy, and 2-field PS and MS PT were created on the patients’ average CT. All the plans delivered 50.4 Gy to the planning target volume (PTV). Overall, 98% of PTV was covered by 95% of the prescription dose and 99% of iCTV received 98% prescription dose. The results show that all the proton plans offer significant lower doses to the left kidney (mean and V{sub 18} {sub Gy}), stomach (mean and V{sub 20} {sub Gy}), and cord (maximum dose) compared with all the photon plans, except 3-field 3DCRT in cord maximum dose. In addition, MS PT also provides lower doses to the right kidney (mean and V{sub 18} {sub Gy}), liver (mean dose), total bowel (V{sub 20} {sub Gy} and mean dose), and small bowel (V{sub 15} {sub Gy} absolute volume ratio) compared with all the photon plans and PS PT. The dosimetric advantage of PT points to the possibility of treating tumor bed and comprehensive nodal areas while providing a more tolerable treatment course that could be used for dose

  5. The role of Cobalt-60 source in Intensity Modulated Radiation Therapy: From modeling finite sources to treatment planning and conformal dose delivery

    NASA Astrophysics Data System (ADS)

    Dhanesar, Sandeep Kaur

    Cobalt-60 (Co-60) units played an integral role in radiation therapy from the mid-1950s to the 1970s. Although they continue to be used to treat cancer in some parts of the world, their role has been significantly reduced due to the invention of medical linear accelerators. A number of groups have indicated a strong potential for Co-60 units in modern radiation therapy. The Medical Physics group at the Cancer Center of the Southeastern Ontario and Queen's University has shown the feasibility of Intensity Modulated Radiation Therapy (IMRT) via simple conformal treatment planning and dose delivery using a Co-60 unit. In this thesis, initial Co-60 tomotherapy planning investigations on simple uniform phantoms are extended to actual clinical cases based on patient CT data. The planning is based on radiation dose data from a clinical Co-60 unit fitted with a multileaf collimator (MLC) and modeled in the EGSnrc Monte Carlo system. An in house treatment planning program is used to calculate IMRT dose distributions. Conformal delivery in a single slice on a uniform phantom based on sequentially delivered pencil beams is verified by Gafchromic film. Volumetric dose distributions for Co-60 serial tomotherapy are then generated for typical clinical sites that had been treated at our clinic by conventional 6MV IMRT using Varian Eclipse treatment plans. The Co-60 treatment plans are compared with the clinical IMRT plans using conventional matrices such as dose volume histograms (DVH). Dose delivery based on simultaneously opened MLC leaves is also explored and a novel MLC segmentation method is proposed. In order to increase efficiency of dose calculations, a novel convolution based fluence model for treatment planning is also proposed. The ion chamber measurements showed that the Monte Carlo modeling of the beam data under the MIMiC MLC is accurate. The film measurements from the uniform phantom irradiations confirm that IMRT plans from our in-house treatment planning system

  6. A planning comparison of 3-dimensional conformal multiple static field, conformal arc, and volumetric modulated arc therapy for the delivery of stereotactic body radiotherapy for early stage lung cancer

    SciTech Connect

    Dickey, Mike; Roa, Wilson; Drodge, Suzanne; Ghosh, Sunita; Murray, Brad; Scrimger, Rufus; Gabos, Zsolt

    2015-01-01

    The primary objective of this study was to compare dosimetric variables as well as treatment times of multiple static fields (MSFs), conformal arcs (CAs), and volumetric modulated arc therapy (VMAT) techniques for the treatment of early stage lung cancer using stereotactic body radiotherapy (SBRT). Treatments of 23 patients previously treated with MSF of 48 Gy to 95% of the planning target volume (PTV) in 4 fractions were replanned using CA and VMAT techniques. Dosimetric parameters of the Radiation Therapy Oncology Group (RTOG) 0915 trial were evaluated, along with the van't Riet conformation number (CN), monitor units (MUs), and actual and calculated treatment times. Paired t-tests for noninferiority were used to compare the 3 techniques. CA had significant dosimetric improvements over MSF for the ratio of the prescription isodose volume to PTV (R{sub 100%}, p < 0.0001), the maximum dose 2 cm away from the PTV (D{sub 2} {sub cm}, p = 0.005), and van't Riet CN (p < 0.0001). CA was not statistically inferior to MSF for the 50% prescription isodose volume to PTV (R{sub 50%}, p = 0.05). VMAT was significantly better than CA for R{sub 100%} (p < 0.0001), R{sub 50%} (p < 0.0001), D{sub 2} {sub cm} (p = 0.006), and CN (p < 0.0001). CA plans had significantly shorter treatment times than those of VMAT (p < 0.0001). Both CA and VMAT planning showed significant dosimetric improvements and shorter treatment times over those of MSF. VMAT showed the most favorable dosimetry of all 3 techniques; however, the dosimetric effect of tumor motion was not evaluated. CA plans were significantly faster to treat, and minimize the interplay of tumor motion and dynamic multileaf collimator (MLC) motion effects. Given these results, CA has become the treatment technique of choice at our facility.

  7. Potential for improved intelligence quotient using volumetric modulated arc therapy compared with conventional 3-dimensional conformal radiation for whole-ventricular radiation in children.

    PubMed

    Qi, X Sharon; Stinauer, Michelle; Rogers, Brion; Madden, Jennifer R; Wilkening, Greta N; Liu, Arthur K

    2012-12-01

    To compare volumetric modulated arc therapy (VMAT) with 3-dimensional conformal radiation therapy (3D-CRT) in the treatment of localized intracranial germinoma. We modeled the effect of the dosimetric differences on intelligence quotient (IQ). Ten children with intracranial germinomas were used for planning. The prescription doses were 23.4 Gy to the ventricles followed by 21.6 Gy to the tumor located in the pineal region. For each child, a 3D-CRT and full arc VMAT was generated. Coverage of the target was assessed by computing a conformity index and heterogeneity index. We also generated VMAT plans with explicit temporal lobe sparing and with smaller ventricular margin expansions. Mean dose to the temporal lobe was used to estimate IQ 5 years after completion of radiation, using a patient age of 10 years. Compared with the 3D-CRT plan, VMAT improved conformality (conformity index 1.10 vs 1.85), with slightly higher heterogeneity (heterogeneity index 1.09 vs 1.06). The averaged mean doses for left and right temporal lobes were 31.3 and 31.7 Gy, respectively, for VMAT plans and 37.7 and 37.6 Gy for 3D-CRT plans. This difference in mean temporal lobe dose resulted in an estimated IQ difference of 3.1 points at 5 years after radiation therapy. When the temporal lobes were explicitly included in the VMAT optimization, the mean temporal lobe dose was reduced 5.6-5.7 Gy, resulting in an estimated IQ difference of an additional 3 points. Reducing the ventricular margin from 1.5 cm to 0.5 cm decreased mean temporal lobe dose 11.4-13.1 Gy, corresponding to an estimated increase in IQ of 7 points. For treatment of children with intracranial pure germinomas, VMAT compared with 3D-CRT provides increased conformality and reduces doses to normal tissue. This may result in improvements in IQ in these children. Copyright © 2012 Elsevier Inc. All rights reserved.

  8. Potential for Improved Intelligence Quotient Using Volumetric Modulated Arc Therapy Compared With Conventional 3-Dimensional Conformal Radiation for Whole-Ventricular Radiation in Children

    SciTech Connect

    Qi, X. Sharon; Stinauer, Michelle; Rogers, Brion; Madden, Jennifer R.; Wilkening, Greta N.; Liu, Arthur K.

    2012-12-01

    Purpose: To compare volumetric modulated arc therapy (VMAT) with 3-dimensional conformal radiation therapy (3D-CRT) in the treatment of localized intracranial germinoma. We modeled the effect of the dosimetric differences on intelligence quotient (IQ). Method and Materials: Ten children with intracranial germinomas were used for planning. The prescription doses were 23.4 Gy to the ventricles followed by 21.6 Gy to the tumor located in the pineal region. For each child, a 3D-CRT and full arc VMAT was generated. Coverage of the target was assessed by computing a conformity index and heterogeneity index. We also generated VMAT plans with explicit temporal lobe sparing and with smaller ventricular margin expansions. Mean dose to the temporal lobe was used to estimate IQ 5 years after completion of radiation, using a patient age of 10 years. Results: Compared with the 3D-CRT plan, VMAT improved conformality (conformity index 1.10 vs 1.85), with slightly higher heterogeneity (heterogeneity index 1.09 vs 1.06). The averaged mean doses for left and right temporal lobes were 31.3 and 31.7 Gy, respectively, for VMAT plans and 37.7 and 37.6 Gy for 3D-CRT plans. This difference in mean temporal lobe dose resulted in an estimated IQ difference of 3.1 points at 5 years after radiation therapy. When the temporal lobes were explicitly included in the VMAT optimization, the mean temporal lobe dose was reduced 5.6-5.7 Gy, resulting in an estimated IQ difference of an additional 3 points. Reducing the ventricular margin from 1.5 cm to 0.5 cm decreased mean temporal lobe dose 11.4-13.1 Gy, corresponding to an estimated increase in IQ of 7 points. Conclusion: For treatment of children with intracranial pure germinomas, VMAT compared with 3D-CRT provides increased conformality and reduces doses to normal tissue. This may result in improvements in IQ in these children.

  9. Stereotactic Radiotherapy of Central Nervous System and Head and Neck Lesions, Using a Conformal Intensity-Modulated Radiotherapy System (Peacock™ System)

    PubMed Central

    Ammirati, Mario; Bernardo, Antonio; Ramsinghani, Nilam; Yakoob, Richard; Al-Ghazi, Matthew; Kuo, Jeffrey; Ammirati, Giuseppe

    2001-01-01

    The objective of this article is to evaluate single-fraction or fractionated stereotactic radiotherapy of central nervous system (CNS) and head and neck lesions using intensity-modulated radiotherapy (IMRT) with a commercially available system (Peacock™, Nomos Corporation, Sewickley, PA). This system allows tomotherapeutic delivery of intensity-modulated radiation, that is, the slice-by-slice treatment of the volume of interest with an intensity-modulated beam, making the delivery of highly conformal radiation to the target possible in both single or multiple fractions mode. During an 18-month period, 43 (21 males and 22 females) patients were treated, using a removable cranial screw-fixation device. Ages ranged from 10 to 77 years (mean, 52.2; median, 53.5). Intra- and extra-axial lesions, including head and neck malignancies and spine metastases, were treated. Clinical target volume ranged from 0.77 to 195 cm3 (mean, 47.8; median, 29.90). The dose distribution was normalized to the maximum and was prescribed, in most cases, at the 80% or 90% isodose line (range, 65 to 96%; median, 85%; mean, 83.4%) and ranged from 14 to 80 Gy (mean, 48; median, 50). The number of fractions ranged from 1 to 40 (mean, 23; median, 25). In all but one patient, 90% of the prescription isodose line covered 100% of the clinical target volume. The heterogeneity index (the ratio between the maximum radiation dose and the prescribed dose) ranged between 1.0 and 1.50, whereas the conformity index (the ratio between the volume encompassed by the prescription isodose line and the clinical target volume) ranged between 1.0 and 4.5. There were no complications related to the radiation treatment. With a median follow-up of 6 months, more than 70% of our patients showed decreased lesion size. Stereotactic IMRT of CNS and head and neck lesions can be delivered safely and accurately. The Peacock system delivers stereotactic radiation in single or multiple fractions and has no volume limitations

  10. Modulation of Multiscale 3D Lattices through Conformational Control: Painting Silk Inverse Opals with Water and Light.

    PubMed

    Wang, Yu; Aurelio, Daniele; Li, Wenyi; Tseng, Peter; Zheng, Zhaozhu; Li, Meng; Kaplan, David L; Liscidini, Marco; Omenetto, Fiorenzo G

    2017-10-01

    Structural proteins from naturally occurring materials are an inspiring template for material design and synthesis at multiple scales. The ability to control the assembly and conformation of such materials offers the opportunity to define fabrication approaches that recapitulate the dimensional hierarchy and structure-function relationships found in nature. A simple and versatile directed assembly method of silk fibroin, which allows the design of structures across multiple dimensional scales by generating and tuning structural color in large-scale, macro defect-free colloidally assembled 3D nanostructures in the form of silk inverse opals (SIOs) is reported. This approach effectively combines bottom-up and top-down techniques to obtain control on the nanoscale (through silk conformational changes), microscale (through patterning), and macroscale (through colloidal assembly), ultimately resulting in a controllable photonic lattice with predefined spectral behavior, with a resulting palette spanning almost the entire visible range. As a demonstration of the approach, examples of "multispectral" SIOs, paired with theoretical calculations and analysis of their response as a function of changes of lattice constants and refractive index contrast are illustrated. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Residues in the membrane-spanning domain core modulate conformation and fusogenicity of the HIV-1 envelope glycoprotein

    SciTech Connect

    Shang Liang; Hunter, Eric

    2010-09-01

    The membrane-spanning domain (MSD) of human immunodeficiency virus type I (HIV-1) envelope glycoprotein (Env) is critical for its biological activity. Initial studies have defined an almost invariant 'core' structure in the MSD and demonstrated that it is crucial for anchoring Env in the membrane and virus entry. We show here that amino acid substitutions in the MSD 'core' do not influence specific virus-cell attachment, nor CD4 receptor and CXCR4 coreceptor recognition by Env. However, substitutions within the MSD 'core' delayed the kinetics and reduced the efficiency of cell-cell fusion mediated by Env. Although we observed no evidence that membrane fusion mediated by the MSD core mutants was arrested at a hemifusion stage, impaired Env fusogenicity was correlated with minor conformational changes in the V2, C1, and C5 regions in gp120 and the immunodominant loop in gp41. These changes could delay initiation of the conformational changes required in the fusion process.

  12. 2-Arachidonoylglycerol metabolism is differently modulated by oligomeric and fibrillar conformations of amyloid beta in synaptic terminals.

    PubMed

    Pascual, Ana C; Gaveglio, Virginia L; Giusto, Norma M; Pasquaré, Susana J

    2017-10-24

    Alzheimer's disease (AD) is the most prevalent disorder of senile dementia mainly characterized by amyloid-beta peptide (Aβ) deposits in the brain. Cannabinoids are relevant to AD as they exert several beneficial effects in many models of this disease. Still, whether the endocannabinoid system is either up- or down-regulated in AD has not yet been fully elucidated. Thus, the aim of the present paper was to analyze endocannabinoid 2-arachidonoylglycerol (2-AG) metabolism in cerebral cortex synaptosomes incubated with Aβ oligomers or fibrils. These Aβ conformations were obtained by "aging" the 1-40 fragment of the peptide under different agitation and time conditions. A diminished availability of 2-AG resulting from a significant decrease in diacylglycerol lipase (DAGL) activity was observed in the presence of large Aβ1-40 oligomers along with synaptosomal membrane damage, as judged by transmission electron microscopy and LDH release. Conversely, a high availability of 2-AG resulting from an increase in DAGL and lysophosphatidic acid phosphohydrolase activities occurred in the presence of Aβ1-40 fibrils although synaptosomal membrane disruption was also observed. Interestingly, neither synaptosomal mitochondrial viability assayed by MTT reduction nor membrane lipid peroxidation assayed by TBARS formation measurements were altered by Aβ1-40 oligomers or fibrils. These results show a differential effect of Aβ1-40 peptide on 2-AG metabolism depending on its conformation. Copyright © 2017 IBRO. Published by Elsevier Ltd. All rights reserved.

  13. AVEC: A Computational Design Environment for Conceptual Innovations

    DTIC Science & Technology

    2008-02-01

    SUPPLEMENTARY NOTES PAO Case Number: AFRL/WS 06-0535, 23 Feb 2006. Report contains color. 14. ABSTRACT This report summarizes programming techniques ...that aid multidisciplinary design programmers in developing computational designs that measure AFRL technology effectiveness. These techniques have...underlying principles of the AVEC environment. This paper describes a number of software techniques already established in AVEC that will help aerospace

  14. Adjuvant external beam radiotherapy after therapeutic groin lymphadenectomy for patients with melanoma: a dosimetric comparison of three-dimensional conformal and intensity-modulated radiotherapy techniques.

    PubMed

    Adams, Gerard; Foote, Matthew; Brown, Simon; Burmeister, Bryan

    2017-02-01

    Radiotherapy after lymph node dissection is recommended in high-risk melanoma cases. The aim of this study is to assess whether intensity-modulated radiotherapy (IMRT) offers advantages over three-dimensional conformal radiotherapy (3DCRT) in the groin nodal basin. Fifteen consecutively treated patients (5 3DCRT and 10 IMRT) were selected. Optimized theoretical plans using the other modality were created - enabling direct comparisons of 3DCRT and IMRT. Target volume and organs at risk constraints were assessed as achieved or as having minor (≤5%) or major (>5%) deviations. The Wilcoxon signed-rank test was used to compare the dose received from each patient plan (3DCRT vs. IMRT), whereas the Mann-Whitney U-test was used to compare clinical plans with theoretical plans. Fisher's exact test was used to compare categorical data. Target coverage was achievable in most patients (major deviations - 1 IMRT and 3 3DCRT). Conformity index improved with IMRT - median 0.65, range 0.48-0.81, versus median 0.44, range 0.29-0.60 for 3DCRT; P value less than 0.001. All 3DCRT plans had major deviations for femoral head/neck constraints. Twelve and 13 IMRT plans achieved the high (V42<5%) and low (V36<35%) constraints; P value less than 0.001. IMRT delivered statistically significant lower doses to small bowel volumes up to 40 ml. There were no differences in beam numbers used nor dosimetric endpoints measured when clinical plans were compared with theoretical plans. IMRT appears to allow superior conformity of dose to the target volume while relatively sparing the adjacent the bowel and femoral head/neck. This may reduce toxicity while maintaining control rates.

  15. pH-Dependent Conformational Changes in the HCV NS3 Protein Modulate Its ATPase and Helicase Activities

    PubMed Central

    Ventura, Gustavo Tavares; da Costa, Emmerson Corrêa Brasil; Capaccia, Anne Miranda; Mohana-Borges, Ronaldo

    2014-01-01

    The hepatitis C virus (HCV) infects 170 to 200 million people worldwide and is, therefore, a major health problem. The lack of efficient treatments that specifically target the viral proteins or RNA and its high chronicity rate make hepatitis C the cause of many deaths and hepatic transplants annually. The NS3 protein is considered an important target for the development of anti-HCV drugs because it is composed of two domains (a serine protease in the N-terminal portion and an RNA helicase/NTPase in the C-terminal portion), which are essential for viral replication and proliferation. We expressed and purified both the NS3 helicase domain (NS3hel) and the full-length NS3 protein (NS3FL) and characterized pH-dependent structural changes associated with the increase in their ATPase and helicase activities at acidic pH. Using intrinsic fluorescence experiments, we have observed that NS3hel was less stable at pH 6.4 than at pH 7.2. Moreover, binding curves using an extrinsic fluorescent probe (bis-ANS) and ATPase assays performed under different pH conditions demonstrated that the hydrophobic clefts of NS3 are significantly more exposed to the aqueous medium at acidic pH. Using fluorescence spectroscopy and anisotropy assays, we have also observed more protein interaction with DNA upon pH acidification, which suggests that the hydrophobic clefts exposure on NS3 might be related to a loss of stability that could lead it to adopt a more open conformation. This conformational change at acidic pH would stimulate both its ATPase and helicase activities, as well as its ability to bind DNA. Taken together, our results indicate that the NS3 protein adopts a more open conformation due to acidification from pH 7.2 to 6.4, resulting in a more active form at a pH that is found near Golgi-derived membranes. This increased activity could better allow NS3 to carry out its functions during HCV replication. PMID:25551442

  16. pH-dependent conformational changes in the HCV NS3 protein modulate its ATPase and helicase activities.

    PubMed

    Ventura, Gustavo Tavares; Costa, Emmerson Corrêa Brasil da; Capaccia, Anne Miranda; Mohana-Borges, Ronaldo

    2014-01-01

    The hepatitis C virus (HCV) infects 170 to 200 million people worldwide and is, therefore, a major health problem. The lack of efficient treatments that specifically target the viral proteins or RNA and its high chronicity rate make hepatitis C the cause of many deaths and hepatic transplants annually. The NS3 protein is considered an important target for the development of anti-HCV drugs because it is composed of two domains (a serine protease in the N-terminal portion and an RNA helicase/NTPase in the C-terminal portion), which are essential for viral replication and proliferation. We expressed and purified both the NS3 helicase domain (NS3hel) and the full-length NS3 protein (NS3FL) and characterized pH-dependent structural changes associated with the increase in their ATPase and helicase activities at acidic pH. Using intrinsic fluorescence experiments, we have observed that NS3hel was less stable at pH 6.4 than at pH 7.2. Moreover, binding curves using an extrinsic fluorescent probe (bis-ANS) and ATPase assays performed under different pH conditions demonstrated that the hydrophobic clefts of NS3 are significantly more exposed to the aqueous medium at acidic pH. Using fluorescence spectroscopy and anisotropy assays, we have also observed more protein interaction with DNA upon pH acidification, which suggests that the hydrophobic clefts exposure on NS3 might be related to a loss of stability that could lead it to adopt a more open conformation. This conformational change at acidic pH would stimulate both its ATPase and helicase activities, as well as its ability to bind DNA. Taken together, our results indicate that the NS3 protein adopts a more open conformation due to acidification from pH 7.2 to 6.4, resulting in a more active form at a pH that is found near Golgi-derived membranes. This increased activity could better allow NS3 to carry out its functions during HCV replication.

  17. Investigation of conformal and intensity-modulated radiation therapy techniques to determine the absorbed fetal dose in pregnant patients with breast cancer

    SciTech Connect

    Öğretici, Akın Akbaş, Uğur; Köksal, Canan; Bilge, Hatice

    2016-07-01

    The aim of this research was to investigate the fetal doses of pregnant patients undergoing conformal radiotherapy or intensity-modulated radiation therapy (IMRT) for breast cancers. An Alderson Rando phantom was chosen to simulate a pregnant patient with breast cancer who is receiving radiation therapy. This phantom was irradiated using the Varian Clinac DBX 600 system (Varian Medical System, Palo Alto, CA) linear accelerator, according to the standard treatment plans of both three-dimensional conformal radiation therapy (3-D CRT) and IMRT techniques. Thermoluminescent dosimeters were used to measure the irradiated phantom's virtually designated uterus area. Thermoluminescent dosimeter measurements (in the phantom) revealed that the mean cumulative fetal dose for 3-D CRT is 1.39 cGy and for IMRT it is 8.48 cGy, for a pregnant breast cancer woman who received radiation treatment of 50 Gy. The fetal dose was confirmed to increase by 70% for 3-D CRT and 40% for IMRT, if it is closer to the irradiated field by 5 cm. The mean fetal dose from 3-D CRT is 1.39 cGy and IMRT is 8.48 cGy, consistent with theoretic calculations. The IMRT technique causes the fetal dose to be 5 times more than that of 3-D CRT. Theoretic knowledge concerning the increase in the peripheral doses as the measurements approached the beam was also practically proven.

  18. Investigation of conformal and intensity-modulated radiation therapy techniques to determine the absorbed fetal dose in pregnant patients with breast cancer.

    PubMed

    Öğretici, Akın; Akbaş, Uğur; Köksal, Canan; Bilge, Hatice

    2016-01-01

    The aim of this research was to investigate the fetal doses of pregnant patients undergoing conformal radiotherapy or intensity-modulated radiation therapy (IMRT) for breast cancers. An Alderson Rando phantom was chosen to simulate a pregnant patient with breast cancer who is receiving radiation therapy. This phantom was irradiated using the Varian Clinac DBX 600 system (Varian Medical System, Palo Alto, CA) linear accelerator, according to the standard treatment plans of both three-dimensional conformal radiation therapy (3-D CRT) and IMRT techniques. Thermoluminescent dosimeters were used to measure the irradiated phantom׳s virtually designated uterus area. Thermoluminescent dosimeter measurements (in the phantom) revealed that the mean cumulative fetal dose for 3-D CRT is 1.39cGy and for IMRT it is 8.48cGy, for a pregnant breast cancer woman who received radiation treatment of 50Gy. The fetal dose was confirmed to increase by 70% for 3-D CRT and 40% for IMRT, if it is closer to the irradiated field by 5cm. The mean fetal dose from 3-D CRT is 1.39cGy and IMRT is 8.48cGy, consistent with theoretic calculations. The IMRT technique causes the fetal dose to be 5 times more than that of 3-D CRT. Theoretic knowledge concerning the increase in the peripheral doses as the measurements approached the beam was also practically proven. Copyright © 2016 American Association of Medical Dosimetrists. Published by Elsevier Inc. All rights reserved.

  19. [Radiotherapy of a glioma in a pregnant woman: evaluation of the foetal dose in conformational 3D or intensity-modulated].

    PubMed

    Lefebvre, L; Doyeux, K; Linca, S; Challand, T; Hanzen, C

    2014-12-01

    The purpose was to assess three treatments planning techniques including one in intensity-modulated radiation therapy (IMRT) for cerebral irradiation of pregnant woman, in order to limit the dose delivered to the foetus. The treatment provided was 60 Gy to the planning target volume. Estimated foetal dose was measured using an anthropomorphic phantom, on the upper and middle part of the uterus. The first plan consisted in four beams in conformational technique delivered from a Varian accelerator with a 120 leaves collimator, the second one used non-coplanar fields and the third one assessed IMRT. With the conformational technique, the dose at the upper part of the uterus was 8.3 mGy and 6.3 mGy at the middle part. The dose delivered to the foetus was higher with the non-coplanar fields. In IMRT, the dose at the upper part of the uterus was 23.8 mGy and 14.3 mGy at the middle part. The three plans used 6 MV X-rays. Because of the use of leaves and non-coplanar fields, IMRT does not seem to be the optimal technique for the treatment of pregnant woman. However, the dose delivered to the foetus remains low and below the dose of 100 mGy recommended by the International Commission of Radiological Protection. It seems possible to consider the use of this technique for a better sparing of organs at risk for the mother.

  20. Cwc21p promotes the second step conformation of the spliceosome and modulates 3′ splice site selection

    PubMed Central

    Gautam, Amit; Grainger, Richard J.; Vilardell, J.; Barrass, J. David; Beggs, Jean D.

    2015-01-01

    Pre-mRNA splicing involves two transesterification steps catalyzed by the spliceosome. How RNA substrates are positioned in each step and the molecular rearrangements involved, remain obscure. Here, we show that mutations in PRP16, PRP8, SNU114 and the U5 snRNA that affect this process interact genetically with CWC21, that encodes the yeast orthologue of the human SR protein, SRm300/SRRM2. Our microarray analysis shows changes in 3′ splice site selection at elevated temperature in a subset of introns in cwc21Δ cells. Considering all the available data, we propose a role for Cwc21p positioning the 3′ splice site at the transition to the second step conformation of the spliceosome, mediated through its interactions with the U5 snRNP. This suggests a mechanism whereby SRm300/SRRM2, might influence splice site selection in human cells. PMID:25740649

  1. Dosimetric study of volumetric arc modulation with RapidArc and intensity-modulated radiotherapy in patients with cervical cancer and comparison with 3-dimensional conformal technique for definitive radiotherapy in patients with cervical cancer

    SciTech Connect

    Guy, Jean-Baptiste; Falk, Alexander T.; Auberdiac, Pierre; Cartier, Lysian; Vallard, Alexis; Ollier, Edouard; Trone, Jane-Chloé; Khodri, Moustapha; Chargari, Cyrus; Magné, Nicolas

    2016-04-01

    Introduction: For patients with cervical cancer, intensity-modulated radiation therapy (IMRT) improves target coverage and allows dose escalation while reducing the radiation dose to organs at risk (OARs). In this study, we compared dosimetric parameters among 3-dimensional conformal radiotherapy (3D-CRT), “step-and-shoot” IMRT, and volumetric intensity-modulated arc radiotherapy (VMAT) in a series of patients with cervical cancer receiving definitive radiotherapy. Computed tomography (CT) scans of 10 patients with histologically proven cervical cancer treated with definitive radiation therapy (RT) from December 2008 to March 2010 at our department were selected for this study. The gross tumor volume (GTV) and clinical target volume (CTV) were delineated following the guidelines of the Gyn IMRT consortium that included cervix, uterus, parametrial tissues, and the pelvic nodes including presacral. The median age was 57 years (range: 30 to 85 years). All 10 patients had squamous cell carcinoma with Federation of Gynecology and Obstetrics (FIGO) stage IB-IIIB. All patients were treated by VMAT. OAR doses were significantly reduced for plans with intensity-modulated technique compared with 3D-CRT except for the dose to the vagina. Between the 2 intensity-modulated techniques, significant difference was observed for the mean dose to the small intestine, to the benefit of VMAT (p < 0.001). There was no improvement in terms of OARs sparing for VMAT although there was a tendency for a slightly decreased average dose to the rectum: − 0.65 Gy but not significant (p = 0.07). The intensity modulation techniques have many advantages in terms of quality indexes, and particularly OAR sparing, compared with 3D-CRT. Following the ongoing technologic developments in modern radiotherapy, it is essential to evaluate the intensity-modulated techniques on prospective studies of a larger scale.

  2. Conformal Nets II: Conformal Blocks

    NASA Astrophysics Data System (ADS)

    Bartels, Arthur; Douglas, Christopher L.; Henriques, André

    2017-08-01

    Conformal nets provide a mathematical formalism for conformal field theory. Associated to a conformal net with finite index, we give a construction of the `bundle of conformal blocks', a representation of the mapping class groupoid of closed topological surfaces into the category of finite-dimensional projective Hilbert spaces. We also construct infinite-dimensional spaces of conformal blocks for topological surfaces with smooth boundary. We prove that the conformal blocks satisfy a factorization formula for gluing surfaces along circles, and an analogous formula for gluing surfaces along intervals. We use this interval factorization property to give a new proof of the modularity of the category of representations of a conformal net.

  3. Conformal Nets II: Conformal Blocks

    NASA Astrophysics Data System (ADS)

    Bartels, Arthur; Douglas, Christopher L.; Henriques, André

    2017-03-01

    Conformal nets provide a mathematical formalism for conformal field theory. Associated to a conformal net with finite index, we give a construction of the `bundle of conformal blocks', a representation of the mapping class groupoid of closed topological surfaces into the category of finite-dimensional projective Hilbert spaces. We also construct infinite-dimensional spaces of conformal blocks for topological surfaces with smooth boundary. We prove that the conformal blocks satisfy a factorization formula for gluing surfaces along circles, and an analogous formula for gluing surfaces along intervals. We use this interval factorization property to give a new proof of the modularity of the category of representations of a conformal net.

  4. Conformity index: a review.

    PubMed

    Feuvret, Loïc; Noël, Georges; Mazeron, Jean-Jacques; Bey, Pierre

    2006-02-01

    We present a critical analysis of the conformity indices described in the literature and an evaluation of their field of application. Three-dimensional conformal radiotherapy, with or without intensity modulation, is based on medical imaging techniques, three-dimensional dosimetry software, compression accessories, and verification procedures. It consists of delineating target volumes and critical healthy tissues to select the best combination of beams. This approach allows better adaptation of the isodose to the tumor volume, while limiting irradiation of healthy tissues. Tools must be developed to evaluate the quality of proposed treatment plans. Dosimetry software provides the dose distribution in each CT section and dose-volume histograms without really indicating the degree of conformity. The conformity index is a complementary tool that attributes a score to a treatment plan or that can compare several treatment plans for the same patient. The future of conformal index in everyday practice therefore remains unclear.

  5. Conformity index: A review

    SciTech Connect

    Feuvret, Loic . E-mail: loic.feuvret@cpo.curie.net; Noel, Georges; Mazeron, Jean-Jacques; Bey, Pierre

    2006-02-01

    We present a critical analysis of the conformity indices described in the literature and an evaluation of their field of application. Three-dimensional conformal radiotherapy, with or without intensity modulation, is based on medical imaging techniques, three-dimensional dosimetry software, compression accessories, and verification procedures. It consists of delineating target volumes and critical healthy tissues to select the best combination of beams. This approach allows better adaptation of the isodose to the tumor volume, while limiting irradiation of healthy tissues. Tools must be developed to evaluate the quality of proposed treatment plans. Dosimetry software provides the dose distribution in each CT section and dose-volume histograms without really indicating the degree of conformity. The conformity index is a complementary tool that attributes a score to a treatment plan or that can compare several treatment plans for the same patient. The future of conformal index in everyday practice therefore remains unclear.

  6. Förster Resonance Energy Transfer and Conformational Stability of Proteins: An Advanced Biophysical Module for Physical Chemistry Students.

    PubMed

    Sanchez, Katheryn M; Schlamadinger, Diana E; Gable, Jonathan E; Kim, Judy E

    2008-09-01

    Protein folding is an exploding area of research in biophysics and physical chemistry. Here, we describe the integration of several techniques, including absorption spectroscopy, fluorescence spectroscopy, and Förster resonance energy transfer (FRET) measurements, to probe important topics in protein folding. Cytochrome c is used as a model protein; comparison of conformational stabilities ( ΔGH2O∘) measured via two chemical denaturants, urea and guanidinium hydrochloride, illustrate important concepts in protein folding and intermolecular interactions. In addition, the determination of intraprotein distances based upon the FRET pair Trp-59 and the heme group for unfolded states of cytochrome c highlights the evolution of the protein structure under unfolding conditions. Analysis and discussion of these results provide opportunities to gain in-depth understanding of models for protein folding while enhancing students' skills with optical techniques. Collectively, the combination of optical spectroscopy, rigorous quantitative analysis, and a focus on biophysics illustrates the significance of fundamental research at the growing intersection of chemistry, biology, and physics.

  7. Förster Resonance Energy Transfer and Conformational Stability of Proteins: An Advanced Biophysical Module for Physical Chemistry Students

    PubMed Central

    Sanchez, Katheryn M.; Schlamadinger, Diana E.; Gable, Jonathan E.; Kim, Judy E.

    2009-01-01

    Protein folding is an exploding area of research in biophysics and physical chemistry. Here, we describe the integration of several techniques, including absorption spectroscopy, fluorescence spectroscopy, and Förster resonance energy transfer (FRET) measurements, to probe important topics in protein folding. Cytochrome c is used as a model protein; comparison of conformational stabilities ( ΔGH2O∘) measured via two chemical denaturants, urea and guanidinium hydrochloride, illustrate important concepts in protein folding and intermolecular interactions. In addition, the determination of intraprotein distances based upon the FRET pair Trp-59 and the heme group for unfolded states of cytochrome c highlights the evolution of the protein structure under unfolding conditions. Analysis and discussion of these results provide opportunities to gain in-depth understanding of models for protein folding while enhancing students’ skills with optical techniques. Collectively, the combination of optical spectroscopy, rigorous quantitative analysis, and a focus on biophysics illustrates the significance of fundamental research at the growing intersection of chemistry, biology, and physics. PMID:19756254

  8. High Affinity vs. Native Fibronectin in the Modulation of αvβ3 Integrin Conformational Dynamics: Insights from Computational Analyses and Implications for Molecular Design

    PubMed Central

    Paladino, Antonella; Civera, Monica; Belvisi, Laura

    2017-01-01

    Understanding how binding events modulate functional motions of multidomain proteins is a major issue in chemical biology. We address several aspects of this problem by analyzing the differential dynamics of αvβ3 integrin bound to wild type (wtFN10, agonist) or high affinity (hFN10, antagonist) mutants of fibronectin. We compare the dynamics of complexes from large-scale domain motions to inter-residue coordinated fluctuations to characterize the distinctive traits of conformational evolution and shed light on the determinants of differential αvβ3 activation induced by different FN sequences. We propose an allosteric model for ligand-based integrin modulation: the conserved integrin binding pocket anchors the ligand, while different residues on the two FN10’s act as the drivers that reorganize relevant interaction networks, guiding the shift towards inactive (hFN10-bound) or active states (wtFN10-bound). We discuss the implications of results for the design of integrin inhibitors. PMID:28114375

  9. Loop Virasoro Lie conformal algebra

    SciTech Connect

    Wu, Henan Chen, Qiufan; Yue, Xiaoqing

    2014-01-15

    The Lie conformal algebra of loop Virasoro algebra, denoted by CW, is introduced in this paper. Explicitly, CW is a Lie conformal algebra with C[∂]-basis (L{sub i} | i∈Z) and λ-brackets [L{sub i} {sub λ} L{sub j}] = (−∂−2λ)L{sub i+j}. Then conformal derivations of CW are determined. Finally, rank one conformal modules and Z-graded free intermediate series modules over CW are classified.

  10. Modulation of constitutive activity and signaling bias of the ghrelin receptor by conformational constraint in the second extracellular loop.

    PubMed

    Mokrosiński, Jacek; Frimurer, Thomas M; Sivertsen, Bjørn; Schwartz, Thue W; Holst, Birgitte

    2012-09-28

    Based on a rare, natural Glu for Ala-204(C+6) variant located six residues after the conserved Cys residue in extracellular loop 2b (ECL2b) associated with selective elimination of the high constitutive signaling of the ghrelin receptor, this loop was subjected to a detailed structure functional analysis. Introduction of Glu in different positions demonstrated that although the constitutive signaling was partly reduced when introduced in position 205(C+7) it was only totally eliminated in position 204(C+6). No charge-charge interaction partner could be identified for the Glu(C+6) variant despite mutational analysis of a number of potential partners in the extracellular loops and outer parts of the transmembrane segments. Systematic probing of position 204(C+6) with amino acid residues of different physicochemical properties indicated that a positively charged Lys surprisingly provided phenotypes similar to those of the negatively charged Glu residue. Computational chemistry analysis indicated that the propensity for the C-terminal segment of extracellular loop 2b to form an extended α-helix was increased from 15% in the wild type to 89 and 82% by introduction in position 204(C+6) of a Glu or a Lys residue, respectively. Moreover, the constitutive activity of the receptor was inhibited by Zn(2+) binding in an engineered metal ion site, stabilizing an α-helical conformation of this loop segment. It is concluded that the high constitutive activity of the ghrelin receptor is dependent upon flexibility in the C-terminal segment of extracellular loop 2 and that mutations or ligand binding that constrains this segment and thereby conceivably the movements of transmembrane domain V relative to transmembrane domain III inhibits the high constitutive signaling.

  11. Origin of the conformational modulation of the 13C NMR chemical shift of methoxy groups in aromatic natural compounds.

    PubMed

    Toušek, Jaromír; Straka, Michal; Sklenář, Vladimír; Marek, Radek

    2013-01-24

    The interpretation of nuclear magnetic resonance (NMR) parameters is essential to understanding experimental observations at the molecular and supramolecular levels and to designing new and more efficient molecular probes. In many aromatic natural compounds, unusual (13)C NMR chemical shifts have been reported for out-of-plane methoxy groups bonded to the aromatic ring (~62 ppm as compared to the typical value of ~56 ppm for an aromatic methoxy group). Here, we analyzed this phenomenon for a series of aromatic natural compounds using Density Functional Theory (DFT) calculations. First, we checked the methodology used to optimize the structure and calculate the NMR chemical shifts in aromatic compounds. The conformational effects of the methoxy group on the (13)C NMR chemical shift then were interpreted by the Natural Bond Orbital (NBO) and Natural Chemical Shift (NCS) approaches, and by excitation analysis of the chemical shifts, breaking down the total nuclear shielding tensor into the contributions from the different occupied orbitals and their magnetic interactions with virtual orbitals. We discovered that the atypical (13)C NMR chemical shifts observed are not directly related to a different conjugation of the lone pair of electrons of the methoxy oxygen with the aromatic ring, as has been suggested. Our analysis indicates that rotation of the methoxy group induces changes in the virtual molecular orbital space, which, in turn, correlate with the predominant part of the contribution of the paramagnetic deshielding connected with the magnetic interactions of the BD(CMet-H)→BD*(CMet-OMet) orbitals, resulting in the experimentally observed deshielding of the (13)C NMR resonance of the out-of-plane methoxy group.

  12. A 4 MV flattening filter-free beam: commissioning and application to conformal therapy and volumetric modulated arc therapy

    NASA Astrophysics Data System (ADS)

    Stevens, S. W.; Rosser, K. E.; Bedford, J. L.

    2011-07-01

    Recent studies have indicated that radiotherapy treatments undertaken on a flattening filter-free (FFF) linear accelerator have a number of advantages over treatments undertaken on a conventional linear accelerator. In addition, 4 MV photon beams may give improved isodose coverage for some treatment volumes at air/tissue interfaces, compared to when utilizing the clinical standard of 6 MV photons. In order to investigate these benefits, FFF beams were established on an Elekta Beam Modulator linear accelerator for 4 MV photons. Commissioning beam data were obtained for open and wedged fields. The measured data were then imported into a treatment planning system and a beam model was commissioned. The beam model was optimized to improve dose calculations at shallow, clinically relevant depths. Following verification, the beam model was utilized in a treatment planning study, including volumetric modulated arc therapy, for a selection of lung, breast/chest wall and larynx patients. Increased dose rates of around 800 MU min-1 were recorded for open fields (relative to 320 MU min-1 for filtered open fields) and reduced head scatter was inferred from output factor measurements. Good agreement between planned and delivered dose was observed in verification of treatment plans. The planning study indicated that with a FFF beam, equivalent (and in some cases improved) isodose profiles could be achieved for small lung and larynx treatment volumes relative to 4 MV filtered treatments. Furthermore, FFF treatments with wedges could be replicated using open fields together with an 'effective wedge' technique and isocentre shift. Clinical feasibility of a FFF beam was therefore demonstrated, with beam modelling, treatment planning and verification being successfully accomplished.

  13. Superiority of helical tomotherapy on liver sparing and dose escalation in hepatocellular carcinoma: a comparison study of three-dimensional conformal radiotherapy and intensity-modulated radiotherapy

    PubMed Central

    Zhao, Qianqian; Wang, Renben; Zhu, Jian; Jin, Linzhi; Zhu, Kunli; Xu, Xiaoqing; Feng, Rui; Jiang, Shumei; Qi, Zhonghua; Yin, Yong

    2016-01-01

    Background and purpose To compare the difference of liver sparing and dose escalation between three-dimensional conformal radiotherapy (3DCRT), intensity-modulated radiotherapy (IMRT), and helical tomotherapy (HT) for hepatocellular carcinoma. Patients and methods Sixteen unresectable HCC patients were enrolled in this study. First, some evaluation factors of 3DCRT, IMRT, and HT plans were calculated with prescription dose at 50 Gy/25 fractions. Then, the doses were increased using HT or IMRT independently until either the plans reached 70 Gy or any normal tissue reached the dose limit according to quantitative analysis of normal tissue effects in the clinic criteria. Results The conformal index of 3DCRT was lower than that of IMRT (P<0.001) or HT (P<0.001), and the homogeneity index of 3DCRT was higher than that of IMRT (P<0.001) or HT (P<0.001). HT took the longest treatment time (P<0.001). For V50% (fraction of normal liver treated to at least 50% of the isocenter dose) of the normal liver, there was a significant difference: 3DCRT > IMRT > HT (P<0.001). HT had a lower Dmean (mean dose) and V20 (Vn, the percentage of organ volume receiving ≥n Gy) of liver compared with 3DCRT (P=0.005 and P=0.005, respectively) or IMRT (P=0.508 and P=0.007, respectively). Dmean of nontarget normal liver and V30 of liver were higher for 3DCRT than IMRT (P=0.005 and P=0.005, respectively) or HT (P=0.005 and P=0.005, respectively). Seven patients in IMRT (43.75%) and nine patients in HT (56.25%) reached the isodose 70 Gy, meeting the dose limit of the organs at risk. Conclusion HT may provide significantly better liver sparing and allow more patients to achieve higher prescription dose in HCC radiotherapy. PMID:27445485

  14. Dosimetric comparison study between intensity modulated radiation therapy and three-dimensional conformal proton therapy for pelvic bone marrow sparing in the treatment of cervical cancer.

    PubMed

    Song, William Y; Huh, Soon N; Liang, Yun; White, Greg; Nichols, R Charles; Watkins, W Tyler; Mundt, Arno J; Mell, Loren K

    2010-08-15

    The objective was to compare intensity-modulated radiation therapy (IMRT) with 3D conformal proton therapy (3DCPT) in the treatment of cervical cancer. In particular, each technique's ability to spare pelvic bone marrow (PBM) was of primary interest in this study. A total of six cervical cancer patients (3 postoperative and 3 intact) were planned and analyzed. All plans had uniform 1.0 cm CTV-PTV margin and satisfied the 95% PTV with 100% isodose (prescription dose = 45 Gy) coverage. Dose-volume histograms (DVH) were analyzed for comparison. The overall PTV and PBM volumes were 1035.9 ± 192.2 cc and 1151.4 ± 198.3 cc, respectively. In terms of PTV dose conformity index (DCI) and dose homogeneity index (DHI), 3DCPT was slightly superior to IMRT with 1.00 ± 0.001, 1.01 ± 0.02, and 1.10 ± 0.02, 1.13 ± 0.01, respectively. In addition, 3DCPT demonstrated superiority in reducing lower doses (i.e., V30 or less) to PBM, small bowel and bladder. Particularly in PBM, average V10 and V20 reductions of 10.8% and 7.4% (p = 0.001 and 0.04), respectively, were observed. However, in the higher dose range, IMRT provided better sparing (> V30). For example, in small bowel and PBM, average reductions in V45 of 4.9% and 10.0% (p = 0.048 and 0.008), respectively, were observed. Due to its physical characteristics such as low entrance dose, spread-out Bragg peak and finite particle range of protons, 3DCPT illustrated superior target coverage uniformity and sparing of the lower doses in PBM and other organs. Further studies are, however, needed to fully exploit the benefits of protons for general use in cervical cancer.

  15. The sigma-1 receptor modulates dopamine transporter conformation and cocaine binding and may thereby potentiate cocaine self-administration in rats.

    PubMed

    Hong, Weimin Conrad; Yano, Hideaki; Hiranita, Takato; Chin, Frederick T; McCurdy, Christopher R; Su, Tsung-Ping; Amara, Susan G; Katz, Jonathan L

    2017-07-07

    The dopamine transporter (DAT) regulates dopamine (DA) neurotransmission by recapturing DA into the presynaptic terminals and is a principal target of the psychostimulant cocaine. The sigma-1 receptor (σ1R) is a molecular chaperone, and its ligands have been shown to modulate DA neuronal signaling, although their effects on DAT activity are unclear. Here, we report that the prototypical σ1R agonist (+)-pentazocine potentiated the dose response of cocaine self-administration in rats, consistent with the effects of the σR agonists PRE-084 and DTG (1,3-di-o-tolylguanidine) reported previously. These behavioral effects appeared to be correlated with functional changes of DAT. Preincubation with (+)-pentazocine or PRE-084 increased the Bmax values of [(3)H]WIN35428 binding to DAT in rat striatal synaptosomes and transfected cells. A specific interaction between σ1R and DAT was detected by co-immunoprecipitation and bioluminescence resonance energy transfer assays. Mutational analyses indicated that the transmembrane domain of σ1R likely mediated this interaction. Furthermore, cysteine accessibility assays showed that σ1R agonist preincubation potentiated cocaine-induced changes in DAT conformation, which were blocked by the specific σ1R antagonist CM304. Moreover, σ1R ligands had distinct effects on σ1R multimerization. CM304 increased the proportion of multimeric σ1Rs, whereas (+)-pentazocine increased monomeric σ1Rs. Together these results support the hypothesis that σ1R agonists promote dissociation of σ1R multimers into monomers, which then interact with DAT to stabilize an outward-facing DAT conformation and enhance cocaine binding. We propose that this novel molecular mechanism underlies the behavioral potentiation of cocaine self-administration by σ1R agonists in animal models. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  16. Single-arc volumetric-modulated arc therapy (sVMAT) as adjuvant treatment for gastric cancer: Dosimetric comparisons with three-dimensional conformal radiotherapy (3D-CRT) and intensity-modulated radiotherapy (IMRT)

    SciTech Connect

    Wang, Xin; Li, Guangjun; Zhang, Yingjie; Bai, Sen; Xu, Feng; Wei, Yuquan; Gong, Youling

    2013-01-01

    To compare the dosimetric differences between the single-arc volumetric-modulated arc therapy (sVMAT), 3-dimensional conformal radiotherapy (3D-CRT), and intensity-modulated radiotherapy (IMRT) techniques in treatment planning for gastric cancer as adjuvant radiotherapy. Twelve patients were retrospectively analyzed. In each patient's case, the parameters were compared based on the dose-volume histogram (DVH) of the sVMAT, 3D-CRT, and IMRT plans, respectively. Three techniques showed similar target dose coverage. The maximum and mean doses of the target were significantly higher in the sVMAT plans than that in 3D-CRT plans and in the 3D-CRT/IMRT plans, respectively, but these differences were clinically acceptable. The IMRT and sVMAT plans successfully achieved better target dose conformity, reduced the V{sub 20/30}, and mean dose of the left kidney, as well as the V{sub 20/30} of the liver, compared with the 3D-CRT plans. And the sVMAT technique reduced the V{sub 20} of the liver much significantly. Although the maximum dose of the spinal cord were much higher in the IMRT and sVMAT plans, respectively (mean 36.4 vs 39.5 and 40.6 Gy), these data were still under the constraints. Not much difference was found in the analysis of the parameters of the right kidney, intestine, and heart. The IMRT and sVMAT plans achieved similar dose distribution to the target, but superior to the 3D-CRT plans, in adjuvant radiotherapy for gastric cancer. The sVMAT technique improved the dose sparings of the left kidney and liver, compared with the 3D-CRT technique, but showed few dosimetric advantages over the IMRT technique. Studies are warranted to evaluate the clinical benefits of the VMAT treatment for patients with gastric cancer after surgery in the future.

  17. Proton Arc Reduces Range Uncertainty Effects and Improves Conformality Compared With Photon Volumetric Modulated Arc Therapy in Stereotactic Body Radiation Therapy for Non-Small Cell Lung Cancer

    SciTech Connect

    Seco, Joao; Gu, Guan; Marcelos, Tiago; Kooy, Hanne; Willers, Henning

    2013-09-01

    Purpose: To describe, in a setting of non-small cell lung cancer (NSCLC), the theoretical dosimetric advantages of proton arc stereotactic body radiation therapy (SBRT) in which the beam penumbra of a rotating beam is used to reduce the impact of range uncertainties. Methods and Materials: Thirteen patients with early-stage NSCLC treated with proton SBRT underwent repeat planning with photon volumetric modulated arc therapy (Photon-VMAT) and an in-house-developed arc planning approach for both proton passive scattering (Passive-Arc) and intensity modulated proton therapy (IMPT-Arc). An arc was mimicked with a series of beams placed at 10° increments. Tumor and organ at risk doses were compared in the context of high- and low-dose regions, represented by volumes receiving >50% and <50% of the prescription dose, respectively. Results: In the high-dose region, conformality index values are 2.56, 1.91, 1.31, and 1.74, and homogeneity index values are 1.29, 1.22, 1.52, and 1.18, respectively, for 3 proton passive scattered beams, Passive-Arc, IMPT-Arc, and Photon-VMAT. Therefore, proton arc leads to a 30% reduction in the 95% isodose line volume to 3-beam proton plan, sparing surrounding organs, such as lung and chest wall. For chest wall, V30 is reduced from 21 cm{sup 3} (3 proton beams) to 11.5 cm{sup 3}, 12.9 cm{sup 3}, and 8.63 cm{sup 3} (P=.005) for Passive-Arc, IMPT-Arc, and Photon-VMAT, respectively. In the low-dose region, the mean lung dose and V20 of the ipsilateral lung are 5.01 Gy(relative biological effectiveness [RBE]), 4.38 Gy(RBE), 4.91 Gy(RBE), and 5.99 Gy(RBE) and 9.5%, 7.5%, 9.0%, and 10.0%, respectively, for 3-beam, Passive-Arc, IMPT-Arc, and Photon-VMAT, respectively. Conclusions: Stereotactic body radiation therapy with proton arc and Photon-VMAT generate significantly more conformal high-dose volumes than standard proton SBRT, without loss of coverage of the tumor and with significant sparing of nearby organs, such as chest wall. In addition

  18. Changes in Pulmonary Function After Three-Dimensional Conformal Radiotherapy, Intensity-Modulated Radiotherapy, or Proton Beam Therapy for Non-Small-Cell Lung Cancer

    SciTech Connect

    Lopez Guerra, Jose L.; Gomez, Daniel R.; Zhuang Yan; Levy, Lawrence B.; Eapen, George; Liu, Hongmei; Mohan, Radhe; Komaki, Ritsuko; Cox, James D.; Liao Zhongxing

    2012-07-15

    Purpose: To investigate the extent of change in pulmonary function over time after definitive radiotherapy for non-small-cell lung cancer (NSCLC) with modern techniques and to identify predictors of changes in pulmonary function according to patient, tumor, and treatment characteristics. Patients and Methods: We analyzed 250 patients who had received {>=}60 Gy radio(chemo)therapy for primary NSCLC in 1998-2010 and had undergone pulmonary function tests before and within 1 year after treatment. Ninety-three patients were treated with three-dimensional conformal radiotherapy, 97 with intensity-modulated radiotherapy, and 60 with proton beam therapy. Postradiation pulmonary function test values were evaluated among individual patients compared with the same patient's preradiation value at the following time intervals: 0-4 (T1), 5-8 (T2), and 9-12 (T3) months. Results: Lung diffusing capacity for carbon monoxide (DLCO) was reduced in the majority of patients along the three time periods after radiation, whereas the forced expiratory volume in 1 s per unit of vital capacity (FEV1/VC) showed an increase and decrease after radiation in a similar percentage of patients. There were baseline differences (stage, radiotherapy dose, concurrent chemotherapy) among the radiation technology groups. On multivariate analysis, the following features were associated with larger posttreatment declines in DLCO: pretreatment DLCO, gross tumor volume, lung and heart dosimetric data, and total radiation dose. Only pretreatment DLCO was associated with larger posttreatment declines in FEV1/VC. Conclusions: Lung diffusing capacity for carbon monoxide is reduced in the majority of patients after radiotherapy with modern techniques. Multiple factors, including gross tumor volume, preradiation lung function, and dosimetric parameters, are associated with the DLCO decline. Prospective studies are needed to better understand whether new radiation technology, such as proton beam therapy or

  19. Adjuvant Radiotherapy for Gastric Cancer: A Dosimetric Comparison of 3-Dimensional Conformal Radiotherapy, Tomotherapy (registered) and Conventional Intensity Modulated Radiotherapy Treatment Plans

    SciTech Connect

    Dahele, Max; Skinner, Matthew; Schultz, Brenda; Cardoso, Marlene; Bell, Chris; Ung, Yee C.

