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Sample records for distort dna substrates

  1. Distortion

    OpenAIRE

    Schultz, Isabella Odorico; Zmylon, Nanna Nielsen; Britze, Juliane

    2014-01-01

    This paper investigates the audience’s perception of the music festival Distortion. By conducting a field-study focusing on the subject’s perception of Distortion, their perception of the Distortion-attendants, and their perception on the promotion of Distortion, the paper will relate the audience perception to the promotion of the event. Using the group’s own research on the promotion of Distortion, the paper points out both the consistencies and the inconsistencies between the promotion and...

  2. Effect of Rap1 binding on DNA distortion and potassium permanganate hypersensitivity.

    Science.gov (United States)

    Le Bihan, Yann-Vaï; Matot, Béatrice; Pietrement, Olivier; Giraud-Panis, Marie-Josèphe; Gasparini, Sylvaine; Le Cam, Eric; Gilson, Eric; Sclavi, Bianca; Miron, Simona; Le Du, Marie-Hélène

    2013-03-01

    Repressor activator protein 1 (Rap1) is an essential factor involved in transcription and telomere stability in the budding yeast Saccharomyces cerevisiae. Its interaction with DNA causes hypersensitivity to potassium permanganate, suggesting local DNA melting and/or distortion. In this study, various Rap1-DNA crystal forms were obtained using specifically designed crystal screens. Analysis of the DNA conformation showed that its distortion was not sufficient to explain the permanganate reactivity. However, anomalous data collected at the Mn edge using a Rap1-DNA crystal soaked in potassium permanganate solution indicated that the DNA conformation in the crystal was compatible with interaction with permanganate ions. Sequence-conservation analysis revealed that double-Myb-containing Rap1 proteins all carry a fully conserved Arg580 at a position that may favour interaction with permanganate ions, although it is not involved in the hypersensitive cytosine distortion. Permanganate reactivity assays with wild-type Rap1 and the Rap1[R580A] mutant demonstrated that Arg580 is essential for hypersensitivity. AFM experiments showed that wild-type Rap1 and the Rap1[R580A] mutant interact with DNA over 16 successive binding sites, leading to local DNA stiffening but not to accumulation of the observed local distortion. Therefore, Rap1 may cause permanganate hypersensitivity of DNA by forming a pocket between the reactive cytosine and Arg580, driving the permanganate ion towards the C5-C6 bond of the cytosine.

  3. Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1

    KAUST Repository

    Rashid, Fahad; Harris, Paul D.; Zaher, Manal S.; Sobhy, Mohamed Abdelmaboud; Joudeh, Luay I; Yan, Chunli; Piwonski, Hubert Marek; Tsutakawa, Susan E; Ivanov, Ivaylo; Tainer, John A; Habuchi, Satoshi; Hamdan, Samir

    2017-01-01

    that efficiently verifies substrate and suppresses off-target cleavage. FEN1 sculpts DNA with diffusion-limited kinetics to test DNA substrate. This DNA distortion mutually 'locks' protein and DNA conformation and enables substrate verification with extreme

  4. Distortion of DNA Origami on Graphene Imaged with Advanced TEM Techniques.

    Science.gov (United States)

    Kabiri, Yoones; Ananth, Adithya N; van der Torre, Jaco; Katan, Allard; Hong, Jin-Yong; Malladi, Sairam; Kong, Jing; Zandbergen, Henny; Dekker, Cees

    2017-08-01

    While graphene may appear to be the ultimate support membrane for transmission electron microscopy (TEM) imaging of DNA nanostructures, very little is known if it poses an advantage over conventional carbon supports in terms of resolution and contrast. Microscopic investigations are carried out on DNA origami nanoplates that are supported onto freestanding graphene, using advanced TEM techniques, including a new dark-field technique that is recently developed in our lab. TEM images of stained and unstained DNA origami are presented with high contrast on both graphene and amorphous carbon membranes. On graphene, the images of the origami plates show severe unwanted distortions, where the rectangular shape of the nanoplates is significantly distorted. From a number of comparative control experiments, it is demonstrated that neither staining agents, nor screening ions, nor the level of electron-beam irradiation cause this distortion. Instead, it is suggested that origami nanoplates are distorted due to hydrophobic interaction of the DNA bases with graphene upon adsorption of the DNA origami nanoplates. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Layered graphene-mica substrates induce melting of DNA origami

    Science.gov (United States)

    Green, Nathaniel S.; Pham, Phi H. Q.; Crow, Daniel T.; Burke, Peter J.; Norton, Michael L.

    2018-04-01

    Monolayer graphene supported on mica substrates induce melting of cross-shaped DNA origami. This behavior can be contrasted with the case of origami on graphene on graphite, where an expansion or partially re-organized structure is observed. On mica, only well-formed structures are observed. Comparison of the morphological differences observed for these probes after adsorption on these substrates provides insights into the sensitivity of DNA based nanostructures to the properties of the graphene monolayer, as modified by its substrate.

  6. Structural factors involved in the recognition of helix distortions in uv-damaged DNA by model peptides

    Energy Technology Data Exchange (ETDEWEB)

    Lang, H; Zimmer, C [Akademie der Wissenschaften der DDR, Jena. Forschungszentrum fuer Molekularbiologie und Medizin

    1977-02-28

    On the basis of our previous and present results concerning conformational changes of DNA after uv-irradiation some conclusions on the structure of DNA double helix in uv-damaged regions were drawn. From the results it appears that local distortions like denaturation or premelting should be excluded. Furthermore it was shown that the thymine dimerization strongly depends on the adjacent nucleic acid bases. By means of a strong binding effect of the oligopeptide netropsin to DNA irradiated at low uv-doses it is concluded that such local distortions in DNA together with a specific sequence-dependent variation of the conformation could act as recognition sites for endonucleases.

  7. Correlation of bistranded clustered abasic DNA lesion processing with structural and dynamic DNA helix distortion

    Science.gov (United States)

    Bignon, Emmanuelle; Gattuso, Hugo; Morell, Christophe; Dehez, François; Georgakilas, Alexandros G.; Monari, Antonio; Dumont, Elise

    2016-01-01

    Clustered apurinic/apyrimidinic (AP; abasic) DNA lesions produced by ionizing radiation are by far more cytotoxic than isolated AP lesion entities. The structure and dynamics of a series of seven 23-bp oligonucleotides featuring simple bistranded clustered damage sites, comprising of two AP sites, zero, one, three or five bases 3′ or 5′ apart from each other, were investigated through 400 ns explicit solvent molecular dynamics simulations. They provide representative structures of synthetically engineered multiply damage sites-containing oligonucleotides whose repair was investigated experimentally (Nucl. Acids Res. 2004, 32:5609-5620; Nucl. Acids Res. 2002, 30: 2800–2808). The inspection of extrahelical positioning of the AP sites, bulge and non Watson–Crick hydrogen bonding corroborates the experimental measurements of repair efficiencies by bacterial or human AP endonucleases Nfo and APE1, respectively. This study provides unprecedented knowledge into the structure and dynamics of clustered abasic DNA lesions, notably rationalizing the non-symmetry with respect to 3′ to 5′ position. In addition, it provides strong mechanistic insights and basis for future studies on the effects of clustered DNA damage on the recognition and processing of these lesions by bacterial or human DNA repair enzymes specialized in the processing of such lesions. PMID:27587587

  8. DNA origami deposition on native and passivated molybdenum disulfide substrates

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    Xiaoning Zhang

    2014-04-01

    Full Text Available Maintaining the structural fidelity of DNA origami structures on substrates is a prerequisite for the successful fabrication of hybrid DNA origami/semiconductor-based biomedical sensor devices. Molybdenum disulfide (MoS2 is an ideal substrate for such future sensors due to its exceptional electrical, mechanical and structural properties. In this work, we performed the first investigations into the interaction of DNA origami with the MoS2 surface. In contrast to the structure-preserving interaction of DNA origami with mica, another atomically flat surface, it was observed that DNA origami structures rapidly lose their structural integrity upon interaction with MoS2. In a further series of studies, pyrene and 1-pyrenemethylamine, were evaluated as surface modifications which might mitigate this effect. While both species were found to form adsorption layers on MoS2 via physisorption, 1-pyrenemethylamine serves as a better protective agent and preserves the structures for significantly longer times. These findings will be beneficial for the fabrication of future DNA origami/MoS2 hybrid electronic structures.

  9. Substrate interactions and promiscuity in a viral DNA packaging motor.

    Science.gov (United States)

    Aathavan, K; Politzer, Adam T; Kaplan, Ariel; Moffitt, Jeffrey R; Chemla, Yann R; Grimes, Shelley; Jardine, Paul J; Anderson, Dwight L; Bustamante, Carlos

    2009-10-01

    The ASCE (additional strand, conserved E) superfamily of proteins consists of structurally similar ATPases associated with diverse cellular activities involving metabolism and transport of proteins and nucleic acids in all forms of life. A subset of these enzymes consists of multimeric ringed pumps responsible for DNA transport in processes including genome packaging in adenoviruses, herpesviruses, poxviruses and tailed bacteriophages. Although their mechanism of mechanochemical conversion is beginning to be understood, little is known about how these motors engage their nucleic acid substrates. Questions remain as to whether the motors contact a single DNA element, such as a phosphate or a base, or whether contacts are distributed over several parts of the DNA. Furthermore, the role of these contacts in the mechanochemical cycle is unknown. Here we use the genome packaging motor of the Bacillus subtilis bacteriophage varphi29 (ref. 4) to address these questions. The full mechanochemical cycle of the motor, in which the ATPase is a pentameric-ring of gene product 16 (gp16), involves two phases-an ATP-loading dwell followed by a translocation burst of four 2.5-base-pair (bp) steps triggered by hydrolysis product release. By challenging the motor with a variety of modified DNA substrates, we show that during the dwell phase important contacts are made with adjacent phosphates every 10-bp on the 5'-3' strand in the direction of packaging. As well as providing stable, long-lived contacts, these phosphate interactions also regulate the chemical cycle. In contrast, during the burst phase, we find that DNA translocation is driven against large forces by extensive contacts, some of which are not specific to the chemical moieties of DNA. Such promiscuous, nonspecific contacts may reflect common translocase-substrate interactions for both the nucleic acid and protein translocases of the ASCE superfamily.

  10. Enzymatic activities and DNA substrate specificity of Mycobacterium tuberculosis DNA helicase XPB.

    Science.gov (United States)

    Balasingham, Seetha V; Zegeye, Ephrem Debebe; Homberset, Håvard; Rossi, Marie L; Laerdahl, Jon K; Bohr, Vilhelm A; Tønjum, Tone

    2012-01-01

    XPB, also known as ERCC3 and RAD25, is a 3' → 5' DNA repair helicase belonging to the superfamily 2 of helicases. XPB is an essential core subunit of the eukaryotic basal transcription factor complex TFIIH. It has two well-established functions: in the context of damaged DNA, XPB facilitates nucleotide excision repair by unwinding double stranded DNA (dsDNA) surrounding a DNA lesion; while in the context of actively transcribing genes, XPB facilitates initiation of RNA polymerase II transcription at gene promoters. Human and other eukaryotic XPB homologs are relatively well characterized compared to conserved homologs found in mycobacteria and archaea. However, more insight into the function of bacterial helicases is central to understanding the mechanism of DNA metabolism and pathogenesis in general. Here, we characterized Mycobacterium tuberculosis XPB (Mtb XPB), a 3'→5' DNA helicase with DNA-dependent ATPase activity. Mtb XPB efficiently catalyzed DNA unwinding in the presence of significant excess of enzyme. The unwinding activity was fueled by ATP or dATP in the presence of Mg(2+)/Mn(2+). Consistent with the 3'→5' polarity of this bacterial XPB helicase, the enzyme required a DNA substrate with a 3' overhang of 15 nucleotides or more. Although Mtb XPB efficiently unwound DNA model substrates with a 3' DNA tail, it was not active on substrates containing a 3' RNA tail. We also found that Mtb XPB efficiently catalyzed ATP-independent annealing of complementary DNA strands. These observations significantly enhance our understanding of the biological roles of Mtb XPB.

  11. Enzymatic activities and DNA substrate specificity of Mycobacterium tuberculosis DNA helicase XPB.

    Directory of Open Access Journals (Sweden)

    Seetha V Balasingham

    Full Text Available XPB, also known as ERCC3 and RAD25, is a 3' → 5' DNA repair helicase belonging to the superfamily 2 of helicases. XPB is an essential core subunit of the eukaryotic basal transcription factor complex TFIIH. It has two well-established functions: in the context of damaged DNA, XPB facilitates nucleotide excision repair by unwinding double stranded DNA (dsDNA surrounding a DNA lesion; while in the context of actively transcribing genes, XPB facilitates initiation of RNA polymerase II transcription at gene promoters. Human and other eukaryotic XPB homologs are relatively well characterized compared to conserved homologs found in mycobacteria and archaea. However, more insight into the function of bacterial helicases is central to understanding the mechanism of DNA metabolism and pathogenesis in general. Here, we characterized Mycobacterium tuberculosis XPB (Mtb XPB, a 3'→5' DNA helicase with DNA-dependent ATPase activity. Mtb XPB efficiently catalyzed DNA unwinding in the presence of significant excess of enzyme. The unwinding activity was fueled by ATP or dATP in the presence of Mg(2+/Mn(2+. Consistent with the 3'→5' polarity of this bacterial XPB helicase, the enzyme required a DNA substrate with a 3' overhang of 15 nucleotides or more. Although Mtb XPB efficiently unwound DNA model substrates with a 3' DNA tail, it was not active on substrates containing a 3' RNA tail. We also found that Mtb XPB efficiently catalyzed ATP-independent annealing of complementary DNA strands. These observations significantly enhance our understanding of the biological roles of Mtb XPB.

  12. pH-Dependent DNA Distortion and Repression of Gene Expression by Pectobacterium atrosepticum PecS.

    Science.gov (United States)

    Deochand, Dinesh K; Meariman, Jacob K; Grove, Anne

    2016-07-15

    Transcriptional activity is exquisitely sensitive to changes in promoter DNA topology. Transcription factors may therefore control gene activity by modulating the relative positioning of -10 and -35 promoter elements. The plant pathogen Pectobacterium atrosepticum, which causes soft rot in potatoes, must alter gene expression patterns to ensure growth in planta. In the related soft-rot enterobacterium Dickeya dadantii, PecS functions as a master regulator of virulence gene expression. Here, we report that P. atrosepticum PecS controls gene activity by altering promoter DNA topology in response to pH. While PecS binds the pecS promoter with high affinity regardless of pH, it induces significant DNA distortion only at neutral pH, the pH at which the pecS promoter is repressed in vivo. At pH ∼8, DNA distortions are attenuated, and PecS no longer represses the pecS promoter. A specific histidine (H142) located in a crevice between the dimerization- and DNA-binding regions is required for pH-dependent changes in DNA distortion and repression of gene activity, and mutation of this histidine renders the mutant protein incapable of repressing the pecS promoter. We propose that protonated PecS induces a DNA conformation at neutral pH in which -10 and -35 promoter elements are suboptimally positioned for RNA polymerase binding; on deprotonation of PecS, binding is no longer associated with significant changes in DNA conformation, allowing gene expression. We suggest that this mode of gene regulation leads to differential expression of the PecS regulon in response to alkalinization of the plant apoplast.

  13. DNA/RNA hybrid substrates modulate the catalytic activity of purified AID.

    Science.gov (United States)

    Abdouni, Hala S; King, Justin J; Ghorbani, Atefeh; Fifield, Heather; Berghuis, Lesley; Larijani, Mani

    2018-01-01

    Activation-induced cytidine deaminase (AID) converts cytidine to uridine at Immunoglobulin (Ig) loci, initiating somatic hypermutation and class switching of antibodies. In vitro, AID acts on single stranded DNA (ssDNA), but neither double-stranded DNA (dsDNA) oligonucleotides nor RNA, and it is believed that transcription is the in vivo generator of ssDNA targeted by AID. It is also known that the Ig loci, particularly the switch (S) regions targeted by AID are rich in transcription-generated DNA/RNA hybrids. Here, we examined the binding and catalytic behavior of purified AID on DNA/RNA hybrid substrates bearing either random sequences or GC-rich sequences simulating Ig S regions. If substrates were made up of a random sequence, AID preferred substrates composed entirely of DNA over DNA/RNA hybrids. In contrast, if substrates were composed of S region sequences, AID preferred to mutate DNA/RNA hybrids over substrates composed entirely of DNA. Accordingly, AID exhibited a significantly higher affinity for binding DNA/RNA hybrid substrates composed specifically of S region sequences, than any other substrates composed of DNA. Thus, in the absence of any other cellular processes or factors, AID itself favors binding and mutating DNA/RNA hybrids composed of S region sequences. AID:DNA/RNA complex formation and supporting mutational analyses suggest that recognition of DNA/RNA hybrids is an inherent structural property of AID. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Effects of a sex-ratio distorting endosymbiont on mtDNA variation in a global insect pest

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    Cook James M

    2009-03-01

    Full Text Available Abstract Background Patterns of mtDNA variation within a species reflect long-term population structure, but may also be influenced by maternally inherited endosymbionts, such as Wolbachia. These bacteria often alter host reproductive biology and can drive particular mtDNA haplotypes through populations. We investigated the impacts of Wolbachia infection and geography on mtDNA variation in the diamondback moth, a major global pest whose geographic distribution reflects both natural processes and transport via human agricultural activities. Results The mtDNA phylogeny of 95 individuals sampled from 10 countries on four continents revealed two major clades. One contained only Wolbachia-infected individuals from Malaysia and Kenya, while the other contained only uninfected individuals, from all countries including Malaysia and Kenya. Within the uninfected group was a further clade containing all individuals from Australasia and displaying very limited sequence variation. In contrast, a biparental nuclear gene phylogeny did not have infected and uninfected clades, supporting the notion that maternally-inherited Wolbachia are responsible for the mtDNA pattern. Only about 5% (15/306 of our global sample of individuals was infected with the plutWB1 isolate and even within infected local populations, many insects were uninfected. Comparisons of infected and uninfected isofemale lines revealed that plutWB1 is associated with sex ratio distortion. Uninfected lines have a 1:1 sex ratio, while infected ones show a 2:1 female bias. Conclusion The main correlate of mtDNA variation in P. xylostella is presence or absence of the plutWB1 infection. This is associated with substantial sex ratio distortion and the underlying mechanisms deserve further study. In contrast, geographic origin is a poor predictor of moth mtDNA sequences, reflecting human activity in moving the insects around the globe. The exception is a clade of Australasian individuals, which may

  15. Flanking bases influence the nature of DNA distortion by platinum 1,2-intrastrand (GG cross-links.

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    Debadeep Bhattacharyya

    Full Text Available The differences in efficacy and molecular mechanisms of platinum anti-cancer drugs cisplatin (CP and oxaliplatin (OX are thought to be partially due to the differences in the DNA conformations of the CP and OX adducts that form on adjacent guanines on DNA, which in turn influence the binding of damage-recognition proteins that control downstream effects of the adducts. Here we report a comprehensive comparison of the structural distortion of DNA caused by CP and OX adducts in the TGGT sequence context using nuclear magnetic resonance (NMR spectroscopy and molecular dynamics (MD simulations. When compared to our previous studies in other sequence contexts, these structural studies help us understand the effect of the sequence context on the conformation of Pt-GG DNA adducts. We find that both the sequence context and the type of Pt-GG DNA adduct (CP vs. OX play an important role in the conformation and the conformational dynamics of Pt-DNA adducts, possibly explaining their influence on the ability of many damage-recognition proteins to bind to Pt-DNA adducts.

  16. Study of the activity of DNA polymerases β and λ using 5-formyluridine containing DNA substrates

    Directory of Open Access Journals (Sweden)

    Lavrik O. I.

    2012-06-01

    Full Text Available Aim. To investigate the TLS-activity of human DNA polymerases β and λ (pols β and λ using 5-formyluridine (5-foU containing DNA duplexes which are imitating the intermediates during replication of the leading DNA strand, and to study the influence of replication factors hRPA and hPCNA on this activity. Methods. The EMSA and the methods of enzyme’s kinetics were used. Results. The capability of pols β and λ to catalyze DNA synthesis across 5-foU was investigated and the kinetic characteristics of this process in the presence and in the absence of protein factors hRPA and hPCNA were evaluated. Conclusions. It was shown that: (i both proteins are able to catalyze TLS on used DNA substrates regardless of the reaction conditions, however, pol λ was more accurate enzyme; (ii hRPA can stimulate the efficacy of the nonmutagenic TLS catalyzed by pol at the nucleotide incorporation directly opposite of 5-foU, at the same time it doesn’t influence the incorporation efficacy if the damage displaced into the duplex; (iii hPCNA doesn’t influence the efficacy of TLS catalyzed by both enzymes.

  17. Unique structural modulation of a non-native substrate by cochaperone DnaJ.

    Science.gov (United States)

    Tiwari, Satyam; Kumar, Vignesh; Jayaraj, Gopal Gunanathan; Maiti, Souvik; Mapa, Koyeli

    2013-02-12

    The role of bacterial DnaJ protein as a cochaperone of DnaK is strongly appreciated. Although DnaJ unaccompanied by DnaK can bind unfolded as well as native substrate proteins, its role as an individual chaperone remains elusive. In this study, we demonstrate that DnaJ binds a model non-native substrate with a low nanomolar dissociation constant and, more importantly, modulates the structure of its non-native state. The structural modulation achieved by DnaJ is different compared to that achieved by the DnaK-DnaJ complex. The nature of structural modulation exerted by DnaJ is suggestive of a unique unfolding activity on the non-native substrate by the chaperone. Furthermore, we demonstrate that the zinc binding motif along with the C-terminal substrate binding domain of DnaJ is necessary and sufficient for binding and the subsequent binding-induced structural alterations of the non-native substrate. We hypothesize that this hitherto unknown structural alteration of non-native states by DnaJ might be important for its chaperoning activity by removing kinetic traps of the folding intermediates.

  18. DNA-binding studies of a tetraalkyl-substituted porphyrin and the mutually adaptive distortion principle.

    Science.gov (United States)

    Ghimire, Srijana; Fanwick, Phillip E; McMillin, David R

    2014-10-20

    This investigation explores DNA-binding interactions of various forms of an alkyl-substituted cationic porphyrin, H2TC3 (5,10,15,20-tetra[3-(3'-methylimidazolium-1'-yl)]porphyrin). The motivating idea is that incorporating alkyl rather than aryl substituents in the meso positions will enhance the prospects for intercalative as well as external binding to DNA hosts. The ligands may also be applicable for photodynamic and/or anticancer therapy. Methods employed include absorbance, circular dichroism, and emission spectroscopies, as well as viscometry and X-ray crystallography. By comparison with the classical H2T4 system, H2TC3 exhibits a higher molar extinction coefficient but is more prone to self-association. Findings of note include that the copper(II)-containing form Cu(TC3) is adept at internalizing into single-stranded as well as B-form DNA, regardless of the base composition. Surprisingly, however, external binding of H2TC3 occurs within domains that are rich in adenine-thymine base pairs. The difference in the deformability of H2TC3 versus Cu(TC3) probably accounts for the reactivity difference. Finally, Zn(TC3) binds externally, as the metal center remains five-coordinate.

  19. Trigger Factor and DnaK possess overlapping substrate pools and binding specificities.

    Science.gov (United States)

    Deuerling, Elke; Patzelt, Holger; Vorderwülbecke, Sonja; Rauch, Thomas; Kramer, Günter; Schaffitzel, Elke; Mogk, Axel; Schulze-Specking, Agnes; Langen, Hanno; Bukau, Bernd

    2003-03-01

    Ribosome-associated Trigger Factor (TF) and the DnaK chaperone system assist the folding of newly synthesized proteins in Escherichia coli. Here, we show that DnaK and TF share a common substrate pool in vivo. In TF-deficient cells, deltatig, depleted for DnaK and DnaJ the amount of aggregated proteins increases with increasing temperature, amounting to 10% of total soluble protein (approximately 340 protein species) at 37 degrees C. A similar population of proteins aggregated in DnaK depleted tig+ cells, albeit to a much lower extent. Ninety-four aggregated proteins isolated from DnaK- and DnaJ-depleted deltatig cells were identified by mass spectrometry and found to include essential cytosolic proteins. Four potential in vivo substrates were screened for chaperone binding sites using peptide libraries. Although TF and DnaK recognize different binding motifs, 77% of TF binding peptides also associated with DnaK. In the case of the nascent polypeptides TF and DnaK competed for binding, however, with competitive advantage for TF. In vivo, the loss of TF is compensated by the induction of the heat shock response and thus enhanced levels of DnaK. In summary, our results demonstrate that the co-operation of the two mechanistically distinct chaperones in protein folding is based on their overlap in substrate specificities.

  20. Recognition and processing of a new repertoire of DNA substrates by human 3-methyladenine DNA glycosylase (AAG).

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    Lee, Chun-Yue I; Delaney, James C; Kartalou, Maria; Lingaraju, Gondichatnahalli M; Maor-Shoshani, Ayelet; Essigmann, John M; Samson, Leona D

    2009-03-10

    The human 3-methyladenine DNA glycosylase (AAG) recognizes and excises a broad range of purines damaged by alkylation and oxidative damage, including 3-methyladenine, 7-methylguanine, hypoxanthine (Hx), and 1,N(6)-ethenoadenine (epsilonA). The crystal structures of AAG bound to epsilonA have provided insights into the structural basis for substrate recognition, base excision, and exclusion of normal purines and pyrimidines from its substrate recognition pocket. In this study, we explore the substrate specificity of full-length and truncated Delta80AAG on a library of oligonucleotides containing structurally diverse base modifications. Substrate binding and base excision kinetics of AAG with 13 damaged oligonucleotides were examined. We found that AAG bound to a wide variety of purine and pyrimidine lesions but excised only a few of them. Single-turnover excision kinetics showed that in addition to the well-known epsilonA and Hx substrates, 1-methylguanine (m1G) was also excised efficiently by AAG. Thus, along with epsilonA and ethanoadenine (EA), m1G is another substrate that is shared between AAG and the direct repair protein AlkB. In addition, we found that both the full-length and truncated AAG excised 1,N(2)-ethenoguanine (1,N(2)-epsilonG), albeit weakly, from duplex DNA. Uracil was excised from both single- and double-stranded DNA, but only by full-length AAG, indicating that the N-terminus of AAG may influence glycosylase activity for some substrates. Although AAG has been primarily shown to act on double-stranded DNA, AAG excised both epsilonA and Hx from single-stranded DNA, suggesting the possible significance of repair of these frequent lesions in single-stranded DNA transiently generated during replication and transcription.

  1. Substrate sequence selectivity of APOBEC3A implicates intra-DNA interactions.

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    Silvas, Tania V; Hou, Shurong; Myint, Wazo; Nalivaika, Ellen; Somasundaran, Mohan; Kelch, Brian A; Matsuo, Hiroshi; Kurt Yilmaz, Nese; Schiffer, Celia A

    2018-05-14

    The APOBEC3 (A3) family of human cytidine deaminases is renowned for providing a first line of defense against many exogenous and endogenous retroviruses. However, the ability of these proteins to deaminate deoxycytidines in ssDNA makes A3s a double-edged sword. When overexpressed, A3s can mutate endogenous genomic DNA resulting in a variety of cancers. Although the sequence context for mutating DNA varies among A3s, the mechanism for substrate sequence specificity is not well understood. To characterize substrate specificity of A3A, a systematic approach was used to quantify the affinity for substrate as a function of sequence context, length, secondary structure, and solution pH. We identified the A3A ssDNA binding motif as (T/C)TC(A/G), which correlated with enzymatic activity. We also validated that A3A binds RNA in a sequence specific manner. A3A bound tighter to substrate binding motif within a hairpin loop compared to linear oligonucleotide, suggesting A3A affinity is modulated by substrate structure. Based on these findings and previously published A3A-ssDNA co-crystal structures, we propose a new model with intra-DNA interactions for the molecular mechanism underlying A3A sequence preference. Overall, the sequence and structural preferences identified for A3A leads to a new paradigm for identifying A3A's involvement in mutation of endogenous or exogenous DNA.

  2. Distortion of genetically modified organism quantification in processed foods: influence of particle size compositions and heat-induced DNA degradation.

    Science.gov (United States)

    Moreano, Francisco; Busch, Ulrich; Engel, Karl-Heinz

    2005-12-28

    Milling fractions from conventional and transgenic corn were prepared at laboratory scale and used to study the influence of sample composition and heat-induced DNA degradation on the relative quantification of genetically modified organisms (GMO) in food products. Particle size distributions of the obtained fractions (coarse grits, regular grits, meal, and flour) were characterized using a laser diffraction system. The application of two DNA isolation protocols revealed a strong correlation between the degree of comminution of the milling fractions and the DNA yield in the extracts. Mixtures of milling fractions from conventional and transgenic material (1%) were prepared and analyzed via real-time polymerase chain reaction. Accurate quantification of the adjusted GMO content was only possible in mixtures containing conventional and transgenic material in the form of analogous milling fractions, whereas mixtures of fractions exhibiting different particle size distributions delivered significantly over- and underestimated GMO contents depending on their compositions. The process of heat-induced nucleic acid degradation was followed by applying two established quantitative assays showing differences between the lengths of the recombinant and reference target sequences (A, deltal(A) = -25 bp; B, deltal(B) = +16 bp; values related to the amplicon length of the reference gene). Data obtained by the application of method A resulted in underestimated recoveries of GMO contents in the samples of heat-treated products, reflecting the favored degradation of the longer target sequence used for the detection of the transgene. In contrast, data yielded by the application of method B resulted in increasingly overestimated recoveries of GMO contents. The results show how commonly used food technological processes may lead to distortions in the results of quantitative GMO analyses.

  3. Nanofabricated racks of aligned and anchored DNA substrates for single-molecule imaging.

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    Gorman, Jason; Fazio, Teresa; Wang, Feng; Wind, Shalom; Greene, Eric C

    2010-01-19

    Single-molecule studies of biological macromolecules can benefit from new experimental platforms that facilitate experimental design and data acquisition. Here we develop new strategies to construct curtains of DNA in which the molecules are aligned with respect to one another and maintained in an extended configuration by anchoring both ends of the DNA to the surface of a microfluidic sample chamber that is otherwise coated with an inert lipid bilayer. This "double-tethered" DNA substrate configuration is established through the use of nanofabricated rack patterns comprised of two distinct functional elements: linear barriers to lipid diffusion that align DNA molecules anchored by one end to the bilayer and antibody-coated pentagons that provide immobile anchor points for the opposite ends of the DNA. These devices enable the alignment and anchoring of thousands of individual DNA molecules, which can then be visualized using total internal reflection fluorescence microscopy under conditions that do not require continuous application of buffer flow to stretch the DNA. This unique strategy offers the potential for studying protein-DNA interactions on large DNA substrates without compromising measurements through application of hydrodynamic force. We provide a proof-of-principle demonstration that double-tethered DNA curtains made with nanofabricated rack patterns can be used in a one-dimensional diffusion assay that monitors the motion of quantum dot-tagged proteins along DNA.

  4. Binding of Substrate Locks the Electrochemistry of CRY-DASH into DNA Repair.

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    Gindt, Yvonne M; Messyasz, Adriana; Jumbo, Pamela I

    2015-05-12

    VcCry1, a member of the CRY-DASH family, may serve two diverse roles in vivo, including blue-light signaling and repair of UV-damaged DNA. We have discovered that the electrochemistry of the flavin adenine dinucleotide cofactor of VcCry1 is locked to cycle only between the hydroquinone and neutral semiquinone states when UV-damaged DNA is present. Other potential substrates, including undamaged DNA and ATP, have no discernible effect on the electrochemistry, and the kinetics of the reduction is unaffected by damaged DNA. Binding of the damaged DNA substrate determines the role of the protein and prevents the presumed photochemistry required for blue-light signaling.

  5. Preparation of Mica and Silicon Substrates for DNA Origami Analysis and Experimentation

    Science.gov (United States)

    Pillers, Michelle A.; Shute, Rebecca; Farchone, Adam; Linder, Keenan P.; Doerfler, Rose; Gavin, Corey; Goss, Valerie; Lieberman, Marya

    2015-01-01

    The designed nature and controlled, one-pot synthesis of DNA origami provides exciting opportunities in many fields, particularly nanoelectronics. Many of these applications require interaction with and adhesion of DNA nanostructures to a substrate. Due to its atomically flat and easily cleaned nature, mica has been the substrate of choice for DNA origami experiments. However, the practical applications of mica are relatively limited compared to those of semiconductor substrates. For this reason, a straightforward, stable, and repeatable process for DNA origami adhesion on derivatized silicon oxide is presented here. To promote the adhesion of DNA nanostructures to silicon oxide surface, a self-assembled monolayer of 3-aminopropyltriethoxysilane (APTES) is deposited from an aqueous solution that is compatible with many photoresists. The substrate must be cleaned of all organic and metal contaminants using Radio Corporation of America (RCA) cleaning processes and the native oxide layer must be etched to ensure a flat, functionalizable surface. Cleanrooms are equipped with facilities for silicon cleaning, however many components of DNA origami buffers and solutions are often not allowed in them due to contamination concerns. This manuscript describes the set-up and protocol for in-lab, small-scale silicon cleaning for researchers who do not have access to a cleanroom or would like to incorporate processes that could cause contamination of a cleanroom CMOS clean bench. Additionally, variables for regulating coverage are discussed and how to recognize and avoid common sample preparation problems is described. PMID:26274888

  6. Substrate specificity of Micrococcus luteus uv endonuclease and its overlap with DNA photolyase activity

    International Nuclear Information System (INIS)

    Patrick, M.H.

    1975-01-01

    The action of an endonuclease from Micrococcus luteus that operates on uv damage in DNA overlaps with that of DNA photolyase from yeast: homo- and heterocyclobutane dipyrimidines in DNA are substrates for both enzymes, but pyrimidine adducts or the spore photoproduct in DNA are not. As expected from this overlap, the action of the two enzymes is mutually interfering: single-strand nicks introduced by the endonuclease effectively preclude photoreactivation; conversely, formation of a photolyase-cyclobutane dipyrimidine complex can prevent nicking by the endonuclease

  7. Direct quantification of fungal DNA from soil substrate using real-time PCR.

    Science.gov (United States)

    Filion, Martin; St-Arnaud, Marc; Jabaji-Hare, Suha H

    2003-04-01

    Detection and quantification of genomic DNA from two ecologically different fungi, the plant pathogen Fusarium solani f. sp. phaseoli and the arbuscular mycorrhizal fungus Glomus intraradices, was achieved from soil substrate. Specific primers targeting a 362-bp fragment from the SSU rRNA gene region of G. intraradices and a 562-bp fragment from the F. solani f. sp. phaseoli translation elongation factor 1 alpha gene were used in real-time polymerase chain reaction (PCR) assays conjugated with the fluorescent SYBR(R) Green I dye. Standard curves showed a linear relation (r(2)=0.999) between log values of fungal genomic DNA of each species and real-time PCR threshold cycles and were quantitative over 4-5 orders of magnitude. Real-time PCR assays were applied to in vitro-produced fungal structures and sterile and non-sterile soil substrate seeded with known propagule numbers of either fungi. Detection and genomic DNA quantification was obtained from the different treatments, while no amplicon was detected from non-seeded non-sterile soil samples, confirming the absence of cross-reactivity with the soil microflora DNA. A significant correlation (Pgenomic DNA of F. solani f. sp. phaseoli or G. intraradices detected and the number of fungal propagules present in seeded soil substrate. The DNA extraction protocol and real-time PCR quantification assay can be performed in less than 2 h and is adaptable to detect and quantify genomic DNA from other soilborne fungi.

  8. DNA-assisted binding of microspheres on glass substrates and their laser-induced release

    International Nuclear Information System (INIS)

    Kim, Sejong; Geiss, Erik; Yu, Phillip; Papadimitrakopoulos, Fotios; Marcus, Harris L.

    2006-01-01

    DNA hybridization has been increasingly adopted in materials sciences due to its complementary nature of single stranded DNAs. This unique property could be potentially used in the realization of 2 dimensional (2D) arrays of colloidal microspheres as a precursor to further build more complicated superstructures. In order to precisely understand this DNA-assisted assembly of colloidal particles, we quantitatively assessed the surface density of grafted and hybridizing accessible DNA oligomers on both substrate and colloidal particles. The DNA grafting densities were determined by UV-Vis of dye-functionalized complementary DNA oligomers, in conjunction with theoretical models. The variations of the concentration of hybridized DNA as a function of parameters such as the number of DNA base pairs (bp), the length of spacer and the size of sphere were also investigated to determine the immobilization strength of colloidal microspheres on the substrate. Dehybridization of the particle was conducted by utilizing a focused laser beam. These results were also compared with the particle hybridization energies and modeled according to the sum of DNA bindings as a function of the number of hybridized bases

  9. Selective DNA-Mediated Assembly of Gold Nanoparticles on Electroded Substrates

    Science.gov (United States)

    2008-06-01

    might use the Watson - Crick base-pairing of DNA as a means for ultrahigh-precision engineering is well- known.5,6 The idea is to use the highly specific...Selective DNA -Mediated Assembly of Gold Nanoparticles on Electroded Substrates K. E. Sapsford,†,‡,∇ D. Park,§ E. R. Goldman,‡ E. E. Foos,| S. A...electrodes via DNA hybridization. Protocols are demonstrated for maximizing selectivity and coverage using 15mers as the active binding agents. Detailed

  10. Precise Sequential DNA Ligation on A Solid Substrate: Solid-Based Rapid Sequential Ligation of Multiple DNA Molecules

    Science.gov (United States)

    Takita, Eiji; Kohda, Katsunori; Tomatsu, Hajime; Hanano, Shigeru; Moriya, Kanami; Hosouchi, Tsutomu; Sakurai, Nozomu; Suzuki, Hideyuki; Shinmyo, Atsuhiko; Shibata, Daisuke

    2013-01-01

    Ligation, the joining of DNA fragments, is a fundamental procedure in molecular cloning and is indispensable to the production of genetically modified organisms that can be used for basic research, the applied biosciences, or both. Given that many genes cooperate in various pathways, incorporating multiple gene cassettes in tandem in a transgenic DNA construct for the purpose of genetic modification is often necessary when generating organisms that produce multiple foreign gene products. Here, we describe a novel method, designated PRESSO (precise sequential DNA ligation on a solid substrate), for the tandem ligation of multiple DNA fragments. We amplified donor DNA fragments with non-palindromic ends, and ligated the fragment to acceptor DNA fragments on solid beads. After the final donor DNA fragments, which included vector sequences, were joined to the construct that contained the array of fragments, the ligation product (the construct) was thereby released from the beads via digestion with a rare-cut meganuclease; the freed linear construct was circularized via an intra-molecular ligation. PRESSO allowed us to rapidly and efficiently join multiple genes in an optimized order and orientation. This method can overcome many technical challenges in functional genomics during the post-sequencing generation. PMID:23897972

  11. Caulobacter crescentus Cell Cycle-Regulated DNA Methyltransferase Uses a Novel Mechanism for Substrate Recognition.

    Science.gov (United States)

    Woodcock, Clayton B; Yakubov, Aziz B; Reich, Norbert O

    2017-08-01

    Caulobacter crescentus relies on DNA methylation by the cell cycle-regulated methyltransferase (CcrM) in addition to key transcription factors to control the cell cycle and direct cellular differentiation. CcrM is shown here to efficiently methylate its cognate recognition site 5'-GANTC-3' in single-stranded and hemimethylated double-stranded DNA. We report the K m , k cat , k methylation , and K d for single-stranded and hemimethylated substrates, revealing discrimination of 10 7 -fold for noncognate sequences. The enzyme also shows a similar discrimination against single-stranded RNA. Two independent assays clearly show that CcrM is highly processive with single-stranded and hemimethylated DNA. Collectively, the data provide evidence that CcrM and other DNA-modifying enzymes may use a new mechanism to recognize DNA in a key epigenetic process.

  12. Synthesis of dihydrothymidine and thymidine glycol 5'-triphosphates and their ability to serve as substrates for Escherichia coli DNA polymerase I

    International Nuclear Information System (INIS)

    Ide, H.; Melamede, R.J.; Wallace, S.S.

    1987-01-01

    5,6-Dihydrothymidine 5'-triphosphate (DHdTTP) was synthesized by catalytic hydrogenation of thymidine 5'-triphosphate (dTTP). Thymidine glycol 5'-triphosphate (dTTP-GLY) was prepared by bromination of dTTP followed by treatment with Ag 2 O. The modified nucleotides were extensively purified by anion-exchange high-performance liquid chromatography (HPLC). Alkaline phosphatase digestion of DHdTTP and dTTP-GLY gave the expected products (5,6-dihydrothymidine and cis-thymidine glycol), the identities of which were confirmed by reverse-phase HPLC using authentic markers. HPLC analysis of the alkaline phosphatase digested DHdTTP revealed that DHdTTP was a mixture of C5 diastereoisomers [(5S)- and (5R)-DHdTTP]. Despite the significant distortion of the pyrimidine ring in DHdTTP, it was incorporated in place of dTTP during primer elongation catalyzed by Escherichia coli DNA polymerase I Klenow fragment. The rate of incorporation of DHdTTP was about 10-25-fold lower than that of dTTP. On the other hand, dTTP-GLY, which also has a distorted pyrimidine ring, did not replace dTTP, and no elongation of the primer was observed. In order to study the preference of incorporation of the diastereoisomers of DHdTTP into DNA, salmon testes DNA, activated by exonuclease III, was used as a template for DNA polymerase I Klenow fragment in the presence of [ 3 H]DHdTTP (S and R mixture) and normal nucleotides. After enzymatic digestion of the DNA to nucleosides, the products were analyzed by HPLC. The result suggests that Escherichia coli DNA polymerase I uses both isomers of DHdTTP as substrates and that the overall efficiency of incorporation is primarily determined by the concentration of the isomers in the nucleotide pool

  13. DNA and Protein Requirements for Substrate Conformational Changes Necessary for Human Flap Endonuclease-1-catalyzed Reaction*

    Science.gov (United States)

    Algasaier, Sana I.; Exell, Jack C.; Bennet, Ian A.; Thompson, Mark J.; Gotham, Victoria J. B.; Shaw, Steven J.; Craggs, Timothy D.; Finger, L. David; Grasby, Jane A.

    2016-01-01

    Human flap endonuclease-1 (hFEN1) catalyzes the essential removal of single-stranded flaps arising at DNA junctions during replication and repair processes. hFEN1 biological function must be precisely controlled, and consequently, the protein relies on a combination of protein and substrate conformational changes as a prerequisite for reaction. These include substrate bending at the duplex-duplex junction and transfer of unpaired reacting duplex end into the active site. When present, 5′-flaps are thought to thread under the helical cap, limiting reaction to flaps with free 5′-termini in vivo. Here we monitored DNA bending by FRET and DNA unpairing using 2-aminopurine exciton pair CD to determine the DNA and protein requirements for these substrate conformational changes. Binding of DNA to hFEN1 in a bent conformation occurred independently of 5′-flap accommodation and did not require active site metal ions or the presence of conserved active site residues. More stringent requirements exist for transfer of the substrate to the active site. Placement of the scissile phosphate diester in the active site required the presence of divalent metal ions, a free 5′-flap (if present), a Watson-Crick base pair at the terminus of the reacting duplex, and the intact secondary structure of the enzyme helical cap. Optimal positioning of the scissile phosphate additionally required active site conserved residues Tyr40, Asp181, and Arg100 and a reacting duplex 5′-phosphate. These studies suggest a FEN1 reaction mechanism where junctions are bound and 5′-flaps are threaded (when present), and finally the substrate is transferred onto active site metals initiating cleavage. PMID:26884332

  14. Energy buffering of DNA structure fails when Escherichia coli runs out of substrate

    DEFF Research Database (Denmark)

    Jensen, Peter Ruhdal; Loman, Leine; Petra, Bob

    1995-01-01

    To study how changes in the (ATP)/(ADP) ratio affect the level of DNA supercoiling in Escherichia coli, the cellular content of H+-ATPase was modulated around the wild-type level. A relatively large drop in the (ATP)/(ADP) ratio from the normal ratio resulted in a small increase in the linking...... number of our reporter plasmid (corresponding to a small decrease in negative supercoiling). However, when cells depleted their carbon and energy source, the ensuing drop in energy state was accompanied by a strong increase in linking number. This increase was not due to reduced transcription of the DNA...... in the absence of growth substrate, since rifampin had virtually no effect on the plasmid linking number. To examine whether DNA supercoiling depends more strongly on the cellular energy state at low (ATP)/(ADP) ratios than at high ratios, we used cells that were already at a low energy state after substrate...

  15. Colorimetric determination of DNase I activity with a DNA-methyl green substrate.

    Science.gov (United States)

    Sinicropi, D; Baker, D L; Prince, W S; Shiffer, K; Shak, S

    1994-11-01

    A simple, high throughput, and precise assay was developed for quantification of deoxyribonuclease I (DNase; IUB 3.1.21.1) activity. The method was adapted from the procedure devised by Kurnick which employs a substrate comprised of highly polymerized native DNA complexed with methyl green. Hydrolysis of the DNA produced unbound methyl green and a decrease in the absorbance of the solution at 620 nm. By adjusting the time and temperature of the reaction, the assay permits quantification of DNase activity over a wide concentration range (0.4 to 8900 ng/ml). Samples and standards were added to the substrate in microtiter plates and were incubated for 1-24 h at 25-37 degrees C to achieve the desired assay range. The DNase activity of the samples was interpolated from a standard curve generated with Pulmozyme recombinant human deoxyribonuclease I (rhDNase). Interassay precision was less than 12% CV and recovery was within 100 +/- 11%. Activity determination by the DNA-methyl green method correlated well with that determined by the widely used "hyperchromicity" method originated by Kunitz, which is based on the increase in absorbance at 260 nm upon hydrolysis of DNA. The DNA-methyl green assay was simpler and more versatile than the hyperchromicity method and was used to characterize the activity of rhDNase and DNase isolated from human urine.

  16. Influence of the surface free energy of silane-coupled mica substrate on the fixing and straightening of DNA

    International Nuclear Information System (INIS)

    Sasou, Megumi; Sugiyama, Shigeru; Ishida, Takao; Ohtani, Toshio; Miyake, Koji

    2009-01-01

    Methyltrimethoxysilane (MTMS)-coupled mica substrate is reportedly suitable for fixing and straightening of DNA, but 3-aminopropyltriethoxysilane (APTES)-coupled mica substrate has been found less suitable. On MTMS-coupled mica substrate, the straightness of fixed DNA was sufficient, and the adsorption of contaminants was not observed using fluorescence microscopy and atomic force microscopy. For the APTES-coupled mica substrate, however, aggregated or curved DNA and adsorption of contaminants were observed. To clarify the surface factors that are responsible for this suitability, we analyzed the surface free energies of these substrates using the extended Fowkes theory. In each of the surface free energy components, the dispersion force component in the MTMS-coupled mica substrate was lower than that in the APTES-coupled mica substrate. The ratio of the polar force component on the MTMS-coupled mica substrate was about one order of magnitude on the APTES-coupled mica substrate. In addition, the ratio of the hydrogen-bonding force component for the MTMS-coupled mica substrate was about two times larger than that of the APTES-coupled mica substrate. These results suggest that the polar force and hydrogen-bonding force components are important factors for the fixation and straightening of DNA and that the dispersion force components influence the production and adsorption of contaminants.

  17. Glycosylase-mediated repair of radiation-induced DNA bases: substrate specificities and mechanisms

    International Nuclear Information System (INIS)

    D'ham, Cedric

    1998-01-01

    Cellular DNA is subject to permanent damage and repair processes. One way to restore the integrity of DNA involves the base excision repair pathway. Glycosylases are the key-enzymes of this process. The present work deals with the determination of the substrate specificity and the mechanism of action of three glycosylases: endonuclease III and Fpg of Escherichia coli and Ogg1 of Saccharomyces cerevisiae. The present manuscript is divided into four parts: Endonuclease III-mediated excision of 5,6-dihydro-thymine and 5-hydroxy-5,6-dihydro-thymine from γ-irradiated DNA was analyzed by a gas chromatography-mass spectrometry assay, including a liquid chromatography pre-purification step. This was found to be necessary in order to separate the cis and trans isomers of 6-hydroxy-5,6-dihydro-thymine from the 5-hydroxy-5,6-dihydro-thymine. Modified oligonucleotides that contained a unique lesion, including thymine glycol, 5,6-dihydro-thymine and 5-hydroxy-cytosine were synthesized to assess the substrate specificity of endonuclease III and Fpg. The order of preference of the enzymes for the substrates was determined by the measurement of the Michaelis constants of the kinetics. Furthermore, the mechanism of action of endonuclease III has been reconsidered, after analysis using the MALDI mass spectrometry technique. These studies reveal that hydrolysis is the main pathway by which endonuclease III cleaves the DNA backbone. Using a modified oligonucleotide, 8-oxo-7,8-dihydro-adenine was shown to be a product of excision of the Ogg1 enzyme. The role of the complementary base towards the lesion was found to be preponderant in the damage excision. A last chapter concerns the synthesis and the characterization of the four isomers of 5(6)-hydroxy-6(5)-hydroperoxides of thymine. These products may be substrates for endonuclease III or Fpg. (author) [fr

  18. A Simple Thermoplastic Substrate Containing Hierarchical Silica Lamellae for High-Molecular-Weight DNA Extraction.

    Science.gov (United States)

    Zhang, Ye; Zhang, Yi; Burke, Jeffrey M; Gleitsman, Kristin; Friedrich, Sarah M; Liu, Kelvin J; Wang, Tza-Huei

    2016-12-01

    An inexpensive, magnetic thermoplastic nanomaterial is developed utilizing a hierarchical layering of micro- and nanoscale silica lamellae to create a high-surface-area and low-shear substrate capable of capturing vast amounts of ultrahigh-molecular-weight DNA. Extraction is performed via a simple 45 min process and is capable of achieving binding capacities up to 1 000 000 times greater than silica microparticles. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. The oxidative DNA glycosylases of Mycobacterium tuberculosis exhibit different substrate preferences from their Escherichia coli counterparts.

    Science.gov (United States)

    Guo, Yin; Bandaru, Viswanath; Jaruga, Pawel; Zhao, Xiaobei; Burrows, Cynthia J; Iwai, Shigenori; Dizdaroglu, Miral; Bond, Jeffrey P; Wallace, Susan S

    2010-02-04

    The DNA glycosylases that remove oxidized DNA bases fall into two general families: the Fpg/Nei family and the Nth superfamily. Based on protein sequence alignments, we identified four putative Fpg/Nei family members, as well as a putative Nth protein in Mycobacterium tuberculosis H37Rv. All four Fpg/Nei proteins were successfully overexpressed using a bicistronic vector created in our laboratory. The MtuNth protein was also overexpressed in soluble form. The substrate specificities of the purified enzymes were characterized in vitro with oligodeoxynucleotide substrates containing single lesions. Some were further characterized by gas chromatography/mass spectrometry (GC/MS) analysis of products released from gamma-irradiated DNA. MtuFpg1 has substrate specificity similar to that of EcoFpg. Both EcoFpg and MtuFpg1 are more efficient at removing spiroiminodihydantoin (Sp) than 7,8-dihydro-8-oxoguanine (8-oxoG). However, MtuFpg1 shows a substantially increased opposite base discrimination compared to EcoFpg. MtuFpg2 contains only the C-terminal domain of an Fpg protein and has no detectable DNA binding activity or DNA glycosylase/lyase activity and thus appears to be a pseudogene. MtuNei1 recognizes oxidized pyrimidines on both double-stranded and single-stranded DNA and exhibits uracil DNA glycosylase activity. MtuNth recognizes a variety of oxidized bases, including urea, 5,6-dihydrouracil (DHU), 5-hydroxyuracil (5-OHU), 5-hydroxycytosine (5-OHC) and methylhydantoin (MeHyd). Both MtuNei1 and MtuNth excise thymine glycol (Tg); however, MtuNei1 strongly prefers the (5R) isomers, whereas MtuNth recognizes only the (5S) isomers. MtuNei2 did not demonstrate activity in vitro as a recombinant protein, but like MtuNei1 when expressed in Escherichia coli, it decreased the spontaneous mutation frequency of both the fpg mutY nei triple and nei nth double mutants, suggesting that MtuNei2 is functionally active in vivo recognizing both guanine and cytosine oxidation products

  20. Activation of the DnaK-ClpB Complex is Regulated by the Properties of the Bound Substrate.

    Science.gov (United States)

    Fernández-Higuero, Jose Angel; Aguado, Alejandra; Perales-Calvo, Judit; Moro, Fernando; Muga, Arturo

    2018-04-11

    The chaperone ClpB in bacteria is responsible for the reactivation of aggregated proteins in collaboration with the DnaK system. Association of these chaperones at the aggregate surface stimulates ATP hydrolysis, which mediates substrate remodeling. However, a question that remains unanswered is whether the bichaperone complex can be selectively activated by substrates that require remodeling. We find that large aggregates or bulky, native-like substrates activates the complex, whereas a smaller, permanently unfolded protein or extended, short peptides fail to stimulate it. Our data also indicate that ClpB interacts differently with DnaK in the presence of aggregates or small peptides, displaying a higher affinity for aggregate-bound DnaK, and that DnaK-ClpB collaboration requires the coupled ATPase-dependent remodeling activities of both chaperones. Complex stimulation is mediated by residues at the β subdomain of DnaK substrate binding domain, which become accessible to the disaggregase when the lid is allosterically detached from the β subdomain. Complex activation also requires an active NBD2 and the integrity of the M domain-ring of ClpB. Disruption of the M-domain ring allows the unproductive stimulation of the DnaK-ClpB complex in solution. The ability of the DnaK-ClpB complex to discrimínate different substrate proteins might allow its activation when client proteins require remodeling.

  1. Analysis of substrate specificity of Schizosaccharomyces pombe Mag1 alkylpurine DNA glycosylase

    Energy Technology Data Exchange (ETDEWEB)

    Adhikary, Suraj; Eichman, Brandt F. (Vanderbilt)

    2014-10-02

    DNA glycosylases specialized for the repair of alkylation damage must identify, with fine specificity, a diverse array of subtle modifications within DNA. The current mechanism involves damage sensing through interrogation of the DNA duplex, followed by more specific recognition of the target base inside the active site pocket. To better understand the physical basis for alkylpurine detection, we determined the crystal structure of Schizosaccharomyces pombe Mag1 (spMag1) in complex with DNA and performed a mutational analysis of spMag1 and the close homologue from Saccharomyces cerevisiae (scMag). Despite strong homology, spMag1 and scMag differ in substrate specificity and cellular alkylation sensitivity, although the enzymological basis for their functional differences is unknown. We show that Mag preference for 1,N{sup 6}-ethenoadenine ({var_epsilon}A) is influenced by a minor groove-interrogating residue more than the composition of the nucleobase-binding pocket. Exchanging this residue between Mag proteins swapped their {var_epsilon}A activities, providing evidence that residues outside the extrahelical base-binding pocket have a role in identification of a particular modification in addition to sensing damage.

  2. hnRNP-U is a specific DNA-dependent protein kinase substrate phosphorylated in response to DNA double-strand breaks

    International Nuclear Information System (INIS)

    Berglund, Fredrik M.; Clarke, Paul R.

    2009-01-01

    Cellular responses to DNA damage are orchestrated by the large phosphoinositol-3-kinase related kinases ATM, ATR and DNA-PK. We have developed a cell-free system to dissect the biochemical mechanisms of these kinases. Using this system, we identify heterogeneous nuclear ribonucleoprotein U (hnRNP-U), also termed scaffold attachment factor A (SAF-A), as a specific substrate for DNA-PK. We show that hnRNP-U is phosphorylated at Ser59 by DNA-PK in vitro and in cells in response to DNA double-strand breaks. Phosphorylation of hnRNP-U suggests novel functions for DNA-PK in the response to DNA damage.

  3. Architecture and Assembly of HIV Integrase Multimers in the Absence of DNA Substrates*

    Science.gov (United States)

    Bojja, Ravi Shankar; Andrake, Mark D.; Merkel, George; Weigand, Steven; Dunbrack, Roland L.; Skalka, Anna Marie

    2013-01-01

    We have applied small angle x-ray scattering and protein cross-linking coupled with mass spectrometry to determine the architectures of full-length HIV integrase (IN) dimers in solution. By blocking interactions that stabilize either a core-core domain interface or N-terminal domain intermolecular contacts, we show that full-length HIV IN can form two dimer types. One is an expected dimer, characterized by interactions between two catalytic core domains. The other dimer is stabilized by interactions of the N-terminal domain of one monomer with the C-terminal domain and catalytic core domain of the second monomer as well as direct interactions between the two C-terminal domains. This organization is similar to the “reaching dimer” previously described for wild type ASV apoIN and resembles the inner, substrate binding dimer in the crystal structure of the PFV intasome. Results from our small angle x-ray scattering and modeling studies indicate that in the absence of its DNA substrate, the HIV IN tetramer assembles as two stacked reaching dimers that are stabilized by core-core interactions. These models of full-length HIV IN provide new insight into multimer assembly and suggest additional approaches for enzyme inhibition. PMID:23322775

  4. The use of AMPPD as an alternative substrate for AP-mediated detection of nonradiolabeled DNA probes in Eucalyptus saligna

    OpenAIRE

    De Moura Campos Pardini, M. I. [UNESP; Wolff, J. L C [UNESP; Lopes, C. R. [UNESP

    1993-01-01

    We present a non-radioactive alternative to Southern's (J. Mol. Biol. 98: 503-517, 1975) DNA-DNA hybridization technique. The use of AMPPD - Disodium 3-(4-Methoxyspiro {1,2-dioxetane-3,2'tricyclo[3.3.1.1(3,7)]decan}-4-yl)phyenyl phosphate as an alternative substrate for AP-mediated detection of digoxigenin-11 dUTP-labeled probes made possible the simple and nonhazardous reuse of blots. We used 0.8 % agarose gels containing 30 mug per lane of Eucalyptus saligna DNA, digested with Eco RI, elect...

  5. Characterization of DNA substrate specificities of apurinic/apyrimidinic endonucleases from Mycobacterium tuberculosis.

    Science.gov (United States)

    Abeldenov, Sailau; Talhaoui, Ibtissam; Zharkov, Dmitry O; Ishchenko, Alexander A; Ramanculov, Erlan; Saparbaev, Murat; Khassenov, Bekbolat

    2015-09-01

    Apurinic/apyrimidinic (AP) endonucleases are key enzymes involved in the repair of abasic sites and DNA strand breaks. Pathogenic bacteria Mycobacterium tuberculosis contains two AP endonucleases: MtbXthA and MtbNfo members of the exonuclease III and endonuclease IV families, which are exemplified by Escherichia coli Xth and Nfo, respectively. It has been shown that both MtbXthA and MtbNfo contain AP endonuclease and 3'→5' exonuclease activities. However, it remains unclear whether these enzymes hold 3'-repair phosphodiesterase and nucleotide incision repair (NIR) activities. Here, we report that both mycobacterial enzymes have 3'-repair phosphodiesterase and 3'-phosphatase, and MtbNfo contains in addition a very weak NIR activity. Interestingly, depending on pH, both enzymes require different concentrations of divalent cations: 0.5mM MnCl2 at pH 7.6 and 10 mM at pH 6.5. MtbXthA requires a low ionic strength and 37 °C, while MtbNfo requires high ionic strength (200 mM KCl) and has a temperature optimum at 60 °C. Point mutation analysis showed that D180 and N182 in MtbXthA and H206 and E129 in MtbNfo are critical for enzymes activities. The steady-state kinetic parameters indicate that MtbXthA removes 3'-blocking sugar-phosphate and 3'-phosphate moieties at DNA strand breaks with an extremely high efficiency (kcat/KM=440 and 1280 μM(-1)∙min(-1), respectively), while MtbNfo exhibits much lower 3'-repair activities (kcat/KM=0.26 and 0.65 μM(-1)∙min(-1), respectively). Surprisingly, both MtbXthA and MtbNfo exhibited very weak AP site cleavage activities, with kinetic parameters 100- and 300-fold lower, respectively, as compared with the results reported previously. Expression of MtbXthA and MtbNfo reduced the sensitivity of AP endonuclease-deficient E. coli xth nfo strain to methylmethanesulfonate and H2O2 to various degrees. Taken together, these data establish the DNA substrate specificity of M. tuberculosis AP endonucleases and suggest their possible role

  6. Amplifier Distortion

    Science.gov (United States)

    Keeports, David

    2006-12-01

    By definition, a high fidelity amplifier's instantaneous output voltage is directly proportional to its instantaneous input voltage. While high fidelity is generally valued in the amplification of recorded music, nonlinearity, also known as distortion, is desirable in the amplification of some musical instruments. In particular, guitar amplifiers exploit nonlinearity to increase both the harmonic content and sustain of a guitar's sound. I will discuss how both modifications in sound result from saturation of triode tubes and transistors. Additionally, I will describe the difference in the symmetry of saturation curves for transistors and tubes and the reason why tube guitar amplifiers are generally considered to be superior to solid-state amplifiers. Finally, I will discuss attempts to use solid-state electronics to replicate the sound of tube amplifiers.

  7. Mycobacterium tuberculosis RecG binds and unwinds model DNA substrates with a preference for Holliday junctions.

    Science.gov (United States)

    Zegeye, Ephrem Debebe; Balasingham, Seetha V; Laerdahl, Jon K; Homberset, Håvard; Tønjum, Tone

    2012-08-01

    The RecG enzyme, a superfamily 2 helicase, is present in nearly all bacteria. Here we report for the first time that the recG gene is also present in the genomes of most vascular plants as well as in green algae, but is not found in other eukaryotes or archaea. The precise function of RecG is poorly understood, although ample evidence shows that it plays critical roles in DNA repair, recombination and replication. We further demonstrate that Mycobacterium tuberculosis RecG (RecG(Mtb)) DNA binding activity had a broad substrate specificity, whereas it only unwound branched-DNA substrates such as Holliday junctions (HJs), replication forks, D-loops and R-loops, with a strong preference for the HJ as a helicase substrate. In addition, RecG(Mtb) preferentially bound relatively long (≥40 nt) ssDNA, exhibiting a higher affinity for the homopolymeric nucleotides poly(dT), poly(dG) and poly(dC) than for poly(dA). RecG(Mtb) helicase activity was supported by hydrolysis of ATP or dATP in the presence of Mg(2+), Mn(2+), Cu(2+) or Fe(2+). Like its Escherichia coli orthologue, RecG(Mtb) is also a strictly DNA-dependent ATPase.

  8. Structural and mutational analysis of Escherichia coli AlkB provides insight into substrate specificity and DNA damage searching.

    Directory of Open Access Journals (Sweden)

    Paul J Holland

    Full Text Available BACKGROUND: In Escherichia coli, cytotoxic DNA methyl lesions on the N1 position of purines and N3 position of pyrimidines are primarily repaired by the 2-oxoglutarate (2-OG iron(II dependent dioxygenase, AlkB. AlkB repairs 1-methyladenine (1-meA and 3-methylcytosine (3-meC lesions, but it also repairs 1-methylguanine (1-meG and 3-methylthymine (3-meT at a much less efficient rate. How the AlkB enzyme is able to locate and identify methylated bases in ssDNA has remained an open question. METHODOLOGY/PRINCIPAL FINDINGS: We determined the crystal structures of the E. coli AlkB protein holoenzyme and the AlkB-ssDNA complex containing a 1-meG lesion. We coupled this to site-directed mutagenesis of amino acids in and around the active site, and tested the effects of these mutations on the ability of the protein to bind both damaged and undamaged DNA, as well as catalyze repair of a methylated substrate. CONCLUSIONS/SIGNIFICANCE: A comparison of our substrate-bound AlkB-ssDNA complex with our unliganded holoenzyme reveals conformational changes of residues within the active site that are important for binding damaged bases. Site-directed mutagenesis of these residues reveals novel insight into their roles in DNA damage recognition and repair. Our data support a model that the AlkB protein utilizes at least two distinct conformations in searching and binding methylated bases within DNA: a "searching" mode and "repair" mode. Moreover, we are able to functionally separate these modes through mutagenesis of residues that affect one or the other binding state. Finally, our mutagenesis experiments show that amino acid D135 of AlkB participates in both substrate specificity and catalysis.

  9. Analysis of DNA binding by human factor xeroderma pigmentosum complementation group A (XPA) provides insight into its interactions with nucleotide excision repair substrates.

    Science.gov (United States)

    Sugitani, Norie; Voehler, Markus W; Roh, Michelle S; Topolska-Woś, Agnieszka M; Chazin, Walter J

    2017-10-13

    Xeroderma pigmentosum (XP) complementation group A (XPA) is an essential scaffolding protein in the multiprotein nucleotide excision repair (NER) machinery. The interaction of XPA with DNA is a core function of this protein; a number of mutations in the DNA-binding domain (DBD) are associated with XP disease. Although structures of the central globular domain of human XPA and data on binding of DNA substrates have been reported, the structural basis for XPA's DNA-binding activity remains unknown. X-ray crystal structures of the central globular domain of yeast XPA (Rad14) with lesion-containing DNA duplexes have provided valuable insights, but the DNA substrates used for this study do not correspond to the substrates of XPA as it functions within the NER machinery. To better understand the DNA-binding activity of human XPA in NER, we used NMR to investigate the interaction of its DBD with a range of DNA substrates. We found that XPA binds different single-stranded/double-stranded junction DNA substrates with a common surface. Comparisons of our NMR-based mapping of binding residues with the previously reported Rad14-DNA crystal structures revealed similarities and differences in substrate binding between XPA and Rad14. This includes direct evidence for DNA contacts to the residues extending C-terminally from the globular core, which are lacking in the Rad14 construct. Moreover, mutation of the XPA residue corresponding to Phe-262 in Rad14, previously reported as being critical for DNA binding, had only a moderate effect on the DNA-binding activity of XPA. The DNA-binding properties of several disease-associated mutations in the DBD were investigated. These results suggest that for XPA mutants exhibiting altered DNA-binding properties, a correlation exists between the extent of reduction in DNA-binding affinity and the severity of symptoms in XP patients. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  10. Compression of the DNA substrate by a viral packaging motor is supported by removal of intercalating dye during translocation.

    Science.gov (United States)

    Dixit, Aparna Banerjee; Ray, Krishanu; Black, Lindsay W

    2012-12-11

    Viral genome packaging into capsids is powered by high-force-generating motor proteins. In the presence of all packaging components, ATP-powered translocation in vitro expels all detectable tightly bound YOYO-1 dye from packaged short dsDNA substrates and removes all aminoacridine dye from packaged genomic DNA in vivo. In contrast, in the absence of packaging, the purified T4 packaging ATPase alone can only remove up to ∼1/3 of DNA-bound intercalating YOYO-1 dye molecules in the presence of ATP or ATP-γ-S. In sufficient concentration, intercalating dyes arrest packaging, but rare terminase mutations confer resistance. These distant mutations are highly interdependent in acquiring function and resistance and likely mark motor contact points with the translocating DNA. In stalled Y-DNAs, FRET has shown a decrease in distance from the phage T4 terminase C terminus to portal consistent with a linear motor, and in the Y-stem DNA compression between closely positioned dye pairs. Taken together with prior FRET studies of conformational changes in stalled Y-DNAs, removal of intercalating compounds by the packaging motor demonstrates conformational change in DNA during normal translocation at low packaging resistance and supports a proposed linear "DNA crunching" or torsional compression motor mechanism involving a transient grip-and-release structural change in B form DNA.

  11. Analysis of the substrate recognition state of TDP-43 to single-stranded DNA using fluorescence correlation spectroscopy

    Directory of Open Access Journals (Sweden)

    Akira Kitamura

    2018-07-01

    Full Text Available Normal function and abnormal aggregation of transactivation response (TAR DNA/RNA-binding protein 43 kDa (TDP-43 are directly associated with the lethal genetic diseases: cystic fibrosis, amyotrophic lateral sclerosis (ALS, and frontotemporal lobar degeneration (FTLD. The binding of TDP-43 to single-stranded DNA (ssDNA or RNA is involved in transcriptional repression, regulation of RNA splicing, and RNA stabilization. Equilibrium dissociation constants (Kd of TDP-43 and ssDNA or RNA have been determined using various methods; however, methods that can measure Kd with high sensitivity in a short time using a small amount of TDP-43 in solution would be advantageous. Here, in order to determine the Kd of TDP-43 and fluorescence-labeled ssDNA as well as the binding stoichiometry, we use fluorescence correlation spectroscopy (FCS, which detects the slowed diffusion of molecular interactions in solution with single-molecule sensitivity, in addition to electrophoretic mobility shift assay (EMSA. Using tandem affinity chromatography of TDP-43 dually tagged with glutathione-S-transferase and poly-histidine tags, highly purified protein was obtained. FCS successfully detected specific interaction between purified TDP-43 and TG ssDNA repeats, with a Kd in the nanomolar range. The Kd of the TDP-43 mutant was not different from the wild type, although mutant oligomers, which did not bind ssDNA, were observed. Analysis of the fluorescence brightness per dimerized TDP-43/ssDNA complex was used to evaluate their binding stoichiometry. The results suggest that an assay combining FCS and EMSA can precisely analyze ssDNA recognition mechanisms, and that FCS may be applied for the rapid and quantitative determination of the interaction strength between TDP-43 and ssDNA or RNA. These methods will aid in the elucidation of the substrate recognition mechanism of ALS- and FTLD-associated variants of TDP-43.

  12. The Fanconi anemia associated protein FAAP24 uses two substrate specific binding surfaces for DNA recognition

    NARCIS (Netherlands)

    Wienk, H.L.J.; Slootweg, J.C.; Speerstra, S.; Kaptein, R.; Boelens, R.; Folkers, G.E.

    2013-01-01

    To maintain the integrity of the genome, multiple DNA repair systems exist to repair damaged DNA. Recognition of altered DNA, including bulky adducts, pyrimidine dimers and interstrand crosslinks (ICL), partially depends on proteins containing helix-hairpin-helix (HhH) domains. To understand how ICL

  13. Dynamics of bleomycin interaction with a strongly bound hairpin DNA substrate, and implications for cleavage of the bound DNA.

    Science.gov (United States)

    Bozeman, Trevor C; Nanjunda, Rupesh; Tang, Chenhong; Liu, Yang; Segerman, Zachary J; Zaleski, Paul A; Wilson, W David; Hecht, Sidney M

    2012-10-31

    Recent studies involving DNAs bound strongly by bleomycins have documented that such DNAs are degraded by the antitumor antibiotic with characteristics different from those observed when studying the cleavage of randomly chosen DNAs in the presence of excess Fe·BLM. In the present study, surface plasmon resonance has been used to characterize the dynamics of BLM B(2) binding to a strongly bound hairpin DNA, to define the effects of Fe(3+), salt, and temperature on BLM-DNA interaction. One strong primary DNA binding site, and at least one much weaker site, were documented. In contrast, more than one strong cleavage site was found, an observation also made for two other hairpin DNAs. Evidence is presented for BLM equilibration between the stronger and weaker binding sites in a way that renders BLM unavailable to other, less strongly bound DNAs. Thus, enhanced binding to a given site does not necessarily result in increased DNA degradation at that site; i.e., for strongly bound DNAs, the facility of DNA cleavage must involve other parameters in addition to the intrinsic rate of C-4' H atom abstraction from DNA sugars.

  14. Alignment of Gold Nanoparticle-Decorated DNA Origami Nanotubes: Substrate Prepatterning versus Molecular Combing.

    Science.gov (United States)

    Teschome, Bezu; Facsko, Stefan; Gothelf, Kurt V; Keller, Adrian

    2015-11-24

    DNA origami has become an established technique for designing well-defined nanostructures with any desired shape and for the controlled arrangement of functional nanostructures with few nanometer resolution. These unique features make DNA origami nanostructures promising candidates for use as scaffolds in nanoelectronics and nanophotonics device fabrication. Consequently, a number of studies have shown the precise organization of metallic nanoparticles on various DNA origami shapes. In this work, we fabricated large arrays of aligned DNA origami decorated with a high density of gold nanoparticles (AuNPs). To this end, we first demonstrate the high-yield assembly of high-density AuNP arrangements on DNA origami adsorbed to Si surfaces with few unbound background nanoparticles by carefully controlling the concentrations of MgCl2 and AuNPs in the hybridization buffer and the hybridization time. Then, we evaluate two methods, i.e., hybridization to prealigned DNA origami and molecular combing in a receding meniscus, with respect to their potential to yield large arrays of aligned AuNP-decorated DNA origami nanotubes. Because of the comparatively low MgCl2 concentration required for the efficient immobilization of the AuNPs, the prealigned DNA origami become mobile and displaced from their original positions, thereby decreasing the alignment yield. This increased mobility, on the other hand, makes the adsorbed origami susceptible to molecular combing, and a total alignment yield of 86% is obtained in this way.

  15. DndEi Exhibits Helicase Activity Essential for DNA Phosphorothioate Modification and ATPase Activity Strongly Stimulated by DNA Substrate with a GAAC/GTTC Motif.

    Science.gov (United States)

    Zheng, Tao; Jiang, Pan; Cao, Bo; Cheng, Qiuxiang; Kong, Lingxin; Zheng, Xiaoqing; Hu, Qinghai; You, Delin

    2016-01-15

    Phosphorothioate (PT) modification of DNA, in which the non-bridging oxygen of the backbone phosphate group is replaced by sulfur, is governed by the DndA-E proteins in prokaryotes. To better understand the biochemical mechanism of PT modification, functional analysis of the recently found PT-modifying enzyme DndEi, which has an additional domain compared with canonical DndE, from Riemerella anatipestifer is performed in this study. The additional domain is identified as a DNA helicase, and functional deletion of this domain in vivo leads to PT modification deficiency, indicating an essential role of helicase activity in PT modification. Subsequent analysis reveals that the additional domain has an ATPase activity. Intriguingly, the ATPase activity is strongly stimulated by DNA substrate containing a GAAC/GTTC motif (i.e. the motif at which PT modifications occur in R. anatipestifer) when the additional domain and the other domain (homologous to canonical DndE) are co-expressed as a full-length DndEi. These results reveal that PT modification is a biochemical process with DNA strand separation and intense ATP hydrolysis. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  16. Photolithographic Synthesis of High-Density DNA and RNA Arrays on Flexible, Transparent, and Easily Subdivided Plastic Substrates.

    Science.gov (United States)

    Holden, Matthew T; Carter, Matthew C D; Wu, Cheng-Hsien; Wolfer, Jamison; Codner, Eric; Sussman, Michael R; Lynn, David M; Smith, Lloyd M

    2015-11-17

    The photolithographic fabrication of high-density DNA and RNA arrays on flexible and transparent plastic substrates is reported. The substrates are thin sheets of poly(ethylene terephthalate) (PET) coated with cross-linked polymer multilayers that present hydroxyl groups suitable for conventional phosphoramidite-based nucleic acid synthesis. We demonstrate that by modifying array synthesis procedures to accommodate the physical and chemical properties of these materials, it is possible to synthesize plastic-backed oligonucleotide arrays with feature sizes as small as 14 μm × 14 μm and feature densities in excess of 125 000/cm(2), similar to specifications attainable using rigid substrates such as glass or glassy carbon. These plastic-backed arrays are tolerant to a wide range of hybridization temperatures, and improved synthetic procedures are described that enable the fabrication of arrays with sequences up to 50 nucleotides in length. These arrays hybridize with S/N ratios comparable to those fabricated on otherwise identical arrays prepared on glass or glassy carbon. This platform supports the enzymatic synthesis of RNA arrays and proof-of-concept experiments are presented showing that the arrays can be readily subdivided into smaller arrays (or "millichips") using common laboratory-scale laser cutting tools. These results expand the utility of oligonucleotide arrays fabricated on plastic substrates and open the door to new applications for these important bioanalytical tools.

  17. Single-molecule FRET unveils induced-fit mechanism for substrate selectivity in flap endonuclease 1

    KAUST Repository

    Rashid, Fahad

    2017-02-23

    Human flap endonuclease 1 (FEN1) and related structure-specific 5\\'nucleases precisely identify and incise aberrant DNA structures during replication, repair and recombination to avoid genomic instability. Yet, it is unclear how the 5\\'nuclease mechanisms of DNA distortion and protein ordering robustly mediate efficient and accurate substrate recognition and catalytic selectivity. Here, single-molecule sub-millisecond and millisecond analyses of FEN1 reveal a protein-DNA induced-fit mechanism that efficiently verifies substrate and suppresses off-target cleavage. FEN1 sculpts DNA with diffusion-limited kinetics to test DNA substrate. This DNA distortion mutually \\'locks\\' protein and DNA conformation and enables substrate verification with extreme precision. Strikingly, FEN1 never misses cleavage of its cognate substrate while blocking probable formation of catalytically competent interactions with noncognate substrates and fostering their pre-incision dissociation. These findings establish FEN1 has practically perfect precision and that separate control of induced-fit substrate recognition sets up the catalytic selectivity of the nuclease active site for genome stability.

  18. Tyrosyl-DNA Phosphodiesterase I Catalytic Mutants Reveal an Alternative Nucleophile That Can Catalyze Substrate Cleavage*

    Science.gov (United States)

    Comeaux, Evan Q.; Cuya, Selma M.; Kojima, Kyoko; Jafari, Nauzanene; Wanzeck, Keith C.; Mobley, James A.; Bjornsti, Mary-Ann; van Waardenburg, Robert C. A. M.

    2015-01-01

    Tyrosyl-DNA phosphodiesterase I (Tdp1) catalyzes the repair of 3′-DNA adducts, such as the 3′-phosphotyrosyl linkage of DNA topoisomerase I to DNA. Tdp1 contains two conserved catalytic histidines: a nucleophilic His (Hisnuc) that attacks DNA adducts to form a covalent 3′-phosphohistidyl intermediate and a general acid/base His (Hisgab), which resolves the Tdp1-DNA linkage. A Hisnuc to Ala mutant protein is reportedly inactive, whereas the autosomal recessive neurodegenerative disease SCAN1 has been attributed to the enhanced stability of the Tdp1-DNA intermediate induced by mutation of Hisgab to Arg. However, here we report that expression of the yeast HisnucAla (H182A) mutant actually induced topoisomerase I-dependent cytotoxicity and further enhanced the cytotoxicity of Tdp1 Hisgab mutants, including H432N and the SCAN1-related H432R. Moreover, the HisnucAla mutant was catalytically active in vitro, albeit at levels 85-fold less than that observed with wild type Tdp1. In contrast, the HisnucPhe mutant was catalytically inactive and suppressed Hisgab mutant-induced toxicity. These data suggest that the activity of another nucleophile when Hisnuc is replaced with residues containing a small side chain (Ala, Asn, and Gln), but not with a bulky side chain. Indeed, genetic, biochemical, and mass spectrometry analyses show that a highly conserved His, immediately N-terminal to Hisnuc, can act as a nucleophile to catalyze the formation of a covalent Tdp1-DNA intermediate. These findings suggest that the flexibility of Tdp1 active site residues may impair the resolution of mutant Tdp1 covalent phosphohistidyl intermediates and provide the rationale for developing chemotherapeutics that stabilize the covalent Tdp1-DNA intermediate. PMID:25609251

  19. Quantitative assessment of phytopathogenic fungi in various substrates using a DNA macroarray

    NARCIS (Netherlands)

    Lievens, B.; Brouwer, M.; Vanachter, A.C.R.C.; Lévesque, C.A.; Cammue, B.P.A.; Thomma, B.P.H.J.

    2005-01-01

    Detection, identification and quantification of plant pathogens are the cornerstones of preventive plant disease management. To detect multiple pathogens in a single assay, DNA array technology currently is the most suitable technique. However, for sensitive detection, polymerase chain reaction

  20. Eggshell membrane: A natural substrate for immobilization and detection of DNA

    Energy Technology Data Exchange (ETDEWEB)

    Ray, Preetam Guha; Roy, Somenath, E-mail: sroy@cgcri.res.in

    2016-02-01

    Chemically modified eggshell membranes (ESM) have been explored as potentially novel platforms for immobilization of oligonucleotides and subsequent detection of target DNA. The fibrous network of the native ESM as well those functionalized with acetic acid or n-butyl acetate has been examined by field-emission scanning electron microscopy (FESEM). The formation of surface functional moieties has been confirmed by Fourier-transform infrared spectroscopy (FTIR). DNA molecules, with an end terminal − NH{sub 2} group (at 5′ end) have been immobilized on the chemically modified ESM surface. The effect of surface modification on the DNA immobilization efficiency has been investigated using fluorescence microscopy and atomic force microscopy (AFM). The above studies concurrently suggest that functionalization of ESM with n-butyl acetate causes a better homogeneity of the DNA probes on the membrane surface. On-chip hybridization of the target DNA with the surface bound capture probes has been performed on the functionalized membranes. It is observed that n-butyl acetate modification of ESM pushes the limit of detection (LOD) of the DNA sensors by at least an order of magnitude compared to the other modification method. - Graphical abstract: Eggshell membranes (ESM) have been chemically modified with acetic acid or n-butyl acetate for immobilization of aminated capture probes and subsequent detection of fluorophore-tagged target DNA molecules. n-Butyl acetate modified ESM exhibits superior homogeneity of capture probe immobilization and lower limit of detection for the target DNA molecules. - Highlights: • Eggshell membranes (ESM) have been explored as potentially novel platforms for immobilization of oligonucleotides. • Compared to native ESM, those modified with acetic acid or n-butyl acetate have shown more efficient loading of DNA probes. • ESM modified with n-butyl acetate pushed the lower limit of detection (LOD) of the sensor down to 10 nM of target DNA

  1. Surface-enhanced Raman scattering biosensor for DNA detection on nanoparticle island substrates

    DEFF Research Database (Denmark)

    Yuan, Scott Wu; Ho, Ho Pui; Lee, Rebecca K.Y.

    2009-01-01

    We present a study on the surface-enhanced Raman scattering (SERS) properties of Ag nanoparticle island substrates (NIS) and their applications for target oligonucleotide (OND) detection. It has been found that the surface nanostructure of NIS samples can be controlled with a good degree of repro......We present a study on the surface-enhanced Raman scattering (SERS) properties of Ag nanoparticle island substrates (NIS) and their applications for target oligonucleotide (OND) detection. It has been found that the surface nanostructure of NIS samples can be controlled with a good degree...

  2. Saccharomyces cerevisiae Hrq1 requires a long 3′-tailed DNA substrate for helicase activity

    International Nuclear Information System (INIS)

    Kwon, Sung-Hun; Choi, Do-Hee; Lee, Rina; Bae, Sung-Ho

    2012-01-01

    Highlights: ► Hrq1 has intrinsic 3′–5′ helicase and DNA strand annealing activities. ► Hrq1 requires a long 3′-tail for efficient DNA unwinding. ► Helicase activity of Hrq1 is stimulated by a fork structure. ► Hrq1 is a moderately processive helicase. -- Abstract: RecQ helicases are well conserved proteins from bacteria to human and function in various DNA metabolism for maintenance of genome stability. Five RecQ helicases are found in humans, whereas only one RecQ helicase has been described in lower eukaryotes. However, recent studies predicted the presence of a second RecQ helicase, Hrq1, in fungal genomes and verified it as a functional gene in fission yeast. Here we show that 3′–5′ helicase activity is intrinsically associated with Hrq1 of Saccharomyces cerevisiae. We also determined several biochemical properties of Hrq1 helicase distinguishable from those of other RecQ helicase members. Hrq1 is able to unwind relatively long duplex DNA up to 120-bp and is significantly stimulated by a preexisting fork structure. Further, the most striking feature of Hrq1 is its absolute requirement for a long 3′-tail (⩾70-nt) for efficient unwinding of duplex DNA. We also found that Hrq1 has potent DNA strand annealing activity. Our results indicate that Hrq1 has vigorous helicase activity that deserves further characterization to expand our understanding of RecQ helicases.

  3. Dynamics of translocation and substrate binding in individual complexes formed with active site mutants of {phi}29 DNA polymerase.

    Science.gov (United States)

    Dahl, Joseph M; Wang, Hongyun; Lázaro, José M; Salas, Margarita; Lieberman, Kate R

    2014-03-07

    The Φ29 DNA polymerase (DNAP) is a processive B-family replicative DNAP. Fluctuations between the pre-translocation and post-translocation states can be quantified from ionic current traces, when individual Φ29 DNAP-DNA complexes are held atop a nanopore in an electric field. Based upon crystal structures of the Φ29 DNAP-DNA binary complex and the Φ29 DNAP-DNA-dNTP ternary complex, residues Tyr-226 and Tyr-390 in the polymerase active site were implicated in the structural basis of translocation. Here, we have examined the dynamics of translocation and substrate binding in complexes formed with the Y226F and Y390F mutants. The Y226F mutation diminished the forward and reverse rates of translocation, increased the affinity for dNTP in the post-translocation state by decreasing the dNTP dissociation rate, and increased the affinity for pyrophosphate in the pre-translocation state. The Y390F mutation significantly decreased the affinity for dNTP in the post-translocation state by decreasing the association rate ∼2-fold and increasing the dissociation rate ∼10-fold, implicating this as a mechanism by which this mutation impedes DNA synthesis. The Y390F dissociation rate increase is suppressed when complexes are examined in the presence of Mn(2+) rather than Mg(2+). The same effects of the Y226F or Y390F mutations were observed in the background of the D12A/D66A mutations, located in the exonuclease active site, ∼30 Å from the polymerase active site. Although translocation rates were unaffected in the D12A/D66A mutant, these exonuclease site mutations caused a decrease in the dNTP dissociation rate, suggesting that they perturb Φ29 DNAP interdomain architecture.

  4. Saccharomyces cerevisiae Hrq1 requires a long 3'-tailed DNA substrate for helicase activity.

    Science.gov (United States)

    Kwon, Sung-Hun; Choi, Do-Hee; Lee, Rina; Bae, Sung-Ho

    2012-10-26

    RecQ helicases are well conserved proteins from bacteria to human and function in various DNA metabolism for maintenance of genome stability. Five RecQ helicases are found in humans, whereas only one RecQ helicase has been described in lower eukaryotes. However, recent studies predicted the presence of a second RecQ helicase, Hrq1, in fungal genomes and verified it as a functional gene in fission yeast. Here we show that 3'-5' helicase activity is intrinsically associated with Hrq1 of Saccharomyces cerevisiae. We also determined several biochemical properties of Hrq1 helicase distinguishable from those of other RecQ helicase members. Hrq1 is able to unwind relatively long duplex DNA up to 120-bp and is significantly stimulated by a preexisting fork structure. Further, the most striking feature of Hrq1 is its absolute requirement for a long 3'-tail (⩾70-nt) for efficient unwinding of duplex DNA. We also found that Hrq1 has potent DNA strand annealing activity. Our results indicate that Hrq1 has vigorous helicase activity that deserves further characterization to expand our understanding of RecQ helicases. Copyright © 2012 Elsevier Inc. All rights reserved.

  5. Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation | Center for Cancer Research

    Science.gov (United States)

    Dubbed "Tom's T" by Dhruba Chattoraj, the unusually conserved thymine at position +7 in bacteriophage P1 plasmid RepA DNA binding sites rises above repressor and acceptor sequence logos. The T appears to represent base flipping prior to helix opening in this DNA replication initation protein.

  6. Conformational Dynamics of a Y-Family DNA Polymerase during Substrate Binding and Catalysis As Revealed by Interdomain F?rster Resonance Energy Transfer

    OpenAIRE

    Maxwell, Brian A.; Xu, Cuiling; Suo, Zucai

    2014-01-01

    Numerous kinetic, structural, and theoretical studies have established that DNA polymerases adjust their domain structures to enclose nucleotides in their active sites and then rearrange critical active site residues and substrates for catalysis, with the latter conformational change acting to kinetically limit the correct nucleotide incorporation rate. Additionally, structural studies have revealed a large conformational change between the apoprotein and the DNA?protein binary state for Y-fa...

  7. Noncanonical substrate preference of lambda exonuclease for 5'-nonphosphate-ended dsDNA and a mismatch-induced acceleration effect on the enzymatic reaction.

    Science.gov (United States)

    Wu, Tongbo; Yang, Yufei; Chen, Wei; Wang, Jiayu; Yang, Ziyu; Wang, Shenlin; Xiao, Xianjin; Li, Mengyuan; Zhao, Meiping

    2018-04-06

    Lambda exonuclease (λ exo) plays an important role in the resection of DNA ends for DNA repair. Currently, it is also a widely used enzymatic tool in genetic engineering, DNA-binding protein mapping, nanopore sequencing and biosensing. Herein, we disclose two noncanonical properties of this enzyme and suggest a previously undescribed hydrophobic interaction model between λ exo and DNA substrates. We demonstrate that the length of the free portion of the substrate strand in the dsDNA plays an essential role in the initiation of digestion reactions by λ exo. A dsDNA with a 5' non-phosphorylated, two-nucleotide-protruding end can be digested by λ exo with very high efficiency. Moreover, we show that when a conjugated structure is covalently attached to an internal base of the dsDNA, the presence of a single mismatched base pair at the 5' side of the modified base may significantly accelerate the process of digestion by λ exo. A detailed comparison study revealed additional π-π stacking interactions between the attached label and the amino acid residues of the enzyme. These new findings not only broaden our knowledge of the enzyme but will also be very useful for research on DNA repair and in vitro processing of nucleic acids.

  8. Noncanonical substrate preference of lambda exonuclease for 5′-nonphosphate-ended dsDNA and a mismatch-induced acceleration effect on the enzymatic reaction

    Science.gov (United States)

    Yang, Yufei; Chen, Wei; Wang, Jiayu; Yang, Ziyu; Wang, Shenlin; Xiao, Xianjin; Li, Mengyuan

    2018-01-01

    Abstract Lambda exonuclease (λ exo) plays an important role in the resection of DNA ends for DNA repair. Currently, it is also a widely used enzymatic tool in genetic engineering, DNA-binding protein mapping, nanopore sequencing and biosensing. Herein, we disclose two noncanonical properties of this enzyme and suggest a previously undescribed hydrophobic interaction model between λ exo and DNA substrates. We demonstrate that the length of the free portion of the substrate strand in the dsDNA plays an essential role in the initiation of digestion reactions by λ exo. A dsDNA with a 5′ non-phosphorylated, two-nucleotide-protruding end can be digested by λ exo with very high efficiency. Moreover, we show that when a conjugated structure is covalently attached to an internal base of the dsDNA, the presence of a single mismatched base pair at the 5′ side of the modified base may significantly accelerate the process of digestion by λ exo. A detailed comparison study revealed additional π–π stacking interactions between the attached label and the amino acid residues of the enzyme. These new findings not only broaden our knowledge of the enzyme but will also be very useful for research on DNA repair and in vitro processing of nucleic acids. PMID:29490081

  9. Distortion Control during Welding

    NARCIS (Netherlands)

    Akbari Pazooki, A.M.

    2014-01-01

    The local material expansion and contraction involved in welding result in permanent deformations or instability i.e., welding distortion. Considerable efforts have been made in controlling welding distortion prior to, during or after welding. Thermal Tensioning (TT) describes a group of in-situ

  10. Differences in substrate specificity of C(5)-substituted or C(5)-unsubstituted pyrimidine nucleotides by DNA polymerases from thermophilic bacteria, archaea, and phages.

    Science.gov (United States)

    Sawai, Hiroaki; Nagashima, Junichi; Kuwahara, Msayasu; Kitagata, Rina; Tamura, Takehiro; Matsui, Ikuo

    2007-09-01

    The pyrimidine bases of RNA are uracil (U) and cytosine (C), while thymine (T) and C are used for DNA. The C(5) position of C and U is unsubstituted, whereas the C(5) of T is substituted with a Me group. Miller et al. hypothesized that various C(5)-substituted uracil derivatives were formed during chemical evolution, and that C(5)-substituted U derivatives may have played important roles in the transition from an 'RNA world' to a 'DNA-RNA-protein world'. Hyperthermophilic bacteria and archaea are considered to be primitive organisms that are evolutionarily close to the universal ancestor of all life on earth. Thus, we examined the substrate specificity of several C(5)-substituted or C(5)-unsubstituted dUTP and dCTP analogs for several DNA polymerases from hyperthermophilic bacteria, hyperthermophilic archaea, and viruses during PCR or primer extension reaction. The substrate specificity of the C(5)-substituted or C(5)-unsubstituted pyrimidine nucleotides varied greatly depending on the type of DNA polymerase. The significance of this difference in substrate specificity in terms of the origin and evolution of the DNA replication system is discussed briefly.

  11. TERRA mimicking ssRNAs prevail over the DNA substrate for telomerase in vitro due to interactions with the alternative binding site.

    Science.gov (United States)

    Azhibek, Dulat; Skvortsov, Dmitry; Andreeva, Anna; Zatsepin, Timofei; Arutyunyan, Alexandr; Zvereva, Maria; Dontsova, Olga

    2016-06-01

    Telomerase is a key component of the telomere length maintenance system in the majority of eukaryotes. Telomerase displays maximal activity in stem and cancer cells with high proliferative potential. In humans, telomerase activity is regulated by various mechanisms, including the interaction with telomere ssDNA overhangs that contain a repetitive G-rich sequence, and with noncoding RNA, Telomeric repeat-containing RNA (TERRA), that contains the same sequence. So these nucleic acids can compete for telomerase RNA templates in the cell. In this study, we have investigated the ability of different model substrates mimicking telomere DNA overhangs and TERRA RNA to compete for telomerase in vitro through a previously developed telomerase inhibitor assay. We have shown in this study that RNA oligonucleotides are better competitors for telomerase that DNA ones as RNA also use an alternative binding site on telomerase, and the presence of 2'-OH groups is significant in these interactions. In contrast to DNA, the possibility of forming intramolecular G-quadruplex structures has a minor effect for RNA binding to telomerase. Taking together our data, we propose that TERRA RNA binds better to telomerase compared with its native substrate - the 3'-end of telomere DNA overhang. As a result, some specific factor may exist that participates in switching telomerase from TERRA to the 3'-end of DNA for telomere elongation at the distinct period of a cell cycle in vivo. Copyright © 2015 John Wiley & Sons, Ltd. Copyright © 2015 John Wiley & Sons, Ltd.

  12. Isolation of a cDNA clone complementary to sequences for a 34-kilodalton protein which is a pp60v-src substrate.

    OpenAIRE

    Tomasiewicz, H G; Cook-Deegan, R; Chikaraishi, D M

    1984-01-01

    We have isolated a partial cDNA clone containing sequences complementary to a mRNA encoding a 34- to 36-kilodalton normal chicken cell protein which is a substrate for pp60v-src kinase activity. Using this 34-kilodalton cDNA clone as a probe, we determined that the size of the 34-kilodalton mRNA was 1,100 nucleotides and the level of the 34-kilodalton RNA was the same in various tissues of mature chickens but was significantly higher in chicken embryo fibroblast cells.

  13. The mismatch repair and meiotic recombination endonuclease Mlh1-Mlh3 is activated by polymer formation and can cleave DNA substrates in trans.

    Science.gov (United States)

    Manhart, Carol M; Ni, Xiaodan; White, Martin A; Ortega, Joaquin; Surtees, Jennifer A; Alani, Eric

    2017-04-01

    Crossing over between homologs is initiated in meiotic prophase by the formation of DNA double-strand breaks that occur throughout the genome. In the major interference-responsive crossover pathway in baker's yeast, these breaks are resected to form 3' single-strand tails that participate in a homology search, ultimately forming double Holliday junctions (dHJs) that primarily include both homologs. These dHJs are resolved by endonuclease activity to form exclusively crossovers, which are critical for proper homolog segregation in Meiosis I. Recent genetic, biochemical, and molecular studies in yeast are consistent with the hypothesis of Mlh1-Mlh3 DNA mismatch repair complex acting as the major endonuclease activity that resolves dHJs into crossovers. However, the mechanism by which the Mlh1-Mlh3 endonuclease is activated is unknown. Here, we provide evidence that Mlh1-Mlh3 does not behave like a structure-specific endonuclease but forms polymers required to generate nicks in DNA. This conclusion is supported by DNA binding studies performed with different-sized substrates that contain or lack polymerization barriers and endonuclease assays performed with varying ratios of endonuclease-deficient and endonuclease-proficient Mlh1-Mlh3. In addition, Mlh1-Mlh3 can generate religatable double-strand breaks and form an active nucleoprotein complex that can nick DNA substrates in trans. Together these observations argue that Mlh1-Mlh3 may not act like a canonical, RuvC-like Holliday junction resolvase and support a novel model in which Mlh1-Mlh3 is loaded onto DNA to form an activated polymer that cleaves DNA.

  14. DNA Damage: Quantum Mechanics/Molecular Mechanics Study on the Oxygen Binding and Substrate Hydroxylation Step in AlkB Repair Enzymes

    Science.gov (United States)

    Quesne, Matthew G; Latifi, Reza; Gonzalez-Ovalle, Luis E; Kumar, Devesh; de Visser, Sam P

    2014-01-01

    AlkB repair enzymes are important nonheme iron enzymes that catalyse the demethylation of alkylated DNA bases in humans, which is a vital reaction in the body that heals externally damaged DNA bases. Its mechanism is currently controversial and in order to resolve the catalytic mechanism of these enzymes, a quantum mechanics/molecular mechanics (QM/MM) study was performed on the demethylation of the N1-methyladenine fragment by AlkB repair enzymes. Firstly, the initial modelling identified the oxygen binding site of the enzyme. Secondly, the oxygen activation mechanism was investigated and a novel pathway was found, whereby the catalytically active iron(IV)–oxo intermediate in the catalytic cycle undergoes an initial isomerisation assisted by an Arg residue in the substrate binding pocket, which then brings the oxo group in close contact with the methyl group of the alkylated DNA base. This enables a subsequent rate-determining hydrogen-atom abstraction on competitive σ-and π-pathways on a quintet spin-state surface. These findings give evidence of different locations of the oxygen and substrate binding channels in the enzyme and the origin of the separation of the oxygen-bound intermediates in the catalytic cycle from substrate. Our studies are compared with small model complexes and the effect of protein and environment on the kinetics and mechanism is explained. PMID:24339041

  15. DNA Modified with Metal Nanoparticles: Preparation and Characterization of Ordered Metal-DNA Nanostructures in a Solution and on a Substrate

    Directory of Open Access Journals (Sweden)

    Nina Kasyanenko

    2016-01-01

    Full Text Available DNA interaction with silver and aluminum nanoparticles in a solution has been investigated with the AFM, SEM, dynamic light scattering, viscometry, and spectral methods. The comparison of DNA interaction with nanoparticles synthesized by the reduction of Ag+ ions and with nanoparticles obtained by the electric discharge plasma method was done. DNA metallization in a solution and on n-silicon surface with metal nanoparticles or by the reduction of silver ions after their binding to DNA was executed and studied. It was shown that DNA strands with regular location of silver or aluminum nanoparticles can be prepared. The conditions for the formation of silver nanoparticles and silver nanoclusters on DNA were analyzed.

  16. Highly selective and sensitive detection of miRNA based on toehold-mediated strand displacement reaction and DNA tetrahedron substrate.

    Science.gov (United States)

    Li, Wei; Jiang, Wei; Ding, Yongshun; Wang, Lei

    2015-09-15

    MicroRNAs (miRNAs) play important roles in a variety of biological processes and have been regarded as tumor biomarkers in cancer diagnosis and prognosis. In this work, a single-molecule counting method for miRNA analysis was proposed based on toehold-mediated strand displacement reaction (SDR) and DNA tetrahedron substrate. Firstly, a specially designed DNA tetrahedron was assembled with a hairpin at one of the vertex, which has an overhanging toehold domain. Then, the DNA tetrahedron was immobilized on the epoxy-functional glass slide by epoxy-amine reaction, forming a DNA tetrahedron substrate. Next, the target miRNA perhybridized with the toehold domain and initiated a strand displacement reaction along with the unfolding of the hairpin, realizing the selective recognization of miRNA. Finally, a biotin labeled detection DNA was hybridized with the new emerging single strand and the streptavidin coated QDs were used as fluorescent probes. Fluorescent images were acquired via epi-fluorescence microscopy, the numbers of fluorescence dots were counted one by one for quantification. The detection limit is 5 fM, which displayed an excellent sensitivity. Moreover, the proposed method which can accurately be identified the target miRNA among its family members, demonstrated an admirable selectivity. Furthermore, miRNA analysis in total RNA samples from human lung tissues was performed, suggesting the feasibility of this method for quantitative detection of miRNA in biomedical research and early clinical diagnostics. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. DNA Polymerase Fidelity: Comparing Direct Competition of Right and Wrong dNTP Substrates with Steady State and Presteady State Kinetics†

    Science.gov (United States)

    Bertram, Jeffrey G.; Oertell, Keriann; Petruska, John; Goodman, Myron F.

    2009-01-01

    DNA polymerase fidelity is defined as the ratio of right (R) to wrong (W) nucleotide incorporations when dRTP and dWTP substrates compete at equal concentrations for primer extension at the same site in the polymerase-primer-template DNA complex. Typically, R incorporation is favored over W by 103 – 105, even in the absence of 3′-exonuclease proofreading. Straightforward in principal, a direct competition fidelity measurement is difficult to perform in practice because detection of a small amount of W is masked by a large amount of R. As an alternative, enzyme kinetics measurements to evaluate kcat/Km for R and W in separate reactions are widely used to measure polymerase fidelity indirectly, based on a steady-state derivation by Fersht. A systematic comparison between direct competition and kinetics has not been made until now. By separating R and W products using electrophoresis, we have successfully made accurate fidelity measurements for directly competing R and W dNTP substrates for 9 of the 12 natural base mispairs. We compare our direct competition results with steady state and presteady state kinetic measurements of fidelity at the same template site, using the proofreading-deficient mutant of Klenow Fragment (KF−) DNA polymerase. All the data are in quantitative agreement. PMID:20000359

  18. Distortion dependent intersystem crossing

    DEFF Research Database (Denmark)

    Stephansen, Anne Boutrup; Sølling, Theis Ivan

    2017-01-01

    . The effect is observed to increase in the presence of methyl-groups on the pinnacle carbon-atoms, where largest extents of r and p orbital-mixing are observed. This is fully consistent with the time-resolved spectroscopy data: Toluene and p-xylene show evidence for ultrafast triplet formation competing......The competition between ultrafast intersystem crossing and internal conversion in benzene, toluene, and p-xylene is investigated with time-resolved photoelectron spectroscopy and quantum chemical calculations. By exciting to S2 out-of-plane symmetry breaking, distortions are activated at early...... times whereupon spin-forbidden intersystem crossing becomes (partly) allowed. Natural bond orbital analysis suggests that the pinnacle carbon atoms distorting from the aromatic plane change hybridization between the planar Franck-Condon geometry and the deformed (boat-shaped) S2 equilibrium geometry...

  19. PIP degron proteins, substrates of CRL4Cdt2, and not PIP boxes, interfere with DNA polymerase η and κ focus formation on UV damage.

    Science.gov (United States)

    Tsanov, Nikolay; Kermi, Chames; Coulombe, Philippe; Van der Laan, Siem; Hodroj, Dana; Maiorano, Domenico

    2014-04-01

    Proliferating cell nuclear antigen (PCNA) is a well-known scaffold for many DNA replication and repair proteins, but how the switch between partners is regulated is currently unclear. Interaction with PCNA occurs via a domain known as a PCNA-Interacting Protein motif (PIP box). More recently, an additional specialized PIP box has been described, the « PIP degron », that targets PCNA-interacting proteins for proteasomal degradation via the E3 ubiquitin ligase CRL4(Cdt2). Here we provide evidence that CRL4(Cdt2)-dependent degradation of PIP degron proteins plays a role in the switch of PCNA partners during the DNA damage response by facilitating accumulation of translesion synthesis DNA polymerases into nuclear foci. We show that expression of a nondegradable PIP degron (Cdt1) impairs both Pol η and Pol κ focus formation on ultraviolet irradiation and reduces cell viability, while canonical PIP box-containing proteins have no effect. Furthermore, we identify PIP degron-containing peptides from several substrates of CRL4(Cdt2) as efficient inhibitors of Pol η foci formation. By site-directed mutagenesis we show that inhibition depends on a conserved threonine residue that confers high affinity for PCNA-binding. Altogether these findings reveal an important regulative role for the CRL4(Cdt2) pathway in the switch of PCNA partners on DNA damage.

  20. Distorted Fingerprint Verification System

    Directory of Open Access Journals (Sweden)

    Divya KARTHIKAESHWARAN

    2011-01-01

    Full Text Available Fingerprint verification is one of the most reliable personal identification methods. Fingerprint matching is affected by non-linear distortion introduced in fingerprint impression during the image acquisition process. This non-linear deformation changes both the position and orientation of minutiae. The proposed system operates in three stages: alignment based fingerprint matching, fuzzy clustering and classifier framework. First, an enhanced input fingerprint image has been aligned with the template fingerprint image and matching score is computed. To improve the performance of the system, a fuzzy clustering based on distance and density has been used to cluster the feature set obtained from the fingerprint matcher. Finally a classifier framework has been developed and found that cost sensitive classifier produces better results. The system has been evaluated on fingerprint database and the experimental result shows that system produces a verification rate of 96%. This system plays an important role in forensic and civilian applications.

  1. Limited distortion in LSB steganography

    Science.gov (United States)

    Kim, Younhee; Duric, Zoran; Richards, Dana

    2006-02-01

    It is well known that all information hiding methods that modify the least significant bits introduce distortions into the cover objects. Those distortions have been utilized by steganalysis algorithms to detect that the objects had been modified. It has been proposed that only coefficients whose modification does not introduce large distortions should be used for embedding. In this paper we propose an effcient algorithm for information hiding in the LSBs of JPEG coefficients. Our algorithm uses parity coding to choose the coefficients whose modifications introduce minimal additional distortion. We derive the expected value of the additional distortion as a function of the message length and the probability distribution of the JPEG quantization errors of cover images. Our experiments show close agreement between the theoretical prediction and the actual additional distortion.

  2. Stereospecific suppression of active site mutants by methylphosphonate substituted substrates reveals the stereochemical course of site-specific DNA recombination

    OpenAIRE

    Rowley, Paul A.; Kachroo, Aashiq H.; Ma, Chien-Hui; Maciaszek, Anna D.; Guga, Piotr; Jayaram, Makkuni

    2015-01-01

    Tyrosine site-specific recombinases, which promote one class of biologically important phosphoryl transfer reactions in DNA, exemplify active site mechanisms for stabilizing the phosphate transition state. A highly conserved arginine duo (Arg-I; Arg-II) of the recombinase active site plays a crucial role in this function. Cre and Flp recombinase mutants lacking either arginine can be rescued by compensatory charge neutralization of the scissile phosphate via methylphosphonate (MeP) modificati...

  3. Determination of DNA by solid substrate room temperature phosphorescence enhancing method based on the Morin.SiO2 luminescent nanoparticles-Pd system as a phosphorescence probe

    International Nuclear Information System (INIS)

    Liu Jiaming; Yang Tianlong; Gao Fei; Hu Lixiang; He Hangxia; Liu Qinying; Liu Zhenbo; Huang Xiaomei; Zhu Guohui

    2006-01-01

    Sodium carbonate (Na 2 SiO 3 ) as the precursor, was mixed with Morin organic dye to synthesize silicon dioxide luminescent nanoparticles containing Morin (Morin.SiO 2 ) by sol-gel method. The particle sizes of SiO 2 .nH 2 O and Morin.SiO 2 were both 50 nm, measured with TEM (transmission electron microscope). Morin.SiO 2 modified by HS-CH 2 COOH could be dissolved by water. In the HMTA (hexamethylenetetramine)-HCl buffer solution, Pd 2+ could coordinate with Morin in Morin.SiO 2 to form complex Pd 2+ -Morin.SiO 2 , which could emit phosphorescence on polyamide membrane. And DNA (deoxyribonucleic acid) could cause a sharp enhancement of the room temperature phosphorescence (RTP) intensity of complex Pd 2+ -Morin.SiO 2 . Thus a new method of solid substrate room temperature phosphorescence (SS-RTP) enhancing for the determination of DNA was established based on the Morin.SiO 2 luminescent nanoparticles-Pd system as a phosphorescence probe. The ΔIp is directly proportional to the content of DNA in the range of 4.00-1000.0 fg spot -1 (corresponding concentration: 0.010-2.50 ng ml -1 ). The regression equation of working curve was ΔIp = 21.13 + 0.2076m DNA (fg spot -1 ) (r = 0.9990) and the detection limit was 0.61 fg spot -1 (corresponding concentration: 1.5 pg ml -1 ). This method had a wide linear range, high sensitivity, convenience, rapidity and only a little sample was needed. Samples containing 0.10 and 25.0 ng ml -1 DNA were measured repeatedly for 11 times and RSDs were 3.2 and 4.1% (n = 11), respectively, which indicated that the method had a good repeatability. Disturbance of common ions, such as Mg 2+ , K + , and Ca 2+ , was small, and there was no disturbance in the presence of protein and RNA. This method has been applied to the determination of DNA in nectar successfully

  4. A KAS2 cDNA complements the phenotypes of the Arabidopsis fab1 mutant that differs in a single residue bordering the substrate binding pocket

    DEFF Research Database (Denmark)

    Carlsson, A.S.; LaBrie, S.T.; Kinney, A.J.

    2002-01-01

    The fab1 mutant of Arabidopsis is partially deficient in activity of ß-ketoacyl-[acyl carrier protein] synthase II (KAS II). This defect results in increased levels of 16 : 0 fatty acid and is associated with damage and death of the mutants at low temperature. Transformation of fab1 plants with a c......DNA from Brassica napus encoding a KAS II enzyme resulted in complementation of both mutant phenotypes. The dual complementation by expression of the single gene proves that low-temperature damage is a consequence of altered membrane unsaturation. The fab1 mutation is a single nucleotide change...... chain to bend. For functional analysis the equivalent Leu207Phe mutation was introduced into the fabB gene encoding the E. coli KAS I enzyme. Compared to wild-type, the Leu207Phe protein showed a 10-fold decrease in binding affinity for the fatty acid substrate, exhibited a modified behavior during size...

  5. From nucleotides to DNA analysis by a SERS substrate of a self similar chain of silver nanospheres

    KAUST Repository

    Coluccio, M L

    2015-11-01

    In this work we realized a device of silver nanostructures designed so that they have a great ability to sustain the surface-enhanced Raman scattering effect. The nanostructures were silver self-similar chains of three nanospheres, having constant ratios between their diameters and between their reciprocal distances. They were realized by electron beam lithography, to write the pattern, and by silver electroless deposition technique, to fill it with the metal. The obtained device showed the capability to increase the Raman signal coming from the gap between the two smallest nanospheres (whose size is around 10 nm) and so it allows the detection of biomolecules fallen into this hot spot. In particular, oligonucleotides with 6 DNA bases, deposited on these devices with a drop coating method, gave a Raman spectrum characterized by a clear fingerprint coming from the hot spot and, with the help of a fitting method, also oligonucleotides of 9 bases, which are less than 3 nm long, were resolved. In conclusion the silver nanolens results in a SERS device able to measure all the molecules, or part of them, held into the hot spot of the nanolenses, and thus it could be a future instrument with which to analyze DNA portions.