    2010-07-01

    Some patients with gastric cancer benefit from post-operative chemo-radiotherapy, but adequately irradiating the planning target volume (PTV) whilst avoiding organs at risk (OAR) can be difficult. We evaluate 3-dimensional conformal radiotherapy (CRT), conventional intensity-modulated radiotherapy (IMRT) and helical tomotherapy (TT). TT, 2 and 5-field (F) CRT and IMRT treatment plans with the same PTV coverage were generated for 5 patients and compared. Median values are reported. The volume of left/right kidney receiving at least 20Gy (V20) was 57/51% and 51/60% for 2 and 5F-CRT, and 28/14% for TT and 27/19% for IMRT. The volume of liver receiving at least 30Gy (V30) was 45% and 62% for 2 and 5F-CRT, and 37% for TT and 35% for IMRT. With TT, 98% of the PTV received 95-105% of the prescribed dose, compared with 45%, 34% and 28% for 2F-CRT, 5F-CRT and IMRT respectively. Using conventional metrics, conventional IMRT can achieve comparable PTV coverage and OAR sparing to TT, but at the expense of PTV dose heterogeneity. Both irradiate large volumes of normal tissue to low doses. Additional studies are needed to demonstrate the clinical impact of these technologies.

  20. Dosimetric evaluation of the skin-sparing effects of 3-dimensional conformal radiotherapy and intensity-modulated radiotherapy for left breast cancer.

    PubMed

    Jo, In Young; Kim, Shin-Wook; Son, Seok Hyun

    2017-01-10

    The purpose of this study was to evaluate the skin-sparing effects of 3-dimensional conformal radiotherapy (3D-CRT) and intensity-modulated radiotherapy (IMRT) in patients with early left-sided breast cancer. Twenty left breast cancer patients treated with whole breast radiotherapy following breast-conserving surgery were enrolled in this study, and the 3D-CRT and IMRT plans were generated for each patient. To evaluate the dose delivered to the skin, 2 mm thickness skin (2-mm skin) and 3 mm thickness skin (3-mm skin) were contoured and a dosimetric comparison between the 2 plans was performed. The target volume coverage was better in IMRT than in 3D-CRT. The mean dose was 50.8 Gy for 3D-CRT and 51.1 Gy for IMRT. V40Gy was 99.4% for 3D-CRT and 99.9% for IMRT. In the case of skin, the mean dose was higher in 3D-CRT than in IMRT (mean dose of 2-mm skin: 32.8 Gy and 24.2 Gy; mean dose of 3-mm skin: 37.2 Gy and 27.8 Gy, for 3D-CRT and IMRT, respectively). These results indicated that the skin-sparing effect is more prominent in IMRT compared to 3D-CRT without compromising the target volume coverage.

  1. Docosahexaenoic acid phospholipid differentially modulates the conformation of G90V and N55K rhodopsin mutants associated with retinitis pigmentosa.

    PubMed

    Dong, Xiaoyun; Herrera-Hernández, María Guadalupe; Ramon, Eva; Garriga, Pere

    2017-05-01

    Rhodopsin is the visual photoreceptor of the retinal rod cells that mediates dim light vision and a prototypical member of the G protein-coupled receptor superfamily. The structural stability and functional performance of rhodopsin are modulated by membrane lipids. Docosahexaenoic acid has been shown to interact with native rhodopsin but no direct evidence has been established on the effect of such lipid on the stability and regeneration of rhodopsin mutants associated with retinal diseases. The stability and regeneration of two thermosensitive mutants G90V and N55K, associated with the retinal degenerative disease retinitis pigmentosa, have been analyzed in docosohexaenoic phospholipid (1,2-didocosa-hexaenoyl-sn-glycero-3-phosphocholine; DDHA-PC) liposomes. G90V mutant reconstituted in DDHA-PC liposomes significantly increased its thermal stability, but N55K mutant showed similar thermal sensitivity both in dodecyl maltoside detergent solution and in DDHA-PC liposomes. The retinal release process, measured by fluorescence spectroscopy, became faster in the lipid system for the two mutants. The opsin conformation was stabilized for the G90V mutant allowing improved retinal uptake whereas no chromophore binding could be detected for N55K opsin after photoactivation. The results emphasize the distinct role of DHA on different phenotypic rhodopsin mutations associated with classical (G90V) and sector (N55K) retinitis pigmentosa. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Transportation Conformity

    EPA Pesticide Factsheets

    This section provides information on: current laws, regulations and guidance, policy and technical guidance, project-level conformity, general information, contacts and training, adequacy review of SIP submissions

  3. A comparison of liver protection among 3-D conformal radiotherapy, intensity-modulated radiotherapy and RapidArc for hepatocellular carcinoma

    PubMed Central

    2014-01-01

    Purpose The analysis was designed to compare dosimetric parameters among 3-D conformal radiotherapy (3DCRT), intensity-modulated radiotherapy (IMRT) and RapidArc (RA) to identify which can achieve the lowest risk of radiation-induced liver disease (RILD) for hepatocellular carcinoma (HCC). Methods Twenty patients with HCC were enrolled in this study. Dosimetric values for 3DCRT, IMRT, and RA were calculated for total dose of 50 Gy/25f. The percentage of the normal liver volume receiving >40, >30, >20, >10, and >5 Gy (V40, V30, V20, V10 and V5) were evaluated to determine liver toxicity. V5, V10, V20, V30 and Dmean of liver were compared as predicting parameters for RILD. Other parameters included the conformal index (CI), homogeneity index (HI), and hot spot (V110%) for the planned target volume (PTV) as well as the monitor units (MUs) for plan efficiency, the mean dose (Dmean) for the organs at risk (OARs) and the maximal dose at 1% volume (D1%) for the spinal cord. Results The Dmean of IMRT was higher than 3DCRT (p = 0.045). For V5, there was a significant difference: RA > IMRT >3DCRT (p <0.05). 3DCRT had a lower V10 and higher V20, V30 values for liver than RA (p <0.05). RA and IMRT achieved significantly better CI and lower V110% values than 3DCRT (p <0.05). RA had better HI, lower MUs and shorter delivery time than 3DCRT or IMRT (p <0.05). Conclusion For right lobe tumors, RapidArc may have the lowest risk of RILD with the lowest V20 and V30 compared with 3DCRT or IMRT. For diameters of tumors >8 cm in our study, the value of Dmean for 3DCRT was lower than IMRT or RapidArc. This may indicate that 3DCRT is more suitable for larger tumors. PMID:24502643

  4. Late Side Effects After Image Guided Intensity Modulated Radiation Therapy Compared to 3D-Conformal Radiation Therapy for Prostate Cancer: Results From 2 Prospective Cohorts.

    PubMed

    Wortel, Ruud C; Incrocci, Luca; Pos, Floris J; van der Heide, Uulke A; Lebesque, Joos V; Aluwini, Shafak; Witte, Marnix G; Heemsbergen, Wilma D

    2016-06-01

    Technical developments in the field of external beam radiation therapy (RT) enabled the clinical introduction of image guided intensity modulated radiation therapy (IG-IMRT), which improved target conformity and allowed reduction of safety margins. Whether this had an impact on late toxicity levels compared to previously applied three-dimensional conformal radiation therapy (3D-CRT) is currently unknown. We analyzed late side effects after treatment with IG-IMRT or 3D-CRT, evaluating 2 prospective cohorts of men treated for localized prostate cancer to investigate the hypothesized reductions in toxicity. Patients treated with 3D-CRT (n=189) or IG-IMRT (n=242) to 78 Gy in 39 fractions were recruited from 2 Dutch randomized trials with identical toxicity scoring protocols. Late toxicity (>90 days after treatment) was derived from self-assessment questionnaires and case report forms, according to Radiation Therapy Oncology Group/European Organization for Research and Treatment of Cancer (RTOG-EORTC) scoring criteria. Grade ≥2 endpoints included gastrointestinal (GI) rectal bleeding, increased stool frequency, discomfort, rectal incontinence, proctitis, and genitourinary (GU) obstruction, increased urinary frequency, nocturia, urinary incontinence, and dysuria. The Cox proportional hazards regression model was used to compare grade ≥2 toxicities between both techniques, adjusting for other modifying factors. The 5-year cumulative incidence of grade ≥2 GI toxicity was 24.9% for IG-IMRT and 37.6% following 3D-CRT (adjusted hazard ratio [HR]: 0.59, P=.005), with significant reductions in proctitis (HR: 0.37, P=.047) and increased stool frequency (HR: 0.23, P<.001). GU grade ≥2 toxicity levels at 5 years were comparable with 46.2% and 36.4% following IG-IMRT and 3D-CRT, respectively (adjusted HR: 1.19, P=.33). Other strong predictors (P<.01) of grade ≥2 late toxicity were baseline complaints, acute toxicity, and age. Treatment with IG-IMRT reduced the risk of

  5. Propensity Score-based Comparison of Long-term Outcomes With 3-Dimensional Conformal Radiotherapy vs Intensity-Modulated Radiotherapy for Esophageal Cancer

    SciTech Connect

    Lin, Steven H.; Wang Lu; Myles, Bevan; Thall, Peter F.; Hofstetter, Wayne L.; Swisher, Stephen G.; Ajani, Jaffer A.; Cox, James D.; Komaki, Ritsuko; Liao Zhongxing

    2012-12-01

    Purpose: Although 3-dimensional conformal radiotherapy (3D-CRT) is the worldwide standard for the treatment of esophageal cancer, intensity modulated radiotherapy (IMRT) improves dose conformality and reduces the radiation exposure to normal tissues. We hypothesized that the dosimetric advantages of IMRT should translate to substantive benefits in clinical outcomes compared with 3D-CRT. Methods and Materials: An analysis was performed of 676 nonrandomized patients (3D-CRT, n=413; IMRT, n=263) with stage Ib-IVa (American Joint Committee on Cancer 2002) esophageal cancers treated with chemoradiotherapy at a single institution from 1998-2008. An inverse probability of treatment weighting and inclusion of propensity score (treatment probability) as a covariate were used to compare overall survival time, interval to local failure, and interval to distant metastasis, while accounting for the effects of other clinically relevant covariates. The propensity scores were estimated using logistic regression analysis. Results: A fitted multivariate inverse probability weighted-adjusted Cox model showed that the overall survival time was significantly associated with several well-known prognostic factors, along with the treatment modality (IMRT vs 3D-CRT, hazard ratio 0.72, P<.001). Compared with IMRT, 3D-CRT patients had a significantly greater risk of dying (72.6% vs 52.9%, inverse probability of treatment weighting, log-rank test, P<.0001) and of locoregional recurrence (P=.0038). No difference was seen in cancer-specific mortality (Gray's test, P=.86) or distant metastasis (P=.99) between the 2 groups. An increased cumulative incidence of cardiac death was seen in the 3D-CRT group (P=.049), but most deaths were undocumented (5-year estimate, 11.7% in 3D-CRT vs 5.4% in IMRT group, Gray's test, P=.0029). Conclusions: Overall survival, locoregional control, and noncancer-related death were significantly better after IMRT than after 3D-CRT. Although these results need

  6. Protection of organs at risk during neoadjuvant chemoradiotherapy for gastric cancer based on a comparison between conformal and intensity-modulated radiation therapy

    PubMed Central

    HAWRYLEWICZ, LESZEK; LESZCZYŃSKI, WOJCIECH; NAMYSŁ-KALETKA, AGNIESZKA; BRONCLIK, IWONA; WYDMAŃSKI, JERZY

    2016-01-01

    The aim of the present study was to compare the techniques of dynamic intensity-modulated radiation therapy (IMRT) and three-dimensional conformal radiotherapy (3DCRT) in patients with gastric cancer. Implementation of the IMRT technique does not significantly affect the minimum and maximum dose levels in the planning target volume (PTV), but more effectively protects the critical organs. The study group consisted of 25 patients. The results of the analysis of the conformity index (CI) and the homogeneity index (HI) showed that the doses in the PTV regions were at a comparable level. The CI for the PTV was 0.95 for the 2-field technique, 0.95 for the 3-field technique, 0.96 for the 4-field technique and 0.94 for the IMRT technique. The CIs for these techniques for the clinical target volume (CTV) were 0.96, 0.96, 0.97 and 0.96, respectively, and the CIs for the gross tumor volume (GTV) were 0.99, 0.99, 0.99 and 0.98, respectively. The HI values for the PTV were 1.12 for the 2-field technique, 1.12 for the 3-field technique, 1.09 for the 4-field technique and 1.09 for the IMRT technique, and the HI values for the CTV were 1.12, 1.12, 1.09 and 1.08 for the same techniques, respectively. The HI values for the GTV were 1.09, 1.09, 1.07 and 1.06, respectively, which indicated significantly superior performance in the regions of healthy tissue. Statistical study was based on Friedman's rank analysis of variance to determine the level of reliability of the tested groups of variables (P<0.001). The present study demonstrated that the IMRT technique in the pre-operative radiotherapy of gastric cancer patients results in superior treatment tolerance and reduces the risk of damage to healthy tissue that is in close proximity to the irradiated area. PMID:27347202

  7. In-vitro investigation of out-of-field cell survival following the delivery of conformal, intensity-modulated radiation therapy (IMRT) and volumetric modulated arc therapy (VMAT) plans

    NASA Astrophysics Data System (ADS)

    McGarry, Conor K.; Butterworth, Karl T.; Trainor, Colman; McMahon, Stephen J.; O'Sullivan, Joe M.; Prise, Kevin M.; Hounsell, Alan R.

    2012-10-01

    The aim of this work is to determine the out-of-field survival of cells irradiated with either the primary field or scattered radiation in the presence and absence of intercellular communication following delivery of conformal, IMRT and VMAT treatment plans. Single beam, conformal, IMRT and VMAT plans were created to deliver 3 Gy to half the area of a T80 flask containing either DU-145 or AGO-1522 cells allowing intercellular communication between the in- and out-of-field cell populations. The same plans were delivered to a similar custom made phantom used to hold two T25 culture flasks, one flask in-field and one out-of-field to allow comparison of cell survival responses when intercellular communication is physically inhibited. Plans were created for the delivery of 8 Gy to the more radio-resistant DU-145 cells only in the presence and absence of intercellular communication. Cell survival was determined by clonogenic assay. In both cell lines, the out-of-field survival was not statistically different between delivery techniques for either cell line or dose. There was however, a statistically significant difference between survival out-of-field when intercellular communication was intact (single T80 culture flask) or inhibited (multiple T25 culture flasks) to in-field for all plans. No statistically significant difference was observed in-field with or without cellular communication to out-of-field for all plans. These data demonstrate out-of-field effects as important determinants of cell survival following exposure to modulated irradiation fields when cellular communication between differentially irradiated cell populations is present. This data is further evidence that refinement of existing radiobiological models to include indirect cell killing effects is required.

  8. Volumetric Modulation Arc Radiotherapy With Flattening Filter-Free Beams Compared With Static Gantry IMRT and 3D Conformal Radiotherapy for Advanced Esophageal Cancer: A Feasibility Study

    SciTech Connect

    Nicolini, Giorgia; Ghosh-Laskar, Sarbani; Shrivastava, Shyam Kishore; Banerjee, Sushovan; Chaudhary, Suresh; Agarwal, Jai Prakash; Munshi, Anusheel; Clivio, Alessandro; Fogliata, Antonella; Mancosu, Pietro; Vanetti, Eugenio; Cozzi, Luca

    2012-10-01

    Purpose: A feasibility study was performed to evaluate RapidArc (RA), and the potential benefit of flattening filter-free beams, on advanced esophageal cancer against intensity-modulated radiotherapy (IMRT) and three-dimensional conformal radiotherapy (3D-CRT). Methods and Materials: The plans for 3D-CRT and IMRT with three to seven and five to seven fixed beams were compared against double-modulated arcs with avoidance sectors to spare the lungs for 10 patients. All plans were optimized for 6-MV photon beams. The RA plans were studied for conventional and flattening filter-free (FFF) beams. The objectives for the planning target volume were the volume receiving {>=}95% or at most 107% of the prescribed dose of <1% with a dose prescription of 59.4 Gy. For the organs at risk, the lung volume (minus the planning target volume) receiving {>=}5 Gy was <60%, that receiving 20 Gy was <20%-30%, and the mean lung dose was <15.0 Gy. The heart volume receiving 45 Gy was <20%, volume receiving 30 Gy was <50%. The spinal dose received by 1% was <45 Gy. The technical delivery parameters for RA were assessed to compare the normal and FFF beam characteristics. Results: RA and IMRT provided equivalent coverage and homogeneity, slightly superior to 3D-CRT. The conformity index was 1.2 {+-} 0.1 for RA and IMRT and 1.5 {+-} 0.2 for 3D-CRT. The mean lung dose was 12.2 {+-} 4.5 for IMRT, 11.3 {+-} 4.6 for RA, and 10.8 {+-} 4.4 for RA with FFF beams, 18.2 {+-} 8.5 for 3D-CRT. The percentage of volume receiving {>=}20 Gy ranged from 23.6% {+-} 9.1% to 21.1% {+-} 9.7% for IMRT and RA (FFF beams) and 39.2% {+-} 17.0% for 3D-CRT. The heart and spine objectives were met by all techniques. The monitor units for IMRT and RA were 457 {+-} 139, 322 {+-} 20, and 387 {+-} 40, respectively. RA with FFF beams showed, compared with RA with normal beams, a {approx}20% increase in monitor units per Gray, a 90% increase in the average dose rate, and 20% reduction in beam on time (owing to different

  9. A Comparison of Out-of-Field Dose and Its Constituent Components for Intensity-Modulated Radiation Therapy Versus Conformal Radiation Therapy: Implications for Carcinogenesis

    SciTech Connect

    Ruben, Jeremy D.; Lancaster, Craig M.; Jones, Phillip; Smith, Ryan L.

    2011-12-01

    Purpose: To investigate differences in scatter and leakage between 6-MV intensity-modulated radiation therapy (IMRT) and three-dimensional conformal radiation therapy (3DCRT); to describe the relative contributions of internal patient scatter, collimator scatter, and head leakage; and to discuss implications for second cancer induction. Methods and Materials: Dose was measured at increasing distances from the field edge in a water bath with a sloping wall (1) under full scatter conditions, (2) with the field edge abutting but outside the bath to prevent internal (water) scatter, and (3) with the beam aperture plugged to reflect leakage only. Results: Internal patient scatter from IMRT is 11% lower than 3DCRT, but collimator scatter and head leakage are five and three times higher, respectively. Ultimately, total scattered dose is 80% higher with IMRT; however this difference is small in absolute terms, being 0.14% of prescribed dose. Secondary dose from 3DCRT is mostly due to internal patient scatter, which contributes 70% of the total and predominates until 25 cm from the field edge. For IMRT, however, machine scatter/leakage is the dominant source, contributing 65% of the secondary dose. Internal scatter predominates for just the first 10 cm from field edge, collimator scatter for the next 10 cm, and head leakage thereafter. Conclusions: Out-of-field dose is 80% higher with IMRT, but differences are tiny in absolute terms. Reductions in internal patient scatter with IMRT are outweighed by increased machine scatter and leakage, at least for small fields. Reductions from IMRT in dose to tissues within the portals and in internal scatter, which predominates close to the field edge, means that calculations based solely on dose to distant tissues may overestimate carcinogenic risks.

  10. A comparison of out-of-field dose and its constituent components for intensity-modulated radiation therapy versus conformal radiation therapy: implications for carcinogenesis.

    PubMed

    Ruben, Jeremy D; Lancaster, Craig M; Jones, Phillip; Smith, Ryan L

    2011-12-01

    To investigate differences in scatter and leakage between 6-MV intensity-modulated radiation therapy (IMRT) and three-dimensional conformal radiation therapy (3DCRT); to describe the relative contributions of internal patient scatter, collimator scatter, and head leakage; and to discuss implications for second cancer induction. Dose was measured at increasing distances from the field edge in a water bath with a sloping wall (1) under full scatter conditions, (2) with the field edge abutting but outside the bath to prevent internal (water) scatter, and (3) with the beam aperture plugged to reflect leakage only. Internal patient scatter from IMRT is 11% lower than 3DCRT, but collimator scatter and head leakage are five and three times higher, respectively. Ultimately, total scattered dose is 80% higher with IMRT; however this difference is small in absolute terms, being 0.14% of prescribed dose. Secondary dose from 3DCRT is mostly due to internal patient scatter, which contributes 70% of the total and predominates until 25 cm from the field edge. For IMRT, however, machine scatter/leakage is the dominant source, contributing 65% of the secondary dose. Internal scatter predominates for just the first 10 cm from field edge, collimator scatter for the next 10 cm, and head leakage thereafter. Out-of-field dose is 80% higher with IMRT, but differences are tiny in absolute terms. Reductions in internal patient scatter with IMRT are outweighed by increased machine scatter and leakage, at least for small fields. Reductions from IMRT in dose to tissues within the portals and in internal scatter, which predominates close to the field edge, means that calculations based solely on dose to distant tissues may overestimate carcinogenic risks. Crown Copyright © 2011. Published by Elsevier Inc. All rights reserved.

  11. A comparative analysis of 3D conformal deep inspiratory–breath hold and free-breathing intensity-modulated radiation therapy for left-sided breast cancer

    SciTech Connect

    Reardon, Kelli A.; Read, Paul W.; Morris, Monica M.; Reardon, Michael A.; Geesey, Constance; Wijesooriya, Krishni

    2013-07-01

    Patients undergoing radiation for left-sided breast cancer have increased rates of coronary artery disease. Free-breathing intensity-modulated radiation therapy (FB-IMRT) and 3-dimensional conformal deep inspiratory–breath hold (3D-DIBH) reduce cardiac irradiation. The purpose of this study is to compare the dose to organs at risk in FB-IMRT vs 3D-DIBH for patients with left-sided breast cancer. Ten patients with left-sided breast cancer had 2 computed tomography scans: free breathing and voluntary DIBH. Optimization of the IMRT plan was performed on the free-breathing scan using 6 noncoplanar tangential beams. The 3D-DIBH plan was optimized on the DIBH scan and used standard tangents. Mean volumes of the heart, the left anterior descending coronary artery (LAD), the total lung, and the right breast receiving 5% to 95% (5% increments) of the prescription dose were calculated. Mean volumes of the heart and the LAD were lower (p<0.05) in 3D-DIBH for volumes receiving 5% to 80% of the prescription dose for the heart and 5% for the LAD. Mean dose to the LAD and heart were lower in 3D-DIBH (p≤0.01). Mean volumes of the total lung were lower in FB-IMRT for dose levels 20% to 75% (p<0.05), but mean dose was not different. Mean volumes of the right breast were not different for any dose; however, mean dose was lower for 3D-DIBH (p = 0.04). 3D-DIBH is an alternative approach to FB-IMRT that provides a clinically equivalent treatment for patients with left-sided breast cancer while sparing organs at risk with increased ease of implementation.

  12. Intensity-Modulated Radiotherapy Might Increase Pneumonitis Risk Relative to Three-Dimensional Conformal Radiotherapy in Patients Receiving Combined Chemotherapy and Radiotherapy: A Modeling Study of Dose Dumping

    SciTech Connect

    Vogelius, Ivan S.; Westerly, David C.; Cannon, George M.; Mackie, Thomas R.; Mehta, Minesh P.; Sugie, Chikao; Bentzen, Soren M.

    2011-07-01

    Purpose: To model the possible interaction between cytotoxic chemotherapy and the radiation dose distribution with respect to the risk of radiation pneumonitis. Methods and Materials: A total of 18 non-small-cell lung cancer patients previously treated with helical tomotherapy at the University of Wisconsin were selected for the present modeling study. Three treatment plans were considered: the delivered tomotherapy plans; a three-dimensional conformal radiotherapy (3D-CRT) plan; and a fixed-field intensity-modulated radiotherapy (IMRT) plan. The IMRT and 3D-CRT plans were generated specifically for the present study. The plans were optimized without adjusting for the chemotherapy effect. The effect of chemotherapy was modeled as an independent cell killing process by considering a uniform chemotherapy equivalent radiation dose added to all voxels of the organ at risk. The risk of radiation pneumonitis was estimated for all plans using the Lyman and the critical volume models. Results: For radiotherapy alone, the critical volume model predicts that the two IMRT plans are associated with a lower risk of radiation pneumonitis than the 3D-CRT plan. However, when the chemotherapy equivalent radiation dose exceeds a certain threshold, the radiation pneumonitis risk after IMRT is greater than after 3D-CRT. This threshold dose is in the range estimated from clinical chemoradiotherapy data sets. Conclusions: Cytotoxic chemotherapy might affect the relative merit of competing radiotherapy plans. More work is needed to improve our understanding of the interaction between chemotherapy and the radiation dose distribution in clinical settings.

  13. Quality of Life and Survival Outcome for Patients With Nasopharyngeal Carcinoma Receiving Three-Dimensional Conformal Radiotherapy vs. Intensity-Modulated Radiotherapy-A Longitudinal Study

    SciTech Connect

    Fang, F.-M. Chien, C.-Y.; Tsai, W.-L.; Chen, H.-C.; Hsu, H.-C.; Lui, C.-C.; Huang, T.-L.

    2008-10-01

    Purpose: To investigate the changes of quality of life (QoL) and survival outcomes for patients with nasopharyngeal carcinoma (NPC) treated by three-dimensional conformal radiotherapy (3D-CRT) vs. intensity-modulated radiotherapy (IMRT). Methods and Materials: Two hundred and three newly diagnosed NPC patients, who were curatively treated by 3D-CRT (n = 93) or IMRT (n = 110) between March 2002 and July 2004, were analyzed. The distributions of clinical stage according to American Joint Committee on Cancer 1997 were I: 15 (7.4%), II: 78 (38.4%), III: 74 (36.5%), and IV: 36 (17.7%). QoL was longitudinally assessed by the European Organization for Research and Treatment of Cancer (EORTC) QLQ-C30 and the EORTC QLQ-H and N35 questionnaires at the five time points: before RT, during RT (36 Gy), and 3 months, 12 months, and 24 months after RT. Results: The 3-year locoregional control, metastasis-free survival, and overall survival rates were 84.8%, 76.7%, and 81.7% for the 3D-CRT group, respectively, compared with 84.2%, 82.6%, and 85.4% for the IMRT group (p value > 0.05). A general trend of maximal deterioration in most QoL scales was observed during RT, followed by a gradual recovery thereafter. There was no significant difference in most scales between the two groups at each time point. The exception was that patients treated by IMRT had a both statistically and clinically significant improvement in global QoL, fatigue, taste/smell, dry mouth, and feeling ill at the time point of 3 months after RT. Conclusions: The potential advantage of IMRT over 3D-CRT in treating NPC patients might occur in QoL outcome during the recovery phase of acute toxicity.

  14. Contribution of three-dimensional conformal intensity-modulated radiation therapy for women affected by bulky stage II supradiaphragmatic Hodgkin disease.

    PubMed

    Antoni, Delphine; Natarajan-Ame, Shanti; Meyer, Philippe; Niederst, Claudine; Bourahla, Khalil; Noel, Georges

    2013-05-02

    To analyze the outcome and dose distribution of intensity-modulated radiation therapy (IMRT) by helical tomotherapy in women treated for large supradiaphragmatic Hodgkin's disease. A total of 13 patients received adjuvant radiation at a dose of 30 Gy to the initially involved sites with a boost of 6 Gy to those areas suspected of harboring residual disease on the simulation CT scan. With a median follow-up of 23 months, the two-year progression-free survival was 91.6%, and the 2- and 3-year overall survivals were 100%. We did not report any heart or lung acute side effects. The conformity index of PTV (Planning Target Volume) was better for IMRT than for 3D-CRT (p=0.001). For the breasts, lungs, heart, thyroid and esophagus, the volume distributions favored the IMRT plans. For the breasts, the V(20Gy), V(25Gy) and V(30Gy) were 1.5, 2.5 and 3.5 times lower, respectively, for IMRT than for 3D-CRT. For the lung tissues, the V(20Gy) and V(30Gy) were 2 times and 4.5 times lower, respectively, for IMRT than for 3D-CRT. For the heart, the V(20Gy) and V(30Gy) were 1.4 and 2 times lower, respectively, for IMRT than for 3D-CRT. For the esophagus, the V(35Gy) was 1.7 lower for IMRT than for 3D-CRT, and for the thyroid, the V(30Gy) was 1.2 times lower for IMRT. IMRT by helical tomotherapy improved the PTV coverage and dramatically decreased the dose in organs at risk. The treatment was well tolerated, but a longer follow-up is necessary to prove a translation of these dosimetric improvements in the outcome of the patients.

  15. Contribution of three-dimensional conformal intensity-modulated radiation therapy for women affected by bulky stage II supradiaphragmatic Hodgkin disease

    PubMed Central

    2013-01-01

    Purpose To analyze the outcome and dose distribution of intensity-modulated radiation therapy (IMRT) by helical tomotherapy in women treated for large supradiaphragmatic Hodgkin’s disease. Material and methods A total of 13 patients received adjuvant radiation at a dose of 30 Gy to the initially involved sites with a boost of 6 Gy to those areas suspected of harboring residual disease on the simulation CT scan. Results With a median follow-up of 23 months, the two-year progression-free survival was 91.6%, and the 2- and 3-year overall survivals were 100%. We did not report any heart or lung acute side effects. The conformity index of PTV (Planning Target Volume) was better for IMRT than for 3D-CRT (p=0.001). For the breasts, lungs, heart, thyroid and esophagus, the volume distributions favored the IMRT plans. For the breasts, the V20Gy, V25Gy and V30Gy were 1.5, 2.5 and 3.5 times lower, respectively, for IMRT than for 3D-CRT. For the lung tissues, the V20Gy and V30Gy were 2 times and 4.5 times lower, respectively, for IMRT than for 3D-CRT. For the heart, the V20Gy and V30Gy were 1.4 and 2 times lower, respectively, for IMRT than for 3D-CRT. For the esophagus, the V35Gy was 1.7 lower for IMRT than for 3D-CRT, and for the thyroid, the V30Gy was 1.2 times lower for IMRT. Conclusion IMRT by helical tomotherapy improved the PTV coverage and dramatically decreased the dose in organs at risk. The treatment was well tolerated, but a longer follow-up is necessary to prove a translation of these dosimetric improvements in the outcome of the patients. PMID:23638873

  16. A comparative analysis of 3D conformal deep inspiratory-breath hold and free-breathing intensity-modulated radiation therapy for left-sided breast cancer.

    PubMed

    Reardon, Kelli A; Read, Paul W; Morris, Monica M; Reardon, Michael A; Geesey, Constance; Wijesooriya, Krishni

    2013-01-01

    Patients undergoing radiation for left-sided breast cancer have increased rates of coronary artery disease. Free-breathing intensity-modulated radiation therapy (FB-IMRT) and 3-dimensional conformal deep inspiratory-breath hold (3D-DIBH) reduce cardiac irradiation. The purpose of this study is to compare the dose to organs at risk in FB-IMRT vs 3D-DIBH for patients with left-sided breast cancer. Ten patients with left-sided breast cancer had 2 computed tomography scans: free breathing and voluntary DIBH. Optimization of the IMRT plan was performed on the free-breathing scan using 6 noncoplanar tangential beams. The 3D-DIBH plan was optimized on the DIBH scan and used standard tangents. Mean volumes of the heart, the left anterior descending coronary artery (LAD), the total lung, and the right breast receiving 5% to 95% (5% increments) of the prescription dose were calculated. Mean volumes of the heart and the LAD were lower (p<0.05) in 3D-DIBH for volumes receiving 5% to 80% of the prescription dose for the heart and 5% for the LAD. Mean dose to the LAD and heart were lower in 3D-DIBH (p≤0.01). Mean volumes of the total lung were lower in FB-IMRT for dose levels 20% to 75% (p<0.05), but mean dose was not different. Mean volumes of the right breast were not different for any dose; however, mean dose was lower for 3D-DIBH (p = 0.04). 3D-DIBH is an alternative approach to FB-IMRT that provides a clinically equivalent treatment for patients with left-sided breast cancer while sparing organs at risk with increased ease of implementation.

  17. Two-Year and Lifetime Cost-Effectiveness of Intensity Modulated Radiation Therapy Versus 3-Dimensional Conformal Radiation Therapy for Head-and-Neck Cancer

    SciTech Connect

    Kohler, Racquel E.; Sheets, Nathan C.; Wheeler, Stephanie B.; Nutting, Chris; Hall, Emma; Chera, Bhishamjit S.

    2013-11-15

    Purpose: To assess the cost-effectiveness of intensity modulated radiation therapy (IMRT) versus 3-dimensional conformal radiation therapy (3D-CRT) in the treatment of head-and neck-cancer (HNC). Methods and Materials: We used a Markov model to simulate radiation therapy-induced xerostomia and dysphagia in a hypothetical cohort of 65-year-old HNC patients. Model input parameters were derived from PARSPORT (CRUK/03/005) patient-level trial data and quality-of-life and Medicare cost data from published literature. We calculated average incremental cost-effectiveness ratios (ICERs) from the US health care perspective as cost per quality-adjusted life-year (QALY) gained and compared our ICERs with current cost-effectiveness standards whereby treatment comparators less than $50,000 per QALY gained are considered cost-effective. Results: In the first 2 years after initial treatment, IMRT is not cost-effective compared with 3D-CRT, given an average ICER of $101,100 per QALY gained. However, over 15 years (remaining lifetime on the basis of average life expectancy of a 65-year-old), IMRT is more cost-effective at $34,523 per QALY gained. Conclusion: Although HNC patients receiving IMRT will likely experience reduced xerostomia and dysphagia symptoms, the small quality-of-life benefit associated with IMRT is not cost-effective in the short term but may be cost-effective over a patient's lifetime, assuming benefits persist over time and patients are healthy and likely to live for a sustained period. Additional data quantifying the long-term benefits of IMRT, however, are needed.

  18. Intensity modulated radiation therapy (IMRT) is not superior to three-dimensional conformal radiation (3DCRT) for adjuvant gastric radiation: A matched pair analysis.

    PubMed

    Chopra, Supriya; Agarwal, Aditi; Engineer, Reena; Dora, Tapas; Thomas, Biji; Sonawone, Supriya; Paul, Siji N; Kannan, Sadhna; Patil, Prachi; Mehta, Shaesta; Shrivastava, Shyam Kishore

    2015-01-01

    To compare three-dimensional conformal radiation (3DCRT) and Intensity Modulated Radiation Therapy (IG-IMRT) for adjuvant gastric irradiation. From Jan 2010-Aug 2013, all patients undergoing 3DCRT and IG-IMRT were included. Systemic chemotherapy included 1 cycle before and 2 cycles after chemoradiation. Planning Target Volume (PTV) received 45 Gy/25 fractions/5 weeks with concurrent capcetabine 825 mg/m2 bid. Matched pair analysis was performed to evaluate imbalance in two cohorts if any. Common Toxicity Criteria for Adverse Event (CTCAE) vs 3.0 was used to record gastrointestinal (GI), hematological (HL), and renal toxicity during treatment and follow-up. Patterns of recurrence were documented. Mann-Whitney U test was used for statistical comparison. Of the 51 patients, 26 received 3DCRT and 25 IMRT. IMRT led to decrease in dose received by right and left kidney (12.4 Gy and 7.1 Gy and 29 Gy vs 8.2 Gy; P<0.001). Overall, 17.6% and 19.6% patients had grade II GI and HL toxicity and 3.9% and 5.9% had grade III GI and HL toxicity. No difference was observed in acute grade II-V GI or HL toxicity (11.5% vs 24%, P=0.07; 7.6% vs 20% P=0.20) or late GI, HL, or renal toxicity between 3DCRT and IMRT. No difference was observed in patterns of local relapse (11.5% vs 12%, P=0.14) or overall survival (39% and 38% (P=0.97)) between 3DCRT and IMRT. 3DCRT and IMRT are equivalent in terms of toxicity and local control.

  19. Dosimetric impact of inter-observer variability for 3D conformal radiotherapy and volumetric modulated arc therapy: the rectal tumor target definition case

    PubMed Central

    2013-01-01

    Background To assess the dosimetric effect induced by inter-observer variability in target definition for 3D-conformal RT (3DCRT) and volumetric modulated arc therapy by RapidArc (RA) techniques for rectal cancer treatment. Methods Ten patients with rectal cancer subjected to neo-adjuvant RT were randomly selected from the internal database. Four radiation oncologists independently contoured the clinical target volume (CTV) in blind mode. Planning target volume (PTV) was defined as CTV + 7 mm in the three directions. Afterwards, shared guidelines between radiation oncologists were introduced to give general criteria for the contouring of rectal target and the four radiation oncologists defined new CTV following the guidelines. For each patient, six intersections (I) and unions (U) volumes were calculated coupling the contours of the various oncologists. This was repeated for the contours drawn after the guidelines. Agreement Index (AI = I/U) was calculated pre and post guidelines. Two RT plans (one with 3DCRT technique using 3–4 fields and one with RA using a single modulated arc) were optimized on each radiation oncologist’s PTV. For each plan the PTV volume receiving at least 95% of the prescribed dose (PTV V95%) was calculated for both target and non-target PTVs. Results The inter-operator AI pre-guidelines was 0.57 and was increased up to 0.69 post-guidelines. The maximum volume difference between the various CTV couples, drawn for each patient, passed from 380 ± 147 cm3 to 137 ± 83 cm3 after the introduction of guidelines. The mean percentage for the non-target PTV V95% was 93.7 ± 9.2% before and 96.6 ± 4.9%after the introduction of guidelines for the 3DCRT, for RA the increase was more relevant, passing from 86.5 ± 13.8% (pre) to 94.5 ± 7.5% (post). The OARs were maximally spared with VMAT technique while the variability between pre and post guidelines was not relevant in both techniques. Conclusions The contouring

  20. Dosimetric impact of inter-observer variability for 3D conformal radiotherapy and volumetric modulated arc therapy: the rectal tumor target definition case.

    PubMed

    Lobefalo, Francesca; Bignardi, Mario; Reggiori, Giacomo; Tozzi, Angelo; Tomatis, Stefano; Alongi, Filippo; Fogliata, Antonella; Gaudino, Anna; Navarria, Piera; Cozzi, Luca; Scorsetti, Marta; Mancosu, Pietro

    2013-07-09

    To assess the dosimetric effect induced by inter-observer variability in target definition for 3D-conformal RT (3DCRT) and volumetric modulated arc therapy by RapidArc (RA) techniques for rectal cancer treatment. Ten patients with rectal cancer subjected to neo-adjuvant RT were randomly selected from the internal database. Four radiation oncologists independently contoured the clinical target volume (CTV) in blind mode. Planning target volume (PTV) was defined as CTV + 7 mm in the three directions. Afterwards, shared guidelines between radiation oncologists were introduced to give general criteria for the contouring of rectal target and the four radiation oncologists defined new CTV following the guidelines. For each patient, six intersections (I) and unions (U) volumes were calculated coupling the contours of the various oncologists. This was repeated for the contours drawn after the guidelines. Agreement Index (AI = I/U) was calculated pre and post guidelines. Two RT plans (one with 3DCRT technique using 3-4 fields and one with RA using a single modulated arc) were optimized on each radiation oncologist's PTV. For each plan the PTV volume receiving at least 95% of the prescribed dose (PTV V95%) was calculated for both target and non-target PTVs. The inter-operator AI pre-guidelines was 0.57 and was increased up to 0.69 post-guidelines. The maximum volume difference between the various CTV couples, drawn for each patient, passed from 380 ± 147 cm³ to 137 ± 83 cm³ after the introduction of guidelines. The mean percentage for the non-target PTV V95% was 93.7 ± 9.2% before and 96.6 ± 4.9%after the introduction of guidelines for the 3DCRT, for RA the increase was more relevant, passing from 86.5 ± 13.8% (pre) to 94.5 ± 7.5% (post). The OARs were maximally spared with VMAT technique while the variability between pre and post guidelines was not relevant in both techniques. The contouring inter-observer variability has dosimetric

  1. Intensity modulated radiation therapy versus three-dimensional conformal radiation therapy for the treatment of high grade glioma: a dosimetric comparison.

    PubMed

    MacDonald, Shannon M; Ahmad, Salahuddin; Kachris, Stefanos; Vogds, Betty J; DeRouen, Melissa; Gittleman, Alicia E; DeWyngaert, Keith; Vlachaki, Maria T

    2007-04-19

    The present study compared the dosimetry of intensity-modulated radiation therapy (IMRT) and three-dimensional conformal radiation therapy (3D-CRT) techniques in patients treated for high-grade glioma. A total of 20 patients underwent computed tomography treatment planning in conjunction with magnetic resonance imaging fusion. Prescription dose and normal-tissue constraints were identical for the 3D-CRT and IMRT plans. The prescribed dose was 59.4 Gy delivered at 1.8 Gy per fraction using 4-10 MV photons. Normal-tissue dose constraints were 50-54 Gy for the optic chiasm and nerves, and 55-60 Gy for the brainstem. The IMRT plan yielded superior target coverage as compared with the 3D-CRT plan. Specifically, minimum and mean planning target volume cone down doses were 54.52 Gy and 61.74 Gy for IMRT and 50.56 Gy and 60.06 Gy for 3D-CRT (p < or = 0.01). The IMRT plan reduced the percent volume of brainstem receiving a dose greater than 45 Gy by 31% (p = 0.004) and the percent volume of brain receiving a dose greater than 18 Gy, 24 Gy, and 45 Gy by 10% (p = 0.059), 14% (p = 0.015), and 40% (p < or = 0.0001) respectively. With IMRT, the percent volume of optic chiasm receiving more than 45 Gy was also reduced by 30.40% (p = 0.047). As compared with 3D-CRT, IMRT significantly increased the tumor control probability (p < or = 0.005) and lowered the normal-tissue complication probability for brain and brainstem (p < 0.033). Intensity-modulated radiation therapy improved target coverage and reduced radiation dose to the brain, brainstem, and optic chiasm. With the availability of new cancer imaging tools and more effective systemic agents, IMRT may be used to intensify tumor doses while minimizing toxicity, therefore potentially improving outcomes in patients with high-grade glioma.

  2. Conformal Infinity

    NASA Astrophysics Data System (ADS)

    Frauendiener, Jörg

    2004-12-01

    The notion of conformal infinity has a long history within the research in Einstein's theory of gravity. Today, "conformal infinity" is related to almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved from physical issues, namely the need to understand gravitational radiation and isolated systems within the theory of gravitation, and how it lends itself very naturally to the solution of radiation problems in numerical relativity. The fundamental concept of null-infinity is introduced. Friedrich's regular conformal field equations are presented and various initial value problems for them are discussed. Finally, it is shown that the conformal field equations provide a very powerful method within numerical relativity to study global problems such as gravitational wave propagation and detection.

  3. General Conformity

    EPA Pesticide Factsheets

    The General Conformity requirements ensure that the actions taken by federal agencies in nonattainment and maintenance areas do not interfere with a state’s plans to meet national standards for air quality.

  4. Improvement in toxicity in high risk prostate cancer patients treated with image-guided intensity-modulated radiotherapy compared to 3D conformal radiotherapy without daily image guidance

    PubMed Central

    2014-01-01

    Background Image-guided radiotherapy (IGRT) facilitates the delivery of a very precise radiation dose. In this study we compare the toxicity and biochemical progression-free survival between patients treated with daily image-guided intensity-modulated radiotherapy (IG-IMRT) and 3D conformal radiotherapy (3DCRT) without daily image guidance for high risk prostate cancer (PCa). Methods A total of 503 high risk PCa patients treated with radiotherapy (RT) and endocrine treatment between 2000 and 2010 were retrospectively reviewed. 115 patients were treated with 3DCRT, and 388 patients were treated with IG-IMRT. 3DCRT patients were treated to 76 Gy and without daily image guidance and with 1–2 cm PTV margins. IG-IMRT patients were treated to 78 Gy based on daily image guidance of fiducial markers, and the PTV margins were 5–7 mm. Furthermore, the dose-volume constraints to both the rectum and bladder were changed with the introduction of IG-IMRT. Results The 2-year actuarial likelihood of developing grade > = 2 GI toxicity following RT was 57.3% in 3DCRT patients and 5.8% in IG-IMRT patients (p < 0.001). For GU toxicity the numbers were 41.8% and 29.7%, respectively (p = 0.011). On multivariate analysis, 3DCRT was associated with a significantly increased risk of developing grade > = 2 GI toxicity compared to IG-IMRT (p < 0.001, HR = 11.59 [CI: 6.67-20.14]). 3DCRT was also associated with an increased risk of developing GU toxicity compared to IG-IMRT. The 3-year actuarial biochemical progression-free survival probability was 86.0% for 3DCRT and 90.3% for IG-IMRT (p = 0.386). On multivariate analysis there was no difference in biochemical progression-free survival between 3DCRT and IG-IMRT. Conclusion The difference in toxicity can be attributed to the combination of the IMRT technique with reduced dose to organs-at-risk, daily image guidance and margin reduction. PMID:24495815

  5. Intensity-Modulated Radiotherapy Causes Fewer Side Effects than Three-Dimensional Conformal Radiotherapy When Used in Combination With Brachytherapy for the Treatment of Prostate Cancer

    SciTech Connect

    Forsythe, Kevin; Blacksburg, Seth; Stone, Nelson; Stock, Richard G.

    2012-06-01

    Purpose: To measure the benefits of intensity-modulated radiotherapy (IMRT) compared with three-dimensional conformal radiotherapy (3D-CRT) when used in combination with brachytherapy for the treatment of prostate cancer. Methods and Materials: We conducted a retrospective review of all patients with localized prostate cancer who received external-beam radiotherapy (EBRT) in combination with brachytherapy with at least 1 year follow-up (n = 812). Combination therapy consisted of {sup 103}Pd or {sup 125}I implant, followed by a course of EBRT. From 1993 to March 2003 521 patients were treated with 3D-CRT, and from April 2003 to March 2009 291 patients were treated with IMRT. Urinary symptoms were prospectively measured with the International Prostate Symptom Score questionnaire with a single quality of life (QOL) question; rectal bleeding was assessed per the Radiation Therapy Oncology Group/European Organization for Research and Treatment of Cancer Late Radiation Morbidity Scoring Schema. The Pearson {chi}{sup 2} test was used to compare toxicities experienced by patients who were treated with either IMRT or 3D-CRT. Logistic regression analyses were also performed to rule out possible confounding factors. Results: Within the first 3 months after treatment, patients treated with 3D-CRT scored their urinary symptoms as follows: 19% mild, 44% moderate, and 37% severe; patients treated with IMRT scored their urinary symptoms as follows: 36% mild, 47% moderate, and 17% severe (p < 0.001). The 3D-CRT patients rated their QOL as follows: 35% positive, 20% neutral, and 45% negative; IMRT patients rated their QOL as follows: 51% positive, 18% neutral, and 31% negative (p < 0.001). After 1 year of follow-up there was no longer any difference in urinary morbidity between the two groups. Logistic regression confirmed the differences in International Prostate Symptom Score and QOL in the acute setting (p < 0.001 for both). Grade {>=}2 rectal bleeding was reported by 11% of 3D

  6. Intensity-modulated radiotherapy improves lymph node coverage and dose to critical structures compared with three-dimensional conformal radiation therapy in clinically localized prostate cancer

    SciTech Connect

    Wang-Chesebro, Alice . E-mail: awang@radonc17.ucsf.edu; Xia Ping; Coleman, Joy; Akazawa, Clayton C.; Roach, Mack

    2006-11-01

    Purpose: The aim of this study was to quantify gains in lymph node coverage and critical structure dose reduction for whole-pelvis (WP) and extended-field (EF) radiotherapy in prostate cancer using intensity-modulated radiotherapy (IMRT) compared with three-dimensional conformal radiotherapy (3DCRT) for the first treatment phase of 45 Gy in the concurrent treatment of lymph nodes and prostate. Methods and Materials: From January to August 2005, 35 patients with localized prostate cancer were treated with pelvic IMRT; 7 had nodes defined up to L5-S1 (Group 1), and 28 had nodes defined above L5-S1 (Group 2). Each patient had 2 plans retrospectively generated: 1 WP 3DCRT plan using bony landmarks, and 1 EF 3DCRT plan to cover the vascular defined volumes. Dose-volume histograms for the lymph nodes, rectum, bladder, small bowel, and penile bulb were compared by group. Results: For Group 1, WP 3DCRT missed 25% of pelvic nodes with the prescribed dose 45 Gy and missed 18% with the 95% prescribed dose 42.75 Gy, whereas WP IMRT achieved V{sub 45Gy} = 98% and V{sub 42.75Gy} = 100%. Compared with WP 3DCRT, IMRT reduced bladder V{sub 45Gy} by 78%, rectum V{sub 45Gy} by 48%, and small bowel V{sub 45Gy} by 232 cm{sup 3}. EF 3DCRT achieved 95% coverage of nodes for all patients at high cost to critical structures. For Group 2, IMRT decreased bladder V{sub 45Gy} by 90%, rectum V{sub 45Gy} by 54% and small bowel V{sub 45Gy} by 455 cm{sup 3} compared with EF 3DCRT. Conclusion: In this study WP 3DCRT missed a significant percentage of pelvic nodes. Although EF 3DCRT achieved 95% pelvic nodal coverage, it increased critical structure doses. IMRT improved pelvic nodal coverage while decreasing dose to bladder, rectum, small bowel, and penile bulb. For patients with extended node involvement, IMRT especially decreases small bowel dose.

  7. Variations in energy spectra and water-to-material stopping-power ratios in three-dimensional conformal and intensity-modulated photon fields

    SciTech Connect

    Jang, Si Young; Liu, H. Helen; Mohan, Radhe; Siebers, Jeffrey V.

    2007-04-15

    Because of complex dose distributions and dose gradients that are created in three-dimensional conformal radiotherapy (3D-CRT) and intensity-modulated radiation therapy (IMRT), photon- and electron-energy spectra might change significantly with spatial locations and doses. This study examined variations in photon- and electron-energy spectra in 3D-CRT and IMRT photon fields. The effects of spectral variations on water-to-material stopping-power ratios used in Monte Carlo treatment planning systems and the responses of energy-dependent dosimeters, such as thermoluminescent dosimeters (TLDs) and radiographic films were further studied. The EGSnrc Monte Carlo code was used to simulate megavoltage 3D-CRT and IMRT photon fields. The photon- and electron-energy spectra were calculated in 3D water phantoms and anthropomorphic phantoms based on the fluence scored in voxel grids. We then obtained the water-to-material stopping-power ratios in the local voxels using the Spencer-Attix cavity theory. Changes in the responses of films and TLDs were estimated based on the calculated local energy spectra and published data on the dosimeter energy dependency. Results showed that the photon-energy spectra strongly depended on spatial positions and doses in both the 3D-CRT and IMRT fields. The relative fraction of low-energy photons (<100 keV) increased inversely with the photon dose in low-dose regions of the fields. A similar but smaller effect was observed for electrons in the phantoms. The maximum variation of the water-to-material stopping-power ratio over the range of calculated dose for both 3D-CRT and IMRT was negligible (<1.0%) for ICRU tissue, cortical bone, and soft bone and less than 3.6% for dry air and lung. Because of spectral softening at low doses, radiographic films in the phantoms could over-respond to dose by more than 30%, whereas the over-response of TLDs was less than 10%. Thus, spatial variations of the photon- and electron-energy spectra should be considered

  8. Variations in energy spectra and water-to-material stopping-power ratios in three-dimensional conformal and intensity-modulated photon fields.

    PubMed

    Jang, Si Young; Liu, H Helen; Mohan, Radhe; Siebers, Jeffrey V

    2007-04-01

    Because of complex dose distributions and dose gradients that are created in three-dimensional conformal radiotherapy (3D-CRT) and intensity-modulated radiation therapy (IMRT), photon- and electron-energy spectra might change significantly with spatial locations and doses. This study examined variations in photon- and electron-energy spectra in 3D-CRT and IMRT photon fields. The effects of spectral variations on water-to-material stopping-power ratios used in Monte Carlo treatment planning systems and the responses of energy-dependent dosimeters, such as thermoluminescent dosimeters (TLDs) and radiographic films were further studied. The EGSnrc Monte Carlo code was used to simulate megavoltage 3D-CRT and IMRT photon fields. The photon- and electron-energy spectra were calculated in 3D water phantoms and anthropomorphic phantoms based on the fluence scored in voxel grids. We then obtained the water-to-material stopping-power ratios in the local voxels using the Spencer-Attix cavity theory. Changes in the responses of films and TLDs were estimated based on the calculated local energy spectra and published data on the dosimeter energy dependency. Results showed that the photon-energy spectra strongly depended on spatial positions and doses in both the 3D-CRT and IMRT fields. The relative fraction of low-energy photons (< 100 keV) increased inversely with the photon dose in low-dose regions of the fields. A similar but smaller effect was observed for electrons in the phantoms. The maximum variation of the water-to-material stopping-power ratio over the range of calculated dose for both 3D-CRT and IMRT was negligible (< 1.0%) for ICRU tissue, cortical bone, and soft bone and less than 3.6% for dry air and lung. Because of spectral softening at low doses, radiographic films in the phantoms could over-respond to dose by more than 30%, whereas the over-response of TLDs was less than 10%. Thus, spatial variations of the photon- and electron-energy spectra should be

  9. Conformational and thermodynamic properties modulate the nucleotide excision repair of 2-aminofluorene and 2-acetylaminofluorene dG adducts in the NarI sequence

    PubMed Central

    Jain, Vipin; Hilton, Benjamin; Patnaik, Satyakam; Zou, Yue; Chiarelli, M. Paul; Cho, Bongsup P.