  6. Distortions in Judged Spatial Relations.

    Science.gov (United States)

    Stevens, Albert

    1978-01-01

    Distortions in judgments of relative geographical relations were observed, particularly when the locations were in different geographical or political units. Subjects distorted the judged relation to conform with the relation of the superordinate political unit. A model for the hierachical storage of spatial information is presented. (Author/RD)

  7. Volterra Series Based Distortion Effect

    DEFF Research Database (Denmark)

    Agerkvist, Finn T.

    2010-01-01

    A large part of the characteristic sound of the electric guitar comes from nonlinearities in the signal path. Such nonlinearities may come from the input- or output-stage of the amplier, which is often equipped with vacuum tubes or a dedicated distortion pedal. In this paper the Volterra series...... expansion for non linear systems is investigated with respect to generating good distortion. The Volterra series allows for unlimited adjustment of the level and frequency dependency of each distortion component. Subjectively relevant ways of linking the dierent orders are discussed....

  8. Lipofection and nucleofection of substrate plasmid can generate widely different readings of DNA end-joining efficiency in different cell lines.

    Science.gov (United States)

    Magin, Simon; Saha, Janapriya; Wang, Minli; Mladenova, Veronika; Coym, Nadine; Iliakis, George

    2013-02-01

    In vivo plasmid end-joining assays are valuable tools for dissecting important qualitative and quantitative aspects of non-homologous end-joining (NHEJ)--a key mechanism for the repair of DNA double-strand breaks (DSBs) in higher eukaryotes. They enable the use of defined DNA ends as substrates for end-joining and the analysis by sequencing of the resulting junctions to identify the repair pathways engaged. Yet, plasmid assays have generated divergent results of end-joining capacity in the same DSB repair mutants when used under different conditions, which implies contributions from undefined and therefore uncontrolled parameters. To help standardize these assays, we searched for parameters underpinning these variations and identified transfection method as an important determinant. Here, we compare a lipid-based transfection method, lipofection, with an electroporation method, nucleofection, and find large, unanticipated and cell line-dependent differences in percent end-joining without recognizable trends. For example, in rodent cells, transfection using lipofection gives nearly WT end-joining in DNA-PKcs mutants and only mildly inhibited end-joining in Lig4 and Ku mutants. In contrast, transfection using nucleofection shows marked end-joining inhibition in all NHEJ mutants tested as compared to the WT. In human HCT116 cells, end-joining after nucleofection is strongly suppressed even in the WT and the differences to the mutants are small. After lipofection, in contrast, end-joining is high in WT cells and markedly suppressed in the mutants. We conclude that better understanding and control of the physicochemical/biological and analytical parameters underpinning these differences will be required to generate with plasmid assays results with quantitative power comparable to that of well-established methods of DSB analysis such as pulsed-field gel electrophoresis or γ-H2AX foci scoring. Until then, caution is needed in the interpretation of the results obtained

  9. Dielectric coatings on metal substrates

    International Nuclear Information System (INIS)

    Glaros, S.S.; Baker, P.; Milam, D.

    1976-01-01

    Large aperture, beryllium substrate-based mirrors have been used to focus high intensity pulsed laser beams. Finished surfaces have high reflectivity, low wavefront distortion, and high laser damage thresholds. This paper describes the development of a series of metallic coatings, surface finishing techniques, and dielectric overcoatings to meet specified performance requirements. Beryllium substrates were coated with copper, diamond-machined to within 5 micro-inches to final contour, nickel plated, and abrasively figured to final contour. Bond strengths for several bonding processes are presented. Dielectric overcoatings were deposited on finished multimetallic substrates to increase both reflectivity and the damage thresholds. Coatings were deposited using both high and low temperature processes which induce varying stresses in the finished coating substrate system. Data are presented to show the evolution of wavefront distortion, reflectivity, and damage thresholds throughout the many steps involved in fabrication

  10. An Improved Distortion Operator for Insurance Risks

    Institute of Scientific and Technical Information of China (English)

    GAO Jian-wei; QIU Wan-hua

    2002-01-01

    This paper reviews the distortion function approach developed in the actuarial literature for insurance risks. The main aim of this paper is to derive an extensive distortion operator, and to propose a new premium principle based on this extensive distortion operator. Furthermore, the non-robustness of general distortion operator is also discussed. Examples are provided using Bernoulli, Pareto, Lognormal and Gamma distribution assumptions.

  11. Functional Dissection of the DNA Interface of the Nucleotidyltransferase Domain of Chlorella Virus DNA Ligase*

    Science.gov (United States)

    Samai, Poulami; Shuman, Stewart

    2011-01-01

    Chlorella virus DNA ligase (ChVLig) has pluripotent biological activity and an intrinsic nick-sensing function. ChVLig consists of three structural modules that envelop nicked DNA as a C-shaped protein clamp: a nucleotidyltransferase (NTase) domain and an OB domain (these two are common to all DNA ligases) as well as a distinctive β-hairpin latch module. The NTase domain, which performs the chemical steps of ligation, binds the major groove flanking the nick and the minor groove on the 3′-OH side of the nick. Here we performed a structure-guided mutational analysis of the NTase domain, surveying the effects of 35 mutations in 19 residues on ChVLig activity in vivo and in vitro, including biochemical tests of the composite nick sealing reaction and of the three component steps of the ligation pathway (ligase adenylylation, DNA adenylylation, and phosphodiester synthesis). The results highlight (i) key contacts by Thr-84 and Lys-173 to the template DNA strand phosphates at the outer margins of the DNA ligase footprint; (ii) essential contacts of Ser-41, Arg-42, Met-83, and Phe-75 with the 3′-OH strand at the nick; (iii) Arg-176 phosphate contacts at the nick and with ATP during ligase adenylylation; (iv) the role of Phe-44 in forming the protein clamp around the nicked DNA substrate; and (v) the importance of adenine-binding residue Phe-98 in all three steps of ligation. Kinetic analysis of single-turnover nick sealing by ChVLig-AMP underscored the importance of Phe-75-mediated distortion of the nick 3′-OH nucleoside in the catalysis of DNA 5′-adenylylation (step 2) and phosphodiester synthesis (step 3). Induced fit of the nicked DNA into a distorted conformation when bound within the ligase clamp may account for the nick-sensing capacity of ChVLig. PMID:21335605

  12. Functional dissection of the DNA interface of the nucleotidyltransferase domain of chlorella virus DNA ligase.

    Science.gov (United States)

    Samai, Poulami; Shuman, Stewart

    2011-04-15

    Chlorella virus DNA ligase (ChVLig) has pluripotent biological activity and an intrinsic nick-sensing function. ChVLig consists of three structural modules that envelop nicked DNA as a C-shaped protein clamp: a nucleotidyltransferase (NTase) domain and an OB domain (these two are common to all DNA ligases) as well as a distinctive β-hairpin latch module. The NTase domain, which performs the chemical steps of ligation, binds the major groove flanking the nick and the minor groove on the 3'-OH side of the nick. Here we performed a structure-guided mutational analysis of the NTase domain, surveying the effects of 35 mutations in 19 residues on ChVLig activity in vivo and in vitro, including biochemical tests of the composite nick sealing reaction and of the three component steps of the ligation pathway (ligase adenylylation, DNA adenylylation, and phosphodiester synthesis). The results highlight (i) key contacts by Thr-84 and Lys-173 to the template DNA strand phosphates at the outer margins of the DNA ligase footprint; (ii) essential contacts of Ser-41, Arg-42, Met-83, and Phe-75 with the 3'-OH strand at the nick; (iii) Arg-176 phosphate contacts at the nick and with ATP during ligase adenylylation; (iv) the role of Phe-44 in forming the protein clamp around the nicked DNA substrate; and (v) the importance of adenine-binding residue Phe-98 in all three steps of ligation. Kinetic analysis of single-turnover nick sealing by ChVLig-AMP underscored the importance of Phe-75-mediated distortion of the nick 3'-OH nucleoside in the catalysis of DNA 5'-adenylylation (step 2) and phosphodiester synthesis (step 3). Induced fit of the nicked DNA into a distorted conformation when bound within the ligase clamp may account for the nick-sensing capacity of ChVLig.

  13. Possible distortion of autoradiographic results

    Energy Technology Data Exchange (ETDEWEB)

    Kozlov, A.A.; Tumanushvili, G.D. (AN Gruzinskoj SSR, Tbilisi. Inst. Ehksperimental' noj Morfologii)

    1980-01-01

    The effect of radioactive labelling (H/sup 3/-thymidine) on the infusorian division is studied. The presented results show that introduction of labelled compounds results in accelerating infusorian cell division v. Thorough investigation of labelled compound effect with low activity on the parameters of cell division and the search of methods to eliminate distortions able to appear in autoradiographic experiments is expedient.

  14. Distinct DNA-binding surfaces in the ATPase and linker domains of MutLγ determine its substrate specificities and exert separable functions in meiotic recombination and mismatch repair.

    Directory of Open Access Journals (Sweden)

    Corentin Claeys Bouuaert

    2017-05-01

    Full Text Available Mlh1-Mlh3 (MutLγ is a mismatch repair factor with a central role in formation of meiotic crossovers, presumably through resolution of double Holliday junctions. MutLγ has DNA-binding, nuclease, and ATPase activities, but how these relate to one another and to in vivo functions are unclear. Here, we combine biochemical and genetic analyses to characterize Saccharomyces cerevisiae MutLγ. Limited proteolysis and atomic force microscopy showed that purified recombinant MutLγ undergoes ATP-driven conformational changes. In vitro, MutLγ displayed separable DNA-binding activities toward Holliday junctions (HJ and, surprisingly, single-stranded DNA (ssDNA, which was not predicted from current models. MutLγ bound DNA cooperatively, could bind multiple substrates simultaneously, and formed higher-order complexes. FeBABE hydroxyl radical footprinting indicated that the DNA-binding interfaces of MutLγ for ssDNA and HJ substrates only partially overlap. Most contacts with HJ substrates were located in the linker regions of MutLγ, whereas ssDNA contacts mapped within linker regions as well as the N-terminal ATPase domains. Using yeast genetic assays for mismatch repair and meiotic recombination, we found that mutations within different DNA-binding surfaces exert separable effects in vivo. For example, mutations within the Mlh1 linker conferred little or no meiotic phenotype but led to mismatch repair deficiency. Interestingly, mutations in the N-terminal domain of Mlh1 caused a stronger meiotic defect than mlh1Δ, suggesting that the mutant proteins retain an activity that interferes with alternative recombination pathways. Furthermore, mlh3Δ caused more chromosome missegregation than mlh1Δ, whereas mlh1Δ but not mlh3Δ partially alleviated meiotic defects of msh5Δ mutants. These findings illustrate functional differences between Mlh1 and Mlh3 during meiosis and suggest that their absence impinges on chromosome segregation not only via reduced

  15. TPC track distortions IV: post tenebras lux

    CERN Document Server

    Ammosov, V; Boyko, I; Chelkov, G; Dedovitch, D; Dydak, F; Elagin, A; Gostkin, M; Guskov, A; Koreshev, V; Krumshtein, Z; Nefedov, Y; Nikolaev, K; Wotschack, J; Zhemchugov, A

    2007-01-01

    We present a comprehensive discussion and summary of static and dynamic track distortions in the HARP TPC in terms of physical origin, mathematical modelling and correction algorithms. `Static' distortions are constant with time, while `dynamic' distortions are distortions that occur only during the 400 ms long accelerator spill. The measurement of dynamic distortions, their mathematical modelling and the correction algorithms build on our understanding of static distortions. In the course of corroborating the validity of our static distortion corrections, their reliability and precision was further improved. Dynamic TPC distortions originate dominantly from the `stalactite' effect: a column of positive-ion charge starts growing at the begin of the accelerator spill, and continues growing with nearly constant velocity out from the sense-wire plane into the active TPC volume. However, the `stalactite' effect is not able to describe the distortions that are present already at the start of the spill and which ha...

  16. Kinetics and Thermodynamics of DNA Processing by Wild Type DNA-Glycosylase Endo III and Its Catalytically Inactive Mutant Forms

    Directory of Open Access Journals (Sweden)

    Olga A. Kladova

    2018-03-01

    Full Text Available Endonuclease III (Endo III or Nth is one of the key enzymes responsible for initiating the base excision repair of oxidized or reduced pyrimidine bases in DNA. In this study, a thermodynamic analysis of structural rearrangements of the specific and nonspecific DNA-duplexes during their interaction with Endo III is performed based on stopped-flow kinetic data. 1,3-diaza-2-oxophenoxazine (tCO, a fluorescent analog of the natural nucleobase cytosine, is used to record multistep DNA binding and lesion recognition within a temperature range (5–37 °C. Standard Gibbs energy, enthalpy, and entropy of the specific steps are derived from kinetic data using Van’t Hoff plots. The data suggest that enthalpy-driven exothermic 5,6-dihydrouracil (DHU recognition and desolvation-accompanied entropy-driven adjustment of the enzyme–substrate complex into a catalytically active state play equally important parts in the overall process. The roles of catalytically significant amino acids Lys120 and Asp138 in the DNA lesion recognition and catalysis are identified. Lys120 participates not only in the catalytic steps but also in the processes of local duplex distortion, whereas substitution Asp138Ala leads to a complete loss of the ability of Endo III to distort a DNA double chain during enzyme–DNA complex formation.

  17. Mobile Watermarking against Geometrical Distortions

    Directory of Open Access Journals (Sweden)

    Jing Zhang

    2015-08-01

    Full Text Available Mobile watermarking robust to geometrical distortions is still a great challenge. In mobile watermarking, efficient computation is necessary because mobile devices have very limited resources due to power consumption. In this paper, we propose a low-complexity geometrically resilient watermarking approach based on the optimal tradeoff circular harmonic function (OTCHF correlation filter and the minimum average correlation energy Mellin radial harmonic (MACE-MRH correlation filter. By the rotation, translation and scale tolerance properties of the two kinds of filter, the proposed watermark detector can be robust to geometrical attacks. The embedded watermark is weighted by a perceptual mask which matches very well with the properties of the human visual system. Before correlation, a whitening process is utilized to improve watermark detection reliability. Experimental results demonstrate that the proposed watermarking approach is computationally efficient and robust to geometrical distortions.

  18. Guessing and compression subject to distortion

    OpenAIRE

    Hanawal, Manjesh Kumar; Sundaresan, Rajesh

    2010-01-01

    The problem of guessing a random string is revisited. The relation-ship between guessing without distortion and compression is extended to the case when source alphabet size is countably in¯nite. Further, similar relationship is established for the case when distortion allowed by establishing a tight relationship between rate distortion codes and guessing strategies.

  19. Analysis of Brown camera distortion model

    Science.gov (United States)

    Nowakowski, Artur; Skarbek, Władysław

    2013-10-01

    Contemporary image acquisition devices introduce optical distortion into image. It results in pixel displacement and therefore needs to be compensated for many computer vision applications. The distortion is usually modeled by the Brown distortion model, which parameters can be included in camera calibration task. In this paper we describe original model, its dependencies and analyze orthogonality with regard to radius for its decentering distortion component. We also report experiments with camera calibration algorithm included in OpenCV library, especially a stability of distortion parameters estimation is evaluated.

  20. Close encounters for the first time: Helicase interactions with DNA damage.

    Science.gov (United States)

    Khan, Irfan; Sommers, Joshua A; Brosh, Robert M

    2015-09-01

    DNA helicases are molecular motors that harness the energy of nucleoside triphosphate hydrolysis to unwinding structured DNA molecules that must be resolved during cellular replication, DNA repair, recombination, and transcription. In vivo, DNA helicases are expected to encounter a wide spectrum of covalent DNA modifications to the sugar phosphate backbone or the nitrogenous bases; these modifications can be induced by endogenous biochemical processes or exposure to environmental agents. The frequency of lesion abundance can vary depending on the lesion type. Certain adducts such as oxidative base modifications can be quite numerous, and their effects can be helix-distorting or subtle perturbations to DNA structure. Helicase encounters with specific DNA lesions and more novel forms of DNA damage will be discussed. We will also review the battery of assays that have been used to characterize helicase-catalyzed unwinding of damaged DNA substrates. Characterization of the effects of specific DNA adducts on unwinding by various DNA repair and replication helicases has proven to be insightful for understanding mechanistic and biological aspects of helicase function in cellular DNA metabolism. Published by Elsevier B.V.

  1. Space mappings with bounded distortion

    CERN Document Server

    Reshetnyak, Yu G

    1989-01-01

    This book is intended for researchers and students concerned with questions in analysis and function theory. The author provides an exposition of the main results obtained in recent years by Soviet and other mathematicians in the theory of mappings with bounded distortion, an active direction in contemporary mathematics. The mathematical tools presented can be applied to a broad spectrum of problems that go beyond the context of the main topic of investigation. For a number of questions in the theory of partial differential equations and the theory of functions with generalized derivatives, this is the first time they have appeared in an internationally distributed monograph.

  2. Comparison of Methods of Extracting Salmonella enterica Serovar Enteritidis DNA from Environmental Substrates and Quantification of Organisms by Using a General Internal Procedural Control

    NARCIS (Netherlands)

    Klerks, M.M.; Bruggen, van A.H.C.; Zijlstra, C.; Donnikov, M.; Vos, de R.

    2006-01-01

    This paper compares five commercially available DNA extraction methods with respect to DNA extraction efficiency of Salmonella enterica serovar Enteritidis from soil, manure, and compost and uses an Escherichia coli strain harboring a plasmid expressing green fluorescent protein as a general

  3. Molecular distortion and charge transfer effects in ZnPc/Cu(111)

    KAUST Repository

    Amin, B.; Nazir, S.; Schwingenschlö gl, Udo

    2013-01-01

    The adsorption geometry and electronic properties of a zinc-phthalocyanine molecule on a Cu(111) substrate are studied by density functional theory. In agreement with experiment, we find remarkable distortions of the molecule, mainly as the central Zn atom tends towards the substrate to minimize the Zn-Cu distance. As a consequence, the Zn-N chemical bonding and energy levels of the molecule are significantly modified. However, charge transfer induces metallic states on the molecule and therefore is more important for the ZnPc/Cu(111) system than the structural distortions.

  4. Molecular distortion and charge transfer effects in ZnPc/Cu(111)

    KAUST Repository

    Amin, B.

    2013-04-23

    The adsorption geometry and electronic properties of a zinc-phthalocyanine molecule on a Cu(111) substrate are studied by density functional theory. In agreement with experiment, we find remarkable distortions of the molecule, mainly as the central Zn atom tends towards the substrate to minimize the Zn-Cu distance. As a consequence, the Zn-N chemical bonding and energy levels of the molecule are significantly modified. However, charge transfer induces metallic states on the molecule and therefore is more important for the ZnPc/Cu(111) system than the structural distortions.

  5. Differential Salt-Induced Dissociation of the p53 Protein Complexes with Circular and Linear Plasmid DNA Substrates Suggest Involvement of a Sliding Mechanism

    Czech Academy of Sciences Publication Activity Database

    Šebest, Peter; Brázdová, Marie; Fojta, Miroslav; Pivoňková, Hana

    2015-01-01

    Roč. 16, č. 2 (2015), s. 3163-3177 E-ISSN 1422-0067 R&D Projects: GA ČR(CZ) GAP301/11/2076; GA ČR(CZ) GBP206/12/G151 Institutional support: RVO:68081707 Keywords : TUMOR-SUPPRESSOR P53 * CISPLATIN -DAMAGED DNA * SUPERCOILED DNA Subject RIV: BO - Biophysics Impact factor: 3.257, year: 2015

  6. Frequency modulation television analysis: Distortion analysis

    Science.gov (United States)

    Hodge, W. H.; Wong, W. H.

    1973-01-01

    Computer simulation is used to calculate the time-domain waveform of standard T-pulse-and-bar test signal distorted in passing through an FM television system. The simulator includes flat or preemphasized systems and requires specification of the RF predetection filter characteristics. The predetection filters are modeled with frequency-symmetric Chebyshev (0.1-db ripple) and Butterworth filters. The computer was used to calculate distorted output signals for sixty-four different specified systems, and the output waveforms are plotted for all sixty-four. Comparison of the plotted graphs indicates that a Chebyshev predetection filter of four poles causes slightly more signal distortion than a corresponding Butterworth filter and the signal distortion increases as the number of poles increases. An increase in the peak deviation also increases signal distortion. Distortion also increases with the addition of preemphasis.

  7. The selfish Segregation Distorter gene complex of Drosophila melanogaster.

    Science.gov (United States)

    Larracuente, Amanda M; Presgraves, Daven C

    2012-09-01

    Segregation Distorter (SD) is an autosomal meiotic drive gene complex found worldwide in natural populations of Drosophila melanogaster. During spermatogenesis, SD induces dysfunction of SD(+) spermatids so that SD/SD(+) males sire almost exclusively SD-bearing progeny rather than the expected 1:1 Mendelian ratio. SD is thus evolutionarily "selfish," enhancing its own transmission at the expense of its bearers. Here we review the molecular and evolutionary genetics of SD. Genetic analyses show that the SD is a multilocus gene complex involving two key loci--the driver, Segregation distorter (Sd), and the target of drive, Responder (Rsp)--and at least three upward modifiers of distortion. Molecular analyses show that Sd encodes a truncated duplication of the gene RanGAP, whereas Rsp is a large pericentromeric block of satellite DNA. The Sd-RanGAP protein is enzymatically wild type but mislocalized within cells and, for reasons that remain unclear, appears to disrupt the histone-to-protamine transition in drive-sensitive spermatids bearing many Rsp satellite repeats but not drive-insensitive spermatids bearing few or no Rsp satellite repeats. Evolutionary analyses show that the Sd-RanGAP duplication arose recently within the D. melanogaster lineage, exploiting the preexisting and considerably older Rsp satellite locus. Once established, the SD haplotype collected enhancers of distortion and suppressors of recombination. Further dissection of the molecular genetic and cellular basis of SD-mediated distortion seems likely to provide insights into several important areas currently understudied, including the genetic control of spermatogenesis, the maintenance and evolution of satellite DNAs, the possible roles of small interfering RNAs in the germline, and the molecular population genetics of the interaction of genetic linkage and natural selection.

  8. Structural Change Accounting with Labor Market Distortions

    OpenAIRE

    Wenbiao Cai

    2014-01-01

    This paper quantifies the relative importance of sectoral productivity and labor market distortions for structural change. I use a model in which labor productivity is the product of TFP and human capital in each sector, but distortions generate wedges in wage per efficiency worker across sectors. I calculate human capital by sector using micro census data, and use the model to infer TFP and distortions such that it replicates structural change in the US, India, Mexico and Brazil between 1960...

  9. Cognitive Distortions, Humor Styles, and Depression.

    Science.gov (United States)

    Rnic, Katerina; Dozois, David J A; Martin, Rod A

    2016-08-01

    Cognitive distortions are negative biases in thinking that are theorized to represent vulnerability factors for depression and dysphoria. Despite the emphasis placed on cognitive distortions in the context of cognitive behavioural theory and practice, a paucity of research has examined the mechanisms through which they impact depressive symptomatology. Both adaptive and maladaptive styles of humor represent coping strategies that may mediate the relation between cognitive distortions and depressive symptoms. The current study examined the correlations between the frequency and impact of cognitive distortions across both social and achievement-related contexts and types of humor. Cognitive distortions were associated with reduced use of adaptive Affiliative and Self-Enhancing humor styles and increased use of maladaptive Aggressive and Self-Defeating humor. Reduced use of Self-Enhancing humor mediated the relationship between most types of cognitive distortions and depressed mood, indicating that distorted negative thinking may interfere with an individual's ability to adopt a humorous and cheerful outlook on life (i.e., use Self-Enhancing humor) as a way of regulating emotions and coping with stress, thereby resulting in elevated depressive symptoms. Similarly, Self-Defeating humor mediated the association of the social impact of cognitive distortions with depression, such that this humor style may be used as a coping strategy for dealing with distorted thinking that ultimately backfires and results in increased dysphoria.

  10. Protease activity of PprI facilitates DNA damage response: Mn2+-dependence and substrate sequence-specificity of the proteolytic reaction.

    Directory of Open Access Journals (Sweden)

    Yunguang Wang

    Full Text Available The extremophilic bacterium Deinococcus radiodurans exhibits an extraordinary resistance to ionizing radiation. Previous studies established that a protein named PprI, which exists only in the Deinococcus-Thermus family, acts as a general switch to orchestrate the expression of a number of DNA damage response (DDR proteins involved in cellular radio-resistance. Here we show that the regulatory mechanism of PprI depends on its Mn(2+-dependent protease activity toward DdrO, a transcription factor that suppresses DDR genes' expression. Recognition sequence-specificity around the PprI cleavage site is essential for DNA damage repair in vivo. PprI and DdrO mediate a novel DNA damage response pathway differing from the classic LexA-mediated SOS response system found in radiation-sensitive bacterium Escherichia coli. This PprI-mediated pathway in D. radiodurans is indispensable for its extreme radio-resistance and therefore its elucidation significantly advances our understanding of the DNA damage repair mechanism in this amazing organism.

  11. Monitoring DNA damage in wood small-reed (Calamagrostis epigejos) plants growing in a sediment reservoir with substrates from uranium mining

    Czech Academy of Sciences Publication Activity Database

    Ptáček, Ondřej; Mühlfeldová, Zdeňka; Dostálek, J.; Čechák, T.; Gichner, Tomáš

    2002-01-01

    Roč. 4, - (2002), s. 592-595 ISSN 1464-0325 R&D Projects: GA ČR GA521/02/0400 Institutional research plan: CEZ:AV0Z5038910 Keywords : DNA * Calamagrostis epigejos * uranium mining Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.348, year: 2002

  12. Modelling the Perceptual Components of Loudspeaker Distortion

    DEFF Research Database (Denmark)

    Olsen, Sune L.; Agerkvist, Finn T.; MacDonald, Ewen

    2016-01-01

    While non-linear distortion in loudspeakers decreases audio quality, the perceptual consequences can vary substantially. This paper investigates the metric Rnonlin [1] which was developed to predict subjective measurements of sound quality in nonlinear systems. The generalisability of the metric...... the perceptual consequences of non-linear distortion....

  13. Advanced Machining Toolpath for Low Distortion

    Science.gov (United States)

    2017-02-28

    Advanced Machining Toolpath for Low Distortion FINAL STATUS REPORT Prepared by Brian Becker R&D Technology Manager Third Wave Systems, Inc... Machining Toolpath for Low Distortion December 2016 Contract No.: W911W6-16-P-0044 2 Table of Contents 1.0 EXECUTIVE SUMMARY...2 2.1 Task 1: Collect Details of Machining Lab to Support

  14. TPC track distortions III: fiat lux

    CERN Document Server

    Boyko, I; Dydak, F; Elagin, A; Gostkin, M; Guskov, A; Koreshev, V; Nefedov, Y; Nikolaev, K; Veenhof, R; Wotschack, J; Zhemchugov, A

    2005-01-01

    We present a comprehensive overview and final summary of all four types of static track distortions seen in the HARP TPC, in terms of physical origins, mathematical modelling, and correction algorithms. 'Static'™ distortions are defined as not depending on the event time within the 400 ms long accelerator spill. Calculated static distortions are compared with measurements from cosmic-muon tracks. We characterize track distortions by the r phi residuals of cluster positions with respect to the transverse projection of a helical trajectory constrained by hits in the RPC overlap regions. This method provides a fixed TPC-external reference system (by contrast to the co-moving coordinate system associated with a fit) which solely permits to identify individually, and measure quantitatively, the static TPC track distortions arising from (i) the inhomogeneity of the solenoidal magnetic field, (ii) the inhomogeneity of the electric field from the high-voltage mismatch between the inner and outer TPC field cages, (...

  15. Traceless splicing enabled by substrate-induced activation of the Nostoc punctiforme Npu DnaE intein after mutation of a catalytic cysteine to serine.

    Science.gov (United States)

    Cheriyan, Manoj; Chan, Siu-Hong; Perler, Francine

    2014-12-12

    Inteins self-catalytically cleave out of precursor proteins while ligating the surrounding extein fragments with a native peptide bond. Much attention has been lavished on these molecular marvels with the hope of understanding and harnessing their chemistry for novel biochemical transformations including coupling peptides from synthetic or biological origins and controlling protein function. Despite an abundance of powerful applications, the use of inteins is still hampered by limitations in our understanding of their specificity (defined as flanking sequences that permit splicing) and the challenge of inserting inteins into target proteins. We examined the frequently used Nostoc punctiforme Npu DnaE intein after the C-extein cysteine nucleophile (Cys+1) was mutated to serine or threonine. Previous studies demonstrated reduced rates and/or splicing yields with the Npu DnaE intein after mutation of Cys+1 to Ser+1. In this study, genetic selection identified extein sequences with Ser+1 that enabled the Npu DnaE intein to splice with only a 5-fold reduction in rate compared to the wild-type Cys+1 intein and without mutation of the intein itself to activate Ser+1 as a nucleophile. Three different proteins spliced efficiently after insertion of the intein flanked by the selected sequences. We then used this selected specificity to achieve traceless splicing in a targeted enzyme at a location predicted by primary sequence similarity to only the selected C-extein sequence. This study highlights the latent catalytic potential of the Npu DnaE intein to splice with an alternative nucleophile and enables broader intein utility by increasing insertion site choices. Copyright © 2014. Published by Elsevier Ltd.

  16. Offshore Substrate

    Data.gov (United States)

    California Natural Resource Agency — This shapefile displays the distribution of substrate types from Pt. Arena to Pt. Sal in central/northern California. Originally this data consisted of seven paper...

  17. Sonographic ally Detected Architectural Distortion: Clinical Significance

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Shin Kee; Seo, Bo Kyoung; Yi, Ann; Cha, Sang Hoon; Kim, Baek Hyun; Cho, Kyu Ran; Kim, Young Sik; Son, Gil Soo; Kim, Young Soo; Kim, Hee Young [Korea University Ansan Hospital, Ansan (Korea, Republic of)

    2008-12-15

    Architectural distortion is a suspicious abnormality for the diagnosis of breast cancer. The aim of this study was to investigate the clinical significance of sonographic ally detected architectural distortion. From January 2006 to June 2008, 20 patients were identified who had sonographic ally detected architectural distortions without a history of trauma or surgery and abnormal mammographic findings related to an architectural distortion. All of the lesions were pathologically verified. We evaluated the clinical and pathological findings and then assessed the clinical significance of the sonographic ally detected architectural distortions. Based on the clinical findings, one (5%) of the 20 patients had a palpable lump and the remaining 19 patients had no symptoms. No patient had a family history of breast cancer. Based on the pathological findings, three (15%) patients had malignancies. The malignant lesions included invasive ductal carcinomas (n = 2) and ductal carcinoma in situ (n = 1). Four (20%) patients had high-risk lesions: atypical ductal hyperplasia (n = 3) and lobular carcinoma in situ (n = 1). The remaining 13 (65%) patients had benign lesions, however, seven (35%) out of 13 patients had mild-risk lesions (three intraductal papillomas, three moderate or florid epithelial hyperplasia and one sclerosing adenosis). Of the sonographic ally detected architectural distortions, 35% were breast cancers or high-risk lesions and 35% were mild-risk lesions. Thus, a biopsy might be needed for an architectural distortion without an associated mass as depicted on breast ultrasound, even though the mammographic findings are normal

  18. Sonographic ally Detected Architectural Distortion: Clinical Significance

    International Nuclear Information System (INIS)

    Kim, Shin Kee; Seo, Bo Kyoung; Yi, Ann; Cha, Sang Hoon; Kim, Baek Hyun; Cho, Kyu Ran; Kim, Young Sik; Son, Gil Soo; Kim, Young Soo; Kim, Hee Young

    2008-01-01

    Architectural distortion is a suspicious abnormality for the diagnosis of breast cancer. The aim of this study was to investigate the clinical significance of sonographic ally detected architectural distortion. From January 2006 to June 2008, 20 patients were identified who had sonographic ally detected architectural distortions without a history of trauma or surgery and abnormal mammographic findings related to an architectural distortion. All of the lesions were pathologically verified. We evaluated the clinical and pathological findings and then assessed the clinical significance of the sonographic ally detected architectural distortions. Based on the clinical findings, one (5%) of the 20 patients had a palpable lump and the remaining 19 patients had no symptoms. No patient had a family history of breast cancer. Based on the pathological findings, three (15%) patients had malignancies. The malignant lesions included invasive ductal carcinomas (n = 2) and ductal carcinoma in situ (n = 1). Four (20%) patients had high-risk lesions: atypical ductal hyperplasia (n = 3) and lobular carcinoma in situ (n = 1). The remaining 13 (65%) patients had benign lesions, however, seven (35%) out of 13 patients had mild-risk lesions (three intraductal papillomas, three moderate or florid epithelial hyperplasia and one sclerosing adenosis). Of the sonographic ally detected architectural distortions, 35% were breast cancers or high-risk lesions and 35% were mild-risk lesions. Thus, a biopsy might be needed for an architectural distortion without an associated mass as depicted on breast ultrasound, even though the mammographic findings are normal

  19. Determination of DNA by solid substrate room temperature phosphorescence enhancing method based on the Morin.SiO{sub 2} luminescent nanoparticles-Pd system as a phosphorescence probe

    Energy Technology Data Exchange (ETDEWEB)

    Liu Jiaming [Department of Chemistry, Zhangzhou Normal College, Zhangzhou 363000 (China)]. E-mail: zzsyliujiaming@163.com; Yang Tianlong [Department of Chemistry, Zhangzhou Normal College, Zhangzhou 363000 (China); Gao Fei [Department of Chemistry, Zhangzhou Normal College, Zhangzhou 363000 (China); Hu Lixiang [Department of Chemistry, Zhangzhou Normal College, Zhangzhou 363000 (China); He Hangxia [Department of Chemistry, Zhangzhou Normal College, Zhangzhou 363000 (China); Liu Qinying [Department of Chemistry, Zhangzhou Normal College, Zhangzhou 363000 (China); Liu Zhenbo [Department of Orthopedics and Traumatology, Fujian College of Chinese Medicine, Fuzhou 350003 (China); Huang Xiaomei [Department of Food and Chemical Engineering, Zhangzhou Institute of Technology, Zhangzhou 363000 (China); Zhu Guohui [Department of Food and Chemical Engineering, Zhangzhou Institute of Technology, Zhangzhou 363000 (China)

    2006-03-02

    Sodium carbonate (Na{sub 2}SiO{sub 3}) as the precursor, was mixed with Morin organic dye to synthesize silicon dioxide luminescent nanoparticles containing Morin (Morin.SiO{sub 2}) by sol-gel method. The particle sizes of SiO{sub 2}.nH{sub 2}O and Morin.SiO{sub 2} were both 50 nm, measured with TEM (transmission electron microscope). Morin.SiO{sub 2} modified by HS-CH{sub 2}COOH could be dissolved by water. In the HMTA (hexamethylenetetramine)-HCl buffer solution, Pd{sup 2+} could coordinate with Morin in Morin.SiO{sub 2} to form complex Pd{sup 2+}-Morin.SiO{sub 2}, which could emit phosphorescence on polyamide membrane. And DNA (deoxyribonucleic acid) could cause a sharp enhancement of the room temperature phosphorescence (RTP) intensity of complex Pd{sup 2+}-Morin.SiO{sub 2}. Thus a new method of solid substrate room temperature phosphorescence (SS-RTP) enhancing for the determination of DNA was established based on the Morin.SiO{sub 2} luminescent nanoparticles-Pd system as a phosphorescence probe. The {delta}Ip is directly proportional to the content of DNA in the range of 4.00-1000.0 fg spot{sup -1} (corresponding concentration: 0.010-2.50 ng ml{sup -1}). The regression equation of working curve was {delta}Ip = 21.13 + 0.2076m{sub DNA} (fg spot{sup -1}) (r = 0.9990) and the detection limit was 0.61 fg spot{sup -1} (corresponding concentration: 1.5 pg ml{sup -1}). This method had a wide linear range, high sensitivity, convenience, rapidity and only a little sample was needed. Samples containing 0.10 and 25.0 ng ml{sup -1} DNA were measured repeatedly for 11 times and RSDs were 3.2 and 4.1% (n = 11), respectively, which indicated that the method had a good repeatability. Disturbance of common ions, such as Mg{sup 2+}, K{sup +}, and Ca{sup 2+}, was small, and there was no disturbance in the presence of protein and RNA. This method has been applied to the determination of DNA in nectar successfully.

  20. PIP degron proteins, substrates of CRL4Cdt2, and not PIP boxes, interfere with DNA polymerase η and κ focus formation on UV damage

    OpenAIRE

    Tsanov, Nikolay; Kermi, Chames; Coulombe, Philippe; Van der Laan, Siem; Hodroj, Dana; Maiorano, Domenico

    2014-01-01

    Proliferating cell nuclear antigen (PCNA) is a well-known scaffold for many DNA replication and repair proteins, but how the switch between partners is regulated is currently unclear. Interaction with PCNA occurs via a domain known as a PCNA-Interacting Protein motif (PIP box). More recently, an additional specialized PIP box has been described, the « PIP degron », that targets PCNA-interacting proteins for proteasomal degradation via the E3 ubiquitin ligase CRL4Cdt2. Here we provide evidence...

  1. Distortional Modes of Thin-Walled Beams

    DEFF Research Database (Denmark)

    Jönsson, Jeppe; Andreassen, Michael Joachim

    2009-01-01

    The classic thin-walled beam theory for open and closed cross-sections can be generalized by including distortional displacement modes. The introduction of additional displacement modes leads to coupled differential equations, which seems to have prohibited the use of exact shape functions...... in the modelling of coupled torsion and distortion. However, if the distortional displacement modes are chosen as those which decouple the differential equations as in non proportionally damped modal dynamic analysis then it may be possible to use exact shape functions and perform analysis on a reduced problem....... In the recently developed generalized beam theory (GBT) the natural distortional displacement modes are determined on the basis of a quadratic eigenvalue problem. However, as in linear modal dynamic analysis of proportionally damped structures this problem has been solved approximately using linear eigenvalue...

  2. Coulomb Distortion in the Inelastic Regime

    Energy Technology Data Exchange (ETDEWEB)

    Patricia Solvignon, Dave Gaskell, John Arrington

    2009-09-01

    The Coulomb distortion effects have been for a long time neglected in deep inelastic scattering for the good reason that the incident energies were very high. But for energies in the range of earlier data from SLAC or at JLab, the Coulomb distortion could have the potential consequence of affecting the A-dependence of the EMC effect and of the longitudinal to transverse virtual photon absorption cross section ratio $R(x,Q^2)$.

  3. Harmonic distortion in microwave photonic filters.

    Science.gov (United States)

    Rius, Manuel; Mora, José; Bolea, Mario; Capmany, José

    2012-04-09

    We present a theoretical and experimental analysis of nonlinear microwave photonic filters. Far from the conventional condition of low modulation index commonly used to neglect high-order terms, we have analyzed the harmonic distortion involved in microwave photonic structures with periodic and non-periodic frequency responses. We show that it is possible to design microwave photonic filters with reduced harmonic distortion and high linearity even under large signal operation.

  4. Structures and properties of spatially distorted porphyrins

    International Nuclear Information System (INIS)

    Golubchikov, Oleg A; Kuvshinova, Elizaveta M; Pukhovskaya, Svetlana G

    2005-01-01

    The published data on the structures and properties of porphyrins with distorted aromatic macrocycles are generalised and analysed. Data on the crystal structures, spectra and kinetics of formation and dissociation of their coordination derivatives are summarised. It is demonstrated that the distortion of the planar structure of the tetrapyrrole core is one of the most efficient means of controlling spectral, physicochemical and coordination properties of these compounds.

  5. Components of segregation distortion in Drosophila melanogaster

    International Nuclear Information System (INIS)

    Ganetzky, B.

    1977-01-01

    The segregation distorter (SD) complex is a naturally occurring meiotic drive system with the property that males heterozygous for an SD-bearing chromosome 2 and an SD+-bearing homolog transmit the SD-bearing chromosome almost exclusively. This distorted segregation is the consequence of an induced dysfunction of those sperm that receive the SD+ homolog. From previous studies, two loci have been implicated in this phenomenon: the Sd locus which is required to produce distortion, and the Responder (Rsp) locus that is the site at which Sd acts. There are two allelic alternatives of Rsp-sensitive (Rsp/sup sens/) and insensitive (Rsp/sup ins/); a chromosome carrying Rsp/sup ins/ is not distorted by SD. In the present study, the function and location of each of these elements was examined by a genetic and cytological characterization of x-ray-induced mutations at each locus. The results indicate the following: the Rsp locus is located in the proximal heterochromatin of 2R; a deletion for the Rsp locus renders a chromosome insensitive to distortion; the Sd locus is located to the left of pr (2-54.5), in the region from 37D2-D7 to 38A6-B2 of the salivary chromosome map; an SD chromosome deleted for Sd loses its ability to distort; there is another important component of the SD system, E(SD), in or near the proximal heterochromatin of 2L, that behaves as a strong enhancer of distortion. The results of these studies allow a reinterpretation of results from earlier analyses of the SD system and serve to limit the possible mechanisms to account for segregation distortion

  6. Ultrasonographic Findings of Mammographic Architectural Distortion

    International Nuclear Information System (INIS)

    Ma, Jeong Hyun; Kang, Bong Joo; Cha, Eun Suk; Hwangbo, Seol; Kim, Hyeon Sook; Park, Chang Suk; Kim, Sung Hun; Choi, Jae Jeong; Chung, Yong An

    2008-01-01

    To review the sonographic findings of various diseases showing architectural distortion depicted under mammography. We collected and reviewed architectural distortions observed under mammography at our health institution between 1 March 2004, and 28 February 2007. We collected 23 cases of sonographically-detected mammographic architectural distortions that confirmed lesions after surgical resection. The sonographic findings of mammographic architectural distortion were analyzed by use of the BI-RADS lexicon for shape, margin, lesion boundary, echo pattern, posterior acoustic feature and orientation. There were variable diseases that showed architectural distortion depicted under mammography. Fibrocystic disease was the most common presentation (n = 6), followed by adenosis (n = 2), stromal fibrosis (n = 2), radial scar (n = 3), usual ductal hyperplasia (n = 1), atypical ductal hyperplasia (n = 1) and mild fibrosis with microcalcification (n = 1). Malignant lesions such as ductal carcinoma in situ (DCIS) (n = 2), lobular carcinoma in situ (LCIS) (n = 2), invasive ductal carcinoma (n = 2) and invasive lobular carcinoma (n = 1) were observed. As observed by sonography, shape was divided as irregular (n = 22) and round (n = 1). Margin was divided as circumscribed (n = 1), indistinct (n = 7), angular (n = 1), microlobulated (n = 1) and sipculated (n = 13). Lesion boundary was divided as abrupt interface (n = 11) and echogenic halo (n = 12). Echo pattern was divided as hypoechoic (n = 20), anechoic (n = 1), hyperechoic (n = 1) and isoechoic (n = 1). Posterior acoustic feature was divided as posterior acoustic feature (n = 7), posterior acoustic shadow (n = 15) and complex posterior acoustic feature (n = 1). Orientation was divided as parallel (n = 12) and not parallel (n = 11). There were no differential sonographic findings between benign and malignant lesions. This study presented various sonographic findings of mammographic architectural distortion and that it is

  7. Generic distortion model for metrology under optical microscopes

    Science.gov (United States)

    Liu, Xingjian; Li, Zhongwei; Zhong, Kai; Chao, YuhJin; Miraldo, Pedro; Shi, Yusheng

    2018-04-01

    For metrology under optical microscopes, lens distortion is the dominant source of error. Previous distortion models and correction methods mostly rely on the assumption that parametric distortion models require a priori knowledge of the microscopes' lens systems. However, because of the numerous optical elements in a microscope, distortions can be hardly represented by a simple parametric model. In this paper, a generic distortion model considering both symmetric and asymmetric distortions is developed. Such a model is obtained by using radial basis functions (RBFs) to interpolate the radius and distortion values of symmetric distortions (image coordinates and distortion rays for asymmetric distortions). An accurate and easy to implement distortion correction method is presented. With the proposed approach, quantitative measurement with better accuracy can be achieved, such as in Digital Image Correlation for deformation measurement when used with an optical microscope. The proposed technique is verified by both synthetic and real data experiments.

  8. Expertise and processing distorted structure in chess.

    Science.gov (United States)

    Bartlett, James C; Boggan, Amy L; Krawczyk, Daniel C

    2013-01-01

    A classic finding in research on human expertise and knowledge is that of enhanced memory for stimuli in a domain of expertise as compared to either stimuli outside that domain, or within-domain stimuli that have been degraded or distorted in some way. However, we do not understand how experts process degradation or distortion of stimuli within the expert domain (e.g., a face with the eyes, nose, and mouth in the wrong positions, or a chessboard with pieces placed randomly). Focusing on the domain of chess, we present new fMRI evidence that when experts view such distorted/within-domain stimuli, they engage an active search for structure-a kind of exploratory chunking-that involves a component of a prefrontal-parietal network linked to consciousness, attention and working memory.

  9. Lattice shear distortions in fluorite structure oxides

    International Nuclear Information System (INIS)

    Faber, J. Jr.; Mueller, M.H.; Hitterman, R.L.

    1979-01-01

    Crystallographic shear distortions have been observed in fluorite structure, single crystals of UO 2 and Zr(Ca)O 2 /sub-x/ by neutron-diffraction techniques. These distortions localize on the oxygen sublattice and do not require the presence of an external strain. The internal rearrangement mode in UO 2 is a transverse, zone boundary q vector = 2π/a (0.5, 0.0) deformation with amplitude 0.014 A. In Zr(Ca)O/sub 2-x/, the mode is a longitudinal, q vector = 2-/a (0,0,0.5) deformation with amplitude 0.23 A. Cation-anion elastic interactions dominate in selecting the nature of the internal distortion

  10. Density distortion within a rotating body

    International Nuclear Information System (INIS)

    Lanzano, P.

    1975-01-01

    This paper ascertains the distortion of the density distribution within a self-gravitating body in hydrostatic equilibrium under the influence of rotation. For this purpose, the Poisson equation has been solved by using the undistorted density profile within the Laplacian to obtain the distorted density. The Laplacian has been expressed in terms of a system of curvilinear coordinates for which the equipotential surfaces constitute a family of fundamental surfaces. In performing the requisite algebraic manipulations, the Clairaut and Radau equations developed in a previous paper (Lanzano,1974) were utilized to eliminate the derivatives of the elements pertaining to the equipotential surfaces. The density distortion has been obtained up to third-order terms in a small rotational parameter. (Auth.)

  11. 'Distorted structure modelling' - a more physical approach to Rapid Distortion Theory

    International Nuclear Information System (INIS)

    Savill, A.M.

    1979-11-01

    Rapid Distortion Theory is reviewed in the light of the modern mechanistic approach to turbulent motion. The apparent failure of current models, based on this theory, to predict stress intensity ratios accurately in distorted shear flows is attributed to their oversimplistic assumptions concerning the inherent turbulence structure of such flows. A more realistic picture of this structure and the manner in which it responds to distortion is presented in terms of interactions between the mean flow and three principal types of eddies. If Rapid Distortion Theory is modified to account for this it is shown that the stress intensity ratios can be accurately predicted in three test flows. It is concluded that a computational scheme based on Rapid Distortion Theory might ultimately be capable of predicting turbulence parameters in the highly complex geometries of reactor cooling systems. (author)

  12. Holographic measurement of distortion during laser melting: Additive distortion from overlapping pulses

    Science.gov (United States)

    Haglund, Peter; Frostevarg, Jan; Powell, John; Eriksson, Ingemar; Kaplan, Alexander F. H.

    2018-03-01

    Laser - material interactions such as welding, heat treatment and thermal bending generate thermal gradients which give rise to thermal stresses and strains which often result in a permanent distortion of the heated object. This paper investigates the thermal distortion response which results from pulsed laser surface melting of a stainless steel sheet. Pulsed holography has been used to accurately monitor, in real time, the out-of-plane distortion of stainless steel samples melted on one face by with both single and multiple laser pulses. It has been shown that surface melting by additional laser pulses increases the out of plane distortion of the sample without significantly increasing the melt depth. The distortion differences between the primary pulse and subsequent pulses has also been analysed for fully and partially overlapping laser pulses.

  13. Distorted representation in visual tourism research

    DEFF Research Database (Denmark)

    Jensen, Martin Trandberg

    2016-01-01

    how photographic materialities, performativities and sensations contribute to new tourism knowledges. While highlighting the potential of distorted representation, the paper posits a cautionary note in regards to the influential role of academic journals in determining the qualities of visual data....... The paper exemplifies distorted representation through three impressionistic tales derived from ethnographic research on the European rail travel phenomenon: interrail.......Tourism research has recently been informed by non-representational theories to highlight the socio-material, embodied and heterogeneous composition of tourist experiences. These advances have contributed to further reflexivity and called for novel ways to animate representations...

  14. Meiotic drive on aberrant chromosome 1 in the mouse is determined by a linked distorter.

    Science.gov (United States)

    Agulnik, S I; Sabantsev, I D; Orlova, G V; Ruvinsky, A O

    1993-04-01

    An aberrant chromosome 1 carrying an inverted fragment with two amplified DNA regions was isolated from wild populations of Mus musculus. Meiotic drive favouring the aberrant chromosome was demonstrated for heterozygous females. Its cause was preferential passage of aberrant chromosome 1 to the oocyte. Genetic analysis allowed us to identify a two-component system conditioning deviation from equal segregation of the homologues. The system consists of a postulated distorter and responder. The distorter is located on chromosome 1 distally to the responder, between the ln and Pep-3 genes, and it acts on the responder when in trans position. Polymorphism of the distorters was manifested as variation in their effect on meiotic drive level in the laboratory strain and mice from wild populations.

  15. Testing for Distortions in Performance Measures

    DEFF Research Database (Denmark)

    Sloof, Randolph; Van Praag, Mirjam

    2015-01-01

    Distorted performance measures in compensation contracts elicit suboptimal behavioral responses that may even prove to be dysfunctional (gaming). This paper applies the empirical test developed by Courty and Marschke (Review of Economics and Statistics, 90, 428-441) to detect whether the widely...

  16. Synchronization of cubic distortion spontaneous otoacoustic emissions

    NARCIS (Netherlands)

    van Dijk, P; Wit, HP

    A spontaneous otoacoustic emission spectrum may contain equally spaced emission peaks. Then, two peaks, at frequencies, f(1) and f(2), respectively, apparently generate a distortion product at f(d)=2f(1)-f(2) [or 2f(2)-f(1)]. For the three emission peaks of nine of such triplets tin six emission

  17. The possible distortion of autoradiographic results

    International Nuclear Information System (INIS)

    Kozlov, A.A.; Tumanushvili, G.D.

    1980-01-01

    The effect of radioactive labelling (H 3 -thymidine) on the infusorian division is studied. The presented results show that introduction of labelled compounds results in accelerating infusorian cell division v. Thorough inestigation of labelled compound effect with low activity on the parameters of cell division and the search of methods to eliminate distortions able to appear in autoradiographic experiments is expedient [ru

  18. Testing for Distortions in Performance Measures

    DEFF Research Database (Denmark)

    Sloof, Randolph; Van Praag, Mirjam

    Distorted performance measures in compensation contracts elicit suboptimal behavioral responses that may even prove to be dysfunctional (gaming). This paper applies the empirical test developed by Courty and Marschke (2008) to detect whether the widely used class of Residual Income based performa...

  19. Electromagnetic pulse distortion in living tissue

    NARCIS (Netherlands)

    Lepelaars, E.S.A.M.

    1996-01-01

    Insight into the distortion of electromagnetic (EM) signals in living tissue is important for optimising medical applications. To obtain this insight, field calculations have been carried out for a plane-stratified configuration of air, skin, fat, muscle and bone tissue. In this configuration, an EM

  20. DISTORTION ANALYSIS OF TILL -WALLED BOX GIRDERS

    African Journals Online (AJOL)

    NIJOTECH

    bridges, buildings, motor vehicles, ships and aircrafts. Due to thinness of the box walls, generalized loads applied to this structure give rise to warping and distortion of ..... Recommendation for Design of. Intermediate Diaphragms in Box. Girders, Transactions of Japanese. Society of Civil Engineers, Vol. 14,1984, pp 121-126.

  1. Audible Aliasing Distortion in Digital Audio Synthesis

    Directory of Open Access Journals (Sweden)

    J. Schimmel

    2012-04-01

    Full Text Available This paper deals with aliasing distortion in digital audio signal synthesis of classic periodic waveforms with infinite Fourier series, for electronic musical instruments. When these waveforms are generated in the digital domain then the aliasing appears due to its unlimited bandwidth. There are several techniques for the synthesis of these signals that have been designed to avoid or reduce the aliasing distortion. However, these techniques have high computing demands. One can say that today's computers have enough computing power to use these methods. However, we have to realize that today’s computer-aided music production requires tens of multi-timbre voices generated simultaneously by software synthesizers and the most of the computing power must be reserved for hard-disc recording subsystem and real-time audio processing of many audio channels with a lot of audio effects. Trivially generated classic analog synthesizer waveforms are therefore still effective for sound synthesis. We cannot avoid the aliasing distortion but spectral components produced by the aliasing can be masked with harmonic components and thus made inaudible if sufficient oversampling ratio is used. This paper deals with the assessment of audible aliasing distortion with the help of a psychoacoustic model of simultaneous masking and compares the computing demands of trivial generation using oversampling with those of other methods.

  2. Rate-distortion theory and human perception.

    Science.gov (United States)

    Sims, Chris R

    2016-07-01

    The fundamental goal of perception is to aid in the achievement of behavioral objectives. This requires extracting and communicating useful information from noisy and uncertain sensory signals. At the same time, given the complexity of sensory information and the limitations of biological information processing, it is necessary that some information must be lost or discarded in the act of perception. Under these circumstances, what constitutes an 'optimal' perceptual system? This paper describes the mathematical framework of rate-distortion theory as the optimal solution to the problem of minimizing the costs of perceptual error subject to strong constraints on the ability to communicate or transmit information. Rate-distortion theory offers a general and principled theoretical framework for developing computational-level models of human perception (Marr, 1982). Models developed in this framework are capable of producing quantitatively precise explanations for human perceptual performance, while yielding new insights regarding the nature and goals of perception. This paper demonstrates the application of rate-distortion theory to two benchmark domains where capacity limits are especially salient in human perception: discrete categorization of stimuli (also known as absolute identification) and visual working memory. A software package written for the R statistical programming language is described that aids in the development of models based on rate-distortion theory. Copyright © 2016 The Author. Published by Elsevier B.V. All rights reserved.

  3. DNA-cell conjugates

    Science.gov (United States)

    Hsiao, Shih-Chia; Francis, Matthew B.; Bertozzi, Carolyn; Mathies, Richard; Chandra, Ravi; Douglas, Erik; Twite, Amy; Toriello, Nicholas; Onoe, Hiroaki

    2018-05-15

    The present invention provides conjugates of DNA and cells by linking the DNA to a native functional group on the cell surface. The cells can be without cell walls or can have cell walls. The modified cells can be linked to a substrate surface and used in assay or bioreactors.

  4. DNA-cell conjugates

    Science.gov (United States)

    Hsiao, Shih-Chia; Francis, Matthew B.; Bertozzi, Carolyn; Mathies, Richard; Chandra, Ravi; Douglas, Erik; Twite, Amy; Toriello, Nicholas; Onoe, Hiroaki

    2016-05-03

    The present invention provides conjugates of DNA and cells by linking the DNA to a native functional group on the cell surface. The cells can be without cell walls or can have cell walls. The modified cells can be linked to a substrate surface and used in assay or bioreactors.

  5. Convergence of the Distorted Wave Born series

    International Nuclear Information System (INIS)

    MacMillan, D.S.

    1981-01-01

    The aim of this thesis is to begin to understand the idea of reaction mechanisms in nonrelativistic scattering systems. If we have a complete reaction theory of a particular scattering system, then we claim that the theory itself must contain information about important reaction mechanisms in the system. This information can be used to decide what reaction mechanisms should be included in an approximate calculation. To investigate this claim, we studied several solvable models. The primary concept employed in studying our models is the convergence of the multistep series generated by iterating the corresponding scattering integral equation. We known that the eigenvalues of the kernel of the Lippmann-Schwinger equation for potential scattering determine the rate of convergence of the Born series. The Born series will converge only if these eigenvalues all life within the unit circle. We extend these results to a study of the distorted wave Born series for inelastic scattering. The convergence criterion tells us when approximations are valid. We learn how the convergence of the distorted wave series depends upon energy, coupling constants, angular momentum, and angular momentum transfer. In one of our models, we look at several possible distorting potentials to see which one gives the best convergence. We have also applied our results to several actual DWBA or coupled channel calculations in the literature. In addition to the study of models of two-body scattering systems, we have considered the case of rearrangement scattering. We have discussed the formulation of (N greater than or equal to 3)-body distorted wave equations in which the interior dynamics have been redistributed by introducing compact N-body distortion potentials

  6. Forensic image analysis - CCTV distortion and artefacts.

    Science.gov (United States)

    Seckiner, Dilan; Mallett, Xanthé; Roux, Claude; Meuwly, Didier; Maynard, Philip

    2018-04-01

    As a result of the worldwide deployment of surveillance cameras, authorities have gained a powerful tool that captures footage of activities of people in public areas. Surveillance cameras allow continuous monitoring of the area and allow footage to be obtained for later use, if a criminal or other act of interest occurs. Following this, a forensic practitioner, or expert witness can be required to analyse the footage of the Person of Interest. The examination ultimately aims at evaluating the strength of evidence at source and activity levels. In this paper, both source and activity levels are inferred from the trace, obtained in the form of CCTV footage. The source level alludes to features observed within the anatomy and gait of an individual, whilst the activity level relates to activity undertaken by the individual within the footage. The strength of evidence depends on the value of the information recorded, where the activity level is robust, yet source level requires further development. It is therefore suggested that the camera and the associated distortions should be assessed first and foremost and, where possible, quantified, to determine the level of each type of distortion present within the footage. A review of the 'forensic image analysis' review is presented here. It will outline the image distortion types and detail the limitations of differing surveillance camera systems. The aim is to highlight various types of distortion present particularly from surveillance footage, as well as address gaps in current literature in relation to assessment of CCTV distortions in tandem with gait analysis. Future work will consider the anatomical assessment from surveillance footage. Copyright © 2018 Elsevier B.V. All rights reserved.

  7. Quality Evaluation and Nonuniform Compression of Geometrically Distorted Images Using the Quadtree Distortion Map

    Directory of Open Access Journals (Sweden)

    Cristina Costa

    2004-09-01

    Full Text Available The paper presents an analysis of the effects of lossy compression algorithms applied to images affected by geometrical distortion. It will be shown that the encoding-decoding process results in a nonhomogeneous image degradation in the geometrically corrected image, due to the different amount of information associated to each pixel. A distortion measure named quadtree distortion map (QDM able to quantify this aspect is proposed. Furthermore, QDM is exploited to achieve adaptive compression of geometrically distorted pictures, in order to ensure a uniform quality on the final image. Tests are performed using JPEG and JPEG2000 coding standards in order to quantitatively and qualitatively assess the performance of the proposed method.

  8. Evaluation of core distortion in FBR

    International Nuclear Information System (INIS)

    Ikarimoto, I.; Tanaka, M.; Okubo, Y.

    1984-01-01

    The analyses of FBR's core distortion are mainly performed in order to evaluate the following items: 1) Change of reactivity; 2) Force at pads on core assemblies; 3) Withdrawal force at refueling; 4) Loading, refueling and residual deviations of wrapper tubes (core assemblies) at the top; 5) Bowing modes of guide tubes for control rods. The analysis of core distortion are performed by using computer program for two-dimensional row deformation analysis or three-dimensional core deformation if necessary, considering these evaluated items which become design conditions. This report shows the relationship between core deformation analysis and component design, a point of view of choosing an analysis program for design considering core characteristics, and computing examples of core deformation of prototype class reactor by the above code. (author)

  9. Lawful Distortion of Consumers’ Economic Behaviour

    DEFF Research Database (Denmark)

    Trzaskowski, Jan

    2016-01-01

    ‘collateral damage’. In that vein this article discusses situations where consumers may have their economic behaviour distorted by commercial practices that are not unfair under the Directive. It is expected that many consumers will make relatively good decisions most of the time...... Visitors’). The article suggests how behavioural sciences may be applied to understand these situations in order to protect more consumers from having their economic behaviour distorted by commercial practices. It is suggested that per se prohibitions may be advantageous in some instances as long......The Unfair Commercial Practices Directive prohibits unfair business-to-consumer commercial practices with a view to protect consumers’ economic interests. In a market economy such regulation cannot protect the economic interests of all consumers in all situations – there must inevitably be some...

  10. Numerical simulation of distorted crystal Darwin width

    International Nuclear Information System (INIS)

    Wang Li; Xu Zhongmin; Wang Naxiu

    2012-01-01

    A new numerical simulation method according to distorted crystal optical theory was used to predict the direct-cooling crystal monochromator optical properties(crystal Darwin width) in this study. The finite element analysis software was used to calculate the deformed displacements of DCM crystal and to get the local reciprocal lattice vector of distorted crystal. The broadening of direct-cooling crystal Darwin width in meridional direction was estimated at 4.12 μrad. The result agrees well with the experimental data of 5 μrad, while it was 3.89 μrad by traditional calculation method of root mean square (RMS) of the slope error in the center line of footprint. The new method provides important theoretical support for designing and processing of monochromator crystal for synchrotron radiation beamline. (authors)

  11. Redshift-space distortions from vector perturbations

    Science.gov (United States)

    Bonvin, Camille; Durrer, Ruth; Khosravi, Nima; Kunz, Martin; Sawicki, Ignacy

    2018-02-01

    We compute a general expression for the contribution of vector perturbations to the redshift space distortion of galaxy surveys. We show that they contribute to the same multipoles of the correlation function as scalar perturbations and should thus in principle be taken into account in data analysis. We derive constraints for next-generation surveys on the amplitude of two sources of vector perturbations, namely non-linear clustering and topological defects. While topological defects leave a very small imprint on redshift space distortions, we show that the multipoles of the correlation function are sensitive to vorticity induced by non-linear clustering. Therefore future redshift surveys such as DESI or the SKA should be capable of measuring such vector modes, especially with the hexadecapole which appears to be the most sensitive to the presence of vorticity.

  12. Distorted wave calculations for double electron transfer

    International Nuclear Information System (INIS)

    Martinez, A.E.; Rivarola, R.D.; Gayet, R.; Hanssen, J.

    1992-01-01

    The resonant double electron capture by alpha particles in helium targets is studied, at intermediate and high collision energies, using the Continuum Distorted Wave - Eikonal Initial State (CDW-EIS) model. Differential and total cross sections for capture into the He (1 s 2 ) final state are calculated in the framework of an Independent Electron Approximation (IEA). Theoretical results are compared with the experimental data available at present for capture into any final state of helium. (author)

  13. Lattice distortion in hcp rare gas solids

    Science.gov (United States)

    Grechnev, A.; Tretyak, S. M.; Freiman, Yu. A.

    2010-04-01

    The lattice distortion parameter δ ≡c/a-√8/3 has been calculated as a function of molar volume for the hcp phases of He, Ar, Kr, and Xe. Results from both semi-empirical potentials and density functional theory are presented. Our study shows that δ is negative for helium in the entire pressure range. For Ar, Kr, and Xe δ changes sign from negative to positive as the pressure increases, growing rapidly in magnitude at higher pressures.

  14. Distortion of the microwave background by dust

    International Nuclear Information System (INIS)

    Rowan-Robinson, M.

    1981-01-01

    The Woody and Richards distortion of the microwave background has a natural explanation within the framework of the isothermal density fluctuation picture. A pregalactic generation of ''stars'' makes light and metals. The latter are able to condense into dust grains at a redshift approximately 150-225, which then absorb the starlight and reradiate it in the infrared. At the present epoch we see this emission redshifted into the millimetre range of the spectrum

  15. A review of PFR core distortion experience

    International Nuclear Information System (INIS)

    Brook, A.J.

    1984-01-01

    Neutron induced voidage (NIV) swelling and irradiation creep, acting together or individually, produce deformation in core components exposed to a fast neutron flux and can lead to mechanical interaction between them. Today the nature of these processes is reasonably well understood, and reactor designers have two options in attempting to accomodate them: either by employing a flexible free standing design in which contact loadings are low but in which distortion may be high, or more commonly, by some type of restrained core in which inter-component loadings are high, but where distortion is relatively small. The aims of this paper are: a. to describe briefly the various operational limits of core and core component distortion and how they arise, for which a brief description of reactor construction is necessary; b. to outline how the problems of inter-component contact loadings are overcome for the interactive core; c. to describe some other potential problems which arise either from absolute swelling, or from differential swelling between components; of particular relevance here is the problem of contact loadings between absorber rods and their guide tubes; d. to comment on the degree of agreement with, and the feedback provided by, PIE findings; e. to show how the results of the work influence reactor operators and the reload program

  16. CMB spectral distortion constraints on thermal inflation

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Kihyun; Stewart, Ewan D. [Department of Physics, KAIST, Daejeon 34141 (Korea, Republic of); Hong, Sungwook E. [Korea Astronomy and Space Science Institute, Daejeon 34055 (Korea, Republic of); Zoe, Heeseung, E-mail: cho_physics@kaist.ac.kr, E-mail: heezoe@dgist.ac.kr, E-mail: jcap@profstewart.org, E-mail: heezoe@dgist.ac.kr [School of Undergraduate Studies, College of Transdisciplinary Studies, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu 42988 (Korea, Republic of)

    2017-08-01

    Thermal inflation is a second epoch of exponential expansion at typical energy scales V {sup 1/4} ∼ 10{sup 6} {sup ∼} {sup 8} GeV. If the usual primordial inflation is followed by thermal inflation, the primordial power spectrum is only modestly redshifted on large scales, but strongly suppressed on scales smaller than the horizon size at the beginning of thermal inflation, k > k {sub b} = a {sub b} H {sub b}. We calculate the spectral distortion of the cosmic microwave background generated by the dissipation of acoustic waves in this context. For k {sub b} || 10{sup 3} Mpc{sup −1}, thermal inflation results in a large suppression of the μ-distortion amplitude, predicting that it falls well below the standard value of μ ≅ 2× 10{sup −8}. Thus, future spectral distortion experiments, similar to PIXIE, can place new limits on the thermal inflation scenario, constraining k {sub b} ∼> 10{sup 3} Mpc{sup −1} if μ ≅ 2× 10{sup −8} were found.

  17. A directly cooled grating substrate for ALS [Advanced Light Source] undulator beam lines

    International Nuclear Information System (INIS)

    DiGennaro, R.; Swain, T.

    1989-08-01

    Design analyses using finite element methods are presented for thermal distortion of water-cooled diffraction grating substrates for a potential application at the LBL Advanced Light Source, demonstrating that refinements in cooling channel configuration and heat flux distribution can significantly reduce optical surface distortion with high heat loads. Using an existing grating substrate design, sensitivity of tangential slope errors due to thermal distortion is evaluated for a variety of thermal boundary conditions, including coolant flow rate and heat transfer film coefficients, surface illumination area and heat distribution profile, and location of the convection cooling surfaces adjacent to the heated region. 1 ref., 5 figs., 2 tabs

  18. Cognitive Distortions in Depressed Women: Trait, or State Dependent?

    Directory of Open Access Journals (Sweden)

    Sedat BATMAZ

    2015-12-01

    Conclusion: The results have revealed that self-criticism, helplessness, hopelessness and preoccupation with danger related distortions had trait-like features, whereas self-blame related distortions were state dependent. This has clinical implications for the psychotherapeutic treatment of cognitive distortions in depression. Specifically, self-criticism related distortions should be managed during cognitive therapy for depression since the other subscales seem rather problematic. [JCBPR 2015; 4(3.000: 147-152

  19. DNA-binding determinants promoting NHEJ by human Polμ.

    Science.gov (United States)

    Martin, Maria Jose; Juarez, Raquel; Blanco, Luis

    2012-12-01

    Non-homologous end-joining (NHEJ), the preferred pathway to repair double-strand breaks (DSBs) in higher eukaryotes, relies on a collection of molecular tools to process the broken ends, including specific DNA polymerases. Among them, Polµ is unique as it can catalyze DNA synthesis upon connection of two non-complementary ends. Here, we demonstrate that this capacity is intrinsic to Polµ, not conferred by other NHEJ factors. To understand the molecular determinants of its specific function in NHEJ, the interaction of human Polµ with DNA has been directly visualized by electromobility shift assay and footprinting assays. Stable interaction with a DNA gap requires the presence of a recessive 5'-P, thus orienting the catalytic domain for primer and nucleotide binding. Accordingly, recognition of the 5'-P is crucial to align the two DNA substrates of the NHEJ reaction. Site-directed mutagenesis demonstrates the relevance of three specific residues (Lys(249), Arg(253) and Arg(416)) in stabilizing the primer strand during end synapsis, allowing a range of microhomology-induced distortions beneficial for NHEJ. Moreover, our results suggest that the Polµ BRCT domain, thought to be exclusively involved in interaction with NHEJ core factors, has a direct role in binding the DNA region neighbor to the 5'-P, thus boosting Polµ-mediated NHEJ reactions.

  20. Dynamic two-stage mechanism of versatile DNA damage recognition by xeroderma pigmentosum group C protein

    Energy Technology Data Exchange (ETDEWEB)

    Clement, Flurina C.; Camenisch, Ulrike; Fei, Jia; Kaczmarek, Nina; Mathieu, Nadine [Institute of Pharmacology and Toxicology, University of Zuerich-Vetsuisse, Winterthurerstrasse 260, CH-8057 Zuerich (Switzerland); Naegeli, Hanspeter, E-mail: naegelih@vetpharm.uzh.ch [Institute of Pharmacology and Toxicology, University of Zuerich-Vetsuisse, Winterthurerstrasse 260, CH-8057 Zuerich (Switzerland)

    2010-03-01

    The recognition and subsequent repair of DNA damage are essential reactions for the maintenance of genome stability. A key general sensor of DNA lesions is xeroderma pigmentosum group C (XPC) protein, which recognizes a wide variety of helix-distorting DNA adducts arising from ultraviolet (UV) radiation, genotoxic chemicals and reactive metabolic byproducts. By detecting damaged DNA sites, this unique molecular sensor initiates the global genome repair (GGR) pathway, which allows for the removal of all the aforementioned lesions by a limited repertoire of excision factors. A faulty GGR activity causes the accumulation of DNA adducts leading to mutagenesis, carcinogenesis, neurological degeneration and other traits of premature aging. Recent findings indicate that XPC protein achieves its extraordinary substrate versatility by an entirely indirect readout strategy implemented in two clearly discernible stages. First, the XPC subunit uses a dynamic sensor interface to monitor the double helix for the presence of non-hydrogen-bonded bases. This initial screening generates a transient nucleoprotein intermediate that subsequently matures into the ultimate recognition complex by trapping undamaged nucleotides in the abnormally oscillating native strand, in a way that no direct contacts are made between XPC protein and the offending lesion itself. It remains to be elucidated how accessory factors like Rad23B, centrin-2 or the UV-damaged DNA-binding complex contribute to this dynamic two-stage quality control process.

  1. Detection of chromatic and luminance distortions in natural scenes.

    Science.gov (United States)

    Jennings, Ben J; Wang, Karen; Menzies, Samantha; Kingdom, Frederick A A

    2015-09-01

    A number of studies have measured visual thresholds for detecting spatial distortions applied to images of natural scenes. In one study, Bex [J. Vis.10(2), 1 (2010)10.1167/10.2.231534-7362] measured sensitivity to sinusoidal spatial modulations of image scale. Here, we measure sensitivity to sinusoidal scale distortions applied to the chromatic, luminance, or both layers of natural scene images. We first established that sensitivity does not depend on whether the undistorted comparison image was of the same or of a different scene. Next, we found that, when the luminance but not chromatic layer was distorted, performance was the same regardless of whether the chromatic layer was present, absent, or phase-scrambled; in other words, the chromatic layer, in whatever form, did not affect sensitivity to the luminance layer distortion. However, when the chromatic layer was distorted, sensitivity was higher when the luminance layer was intact compared to when absent or phase-scrambled. These detection threshold results complement the appearance of periodic distortions of the image scale: when the luminance layer is distorted visibly, the scene appears distorted, but when the chromatic layer is distorted visibly, there is little apparent scene distortion. We conclude that (a) observers have a built-in sense of how a normal image of a natural scene should appear, and (b) the detection of distortion in, as well as the apparent distortion of, natural scene images is mediated predominantly by the luminance layer and not chromatic layer.

  2. Centi-pixel accurate real-time inverse distortion correction

    CSIR Research Space (South Africa)

    De Villiers, Johan P

    2008-11-01

    Full Text Available Inverse distortion is used to create an undistorted image from a distorted image. For each pixel in the undistorted image it is required to determine which pixel in the distorted image should be used. However the process of characterizing a lens...

  3. Appraisal Distortions and Intimate Partner Violence: Gender, Power, and Interaction

    Science.gov (United States)

    Whiting, Jason B.; Oka, Megan; Fife, Stephen T.

    2012-01-01

    In relationships characterized by control, abuse, or violence, many appraisal distortions occur including denial and minimization. However, the nature of the distortion varies depending on the individual's role in the relationship (i.e., abuser or victim). Reducing these distortions is an important component in treatment success and involves…

  4. Nonthermal ice nucleation observed at distorted contact lines of supercooled water drops.

    Science.gov (United States)

    Yang, Fan; Cruikshank, Owen; He, Weilue; Kostinski, Alex; Shaw, Raymond A

    2018-02-01

    Ice nucleation is the crucial step for ice formation in atmospheric clouds and therefore underlies climatologically relevant precipitation and radiative properties. Progress has been made in understanding the roles of temperature, supersaturation, and material properties, but an explanation for the efficient ice nucleation occurring when a particle contacts a supercooled water drop has been elusive for over half a century. Here, we explore ice nucleation initiated at constant temperature and observe that mechanical agitation induces freezing of supercooled water drops at distorted contact lines. Results show that symmetric motion of supercooled water on a vertically oscillating substrate does not freeze, no matter how we agitate it. However, when the moving contact line is distorted with the help of trace amounts of oil or inhomogeneous pinning on the substrate, freezing can occur at temperatures much higher than in a static droplet, equivalent to ∼10^{10} increase in nucleation rate. Several possible mechanisms are proposed to explain the observations. One plausible explanation among them, decreased pressure due to interface curvature, is explored theoretically and compared with the observational results quasiquantitatively. Indeed, the observed freezing-temperature increase scales with contact line speed in a manner consistent with the pressure hypothesis. Whatever the mechanism, the experiments demonstrate a strong preference for ice nucleation at three-phase contact lines compared to the two-phase interface, and they also show that movement and distortion of the contact line are necessary contributions to stimulating the nucleation process.

  5. Towards distortion-free robust image authentication

    International Nuclear Information System (INIS)

    Coltuc, D

    2007-01-01

    This paper investigates a general framework for distortion-free robust image authentication by multiple marking. First, by robust watermarking a subsampled version of image edges is embedded. Then, by reversible watermarking the information needed to recover the original image is inserted, too. The hiding capacity of the reversible watermarking is the essential requirement for this approach. Thus in case of no attacks not only image is authenticated but also the original is exactly recovered. In case of attacks, reversibility is lost, but image can still be authenticated. Preliminary results providing very good robustness against JPEG compression are presented

  6. Rate dependent image distortions in proportional counters

    International Nuclear Information System (INIS)

    Trow, M.W.; Bento, A.C.; Smith, A.

    1994-01-01

    The positional linearity of imaging proportional counters is affected by the intensity distribution of the incident radiation. A mechanism for this effect is described, in which drifting positive ions in the gas produce a distorting electric field which perturbs the trajectories of the primary electrons. In certain cases, the phenomenon causes an apparent improvement of the position resolution. We demonstrate the effect in a detector filled with a xenon-argon-CO 2 mixture. The images obtained are compared with the results of a simulation. If quantitative predictions for a particular detector are required, accurate values of the absolute detector gain, ion mobility and electron drift velocity are needed. ((orig.))

  7. Multiple shadows from distorted static black holes

    Science.gov (United States)

    Grover, Jai; Kunz, Jutta; Nedkova, Petya; Wittig, Alexander; Yazadjiev, Stoytcho

    2018-04-01

    We study the local shadow of the Schwarzschild black hole with a quadrupole distortion and the influence of the external gravitational field on the photon dynamics. The external matter sources modify the light ring structure and lead to the appearance of multiple shadow images. In the case of negative quadrupole moments we identify the most prominent mechanism causing multiple shadow formation. Furthermore, we obtain a condition under which this mechanism can be realized. This condition depends on the quadrupole moment, but also on the position of the observer and the celestial sphere.

  8. Renormalization of a distorted gauge: invariant theory

    International Nuclear Information System (INIS)

    Hsu, J.P.; Underwood, J.A.

    1976-02-01

    A new type of renormalizable theory involving massive Yang-Mills fields whose mass is generated by an intrinsic breakdown of the usual local gauge symmetry is considered. However, the Lagrangian has a distorted gauge symmetry which leads to the Ward-Takahashi (W-T) identities. Also, the theory is independent of the gauge parameter xi. An explicit renormalization at the oneloop level is completely carried out by exhibiting counter terms, defining the physical parameters and computing all renormalization constants to check the W-T identities

  9. Flow distortion on boom mounted cup anemometers

    DEFF Research Database (Denmark)

    Lindelöw, Per Jonas Petter; Friis Pedersen, Troels; Gottschall, Julia

    In this report we investigate on wind direction dependent errors in the measurement of the horizontal wind speed by boom mounted cup anemometers. The boom mounting on the studied lattice tower is performed according to IEC standard design rules, yet, larger deviations than predicted by flow models...... are observed. The errors on the measurements are likely caused by an underestimation of the flow distortions around the tower. In this paper an experimental method for deriving a correction formula and an in-field calibration is suggested. The method is based on measurements with two cup anemometers mounted...

  10. Redshift distortions of galaxy correlation functions

    International Nuclear Information System (INIS)

    Fry, J.N.; Florida Univ., Gainesville, FL; Gaztanaga, E.; Oxford Univ.

    1993-01-01

    To examine how peculiar velocities can affect the 2-, 3-, and 4-point correlation functions, we evaluate volume-average correlations for configurations that emphasize and minimize distortions for four different volume-limited samples from each of the CfA, SSRS, and IRAS redshift catalogs. We present the results as the correlation length r 0 and power index γ of the 2-point correlation, anti Ξ 2 = (r 0 /r) γ , and as the hierarchical amplitudes of the 3- and 4-point functions, S 3 = anti Ξ 3 /anti Ξ 2 2 and S 4 = anti Ξ/anti Ξ 2 3 . We find a characteristic distortion for anti Ξ 2 : The slope γ is flatter and the correlation length is larger in redshift space than in real space; that is, redshift distortions ''move'' correlations from small to large scales. At the largest scales, extra power in the redshift distribution is compatible with Ω 4/7 /b ∼ 1; we find 0.53 ± 0.15, 1.10 ± 0.16 and 0.84 ± 0.45 for the CfA, SSRS and IRAS catalogs. Higher order correlations anti Ξ 3 and anti Ξ 4 suffer similar redshift distortions, but in such a way that, within the accuracy of our analysis, the normalized amplitudes S 3 and S 4 are insensitive to this effect. The hierarchical amplitudes S 3 and S 4 are constant as a function of scale between 1-12 h -1 Mpc and have similar values in all samples and catalogues, S 3 ∼ 2 and S 4 ∼ 6, despite the fact that anti Ξ 2 , anti Ξ 3 , and anti Ξ 4 differ from one sample to another by large factors. The agreement between the independent estimations of S 3 and S 4 is remarkable given the different criteria in the selection of galaxies and also the difference in the resulting range of densities, luminosities and locations between samples

  11. Ancient DNA

    DEFF Research Database (Denmark)

    Willerslev, Eske; Cooper, Alan

    2004-01-01

    ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair......ancient DNA, palaeontology, palaeoecology, archaeology, population genetics, DNA damage and repair...

  12. Power electronics substrate for direct substrate cooling

    Science.gov (United States)

    Le, Khiet [Mission Viejo, CA; Ward, Terence G [Redondo Beach, CA; Mann, Brooks S [Redondo Beach, CA; Yankoski, Edward P [Corona, CA; Smith, Gregory S [Woodland Hills, CA

    2012-05-01

    Systems and apparatus are provided for power electronics substrates adapted for direct substrate cooling. A power electronics substrate comprises a first surface configured to have electrical circuitry disposed thereon, a second surface, and a plurality of physical features on the second surface. The physical features are configured to promote a turbulent boundary layer in a coolant impinged upon the second surface.

  13. Reducing Field Distortion in Magnetic Resonance Imaging

    Science.gov (United States)

    Eom, Byeong Ho; Penanen, Konstantin; Hahn, Inseob

    2010-01-01

    A concept for a magnetic resonance imaging (MRI) system that would utilize a relatively weak magnetic field provides for several design features that differ significantly from the corresponding features of conventional MRI systems. Notable among these features are a magnetic-field configuration that reduces (relative to the conventional configuration) distortion and blurring of the image, the use of a superconducting quantum interference device (SQUID) magnetometer as the detector, and an imaging procedure suited for the unconventional field configuration and sensor. In a typical application of MRI, a radio-frequency pulse is used to excite precession of the magnetic moments of protons in an applied magnetic field, and the decaying precession is detected for a short time following the pulse. The precession occurs at a resonance frequency proportional to the strengths of the magnetic field and the proton magnetic moment. The magnetic field is configured to vary with position in a known way; hence, by virtue of the aforesaid proportionality, the resonance frequency varies with position in a known way. In other words, position is encoded as resonance frequency. MRI using magnetic fields weaker than those of conventional MRI offers several advantages, including cheaper and smaller equipment, greater compatibility with metallic objects, and higher image quality because of low susceptibility distortion and enhanced spin-lattice-relaxation- time contrast. SQUID MRI is being developed into a practical MRI method for applied magnetic flux densities of the order of only 100 T

  14. Removal of oxygen free-radical-induced 5′,8-purine cyclodeoxynucleosides from DNA by the nucleotide excision-repair pathway in human cells

    Science.gov (United States)

    Kuraoka, Isao; Bender, Christina; Romieu, Anthony; Cadet, Jean; Wood, Richard D.; Lindahl, Tomas

    2000-01-01

    Exposure of cellular DNA to reactive oxygen species generates several classes of base lesions, many of which are removed by the base excision-repair pathway. However, the lesions include purine cyclodeoxynucleoside formation by intramolecular crosslinking between the C-8 position of adenine or guanine and the 5′ position of 2-deoxyribose. This distorting form of DNA damage, in which the purine is attached by two covalent bonds to the sugar-phosphate backbone, occurs as distinct diastereoisomers. It was observed here that both diastereoisomers block primer extension by mammalian and microbial replicative DNA polymerases, using DNA with a site-specific purine cyclodeoxynucleoside residue as template, and consequently appear to be cytotoxic lesions. Plasmid DNA containing either the 5′R or 5′S form of 5′,8-cyclo-2-deoxyadenosine was a substrate for the human nucleotide excision-repair enzyme complex. The R diastereoisomer was more efficiently repaired than the S isomer. No correction of the lesion by direct damage reversal or base excision repair was detected. Dual incision around the lesion depended on the core nucleotide excision-repair protein XPA. In contrast to several other types of oxidative DNA damage, purine cyclodeoxynucleosides are chemically stable and would be expected to accumulate at a slow rate over many years in the DNA of nonregenerating cells from xeroderma pigmentosum patients. High levels of this form of DNA damage might explain the progressive neurodegeneration seen in XPA individuals. PMID:10759556

  15. JET ENGINE INLET DISTORTION SCREEN AND DESCRIPTOR EVALUATION

    Directory of Open Access Journals (Sweden)

    Jiří Pečinka

    2017-02-01

    Full Text Available Total pressure distortion is one of the three basic flow distortions (total pressure, total temperature and swirl distortion that might appear at the inlet of a gas turbine engine (GTE during operation. Different numerical parameters are used for assessing the total pressure distortion intensity and extent. These summary descriptors are based on the distribution of total pressure in the aerodynamic interface plane. There are two descriptors largely spread around the world, however, three or four others are still in use and can be found in current references. The staff at the University of Defence decided to compare the most common descriptors using basic flow distortion patterns in order to select the most appropriate descriptor for future department research. The most common descriptors were identified based on their prevalence in widely accessible publications. The construction and use of these descriptors are reviewed in the paper. Subsequently, they are applied to radial, angular, and combined distortion patterns of different intensities and with varied mass flow rates. The tests were performed on a specially designed test bench using an electrically driven standalone industrial centrifugal compressor, sucking air through the inlet of a TJ100 small turbojet engine. Distortion screens were placed into the inlet channel to create the desired total pressure distortions. Of the three basic distortions, only the total pressure distortion descriptors were evaluated. However, both total and static pressures were collected using a multi probe rotational measurement system.

  16. Prediction of transmission distortion for wireless video communication: analysis.

    Science.gov (United States)

    Chen, Zhifeng; Wu, Dapeng

    2012-03-01

    Transmitting video over wireless is a challenging problem since video may be seriously distorted due to packet errors caused by wireless channels. The capability of predicting transmission distortion (i.e., video distortion caused by packet errors) can assist in designing video encoding and transmission schemes that achieve maximum video quality or minimum end-to-end video distortion. This paper is aimed at deriving formulas for predicting transmission distortion. The contribution of this paper is twofold. First, we identify the governing law that describes how the transmission distortion process evolves over time and analytically derive the transmission distortion formula as a closed-form function of video frame statistics, channel error statistics, and system parameters. Second, we identify, for the first time, two important properties of transmission distortion. The first property is that the clipping noise, which is produced by nonlinear clipping, causes decay of propagated error. The second property is that the correlation between motion-vector concealment error and propagated error is negative and has dominant impact on transmission distortion, compared with other correlations. Due to these two properties and elegant error/distortion decomposition, our formula provides not only more accurate prediction but also lower complexity than the existing methods.

  17. ATLAST ULE mirror segment performance analytical predictions based on thermally induced distortions

    Science.gov (United States)

    Eisenhower, Michael J.; Cohen, Lester M.; Feinberg, Lee D.; Matthews, Gary W.; Nissen, Joel A.; Park, Sang C.; Peabody, Hume L.

    2015-09-01

    The Advanced Technology Large-Aperture Space Telescope (ATLAST) is a concept for a 9.2 m aperture space-borne observatory operating across the UV/Optical/NIR spectra. The primary mirror for ATLAST is a segmented architecture with pico-meter class wavefront stability. Due to its extraordinarily low coefficient of thermal expansion, a leading candidate for the primary mirror substrate is Corning's ULE® titania-silicate glass. The ATLAST ULE® mirror substrates will be maintained at `room temperature' during on orbit flight operations minimizing the need for compensation of mirror deformation between the manufacturing temperature and the operational temperatures. This approach requires active thermal management to maintain operational temperature while on orbit. Furthermore, the active thermal control must be sufficiently stable to prevent time-varying thermally induced distortions in the mirror substrates. This paper describes a conceptual thermal management system for the ATLAST 9.2 m segmented mirror architecture that maintains the wavefront stability to less than 10 pico-meters/10 minutes RMS. Thermal and finite element models, analytical techniques, accuracies involved in solving the mirror figure errors, and early findings from the thermal and thermal-distortion analyses are presented.

  18. Globalization, tax distortions and public sector retrenchment

    DEFF Research Database (Denmark)

    Andersen, Torben M.; Sørensen, Allan

    is strengthened by globalization, it is inferred that the marginal costs of public funds increase and a retrenchment of the public sector follows. We challenge whether these conclusions have support in a general equilibrium model featuring standard effects from open macroeconomics and trade theory. Even though...... income taxation unambiguously worsens wage competitiveness, it does not follow that marginal costs of public funds increase with product market integration due to gains from trade. Moreover, non-cooperative fiscal policies do not have a race-to-the-bottom bias despite that taxes harm competitiveness......It is widely perceived that globalization is a threat to tax financed public sector activities. The argument is that public activities (public consumption and transfers) financed by income taxes distort labour markets and cause higher wages and thus a loss of competitiveness. Since this link...

  19. Distortion compensation in interferometric testing of mirrors

    International Nuclear Information System (INIS)

    Robinson, Brian M.; Reardon, Patrick J.

    2009-01-01

    We present a method to compensate for the imaging distortion encountered in interferometric testing of mirrors, which is introduced by interferometer optics as well as from geometric projection errors. Our method involves placing a mask, imprinted with a regular square grid, over the mirror and finding a transformation that relates the grid coordinates to coordinates in the base plane of the parent surface. This method can be used on finished mirrors since no fiducials have to be applied to the surfaces. A critical step in the process requires that the grid coordinates be projected onto the mirror base plane before the regression is performed. We apply the method successfully during a center-of-curvature null test of an F/2 off-axis paraboloid

  20. Cosmic microwave background distortions at high frequencies

    International Nuclear Information System (INIS)

    Peter, W.; Peratt, A.L.

    1988-01-01

    The authors analyze the deviation of the cosmic background radiation spectrum from the 2.76+-0.02 0 Κ blackbody curve. If the cosmic background radiation is due to absorption and re-emission of synchrotron radiation from galactic-width current filaments, higher-order synchrotron modes are less thermalized than lower-order modes, causing a distortion of the blackbody curve at higher frequencies. New observations of the microwave background spectrum at short wavelengths should provide an indication of the number of synchrotron modes thermalized in this process. The deviation of the spectrum from that of a perfect blackbody can thus be correlated with astronomical observations such as filament temperatures and electron energies. The results are discussed and compared with the theoretical predictions of other models which assume the presence of intergalactic superconducting cosmic strings

  1. A scale distortion theory of anchoring.

    Science.gov (United States)

    Frederick, Shane W; Mochon, Daniel

    2012-02-01

    We propose that anchoring is often best interpreted as a scaling effect--that the anchor changes how the response scale is used, not how the focal stimulus is perceived. Of importance, we maintain that this holds true even for so-called objective scales (e.g., pounds, calories, meters, etc.). In support of this theory of scale distortion, we show that prior exposure to a numeric standard changes respondents' use of that specific response scale but does not generalize to conceptually affiliated judgments rendered on similar scales. Our findings highlight the necessity of distinguishing response language effects from representational effects in places where the need for that distinction has often been assumed away.

  2. Moebius inverse problem for distorted black holes

    International Nuclear Information System (INIS)

    Rosu, H.

    1993-01-01

    Hawking ''thermal'' radiation could be a means to detect black holes of micron sizes, which may be hovering through the universe. We consider these micro-black holes to be distorted by the presence of some distribution of matter representing a convolution factor for their Hawking radiation. One may hope to determine from their Hawking signals the temperature distribution of their material shells by the inverse black body problem. In 1990, Nan-xian Chen has used a so-called modified Moebius transform to solve the inverse black body problem. We discuss and apply this technique to Hawking radiation. Some comments on supersymmetric applications of Moebius function and transform are also added. (author). 22 refs

  3. Distortions in memory for visual displays

    Science.gov (United States)

    Tversky, Barbara

    1989-01-01

    Systematic errors in perception and memory present a challenge to theories of perception and memory and to applied psychologists interested in overcoming them as well. A number of systematic errors in memory for maps and graphs are reviewed, and they are accounted for by an analysis of the perceptual processing presumed to occur in comprehension of maps and graphs. Visual stimuli, like verbal stimuli, are organized in comprehension and memory. For visual stimuli, the organization is a consequence of perceptual processing, which is bottom-up or data-driven in its earlier stages, but top-down and affected by conceptual knowledge later on. Segregation of figure from ground is an early process, and figure recognition later; for both, symmetry is a rapidly detected and ecologically valid cue. Once isolated, figures are organized relative to one another and relative to a frame of reference. Both perceptual (e.g., salience) and conceptual factors (e.g., significance) seem likely to affect selection of a reference frame. Consistent with the analysis, subjects perceived and remembered curves in graphs and rivers in maps as more symmetric than they actually were. Symmetry, useful for detecting and recognizing figures, distorts map and graph figures alike. Top-down processes also seem to operate in that calling attention to the symmetry vs. asymmetry of a slightly asymmetric curve yielded memory errors in the direction of the description. Conceptual frame of reference effects were demonstrated in memory for lines embedded in graphs. In earlier work, the orientation of map figures was distorted in memory toward horizontal or vertical. In recent work, graph lines, but not map lines, were remembered as closer to an imaginary 45 deg line than they had been. Reference frames are determined by both perceptual and conceptual factors, leading to selection of the canonical axes as a reference frame in maps, but selection of the imaginary 45 deg as a reference frame in graphs.

  4. Correction of distortions in a discontinuous image

    International Nuclear Information System (INIS)

    Geagan, M.J.; Chase, B.B.; Muehllehner, G.

    1994-01-01

    Large area position-sensitive NaI detectors have been successfully applied to positron emission tomography (PET). Typical PET studies involve detector singles rates in excess of 500 kcps, which can lead to pile-up and image degradation as a function of countrate. Better high countrate performance can be achieved with a local centroid algorithm, in which the position of each event is calculated from a small group of photomultipliers (PMTs) immediately surrounding the PMT with the highest signal (the peak PMT). The local centroid contains most of the light from the scintillation. If a local centroid of only seven PMTs is used, the position resolution becomes quite stable at high countrates, however, discontinuities appear in the detector flood image as events cluster around each PMT. We therefore developed a method for distortion correction of a discontinuous flood image. For each PMT on the detector, a peak PMT domain is defined. The peak PMT domain is the area on the detector where that PMT could have the highest signal. The peak PMT domains overlap slightly, so that all combinations of peak PMT and position are represented. A collimated source is moved through a regular grid of points - a template - over each peak PMT region. A short collection is performed at each point, and the real and measured position data are recorded. For each point in the spatial range of a given PMT, distortion correction offsets are computed by interpolating between the data points which correspond to that PMT. This new method has been implemented and evaluated. System resolution has been measured at low and high countrates. The high countrate resolution is better with the new method, with no degradation in low countrate resolution. The axial sensitivity profile is also more stable at high countrates, compared to the previously developed method. 3-D brain phantom images show a clear improvement in image quality at high countrates. ((orig.))

  5. Impact of loudspeaker nonlinear distortion on personal sound zones

    DEFF Research Database (Denmark)

    Ma, Xiaohui; J. Hegarty, Patrick; Abildgaard Pedersen, Jan

    2018-01-01

    Personal sound zone systems aim at creating multiple listening zones within a shared space with minimum interference between zones, but the performance is often poorer than simulations predict and effects of nonlinear distortion are sometimes audible. This paper assesses the impact of nonlinear...... distortion on sound zones through simulations and measurements performed under anechoic conditions. Two sound zones, one bright and one dark, are created with acoustic contrast control using two loudspeaker arrays driven at 250 Hz. Nonlinear distortion is modelled using second or third order nonlinearities....... Simulations show that nonlinear distortion degrades the acoustic contrast, which is confirmed by experimental measurements. The harmonic distortion is audible in the dark zone. Frequency resolved measurements reveal that harmonic distortion contributes to contrast loss, but nonlinear effects...

  6. A Cognitive Distortions and Deficits Model of Suicide Ideation

    Directory of Open Access Journals (Sweden)

    Laura L. Fazakas-DeHoog

    2017-05-01

    Full Text Available Although cognitive distortions and deficits are known risk factors for the development and escalation of suicide ideation and behaviour, no empirical work has examined how these variables interact to predict suicide ideation. The current study proposes an integrative model of cognitive distortions (hopelessness and negative evaluations of self and future and deficits (problem solving deficits, problem solving avoidance, and cognitive rigidity. To test the integrity of this model, a sample of 397 undergraduate students completed measures of deficits, distortions, and current suicide ideation. A structural equation model demonstrated excellent fit, and findings indicated that only distortions have a direct effect on suicidal thinking, whereas cognitive deficits may exert their effects on suicide ideation via their reciprocal relation with distortions. Findings underscore the importance of both cognitive distortions and deficits for understanding suicidality, which may have implications for preventative efforts and treatment.

  7. Influence of initial state distortion in ion-atom collisions

    Energy Technology Data Exchange (ETDEWEB)

    Ciappina, M F [CONICET and Departamento de FIsica, Universidad Nacional del Sur, 8000 BahIa Blanca (Argentina); Cravero, W R [CONICET and Departamento de FIsica, Universidad Nacional del Sur, 8000 BahIa Blanca (Argentina); Garibotti, C R [CONICET and Division Colisiones Atomicas, Centro Atomico Bariloche, 8400 Bariloche (Argentina)

    2004-05-28

    We have studied the influence of initial state distortion in a single ionization by ion impact. We have taken a continuum distorted wave type distortion and by taking up to the first order in its asymptotic series expansion we build an eikonal-spherical distortion. In this way the influence of each term in the transition amplitude can be stated. This approximation can be considered an intermediate one between the eikonal initial state and the continuum distorted wave approaches for initial state distortion. We have computed doubly differential cross sections for helium ionization by protons and highly charged ions at high and intermediate impact energy. We have also discussed the contribution of the different terms in electron energy spectra, specially in the vicinity of ECC peak. Very good agreement is found with the available experimental data.

  8. Influence of initial state distortion in ion-atom collisions

    International Nuclear Information System (INIS)

    Ciappina, M F; Cravero, W R; Garibotti, C R

    2004-01-01

    We have studied the influence of initial state distortion in a single ionization by ion impact. We have taken a continuum distorted wave type distortion and by taking up to the first order in its asymptotic series expansion we build an eikonal-spherical distortion. In this way the influence of each term in the transition amplitude can be stated. This approximation can be considered an intermediate one between the eikonal initial state and the continuum distorted wave approaches for initial state distortion. We have computed doubly differential cross sections for helium ionization by protons and highly charged ions at high and intermediate impact energy. We have also discussed the contribution of the different terms in electron energy spectra, specially in the vicinity of ECC peak. Very good agreement is found with the available experimental data

  9. Helical Peierls distortion: Formation of helices of polyketone and polyisocyanide

    Science.gov (United States)

    Cui, Chang-Xing; Kertesz, Miklos

    1990-06-01

    A new type of Peierls-like distortion, the formation of a helix due to the existence of partially filled crossing bands, is reported for polyketone and polyisocyanide. The torsional potential curves, optimized geometries, band structures and phonon dispersion curves are derived. A comparison with the well-known Peierls-distorted all-trans polyacetylene indicates close similarity between the two types of Peierls distortions.

  10. Distortions in the output signals of conventional spectrum analyzers

    International Nuclear Information System (INIS)

    Njau, E.C.

    1988-08-01

    We show that the output signals of conventional spectrum analysers contain distortions which basically originate from the signal processing performed inside the analysers' frequency convertors. Total elimination of these distortions through normal filtering techniques is difficult owing to the closeness of some of their frequencies to the corresponding frequencies of the required signals. Simple design adjustments that can minimize these distortions are suggested. (author). 7 refs, 2 figs

  11. Could unstable relic particles distort the microwave background radiation?

    International Nuclear Information System (INIS)

    Dar, A.; Loeb, A.; Nussinov, S.

    1989-01-01

    Three general classes of possible scenarios for the recently reported distortion of the microwave background radiation (MBR) via decaying relic weakly interacting particles are analyzed. The analysis shows that such particles could not reheat the universe and cause the spectral distortion of the MBR. Gravitational processes such as the early formation of massive black holes may still be plausible energy sources for producing the reported spectral distortion of the MBR at an early cosmological epoch. 24 references

  12. Systems and methods for mirror mounting with minimized distortion

    Science.gov (United States)

    Antonille, Scott R. (Inventor); Wallace, Thomas E. (Inventor); Content, David A. (Inventor); Wake, Shane W. (Inventor)

    2012-01-01

    A method for mounting a mirror for use in a telescope includes attaching the mirror to a plurality of adjustable mounts; determining a distortion in the mirror caused by the plurality adjustable mounts, and, if the distortion is determined to be above a predetermined level: adjusting one or more of the adjustable mounts; and determining the distortion in the mirror caused by the adjustable mounts; and in the event the determined distortion is determined to be at or below the predetermined level, rigidizing the adjustable mounts.

  13. Modeling Kinetics of Distortion in Porous Bi-layered Structures

    DEFF Research Database (Denmark)

    Tadesse Molla, Tesfaye; Frandsen, Henrik Lund; Bjørk, Rasmus

    2013-01-01

    because of different sintering rates of the materials resulting in undesired distortions of the component. An analytical model based on the continuum theory of sintering has been developed to describe the kinetics of densification and distortion in the sintering processes. A new approach is used...... to extract the material parameters controlling shape distortion through optimizing the model to experimental data of free shrinkage strains. The significant influence of weight of the sample (gravity) on the kinetics of distortion is taken in to consideration. The modeling predictions indicate good agreement...

  14. Spectral Distortion in Lossy Compression of Hyperspectral Data

    Directory of Open Access Journals (Sweden)

    Bruno Aiazzi

    2012-01-01

    Full Text Available Distortion allocation varying with wavelength in lossy compression of hyperspectral imagery is investigated, with the aim of minimizing the spectral distortion between original and decompressed data. The absolute angular error, or spectral angle mapper (SAM, is used to quantify spectral distortion, while radiometric distortions are measured by maximum absolute deviation (MAD for near-lossless methods, for example, differential pulse code modulation (DPCM, or mean-squared error (MSE for lossy methods, for example, spectral decorrelation followed by JPEG 2000. Two strategies of interband distortion allocation are compared: given a target average bit rate, distortion may be set to be constant with wavelength. Otherwise, it may be allocated proportionally to the noise level of each band, according to the virtually lossless protocol. Comparisons with the uncompressed originals show that the average SAM of radiance spectra is minimized by constant distortion allocation to radiance data. However, variable distortion allocation according to the virtually lossless protocol yields significantly lower SAM in case of reflectance spectra obtained from compressed radiance data, if compared with the constant distortion allocation at the same compression ratio.

  15. Anomalous Centrifugal Distortion in NH_2

    Science.gov (United States)

    Martin-Drumel, Marie-Aline; Pirali, Olivier; Coudert, L. H.

    2017-06-01

    The NH2 radical spectrum, first observed by Herzberg and Ramsay, is dominated by a strong Renner-Teller effect giving rise to two electronic states: the bent X ^{2}B_1 ground state and the quasi-linear A ^{2}A_1 excited state. The NH2 radical has been the subject of numerous high-resolution investigations and its electronic and ro-vibrational transitions have been measured. Using synchrotron radiation, new rotational transitions have been recently recorded and a value of the rotational quantum number N as large as 26 could be reached. In the X ^{2}B_1 ground state, the NH2 radical behaves like a triatomic molecule displaying spin-rotation splittings. Due to the lightness of the molecule, a strong coupling between the overall rotation and the bending mode arises whose effects increase with N and lead to the anomalous centrifugal distortion evidenced in the new measurements.^d In this talk the Bending-Rotation approach developed to account for the anomalous centrifugal distortion of the water molecule is modified to include spin-rotation coupling and applied to the fitting of high-resolution data pertaining to the ground electronic state of NH2. A preliminary line position analysis of the available data^{c,d} allowed us to account for 1681 transitions with a unitless standard deviation of 1.2. New transitions could also be assigned in the spectrum recorded by Martin-Drumel et al.^d In the talk, the results obtained with the new theoretical approach will be compared to those retrieved with a Watson-type Hamiltonian and the effects of the vibronic coupling between the ground X ^{2}B_1 and the excited A ^{2}A_1 electronic state will be discussed. Herzberg and Ramsay, J. Chem. Phys. 20 (1952) 347 Dressler and Ramsay, Phil. Trans. R. Soc. A 25 (1959) 553 Hadj Bachir, Huet, Destombes, and Vervloet, J. Molec. Spectrosc. 193 (1999) 326 McKellar, Vervloet, Burkholder, and Howard, J. Molec. Spectrosc. 142 (1990) 319 Morino and Kawaguchi, J. Molec. Spectrosc. 182 (1997) 428

  16. About the factors distorting biological dosimetry results

    International Nuclear Information System (INIS)

    Mosseh, I.B.

    1999-01-01

    The row of chemical substances that have not mutagenic effect can strengthen ionising radiation induced cytogenetic effects. For example nitrite sodium and nitrate sodium reinforce mutagenic action of radiation and cause sensitized effect although they aren't mutagens. Presence of residual amount of herbicides in food products can have influence at level of aberration in human cells. It was investigated the influence of herbicide zencor at mutagenic action of radiation. This substance has weak mutagenic activity. In the case of combined action of zencor with irradiation antagonistic effect was observed. Mutation rate turns out to be lower than expected summary value. At the same time many foods products (tea, coffee, cacao, chocolate etc., which contain melanin) are antimutagens and can also change the frequency of radiation induced mutations. Taking of medicine distort the results of dose estimation. The frequency of chromosomal aberrations in blood lymphocytes after acute irradiation is considered to be adequate method of biological dosimetry. In the case of chronic irradiation this analysis becomes complicated with such processes as adaptation (selection and proliferation of cells with more radioresistant genotype) and the origin of genetic un stability which leads to higher radiosensitivity. The estimation of the level of point mutations is the most precise method of biological dosimetry because their existence is less exposed to modifications

  17. TWO NEW TIDALLY DISTORTED WHITE DWARFS

    Energy Technology Data Exchange (ETDEWEB)

    Hermes, J. J.; Montgomery, M. H.; Winget, D. E. [Department of Astronomy, University of Texas at Austin, Austin, TX 78712 (United States); Kilic, Mukremin [Homer L. Dodge Department of Physics and Astronomy, University of Oklahoma, 440 W. Brooks St., Norman, OK 73019 (United States); Brown, Warren R., E-mail: jjhermes@astro.as.utexas.edu [Smithsonian Astrophysical Observatory, 60 Garden St, Cambridge, MA 02138 (United States)

    2012-04-10

    We identify two new tidally distorted white dwarfs (WDs), SDSS J174140.49+652638.7 and J211921.96-001825.8 (hereafter J1741 and J2119). Both stars are extremely low mass (ELM, {<=} 0.2 M{sub Sun }) WDs in short-period, detached binary systems. High-speed photometric observations obtained at the McDonald Observatory reveal ellipsoidal variations and Doppler beaming in both systems; J1741, with a minimum companion mass of 1.1 M{sub Sun }, has one of the strongest Doppler beaming signals ever observed in a binary system (0.59% {+-} 0.06% amplitude). We use the observed ellipsoidal variations to constrain the radius of each WD. For J1741, the star's radius must exceed 0.074 R{sub Sun }. For J2119, the radius exceeds 0.10 R{sub Sun }. These indirect radius measurements are comparable to the radius measurements for the bloated WD companions to A-stars found by the Kepler spacecraft, and they constitute some of the largest radii inferred for any WD. Surprisingly, J1741 also appears to show a 0.23% {+-} 0.06% reflection effect, and we discuss possible sources for this excess heating. Both J1741 and J2119 are strong gravitational wave sources, and the time-of-minimum of the ellipsoidal variations can be used to detect the orbital period decay. This may be possible on a timescale of a decade or less.

  18. Subjective duration distortions mirror neural repetition suppression.

    Science.gov (United States)

    Pariyadath, Vani; Eagleman, David M

    2012-01-01

    Subjective duration is strongly influenced by repetition and novelty, such that an oddball stimulus in a stream of repeated stimuli appears to last longer in duration in comparison. We hypothesize that this duration illusion, called the temporal oddball effect, is a result of the difference in expectation between the oddball and the repeated stimuli. Specifically, we conjecture that the repeated stimuli contract in duration as a result of increased predictability; these duration contractions, we suggest, result from decreased neural response amplitude with repetition, known as repetition suppression. Participants viewed trials consisting of lines presented at a particular orientation (standard stimuli) followed by a line presented at a different orientation (oddball stimulus). We found that the size of the oddball effect correlates with the number of repetitions of the standard stimulus as well as the amount of deviance from the oddball stimulus; both of these results are consistent with a repetition suppression hypothesis. Further, we find that the temporal oddball effect is sensitive to experimental context--that is, the size of the oddball effect for a particular experimental trial is influenced by the range of duration distortions seen in preceding trials. Our data suggest that the repetition-related duration contractions causing the oddball effect are a result of neural repetition suppression. More generally, subjective duration may reflect the prediction error associated with a stimulus and, consequently, the efficiency of encoding that stimulus. Additionally, we emphasize that experimental context effects need to be taken into consideration when designing duration-related tasks.

  19. Distortion Effects on Trojan Horse Applications

    International Nuclear Information System (INIS)

    Pizzone, R. G.; Spitaleri, C.; La Cognata, M.; Lamia, L.; Romano, S.; Mukhamedzhanov, A. M.; Blokhintsev, L. D.; Bertulani, C. A.; Irgaziev, B. F.

    2011-01-01

    The widths of the spectator momentum distributions in several nuclei, which have been used as Trojan Horses, have been obtained as a function of the transferred momentum. Applications of Trojan Horse method will also be discussed. The study of processes relevant for astrophysics involving light nuclei has increased in the last decades due to the development of indirect methods. The present paper will also help to point out the distortion effects which arise at low energies in the study of three-body processes and will suggest some way to by-pass them in Trojan Horse Method (THM) applications. The goal of this paper is to compare the experimental momentum distribution of the spectator in the bound state a = (sx) extracted from the 2 → 3 particles (breakup, or breakup with rearrangement) reactions with the theoretical one. The theoretical momentum distribution has been calculated for the target a = (sx) using the Hulthen potential for a = d and Woods-Saxon one with the standard geometrical parameters, radius r 0 = 1.25 fm and diffuseness a = 0.65 fm, for other nuclei. (author)

  20. Rate-distortion analysis of directional wavelets.

    Science.gov (United States)

    Maleki, Arian; Rajaei, Boshra; Pourreza, Hamid Reza

    2012-02-01

    The inefficiency of separable wavelets in representing smooth edges has led to a great interest in the study of new 2-D transformations. The most popular criterion for analyzing these transformations is the approximation power. Transformations with near-optimal approximation power are useful in many applications such as denoising and enhancement. However, they are not necessarily good for compression. Therefore, most of the nearly optimal transformations such as curvelets and contourlets have not found any application in image compression yet. One of the most promising schemes for image compression is the elegant idea of directional wavelets (DIWs). While these algorithms outperform the state-of-the-art image coders in practice, our theoretical understanding of them is very limited. In this paper, we adopt the notion of rate-distortion and calculate the performance of the DIW on a class of edge-like images. Our theoretical analysis shows that if the edges are not "sharp," the DIW will compress them more efficiently than the separable wavelets. It also demonstrates the inefficiency of the quadtree partitioning that is often used with the DIW. To solve this issue, we propose a new partitioning scheme called megaquad partitioning. Our simulation results on real-world images confirm the benefits of the proposed partitioning algorithm, promised by our theoretical analysis. © 2011 IEEE

  1. Motivational Distortion on 16 PF Primaries by Male Felons.

    Science.gov (United States)

    Wallbrown, Fred H.; And Others

    1989-01-01

    Investigated motivational distortion using the 16 Personality Factor Questionnaire (16 PF) for male (n=331) criminal offenders. Results indicated that ego-strength, free-floating anxiety, ability to bind anxiety, boldness, dominance, emotional sensitivity and suspiciousness contributed most to the motivational distortion scale predictions.…

  2. FSD: Frequency Space Differential measurement of CMB spectral distortions

    Science.gov (United States)

    Mukherjee, Suvodip; Silk, Joseph; Wandelt, Benjamin D.