    2012-01-01

    Nucleotide excision repair (NER) is a major repair pathway that recognizes and corrects various lesions in cellular DNA. We hypothesize that damage recognition is an initial step in NER that senses conformational anomalies in the DNA caused by lesions. We prepared three DNA duplexes containing the carcinogen adduct N-(2′-deoxyguanosin-8-yl)-7-fluoro-2-acetylaminofluorene (FAAF) at G1, G2 or G3 of NarI sequence (5′-CCG1G2CG3CC-3′). Our 19F-NMR/ICD results showed that FAAF at G1 and G3 prefer syn S- and W-conformers, whereas anti B-conformer was predominant for G2. We found that the repair of FAAF occurs in a conformation-specific manner, i.e. the highly S/W-conformeric G3 and -G1 duplexes incised more efficiently than the B-type G2 duplex (G3∼G1 > G2). The melting and thermodynamic data indicate that the S- and W-conformers produce greater DNA distortion and thermodynamic destabilization. The N-deacetylated N-(2′-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene (FAF) adducts in the same NarI sequence are repaired 2- to 3-fold less than FAAF: however, the incision efficiency was in order of G2∼G1 > G3, a reverse trend of the FAAF case. We have envisioned the so-called N-acetyl factor as it could raise conformational barriers of FAAF versus FAF. The present results provide valuable conformational insight into the sequence-dependent UvrABC incisions of the bulky aminofluorene DNA adducts. PMID:22241773

  10. Modulation of Immunogenicity and Conformation of HA1 Subunit of Influenza A Virus H1/N1 Hemagglutinin in Tubular Immunostimulating Complexes.

    PubMed

    Sanina, Nina; Davydova, Ludmila; Chopenko, Natalia; Kostetsky, Eduard; Shnyrov, Valery

    2017-09-03

    The HA1 subunit of the influenza virus hemagglutinin (HA) is a valuable antigen for the development of vaccines against flu due to the availability of most antigenic sites which are conformational. Therefore, a novel adjuvanted antigen delivery system, tubular immunostimulating complexes (TI-complexes) comprising monogalactosyldiacylglycerol (MGDG) from different marine macrophytes as a lipid matrix for an antigen, was applied to enhance the immunogenicity of recombinant HA1 of influenza A H1N1 and to study the relation between its immunogenicity and conformation. The content of anti-HA1 antibodies and cytokines was estimated by ELISA after the immunization of mice with HA1 alone, and HA1 was incorporated in TI-complexes based on different MGDGs isolated from green algae Ulva lactuca, brown algae Sargassum pallidum, and seagrass Zostera marina. Conformational changes of HA1 were estimated by differential scanning calorimetry and intrinsic fluorescence. It was shown that the adjuvant activity of TI-complexes depends on the microviscosity of MGDGs, which differently influence the conformation of HA1. The highest production of anti-HA1 antibodies (compared with the control) was induced by HA1 incorporated in a TI-complex based on MGDG from S. pallidum, which provided the relaxation of the spatial structure and, likely, the proper presentation of the antigen to immunocompetent cells.

  11. Cofactor binding modulates the conformational stabilities and unfolding patterns of NAD(+)-dependent DNA ligases from Escherichia coli and Thermus scotoductus.

    PubMed

    Georlette, Daphné; Blaise, Vinciane; Dohmen, Christophe; Bouillenne, Fabrice; Damien, Benjamin; Depiereux, Eric; Gerday, Charles; Uversky, Vladimir N; Feller, Georges

    2003-12-12

    DNA ligases are important enzymes required for cellular processes such as DNA replication, recombination, and repair. NAD(+)-dependent DNA ligases are essentially restricted to eubacteria, thus constituting an attractive target in the development of novel antibiotics. Although such a project might involve the systematic testing of a vast number of chemical compounds, it can essentially gain from the preliminary deciphering of the conformational stability and structural perturbations associated with the formation of the catalytically active adenylated enzyme. We have, therefore, investigated the adenylation-induced conformational changes in the mesophilic Escherichia coli and thermophilic Thermus scotoductus NAD(+)-DNA ligases, and the resistance of these enzymes to thermal and chemical (guanidine hydrochloride) denaturation. Our results clearly demonstrate that anchoring of the cofactor induces a conformational rearrangement within the active site of both mesophilic and thermophilic enzymes accompanied by their partial compaction. Furthermore, the adenylation of enzymes increases their resistance to thermal and chemical denaturation, establishing a thermodynamic link between cofactor binding and conformational stability enhancement. Finally, guanidine hydrochloride-induced unfolding of NAD(+)-dependent DNA ligases is shown to be a complex process that involves accumulation of at least two equilibrium intermediates, the molten globule and its precursor.

  12. Modulation of Conformational Equilibria in the S-Adenosylmethionine (SAM) II Riboswitch by SAM, Mg(2+), and Trimethylamine N-Oxide.

    PubMed

    McPhie, Peter; Brown, Patrick; Chen, Bin; Dayie, Theodore K; Minton, Allen P

    2016-09-13

    The dependence of the conformation of the S-adenosylmethionine (SAM) II riboswitch on the concentration of added Mg(2+) ions and SAM, individually and in mixtures, was monitored by circular dichroism (CD) spectroscopy and by measurement of the diffusion coefficient. The results are analyzed in the context of two complementary quantitative models, both of which are consistent with a single underlying physical model. Magnesium binding sites in the open state have an affinity on average higher than the affinity of those in the compact state, but formation of the compact state is accompanied by an increase in the number of binding sites. Consequently, at low Mg(2+) concentrations, Mg(2+) binds preferentially to the open state, favoring its formation, but at high concentrations, Mg(2+) binds preferentially to the compact state. The affinity of the riboswitch for SAM increases drastically with an increased level of binding of Mg(2+) to the compact pseudoknot conformation. The effect of increasing concentrations of trimethylamine N-oxide (TMAO), a well-studied molecular crowding agent, on the conformation of the riboswitch and its affinity for SAM were also monitored by CD spectroscopy and measurement of diffusion. In the absence of added Mg(2+), high concentrations of TMAO were found to induce a conformational change compatible with the formation of the pseudoknot form but have only a small effect on the affinity of the RNA for SAM.

  13. Health-Related Quality of Life in Patients With Locally Advanced Prostate Cancer After 76 Gy Intensity-Modulated Radiotherapy vs. 70 Gy Conformal Radiotherapy in a Prospective and Longitudinal Study

    SciTech Connect

    Lips, Irene Dehnad, Human; Kruger, Arto Boeken; Moorselaar, Jeroen van; Heide, Uulke van; Battermann, Jan; Vulpen, Marco van

    2007-11-01

    Purpose: To compare quality of life (QoL) after 70 Gy conformal radiotherapy with QoL after 76 Gy intensity-modulated radiotherapy (IMRT) in patients with locally advanced prostate carcinoma. Methods and Materials: Seventy-eight patients with locally advanced prostate cancer were treated with 70 Gy three-field conformal radiotherapy, and 92 patients received 76 Gy IMRT with fiducial markers for position verification. Quality of life was measured by RAND-36, the European Organization for Research and Treatment of Cancer core questionnaire (EORTC QLQ-C30(+3)), and the prostate-specific EORTC QLQ-PR25, before radiotherapy (baseline) and 1 month and 6 months after treatment. Quality of life changes in time (baseline vs. 1 month and baseline vs. 6 months) of {>=}10 points were considered clinically relevant. Results: Differences between the treatment groups for QoL changes over time occurred in several QoL domains. The 76-Gy group revealed no significant deterioration in QoL compared with the 70-Gy group. The IMRT 76-Gy group even demonstrated a significantly better change in QoL from baseline to 1 month in several domains. The conformal 70-Gy group revealed temporary deterioration in pain, role functioning, and urinary symptoms; for the IMRT 76-Gy group a better QoL in terms of change in health existed after 1 month, which persisted after 6 months. For both treatment groups temporary deterioration in physical role restriction occurred after 1 month, and an improvement in emotional role restriction occurred after 6 months. Sexual activity was reduced after treatment for both groups and remained decreased after 6 months. Conclusions: Intensity-modulated radiotherapy and accurate position verification seem to provide a possibility to increase the radiation dose for prostate cancer without deterioration in QoL.

  14. SU-E-T-645: Treatment of Multiple Brain Metastases Using Stereotactic Radiosurgery with Single-Isocenter Volumetric Modulated Arc Therapy: Comparison with Conventional Dynamic Conformal Arc and Static Beam Stereotactic Radiosurgery.

    PubMed

    Huang, C; Ren, L; Kirkpatrick, J; Wang, Z

    2012-06-01

    To investigate the treatment of multiple brain metastases using stereotactic radiosurgery with single-isocenter volumetric modulated arc therapy (VMAT) compared with conventional multi-isocenter dynamic conformal arc therapy (DCAT) and three-dimensional conformal radiation therapy (3D-CRT). Seventeen patients with 2 to 5 brain metastatic lesions were studied. The number of patients with 5, 4, 3, and 2 lesions were 4, 5, 4, and 4, respectively. For patients treated with DCAT/3D-CRT plans, VMAT plans were retrospectively generated, and vice versa. Single-isocenter set up was employed in VMAT plans while the number of isocenters was proportional to the number of lesions in DCAT/3D-CRT plans. The DCAT/3D-CRT and VMAT plans were generated using iPlan® RT Dose Version 4.1.1 (BrainLAB, Germany) and Eclipse™ Version 8.6 (Varian, USA) treatment planning system, respectively. All plans were designed to be delivered on Novalis Tx™ system (Varian, USA and BrainLAB, Germany), in which the accelerator equipped with a high definition multileaf collimator (HDMLC). Conformity index for VMAT plans were equivalent to or better than that for DCAT/3D-CRT plans. While VMAT and DCAT/3D-CRT plans were similar in target coverage, quality of coverage for VMAT plans was better. However, the volume receiving 5Gy was 46% larger for VMAT plans. In addition, the distance from individual lesion to the VMAT isocenter has no impact on VMAT plans. Compared with DCAT/3D-CRT plans, the mean monitor units (MU) decreased by 42% and the estimated treatment time decreased by 49% for VMAT plans. This work suggests that single-isocenter VMAT is promising for stereotactic radiosurgery in the treatment of multiple brain metastases. Single-isocenter VMAT is able to achieve comparable conformity, target coverage and quality of coverage with significantly superior delivery efficiency. © 2012 American Association of Physicists in Medicine.

  15. Dephosphorylation of F-BAR protein Cdc15 modulates its conformation and stimulates its scaffolding activity at the cell division site

    PubMed Central

    Roberts-Galbraith, Rachel H.; Ohi, Melanie D.; Ballif, Bryan A.; Chen, Jun-Song; McLeod, Ian; McDonald, W. Hayes; Gygi, Steven P.; Yates, John R.; Gould, Kathleen L.

    2010-01-01

    Summary Cytokinesis in Schizosaccharomyces pombe requires the function of Cdc15, founding member of the pombe cdc15 homology (PCH) family of proteins. As an early, abundant contractile ring component with multiple binding partners, Cdc15 plays a key role in organizing the ring. We demonstrate that Cdc15 phosphorylation at many sites generates a closed conformation, inhibits Cdc15 assembly at the division site in interphase, and precludes interaction of Cdc15 with its binding partners. Cdc15 dephosphorylation induces an open conformation, oligomerization, and scaffolding activity during mitosis. Cdc15 mutants with reduced phosphorylation precociously appear at the division site in filament-like structures and display increased association with protein partners and the membrane. Our results indicate that Cdc15 phosphoregulation impels both assembly and disassembly of the contractile apparatus and suggest a regulatory strategy that PCH family and BAR superfamily members might broadly employ to achieve temporal specificity in their roles as linkers between membrane and cytoskeleton. PMID:20603077

  16. Remarks on Polyelectrolyte Conformation

    NASA Astrophysics Data System (ADS)

    de Gennes, P. G.; Pincus, P.; Velasco, R. M.; Brochard, F.

    Nous discutons des conformations de polymères linéaires chargés en faisant les hypothèses suivantes : a) la chaĬne sans charge est flexible, b) la force éctrostatique domine les interactions monomère-monomère c) il n'y a pas de sels. 1) Pour le cas dilué (chaĬne non enchevetrees) en corrigeant le calcul self-consistant fait récemment par Richmond [1a], on trouve une taille des polyions égale a = R ND, qui est une fonction linéaire de l'indice de polymérisation N. Ce rèsultat est en accord avec les prècèdents travaux de Hermans et Overbeek [1b], Kuhn, Kunzle et Katchalsky [1c]. 2) Il existe un domaine pour des concentrations très petites c (c** < c < c*) oò les interactions èlectrostatiques entre les polyions sont supèrieures aux ènergies thermiques, il semble donc possible que les polyions puissent former un rèseau pèriodique à trois dimensions. Nèanmoins, il semble difficile de mettre en èvidence un rèseau si diluè. 3) Jusqu'ici toutes les expériences avec les polyélectrolytes sans sels ont été pratiquement faites à des concentrations c > c*, pour lesquelles les différentes cha.nes sont enchevêtrées. Pour discuter ce régime on s.intéresse uniquement au cas où la charge par unité de longueur est près du (ou audessus du) seuil de condensation, donc il existe une seule longueur ξ(c) caractérisant les corrélations; à trois dimensions 03BE a le même comportement que le rayon de Debye pour les contre-ions. On a considéré quelques conformations possibles : a) un réseau hexagonal de batonnets; b) un réseau cubique de batonnets; c) une phase isotrope de cha.nes partiellement flexibles. Les différentes structures formées de batonnets semblent avoir la même énergie électrostatique. Ce fait suggère que la phase isotrope peut être la plus favorable. On analyse cette dernière phase en utilisant les mêmes méthodes qui se sont révélées efficaces pour les solutions des polymères neutres. Dans le modèle isotrope

  17. Dosimetric comparison of flattened and unflattened beams for stereotactic body radiation therapy: Impact of the size of the PTV on dynamic conformal arc and volumetric modulated arc therapy.

    PubMed

    Vieillevigne, Laure; Bessieres, Sandra; Ouali, Monia; Lanaspeze, Christel

    2016-11-01

    Flattening filter free (FFF) beams are frequently used for stereotactic body radiation therapy with various treatment modalities: conventional static fields, dynamic conformal arc (DCA) or Rapid Arc (RA). The goal of this study was to obtain some criteria to enable a conscious choice of the employment of FFF beams and of the DCA or RA technique, depending on the PTV size. 24 PTVs from 1.52cm(3) to 445.24cm(3) were studied in various sites: virtual phantom, lung and liver. For each PTV, DCA and RA plans were prepared using two flattened (FF) and two unflattened photon beams. Parameters such as conformity index, gradient index, healthy-tissue and organs at risk mean doses, number of monitor units (MU), beam on time (BOT) were used to quantify obtained dose distributions. Friedman tests and Spearman's rank correlation coefficients were also performed. No significant differences were found between FF and FFF beams for RA regarding conformity and gradient indices. For DCA, 10FFF is less suitable and forward planning becomes more challenging as PTV volume increases. FFF beams provided a better sparing of healthy-tissues except for 10FFF used with DCA. 6FFF was slightly better than 10FFF in terms of healthy-tissue mean doses. FFF beams generated significantly reduced BOTs and increased MUs. These effects were more pronounced for larger volumes and especially for RA plans. FFF showed better results than FF beams for the considered plans. 10FFF used with DCA should be used with caution for medium and large volumes. Copyright © 2016. Published by Elsevier Ltd.

  18. SU-F-P-52: A Meta-Analysis of Controlled Clinical Trials Comparing Elective Nodal Irradiation with Involved-Field Irradiation for Conformal Or Intensity-Modulated Radiotherapy in Patients with Esophageal Cancer

    SciTech Connect

    Bai, W; Zhang, R; Zhou, Z; Qiao, X

    2016-06-15

    Purpose: To compare elective nodal irradiation with involved-field irradiation for three-dimensional conformal radiotherapy or intensity-modulated radiotherapy in patients with esophageal cancer by a metaanalysis. Methods: Wanfang, CNKI, VIP, CBM databases, PubMed, Embase and Cochrane Library were searched to identify the controlled clinical trials of elective nodal irradiation with involved-field irradiation for three-dimensional conformal radiotherapy or intensity-modulated radiotherapy in patients with esophageal cancer. The obtained data were analyzed using Stata 11.0. The difference between two groups was estimated by calculating the odds ratio (OR) with 95% confidence interval (95% CI). Results: A total of 12 controlled clinical trials involving 1095 esophageal cancer patients, which were selected according to inclusion and exclusion criteria, were included in this meta-analysis. The meta-analysis showed that the elective nodal irradiation group reduced the rates of out-field failure comparing with involved-field irradiation group (OR=3.727, P=0.007). However, the rates of ≥grades 3 acute radiation pneumonitis and esophagitis were significantly higher in the elective nodal irradiation group than in the involved-field irradiation group (OR=0.348, P=0.001, OR=0.385, P=0.000). 1-, 2-, 3-year local control rates (OR=0.966, P=0.837, OR=0.946, P=0.781; OR=0.732P=0.098) and 1-, 3-, 5-year survival rates were similar in the two groups ( OR=0.966, P=0.837; OR=0.946, P=0.781; OR=0.732, P=0.098; OR=0.952, P=0.756; OR=1.149, P=0.422; OR=0.768, P=0.120). It is the same with the rates of distant metastasis (OR=0.986, P=0.937). Conclusion: Compared with involved-field irradiation, the elective nodal irradiation can reduce the rates of out-field failure for three-dimensional conformal radiotherapy or intensity-modulated radiotherapy in patients with esophageal cancer. However, its advantage of local control and survival rates is not obvious and it increases the incidence

  19. Conformational rearrangements to the intracellular open states of the LeuT and ApcT transporters are modulated by common mechanisms.

    PubMed

    Shi, Lei; Weinstein, Harel

    2010-12-15

    Recent crystallographic studies revealed that five transporter families without much sequence similarities among them have similar structure folds to LeuT, a bacterial neurotransmitter:sodium symporter homolog. The LeuT fold is characterized by an internal twofold structural pseudosymmetry. The transport cycle of some members of each of these families is dependent on a sodium gradient across the membrane, whereas in some others the role of sodium is mimicked by proton. We report on the identification of common structure-dynamics elements of the transporters with LeuT fold, which are recognizable in the conformational transitions related to function. The findings from comparative computational modeling and simulation studies of LeuT, and ApcT from the amino acid-polyamine-organocation transporter family define the intramolecular mechanisms by which Na+ binding couples to the transport process, and single out the lead/active role of TM1a in the transition to inward-open conformation. These mechanistic insights are derived in the context of collaborative investigations of LeuT dynamics with both single-molecule fluorescence and simulations that have produced excellent agreement of the dynamic details, and are found to be generalizable across the transporter families and to transcend sequence and motif similarities.

  20. Comparative study of convolution, superposition, and fast superposition algorithms in conventional radiotherapy, three-dimensional conformal radiotherapy, and intensity modulated radiotherapy techniques for various sites, done on CMS XIO planning system

    PubMed Central

    Muralidhar, K. R.; Murthy, Narayana P.; Raju, Alluri Krishnam; Sresty, NVNM

    2009-01-01

    The aim of this study is to compare the dosimetry results that are obtained by using Convolution, Superposition and Fast Superposition algorithms in Conventional Radiotherapy, Three-Dimensional Conformal Radiotherapy (3D-CRT), and Intensity Modulated Radiotherapy (IMRT) for different sites, and to study the suitability of algorithms with respect to site and technique. For each of the Conventional, 3D-CRT, and IMRT techniques, four different sites, namely, Lung, Esophagus, Prostate, and Hypopharynx were analyzed. Treatment plans were created using 6MV Photon beam quality using the CMS XiO (Computerized Medical System, St.Louis, MO) treatment planning system. The maximum percentage of variation recorded between algorithms was 3.7% in case of Ca.Lung, for the IMRT Technique. Statistical analysis was performed by comparing the mean relative difference, Conformity Index, and Homogeneity Index for target structures. The fast superposition algorithm showed excellent results for lung and esophagus cases for all techniques. For the prostate, the superposition algorithm showed better results in all techniques. In the conventional case of the hypopharynx, the convolution algorithm was good. In case of Ca. Lung, Ca Prostate, Ca Esophagus, and Ca Hypopharynx, OARs got more doses with the superposition algorithm; this progressively decreased for fast superposition and convolution algorithms, respectively. According to this study the dosimetric results using different algorithms led to significant variation and therefore care had to be taken while evaluating treatment plans. The choice of a dose calculation algorithm may in certain cases even influence clinical results. PMID:20126561

  1. Selectivity of stop codon recognition in translation termination is modulated by multiple conformations of GTS loop in eRF1.

    PubMed

    Wong, Leo E; Li, Yan; Pillay, Shubhadra; Frolova, Ludmila; Pervushin, Konstantin

    2012-07-01

    Translation termination in eukaryotes is catalyzed by two release factors eRF1 and eRF3 in a cooperative manner. The precise mechanism of stop codon discrimination by eRF1 remains obscure, hindering drug development targeting aberrations at translation termination. By solving the solution structures of the wild-type N-domain of human eRF1 exhibited omnipotent specificity, i.e. recognition of all three stop codons, and its unipotent mutant with UGA-only specificity, we found the conserved GTS loop adopting alternate conformations. We propose that structural variability in the GTS loop may underline the switching between omnipotency and unipotency of eRF1, implying the direct access of the GTS loop to the stop codon. To explore such feasibility, we positioned N-domain in a pre-termination ribosomal complex using the binding interface between N-domain and model RNA oligonucleotides mimicking Helix 44 of 18S rRNA. NMR analysis revealed that those duplex RNA containing 2-nt internal loops interact specifically with helix α1 of N-domain, and displace C-domain from a non-covalent complex of N-domain and C-domain, suggesting domain rearrangement in eRF1 that accompanies N-domain accommodation into the ribosomal A site.

  2. James Webb Space Telescope (JWST) Integrated Science Instruments Module (ISIM) Electronics Compartment (IEC) Conformal Shields Composite Bond Structure Qualification Test Method

    NASA Technical Reports Server (NTRS)

    Yew, Calinda; Stephens, Matt

    2015-01-01

    The JWST IEC conformal shields are mounted onto a composite frame structure that must undergo qualification testing to satisfy mission assurance requirements. The composite frame segments are bonded together at the joints using epoxy, EA 9394. The development of a test method to verify the integrity of the bonded structure at its operating environment introduces challenges in terms of requirements definition and the attainment of success criteria. Even though protoflight thermal requirements were not achieved, the first attempt in exposing the structure to cryogenic operating conditions in a thermal vacuum environment resulted in approximately 1 bonded joints failure during mechanical pull tests performed at 1.25 times the flight loads. Failure analysis concluded that the failure mode was due to adhesive cracks that formed and propagated along stress concentrated fillets as a result of poor bond squeeze-out control during fabrication. Bond repairs were made and the structures successfully re-tested with an improved LN2 immersion test method to achieve protoflight thermal requirements.

  3. The conformational flexibility of the carboxy terminal residues 105–114 is a key modulator of the catalytic activity and stability of Macrophage Migration Inhibitory Factor (MIF)†

    PubMed Central

    El-Turk, Farah; Cascella, Michele; Ouertatani-Sakouhi, Hajer; Narayanan, Raghavendran Lakshmi; Leng, Lin; Bucala, Richard; Hweckstetter, Markus; Rothlisberger, Ursula; Lashuel, Hilal A.

    2013-01-01

    Macrophage migration inhibitory factor (MIF) is a multifunctional protein and a major mediator of innate immunity. Although X-ray crystallography revealed that MIF exists as a homotrimer, its oligomerization state in vivo as well as the factors governing its oligomerization and stability remain poorly understood. The C-terminal region of MIF is highly conserved and participates in several intramolecular interactions that suggest a role in modulating the stability and biochemical activity of MIF. To determine the importance of these interactions, point mutations (A48P, L46A), insertions (P107) at the monomer-monomer interfaces, and C-terminal deletion (Δ110-114NSTFA and Δ105–114NVGWNNSTFA) variants were designed and their structural properties, thermodynamic stability, oligomerization state, catalytic activity and receptor binding were characterized using a battery of biophysical methods. The C-terminal deletion mutants ΔC5 huMIF1-109 and ΔC10 huMIF1-104 were enzymatically inactive and thermodynamically less stable than wild type MIF. Analytical ultracentrifugation studies demonstrate that both C-terminal mutants sediment as trimers and exhibit similar binding to CD74 as the wild type protein. Disrupting the conformation of the C-terminal region 105–114 and increasing its conformational flexibility through the insertion of a proline residue at position 107 was sufficient to reproduce the structural, biochemical and thermodynamic properties of the deletion mutants. P107 MIF forms an enzymatically inactive trimer and exhibits reduced thermodynamic stability relative to the wild type protein. To provide a rationale for the changes induced by these mutations at the molecular level, we also performed molecular dynamics simulations on these mutants in comparison to the wild type MIF. Together, our studies demonstrate that inter-subunit interactions involving the C-terminal region 105–114, including a salt-bridge interaction between Arg73 of one monomer and the

  4. Conformation and conformational exchange of Olopatadine hydrochloride

    NASA Astrophysics Data System (ADS)

    Lei, Lian-di; Zhu, Chuan-jun; Yang, Chun-hui; Cui, Yu-xin

    2008-12-01

    Besides the assignments of the 13C and 1H shifts by 1D and 2D NMR, the experiment 1H spectra of Olopatadine hydrochloride were recorded at temperature range 228-338 K. The variable-temperature spectra revealed a dynamic NMR effect which is attributed to conformational interconversion of the drug. At low temperature, the solution was shown to contain two conformers and the ration of them was 1:1. A conformational process with a free energy of activation of 56.7 kJ mol -1, coalescence temperature 298 K, was interpreted as geminal 1H exchange. Using molecule simulation, conformational candidates for two conformers are proposed.

  5. Intensity modulated radiotherapy and 3D conformal radiotherapy for whole breast irradiation: a comparative dosimetric study and introduction of a novel qualitative index for plan evaluation, the normal tissue index

    SciTech Connect

    Yim, Jackie; Suttie, Clare; Bromley, Regina; Morgia, Marita; Lamoury, Gillian

    2015-09-15

    We report on a retrospective dosimetric study, comparing 3D conformal radiotherapy (3DCRT) and hybrid intensity modulated radiotherapy (hIMRT). We evaluated plans based on their planning target volume coverage, dose homogeneity, dose to organs at risk (OARs) and exposure of normal tissue to radiation. The Homogeneity Index (HI) was used to assess the dose homogeneity in the target region, and we describe a new index, the normal tissue index (NTI), to assess the dose in the normal tissue inside the tangent treatment portal. Plans were generated for 25 early-stage breast cancer patients, using a hIMRT technique. These were compared with the 3DCRT plans of the treatment previously received by the patients. Plan quality was evaluated using the HI, NTI and dose to OARs. The hIMRT technique was significantly more homogenous than the 3DCRT technique, while maintaining target coverage. The hIMRT technique was also superior at minimising the amount of tissue receiving D{sub 105%} and above (P < 0.0001). The ipsilateral lung and contralateral breast maximum were significantly lower in the hIMRT plans (P < 0.05 and P < 0.005), but the 3DCRT technique achieved a lower mean heart dose in left-sided breast cancer patients (P < 0.05). Hybrid intensity modulated radiotherapy plans achieved improved dose homogeneity compared to the 3DCRT plans and superior outcome with regard to dose to normal tissues. We propose that the addition of both HI and NTI in evaluating the quality of intensity modulated radiotherapy (IMRT) breast plans provides clinically relevant comparators which more accurately reflect the new paradigm of treatment goals and outcomes in the era of breast IMRT.

  6. Intensity-Modulated and 3D-Conformal Radiotherapy for Whole-Ventricular Irradiation as Compared With Conventional Whole-Brain Irradiation in the Management of Localized Central Nervous System Germ Cell Tumors

    SciTech Connect

    Chen, Michael Jenwei; Silva Santos, Adriana da; Sakuraba, Roberto Kenji; Lopes, Cleverson Perceu; Goncalves, Vinicius Demanboro; Weltman, Eduardo; Ferrigno, Robson; Cruz, Jose Carlos

    2010-02-01

    Purpose: To compare the sparing potential of cerebral hemispheres with intensity-modulated radiotherapy (IMRT) and three-dimensional conformal radiotherapy (3D-CRT) for whole-ventricular irradiation (WVI) and conventional whole-brain irradiation (WBI) in the management of localized central nervous system germ cell tumors (CNSGCTs). Methods and Materials: Ten cases of patients with localized CNSGCTs and submitted to WVI by use of IMRT with or without a 'boost' to the primary lesion were selected. For comparison purposes, similar treatment plans were produced by use of 3D-CRT (WVI with or without boost) and WBI (opposed lateral fields with or without boost), and cerebral hemisphere sparing was evaluated at dose levels ranging from 2 Gy to 40 Gy. Results: The median prescription dose for WVI was 30.6 Gy (range, 25.2-37.5 Gy), and that for the boost was 16.5 Gy (range, 0-23.4 Gy). Mean irradiated cerebral hemisphere volumes were lower for WVI with IMRT than for 3D-CRT and were lower for WVI with 3D-CRT than for WBI. Intensity-modulated radiotherapy was associated with the lowest irradiated volumes, with reductions of 7.5%, 12.2%, and 9.0% at dose levels of 20, 30, and 40 Gy, respectively, compared with 3D-CRT. Intensity-modulated radiotherapy provided statistically significant reductions of median irradiated volumes at all dose levels (p = 0.002 or less). However, estimated radiation doses to peripheral areas of the body were 1.9 times higher with IMRT than with 3D-CRT. Conclusions: Although IMRT is associated with increased radiation doses to peripheral areas of the body, its use can spare a significant amount of normal central nervous system tissue compared with 3D-CRT or WBI in the setting of CNSGCT treatment.

  7. Protein conformational populations and functionally relevant substates.

    PubMed

    Ramanathan, Arvind; Savol, Andrej; Burger, Virginia; Chennubhotla, Chakra S; Agarwal, Pratul K

    2014-01-21

    it to attain the transition state, therefore promoting the reaction mechanism. In the long term, this emerging view of proteins with conformational substates has broad implications for improving our understanding of enzymes, enzyme engineering, and better drug design. Researchers have already used photoactivation to modulate protein conformations as a strategy to develop a hypercatalytic enzyme. In addition, the alteration of the conformational substates through binding of ligands at locations other than the active site provides the basis for the design of new medicines through allosteric modulation.

  8. Binding Affinities Controlled by Shifting Conformational Equilibria: Opportunities and Limitations

    PubMed Central

    Michielssens, Servaas; de Groot, Bert L.; Grubmüller, Helmut

    2015-01-01

    Conformational selection is an established mechanism in molecular recognition. Despite its power to explain binding events, it is hardly used in protein/ligand design to modulate molecular recognition. Here, we explore the opportunities and limitations of design by conformational selection. Using appropriate thermodynamic cycles, our approach predicts the effects of a conformational shift on binding affinity and also allows one to disentangle the effects induced by a conformational shift from other effects influencing the binding affinity. The method is assessed and applied to explain the contribution of a conformational shift on the binding affinity of six ubiquitin mutants showing different conformational shifts in six different complexes. PMID:25992736

  9. The Effect of Flattening Filter Free on Three-dimensional Conformal Radiation Therapy (3D-CRT), Intensity-Modulated Radiation Therapy (IMRT), and Volumetric Modulated Arc Therapy (VMAT) Plans for Metastatic Brain Tumors from Non-small Cell Lung Cancer.

    PubMed

    Shi, Li-Wan; Lai, You-Qun; Lin, Qin; Ha, Hui-Ming; Fu, Li-Rong

    2015-07-01

    Flattening filter free (FFF) may affect outcome measures of radiotherapy. The objective of this study is to compare the dosimetric parameters in three types of radiotherapy plans, three-dimensional conformal radiation therapy (3D-CRT), intensity-modulated radiation therapy (IMRT), and volumetric modulated arc therapy (VMAT), with or without the flattening filter (FF), developed for the treatment of metastatic brain tumors from non-small cell lung cancer (NSCLC). From July 2013 to October 2013, 3D-CRT, IMRT, and VMAT treatment plans were designed using 6 MV and 10 MV, with and without FF, for 10 patients with brain metastasis from NSCLC. The evaluation of the treatment plans included homogeneity index (HI), conformity index (CI), monitor units (MU), mean dose (Dmean), treatment time, and the influence of FFF on volumes. There was no difference in CI or HI between FFF and FF models with 3D-CRT, IMRT, and VMAT plans. At 6 MV, a lower Dmean was seen in the FFF model of 3D-CRT and in the VMAT plan at 10 MV. In the IMRT 6 MV, IMRT 10 MV, and VMAT 10 MV plans, higher MUs were seen in the FFF models. FFF treatments are similar in quality to FF plans, generally lead to more monitor units, and are associated with shorter treatment times. FFF plans ranked by the order of superiority in terms of a time advantage are VMAT, 3D-CRT, and IMRT.

  10. Steinberg conformal algebras

    NASA Astrophysics Data System (ADS)

    Mikhalev, A. V.; Pinchuk, I. A.

    2005-06-01

    The structure of Steinberg conformal algebras is studied; these are analogues of Steinberg groups (algebras, superalgebras).A Steinberg conformal algebra is defined as an abstract algebra by a system of generators and relations between the generators. It is proved that a Steinberg conformal algebra is the universal central extension of the corresponding conformal Lie algebra; the kernel of this extension is calculated.

  11. Is intensity-modulated radiotherapy better than conventional radiation treatment and three-dimensional conformal radiotherapy for mediastinal masses in patients with Hodgkin's disease, and is there a role for beam orientation optimization and dose constraints assigned to virtual volumes?

    SciTech Connect

    Girinsky, Theodore . E-mail: girinsky@igr.fr; Pichenot, Charlotte; Beaudre, Anne; Ghalibafian, Mithra; Lefkopoulos, Dimitri

    2006-01-01

    Purpose: To evaluate the role of beam orientation optimization and the role of virtual volumes (VVs) aimed at protecting adjacent organs at risk (OARs), and to compare various intensity-modulated radiotherapy (IMRT) setups with conventional treatment with anterior and posterior fields and three-dimensional conformal radiotherapy (3D-CRT). Methods and Materials: Patients with mediastinal masses in Hodgkin's disease were treated with combined modality therapy (three to six cycles of adriamycin, bleomycin, vinblastine, and dacarbazine [ABVD] before radiation treatment). Contouring and treatment planning were performed with Somavision and CadPlan Helios (Varian Systems, Palo Alto, CA). The gross tumor volume was determined according to the prechemotherapy length and the postchemotherapy width of the mediastinal tumor mass. A 10-mm isotropic margin was added for the planning target volume (PTV). Because dose constraints assigned to OARs led to unsatisfactory PTV coverage, VVs were designed for each patient to protect adjacent OARs. The prescribed dose was 40 Gy to the PTV, delivered according to guidelines from International Commission on Radiation Units and Measurements Report No. 50. Five different IMRT treatment plans were compared with conventional treatment and 3D-CRT. Results: Beam orientation was important with respect to the amount of irradiated normal tissues. The best compromise in terms of PTV coverage and protection of normal tissues was obtained with five equally spaced beams (5FEQ IMRT plan) using dose constraints assigned to VVs. When IMRT treatment plans were compared with conventional treatment and 3D-CRT, dose conformation with IMRT was significantly better, with greater protection of the heart, coronary arteries, esophagus, and spinal cord. The lungs and breasts in women received a slightly higher radiation dose with IMRT compared with conventional treatments. The greater volume of normal tissue receiving low radiation doses could be a cause for

  12. The structure of the Tiam1 PDZ domain/ phospho-syndecan1 complex reveals a ligand conformation that modulates protein dynamics.

    PubMed

    Liu, Xu; Shepherd, Tyson R; Murray, Ann M; Xu, Zhen; Fuentes, Ernesto J

    2013-03-05

    PDZ (PSD-95/Dlg/ZO-1) domains are protein-protein interaction modules often regulated by ligand phosphorylation. Here, we investigated the specificity, structure, and dynamics of Tiam1 PDZ domain/ligand interactions. We show that the PDZ domain specifically binds syndecan1 (SDC1), phosphorylated SDC1 (pSDC1), and SDC3 but not other syndecan isoforms. The crystal structure of the PDZ/SDC1 complex indicates that syndecan affinity is derived from amino acids beyond the four C-terminal residues. Remarkably, the crystal structure of the PDZ/pSDC1 complex reveals a binding pocket that accommodates the phosphoryl group. Methyl relaxation experiments of PDZ/SCD1 and PDZ/pSDC1 complexes reveal that PDZ-phosphoryl interactions dampen dynamic motions in a distal region of the PDZ domain by decoupling them from the ligand-binding site. Our data are consistent with a selection model by which specificity and phosphorylation regulate PDZ/syndecan interactions and signaling events. Importantly, our relaxation data demonstrate that PDZ/phospho-ligand interactions regulate protein dynamics and their coupling to distal sites.

  13. The Structure of the Tiam1 PDZ Domain/Phospho-Syndecan1 Complex Reveals a Ligand Conformation that Modulates Protein Dynamics

    PubMed Central

    Liu, Xu; Shepherd, Tyson R.; Murray, Ann M.; Xu, Zhen; Fuentes, Ernesto J.

    2014-01-01

    SUMMARY PDZ (PSD-95/Dlg/ZO-1) domains are protein-protein interaction modules often regulated by ligand phosphorylation. Here, we investigated the specificity, structure, and dynamics of Tiam1 PDZ domain/ligand interactions. We show that the PDZ domain specifically binds syndecan1 (SDC1), phosphorylated SDC1 (pSDC1), and SDC3 but not other syndecan isoforms. The crystal structure of the PDZ/SDC1 complex indicates that syndecan affinity is derived from amino acids beyond the four C-terminal residues. Remarkably, the crystal structure of the PDZ/pSDC1 complex reveals a binding pocket that accommodates the phosphoryl group. Methyl relaxation experiments of PDZ/SCD1 and PDZ/pSDC1 complexes reveal that PDZ-phosphoryl interactions dampen dynamic motions in a distal region of the PDZ domain by decoupling them from the ligand-binding site. Our data are consistent with a selection model by which specificity and phosphorylation regulate PDZ/syndecan interactions and signaling events. Importantly, our relaxation data demonstrate that PDZ/phospho-ligand interactions regulate protein dynamics and their coupling to distal sites. PMID:23395182

  14. Le Soleil et ses relations avec la Terre

    NASA Astrophysics Data System (ADS)

    Lang, Kenneth; Heidmann, M.

    C'est le 2e livre de K. Lang publié en français, considéré comme texte complementaire au célèbre Vagabonds de l'Espace qui avait gagné en 1994 le prix du livre d'astronomie en France. Maintenant l'auteur se concentre sur le système le plus élémentaire: l'étoile et son planète, et choisit celui qui est le plus intéressant pour nous: le Soleil et la Terre. Il a accumulé les observations terrestres et les plus récentes effectuées par des observatoires spatiales, et ceux des météorologues et géophysiciens, et nous présente un panorama fascinant du Soleil et ses relations avec la Terre. C'est la physique qui a les conséquences les plus fondamentales aux événements qui influencent notre environment, notre vie et même la condition humaine y inclu les arts et la litérature.

  15. Radiological and Clinical Pneumonitis After Stereotactic Lung Radiotherapy: A Matched Analysis of Three-Dimensional Conformal and Volumetric-modulated Arc Therapy Techniques

    SciTech Connect

    Palma, David A.; Senan, Suresh; Haasbeek, Cornelis J.A.; Verbakel, Wilko F.A.R.; Vincent, Andrew; Lagerwaard, Frank

    2011-06-01

    Purpose: Lung fibrosis is common after stereotactic body radiotherapy (SBRT) for lung tumors, but the influence of treatment technique on rates of clinical and radiological pneumonitis is not well described. After implementing volumetric modulated arc therapy (RapidArc [RA]; Varian Medical Systems, Palo Alto, CA) for SBRT, we scored the early pulmonary changes seen with arc and conventional three-dimensional SBRT (3D-CRT). Methods and Materials: Twenty-five SBRT patients treated with RA were matched 1:2 with 50 SBRT patients treated with 3D-CRT. Dose fractionations were based on a risk-adapted strategy. Clinical pneumonitis was scored using Common Terminology Criteria for Adverse Events version 3.0. Acute radiological changes 3 months posttreatment were scored by three blinded observers. Relationships among treatment type, baseline factors, and outcomes were assessed using Spearman's correlation, Cochran-Mantel-Haenszel tests, and logistic regression. Results: The RA and 3D-CRT groups were well matched. Forty-three patients (57%) had radiological pneumonitis 3 months after treatment. Twenty-eight patients (37%) had computed tomography (CT) findings of patchy or diffuse consolidation, and 15 patients (20%) had ground-glass opacities only. Clinical pneumonitis was uncommon, and no differences were seen between 3D-CRT vs. RA patients in rates of grade 2/3 clinical pneumonitis (6% vs. 4%, respectively; p = 0.99), moderate/severe radiological changes (24% vs. 36%, respectively, p = 0.28), or patterns of CT changes (p = 0.47). Radiological severity scores were associated with larger planning target volumes (p = 0.09) and extended fractionation (p = 0.03). Conclusions: Radiological changes after lung SBRT are common with both approaches, but no differences in early clinical or radiological findings were observed after RA. Longer follow-up will be required to exclude late changes.

  16. Evolutionary Conserved Positions Define Protein Conformational Diversity

    PubMed Central

    Saldaño, Tadeo E.; Monzon, Alexander M.; Parisi, Gustavo; Fernandez-Alberti, Sebastian

    2016-01-01

    Conformational diversity of the native state plays a central role in modulating protein function. The selection paradigm sustains that different ligands shift the conformational equilibrium through their binding to highest-affinity conformers. Intramolecular vibrational dynamics associated to each conformation should guarantee conformational transitions, which due to its importance, could possibly be associated with evolutionary conserved traits. Normal mode analysis, based on a coarse-grained model of the protein, can provide the required information to explore these features. Herein, we present a novel procedure to identify key positions sustaining the conformational diversity associated to ligand binding. The method is applied to an adequate refined dataset of 188 paired protein structures in their bound and unbound forms. Firstly, normal modes most involved in the conformational change are selected according to their corresponding overlap with structural distortions introduced by ligand binding. The subspace defined by these modes is used to analyze the effect of simulated point mutations on preserving the conformational diversity of the protein. We find a negative correlation between the effects of mutations on these normal mode subspaces associated to ligand-binding and position-specific evolutionary conservations obtained from multiple sequence-structure alignments. Positions whose mutations are found to alter the most these subspaces are defined as key positions, that is, dynamically important residues that mediate the ligand-binding conformational change. These positions are shown to be evolutionary conserved, mostly buried aliphatic residues localized in regular structural regions of the protein like β-sheets and α-helix. PMID:27008419

  17. Can All Centers Plan Intensity-Modulated Radiotherapy (IMRT) Effectively? An External Audit of Dosimetric Comparisons Between Three-Dimensional Conformal Radiotherapy and IMRT for Adjuvant Chemoradiation for Gastric Cancer

    SciTech Connect

    Chung, Hans T. Lee, Brian; Park, Eileen; Lu, Jiade J.; Xia Ping

    2008-07-15

    Purpose: To compare dosimetric endpoints between three-dimensional conformal radiotherapy (3D-CRT) and intensity-modulated radiotherapy (IMRT) at our center with limited IMRT experience, and to perform an external audit of the IMRT plans. Methods and Materials: Ten patients, who received adjuvant chemoradiation for gastric cancer, formed the study cohort. For standardization, the planning target volume (PTV) and organs at risk were recontoured with the assistance of a study protocol radiologic atlas. The cohort was replanned with CMS Xio to generate coplanar 3D-CRT and IMRT plans. All 10 datasets, including volumes but without the plans (i.e., blinded), were transmitted to an experienced center where IMRT plans were designed using Nomos Corvus (IMRT-C) and ADAC Pinnacle (IMRT-P). All IMRT plans were normalized to D95% receiving 45 Gy. Results: Intensity-modulated radiotherapy yielded higher PTV V45 (volume that receives {>=}45 Gy) (p < 0.001) than 3D-CRT. No difference in V20 was seen in the right (p = 0.9) and left (p 0.3) kidneys, but the liver mean dose (p < 0.001) was superior with IMRT. For the external audit, IMRT-C (p = 0.002) and IMRT-P (p < 0.001) achieved significantly lower left kidney V20 than IMRT, and IMRT-P (p < 0.001) achieved lower right kidney V20 than IMRT. The IMRT-C (p = 0.003) but not IMRT-P (p = 0.6) had lower liver mean doses than IMRT. Conclusions: At our institution with early IMRT experience, IMRT improved PTV dose coverage and liver doses but not kidney doses. An external audit of IMRT plans showed that an experienced center can yield superior IMRT plans.

  18. Acute Toxicity After Image-Guided Intensity Modulated Radiation Therapy Compared to 3D Conformal Radiation Therapy in Prostate Cancer Patients

    SciTech Connect

    Wortel, Ruud C.; Incrocci, Luca; Pos, Floris J.; Lebesque, Joos V.; Witte, Marnix G.; Heide, Uulke A. van der; Herk, Marcel van; Heemsbergen, Wilma D.

    2015-03-15

    Purpose: Image-guided intensity modulated radiation therapy (IG-IMRT) allows significant dose reductions to organs at risk in prostate cancer patients. However, clinical data identifying the benefits of IG-IMRT in daily practice are scarce. The purpose of this study was to compare dose distributions to organs at risk and acute gastrointestinal (GI) and genitourinary (GU) toxicity levels of patients treated to 78 Gy with either IG-IMRT or 3D-CRT. Methods and Materials: Patients treated with 3D-CRT (n=215) and IG-IMRT (n=260) receiving 78 Gy in 39 fractions within 2 randomized trials were selected. Dose surface histograms of anorectum, anal canal, and bladder were calculated. Identical toxicity questionnaires were distributed at baseline, prior to fraction 20 and 30 and at 90 days after treatment. Radiation Therapy Oncology Group (RTOG) grade ≥1, ≥2, and ≥3 endpoints were derived directly from questionnaires. Univariate and multivariate binary logistic regression analyses were applied. Results: The median volumes receiving 5 to 75 Gy were significantly lower (all P<.001) with IG-IMRT for anorectum, anal canal, and bladder. The mean dose to the anorectum was 34.4 Gy versus 47.3 Gy (P<.001), 23.6 Gy versus 44.6 Gy for the anal canal (P<.001), and 33.1 Gy versus 43.2 Gy for the bladder (P<.001). Significantly lower grade ≥2 toxicity was observed for proctitis, stool frequency ≥6/day, and urinary frequency ≥12/day. IG-IMRT resulted in significantly lower overall RTOG grade ≥2 GI toxicity (29% vs 49%, respectively, P=.002) and overall GU grade ≥2 toxicity (38% vs 48%, respectively, P=.009). Conclusions: A clinically meaningful reduction in dose to organs at risk and acute toxicity levels was observed in IG-IMRT patients, as a result of improved technique and tighter margins. Therefore reduced late toxicity levels can be expected as well; additional research is needed to quantify such reductions.

  19. Mise au point du rheometre a cisaillement annulaire pour l'etude de rheologie d'un mastic bitumineux avec verre incorpore =

    NASA Astrophysics Data System (ADS)

    El Mansouri, Souleimane

    Dans le domaine viscoelastique lineaire (VEL, domaine des petites deformations), le comportement thermomecanique du bitume et du mastic bitumineux (melange uniforme de bitume et de fillers) a ete caracterise au Laboratoire des Chaussees et Materiaux Bitumineux (LCMB) de l'Ecole de technologie superieure (ETS) avec l'appui de nos partenaires externes : la Societe des Alcools du Quebec (SAQ) et Eco Entreprises Quebec (EEQ). Les proprietes rheologiques des bitumes et des mastics ont ete mesurees grâce a un nouvel outil d'investigation appele, Rheometre a Cisaillement Annulaire (RCA), sous differentes conditions de chargement. Cet appareil permet non seulement de solliciter des eprouvettes de tailles importantes par rapport a celles utilisees lors des essais classiques, mais aussi d'effectuer des essais en conditions quasi-homogenes, ce qui permet de donner acces a la loi de comportement des materiaux. Les essais sont realises sur une large gamme de temperatures et de frequences (de -15 °C a 45°C et de 0,03Hz a 10 Hz). Cette etude a ete menee principalement pour comparer le comportement d'un bitume avec celui d'un mastic bitumineux dans le domaine des petites deformations. neanmoins, dans une seconde perspective, on s'interesse a l'influence des fillers de verre de post-consommation sur le comportement d'un mastic a faibles niveaux de deformations en comparant l'evolution des modules complexes de cisaillements (G*) d'un mastic avec fillers de verre et un mastic avec fillers conventionnels (calcaire). Enfin, le modele analogique 2S2P1D est utilise pour simuler le comportement viscoelastique lineaire des bitumes et des mastics bitumineux testes lors de la campagne experimentale.

  20. Constituent Components of Out-of-Field Scatter Dose for 18-MV Intensity Modulated Radiation Therapy Versus 3-Dimensional Conformal Radiation Therapy: A Comparison With 6-MV and Implications for Carcinogenesis

    SciTech Connect

    Ruben, Jeremy D.; Smith, Ryan; Lancaster, Craig M.; Haynes, Matthew; Jones, Phillip; Panettieri, Vanessa

    2014-11-01

    Purpose: To characterize and compare the components of out-of-field dose for 18-MV intensity modulated radiation therapy (IMRT) versus 3-dimensional conformal radiation therapy (3D-CRT) and their 6-MV counterparts and consider implications for second cancer induction. Methods and Materials: Comparable plans for each technique/energy were delivered to a water phantom with a sloping wall; under full scatter conditions; with field edge abutting but outside the bath to prevent internal/phantom scatter; and with shielding below the linear accelerator head to attenuate head leakage. Neutron measurements were obtained from published studies. Results: Eighteen-megavolt IMRT produces 1.7 times more out-of-field scatter than 18-MV 3D-CRT. In absolute terms, however, differences are just approximately 0.1% of central axis dose. Eighteen-megavolt IMRT reduces internal/patient scatter by 13%, but collimator scatter (C) is 2.6 times greater than 18-MV 3D-CRT. Head leakage (L) is minimal. Increased out-of-field photon scatter from 18-MV IMRT carries out-of-field second cancer risks of approximately 0.2% over and above the 0.4% from 18-MV 3D-CRT. Greater photoneutron dose from 18-MV IMRT may result in further maximal, absolute increased risk to peripheral tissue of approximately 1.2% over 18-MV 3D-CRT. Out-of-field photon scatter remains comparable for the same modality irrespective of beam energy. Machine scatter (C+L) from 18 versus 6 MV is 1.2 times higher for IMRT and 1.8 times for 3D-CRT. It is 4 times higher for 6-MV IMRT versus 3D-CRT. Reduction in internal scatter with 18 MV versus 6 MV is 27% for 3D-CRT and 29% for IMRT. Compared with 6-MV 3D-CRT, 18-MV IMRT increases out-of-field second cancer risk by 0.2% from photons and adds 0.28-2.2% from neutrons. Conclusions: Out-of-field photon dose seems to be independent of beam energy for both techniques. Eighteen-megavolt IMRT increases out-of-field scatter 1.7-fold over 3D-CRT because of greater collimator scatter despite

  1. Constituent components of out-of-field scatter dose for 18-MV intensity modulated radiation therapy versus 3-dimensional conformal radiation therapy: a comparison with 6-MV and implications for carcinogenesis.

    PubMed

    Ruben, Jeremy D; Smith, Ryan; Lancaster, Craig M; Haynes, Matthew; Jones, Phillip; Panettieri, Vanessa

    2014-11-01

    To characterize and compare the components of out-of-field dose for 18-MV intensity modulated radiation therapy (IMRT) versus 3-dimensional conformal radiation therapy (3D-CRT) and their 6-MV counterparts and consider implications for second cancer induction. Comparable plans for each technique/energy were delivered to a water phantom with a sloping wall; under full scatter conditions; with field edge abutting but outside the bath to prevent internal/phantom scatter; and with shielding below the linear accelerator head to attenuate head leakage. Neutron measurements were obtained from published studies. Eighteen-megavolt IMRT produces 1.7 times more out-of-field scatter than 18-MV 3D-CRT. In absolute terms, however, differences are just approximately 0.1% of central axis dose. Eighteen-megavolt IMRT reduces internal/patient scatter by 13%, but collimator scatter (C) is 2.6 times greater than 18-MV 3D-CRT. Head leakage (L) is minimal. Increased out-of-field photon scatter from 18-MV IMRT carries out-of-field second cancer risks of approximately 0.2% over and above the 0.4% from 18-MV 3D-CRT. Greater photoneutron dose from 18-MV IMRT may result in further maximal, absolute increased risk to peripheral tissue of approximately 1.2% over 18-MV 3D-CRT. Out-of-field photon scatter remains comparable for the same modality irrespective of beam energy. Machine scatter (C+L) from 18 versus 6 MV is 1.2 times higher for IMRT and 1.8 times for 3D-CRT. It is 4 times higher for 6-MV IMRT versus 3D-CRT. Reduction in internal scatter with 18 MV versus 6 MV is 27% for 3D-CRT and 29% for IMRT. Compared with 6-MV 3D-CRT, 18-MV IMRT increases out-of-field second cancer risk by 0.2% from photons and adds 0.28-2.2% from neutrons. Out-of-field photon dose seems to be independent of beam energy for both techniques. Eighteen-megavolt IMRT increases out-of-field scatter 1.7-fold over 3D-CRT because of greater collimator scatter despite reducing internal/patient scatter. Out

  2. Predictors of High-grade Esophagitis After Definitive Three-dimensional Conformal Therapy, Intensity-modulated Radiation Therapy, or Proton Beam Therapy for Non-small cell Lung Cancer

    SciTech Connect

    Gomez, Daniel R.; Tucker, Susan L.; Martel, Mary K.; Mohan, Radhe; Balter, Peter A.; Lopez Guerra, Jose Luis; Liu Hongmei; Komaki, Ritsuko; Cox, James D.; Liao Zhongxing

    2012-11-15

    Introduction: We analyzed the ability of various patient- and treatment-related factors to predict radiation-induced esophagitis (RE) in patients with non-small cell lung cancer (NSCLC) treated with three-dimensional conformal radiation therapy (3D-CRT), intensity-modulated radiation therapy (IMRT), or proton beam therapy (PBT). Methods and Materials: Patients were treated for NSCLC with 3D-CRT, IMRT, or PBT at MD Anderson from 2000 to 2008 and had full dose-volume histogram (DVH) data available. The endpoint was severe (grade {>=}3) RE. The Lyman-Kutcher-Burman (LKB) model was used to analyze RE as a function of the fractional esophageal DVH, with clinical variables included as dose-modifying factors. Results: Overall, 652 patients were included: 405 patients were treated with 3D-CRT, 139 with IMRT, and 108 with PBT; corresponding rates of grade {>=}3 RE were 8%, 28%, and 6%, respectively, with a median time to onset of 42 days (range, 11-93 days). A fit of the fractional DVH LKB model demonstrated that the fractional effective dose was significantly different (P=.046) than 1 (fractional mean dose) indicating that high doses to small volumes are more predictive than mean esophageal dose. The model fit was better for 3D-CRT and PBT than for IMRT. Including receipt of concurrent chemotherapy as a dose-modifying factor significantly improved the LKB model (P=.005), and the model was further improved by including a variable representing treatment with >30 fractions. Examining individual types of chemotherapy agents revealed a trend toward receipt of concurrent taxanes and increased risk of RE (P=.105). Conclusions: Fractional dose (dose rate) and number of fractions (total dose) distinctly affect the risk of severe RE, estimated using the LKB model, and concurrent chemotherapy improves the model fit. This risk of severe RE is underestimated by this model in patients receiving IMRT.

  3. Evolution of radiation techniques in the treatment of mediastinal lymphoma: from 3D conformal radiotherapy (3DCRT) to intensity-modulated RT (IMRT) using helical tomotherapy (HT): a single-centre experience and review of the literature

    PubMed Central

    Besson, Nadia; Pernin, Victor; Zefkili, Sofia

    2016-01-01

    Objective: To evaluate radiation techniques and their toxicity in the treatment of Hodgkin's lymphoma (HL) and non-Hodgkin's lymphoma (NHL) with mediastinal disease over a 10-year period. Methods: Between 2003 and 2015, 173 patients with Stage I–III nodal lymphoma were treated in our institution: some of these patients were irradiated for HL or NHL with mediastinal disease. Some of the patients were treated by three-dimensional conformal radiotherapy (3DCRT), others by intensity-modulated radiotherapy (IMRT). Results: We studied 26 males and 43 females with a median age of 26 years. The median follow-up was 43 months. 49 patients were treated by 3DCRT and 20 patients by IMRT. The median dose received by patients treated for NHL was 40 Gy (range: 36–44 Gy), and the median dose received by patients with HL was 30 Gy (range: 30–36 Gy). Between 2003 and 2006, 16 patients were treated by 3DCRT vs 0 patients by IMRT. Between 2007 and 2009, 16 patients received 3DCRT and one patient received IMRT. Between 2010 and 2015, 19 patients received IMRT, and no patients received 3DCRT. 11 of the 20 (55%) patients treated by IMRT and 35 of the 49 (71.4%) patients treated by 3DCRT experienced acute toxicity. Among the patients treated by 3DCRT, one patient experienced Grade 1 radiation pneumonitis and two patients experienced Grade 1 acute mucositis. No late toxicity was observed in patients treated by IMRT. Conclusion: Improvement of radiation techniques for HL and NHL appears to have improved acute and late clinical safety. Longer follow-up is necessary to evaluate very late toxicity. Advances in knowledge: Improvement of radiation techniques for HL and NHL appears to improve the tolerance. PMID:26744079

  4. Preliminary Toxicity Analysis of 3-Dimensional Conformal Radiation Therapy Versus Intensity Modulated Radiation Therapy on the High-Dose Arm of the Radiation Therapy Oncology Group 0126 Prostate Cancer Trial

    SciTech Connect

    Michalski, Jeff M.; Yan, Yan; Watkins-Bruner, Deborah; Bosch, Walter R.; Winter, Kathryn; Galvin, James M.; Bahary, Jean-Paul; Morton, Gerard C.; Parliament, Matthew B.; Sandler, Howard M.

    2013-12-01

    Purpose: To give a preliminary report of clinical and treatment factors associated with toxicity in men receiving high-dose radiation therapy (RT) on a phase 3 dose-escalation trial. Methods and Materials: The trial was initiated with 3-dimensional conformal RT (3D-CRT) and amended after 1 year to allow intensity modulated RT (IMRT). Patients treated with 3D-CRT received 55.8 Gy to a planning target volume that included the prostate and seminal vesicles, then 23.4 Gy to prostate only. The IMRT patients were treated to the prostate and proximal seminal vesicles to 79.2 Gy. Common Toxicity Criteria, version 2.0, and Radiation Therapy Oncology Group/European Organization for Research and Treatment of Cancer late morbidity scores were used for acute and late effects. Results: Of 763 patients randomized to the 79.2-Gy arm of Radiation Therapy Oncology Group 0126 protocol, 748 were eligible and evaluable: 491 and 257 were treated with 3D-CRT and IMRT, respectively. For both bladder and rectum, the volumes receiving 65, 70, and 75 Gy were significantly lower with IMRT (all P<.0001). For grade (G) 2+ acute gastrointestinal/genitourinary (GI/GU) toxicity, both univariate and multivariate analyses showed a statistically significant decrease in G2+ acute collective GI/GU toxicity for IMRT. There were no significant differences with 3D-CRT or IMRT for acute or late G2+ or 3+ GU toxicities. Univariate analysis showed a statistically significant decrease in late G2+ GI toxicity for IMRT (P=.039). On multivariate analysis, IMRT showed a 26% reduction in G2+ late GI toxicity (P=.099). Acute G2+ toxicity was associated with late G3+ toxicity (P=.005). With dose–volume histogram data in the multivariate analysis, RT modality was not significant, whereas white race (P=.001) and rectal V70 ≥15% were associated with G2+ rectal toxicity (P=.034). Conclusions: Intensity modulated RT is associated with a significant reduction in acute G2+ GI/GU toxicity. There is a trend for a

  5. Conformal Vortex Crystals.

    PubMed

    Menezes, Raí M; Silva, Clécio C de Souza

    2017-10-06

    We investigate theoretically globally nonuniform configurations of quantized-flux vortices in clean superconductors trapped by an external force field that induces a nonuniform vortex density profile. Using an extensive series of numerical simulations, we demonstrate that, for suitable choices of the force field, and bellow a certain transition temperature, the vortex system self-organizes into highly inhomogeneous conformal crystals in a way as to minimize the total energy. These nonuniform structures are topologically ordered and can be mathematically mapped into a triangular Abrikosov lattice via a conformal transformation. Above the crystallization temperature, the conformal vortex crystal becomes unstable and gives place to a nonuniform polycrystalline structure. We propose a simple method to engineer the potential energy profile necessary for the observation of conformal crystals of vortices, which can also be applied to other 2D particle systems, and suggest possible experiments in which conformal or quasi-conformal vortex crystals could be observed in bulk superconductors and in thin films.

  6. The Conformal Bootstrap

    NASA Astrophysics Data System (ADS)

    Simmons-Duffin, David

    These notes are from courses given at TASI and the Advanced Strings School in summer 2015. Starting from principles of quantum field theory and the assumption of a traceless stress tensor, we develop the basics of conformal field theory, including conformal Ward identities, radial quantization, reection positivity, the operator product expansion, and conformal blocks. We end with an introduction to numerical bootstrap methods, focusing on the 2d and 3d Ising models.

  7. A critical evaluation of secondary cancer risk models applied to Monte Carlo dose distributions of 2-dimensional, 3-dimensional conformal and hybrid intensity-modulated radiation therapy for breast cancer

    NASA Astrophysics Data System (ADS)

    Joosten, A.; Bochud, F.; Moeckli, R.

    2014-08-01

    The comparison of radiotherapy techniques regarding secondary cancer risk has yielded contradictory results possibly stemming from the many different approaches used to estimate risk. The purpose of this study was to make a comprehensive evaluation of different available risk models applied to detailed whole-body dose distributions computed by Monte Carlo for various breast radiotherapy techniques including conventional open tangents, 3D conformal wedged tangents and hybrid intensity modulated radiation therapy (IMRT). First, organ-specific linear risk models developed by the International Commission on Radiological Protection (ICRP) and the Biological Effects of Ionizing Radiation (BEIR) VII committee were applied to mean doses for remote organs only and all solid organs. Then, different general non-linear risk models were applied to the whole body dose distribution. Finally, organ-specific non-linear risk models for the lung and breast were used to assess the secondary cancer risk for these two specific organs. A total of 32 different calculated absolute risks resulted in a broad range of values (between 0.1% and 48.5%) underlying the large uncertainties in absolute risk calculation. The ratio of risk between two techniques has often been proposed as a more robust assessment of risk than the absolute risk. We found that the ratio of risk between two techniques could also vary substantially considering the different approaches to risk estimation. Sometimes the ratio of risk between two techniques would range between values smaller and larger than one, which then translates into inconsistent results on the potential higher risk of one technique compared to another. We found however that the hybrid IMRT technique resulted in a systematic reduction of risk compared to the other techniques investigated even though the magnitude of this reduction varied substantially with the different approaches investigated. Based on the epidemiological data available, a reasonable

  8. Dosimetric and radiobiological comparison of helical tomotherapy, forward-planned intensity-modulated radiotherapy and two-phase conformal plans for radical radiotherapy treatment of head and neck squamous cell carcinomas.

    PubMed

    Chatterjee, S; Willis, N; Locks, S M; Mott, J H; Kelly, C G

    2011-12-01

    The usual radical radiotherapy treatment prescribed for head and neck squamous cell carcinoma (HNSCC) is 70 Gy (in 2 Gy per fraction equivalent) administered to the high-risk target volume (TV). This can be planned using either a forward-planned photon-electron junction technique (2P) or a single-phase (1P) forward-planned technique developed in-house. Alternatively, intensity-modulated radiotherapy (IMRT) techniques, including helical tomotherapy (HT), allow image-guided inversely planned treatments. This study was designed to compare these three planning techniques with regards to TV coverage and the dose received by organs at risk. We compared the dose-volume histograms and conformity indices (CI) of the three planning processes in five patients with HNSCC. The tumour control probability (TCP), normal tissue complication probability (NTCP) and uncomplicated tumour control probability (UCP) were calculated for each of the 15 plans. In addition, we explored the radiobiological rationality of a dose-escalation strategy. The CI for the high-risk clinical TV (CTV1) in the 5 patients were 0.78, 0.76, 0.82, 0.72 and 0.81 when HT was used; 0.58, 0.56, 0.47, 0.35 and 0.60 for the single-phase forward-planned technique and 0.46, 0.36, 0.29, 0.22 and 0.49 for the two-phase technique. The TCP for CTV1 with HT were 79.2%, 85.2%, 81.1%, 83.0% and 53.0%; for single-phase forward-planned technique, 76.5%, 86.9%, 73.4%, 81.8% and 31.8% and for the two-phase technique, 38.2%, 86.2%, 42.7%, 0.0% and 3.4%. Dose escalation using HT confirmed the radiobiological advantage in terms of TCP. TCP for the single-phase plans was comparable to that of HT plans, whereas that for the two-phase technique was lower. Centres that cannot provide IMRT for the radical treatment of all patients could implement the single-phase technique as standard to attain comparable TCP. However, IMRT produced better UCP, thereby enabling the exploration of dose escalation.

  9. Static Extraction and Conformance Analysis of Hierarchical Runtime Architectural Structure

    DTIC Science & Technology

    2010-05-14

    Architectural conformance 301 instead of class diagrams as the closer analogy for a runtime architecture (Clements et al. 2003, p. 103). Bauhaus (Raza et al...2006) is a static analysis toolkit that supports a points-to analysis, etc. Bauhaus lets a user specify the high-level module view (or a hypothesis...thereof) and map the concrete modules onto the architecture. Then Bauhaus compares a high-level module view to the concrete modules and their

  10. [Dosimetric evaluation of conformal radiotherapy: conformity factor].

    PubMed

    Oozeer, R; Chauvet, B; Garcia, R; Berger, C; Felix-Faure, C; Reboul, F

    2000-01-01

    The aim of three-dimensional conformal therapy (3DCRT) is to treat the Planning Target Volume (PTV) to the prescribed dose while reducing doses to normal tissues and critical structures, in order to increase local control and reduce toxicity. The evaluation tools used for optimizing treatment techniques are three-dimensional visualization of dose distributions, dose-volume histograms, tumor control probabilities (TCP) and normal tissue complication probabilities (NTCP). These tools, however, do not fully quantify the conformity of dose distributions to the PTV. Specific tools were introduced to measure this conformity for a given dose level. We have extended those definitions to different dose levels, using a conformity index (CI). CI is based on the relative volumes of PTV and outside the PTV receiving more than a given dose. This parameter has been evaluated by a clinical study including 82 patients treated for lung cancer and 82 patients treated for prostate cancer. The CI was low for lung dosimetric studies (0.35 at the prescribed dose 66 Gy) due to build-up around the GTV and to spinal cord sparing. For prostate dosimetric studies, the CI was higher (0.57 at the prescribed dose 70 Gy). The CI has been used to compare treatment plans for lung 3DCRT (2 vs 3 beams) and prostate 3DCRT (4 vs 7 beams). The variation of CI with dose can be used to optimize dose prescription.

  11. Conformations of Substituted Ethanes.

    ERIC Educational Resources Information Center

    Kingsbury, Charles A.

    1979-01-01

    Reviews state-of-the-art of conformational analysis and factors which affect it. Emphasizes sp-3 hybridized acrylic molecules. Provides examples on the importance of certain factors in determining conformation. Purpose, is to provide examples for examination questions. (Author/SA)

  12. Conformal differential invariants

    NASA Astrophysics Data System (ADS)

    Kruglikov, Boris

    2017-03-01

    We compute the Hilbert polynomial and the Poincaré function counting the number of fixed jet-order differential invariants of conformal metric structures modulo local diffeomorphisms, and we describe the field of rational differential invariants separating generic orbits of the diffeomorphism pseudogroup action. This resolves the local recognition problem for conformal structures.

  13. Conformations of Substituted Ethanes.

    ERIC Educational Resources Information Center

    Kingsbury, Charles A.

    1979-01-01

    Reviews state-of-the-art of conformational analysis and factors which affect it. Emphasizes sp-3 hybridized acrylic molecules. Provides examples on the importance of certain factors in determining conformation. Purpose, is to provide examples for examination questions. (Author/SA)

  14. CONSENSUS AND CONFORMITY.

    ERIC Educational Resources Information Center

    ALLEN, VERNON L.; LEVINE, JOHN M.

    IN THIS STUDY, PROFESSOR ALLEN EMPLOYS TWO METHODS OF BREAKING GROUP CONSENSUS, AND HE MEASURES THE EFFECTS ON THE RESPONSES OF COLLEGE SUBJECTS TO BOTH OBJECTIVE AND SUBJECTIVE STIMULI. THE RESULTS SUGGEST THE NEED FOR MODIFICATION OF EXISTING THEORIES OF CONFORMITY BEHAVIOR. IN ADDITION, THESE RESULTS EMPHASIZE THE DIFFERENCES IN CONFORMITY OF…

  15. Spacetime Conformal Fluctuations and Quantum Dephasing

    NASA Astrophysics Data System (ADS)

    Bonifacio, Paolo M.

    2009-06-01

    Any quantum system interacting with a complex environment undergoes decoherence. Empty space is filled with vacuum energy due to matter fields in their ground state and represents an underlying environment that any quantum particle has to cope with. In particular quantum gravity vacuum fluctuations should represent a universal source of decoherence. To study this problem we employ a stochastic approach that models spacetime fluctuations close to the Planck scale by means of a classical, randomly fluctuating metric (random gravity framework). We enrich the classical scheme for metric perturbations over a curved background by also including matter fields and metric conformal fluctuations. We show in general that a conformally modulated metric induces dephasing as a result of an effective nonlinear newtonian potential obtained in the appropriate nonrelativistic limit of a minimally coupled Klein-Gordon field. The special case of vacuum fluctuations is considered and a quantitative estimate of the expected effect deduced. Secondly we address the question of how conformal fluctuations could physically arise. By applying the random gravity framework we first show that standard GR seems to forbid spontaneous conformal metric modulations. Finally we argue that a different result follows within scalar-tensor theories of gravity such as e.g. Brans-Dicke theory. In this case a conformal modulation of the metric arises naturally as a result of the fluctuations in the Brans-Dicke field and quantum dephasing of a test particle is expected to occur. For large negative values of the coupling parameter the conformal fluctuations may also contribute to alleviate the well known problem of the large zero point energy due to quantum matter fields.

  16. Algorithm-supported visual error correction (AVEC) of heart rate measurements in dogs, Canis lupus familiaris.

    PubMed

    Schöberl, Iris; Kortekaas, Kim; Schöberl, Franz F; Kotrschal, Kurt

    2015-12-01

    Dog heart rate (HR) is characterized by a respiratory sinus arrhythmia, and therefore makes an automatic algorithm for error correction of HR measurements hard to apply. Here, we present a new method of error correction for HR data collected with the Polar system, including (1) visual inspection of the data, (2) a standardized way to decide with the aid of an algorithm whether or not a value is an outlier (i.e., "error"), and (3) the subsequent removal of this error from the data set. We applied our new error correction method to the HR data of 24 dogs and compared the uncorrected and corrected data, as well as the algorithm-supported visual error correction (AVEC) with the Polar error correction. The results showed that fewer values were identified as errors after AVEC than after the Polar error correction (p < .001). After AVEC, the HR standard deviation and variability (HRV; i.e., RMSSD, pNN50, and SDNN) were significantly greater than after correction by the Polar tool (all p < .001). Furthermore, the HR data strings with deleted values seemed to be closer to the original data than were those with inserted means. We concluded that our method of error correction is more suitable for dog HR and HR variability than is the customized Polar error correction, especially because AVEC decreases the likelihood of Type I errors, preserves the natural variability in HR, and does not lead to a time shift in the data.

  17. EC declaration of conformity.

    PubMed

    Donawa, M E

    1996-05-01

    The CE-marking procedure requires that manufacturers draw up a written declaration of conformity before placing their products on the market. However, some companies do not realize that this is a requirement for all devices. Also, there is no detailed information concerning the contents and format of the EC declaration of conformity in the medical device Directives or in EC guidance documentation. This article will discuss some important aspects of the EC declaration of conformity and some of the guidance that is available on its contents and format.

  18. Γ-conformal algebras

    NASA Astrophysics Data System (ADS)

    Golenishcheva-Kutuzova, Maria I.; Kac, Victor G.

    1998-04-01

    Γ-conformal algebra is an axiomatic description of the operator product expansion of chiral fields with simple poles at finitely many points. We classify these algebras and their representations in terms of Lie algebras and their representations with an action of the group Γ. To every Γ-conformal algebra and a character of Γ we associate a Lie algebra generated by fields with the OPE with simple poles. Examples include twisted affine Kac-Moody algebras, the sin algebra (which is a "Γ-conformal" analogue of the general linear algebra) and its analogues, the algebra of pseudodifferential operators on the circle, etc.

  19. Conformal Carroll groups

    NASA Astrophysics Data System (ADS)

    Duval, C.; Gibbons, G. W.; Horvathy, P. A.

    2014-08-01

    Conformal extensions of Lévy-Leblond's Carroll group, based on geometric properties analogous to those of Newton-Cartan space-time are proposed. The extensions are labeled by an integer k. This framework includes and extends our recent study of the Bondi-Metzner-Sachs (BMS) and Newman-Unti (NU) groups. The relation to conformal Galilei groups is clarified. Conformal Carroll symmetry is illustrated by ‘Carrollian photons’. Motion both in the Newton-Cartan and Carroll spaces may be related to that of strings in the Bargmann space.

  20. Animal culture: chimpanzee conformity?

    PubMed

    van Schaik, Carel P

    2012-05-22

    Culture-like phenomena in wild animals have received much attention, but how good is the evidence and how similar are they to human culture? New data on chimpanzees suggest their culture may even have an element of conformity.

  1. Coadjoint orbits and conformal field theory

    SciTech Connect

    Taylor, IV, Washington

    1993-08-01

    This thesis is primarily a study of certain aspects of the geometric and algebraic structure of coadjoint orbit representations of infinite-dimensional Lie groups. The goal of this work is to use coadjoint orbit representations to construct conformal field theories, in a fashion analogous to the free-field constructions of conformal field theories. The new results which are presented in this thesis are as follows: First, an explicit set of formulae are derived giving an algebraic realization of coadjoint orbit representations in terms of differential operators acting on a polynomial Fock space. These representations are equivalent to dual Verma module representations. Next, intertwiners are explicitly constructed which allow the construction of resolutions for irreducible representations using these Fock space realizations. Finally, vertex operators between these irreducible representations are explicitly constructed as chain maps between the resolutions; these vertex operators allow the construction of rational conformal field theories according to an algebraic prescription.

  2. Assemblies of Conformal Tanks

    NASA Technical Reports Server (NTRS)

    DeLay, Tom

    2009-01-01

    Assemblies of tanks having shapes that conform to each other and/or conform to other proximate objects have been investigated for use in storing fuels and oxidizers in small available spaces in upper stages of spacecraft. Such assemblies might also prove useful in aircraft, automobiles, boats, and other terrestrial vehicles in which space available for tanks is limited. The basic concept of using conformal tanks to maximize the utilization of limited space is not new in itself: for example, conformal tanks are used in some automobiles to store windshield -washer liquid and coolant that overflows from radiators. The novelty of the present development lies in the concept of an assembly of smaller conformal tanks, as distinguished from a single larger conformal tank. In an assembly of smaller tanks, it would be possible to store different liquids in different tanks. Even if the same liquid were stored in all the tanks, the assembly would offer an advantage by reducing the mechanical disturbance caused by sloshing of fuel in a single larger tank: indeed, the requirement to reduce sloshing is critical in some applications. The figure shows a prototype assembly of conformal tanks. Each tank was fabricated by (1) copper plating a wax tank mandrel to form a liner and (2) wrapping and curing layers of graphite/epoxy composite to form a shell supporting the liner. In this case, the conformal tank surfaces are flat ones where they come in contact with the adjacent tanks. A band of fibers around the outside binds the tanks together tightly in the assembly, which has a quasi-toroidal shape. For proper functioning, it would be necessary to maintain equal pressure in all the tanks.

  3. Logarithmic conformal field theory

    NASA Astrophysics Data System (ADS)

    Gainutdinov, Azat; Ridout, David; Runkel, Ingo

    2013-12-01

    theories including those with boundaries, supersymmetry and galilean relativity. Gurarie has written an historical overview of his seminal contributions to this field, putting his results (and those of his collaborators) in the context of understanding applications to condensed matter physics. This includes the link between the non-diagonalisability of L0 and logarithmic singularities, a study of the c → 0 catastrophe, and a proposed resolution involving supersymmetric partners for the stress-energy tensor and its logarithmic partner field. Henkel and Rouhani describe a direction in which logarithmic singularities are observed in correlators of non-relativistic field theories. Their review covers the appropriate modifications of conformal invariance that are appropriate to non-equilibrium statistical mechanics, strongly anisotropic critical points and certain variants of TMG. The main variation away from the standard relativistic idea of conformal invariance is that time is explicitly distinguished from space when considering dilations and this leads to a variety of algebraic structures to explore. In this review, the link between non-diagonalisable representations and logarithmic singularities in correlators is generalised to these algebras, before two applications of the theory are discussed. Huang and Lepowsky give a non-technical overview of their work on braided tensor structures on suitable categories of representations of vertex operator algebras. They also place their work in historic context and compare it to related approaches. The authors sketch their construction of the so-called P(z)-tensor product of modules of a vertex operator algebra, and the construction of the associativity isomorphisms for this tensor product. They proceed to give a guide to their works leading to the first authorrsquo;s proof of modularity for a class of vertex operator algebras, and to their works, joint with Zhang, on logarithmic intertwining operators and the resulting tensor

  4. Conformational sampling techniques.

    PubMed

    Hatfield, Marcus P D; Lovas, Sándor

    2014-01-01

    The potential energy hyper-surface of a protein relates the potential energy of the protein to its conformational space. This surface is useful in determining the native conformation of a protein or in examining a statistical-mechanical ensemble of structures (canonical ensemble). In determining the potential energy hyper-surface of a protein three aspects must be considered; reducing the degrees of freedom, a method to determine the energy of each conformation and a method to sample the conformational space. For reducing the degrees of freedom the choice of solvent, coarse graining, constraining degrees of freedom and periodic boundary conditions are discussed. The use of quantum mechanics versus molecular mechanics and the choice of force fields are also discussed, as well as the sampling of the conformational space through deterministic and heuristic approaches. Deterministic methods include knowledge-based statistical methods, rotamer libraries, homology modeling, the build-up method, self-consistent electrostatic field, deformation methods, tree-based elimination and eigenvector following routines. The heuristic methods include Monte Carlo chain growing, energy minimizations, metropolis monte carlo and molecular dynamics. In addition, various methods to enhance the conformational search including the deformation or smoothing of the surface, scaling of system parameters, and multi copy searching are also discussed.

  5. Protein Conformational Populations and Functionally Relevant Sub-states

    SciTech Connect

    Agarwal, Pratul K; Burger, Virginia; Savol, Andrej; Ramanathan, Arvind; Chennubhotla, Chakra

    2013-01-01

    it to attain the transition state, therefore promoting the reaction mechanism. In the long term, this emerging view of proteins with conformational substates has broad implications for improving our understanding of enzymes, enzyme engineering, and better drug design. Researchers have already used photoactivation to modulate protein conformations as a strategy to develop a hypercatalytic enzyme. In addition, the alteration of the conformational substates through binding of ligands at locations other than the active site provides the basis for the design of new medicines through allosteric modulation.

  6. Conformity: Implications for ABE Instruction

    ERIC Educational Resources Information Center

    Long, Huey B.

    1977-01-01

    Provides an interpretative review of the literature of conforming behavior with special attention to implications for adult education. Eight different research areas of conformity research are summarized, and five reasons for conformity and three different kinds of conforming behavior are identified and discussed. (SH)

  7. Conformational kinetics reveals affinities of protein conformational states.

    PubMed

    Daniels, Kyle G; Suo, Yang; Oas, Terrence G

    2015-07-28

    Most biological reactions rely on interplay between binding and changes in both macromolecular structure and dynamics. Practical understanding of this interplay requires detection of critical intermediates and determination of their binding and conformational characteristics. However, many of these species are only transiently present and they have often been overlooked in mechanistic studies of reactions that couple binding to conformational change. We monitored the kinetics of ligand-induced conformational changes in a small protein using six different ligands. We analyzed the kinetic data to simultaneously determine both binding affinities for the conformational states and the rate constants of conformational change. The approach we used is sufficiently robust to determine the affinities of three conformational states and detect even modest differences in the protein's affinities for relatively similar ligands. Ligand binding favors higher-affinity conformational states by increasing forward conformational rate constants and/or decreasing reverse conformational rate constants. The amounts by which forward rate constants increase and reverse rate constants decrease are proportional to the ratio of affinities of the conformational states. We also show that both the affinity ratio and another parameter, which quantifies the changes in conformational rate constants upon ligand binding, are strong determinants of the mechanism (conformational selection and/or induced fit) of molecular recognition. Our results highlight the utility of analyzing the kinetics of conformational changes to determine affinities that cannot be determined from equilibrium experiments. Most importantly, they demonstrate an inextricable link between conformational dynamics and the binding affinities of conformational states.

  8. Conformational kinetics reveals affinities of protein conformational states

    PubMed Central

    Daniels, Kyle G.; Suo, Yang; Oas, Terrence G.

    2015-01-01

    Most biological reactions rely on interplay between binding and changes in both macromolecular structure and dynamics. Practical understanding of this interplay requires detection of critical intermediates and determination of their binding and conformational characteristics. However, many of these species are only transiently present and they have often been overlooked in mechanistic studies of reactions that couple binding to conformational change. We monitored the kinetics of ligand-induced conformational changes in a small protein using six different ligands. We analyzed the kinetic data to simultaneously determine both binding affinities for the conformational states and the rate constants of conformational change. The approach we used is sufficiently robust to determine the affinities of three conformational states and detect even modest differences in the protein’s affinities for relatively similar ligands. Ligand binding favors higher-affinity conformational states by increasing forward conformational rate constants and/or decreasing reverse conformational rate constants. The amounts by which forward rate constants increase and reverse rate constants decrease are proportional to the ratio of affinities of the conformational states. We also show that both the affinity ratio and another parameter, which quantifies the changes in conformational rate constants upon ligand binding, are strong determinants of the mechanism (conformational selection and/or induced fit) of molecular recognition. Our results highlight the utility of analyzing the kinetics of conformational changes to determine affinities that cannot be determined from equilibrium experiments. Most importantly, they demonstrate an inextricable link between conformational dynamics and the binding affinities of conformational states. PMID:26162682

  9. Conformers of Gaseous Serine.

    PubMed

    He, Kedan; Allen, Wesley D

    2016-08-09

    The myriad conformers of the neutral form of natural amino acid serine (Ser) have been investigated by systematic computations with reliable electronic wave function methods. A total of 85 unique conformers were located using the MP2/cc-pVTZ level of theory. The 12 lowest-energy conformers of serine fall within a 8 kJ mol(-1) window, and for these species, geometric structures, precise relative energies, equilibrium and vibrationally averaged rotational constants, anharmonic vibrational frequencies, infrared intensities, quartic and sextic centrifugal distortion constants, dipole moments, and (14)N nuclear quadrupole coupling constants were computed. The relative energies were refined through composite focal-point analyses employing basis sets as large as aug-cc-pV5Z and correlation treatments through CCSD(T). The rotational constants for seven conformers measured by Fourier-transform microwave spectroscopy are in good agreement with the vibrationally averaged rotational constants computed in this study. Our anharmonic vibrational frequencies are compared to the large number of experimental vibrational absorptions attributable to at least six conformers.

  10. Conformal perturbation theory

    NASA Astrophysics Data System (ADS)

    Amoretti, Andrea; Magnoli, Nicodemo

    2017-08-01

    Statistical systems near a classical critical point have been intensively studied from both theoretical and experimental points of view. In particular, correlation functions are of relevance in comparing theoretical models with the experimental data of real systems. In order to compute physical quantities near a critical point, one needs to know the model at the critical (conformal) point. In this line, recent progress in the knowledge of conformal field theories, through the conformal bootstrap, gives the hope of getting some interesting results also outside of the critical point. In this paper, we will review and clarify how, starting from the knowledge of the critical correlators, one can calculate in a safe way their behavior outside the critical point. The approach illustrated requires the model to be just scale invariant at the critical point. We will clarify the method by applying it to different kind of perturbations of the 2D Ising model.

  11. La structure de Jordan des matrices de transfert des modeles de boucles et la relation avec les hamiltoniens XXZ

    NASA Astrophysics Data System (ADS)

    Morin-Duchesne, Alexi

    Lattice models such as percolation, the Ising model and the Potts model are useful for the description of phase transitions in two dimensions. Finding analytical solutions is done by calculating the partition function, which in turn requires finding eigenvalues of transfer matrices. At the critical point, the two dimensional statistical models are invariant under conformal transformations and the construction of rational conformal field theories, as the continuum limit of these lattice models, allows one to compute the partition function at the critical point. Many researchers think however that the paradigm of rational conformal conformal field theories can be extended to include models with non diagonalizable transfer matrices. These models would then be described, in the scaling limit, by logarithmic conformal field theories and the representations of the Virasoro algebra coming into play would be indecomposable. We recall the construction of the double-row transfer matrix DN (λ, u) of the Fortuin-Kasteleyn model, seen as an element of the Temperley-Lieb algebra. This transfer matrix comes into play in physical theories through its representation in link modules (or standard modules). The vector space on which this representation acts decomposes into sectors labelled by a physical parameter d, the number of defects, which remains constant or decreases in the link representations. This thesis is devoted to the identification of the Jordan structure of DN(λ, u) in the link representations. The parameter β = 2 cos λ = -(q + q-1) fixes the theory : for instance β = 1 for percolation and 2 for the Ising model. On the geometry of the strip with open boundary conditions, we show that DN(λ, u) has the same Jordan blocks as its highest Fourier coefficient, FN. We study the non-diagonalizability of FN through the divergences of some of the eigenstates of ρ(F N) that appear at the critical values of λ. The Jordan cells we find in ρ(DN(λ, u)) have rank 2 and

  12. Charged conformal Killing spinors

    SciTech Connect

    Lischewski, Andree

    2015-01-15

    We study the twistor equation on pseudo-Riemannian Spin{sup c}-manifolds whose solutions we call charged conformal Killing spinors (CCKSs). We derive several integrability conditions for the existence of CCKS and study their relations to spinor bilinears. A construction principle for Lorentzian manifolds admitting CCKS with nontrivial charge starting from CR-geometry is presented. We obtain a partial classification result in the Lorentzian case under the additional assumption that the associated Dirac current is normal conformal and complete the classification of manifolds admitting CCKS in all dimensions and signatures ≤5 which has recently been initiated in the study of supersymmetric field theories on curved space.

  13. Memory, metamemory, and social cues: Between conformity and resistance.

    PubMed

    Zawadzka, Katarzyna; Krogulska, Aleksandra; Button, Roberta; Higham, Philip A; Hanczakowski, Maciej

    2016-02-01

    When presented with responses of another person, people incorporate these responses into memory reports: a finding termed memory conformity. Research on memory conformity in recognition reveals that people rely on external social cues to guide their memory responses when their own ability to respond is at chance. In this way, conforming to a reliable source boosts recognition performance but conforming to a random source does not impair it. In the present study we assessed whether people would conform indiscriminately to reliable and unreliable (random) sources when they are given the opportunity to exercise metamemory control over their responding by withholding answers in a recognition test. In Experiments 1 and 2, we found the pattern of memory conformity to reliable and unreliable sources in 2 variants of a free-report recognition test, yet at the same time the provision of external cues did not affect the rate of response withholding. In Experiment 3, we provided participants with initial feedback on their recognition decisions, facilitating the discrimination between the reliable and unreliable source. This led to the reduction of memory conformity to the unreliable source, and at the same time modulated metamemory decisions concerning response withholding: participants displayed metamemory conformity to the reliable source, volunteering more responses in their memory report, and metamemory resistance to the random source, withholding more responses from the memory report. Together, the results show how metamemory decisions dissociate various types of memory conformity and that memory and metamemory decisions can be independent of each other.

  14. [A randomized study of intensity-modulated radiation therapy versus three dimensional conformal radiation therapy for pelvic radiation in patients of post-operative treatment with gynecologic malignant tumor].

    PubMed

    Ni, J; Yin, Z M; Yuan, S H; Liu, N F; Li, L; Xu, X X; Lou, H M

    2017-03-25

    Objective: To study the difference between intensity-modulated radiation therapy (IMRT) and three dimensional conformal radiation therapy (3D-CRT) for pelvic radiation of post-operative treatment with gynecologic malignant tumor. Methods: A prospective investigation study was conducted on 183 patients of post-operative patients with whole pelvic radiation therapy of cervical cancer or endometrial cancer in Zhejiang Cancer Hospital [IMRT group (n=85) and 3D-CRT group (n=98)] from Oct. 2015 to Oct. 2016. The two groups received same dose (45 Gy in 25 fractions). Comparison of two groups with radiation dosimetry:the score according to the Radiation Therapy Oncology Group (RTOG) acute radiation injury grading standards before and after radiotherapy reaction, the score from functional assessment of cancer therapy scale-cervix (FACT-Cx) scale and expanded prostate cancer index composite for clinical practice (EPIC-CP) scale were also analyzed. Results: (1) There were no significant effect with age, culture level, family economic condition and ratio of radiochemotherapy between two groups (all P>0.05). (2) Dosimetric comparison for IMRT vs 3D-CRT: the average dose of planning target volume (PTV) decreased (46.1±0.4) vs (46.4±0.5) Gy, V(45) dose percentage increased (95.2±1.0) % vs (93.3±2.0) %, intestinal bag dose of V(4)0 decreased (24.4±6.8) % vs (36.5±15.9) %, rectal V(40) dose percentage decreased (73.9±12.3) % vs (85.4±8.4) %, and lower rectal V(45) dose percentage (32.8±13.4) % vs (71.5±13.7) %, bladder V(40) dose percentage decreased (55.5±13.0) % vs (84.4±13.0) %. Bone marrow V(20) lower: (67.9±5.4) % vs (79.5±6.6) %, V(1)0 lower: (82.1±6.0) % vs (86.3±6.6) %; there were significant differences (all P<0.05). There was no significant difference between the dose of V(45) in the intestinal pouch and bladder (P>0.05). (3) Acute radiation injury classification for IMRT vs 3D-CRT: big or small intestine: Ⅱ-Ⅲ reaction [13% (11/85) vs 24% (24/98); χ(2

  15. Conformal cloak for waves

    SciTech Connect

    Chen Huanyang; Leonhardt, Ulf; Tyc, Tomas

    2011-05-15

    Conformal invisibility devices are only supposed to work within the valid range of geometrical optics. Here, we show by numerical simulations and analytical arguments that for certain quantized frequencies, they are nearly perfect even in a regime that clearly violates geometrical optics. The quantization condition follows from the analogy between the Helmholtz equation and the stationary Schroedinger equation.

  16. Conformational properties of pyrethroids

    NASA Astrophysics Data System (ADS)

    Mullaley, Anne; Taylor, Robin

    1994-04-01

    X-ray database searches and theoretical potential-energy calculations indicate that the acid moieties of pyrethroid cyclopropanecarboxylate esters adopt a well-defined, relatively inflexible conformation. In contrast, the alcohol moieties can exist in many low-energy geometries. One of the least conformationally flexible pyrethroid alcohols is 4-phenylindan-2-ol. The approximate overall conformation adopted at the biological binding site by insecticidal esters of this alcohol can be deduced with reasonable confidence by molecular modelling. Graphics superposition of a variety of pyrethroid acids suggests the existence of a large but rather narrow pocket at the binding site, in which substituents at the 3-position of the cyclopropane ring can be accommodated. This pocket is asymmetric with respect to the plane of the cyclopropane ring, extending further on the side remote from the ester group. The effects of α-substitution on the insecticidal activity of pyrethroid esters may be due to the influence of substituents on the preferred conformations of the molecules. This hypothesis rationalises the paradoxical dependence on absolute stereochemistry of the activities of various allylbenzyl and cinnamyl alcohol derivatives.

  17. Conformal Image Warping

    DTIC Science & Technology

    1988-10-01

    the unit disk Henrici has recently surveyed existing numerical conformal mapping algorithms [8]. For arbitrary shaped regions (which are approximated...22, 3 (August 1988),. 8. Henrici , P., in Applied and computational complex analysis, vol. 3, Wiley, New York,NY, 1986, 402-413. 9. Preparata, F. P

  18. PERSONALITY AND CONFORMITY.

    ERIC Educational Resources Information Center

    BAROCAS, RALPH; GORLOW, LEON

    AN INVESTIGATION WAS MADE OF THE RELATIONSHIP BETWEEN PERSONALITY FACTORS AND CONFORMITY. THE SUBJECTS WERE 243 RANDOMLY SELECTED STUDENTS ENROLLED IN COLLEGE PSYCHOLOGY COURSES WHO WERE DIVIDED INTO GROUPS OF 97, 96, AND 50 SUBJECTS. A PERSONALITY FACTOR INVENTORY WAS OBTAINED FROM RESPONSES TO A LARGE LIST OF TRUE-FALSE PERSONALITY ITEM…

  19. Conformational changes in biopolymers

    NASA Astrophysics Data System (ADS)

    Ivanov, Vassili

    2005-12-01

    Biopolymer conformational changes are involved in many biological processes. This thesis summarizes some theoretical and experimental approaches which I have taken at UCLA to explore conformational changes in biopolymers. The reversible thermal denaturation of the DNA double helix is, perhaps, the simplest example of biopolymer conformational change. I have developed a statistical mechanics model of DNA melting with reduced degrees of freedom, which allows base stacking interaction to be taken into account and treat base pairing and stacking separately. Unlike previous models, this model describes both the unpairing and unstacking parts of the experimental melting curves and explains the observed temperature dependence of the effective thermodynamic parameters used in models of the nearest neighbor type. I developed a basic kinetic model for irreversible thermal denaturation of F-actin, which incorporates depolymerization of F-actin from the ends and breaking of F-actin fiber in the middle. The model explains the cooperativity of F-actin thermal denaturation observed by D. Pavlov et al. in differential calorimetry measurements. CG-rich DNA sequences form left-handed Z-DNA at high ionic strength or upon binding of polyvalent ions and some proteins. I studied experimentally the B-to-Z transition of the (CG)6 dodecamer. Improvement of the locally linearized model used to interpret the data gives evidence for an intermediate state in the B-to-Z transition of DNA, contrary to previous research on this subject. In the past 15 years it has become possible to study the conformational changes of biomolecules using single-molecule techniques. In collaboration with other lab members I performed a single-molecule experiment, where we monitored the displacement of a micrometer-size bead tethered to a surface by a DNA probe undergoing the conformational change. This technique allows probing of conformational changes with subnanometer accuracy. We applied the method to detect

  20. Galilean conformal and superconformal symmetries

    SciTech Connect

    Lukierski, J.

    2012-10-15

    Firstly we discuss briefly three different algebras named as nonrelativistic (NR) conformal: Schroedinger, Galilean conformal, and infinite algebra of local NR conformal isometries. Further we shall consider in some detail Galilean conformal algebra (GCA) obtained in the limit c{yields}{infinity} from relativistic conformal algebraO(d+1, 2) (d-number of space dimensions). Two different contraction limits providing GCA and some recently considered realizations will be briefly discussed. Finally by considering NR contraction of D = 4 superconformal algebra the Galilei conformal superalgebra (GCSA) is obtained, in the formulation using complexWeyl supercharges.

  1. Fast, clash-free RNA conformational morphing using molecular junctions

    DOE PAGES

    Heliou, Amelie; Budday, Dominik; Fonseca, Rasmus; ...

    2017-03-13

    Non-coding ribonucleic acids (ncRNA) are functional RNA molecules that are not translated into protein. They are extremely dynamic, adopting diverse conformational substates, which enables them to modulate their interaction with a large number of other molecules. The flexibility of ncRNA provides a challenge for probing their complex 3D conformational landscape, both experimentally and computationally. As a result, despite their conformational diversity, ncRNAs mostly preserve their secondary structure throughout the dynamic ensemble. Here we present a kinematics-based procedure to morph an RNA molecule between conformational substates, while avoiding inter-atomic clashes. We represent an RNA as a kinematic linkage, with fixed groupsmore » of atoms as rigid bodies and rotatable bonds as degrees of freedom. Our procedure maintains RNA secondary structure by treating hydrogen bonds between base pairs as constraints. The constraints define a lower-dimensional, secondary-structure constraint manifold in conformation space, where motions are largely governed by molecular junctions of unpaired nucleotides. On a large benchmark set, we show that our morphing procedure compares favorably to peer algorithms, and can approach goal conformations to within a low all-atom RMSD by directing fewer than 1% of its atoms. Furthermore, our results suggest that molecular junctions can modulate 3D structural rearrangements, while secondary structure elements guide large parts of the molecule along the transition to the correct final conformation.« less

  2. Conformational Nonequilibrium Enzyme Kinetics: Generalized Michaelis-Menten Equation.

    PubMed

    Piephoff, D Evan; Wu, Jianlan; Cao, Jianshu

    2017-08-03

    In a conformational nonequilibrium steady state (cNESS), enzyme turnover is modulated by the underlying conformational dynamics. On the basis of a discrete kinetic network model, we use an integrated probability flux balance method to derive the cNESS turnover rate for a conformation-modulated enzymatic reaction. The traditional Michaelis-Menten (MM) rate equation is extended to a generalized form, which includes non-MM corrections induced by conformational population currents within combined cyclic kinetic loops. When conformational detailed balance is satisfied, the turnover rate reduces to the MM functional form, explaining its general validity. For the first time, a one-to-one correspondence is established between non-MM terms and combined cyclic loops with unbalanced conformational currents. Cooperativity resulting from nonequilibrium conformational dynamics can be achieved in enzymatic reactions, and we provide a novel, rigorous means of predicting and characterizing such behavior. Our generalized MM equation affords a systematic approach for exploring cNESS enzyme kinetics.

  3. The anti/syn conformation of 8-oxo-7,8-dihydro-2'-deoxyguanosine is modulated by Bacillus subtilis PolX active site residues His255 and Asn263. Efficient processing of damaged 3'-ends.

    PubMed

    Zafra, Olga; Pérez de Ayala, Lucía; de Vega, Miguel

    2017-04-01

    8-oxo-7,8-dihydro-2'-deoxyguanosine (8oxodG) is a major lesion resulting from oxidative stress and found in both DNA and dNTP pools. Such a lesion is usually removed from DNA by the Base Excision Repair (BER), a universally conserved DNA repair pathway. 8oxodG usually adopts the favored and promutagenic syn-conformation at the active site of DNA polymerases, allowing the base to hydrogen bonding with adenine during DNA synthesis. Here, we study the structural determinants that affect the glycosidic torsion-angle of 8oxodGTP at the catalytic active site of the family X DNA polymerase from Bacillus subtilis (PolXBs). We show that, unlike most DNA polymerases, PolXBs exhibits a similar efficiency to stabilize the anti and syn conformation of 8oxodGTP at the catalytic site. Kinetic analyses indicate that at least two conserved residues of the nucleotide binding pocket play opposite roles in the anti/syn conformation selectivity, Asn263 and His255 that favor incorporation of 8oxodGMP opposite dA and dC, respectively. In addition, the presence in PolXBs of Mn(2+)-dependent 3'-phosphatase and 3'-phosphodiesterase activities is also shown. Those activities rely on the catalytic center of the C-terminal Polymerase and Histidinol Phosphatase (PHP) domain of PolXBs and, together with its 3'-5' exonuclease activity allows the enzyme to resume gap-filling after processing of damaged 3' termini.

  4. Transportation Conformity Training and Presentations

    EPA Pesticide Factsheets

    EPA's OTAQ has provided multiple conformity training sessions in the past to assist state and local governments in implementing conformity requirements. As training information is prepared for other venues, it will be posted on this page.

  5. Multiscale conformal pattern transfer

    NASA Astrophysics Data System (ADS)

    Lodewijks, Kristof; Miljkovic, Vladimir; Massiot, Inès; Mekonnen, Addis; Verre, Ruggero; Olsson, Eva; Dmitriev, Alexandre

    2016-06-01

    We demonstrate a method for seamless transfer from a parent flat substrate of basically any lithographic top-down or bottom-up pattern onto essentially any kind of surface. The nano- or microscale patterns, spanning macroscopic surface areas, can be transferred with high conformity onto a large variety of surfaces when such patterns are produced on a thin carbon film, grown on top of a sacrificial layer. The latter allows lifting the patterns from the flat parent substrate onto a water-air interface to be picked up by the host surface of choice. We illustrate the power of this technique by functionalizing broad range of materials including glass, plastics, metals, rough semiconductors and polymers, highlighting the potential applications in in situ colorimetry of the chemistry of materials, anti-counterfeit technologies, biomolecular and biomedical studies, light-matter interactions at the nanoscale, conformal photovoltaics and flexible electronics.

  6. Conformal ALON® windows

    NASA Astrophysics Data System (ADS)

    Goldman, Lee M.; Balasubramanian, Sreeram; Smith, Mark; Nag, Nagendra; Foti, Robyn; Jha, Santosh; Sastri, Suri

    2014-05-01

    Aluminum Oxynitride (ALON® Optical Ceramic) combines broadband transparency with excellent mechanical properties. ALON's cubic structure means that it is transparent in its polycrystalline form, allowing it to be manufactured by conventional powder processing techniques. Surmet controls every aspect of the manufacturing process, beginning with synthesis of ALON® powder, continuing through forming/heat treatment of blanks, ending with optical fabrication of ALON® windows. Surmet has made significant progress in its production capability in recent years. Additional scale up of Surmet's manufacturing capability, for complex geometries, larger sizes and higher quantities, is underway. The requirements for modern aircraft are driving the need for conformal windows for future sensor systems. However, limitations on optical systems and the ability to produce windows in complex geometries currently limit the geometry of existing windows and window assemblies to faceted assemblies of flat windows. Surmet's ability to produce large curved ALON® blanks is an important step in the development of conformal windows for future aircraft applications.

  7. Multiscale conformal pattern transfer

    PubMed Central

    Lodewijks, Kristof; Miljkovic, Vladimir; Massiot, Inès; Mekonnen, Addis; Verre, Ruggero; Olsson, Eva; Dmitriev, Alexandre

    2016-01-01

    We demonstrate a method for seamless transfer from a parent flat substrate of basically any lithographic top-down or bottom-up pattern onto essentially any kind of surface. The nano- or microscale patterns, spanning macroscopic surface areas, can be transferred with high conformity onto a large variety of surfaces when such patterns are produced on a thin carbon film, grown on top of a sacrificial layer. The latter allows lifting the patterns from the flat parent substrate onto a water-air interface to be picked up by the host surface of choice. We illustrate the power of this technique by functionalizing broad range of materials including glass, plastics, metals, rough semiconductors and polymers, highlighting the potential applications in in situ colorimetry of the chemistry of materials, anti-counterfeit technologies, biomolecular and biomedical studies, light-matter interactions at the nanoscale, conformal photovoltaics and flexible electronics. PMID:27329824

  8. Conformal gripping device

    NASA Technical Reports Server (NTRS)

    Vranish, John M. (Inventor)

    2009-01-01

    The present invention relates to a conformal gripping device. In an embodiment of the present invention a conformal gripper device may be disclosed comprising a frame that includes an array of movable pins. The device may also include a roller locking and unlocking system within the frame. The system may comprise a pair of locking rollers for each row of gripper pins to facilitate locking and unlocking the array of gripper pins on a column-by-column basis. The system may also include a striker element that may force the locking rollers to roll along an angled roll surface to facilitate unlocking of the array of pins on a column-by-column basis. The system may further include an electromagnetic actuator or solenoid and permanent magnets to facilitate movement of the striker element and the locking rollers.

  9. Conformational flexibility of aspartame.

    PubMed

    Toniolo, Claudio; Temussi, Pierandrea

    2016-05-01

    L-Aspartyl-L-phenylalanine methyl ester, better known as aspartame, is not only one of the most used artificial sweeteners, but also a very interesting molecule with respect to the correlation between molecular structure and taste. The extreme conformational flexibility of this dipeptide posed a huge difficulty when researchers tried to use it as a lead compound to design new sweeteners. In particular, it was difficult to take advantage of its molecular model as a mold to infer the shape of the, then unknown, active site of the sweet taste receptor. Here, we follow the story of the 3D structural aspects of aspartame from early conformational studies to recent docking into homology models of the receptor. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 376-384, 2016. © 2016 Wiley Periodicals, Inc.

  10. Conformal scalar field wormholes

    NASA Technical Reports Server (NTRS)

    Halliwell, Jonathan J.; Laflamme, Raymond

    1989-01-01

    The Euclidian Einstein equations with a cosmological constant and a conformally coupled scalar field are solved, taking the metric to be of the Robertson-Walker type. In the case Lambda = 0, solutions are found which represent a wormhole connecting two asymptotically flat Euclidian regions. In the case Lambda greater than 0, the solutions represent tunneling from a small Tolman-like universe to a large Robertson-Walker universe.

  11. Ordering in Conformal Crystals

    NASA Astrophysics Data System (ADS)

    Soni, Vishal; Gomez, Leopoldo; Irvine, William

    2014-03-01

    Condensed matter systems commonly undergo ordering processes that are frustrated by geometric constraints. Experiments on interfacial colloidal systems have resulted in several recent insights into the two dimensional ordering of crystalline lattices frustrated by Gaussian curvature. We study the ordering of flat colloidal Wigner crystals immersed in an axially symmetric potential. By relating the resulting inhomogenous structure to a lattice with Gaussian curvature, we investigate the role of topological defects in organizing the conformal crystal-like ground state.

  12. Conformal scalar field wormholes

    NASA Technical Reports Server (NTRS)

    Halliwell, Jonathan J.; Laflamme, Raymond

    1989-01-01

    The Euclidian Einstein equations with a cosmological constant and a conformally coupled scalar field are solved, taking the metric to be of the Robertson-Walker type. In the case Lambda = 0, solutions are found which represent a wormhole connecting two asymptotically flat Euclidian regions. In the case Lambda greater than 0, the solutions represent tunneling from a small Tolman-like universe to a large Robertson-Walker universe.

  13. The conformal bootstrap

    NASA Astrophysics Data System (ADS)

    Poland, David; Simmons-Duffin, David

    2016-06-01

    The conformal bootstrap was proposed in the 1970s as a strategy for calculating the properties of second-order phase transitions. After spectacular success elucidating two-dimensional systems, little progress was made on systems in higher dimensions until a recent renaissance beginning in 2008. We report on some of the main results and ideas from this renaissance, focusing on new determinations of critical exponents and correlation functions in the three-dimensional Ising and O(N) models.

  14. Conformations of organophosphine oxides

    SciTech Connect

    De Silva, Nuwan; Zahariev, Federico; Hay, Benjamin P.; Gordon, Mark S.; Windus, Theresa L.

    2015-07-17

    The conformations of a series of organophosphine oxides, OP(CH3)2R, where R = methyl, ethyl, isopropyl, tert-butyl, vinyl, and phenyl, are predicted using the MP2/cc-pVTZ level of theory. Comparison of potential energy surfaces for rotation about P–C bonds with crystal structure data reveals a strong correlation between predicted location and energetics of minima and histograms of dihedral angle distributions observed in the solid state. In addition, the most stable conformers are those that minimize the extent of steric repulsion between adjacent rotor substituents, and the torsional barriers tend to increase with the steric bulk of the rotating alkyl group. MM3 force field parameters were adjusted to fit the MP2 results, providing a fast and accurate model for predicting organophosphine oxides shapes—an essential part of understanding the chemistry of these compounds. As a result, the predictive power of the modified MM3 model was tested against MP2/cc-pVTZ conformations for triethylphosphine oxide, OP(CH2CH3)3, and triphenylphosphine oxide, OP(Ph)3.