    2018-04-01

    Although the Cosmic Microwave Background agrees with a perfect blackbody spectrum within the current experimental limits, it is expected to exhibit certain spectral distortions with known spectral properties. We propose a new method, Frequency Space Differential (FSD) to measure the spectral distortions in the CMB spectrum by using the inter-frequency differences of the brightness temperature. The difference between the observed CMB temperature at different frequencies must agree with the frequency derivative of the blackbody spectrum, in the absence of any distortion. However, in the presence of spectral distortions, the measured inter-frequency differences would also exhibit deviations from blackbody which can be modeled for known sources of spectral distortions like y & μ. Our technique uses FSD information for the CMB blackbody, y, μ or any other sources of spectral distortions to model the observed signal. Successful application of this method in future CMB missions can provide an alternative method to extract spectral distortion signals and can potentially make it feasible to measure spectral distortions without an internal blackbody calibrator.

  3. Audiovisual Cues and Perceptual Learning of Spectrally Distorted Speech

    Science.gov (United States)

    Pilling, Michael; Thomas, Sharon

    2011-01-01

    Two experiments investigate the effectiveness of audiovisual (AV) speech cues (cues derived from both seeing and hearing a talker speak) in facilitating perceptual learning of spectrally distorted speech. Speech was distorted through an eight channel noise-vocoder which shifted the spectral envelope of the speech signal to simulate the properties…

  4. Distortion of Probability and Outcome Information in Risky Decisions

    Science.gov (United States)

    DeKay, Michael L.; Patino-Echeverri, Dalia; Fischbeck, Paul S.

    2009-01-01

    Substantial evidence indicates that information is distorted during decision making, but very few studies have assessed the distortion of probability and outcome information in risky decisions. In two studies involving six binary decisions (e.g., banning blood donations from people who have visited England, because of "mad cow disease"),…

  5. Method and device for monitoring distortion in an optical network

    NARCIS (Netherlands)

    2012-01-01

    A method and a device for monitoring of distortion in an optical network are provided, wherein at least one reference signal and at least one data signal are conveyed via an optical link and wherein a distortion of the at least one data signal is determined based on the at least one reference

  6. How Distorted Thinking Influence Arab Children Academic Achievement in Israel?

    Science.gov (United States)

    Gith, Emad

    2018-01-01

    The purpose of the current study was to examine the relation between the parents Cognitive Distortion and Arab children academic achievements in Israel. 52 fifth grade Arab Children and their parents from Israel were participated. The results indicated that parent's cognitive distortion related negatively to children academic achievements; there…

  7. Distortions caused by the signal processing in analog AM modulators

    International Nuclear Information System (INIS)

    Njau, E.C.

    1988-08-01

    Complete analytical expressions for distortions caused by signal processing in analog AM modulators are developed. The salient features in these expressions are shown to be consistent with displays of actual spectra of AM signals. Finally suggestions are given on how the distortions may be practically minimized. (author). 6 refs, 3 figs

  8. Distorted Risk Measures with Application to Military Capability Shortfalls

    Science.gov (United States)

    2005-12-15

    effects of different distortions and to make basic recommendations regarding the appropriateness of certain distortion functions and parameters using...and increased limits ratemaking by proportional hazards transforms. Insurance: Mathematics and Economics, 17: 43-54. [9] Wang, S. (1996a). Premium

  9. Fisheye image rectification using spherical and digital distortion models

    Science.gov (United States)

    Li, Xin; Pi, Yingdong; Jia, Yanling; Yang, Yuhui; Chen, Zhiyong; Hou, Wenguang

    2018-02-01

    Fisheye cameras have been widely used in many applications including close range visual navigation and observation and cyber city reconstruction because its field of view is much larger than that of a common pinhole camera. This means that a fisheye camera can capture more information than a pinhole camera in the same scenario. However, the fisheye image contains serious distortion, which may cause trouble for human observers in recognizing the objects within. Therefore, in most practical applications, the fisheye image should be rectified to a pinhole perspective projection image to conform to human cognitive habits. The traditional mathematical model-based methods cannot effectively remove the distortion, but the digital distortion model can reduce the image resolution to some extent. Considering these defects, this paper proposes a new method that combines the physical spherical model and the digital distortion model. The distortion of fisheye images can be effectively removed according to the proposed approach. Many experiments validate its feasibility and effectiveness.

  10. Deep subcritical levels measurements dependents upon kinetic distortion factors

    International Nuclear Information System (INIS)

    Pan Shibiao; Li Xiang; Fu Guo'en; Huang Liyuan; Mu Keliang

    2013-01-01

    The measurement of deep subcritical levels, with the increase of subcriticality, showed that the results impact on the kinetic distortion effect, along with neutron flux strongly deteriorated. Using the diffusion theory, calculations have been carried out to quantify the kinetic distortion correction factors in subcritical systems, and these indicate that epithermal neutron distributions are strongly affected by kinetic distortion. Subcriticality measurements in four different rod-state combination at the zero power device was carried out. The test data analysis shows that, with increasing subcriticality, kinetic distortion effect correction factor gradually increases from 1.052 to 1.065, corresponding reactive correction amount of 0.78β eff ∼ 3.01β eff . Thus, it is necessary to consider the kinetic distortion effect in the deep subcritical reactivity measurements. (authors)

  11. Effects of image distortion correction on voxel-based morphometry

    International Nuclear Information System (INIS)

    Goto, Masami; Abe, Osamu; Kabasawa, Hiroyuki

    2012-01-01

    We aimed to show that correcting image distortion significantly affects brain volumetry using voxel-based morphometry (VBM) and to assess whether the processing of distortion correction reduces system dependency. We obtained contiguous sagittal T 1 -weighted images of the brain from 22 healthy participants using 1.5- and 3-tesla magnetic resonance (MR) scanners, preprocessed images using Statistical Parametric Mapping 5, and tested the relation between distortion correction and brain volume using VBM. Local brain volume significantly increased or decreased on corrected images compared with uncorrected images. In addition, the method used to correct image distortion for gradient nonlinearity produced fewer volumetric errors from MR system variation. This is the first VBM study to show more precise volumetry using VBM with corrected images. These results indicate that multi-scanner or multi-site imaging trials require correction for distortion induced by gradient nonlinearity. (author)

  12. A versatile non-radioactive assay for DNA methyltransferase activity and DNA binding

    Science.gov (United States)

    Frauer, Carina; Leonhardt, Heinrich

    2009-01-01

    We present a simple, non-radioactive assay for DNA methyltransferase activity and DNA binding. As most proteins are studied as GFP fusions in living cells, we used a GFP binding nanobody coupled to agarose beads (GFP nanotrap) for rapid one-step purification. Immobilized GFP fusion proteins were subsequently incubated with different fluorescently labeled DNA substrates. The absolute amounts and molar ratios of GFP fusion proteins and bound DNA substrates were determined by fluorescence spectroscopy. In addition to specific DNA binding of GFP fusion proteins, the enzymatic activity of DNA methyltransferases can also be determined by using suicide DNA substrates. These substrates contain the mechanism-based inhibitor 5-aza-dC and lead to irreversible covalent complex formation. We obtained covalent complexes with mammalian DNA methyltransferase 1 (Dnmt1), which were resistant to competition with non-labeled canonical DNA substrates, allowing differentiation between methyltransferase activity and DNA binding. By comparison, the Dnmt1C1229W catalytic site mutant showed DNA-binding activity, but no irreversible covalent complex formation. With this assay, we could also confirm the preference of Dnmt1 for hemimethylated CpG sequences. The rapid optical read-out in a multi-well format and the possibility to test several different substrates in direct competition allow rapid characterization of sequence-specific binding and enzymatic activity. PMID:19129216

  13. Subjective duration distortions mirror neural repetition suppression.

    Directory of Open Access Journals (Sweden)

    Vani Pariyadath

    Full Text Available Subjective duration is strongly influenced by repetition and novelty, such that an oddball stimulus in a stream of repeated stimuli appears to last longer in duration in comparison. We hypothesize that this duration illusion, called the temporal oddball effect, is a result of the difference in expectation between the oddball and the repeated stimuli. Specifically, we conjecture that the repeated stimuli contract in duration as a result of increased predictability; these duration contractions, we suggest, result from decreased neural response amplitude with repetition, known as repetition suppression.Participants viewed trials consisting of lines presented at a particular orientation (standard stimuli followed by a line presented at a different orientation (oddball stimulus. We found that the size of the oddball effect correlates with the number of repetitions of the standard stimulus as well as the amount of deviance from the oddball stimulus; both of these results are consistent with a repetition suppression hypothesis. Further, we find that the temporal oddball effect is sensitive to experimental context--that is, the size of the oddball effect for a particular experimental trial is influenced by the range of duration distortions seen in preceding trials.Our data suggest that the repetition-related duration contractions causing the oddball effect are a result of neural repetition suppression. More generally, subjective duration may reflect the prediction error associated with a stimulus and, consequently, the efficiency of encoding that stimulus. Additionally, we emphasize that experimental context effects need to be taken into consideration when designing duration-related tasks.

  14. Prussian phenomenon and its historical distortion

    Directory of Open Access Journals (Sweden)

    Oleg Y. Plenkov

    2016-03-01

    Full Text Available The article deals with the phenomenon of Prussia. Once, Prussia had been the largest continental Protestant state in Europe. The main issue of this phenomenon is that upon the tragic events of the World War II Prussian history and heritage had been considerably distorted, in order to compensate somehow for the dreadful casualties suffered by the victorious powers. The common European misconception implied that Prussia had been the bulwark of militarism, and therefore had to bear all the responsibility for the atrocities of war. Unfortunately, the majority of modern German historians share such misinterpretation of Prussian heritage in order to please false political correctness, perhaps, as an act of contrition for National Socialism and its crimes. However, the Prussian tradition and history go far beyond this militarism, and this article explains what ways. The authors believe that there should not be any prejudices and biases, that any subject should be examined sine ira et studio. Moreover, given that it is possible to characterize the Great French Revolution as a juristic one, and the Great October revolution – as a social one, the Prussian revolution “from above”, led by the first representatives of the Hohenzollern family, may be well considered as a pedagogical revolution. This revolution did bring definitely positive changes; they are surveyed in the article. The French Revolution has not eliminated the covetousness of the bourgeoisie after 1789; despotism of the authorities and people’s passiveness similarly have remained unaltered in Russia after 1917. On the contrary, Federal Republic of Germany of nowadays, distinctive for its law, order and effective responsible government is unthinkable without Prussian heritage.

  15. Structural, optical and electrical characteristics of ITO thin films deposited by sputtering on different polyester substrates

    International Nuclear Information System (INIS)

    Guillen, C.; Herrero, J.

    2008-01-01

    Indium tin oxide (ITO) thin films were deposited by sputtering at room temperature on glass and different polyester substrates; namely polyarylate (PA), polycarbonate (PC) and polyethylene terephtalate (PET). The influence of the substrate on the structural, optical and electrical characteristics of the ITO layers was investigated. The sputtered films exhibited crystallization in the (2 2 2) orientation, with higher mean crystallite size and lower structural distortion onto PET than onto PA, PC or glass substrates. ITO films deposited onto PET showed also higher band gap energy, higher carrier concentration and lower resistivity than the ITO layers onto the other tested substrates. These optical and electrical characteristics have been related to the structural distortion that was found dependent on the specific polyester substrate

  16. A structural classification of substrate-binding proteins

    NARCIS (Netherlands)

    Berntsson, Ronnie P. -A.; Smits, Sander H. J.; Schmitt, Lutz; Slotboom, Dirk-Jan; Poolman, Bert

    2010-01-01

    Substrate-binding proteins (SBP) are associated with a wide variety of protein complexes. The proteins are part of ATP-binding cassette transporters for substrate uptake, ion gradient driven transporters, DNA-binding proteins, as well as channels and receptors from both pro-and eukaryotes. A wealth

  17. Structure-based domain assignment in Leishmania infantum EndoG: characterization of a pH-dependent regulatory switch and a C-terminal extension that largely dictates DNA substrate preferences.

    Science.gov (United States)

    Oliva, Cristina; Sánchez-Murcia, Pedro A; Rico, Eva; Bravo, Ana; Menéndez, Margarita; Gago, Federico; Jiménez-Ruiz, Antonio

    2017-09-06

    Mitochondrial endonuclease G from Leishmania infantum (LiEndoG) participates in the degradation of double-stranded DNA (dsDNA) during parasite cell death and is catalytically inactive at a pH of 8.0 or above. The presence, in the primary sequence, of an acidic amino acid-rich insertion exclusive to trypanosomatids and its spatial position in a homology-built model of LiEndoG led us to postulate that this peptide stretch might act as a pH sensor for self-inhibition. We found that a LiEndoG variant lacking residues 145-180 is indeed far more active than its wild-type counterpart at pH values >7.0. In addition, we discovered that (i) LiEndoG exists as a homodimer, (ii) replacement of Ser211 in the active-site SRGH motif with the canonical aspartate from the DRGH motif of other nucleases leads to a catalytically deficient enzyme, (iii) the activity of the S211D variant can be restored upon the concomitant replacement of Ala247 with Arg and (iv) a C-terminal extension is responsible for the observed preferential cleavage of single-stranded DNA (ssDNA) and ssDNA-dsDNA junctions. Taken together, our results support the view that LiEndoG is a multidomain molecular machine whose nuclease activity can be subtly modulated or even abrogated through architectural changes brought about by environmental conditions and interaction with other binding partners. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Improvement of vector compensation method for vehicle magnetic distortion field

    Energy Technology Data Exchange (ETDEWEB)

    Pang, Hongfeng, E-mail: panghongfeng@126.com; Zhang, Qi; Li, Ji; Luo, Shitu; Chen, Dixiang; Pan, Mengchun; Luo, Feilu

    2014-03-15

    Magnetic distortions such as eddy-current field and low frequency magnetic field have not been considered in vector compensation methods. A new compensation method is proposed to suppress these magnetic distortions and improve compensation performance, in which the magnetic distortions related to measurement vectors and time are considered. The experimental system mainly consists of a three-axis fluxgate magnetometer (DM-050), an underwater vehicle and a proton magnetometer, in which the scalar value of magnetic field is obtained with the proton magnetometer and considered to be the true value. Comparing with traditional compensation methods, experimental results show that the magnetic distortions can be further reduced by two times. After compensation, error intensity and RMS error are reduced from 11684.013 nT and 7794.604 nT to 16.219 nT and 5.907 nT respectively. It suggests an effective way to improve the compensation performance of magnetic distortions. - Highlights: • A new vector compensation method is proposed for vehicle magnetic distortion. • The proposed model not only includes magnetometer error but also considers magnetic distortion. • Compensation parameters are computed directly by solving nonlinear equations. • Compared with traditional methods, the proposed method is not related with rotation angle rate. • Error intensity and RMS error can be reduced to 1/2 of the error with traditional methods.

  19. Improvement of vector compensation method for vehicle magnetic distortion field

    International Nuclear Information System (INIS)

    Pang, Hongfeng; Zhang, Qi; Li, Ji; Luo, Shitu; Chen, Dixiang; Pan, Mengchun; Luo, Feilu

    2014-01-01

    Magnetic distortions such as eddy-current field and low frequency magnetic field have not been considered in vector compensation methods. A new compensation method is proposed to suppress these magnetic distortions and improve compensation performance, in which the magnetic distortions related to measurement vectors and time are considered. The experimental system mainly consists of a three-axis fluxgate magnetometer (DM-050), an underwater vehicle and a proton magnetometer, in which the scalar value of magnetic field is obtained with the proton magnetometer and considered to be the true value. Comparing with traditional compensation methods, experimental results show that the magnetic distortions can be further reduced by two times. After compensation, error intensity and RMS error are reduced from 11684.013 nT and 7794.604 nT to 16.219 nT and 5.907 nT respectively. It suggests an effective way to improve the compensation performance of magnetic distortions. - Highlights: • A new vector compensation method is proposed for vehicle magnetic distortion. • The proposed model not only includes magnetometer error but also considers magnetic distortion. • Compensation parameters are computed directly by solving nonlinear equations. • Compared with traditional methods, the proposed method is not related with rotation angle rate. • Error intensity and RMS error can be reduced to 1/2 of the error with traditional methods

  20. The evolution of costly mate choice against segregation distorters.

    Science.gov (United States)

    Manser, Andri; Lindholm, Anna K; Weissing, Franz J

    2017-12-01

    The evolution of female preference for male genetic quality remains a controversial topic in sexual selection research. One well-known problem, known as the lek paradox, lies in understanding how variation in genetic quality is maintained in spite of natural selection and sexual selection against low-quality alleles. Here, we theoretically investigate a scenario where females pay a direct fitness cost to avoid males carrying an autosomal segregation distorter. We show that preference evolution is greatly facilitated under such circumstances. Because the distorter is transmitted in a non-Mendelian fashion, it can be maintained in the population despite directional sexual selection. The preference helps females avoid fitness costs associated with the distorter. Interestingly, we find that preference evolution is limited if the choice allele induces a very strong preference or if distortion is very strong. Moreover, the preference can only persist in the presence of a signal that reliably indicates a male's distorter genotype. Hence, even in a system where the lek paradox does not play a major role, costly preferences can only spread under specific circumstances. We discuss the importance of distorter systems for the evolution of costly female choice and potential implications for the use of artificial distorters in pest control. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  1. Bilateral Symmetry of Distortions of Tactile Size Perception.

    Science.gov (United States)

    Longo, Matthew R; Ghosh, Arko; Yahya, Tasneem

    2015-01-01

    The perceived distance between touches on the limbs is generally bigger for distances oriented across the width of the limb than for distances oriented along the length of the limb. The present study aimed to investigate the coherence of such distortions of tactile size perception across different skin surfaces. We investigated distortions of tactile size perception on the dorsal and palmar surfaces of both the left and right hands as well as the forehead. Participants judged which of two tactile distances felt larger. One distance was aligned with the proximodistal axis (along the body), the other with the mediolateral axis (across the body). Clear distortions were found on all five skin surfaces, with stimuli oriented across the width of the body being perceived as farther apart than those oriented along the length of the body. Consistent with previous results, distortions were smaller on the palmar than on the dorsal hand surface. Distortion on the forehead was intermediate between the dorsal and palmar surfaces. There were clear correlations between distortion on the left and right hands, for both the dorsal and palmar skin surfaces. In contrast, within each hand, there was no significant correlation between the two skin surfaces. Distortion on the forehead was not significantly correlated with that on any of the other skin surfaces. These results provide evidence for bilaterally symmetric representations underlying tactile size perception. © The Author(s) 2015.

  2. CMB spectral distortions as solutions to the Boltzmann equations

    Energy Technology Data Exchange (ETDEWEB)

    Ota, Atsuhisa, E-mail: a.ota@th.phys.titech.ac.jp [Department of Physics, Tokyo Institute of Technology, Tokyo 152-8551 (Japan)

    2017-01-01

    We propose to re-interpret the cosmic microwave background spectral distortions as solutions to the Boltzmann equation. This approach makes it possible to solve the second order Boltzmann equation explicitly, with the spectral y distortion and the momentum independent second order temperature perturbation, while generation of μ distortion cannot be explained even at second order in this framework. We also extend our method to higher order Boltzmann equations systematically and find new type spectral distortions, assuming that the collision term is linear in the photon distribution functions, namely, in the Thomson scattering limit. As an example, we concretely construct solutions to the cubic order Boltzmann equation and show that the equations are closed with additional three parameters composed of a cubic order temperature perturbation and two cubic order spectral distortions. The linear Sunyaev-Zel'dovich effect whose momentum dependence is different from the usual y distortion is also discussed in the presence of the next leading order Kompaneets terms, and we show that higher order spectral distortions are also generated as a result of the diffusion process in a framework of higher order Boltzmann equations. The method may be applicable to a wider class of problems and has potential to give a general prescription to non-equilibrium physics.

  3. Spatial distortion in MRI with application to stereotactic neurosurgery

    International Nuclear Information System (INIS)

    Morgan, P.S.

    1999-05-01

    The aim of this work was to implement a thorough method for quantifying the errors introduced to frame-based neurosurgical stereotactic procedures by the use of MRI. Chang and Fitzpatrick's reversed gradient distortion correction method was used, in combination with a phantom, to measure these errors. Spatial distortion in MR images of between 1 mm and 2 mm was measured. Further analysis showed that this typically introduced an additional error in the coordinate of the actual treatment point of 0.7 mm. The implications of this are discussed. The main source of distortion in the MR images used for stereotaxis was found to be the head ring. A comparison between imaging sequences and MR scanners revealed that the spatial distortion depends mainly on the bandwidth per pixel of the sequence rather than other differences in the imaging sequences. By comparison with a phase map distortion correction technique, the imaging parameters required to allow successful distortion correction with the reversed gradient method were identified. The most important was the use of full Fourier spin echo acquisitions. The reversed gradient correction method was applied to two contemporary EPI techniques. Considerable improvement was seen in the production of ADC maps after the images had been corrected for distortion. The method also was shown to be valid in application to BOLD fMRl data. (author)

  4. Market distortions and aggregate productivity: Evidence from Chinese energy enterprises

    International Nuclear Information System (INIS)

    Dai, Xiaoyong; Cheng, Liwei

    2016-01-01

    Market distortions can generate resource misallocations across heterogeneous firms and reduce aggregate productivity. This paper measures market distortions and aggregate productivity growth in China's energy sector. We use the wedge between output elasticities and factor shares in revenues to recover a measure of firm-level market distortions. Using data on a large sample of Chinese energy enterprises from 1999 to 2007, our estimations provide strong evidence of the existence of both factor and product market distortions within and across China's various energy industries. The productivity aggregation and decomposition results demonstrate that the estimated aggregate productivity growth (APG) is, on average, 2.595% points per year, of which technological change, resource reallocation, and firm entries and exits account for 1.981, 0.068, and 0.546% points, respectively. The weak contributions of resource reallocation and firm turnover to APG are also found in energy sub-industries, except in the coal industry. Our research suggests that China's energy sector has major potential for productivity gains from resource reallocation through the reduction of market distortions. - Highlights: •We estimate market distortions and productivity growth of China's energy sector. •We use a large sample of Chinese energy enterprises. •There are evidences of the existence of factor and product market distortions. •Aggregate productivity growth is largely driven by firm-level technological change. •China's energy sector can realize productivity gains from resource reallocations.

  5. Word Recognition for Temporally and Spectrally Distorted Materials

    DEFF Research Database (Denmark)

    Smith, Sherri L.; Pichora-Fuller, Margaret Kathleen; Wilson, Richard H.

    2012-01-01

    listeners with near-normal hearing and hearing loss performed best in the unaltered condition, followed by the jitter and smear conditions, with the poorest performance in the combined jitter-smear condition in both quiet and noise. Overall, listeners with near-normal hearing performed better than listeners...... to predict group differences, but not the effects of distortion. Individual differences in performance were similar across all distortion conditions with both age and hearing loss being implicated. The speech materials needed to be both spectrally and temporally distorted to mimic the effects of age...

  6. Perceptual distortion analysis of color image VQ-based coding

    Science.gov (United States)

    Charrier, Christophe; Knoblauch, Kenneth; Cherifi, Hocine

    1997-04-01

    It is generally accepted that a RGB color image can be easily encoded by using a gray-scale compression technique on each of the three color planes. Such an approach, however, fails to take into account correlations existing between color planes and perceptual factors. We evaluated several linear and non-linear color spaces, some introduced by the CIE, compressed with the vector quantization technique for minimum perceptual distortion. To study these distortions, we measured contrast and luminance of the video framebuffer, to precisely control color. We then obtained psychophysical judgements to measure how well these methods work to minimize perceptual distortion in a variety of color space.

  7. Operation of static series compensator under distorted utility conditions

    DEFF Research Database (Denmark)

    Awad, H.; Nelsen, H.; Blaabjerg, Frede

    2005-01-01

    in the case of distorted grid voltage. Furthermore, a selective harmonic compensation strategy is applied to filter out the grid harmonics. The operation of the SSC under distorted utility conditions and voltage dips is discussed. The validity of the proposed controller is verified by experiments, carried out...... on a 10-kV SSC laboratory setup. Experimental results have shown the ability of the SSC to mitigate voltage dips and harmonics. It is also shown that the proposed controller has improved the transient performance of the SSC even under distorted utility conditions....

  8. cDNA sequence and tissue distribution of the mRNA for bovine and murine p11, the S100-related light chain of the protein-tyrosine kinase substrate p36 (calpactin I)

    DEFF Research Database (Denmark)

    Saris, Chris J M; Kristensen, Torsten; D’Eustachio, Peter

    1987-01-01

    We have isolated and sequenced cDNA clones of bovine nd murine pl 1 mRNAs. The nonpolyadenylated mRNAs are predicted to be 614 and 600 nucleotides, respectively. The p l l mRNAs both contain a 291 nucleotide open reading frame, preceded by a 5”untranslated region of 73 nucleotides in bovine p l l m...

  9. DNA repair deficiency in neurodegeneration

    DEFF Research Database (Denmark)

    Jeppesen, Dennis Kjølhede; Bohr, Vilhelm A; Stevnsner, Tinna V.

    2011-01-01

    Deficiency in repair of nuclear and mitochondrial DNA damage has been linked to several neurodegenerative disorders. Many recent experimental results indicate that the post-mitotic neurons are particularly prone to accumulation of unrepaired DNA lesions potentially leading to progressive...... neurodegeneration. Nucleotide excision repair is the cellular pathway responsible for removing helix-distorting DNA damage and deficiency in such repair is found in a number of diseases with neurodegenerative phenotypes, including Xeroderma Pigmentosum and Cockayne syndrome. The main pathway for repairing oxidative...... base lesions is base excision repair, and such repair is crucial for neurons given their high rates of oxygen metabolism. Mismatch repair corrects base mispairs generated during replication and evidence indicates that oxidative DNA damage can cause this pathway to expand trinucleotide repeats, thereby...

  10. Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations

    Science.gov (United States)

    Zeida, Ari; Machado, Matías Rodrigo; Dans, Pablo Daniel; Pantano, Sergio

    2012-08-01

    Bending of the seemingly stiff DNA double helix is a fundamental physical process for any living organism. Specialized proteins recognize DNA inducing and stabilizing sharp curvatures of the double helix. However, experimental evidence suggests a high protein-independent flexibility of DNA. On the basis of coarse-grained simulations, we propose that DNA experiences thermally induced kinks associated with the spontaneous formation of internal bubbles. Comparison of the protein-induced DNA curvature calculated from the Protein Data Bank with that sampled by our simulations suggests that thermally induced distortions can account for ˜80% of the DNA curvature present in experimentally solved structures.

  11. Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations.

    Science.gov (United States)

    Zeida, Ari; Machado, Matías Rodrigo; Dans, Pablo Daniel; Pantano, Sergio

    2012-08-01

    Bending of the seemingly stiff DNA double helix is a fundamental physical process for any living organism. Specialized proteins recognize DNA inducing and stabilizing sharp curvatures of the double helix. However, experimental evidence suggests a high protein-independent flexibility of DNA. On the basis of coarse-grained simulations, we propose that DNA experiences thermally induced kinks associated with the spontaneous formation of internal bubbles. Comparison of the protein-induced DNA curvature calculated from the Protein Data Bank with that sampled by our simulations suggests that thermally induced distortions can account for ~80% of the DNA curvature present in experimentally solved structures.

  12. Journal Afrika Statistika ISSN 0852-0305 Distortion risk measures ...

    African Journals Online (AJOL)

    la somme et sur la structure de dépendance des risques, représentée par une copule. ... Key words: Coherence; Dependence structure; Distortion function; Risk measure; Risk theory; insurance; Wang ..... Weighted risk capital allocations.

  13. A method to correct coordinate distortion in EBSD maps

    International Nuclear Information System (INIS)

    Zhang, Y.B.; Elbrønd, A.; Lin, F.X.

    2014-01-01

    Drift during electron backscatter diffraction mapping leads to coordinate distortions in resulting orientation maps, which affects, in some cases significantly, the accuracy of analysis. A method, thin plate spline, is introduced and tested to correct such coordinate distortions in the maps after the electron backscatter diffraction measurements. The accuracy of the correction as well as theoretical and practical aspects of using the thin plate spline method is discussed in detail. By comparing with other correction methods, it is shown that the thin plate spline method is most efficient to correct different local distortions in the electron backscatter diffraction maps. - Highlights: • A new method is suggested to correct nonlinear spatial distortion in EBSD maps. • The method corrects EBSD maps more precisely than presently available methods. • Errors less than 1–2 pixels are typically obtained. • Direct quantitative analysis of dynamic data are available after this correction

  14. Off-shell distortions of multichannel atomic processes

    Science.gov (United States)

    Barrachina, R. O.; Clauser, C. F.

    2017-10-01

    Any multichannel problem can be reduced to a succession of two-body events. However, these basic building blocks of many-body theories do not correspond to elastic processes but are off-the-energy-shell. In view of this difficulty, the great majority of the Distorted-Wave models includes a subsidiary approximation where these off-shell terms are arbitrarily forced to lie on the energy shell. At a first glance, since the energy deficiency is negligible for high enough velocities, the on-shell assumption seems to be completely justified. However, for the case of Coulomb interactions, the two-body off-shell distortions have branch-point singularities on the on-shell limit. In this article we demonstrate that these singularities might produce sizeable distortions of multiple scattering amplitudes, mainly when dealing with ion-ion collisions. Finally, we propose a method of including these distortions that might lead to better results that removing them completely.

  15. FPGA Based Compensation Method for Correcting Distortion in Voltage Inverters

    National Research Council Canada - National Science Library

    Williamson, Kenya D

    2007-01-01

    ...) voltage source inverters. Blanking time distortion is caused by the delay inserted to prevent the short circuit that would occur if the two transistors in the same inverter leg are both on at the same time...

  16. Correcting the Chromatic Aberration in Barrel Distortion of Endoscopic Images

    Directory of Open Access Journals (Sweden)

    Y. M. Harry Ng

    2003-04-01

    Full Text Available Modern endoscopes offer physicians a wide-angle field of view (FOV for minimally invasive therapies. However, the high level of barrel distortion may prevent accurate perception of image. Fortunately, this kind of distortion may be corrected by digital image processing. In this paper we investigate the chromatic aberrations in the barrel distortion of endoscopic images. In the past, chromatic aberration in endoscopes is corrected by achromatic lenses or active lens control. In contrast, we take a computational approach by modifying the concept of image warping and the existing barrel distortion correction algorithm to tackle the chromatic aberration problem. In addition, an error function for the determination of the level of centroid coincidence is proposed. Simulation and experimental results confirm the effectiveness of our method.

  17. A search for transmission ratio distortions in offspring from crosses ...

    Indian Academy of Sciences (India)

    differential embryonic mortality, nondisjunction and gene conversion that are rather irregular forms of ... Keywords. transmission ratio distortion; meiotic drive; inbred mice. ..... Sapienza 2000 Heritability of the maternal meiotic drive system.

  18. Estimates of Atmospheric Distortion Number for Nonlinear Refraction

    National Research Council Canada - National Science Library

    Roadcap, J. R; McNicholl, P. J; Beland, R. R; Jumper, G. Y

    2007-01-01

    A characteristic nondimensional distortion number Nd was derived in the 1970s that allows inference of the degree of nonlinear refraction or thermal blooming associated with an atmospheric laser path...

  19. SBS [stimulated Brillouin scattering] pulse distortion in multimode optical fibers

    International Nuclear Information System (INIS)

    Smith, J.R.; Hawkins, R.J.; Laumann, C.W.; Hatch, J.

    1989-01-01

    We have observed sever temporal-pulse-shape distortion due to stimulated Brillouin scattering (SBS) in multimode optical fibers used to diagnose 351 m laser pulses on the Nova laser system. Our measurements can be fit by a basic model of SBS and provide a clear indication of the intensity and temporal regimes where significant SBS-induced temporal-pulse-shape distortion can be avoided. 15 refs., 3 figs., 1 tab

  20. Reactivity analysis of core distortion effects in the FFTF

    International Nuclear Information System (INIS)

    Knutson, B.J.

    1982-01-01

    An improved technique for evaluating core distortion reactivity effects was developed using reactivity analyses of two core geometry models (R-Z and HEX). This technique is incorporated into a new processor code called CORDIS. The advantages of this technique over existing reactivity models are that is preserves core heterogeneity, provides a control rod insertion effect model, uses row-dependent axial shape functions, and provides a flexible and cost efficient core distortion reactivity analysis method

  1. Pulse Distortion in Saturated Fiber Optical Parametric Chirped Pulse Amplification

    DEFF Research Database (Denmark)

    Lali-Dastjerdi, Zohreh; Da Ros, Francesco; Rottwitt, Karsten

    2012-01-01

    Fiber optical parametric chirped pulse amplification is experimentally compared for different chirped pulses in the picosecond regime. The amplified chirped pulses show distortion appearing as pedestals after recompression when the amplifier is operated in saturation.......Fiber optical parametric chirped pulse amplification is experimentally compared for different chirped pulses in the picosecond regime. The amplified chirped pulses show distortion appearing as pedestals after recompression when the amplifier is operated in saturation....

  2. Distorted eikonal cross sections: A time-dependent view

    International Nuclear Information System (INIS)

    Turner, R.E.

    1982-01-01

    For Hamiltonians with two potentials, differential cross sections are written as time-correlation functions of reference and distorted transition operators. Distorted eikonal differential cross sections are defined in terms of straight-line and reference classical trajectories. Both elastic and inelastic results are obtained. Expressions for the inelastic cross sections are presented in terms of time-ordered cosine and sine memory functions through the use of the Zwanzig-Feshbach projection-operator method

  3. Correlation of lattice distortion with photocatalytic activity of titanium dioxide

    International Nuclear Information System (INIS)

    Wang Xia; Shui Miao; Li Rongsheng; Song Yue

    2008-01-01

    The photocatalytic activity of titanium dioxide dispersions on X-3B pigment degradation has been investigated. A variety of factors that would influence the photocatalytic activity such as crystallite size, lattice distortion, and anatase content are discussed in detail. It is found that lattice distortion is the most important one among these factors and is expected to inhibit the hole and electron pair recombination. It determines, to some extent, the photocatalytic efficiency of titanium dioxide dispersions

  4. Nonlinear distortion in wireless systems modeling and simulation with Matlab

    CERN Document Server

    Gharaibeh, Khaled M

    2011-01-01

    This book covers the principles of modeling and simulation of nonlinear distortion in wireless communication systems with MATLAB simulations and techniques In this book, the author describes the principles of modeling and simulation of nonlinear distortion in single and multichannel wireless communication systems using both deterministic and stochastic signals. Models and simulation methods of nonlinear amplifiers explain in detail how to analyze and evaluate the performance of data communication links under nonlinear amplification. The book addresses the analysis of nonlinear systems

  5. Elliptical Galaxies: Rotationally Distorted, After All

    Directory of Open Access Journals (Sweden)

    Caimmi, R.

    2009-12-01

    .15$, and low rotationparameters $(0lechi_v^2<0.15$, while fastrotators show large ellipticities $(0.2lehat{e}<0.65$, large anisotropy parameters$(0.15ledelta<0.35$, and large rotationparameters $(0.15lechi_v^2<0.5$. Analternative kinematic classification withrespect to earlier attempts (Emsellem etal. 2007 requires larger samples for providingadditional support to the above mentionedresults. A possible interpretation of slowrotators as nonrotating at all and elongated due to negative anisotropy parameters,instead of flattened due to positiveanisotropy parameters, is exploited.Finally, the elliptical side of the Hubblemorphological sequence is interpreted as asequence of equilibrium (adjoint configurations where the ellipticity is an increasing functionof the rotation parameter, slow rotators correspond to early classes (E0-E2 in the oblate limit and E2-E0 in the prolate limitand fast rotators to late classes (E3-E6.In this view, boundaries are rotationally distorted regardless of angular momentumand stress tensor, where rotation has tobe intended as due to additional kinetic energy of tangential equatorial velocity components,with respect to spherical configurations with isotropic stress tensor.

  6. Positioning the 5'-flap junction in the active site controls the rate of flap endonuclease-1-catalyzed DNA cleavage

    KAUST Repository

    Song, Bo

    2018-02-09

    Flap endonucleases catalyze cleavage of single-stranded DNA flaps formed during replication, repair and recombination, and are therefore essential for genome processing and stability. Recent crystal structures of DNA-bound human flap endonuclease (hFEN1) offer new insights into how conformational changes in the DNA and hFEN1 may facilitate the reaction mechanism. For example, previous biochemical studies of DNA conformation performed under non-catalytic conditions with Ca2+ have suggested that base unpairing at the 5\\'-flap:template junction is an important step in the reaction, but the new structural data suggest otherwise. To clarify the role of DNA changes in the kinetic mechanism, we measured a series of transient steps - from substrate binding to product release - during the hFEN1-catalyzed reaction in the presence of Mg2+. We found that while hFEN1 binds and bends DNA at a fast, diffusion-limited rate, much slower Mg2+-dependent conformational changes in DNA around the active site are subsequently necessary and rate-limiting for 5\\'-flap cleavage. These changes are reported overall by fluorescence of 2-aminopurine at the 5\\'-flap:template junction, indicating that local DNA distortion (e.g., disruption of base stacking observed in structures), associated with positioning the 5\\'-flap scissile phosphodiester bond in the hFEN1 active site, controls catalysis. hFEN1 residues with distinct roles in the catalytic mechanism, including those binding metal ions (Asp-34, Asp-181), steering the 5\\'-flap through the active site and binding the scissile phosphate (Lys-93, Arg-100), and stacking against the base 5\\' to the scissile phosphate (Tyr-40), all contribute to these rate-limiting conformational changes, ensuring efficient and specific cleavage of 5\\'-flaps.

  7. Positioning the 5'-flap junction in the active site controls the rate of flap endonuclease-1-catalyzed DNA cleavage

    KAUST Repository

    Song, Bo; Hamdan, Samir; Hingorani, Manju M

    2018-01-01

    Flap endonucleases catalyze cleavage of single-stranded DNA flaps formed during replication, repair and recombination, and are therefore essential for genome processing and stability. Recent crystal structures of DNA-bound human flap endonuclease (hFEN1) offer new insights into how conformational changes in the DNA and hFEN1 may facilitate the reaction mechanism. For example, previous biochemical studies of DNA conformation performed under non-catalytic conditions with Ca2+ have suggested that base unpairing at the 5'-flap:template junction is an important step in the reaction, but the new structural data suggest otherwise. To clarify the role of DNA changes in the kinetic mechanism, we measured a series of transient steps - from substrate binding to product release - during the hFEN1-catalyzed reaction in the presence of Mg2+. We found that while hFEN1 binds and bends DNA at a fast, diffusion-limited rate, much slower Mg2+-dependent conformational changes in DNA around the active site are subsequently necessary and rate-limiting for 5'-flap cleavage. These changes are reported overall by fluorescence of 2-aminopurine at the 5'-flap:template junction, indicating that local DNA distortion (e.g., disruption of base stacking observed in structures), associated with positioning the 5'-flap scissile phosphodiester bond in the hFEN1 active site, controls catalysis. hFEN1 residues with distinct roles in the catalytic mechanism, including those binding metal ions (Asp-34, Asp-181), steering the 5'-flap through the active site and binding the scissile phosphate (Lys-93, Arg-100), and stacking against the base 5' to the scissile phosphate (Tyr-40), all contribute to these rate-limiting conformational changes, ensuring efficient and specific cleavage of 5'-flaps.

  8. Two dimensional spatial distortion correction algorithm for scintillation GAMMA cameras

    International Nuclear Information System (INIS)

    Chaney, R.; Gray, E.; Jih, F.; King, S.E.; Lim, C.B.

    1985-01-01

    Spatial distortion in an Anger gamma camera originates fundamentally from the discrete nature of scintillation light sampling with an array of PMT's. Historically digital distortion correction started with the method based on the distortion measurement by using 1-D slit pattern and the subsequent on-line bi-linear approximation with 64 x 64 look-up tables for X and Y. However, the X, Y distortions are inherently two-dimensional in nature, and thus the validity of this 1-D calibration method becomes questionable with the increasing distortion amplitude in association with the effort to get better spatial and energy resolutions. The authors have developed a new accurate 2-D correction algorithm. This method involves the steps of; data collection from 2-D orthogonal hole pattern, 2-D distortion vector measurement, 2-D Lagrangian polynomial interpolation, and transformation to X, Y ADC frame. The impact of numerical precision used in correction and the accuracy of bilinear approximation with varying look-up table size have been carefully examined through computer simulation by using measured single PMT light response function together with Anger positioning logic. Also the accuracy level of different order Lagrangian polynomial interpolations for correction table expansion from hole centroids were investigated. Detailed algorithm and computer simulation are presented along with camera test results

  9. Economic choices reveal probability distortion in macaque monkeys.

    Science.gov (United States)

    Stauffer, William R; Lak, Armin; Bossaerts, Peter; Schultz, Wolfram

    2015-02-18

    Economic choices are largely determined by two principal elements, reward value (utility) and probability. Although nonlinear utility functions have been acknowledged for centuries, nonlinear probability weighting (probability distortion) was only recently recognized as a ubiquitous aspect of real-world choice behavior. Even when outcome probabilities are known and acknowledged, human decision makers often overweight low probability outcomes and underweight high probability outcomes. Whereas recent studies measured utility functions and their corresponding neural correlates in monkeys, it is not known whether monkeys distort probability in a manner similar to humans. Therefore, we investigated economic choices in macaque monkeys for evidence of probability distortion. We trained two monkeys to predict reward from probabilistic gambles with constant outcome values (0.5 ml or nothing). The probability of winning was conveyed using explicit visual cues (sector stimuli). Choices between the gambles revealed that the monkeys used the explicit probability information to make meaningful decisions. Using these cues, we measured probability distortion from choices between the gambles and safe rewards. Parametric modeling of the choices revealed classic probability weighting functions with inverted-S shape. Therefore, the animals overweighted low probability rewards and underweighted high probability rewards. Empirical investigation of the behavior verified that the choices were best explained by a combination of nonlinear value and nonlinear probability distortion. Together, these results suggest that probability distortion may reflect evolutionarily preserved neuronal processing. Copyright © 2015 Stauffer et al.

  10. Quantitive DNA Fiber Mapping

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Chun-Mei; Wang, Mei; Greulich-Bode, Karin M.; Weier, Jingly F.; Weier, Heinz-Ulli G.

    2008-01-28

    Several hybridization-based methods used to delineate single copy or repeated DNA sequences in larger genomic intervals take advantage of the increased resolution and sensitivity of free chromatin, i.e., chromatin released from interphase cell nuclei. Quantitative DNA fiber mapping (QDFM) differs from the majority of these methods in that it applies FISH to purified, clonal DNA molecules which have been bound with at least one end to a solid substrate. The DNA molecules are then stretched by the action of a receding meniscus at the water-air interface resulting in DNA molecules stretched homogeneously to about 2.3 kb/{micro}m. When non-isotopically, multicolor-labeled probes are hybridized to these stretched DNA fibers, their respective binding sites are visualized in the fluorescence microscope, their relative distance can be measured and converted into kilobase pairs (kb). The QDFM technique has found useful applications ranging from the detection and delineation of deletions or overlap between linked clones to the construction of high-resolution physical maps to studies of stalled DNA replication and transcription.

  11. Flexible 2D Crystals of Polycyclic Aromatics Stabilized by Static Distortion Waves.

    Science.gov (United States)

    Meissner, Matthias; Sojka, Falko; Matthes, Lars; Bechstedt, Friedhelm; Feng, Xinliang; Müllen, Klaus; Mannsfeld, Stefan C B; Forker, Roman; Fritz, Torsten

    2016-07-26

    The epitaxy of many organic films on inorganic substrates can be classified within the framework of rigid lattices which helps to understand the origin of energy gain driving the epitaxy of the films. Yet, there are adsorbate-substrate combinations with distinct mutual orientations for which this classification fails and epitaxy cannot be explained within a rigid lattice concept. It has been proposed that tiny shifts in atomic positions away from ideal lattice points, so-called static distortion waves (SDWs), are responsible for the observed orientational epitaxy in such cases. Using low-energy electron diffraction and scanning tunneling microscopy, we provide direct experimental evidence for SDWs in organic adsorbate films, namely hexa-peri-hexabenzocoronene on graphite. They manifest as wave-like sub-Ångström molecular displacements away from an ideal adsorbate lattice which is incommensurate with graphite. By means of a density-functional-theory based model, we show that, due to the flexibility in the adsorbate layer, molecule-substrate energy is gained by straining the intermolecular bonds and that the resulting total energy is minimal for the observed domain orientation, constituting the orientational epitaxy. While structural relaxation at an interface is a common assumption, the combination of the precise determination of the incommensurate epitaxial relation, the direct observation of SDWs in real space, and their identification as the sole source of epitaxial energy gain constitutes a comprehensive proof of this effect.

  12. Cognitive distortions among older adult gamblers in an Asian context.

    Directory of Open Access Journals (Sweden)

    Mythily Subramaniam

    Full Text Available The study aims to describe the construct of cognitive distortions based on the narratives of older adult gamblers (aged 60 years and above in Singapore.Singapore residents (citizens or permanent residents aged 60 years and above, who were current or past regular gamblers were included in the study. Participants were recruited using a combination of venue based approach, referrals from service providers as well as by snowball sampling. In all, 25 in-depth interviews were conducted with older adult gamblers. The six-step thematic network analysis methodology was adopted for data analysis.The mean age of the participants was 66.2 years. The majority were male (n = 18, of Chinese ethnicity (n = 16, with a mean age of gambling initiation at 24.5 years. Among older adult gamblers, cognitive distortions emerged as a significant global theme comprising three organizing themes-illusion of control, probability control and interpretive control. The organizing themes comprised nine basic themes: perception of gambling as a skill, near miss, concept of luck, superstitious beliefs, entrapment, gambler's fallacy, chasing wins, chasing losses, and beliefs that wins are more than losses.Cognitive distortions were endorsed by all gamblers in the current study and were shown to play a role in both maintaining and escalating the gambling behaviour. While the surface characteristics of the distortions had a culture-specific appearance, the deeper characteristics of the distortions may in fact be more universal than previously thought. Future research must include longitudinal studies to understand causal relationships between cognitive distortions and gambling as well as the role of culture-specific distortions both in the maintenance and treatment of the disorder.

  13. DNA stable-isotope probing (DNA-SIP).

    Science.gov (United States)

    Dunford, Eric A; Neufeld, Josh D

    2010-08-02

    DNA stable-isotope probing (DNA-SIP) is a powerful technique for identifying active microorganisms that assimilate particular carbon substrates and nutrients into cellular biomass. As such, this cultivation-independent technique has been an important methodology for assigning metabolic function to the diverse communities inhabiting a wide range of terrestrial and aquatic environments. Following the incubation of an environmental sample with stable-isotope labelled compounds, extracted nucleic acid is subjected to density gradient ultracentrifugation and subsequent gradient fractionation to separate nucleic acids of differing densities. Purification of DNA from cesium chloride retrieves labelled and unlabelled DNA for subsequent molecular characterization (e.g. fingerprinting, microarrays, clone libraries, metagenomics). This JoVE video protocol provides visual step-by-step explanations of the protocol for density gradient ultracentrifugation, gradient fractionation and recovery of labelled DNA. The protocol also includes sample SIP data and highlights important tips and cautions that must be considered to ensure a successful DNA-SIP analysis.

  14. Efficient Sleeping Beauty DNA Transposition From DNA Minicircles

    Directory of Open Access Journals (Sweden)

    Nynne Sharma

    2013-01-01

    Full Text Available DNA transposon-based vectors have emerged as new potential delivery tools in therapeutic gene transfer. Such vectors are now showing promise in hematopoietic stem cells and primary human T cells, and clinical trials with transposon-engineered cells are on the way. However, the use of plasmid DNA as a carrier of the vector raises safety concerns due to the undesirable administration of bacterial sequences. To optimize vectors based on the Sleeping Beauty (SB DNA transposon for clinical use, we examine here SB transposition from DNA minicircles (MCs devoid of the bacterial plasmid backbone. Potent DNA transposition, directed by the hyperactive SB100X transposase, is demonstrated from MC donors, and the stable transfection rate is significantly enhanced by expressing the SB100X transposase from MCs. The stable transfection rate is inversely related to the size of circular donor, suggesting that a MC-based SB transposition system benefits primarily from an increased cellular uptake and/or enhanced expression which can be observed with DNA MCs. DNA transposon and transposase MCs are easily produced, are favorable in size, do not carry irrelevant DNA, and are robust substrates for DNA transposition. In accordance, DNA MCs should become a standard source of DNA transposons not only in therapeutic settings but also in the daily use of the SB system.

  15. Genome instabilities arising from ribonucleotides in DNA.

    Science.gov (United States)

    Klein, Hannah L

    2017-08-01

    Genomic DNA is transiently contaminated with ribonucleotide residues during the process of DNA replication through misincorporation by the replicative DNA polymerases α, δ and ε, and by the normal replication process on the lagging strand, which uses RNA primers. These ribonucleotides are efficiently removed during replication by RNase H enzymes and the lagging strand synthesis machinery. However, when ribonucleotides remain in DNA they can distort the DNA helix, affect machineries for DNA replication, transcription and repair, and can stimulate genomic instabilities which are manifest as increased mutation, recombination and chromosome alterations. The genomic instabilities associated with embedded ribonucleotides are considered here, along with a discussion of the origin of the lesions that stimulate particular classes of instabilities. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Standard test method for measurement of roll wave optical distortion in heat-treated flat glass

    CERN Document Server

    American Society for Testing and Materials. Philadelphia

    2008-01-01

    1.1 This test method is applicable to the determination of the peak-to-valley depth and peak-to-peak distances of the out-of-plane deformation referred to as roll wave which occurs in flat, heat-treated architectural glass substrates processed in a heat processing continuous or oscillating conveyance oven. 1.2 The values stated in inch-pound units are to be regarded as standard. The values given in parentheses are mathematical conversions to SI units that are provided for information only and are not considered standard. 1.3 This test method does not address other flatness issues like edge kink, ream, pocket distortion, bow, or other distortions outside of roll wave as defined in this test method. 1.4 This standard does not purport to address all of the safety concerns, if any, associated with its use. It is the responsibility of the user of this standard to establish appropriate safety and health practices and determine the applicability of regulatory limitations prior to use.

  17. Distortion definition and correction in off-axis systems

    Science.gov (United States)

    Da Deppo, Vania; Simioni, Emanuele; Naletto, Giampiero; Cremonese, Gabriele

    2015-09-01

    Off-axis optical configurations are becoming more and more used in a variety of applications, in particular they are the most preferred solution for cameras devoted to Solar System planets and small bodies (i.e. asteroids and comets) study. Off-axis designs, being devoid of central obstruction, are able to guarantee better PSF and MTF performance, and thus higher contrast imaging capabilities with respect to classical on-axis designs. In particular they are suitable for observing extended targets with intrinsic low contrast features, or scenes where a high dynamical signal range is present. Classical distortion theory is able to well describe the performance of the on-axis systems, but it has to be adapted for the off-axis case. A proper way to deal with off-axis distortion definition is thus needed together with dedicated techniques to accurately measure and hence remove the distortion effects present in the acquired images. In this paper, a review of the distortion definition for off-axis systems will be given. In particular the method adopted by the authors to deal with the distortion related issues (definition, measure, removal) in some off-axis instruments will be described in detail.

  18. Distortion-Based Link Adaptation for Wireless Video Transmission

    Directory of Open Access Journals (Sweden)

    Andrew Nix

    2008-06-01

    Full Text Available Wireless local area networks (WLANs such as IEEE 802.11a/g utilise numerous transmission modes, each providing different throughputs and reliability levels. Most link adaptation algorithms proposed in the literature (i maximise the error-free data throughput, (ii do not take into account the content of the data stream, and (iii rely strongly on the use of ARQ. Low-latency applications, such as real-time video transmission, do not permit large numbers of retransmission. In this paper, a novel link adaptation scheme is presented that improves the quality of service (QoS for video transmission. Rather than maximising the error-free throughput, our scheme minimises the video distortion of the received sequence. With the use of simple and local rate distortion measures and end-to-end distortion models at the video encoder, the proposed scheme estimates the received video distortion at the current transmission rate, as well as on the adjacent lower and higher rates. This allows the system to select the link-speed which offers the lowest distortion and to adapt to the channel conditions. Simulation results are presented using the MPEG-4/AVC H.264 video compression standard over IEEE 802.11g. The results show that the proposed system closely follows the optimum theoretic solution.

  19. Distortion of digital panoramic radiographs used for implant site assessment

    Directory of Open Access Journals (Sweden)

    Rayyan Abdulhamid Kayal

    2016-01-01

    Full Text Available Aims: This study is conducted to determine the amount of distortion of digital panoramic radiographs. Materials and Methods: Panoramic radiographs of all patients who received dental implants in the years 2012 and 2013 were selected from the records at the faculty of dentistry, King Abdulaziz University. Radiographs were analyzed using the R4 Kodak Software for linear measurements of implants length and width. The measurements were compared to the actual size of the implant, and the amount of distortion was calculated. Results: A total of 169 implants were analyzed. Horizontally, there was a statistically significant increase of 0.4 mm in width in the radiographic measurement compared to the actual size in the incisor region. Vertically, the sample overall exhibited a decrease by 0.4 mm compared to the actual size. Incisors had the highest difference with a decrease of 1.7 mm in the radiographic measurements compared to actual size. The highest distortion was found in the incisor region for both diameter and length (1.1 and 0.86, respectively. Conclusion: Digital panoramic radiographs show minimal to no distortion. The highest distortion is found in the anterior area.

  20. Accuracy evaluation of optical distortion calibration by digital image correlation

    Science.gov (United States)

    Gao, Zeren; Zhang, Qingchuan; Su, Yong; Wu, Shangquan

    2017-11-01

    Due to its convenience of operation, the camera calibration algorithm, which is based on the plane template, is widely used in image measurement, computer vision and other fields. How to select a suitable distortion model is always a problem to be solved. Therefore, there is an urgent need for an experimental evaluation of the accuracy of camera distortion calibrations. This paper presents an experimental method for evaluating camera distortion calibration accuracy, which is easy to implement, has high precision, and is suitable for a variety of commonly used lens. First, we use the digital image correlation method to calculate the in-plane rigid body displacement field of an image displayed on a liquid crystal display before and after translation, as captured with a camera. Next, we use a calibration board to calibrate the camera to obtain calibration parameters which are used to correct calculation points of the image before and after deformation. The displacement field before and after correction is compared to analyze the distortion calibration results. Experiments were carried out to evaluate the performance of two commonly used industrial camera lenses for four commonly used distortion models.