  15. Conformations of organophosphine oxides

    DOE PAGES

    De Silva, Nuwan; Zahariev, Federico; Hay, Benjamin P.; ...

    2015-07-17

    The conformations of a series of organophosphine oxides, OP(CH3)2R, where R = methyl, ethyl, isopropyl, tert-butyl, vinyl, and phenyl, are predicted using the MP2/cc-pVTZ level of theory. Comparison of potential energy surfaces for rotation about P–C bonds with crystal structure data reveals a strong correlation between predicted location and energetics of minima and histograms of dihedral angle distributions observed in the solid state. In addition, the most stable conformers are those that minimize the extent of steric repulsion between adjacent rotor substituents, and the torsional barriers tend to increase with the steric bulk of the rotating alkyl group. MM3 forcemore » field parameters were adjusted to fit the MP2 results, providing a fast and accurate model for predicting organophosphine oxides shapes—an essential part of understanding the chemistry of these compounds. As a result, the predictive power of the modified MM3 model was tested against MP2/cc-pVTZ conformations for triethylphosphine oxide, OP(CH2CH3)3, and triphenylphosphine oxide, OP(Ph)3.« less

  16. Hot conformal gauge theories

    NASA Astrophysics Data System (ADS)

    Mojaza, Matin; Pica, Claudio; Sannino, Francesco

    2010-12-01

    We compute the nonzero temperature free energy up to the order g6ln⁡(1/g) in the coupling constant for vectorlike SU(N) gauge theories featuring matter transforming according to different representations of the underlying gauge group. The number of matter fields, i.e. flavors, is arranged in such a way that the theory develops a perturbative stable infrared fixed point at zero temperature. Because of large distance conformality we trade the coupling constant with its fixed point value and define a reduced free energy which depends only on the number of flavors, colors, and matter representation. We show that the reduced free energy changes sign, at the second, fifth, and sixth order in the coupling, when decreasing the number of flavors from the upper end of the conformal window. If the change in sign is interpreted as a signal of an instability of the system then we infer a critical number of flavors. Surprisingly this number, if computed to the order g2, agrees with previous predictions for the lower boundary of the conformal window for nonsupersymmetric gauge theories. The higher order results tend to predict a higher number of critical flavors. These are universal properties, i.e. they are independent of the specific matter representation.

  17. Electrical control of protein conformation.

    PubMed

    Wan, Alwin M D; Schur, Rebecca M; Ober, Christopher K; Fischbach, Claudia; Gourdon, Delphine; Malliaras, George G

    2012-05-08

    Conducting polymer devices that enable precise control of fibronectin conformation over macroscopic areas are reported. Single conformations as well as conformation gradients are achieved by applying an appropriate potential. These surfaces remain biologically relevant and support cell culture; hence, they may serve as a model to understand and control cell-surface interactions, with applications in basic research, medical diagnostics, and tissue engineering.

  18. Probing conformation and conformational change in proteins is optimally undertaken in relative mode.

    PubMed

    Errington, Neil; Rowe, Arthur J

    2003-08-01

    Hydrodynamic bead modelling has been widely used in attempts to assess the 3D conformation of proteins in solution. Initially, simple models employing only a small number of beads were used, with a considerable degree of success. Latterly, high-resolution bead models based upon atomic coordinates have been developed, and much more sophisticated questions can in principle be addressed. A detailed analysis is presented of the errors involved in the generation of such models and associated prediction of (translational friction) parameters, and in the practical measurement of these parameters for comparison. It is shown that in most cases, for a particle of only moderate asymmetry, the errors are such that it is not feasible to determine, on an absolute basis, which of a range of candidate conformers is the "correct" one. However, when the properties of the candidate conformers can be compared in relation to those of a "paradigm conformer", whose structure in solution, on the basis of external evidence, can be accepted as correct, then errors cancel and very precise comparisons become possible. The generation of 3D bead models (and hence 3D data files) for a range of candidate conformers is a simple matter, using the existing program MacBEADS, further facilitated by a 3D display module (pro Fit).

  19. Logarithmic conformal field theory: beyond an introduction

    NASA Astrophysics Data System (ADS)

    Creutzig, Thomas; Ridout, David

    2013-12-01

    This article aims to review a selection of central topics and examples in logarithmic conformal field theory. It begins with the remarkable observation of Cardy that the horizontal crossing probability of critical percolation may be computed analytically within the formalism of boundary conformal field theory. Cardy’s derivation relies on certain implicit assumptions which are shown to lead inexorably to indecomposable modules and logarithmic singularities in correlators. For this, a short introduction to the fusion algorithm of Nahm, Gaberdiel and Kausch is provided. While the percolation logarithmic conformal field theory is still not completely understood, there are several examples for which the formalism familiar from rational conformal field theory, including bulk partition functions, correlation functions, modular transformations, fusion rules and the Verlinde formula, has been successfully generalized. This is illustrated for three examples: the singlet model \\mathfrak {M} (1,2), related to the triplet model \\mathfrak {W} (1,2), symplectic fermions and the fermionic bc ghost system; the fractional level Wess-Zumino-Witten model based on \\widehat{\\mathfrak {sl}} \\left( 2 \\right) at k=-\\frac{1}{2}, related to the bosonic βγ ghost system; and the Wess-Zumino-Witten model for the Lie supergroup \\mathsf {GL} \\left( 1 {\\mid} 1 \\right), related to \\mathsf {SL} \\left( 2 {\\mid} 1 \\right) at k=-\\frac{1}{2} and 1, the Bershadsky-Polyakov algebra W_3^{(2)} and the Feigin-Semikhatov algebras W_n^{(2)}. These examples have been chosen because they represent the most accessible, and most useful, members of the three best-understood families of logarithmic conformal field theories. The logarithmic minimal models \\mathfrak {W} (q,p), the fractional level Wess-Zumino-Witten models, and the Wess-Zumino-Witten models on Lie supergroups (excluding \\mathsf {OSP} \\left( 1 {\\mid} 2n \\right)). In this review, the emphasis lies on the representation theory

  20. Conformal Janus on Euclidean sphere

    NASA Astrophysics Data System (ADS)

    Bak, Dongsu; Gustavsson, Andreas; Rey, Soo-Jong

    2016-12-01

    We interpret Janus as an interface in a conformal field theory and study its properties. The Janus is created by an exactly marginal operator and we study its effect on the interface conformal field theory on the Janus. We do this by utilizing the AdS/CFT correspondence. We compute the interface free energy both from leading correction to the Euclidean action in the dual gravity description and from conformal perturbation theory in the conformal field theory. We find that the two results agree each other and that the interface free energy scales precisely as expected from the conformal invariance of the Janus interface.

  1. Conformal vectors and stellar models

    NASA Astrophysics Data System (ADS)

    Manjonjo, A. M.; Maharaj, S. D.; Moopanar, S.

    2017-02-01

    The relationship between conformal symmetries and relativistic spheres in astrophysics is studied. We use the nonvanishing components of the Weyl tensor to classify the conformal symmetries in static spherical spacetimes. It is possible to find an explicit connection between the two gravitational potentials for both conformally flat and nonconformally flat cases. We show that the conformal Killing vector admits time dependence in terms of quadratic, trigonometric and hyperbolic functions. The Einstein and Einstein-Maxwell field equations can be written in terms of a single potential, any choice of which leads to an exact solution. Previous results of conformally invariant static spheres are contained in our treatment.

  2. Conformational flexibility in biochemical regulation

    SciTech Connect

    Trewhella, J.

    1993-09-01

    Small-angle X-ray and neutron scattering have proven extremely useful for studying the evolutionarily related dumbbell-shaped Ca {sup 2+} -binding proteins calmodulin and troponin C and their interactions with the target proteins whose activity they regulate. Calmodulin contracts about target enzyme binding domains with the common characteristic of having a high propensity for forming a basic, amphipathic a-helix. The contraction is achieved via flexibility in the interconnecting helix region of the molecule that links its two globular domains. This flexibility allows calmodulin to optimize its binding to different arrangements of hydrophobic and charged residues important in forming these complexes. In contrast calmodulin remains extended in its interaction with the catalytic subunit of phosphorylase kinase. There are structural and functional similarities between this interaction and that of troponin C and troponin I. Our most recent neutron scattering experiments confirm our prediction that troponin C also remains extended in this complex. The ability of the dumbbell-shaped Ca {sup 2+} -binding proteins to modulate their conformations via flexibility in the interconnecting helix region in order to accommodate different target binding domains is a remarkable example nature building functional diversity as well as specificity into a compact and unusual shape.

  3. Rupture diaphragmatique droite avec passage total et isolé du foie en intra-thoracique

    PubMed Central

    Turki, Mohamed; Barhoumi, Mohamed Hafed; Hajji, Hassen; Chemchik, Heithem; M'barek, Bechir

    2011-01-01

    La rupture traumatique de la coupole diaphragmatique droite avec hernie du foie dans le thorax est une lésion rare. Elle est souvent intégrée dans le cadre d'un poly-traumatisme, dont elle est un critère de gravité. Elle expose, précocement ou tardivement, à des complications cardio-pulmonaires par compression. Le diagnostic d'une rupture diaphragmatique droite est difficile à établir. En effet, ses signes cliniques sont peu spécifiques et l'imagerie peut être prise en défaut du faite qu'elle visualise les organes ascensionnés mais plus difficilement la rupture elle-même. La voie d'abord thoracique est souvent préférée du fait des difficultés de l'exposition du diaphragme en présence du foie. Nous rapportons un cas d'une rupture diaphragmatique droite avec passage isolé et total du foie en intra-thoracique diagnostiquée au cinquième jour d'hospitalisation chez un polytraumatisé. PMID:22187610

  4. OSI Conformance Testing for Bibliographic Applications.

    ERIC Educational Resources Information Center

    Arbez, Gilbert; Swain, Leigh

    1990-01-01

    Describes the development of Open Systems Interconnection (OSI) conformance testing sites, conformance testing tools, and conformance testing services. Discusses related topics such as interoperability testing, arbitration testing, and international harmonization of conformance testing. A glossary is included. (24 references) (SD)

  5. OSI Conformance Testing for Bibliographic Applications.

    ERIC Educational Resources Information Center

    Arbez, Gilbert; Swain, Leigh

    1990-01-01

    Describes the development of Open Systems Interconnection (OSI) conformance testing sites, conformance testing tools, and conformance testing services. Discusses related topics such as interoperability testing, arbitration testing, and international harmonization of conformance testing. A glossary is included. (24 references) (SD)

  6. Leaf growth is conformal

    NASA Astrophysics Data System (ADS)

    Alim, Karen; Armon, Shahaf; Shraiman, Boris I.; Boudaoud, Arezki

    2016-10-01

    Growth pattern dynamics lie at the heart of morphogenesis. Here, we investigate the growth of plant leaves. We compute the conformal transformation that maps the contour of a leaf at a given stage onto the contour of the same leaf at a later stage. Based on the mapping we predict the local displacement field in the leaf blade and find it to agree with the experimentally measured displacement field to 92%. This approach is applicable to any two-dimensional system with locally isotropic growth, enabling the deduction of the whole growth field just from observation of the tissue contour.

  7. Metamaterials with conformational nonlinearity

    PubMed Central

    Lapine, Mikhail; Shadrivov, Ilya V.; Powell, David A.; Kivshar, Yuri S.

    2011-01-01

    Within a decade of fruitful development, metamaterials became a prominent area of research, bridging theoretical and applied electrodynamics, electrical engineering and material science. Being man-made structures, metamaterials offer a particularly useful playground to develop interdisciplinary concepts. Here we demonstrate a novel principle in metamaterial assembly which integrates electromagnetic, mechanical, and thermal responses within their elements. Through these mechanisms, the conformation of the meta-molecules changes, providing a dual mechanism for nonlinearity and offering nonlinear chirality. Our proposal opens a wide road towards further developments of nonlinear metamaterials and photonic structures, adding extra flexibility to their design and control. PMID:22355655

  8. Eikonalization of conformal blocks

    DOE PAGES

    Fitzpatrick, A. Liam; Kaplan, Jared; Walters, Matthew T.; ...

    2015-09-03

    Classical field configurations such as the Coulomb potential and Schwarzschild solution are built from the t-channel exchange of many light degrees of freedom. We study the CFT analog of this phenomenon, which we term the 'eikonalization' of conformal blocks. We show that when an operator T appears in the OPE Ο(x)Ο(0), then the large spin Fock space states [TT···T]ℓ also appear in this OPE with a computable coefficient. The sum over the exchange of these Fock space states in an correlator build the classical 'T field' in the dual AdS description. In some limits the sum of all Fock spacemore » exchanges can be represented as the exponential of a single T exchange in the 4-pt correlator of O. Our results should be useful for systematizing 1/ℓ perturbation theory in general CFTs and simplifying the computation of large spin OPE coefficients. As examples we obtain the leading log ℓ dependence of Fock space conformal block coefficients, and we directly compute the OPE coefficients of the simplest ‘triple-trace’ operators.« less

  9. Eikonalization of conformal blocks

    SciTech Connect

    Fitzpatrick, A. Liam; Kaplan, Jared; Walters, Matthew T.; Wang, Junpu

    2015-09-03

    Classical field configurations such as the Coulomb potential and Schwarzschild solution are built from the t-channel exchange of many light degrees of freedom. We study the CFT analog of this phenomenon, which we term the 'eikonalization' of conformal blocks. We show that when an operator T appears in the OPE Ο(x)Ο(0), then the large spin Fock space states [TT···T] also appear in this OPE with a computable coefficient. The sum over the exchange of these Fock space states in an correlator build the classical 'T field' in the dual AdS description. In some limits the sum of all Fock space exchanges can be represented as the exponential of a single T exchange in the 4-pt correlator of O. Our results should be useful for systematizing 1/ℓ perturbation theory in general CFTs and simplifying the computation of large spin OPE coefficients. As examples we obtain the leading log ℓ dependence of Fock space conformal block coefficients, and we directly compute the OPE coefficients of the simplest ‘triple-trace’ operators.

  10. Supergravitational conformal Galileons

    NASA Astrophysics Data System (ADS)

    Deen, Rehan; Ovrut, Burt

    2017-08-01

    The worldvolume actions of 3+1 dimensional bosonic branes embedded in a five-dimensional bulk space can lead to important effective field theories, such as the DBI conformal Galileons, and may, when the Null Energy Condition is violated, play an essential role in cosmological theories of the early universe. These include Galileon Genesis and "bouncing" cosmology, where a pre-Big Bang contracting phase bounces smoothly to the presently observed expanding universe. Perhaps the most natural arena for such branes to arise is within the context of superstring and M -theory vacua. Here, not only are branes required for the consistency of the theory, but, in many cases, the exact spectrum of particle physics occurs at low energy. However, such theories have the additional constraint that they must be N = 1 supersymmetric. This motivates us to compute the worldvolume actions of N = 1 supersymmetric three-branes, first in flat superspace and then to generalize them to N = 1 supergravitation. In this paper, for simplicity, we begin the process, not within the context of a superstring vacuum but, rather, for the conformal Galileons arising on a co-dimension one brane embedded in a maximally symmetric AdS 5 bulk space. We proceed to N = 1 supersymmetrize the associated worldvolume theory and then generalize the results to N = 1 supergravity, opening the door to possible new cosmological scenarios

  11. Conformally symmetric traversable wormholes

    SciTech Connect

    Boehmer, Christian G.; Harko, Tiberiu; Lobo, Francisco S. N.

    2007-10-15

    Exact solutions of traversable wormholes are found under the assumption of spherical symmetry and the existence of a nonstatic conformal symmetry, which presents a more systematic approach in searching for exact wormhole solutions. In this work, a wide variety of solutions are deduced by considering choices for the form function, a specific linear equation of state relating the energy density and the pressure anisotropy, and various phantom wormhole geometries are explored. A large class of solutions impose that the spatial distribution of the exotic matter is restricted to the throat neighborhood, with a cutoff of the stress-energy tensor at a finite junction interface, although asymptotically flat exact solutions are also found. Using the 'volume integral quantifier', it is found that the conformally symmetric phantom wormhole geometries may, in principle, be constructed by infinitesimally small amounts of averaged null energy condition violating matter. Considering the tidal acceleration traversability conditions for the phantom wormhole geometry, specific wormhole dimensions and the traversal velocity are also deduced.

  12. Amitriptylinium picrate: conformational disorder.

    PubMed

    Bindya, S; Wong, Wing-Tak; Ashok, M A; Yathirajan, H S; Rathore, R S

    2007-09-01

    In the structure of the title salt [systematic name: 3-(10,11-dihydro-5H-dibenzo[a,d][7]annulen-5-ylidene)-N,N-dimethylpropan-1-aminium 2,4,6-trinitrophenolate] of a tricyclic antidepressant, C(20)H(24)N+.C(6)H(2)N(3)O(7)-, the dimethylaminopropyl subunit possesses a classical static conformational disorder. The central cycloheptadiene ring adopts a bent conformation that is intermediate between boat and chair forms, leading to a butterfly shape for the hetero-tricyclic moiety. In a complementary fashion, donors from amitriptyline and acceptors from picrate form intermolecular C-H...O hydrogen bonds and N-H...O salt bridges. These hydrogen bonds cluster amitriptyline and picrate ions into a closed R4(4)(36) hetero-tetramer, whereas intermolecular C-H...pi interactions between amitriptyline ions cluster them into homo-dimers. Significant pi-pi stacking interactions are also observed between aromatic rings of amitriptyline and picrate, and these, combined with the C-H...pi interactions, associate molecules into linear arrays along the [111] direction.

  13. Conformationally constrained analogues of L-prolyl-l-leucylglycinamide

    SciTech Connect

    Yu, K.L.

    1986-01-01

    The tripeptide, L-prolyl-L-leucylglycinamide (PLG), has been shown to modulate the pharmacological response of the neurotransmitter, dopamine, in the central nervous system. Many physical studies have suggested that PLG can exist in a type II ..beta..-bend conformation. In this study several types of conformationally constrained analogues capable of mimicking different types of conformations of PLG have been designed to answer two questions: (1) Is the type II ..beta..-bend the bioactive conformation of PLG. (2) Does the Leu-Gly amide bond of PLG need to be in a cis or trans configuration in order for it to bind to its receptor. The analogues of PLG that have been synthesized include the following: (1) Lactam analogues, (2) Cyclic peptides, (3) Olefinic analogue, and (4) Tetazole analogues. The analogues synthesized were tested in a (/sup 3/H)-ADTN binding assay to determine their ability to enhance the binding of this dopamine agonist to dopamine receptors.

  14. On classification of extremal non-holomorphic conformal field theories

    NASA Astrophysics Data System (ADS)

    Tener, James E.; Wang, Zhenghan

    2017-03-01

    Rational chiral conformal field theories are organized according to their genus, which consists of a modular tensor category C and a central charge c. A long-term goal is to classify unitary rational conformal field theories based on a classification of unitary modular tensor categories. We conjecture that for any unitary modular tensor category C , there exists a unitary chiral conformal field theory V so that its modular tensor category {{C}V} is C . In this paper, we initiate a mathematical program in and around this conjecture. We define a class of extremal vertex operator algebras with minimal conformal dimensions as large as possible for their central charge, and non-trivial representation theory. We show that there are finitely many different characters of extremal vertex operator algebras V possessing at most three different irreducible modules. Moreover, we list all of the possible characters for such vertex operator algebras with c≤slant 48 .

  15. Plasmonic organic thin-film solar cell: light trapping by using conformal vs. non-conformal relief gratings

    NASA Astrophysics Data System (ADS)

    Keshmiri, Hamid; Dostlek, Jakub

    2015-05-01

    Theoretical study of light management in thin film organic photovoltaic cell that utilizes diffraction coupling to guided waves is presented. As a model system, a regular solar cell geometry with P3HT:PCBM active layer, transparent ITO electrode and Al backside electrode is used. The paper discusses enhancement of absorption of incident photons selectively in the active layer by the interplay of surface plasmon polariton and optical waveguide waves, the effect on the profile of their field and damping that affects the spatial distribution of dissipated light energy in the layer structure. The model shows that for optimized grating period and modulation depth the number of absorbed photons in the active layer can be increased by 24 per cent. The comparison of the geometry with conformal and non-conformally corrugated layers reveals that the conformal structure outperforms the non-conformal in the enhancing of photon absorption in the wavelength range of 350-800 nm.

  16. Recent Advances in Conformal Gravity

    NASA Astrophysics Data System (ADS)

    O'Brien, James; Chaykov, Spasen

    2016-03-01

    In recent years, significant advances have been made in alternative gravitational theories. Although MOND remains the leading candidate among the alternative models, Conformal Gravity has been studied by Mannheim and O'Brien to solve the rotation curve problem without the need for dark matter. Recently, Mannheim, O'Brien and Chaykov have begun solving other gravitational questions in Conformal Gravity. In this presentation, we highlight the new work of Conformal Gravity's application to random motions of clusters (the original Zwicky problem), gravitational bending of light, gravitational lensing and a very recent survey of dwarf galaxy rotation curves. We will show in each case that Conformal Gravity can provide an accurate explanation and prediction of the data without the need for dark matter. Coupled with the fact that Conformal Gravity is a fully re-normalizable metric theory of gravity, these results help to push Conformal Gravity onto a competitive stage against other alternative models.

  17. Development of conformal respirator monitoring technology

    SciTech Connect

    Shonka, J.J.; Weismann, J.J.; Logan, R.J.

    1997-04-01

    This report summarizes the results of a Small Business Innovative Research Phase II project to develop a modular, surface conforming respirator monitor to improve upon the manual survey techniques presently used by the nuclear industry. Research was performed with plastic scintillator and gas proportional modules in an effort to find the most conducive geometry for a surface conformal, position sensitive monitor. The respirator monitor prototype developed is a computer controlled, position-sensitive detection system employing 56 modular proportional counters mounted in molds conforming to the inner and outer surfaces of a commonly used respirator (Scott Model 801450-40). The molds are housed in separate enclosures and hinged to create a {open_quotes}waffle-iron{close_quotes} effect so that the closed monitor will simultaneously survey both surfaces of the respirator. The proportional counter prototype was also designed to incorporate Shonka Research Associates previously developed charge-division electronics. This research provided valuable experience into pixellated position sensitive detection systems. The technology developed can be adapted to other monitoring applications where there is a need for deployment of many traditional radiation detectors.

  18. Fermion-scalar conformal blocks

    DOE PAGES

    Iliesiu, Luca; Kos, Filip; Poland, David; ...

    2016-04-13

    In this study, we compute the conformal blocks associated with scalar-scalar-fermionfermion 4-point functions in 3D CFTs. Together with the known scalar conformal blocks, our result completes the task of determining the so-called ‘seed blocks’ in three dimensions. In addition, conformal blocks associated with 4-point functions of operators with arbitrary spins can now be determined from these seed blocks by using known differential operators.

  19. Fermion-scalar conformal blocks

    SciTech Connect

    Iliesiu, Luca; Kos, Filip; Poland, David; Pufu, Silviu S.; Simmons-Duffin, David; Yacoby, Ran

    2016-04-13

    In this study, we compute the conformal blocks associated with scalar-scalar-fermionfermion 4-point functions in 3D CFTs. Together with the known scalar conformal blocks, our result completes the task of determining the so-called ‘seed blocks’ in three dimensions. In addition, conformal blocks associated with 4-point functions of operators with arbitrary spins can now be determined from these seed blocks by using known differential operators.

  20. Conformal array antenna subsystem

    NASA Astrophysics Data System (ADS)

    1985-04-01

    An antenna subsystem to communicate between Ariane 4 and a data relay satellite was studied, concluding that the original ideas on ring antennas should be corrected due to the wide margin of coverage required in elevation for such antennas, which implies the need of splitting the coverage. Nevertheless, the study of cylindrical and conical conformal arrays was continued in view of their intrinsic interest. Needed coverages with specified gain can be obtained with a set of microstrip circular patch antennas. For the lower stage, a single patch is enough. For geostationary missions, one horizontal array is used, and for heliosynchronous missions two horizontal arrays and a vertical one. The numerical study carried out on omniazimuthal ring antennas shows that a tendency to omnidirectional pattern exists in spite of the directivity of the elementary radiators. A small pointing improvement of the meridian pattern can be obtained by means of conical arrays instead of the cylindrical ones.

  1. Capturing Chromosome Conformation

    NASA Astrophysics Data System (ADS)

    Dekker, Job; Rippe, Karsten; Dekker, Martijn; Kleckner, Nancy

    2002-02-01

    We describe an approach to detect the frequency of interaction between any two genomic loci. Generation of a matrix of interaction frequencies between sites on the same or different chromosomes reveals their relative spatial disposition and provides information about the physical properties of the chromatin fiber. This methodology can be applied to the spatial organization of entire genomes in organisms from bacteria to human. Using the yeast Saccharomyces cerevisiae, we could confirm known qualitative features of chromosome organization within the nucleus and dynamic changes in that organization during meiosis. We also analyzed yeast chromosome III at the G1 stage of the cell cycle. We found that chromatin is highly flexible throughout. Furthermore, functionally distinct AT- and GC-rich domains were found to exhibit different conformations, and a population-average 3D model of chromosome III could be determined. Chromosome III emerges as a contorted ring.

  2. Thermal insulating conformal blanket

    NASA Technical Reports Server (NTRS)

    Barney, Andrea (Inventor); Whittington, Charles A (Inventor); Eilertson, Bryan (Inventor); Siminski, Zenon (Inventor)

    2003-01-01

    The conformal thermal insulating blanket may have generally rigid batting material covered by an outer insulating layer formed of a high temperature resistant woven ceramic material and an inner insulating layer formed of a woven ceramic fiber material. The batting and insulating layers may be fastened together by sewing or stitching using an outer mold layer thread fabricated of a high temperature resistant material and an inner mold layer thread of a ceramic fiber material. The batting may be formed to a composite structure that may have a firmness factor sufficient to inhibit a pillowing effect after the stitching to not more than 0.03 inch. The outer insulating layer and an upper portion of the batting adjacent the outer insulating layer may be impregnated with a ceramic coating material.

  3. Conformally symmetric relativistic star

    NASA Astrophysics Data System (ADS)

    Rahaman, Farook; Maharaj, Sunil D.; Sardar, Iftikar Hossain; Chakraborty, Koushik

    2017-03-01

    We investigate whether compact stars having Tolman-like interior geometry admit conformal symmetry. Taking anisotropic pressure along the two principal directions within the compact object, we obtain physically relevant quantities such as transverse and radial pressure, density and redshift function. We study the equation of state (EOS) for the matter distribution inside the star. From the relation between pressure and density function of the constituent matter, we explore the nature and properties of the interior matter. The redshift function and compactness parameter are found to be physically reasonable. The matter inside the star satisfies the null, weak and strong energy conditions. Finally, we compare the masses and radii predicted from the model with corresponding values in some observed stars.

  4. Conformal model of gravitons

    NASA Astrophysics Data System (ADS)

    Donoghue, John F.

    2017-08-01

    In the description of general covariance, the vierbein and the Lorentz connection can be treated as independent fundamental fields. With the usual gauge Lagrangian, the Lorentz connection is characterized by an asymptotically free running coupling. When running from high energy, the coupling gets large at a scale which can be called the Planck mass. If the Lorentz connection is confined at that scale, the low energy theory can have the Einstein Lagrangian induced at low energy through dimensional transmutation. However, in general there will be new divergences in such a theory and the Lagrangian basis should be expanded. I construct a conformally invariant model with a larger basis size which potentially may have the same property.

  5. Conformal Aspects of QCD

    SciTech Connect

    Brodsky, S

    2003-11-19

    Theoretical and phenomenological evidence is now accumulating that the QCD coupling becomes constant at small virtuality; i.e., {alpha}{sub s}(Q{sup 2}) develops an infrared fixed point in contradiction to the usual assumption of singular growth in the infrared. For example, the hadronic decays of the {tau} lepton can be used to determine the effective charge {alpha}{sub {tau}}(m{sub {tau}{prime}}{sup 2}) for a hypothetical {tau}-lepton with mass in the range 0 < m{sub {tau}{prime}} < m{sub {tau}}. The {tau} decay data at low mass scales indicates that the effective charge freezes at a value of s = m{sub {tau}{prime}}{sup 2} of order 1 GeV{sup 2} with a magnitude {alpha}{sub {tau}} {approx} 0.9 {+-} 0.1. The near-constant behavior of effective couplings suggests that QCD can be approximated as a conformal theory even at relatively small momentum transfer and why there are no significant running coupling corrections to quark counting rules for exclusive processes. The AdS/CFT correspondence of large N{sub c} supergravity theory in higher-dimensional anti-de Sitter space with supersymmetric QCD in 4-dimensional space-time also has interesting implications for hadron phenomenology in the conformal limit, including an all-orders demonstration of counting rules for exclusive processes and light-front wavefunctions. The utility of light-front quantization and light-front Fock wavefunctions for analyzing nonperturbative QCD and representing the dynamics of QCD bound states is also discussed.

  6. Elaboration de revetements nanocomposites avec des proprietes superhydrophobes, semi-conductrices et photocatalytiques

    NASA Astrophysics Data System (ADS)

    Madidi, Fatima Zahra

    Les lignes aeriennes de transport et de distribution de l'energie electrique sont souvent exposees a diverses contraintes. Parmi celles-ci, la pollution des isolateurs constitue l'un des facteurs de premiere importance dans la fiabilite du transport d'energie. En effet, la presence de pollution sur les isolateurs lorsqu'elle est humidifiee entraine la diminution de leur performance electrique en favorisant l'apparition d'arcs de contournement. De telles pannes peuvent parfois causer des impacts socioeconomiques importants. Par ailleurs, le developpement de nouveaux revetements pour ces isolateurs peut s'averer un moyen efficace pour les proteger contre l'apparition de l'arc de contournement. Les revetements superhydrophobes ont fait l'objet de nombreuses etudes au cours de ces dernieres annees. Ces surfaces sont preparees en combinant une rugosite nano-microstructuree avec une faible energie de surface. En outre, de telles surfaces ont de nombreuses applications si elles sont durables et n'ont pas d'effets nocifs sur l'environnement. L'objectif principal de la presente etude vise d'abord l'elaboration de revetements superhydrophobes, puis l'etude de leur duree de vie, leurs proprietes dielectriques et photocatalytiques. Une grande variete de materiaux a faible energie de surface peuvent etre utilises pour le developpement de ces revetements. Dans cette recherche, le caoutchouc de silicone (CS) est employe car il presente de nombreuses proprietes, notamment une forte hydrophobie, une resistance aux rayonnements ultraviolets, et une bonne tenue au feu sans degagement de produits toxiques. Toutefois, le point faible de ces materiaux est la degradation de leurs proprietes hydrophobes. Afin d'ameliorer certaines proprietes du caoutchouc de silicone, des nanoparticules seront additionnees au polymere de base. La technique d'elaboration des revetements consiste a ajouter des nanoparticules de dioxyde de titane (TiO2) au polymere de base, par des methodes ayant un

  7. Replacement between conformity and counter-conformity in consumption decisions.

    PubMed

    Chou, Ting-Jui; Chang, En-Chung; Dai, Qi; Wong, Veronica

    2013-02-01

    This study assessed, in a Chinese context, how self-esteem interacts with perceived similarity and uniqueness to yield cognitive dissonance, and whether the dissonance leads to self-reported conformity or counter-conformity behavior. Participants were 408 respondents from 4 major Chinese cities (M age = 33.0 yr., SD = 4.3; 48% men). Self-perceptions of uniqueness, similarity, cognitive dissonance, self-esteem and need to behave in conformity or counter-conformity were measured. A theoretical model was assessed in four situations, relating the ratings of self-esteem and perceived similarity/uniqueness to the way other people at a wedding were dressed, and the resultant cognitive dissonance and conformity/ counter-conformity behavior. Regardless of high or low self-esteem, all participants reported cognitive dissonance when they were told that they were dressed extremely similarly to or extremely differently from the other people attending the wedding. However, the conforming/counter-conforming strategies used by participants to resolve the cognitive dissonance differed. When encountering dissonance induced by the perceived extreme uniqueness of dress, participants with low self-esteem tended to say they would dress next time so as to conform with the way others were dressed, while those with high self-esteem indicated they would continue their counter-conformity in attire. When encountering dissonance induced by the perceived extreme similarity to others, both those with high and low self-esteem tended to say they would dress in an unorthodox manner to surprise other people in the future.

  8. Counselor Identity: Conformity or Distinction?

    ERIC Educational Resources Information Center

    McLaughlin, Jerry E.; Boettcher, Kathryn

    2009-01-01

    The authors explore 3 debates in other disciplines similar to counseling's identity debate in order to learn about common themes and outcomes. Conformity, distinction, and cohesion emerged as common themes. They conclude that counselors should retain their distinctive, humanistic approach rather than conforming to the dominant, medical approach.

  9. Recent advancements in conformal gravity

    NASA Astrophysics Data System (ADS)

    O'Brien, James G.; Chaykov, Spasen S.; Dentico, Jeremy; Stulge, Modestas; Stefanski, Brian; Moss, Robert J.

    2017-05-01

    In recent years, due to the lack of direct observed evidence of cold dark matter, coupled with the shrinking parameter space to search for new dark matter particles, there has been increased interest in Alternative Gravitational theories. This paper, addresses three recent advances in conformal gravity, a fourth order renormalizable metric theory of gravitation originally formulated by Weyl, and later advanced by Mannheim and Kazanas. The first section of the paper applies conformal gravity to the rotation curves of the LITTLE THINGS survey, extending the total number of rotation curves successfully fit by conformal gravity to well over 200 individual data sets without the need for additional dark matter. Further, in this rotation curve study, we show how MOND and conformal gravity compare for each galaxy in the sample. Second, we look at the original Zwicky problem of applying the virial theorem to the Coma cluster in order to get an estimate for the cluster mass. However, instead of using the standard Newtonian potential, here we use the weak field approximation of conformal gravity. We show that in the conformal case we can get a much smaller mass estimate and thus there is no apparent need to include dark matter. We then show that this calculation is in agreement with the observational data from other well studied clusters. Last, we explore the calculation of the deflection of starlight through conformal gravity, as a first step towards applying conformal gravity to gravitaitonal lensing.

  10. Conformal Transformations and Space Travel.

    PubMed

    Gupta, S N

    1961-10-27

    Conformal transformations are applied to the motion of a space ship experiencing a constant acceleration. The role of proper time is interpreted in terms of atomic periods, and the relationship between the conformal transformations and the general theory of relativity is clarified.

  11. Conformal Fermi Coordinates

    SciTech Connect

    Dai, Liang; Pajer, Enrico; Schmidt, Fabian E-mail: Enrico.pajer@gmail.com

    2015-11-01

    Fermi Normal Coordinates (FNC) are a useful frame for isolating the locally observable, physical effects of a long-wavelength spacetime perturbation. Their cosmological application, however, is hampered by the fact that they are only valid on scales much smaller than the horizon. We introduce a generalization that we call Conformal Fermi Coordinates (CFC). CFC preserve all the advantages of FNC, but in addition are valid outside the horizon. They allow us to calculate the coupling of long- and short-wavelength modes on all scales larger than the sound horizon of the cosmological fluid, starting from the epoch of inflation until today, by removing the complications of the second order Einstein equations to a large extent, and eliminating all gauge ambiguities. As an application, we present a calculation of the effect of long-wavelength tensor modes on small scale density fluctuations. We recover previous results, but clarify the physical content of the individual contributions in terms of locally measurable effects and ''projection'' terms.

  12. Imaging of conformational changes

    SciTech Connect

    Michl, Josef

    2016-03-13

    Control of intramolecular conformational change in a small number of molecules or even a single one by an application of an outside electric field defined by potentials on nearby metal or dielectric surfaces has potential applications in both 3-D and 2-D nanotechnology. Specifically, the synthesis, characterization, and understanding of designed solids with controlled built-in internal rotational motion of a dipole promises a new class of materials with intrinsic dielectric, ferroelectric, optical and optoelectronic properties not found in nature. Controlled rotational motion is of great interest due to its expected utility in phenomena as diverse as transport, current flow in molecular junctions, diffusion in microfluidic channels, and rotary motion in molecular machines. A direct time-resolved observation of the dynamics of motion on ps or ns time scale in a single molecule would be highly interesting but is also very difficult and has yet to be accomplished. Much can be learned from an easier but still challenging comparison of directly observed initial and final orientational states of a single molecule, which is the basis of this project. The project also impacts the understanding of surface-enhanced Raman spectroscopy (SERS) and single-molecule spectroscopic detection, as well as the synthesis of solid-state materials with tailored properties from designed precursors.

  13. Dynamics of protein conformations

    NASA Astrophysics Data System (ADS)

    Stepanova, Maria

    2010-10-01

    A novel theoretical methodology is introduced to identify dynamic structural domains and analyze local flexibility in proteins. The methodology employs a multiscale approach combining identification of essential collective coordinates based on the covariance analysis of molecular dynamics trajectories, construction of the Mori projection operator with these essential coordinates, and analysis of the corresponding generalized Langevin equations [M.Stepanova, Phys.Rev.E 76(2007)051918]. Because the approach employs a rigorous theory, the outcomes are physically transparent: the dynamic domains are associated with regions of relative rigidity in the protein, whereas off-domain regions are relatively soft. This also allows scoring the flexibility in the macromolecule with atomic-level resolution [N.Blinov, M.Berjanskii, D.S.Wishart, and M.Stepanova, Biochemistry, 48(2009)1488]. The applications include the domain coarse-graining and characterization of conformational stability in protein G and prion proteins. The results are compared with published NMR experiments. Potential applications for structural biology, bioinformatics, and drug design are discussed.

  14. Flexible backbone sampling methods to model and design protein alternative conformations.

    PubMed

    Ollikainen, Noah; Smith, Colin A; Fraser, James S; Kortemme, Tanja

    2013-01-01

    Sampling alternative conformations is key to understanding how proteins work and engineering them for new functions. However, accurately characterizing and modeling protein conformational ensembles remain experimentally and computationally challenging. These challenges must be met before protein conformational heterogeneity can be exploited in protein engineering and design. Here, as a stepping stone, we describe methods to detect alternative conformations in proteins and strategies to model these near-native conformational changes based on backrub-type Monte Carlo moves in Rosetta. We illustrate how Rosetta simulations that apply backrub moves improve modeling of point mutant side-chain conformations, native side-chain conformational heterogeneity, functional conformational changes, tolerated sequence space, protein interaction specificity, and amino acid covariation across protein-protein interfaces. We include relevant Rosetta command lines and RosettaScripts to encourage the application of these types of simulations to other systems. Our work highlights that critical scoring and sampling improvements will be necessary to approximate conformational landscapes. Challenges for the future development of these methods include modeling conformational changes that propagate away from designed mutation sites and modulating backbone flexibility to predictively design functionally important conformational heterogeneity. Copyright © 2013 Elsevier Inc. All rights reserved.

  15. Benchmarking Commercial Conformer Ensemble Generators.

    PubMed

    Friedrich, Nils-Ole; de Bruyn Kops, Christina; Flachsenberg, Florian; Sommer, Kai; Rarey, Matthias; Kirchmair, Johannes

    2017-10-02

    We assess and compare the performance of eight commercial conformer ensemble generators (ConfGen, ConfGenX, cxcalc, iCon, MOE LowModeMD, MOE Stochastic, MOE Conformation Import and OMEGA) and one leading free algorithm, the distance geometry (DG) algorithm implemented in RDKit. The comparative study is based on a new version of the Platinum Diverse Dataset, a high-quality benchmarking dataset of 2859 protein-bound ligand conformations extracted from the PDB. Differences in the performance of commercial algorithms are much smaller than those observed for free algorithms in our previous study (J. Chem. Inf. 2017, 57, 529-539). For commercial algorithms the median minimum RMSDs measured between protein-bound ligand conformations and ensembles of a maximum of 250 conformers are between 0.46 and 0.61 Å. Commercial conformer ensemble generators are characterized by their high robustness, with at least 99% of all input molecules successfully processed and few or even no substantial geometrical errors detectable in their output conformations. The RDKit DG algorithm (with minimization enabled) appears to be a good free alternative since its performance is comparable to that of the mid-ranked commercial algorithms. Based on a statistical analysis, we elaborate on which algorithms to use and how to parameterize them for best performance in different application scenarios.

  16. Conformal optics risk reduction demonstration

    NASA Astrophysics Data System (ADS)

    Knapp, David J.; Mills, James P.; Hegg, Ronald G.; Trotta, Patrick A.; Smith, Christopher B.

    2001-09-01

    For the past three years, the Precision Conformal Optics Consortium has been developing a revolutionary new class of optics. These optics are characterized by outer window elements that conform to aerodynamic rather than optical requirements. Conformal optical elements can greatly improve the aerodynamic performance of the host platform. To make conformal optics a reality, challenges had to be overcome in design, fabrication, and testing. This was accomplished in October 1999 when Raytheon demonstrated the world's first conformal optical system. This fineness ratio one system was a risk reduction effort to develop technology for later systems. It is comprised of a calcium fluoride conformal optical dome, a TI-1173 aspheric corrector, and a calcium fluoride solid catadioptric telescope. The design involved overcoming large amounts of aberration that varied with gimbal look angle. Efforts also included aligning the system to tight tolerances and testing highly aspheric optical elements. Overall, the actual system performance compared very favorably with the design model. With the proven success of this risk reduction demonstration, the path was cleared for new higher performance conformal optical systems.

  17. Conformal Lorentz geometry revisited

    NASA Astrophysics Data System (ADS)

    Teleman, Kostake

    1996-02-01

    The group U(2,2) and its subgroup SU(2,2) were considered by Penrose in his study of the conformal compactification M of the Minkowski space M [R. Penrose and W. Rindler, Spinors and Space-Time (Cambridge University, Cambridge, 1986) and R. O. Wells, Jr., Bull. Am. Math. Soc. I, 2 (1979)]. The standard representation of SU(2,2) in C4 and in M are the corner stones of twistor theory, which was created by Penrose to the double purpose of obtaining new solutions of Einstein equations and new insights on gravitational radiation. We think that other representations of SU(2,2) or U(2,2) could also bring some information in relativity [see also, Barut O. Asjim, in Noncompact Lie Groups and some of their Applications, edited by E. A. Tanner and R. Wilson (Kluwer Academic, Dordrecht, 1994), p. 103] and, accordingly, we propose an extension of Penrose twistor program. In this paper we deal with a new U(2,2)-space, which we denote by W. We show first that the SU(2,2)-space M introduced by Penrose is isomorphic to U(2), endowed with an action of SU(2,2) given by non-Abelian homographic transformations. These transformations keep invariant the equation det(u-v)=0, characterizing the pairs (u,v)∈U(2)×U(2) such that ``u lies on the light-cone of v.'' By definition, our space W consists of all pairs (u,v)∈U(2)×U(2) satisfying the condition det(u-v)≠0. The starting point of this article is the observation that W carries an SU(2,2)-invariant pseudo-Riemannian metric L:=Tr[(u-v)-1u˙ ×(u-v)-1v˙], of signature (4,4). (W,L) is in fact an irreducible symmetric space in Cartan's sense, which is isomorphic to the quotient SO(2,4)/S[O(1,1)×O(1,3)]. As an irreducible symmetric space, it is an 8-dimensional Einstein space, whose Ricci tensor is proportional to the metric tensor. We study the geodesic paths of this space giving the general solutions in terms of initial data and studying the constants of motion. In particular we determine the geodesic paths which exhibit two periods

  18. CONFORMANCE IMPROVEMENT USING GELS

    SciTech Connect

    Randall S. Seright

    2002-02-28

    This technical progress report describes work performed from June 20 through December 19, 2001, for the project, ''Conformance Improvement Using Gels''. Interest has increased in some new polymeric products that purport to substantially reduce permeability to water while causing minimum permeability reduction to oil. In view of this interest, we are currently studying BJ's Aqua Con. Results from six corefloods revealed that the Aqua Con gelant consistently reduced permeability to water more than that to oil. However, the magnitude of the disproportionate permeability reduction varied significantly for the various experiments. Thus, as with most materials tested to date, the issue of reproducibility and control of the disproportionate permeability remains to be resolved. Concern exists about the ability of gels to resist washout after placement in fractures. We examined whether a width constriction in the middle of a fracture would cause different gel washout behavior upstream versus downstream of the constriction. Tests were performed using a formed Cr(III)-acetate-HPAM gel in a 48-in.-long fracture with three sections of equal length, but with widths of 0.08-, 0.02-, and 0.08-in., respectively. The pressure gradients during gel extrusion (i.e., placement) were similar in the two 0.08-in.-wide fracture sections, even though they were separated by a 0.02-in.-wide fracture section. The constriction associated with the middle fracture section may have inhibited gel washout during the first pulse of brine injection after gel placement. However, during subsequent phases of brine injection, the constriction did not inhibit washout in the upstream fracture section any more than in the downstream section.

  19. Predicting conformational switches in proteins.

    PubMed Central

    Young, M.; Kirshenbaum, K.; Dill, K. A.; Highsmith, S.

    1999-01-01

    We describe a new computational technique to predict conformationally switching elements in proteins from their amino acid sequences. The method, called ASP (Ambivalent Structure Predictor), analyzes results from a secondary structure prediction algorithm to identify regions of conformational ambivalence. ASP identifies ambivalent regions in 16 test protein sequences for which function involves substantial backbone rearrangements. In the test set, all sites previously described as conformational switches are correctly predicted to be structurally ambivalent regions. No such regions are predicted in three negative control protein sequences. ASP may be useful as a guide for experimental studies on protein function and motion in the absence of detailed three-dimensional structural data. PMID:10493576

  20. Conformal tensors via Lovelock gravity

    NASA Astrophysics Data System (ADS)

    Kastor, David

    2013-10-01

    Constructs from conformal geometry are important in low dimensional gravity models, while in higher dimensions the higher curvature interactions of Lovelock gravity are similarly prominent. Considering conformal invariance in the context of Lovelock gravity leads to natural, higher curvature generalizations of the Weyl, Schouten, Cotton and Bach tensors, with properties that straightforwardly extend those of their familiar counterparts. As a first application, we introduce a new set of conformally invariant gravity theories in D = 4k dimensions, based on the squares of the higher curvature Weyl tensors.

  1. Conformational changes of adsorbed proteins

    NASA Astrophysics Data System (ADS)

    Allen, Scott

    2005-03-01

    The adsorption of bovine serum albumin (BSA) and pepsin to gold surfaces has been studied using surface plasmon resonance (SPR). Proteins are adsorbed from solution onto a gold surface and changes in the conformation of the adsorbed proteins are induced by changing the buffer solution. We selected pH and ionic strength values for the buffer solutions that are known from our circular dichroism measurements to cause conformational changes of the proteins in bulk solution. We find that for both BSA and pepsin the changes in conformation are impeded by the interaction of the protein with the gold surface.

  2. Conformational Landscape of Nicotinoids: Solving the "conformational - Rity" of Anabasine

    NASA Astrophysics Data System (ADS)

    Lesarri, Alberto; Cocinero, Emilio J.; Evangelisti, Luca; Suenram, Richard D.; Caminati, Walther; Grabow, Jens-Uwe

    2010-06-01

    The conformational landscape of the alkaloid anabasine (neonicotine) has been investigated using rotational spectroscopy and ab initio calculations. The results allow a detailed comparison of the structural properties of the prototype piperidinic and pyrrolidinic nicotinoids (anabasine vs. nicotine). Anabasine adopts two most stable conformations in isolation conditions, for which we determined accurate rotational and nuclear quadrupole coupling parameters. The preferred conformations are characterized by an equatorial pyridine moiety and additional N-H equatorial stereochemistry at the piperidine ring (Eq-Eq). The two rings of anabasine are close to a bisecting arrangement, with the observed conformations differing in a ca. 180° rotation of the pyridine subunit, denoted either Syn or Anti. The preference of anabasine for the Eq-Eq-Syn conformation has been established by relative intensity measurements (Syn/Anti˜5(2)). The conformational preferences of free anabasine are directed by a N\\cdot\\cdot\\cdotH-C weak hydrogen bond interaction between the nitrogen lone pair at piperidine and the closest hydrogen bond in pyridine, with N\\cdot\\cdot\\cdotN distances ranging from 4.750 Å (Syn) to 4.233 Å (Anti). R. J. Lavrich, R. D. Suenram, D. F. Plusquellic and S. Davis, 58^th OSU Int. Symp. on Mol. Spectrosc., Columbus, OH, 2003, Comm. RH13.

  3. Regles de fusion en theorie des champs conformes

    NASA Astrophysics Data System (ADS)

    Begin, Luc

    1999-10-01

    Les théories de champs conformes constituent un domaine de recherche très actif avec de nombreuses applications en physique statistique, en matière condensée, en théorie des cordes, en mathématiques, etc. Nous analysons ici le calcul des règles de fusion dans les modèles Wess- Zumino-Witten par des méthodes positives. Les règles de fusion sont des quantités importantes puisqu'elles indiquent comment se combinent les champs primaires de la théorie. L'approche présentée est basée sur l'hypothèse que les règles de fusion sont décrites par un système d'inéquations linéaire et homogène et mène au concept original de «base de fusion». Cette approche simple et générale permet d'utiliser les méthodes combinatoires et de programmation linéaire pour construire les fonctions génératrices et les bases de fusion. Cette méthode permet d'obtenir des résultats originaux et explicites pour les algèbres su (3), su (4) et sp (4).

  4. Ligand-driven conformational changes of MurD visualized by paramagnetic NMR.

    PubMed

    Saio, Tomohide; Ogura, Kenji; Kumeta, Hiroyuki; Kobashigawa, Yoshihiro; Shimizu, Kazumi; Yokochi, Masashi; Kodama, Kota; Yamaguchi, Hiroto; Tsujishita, Hideki; Inagaki, Fuyuhiko

    2015-11-19

    Proteins, especially multi-domain proteins, often undergo drastic conformational changes upon binding to ligands or by post-translational modifications, which is a key step to regulate their function. However, the detailed mechanisms of such dynamic regulation of the functional processes are poorly understood because of the lack of an efficient tool. We here demonstrate detailed characterization of conformational changes of MurD, a 47 kDa protein enzyme consisting of three domains, by the use of solution NMR equipped with paramagnetic lanthanide probe. Quantitative analysis of pseudocontact shifts has identified a novel conformational state of MurD, named semi-closed conformation, which is found to be the key to understand how MurD regulates the binding of the ligands. The modulation of the affinity coupled with conformational changes accentuates the importance of conformational state to be evaluated in drug design.

  5. Conformation Distributions in Adsorbed Proteins.

    NASA Astrophysics Data System (ADS)

    Meuse, Curtis W.; Hubbard, Joseph B.; Vrettos, John S.; Smith, Jackson R.; Cicerone, Marcus T.

    2007-03-01

    While the structural basis of protein function is well understood in the biopharmaceutical and biotechnology industries, few methods for the characterization and comparison of protein conformation distributions are available. New methods capable of measuring the stability of protein conformations and the integrity of protein-protein, protein-ligand and protein-surface interactions both in solution and on surfaces are needed to help the development of protein-based products. We are developing infrared spectroscopy methods for the characterization and comparison of molecular conformation distributions in monolayers and in solutions. We have extracted an order parameter describing the orientational and conformational variations of protein functional groups around the average molecular values from a single polarized spectrum. We will discuss the development of these methods and compare them to amide hydrogen/deuterium exchange methods for albumin in solution and on different polymer surfaces to show that our order parameter is related to protein stability.

  6. Graphene-based conformal devices.

    PubMed

    Park, Yong Ju; Lee, Seoung-Ki; Kim, Min-Seok; Kim, Hyunmin; Ahn, Jong-Hyun

    2014-08-26

    Despite recent progress in bendable and stretchable thin-film transistors using novel designs and materials, the development of conformal devices remains limited by the insufficient flexibility of devices. Here, we demonstrate the fabrication of graphene-based conformal and stretchable devices such as transistor and tactile sensor on a substrate with a convoluted surface by scaling down the device thickness. The 70 nm thick graphene-based conformal devices displayed a much lower bending stiffness than reported previously. The demonstrated devices provided excellent conformal coverage over an uneven animal hide surface without the need for an adhesive. In addition, the ultrathin graphene devices formed on the three-dimensionally curved animal hide exhibited stable electrical characteristics, even under repetitive bending and twisting. The advanced performance and flexibility demonstrated here show promise for the development and adoption of wearable electronics in a wide range of future applications.

  7. Solution NMR conformation of glycosaminoglycans.

    PubMed

    Pomin, Vitor H

    2014-04-01

    Nuclear magnetic resonance (NMR) spectroscopy has been giving a pivotal contribution to the progress of glycomics, mostly by elucidating the structural, dynamical, conformational and intermolecular binding aspects of carbohydrates. Particularly in the field of conformation, NOE resonances, scalar couplings, residual dipolar couplings, and chemical shift anisotropy offsets have been the principal NMR parameters utilized. Molecular dynamics calculations restrained by NMR-data input are usually employed in conjunction to generate glycosidic bond dihedral angles. Glycosaminoglycans (GAGs) are a special class of sulfated polysaccharides extensively studied worldwide. Besides regulating innumerous physiological processes, these glycans are also widely explored in the global market as either clinical or nutraceutical agents. The conformational aspects of GAGs are key regulators to the quality of interactions with the functional proteins involved in biological events. This report discusses the solution conformation of each GAG type analyzed by one or more of the above-mentioned methods.

  8. Conformal mapping of rectangular heptagons

    SciTech Connect

    Bogatyrev, Andrei B

    2012-12-31

    A new effective approach to calculating the direct and inverse conformal mapping of rectangular polygons onto a half-plane is put forward; it is based on the use of Riemann theta functions. Bibliography: 14 titles.

  9. Conformal invariance for Wilson actions

    NASA Astrophysics Data System (ADS)

    Sonoda, H.