  1. Complex DNA structures and structures of DNA complexes

    International Nuclear Information System (INIS)

    Chazin, W.J.; Carlstroem, G.; Shiow-Meei Chen; Miick, S.; Gomez-Paloma, L.; Smith, J.; Rydzewski, J.

    1994-01-01

    Complex DNA structures (for example, triplexes, quadruplexes, junctions) and DNA-ligand complexes are more difficult to study by NMR than standard DNA duplexes are because they have high molecular weights, show nonstandard or distorted local conformations, and exhibit large resonance linewidths and severe 1 H spectral overlap. These systems also tend to have limited solubility and may require specialized solution conditions to maintain favorable spectral characteristics, which adds to the spectroscopic difficulties. Furthermore, with more atoms in the system, both assignment and structure calculation become more challenging. In this article, we focus on demonstrating the current status of NMR studies of such systems and the limitations to further progress; we also indicate in what ways isotopic enrichment can be useful

  2. Complex DNA structures and structures of DNA complexes

    Energy Technology Data Exchange (ETDEWEB)

    Chazin, W.J.; Carlstroem, G.; Shiow-Meei Chen; Miick, S.; Gomez-Paloma, L.; Smith, J.; Rydzewski, J. [Scripps Research Institute, La Jolla, CA (United States)

    1994-12-01

    Complex DNA structures (for example, triplexes, quadruplexes, junctions) and DNA-ligand complexes are more difficult to study by NMR than standard DNA duplexes are because they have high molecular weights, show nonstandard or distorted local conformations, and exhibit large resonance linewidths and severe {sup 1}H spectral overlap. These systems also tend to have limited solubility and may require specialized solution conditions to maintain favorable spectral characteristics, which adds to the spectroscopic difficulties. Furthermore, with more atoms in the system, both assignment and structure calculation become more challenging. In this article, we focus on demonstrating the current status of NMR studies of such systems and the limitations to further progress; we also indicate in what ways isotopic enrichment can be useful.

  3. Efficient DNA ligation in DNA–RNA hybrid helices by Chlorella virus DNA ligase

    Science.gov (United States)

    Lohman, Gregory J. S.; Zhang, Yinhua; Zhelkovsky, Alexander M.; Cantor, Eric J.; Evans, Thomas C.

    2014-01-01

    Single-stranded DNA molecules (ssDNA) annealed to an RNA splint are notoriously poor substrates for DNA ligases. Herein we report the unexpectedly efficient ligation of RNA-splinted DNA by Chlorella virus DNA ligase (PBCV-1 DNA ligase). PBCV-1 DNA ligase ligated ssDNA splinted by RNA with kcat ≈ 8 x 10−3 s−1 and KM DNA ligase produced only 5′-adenylylated DNA with a 20-fold lower kcat and a KM ≈ 300 nM. The rate of ligation increased with addition of Mn2+, but was strongly inhibited by concentrations of NaCl >100 mM. Abortive adenylylation was suppressed at low ATP concentrations (8, leading to increased product yields. The ligation reaction was rapid for a broad range of substrate sequences, but was relatively slower for substrates with a 5′-phosphorylated dC or dG residue on the 3′ side of the ligation junction. Nevertheless, PBCV-1 DNA ligase ligated all sequences tested with 10-fold less enzyme and 15-fold shorter incubation times than required when using T4 DNA ligase. Furthermore, this ligase was used in a ligation-based detection assay system to show increased sensitivity over T4 DNA ligase in the specific detection of a target mRNA. PMID:24203707

  4. Repair of Clustered Damage and DNA Polymerase Iota.

    Science.gov (United States)

    Belousova, E A; Lavrik, O I

    2015-08-01

    Multiple DNA lesions occurring within one or two turns of the DNA helix known as clustered damage are a source of double-stranded DNA breaks, which represent a serious threat to the cells. Repair of clustered lesions is accomplished in several steps. If a clustered lesion contains oxidized bases, an individual DNA lesion is repaired by the base excision repair (BER) mechanism involving a specialized DNA polymerase after excising DNA damage. Here, we investigated DNA synthesis catalyzed by DNA polymerase iota using damaged DNA templates. Two types of DNA substrates were used as model DNAs: partial DNA duplexes containing breaks of different length, and DNA duplexes containing 5-formyluracil (5-foU) and uracil as a precursor of apurinic/apyrimidinic sites (AP) in opposite DNA strands. For the first time, we showed that DNA polymerase iota is able to catalyze DNA synthesis using partial DNA duplexes having breaks of different length as substrates. In addition, we found that DNA polymerase iota could catalyze DNA synthesis during repair of clustered damage via the BER system by using both undamaged and 5-foU-containing templates. We found that hPCNA (human proliferating cell nuclear antigen) increased efficacy of DNA synthesis catalyzed by DNA polymerase iota.

  5. An Exact Formula for Calculating Inverse Radial Lens Distortions

    Directory of Open Access Journals (Sweden)

    Pierre Drap

    2016-06-01

    Full Text Available This article presents a new approach to calculating the inverse of radial distortions. The method presented here provides a model of reverse radial distortion, currently modeled by a polynomial expression, that proposes another polynomial expression where the new coefficients are a function of the original ones. After describing the state of the art, the proposed method is developed. It is based on a formal calculus involving a power series used to deduce a recursive formula for the new coefficients. We present several implementations of this method and describe the experiments conducted to assess the validity of the new approach. Such an approach, non-iterative, using another polynomial expression, able to be deduced from the first one, can actually be interesting in terms of performance, reuse of existing software, or bridging between different existing software tools that do not consider distortion from the same point of view.

  6. Multiview Trajectory Mapping Using Homography with Lens Distortion Correction

    Directory of Open Access Journals (Sweden)

    Andrea Cavallaro

    2008-11-01

    Full Text Available We present a trajectory mapping algorithm for a distributed camera setting that is based on statistical homography estimation accounting for the distortion introduced by camera lenses. Unlike traditional approaches based on the direct linear transformation (DLT algorithm and singular value decomposition (SVD, the planar homography estimation is derived from renormalization. In addition to this, the algorithm explicitly introduces a correction parameter to account for the nonlinear radial lens distortion, thus improving the accuracy of the transformation. We demonstrate the proposed algorithm by generating mosaics of the observed scenes and by registering the spatial locations of moving objects (trajectories from multiple cameras on the mosaics. Moreover, we objectively compare the transformed trajectories with those obtained by SVD and least mean square (LMS methods on standard datasets and demonstrate the advantages of the renormalization and the lens distortion correction.

  7. Multiview Trajectory Mapping Using Homography with Lens Distortion Correction

    Directory of Open Access Journals (Sweden)

    Kayumbi Gabin

    2008-01-01

    Full Text Available Abstract We present a trajectory mapping algorithm for a distributed camera setting that is based on statistical homography estimation accounting for the distortion introduced by camera lenses. Unlike traditional approaches based on the direct linear transformation (DLT algorithm and singular value decomposition (SVD, the planar homography estimation is derived from renormalization. In addition to this, the algorithm explicitly introduces a correction parameter to account for the nonlinear radial lens distortion, thus improving the accuracy of the transformation. We demonstrate the proposed algorithm by generating mosaics of the observed scenes and by registering the spatial locations of moving objects (trajectories from multiple cameras on the mosaics. Moreover, we objectively compare the transformed trajectories with those obtained by SVD and least mean square (LMS methods on standard datasets and demonstrate the advantages of the renormalization and the lens distortion correction.

  8. Metering error quantification under voltage and current waveform distortion

    Science.gov (United States)

    Wang, Tao; Wang, Jia; Xie, Zhi; Zhang, Ran

    2017-09-01

    With integration of more and more renewable energies and distortion loads into power grid, the voltage and current waveform distortion results in metering error in the smart meters. Because of the negative effects on the metering accuracy and fairness, it is an important subject to study energy metering combined error. In this paper, after the comparing between metering theoretical value and real recorded value under different meter modes for linear and nonlinear loads, a quantification method of metering mode error is proposed under waveform distortion. Based on the metering and time-division multiplier principles, a quantification method of metering accuracy error is proposed also. Analyzing the mode error and accuracy error, a comprehensive error analysis method is presented which is suitable for new energy and nonlinear loads. The proposed method has been proved by simulation.

  9. Lepton asymmetry, neutrino spectral distortions, and big bang nucleosynthesis

    Science.gov (United States)

    Grohs, E.; Fuller, George M.; Kishimoto, C. T.; Paris, Mark W.

    2017-03-01

    We calculate Boltzmann neutrino energy transport with self-consistently coupled nuclear reactions through the weak-decoupling-nucleosynthesis epoch in an early universe with significant lepton numbers. We find that the presence of lepton asymmetry enhances processes which give rise to nonthermal neutrino spectral distortions. Our results reveal how asymmetries in energy and entropy density uniquely evolve for different transport processes and neutrino flavors. The enhanced distortions in the neutrino spectra alter the expected big bang nucleosynthesis light element abundance yields relative to those in the standard Fermi-Dirac neutrino distribution cases. These yields, sensitive to the shapes of the neutrino energy spectra, are also sensitive to the phasing of the growth of distortions and entropy flow with time/scale factor. We analyze these issues and speculate on new sensitivity limits of deuterium and helium to lepton number.

  10. Time distortion for expert and novice online game players.

    Science.gov (United States)

    Rau, Pei-Luen Patrick; Peng, Shu-Yun; Yang, Chin-Chow

    2006-08-01

    Online game addiction is a new mental disorder. This disorder is difficult to describe because of its comprehensive nature. Many online game players have problems controlling their playing time. They cannot stop playing a game that they enjoy. This research surveyed the past literature on "flow" and time disorder theory. A time distortion experiment was conducted. This research invited 64 children, teenagers, and young adults to investigate player skill and playing time effects on online game break-off. The playing experience and degree of time distortion were measured and analyzed. The results showed that both novice and expert online game players were subject to time distortion. The participants had difficulty breaking off from the game without intrusion by others in the real world. This research also suggests eight questions for self-evaluation for online game addiction.

  11. Geometrical theory of nonlinear phase distortion of intense laser beams

    International Nuclear Information System (INIS)

    Glaze, J.A.; Hunt, J.T.; Speck, D.R.

    1975-01-01

    Phase distortion arising from whole beam self-focusing of intense laser pulses with arbitrary spatial profiles is treated in the limit of geometrical optics. The constant shape approximation is used to obtain the phase and angular distribution of the geometrical rays in the near field. Conditions for the validity of this approximation are discussed. Geometrical focusing of the aberrated beam is treated for the special case of a beam with axial symmetry. Equations are derived that show both the shift of the focus and the distortion of the intensity distribution that are caused by the nonlinear index of refraction of the optical medium. An illustrative example treats the case of beam distortion in a Nd:Glass amplifier

  12. Distorted Images of Islam: The Case of Former Yugoslavia

    Directory of Open Access Journals (Sweden)

    Fikret Karčić

    1995-12-01

    Full Text Available Since the 1980s, the former Yugoslavia has witnessed increasing distortion of images of Islam in academic publications, media, and public life. This process has been connected with the changes in power structure in Serbia, and with the new ideological orientation of the Serbian leadership which opted for national exclusivism (ethno fascism. The Muslims have been portrayed as a threat to the realization of the Serbian hegemonist project. In order to mobilize domestic public opinion against the Muslims and to justify future acts against them in the eyes of the West, the Serbian leadership needed an image of Islam as a totalitarian, inherently violent, and culturally alien system on European soil. Such a distorted image has been provided by some influential Serbian orientalists, the Orthodox Church, and some historians. Due to these distortions, these Serbian intellectual circles have become accomplices in the crimes committed against the Muslims in former Yugoslavia during 1992-1995.

  13. Testing inflation and curvaton scenarios with CMB distortions

    International Nuclear Information System (INIS)

    Clesse, Sébastien; Garbrecht, Björn; Zhu, Yi

    2014-01-01

    Prior to recombination, Silk damping causes the dissipation of energy from acoustic waves into the monopole of the Cosmic Microwave Background (CMB), resulting in spectral distortions. These can be used to probe the primordial scalar power spectrum on smaller scales than it is possible with CMB anisotropies. An enhancement of power on these scales is nevertheless required for the resulting distortions to be detectable by future experiments like PIXIE. In this paper, we examine all 49 single-field inflation models listed by Martin et al. in the Encyclopaedia Inflationaris [1] and find that only one of these may lead to a detectable level of distortions in a tuned region of its parameter space, namely the original hybrid model. Three effective multi-field scenarios are also studied: with softly and suddenly turning trajectories, and with a mild waterfall trajectory. Softly turning trajectories do not induce distortions at any detectable level, whereas a sudden turn in the field space or a mild waterfall trajectory predicts a peak (plus damped oscillations in the sudden turn case) in the scalar power spectrum, which can lead to an observable amount of CMB distortions. Finally, another scenario leading to potentially detectable distortions involves a curvaton whose blue spectrum is subdominant on CMB angular scales and overtakes the inflaton spectrum on smaller scales. In this case however, we show that the bounds from ultra compact minihaloes are not satisfied. Expectations for an ultimate PRISM-class experiment characterized by an improvement in sensitivity by a factor of ten are discussed for some models

  14. Testing inflation and curvaton scenarios with CMB distortions

    Science.gov (United States)

    Clesse, Sébastien; Garbrecht, Björn; Zhu, Yi

    2014-10-01

    Prior to recombination, Silk damping causes the dissipation of energy from acoustic waves into the monopole of the Cosmic Microwave Background (CMB), resulting in spectral distortions. These can be used to probe the primordial scalar power spectrum on smaller scales than it is possible with CMB anisotropies. An enhancement of power on these scales is nevertheless required for the resulting distortions to be detectable by future experiments like PIXIE. In this paper, we examine all 49 single-field inflation models listed by Martin et al. in the Encyclopaedia Inflationaris [1] and find that only one of these may lead to a detectable level of distortions in a tuned region of its parameter space, namely the original hybrid model. Three effective multi-field scenarios are also studied: with softly and suddenly turning trajectories, and with a mild waterfall trajectory. Softly turning trajectories do not induce distortions at any detectable level, whereas a sudden turn in the field space or a mild waterfall trajectory predicts a peak (plus damped oscillations in the sudden turn case) in the scalar power spectrum, which can lead to an observable amount of CMB distortions. Finally, another scenario leading to potentially detectable distortions involves a curvaton whose blue spectrum is subdominant on CMB angular scales and overtakes the inflaton spectrum on smaller scales. In this case however, we show that the bounds from ultra compact minihaloes are not satisfied. Expectations for an ultimate PRISM-class experiment characterized by an improvement in sensitivity by a factor of ten are discussed for some models.

  15. Anisotropic extinction distortion of the galaxy correlation function

    International Nuclear Information System (INIS)

    Fang Wenjuan; Hui Lam; Menard, Brice; May, Morgan; Scranton, Ryan

    2011-01-01

    Similar to the magnification of the galaxies' fluxes by gravitational lensing, the extinction of the fluxes by comic dust, whose existence is recently detected by [B. Menard, R. Scranton, M. Fukugita, and G. Richards, Mon. Not. R. Astron. Soc. 405, 1025 (2010).], also modifies the distribution of a flux-selected galaxy sample. We study the anisotropic distortion by dust extinction to the 3D galaxy correlation function, including magnification bias and redshift distortion at the same time. We find the extinction distortion is most significant along the line of sight and at large separations, similar to that by magnification bias. The correction from dust extinction is negative except at sufficiently large transverse separations, which is almost always opposite to that from magnification bias (we consider a number count slope s>0.4). Hence, the distortions from these two effects tend to reduce each other. At low z (< or approx. 1), the distortion by extinction is stronger than that by magnification bias, but at high z, the reverse holds. We also study how dust extinction affects probes in real space of the baryon acoustic oscillations (BAO) and the linear redshift distortion parameter β. We find its effect on BAO is negligible. However, it introduces a positive scale-dependent correction to β that can be as large as a few percent. At the same time, we also find a negative scale-dependent correction from magnification bias, which is up to percent level at low z, but to ∼40% at high z. These corrections are non-negligible for precision cosmology, and should be considered when testing General Relativity through the scale-dependence of β.

  16. DNA-mediated self-assembly of carbon nanotubes on gold

    International Nuclear Information System (INIS)

    Sanchez-Pomales, Germarie; Rivera-Velez, Nelson E; Cabrera, Carlos R

    2007-01-01

    This report presents the use of disulfide-modified single-stranded DNA (ssDNA) to form DNA self-assembled monolayers (SAMs) and mixed DNA-carbon nanotube (CNT) hybrids SAMs on gold substrates. Mixed DNA-CNT SAMs are composed of DNA, mercaptohexanol (MCH) and DNA-CNT aggregates. Both, DNA-CNT and DNA areas of the mixed SAMs were analyzed and compared to traditional DNA SAMs. The results suggest the formation of a more compact and densely packed monolayer of DNA-CNT in comparison with DNA. The use of DNA-CNT hybrids to form SAMs on gold substrates might represent a new approach to improve the immobilization of DNA strands on gold, and might therefore help with the development of enhanced DNA sensors

  17. Coil extensions improve line shapes by removing field distortions

    Science.gov (United States)

    Conradi, Mark S.; Altobelli, Stephen A.; McDowell, Andrew F.

    2018-06-01

    The static magnetic susceptibility of the rf coil can substantially distort the field B0 and be a dominant source of line broadening. A scaling argument shows that this may be a particular problem in microcoil NMR. We propose coil extensions to reduce the distortion. The actual rf coil is extended to a much longer overall length by abutted coil segments that do not carry rf current. The result is a long and nearly uniform sheath of copper wire, in terms of the static susceptibility. The line shape improvement is demonstrated at 43.9 MHz and in simulation calculations.

  18. Analytical evaluation of nonlinear distortion effects on multicarrier signals

    CERN Document Server

    Araújo, Theresa

    2015-01-01

    Due to their ability to support reliable high quality of service as well as spectral and power efficiency, multicarrier modulation systems have found increasing use in modern communications services. However, one of the main drawbacks of these systems is their vulnerability to nonlinear distortion effects. Analytical Evaluation of Nonlinear Distortion Effects on Multicarrier Signals details a unified approach to well-known analytical results on memoryless nonlinearities that takes advantage of the Gaussian behavior of multicarrier signals.Sharing new insights into the behavior of nonlinearly d

  19. Visualization and spectral synthesis of rotationally distorted stars

    International Nuclear Information System (INIS)

    Dall, T H; Sbordone, L

    2011-01-01

    Simple spherical, non-rotating stellar models are inadequate when describing real stars in the limit of very fast rotation: Both the observable spectrum and the geometrical shape of the star deviate strongly from simple models. We attempt to approach the problem of modeling geometrically distorted, rapidly rotating stars from a new angle: By constructing distorted geometrical models and integrating standard stellar models with varying temperature, gravity, and abundances, over the entire surface, we attempt a semi-empirical approach to modeling. Here we present our methodology, and present simple examples of applications.

  20. Sudden distortion of turbulence at a forest edge

    DEFF Research Database (Denmark)

    Mann, Jakob; Dellwik, Ebba

    2014-01-01

    Dellwik et al. (2013) presented data from a forest edge experiment based on two meteorological towers instrumented with sonic anemometers. The experiment was performed at a dense edge of the Tromnæs Forest, which is a 24 m tall mature beech stand on the island Falster, Denmark. The topography...... in the lateral variance, whereas the streamwise variance remained approximately constant. This result is in contrast to the predictions by homogeneous rapid distortion theory. We apply and develop an alternative framework based on inhomogeneous rapid distortion theory, also called blocking, in combination...

  1. Information theory and rate distortion theory for communications and compression

    CERN Document Server

    Gibson, Jerry

    2013-01-01

    This book is very specifically targeted to problems in communications and compression by providing the fundamental principles and results in information theory and rate distortion theory for these applications and presenting methods that have proved and will prove useful in analyzing and designing real systems. The chapters contain treatments of entropy, mutual information, lossless source coding, channel capacity, and rate distortion theory; however, it is the selection, ordering, and presentation of the topics within these broad categories that is unique to this concise book. While the cover

  2. A method to correct coordinate distortion in EBSD maps

    DEFF Research Database (Denmark)

    Zhang, Yubin; Elbrønd, Andreas Benjamin; Lin, Fengxiang

    2014-01-01

    Drift during electron backscatter diffraction mapping leads to coordinate distortions in resulting orientation maps, which affects, in some cases significantly, the accuracy of analysis. A method, thin plate spline, is introduced and tested to correct such coordinate distortions in the maps after...... the electron backscatter diffraction measurements. The accuracy of the correction as well as theoretical and practical aspects of using the thin plate spline method is discussed in detail. By comparing with other correction methods, it is shown that the thin plate spline method is most efficient to correct...

  3. Temperature and distortion transients in gas tungsten-arc weldments

    International Nuclear Information System (INIS)

    Glickstein, S.S.; Friedman, E.

    1979-10-01

    An analysis and test program to develop a fundamental understanding of the gas tungsten-arc welding process has been undertaken at the Bettis Atomic Power Laboratory to develop techniques to determine and control the various welding parameters and weldment conditions so as to result in optimum weld response characteristics. These response characteristics include depth of penetration, weld bead configuration, weld bead sink and roll, distortion, and cracking sensitivity. The results are documented of that part of the program devoted to analytical and experimental investigations of temperatures, weld bead dimensions, and distortions for moving gas tungsten-arc welds applied to Alloy 600 plates

  4. Naked singularities are not singular in distorted gravity

    Energy Technology Data Exchange (ETDEWEB)

    Garattini, Remo, E-mail: Remo.Garattini@unibg.it [Università degli Studi di Bergamo, Facoltà di Ingegneria, Viale Marconi 5, 24044 Dalmine (Bergamo) (Italy); I.N.F.N. – sezione di Milano, Milan (Italy); Majumder, Barun, E-mail: barunbasanta@iitgn.ac.in [Indian Institute of Technology Gandhinagar, Ahmedabad, Gujarat 382424 (India)

    2014-07-15

    We compute the Zero Point Energy (ZPE) induced by a naked singularity with the help of a reformulation of the Wheeler–DeWitt equation. A variational approach is used for the calculation with Gaussian Trial Wave Functionals. The one loop contribution of the graviton to the ZPE is extracted keeping under control the UltraViolet divergences by means of a distorted gravitational field. Two examples of distortion are taken under consideration: Gravity's Rainbow and Noncommutative Geometry. Surprisingly, we find that the ZPE is no more singular when we approach the singularity.

  5. Naked singularities are not singular in distorted gravity

    Science.gov (United States)

    Garattini, Remo; Majumder, Barun

    2014-07-01

    We compute the Zero Point Energy (ZPE) induced by a naked singularity with the help of a reformulation of the Wheele-DeWitt equation. A variational approach is used for the calculation with Gaussian Trial Wave Functionals. The one loop contribution of the graviton to the ZPE is extracted keeping under control the UltraViolet divergences by means of a distorted gravitational field. Two examples of distortion are taken under consideration: Gravity's Rainbow and Noncommutative Geometry. Surprisingly, we find that the ZPE is no more singular when we approach the singularity.

  6. Naked singularities are not singular in distorted gravity

    International Nuclear Information System (INIS)

    Garattini, Remo; Majumder, Barun

    2014-01-01

    We compute the Zero Point Energy (ZPE) induced by a naked singularity with the help of a reformulation of the Wheeler–DeWitt equation. A variational approach is used for the calculation with Gaussian Trial Wave Functionals. The one loop contribution of the graviton to the ZPE is extracted keeping under control the UltraViolet divergences by means of a distorted gravitational field. Two examples of distortion are taken under consideration: Gravity's Rainbow and Noncommutative Geometry. Surprisingly, we find that the ZPE is no more singular when we approach the singularity

  7. Studies of radial distortions of the ATLAS Inner Detector

    CERN Document Server

    The ATLAS collaboration

    2018-01-01

    The measurement of the absolute momentum scale of charged particles provided by the ATLAS inner detector is affected by biases related to geometrical deformations which are not well constrained by the track-based alignment procedure. The focus of this note is on momentum biases related to radial distortions of the inner detector. The $J/\\psi$, $\\Upsilon$, and $Z$-boson resonances decaying into pairs of muons are used to study and quantify such radial distortions in the barrel region of the inner detector. The analysis is performed on data collected in 2016 during Run 2 of the Large Hadron Collider, and corresponding to 33 fb$^{-1}$ of integrated luminosity.

  8. Identification and control of harmonic distortions report on Furnas experience

    Energy Technology Data Exchange (ETDEWEB)

    Mantuano Filho, Salvatore; Medeiros, Jose Roberto de; Bezerra, Luiz Roberto; Oliveira, Denise Borges de; Praca, Antonio Augusto Souza; Paiva Fontes, Marco Antonio de; Marques, Luiz Carlos Borges C. [FURNAS, Rio de Janeiro, RJ (Brazil)

    1994-12-31

    This paper describes FURNAS experience on identification and control of harmonic distortions obtained from conservation of system operation and research for solutions. Special attention is paid to the harmonic overload observed at Ibiuna substation, the receiving end of the FURNAS HVDC transmission of the Itaipu 50 Hz energy, and the solutions that have been adopted. Methods of measurement and digital simulation have been developed and successfully tested so far. The present stage of those methods will be described. Not less important is the need for a specific legislation on harmonic distortion as explained in this paper. (author) 6 refs., 2 figs.

  9. Improved distorted wave theory with the localized virial conditions

    Science.gov (United States)

    Hahn, Y. K.; Zerrad, E.

    2009-12-01

    The distorted wave theory is operationally improved to treat the full collision amplitude, such that the corrections to the distorted wave Born amplitude can be systematically calculated. The localized virial conditions provide the tools necessary to test the quality of successive approximations at each stage and to optimize the solution. The details of the theoretical procedure are explained in concrete terms using a collisional ionization model and variational trial functions. For the first time, adjustable parameters associated with an approximate scattering solution can be fully determined by the theory. A small number of linear parameters are introduced to examine the convergence property and the effectiveness of the new approach.

  10. Contrast distortion induced by modulation voltage in scanning capacitance microscopy

    Science.gov (United States)

    Chang, M. N.; Hu, C. W.; Chou, T. H.; Lee, Y. J.

    2012-08-01

    With a dark-mode scanning capacitance microscopy (SCM), we directly observed the influence of SCM modulation voltage (MV) on image contrasts. For electrical junctions, an extensive modulated area induced by MV may lead to noticeable changes in the SCM signal phase and intensity, resulting in a narrowed junction image and a broadened carrier concentration profile. This contrast distortion in SCM images may occur even if the peak-to-peak MV is down to 0.3 V. In addition, MV may shift the measured electrical junction depth. The balance of SCM signals components explain these MV-induced contrast distortions.

  11. Sources of PCR-induced distortions in high-throughput sequencing data sets

    Science.gov (United States)

    Kebschull, Justus M.; Zador, Anthony M.

    2015-01-01

    PCR permits the exponential and sequence-specific amplification of DNA, even from minute starting quantities. PCR is a fundamental step in preparing DNA samples for high-throughput sequencing. However, there are errors associated with PCR-mediated amplification. Here we examine the effects of four important sources of error—bias, stochasticity, template switches and polymerase errors—on sequence representation in low-input next-generation sequencing libraries. We designed a pool of diverse PCR amplicons with a defined structure, and then used Illumina sequencing to search for signatures of each process. We further developed quantitative models for each process, and compared predictions of these models to our experimental data. We find that PCR stochasticity is the major force skewing sequence representation after amplification of a pool of unique DNA amplicons. Polymerase errors become very common in later cycles of PCR but have little impact on the overall sequence distribution as they are confined to small copy numbers. PCR template switches are rare and confined to low copy numbers. Our results provide a theoretical basis for removing distortions from high-throughput sequencing data. In addition, our findings on PCR stochasticity will have particular relevance to quantification of results from single cell sequencing, in which sequences are represented by only one or a few molecules. PMID:26187991

  12. Sensor Substrate Development

    Data.gov (United States)

    National Aeronautics and Space Administration — Novel substrates, such as aerogels and porous, low density ceramics may increase the sensitivities of chemical reaction-based sensors for toxic vapors. These sensors...

  13. Experimental Investigation of Inlet Distortion in a Multistage Axial Compressor

    Science.gov (United States)

    Rusu, Razvan

    The primary objective of this research is to present results and methodologies used to study total pressure inlet distortion in a multi-stage axial compressor environment. The study was performed at the Purdue 3-Stage Axial Compressor Facility (P3S) which models the final three stages of a production turbofan engine's high-pressure compressor (HPC). The goal of this study was twofold; first, to design, implement, and validate a circumferentially traversable total pressure inlet distortion generation system, and second, to demonstrate data acquisition methods to characterize the inter-stage total pressure flow fields to study the propagation and attenuation of a one-per-rev total pressure distortion. The datasets acquired for this study are intended to support the development and validation of novel computational tools and flow physics models for turbomachinery flow analysis. Total pressure inlet distortion was generated using a series of low-porosity wire gauze screens placed upstream of the compressor in the inlet duct. The screens are mounted to a rotatable duct section that can be precisely controlled. The P3S compressor features fixed instrumentation stations located at the aerodynamic interface plane (AIP) and downstream and upstream of each vane row. Furthermore, the compressor features individually indexable stator vanes which can be traverse by up to two vane passages. Using a series of coordinated distortion and vane traverses, the total pressure flow field at the AIP and subsequent inter-stage stations was characterized with a high circumferential resolution. The uniformity of the honeycomb carrier was demonstrated by characterizing the flow field at the AIP while no distortion screens where installed. Next, the distortion screen used for this study was selected following three iterations of porosity reduction. The selected screen consisted of a series of layered screens with a 100% radial extent and a 120° circumferential extent. A detailed total

  14. Anthraquinones quinizarin and danthron unwind negatively supercoiled DNA and lengthen linear DNA

    International Nuclear Information System (INIS)

    Verebová, Valéria; Adamcik, Jozef; Danko, Patrik; Podhradský, Dušan; Miškovský, Pavol; Staničová, Jana

    2014-01-01

    Highlights: • Anthraquinones quinizarin and danthron unwind negatively supercoiled DNA. • Anthraquinones quinizarin and danthron lengthen linear DNA. • Anthraquinones quinizarin and danthron possess middle binding affinity to DNA. • Anthraquinones quinizarin and danthron interact with DNA by intercalating mode. - Abstract: The intercalating drugs possess a planar aromatic chromophore unit by which they insert between DNA bases causing the distortion of classical B-DNA form. The planar tricyclic structure of anthraquinones belongs to the group of chromophore units and enables anthraquinones to bind to DNA by intercalating mode. The interactions of simple derivatives of anthraquinone, quinizarin (1,4-dihydroxyanthraquinone) and danthron (1,8-dihydroxyanthraquinone), with negatively supercoiled and linear DNA were investigated using a combination of the electrophoretic methods, fluorescence spectrophotometry and single molecule technique an atomic force microscopy. The detection of the topological change of negatively supercoiled plasmid DNA, unwinding of negatively supercoiled DNA, corresponding to appearance of DNA topoisomers with the low superhelicity and an increase of the contour length of linear DNA in the presence of quinizarin and danthron indicate the binding of both anthraquinones to DNA by intercalating mode

  15. Anthraquinones quinizarin and danthron unwind negatively supercoiled DNA and lengthen linear DNA

    Energy Technology Data Exchange (ETDEWEB)

    Verebová, Valéria [Institute of Biophysics, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice (Slovakia); Adamcik, Jozef [Food and Soft Materials Science, Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 9, CH-8092 Zürich (Switzerland); Danko, Patrik; Podhradský, Dušan [Department of Biochemistry, Institute of Chemistry, Faculty of Sciences, P.J. Šafárik University, Moyzesova 11, 041 54 Košice (Slovakia); Miškovský, Pavol [Department of Biophysics, Faculty of Sciences, P.J. Šafárik University, Jesenná 5, 041 54 Košice (Slovakia); Center for Interdisciplinary Biosciences, Faculty of Sciences, P.J. Šafárik University, Jesenná 5, 041 54 Košice (Slovakia); Staničová, Jana, E-mail: jana.stanicova@uvlf.sk [Institute of Biophysics, University of Veterinary Medicine and Pharmacy, Komenského 73, 041 81 Košice (Slovakia)

    2014-01-31

    Highlights: • Anthraquinones quinizarin and danthron unwind negatively supercoiled DNA. • Anthraquinones quinizarin and danthron lengthen linear DNA. • Anthraquinones quinizarin and danthron possess middle binding affinity to DNA. • Anthraquinones quinizarin and danthron interact with DNA by intercalating mode. - Abstract: The intercalating drugs possess a planar aromatic chromophore unit by which they insert between DNA bases causing the distortion of classical B-DNA form. The planar tricyclic structure of anthraquinones belongs to the group of chromophore units and enables anthraquinones to bind to DNA by intercalating mode. The interactions of simple derivatives of anthraquinone, quinizarin (1,4-dihydroxyanthraquinone) and danthron (1,8-dihydroxyanthraquinone), with negatively supercoiled and linear DNA were investigated using a combination of the electrophoretic methods, fluorescence spectrophotometry and single molecule technique an atomic force microscopy. The detection of the topological change of negatively supercoiled plasmid DNA, unwinding of negatively supercoiled DNA, corresponding to appearance of DNA topoisomers with the low superhelicity and an increase of the contour length of linear DNA in the presence of quinizarin and danthron indicate the binding of both anthraquinones to DNA by intercalating mode.

  16. The effect of polyamines on the photochemical reactivity of DNA

    International Nuclear Information System (INIS)

    Ben-Hur, E.; Hebrew Univ., Jerusalem

    1975-01-01

    The effects of diaminopentane (cadaverine), diaminoethane and the polyamine, spermine, on the photoreactions of 4,5', 8-trimethylpsoralen with DNA were studied. Near ultraviolet (UV) light (360 nm) irradiation of psoralen with DNA results in the formation of psoralen monoadducts with pyrimidine bases and DNA interstrand crosslinks. The polyamines studied reduced the rate of both photoreactions to the same extent by a factor of 1.5-2.0. The magnitude of the effect increased with polyamine concentration. Effectiveness was in the order spermine > cadaverine > diaminoethane. This is also the same order for stabilization of the DNA double-helix. Under conditions of higher DNA stability (higher ionic strength), higher polyamine concentrations were required to obtain an effect which was smaller than at low ionic strength. It is concluded that the photoreactions of psoralen with pyrimidines in DNA require some distortion of the double-helix. This distortion is made more difficult in the presence of stabilizing agents like polyamines and therefore the rate of the reaction is reduced. If crosslinking of DNA by psoralen is a two-step reaction then it must be concluded that the second step does not require further distortion. Consistently with the above, polyamines also reduced the UV-induced dimerization of thymine in DNA, although to a lesser extent. (author)

  17. The International Criminal Tribunal for Rwanda: A Distorting Mirror ...

    African Journals Online (AJOL)

    Angela

    certainly at work in Rwanda, where an estimated one million people from a ... See Office of the Press Secretary, The White House, US Efforts to Promote Human .... Part 2 of the article provides a tour d'horizon of Rwanda's history, aimed at bringing ..... misleading and distorts the overall vision and dialectics necessary for the.

  18. Body Dysmorphic Disorder: Easing the Distress of Distortion.

    Science.gov (United States)

    Fore, Cynthia M.

    People who suffer from body dysmorphic disorder believe that their body is defected and that this defect makes them ugly. Their distorted body image can be precipitated by many internal and external factors and as a result of their imagined defect, these normal-appearing individuals exhibit self-defeating behaviors. The disorder can lead to the…

  19. Alternative agricultural price distortions for CGE analysis, 2007 and 2011

    DEFF Research Database (Denmark)

    Jensen, Hans Grinsted; Anderson, Kym

    A recent World Bank research project has generated an annual time series of distortions to agricultural incentives over the past half century for 82 countries, the majority of which are low-and middle-income countries. In this memorandum, the current GTAP version 8 Data Base may be modified to in...

  20. A new interpretation of distortion artifacts in sweep measurements

    DEFF Research Database (Denmark)

    Torras Rosell, Antoni; Jacobsen, Finn

    2011-01-01

    The characterization of acoustical spaces by means of impulse response measurements is often biased by the nonlinear behavior of the loudspeaker used to excite the system under test. In this context the distortion immunity provided by the sweep technique has been investigated. The results show...

  1. Electromagnetic hammer removes weld distortions from aluminum tanks

    Science.gov (United States)

    Schwinghamer, R. J.

    1965-01-01

    Distortions around weld areas on sheet-aluminum tanks and other structures are removed with a portable electromagnetic hammer. The hammer incorporates a coil that generates a controlled high-energy pulsed magnetic field over localized areas on the metal surface.

  2. Effects of galvanic distortions on magnetotelluric data: Interpretation ...

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    But in the case of field data the problem is ... The distorted data set is corrected using the MT response for DRS model and further ... ments, the apparent resistivity and phase at differ- ... from the telluric field, which is of galvanic or inductive ...

  3. Phantom limb phenomenon as an example of body image distortion

    Directory of Open Access Journals (Sweden)

    Razmus Magdalena

    2017-06-01

    Full Text Available Introduction: The perception of one’s own body, its mental representation, and emotional attitude to it are the components of so-called “body image” [1]. The aim of the research was to analyse phantom pain and non-painful phantom sensations as results of limb loss and to explain them in terms of body image distortion.

  4. Distortion Estimation in Compressed Music Using Only Audio Fingerprints

    NARCIS (Netherlands)

    Doets, P.J.O.; Lagendijk, R.L.

    2008-01-01

    An audio fingerprint is a compact yet very robust representation of the perceptually relevant parts of an audio signal. It can be used for content-based audio identification, even when the audio is severely distorted. Audio compression changes the fingerprint slightly. We show that these small

  5. Mode distortion measurements on the Jefferson lab IR FEL

    CERN Document Server

    Benson, S V; Shinn, M

    2002-01-01

    We have previously reported on the analytical calculations of mirror distortion in a high-power FEL with a near-concentric cavity. This analysis allowed us to estimate the power level at which the FEL interaction would be affected, though no exact theory of FEL power vs. distortion exists at this point. Recently we have directly measured the mode size and beam quality as a function of power using a resonator with a center wavelength of 5 mu m. The resonator mirrors were calcium fluoride. This particular material exhibits a large amount of distortion for a given power but, due to the negative slope of refractive index vs. temperature, adds almost no optical phase distortion on the laser output. The mode in the cavity can thus be directly calculated from the measurements at the resonator output. The presence of angular jitter produced raw measurements inconsistent with cold cavity expectations. Removing the effects of the angular jitter, we derive results in agreement with cold cavity measurements. The result i...

  6. Analysis of tractable distortion metrics for EEG compression applications

    International Nuclear Information System (INIS)

    Bazán-Prieto, Carlos; Blanco-Velasco, Manuel; Cruz-Roldán, Fernando; Cárdenas-Barrera, Julián

    2012-01-01

    Coding distortion in lossy electroencephalographic (EEG) signal compression methods is evaluated through tractable objective criteria. The percentage root-mean-square difference, which is a global and relative indicator of the quality held by reconstructed waveforms, is the most widely used criterion. However, this parameter does not ensure compliance with clinical standard guidelines that specify limits to allowable noise in EEG recordings. As a result, expert clinicians may have difficulties interpreting the resulting distortion of the EEG for a given value of this parameter. Conversely, the root-mean-square error is an alternative criterion that quantifies distortion in understandable units. In this paper, we demonstrate that the root-mean-square error is better suited to control and to assess the distortion introduced by compression methods. The experiments conducted in this paper show that the use of the root-mean-square error as target parameter in EEG compression allows both clinicians and scientists to infer whether coding error is clinically acceptable or not at no cost for the compression ratio. (paper)

  7. Modeling Distortion Effects in Class-D Amplifier Filter Inductors

    DEFF Research Database (Denmark)

    Knott, Arnold; Stegenborg-Andersen, Tore; Thomsen, Ole Cornelius

    2010-01-01

    Distortion is generally accepted as a quantifier to judge the quality of audio power amplifiers. In switchmode power amplifiers various mechanisms influence this performance measure. After giving an overview of those, this paper focuses on the particular effect of the nonlinearity of the output f...

  8. Spectral Behavior of Weakly Compressible Aero-Optical Distortions

    Science.gov (United States)

    Mathews, Edwin; Wang, Kan; Wang, Meng; Jumper, Eric

    2016-11-01

    In classical theories of optical distortions by atmospheric turbulence, an appropriate and key assumption is that index-of-refraction variations are dominated by fluctuations in temperature and the effects of turbulent pressure fluctuations are negligible. This assumption is, however, not generally valid for aero-optical distortions caused by turbulent flow over an optical aperture, where both temperature and pressures fluctuations may contribute significantly to the index-of-refraction fluctuations. A general expression for weak fluctuations in refractive index is derived using the ideal gas law and Gladstone-Dale relation and applied to describe the spectral behavior of aero-optical distortions. Large-eddy simulations of weakly compressible, temporally evolving shear layers are then used to verify the theoretical results. Computational results support theoretical findings and confirm that if the log slope of the 1-D density spectrum in the inertial range is -mρ , the optical phase distortion spectral slope is given by - (mρ + 1) . The value of mρ is then shown to be dependent on the ratio of shear-layer free-stream densities and bounded by the spectral slopes of temperature and pressure fluctuations. Supported by HEL-JTO through AFOSR Grant FA9550-13-1-0001 and Blue Waters Graduate Fellowship Program.

  9. Effects Of Field Distortions In Ih-apf Linac

    CERN Document Server

    Kapin, Valery; Yamada, S

    2004-01-01

    The project on developing compact medical accelera-tors for the tumor therapy using carbon ions has been started at the National Institute of Radiological Sciences (NIRS). Alternating-phase-focused (APF) linac using an interdigital H-mode (IH) cavity has been proposed for the injector linac. The IH-cavity is doubly ridged circular resonator loaded by the drift-tubes mounted on ridges with supporting stems. The effects of intrinsic and random field distortions in a practical design of the 4-MeV/u 200 MHz IH-APF linac are considered. The intrinsic field distortions in IH-cavity are caused by the asymmetry of the gap field due to presence of the drift-tube supporting stems and pair of ridges. The random field distortions are caused by drift-tube misalignments and non-regular deviations of the voltage distribution from programmed law. The RF fields in IH-cavity have been calculated using Microwave Studio (MWS) code. The effects of field distortions on beam dynamics have been simulated numerically.

  10. Multiaxial ratcheting with advanced kinematic and directional distortional hardening rules

    Czech Academy of Sciences Publication Activity Database

    Feigenbaum, H. P.; Dugdale, J.; Dafalias, Y.F.; Kourousis, K. I.; Plešek, Jiří

    2012-01-01

    Roč. 49, č. 22 (2012), s. 3063-3076 ISSN 0020-7683 R&D Projects: GA MŠk(CZ) ME10024 Institutional research plan: CEZ:AV0Z20760514 Keywords : plasticity * directional distortional hardening * thermodynamics Subject RIV: JJ - Other Materials Impact factor: 1.871, year: 2012 http://www.sciencedirect.com/science/article/pii/S0020768312002612

  11. Determination of Total Harmonic Distortion (THD) on a 33kv ...

    African Journals Online (AJOL)

    Modern day AC power systems are proliferated by the introduction of several kinds of nonlinear loads which generate harmonics in a power system and this has a cumulative negative effect on power quality. Examples of nonlinear loads are power electronic devices, which cause distortion of voltage and current waveforms ...

  12. Distortion effects in pion-induced knock-out reactions

    International Nuclear Information System (INIS)

    Jain, B.K.

    The cross-section for (π + ,π + p) reaction on 12 C is calculated in DWIA at 100 and 180 MeV incident energy. The effect of pion distortion is found to be strong. Around 180 MeV the effect is strongly absorptive while around 10O MeV it is mainly dispersive. (auth.)

  13. Sensitivity Analysis of Structures by Virtual Distortion Method

    DEFF Research Database (Denmark)

    Gierlinski, J.T.; Holnicki-Szulc, J.; Sørensen, John Dalsgaard

    1991-01-01

    are used in structural optimization, see Haftka [4]. The recently developed Virtual Distortion Method (VDM) is a numerical technique which offers an efficient approach to calculation of the sensitivity derivatives. This method has been orginally applied to structural remodelling and collapse analysis, see...

  14. Investigation of the Geometrical Distortions in the Nuclear Emulsion

    International Nuclear Information System (INIS)

    Batusov, Yu.A.; Rumyantseva, V.P.; Soroko, L.M.; Tereshchenko, V.V.

    1994-01-01

    The geometrical distortions in the nuclear emulsion were investigated by means of two devices: 1) stereoscopic meso-optical Fourier transform microscope (MFTM) and 2) traditional optical microscope (KSM-1) designed for precise measurements. The particle tracks were produced by primary Oxygen-nuclei with impulse 65.6 GeV/c and by secondary α-particles in various regions of the nuclear emulsion. The measurement errors were: 1.8' (angular minute) for orientation angle θ xy ; 2.7' (angular minute) for dip angle θ z ; 0.3 μm for transverse coordinate x; 0.1 μm for longitudinal coordinate y and 0.3 μm for depth coordinate z. The effect of the global forced bending of the nuclear emulsion glass support was detected and estimated as dθ z /dy=2' (angular minute) per mm. To suppress the local geometrical distortions, a difference plot was calculated for two secondary α-particles going very close within ≤ 10 μm over the distance 6 mm. It was shown that this mode of the local geometrical distortions is kept constant over the mutual transverse distances up to 0.6 mm. By observing the zy-plots of four secondary α-particles we have isolated the rotating mode of the local geometrical distortions in the nuclear emulsion. 5 refs., 11 figs

  15. Distributed Remote Vector Gaussian Source Coding with Covariance Distortion Constraints

    DEFF Research Database (Denmark)

    Zahedi, Adel; Østergaard, Jan; Jensen, Søren Holdt

    2014-01-01

    In this paper, we consider a distributed remote source coding problem, where a sequence of observations of source vectors is available at the encoder. The problem is to specify the optimal rate for encoding the observations subject to a covariance matrix distortion constraint and in the presence...

  16. Source Coding in Networks with Covariance Distortion Constraints

    DEFF Research Database (Denmark)

    Zahedi, Adel; Østergaard, Jan; Jensen, Søren Holdt

    2016-01-01

    results to a joint source coding and denoising problem. We consider a network with a centralized topology and a given weighted sum-rate constraint, where the received signals at the center are to be fused to maximize the output SNR while enforcing no linear distortion. We show that one can design...

  17. Factors associated with body image distortion in Korean adolescents

    Directory of Open Access Journals (Sweden)

    Hyun MY

    2014-05-01

    Full Text Available Mi-Yeul Hyun,1 Young-Eun Jung,2 Moon-Doo Kim,2 Young-Sook Kwak,2 Sung-Chul Hong,3 Won-Myong Bahk,4 Bo-Hyun Yoon,5 Hye Won Yoon,6 Bora Yoo61College of Nursing, Jeju National University, Jeju, Korea; 2Department of Psychiatry, School of Medicine, Jeju National University, Jeju, Korea; 3Department of Preventive Medicine, School of Medicine, Jeju National University, Jeju, Korea; 4Department of Psychiatry, Yeouido St Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea; 5Department of Psychiatry, Naju National Hospital, Naju, Korea; 6School of Medicine, Jeju National University, Jeju, KoreaPurpose: Body image incorporates cognitive and affective components as well as behaviors related to own body perception. This study evaluated the occurrence of body image distortion and its correlates in Korean adolescents.Methods: In a school-based cross-sectional survey, a total of 2,117 adolescents were recruited. They filled out self-completing questionnaires on body image distortion, eating attitudes, and behaviors (Eating Attitude Test-26 and related factors.Results: Body image distortions were found in 51.8 percent of adolescents. Univariate analyses showed that boys and older adolescents had higher rates of body image distortion. In the multivariate analyses, body image distortion was associated with high risk for eating disorders (odds ratio [OR] =1.69; 95% confidence interval [CI] 1.11–2.58; P=0.015 and being over weight (OR =33.27; 95% CI 15.51–71.35; P<0.001 or obese (OR =9.37; 95% CI 5.06–17.34; P<0.001.Conclusion: These results suggest that body image distortion is relatively common in Korean adolescents, which has implications for adolescents at risk of developing eating disorders.Keywords: body image distortion, high risk for eating disorders, Korean adolescent

  18. Influence of DNA Lesions on Polymerase-Mediated DNA Replication at Single-Molecule Resolution.

    Science.gov (United States)

    Gahlon, Hailey L; Romano, Louis J; Rueda, David

    2017-11-20

    Faithful replication of DNA is a critical aspect in maintaining genome integrity. DNA polymerases are responsible for replicating DNA, and high-fidelity polymerases do this rapidly and at low error rates. Upon exposure to exogenous or endogenous substances, DNA can become damaged and this can alter the speed and fidelity of a DNA polymerase. In this instance, DNA polymerases are confronted with an obstacle that can result in genomic instability during replication, for example, by nucleotide misinsertion or replication fork collapse. It is important to know how DNA polymerases respond to damaged DNA substrates to understand the mechanism of mutagenesis and chemical carcinogenesis. Single-molecule techniques have helped to improve our current understanding of DNA polymerase-mediated DNA replication, as they enable the dissection of mechanistic details that can otherwise be lost in ensemble-averaged experiments. These techniques have also been used to gain a deeper understanding of how single DNA polymerases behave at the site of the damage in a DNA substrate. In this review, we evaluate single-molecule studies that have examined the interaction between DNA polymerases and damaged sites on a DNA template.

  19. Human DNA ligase III bridges two DNA ends to promote specific intermolecular DNA end joining

    Science.gov (United States)

    Kukshal, Vandna; Kim, In-Kwon; Hura, Gregory L.; Tomkinson, Alan E.; Tainer, John A.; Ellenberger, Tom

    2015-01-01

    Mammalian DNA ligase III (LigIII) functions in both nuclear and mitochondrial DNA metabolism. In the nucleus, LigIII has functional redundancy with DNA ligase I whereas LigIII is the only mitochondrial DNA ligase and is essential for the survival of cells dependent upon oxidative respiration. The unique LigIII zinc finger (ZnF) domain is not required for catalytic activity but senses DNA strand breaks and stimulates intermolecular ligation of two DNAs by an unknown mechanism. Consistent with this activity, LigIII acts in an alternative pathway of DNA double strand break repair that buttresses canonical non-homologous end joining (NHEJ) and is manifest in NHEJ-defective cancer cells, but how LigIII acts in joining intermolecular DNA ends versus nick ligation is unclear. To investigate how LigIII efficiently joins two DNAs, we developed a real-time, fluorescence-based assay of DNA bridging suitable for high-throughput screening. On a nicked duplex DNA substrate, the results reveal binding competition between the ZnF and the oligonucleotide/oligosaccharide-binding domain, one of three domains constituting the LigIII catalytic core. In contrast, these domains collaborate and are essential for formation of a DNA-bridging intermediate by adenylated LigIII that positions a pair of blunt-ended duplex DNAs for efficient and specific intermolecular ligation. PMID:26130724

  20. High resolution microstructure characterization of the interface between cold sprayed Al coating and Mg alloy substrate

    International Nuclear Information System (INIS)

    Wang, Qiang; Qiu, Dong; Xiong, Yuming; Birbilis, Nick; Zhang, Ming-Xing

    2014-01-01

    High-resolution transmission electron microscopy (HR-TEM) has validated the intimate metallurgical (atomic) bond formed along the interface of a cold-sprayed Al coating upon an Mg-alloy (AZ91) substrate. The compressive impact led to the formation of nanostructured layers of about 300–500 nm into the substrate. A highly distorted lattice structure with the inclusion of small amorphous zones was observed at the periphery of the particle/substrate interface, as a result of adiabatic shear plastic deformation at a high strain rate.

  1. Modeling DNA

    Science.gov (United States)

    Robertson, Carol

    2016-01-01

    Deoxyribonucleic acid (DNA) is life's most amazing molecule. It carries the genetic instructions that almost every organism needs to develop and reproduce. In the human genome alone, there are some three billion DNA base pairs. The most difficult part of teaching DNA structure, however, may be getting students to visualize something as small as a…

  2. Coating of substrates

    International Nuclear Information System (INIS)

    Cairns, J.A.; Nelson, R.L.; Woodhead, J.L.

    1979-01-01

    The process is concerned with providing substrates with coatings obtainable from sols, for example to protect the substrate (such as in nuclear reactors or hydrocarbon cracking plant) or to provide a carrier for catalytically active material. Hitherto, coatings obtained from sols have had a high porosity and high surface area so that they have not been entirely satisfactory for the above applications. In the process described, dense, low-porosity coatings are provided by contacting the substrate with a sol of refractory material (e.g. CeO 2 or SiO 2 ) convertible to a gel of density at least 40% of the theoretical density of the refractory material, and converting the sol to the gel. Optionally, the gel may be converted to a ceramic coating by firing. (author)

  3. Robust plasmonic substrates

    DEFF Research Database (Denmark)

    Kostiučenko, Oksana; Fiutowski, Jacek; Tamulevicius, Tomas

    2014-01-01

    Robustness is a key issue for the applications of plasmonic substrates such as tip-enhanced Raman spectroscopy, surface-enhanced spectroscopies, enhanced optical biosensing, optical and optoelectronic plasmonic nanosensors and others. A novel approach for the fabrication of robust plasmonic...... substrates is presented, which relies on the coverage of gold nanostructures with diamond-like carbon (DLC) thin films of thicknesses 25, 55 and 105 nm. DLC thin films were grown by direct hydrocarbon ion beam deposition. In order to find the optimum balance between optical and mechanical properties...

  4. Substrate system for spray forming

    Energy Technology Data Exchange (ETDEWEB)

    Chu, Men G. (Export, PA); Chernicoff, William P. (Harrisburg, PA)

    2002-01-01

    A substrate system for receiving a deposit of sprayed metal droplets including a movable outer substrate on which the sprayed metal droplets are deposited. The substrate system also includes an inner substrate disposed adjacent the outer substrate where the sprayed metal droplets are deposited on the outer substrate. The inner substrate includes zones of differing thermal conductivity to resist substrate layer porosity and to resist formation of large grains and coarse constituent particles in a bulk layer of the metal droplets which have accumulated on the outer substrate. A spray forming apparatus and associated method of spray forming a molten metal to form a metal product using the substrate system of the invention is also provided.

  5. Wetting on structured substrates

    International Nuclear Information System (INIS)

    Dietrich, S; Popescu, M N; Rauscher, M

    2005-01-01

    Chemically patterned surfaces are of significant interest in the context of microfluidic applications, and miniaturization of such devices aims at generating structures on the nano-scale. Whereas on the micron scale purely macroscopic descriptions of liquid flow are valid, on the nanometre scale long-ranged inter-molecular interactions, thermal fluctuations such as capillary waves, and finally the molecular structure of the liquid become important. We discuss the most important conceptual differences between flow on chemically patterned substrates on the micron scale and on the nanometre scale, and formulate four design issues for nanofluidics related to channel width, channel separation, and channel bending radius. As a specific example of nano-scale transport we present a microscopic model for the dynamics of spreading of monolayers on homogeneous substrates. Kinetic Monte Carlo simulations of this model on a homogeneous substrate reveal a complex spatio-temporal structure of the extracted monolayer, which includes the emergence of interfaces and of scaling properties of density profiles. These features are discussed and rationalized within the corresponding continuum limit derived from the microscopic dynamics. The corresponding spreading behaviour on a patterned substrate is briefly addressed

  6. Quantitation of structural distortion with gradient-echo imaging techniques

    International Nuclear Information System (INIS)

    Tien, R.D.; Schwaighofer, B.W.; Hesselink, J.R.; Chu, P.K.

    1990-01-01

    This paper determines the structural distortion and measurement error associated with fast MR imaging of the spinal neural foramina. Dry skeletal specimens and a thin cadaveric sagittal section through the neural foramina were placed in a water bath. MR images were obtained with a 1.5-T unit in different planes and with various pulse sequences. The size and shape of each neural foramen were carefully measured on the images and on the skeletal specimens. Gradient-echo (GRE) techniques (gradient recalled acquisition in a steady state, MPGR, three-dimensional volume acquisition) resulted in structural distortion in up to 10% on the fresh skeleton and 30% of the dry skeleton specimens when a small TE was used (the foramina appear narrower on the images)

  7. Simulation of Welding Distortions in Theory and Practice

    DEFF Research Database (Denmark)

    Birk-Sørensen, Martin; Kierkegaard, Henning

    1997-01-01

    by an optimised welding order. Welding test samples prove that the constraint of the sample and the time between each pass in a multipass weld affect the magnitude of distortion. Experiments with welding specimens in the form of butt-and fillet welds have been carried out. They show angular deflections as well......In the last few years the use of robot welding processes has increased significatnly. The programming of the robots has until now mainly focused on high efficiency, i.e.high torch rate time, and hence, minimising the inefficient "travelling" time. Together with developing high-performance welding...... due to cutting and welding and parlty in the form of dimensional variation due to human factors. Measurements have been made of the production line for assemblies. The measurements show that distortions related to the multirobot welding are a factor which can rather easily be controlled...

  8. Can components in distortion-product otoacoustic emissions be separated?

    DEFF Research Database (Denmark)

    Christensen, Anders Tornvig; W. Purcell, David; Christensen, Flemming

    2012-01-01

    Otoacoustic emissions are signals emitted from the cochlea, either spontaneously or evoked by stimuli. Measured with an acoustic probe sealed in the ear-canal, they reveal information about a part of the mechanism of hearing that is otherwise inaccessible. Outer hair cells in the cochlea work...... to improve hearing sensitivity by means of nonlinear amplification, which produces distortion. In the measurement of otoacoustic emissions, two tones can be delivered to the cochlea to invoke this nonlinearity and elicit the distortion-product otoacoustic emission (DPOAE). DPOAEs arise mainly from two...... spatially separated generation mechanisms, thus making interpretation of DPOAE measurements complicated. In this study, we test whether or not source separation by group delays is equivalent to separation by time delays – either result is equally interesting to understand given the complexity of the cochlea...

  9. The Dark Side of Context: Context Reinstatement Can Distort Memory.

    Science.gov (United States)

    Doss, Manoj K; Picart, Jamila K; Gallo, David A

    2018-04-01

    It is widely assumed that context reinstatement benefits memory, but our experiments revealed that context reinstatement can systematically distort memory. Participants viewed pictures of objects superimposed over scenes, and we later tested their ability to differentiate these old objects from similar new objects. Context reinstatement was manipulated by presenting objects on the reinstated or switched scene at test. Not only did context reinstatement increase correct recognition of old objects, but it also consistently increased incorrect recognition of similar objects as old ones. This false recognition effect was robust, as it was found in several experiments, occurred after both immediate and delayed testing, and persisted with high confidence even after participants were warned to avoid the distorting effects of context. To explain this memory illusion, we propose that context reinstatement increases the likelihood of confusing conceptual and perceptual information, potentially in medial temporal brain regions that integrate this information.

  10. In situ visualization of thermal distortions of synchrotron radiation optics

    International Nuclear Information System (INIS)

    Revesz, P.; Kazimirov, A.; Bazarov, I.

    2007-01-01

    We have developed a new in situ method to measure heating-induced distortions of the surface of the first monochromator crystal exposed to high-power white synchrotron radiation beam. The method is based on recording the image of a stationary grid of dots captured by a CCD camera as reflected from the surface of a crystal with and without a heat load. The three-dimensional surface profile (heat bump) is then reconstructed from the distortions of the original pattern. In experiments performed at the CHESS A2 wiggler beam line we measured the heat bumps with the heights of up to 600 nm produced by a wiggler beam with total power in the range of 15-60 W incident on the (1 1 1) Si crystal at various angles between 3 deg. and 15 deg

  11. Internal process: what is abstraction and distortion process?

    Science.gov (United States)

    Fiantika, F. R.; Budayasa, I. K.; Lukito, A.

    2018-03-01

    Geometry is one of the branch of mathematics that plays a major role in the development of science and technology. Thus, knowing the geometry concept is needed for students from their early basic level of thinking. A preliminary study showed that the elementary students have difficulty in perceiving parallelogram shape in a 2-dimention of a cube drawing as a square shape. This difficulty makes the students can not solve geometrical problems correctly. This problem is related to the internal thinking process in geometry. We conducted the exploration of students’ internal thinking processes in geometry particularly in distinguishing the square and parallelogram shape. How the students process their internal thinking through distortion and abstraction is the main aim of this study. Analysis of the geometrical test and deep interview are used in this study to obtain the data. The result of this study is there are two types of distortion and abstraction respectively in which the student used in their internal thinking processes.

  12. Distortional Mechanics of Thin-Walled Structural Elements

    DEFF Research Database (Denmark)

    Andreassen, Michael Joachim

    In several industries such as civil, mechanical, and aerospace, thin-walled structures are often used due to the high strength and effective use of the materials. Because of the increased consumption there has been increasing focus on optimizing and more detailed calculations. However, finely...... number of degrees of freedom. This means that the classical Vlasov thin-walled beam theory for open and closed cross sections is generalized as part of a semi-discretization process by including distortional displacement fields. A novel finite-element-based displacement approach is used in combination...... by discretization of the cross section are now solved analytically and the formulation is valid without special attention and approximation also for closed single or multi-cell cross sections. Furthermore, the found eigenvalues have clear mechanical meaning, since they represent the attenuation of the distortional...

  13. Harmonic Distortion of Rectifier Topologies for Adjustable Speed Drives

    DEFF Research Database (Denmark)

    Hansen, Steffan

    This thesis deals with the harmonic distortion of the diode rectifier and a number of alternative rectifier topologies for adjustable speed drives. The main intention of this thesis is to provide models and tools that allow easy prediction of the harmonic distortion of ASD’s in a given system...... rectifier are presented. The first level is an ideal model where the diode rectifier basically is treated as an independent (harmonic) current source. The second level is an empirical model, where simulated (or measured) values of the harmonic currents of the diode rectifier for different parameters......-angle of the individual harmonic currents of different diode rectifier types is analyzed. Four selected rectifier topologies with a high input power factor are presented. It is shown that using ac- or dc-coils is a very simple and efficient method to reduce the harmonic currents compared to the basic diode rectifier...

  14. Analysis and validation of laser spot weld-induced distortion

    Energy Technology Data Exchange (ETDEWEB)

    Knorovsky, G.A.; Kanouff, M.P.; Maccallum, D.O.; Fuerschbach, P.W.

    1999-12-09

    Laser spot welding is an ideal process for joining small parts with tight tolerances on weld size, location, and distortion, particularly those with near-by heat sensitive features. It is also key to understanding the overlapping laser spot seam welding process. Rather than attempting to simulate the laser beam-to-part coupling (particularly if a keyhole occurs), it was measured by calorimetry. This data was then used to calculate the thermal and structural response of a laser spot welded SS304 disk using the finite element method. Five combinations of process parameter values were studied. Calculations were compared to experimental data for temperature and distortion profiles measured by thermocouples and surface profiling. Results are discussed in terms of experimental and modeling factors. The authors then suggest appropriate parameters for laser spot welding.

  15. Probing correlations of early magnetic fields using mu-distortion

    DEFF Research Database (Denmark)

    Ganc, Jonathan; Sloth, Martin Snoager

    2014-01-01

    the perturbations which produce the $\\mu$-distortion will be much smaller scale than the relevant density perturbations, the observation of this correlation is sensitive to the squeezed limit of $\\langle B^2\\zeta\\rangle$, which is naturally parameterized by $b_{\\text{NL}}$ (a parameter defined analogously to $f_{\\text......{NL}}$). We find that a PIXIE-like CMB experiments has a signal to noise $S/N\\approx 1.0 \\times b_{\\text{NL}} (\\tilde B_\\mu/10\\text{ nG})^2$, where $\\tilde B_\\mu$ is the magnetic field's strength on $\\mu$-distortion scales normalized to today's redshift; thus, a 10 nG field would be detectable with $b_{\\text...

  16. Labor Market Distortions in Côte d'Ivoire:

    DEFF Research Database (Denmark)

    Kristensen, Nicolai; Verner, Dorte

    2008-01-01

    This paper investigates the extent and nature of distortions in the labor market in the Republic of Côte d'Ivoire by using quantile regression analysis on employer-employee data from the manufacturing sector. We found that the labor markets in Côte d'Ivoire do not seem to be much distorted. Unions...... may influence employment through tenure but do not seem to influence wages directly except for vulnerable minorities that seem protected by unions. Establishment-size wage effects are pronounced and highest for white-collar workers. This may be explained by the efficiency wage theory, so that, even...... in the absence of unions, segmentation and inefficiencies will still be present as long as firms seek to retain their employees by paying wages above the market clearing level. The inefficiency arising from establishment-size wage effects can be mitigated by education....

  17. Mapping flow distortion on oceanographic platforms using computational fluid dynamics

    Directory of Open Access Journals (Sweden)

    N. O'Sullivan

    2013-10-01

    Full Text Available Wind speed measurements over the ocean on ships or buoys are affected by flow distortion from the platform and by the anemometer itself. This can lead to errors in direct measurements and the derived parametrisations. Here we computational fluid dynamics (CFD to simulate the errors in wind speed measurements caused by flow distortion on the RV Celtic Explorer. Numerical measurements were obtained from the finite-volume CFD code OpenFOAM, which was used to simulate the velocity fields. This was done over a range of orientations in the test domain from −60 to +60° in increments of 10°. The simulation was also set up for a range of velocities, ranging from 5 to 25 m s−1 in increments of 0.5 m s−1. The numerical analysis showed close agreement to experimental measurements.

  18. Predicting Harmonic Distortion of Multiple Converters in a Power System

    Directory of Open Access Journals (Sweden)

    P. M. Ivry

    2017-01-01

    Full Text Available Various uncertainties arise in the operation and management of power systems containing Renewable Energy Sources (RES that affect the systems power quality. These uncertainties may arise due to system parameter changes or design parameter choice. In this work, the impact of uncertainties on the prediction of harmonics in a power system containing multiple Voltage Source Converters (VSCs is investigated. The study focuses on the prediction of harmonic distortion level in multiple VSCs when some system or design parameters are only known within certain constraints. The Univariate Dimension Reduction (UDR method was utilized in this study as an efficient predictive tool for the level of harmonic distortion of the VSCs measured at the Point of Common Coupling (PCC to the grid. Two case studies were considered and the UDR technique was also experimentally validated. The obtained results were compared with that of the Monte Carlo Simulation (MCS results.

  19. Numerical implementation of a model with directional distortional hardening

    Czech Academy of Sciences Publication Activity Database

    Marek, René; Plešek, Jiří; Hrubý, Zbyněk; Parma, Slavomír; Feigenbaum, H. P.; Dafalias, Y.F.

    2015-01-01

    Roč. 141, č. 12 (2015), 04015048-04015048 ISSN 0733-9399 R&D Projects: GA MŠk LH14018; GA ČR(CZ) GA15-20666S Institutional support: RVO:61388998 Keywords : plasticity * directional distortional hardening * finite-element procedures Subject RIV: JG - Metallurgy Impact factor: 1.346, year: 2015 http://ascelibrary.org/doi/abs/10.1061/%28ASCE%29EM.1943-7889.0000954

  20. Distortion risk measures for sums of dependent losses | Brahimi ...

    African Journals Online (AJOL)

    ... of losses and possible correlations between risk components. Resume. Nous discutons deux approches distinctes, de distortion des mesures de risque de la somme de variables al´eatoires d´ependantes, qui conservent la propri´et´e de coh´erence. La premi`ere, bas´ee sur les esp´erances distordues, agit sur la fonction ...

  1. Potential constants and centrifugal distortion constants of octahedral hexafluoride molecules

    Energy Technology Data Exchange (ETDEWEB)

    Manivannan, G [Government Thirumagal Mill' s Coll., Gudiyattam, Tamil Nadu (India)

    1981-04-01

    The kinetic constants method outlined by Thirugnanasambandham (1964) based on Wilson's (1955) group theory has been adapted in evaluating the potential constants for SF/sub 6/, SeF/sub 6/, WF/sub 6/, IrF/sub 6/, UF/sub 6/, NpF/sub 6/, and PuF/sub 6/ using the experimentally observed vibrational frequency data. These constants are used to calculate the centrifugal distortion constants for the first time.

  2. Distortions Imposed By Inflation on Historical-Cost Depreciation

    OpenAIRE

    Bravo-Ureta, Boris E.

    1983-01-01

    The use of historical-cost depreciation in periods of persistent inflation decreases the present value of depreciation deductions, thus understating the true economic cost of capital and increasing the real after-tax rate of return required by potential investors. Efforts to correct these problems by adopting depreciation methods that allow for artificially short recovery periods or accelerated rates do not provide an adequate solution. Distortions imposed by inflation on historical-cost depr...

  3. Unstable system with Coulomb interaction distorted near the origin

    International Nuclear Information System (INIS)

    Kerbikov, B.O.

    1981-01-01

    An unstable system with Coulomb interaction distorted at small distances is considered. The results are applicable to hadronic atoms analysis. A detailed investigation of the model which can be solved exactly is presented. This model contains the separable short-range potential with the Yamaguchi form factor. Closed expressions for the modified effective range function and the Coulomb-modified scattering length ase obtained [ru

  4. The Uruguay Round and Welfare in Some Distorted Agricultural Economies

    OpenAIRE

    James E. Anderson

    1997-01-01

    There is widespread concern that the Uruguay Round may reduce the welfare of developing countries through its effect on world agricultural prices. Reduced agricultural price distortions among major supplying nations are predicted to increase basic food prices and decrease some important export prices such as those for coffee and cotton. It appears that raising food prices paid by food importers must be bad for them, while reducing world coffee and cotton prices appears bad for exporters of th...

  5. Topology Optimization for Reducing Additive Manufacturing Processing Distortions

    Science.gov (United States)

    2017-12-01

    distribution is unlimited. 1. Introduction Additive manufacturing (AM) is a production method that involves gradual, layer- by-layer building of material... design space—allowing the production of pre- viously unmanufacturable topologically optimized structures—constraints remain. One constraint, for...ARL-TR-8242•DEC 2017 US Army Research Laboratory Topology Optimization for ReducingAdditive Manufacturing ProcessingDistortions by Raymond A Wildman

  6. Experimental dead-time distortions of Poisson processes

    International Nuclear Information System (INIS)

    Faraci, G.; Pennisi, A.R.; Consiglio Nazionale delle Ricerche, Catania

    1983-01-01

    In order to check the distortions, introduced by a non-extended dead time on the Poisson statistics, accurate experiments have been made in single channel counting. At a given measuring time, the dependence on the choice of the time origin and on the width of the dead time has been verified. An excellent agreement has been found between the theoretical expressions and the experimental curves. (orig.)

  7. Measuring redshift-space distortions using photometric surveys

    OpenAIRE

    Ross, Ashley; Percival, Will; Crocce, M.; Cabre, A.; Gaztanaga, E.

    2011-01-01

    We outline how redshift-space distortions (RSD) can be measured from the angular correlation function w({\\theta}), of galaxies selected from photometric surveys. The natural degeneracy between RSD and galaxy bias can be minimized by comparing results from bins with top-hat galaxy selection in redshift, and bins based on the radial position of galaxy pair centres. This comparison can also be used to test the accuracy of the photometric redshifts. The presence of RSD will be clearly detectable ...

  8. Welding distortion control in double walled KSTAR vacuum vessel fabrication

    International Nuclear Information System (INIS)

    Oh, D. W.; Lee, G. T.; Kim, H. K.; Yang, H. L.; Bak, J. S.

    2004-01-01

    The KSTAR(Korea Superconducting Tokamak Advanced Research) vacuum vessel is designed to be a double walled structure made of 12mm thick 316LN stainless steel with a D shaped cross-section about 4 m height. Vacuum vessel was pre-fabricated in two parts, 180 degree and 157.5 degree sectors in toroidal direction to meet the transportation purpose. These two parts have to be welded on site with ±2mm allowable fabrication tolerances. 1/3 scaled mock-up model was used to estimate the welding distortion and to ensure the weld quality of vacuum vessel. Gas Tungsten Arc Welding(GTAW), which has been approved by procedure qualification test, was used during mock-up test and vacuum vessel site fabrication. Welding distortion could be managed by allowing for distortion in opposite direction, by applying high restraint using lots of strong backs, by controlling the welding heat input with symmetrical welding sequence. The integrity of the site welding joint was assured by radiographic test, ultrasonic test and leak test with helium detecting method

  9. Damage to insula abolishes cognitive distortions during simulated gambling.

    Science.gov (United States)

    Clark, Luke; Studer, Bettina; Bruss, Joel; Tranel, Daniel; Bechara, Antoine

    2014-04-22

    Gambling is a naturalistic example of risky decision-making. During gambling, players typically display an array of cognitive biases that create a distorted expectancy of winning. This study investigated brain regions underpinning gambling-related cognitive distortions, contrasting patients with focal brain lesions to the ventromedial prefrontal cortex (vmPFC), insula, or amygdala ("target patients") against healthy comparison participants and lesion comparison patients (i.e., with lesions that spare the target regions). A slot machine task was used to deliver near-miss outcomes (i.e., nonwins that fall spatially close to a jackpot), and a roulette game was used to examine the gambler's fallacy (color decisions following outcome runs). Comparison groups displayed a heightened motivation to play following near misses (compared with full misses), and manifested a classic gambler's fallacy effect. Both effects were also observed in patients with vmPFC and amygdala damage, but were absent in patients with insula damage. Our findings indicate that the distorted cognitive processing of near-miss outcomes and event sequences may be ordinarily supported by the recruitment of the insula. Interventions to reduce insula reactivity could show promise in the treatment of disordered gambling.

  10. Vacuum energy density near static distorted black holes

    International Nuclear Information System (INIS)

    Frolov, V.P.; Sanchez, N.

    1986-01-01

    We investigate the contribution of massless fields of spins 0, 1/2, and 1 to the vacuum polarization near the event horizon of static Ricci-flat space-times. We do not assume any particular spatial symmetry. Within the Page-Brown ''ansatz'' we calculate 2 >/sup ren/ and /sup ren/ near static distorted black holes, for both the Hartle-Hawking (Vertical Bar>/sub H/) and Boulware (Vertical Bar>/sub B/) vacua. Using Israel's description of static space-times, we express these quantities in an invariant geometric way. We obtain that 2 >/sub H//sup ren/ and /sub H//sup ren/ near the horizon depend only on the two-dimensional geometry of the horizon surface. We find 2 >/sub H//sup ren/ = (1/48π 2 )K 0 , 0 0 >/sub H//sup ren/ = (7α+12β )K 0 2 -α/sup( 2 )ΔK 0 . $K sub 0: is the Gaussian curvature of the horizon, and α and β are numerical coefficients depending on the spin of a field. The term in /sup( 2 )ΔK 0 is characteristic of the distortion of the black hole. When the event horizon is not distorted, K 0 is a constant and this term disappears

  11. Emittance and beam size distortion due to linear coupling

    International Nuclear Information System (INIS)

    Parzen, G.

    1993-01-01

    At injection, the presence of linear coupling may result in an increased beam emittance and in increased beam dimensions. Results for the emittance in the presence of linear coupling will be found. These results for the emittance distortion show that the harmonics of the skew quadrupole field close to ν x + ν y are the important harmonics. Results will be found for the important driving terms for the emittance distortion. It will be shown that if these driving terms are corrected, then the total emittance is unchanged, var-epsilon x + var-epsilon y = var-epsilon 1 + var-epsilon 2 . Also, the increase in the beam dimensions will be limited to a factor which is less than 1.414. If the correction is good enough, see below for details, one can achieve var-epsilon 1 = var-epsilon x , var-epsilon 2 = var-epsilon where var-epsilon 1 , var-epsilon 2 are the emittances in the presence of coupling, and the beam dimensions are unchanged. Global correction of the emittance and beam size distortion appears possible

  12. [An improved low spectral distortion PCA fusion method].

    Science.gov (United States)

    Peng, Shi; Zhang, Ai-Wu; Li, Han-Lun; Hu, Shao-Xing; Meng, Xian-Gang; Sun, Wei-Dong

    2013-10-01

    Aiming at the spectral distortion produced in PCA fusion process, the present paper proposes an improved low spectral distortion PCA fusion method. This method uses NCUT (normalized cut) image segmentation algorithm to make a complex hyperspectral remote sensing image into multiple sub-images for increasing the separability of samples, which can weaken the spectral distortions of traditional PCA fusion; Pixels similarity weighting matrix and masks were produced by using graph theory and clustering theory. These masks are used to cut the hyperspectral image and high-resolution image into some sub-region objects. All corresponding sub-region objects between the hyperspectral image and high-resolution image are fused by using PCA method, and all sub-regional integration results are spliced together to produce a new image. In the experiment, Hyperion hyperspectral data and Rapid Eye data were used. And the experiment result shows that the proposed method has the same ability to enhance spatial resolution and greater ability to improve spectral fidelity performance.

  13. Applying image quality in cell phone cameras: lens distortion

    Science.gov (United States)

    Baxter, Donald; Goma, Sergio R.; Aleksic, Milivoje

    2009-01-01

    This paper describes the framework used in one of the pilot studies run under the I3A CPIQ initiative to quantify overall image quality in cell-phone cameras. The framework is based on a multivariate formalism which tries to predict overall image quality from individual image quality attributes and was validated in a CPIQ pilot program. The pilot study focuses on image quality distortions introduced in the optical path of a cell-phone camera, which may or may not be corrected in the image processing path. The assumption is that the captured image used is JPEG compressed and the cellphone camera is set to 'auto' mode. As the used framework requires that the individual attributes to be relatively perceptually orthogonal, in the pilot study, the attributes used are lens geometric distortion (LGD) and lateral chromatic aberrations (LCA). The goal of this paper is to present the framework of this pilot project starting with the definition of the individual attributes, up to their quantification in JNDs of quality, a requirement of the multivariate formalism, therefore both objective and subjective evaluations were used. A major distinction in the objective part from the 'DSC imaging world' is that the LCA/LGD distortions found in cell-phone cameras, rarely exhibit radial behavior, therefore a radial mapping/modeling cannot be used in this case.

  14. Mesoscopic Elastic Distortions in GaAs Quantum Dot Heterostructures.

    Science.gov (United States)

    Pateras, Anastasios; Park, Joonkyu; Ahn, Youngjun; Tilka, Jack A; Holt, Martin V; Reichl, Christian; Wegscheider, Werner; Baart, Timothy A; Dehollain, Juan Pablo; Mukhopadhyay, Uditendu; Vandersypen, Lieven M K; Evans, Paul G

    2018-05-09

    Quantum devices formed in high-electron-mobility semiconductor heterostructures provide a route through which quantum mechanical effects can be exploited on length scales accessible to lithography and integrated electronics. The electrostatic definition of quantum dots in semiconductor heterostructure devices intrinsically involves the lithographic fabrication of intricate patterns of metallic electrodes. The formation of metal/semiconductor interfaces, growth processes associated with polycrystalline metallic layers, and differential thermal expansion produce elastic distortion in the active areas of quantum devices. Understanding and controlling these distortions present a significant challenge in quantum device development. We report synchrotron X-ray nanodiffraction measurements combined with dynamical X-ray diffraction modeling that reveal lattice tilts with a depth-averaged value up to 0.04° and strain on the order of 10 -4 in the two-dimensional electron gas (2DEG) in a GaAs/AlGaAs heterostructure. Elastic distortions in GaAs/AlGaAs heterostructures modify the potential energy landscape in the 2DEG due to the generation of a deformation potential and an electric field through the piezoelectric effect. The stress induced by metal electrodes directly impacts the ability to control the positions of the potential minima where quantum dots form and the coupling between neighboring quantum dots.

  15. DNA Camouflage

    Science.gov (United States)

    2016-01-08

    1 DNA Camouflage Supplementary Information Bijan Zakeri1,2*, Timothy K. Lu1,2*, Peter A. Carr2,3* 1Department of Electrical Engineering and...ll.mit.edu). Distribution A: Public Release   2 Supplementary Figure 1 DNA camouflage with the 2-state device. (a) In the presence of Cre, DSD-2[α...10 1 + Cre 1 500 1,000 length (bp) chromatogram alignment template − Cre   4 Supplementary Figure 3 DNA camouflage with a switchable

  16. Radicals of DNA and DNA nucleotides generated by ionising radiation

    International Nuclear Information System (INIS)

    Przybytniak, G.

    2004-01-01

    A first stage of cell processes leading to DNA damage of initiated by radical reactions. In a model system such transformations were generated by ionising radiation which involves production of electron loss and electron gain centers of the substrate and radical formation. Using cryogenic ESR spectroscopy it was found that the DNA nucleotides, which convert to radical anions upon electron capture undergo the separation of unpaired spin and charge due to protonation. Circular and linear dichroism studies enabled to conclude that iron ions(III) induce strong changes in the DNA helical structure indicating their coordination with nitrogen bases. The repair of DNA radicals produced via radiolytic oxidation, i.e. the guanine radical cation and the allyl type radical of thymine, is possible at elevated temperatures due to the involvement of sulphydryl groups. The influence of the thiol charge is then limited

  17. Collaborating functions of BLM and DNA topoisomerase I in regulating human rDNA transcription

    International Nuclear Information System (INIS)

    Grierson, Patrick M.; Acharya, Samir; Groden, Joanna

    2013-01-01

    Bloom's syndrome (BS) is an inherited disorder caused by loss of function of the recQ-like BLM helicase. It is characterized clinically by severe growth retardation and cancer predisposition. BLM localizes to PML nuclear bodies and to the nucleolus; its deficiency results in increased intra- and inter-chromosomal recombination, including hyper-recombination of rDNA repeats. Our previous work has shown that BLM facilitates RNA polymerase I-mediated rRNA transcription in the nucleolus (Grierson et al., 2012 [18]). This study uses protein co-immunoprecipitation and in vitro transcription/translation (IVTT) to identify a direct interaction of DNA topoisomerase I with the C-terminus of BLM in the nucleolus. In vitro helicase assays demonstrate that DNA topoisomerase I stimulates BLM helicase activity on a nucleolar-relevant RNA:DNA hybrid, but has an insignificant effect on BLM helicase activity on a control DNA:DNA duplex substrate. Reciprocally, BLM enhances the DNA relaxation activity of DNA topoisomerase I on supercoiled DNA substrates. Our study suggests that BLM and DNA topoisomerase I function coordinately to modulate RNA:DNA hybrid formation as well as relaxation of DNA supercoils in the context of nucleolar transcription

  18. Collaborating functions of BLM and DNA topoisomerase I in regulating human rDNA transcription

    Energy Technology Data Exchange (ETDEWEB)

    Grierson, Patrick M. [Department of Microbiology, Immunology and Medical Genetics, The Ohio State University College of Medicine, Columbus, OH 43210 (United States); Acharya, Samir, E-mail: samir.acharya@osumc.edu [Department of Microbiology, Immunology and Medical Genetics, The Ohio State University College of Medicine, Columbus, OH 43210 (United States); Groden, Joanna [Department of Microbiology, Immunology and Medical Genetics, The Ohio State University College of Medicine, Columbus, OH 43210 (United States)

    2013-03-15

    Bloom's syndrome (BS) is an inherited disorder caused by loss of function of the recQ-like BLM helicase. It is characterized clinically by severe growth retardation and cancer predisposition. BLM localizes to PML nuclear bodies and to the nucleolus; its deficiency results in increased intra- and inter-chromosomal recombination, including hyper-recombination of rDNA repeats. Our previous work has shown that BLM facilitates RNA polymerase I-mediated rRNA transcription in the nucleolus (Grierson et al., 2012 [18]). This study uses protein co-immunoprecipitation and in vitro transcription/translation (IVTT) to identify a direct interaction of DNA topoisomerase I with the C-terminus of BLM in the nucleolus. In vitro helicase assays demonstrate that DNA topoisomerase I stimulates BLM helicase activity on a nucleolar-relevant RNA:DNA hybrid, but has an insignificant effect on BLM helicase activity on a control DNA:DNA duplex substrate. Reciprocally, BLM enhances the DNA relaxation activity of DNA topoisomerase I on supercoiled DNA substrates. Our study suggests that BLM and DNA topoisomerase I function coordinately to modulate RNA:DNA hybrid formation as well as relaxation of DNA supercoils in the context of nucleolar transcription.

  19. Sequential and Multistep Substrate Interrogation Provides the Scaffold for Specificity in Human Flap Endonuclease 1

    KAUST Repository

    Sobhy, M.; Joudeh, L.; Huang, X.; Takahashi, Masateru; Hamdan, S.

    2013-01-01

    Human flap endonuclease 1 (FEN1), one of the structure-specific 5' nucleases, is integral in replication, repair, and recombination of cellular DNA. The 5' nucleases share significant unifying features yet cleave diverse substrates at similar positions relative to 5' end junctions. Using single-molecule Förster resonance energy transfer, we find a multistep mechanism that verifies all substrate features before inducing the intermediary-DNA bending step that is believed to unify 5' nuclease mechanisms. This is achieved by coordinating threading of the 5' flap of a nick junction into the conserved capped-helical gateway, overseeing the active site, and bending by binding at the base of the junction. We propose that this sequential and multistep substrate recognition process allows different 5' nucleases to recognize different substrates and restrict the induction of DNA bending to the last common step. Such mechanisms would also ensure the protection ofDNA junctions from nonspecific bending and cleavage. 2013 The Authors.

  20. Sequential and Multistep Substrate Interrogation Provides the Scaffold for Specificity in Human Flap Endonuclease 1

    KAUST Repository

    Sobhy, M.

    2013-06-06

    Human flap endonuclease 1 (FEN1), one of the structure-specific 5\\' nucleases, is integral in replication, repair, and recombination of cellular DNA. The 5\\' nucleases share significant unifying features yet cleave diverse substrates at similar positions relative to 5\\' end junctions. Using single-molecule Förster resonance energy transfer, we find a multistep mechanism that verifies all substrate features before inducing the intermediary-DNA bending step that is believed to unify 5\\' nuclease mechanisms. This is achieved by coordinating threading of the 5\\' flap of a nick junction into the conserved capped-helical gateway, overseeing the active site, and bending by binding at the base of the junction. We propose that this sequential and multistep substrate recognition process allows different 5\\' nucleases to recognize different substrates and restrict the induction of DNA bending to the last common step. Such mechanisms would also ensure the protection ofDNA junctions from nonspecific bending and cleavage. 2013 The Authors.

  1. Multiple conformational states of DnaA protein regulate its interaction with DnaA boxes in the initiation of DNA replication.

    Science.gov (United States)

    Patel, Meera J; Bhatia, Lavesh; Yilmaz, Gulden; Biswas-Fiss, Esther E; Biswas, Subhasis B

    2017-09-01

    DnaA protein is the initiator of genomic DNA replication in prokaryotes. It binds to specific DNA sequences in the origin of DNA replication and unwinds small AT-rich sequences downstream for the assembly of the replisome. The mechanism of activation of DnaA that enables it to bind and organize the origin DNA and leads to replication initiation remains unclear. In this study, we have developed double-labeled fluorescent DnaA probes to analyze conformational states of DnaA protein upon binding DNA, nucleotide, and Soj sporulation protein using Fluorescence Resonance Energy Transfer (FRET). Our studies demonstrate that DnaA protein undergoes large conformational changes upon binding to substrates and there are multiple distinct conformational states that enable it to initiate DNA replication. DnaA protein adopted a relaxed conformation by expanding ~15Å upon binding ATP and DNA to form the ATP·DnaA·DNA complex. Hydrolysis of bound ATP to ADP led to a contraction of DnaA within the complex. The relaxed conformation of DnaA is likely required for the formation of the multi-protein ATP·DnaA·DNA complex. In the initiation of sporulation, Soj binding to DnaA prevented relaxation of its conformation. Soj·ADP appeared to block the activation of DnaA, suggesting a mechanism for Soj·ADP in switching initiation of DNA replication to sporulation. Our studies demonstrate that multiple conformational states of DnaA protein regulate its binding to DNA in the initiation of DNA replication. Copyright © 2017 Elsevier B.V. All rights reserved.

  2. Structural and magnetic properties of (NdBa)MnO3 films on lattice-matched substrates

    DEFF Research Database (Denmark)

    Khoryushin, Alexey V.; Mozhaeva, Julia E.; Mozhaev, Peter B.

    2013-01-01

    Structural and magnetic properties of (NdBa)MnO3 thin films grown on several perovskite substrates by pulsed laser deposition are presented. A high crystal quality epitaxial film with smooth surface and low level of internal strain may be grown up to thicknesses of 70 nm. The in-plane distortion ...

  3. DNA glue

    DEFF Research Database (Denmark)

    Filichev, Vyacheslav V; Astakhova, Irina V.; Malakhov, Andrei D.

    2008-01-01

    Significant alterations in thermal stability of parallel DNA triplexes and antiparallel duplexes were observed upon changing the attachment of ethynylpyrenes from para to ortho in the structure of phenylmethylglycerol inserted as a bulge into DNA (TINA). Insertions of two ortho-TINAs as a pseudo...

  4. Hyperstretching DNA

    NARCIS (Netherlands)

    Schakenraad, Koen; Biebricher, Andreas S.; Sebregts, Maarten; Ten Bensel, Brian; Peterman, Erwin J.G.; Wuite, Gijs J L; Heller, Iddo; Storm, Cornelis; Van Der Schoot, Paul

    2017-01-01

    The three-dimensional structure of DNA is highly susceptible to changes by mechanical and biochemical cues in vivo and in vitro. In particular, large increases in base pair spacing compared to regular B-DNA are effected by mechanical (over)stretching and by intercalation of compounds that are widely

  5. DNA: Polymer and molecular code

    Science.gov (United States)

    Shivashankar, G. V.

    1999-10-01

    gene expression a prime example of a biological code. We developed a novel method of making DNA micro- arrays, the so-called DNA chip. Using the optical tweezer concept, we were able to pattern biomolecules on a solid substrate, developing a new type of sub-micron laser lithography. A laser beam is focused onto a thin gold film on a glass substrate. Laser ablation of gold results in local aggregation of nanometer scale beads conjugated with small DNA oligonucleotides, with sub-micron resolution. This leads to specific detection of cDNA and RNA molecules. We built a simple micro-array fabrication and detection in the laboratory, based on this method, to probe addressable pools (genes, proteins or antibodies). We have lately used molecular beacons (single stranded DNA with a stem-loop structure containing a fluorophore and quencher), for the direct detection of unlabelled mRNA. As a first step towards a study of the dynamics of the biological code, we have begun to examine the patterns of gene expression during virus (T7 phage) infection of E-coli bacteria.

  6. Pump-induced optical distortions in disk amplifier modules: holographic and interferometric measurements

    International Nuclear Information System (INIS)

    Linford, G.J.; Chau, H.H.; Glaze, J.A.; Layne, C.B.; Rainer, F.

    1975-01-01

    Interferometric measurements have been made of the optical distortions induced in laser disk amplifiers during the flashlamp pumping pulse. Both conventional interferometric methods and the techniques of double exposure holographic interferometry were used to identify four major sources of pump-induced optical distortions: subsonic intrusion of hot gas (traced to leakage of atmospheric oxygen into the amplifier), microexplosions of dust particles, thermally induced optical distortions in the glass disks, and gaseous optical distortion effects caused by turbulent flow of the purging nitrogen gas supply used within the laser amplifier head. Methods for reducing or eliminating the effects of each of these optical distortions are described

  7. On the relationship between perceptual impact of source and channel distortions in video sequences

    DEFF Research Database (Denmark)

    Korhonen, Jari; Reiter, Ulrich; You, Junyong

    2010-01-01

    It is known that peak signal-to-noise ratio (PSNR) can be used for assessing the relative qualities of distorted video sequences meaningfully only if the compared sequences contain similar types of distortions. In this paper, we propose a model for rough assessment of the bias in PSNR results, when...... video sequences with both channel and source distortion are compared against video sequences with source distortion only. The proposed method can be used to compare the relative perceptual quality levels of video sequences with different distortion types more reliably than using plain PSNR....

  8. System performance enhancement with pre-distorted OOFDM signal waveforms in DM/DD systems.

    Science.gov (United States)

    Sánchez, C; Ortega, B; Capmany, J

    2014-03-24

    In this work we propose a pre-distortion technique for the mitigation of the nonlinear distortion present in directly modulated/detected OOFDM systems and explore the system performance achieved under varying system parameters. Simulation results show that the proposed pre-distortion technique efficiently mitigates the nonlinear distortion, achieving transmission information rates around 40 Gbits/s and 18.5 Gbits/s over 40 km and 100 km of single mode fiber links, respectively, under optimum operating conditions. Moreover, the proposed pre-distortion technique can potentially provide higher system performance to that obtained with nonlinear equalization at the receiver.

  9. Preparation and optical characterization of DNA-riboflavin thin films

    Science.gov (United States)

    Paulson, Bjorn; Shin, Inchul; Kong, Byungjoo; Sauer, Gregor; Dugasani, Sreekantha Reddy; Khazaeinezhad, Reza; Jung, Woohyun; Joo, Boram; Oh, Kyunghwan

    2016-09-01

    Thin films of DNA biopolymer thin film are fabricated by a drop casting process on glass and silicon substrates, as well as freestanding. The refractive index is measured by elliposmetry and in bulk DNA film the refractive index is shown to be increased in the 600 to 900 nm DNA transparency window by doping with riboflavin. Further analysis with FT-IR, Raman, and XRD are used to determine whether binding between riboflavin and DNA occurs.

  10. Latency and distortion of electromagnetic trackers for augmented reality systems

    CERN Document Server

    Himberg, Henry

    2014-01-01

    Augmented reality (AR) systems are often used to superimpose virtual objects or information on a scene to improve situational awareness. Delays in the display system or inaccurate registration of objects destroy the sense of immersion a user experiences when using AR systems. AC electromagnetic trackers are ideal for these applications when combined with head orientation prediction to compensate for display system delays. Unfortunately, these trackers do not perform well in environments that contain conductive or ferrous materials due to magnetic field distortion without expensive calibration

  11. MRI, geometric distortion of the image and stereotaxy

    International Nuclear Information System (INIS)

    Derosier, C.; Delegue, G.; Munier, T.; Pharaboz, C.; Cosnard, G.

    1991-01-01

    The MRI technology may be the starting-point of geometric distortion. The mathematical preciseness of a spatial location may be disturbed and alter the guidance of a MRI interventional act, especially in stereotactic brain biopsy. A review of the literature shows errors of 1 to 1.5 mm. Our results show an error of 0.16±0.66. The control of quality: homogeneity and calibration of magnetic-field gradients, permit an improve of the ballistic preciseness and give permission to realize the guidance of a stereotactic brain biopsy with the alone MRI

  12. Optical distortions in electron/positron storage rings

    International Nuclear Information System (INIS)

    Brown, K.L.; Donald, M.; Servranckx, R.

    1983-01-01

    We have studied the optical distortions in the PEP electron/positron storage ring for various optical configurations using the computer programs DIMAT, HARMON, PATRICIA, and TURTLE. The results are shown graphically by tracing several thousand trajectories from one interaction region to the next using TURTLE and by tracing a few selected rays several hundred turns using the programs DIMAT and PATRICIA. The results show an interesting correlation between the calculated optical cleanliness of a particular lattice configuration and the observed operating characteristics of the machine

  13. Spatial affects and imitations in OWS and Distortion

    DEFF Research Database (Denmark)

    Samson, Kristine

    the notions of affect (Thrift 2008, Ash & Amin 2002, Anderson & Holden 2008) and imitation (Tarde 1903), the paper will discuss recent urban crowd movements. OWS has spread a global social activist movement using affective bodily means of communication, whereas Distortion is a cultural street festival taking...... manner. For instance, both crowds do not merely gather and organize in terms of verbal communication, rather they organize virally, visually and through bodily affects and imitation. In that sense they appropriate urban space and its architectural design ”like viruses that hop between people, thereby...

  14. Distortion-product otoacoustic emission at low frequencies in humans

    DEFF Research Database (Denmark)

    Christensen, Anders Tornvig

    -frequency hearing has not yet been characterized by measurement of low-frequency emissions from the cochlea. Low-frequency emissions are expected to be covered in sounds of breathing, blood circulation, and so on, if they exist at all at measurable levels. The present study shows, in essence, that the human ear...... emits distortion at least 1-2 octaves lower in frequency than has previously been shown. The emission is promising for further exploratory and clinical assessment of cochlear activity associated with low-frequency hearing. Anders received his M.Sc. degree in acoustics in 2012 from Aalborg University...

  15. Luminosity Optimization With Offset, Crossing Angle, and Distortion

    CERN Document Server

    Wu, Juhao

    2005-01-01

    In a linear collider, sources of beam jitter due to kicker noise, quadrupole vibration and long-range transverse wakefields will lead to beam offsets and tilts at the Intersection Point (IP). In addition, sources of emittance dilution such as short-range transverse wakefields or dispersive errors will lead to internal beam distortions. When the IP disruption parameter is large, these beam imperfections will be amplified by a single bunch kink instability which will lead to luminosity loss. In this paper, we study the luminosity loss and then the optimization required to cancel the luminosity loss first analytically and then with simulation.

  16. Beam-beam diagnostics from closed-orbit distortion

    International Nuclear Information System (INIS)

    Furman, M.; Chin, Y.H.; Eden, J.; Kozanecki, W.; Tennyson, J.; Ziemann, V.

    1992-07-01

    We study the applicability of beam-beam deflection techniques as a tuning tool for asymmetric B factories, focusing on PEP-II as an example. Assuming that the closed orbits of the two beams are separated vertically at the interaction point by a local orbit bump that is nominally closed, we calculate the residual beam orbit distortions due to the beam-beam interaction. Difference orbit measurements, performed at points conveniently distant from the interaction point (IP), provide distinct signatures that can be used to maintain the beams in collision and perform detailed optical diagnostics at the IP. A proposal to test this method experimentally at the TRISTAN ring is briefly discussed

  17. Memory of AMR coded speech distorted by packet loss

    OpenAIRE

    Nykänen, Arne; Lindegren, David; Wruck, Louisa; Ljung, Robert; Odelius, Johan; Möller, Sebastian

    2014-01-01

    Previous studies have shown that free recall of spoken word lists is impaired if the speech is presented in background noise, even if the signal-to-noise ratio is kept at a level allowing full word identification. The objective of this study was to examine recall rates for word lists presented in noise and word lists coded by an AMR (Adaptive Multi Rate) telephone codec distorted by packet loss. Twenty subjects performed a word recall test. Word lists consisting of ten words were played to th...

  18. Base Station Antenna Pattern Distortion in Practical Urban Deployment Scenarios

    DEFF Research Database (Denmark)

    Rodriguez Larrad, Ignacio; Nguyen, Huan Cong; Sørensen, Troels Bundgaard

    2014-01-01

    In real urban deployments, base station antennas are typically not placed in free space conditions. Therefore, the radiation pattern can be affected by mounting structures and nearby obstacles located in the proximity of the antenna (near-field), which are often not taken into consideration. Also...... presents a combination of near-field and far-field simulations aimed to provide an overview of the distortion experienced by the base station antenna pattern in two different urban deployment scenarios: rooftop and telecommunications tower. The study illustrates how, in comparison with the near...

  19. An analytic distorted wave approximation for intermediate energy proton scattering

    International Nuclear Information System (INIS)

    Di Marzio, F.; Amos, K.

    1982-01-01

    An analytic Distorted Wave approximation has been developed for use in analyses of intermediate energy proton inelastic scattering from nuclei. Applications are made to analyse 402 and 800 MeV data from the isoscalar and isovector 1 + and 2 + states in 12 C and to the 800 MeV data from the excitation of the 2 - (8.88MeV) state in 16 O. Comparisons of predictions made using different model two-nucleon t-matrices and different models of nuclear structure are given

  20. Mirror distortion of the levels of a compound system

    International Nuclear Information System (INIS)

    Khvalchenko, I.I.

    1995-01-01

    The problem of the action of an arbitrary perturbation on a system of two identical atoms in the radiation field is analyzed. For simplicity, only two-level atoms are considered, the field is assumed to be classical, and the spontaneous transitions are ignored. The polarizations are calculated for the open-quotes two atoms + fieldclose quotes and open-quotes two atoms + field + particleclose quotes systems. A comparison of the obtained relationships allows us to clarify the character of the level distortions caused by the external perturbation in the compound system. 10 refs

  1. Distortion product otoacoustic emission fine structure of symphony orchestra musicians

    DEFF Research Database (Denmark)

    Reuter, Karen; Hammershøi, Dorte

    2006-01-01

    Otoacoustic emissions (OAE) are sounds produced by the healthy inner ear. They can be measured as low-level signals in the ear canal and are used to monitor the functioning of outer hair cells.Several studies indicate that OAE might be a more sensitive measure to detect early noise-induced hearing...... losses than puretone audiometry. The distortion product otoacoustic emission (DPOAE) fine structure is obtained when the ear is stimulated by dual tone stimuli using a high frequency resolution. It is characterized by quasi-periodic variations across frequency, as it can be observed in the hearing...

  2. Influence of the film thickness on the structure, optical and electrical properties of ITO coatings deposited by sputtering at room temperature on glass and plastic substrates

    International Nuclear Information System (INIS)

    Guillén, C; Herrero, J

    2008-01-01

    Transparent and conductive indium tin oxide (ITO) films with thickness between 0.2 and 0.7 µm were deposited by sputtering at room temperature on glass and polyethylene terephthalate (PET) substrates. All films were polycrystalline, with crystallite size increasing and lattice distortion decreasing when the film thickness was increased. Besides, transmission in the near-infrared region is found to be decreasing and carrier concentration increasing when the film thickness was increased. For the same thickness, the lattice distortion is slightly lower and the carrier concentration higher for the layers grown on PET substrates. A direct relationship between the lattice distortion and the free carrier concentration has been established, applying to the films grown on glass and plastic substrates. By adjusting ITO coating thickness, sheet resistance below 15 Ω sq −1 and average visible transmittance about 90% have been achieved by sputtering at room temperature

  3. Characterization, prediction, and correction of geometric distortion in 3 T MR images

    International Nuclear Information System (INIS)

    Baldwin, Lesley N.; Wachowicz, Keith; Thomas, Steven D.; Rivest, Ryan; Gino Fallone, B.

    2007-01-01

    The work presented herein describes our methods and results for predicting, measuring and correcting geometric distortions in a 3 T clinical magnetic resonance (MR) scanner for the purpose of image guidance in radiation treatment planning. Geometric inaccuracies due to both inhomogeneities in the background field and nonlinearities in the applied gradients were easily visualized on the MR images of a regularly structured three-dimensional (3D) grid phantom. From a computed tomography scan, the locations of just under 10 000 control points within the phantom were accurately determined in three dimensions using a MATLAB-based computer program. MR distortion was then determined by measuring the corresponding locations of the control points when the phantom was imaged using the MR scanner. Using a reversed gradient method, distortions due to gradient nonlinearities were separated from distortions due to inhomogeneities in the background B 0 field. Because the various sources of machine-related distortions can be individually characterized, distortions present in other imaging sequences (for which 3D distortion cannot accurately be measured using phantom methods) can be predicted negating the need for individual distortion calculation for a variety of other imaging sequences. Distortions were found to be primarily caused by gradient nonlinearities and maximum image distortions were reported to be less than those previously found by other researchers at 1.5 T. Finally, the image slices were corrected for distortion in order to provide geometrically accurate phantom images

  4. DNA probes

    International Nuclear Information System (INIS)

    Castelino, J.

    1992-01-01

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with 32 P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism's genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens

  5. DNA probes

    Energy Technology Data Exchange (ETDEWEB)

    Castelino, J

    1993-12-31

    The creation of DNA probes for detection of specific nucleotide segments differs from ligand detection in that it is a chemical rather than an immunological reaction. Complementary DNA or RNA is used in place of the antibody and is labelled with {sup 32}P. So far, DNA probes have been successfully employed in the diagnosis of inherited disorders, infectious diseases, and for identification of human oncogenes. The latest approach to the diagnosis of communicable and parasitic infections is based on the use of deoxyribonucleic acid (DNA) probes. The genetic information of all cells is encoded by DNA and DNA probe approach to identification of pathogens is unique because the focus of the method is the nucleic acid content of the organism rather than the products that the nucleic acid encodes. Since every properly classified species has some unique nucleotide sequences that distinguish it from every other species, each organism`s genetic composition is in essence a finger print that can be used for its identification. In addition to this specificity, DNA probes offer other advantages in that pathogens may be identified directly in clinical specimens 10 figs, 2 tabs

  6. Theoretical study on onset of cubic distortion product otoacoustic emissions

    Science.gov (United States)

    Vencovský, Václav; Vetešník, Aleš

    2018-05-01

    The distortion product otoacoustic emissions (DPOAEs) are generated when the cochlea is stimulated by two pure tones with different frequencies f1 and f2. Onset of the DPOAE amplitude may have a nonmonotonic complex shape when the f2 is pulsed during a stationary f1 input. Observed complexities have been explained as (1) due to the secondary source of the DPOAE at the distortion product (DP) characteristic site, and (2) due to the spatial distribution of DP sources with different phases. There is also a third possibility that the complexities are due to the suppression of the f1 basilar membrane (BM) response during the f2 onset. In this study, a hydrodynamic cochlea model is used to examine influence of f1 suppression on the time course of DPOAE onset. In particular, a set of simulations was performed for frequency ratio f2/f1 = 1.26 and various levels of the primary tones (L1 and L2=30-70 dB SPL) to determine the relationship between time dependencies of the DPOAE onset and the suppression of the f1 BM response. The model predicts that suppression of the f1 BM response can cause suppression of DPOAE amplitude during the onset period.

  7. Distortions in power spectra of digitized signals - II: Suggested solution

    International Nuclear Information System (INIS)

    Njau, E.C.

    1982-04-01

    In Part I of this report we developed analytical expressions which represent exactly the energy density spectra of ''digitization processes'' that are essentially involved in spectral analysis of continuous signals. Besides, we related the spectral energy density of each digitization process to the parameters of the exact spectral energy density of the corresponding signal. On this basis, we briefly discussed the forms of distortions (or false structures) which are present in normally computed power spectra when the corresponding spectra of the digitization processes are not sufficiently decoupled from or nullified in the computed spectra. The biggest worry with regard to these distortions is not only that they may mask the actual information contained in the original signal, but also they may tempt the researcher to establish false characteristics about the signal involved. It is, in this context, that any reasonable method that could be used (even conditionally) to pinpoint false structures in computed power spectra would be both timely and useful. A simple, handy guidance through which some portions of computed energy density spectra which are dominated by the false structures mentioned above, can be located is presented herein. Equations are presented which give the various frequencies at which false peaks may be located in such ''contaminated'' portions of computed energy density spectra. The occurrence of frequency shifts in computed power spectra is also briefly discussed. (author)

  8. Multipole analysis of redshift-space distortions around cosmic voids

    Energy Technology Data Exchange (ETDEWEB)

    Hamaus, Nico; Weller, Jochen [Universitäts-Sternwarte München, Fakultät für Physik, Ludwig-Maximilians Universität, Scheinerstr. 1, D-81679 München (Germany); Cousinou, Marie-Claude; Pisani, Alice; Aubert, Marie; Escoffier, Stéphanie, E-mail: hamaus@usm.lmu.de, E-mail: cousinou@cppm.in2p3.fr, E-mail: pisani@cppm.in2p3.fr, E-mail: maubert@cppm.in2p3.fr, E-mail: escoffier@cppm.in2p3.fr, E-mail: jochen.weller@usm.lmu.de [Aix Marseille Univ., CNRS/IN2P3, CPPM, 163 avenue de Luminy, F-13288, Marseille (France)

    2017-07-01

    We perform a comprehensive redshift-space distortion analysis based on cosmic voids in the large-scale distribution of galaxies observed with the Sloan Digital Sky Survey. To this end, we measure multipoles of the void-galaxy cross-correlation function and compare them with standard model predictions in cosmology. Merely considering linear-order theory allows us to accurately describe the data on the entire available range of scales and to probe void-centric distances down to about 2 h {sup −1}Mpc. Common systematics, such as the Fingers-of-God effect, scale-dependent galaxy bias, and nonlinear clustering do not seem to play a significant role in our analysis. We constrain the growth rate of structure via the redshift-space distortion parameter β at two median redshifts, β( z-bar =0.32)=0.599{sup +0.134}{sub −0.124} and β( z-bar =0.54)=0.457{sup +0.056}{sub −0.054}, with a precision that is competitive with state-of-the-art galaxy-clustering results. While the high-redshift constraint perfectly agrees with model expectations, we observe a mild 2σ deviation at z-bar =0.32, which increases to 3σ when the data is restricted to the lowest available redshift range of 0.15< z <0.33.

  9. Multipole analysis of redshift-space distortions around cosmic voids

    Science.gov (United States)

    Hamaus, Nico; Cousinou, Marie-Claude; Pisani, Alice; Aubert, Marie; Escoffier, Stéphanie; Weller, Jochen

    2017-07-01

    We perform a comprehensive redshift-space distortion analysis based on cosmic voids in the large-scale distribution of galaxies observed with the Sloan Digital Sky Survey. To this end, we measure multipoles of the void-galaxy cross-correlation function and compare them with standard model predictions in cosmology. Merely considering linear-order theory allows us to accurately describe the data on the entire available range of scales and to probe void-centric distances down to about 2 h-1Mpc. Common systematics, such as the Fingers-of-God effect, scale-dependent galaxy bias, and nonlinear clustering do not seem to play a significant role in our analysis. We constrain the growth rate of structure via the redshift-space distortion parameter β at two median redshifts, β(bar z=0.32)=0.599+0.134-0.124 and β(bar z=0.54)=0.457+0.056-0.054, with a precision that is competitive with state-of-the-art galaxy-clustering results. While the high-redshift constraint perfectly agrees with model expectations, we observe a mild 2σ deviation at bar z=0.32, which increases to 3σ when the data is restricted to the lowest available redshift range of 0.15

  10. The magnetic-distortion probe: velocimetry in conducting fluids.

    Science.gov (United States)

    Miralles, Sophie; Verhille, Gautier; Plihon, Nicolas; Pinton, Jean-François

    2011-09-01

    A new type of velocimeter, capable of local velocity measurements in conducting fluids, is introduced. The principle of the "magnetic-distortion probe" is based on the measurement of the induced magnetic field by the flow of a conducting fluid in the vicinity of a localized magnetic field. The new velocimeter has no moving parts, and can be enclosed in a sealed cap, easing the implementation in harsh environments, such as liquid metals. The proposed method allows one to probe both the continuous part and fluctuations of the velocity, the temporal and spatial resolution being linked to the actual geometric configuration of the probe. A prototype probe has been tested in a gallinstan pipe flow and in a fully turbulent flow of liquid gallium generated by the counter rotation of two coaxial impellers in a cylinder. The signals have been compared to a reference potential probe and show very good agreement both for time-averaged velocities and turbulent fluctuations. The prototype is shown to detect motion from a few cm s(-1) to a few m s(-1). Moreover, the use of the magnetic-distortion probe with large-scale applied magnetic field is discussed. © 2011 American Institute of Physics

  11. Vertical dispersion produced by random closed orbit distortions and sextupoles

    International Nuclear Information System (INIS)

    Suzuki, Toshio.