    2017-08-01

    We discuss the realization of conformal invariance for Wilson actions using the formalism of the exact renormalization group. This subject has been studied extensively in the recent works of O. J. Rosten. The main purpose of this paper is to reformulate Rosten's formulas for conformal transformations using a method developed earlier for the realization of any continuous symmetry in the exact renormalization group formalism. The merit of the reformulation is simplicity and transparency via the consistent use of equation-of-motion operators. We derive equations that imply the invariance of the Wilson action under infinitesimal conformal transformations which are non-linearly realized but form a closed conformal algebra. The best effort has been made to make the paper self-contained; ample background on the formalism is provided.

  10. Lattice Simulations and Infrared Conformality

    DOE PAGES

    Appelquist, Thomas; Fleming, George T.; Lin, Meifeng; ...

    2011-09-01

    We examine several recent lattice-simulation data sets, asking whether they are consistent with infrared conformality. We observe, in particular, that for an SU(3) gauge theory with 12 Dirac fermions in the fundamental representation, recent simulation data can be described assuming infrared conformality. Lattice simulations include a fermion mass m which is then extrapolated to zero, and we note that this data can be fit by a small-m expansion, allowing a controlled extrapolation. We also note that the conformal hypothesis does not work well for two theories that are known or expected to be confining and chirally broken, and that itmore » does work well for another theory expected to be infrared conformal.« less

  11. Conformity Adequacy Review: Region 5

    EPA Pesticide Factsheets

    Resources are for air quality and transportation government and community leaders. Information on the conformity SIP adequacy/inadequacy of state implementation plans (SIPs) in EPA Region 5 (IL, IN, MI, OH, WI) is provided here.

  12. CONFORMANCE IMPROVEMENT USING GELS

    SciTech Connect

    Randall S. Seright

    2004-09-30

    This report describes work performed during the third and final year of the project, ''Conformance Improvement Using Gels.'' Corefloods revealed throughput dependencies of permeability reduction by polymers and gels that were much more prolonged during oil flow than water flow. This behavior was explained using simple mobility ratio arguments. A model was developed that quantitatively fits the results and predicts ''clean up'' times for oil productivity when production wells are returned to service after application of a polymer or gel treatment. X-ray computed microtomography studies of gels in strongly water-wet Berea sandstone and strongly oil-wet porous polyethylene suggested that oil penetration through gel-filled pores occurs by a gel-dehydration mechanism, rather than gel-ripping or gel-displacement mechanisms. In contrast, analysis of data from the University of Kansas suggests that the gel-ripping or displacement mechanisms are more important in more permeable, strongly water-wet sandpacks. These findings help to explain why aqueous gels can reduce permeability to water more than to oil under different conditions. Since cement is the most commonly used material for water shutoff, we considered when gels are preferred over cements. Our analysis and experimental results indicated that cement cannot be expected to completely fill (top to bottom) a vertical fracture of any width, except near the wellbore. For vertical fractures with apertures less than 4 mm, the cement slurry will simply not penetrate very far into the fracture. For vertical fractures with apertures greater than 4 mm, the slurry may penetrate a substantial distance into the bottom part of the fracture. However, except near the wellbore, the upper part of the fracture will remain open due to gravity segregation. We compared various approaches to plugging fractures using gels, including (1) varying polymer content, (2) varying placement (extrusion) rate, (3) using partially formed gels, (4

  13. CONFORMANCE IMPROVEMENT USING GELS

    SciTech Connect

    Randall S. Seright

    2004-03-01

    This technical progress report describes work performed from September 1, 2003, through February 29, 2004, for the project, ''Conformance Improvement Using Gels.'' We examined the properties of several ''partially formed'' gels that were formulated with a combination of high and low molecular weight HPAM polymers. After placement in 4-mm-wide fractures, these gels required about 25 psi/ft for brine to breach the gel (the best performance to date in fractures this wide). After this breach, stabilized residual resistance factors decreased significantly with increased flow rate. Also, residual resistance factors were up to 9 times greater for water than for oil. Nevertheless, permeability reduction factors were substantial for both water and oil flow. Gel with 2.5% chopped fiberglass effectively plugged 4-mm-wide fractures if a 0.5-mm-wide constriction was present. The ability to screen-out at a constriction appears crucial for particulate incorporation to be useful in plugging fractures. In addition to fiberglass, we examined incorporation of polypropylene fibers into gels. Once dispersed in brine or gelant, the polypropylene fibers exhibited the least gravity segregation of any particulate that we have tested to date. In fractures with widths of at least 2 mm, 24-hr-old gels (0.5% high molecular weight HPAM) with 0.5% fiber did not exhibit progressive plugging during placement and showed extrusion pressure gradients similar to those of gels without the fiber. The presence of the fiber roughly doubled the gel's resistance to first breach by brine flow. The breaching pressure gradients were not as large as for gels made with high and low molecular weight polymers (mentioned above). However, their material requirements and costs (i.e., polymer and/or particulate concentrations) were substantially lower than for those gels. A partially formed gel made with 0.5% HPAM did not enter a 0.052-mm-wide fracture when applying a pressure gradient of 65 psi/ft. This result

  14. Scale invariance vs conformal invariance

    NASA Astrophysics Data System (ADS)

    Nakayama, Yu

    2015-03-01

    In this review article, we discuss the distinction and possible equivalence between scale invariance and conformal invariance in relativistic quantum field theories. Under some technical assumptions, we can prove that scale invariant quantum field theories in d = 2 space-time dimensions necessarily possess the enhanced conformal symmetry. The use of the conformal symmetry is well appreciated in the literature, but the fact that all the scale invariant phenomena in d = 2 space-time dimensions enjoy the conformal property relies on the deep structure of the renormalization group. The outstanding question is whether this feature is specific to d = 2 space-time dimensions or it holds in higher dimensions, too. As of January 2014, our consensus is that there is no known example of scale invariant but non-conformal field theories in d = 4 space-time dimensions under the assumptions of (1) unitarity, (2) Poincaré invariance (causality), (3) discrete spectrum in scaling dimensions, (4) existence of scale current and (5) unbroken scale invariance in the vacuum. We have a perturbative proof of the enhancement of conformal invariance from scale invariance based on the higher dimensional analogue of Zamolodchikov's c-theorem, but the non-perturbative proof is yet to come. As a reference we have tried to collect as many interesting examples of scale invariance in relativistic quantum field theories as possible in this article. We give a complementary holographic argument based on the energy-condition of the gravitational system and the space-time diffeomorphism in order to support the claim of the symmetry enhancement. We believe that the possible enhancement of conformal invariance from scale invariance reveals the sublime nature of the renormalization group and space-time with holography. This review is based on a lecture note on scale invariance vs conformal invariance, on which the author gave lectures at Taiwan Central University for the 5th Taiwan School on Strings and

  15. Conformal anomalies and gravitational waves

    NASA Astrophysics Data System (ADS)

    Meissner, Krzysztof A.; Nicolai, Hermann

    2017-09-01

    We argue that the presence of conformal anomalies in gravitational theories can lead to observable modifications to Einstein's equations via the induced anomalous effective actions, whose non-localities can overwhelm the smallness of the Planck scale. The fact that no such effects have been seen in recent cosmological or gravitational wave observations therefore imposes strong restrictions on the field content of possible extensions of Einstein's theory: all viable theories should have vanishing conformal anomalies. We then show that a complete cancellation of conformal anomalies in D = 4 for both the C2 invariant and the Euler (Gauss-Bonnet) invariant E4 can only be achieved for N-extended supergravity multiplets with N ⩾ 5, as well as for M theory compactified to four dimensions. Although there remain open questions, in particular concerning the true significance of conformal anomalies in non-conformal theories, as well as their possible gauge dependence for spin s ⩾3/2, these cancellations suggest a hidden conformal structure of unknown type in these theories.

  16. Reconnaissance Invariante des Formes avec le Filtre de Fourier-Mellin et un Reseau Neuronique

    NASA Astrophysics Data System (ADS)

    Lejeune, Claude

    Le filtre de Fourier-Mellin est applique a un ensemble d'objets pour generer des vecteurs invariants sous translation, rotation et changement d'echelle. C'est la premiere methode permettant d'obtenir ces trois invariants simultanement. Le calcul des vecteurs invariants est fait numeriquement et optiquement. Les vecteurs ainsi obtenus sont utilises comme entrees dans un reseau neuronique backpropagation pour faire la classification des prototypes qui lui sont presentes. Les dimensions des vecteurs invariants sont tres petites par rapport aux objets d'entree et permettent d'utiliser un reseau possedant un nombre restreint de connexions. Il devient possible d'entrai ner le reseau dans des temps relativement courts sur un ordinateur du type PC. Une fois le reseau entrai ne, nous lui presentons des vecteurs invariants provenant d'objets se retrouvant dans l'ensemble d'entrai nement mais ayant subi des rotations et des changements d'echelle. Ce nouveau groupe represente l'ensemble de rappel. La performance de la methode est tres bonne avec des taux de succes superieurs a 85%.

  17. Association de neuroleptiques atypiques avec les anticonvulsivants et syndrome malin (à propos de deux cas)

    PubMed Central

    Nabih, Fadoua Oueriagli; Benali, Abdeslam; adali, Imane; Manoudi, Fatiha; Asri, Fatima

    2014-01-01

    Le syndrome malin des neuroleptiques (SMN) est une complication rare mais grave du traitement par les neuroleptiques, pouvant engager le pronostic vital. Les auteurs rapportent deux observations, la première d'une jeune patiente de 18 ans, suivie pour une épilepsie partielle temporale, sous carbamazépine (800mg/jour) depuis 13 ans, et qui a développé un SMN après introduction d'amisulpride (600 mg/jour). La deuxième observation d'un jeune patient de 28 ans sous valproate sodium (750mg/jour) depuis 10 ans et qui a présenté un SMN après association d'olanzapine (20mg/jour). Les cliniciens doivent être vigilants par rapport au risque d'induction d'un SMN après introduction de neuroleptiques atypiques chez des patients traités pendant une longue durée avec des anticonvulsivants. PMID:25422695

  18. Pneumopathie grave avec atteinte bronchique compliquant une varicelle chez un adulte immunocompétent

    PubMed Central

    Serghini, Issam; Chkoura, Khalid; Hjira, Nawfal; Zoubir, Mohamed; Lalaoui; Boughalem, Mohamed

    2014-01-01

    La varicelle est une infection virale cosmopolite, très contagieuse, due au virus varicelle-zona (VZV) et caractérisée par de la fièvre et une éruption papulo-vésiculeuse prurigineuse. L'incidence de la varicelle a significativement augmenté dans les dernières décennies en Europe et aux États-Unis. Chez l'enfant, la varicelle est une infection habituellement bénigne. Chez l'adulte, son évolution peut être émaillée de complications. La pneumonie varicelleuse est la plus fréquente des complications graves de la varicelle chez l'adulte, avec une incidence estimée de 16 à 33% et une mortalité pouvant atteindre 20%. Nous rapportons un cas de varicelle compliquée d'une pneumopathie hypoxémiante. L'examen endoscopique bronchique met en évidence des lésions vésiculeuses de la muqueuse bronchique. Sous traitement antiviral, l’évolution est favorable. PMID:25829973

  19. Takiff superalgebras and conformal field theory

    NASA Astrophysics Data System (ADS)

    Babichenko, Andrei; Ridout, David

    2013-03-01

    A class of non-semisimple extensions of Lie superalgebras is studied. They are obtained by adjoining to the superalgebra its adjoint representation as an Abelian ideal. When the superalgebra is of affine Kac-Moody type, a generalization of Sugawara’s construction is shown to give rise to a copy of the Virasoro algebra and so, presumably, to a conformal field theory. Evidence for this is detailed for the extension of the affinization of the superalgebra \\mathfrak {gl} ( 1 \\vert 1): its highest weight irreducible modules are classified using spectral flow, the irreducible supercharacters are computed and a continuum version of the Verlinde formula is verified to give non-negative integer structure coefficients. Interpreting these coefficients as those of the Grothendieck ring of fusion, partial results on the true fusion ring and its indecomposable structures are deduced.

  20. Free □ k scalar conformal field theory

    NASA Astrophysics Data System (ADS)

    Brust, Christopher; Hinterbichler, Kurt

    2017-02-01

    We consider the generalizations of the free U( N ) and O( N ) scalar conformal field theories to actions with higher powers of the Laplacian □ k , in general dimension d. We study the spectra, Verma modules, anomalies and OPE of these theories. We argue that in certain d and k, the spectrum contains zero norm operators which are both primary and descendant, as well as extension operators which are neither primary nor descendant. In addition, we argue that in even dimensions d ≤ 2 k, there are well-defined operator algebras which are related to the □ k theories and are novel in that they have a finite number of single-trace states.

  1. Metal complexes and metalloproteases: targeting conformational diseases.

    PubMed

    Grasso, Giuseppe; Bonnet, Sylvestre

    2014-08-01

    In recent years many metalloproteases (MPs) have been shown to play important roles in the development of various pathological conditions. Although most of the literature is focused on matrix MPs (MMPs), many other MPs have been demonstrated to be involved in the degradation of peptides or proteins whose accumulation and dyshomeostasis are considered as being responsible for the development of conformational diseases, i.e., diseases where non-native protein conformations lead to protein aggregation. It seems clear that, at least in principle, it must be possible to control the levels of many aggregation-prone proteins not only by reducing their production, but also by enhancing their catabolism. Metal complexes that can perform this function were designed and tested according to at least two different strategies: (i) intervening on the endogenous MPs by directly or indirectly modulating their activity; (ii) acting as artificial MPs, replacing or synergistically functioning with endogenous MPs. These two different bioinorganic approaches are widely represented in the current literature and the aim of this review is to rationally organize and discuss both of them so as to give a critical insight into these approaches and highlighting their limitations and future perspectives.

  2. Thermality of eigenstates in conformal field theories

    NASA Astrophysics Data System (ADS)

    Basu, Pallab; Das, Diptarka; Datta, Shouvik; Pal, Sridip

    2017-08-01

    The eigenstate thermalization hypothesis (ETH) provides a way to understand how an isolated quantum mechanical system can be approximated by a thermal density matrix. We find a class of operators in (1+1)-dimensional conformal field theories, consisting of quasiprimaries of the identity module, which satisfy the hypothesis only at the leading order in large central charge. In the context of subsystem ETH, this plays a role in the deviation of the reduced density matrices, corresponding to a finite energy density eigenstate from its hypothesized thermal approximation. The universal deviation in terms of the square of the trace-square distance goes as the eighth power of the subsystem fraction and is suppressed by powers of inverse central charge (c ). Furthermore, the nonuniversal deviations from subsystem ETH are found to be proportional to the heavy-light-heavy structure constants which are typically exponentially suppressed in √{h /c }, where h is the conformal scaling dimension of the finite energy density state. We also examine the effects of the leading finite-size corrections.

  3. CONFORMANCE IMPROVEMENT USING GELS

    SciTech Connect

    Randall S. Seright

    2003-09-01

    This report describes work performed during the second year of the project, ''Conformance Improvement Using Gels.'' The project has two objectives. The first objective is to identify gel compositions and conditions that substantially reduce flow through fractures that allow direct channeling between wells, while leaving secondary fractures open so that high fluid injection and production rates can be maintained. The second objective is to optimize treatments in fractured production wells, where the gel must reduce permeability to water much more than that to oil. Pore-level images from X-ray computed microtomography were re-examined for Berea sandstone and porous polyethylene. This analysis suggests that oil penetration through gel-filled pores occurs by a gel-dehydration mechanism, rather than a gel-ripping mechanism. This finding helps to explain why aqueous gels can reduce permeability to water more than to oil. We analyzed a Cr(III)-acetate-HPAM gel treatment in a production well in the Arbuckle formation. The availability of accurate pressure data before, during, and after the treatment was critical for the analysis. After the gel treatment, water productivity was fairly constant at about 20% of the pre-treatment value. However, oil productivity was stimulated by a factor of 18 immediately after the treatment. During the six months after the treatment, oil productivity gradually decreased to approach the pre-treatment value. To explain this behavior, we proposed that the fracture area open to oil flow was increased substantially by the gel treatment, followed by a gradual closing of the fractures during subsequent production. For a conventional Cr(III)-acetate-HPAM gel, the delay between gelant preparation and injection into a fracture impacts the placement, leakoff, and permeability reduction behavior. Formulations placed as partially formed gels showed relatively low pressure gradients during placement, and yet substantially reduced the flow capacity of

  4. To conform or not to conform: spontaneous conformity diminishes the sensitivity to monetary outcomes.

    PubMed

    Yu, Rongjun; Sun, Sai

    2013-01-01

    When people have different opinions in a group, they often adjust their own attitudes and behaviors to match the group opinion, known as social conformity. The affiliation account of normative conformity states that people conform to norms in order to 'fit in', whereas the accuracy account of informative conformity posits that the motive to learn from others produces herding. Here, we test another possibility that following the crowd reduces the experienced negative emotion when the group decision turns out to be a bad one. Using event related potential (ERP) combined with a novel group gambling task, we found that participants were more likely to choose the option that was predominately chosen by other players in previous trials, although there was little explicit normative pressure at the decision stage and group choices were not informative. When individuals' choices were different from others, the feedback related negativity (FRN), an ERP component sensitive to losses and errors, was enhanced, suggesting that being independent is aversive. At the outcome stage, the losses minus wins FRN effect was significantly reduced following conformity choices than following independent choices. Analyses of the P300 revealed similar patterns both in the response and outcome period. Our study suggests that social conformity serves as an emotional buffer that protects individuals from experiencing strong negative emotion when the outcomes are bad.

  5. To Conform or Not to Conform: Spontaneous Conformity Diminishes the Sensitivity to Monetary Outcomes

    PubMed Central

    2013-01-01

    When people have different opinions in a group, they often adjust their own attitudes and behaviors to match the group opinion, known as social conformity. The affiliation account of normative conformity states that people conform to norms in order to ‘fit in’, whereas the accuracy account of informative conformity posits that the motive to learn from others produces herding. Here, we test another possibility that following the crowd reduces the experienced negative emotion when the group decision turns out to be a bad one. Using event related potential (ERP) combined with a novel group gambling task, we found that participants were more likely to choose the option that was predominately chosen by other players in previous trials, although there was little explicit normative pressure at the decision stage and group choices were not informative. When individuals' choices were different from others, the feedback related negativity (FRN), an ERP component sensitive to losses and errors, was enhanced, suggesting that being independent is aversive. At the outcome stage, the losses minus wins FRN effect was significantly reduced following conformity choices than following independent choices. Analyses of the P300 revealed similar patterns both in the response and outcome period. Our study suggests that social conformity serves as an emotional buffer that protects individuals from experiencing strong negative emotion when the outcomes are bad. PMID:23691242

  6. Elements and modulation of functional dynamics.

    PubMed

    Gibbs, Alan C

    2014-10-09

    The existing structure-function paradigm of drug discovery has been evolving toward the essential incorporation of dynamics data. This new functional dynamics paradigm emphasizes conformational entropy as a driving force of protein function and intermolecular recognition. Conformational dynamics (a proxy of conformational entropy) impacts the degree of protein (dis)order and the constitution of the conformational ensemble, the mechanisms of allostery and drug resistance, and the free energy of ligand binding. Specific protein and ligand conformations facilitate favorable, reciprocal interactions. The number of protein and ligand conformers that exhibit favorable binding interactions will vary from system to system. All binding scenarios can modulate protein dynamics by various levels of enthalpic and entropic contribution, with significant influence on the functional dynamics of the system. Analysis and consideration of resulting changes of activity, signaling, catalysis, and subsequent phenotypic outcome are powerful motivations in the drug design process.

  7. Microwave Spectroscopy of Alkaloids: the Conformational Shapes of Nicotine

    NASA Astrophysics Data System (ADS)

    Grabow, Jens-Uwe; Mata, S.; López, J. C.; Peńa, I.; Cabezas, C.; Blanco, S.; Alonso, J. L.

    2010-06-01

    Nicotinoid alkaloids consist of two ring systems connected via a C-C σ-bond: Joining pyridine either with a (substituted) pyrrolidine or piperidine ring system, pyrrolidinic or piperidinic nicotinoids are formed. Nicotine itself, consisting of pyridine and N-methylpyrrolidine, is the prototype pyrrolidinic nicotinoid. Its coupled heteoaromatic and heteroaliphatic ring systems exhibit three sites that allow for conformational flexibility: (I) puckering of the pyrrolidine ring (Eq./Ax. positions of the pyridine), (II) inversion of the N-methyl group (Eq./Ax. positions of the hydrogen), and (III) relative orientation of the two rings (Syn-Anti). Two conformations of nicotine have been observed using the In-phase/quadrature-phase-Modulation Passage-Acquired-Coherence Technique (IMPACT) Fourier Transform Microwave (FTMW) spectrometer in Valladolid. The preferred conformations are characterized by an equatorial (Eq.) pyridine moiety and equatorial (Eq.) N-CH_3 stereochemistry. The planes of two rings are almost perpendicular with respect to each other while exhibiting two low energy conformations, Syn and Anti, that differ by a 180° rotation about the C-C σ-bond. The Eq.-Eq. conformational preference is likely due to a weak hydrogen bond interaction between the nitrogen lone pair at the N-methylpyrroline and the closest hydrogen in pyridine. Supporting quantum-chemical calculations are also provided. Lavrich, R. J.; Suenram, R. D.; Plusquellic, D. F.; Davis, S. 58th International Symposium on Molecular Spectroscopy, Columbus, OH 2003, RH13.

  8. HAMP domain conformers that propagate opposite signals in bacterial chemoreceptors.

    PubMed

    Airola, Michael V; Sukomon, Nattakan; Samanta, Dipanjan; Borbat, Peter P; Freed, Jack H; Watts, Kylie J; Crane, Brian R

    2013-01-01

    HAMP domains are signal relay modules in >26,000 receptors of bacteria, eukaryotes, and archaea that mediate processes involved in chemotaxis, pathogenesis, and biofilm formation. We identify two HAMP conformations distinguished by a four- to two-helix packing transition at the C-termini that send opposing signals in bacterial chemoreceptors. Crystal structures of signal-locked mutants establish the observed structure-to-function relationships. Pulsed dipolar electron spin resonance spectroscopy of spin-labeled soluble receptors active in cells verify that the crystallographically defined HAMP conformers are maintained in the receptors and influence the structure and activity of downstream domains accordingly. Mutation of HR2, a key residue for setting the HAMP conformation and generating an inhibitory signal, shifts HAMP structure and receptor output to an activating state. Another HR2 variant displays an inverted response with respect to ligand and demonstrates the fine energetic balance between "on" and "off" conformers. A DExG motif found in membrane proximal HAMP domains is shown to be critical for responses to extracellular ligand. Our findings directly correlate in vivo signaling with HAMP structure, stability, and dynamics to establish a comprehensive model for HAMP-mediated signal relay that consolidates existing views on how conformational signals propagate in receptors. Moreover, we have developed a rational means to manipulate HAMP structure and function that may prove useful in the engineering of bacterial taxis responses.

  9. Group Cohesiveness, Deviation, Stress, and Conformity

    DTIC Science & Technology

    1993-08-11

    assessed pre- and post- conformity pressure (see Appendix VIII). Components of group influences , Offer of Reward for Conformity (ORC), and Threat of...Cohesiveness Pressures to Uniformity Studies . . . . Evidence Supporting a Group Cohesiveness- Conformity Relationship . . . . . . Evidence Supporting a...Response and Conformity Pressure . . . . Stress and ORC and TPN . . . . . . . . TPN and Space Crews . . . . . . . . . . Summary of Group

  10. Treatment planning for conformal proton radiation therapy.

    PubMed

    Bussière, Mark R; Adams, Judith A

    2003-10-01

    Clinical results from various trials have demonstrated the viability of protons in radiation therapy and radiosurgery. This has motivated a few large medical centers to design and build expensive hospital based proton facilities based proton facilities (current cost estimates for a proton facility is around 100 million US dollars). Until this development proton therapy was done using retrofitted equipment originally designed for nuclear experiments. There are presently only three active proton therapy centers in the United States, 22 worldwide. However, more centers are under construction and being proposed in the US and abroad. The important difference between proton and x-ray therapy is in the dose distribution. X-rays deposit most of their dose at shallow depths of a few centimeters with a gradual decay with depth in the patient. Protons deliver most of their dose in the Bragg peak, which can be delivered at most clinically required depths followed by a sharp fall-off. This sharp falloff makes protons sensitive to variations in treatment depths within patients. Treatment planning incorporates all the knowledge of protons into a process, which allows patients to be treated accurately and reliably. This process includes patient immobilization, imaging, targeting, and modeling of planned dose distributions. Although the principles are similar to x-ray therapy some significant differences exist in the planning process, which described in this paper. Target dose conformality has recently taken on much momentum with the advent of intensity modulated radiation therapy (IMRT) with photon beams. Proton treatments provide a viable alternative to IMRT because they are inherently conformal avoiding normal tissue while irradiating the intended targets. Proton therapy will soon bring conformality to a new high with the development of intensity modulated proton therapy (IMPT). Future challenges include keeping the cost down, increasing access to conventional proton therapy as

  11. Self-Dual Conformal Gravity

    NASA Astrophysics Data System (ADS)

    Dunajski, Maciej; Tod, Paul

    2014-10-01

    We find necessary and sufficient conditions for a Riemannian four-dimensional manifold ( M, g) with anti-self-dual Weyl tensor to be locally conformal to a Ricci-flat manifold. These conditions are expressed as the vanishing of scalar and tensor conformal invariants. The invariants obstruct the existence of parallel sections of a certain connection on a complex rank-four vector bundle over M. They provide a natural generalisation of the Bach tensor which vanishes identically for anti-self-dual conformal structures. We use the obstructions to demonstrate that LeBrun's anti-self-dual metrics on connected sums of s are not conformally Ricci-flat on any open set. We analyze both Riemannian and neutral signature metrics. In the latter case we find all anti-self-dual metrics with a parallel real spinor which are locally conformal to Einstein metrics with non-zero cosmological constant. These metrics admit a hyper-surface orthogonal null Killing vector and thus give rise to projective structures on the space of β-surfaces.

  12. A proposed bioactive conformation of Peptide T

    NASA Astrophysics Data System (ADS)

    Centeno, Nuria B.; Perez, Juan J.

    1998-01-01

    The conformational profiles of Peptide T, (5-8)Peptide T, [Abu5](4-8)Peptide T and (4-8)Peptide T were computed independently to assess the geometrical characteristics of the bioactive conformation of Peptide T. The conformational profiles of the peptides were computed within the molecular mechanics framework using an effective dielectric constant of 80. The conformational space was thoroughly sampled using an iterative simulated annealing protocol. The bioactive conformation was assessed by pairwise cross comparisons of each of the unique low energy conformations found for each of the different analogs studied. After a putative bioactive conformation was selected, in order to further validate our hypothesis the conformational profile of the potent compound cyclo(Thr-Thr-Asn-Tyr-Thr-Asp) was computed and the putative bioactive conformation was found. The conformation exhibits a pseudo β-turn involving the side chain of Thr5 and the carbonyl oxygen of Tyr7 forming a C12 ring.

  13. Partial masslessness and conformal gravity

    NASA Astrophysics Data System (ADS)

    Deser, S.; Joung, E.; Waldron, A.

    2013-05-01

    We use conformal, but ghostful, Weyl gravity to study its ghost-free, second derivative, partially massless (PM) spin-2 component in the presence of Einstein gravity with positive cosmological constant. Specifically, we consider both gravitational- and self-interactions of PM via the fully nonlinear factorization of conformal gravity’s Bach tensor into Einstein times Schouten operators. We find that extending PM beyond linear order suffers from familiar higher spin consistency obstructions: it propagates only in Einstein backgrounds, and the conformal gravity route generates only the usual safe, Noether, cubic order vertices. This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical devoted to ‘Higher spin theories and holography’.

  14. Quantum cosmology and conformal invariance.

    PubMed

    Pioline, B; Waldron, A

    2003-01-24

    According to Belinsky, Khalatnikov, and Lifshitz, gravity near a spacelike singularity reduces to a set of decoupled one-dimensional mechanical models at each point in space. We point out that these models fall into a class of conformal mechanical models first introduced by de Alfaro, Fubini, and Furlan (DFF). The deformation used by DFF to render the spectrum discrete corresponds to a negative cosmological constant. The wave function of the Universe is the zero-energy eigenmode of the Hamiltonian, or the spherical vector of the representation of the conformal group SO(1,2). A new class of conformal quantum mechanical models with enhanced ADE symmetry is constructed, based on the quantization of nilpotent coadjoint orbits.

  15. Toward Understanding the Conformal Gravity

    NASA Astrophysics Data System (ADS)

    Berezin, V. A.; Dokuchaev, V. I.; Eroshenko, Yu. N.

    2017-03-01

    We constructed the conformally invariant model for scalar particle creation induced by strong gravitational fields. Starting from the usual hydrodynamic description of the particle motion written in the Eulerian coordinates, we substituted the particle number conservation law (which enters the formalism) by the particle creation law, proportional to the square of the Weyl tensor, following the famous result by Ya. B. Zel'dovich and A. A. Starobinsky. Then, demanding the conformal invariance of the whole dynamical system, we have got both the Weyl-conformal gravity and the Einstein-Hilbert dilaton gravity action integral. Thus, we obtained something like the induced gravity suggested first by A. D. Sakharov. It is shown that the resulting system is self-consistent.

  16. Toward Understanding the Conformal Gravity

    NASA Astrophysics Data System (ADS)

    Berezin, V. A.; Dokuchaev, V. I.; Eroshenko, Yu. N.

    2017-03-01

    We constructed the conformally invariant model for scalar particle creation induced by strong gravitational fields. Starting from the usual hydrodynamic description of the particle motion written in the Eulerian coordinates, we substituted the particle number conservation law (which enters the formalism) by the particle creation law, proportional to the square of the Weyl tensor, following the famous result by Ya. B. Zel'dovich and A. A. Starobinsky. Then, demanding the conformal invariance of the whole dynamical system, we have got both the Weyl-conformal gravity and the Einstein-Hilbert dilaton gravity action integral. Thus, we obtained something like the induced gravity suggested first by A. D. Sakharov. It is shown that the resulting system is self-consistent.

  17. Conformal semi-slant submersions

    NASA Astrophysics Data System (ADS)

    Akyol, Mehmet Akif

    Park and Prasad [Semi-slant submersions, Bull. Korean Math. Soc. 50(3) (2013) 951-962.] defined and studied semi-slant submersions as a generalization of slant submersions, semi-invariant submersions, anti-invariant submersions. As a generalization of semi-slant submersions, we introduce conformal semi-slant submersions and study the new submersions from almost Hermitian manifolds onto Riemannian manifolds. We study the integrability of ditributions and the geometry of leaves of a conformal submersion. Moreover, we show that there are certain product structures on base manifold of a conformal semi-slant submersion. We also obtain totally geodesic conditions for such maps. Finally, we give lots of examples.

  18. Universality class in conformal inflation

    SciTech Connect

    Kallosh, Renata; Linde, Andrei E-mail: alinde@stanford.edu

    2013-07-01

    We develop a new class of chaotic inflation models with spontaneously broken conformal invariance. Observational consequences of a broad class of such models are stable with respect to strong deformations of the scalar potential. This universality is a critical phenomenon near the point of enhanced symmetry, SO(1,1), in case of conformal inflation. It appears because of the exponential stretching of the moduli space and the resulting exponential flattening of scalar potentials upon switching from the Jordan frame to the Einstein frame in this class of models. This result resembles stretching and flattening of inhomogeneities during inflationary expansion. It has a simple interpretation in terms of velocity versus rapidity near the Kähler cone in the moduli space, similar to the light cone of special theory of relativity. This effect makes inflation possible even in the models with very steep potentials. We describe conformal and superconformal versions of this cosmological attractor mechanism.

  19. Cyclic AMP Analog Blocks Kinase Activation by Stabilizing Inactive Conformation: Conformational Selection Highlights a New Concept in Allosteric Inhibitor Design*

    PubMed Central

    Badireddy, Suguna; Yunfeng, Gao; Ritchie, Mark; Akamine, Pearl; Wu, Jian; Kim, Choel W.; Taylor, Susan S.; Qingsong, Lin; Swaminathan, Kunchithapadam; Anand, Ganesh S.

    2011-01-01

    The regulatory (R) subunit of protein kinase A serves to modulate the activity of protein kinase A in a cAMP-dependent manner and exists in two distinct and structurally dissimilar, end point cAMP-bound “B” and C-subunit-bound “H”-conformations. Here we report mechanistic details of cAMP action as yet unknown through a unique approach combining x-ray crystallography with structural proteomics approaches, amide hydrogen/deuterium exchange and ion mobility mass spectrometry, applied to the study of a stereospecific cAMP phosphorothioate analog and antagonist((Rp)-cAMPS). X-ray crystallography shows cAMP-bound R-subunit in the B form but surprisingly the antagonist Rp-cAMPS-bound R-subunit crystallized in the H conformation, which was previously assumed to be induced only by C-subunit-binding. Apo R-subunit crystallized in the B form as well but amide exchange mass spectrometry showed large differences between apo, agonist and antagonist-bound states of the R-subunit. Further ion mobility reveals the apo R-subunit as an ensemble of multiple conformations with collisional cross-sectional areas spanning both the agonist and antagonist-bound states. Thus contrary to earlier studies that explained the basis for cAMP action through “induced fit” alone, we report evidence for conformational selection, where the ligand-free apo form of the R-subunit exists as an ensemble of both B and H conformations. Although cAMP preferentially binds the B conformation, Rp-cAMPS interestingly binds the H conformation. This reveals the unique importance of the equatorial oxygen of the cyclic phosphate in mediating conformational transitions from H to B forms highlighting a novel approach for rational structure-based drug design. Ideal inhibitors such as Rp-cAMPS are those that preferentially “select” inactive conformations of target proteins by satisfying all “binding” constraints alone without inducing conformational changes necessary for activation. PMID:21081668

  20. Cyclic AMP analog blocks kinase activation by stabilizing inactive conformation: conformational selection highlights a new concept in allosteric inhibitor design.

    PubMed

    Badireddy, Suguna; Yunfeng, Gao; Ritchie, Mark; Akamine, Pearl; Wu, Jian; Kim, Choel W; Taylor, Susan S; Qingsong, Lin; Swaminathan, Kunchithapadam; Anand, Ganesh S

    2011-03-01

    The regulatory (R) subunit of protein kinase A serves to modulate the activity of protein kinase A in a cAMP-dependent manner and exists in two distinct and structurally dissimilar, end point cAMP-bound "B" and C-subunit-bound "H"-conformations. Here we report mechanistic details of cAMP action as yet unknown through a unique approach combining x-ray crystallography with structural proteomics approaches, amide hydrogen/deuterium exchange and ion mobility mass spectrometry, applied to the study of a stereospecific cAMP phosphorothioate analog and antagonist((Rp)-cAMPS). X-ray crystallography shows cAMP-bound R-subunit in the B form but surprisingly the antagonist Rp-cAMPS-bound R-subunit crystallized in the H conformation, which was previously assumed to be induced only by C-subunit-binding. Apo R-subunit crystallized in the B form as well but amide exchange mass spectrometry showed large differences between apo, agonist and antagonist-bound states of the R-subunit. Further ion mobility reveals the apo R-subunit as an ensemble of multiple conformations with collisional cross-sectional areas spanning both the agonist and antagonist-bound states. Thus contrary to earlier studies that explained the basis for cAMP action through "induced fit" alone, we report evidence for conformational selection, where the ligand-free apo form of the R-subunit exists as an ensemble of both B and H conformations. Although cAMP preferentially binds the B conformation, Rp-cAMPS interestingly binds the H conformation. This reveals the unique importance of the equatorial oxygen of the cyclic phosphate in mediating conformational transitions from H to B forms highlighting a novel approach for rational structure-based drug design. Ideal inhibitors such as Rp-cAMPS are those that preferentially "select" inactive conformations of target proteins by satisfying all "binding" constraints alone without inducing conformational changes necessary for activation.

  1. Conformal deposition of LPCVD TEOS

    NASA Astrophysics Data System (ADS)

    McCann, Paul; Somasundram, Kumar; Byrne, Stephen; Nevin, Andrew

    2001-09-01

    The step coverage of dielectrics is important for the microelectronics industry and critical to Micro-machined products and High Voltage MEMS drivers. The techniques used to fabricate MEMS structures require void free refill processes and even film deposition along deep trenches to protect against etch chemistries. High voltage drivers used to actuate MEMS devices benefit from dielectric isolation, which reduces the need for large tub formation between devices. It also enables 'system on chip' solutions for MEMs devices and protection against voltage spikes. This paper presents a process developed at Analog Devices Belfast that enables an LPCVD TEOS furnace to perform a highly conformal trench refill without equipment modification. The conformality is over 95% for 20 micrometer deep trenches and maintains a conformality greater than 85% in 50 micrometer deep trenches. This compares with 75% conformality which is considered excellent for 20 micrometer trench refills obtained using previous LPCVD TEOS processing. The process is shown to have benefits in conformality, breakdown voltage, and stress over standard trench fill processes including Ozone TEOS. The densification of the TEOS film has been optimized for electrical parameters using CV and IV techniques, while XPS, FTIR and spectroscopic ellipsometry are used for physical characterization. Stress is a very important parameter for micro-machining and the conformal TEOS has a film stress which is tensile 30 - 40 MPa as deposited and compressive 100 MPa after densification. The breakdown voltage has been measured at 8.5 MV/cm compared to 7.5 - 9 MV/cm for a typical densified TEOS film and the refractive index is 1.456 compared to 1.465 for a thermal oxide. Analog Devices Belfast is part of the Micro-machined Products division and provides SOI and customized SOI for the MEMs and IC market.

  2. Nonlocal gravity: Conformally flat spacetimes

    NASA Astrophysics Data System (ADS)

    Bini, Donato; Mashhoon, Bahram

    2016-04-01

    The field equations of the recent nonlocal generalization of Einstein’s theory of gravitation are presented in a form that is reminiscent of general relativity. The implications of the nonlocal field equations are studied in the case of conformally flat spacetimes. Even in this simple case, the field equations are intractable. Therefore, to gain insight into the nature of these equations, we investigate the structure of nonlocal gravity (NLG) in 2D spacetimes. While any smooth 2D spacetime is conformally flat and satisfies Einstein’s field equations, only a subset containing either a Killing vector or a homothetic Killing vector can satisfy the field equations of NLG.

  3. Social influence: compliance and conformity.

    PubMed

    Cialdini, Robert B; Goldstein, Noah J

    2004-01-01

    This review covers recent developments in the social influence literature, focusing primarily on compliance and conformity research published between 1997 and 2002. The principles and processes underlying a target's susceptibility to outside influences are considered in light of three goals fundamental to rewarding human functioning. Specifically, targets are motivated to form accurate perceptions of reality and react accordingly, to develop and preserve meaningful social relationships, and to maintain a favorable self-concept. Consistent with the current movement in compliance and conformity research, this review emphasizes the ways in which these goals interact with external forces to engender social influence processes that are subtle, indirect, and outside of awareness.

  4. SUSY Unparticle and Conformal Sequestering

    SciTech Connect

    Nakayama, Yu; Nakayama, Yu

    2007-07-17

    We investigate unparticle physics with supersymmetry (SUSY). The SUSY breaking effects due to the gravity mediation induce soft masses for the SUSY unparticles and hence break the conformal invariance. The unparticle physics observable in near future experiments is only consistent if the SUSY breakingeffects from the hidden sector to the standard model sector are dominated by the gauge mediation, or if the SUSY breaking effects to the unparticle sector are sufficiently sequestered. We argue that the natural realization of the latter possibility is the conformal sequestering scenario.

  5. Methods of determining DNA conformation

    SciTech Connect

    Mayes, E.L.

    1994-04-01

    While the basic structure of DNA has been known since 1953, there is still a great void in terms of knowing how DNA interacts with its surroundings. Because the structure of biological molecules determines their function, the conformation of DNA is of prime importance in understanding its role in living organisms. We present two methods of determining some components of DNA`s conformation. One uses atomic force microscopy to determine the dimensions of DNA`s base pairs, and the other seeks to computationally determine the structure of DNA in different chemical environments.

  6. Algebraic orbifold conformal field theories

    PubMed Central

    Xu, Feng

    2000-01-01

    The unitary rational orbifold conformal field theories in the algebraic quantum field theory and subfactor theory framework are formulated. Under general conditions, it is shown that the orbifold of a given unitary rational conformal field theory generates a unitary modular category. Many new unitary modular categories are obtained. It is also shown that the irreducible representations of orbifolds of rank one lattice vertex operator algebras give rise to unitary modular categories and determine the corresponding modular matrices, which has been conjectured for some time. PMID:11106383

  7. Epigenetic Dominance of Prion Conformers

    PubMed Central

    Saijo, Eri; Kang, Hae-Eun; Bian, Jifeng; Bowling, Kristi G.; Browning, Shawn; Kim, Sehun; Hunter, Nora; Telling, Glenn C.

    2013-01-01

    Although they share certain biological properties with nucleic acid based infectious agents, prions, the causative agents of invariably fatal, transmissible neurodegenerative disorders such as bovine spongiform encephalopathy, sheep scrapie, and human Creutzfeldt Jakob disease, propagate by conformational templating of host encoded proteins. Once thought to be unique to these diseases, this mechanism is now recognized as a ubiquitous means of information transfer in biological systems, including other protein misfolding disorders such as those causing Alzheimer's and Parkinson's diseases. To address the poorly understood mechanism by which host prion protein (PrP) primary structures interact with distinct prion conformations to influence pathogenesis, we produced transgenic (Tg) mice expressing different sheep scrapie susceptibility alleles, varying only at a single amino acid at PrP residue 136. Tg mice expressing ovine PrP with alanine (A) at (OvPrP-A136) infected with SSBP/1 scrapie prions propagated a relatively stable (S) prion conformation, which accumulated as punctate aggregates in the brain, and produced prolonged incubation times. In contrast, Tg mice expressing OvPrP with valine (V) at 136 (OvPrP-V136) infected with the same prions developed disease rapidly, and the converted prion was comprised of an unstable (U), diffusely distributed conformer. Infected Tg mice co-expressing both alleles manifested properties consistent with the U conformer, suggesting a dominant effect resulting from exclusive conversion of OvPrP-V136 but not OvPrP-A136. Surprisingly, however, studies with monoclonal antibody (mAb) PRC5, which discriminates OvPrP-A136 from OvPrP-V136, revealed substantial conversion of OvPrP-A136. Moreover, the resulting OvPrP-A136 prion acquired the characteristics of the U conformer. These results, substantiated by in vitro analyses, indicated that co-expression of OvPrP-V136 altered the conversion potential of OvPrP-A136 from the S to the

  8. Dynamical spacetimes in conformal gravity

    NASA Astrophysics Data System (ADS)

    Zhang, Hongsheng; Zhang, Yi; Li, Xin-Zhou

    2017-08-01

    The conformal gravity remarkably boosts our prehension of gravity theories. We find a series of dynamical solutions in the W2-conformal gravity, including generalized Schwarzschild-Friedmann-Robertson-Walker (GSFRW), charged generalized Schwarzschild-Friedmann-Robertson-Walker (CGSFRW), especially rotating Friedmann-Robertson-Walker (RFRW), charged rotating Friedmann-Robertson-Walker (CRFRW), and a dynamical cylindrically symmetric solutions. The RFRW, CRFRW and the dynamical cylindrically symmetric solutions are never found in the Einstein gravity and modified gravities. The GSFRW and CGSFRW solutions take different forms from the corresponding solutions in the Einstein gravity.

  9. Dynamic conformational changes in munc18 prevent syntaxin binding.

    PubMed

    Bar-On, Dana; Nachliel, Esther; Gutman, Menachem; Ashery, Uri

    2011-03-01

    The Sec1/munc18 protein family is essential for vesicle fusion in eukaryotic cells via binding to SNARE proteins. Protein kinase C modulates these interactions by phosphorylating munc18a thereby reducing its affinity to one of the central SNARE members, syntaxin-1a. The established hypothesis is that the reduced affinity of the phosphorylated munc18a to syntaxin-1a is a result of local electrostatic repulsion between the two proteins, which interferes with their compatibility. The current study challenges this paradigm and offers a novel mechanistic explanation by revealing a syntaxin-non-binding conformation of munc18a that is induced by the phosphomimetic mutations. In the present study, using molecular dynamics simulations, we explored the dynamics of the wild-type munc18a versus phosphomimetic mutant munc18a. We focused on the structural changes that occur in the cavity between domains 3a and 1, which serves as the main syntaxin-binding site. The results of the simulations suggest that the free wild-type munc18a exhibits a dynamic equilibrium between several conformations differing in the size of its cavity (the main syntaxin-binding site). The flexibility of the cavity's size might facilitate the binding or unbinding of syntaxin. In silico insertion of phosphomimetic mutations into the munc18a structure induces the formation of a conformation where the syntaxin-binding area is rigid and blocked as a result of interactions between residues located on both sides of the cavity. Therefore, we suggest that the reduced affinity of the phosphomimetic mutant/phosphorylated munc18a is a result of the closed-cavity conformation, which makes syntaxin binding energetically and sterically unfavorable. The current study demonstrates the potential of phosphorylation, an essential biological process, to serve as a driving force for dramatic conformational changes of proteins modulating their affinity to target proteins.

  10. Logarithmic conformal field theory, log-modular tensor categories and modular forms

    NASA Astrophysics Data System (ADS)

    Creutzig, Thomas; Gannon, Terry

    2017-10-01

    The two pillars of rational conformal field theory and rational vertex operator algebras are modularity of characters, and the interpretation of its category of modules as a modular tensor category. Overarching these pillars is the Verlinde formula. In this paper we consider the more general class of logarithmic conformal field theories and C 2-cofinite vertex operator algebras. We suggest logarithmic variants of those pillars and of Verlinde’s formula. We illustrate our ideas with the \

  11. Molecular mechanics conformational analysis of tylosin

    NASA Astrophysics Data System (ADS)

    Ivanov, Petko M.

    1998-01-01

    The conformations of the 16-membered macrolide antibiotic tylosin were studied with molecular mechanics (AMBER∗ force field) including modelling of the effect of the solvent on the conformational preferences (GB/SA). A Monte Carlo conformational search procedure was used for finding the most probable low-energy conformations. The present study provides complementary data to recently reported analysis of the conformations of tylosin based on NMR techniques. A search for the low-energy conformations of protynolide, a 16-membered lactone containing the same aglycone as tylosin, was also carried out, and the results were compared with the observed conformation in the crystal as well as with the most probable conformations of the macrocyclic ring of tylosin. The dependence of the results on force field was also studied by utilizing the MM3 force field. Some particular conformations were computed with the semiempirical molecular orbital methods AM1 and PM3.

  12. Conformal mapping for multiple terminals.

    PubMed

    Wang, Weimin; Ma, Wenying; Wang, Qiang; Ren, Hao

    2016-11-10

    Conformal mapping is an important mathematical tool that can be used to solve various physical and engineering problems in many fields, including electrostatics, fluid mechanics, classical mechanics, and transformation optics. It is an accurate and convenient way to solve problems involving two terminals. However, when faced with problems involving three or more terminals, which are more common in practical applications, existing conformal mapping methods apply assumptions or approximations. A general exact method does not exist for a structure with an arbitrary number of terminals. This study presents a conformal mapping method for multiple terminals. Through an accurate analysis of boundary conditions, additional terminals or boundaries are folded into the inner part of a mapped region. The method is applied to several typical situations, and the calculation process is described for two examples of an electrostatic actuator with three electrodes and of a light beam splitter with three ports. Compared with previously reported results, the solutions for the two examples based on our method are more precise and general. The proposed method is helpful in promoting the application of conformal mapping in analysis of practical problems.

  13. Conformal mapping for multiple terminals

    NASA Astrophysics Data System (ADS)

    Wang, Weimin; Ma, Wenying; Wang, Qiang; Ren, Hao

    2016-11-01

    Conformal mapping is an important mathematical tool that can be used to solve various physical and engineering problems in many fields, including electrostatics, fluid mechanics, classical mechanics, and transformation optics. It is an accurate and convenient way to solve problems involving two terminals. However, when faced with problems involving three or more terminals, which are more common in practical applications, existing conformal mapping methods apply assumptions or approximations. A general exact method does not exist for a structure with an arbitrary number of terminals. This study presents a conformal mapping method for multiple terminals. Through an accurate analysis of boundary conditions, additional terminals or boundaries are folded into the inner part of a mapped region. The method is applied to several typical situations, and the calculation process is described for two examples of an electrostatic actuator with three electrodes and of a light beam splitter with three ports. Compared with previously reported results, the solutions for the two examples based on our method are more precise and general. The proposed method is helpful in promoting the application of conformal mapping in analysis of practical problems.

  14. Correct Representation of Conformational Equilibria.

    ERIC Educational Resources Information Center

    Fulop, F.; And Others

    1983-01-01

    In representing conformational equilibria of compounds having only one chiral center, erroneous formulas showing different antipodes on the two sides of the equilibrium are rare. In contrast, with compounds having two or more chiral centers especially with saturated heterocycles, this erroneous representation occurs frequently in the chemical…

  15. Temperature: Human Regulating, Ants Conforming

    ERIC Educational Resources Information Center

    Clopton, Joe R.

    2007-01-01

    Biological processes speed up as temperature rises. Procedures for demonstrating this with ants traveling on trails, and data gathered by students on the Argentine ant ("Linepithema humile") are presented. The concepts of temperature regulation and conformity are detailed with a focus on the processes rather than on terms that label the organisms.

  16. Conformational analysis of oligomeric flavanoids

    Treesearch

    Jan P. Steynberg; E. Vincent Brandt; Daneel Ferreira; Carin A. Helfer; Wayne L. Mattice; Dominika Gornik; Richard W. Hemingway

    1995-01-01

    The profisetinidins are the most important polyflavanoids of commerce, making up the major constituents of wattle and quebracho tannins. Even within the dimeric profisetinidins, substantial complexity exists because of stereo-, regio-, rotational and conformational isomers. Definition of the stereochemistry of the upper and lower flavan units, the location of the...

  17. Conformation analysis of oligomeric flavanoids

    Treesearch

    Jan P. Steynberg; E. Vincent Brandt; Daneel Ferreira; Carin A. Helfer; Wayne L. Mattice; Dominika Gornik; Richard W. Hemingway

    1995-01-01

    The profisetinidins are the most important polyflavanoids of commerce, making up the major constituents of wattle and quebracho tannins. Within the dimeric profisetinidins, substantial complexity exists because of stereo-, regio, rotational and conformational isomers. Definition of the stereochemistry of the upper and lower flavan units, the location of the...

  18. Parsimony in Protein Conformational Change.

    PubMed

    Chapman, Brynmor K; Davulcu, Omar; Skalicky, Jack J; Brüschweiler, Rafael P; Chapman, Michael S

    2015-07-07

    Protein conformational change is analyzed by finding the minimalist backbone torsion angle rotations that superpose crystal structures within experimental error. Of several approaches for enforcing parsimony during flexible least-squares superposition, an ℓ(1)-norm restraint provided greatest consistency with independent indications of flexibility from nuclear magnetic resonance relaxation dispersion and chemical shift perturbation in arginine kinase and four previously studied systems. Crystallographic cross-validation shows that the dihedral parameterization describes conformational change more accurately than rigid-group approaches. The rotations that superpose the principal elements of structure constitute a small fraction of the raw (φ, ψ) differences that also reflect local conformation and experimental error. Substantial long-range displacements can be mediated by modest dihedral rotations, accommodated even within α helices and β sheets without disruption of hydrogen bonding at the hinges. Consistency between ligand-associated and intrinsic motions (in the unliganded state) implies that induced changes tend to follow low-barrier paths between conformational sub-states that are in intrinsic dynamic equilibrium. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Conformal invariant vacuum nonlinear electrodynamics

    NASA Astrophysics Data System (ADS)

    Denisov, V. I.; Dolgaya, E. E.; Sokolov, V. A.; Denisova, I. P.

    2017-08-01

    In this paper, a general case of conformal invariant vacuum nonlinear electrodynamics is studied. We analyze the consistency of this electrodynamics model with fundamental principles such as causality, unitarity, and the Ellis-Hawking dominant energy condition. Certain features of the electromagnetic waves in this model are investigated.

  20. Temperature: Human Regulating, Ants Conforming

    ERIC Educational Resources Information Center

    Clopton, Joe R.

    2007-01-01

    Biological processes speed up as temperature rises. Procedures for demonstrating this with ants traveling on trails, and data gathered by students on the Argentine ant ("Linepithema humile") are presented. The concepts of temperature regulation and conformity are detailed with a focus on the processes rather than on terms that label the organisms.

  1. Conformal mapping for multiple terminals

    PubMed Central

    Wang, Weimin; Ma, Wenying; Wang, Qiang; Ren, Hao

    2016-01-01

    Conformal mapping is an important mathematical tool that can be used to solve various physical and engineering problems in many fields, including electrostatics, fluid mechanics, classical mechanics, and transformation optics. It is an accurate and convenient way to solve problems involving two terminals. However, when faced with problems involving three or more terminals, which are more common in practical applications, existing conformal mapping methods apply assumptions or approximations. A general exact method does not exist for a structure with an arbitrary number of terminals. This study presents a conformal mapping method for multiple terminals. Through an accurate analysis of boundary conditions, additional terminals or boundaries are folded into the inner part of a mapped region. The method is applied to several typical situations, and the calculation process is described for two examples of an electrostatic actuator with three electrodes and of a light beam splitter with three ports. Compared with previously reported results, the solutions for the two examples based on our method are more precise and general. The proposed method is helpful in promoting the application of conformal mapping in analysis of practical problems. PMID:27830746

  2. De novo designed coiled-coil proteins with variable conformations as components of molecular electronic devices.

    PubMed

    Shlizerman, Clara; Atanassov, Alexander; Berkovich, Inbal; Ashkenasy, Gonen; Ashkenasy, Nurit

    2010-04-14

    Conformational changes of proteins are widely used in nature for controlling cellular functions, including ligand binding, oligomerization, and catalysis. Despite the fact that different proteins and artificial peptides have been utilized as electron-transfer mediators in electronic devices, the unique propensity of proteins to switch between different conformations has not been used as a mechanism to control device properties and performance. Toward this aim, we have designed and prepared new dimeric coiled-coil proteins that adopt different conformations due to parallel or antiparallel relative orientations of their monomers. We show here that controlling the conformation of these proteins attached as monolayers to gold, which dictates the direction and magnitude of the molecular dipole relative to the surface, results in quantitative modulation of the gold work function. Furthermore, charge transport through the proteins as molecular bridges is controlled by the different protein conformations, producing either rectifying or ohmic-like behavior.

  3. Conformational activation of ADAMTS13.

    PubMed

    South, Kieron; Luken, Brenda M; Crawley, James T B; Phillips, Rebecca; Thomas, Mari; Collins, Richard F; Deforche, Louis; Vanhoorelbeke, Karen; Lane, David A

    2014-12-30

    A disintegrin and metalloprotease with thrombospondin motifs 13 (ADAMTS13) is a metalloprotease that regulates von Willebrand factor (VWF) function. ADAMTS13-mediated proteolysis is determined by conformational changes in VWF, but also may depend on its own conformational activation. Kinetic analysis of WT ADAMTS13 revealed ∼ 2.5-fold reduced activity compared with ADAMTS13 lacking its C-terminal tail (MDTCS) or its CUB1-2 domains (WTΔCUB1-2), suggesting that the CUB domains naturally limit ADAMTS13 function. Consistent with this suggestion, WT ADAMTS13 activity was enhanced ∼ 2.5-fold by preincubation with either an anti-CUB mAb (20E9) or VWF D4CK (the natural binding partner for the CUB domains). Furthermore, the isolated CUB1-2 domains not only bound MDTCS, but also inhibited activity by up to 2.5-fold. Interestingly, a gain-of-function (GoF) ADAMTS13 spacer domain variant (R568K/F592Y/R660K/Y661F/Y665F) was ∼ 2.5-fold more active than WT ADAMTS13, but could not be further activated by 20E9 mAb or VWF D4CK and was unable to bind or to be inhibited by the CUB1-2 domains, suggesting that the inhibitory effects of the CUB domains involve an interaction with the spacer domain that is disrupted in GoF ADAMTS13. Electron microscopy demonstrated a "closed" conformation of WT ADAMTS13 and suggested a more "open" conformation for GoF ADAMTS13. The cryptic spacer domain epitope revealed by conformational unfolding also represents the core antigenic target for autoantibodies in thrombotic thrombocytopenic purpura. We propose that ADAMTS13 circulates in a closed conformation, which is maintained by a CUB-spacer domain binding interaction. ADAMTS13 becomes conformationally activated on demand through interaction of its C-terminal CUB domains with VWF, making it susceptible to immune recognition.

  4. Conformal consistency relations for single-field inflation

    SciTech Connect

    Creminelli, Paolo; Noreña, Jorge; Simonović, Marko E-mail: jorge.norena@gmail.com

    2012-07-01

    We generalize the single-field consistency relations to capture not only the leading term in the squeezed limit — going as 1/q{sup 3}, where q is the small wavevector — but also the subleading one, going as 1/q{sup 2}. This term, for an (n+1)-point function, is fixed in terms of the variation of the n-point function under a special conformal transformation; this parallels the fact that the 1/q{sup 3} term is related with the scale dependence of the n-point function. For the squeezed limit of the 3-point function, this conformal consistency relation implies that there are no terms going as 1/q{sup 2}. We verify that the squeezed limit of the 4-point function is related to the conformal variation of the 3-point function both in the case of canonical slow-roll inflation and in models with reduced speed of sound. In the second case the conformal consistency conditions capture, at the level of observables, the relation among operators induced by the non-linear realization of Lorentz invariance in the Lagrangian. These results mean that, in any single-field model, primordial correlation functions of ζ are endowed with an SO(4,1) symmetry, with dilations and special conformal transformations non-linearly realized by ζ. We also verify the conformal consistency relations for any n-point function in models with a modulation of the inflaton potential, where the scale dependence is not negligible. Finally, we generalize (some of) the consistency relations involving tensors and soft internal momenta.

  5. Shear-induced conformation change in α-crystalline nylon6

    SciTech Connect

    Arabnejad, Saeid; Manzhos, Sergei; Shim, V. P. W.; He, Chaobin

    2014-12-01

    A study of shear deformation of α-crystalline nylon6 is undertaken, using dispersion-corrected density functional theory. The shear stress-strain relationship and shear strength for interlayer shear deformation are computed. A conformation change induced by shear is identified along twinning deformation, whereby the conformation of chains, specifically the location of non-H-bonded hydrogen atoms, changes continuously. This paves a way for the modulation of properties of this group of materials by small shear deformation, if the non-H-bonded hydrogens are chemically substituted to form non-equivalent conformations when deformed.

  6. Fake conformal symmetry in unimodular gravity

    NASA Astrophysics Data System (ADS)

    Oda, Ichiro

    2016-08-01

    We study Weyl symmetry (local conformal symmetry) in unimodular gravity. It is shown that the Noether currents for both Weyl symmetry and global scale symmetry vanish exactly as in conformally invariant scalar-tensor gravity. We clearly explain why in the class of conformally invariant gravitational theories, the Noether currents vanish by starting with conformally invariant scalar-tensor gravity. Moreover, we comment on both classical and quantum-mechanical equivalences in Einstein's general relativity, conformally invariant scalar-tensor gravity, and the Weyl-transverse gravity. Finally, we discuss the Weyl current in the conformally invariant scalar action and see that it is also vanishing.

  7. L’identification et traitement du trouble panique avec ou sans agoraphobie

    PubMed Central

    Foldes-Busque, Guillaume; Marchand, André; Landry, Pierre

    2007-01-01

    RÉSUMÉ OBJECTIF Renseigner les médecins de première ligne au sujet de l’identification précoce, du diagnostic et du traitement du trouble panique avec ou sans agoraphobie (TP/A). QUALITÉ DES DONNÉES Les données et recommandations présentées proviennent d’une recension des écrits scientifiques réalisée via les banques de données PsycLIT, PsyINFO et MEDLINE (1985 à 2006) en utilisant les descripteurs panic disorder, psychotherapy, psychosocial treatment, treatment et pharmacotherapy. Les recommandations formulées par les auteurs s’appuient sur des données probantes provenant d’études d’excellente qualité. Les informations concernant le diagnostic et l’évaluation du TP/A proviennent d’études épidémiologiques récentes, de consensus et d’opinions d’experts. PRINCIPAL MESSAGE Le TP/A est un trouble psychiatrique souvent rencontré en médecine de première ligne, mais il est fréquemment sous-diagnostiqué et sous-traité. L’identification précoce de ce trouble demande une attention particulière aux symptômes médicalement inexpliqués et, le cas échéant, le médecin doit utiliser des questions spécifiques permettant d’identifier d’éventuelles attaques de panique et de cerner leur signification pour le patient. Le traitement de premier choix pour ce trouble est une psychothérapie d’orientation cognitivo-comportementale administrée par un psychologue ou un psychiatre spécialisé. Si de telles ressources ne sont pas disponibles, le médecin peut opter pour un traitement psychopharmacologique. CONCLUSION Les médecins de famille peuvent jouer un rôle central dans l’identification et le traitement des patients souffrant d’un TP/A. PMID:17934032

  8. Clinical Applications of 3-D Conformal Radiotherapy

    NASA Astrophysics Data System (ADS)

    Miralbell, Raymond

    Although a significant improvement in cancer cure (i.e. 20% increment) has been obtained in the last 2-3 decades, 30-40% of patients still fail locally after curative radiotherapy. In order to improve local tumor control rates with radiotherapy high doses to the tumor volume are frequently necessary. Three-dimensional conformal radiation therapy (3-D CRT) is used to denote a spectrum of radiation planning and delivery techniques that rely on three-dimensional imaging to define the target (tumor) and to distinguish it from normal tissues. Modern, high-precision radiotherapy (RT) techniques are needed in order to implement the goal of optimal tumor destruction delivering minimal dose to the non-target normal tissues. A better target definition is nowadays possible with contemporary imaging (computerized tomography, magnetic resonance imaging, and positron emission tomography) and image registration technology. A highly precise dose distributions can be obtained with optimal 3-D CRT treatment delivery techniques such as stereotactic RT, intensity modulated RT (IMRT), or protontherapy (the latter allowing for in-depth conformation). Patient daily set-up repositioning and internal organ immobilization systems are necessary before considering to undertake any of the above mentioned high-precision treatment approaches. Prostate cancer, brain tumors, and base of skull malignancies are among the sites most benefitting of dose escalation approaches. Nevertheless, a significant dose reduction to the normal tissues in the vicinity of the irradiated tumor also achievable with optimal 3-D CRT may also be a major issue in the treatment of pediatric tumors in order to preserve growth, normal development, and to reduce the risk of developing radiation induced diseases such as cancer or endocrinologic disorders.

  9. Double conformal space-time algebra

    NASA Astrophysics Data System (ADS)

    Easter, Robert Benjamin; Hitzer, Eckhard

    2017-01-01

    The Double Conformal Space-Time Algebra (DCSTA) is a high-dimensional 12D Geometric Algebra G 4,8that extends the concepts introduced with the Double Conformal / Darboux Cyclide Geometric Algebra (DCGA) G 8,2 with entities for Darboux cyclides (incl. parabolic and Dupin cyclides, general quadrics, and ring torus) in spacetime with a new boost operator. The base algebra in which spacetime geometry is modeled is the Space-Time Algebra (STA) G 1,3. Two Conformal Space-Time subalgebras (CSTA) G 2,4 provide spacetime entities for points, flats (incl. worldlines), and hyperbolics, and a complete set of versors for their spacetime transformations that includes rotation, translation, isotropic dilation, hyperbolic rotation (boost), planar reflection, and (pseudo)spherical inversion in rounds or hyperbolics. The DCSTA G 4,8 is a doubling product of two G 2,4 CSTA subalgebras that inherits doubled CSTA entities and versors from CSTA and adds new bivector entities for (pseudo)quadrics and Darboux (pseudo)cyclides in spacetime that are also transformed by the doubled versors. The "pseudo" surface entities are spacetime hyperbolics or other surface entities using the time axis as a pseudospatial dimension. The (pseudo)cyclides are the inversions of (pseudo)quadrics in rounds or hyperbolics. An operation for the directed non-uniform scaling (anisotropic dilation) of the bivector general quadric entities is defined using the boost operator and a spatial projection. DCSTA allows general quadric surfaces to be transformed in spacetime by the same complete set of doubled CSTA versor (i.e., DCSTA versor) operations that are also valid on the doubled CSTA point entity (i.e., DCSTA point) and the other doubled CSTA entities. The new DCSTA bivector entities are formed by extracting values from the DCSTA point entity using specifically defined inner product extraction operators. Quadric surface entities can be boosted into moving surfaces with constant velocities that display the length

  10. Flow of structural information between four DNA conformational levels.

    PubMed

    Levin-Zaidman, S; Reich, Z; Wachtel, E J; Minsky, A

    1996-03-05

    Closed-circular supercoiled DNA molecules have been shown to form a cholesteric assembly within bacteria as well as in vitro under physiological DNA and salt concentrations. Circular dichroism and X-ray scattering studies indicate that the macroscopic structural properties of the chiral mesophase are directly and uniquely dictated by the supercoiling parameters of the constituent molecules. Specifically, we find that the pitch of the DNA cholesteric phase derived from supercoiled DNA is determined by the superhelical density, which, in turn, is modulated by secondary conformational changes. A direct interrelationship among four DNA structural levels, namely, DNA sequence, secondary structural transitions, the tertiary superhelical conformation, and the quaternary, supramolecular organization is accordingly pointed out. Since secondary conformational changes are both sequence and environment dependent, alterations of cellular conditions may effectively modulate the properties of the packed DNA organization, through their effects on secondary structural transitions and hence on the superhelical parameters. On the basis of these results we suggest that liquid crystallinity represents an effectively regulated packaging mode of plectonemic, nucleosome-free DNA molecules in living systems.

  11. Conformational Preferences of α-Substituted Proline Analogues

    PubMed Central

    Flores-Ortega, Alejandra; Jiménez, Ana I.; Cativiela, Carlos; Nussinov, Ruth; Alemán, Carlos; Casanovas, Jordi

    2009-01-01

    DFT calculations at the B3LYP/6-31+G(d,p) level have been used to investigate how the replacement of the α hydrogen by a more sterically demanding group affects the conformational preferences of proline. Specifically, the N-acetyl-N’-methylamide derivatives of L-proline, L-α-methylproline and L-α-phenylproline have been calculated, with both the cis/trans isomerism of the peptide bonds and the puckering of the pyrrolidine ring being considered. The effects of solvation have been evaluated using a Self Consistent Reaction Field model. As expected, tetrasubstitution at the α carbon destabilizes the conformers with one or more peptide bonds arranged in cis. The lowest energy minimum has been found to be identical for the three compounds investigated, but important differences are observed regarding other energetically accessible backbone conformations. The results obtained provide evidence that the distinct steric requirements of the substituent at Cα may play a significant role in modulating the conformational preferences of proline. PMID:18351745

  12. Dopamine-Induced Conformational Changes in Alpha-Synuclein

    PubMed Central

    Outeiro, Tiago F.; Klucken, Jochen; Bercury, Kathryn; Tetzlaff, Julie; Putcha, Preeti; Oliveira, Luis M. A.; Quintas, Alexandre; McLean, Pamela J.; Hyman, Bradley T.

    2009-01-01

    Background Oligomerization and aggregation of α-synuclein molecules play a major role in neuronal dysfunction and loss in Parkinson's disease [1]. However, α-synuclein oligomerization and aggregation have mostly been detected indirectly in cells using detergent extraction methods [2], [3], [4]. A number of in vitro studies showed that dopamine can modulate the aggregation of α-synuclein by inhibiting the formation of or by disaggregating amyloid fibrils [5], [6], [7]. Methodology/Principal Findings Here, we show that α-synuclein adopts a variety of conformations in primary neuronal cultures using fluorescence lifetime imaging microscopy (FLIM). Importantly, we found that dopamine, but not dopamine agonists, induced conformational changes in α-synuclein which could be prevented by blocking dopamine transport into the cell. Dopamine also induced conformational changes in α-synuclein expressed in neuronal cell lines, and these changes were also associated with alterations in oligomeric/aggregated species. Conclusion/Significance Our results show, for the first time, a direct effect of dopamine on the conformation of α-synuclein in neurons, which may help explain the increased vulnerability of dopaminergic neurons in Parkinson's disease. PMID:19730729

  13. Conformal Window and Correlation Functions in Lattice Conformal QCD

    NASA Astrophysics Data System (ADS)

    Iwasaki, Y.

    We discuss various aspects of Conformal Field Theories on the Lattice. We mainly investigate the SU(3) gauge theory with Nf degenerate fermions in the fundamental representation, employing the one-plaquette gauge action and the Wilson fermion action. First we make a brief review of our previous works on the phase structure of lattice gauge theories in terms of the gauge coupling constant and the quark mass. We thereby clarify the reason why we conjecture that the conformal window is 7 ≤ Nf ≤ 16. Secondly, we introduce a new concept, "conformal theories with IR cutof" and point out that any numerical simulation on a lattice is bounded by an IR cutoff ∧IR. Then we make predictions that when Nf is within the conformal window, the propagator of a meson G(t) behaves at large t, as G(t) = c exp (-mHt)/tα, that is, a modified Yukawa-type decay form, instead of the usual exponential decay form exp (-mHt), in the small quark mass region. This holds on an any lattice for any coupling constant g, as far as g is between 0 and g*, where g* is the IR fixed point. We verify that numerical results really satisfy the predictions for the Nf = 7 case and the Nf = 16 case. Thirdly, we discuss small number of flavors (Nf = 2 ˜ 6) QCD at finite temperatures. We point out theoretically and verify numerically that the correlation functions at T/Tc > 1 exhibit the characteristics of the conformal function with IR cutoff, an exponential decay with power correction. Investigating our numerical data by a new method which we call the "local-analysis" of propagators, we observe that the Nf = 7 case and the Nf = 2 at T ˜ 2Tc case are similar to each other, while the Nf = 16 case and the Nf = 2 at T = 102 ˜ 105Tc cases are similar to each other. Further, we observe our data are consistent with the picture that the Nf = 7 case and the Nf = 2 at T ˜ 2Tc case are close to the meson unparticle model. On the other hand, the Nf = 16 case and the Nf = 2 at T = 102 ˜ 105Tc cases are close to

  14. Killing Initial Data on spacelike conformal boundaries

    NASA Astrophysics Data System (ADS)

    Paetz, Tim-Torben

    2016-08-01

    We analyze Killing Initial Data on Cauchy surfaces in conformally rescaled vacuum space-times satisfying Friedrich's conformal field equations. As an application, we derive the KID equations on a spacelike ℐ-.

  15. Conformal Antennas and Integrated Design Procedures

    DTIC Science & Technology

    2006-10-01

    Conformal Antennas and Integrated Design Procedures Mauro Bandinelli, Aldo Citriniti , Antonio Guidoni IDS Ingegneria Dei Sistemi SpA Via Livornese...UNCLASSIFIED/UNLIMITED Bandinelli, M.; Citriniti , A.; Guidoni, A. (2006) Conformal Antennas and Integrated Design Procedures. In Multifunctional

  16. Gauge natural formulation of conformal gravity

    SciTech Connect

    Campigotto, M.; Fatibene, L.

    2015-03-15

    We consider conformal gravity as a gauge natural theory. We study its conservation laws and superpotentials. We also consider the Mannheim and Kazanas spherically symmetric vacuum solution and discuss conserved quantities associated to conformal and diffeomorphism symmetries.

  17. Boundary terms of conformal anomaly

    NASA Astrophysics Data System (ADS)

    Solodukhin, Sergey N.

    2016-01-01

    We analyze the structure of the boundary terms in the conformal anomaly integrated over a manifold with boundaries. We suggest that the anomalies of type B, polynomial in the Weyl tensor, are accompanied with the respective boundary terms of the Gibbons-Hawking type. Their form is dictated by the requirement that they produce a variation which compensates the normal derivatives of the metric variation on the boundary in order to have a well-defined variational procedure. This suggestion agrees with recent findings in four dimensions for free fields of various spins. We generalize this consideration to six dimensions and derive explicitly the respective boundary terms. We point out that the integrated conformal anomaly in odd dimensions is non-vanishing due to the boundary terms. These terms are specified in three and five dimensions.

  18. Conformal Bootstrap in Mellin Space.

    PubMed

    Gopakumar, Rajesh; Kaviraj, Apratim; Sen, Kallol; Sinha, Aninda

    2017-02-24

    We propose a new approach towards analytically solving for the dynamical content of conformal field theories (CFTs) using the bootstrap philosophy. This combines the original bootstrap idea of Polyakov with the modern technology of the Mellin representation of CFT amplitudes. We employ exchange Witten diagrams with built-in crossing symmetry as our basic building blocks rather than the conventional conformal blocks in a particular channel. Demanding consistency with the operator product expansion (OPE) implies an infinite set of constraints on operator dimensions and OPE coefficients. We illustrate the power of this method in the ε expansion of the Wilson-Fisher fixed point by reproducing anomalous dimensions and, strikingly, obtaining OPE coefficients to higher orders in ε than currently available using other analytic techniques (including Feynman diagram calculations). Our results enable us to get a somewhat better agreement between certain observables in the 3D Ising model and the precise numerical values that have been recently obtained.

  19. Generative models of conformational dynamics.

    PubMed

    Langmead, Christopher James

    2014-01-01

    Atomistic simulations of the conformational dynamics of proteins can be performed using either Molecular Dynamics or Monte Carlo procedures. The ensembles of three-dimensional structures produced during simulation can be analyzed in a number of ways to elucidate the thermodynamic and kinetic properties of the system. The goal of this chapter is to review both traditional and emerging methods for learning generative models from atomistic simulation data. Here, the term 'generative' refers to a model of the joint probability distribution over the behaviors of the constituent atoms. In the context of molecular modeling, generative models reveal the correlation structure between the atoms, and may be used to predict how the system will respond to structural perturbations. We begin by discussing traditional methods, which produce multivariate Gaussian models. We then discuss GAMELAN (GRAPHICAL MODELS OF ENERGY LANDSCAPES), which produces generative models of complex, non-Gaussian conformational dynamics (e.g., allostery, binding, folding, etc.) from long timescale simulation data.

  20. Conformal compactifications from spinor geometry

    SciTech Connect

    Budinich, P. )

    1993-06-01

    Compactified Minkowski spacetime is suggested by conformal covariance of Maxwell equations, while E. Cartan's definition of simple spinors leads to the idea of compactified momentum space. Assuming both diffeomorphic to (S[sub 3] [times] S[sub 1])/Z[sub 2], one may obtain in the conformally flat stereographic projection field theories both infrared and ultraviolet regularized. On the compact manifold themselves instead, Fourier integrals of wave-field oscillations would have to be replaced by Fourier series summed over indices of spherical eigenfunctions: n, l, m, m[prime]. Tentatively identifying those wave structures with spacetime itself (in the frame of Big-Bang) and/or with matter and radiation distribution, some large-scale (hydrogenic) and small-scale (lattice) space structures are conjectured. 14 refs.

  1. Conformal FDTD modeling wake fields

    SciTech Connect

    Jurgens, T.; Harfoush, F.

    1991-05-01

    Many computer codes have been written to model wake fields. Here we describe the use of the Conformal Finite Difference Time Domain (CFDTD) method to model the wake fields generated by a rigid beam traveling through various accelerating structures. The non- cylindrical symmetry of some of the problems considered here requires the use of a three dimensional code. In traditional FDTD codes, curved surfaces are approximated by rectangular steps. The errors introduced in wake field calculations by such an approximation can be reduced by increasing the mesh size, therefore increasing the cost of computing. Another approach, validated here, deforms Ampere and Faraday contours near a media interface so as to conform to the interface. These improvements of the FDTD method result in better accuracy of the fields at asymptotically no computational cost. This method is also capable of modeling thin wires as found in beam profile monitors, and slots and cracks as found in resistive wall motions. 4 refs., 5 figs.

  2. Conformal Bootstrap in Mellin Space

    NASA Astrophysics Data System (ADS)

    Gopakumar, Rajesh; Kaviraj, Apratim; Sen, Kallol; Sinha, Aninda

    2017-02-01

    We propose a new approach towards analytically solving for the dynamical content of conformal field theories (CFTs) using the bootstrap philosophy. This combines the original bootstrap idea of Polyakov with the modern technology of the Mellin representation of CFT amplitudes. We employ exchange Witten diagrams with built-in crossing symmetry as our basic building blocks rather than the conventional conformal blocks in a particular channel. Demanding consistency with the operator product expansion (OPE) implies an infinite set of constraints on operator dimensions and OPE coefficients. We illustrate the power of this method in the ɛ expansion of the Wilson-Fisher fixed point by reproducing anomalous dimensions and, strikingly, obtaining OPE coefficients to higher orders in ɛ than currently available using other analytic techniques (including Feynman diagram calculations). Our results enable us to get a somewhat better agreement between certain observables in the 3D Ising model and the precise numerical values that have been recently obtained.

  3. DoD Biometric Conformity Assessment Initiative

    DTIC Science & Technology

    2005-04-01

    REPORT DATE APR 2005 2. REPORT TYPE 3. DATES COVERED 00-04-2005 to 00-06-2005 4. TITLE AND SUBTITLE DoD Biometric Conformity Assessment...Prescribed by ANSI Std Z39-18 dsp.dla.mil 21 DSP JOURNAL April/June 200522 The comprehensive discipline of conformity assess- ment involves conformance ... conformity assessment, and details the steps the DoD Biometrics Management Office (BMO) and its subordinate technology center, the DoD Biometrics Fusion

  4. Stabilizing the boat conformation of cyclohexane rings

    SciTech Connect

    Dasgupta, S.; Goddard, W.A. III; Moldowan, J.M.; Carlson, R.M.K.; Goddard, W.A. III.

    1995-06-21

    In calculating the energetics for various conformers of the A, B, and C series of hopanoid hydrocarbons present in mature oil reservoirs, we find that the B series prefers the boat conformation (by 1.3-2.5 kcal/mol) for the D cyclohexane ring. We analyze the structural elements responsible for stabilizing this boat conformation, identify the key features, and illustrate how one might stabilize boat conformations of other systems. 5 refs., 3 figs., 2 tabs.

  5. Holographic multiverse and conformal invariance

    SciTech Connect

    Garriga, Jaume; Vilenkin, Alexander E-mail: vilenkin@cosmos.phy.tufts.edu

    2009-11-01

    We consider a holographic description of the inflationary multiverse, according to which the wave function of the universe is interpreted as the generating functional for a lower dimensional Euclidean theory. We analyze a simple model where transitions between inflationary vacua occur through bubble nucleation, and the inflating part of spacetime consists of de Sitter regions separated by thin bubble walls. In this model, we present some evidence that the dual theory is conformally invariant in the UV.

  6. Conformal microstrip arrays on cylinders

    NASA Astrophysics Data System (ADS)

    Ashkenazy, J.; Shtrikman, S.; Treves, D.

    1988-04-01

    Design and measured results for two X-band conformal microstrip arrays are presented. The two 4 x 4 arrays are built on the surface of a cylinder of small radius. They differ by the orientation of small radius. They differ by the orientation of the elements relative to the cylinder axis. The measured directivities and radiation patterns are in reasonable agreement with theoretical predictions.

  7. Metamaterials and Conformal Antenna Technologies

    DTIC Science & Technology

    2013-03-01

    AFRL-RY-HS-TR-2010-0030 METAMATERIALS AND CONFORMAL ANTENNA TECHNOLOGIES Srinivas Sridhar, Mehmet Dokmeci, Hossein Mosallaei, Latika... Mehmet Dokmeci, Hossein Mosallaei, Latika Menon, Jeffrey Sokoloff, and Don Heiman 5d. PROJECT NUMBER 4916 5e. TASK NUMBER HA 5f. WORK UNIT...Platform, Nishant Khanduja, Selvapraba Selvarasah, Chia-Ling Chen, Mehmet R. Dokmeci, Xugang Xiong, Prashanth Makaram, and Ahmed Busnaina, Appl

  8. Spiral pocketing by conformal mappings

    NASA Astrophysics Data System (ADS)

    Romero-Carrillo, P.; Dorado, R.; Diaz-Garrido, F. A.; Lopez-Garcia, R.

    2012-04-01

    Pocketing is usual in numerical control (NC) machining applications like die and mould operations. The usual parallel cuts or offset curves strategies show C1 discontinuities, thus they are not well fitted for high speed machining. In order to alleviate this drawback, we propose a C∝. path that fills a target region and it is computed via a conformal mapping of an Archimedes' spiral. Regarding continuity, machining time and overcut, our spirals are adequate if they are compared to CAM system strategies.

  9. Conformal Antenna Array Design Handbook

    DTIC Science & Technology

    1981-09-01

    PLANAR ARRAY PHASE C LbP=IowITH CORRECT CONFORMAL ARRAY PHASE C NbPt NOe OF PhS&. SH-IFT UITSPII- NoP*.GT*1O CONRCLT PHASES ARE USED C TAP19PATTLRN...of Antenna Arrays, Radio Science , Vol. 3, May 1968, pp. 401-522. M. T. Ma, "Theory and Application of Antenna Arrays", Wiley, New York, 1974, Chapter

  10. Conformal Invariance of Graphene Sheets

    PubMed Central

    Giordanelli, I.; Posé, N.; Mendoza, M.; Herrmann, H. J.

    2016-01-01

    Suspended graphene sheets exhibit correlated random deformations that can be studied under the framework of rough surfaces with a Hurst (roughness) exponent 0.72 ± 0.01. Here, we show that, independent of the temperature, the iso-height lines at the percolation threshold have a well-defined fractal dimension and are conformally invariant, sharing the same statistical properties as Schramm-Loewner evolution (SLEκ) curves with κ = 2.24 ± 0.07. Interestingly, iso-height lines of other rough surfaces are not necessarily conformally invariant even if they have the same Hurst exponent, e.g. random Gaussian surfaces. We have found that the distribution of the modulus of the Fourier coefficients plays an important role on this property. Our results not only introduce a new universality class and place the study of suspended graphene membranes within the theory of critical phenomena, but also provide hints on the long-standing question about the origin of conformal invariance in iso-height lines of rough surfaces. PMID:26961723

  11. Electrophysiological precursors of social conformity.

    PubMed

    Shestakova, Anna; Rieskamp, Jörg; Tugin, Sergey; Ossadtchi, Alexey; Krutitskaya, Janina; Klucharev, Vasily

    2013-10-01

    Humans often change their beliefs or behavior due to the behavior or opinions of others. This study explored, with the use of human event-related potentials (ERPs), whether social conformity is based on a general performance-monitoring mechanism. We tested the hypothesis that conflicts with a normative group opinion evoke a feedback-related negativity (FRN) often associated with performance monitoring and subsequent adjustment of behavior. The experimental results show that individual judgments of facial attractiveness were adjusted in line with a normative group opinion. A mismatch between individual and group opinions triggered a frontocentral negative deflection with the maximum at 200 ms, similar to FRN. Overall, a conflict with a normative group opinion triggered a cascade of neuronal responses: from an earlier FRN response reflecting a conflict with the normative opinion to a later ERP component (peaking at 380 ms) reflecting a conforming behavioral adjustment. These results add to the growing literature on neuronal mechanisms of social influence by disentangling the conflict-monitoring signal in response to the perceived violation of social norms and the neural signal of a conforming behavioral adjustment.

  12. Conformational Study of Dibenzyl Ether

    NASA Astrophysics Data System (ADS)

    Hernandez-Castillo, Alicia O.; Abeysekera, Chamara; Hewett, Daniel M.; Zwier, Timothy S.

    2017-06-01

    Understanding the initial stages of polycyclic aromatic hydrocarbon (PAH) aggregation, the onset of soot formation, is an important goal on the pathway to cleaner combustion processes. PAHs with short alkyl chains, present in fuel-rich combustion environments, can undergo reactions that will chemically link aromatic rings together. One such example of a linked diaryl compound is dibenzyl ether, C_{6}H_{5}-CH_{2}-O-CH_{2}-C_{6}H_{5}. The -CH_{2}-O-CH_{2}- linkage has a length and flexibility well-suited to forming a π-stacked conformation between the two phenyl rings. In this talk, we will explore the single-conformation spectroscopy of dibenzyl ether under jet-cooled conditions in the gas phase. Laser-induced fluorescence, chirped pulse Fourier transform microwave (8-18 GHz region), and single-conformation infrared spectroscopy in the alkyl CH stretch region were all carried out on the molecule, thereby interrogating its full array of electronic, vibrational and rotational degrees of freedom. This work is the first step in a broader study to determine the extent of π-stacking in linked aryl compounds as a function of linkage and PAH size.

  13. A conformal block Farey tail

    NASA Astrophysics Data System (ADS)

    Maloney, Alexander; Maxfield, Henry; Ng, Gim Seng

    2017-06-01

    We investigate the constraints of crossing symmetry on CFT correlation functions. Four point conformal blocks are naturally viewed as functions on the upper-half plane, on which crossing symmetry acts by PSL(2, Z ) modular transformations. This allows us to construct a unique, crossing symmetric function out of a given conformal block by averaging over PSL(2, Z ). In some two dimensional CFTs the correlation functions are precisely equal to the modular average of the contributions of a finite number of light states. For example, in the two dimensional Ising and tri-critical Ising model CFTs, the correlation functions of identical operators are equal to the PSL(2, Z ) average of the Virasoro vacuum block; this determines the 3 point function coefficients uniquely in terms of the central charge. The sum over PSL(2, Z ) in CFT2 has a natural AdS3 interpretation as a sum over semi-classical saddle points, which describe particles propagating along rational tangles in the bulk. We demonstrate this explicitly for the correlation function of certain heavy operators, where we compute holographically the semi-classical conformal block with a heavy internal operator.

  14. New potentials for conformal mechanics

    NASA Astrophysics Data System (ADS)

    Papadopoulos, G.

    2013-04-01

    We find under some mild assumptions that the most general potential of one-dimensional conformal systems with time-independent couplings is expressed as V = V0 + V1, where V0 is a homogeneous function with respect to a homothetic motion in configuration space and V1 is determined from an equation with source a homothetic potential. Such systems admit at most an SL(2,{R}) conformal symmetry which, depending on the couplings, is embedded in {Diff}({R}) in three different ways. In one case, SL(2,{R}) is also embedded in Diff(S1). Examples of such models include those with potential V = αx2 + βx-2 for arbitrary couplings α and β, the Calogero models with harmonic oscillator couplings and nonlinear models with suitable metrics and potentials. In addition, we give the conditions on the couplings for a class of gauge theories to admit a SL(2,{R}) conformal symmetry. We present examples of such systems with general gauge groups and global symmetries that include the isometries of AdS2 × S3 and AdS2 × S3 × S3 which arise as backgrounds in AdS2/CFT1.

  15. Anomalies, conformal manifolds, and spheres

    SciTech Connect

    Gomis, Jaume; Hsin, Po-Shen; Komargodski, Zohar; Schwimmer, Adam; Seiberg, Nathan; Theisen, Stefan

    2016-03-04

    The two-point function of exactly marginal operators leads to a universal contribution to the trace anomaly in even dimensions. We study aspects of this trace anomaly, emphasizing its interpretation as a sigma model, whose target space $M$ is the space of conformal field theories (a.k.a. the conformal manifold). When the underlying quantum field theory is supersymmetric, this sigma model has to be appropriately supersymmetrized. As examples, we consider in some detail $N$ = (2; 2) and $N$ = (0; 2) supersymmetric theories in d = 2 and $N$ = 2 supersymmetric theories in d = 4. This reasoning leads to new information about the conformal manifolds of these theories, for example, we show that the manifold is K ahler-Hodge and we further argue that it has vanishing K ahler class. For $N$ = (2; 2) theories in d = 2 and N = 2 theories in d = 4 we also show that the relation between the sphere partition function and the K ahler potential of $M$ follows immediately from the appropriate sigma models that we construct. Ultimately, along the way we find several examples of potential trace anomalies that obey the Wess-Zumino consistency conditions, but can be ruled out by a more detailed analysis.

  16. The Conformational Landscape of Serinol

    NASA Astrophysics Data System (ADS)

    Sanz, M. Eugenia; Loru, Donatella; Peña, Isabel; Alonso, José L.

    2014-06-01

    The rotational spectrum of the amino alcohol serinol CH_2OH--CH(NH_2)--CH_2OH, which constitutes the hydrophilic head of the lipid sphingosine, has been investigated using chirped-pulsed Fourier transform microwave spectroscopy in combination with laser ablation Five different forms of serinol have been observed and conclusively identified by the comparison between the experimental values of their rotational and 14N quadrupole coupling constants and those predicted by ab initio calculations. In all observed conformers several hydrogen bonds are established between the two hydroxyl groups and the amino groups in a chain or circular arrangement. The most abundant conformer is stabilised by O--H···N and N--H···O hydrogen bonds forming a chain rather than a cycle. One of the detected conformers presents a tunnelling motion of the hydrogen atoms of the functional groups similar to that observed in glycerol. S. Mata, I. Peña, C. Cabezas, J. C. López, J. L. Alonso, J. Mol. Spectrosc. 2012, 280, 91 V. V. Ilyushin, R. A. Motiyenko, F. J. Lovas, D. F. Plusquellic, J. Mol. Spectrosc. 2008, 251, 129.

  17. Electrophysiological precursors of social conformity

    PubMed Central

    Rieskamp, Jörg; Tugin, Sergey; Ossadtchi, Alexey; Krutitskaya, Janina; Klucharev, Vasily

    2013-01-01

    Humans often change their beliefs or behavior due to the behavior or opinions of others. This study explored, with the use of human event-related potentials (ERPs), whether social conformity is based on a general performance-monitoring mechanism. We tested the hypothesis that conflicts with a normative group opinion evoke a feedback-related negativity (FRN) often associated with performance monitoring and subsequent adjustment of behavior. The experimental results show that individual judgments of facial attractiveness were adjusted in line with a normative group opinion. A mismatch between individual and group opinions triggered a frontocentral negative deflection with the maximum at 200 ms, similar to FRN. Overall, a conflict with a normative group opinion triggered a cascade of neuronal responses: from an earlier FRN response reflecting a conflict with the normative opinion to a later ERP component (peaking at 380 ms) reflecting a conforming behavioral adjustment. These results add to the growing literature on neuronal mechanisms of social influence by disentangling the conflict-monitoring signal in response to the perceived violation of social norms and the neural signal of a conforming behavioral adjustment. PMID:22683703

  18. Anomalies, conformal manifolds, and spheres

    DOE PAGES

    Gomis, Jaume; Hsin, Po-Shen; Komargodski, Zohar; ...

    2016-03-04

    The two-point function of exactly marginal operators leads to a universal contribution to the trace anomaly in even dimensions. We study aspects of this trace anomaly, emphasizing its interpretation as a sigma model, whose target space $M$ is the space of conformal field theories (a.k.a. the conformal manifold). When the underlying quantum field theory is supersymmetric, this sigma model has to be appropriately supersymmetrized. As examples, we consider in some detail $N$ = (2; 2) and $N$ = (0; 2) supersymmetric theories in d = 2 and $N$ = 2 supersymmetric theories in d = 4. This reasoning leads tomore » new information about the conformal manifolds of these theories, for example, we show that the manifold is K ahler-Hodge and we further argue that it has vanishing K ahler class. For $N$ = (2; 2) theories in d = 2 and N = 2 theories in d = 4 we also show that the relation between the sphere partition function and the K ahler potential of $M$ follows immediately from the appropriate sigma models that we construct. Ultimately, along the way we find several examples of potential trace anomalies that obey the Wess-Zumino consistency conditions, but can be ruled out by a more detailed analysis.« less

  19. 40 CFR 52.2133 - General conformity.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 4 2010-07-01 2010-07-01 false General conformity. 52.2133 Section 52...) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS (CONTINUED) South Carolina § 52.2133 General conformity. The General Conformity regulations adopted into the South Carolina State Implementation Plan...

  20. 40 CFR 52.938 - General conformity.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 3 2010-07-01 2010-07-01 false General conformity. 52.938 Section 52...) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS Kentucky § 52.938 General conformity. The General Conformity regulations were submitted on November 10, 1995, and adopted into the Kentucky...

  1. Molecular Orbital Studies of Ethylenediamine Conformations

    PubMed Central

    Jhon, Mu Shik; Cho, Ung-Ln; Kier, Lemont B.; Eyring, Henry

    1972-01-01

    Semiempirical quantum mechanical treatments are applied to the ethylenediamine di-cation, mono-action, and neutral molecule by the use of the extended Huckel theory. The minimum energies of conformations of molecules for rotation about the CH2-CH2 axis is found. The theoretical predictions for the conformation with minimum values. The importance of the ethylenediamine conformations are discussed. PMID:16591963

  2. 40 CFR 52.799 - Transportation conformity.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 3 2012-07-01 2012-07-01 false Transportation conformity. 52.799... (CONTINUED) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS Indiana § 52.799 Transportation conformity. On June 4, 2010, Indiana submitted the Transportation Conformity Consultation SIP consisting of...

  3. 40 CFR 52.799 - Transportation conformity.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 3 2013-07-01 2013-07-01 false Transportation conformity. 52.799... (CONTINUED) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS Indiana § 52.799 Transportation conformity. On June 4, 2010, Indiana submitted the Transportation Conformity Consultation SIP consisting of...

  4. 40 CFR 52.799 - Transportation conformity.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 3 2014-07-01 2014-07-01 false Transportation conformity. 52.799... (CONTINUED) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS Indiana § 52.799 Transportation conformity. On June 4, 2010, Indiana submitted the Transportation Conformity Consultation SIP consisting of...

  5. 40 CFR 52.2133 - General conformity.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 4 2011-07-01 2011-07-01 false General conformity. 52.2133 Section 52...) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS (CONTINUED) South Carolina § 52.2133 General conformity. The General Conformity regulations adopted into the South Carolina State Implementation Plan...

  6. 40 CFR 52.938 - General conformity.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 3 2011-07-01 2011-07-01 false General conformity. 52.938 Section 52...) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS Kentucky § 52.938 General conformity. The General Conformity regulations were submitted on November 10, 1995, and adopted into the Kentucky...

  7. An extension theorem for conformal gauge singularities

    NASA Astrophysics Data System (ADS)

    Lübbe, Christian; Tod, Paul

    2009-11-01

    We analyze conformal gauge, or isotropic, singularities in cosmological models in general relativity. Using the calculus of tractors, we find conditions in terms of tractor curvature for a local extension of the conformal structure through a cosmological singularity and prove a local extension theorem along a congruence of timelike conformal geodesics.

  8. 40 CFR 52.799 - Transportation conformity.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 3 2011-07-01 2011-07-01 false Transportation conformity. 52.799... (CONTINUED) APPROVAL AND PROMULGATION OF IMPLEMENTATION PLANS Indiana § 52.799 Transportation conformity. On June 4, 2010, Indiana submitted the Transportation Conformity Consultation SIP consisting of...

  9. On staggered indecomposable Virasoro modules

    NASA Astrophysics Data System (ADS)

    Kytölä, Kalle; Ridout, David

    2009-12-01

    In this article, certain indecomposable Virasoro modules are studied. Specifically, the Virasoro mode L0 is assumed to be nondiagonalizable, possessing Jordan blocks of rank 2. Moreover, the module is further assumed to have a highest weight submodule, the "left module," and that the quotient by this submodule yields another highest weight module, the "right module." Such modules, which have been called staggered, have appeared repeatedly in the logarithmic conformal field theory literature, but their theory has not been explored in full generality. Here, such a theory is developed for the Virasoro algebra using rather elementary techniques. The focus centers on two different but related questions typically encountered in practical studies: How can one identify a given staggered module, and how can one demonstrate the existence of a proposed staggered module. Given just the values of the highest weights of the left and right modules, themselves subject to simple necessary conditions, invariants are defined which together with the knowledge of the left and right modules uniquely identify a staggered module. The possible values of these invariants form a vector space of dimension 0, 1, or 2, and the structures of the left and right modules limit the isomorphism classes of the corresponding staggered modules to an affine subspace (possibly empty). The number of invariants and affine restrictions is purely determined by the structures of the left and right modules. Moreover, in order to facilitate applications, the expressions for the invariants and restrictions are given by formulas as explicit as possible (they generally rely on expressions for Virasoro singular vectors). Finally, the text is liberally peppered throughout with examples illustrating the general concepts. These have been carefully chosen for their physical relevance or for the novel features they exhibit.

  10. On probing conformation of microtubules by second-harmonic generation

    NASA Astrophysics Data System (ADS)

    Sharoukhov, Denis; Lim, Hyungsik

    2016-01-01

    Microtubule (MT) is a component of cytoskeleton playing an important role in a variety of cellular processes. Altering the structure of MT is a crucial mechanism of modulating the function, but it is difficult to measure the in vivo conformation. We present here the use of second-harmonic generation (SHG) for acquiring information about the architecture of MTs in living tissue. Axonal MTs were imaged by polarization-resolved SHG and anisotropy in the molecular structure was determined by means of the second-order tensor analysis. The feasibility of the second-order tensor analysis was tested for measuring the conformational changes induced by MT-stabilizing drug. It demonstrates that the new optical contrast may be useful for investigating the dynamics of MT cytoskeleton in vivo.

  11. Conformational studies of proline-, thiaproline- and dimethylsilaproline-containing diketopiperazines.

    PubMed

    Cavelier, Florine; Marchand, Damien; Mbassi, Patrick; Martinez, Jean; Marraud, Michel

    2006-10-01

    As proline plays an important role in biologically active peptides, many analogues of this residue have been developed to modulate the proportion of cis and trans conformers. A correlation between the pyrrolidine ring shape and structural properties of proline has been established. Diketopiperazine (DKP) is the model of choice to study the influence of the proline ring modification. In this contribution, cyclo(Gly-Pro) and two analogues cyclo(Sip-Pro) and cyclo(Thz-Pro) have been studied with proton NMR. We showed that both analogues with heteroatoms in gamma position, silicon and sulfur respectively, display a more rigid five-member ring. The usual flexibility of proline ring is restrained in both cases and only the two C(beta)-exo and C(beta)-endo conformations are observed.

  12. Conformational Switching in the Fungal Light Sensor Vivid

    SciTech Connect

    Zoltowski,B.; Schwerdtgeger, C.; Widom, J.; Loros, J.; Bilwes, A.; Dunlap, J.; Crane, B.

    2007-01-01

    The Neurospora crassa photoreceptor Vivid tunes blue-light responses and modulates gating of the circadian clock. Crystal structures of dark-state and light-state Vivid reveal a light, oxygen, or voltage Per-Arnt-Sim domain with an unusual N-terminal cap region and a loop insertion that accommodates the flavin cofactor. Photoinduced formation of a cystein-flavin adduct drives flavin protonation to induce an N-terminal conformational change. A cysteine-to-serine substitution remote from the flavin adenine dinucleotide binding site decouples conformational switching from the flavin photocycle and prevents Vivid from sending signals in Neurospora. Key elements of this activation mechanism are conserved by other photosensors such as White Collar-1, ZEITLUPE, ENVOY, and flavin-binding, kelch repeat, F-BOX 1 (FKF1).

  13. Conformational dynamics of amyloid proteins at the aqueous interface

    NASA Astrophysics Data System (ADS)

    Armbruster, Matthew; Horst, Nathan; Aoki, Brendy; Malik, Saad; Soto, Patricia

    2013-03-01

    Amyloid proteins is a class of proteins that exhibit distinct monomeric and oligomeric conformational states hallmark of deleterious neurological diseases for which there are not yet cures. Our goal is to examine the extent of which the aqueous/membrane interface modulates the folding energy landscape of amyloid proteins. To this end, we probe the dynamic conformational ensemble of amyloids (monomer prion protein and Alzheimer's Ab protofilaments) interacting with model bilayers. We will present the results of our coarse grain molecular modeling study in terms of the existence of preferential binding spots of the amyloid to the bilayer and the response of the bilayer to the interaction with the amyloid. NSF Nebraska EPSCoR First Award

  14. Morpheus: a conformation-activity relationships and receptor modeling package.

    PubMed

    Andrews, P R; Quint, G; Winkler, D A; Richardson, D; Sadek, M; Spurling, T H

    1989-09-01

    Our molecular modeling software package, MORPHEUS, allows the study of the interactions between biologically active molecules and their receptors. The package is capable of exploring the multidimensional conformational space accessible to each molecule of the data set under study. By specifying distance constraints or hypothetical receptor binding points, the package is able to filter the biologically accessible conformations of each active compound and deduce a three-dimensional model of the binding sites consistent with the properties of the agonists (or antagonists) under scrutiny. The electrostatic potentials in the environment of a putative binding site can also be investigated using the MORPHEUS package. The molecular modeling module CRYS-X, which is written in FORTRAN 77 for IBM PC machines, is capable of building, displaying and manipulating molecules.

  15. Un syndrome confusionnel révélant un syndrome de Fahr avec hyperparathyroïdie

    PubMed Central

    Rharrabti, Souad; Darouich, Ilhame; Benbrahim, Mohamed; Belahsen, Fawzi; Rammouz, Ismail; Alouane, Rachid

    2013-01-01

    Le syndrome de Fahr est une entité anatomo-clinique rare, caractérisée par des calcifications intracérébrales bilatérales et symétriques, localisées dans les noyaux gris centraux, le plus souvent associées à des troubles du métabolisme phosphocalcique. L'hypoparathyroïdie, primitive ou postopératoire, est l'anomalie la plus classique. L'hyperparathyroïdie est exceptionnellement rapportée comme cause du syndrome de Fahr. Nous rapportons le cas d'une fille de 17 ans suivie depuis l’âge de 12 ans pour une épilepsie avec la notion d'un retard mental depuis l'enfance, qui a présenté un syndrome confusionnel révélant un syndrome de Fahr avec la particularité de l'existence d'une hyperparathyroïdie. PMID:23734268

  16. Jumelage eolien-diesel avec stockage d'air comprime: Modelisation de Ia suralimentation du moteur diesel

    NASA Astrophysics Data System (ADS)

    Beaulac, Philippe

    Ce memoire est le resultat d'une recherche qui visait le developpement d'un modele de moteur diesel a I' aide d'un logiciel commercial, GT Power. Ce modele permet de tester certaines hypotheses pour optimiser la recuperation d'energie d'un systeme hybride eolien-diesel avec stockage d'air comprime. L'energie stockee sous forme d'air comprime pourrait etre utilisee afin de reduire la consommation en carburant du moteur diesel. Les resultats anticipes pourraient etre utilises dans des sites isoles du nord canadien, ou l'energie est beaucoup plus dispendieuse a rendre disponible aux consommateurs. La methodologie preconisee consistait a relever des donnees de performances sur un groupe electrogene modifie avec des capteurs, charges resistantes, interface et apport d'air comprime. Les donnees pouvaient etre utilisees afin d'ajuster le modele developpe. Une fois le modele bien ajuste, les hypotheses d'optimisation sont mises a l'essai avant de tenter de modifier le moteur physique en tant que tel. Les resultats obtenus ne sont pas aussi concluants que desires, compte tenu du bris d'un capteur de pression critique et d'echeanciers trop serres pour permettre de reprendre les essais. Par contre, les donnees colligees de la simulation du modele demontrent que le modele et done le logiciel GT Power peuvent bel et bien foumir l'outil de confirmation souhaite pour justifier des travaux de modification de concept de moteur.

  17. Un cas de fracture luxation négligée du coude avec conservation de la fonction du coude

    PubMed Central

    Lahrach, Kamal; Ammoumri, Oussama; Mezzani, Amine; Benabid, Mounir; Marzouki, Amine; Boutayeb, Fawzi

    2015-01-01

    Les fractures luxations du coude sont rares et souvent mal tolérées chez les sujets jeunes actifs. Nous rapportons un cas de fracture-luxation du coude remontant à 20 ans. C'est un jeune de 35 ans, victime il y a 20 ans d'un traumatisme fermé, suite à une chute lors d'un match du football, de son coude gauche occasionnant une fracture-luxation du coude. Le patient a refusé une intervention chirurgicale avec une auto-rééducation. L'examen a mis en évidence une conservation de la fonction du coude. Un bilan radiologique a montré une fracture luxation du coude avec remaniement de la palette humérale. Une abstention thérapeutique a été décidée devant l'ancienneté de la fracture-luxation et la gêne fonctionnelle minime engendrée. Contrairement aux autres séries, la fracture-luxation dans notre cas était bien tolérée malgré le jeune âge du patient. PMID:26113930

  18. Carcinome métaplasique du sein avec différenciation osseuse extensive: à propos d'un cas

    PubMed Central

    Benlemlih, Amal; Bendahou, Mouhcine; Znati, Kaoutar; Sekkal, Mohamed; Chahbouni, Sanae; Mahmoud, Samia; Banani, Mohamed; Afaf, Amarti

    2013-01-01

    Le carcinome métaplasique du sein est une entité rare et bien individualisé par l'OMS. Il représente moins de 1% des cancers invasifs du sein et constitue un groupe tumoral hétérogène soit purement épithélial soit à doublecontingent épithélial et mésenchymateuse. Le carcinome métaplasique avec différenciation osseuse extensive est très rare. Il représente 0.2% des carcinomes du sein. Nous rapportant un cas exceptionnel d'un carcinome métaplasique du sein avec différenciation osseuse extensive chez une patiente de 53 ans. A travers ce cas et une revue de la littérature, les caractéristiques anatomo-cliniques, radiologique, thérapeutiques et évolutives seront discutées. PMID:24570796

  19. Etude de la photosensibilite dans la silice implantee avec des ions de haute energie

    NASA Astrophysics Data System (ADS)

    Verhaegen, Marc

    La photosensibilite est la propriete par laquelle une materiau donne voit son indice de refraction changer sous l'effet d'une exposition lumineuse. Malgre le nombre croissant de dispositif base sur ce phenomene, les mecanismes a la base de la photosensibilite sont encore debattus. Nous apportons dans cette these un eclairage original sur ce sujet en etudiant la matrice de silice pure non dopee rendue photosensible par implantation d'ion de haute energie. L'implantation d'ions silicium de S MeV modifie l'indice de refraction principalement en densifiant une couche mince dont l'epaisseur est de l'ordre de quelques microns. Nos mesures montrent qu'un guide plan supportant les modes TEi et TMi (i = 0,1) est forme et que l'indice effectif du mode TE0 suit l'evolution de la densification en fonction de la dose de silicium implantee. Nous montrerons egalement que l'augmentation d'indice et la densification produites par implantation atteignent un palier pour une dose de 3 x 1014Si/cm 2, alors que la production de defauts par implantation atteint son palier pour une dose plus faible d'un ordre de grandeur soit 3 x 1013Si/cm2. Le profil d'indice longitudinal produit par l'implantation ionique est calcule a partir des mesures des indices effectifs des modes guides. Ce profil suggere que l'augmentation d'indice comprend une contribution dues collisions et une contribution dues aux pertes d'energie par ionisation. La contribution des pertes par ionisation influence significativement le profil d'indice pour des valeurs de pertes d'energie par unite de longueur (dE/dx) de l'ordre de 2 keV/nm. Lorsque la silice implantee est soumise a un rayonnement ultraviolet d'un laser a excimeres, il en resulte une diminution d'indice de refraction de l'ordre de 10-3 avec une efficacite plus grande si la longueur d'onde d'exposition est 193nm (ArF) plutot que 248nm (KrF). Deux regimes d'exposition lumineuse de la silice implantee a 193nm sont observes. Le premier regime produit une diminution

  20. Modulation techniques

    NASA Technical Reports Server (NTRS)

    Schilling, D. L.

    1982-01-01

    Bandwidth efficient digital modulation techniques, proposed for use on and/or applied to satellite channels, are reviewed. In a survey of recent works on digital modulation techniques, the performance of several schemes operating in various environments are compared. Topics covered include: (1) quadrature phase shift keying; (2) offset - QPSK and MSK; (3) combined modulation and coding; and (4) spectrally efficient modulation techniques.

  1. Conformation and chirality in liquid crystals

    NASA Astrophysics Data System (ADS)

    West, John L.; Zhao, Lei

    2013-09-01

    High helical twisting powerchiral additives are required for an expanding variety of liquid crystal displays and devices. Molecular conformation plays a critical role in determining the helical twisting power, HTP, of chiral additives. We studied additives based on an isosorbide benzoate ester core. Molecular modeling revealed two low energy states with very different conformations for this core The ultra-violet absorption and NMR spectra show two stable isosorbide conformers These spectra reveal how the relative populations of these two conformations change with temperature and how this is related to the helical twisting power. Conformation changes can explain many of the observed anomalous responses of HPT to temperature.

  2. A chemical chaperone induces inhomogeneous conformational changes in flexible proteins.

    PubMed

    Hamdane, Djemel; Velours, Christophe; Cornu, David; Nicaise, Magali; Lombard, Murielle; Fontecave, Marc

    2016-07-27

    Organic osmolytes also known as chemical chaperones are major cellular compounds that favor, by an unclear mechanism, protein's compaction and stabilization of the native state. Here, we have examined the chaperone effect of the naturally occurring trimethylamine N-oxide (TMAO) osmolyte on a loosely packed protein (LPP), known to be a highly flexible form, using an apoprotein mutant of the flavin-dependent RNA methyltransferase as a model. Thermal and chemical denaturation experiments showed that TMAO stabilizes the structural integrity of the apoprotein dramatically. The denaturation reaction is irreversible indicating that the stability of the apoprotein is under kinetic control. This result implies that the stabilization is due to a TMAO-induced reconfiguration of the flexible LPP state, which leads to conformational limitations of the apoprotein likely driven by favorable entropic contribution. Evidence for the conformational perturbation of the apoprotein had been obtained through several biophysical approaches notably analytical ultracentrifugation, circular dichroism, fluorescence spectroscopy, labelling experiments and proteolysis coupled to mass spectrometry. Unexpectedly, TMAO promotes an overall elongation or asymmetrical changes of the hydrodynamic shape of the apoprotein without alteration of the secondary structure. The modulation of the hydrodynamic properties of the protein is associated with diverse inhomogenous conformational changes: loss of the solvent accessible cavities resulting in a dried protein matrix; some side-chain residues initially buried become solvent exposed while some others become hidden. Consequently, the TMAO-induced protein state exhibits impaired capability in the flavin binding process. Our study suggests that the nature of protein conformational changes induced by the chemical chaperones may be specific to protein packing and plasticity. This could be an efficient mechanism by which the cell controls and finely tunes the

  3. Logarithmic conformal field theory: a lattice approach

    NASA Astrophysics Data System (ADS)

    Gainutdinov, A. M.; Jacobsen, J. L.; Read, N.; Saleur, H.; Vasseur, R.

    2013-12-01

    Logarithmic conformal field theories (LCFT) play a key role, for instance, in the description of critical geometrical problems (percolation, self-avoiding walks, etc), or of critical points in several classes of disordered systems (transition between plateaux in the integer and spin quantum Hall effects). Much progress in their understanding has been obtained by studying algebraic features of their lattice regularizations. For reasons which are not entirely understood, the non-semi-simple associative algebras underlying these lattice models—such as the Temperley-Lieb algebra or the blob algebra—indeed exhibit, in finite size, properties that are in full correspondence with those of their continuum limits. This applies not only to the structure of indecomposable modules, but also to fusion rules, and provides an ‘experimental’ way of measuring couplings, such as the ‘number b’ quantifying the logarithmic coupling of the stress-energy tensor with its partner. Most results obtained so far have concerned boundary LCFTs and the associated indecomposability in the chiral sector. While the bulk case is considerably more involved (mixing in general left and right moving sectors), progress has also recently been made in this direction, uncovering fascinating structures. This study provides a short general review of our work in this area.

  4. Cryptographie quantique avec des états cohérents à longueur d'onde télécom

    NASA Astrophysics Data System (ADS)

    Lodewyck, J.; Tualle-Brouri, R.; Debuisschert, T.; Grangier, P.

    2006-10-01

    Nous proposons un système de distribution quantique de clé avec des variables continues, implémenté avec des technologies télécom à 1550 nm. Le dispositif actuel nous a permis de transmettre une clé secrète brute au taux de 1 Mb/s sur une distance de quelques mètres. Une extension en cours de réalisation nous permettra de transmettre des clés sur des distances allant jusqu'à plusieurs dizaines dekilomètres.

  5. Modulating NHC catalysis with fluorine.

    PubMed

    Rey, Yannick P; Gilmour, Ryan

    2013-01-01

    Fluorination often confers a range of advantages in modulating the conformation and reactivity of small molecule organocatalysts. By strategically introducing fluorine substituents, as part of a β-fluoroamine motif, in a triazolium pre-catalyst, it was possible to modulate the behaviour of the corresponding N-heterocyclic carbene (NHC) with minimal steric alterations to the catalyst core. In this study, the effect of hydrogen to fluorine substitution was evaluated as part of a molecular editing study. X-ray crystallographic analyses of a number of derivatives are presented and the conformations are discussed. Upon deprotonation, the fluorinated triazolium salts generate catalytically active N-heterocyclic carbenes, which can then participate in the enantioselective Steglich rearrangement of oxazolyl carbonates to C-carboxyazlactones (e.r. up to 87.0:13.0).

  6. Gauge Choice in Conformal Gravity

    NASA Astrophysics Data System (ADS)

    Sultana, Joseph; Kazanas, Demosthenes

    2017-01-01

    In a recent paper (MNRAS 458, 4122 (2016)) K. Horne examined the effect of a conformally coupled scalar field (referred to as Higgs field) on the Mannheim-Kazanas metric gμν, i.e. the static spherically symmetric metric within the context of conformal gravity (CG), and studied its effect on the rotation curves of galaxies. He showed that for a Higgs field of the form S(r) = S0a/(r + a), where a is a radial length scale, the equivalent Higgs-frame Mannheim-Kazanas metric tilde{g}_{μ ν } = Ω ^2 g_{μ ν }, with Ω = S(r)/S0, lacks the linear γr term, which has been employed in the fitting of the galactic rotation curves without the need to invoke dark matter. In this brief note we point out that the representation of the Mannheim-Kazanas metric in a gauge where it lacks the linear term has already been presented by others, including Mannheim and Kazanas themselves, without the need to introduce a conformally coupled Higgs field. Furthermore, Horne argues that the absence of the linear term resolves the issue of light bending in the wrong direction, i.e. away from the gravitating mass, if γr > 0 in the Mannheim-Kazanas metric, a condition necessary to resolve the galactic dynamics in the absence of dark matter. In this case we also point out that the elimination of the linear term is not even required because the sign of the γr term in the metric can be easily reversed by a simple gauge transformation, and also that the effects of this term are indeed too small to be observed.

  7. The biological bases of conformity.

    PubMed

    Morgan, T J H; Laland, K N

    2012-01-01

    Humans are characterized by an extreme dependence on culturally transmitted information and recent formal theory predicts that natural selection should favor adaptive learning strategies that facilitate effective copying and decision making. One strategy that has attracted particular attention is conformist transmission, defined as the disproportionately likely adoption of the most common variant. Conformity has historically been emphasized as significant in the social psychology literature, and recently there have also been reports of conformist behavior in non-human animals. However, mathematical analyses differ in how important and widespread they expect conformity to be, and relevant experimental work is scarce, and generates findings that are both mutually contradictory and inconsistent with the predictions of the models. We review the relevant literature considering the causation, function, history, and ontogeny of conformity, and describe a computer-based experiment on human subjects that we carried out in order to resolve ambiguities. We found that only when many demonstrators were available and subjects were uncertain was subject behavior conformist. A further analysis found that the underlying response to social information alone was generally conformist. Thus, our data are consistent with a conformist use of social information, but as subjects' behavior is the result of both social and asocial influences, the resultant behavior may not be conformist. We end by relating these findings to an embryonic cognitive neuroscience literature that has recently begun to explore the neural bases of social learning. Here conformist transmission may be a particularly useful case study, not only because there are well-defined and tractable opportunities to characterize the biological underpinnings of this form of social learning, but also because early findings imply that humans may possess specific cognitive adaptations for effective social learning.

  8. Conformance Testing: Measurement Decision Rules

    NASA Technical Reports Server (NTRS)

    Mimbs, Scott M.

    2010-01-01

    The goal of a Quality Management System (QMS) as specified in ISO 9001 and AS9100 is to provide assurance to the customer that end products meet specifications. Measuring devices, often called measuring and test equipment (MTE), are used to provide the evidence of product conformity to specified requirements. Unfortunately, processes that employ MTE can become a weak link to the overall QMS if proper attention is not given to the measurement process design, capability, and implementation. Documented "decision rules" establish the requirements to ensure measurement processes provide the measurement data that supports the needs of the QMS. Measurement data are used to make the decisions that impact all areas of technology. Whether measurements support research, design, production, or maintenance, ensuring the data supports the decision is crucial. Measurement data quality can be critical to the resulting consequences of measurement-based decisions. Historically, most industries required simplistic, one-size-fits-all decision rules for measurements. One-size-fits-all rules in some cases are not rigorous enough to provide adequate measurement results, while in other cases are overly conservative and too costly to implement. Ideally, decision rules should be rigorous enough to match the criticality of the parameter being measured, while being flexible enough to be cost effective. The goal of a decision rule is to ensure that measurement processes provide data with a sufficient level of quality to support the decisions being made - no more, no less. This paper discusses the basic concepts of providing measurement-based evidence that end products meet specifications. Although relevant to all measurement-based conformance tests, the target audience is the MTE end-user, which is anyone using MTE other than calibration service providers. Topics include measurement fundamentals, the associated decision risks, verifying conformance to specifications, and basic measurement

  9. Solvent interactions determine carbohydrate conformation

    PubMed Central

    Kirschner, Karl N.; Woods, Robert J.

    2001-01-01

    The relationship between the three-dimensional structures of oligosaccharides and polysaccharides and their biological properties has been the focus of many recent studies. The overall conformation of an oligosaccharide depends primarily on the orientation of the torsion angles (φ, ψ, and ω) between glycosyl residues. Numerous experimental studies have shown that in glucopyranosides the ω-torsion angle (O6-C6-C5-O5) displays a preference for gauche orientations, in disagreement with predictions based on gas-phase quantum mechanics calculations. In contrast, the ω-angle in galactopyranosides displays a high proportion of the anti-orientation. For oligosaccharides containing glycosidic linkages at the 6-position (1→6 linked), variations in rotamer population have a direct effect on the oligosaccharides' structure and function, and yet the physical origin of these conformational preferences remains unclear. Although it is generally recognized that the gauche effect in carbohydrates is a solvent-dependent phenomenon, the mechanism through which solvent induces the gauche preference is not understood. In the present work, quantum mechanics and solvated molecular dynamics calculations were performed on two representative carbohydrates, methyl α-d-glucopyranoside and methyl α-d-galactopyranoside. We show that correct reproduction of the experimental rotamer distributions about the ω-angles is obtained only after explicit water is included in the molecular dynamics simulations. The primary role of the water appears to be to disrupt the hydrogen bonding within the carbohydrate, thereby allowing the rotamer populations to be determined by internal electronic and steric repulsions between the oxygen atoms. The results reported here provide a quantitative explanation of the conformational behavior of (1→6)-linked carbohydrates. PMID:11526221

  10. Gauge choice in conformal gravity

    NASA Astrophysics Data System (ADS)

    Sultana, Joseph; Kazanas, Demosthenes

    2017-04-01

    In a recent paper, K. Horne examined the effect of a conformally coupled scalar field (referred to as Higgs field) on the Mannheim-Kazanas metric gμν, i.e. the static spherically symmetric metric within the context of conformal gravity, and studied its effect on the rotation curves of galaxies. He showed that for a Higgs field of the form S(r) = S0a/(r + a), where a is a radial length-scale, the equivalent Higgs-frame Mannheim-Kazanas metric \\tilde{g}_{μ ν } = Ω ^2 g_{μ ν }, with Ω = S(r)/S0, lacks the linear γr term, which has been employed in the fitting of the galactic rotation curves without the need to invoke dark matter. In this brief note, we point out that the representation of the Mannheim-Kazanas metric in a gauge, where it lacks the linear term, has already been presented by others, including Mannheim and Kazanas themselves, without the need to introduce a conformally coupled Higgs field. Furthermore, Horne argues that the absence of the linear term resolves the issue of light bending in the wrong direction, i.e. away from the gravitating mass, if γr > 0 in the Mannheim-Kazanas metric, a condition necessary to resolve the galactic dynamics in the absence of dark matter. In this case, we also point out that the elimination of the linear term is not even required because the sign of the γr term in the metric can be easily reversed by a simple gauge transformation, and also that the effects of this term are indeed too small to be observed.

  11. The Biological Bases of Conformity

    PubMed Central

    Morgan, T. J. H.; Laland, K. N.

    2012-01-01

    Humans are characterized by an extreme dependence on culturally transmitted information and recent formal theory predicts that natural selection should favor adaptive learning strategies that facilitate effective copying and decision making. One strategy that has attracted particular attention is conformist transmission, defined as the disproportionately likely adoption of the most common variant. Conformity has historically been emphasized as significant in the social psychology literature, and recently there have also been reports of conformist behavior in non-human animals. However, mathematical analyses differ in how important and widespread they expect conformity to be, and relevant experimental work is scarce, and generates findings that are both mutually contradictory and inconsistent with the predictions of the models. We review the relevant literature considering the causation, function, history, and ontogeny of conformity, and describe a computer-based experiment on human subjects that we carried out in order to resolve ambiguities. We found that only when many demonstrators were available and subjects were uncertain was subject behavior conformist. A further analysis found that the underlying response to social information alone was generally conformist. Thus, our data are consistent with a conformist use of social information, but as subjects’ behavior is the result of both social and asocial influences, the resultant behavior may not be conformist. We end by relating these findings to an embryonic cognitive neuroscience literature that has recently begun to explore the neural bases of social learning. Here conformist transmission may be a particularly useful case study, not only because there are well-defined and tractable opportunities to characterize the biological underpinnings of this form of social learning, but also because early findings imply that humans may possess specific cognitive adaptations for effective social learning. PMID:22712006

  12. Chromosome Conformation Capture in Drosophila.

    PubMed

    Li, Hua-Bing

    2016-01-01

    Linear chromatin fiber is packed inside the nuclei as a complex three-dimensional structure, and the organization of the chromatin has important roles in the appropriate spatial and temporal regulation of gene expression. To understand how chromatin organizes inside nuclei, and how regulatory proteins physically interact with genes, chromosome conformation capture (3C) technique provides a powerful and sensitive tool to detect both short- and long-range DNA-DNA interaction. Here I describe the 3C technique to detect the DNA-DNA interactions mediated by insulator proteins that are closely related to PcG in Drosophila, which is also broadly applicable to other systems.

  13. From conformal to Einstein gravity

    NASA Astrophysics Data System (ADS)

    Anastasiou, Giorgos; Olea, Rodrigo

    2016-10-01

    We provide a simple derivation of the equivalence between Einstein and conformal gravity (CG) with Neumann boundary conditions given by Maldacena. As Einstein spacetimes are Bach flat, a generic solution to CG would contain both Einstein and non-Einstein parts. Using this decomposition of the spacetime curvature in the Weyl tensor makes manifest the equivalence between the two theories, both at the level of the action and the variation of it. As a consequence, we show that the on-shell action for critical gravity in four dimensions is given uniquely in terms of the Bach tensor.

  14. Toward TeV Conformality

    SciTech Connect

    Appelquist, T; Avakian, A; Babich, R; Brower, R C; Cheng, M; Clark, M A; Cohen, S D; Fleming, G T; Kiskis, J; Neil, E T; Osborn, J C; Rebbi, C; Schaich, D; Soltz, R; Vranas, P

    2009-11-30

    We study the chiral condensate <{bar {psi}}{psi}> for an SU(3) gauge theory with N{sub f} massless Dirac fermions in the fundamental representation when N{sub f} is increased from 2 to 6. For N{sub f} = 2, our lattice simulations of <{bar {psi}}{psi}>/F{sup 3}, where F is the Nambu-Goldstone-boson decay constant, agree with the measured QCD value. For N{sub f} = 6, this ratio shows significant enhancement, presaging an even larger enhancement anticipated as N{sub f} increases further, toward the critical value for transition from confinement to infrared conformality.

  15. Applications of Numerical Conformal Mapping.

    DTIC Science & Technology

    1980-07-01

    Al A095 886 CAMBRIDGE HYDRODYNAMICS INC MA F/ A2 - APPL ICAI IONS OF NUMERICAL CONFORMAL MAPPING U) JUL AD D I MEIRON , S A ORSZAG. M ISRAELI NOI0iN...CLASSIFICATION OF THIS1 PAGE flle Dol Sneered) Q___Y , REPORT OCUMENTATION PAGE ~RAD ISTRUCTIONS~ I. REPORT NUM@Et is GOVT ACCESSION No. S . RECIPIENT’S...CATALOG NMER-...o . __ , 4. TITLE (and S uo) As O L Tm U #o V Cambridge Hydrodynamics Report No..34 Interim /echnical /pm t. Applications of Numerical

  16. Conformational Transitions in Molecular Systems

    NASA Astrophysics Data System (ADS)

    Bachmann, M.; Janke, W.

    2008-11-01

    Proteins are the "work horses" in biological systems. In almost all functions specific proteins are involved. They control molecular transport processes, stabilize the cell structure, enzymatically catalyze chemical reactions; others act as molecular motors in the complex machinery of molecular synthetization processes. Due to their significance, misfolds and malfunctions of proteins typically entail disastrous diseases, such as Alzheimer's disease and bovine spongiform encephalopathy (BSE). Therefore, the understanding of the trinity of amino acid composition, geometric structure, and biological function is one of the most essential challenges for the natural sciences. Here, we glance at conformational transitions accompanying the structure formation in protein folding processes.

  17. Conformational isomers of linear rotaxanes

    NASA Astrophysics Data System (ADS)

    Sevick, Edith M.; Williams, David R. M.

    2014-09-01

    We examine a simple model of rotaxane structure, with 3 asymmetric rings interacting via repulsive power-law forces. This interlocked molecule exhibits conformational isomerisation which is different from that of molecules whose connectedness is through covalent bonds. The rings are free to translate along and rotate around the axle, and hence weak interaction forces between the rings can lead to distinct rotamer states. We use energy minimisation to determine these states exactly, and show that there can be transitions from asymmetric to symmetric states by varying the bond lengths. We also use classical statistical mechanics to show the effect of thermal noise.

  18. Les astronomes européens auscultent les cieux avec le plus grand télescope du monde

    NASA Astrophysics Data System (ADS)

    Malbet, F.

    2008-09-01

    À l'heure des projets de télescopes extrêmement grands, l'Europe a déjà une longueur d'avance. Le télescope européen (VLT), en mode interférométrique avec l'instrument AMBER devient le plus grand télescope jamais utilisé dans le domaine optique aussi bien en surface de miroir (plus de 150 m2) qúen finesse de résolution qui atteint celle d'un télescope de 130 m de diamètre. Le journal professionnel Astronomy & Astrophysics a publié en 2007 un numéro spécial qui rapporte les premiers résultats obtenus avec l'instrument AMBER (Astronomical MultiBEam Recombiner) par le très grand télescope européen. Ces articles couvrent pratiquement tous les stades de l'évolution stellaire depuis la formation des étoiles et des planètes jusqu'a l'observation de l'explosion de type nova dans un système stellaire évolué. Ces résultats inédits ont été obtenus en utilisant simultanément 3 des 4 télescopes du VLT basés à l'Observatoire européen austral du mont Paranal au Chili. L'instrument AMBER équipant le VLTI (mode interférométrique du VLT) permet dâatteindre une résolution angulaire inégalée de l'ordre du millième de seconde d'angle autorisant l'observation des astres dans différentes longueurs d'onde, dans l'infrarouge proche. Les astronomes obtiennent donc des observations avec une finesse 13 fois plus importante que celle d'un télescope seul. Il devient alors possible de sonder les régions de formation de planètes, d'observer les vents des étoiles en rotation très rapide, d'étudier les différents types de matières éjectées par une étoile massive, de séparer les deux composantes d'une étoile double serrée et de voir en direct l'évolution d'une nova quelques jours seulement après son explosion.

  19. Coexisting stable conformations of gaseous protein ions.

    PubMed Central

    Suckau, D; Shi, Y; Beu, S C; Senko, M W; Quinn, J P; Wampler, F M; McLafferty, F W

    1993-01-01

    For further insight into the role of solvent in protein conformer stabilization, the structural and dynamic properties of protein ions in vacuo have been probed by hydrogen-deuterium exchange in a Fourier-transform mass spectrometer. Multiply charged ions generated by electrospray ionization of five proteins show exchange reactions with 2H2O at 10(-7) torr (1 torr = 133.3 Pa) exhibiting pseudo-first-order kinetics. Gas-phase compactness of the S-S cross-linked RNase A relative to denatured S-derivatized RNase A is indicated by exchange of 35 and 135 hydrogen atoms, respectively. For pure cytochrome c ions, the existence of at least three distinct gaseous conformers is indicated by the substantially different values--52, 113, and 74--of reactive H atoms; the observation of these same values for ions of a number--2, 7, and 5, respectively--of different charge states indicates conformational insensitivity to coulombic forces. For each of these conformers, the compactness in vacuo indicated by these values corresponds directly to that of a known conformer structure in the solution from which the conformer ions are produced by electrospray. S-derivatized RNase A ions also exist as at least two gaseous conformers exchanging 50-140 H atoms. Gaseous conformer ions are isometrically stable for hours; removal of solvent greatly increases conformational rigidity. More specific ion-molecule reactions could provide further details of conformer structures. Images PMID:8381533

  20. Generative Models of Conformational Dynamics

    PubMed Central

    Langmead, Christopher James

    2014-01-01

    Atomistic simulations of the conformational dynamics of proteins can be performed using either Molecular Dynamics or Monte Carlo procedures. The ensembles of three-dimensional structures produced during simulation can be analyzed in a number of ways to elucidate the thermodynamic and kinetic properties of the system. The goal of this chapter is to review both traditional and emerging methods for learning generative models from atomistic simulation data. Here, the term ‘generative’ refers to a model of the joint probability distribution over the behaviors of the constituent atoms. In the context of molecular modeling, generative models reveal the correlation structure between the atoms, and may be used to predict how the system will respond to structural perturbations. We begin by discussing traditional methods, which produce multivariate Gaussian models. We then discuss GAMELAN (GrAphical Models of Energy LANdscapes), which produces generative models of complex, non-Gaussian conformational dynamics (e.g., allostery, binding, folding, etc) from long timescale simulation data. PMID:24446358

  1. Conformal ALON® and spinel windows

    NASA Astrophysics Data System (ADS)

    Goldman, Lee M.; Smith, Mark; Ramisetty, Mohan; Jha, Santosh; Sastri, Suri

    2017-05-01

    The requirements for modern aircraft based reconnaissance systems are driving the need for conformal windows for future sensor systems. However, limitations on optical systems and the ability to produce windows in complex geometries currently limit the geometry of existing windows and window assemblies to faceted assemblies of flat windows. ALON consists primarily of aluminum and oxygen, similar to that of alumina, with a small amount of nitrogen added to help stabilize the cubic gamma-AlON phase. ALON's chemical similarity to alumina, translates into a robust manufacturing process. This ease of processing has allowed Surmet to produce ALON windows and domes in a wide variety of geometries and sizes. Spinel (MgAl2O4) contains equal molar amounts of MgO and Al2O3, and is a cubic material, that transmits further into the Infrared than ALON. Spinel is produced via powder processing techniques similar to those used to produce ALON. Surmet is now applying the lessons learned with ALON to produce conformal spinel windows and domes as well.

  2. Local Order in the Unfolded State: Conformational Biases and Nearest Neighbor Interactions

    PubMed Central

    Toal, Siobhan; Schweitzer-Stenner, Reinhard

    2014-01-01

    The discovery of Intrinsically Disordered Proteins, which contain significant levels of disorder yet perform complex biologically functions, as well as unwanted aggregation, has motivated numerous experimental and theoretical studies aimed at describing residue-level conformational ensembles. Multiple lines of evidence gathered over the last 15 years strongly suggest that amino acids residues display unique and restricted conformational preferences in the unfolded state of peptides and proteins, contrary to one of the basic assumptions of the canonical random coil model. To fully understand residue level order/disorder, however, one has to gain a quantitative, experimentally based picture of conformational distributions and to determine the physical basis underlying residue-level conformational biases. Here, we review the experimental, computational and bioinformatic evidence for conformational preferences of amino acid residues in (mostly short) peptides that can be utilized as suitable model systems for unfolded states of peptides and proteins. In this context particular attention is paid to the alleged high polyproline II preference of alanine. We discuss how these conformational propensities may be modulated by peptide solvent interactions and so called nearest-neighbor interactions. The relevance of conformational propensities for the protein folding problem and the understanding of IDPs is briefly discussed. PMID:25062017

  3. Hyperemesis gravidarum avec troubles ioniques sévères: à propos d'un cas

    PubMed Central

    Jarraya, Anouar; Elleuch, Sahar; Zouari, Jawhar; Trigui, Khaled; Sofiene, Abidi; Smaoui, Mohamed; Kolsi, Kamel

    2015-01-01

    L'hyperemesis gravidarum s'accompagne habituellement d'une perte de poids, d'une acétonurie et de troubles hydro-électrolytiques comme il peut également s'accompagner d'anomalies du bilan hépatique. Nous rapportons un cas de vomissements gravidiques à 10 semaines d'aménorrhée non traité et vu tardivement avec des troubles ioniques sévères associés à des répercussions cliniques dans un contexte de cytolyse, de cholestase et d'insuffisance rénale aigue. Ce cas a bien répondu au traitement médical. PMID:26161187

  4. Lipome du corps calleux: à propos d'un cas avec revue de littérature

    PubMed Central

    Zhari, Bouchra; Mattiche, Houda; Boumdine, Hassan; Amil, Touriya; Ennouali, Hassan

    2015-01-01

    Le lipome du corps calleux est une malformation congénitale très rare, qui peut être associée à des degrés divers de dysgénésie du corps calleux. Son extension dans le ventricule latéral est encore plus rare. Il est souvent asymptomatique, mais peut se présenter par une épilepsie, hémiplégie, démence ou de simples céphalées. La tomodensitométrie et l'imagerie par résonance magnétique permettent facilement le diagnostic. Nous rapportons le cas d'une jeune fille de 14 ans, souffrant de simples céphalées, chez qui on découvre un lipome du corps calleux avec extension au ventricule latéral. PMID:26526933

  5. On the conformation of the propranolol molecule

    NASA Astrophysics Data System (ADS)

    Sadlej-Sosnowska, N.; Dobrowolski, J. Cz; Mazurek, A. P.

    2000-03-01

    The structure of the propranolol molecule has been optimized within the AM1 and PM3 semiempirical framework followed by ab initio HF/6-31G ∗ refinement. On each calculation level the conformational space was sampled to search for the lowest-energy conformer(s) from among a few hundreds of conformers at the semiempirical step and next from among a few dozens of conformers at the ab initio level. Finally, five stable conformers were found; each stabilized by one or two of the three possible hydrogen bonds. The geometrical and electronic parameters were established and found to differ only slightly in the structures with the hydrogen bond either present or not.

  6. Measuring the mechanical properties of molecular conformers

    NASA Astrophysics Data System (ADS)

    Jarvis, S. P.; Taylor, S.; Baran, J. D.; Champness, N. R.; Larsson, J. A.; Moriarty, P.

    2015-09-01

    Scanning probe-actuated single molecule manipulation has proven to be an exceptionally powerful tool for the systematic atomic-scale interrogation of molecular adsorbates. To date, however, the extent to which molecular conformation affects the force required to push or pull a single molecule has not been explored. Here we probe the mechanochemical response of two tetra(4-bromophenyl)porphyrin conformers using non-contact atomic force microscopy where we find a large difference between the lateral forces required for manipulation. Remarkably, despite sharing very similar adsorption characteristics, variations in the potential energy surface are capable of prohibiting probe-induced positioning of one conformer, while simultaneously permitting manipulation of the alternative conformational form. Our results are interpreted in the context of dispersion-corrected density functional theory calculations which reveal significant differences in the diffusion barriers for each conformer. These results demonstrate that conformational variation significantly modifies the mechanical response of even simple porpyhrins, potentially affecting many other flexible molecules.

  7. Measuring the mechanical properties of molecular conformers.

    PubMed

    Jarvis, S P; Taylor, S; Baran, J D; Champness, N R; Larsson, J A; Moriarty, P

    2015-09-21

    Scanning probe-actuated single molecule manipulation has proven to be an exceptionally powerful tool for the systematic atomic-scale interrogation of molecular adsorbates. To date, however, the extent to which molecular conformation affects the force required to push or pull a single molecule has not been explored. Here we probe the mechanochemical response of two tetra(4-bromophenyl)porphyrin conformers using non-contact atomic force microscopy where we find a large difference between the lateral forces required for manipulation. Remarkably, despite sharing very similar adsorption characteristics, variations in the potential energy surface are capable of prohibiting probe-induced positioning of one conformer, while simultaneously permitting manipulation of the alternative conformational form. Our results are interpreted in the context of dispersion-corrected density functional theory calculations which reveal significant differences in the diffusion barriers for each conformer. These results demonstrate that conformational variation significantly modifies the mechanical response of even simple porpyhrins, potentially affecting many other flexible molecules.

  8. Conformal basis for flat space amplitudes

    NASA Astrophysics Data System (ADS)

    Pasterski, Sabrina; Shao, Shu-Heng

    2017-09-01

    We study solutions of the Klein-Gordon, Maxwell, and linearized Einstein equations in R1 ,d +1 that transform as d -dimensional conformal primaries under the Lorentz group S O (1 ,d +1 ). Such solutions, called conformal primary wavefunctions, are labeled by a conformal dimension Δ and a point in Rd, rather than an on-shell (d +2 )-dimensional momentum. We show that the continuum of scalar conformal primary wavefunctions on the principal continuous series Δ ∈d/2 +i R of S O (1 ,d +1 ) spans a complete set of normalizable solutions to the wave equation. In the massless case, with or without spin, the transition from momentum space to conformal primary wavefunctions is implemented by a Mellin transform. As a consequence of this construction, scattering amplitudes in this basis transform covariantly under S O (1 ,d +1 ) as d -dimensional conformal correlators.

  9. Conformal regularization of Einstein's field equations

    NASA Astrophysics Data System (ADS)

    Röhr, Niklas; Uggla, Claes

    2005-09-01

    To study asymptotic structures, we regularize Einstein's field equations by means of conformal transformations. The conformal factor is chosen so that it carries a dimensional scale that captures crucial asymptotic features. By choosing a conformal orthonormal frame, we obtain a coupled system of differential equations for a set of dimensionless variables, associated with the conformal dimensionless metric, where the variables describe ratios with respect to the chosen asymptotic scale structure. As examples, we describe some explicit choices of conformal factors and coordinates appropriate for the situation of a timelike congruence approaching a singularity. One choice is shown to just slightly modify the so-called Hubble-normalized approach, and one leads to dimensionless first-order symmetric hyperbolic equations. We also discuss differences and similarities with other conformal approaches in the literature, as regards, e.g., isotropic singularities.

  10. Conformational Analysis on structural perturbations of the zinc finger NEMO

    NASA Astrophysics Data System (ADS)

    Godwin, Ryan; Salsbury, Freddie; Salsbury Group Team

    2014-03-01

    The NEMO (NF-kB Essential Modulator) Zinc Finger protein (2jvx) is a functional Ubiquitin-binding domain, and plays a role in signaling pathways for immune/inflammatory responses, apoptosis, and oncogenesis [Cordier et al., 2008]. Characterized by 3 cysteines and 1 histidine residue at the active site, the biologically occurring, bound zinc configuration is a stable structural motif. Perturbations of the zinc binding residues suggest conformational changes in the 423-atom protein characterized via analysis of all-atom molecular dynamics simulations. Structural perturbations include simulations with and without a zinc ion and with and without de-protonated cysteines, resulting in four distinct configurations. Simulations of various time scales show consistent results, yet the longest, GPU driven, microsecond runs show more drastic structural and dynamic fluctuations when compared to shorter duration time-scales. The last cysteine residue (26 of 28) and the helix on which it resides exhibit a secondary, locally unfolded conformation in addition to its normal bound conformation. Combined analytics elucidate how the presence of zinc and/or protonated cysteines impact the dynamics and energetic fluctuations of NEMO. Comprehensive Cancer Center of Wake Forest University Computational Biosciences shared resource supported by NCI CCSG P30CA012197.

  11. Présentation atypique d'une granulomatose avec polyangeite: à propos d'une observation pédiatrique

    PubMed Central

    Berriche, Olfa; Younes, Samia; Ammari, Wafa; Alaya, Wafa; Kessomtini, Wassia; Hammami, Sonia

    2015-01-01

    La granulomatose avec polyangéite (GPA) est une vascularite nécrosante systémique, caractérisée par une inflammation granulomateuse, une nécrose tissulaire et une vascularite touchant les vaisseaux de moyen et, surtout, de petit calibre, elle touche rarement l'enfant. PMID:26327978

  12. Conformational dynamic of fibrinogen by dielectric spectroscopy

    NASA Astrophysics Data System (ADS)

    Berest, Vladimir P.; Gatash, Sergiy V.

    1999-12-01

    The information concerning the structural changes of fibrinogen molecule at temperatures form 4 to 52 degrees C has ben obtained by means of dielectric-spectroscopy method. Besides the known conformational transition II, under physiological conditions conformational transition at 20-22 degrees C has been observed in fibrinogen. This transition might be connected with structural transition in peripheral domain of fibrinogen. Revealed conformational transition, probably, determines the character of the temperature dependence of blood platelet aggregation.

  13. Conformal Electromagnetic Particle in Cell: A Review

    SciTech Connect

    Meierbachtol, Collin S.; Greenwood, Andrew D.; Verboncoeur, John P.; Shanker, Balasubramaniam

    2015-10-26

    We review conformal (or body-fitted) electromagnetic particle-in-cell (EM-PIC) numerical solution schemes. Included is a chronological history of relevant particle physics algorithms often employed in these conformal simulations. We also provide brief mathematical descriptions of particle-tracking algorithms and current weighting schemes, along with a brief summary of major time-dependent electromagnetic solution methods. Several research areas are also highlighted for recommended future development of new conformal EM-PIC methods.

  14. Scattering Via Conformal Higher Spin Exchanges

    NASA Astrophysics Data System (ADS)

    Tseytlin, A. A.

    We consider a model of massless scalars interacting (via bilinear conserved currents) with conformal higher spin fields in flat space. We compute the tree-level four-scalar scattering amplitude using a natural prescription for summation over an infinite set of conformal higher spin exchanges and find that it vanishes. Independently, we show that the vanishing of the scalar scattering amplitude is, in fact, implied by the global conformal higher spin symmetry of this model.

  15. Conformal Electromagnetic Particle in Cell: A Review

    DOE PAGES

    Meierbachtol, Collin S.; Greenwood, Andrew D.; Verboncoeur, John P.; ...

    2015-10-26

    We review conformal (or body-fitted) electromagnetic particle-in-cell (EM-PIC) numerical solution schemes. Included is a chronological history of relevant particle physics algorithms often employed in these conformal simulations. We also provide brief mathematical descriptions of particle-tracking algorithms and current weighting schemes, along with a brief summary of major time-dependent electromagnetic solution methods. Several research areas are also highlighted for recommended future development of new conformal EM-PIC methods.

  16. Solution conformational study of Scyliorhinin I analogues with conformational constraints by two-dimensional NMR and theoretical conformational analysis.

    PubMed

    Rodziewicz-Motowidło, S; Legowska, A; Qi, X F; Czaplewski, C; Liwo, A; Sowiński, P; Mozga, W; Olczak, J; Zabrocki, J; Rolka, K

    2000-09-01

    Two analogues of Scyliorhinin I (Scyl), a tachykinin with N-MeLeu in position 8 and a 1,5-disubstituted tetrazole ring between positions 7 and 8, introduced in order to generate local conformational constraints, were synthesized using the solid-phase method. Conformational studies in water and DMSO-d6 were performed on these peptides using a combination of the two-dimensional NMR technique and theoretical conformational analysis. The algorithm of conformational search consisted of the following three stages: (i) extensive global conformational analysis in order to find all low-energy conformations; (ii) calculation of the NOE effects and vicinal coupling constants for each of the low energy conformations; (iii) determining the statistical weights of these conformations by means of a nonlinear least-squares procedure, in order to obtain the best fit of the averaged simulated spectrum to the experimental one. In both solvents the three-dimensional structure of the analogues studied can be interpreted only in terms of an ensemble of multiple conformations. For [MeLeu8]Scyl, the C-terminal 6-10 fragment adopts more rigid structure than the N-terminal one. In the case of the analogue with the tetrazole ring in DMSO-d6 the three-dimensional structure is characterized by two dominant conformers with similar geometry of their backbones. They superimpose especially well (RMSD = 0.28 A) in the 6-9 fragments. All conformers calculated in both solvents superimpose in their C-terminal fragments much better than those of the first analogue. The results obtained indicate that the introduction of the tetrazole ring into the Scyl molecule rigidifies its structure significantly more than that of MeLeu.

  17. Rotational Spectroscopy Unveils Eleven Conformers of Adrenaline

    NASA Astrophysics Data System (ADS)

    Cabezas, C.; Cortijo, V.; Mata, S.; Lopez, J. C.; Alonso, J. L.

    2013-06-01

    Recent improvements in our LA-MB-FTMW instrumentation have allowed the characterization of eleven and eight conformers for the neurotransmitters adrenaline and noradrenaline respectively. The observation of this rich conformational behavior is in accordance with the recent observation of seven conformers for dopamine and in sharp contrast with the conformational reduction proposed for catecholamines. C. Cabezas, I. Peña, J. C. López, J. L. Alonso J. Phys. Chem. Lett. 2013, 4, 486. H. Mitsuda, M. Miyazaki, I. B. Nielsen, P. Carcabal,C. Dedonder, C. Jouvet, S. Ishiuchi, M. Fujii J. Phys. Chem. Lett. 2010, 1, 1130.

  18. Kinetically accessible compact conformations of chain molecules

    NASA Astrophysics Data System (ADS)

    Yoshie, Naoko; Yamamoto, Keigo

    1998-05-01

    The kinetic accessibility of various compact conformations of chain molecules is studied using a short self-avoiding chain on a three-dimensional cubic lattice. The kinetic accessibility of a compact conformation depends on the conformational energy and the distances from the other conformations along kinetically possible trajectories. We focus on the kinetic distances. We consider a chain in a poor solvent, having multiple lowest-energy compact conformations. The chain collapse from an arbitrary conformation to one of the lowest energy conformations is investigated. Though the lowest energy states would be occupied with the same probability in equilibrium, the probabilities for a first hit are not necessarily all the same and they indeed are not. We show that the hit probability at low temperature can be used as a measure of the kinetic distances from other conformations. The hit probability is investigated under two kinetic processes. One is a Monte Carlo dynamic process and the other is a "contact-set stepping" process, in which kinetic distances between conformations are defined based on sets of contacts. The two kinetic processes exhibit similar results showing that both processes well reproduce the kinetic behavior of chain molecules. Through the characterization of the states with large hit probability at low temperature, we show that the influence of the kinetic distances on the kinetic accessibility can be explained by domain structure or locality of contacts.

  19. Conformity in condylar replacement knee prosthesis.

    PubMed

    Walker, P S; Hsieh, H H

    1977-05-01

    Experiments were carried out to determine the optimum conformity between the femoral and tibial condyles in condylar replacement knee prostheses. Wear tests and observations from removed prostheses indicated that both high and low conformity produced characteristic abrasion and fatigue. Partly conforming condyles provided stability under load-bearing but allowed laxity to occur. Fixation to resist the various forces on the tibial components was enhanced by a short central intramedullary peg. Partial conformity is proposed as the optimum configuration between femoral and tibial components.

  20. Proline Conformation in a Functional Tau Fragment.

    PubMed

    Ahuja, Puneet; Cantrelle, François-Xavier; Huvent, Isabelle; Hanoulle, Xavier; Lopez, Juan; Smet, Caroline; Wieruszeski, Jean-Michel; Landrieu, Isabelle; Lippens, G

    2016-01-16

    The conformational state of distinct prolines can determine the folding of a protein but equally other biological processes when coupled to a conformation-sensitive secondary reaction. For the neuronal tau protein, the importance of proline conformation is underscored by its interaction with different prolyl cis/trans isomerases. The proline conformation would gain even further importance after phosphorylation of the preceding residue by various proline-directed kinases. A number of molecular diseases including Alzheimer's disease and traumatic brain injury were thereby recently qualified as "cistauosis", as they would imply a cis conformation for the pThr231-Pro232 prolyl bond. We here investigate by NMR spectroscopy the conformation of all prolines in a functional Tau fragment, Tau[208-324]. Although we can detect and identify some minor conformers in the cis form, we show that all prolines are for over 90% in the trans conformation. Phosphorylation by CDK2/CycA3, which notably leads to complete modification of the Thr231 residue, does not change this conclusion. Our data hence disagree with the notion that specific prolyl bonds in tau would adopt preferentially the cis conformation.

  1. Conformal and projective symmetries in Newtonian cosmology

    NASA Astrophysics Data System (ADS)

    Duval, C.; Gibbons, G. W.; Horváthy, P. A.

    2017-02-01

    Definitions of non-relativistic conformal transformations are considered both in the Newton-Cartan and in the Kaluza-Klein-type Eisenhart/Bargmann geometrical frameworks. The symmetry groups that come into play are exemplified by the cosmological, and also the Newton-Hooke solutions of Newton's gravitational field equations. It is shown, in particular, that the maximal symmetry group of the standard cosmological model is isomorphic to the 13-dimensional conformal-Newton-Cartan group whose conformal-Bargmann extension is explicitly worked out. Attention is drawn to the appearance of independent space and time dilations, in contrast with the Schrödinger group or the Conformal Galilei Algebra.

  2. Light gauginos and conformal sequestering

    SciTech Connect

    Hanaki, Kentaro; Ookouchi, Yutaka

    2011-06-15

    In a wide class of direct and semidirect gauge mediation models, it has been observed that the gaugino masses vanish at leading order. It implies that there is a hierarchy between the gaugino and sfermion masses, invoking a fine-tuning problem in the Higgs sector via radiative corrections. In this paper, we explore the possibility of solving this anomalously light gaugino problem exploiting strong conformal dynamics in the hidden sector. With a mild assumption on the anomalous dimensions of the hidden sector operators, we show that the next-to-leading order contributions to the gaugino masses can naturally be in the same order as the sfermion masses. The {mu}/B{sub {mu}} problem is also discussed.

  3. Conformable eddy current array delivery

    NASA Astrophysics Data System (ADS)

    Summan, Rahul; Pierce, Gareth; Macleod, Charles; Mineo, Carmelo; Riise, Jonathan; Morozov, Maxim; Dobie, Gordon; Bolton, Gary; Raude, Angélique; Dalpé, Colombe; Braumann, Johannes

    2016-02-01

    The external surface of stainless steel containers used for the interim storage of nuclear material may be subject to Atmospherically Induced Stress Corrosion Cracking (AISCC). The inspection of such containers poses a significant challenge due to the large quantities involved; therefore, automating the inspection process is of considerable interest. This paper reports upon a proof-of-concept project concerning the automated NDT of a set of test containers containing artificially generated AISCCs. An Eddy current array probe with a conformable padded surface from Eddyfi was used as the NDT sensor and end effector on a KUKA KR5 arc HW robot. A kinematically valid cylindrical raster scan path was designed using the KUKA|PRC path planning software. Custom software was then written to interface measurement acquisition from the Eddyfi hardware with the motion control of the robot. Preliminary results and analysis are presented from scanning two canisters.

  4. Conformal frame dependence of inflation

    SciTech Connect

    Domènech, Guillem; Sasaki, Misao E-mail: misao@yukawa.kyoto-u.ac.jp

    2015-04-01

    Physical equivalence between different conformal frames in scalar-tensor theory of gravity is a known fact. However, assuming that matter minimally couples to the metric of a particular frame, which we call the matter Jordan frame, the matter point of view of the universe may vary from frame to frame. Thus, there is a clear distinction between gravitational sector (curvature and scalar field) and matter sector. In this paper, focusing on a simple power-law inflation model in the Einstein frame, two examples are considered; a super-inflationary and a bouncing universe Jordan frames. Then we consider a spectator curvaton minimally coupled to a Jordan frame, and compute its contribution to the curvature perturbation power spectrum. In these specific examples, we find a blue tilt at short scales for the super-inflationary case, and a blue tilt at large scales for the bouncing case.

  5. Recherche De Correlations Temporelles Des Muons Cosmiques Avec Macro Et Perte D'Energie Des Nuclearites

    NASA Astrophysics Data System (ADS)

    Moussa, A.

    2009-11-01

    The first parts of the thesis recalls the main features of the large MACRO experiment at the underground Gran Sasso Laboratory. It then describes the atmospheric muons measured by the experiment and the selection criteria to obtain and analyze a large sample of cosmic muons. The time series of MACRO muons was analyzed with two complementary approaches: search for the occurrence of bursts of muon events and search for periodicities in the muon time distribution. The Scan Statistics method was used in the first case and the Lomb-Scargle spectral analysis in the second case. The two techniques complete early analyses performed with "folding" methods. It is confirmed that the seasonal variation is the dominant periodic variation, and one also confirms the solar diurnal and sidereal modulations. A separate study concerns the analysis of the energy losses of the hypothetical Nuclearites in different materials and detectors; their importance for the searches performed by the MACRO and the SLIM experiments is discussed.

  6. Module Configuration

    DOEpatents

    Oweis, Salah; D'Ussel, Louis; Chagnon, Guy; Zuhowski, Michael; Sack, Tim; Laucournet, Gaullume; Jackson, Edward J.

    2002-06-04

    A stand alone battery module including: (a) a mechanical configuration; (b) a thermal management configuration; (c) an electrical connection configuration; and (d) an electronics configuration. Such a module is fully interchangeable in a battery pack assembly, mechanically, from the thermal management point of view, and electrically. With the same hardware, the module can accommodate different cell sizes and, therefore, can easily have different capacities. The module structure is designed to accommodate the electronics monitoring, protection, and printed wiring assembly boards (PWAs), as well as to allow airflow through the module. A plurality of modules may easily be connected together to form a battery pack. The parts of the module are designed to facilitate their manufacture and assembly.

  7. Probing the role of water in protein conformation and function.

    PubMed Central

    Rand, R P

    2004-01-01

    Life began in a bath of water and has never escaped it. Cellular function has forced the evolution of many mechanisms ensuring that cellular water concentration has never changed significantly. To free oneself of any conceptual distinction among all small molecules, solutes and solvents, means that experiments to probe water's specific role in molecular function can be designed like any classical chemical reaction. Such an 'osmotic stress' strategy will be described in general and for an enzyme, hexokinase. Water behaves like a reactant that competes with glucose in binding to hexokinase, and modulates its conformational change and activity. This 'osmotic stress' strategy, now applied to many very different systems, shows that water plays a significant role, energetically, in most macromolecular reactions. It can be required to fill obligatory space, it dominates nearest non-specific interactions between large surfaces, it can be a reactant modulating conformational change; all this in addition to its more commonly perceived static role as an integral part of stereospecific intramolecular structure. PMID:15306382

  8. ANTIGENIC MODULATION

    PubMed Central

    Old, Lloyd J.; Stockert, Elisabeth; Boyse, Edward A.; Kim, Jae Ho

    1968-01-01

    Antigenic modulation (the loss of TL antigens from TL+ cells exposed to TL antibody in the absence of lytic complement) has been demonstrated in vitro. An ascites leukemia, phenotype TL.1,2,3, which modulates rapidly and completely when incubated with TL antiserum in vitro, was selected for further study of the phenomenon. Over a wide range of TL antibody concentrations modulation at 37°C was detectable within 10 min and was complete within approximately 1 hr. The cells were initially sensitized to C' by their contact with antibody, thereafter losing this sensitivity to C' lysis together with their sensitivity to TL antibody and C' in the cytotoxic test. The capacity of the cells to undergo modulation was abolished by actinomycin D and by iodoacetamide, and by reducing the temperature of incubation to 0°C. Thus modulation apparently is an active cellular process. Antigens TL. 1,2, and 3 are all modulated by anti-TL.1,3 serum and by anti-TL.3 serum. This modulation affects all three TL components together, even when antibody to one or two of them is lacking. aAnti-TL.2 serum does not induce modulation and in fact impairs modulation by the other TL antibodies. The influence of the TL phenotype of cells upon the demonstrable content of H-2 (D region) isoantigen, first shown in cells modulated in vivo, has been observed with cells modulated in vitro. Cells undergoing modulation show a progressive increase in H-2 (D region) antigen over a period of 4 hr, with no change in H-2 antigens of the K region. Restoration of the TL+ phenotype of modulated cells after removal of antibody is less rapid than TL+ → TL- modulation and may require several cell divisions. PMID:5636556

  9. Conformal, concircular, quasi-conformal and conharmonic flatness on normal complex contact metric manifolds

    NASA Astrophysics Data System (ADS)

    Turgut Vanli, Aysel; Unal, Inan

    Conformal, concircular, quasi-conformal and conharmonic curvature tensors play an important role in Riemannian geometry. In this paper, we study on normal complex contact metric manifolds under flatness conditions of these tensors.

  10. Conformational analysis of thiophene analogs of propranolol

    NASA Astrophysics Data System (ADS)

    Corral, Carlos; Donoso, Rosa; Elguero, Jose; Goya, Pilar; Lissavetzky, Jaime; Rozas, Isabel

    1990-10-01

    Conformation of 3-tert-butylamino-1-thienyloxy-2-propanol, a thiophene analogue of propanolol, have been theoretically investigated by molecular mechanics and semiempirical calculations. The conformational minima obtained have been compared with those reported for propranolol using molecular graphics. The good "fit" obtained can account for the similar biological activity of these compounds.

  11. 40 CFR 93.154 - Conformity analysis.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Conformity analysis. 93.154 Section 93... General Federal Actions to State or Federal Implementation Plans § 93.154 Conformity analysis. Any Federal... choose to adopt the analysis of another Federal agency or develop its own analysis in order to make its...

  12. 40 CFR 51.854 - Conformity analysis.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 2 2010-07-01 2010-07-01 false Conformity analysis. 51.854 Section 51... Federal Actions to State or Federal Implementation Plans § 51.854 Conformity analysis. Link to an... for various aspects of a project, a Federal agency may choose to adopt the analysis of another Federal...

  13. Starkweather Social Conformity Test for Preschool Children.

    ERIC Educational Resources Information Center

    Starkweather, Elizabeth K.

    The Starkweather Social Conformity Test is a research instrument designed to measure conforming and nonconforming behavior by providing the young child with opportunities to make choices in a situation in which he can follow a model or respond freely according to his own preferences. The test discriminates between compulsive conformists or…

  14. Regulatory Conformance Checking: Logic and Logical Form

    ERIC Educational Resources Information Center

    Dinesh, Nikhil

    2010-01-01

    We consider the problem of checking whether an organization conforms to a body of regulation. Conformance is studied in a runtime verification setting. The regulation is translated to a logic, from which we synthesize monitors. The monitors are evaluated as the state of an organization evolves over time, raising an alarm if a violation is…

  15. A model of protein conformational substates

    PubMed Central

    Stein, D. L.

    1985-01-01

    Many proteins have been observed to exist in a large number of conformations that are believed to play an important role in their dynamics. A model of protein conformational substates that incorporates the ideas of frustration and disorder in analogy to glasses and spin glasses is proposed. Applications to x-ray diffraction, Mössbauer studies, and recombination experiments are discussed. PMID:16593568

  16. Conformational Sampling of Peptides in Cellular Environments☆

    PubMed Central

    Tanizaki, Seiichiro; Clifford, Jacob; Connelly, Brian D.; Feig, Michael

    2008-01-01

    Abstract Biological systems provide a complex environment that can be understood in terms of its dielectric properties. High concentrations of macromolecules and cosolvents effectively reduce the dielectric constant of cellular environments, thereby affecting the conformational sampling of biomolecules. To examine this effect in more detail, the conformational preference of alanine dipeptide, poly-alanine, and melittin in different dielectric environments is studied with computer simulations based on recently developed generalized Born methodology. Results from these simulations suggest that extended conformations are favored over α-helical conformations at the dipeptide level at and below dielectric constants of 5–10. Furthermore, lower-dielectric environments begin to significantly stabilize helical structures in poly-alanine at ɛ = 20. In the more complex peptide melittin, different dielectric environments shift the equilibrium between two main conformations: a nearly fully extended helix that is most stable in low dielectrics and a compact, V-shaped conformation consisting of two helices that is preferred in higher dielectric environments. An additional conformation is only found to be significantly populated at intermediate dielectric constants. Good agreement with previous studies of different peptides in specific, less-polar solvent environments, suggest that helix stabilization and shifts in conformational preferences in such environments are primarily due to a reduced dielectric environment rather than specific molecular details. The findings presented here make predictions of how peptide sampling may be altered in dense cellular environments with reduced dielectric response. PMID:17905846

  17. Conformity to Peer Pressure in Preschool Children

    ERIC Educational Resources Information Center

    Haun, Daniel B. M.; Tomasello, Michael

    2011-01-01

    Both adults and adolescents often conform their behavior and opinions to peer groups, even when they themselves know better. The current study investigated this phenomenon in 24 groups of 4 children between 4;2 and 4;9 years of age. Children often made their judgments conform to those of 3 peers, who had made obviously erroneous but unanimous…

  18. Regulatory Conformance Checking: Logic and Logical Form

    ERIC Educational Resources Information Center

    Dinesh, Nikhil

    2010-01-01

    We consider the problem of checking whether an organization conforms to a body of regulation. Conformance is studied in a runtime verification setting. The regulation is translated to a logic, from which we synthesize monitors. The monitors are evaluated as the state of an organization evolves over time, raising an alarm if a violation is…

  19. Conformity to Peer Pressure in Preschool Children