    1977-01-01

    Vertical dispersion appears even in a machine designed with plane symmetry because of vertical closed orbit distortions, linear coupling and coupling due to sextupoles. This gives rise to several undesirable effects in an electron-positron storage ring such as PEP. Vertical dispersion at the interaction point will increase beam height and reduce luminosity. Vertical dispersion around the ring will modify vertical emittance and partition numbers for synchrotron radiation damping. It will also induce betatron-synchrotron resonance and affect chromaticity correction. Vertical dispersion due to random closed orbit distortions and sextupoles has been studied by Piwinski, and he has indicated that correction of chromaticity and chromatic change of β-function is important. However, he has assumed one error element and evaluated the dispersion at the position of the element. We generalize his argument to a more realistic case and derive more precise criteria for the correction of vertical dispersion. Horizontal dispersion due to perturbations is also studied. Vertical dispersion due to linear coupling is neglected in this note, since it has been studied by other authors. 7 refs

  12. Optical technique to measure distortion on heat treated parts

    Science.gov (United States)

    Sciammarella, Federico Mariano

    The use of aluminum for structural applications grows with the continual improvement of their physical properties. Through the various amounts of heat treatments that are available, aluminum can vary in properties for all different types of applications. The automotive industry has benefited the most from the use of aluminum and they continue to seek more uses. The heat treatments of these parts are very vital in providing the properties needed for their particular applications. Moreover understanding the effects of heat treatments that may cause distortion to a part is critical. Most of the work carried out in this field is a pre and post measurement after part has experienced its treatment. In this study, we carry out in-situ measurements of the distortions that a heat-treated part undergoes when subjected to temperatures near melting followed by a slow cooling. In order to confirm the experimental measurements we used HOTPOINT to simulate the experiment and compare results. This study will provide much needed insight to the complex occurrences that aluminum parts undergo during heat treatment.

  13. Distortion and regulation characterization of a Mapham inverter

    Science.gov (United States)

    Sundberg, Richard C.; Brush, Andrew S.; Button, Robert M.; Patterson, Alexander G.

    1989-01-01

    Output voltage Total Harmonic Distortion (THD) of a 20kHz, 6kVA Mapham resonant inverter is characterized as a function of its switching-to-resonant frequency ratio, f sub s/f sub r, using the EASY5 engineering analysis system. EASY5 circuit simulation results are compared with hardware test results to verify the accuracy of the simulations. The effects of load on the THD versus f sub s/f sub r ratio is investigated for resistive, leading, and lagging power factor load impedances. The effect of the series output capacitor on the Mapham inverter output voltage distortion and inherent load regulation is characterized under loads of various power factors and magnitudes. An optimum series capacitor value which improves the inherent load regulation to better than 3 percent is identified. The optimum series capacitor value is different than the value predicted from a modeled frequency domain analysis. An explanation is proposed which takes into account the conduction overlap in the inductor pairs during steady-state inverter operation, which decreases the effective inductance of a Mapham inverter. A fault protection and current limit method is discussed which allows the Mapham inverter to operate into a short circuit, even when the inverter resonant circuit becomes overdamped.

  14. Multipole analysis of redshift-space distortions around cosmic voids

    International Nuclear Information System (INIS)

    Hamaus, Nico; Weller, Jochen; Cousinou, Marie-Claude; Pisani, Alice; Aubert, Marie; Escoffier, Stéphanie

    2017-01-01

    We perform a comprehensive redshift-space distortion analysis based on cosmic voids in the large-scale distribution of galaxies observed with the Sloan Digital Sky Survey. To this end, we measure multipoles of the void-galaxy cross-correlation function and compare them with standard model predictions in cosmology. Merely considering linear-order theory allows us to accurately describe the data on the entire available range of scales and to probe void-centric distances down to about 2 h −1 Mpc. Common systematics, such as the Fingers-of-God effect, scale-dependent galaxy bias, and nonlinear clustering do not seem to play a significant role in our analysis. We constrain the growth rate of structure via the redshift-space distortion parameter β at two median redshifts, β( z-bar =0.32)=0.599 +0.134 −0.124 and β( z-bar =0.54)=0.457 +0.056 −0.054 , with a precision that is competitive with state-of-the-art galaxy-clustering results. While the high-redshift constraint perfectly agrees with model expectations, we observe a mild 2σ deviation at z-bar =0.32, which increases to 3σ when the data is restricted to the lowest available redshift range of 0.15< z <0.33.

  15. [Distorted cognition of bodily sensations in subtypes of social anxiety].

    Science.gov (United States)

    Kanai, Yoshihiro; Sasaki, Shoko; Iwanaga, Makoto; Seiwa, Hidetoshi

    2010-02-01

    The purpose of this study was to investigate the relationship between subtypes of social anxiety and distorted cognition of bodily sensations. The package of questionnaires including the Social Phobia Scale (SPS) and the Social Interaction Anxiety Scale (SIAS) was administered to 582 undergraduate students. To identify subtypes of social anxiety, cluster analysis was conducted using scores of the SPS and SIAS. Five clusters were identified and labeled as follows: Generalized type characterized by intense anxiety in most social situations, Non-anxious type characterized by low anxiety levels in social situations, Averaged type whose anxiety levels are averaged, Interaction anxiety type who feels anxiety mainly in social interaction situations, and Performance anxiety type who feels anxiety mainly in performance situations. Results of an ANOVA indicated that individuals with interaction type fear the negative evaluation from others regarding their bodily sensations whereas individuals with performance type overestimate the visibility of their bodily sensations to others. Differences in salient aspects of cognitive distortion among social anxiety subtypes may show necessity to select intervention techniques in consideration of subtypes.

  16. The UV Plasmonic Behavior of Distorted Rhodium Nanocubes

    Directory of Open Access Journals (Sweden)

    Yael Gutiérrez

    2017-12-01

    Full Text Available For applications of surface-enhanced spectroscopy and photocatalysis, the ultraviolet (UV plasmonic behavior and charge distribution within rhodium nanocubes is explored by a detailed numerical analysis. The strongest plasmonic hot-spots and charge concentrations are located at the corners and edges of the nanocubes, exactly where they are the most spectroscopically and catalytically active. Because intense catalytic activity at corners and edges will reshape these nanoparticles, distortions of the cubical shape, including surface concavity, surface convexity, and rounded corners and edges, are also explored to quantify how significantly these distortions deteriorate their plasmonic and photocatalytic properties. The fact that the highest fields and highest carrier concentrations occur in the corners and edges of Rh nanocubes (NCs confirms their tremendous potential for plasmon-enhanced spectroscopy and catalysis. It is shown that this opportunity is fortuitously enhanced by the fact that even higher field and charge concentrations reside at the interface between the metal nanoparticle and a dielectric or semiconductor support, precisely where the most chemically active sites are located.

  17. Interliminal Design: Understanding cognitive heuristics to mitigate design distortion

    Directory of Open Access Journals (Sweden)

    Andrew McCollough

    2014-12-01

    Full Text Available Cognitive heuristics are mental shortcuts adapted over time to enable rapid interpretation of our complex environment. They are intrinsic to human cognition and resist modification. Heuristics applied outside the context to which they are best suited are termed cognitive bias, and are the cause of systematic errors in judgment and reasoning. As both a cognitive and intuitive discipline, design by individuals is vulnerable to context-inappropriate heuristic usage. Designing in groups can act positively to counterbalance these tendencies, but is subject to heuristic misuse and biases particular to social environments. Mismatch between desired and actual outcomes– termed here, design distortion – occurs when such usage goes unnoticed and unaddressed, and can affect multiple dimensions of a system. We propose a methodology, interliminal design, emerging from the Program in Collaborative Design at Pacific Northwest College of Art, to specifically address the influence of cognitive heuristics in design. This adaptive approach involves reflective, dialogic, inquiry-driven practices intended to increase awareness of heuristic usage, and identify aspects of the design process vulnerable to misuse on both individual and group levels. By facilitating the detection and mitigation of potentially costly errors in judgment and decision-making that create distortion, such metacognitive techniques can meaningfully improve design.

  18. Radiolabelled substrates for studying biological effects of trace contaminants

    International Nuclear Information System (INIS)

    1975-01-01

    A programme of coordinated isotopic tracer-aided investigations of the biological side-effects of foreign chemical residues in food and agriculture, initiated in 1973, was reviewed. The current status of representative investigations from the point of view of techniques and priorities was assessed. Such investigations involved radioactive substrates for studying DNA injury and its repair; 14 C-labelled acetylcholine as substrate for measuring enzyme inhibition due to the presence of, or exposure to, anticholinesteratic contaminants; radioactive substrates as indication of side-effects in non-target organisms and of their comparative susceptibilities; radioactive substrates as indicators of persistence or biodegradability of trace contaminants of soil or water; and labelled pools for studying the biological side-effects of trace contaminants. Priorities were identified

  19. Solid substrate fermentation

    Energy Technology Data Exchange (ETDEWEB)

    Tengerdy, R P

    1985-04-01

    Solid Substrate Fermentation (SSF) describes the microbiological tranformation of biological materials in their natural state, in contrast with liquid or submerged fermentations which are carried out in dilute solutions or slurries. The most important industrial microorganisms used in SSF are filamentous fungi and the critical factors in their growth are the control of the moisture level and the temperature. Traditionally, most SSFs are conducted in shallow trays (so that heat build up is avoided) and stacked in a moist chamber, however, the modern SSF should be able to mix large amounts of substrate for a uniform fermentation, maximum automization scale-up of the process, continuous operation and fermentation control and a promising new design is the Helical screw fermenter. At the present time SSF is used in the production of foods (e.g. mushrooms and oriental foods) in municipal, agricultural and industrial solid waste disposal and in the production of enzymes and speciality chemicals but it does not seem likely that it will replace prevalent liquid fermentation technologies. 29 references.

  20. Numerical correction of distorted images in full-field optical coherence tomography

    Science.gov (United States)

    Min, Gihyeon; Kim, Ju Wan; Choi, Woo June; Lee, Byeong Ha

    2012-03-01

    We propose a numerical method which can numerically correct the distorted en face images obtained with a full field optical coherence tomography (FF-OCT) system. It is shown that the FF-OCT image of the deep region of a biological sample is easily blurred or degraded because the sample has a refractive index (RI) much higher than its surrounding medium in general. It is analyzed that the focal plane of the imaging system is segregated from the imaging plane of the coherence-gated system due to the RI mismatch. This image-blurring phenomenon is experimentally confirmed by imaging the chrome pattern of a resolution test target through its glass substrate in water. Moreover, we demonstrate that the blurred image can be appreciably corrected by using the numerical correction process based on the Fresnel-Kirchhoff diffraction theory. The proposed correction method is applied to enhance the image of a human hair, which permits the distinct identification of the melanin granules inside the cortex layer of the hair shaft.

  1. Direct Fourier imaging of distortions in LaAlO{sub 3} films

    Energy Technology Data Exchange (ETDEWEB)

    Schlueter, Christoph; Zegenhagen, Joerg [ESRF, Grenoble (France); Lee, Tien-Lin [Diamond Light Source Ltd, Didcot (United Kingdom); Aruta, Carmela [CNR-SPIN, Naples (Italy)

    2012-07-01

    The formation of a quasi-2dimensional electron gas at interface of SrTiO{sub 3} (STO) and LaAlO{sub 3} (LAO) attracted considerable attention in the recent years. The polar LAO layer was expected to cause the build-up of an electric potential. Distortions in the overlayer are discussed as one possible response of the system. The highly sensitive X-ray standing wave (XSW) imaging technique is well suited to study theses films because of its chemical and spacial resolution. LAO thin films below and above the critical thickness for conductivity were studied at the hard X-ray photo electron spectroscopy end station of ID32 at the ESRF. The XSW modulated core level photo electron yield was recorded for the five elements present in film and substrate for seven different Bragg reflections. Subsequent analysis provided for each reflection and element the amplitude and phase of one Fourier coefficient of the elemental atomic distribution function. The three dimensional real space image of the atomic distribution for each of the elements is reconstructed by direct Fourier inversion. The reconstructed 3D images obtained by this model free approach reveal significant atomic displacements.

  2. Maintainable substrate carrier for electroplating

    Science.gov (United States)

    Chen, Chen-An [Milpitas, CA; Abas, Emmanuel Chua [Laguna, PH; Divino, Edmundo Anida [Cavite, PH; Ermita, Jake Randal G [Laguna, PH; Capulong, Jose Francisco S [Laguna, PH; Castillo, Arnold Villamor [Batangas, PH; Ma,; Xiaobing, Diana [Saratoga, CA

    2012-07-17

    One embodiment relates to a substrate carrier for use in electroplating a plurality of substrates. The carrier includes a non-conductive carrier body on which the substrates are placed and conductive lines embedded within the carrier body. A plurality of conductive clip attachment parts are attached in a permanent manner to the conductive lines embedded within the carrier body. A plurality of contact clips are attached in a removable manner to the clip attachment parts. The contact clips hold the substrates in place and conductively connecting the substrates with the conductive lines. Other embodiments, aspects and features are also disclosed.

  3. Marvels of enzyme catalysis at true atomic resolution: distortions, bond elongations, hidden flips, protonation states and atom identities.

    Science.gov (United States)

    Neumann, Piotr; Tittmann, Kai

    2014-12-01

    Although general principles of enzyme catalysis are fairly well understood nowadays, many important details of how exactly the substrate is bound and processed in an enzyme remain often invisible and as such elusive. In fortunate cases, structural analysis of enzymes can be accomplished at true atomic resolution thus making possible to shed light on otherwise concealed fine-structural traits of bound substrates, intermediates, cofactors and protein groups. We highlight recent structural studies of enzymes using ultrahigh-resolution X-ray protein crystallography showcasing its enormous potential as a tool in the elucidation of enzymatic mechanisms and in unveiling fundamental principles of enzyme catalysis. We discuss the observation of seemingly hyper-reactive, physically distorted cofactors and intermediates with elongated scissile substrate bonds, the detection of 'hidden' conformational and chemical equilibria and the analysis of protonation states with surprising findings. In delicate cases, atomic resolution is required to unambiguously disclose the identity of atoms as demonstrated for the metal cluster in nitrogenase. In addition to the pivotal structural findings and the implications for our understanding of enzyme catalysis, we further provide a practical framework for resolution enhancement through optimized data acquisition and processing. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. Laboratory simulation of atmospheric turbulence induced optical wavefront distortion

    Science.gov (United States)

    Taylor, Travis Shane

    1999-11-01

    Many creative approaches have been taken in the past for simulating the effect that atmospheric turbulence has on optical beams. Most of the experimental architectures have been complicated and consisted of many optical elements as well as moving components. These techniques have shown a modicum of success; however, they are not completely controllable or predictable. A benchtop technique for experimentally producing one important effect that atmospheric turbulence has on optical beams (phase distortion) is presented here. The system is completely controllable and predictable while accurately representing the statistical nature of the problem. Previous experimentation in optical processing through turbulent media has demonstrated that optical wavefront distortions can be produced via spatial light modulating (SLM) devices, and most turbulence models and experimental results indicate that turbulence can be represented as a phase fluctuation. The amplitude distributions in the resulting far field are primarily due to propagation of the phase. Operating a liquid crystal television (LCTV) in the ``phase- mostly'' mode, a phase fluctuation type model for turbulence is utilized in the present investigation, and a real-time experiment for demonstrating the effects was constructed. For an optical system to simulate optical wavefront distortions due to atmospheric turbulence, the following are required: (1)An optical element that modulates the phasefront of an optical beam (2)A model and a technique for generating spatially correlated turbulence simulating distributions (3)Hardware and software for displaying and manipulating the information addressing the optical phase modulation device The LCTV is ideal for this application. When operated in the ``phase-mostly'' mode some LCTVs can modulate the phasefront of an optical beam by as much as 2π and an algorithm for generating spatially correlated phase screens can be constructed via mathematical modeling software such as

  5. Inhibiting DNA Polymerases as a Therapeutic Intervention against Cancer

    Directory of Open Access Journals (Sweden)

    Anthony J. Berdis

    2017-11-01

    Full Text Available Inhibiting DNA synthesis is an important therapeutic strategy that is widely used to treat a number of hyperproliferative diseases including viral infections, autoimmune disorders, and cancer. This chapter describes two major categories of therapeutic agents used to inhibit DNA synthesis. The first category includes purine and pyrmidine nucleoside analogs that directly inhibit DNA polymerase activity. The second category includes DNA damaging agents including cisplatin and chlorambucil that modify the composition and structure of the nucleic acid substrate to indirectly inhibit DNA synthesis. Special emphasis is placed on describing the molecular mechanisms of these inhibitory effects against chromosomal and mitochondrial DNA polymerases. Discussions are also provided on the mechanisms associated with resistance to these therapeutic agents. A primary focus is toward understanding the roles of specialized DNA polymerases that by-pass DNA lesions produced by DNA damaging agents. Finally, a section is provided that describes emerging areas in developing new therapeutic strategies targeting specialized DNA polymerases.

  6. DNA methylation

    DEFF Research Database (Denmark)

    Williams, Kristine; Christensen, Jesper; Helin, Kristian

    2012-01-01

    DNA methylation is involved in key cellular processes, including X-chromosome inactivation, imprinting and transcriptional silencing of specific genes and repetitive elements. DNA methylation patterns are frequently perturbed in human diseases such as imprinting disorders and cancer. The recent...... discovery that the three members of the TET protein family can convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) has provided a potential mechanism leading to DNA demethylation. Moreover, the demonstration that TET2 is frequently mutated in haematopoietic tumours suggests that the TET...... proteins are important regulators of cellular identity. Here, we review the current knowledge regarding the function of the TET proteins, and discuss various mechanisms by which they contribute to transcriptional control. We propose that the TET proteins have an important role in regulating DNA methylation...

  7. DNA data

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Raw DNA chromatogram data produced by the ABI 373, 377, 3130 and 3730 automated sequencing machines in ABI format. These are from fish (primarily Sebastes spp.,...

  8. DNA nanotechnology

    Science.gov (United States)

    Seeman, Nadrian C.; Sleiman, Hanadi F.

    2018-01-01

    DNA is the molecule that stores and transmits genetic information in biological systems. The field of DNA nanotechnology takes this molecule out of its biological context and uses its information to assemble structural motifs and then to connect them together. This field has had a remarkable impact on nanoscience and nanotechnology, and has been revolutionary in our ability to control molecular self-assembly. In this Review, we summarize the approaches used to assemble DNA nanostructures and examine their emerging applications in areas such as biophysics, diagnostics, nanoparticle and protein assembly, biomolecule structure determination, drug delivery and synthetic biology. The introduction of orthogonal interactions into DNA nanostructures is discussed, and finally, a perspective on the future directions of this field is presented.

  9. DNA expressions - A formal notation for DNA

    NARCIS (Netherlands)

    Vliet, Rudy van

    2015-01-01

    We describe a formal notation for DNA molecules that may contain nicks and gaps. The resulting DNA expressions denote formal DNA molecules. Different DNA expressions may denote the same molecule. Such DNA expressions are called equivalent. We examine which DNA expressions are minimal, which

  10. Does energy-price regulation benefit China's economy and environment? Evidence from energy-price distortions

    International Nuclear Information System (INIS)

    Ju, Keyi; Su, Bin; Zhou, Dequn; Wu, Junmin

    2017-01-01

    China's energy prices have long been regulated due to the critical role energy plays in economic growth and social development, which leads to energy-price distortion to some extent. To figure out whether energy-price regulations will benefit China's economy (measured by GDP growth) and environment (measured by carbon emissions), we conducted an in-depth simulation using path analysis, where five energy products (natural gas, gasoline, fuel oil, steam coal, and coking coal) are selected and three measurements (absolute, relative, and moving) of energy-price distortions are calculated. The results indicate that, with a series of energy pricing policies, the price distortion for a single type of energy has gradually transformed, while the energy pricing system in China is not fully market-oriented yet. Furthermore, China's economy benefits from relative and moving distortions, while the absolute distortions of energy prices have negative impacts on economic growth. Finally, with regard to the environment, carbon emissions call for fewer distortions. - Highlights: • Price distortion for a single type of energy has gradually transformed. • Energy pricing system in China is not yet fully market-oriented. • China's economy benefits from relative and moving distortions. • Absolute distortions of energy prices have negative effects on economic growth. • Carbon emissions call for less pricing distortions.

  11. An Iterative Optimization Algorithm for Lens Distortion Correction Using Two-Parameter Models

    Directory of Open Access Journals (Sweden)

    Daniel Santana-Cedrés

    2016-12-01

    Full Text Available We present a method for the automatic estimation of two-parameter radial distortion models, considering polynomial as well as division models. The method first detects the longest distorted lines within the image by applying the Hough transform enriched with a radial distortion parameter. From these lines, the first distortion parameter is estimated, then we initialize the second distortion parameter to zero and the two-parameter model is embedded into an iterative nonlinear optimization process to improve the estimation. This optimization aims at reducing the distance from the edge points to the lines, adjusting two distortion parameters as well as the coordinates of the center of distortion. Furthermore, this allows detecting more points belonging to the distorted lines, so that the Hough transform is iteratively repeated to extract a better set of lines until no improvement is achieved. We present some experiments on real images with significant distortion to show the ability of the proposed approach to automatically correct this type of distortion as well as a comparison between the polynomial and division models.

  12. Distortions in power spectra of digitized signals - I: General formulations

    International Nuclear Information System (INIS)

    Njau, E.C.

    1982-04-01

    When a continuous signal f(t) is digitized and then spectrally analysed, the resultant energy spectral density R(ω) is given as R(ω) = |F(ω) * D(ω)| 2 , where F(ω) is the exact Fourier transform of f(t), D(ω) is the exact Fourier transform of the digitization process and * denotes convolution operation. A notable practical problem in spectral analysis is how to adequately decouple D(ω) from R(ω) and hence obtain the exact energy spectral density of f(t), i.e. |F(ω)| 2 , since R(ω) → |F(ω)| 2 only if D(ω) → delta(ω) or (under certain conditions) when D(ω) → delta(ω-ω 0 ) or if D(ω) → Σsub(n) delta(ω-ωsub(n)), where the latter is a sufficiently spaced series of delta functions and ωsub(j) is constant for a given j. A solution to this problem requires, among others, thorough understanding of D(ω), how it relates to F(ω) and hence the manner or degree to which D(ω) distorts or contaminates F(ω) to form R(ω). In this paper, we have developed exact analytical expressions of D(ω) that are well related to the corresponding F(ω) in the cases when f(t) is a simple sinusoid as well as when it is in the form of a more complex function. It is established that in either of these cases, D(ω) is a clear function of the salient parameters of both f(t) and F(ω). The contents of this paper are used in Part II to examine the manner and extent to which D(ω) causes distortions in R(ω) under given conditions, and also to establish a procedure by which such distortions may be decoupled from a practically computed R(ω). Other related issues such as frequency shifts in computed power spectra are also discussed therein. (author)

  13. What Is Mitochondrial DNA?

    Science.gov (United States)

    ... DNA What is mitochondrial DNA? What is mitochondrial DNA? Although most DNA is packaged in chromosomes within ... proteins. For more information about mitochondria and mitochondrial DNA: Molecular Expressions, a web site from the Florida ...

  14. Cells immobilized on patterns printed in DNA by an inkjet printer.

    Science.gov (United States)

    Sakurai, Kengo; Teramura, Yuji; Iwata, Hiroo

    2011-05-01

    The ability to two-dimensionally align various kinds of cells freely onto substrate would be a useful tool for analysis of cell-cell interactions. In this study, we aimed to establish a method for attaching cells to the substrate, in which the pattern is drawn by an inkjet printer. Poly-deoxyribonucleic acid (DNA) was immobilized onto the cell surface by use of DNA-conjugated poly(ethylene) glycol-phospholipid (DNA-PEG-lipid), which is the amphiphilic conjugate of PEG-lipid and single-stranded DNA. The surface of the substrate was then modified with the complementary DNA using an inkjet printer. Finally, DNA-immobilized cells were attached onto the substrate through DNA hybridization. The use of the inkjet printer enabled us to draw the DNA pattern accurately on the substrate with a resolution of a few hundred micrometers. DNA-immobilized cells could be attached precisely along the DNA pattern on the substrate. In addition, various kinds of cells could be attached simultaneously by using various sequences of DNA. Our technique is promising for analysis of cell-cell interactions and differentiation induction in stem cell research. Copyright © 2011 Elsevier Ltd. All rights reserved.

  15. Effects of Visual Feedback Distortion on Gait Adaptation: Comparison of Implicit Visual Distortion Versus Conscious Modulation on Retention of Motor Learning.

    Science.gov (United States)

    Kim, Seung-Jae; Ogilvie, Mitchell; Shimabukuro, Nathan; Stewart, Trevor; Shin, Joon-Ho

    2015-09-01

    Visual feedback can be used during gait rehabilitation to improve the efficacy of training. We presented a paradigm called visual feedback distortion; the visual representation of step length was manipulated during treadmill walking. Our prior work demonstrated that an implicit distortion of visual feedback of step length entails an unintentional adaptive process in the subjects' spatial gait pattern. Here, we investigated whether the implicit visual feedback distortion, versus conscious correction, promotes efficient locomotor adaptation that relates to greater retention of a task. Thirteen healthy subjects were studied under two conditions: (1) we implicitly distorted the visual representation of their gait symmetry over 14 min, and (2) with help of visual feedback, subjects were told to walk on the treadmill with the intent of attaining the gait asymmetry observed during the first implicit trial. After adaptation, the visual feedback was removed while subjects continued walking normally. Over this 6-min period, retention of preserved asymmetric pattern was assessed. We found that there was a greater retention rate during the implicit distortion trial than that of the visually guided conscious modulation trial. This study highlights the important role of implicit learning in the context of gait rehabilitation by demonstrating that training with implicit visual feedback distortion may produce longer lasting effects. This suggests that using visual feedback distortion could improve the effectiveness of treadmill rehabilitation processes by influencing the retention of motor skills.

  16. India’s Distorted Sex Ratio: Dire Consequences for Girls

    Science.gov (United States)

    Roberts, Lisa R.; Montgomery, Susanne B.

    2017-01-01

    Female gender discrimination related to cultural preference for males is a common global problem, especially in Asian countries. Numerous laws intended to prevent discrimination on the basis of gender have been passed in India, yet the distorted female-to-male sex ratio seems to show worsening tendencies. Using detailed, two-year longitudinal chart abstraction data about delivery records of a private mission hospital in rural India, we explored if hospital birth ratio data differed in comparison to regional data, and what demographic and contextual variables may have influenced these outcomes. Using quantitative chart abstraction and qualitative contextual data, study results showed the female-to-male ratio was lower than the reported state ratio at birth. In the context of India’s patriarchal structure, with its strong son preference, women are under tremendous pressure or coerced to access community-based, sex-selective identification and female fetus abortion. Nurses may be key to turning the tide. PMID:28286369

  17. Closed orbit distortion and the beam-beam interaction

    Energy Technology Data Exchange (ETDEWEB)

    Furman, M.; Chin, Y.H.; Eden, J. [Lawrence Berkeley Lab., CA (United States); Kozanecki, W. [CEA Centre d`Etudes Nucleaires de Saclay, 91 - Gif-sur-Yvette (France)]|[Stanford Linear Accelerator Center, Menlo Park, CA (United States); Tennyson, J.; Ziemann, V. [Stanford Linear Accelerator Center, Menlo Park, CA (United States)

    1992-06-01

    We study the applicability of beam-beam deflection techniques as a tuning tool for the SLAC/LBL/LLNL B factory, PEP-II. Assuming that the closed orbits of the two beams are separated vertically at the interaction point by a local orbit bump that is nominally closed, we calculate the residual beam orbit distortions due to the beam-beam interaction. Difference orbit measurements, performed at points conveniently distant from the IP, provide distinct coordinate- or frequency-space signatures that can be used to maintain the beams in collision and perform detailed optical diagnostics at the IP. A proposal to test this method experimentally at the TRISTAN ring is briefly discussed.

  18. Spectral distortion due to scattered cold neutrons in beryllium filter

    International Nuclear Information System (INIS)

    Sakamoto, Yukio; Inoue, Kazuhiko

    1980-01-01

    Polycrystalline beryllium filters are used to discriminate the cold neutrons from the thermal neutrons with energies above Bragg cut-off energy. The cold neutron scattering cross section is very small, but the remaining cross section is not zero. Then the neutrons scattered once from the filter in the cold neutron energy region have chance of impinging on the outlet of filter. Those neutrons are almost upscattered and develop into thermal neutrons; thus the discriminated cold neutrons include a small spectral distortion due to the thermal neutrons. In the present work we have evaluated the effect on the cold neutron spectrum due to the repeatedly scattered and transmitted neutrons by using a Monte Carlo calculation method. (author)

  19. Orbit and Optics Distortion in a Nonscaling Muon FFAG

    International Nuclear Information System (INIS)

    Machida, Shinji

    2008-01-01

    Finite chromaticity in a nonscaling FFAG makes transverse tunes move during acceleration. Particles have to cross many integer and half-integer resonances although all those tunes are imperfection ones. Plausible argument is that the acceleration is so fast that effects of those resonance crossings are marginal. We did a tracking study in a lattice with alignment and gradient errors to see how the orbit and optics distortion is excited. We found that in a time scale of the muon acceleration, namely total tune changes about one unit per turn, the resonance is not a proper way to describe the beam dynamics. Instead, a random walk model, in which we assume that alignment and gradient errors kick a particle randomly in phase space, well explains the tracking results

  20. Distorted wave method in reactions with composite particles

    International Nuclear Information System (INIS)

    Zelenskaya, N.S.; Teplov, I.B.

    1980-01-01

    The work deals with the distorbed wave method with a finite radius of interaction (DWBAFR) as applied to quantitative analysis of direct nuclear reactions with composite particles (including heavy ions) considering the reaction mechanisms other than the cluster stripping mechanism, in particular the exchange processes. The accurate equations of the distorbed-wave method in the three-body problem and the general formula dor calculating differential cross-sections of arbitrary binary reactions by DWBAFR are presented. Accurate and approximate methods allowing for finite interaction radius are discussed. Two main versions of exact account of recoil effects: separation of variables in wave functions of relative motion of particles and in interaction potentials and separation of variables in distorted waves are analysed. Given is a characteristic of the known calculated programs approximately and exactly taking account of recoil effects for direct and exchange processes [ru

  1. Image distortion due to refraction by planar surfaces

    International Nuclear Information System (INIS)

    Arizaga, R; Cap, N; Rabal, H; Trivi, M

    2010-01-01

    The term 'apparent depth' is commonly treated in textbooks as an issue easily understandable from the point of view of paraxial optical geometrical optics. Nevertheless, everyday life tells us that most of the time the observation of objects immersed in water is made under a great range of visual angles where the paraxial approximation is not valid. Here we developed a non-paraxial treatment to calculate the position and shape of the image of objects immersed in liquids of different refractive indices. The approach was focused on the parametric positions of the images of a single point at different viewing angles. Then we calculated how the image of an extended object is distorted. By using the Matlab software, it is possible to visualize the images for different geometrical conditions. We also include the analysis for refractive index with negative values as is the case of metamaterials.

  2. Process induced residual stresses and distortions in pultrusion

    DEFF Research Database (Denmark)

    Baran, Ismet; Tutum, Cem Celal; Nielsen, Michael Wenani

    2013-01-01

    In the present study, a coupled 3D transient Eulerian thermo-chemical analysis together with a 2D plane strain Lagrangian mechanical analysis of the pultrusion process, which has not been considered until now, is carried out. The development of the process induced residual stresses and strains...... together with the distortions are predicted during the pultrusion in which the cure hardening instantaneous linear elastic (CHILE) approach is implemented. At the end of the process, tension stresses prevail for the inner region of the composite since the curing rate is higher here as compared to the outer...... regions where compression stresses are obtained. The separation between the heating die and the part due to shrinkage is also investigated using a mechanical contact formulation at the die-part interface. The proposed approach is found to be efficient and fast for the calculation of the residual stresses...

  3. Image distortion due to refraction by planar surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Arizaga, R; Cap, N; Rabal, H; Trivi, M [Centro de Investigaciones Opticas (CONICET La Plata-CIC) and OPTIMO Dto de Ciencias Basicas, Fac. de Ingenieria UNLP, PO Box 3, 1897 Gonnet, La Plata (Argentina)

    2010-01-15

    The term 'apparent depth' is commonly treated in textbooks as an issue easily understandable from the point of view of paraxial optical geometrical optics. Nevertheless, everyday life tells us that most of the time the observation of objects immersed in water is made under a great range of visual angles where the paraxial approximation is not valid. Here we developed a non-paraxial treatment to calculate the position and shape of the image of objects immersed in liquids of different refractive indices. The approach was focused on the parametric positions of the images of a single point at different viewing angles. Then we calculated how the image of an extended object is distorted. By using the Matlab software, it is possible to visualize the images for different geometrical conditions. We also include the analysis for refractive index with negative values as is the case of metamaterials.

  4. Bond-Length Distortions in Strained Semiconductor Alloys

    International Nuclear Information System (INIS)

    Woicik, J.C.; Pellegrino, J.G.; Steiner, B.; Miyano, K.E.; Bompadre, S.G.; Sorensen, L.B.; Lee, T.; Khalid, S.

    1997-01-01

    Extended x-ray absorption fine structure measurements performed at In-K edge have resolved the outstanding issue of bond-length strain in semiconductor-alloy heterostructures. We determine the In-As bond length to be 2.581±0.004 Angstrom in a buried, 213 Angstrom thick Ga 0.78 In 0.22 As layer grown coherently on GaAs(001). This bond length corresponds to a strain-induced contraction of 0.015±0.004 Angstrom relative to the In-As bond length in bulk Ga 1-x In x As of the same composition; it is consistent with a simple model which assumes a uniform bond-length distortion in the epilayer despite the inequivalent In-As and Ga-As bond lengths. copyright 1997 The American Physical Society

  5. Vector neural net identifying many strongly distorted and correlated patterns

    Science.gov (United States)

    Kryzhanovsky, Boris V.; Mikaelian, Andrei L.; Fonarev, Anatoly B.

    2005-01-01

    We suggest an effective and simple algorithm providing a polynomial storage capacity of a network of the form M ~ N2s+1, where N is the dimension of the stored binary patterns. In this problem the value of the free parameter s is restricted by the inequalities N >> slnN >= 1. The algorithm allows us to identify a large number of highly distorted similar patterns. The negative influence of correlations of the patterns is suppressed by choosing a sufficiently large value of the parameter s. We show the efficiency of the algorithm by the example of a perceptron identifier, but it also can be used to increase the storage capacity of full connected systems of associative memory.

  6. India's Distorted Sex Ratio: Dire Consequences for Girls.

    Science.gov (United States)

    Roberts, Lisa R; Montgomery, Susanne B

    2016-01-01

    Female gender discrimination related to cultural preference for males is a common global problem, especially in Asian countries. Numerous laws intended to prevent discrimination on the basis of gender have been passed in India, yet the distorted female-to-male sex ratio seems to show worsening tendencies. Using detailed, two-year longitudinal chart abstraction data about delivery records of a private mission hospital in rural India, we explored if hospital birth ratio data differed in comparison to regional data, and what demographic and contextual variables may have influenced these outcomes. Using quantitative chart abstraction and qualitative contextual data, study results showed the female-to-male ratio was lower than the reported state ratio at birth. In the context of India's patriarchal structure, with its strong son preference, women are under tremendous pressure or coerced to access community-based, sex-selective identification and female fetus abortion. Nurses may be key to turning the tide.

  7. The correlation algorithm on the basis of hodograph distortions

    Energy Technology Data Exchange (ETDEWEB)

    Belkina, V.A.

    1982-01-01

    Results are given from studying the distortion of seismic temporary fields. From the examined distributions: of the normal, Student-t-distribution with two degrees of freedom and a mix of two normal distributions they are best described as a mix of normal distributions. Starting from this, a more precise criterion of correlating seismic waves is proposed. The effectiveness of this criterion is studied on modal material within the limits of a two-stage method for solving correlation problems consisting of a preliminary trace and search for related correlation variants. Practical use of the criterion makes it possible to increase the reliability of automatic correlation and, subsequently, to increase the accuracy of the final results of the seismic investigations.

  8. Closed orbit distortion and the beam-beam interaction

    International Nuclear Information System (INIS)

    Furman, M.; Chin, Y.H.; Eden, J.; Kozanecki, W.; Tennyson, J.; Ziemann, V.

    1992-01-01

    We study the applicability of beam-beam deflection techniques as a tuning tool for the SLAC/LBL/LLNL B factory, PEP-II. Assuming that the closed orbits of the two beams are separated vertically at the interaction point by a local orbit bump that is nominally closed, we calculate the residual beam orbit distortions due to the beam-beam interaction. Difference orbit measurements, performed at points conveniently distant from the IP, provide distinct coordinate- or frequency-space signatures that can be used to maintain the beams in collision and perform detailed optical diagnostics at the IP. A proposal to test this method experimentally at the TRISTAN ring is briefly discussed

  9. Asymmetric Hardware Distortions in Receive Diversity Systems: Outage Performance Analysis

    KAUST Repository

    Javed, Sidrah; Amin, Osama; Ikki, Salama S.; Alouini, Mohamed-Slim

    2017-01-01

    This paper studies the impact of asymmetric hardware distortion (HWD) on the performance of receive diversity systems using linear and switched combining receivers. The asymmetric attribute of the proposed model motivates the employment of improper Gaussian signaling (IGS) scheme rather than the traditional proper Gaussian signaling (PGS) scheme. The achievable rate performance is analyzed for the ideal and non-ideal hardware scenarios using PGS and IGS transmission schemes for different combining receivers. In addition, the IGS statistical characteristics are optimized to maximize the achievable rate performance. Moreover, the outage probability performance of the receive diversity systems is analyzed yielding closed form expressions for both PGS and IGS based transmission schemes. HWD systems that employ IGS is proven to efficiently combat the self interference caused by the HWD. Furthermore, the obtained analytic expressions are validated through Monte-Carlo simulations. Eventually, non-ideal hardware transceivers degradation and IGS scheme acquired compensation are quantified through suitable numerical results.

  10. New Geometric-distortion Solution for STIS FUV-MAMA

    Science.gov (United States)

    Sohn, S. Tony

    2018-04-01

    We derived a new geometric distortion solution for the STIS FUV-MAMA detector. To do this, positions of stars in 89 FUV-MAMA observations of NGC 6681 were compared to an astrometric standard catalog created using WFC3/UVIS imaging data to derive a fourth-order polynomial solution that transforms raw (x, y) positions to geometrically- corrected (x, y) positions. When compared to astrometric catalog positions, the FUV- MAMA position measurements based on the IDCTAB showed residuals with an RMS of ∼ 30 mas in each coordinate. Using the new IDCTAB, the RMS is reduced to ∼ 4 mas, or 0.16 FUV-MAMA pixels, in each coordinate. The updated IDCTAB is now being used in the HST STIS pipeline to process all STIS FUV-MAMA images.

  11. Financial Indicators of Performance Measurement: Reality, Relevance and Distortion

    Directory of Open Access Journals (Sweden)

    Flavius-Andrei Guinea

    2016-01-01

    Full Text Available The main criticism brought to managers and to managerial accounting systems was the lack of emphasis on the return of the use of invested capital and the excessive focus on the efficiency of production processes. This fact forced the transition to a new view on the way of establishing the strategic objectives measured by financial indicators. The aim of this paper is to demonstrate, through case studies, the relevance and possibilities of manipulation of a series of indicators used for assessing performance: return on investment, residual profit, economic added value, commercial profitability. The relativity and the criticized appraisal of performance only through the means of profit were thought to be solved by implementing other indicators that would link several ingredients of profitability. The conclusions highlight that the remedy promoted by the new sets of financial indicators imposes a considerable cost, represented by the temptation of information distortion.

  12. Modeling Macroscopic Shape Distortions during Sintering of Multi-layers

    DEFF Research Database (Denmark)

    Tadesse Molla, Tesfaye

    as to help achieve defect free multi-layer components. The initial thickness ratio between the layers making the multi-layer has also significant effect on the extent of camber evolution depending on the material systems. During sintering of tubular bi-layer structures, tangential (hoop) stresses are very...... large compared to radial stresses. The maximum value of hoop stress, which can generate processing defects such as cracks and coating peel-offs, occurs at the beginning of the sintering cycle. Unlike most of the models defining material properties based on porosity and grain size only, the multi...... (firing). However, unintended features like shape instabilities of samples, cracks or delamination of layers may arise during sintering of multi-layer composites. Among these defects, macroscopic shape distortions in the samples can cause problems in the assembly or performance of the final component...

  13. Over-exposure effects on the distortion product otoacoustic emission

    DEFF Research Database (Denmark)

    Reuter, Karen

    , however. In the present study it was investigated, whether Distortion Product OtoAcoustic Emission (DPOAE) parameters exist, which indicate the early stage of a hearing loss. DPOAE was obtained with high frequency resolution, and its characteristic spectral fine structure was analyzed. Data of subjects...... belonging to different groups of age and exposure history were obtained and compared. Controlled sound/ noise exposure experiments were performed to observe changes in DPOAE characteristics. The DPOAE of all tested subjects feature the typical fine structure pattern. The fine structure pattern is highly...... individual and stable over time. No unequivocal relation between the characteristics of the DPOAE fine structure and the state of hearing could be found. It is suggested to eliminate the DPOAE fine structure in the DPOAE measurement and to establish a reference zero from a large amount of DPOAE data...

  14. Improvements on Semi-Classical Distorted-Wave model

    Energy Technology Data Exchange (ETDEWEB)

    Sun Weili; Watanabe, Y.; Kuwata, R. [Kyushu Univ., Fukuoka (Japan); Kohno, M.; Ogata, K.; Kawai, M.

    1998-03-01

    A method of improving the Semi-Classical Distorted Wave (SCDW) model in terms of the Wigner transform of the one-body density matrix is presented. Finite size effect of atomic nuclei can be taken into account by using the single particle wave functions for harmonic oscillator or Wood-Saxon potential, instead of those based on the local Fermi-gas model which were incorporated into previous SCDW model. We carried out a preliminary SCDW calculation of 160 MeV (p,p`x) reaction on {sup 90}Zr with the Wigner transform of harmonic oscillator wave functions. It is shown that the present calculation of angular distributions increase remarkably at backward angles than the previous ones and the agreement with the experimental data is improved. (author)

  15. Video quality pooling adaptive to perceptual distortion severity.

    Science.gov (United States)

    Park, Jincheol; Seshadrinathan, Kalpana; Lee, Sanghoon; Bovik, Alan Conrad

    2013-02-01

    It is generally recognized that severe video distortions that are transient in space and/or time have a large effect on overall perceived video quality. In order to understand this phenomena, we study the distribution of spatio-temporally local quality scores obtained from several video quality assessment (VQA) algorithms on videos suffering from compression and lossy transmission over communication channels. We propose a content adaptive spatial and temporal pooling strategy based on the observed distribution. Our method adaptively emphasizes "worst" scores along both the spatial and temporal dimensions of a video sequence and also considers the perceptual effect of large-area cohesive motion flow such as egomotion. We demonstrate the efficacy of the method by testing it using three different VQA algorithms on the LIVE Video Quality database and the EPFL-PoliMI video quality database.

  16. Asymmetric Hardware Distortions in Receive Diversity Systems: Outage Performance Analysis

    KAUST Repository

    Javed, Sidrah

    2017-02-22

    This paper studies the impact of asymmetric hardware distortion (HWD) on the performance of receive diversity systems using linear and switched combining receivers. The asymmetric attribute of the proposed model motivates the employment of improper Gaussian signaling (IGS) scheme rather than the traditional proper Gaussian signaling (PGS) scheme. The achievable rate performance is analyzed for the ideal and non-ideal hardware scenarios using PGS and IGS transmission schemes for different combining receivers. In addition, the IGS statistical characteristics are optimized to maximize the achievable rate performance. Moreover, the outage probability performance of the receive diversity systems is analyzed yielding closed form expressions for both PGS and IGS based transmission schemes. HWD systems that employ IGS is proven to efficiently combat the self interference caused by the HWD. Furthermore, the obtained analytic expressions are validated through Monte-Carlo simulations. Eventually, non-ideal hardware transceivers degradation and IGS scheme acquired compensation are quantified through suitable numerical results.

  17. Environmental DNA mapping of Zebra Mussel populations

    Science.gov (United States)

    Amberg, Jon J.; Merkes, Christopher

    2016-01-01

    Environmental DNA (eDNA) has become a popular tool for detecting aquatic invasive species, but advancements have made it possible to potentially answer other questions like reproduction, movement, and abundance of the targeted organism. In this study we developed a Zebra Mussel (Dreissena polymorpha) eDNA protocol. We then determined if this assay could be used to help determine Zebra Mussel biomass in a lake with a well-established population of Zebra Mussels and a lake with an emerging population of mussels. Our eDNA assay detected DNA of Zebra Mussels but not DNA from more than 20 other species of fish and mussels, many commonly found in Minnesota waters. Our assay did not predict biomass. We did find that DNA from Zebra Mussels accumulated in softer substrates in both lakes, even though the mussels were predominately on the harder substrates. Therefore, we concluded that eDNA may be useful to detect the presence of Zebra Mussels in these lakes but our assay/approach could not predict biomass.

  18. Studi Molekuler pada Instabilitas Genetik : Mekanisme Kerusakan DNA dan Proses Perbaikannya

    Directory of Open Access Journals (Sweden)

    Yani Corvianindya

    2015-11-01

    Full Text Available The life survival of individuals depends on their DNA stability. Radiation exposure, physical and chemical change, and also replication errors can induce DNA lesions. Multiple pathways are involved in the maintenance of genetic integrity, most link to the cell cycle. By arresting the cell cycle, checkpoints allow cells to repair DNA when damage to the genome is detected. Genes induced in genetic instability to respond to DNA damage include ATM, p53, p21, BRCA1 and Chk2. Cells have various DNA repair systems to keep homeostasis condition with enzymes that search for some changes or distortion to be repaired.

  19. Susceptibility to cognitive distortions: the role of eating pathology.

    Science.gov (United States)

    Coelho, Jennifer S; Ouellet-Courtois, Catherine; Purdon, Christine; Steiger, Howard

    2015-01-01

    Thought-Shape Fusion (TSF) and Thought-Action Fusion (TAF) are cognitive distortions that are associated with eating and obsessional pathology respectively. Both involve the underlying belief that mere thoughts and mental images can lead to negative outcomes. TSF involves the belief that food-related thoughts lead to weight gain, body dissatisfaction, and perceptions of moral wrong-doing. TAF is more general, and involves the belief that merely thinking about a negative event (e.g., a loved one getting into a car accident) can make this event more likely to happen, and leads to perceptions of moral wrong-doing. However, the shared susceptibility across related cognitive distortions-TAF and TSF-has not yet been studied. The effects of TSF and TAF inductions in women with an eating disorder (n = 21) and a group of healthy control women with no history of an eating disorder (n = 23) were measured. A repeated-measures design was employed, with all participants exposed to a TSF, TAF and neutral induction during three separate experimental sessions. Participants' cognitive and behavioral responses were assessed. Individuals with eating disorders were more susceptible to TSF and TAF than were control participants, demonstrating more neutralization behavior after TSF and TAF inductions (i.e., actions to try to reduce the negative effects of the induction), and reporting higher levels of trait TAF and TSF than did controls. Individuals with eating disorders are particularly susceptible to both TAF and TSF. Clinical implications of these findings will be discussed.

  20. How emission certificate allocations distort fossil investments: The German example

    International Nuclear Information System (INIS)

    Pahle, Michael; Fan Lin; Schill, Wolf-Peter

    2011-01-01

    Despite political activities to foster a low-carbon energy transition, Germany currently sees a considerable number of new coal power plants being added to its power mix. There are several possible drivers for this 'dash for coal', but it is widely accepted that windfall profits gained through free allocation of ETS certificates play an important role. Yet the quantification of allocation-related investment distortions has been limited to back-of-the envelope calculations and stylized models so far. We close this gap with a numerical model integrating both Germany's particular allocation rules and its specific power generation structure. We find that technology specific new entrant provisions have substantially increased incentives to invest in hard coal plants red to natural gas at the time of the ETS onset. More precisely, disproportionate windfall profits compared more than half the total capital costs of a hard coal plant. Moreover, shorter periods of free allocations would not have turned investors' favours towards the cleaner natural gas technology because of pre-existing economic advantages for coal. In contrast, full auctioning of permits or a single best available technology benchmark would have made natural gas the predominant technology of choice. - Research highlights: → We study how early emission certificate allocations in Germany distort fossil investments. → We examine the role of windfall profits in the overall profitabilities of a new hard coal compared to a natural gas plant. → We find that technology specific grandfathering over any period does not induce a change in preferences away from hard coal. → Natural gas would have been preferred under auctioning or a technology neutral allocation though.

  1. Selecting Map Projections in Minimizing Area Distortions in GIS Applications

    Directory of Open Access Journals (Sweden)

    Ahmet Kaya

    2008-12-01

    Full Text Available Varioussoftware for Geographical Information Systems (GISs have been developed and used in many different engineering projects. In GIS applications, map coverage is important in terms of performing reliable and meaningful queries. Map projections can be conformal, equal-area and equidistant. The goal of an application plays an important role in choosing one of those projections. Choosing the equal-area projection for an application in which area information is used (forestry, agriculture, ecosystem etc reduces the amount of distortion on the area, but many users using GIS ignore this fact and continue to use applications with present map sheets no matter in what map projection it is. For example, extracting area information from data whose country system’s map sheet is in conformal projection is relatively more distorted, compared to an equal-area projection one. The goal of this study is to make the best decision in choosing the most proper equal-area projection among the choices provided by ArcGIS 9.0, which is a popular GIS software package, and making a comparison on area errors when conformal projection is used. In this study, the area of parcels chosen in three different regions and geographic coordinates and whose sizes vary between 0.01 to 1,000,000 ha are calculated according to Transversal Mercator (TM, 3°, Universal Transversal Mercator (UTM, 6° and 14 different equal-area projections existing in the ArcGIS 9.0 GIS software package. The parcel areas calculated with geographical coordinates are accepted as definite. The difference between the sizes calculated according to projection coordinates and real sizes of the parcels are determined. Consequently, the appropriate projections are decided for the areas smaller and equal than 1,000 ha and greater than 1,000 ha in the GIS software package.

  2. Distortion-product otoacoustic emission growth curves in neonates

    Directory of Open Access Journals (Sweden)

    Tania Alves Barbosa

    2014-12-01

    Full Text Available Background: The recording of otoacoustic emissions (OAE enabled us to prove that the cochlea is able not only to receive sounds but also to produce acoustic energy. Through the use of distortion-product otoacoustic emission measurements, the growth of the response was seen according to the intensity of the sound stimulus presented (growth curve. Objective: to determine the thresholds for the emergence of distortion-product otoacoustic emissions (DPOAE on frequencies of 2000 and 4000 Hz with a stimulus varying from 20 to 65dB SPL, and to establish the slope values obtained in the growth curves. Methods: 39 neonates aged 5 to 28 days without risk indicators of hearing loss were studied. The DPOAE growth curves were obtained on the frequencies from 2000 Hz and 4000 Hz with a level of intensity ranging from 20 to 65dB SPL divided into two paradigms (20 to 40dB SPL and 40-65dB SPL. Results: there was a statistically significant difference in the thresholds for the emergence of DPOAE depending on the criteria used. The thresholds were on average higher at 4000 Hz than 2000 Hz and the slope was higher on average at 2000 Hz than 4000 Hz, although not statistically significant in either case. Conclusion: the thresholds were on average 30dB SPL at 2000Hz and 35dB SPL at 4000Hz. The slope values varied between 3 and 4 on average, reaching 15 in some cases.

  3. Distortion of liquid film discharging from twin-fluid atomizer

    Science.gov (United States)

    Mehring, C.; Sirignano, W. A.

    2001-11-01

    The nonlinear distortion and disintegration of a thin liquid film exiting from a two-dimensional twin-fluid atomizer is analyzed numerically. Pulsed gas jets impacting on both sides of the discharging liquid film at the atomizer exit generate dilational and/or sinuous deformations of the film. Both liquid phase and gas phase are inviscid and incompressible. For the liquid phase the so-called long-wavelength approximation is employed yielding a system of unsteady one-dimensional equations for the planar film. Solution of Laplace's equation for the velocity potential yields the gas-phase velocity field on both sides of the liquid stream. Coupling between both phases is described through kinematic and dynamic boundary conditions at the phase interfaces, and includes the solution of the unsteady Bernoulli equation to determine the gas-phase pressure along the interfaces. Both gas- and liquid-phase equations are solved simultaneously. Solution of Laplace's equation for the gas streams is obtained by means of a boundary-element method. Numerical solutions for the liquid phase use the Lax-Wendroff method with Richtmyer splitting. Sheet distortion resulting from the stagnation pressure of the impacting gas jets and subsequent disturbance amplification due to Kelvin-Helmholtz effects are studied for various combinations of gas-pulse timing, gas-jet impact angles, gas-to-liquid-density ratio, liquid-phase Weber number and gas-jet-to-liquid-jet-momentum ratio. Dilational and sinuous oscillations of the liquid are examined and film pinch-off is predicted.

  4. PLZT capacitor on glass substrate

    Science.gov (United States)

    Fairchild, M. Ray; Taylor, Ralph S.; Berlin, Carl W.; Wong, Celine W. K.; Ma, Beihai; Balachandran, Uthamalingam

    2016-01-05

    A lead-lanthanum-zirconium-titanate (PLZT) capacitor on a substrate formed of glass. The first metallization layer is deposited on a top side of the substrate to form a first electrode. The dielectric layer of PLZT is deposited over the first metallization layer. The second metallization layer deposited over the dielectric layer to form a second electrode. The glass substrate is advantageous as glass is compatible with an annealing process used to form the capacitor.

  5. Structure formation in bis(terpyridine) derivative adlayers: molecule-substrate versus molecule-molecule interactions.

    Science.gov (United States)

    Hoster, Harry E; Roos, Matthias; Breitruck, Achim; Meier, Christoph; Tonigold, Katrin; Waldmann, Thomas; Ziener, Ulrich; Landfester, Katharina; Behm, R Jürgen

    2007-11-06

    The influence of the substrate and the deposition conditions-vapor deposition versus deposition from solution-on the structures formed upon self-assembly of deposited bis(terpyridine) derivative (2,4'-BTP) monolayers on different hexagonal substrates, including highly oriented pyrolytic graphite (HOPG), Au(111), and (111)-oriented Ag thin films, was investigated by high-resolution scanning tunneling microscopy and by model calculations of the intermolecular energies and the lateral corrugation of the substrate-adsorbate interaction. Similar quasi-quadratic network structures with almost the same lattice constants obtained on all substrates are essentially identical to the optimum configuration expected from an optimization of the adlayer structure with C-H...N-type bridging bonds as a structure-determining factor, which underlines a key role of the intermolecular interactions in adlayer order. Slight distortions from the optimum values to form commensurate adlayer structures on the metal substrates and the preferential orientation of the adlayer with respect to the substrate are attributed to the substrate-adsorbate interactions, specifically, the lateral corrugation in the substrate-adsorbate interaction upon lateral displacement and rotation of the adsorbed BTP molecules. The fact that similar adlayer structures are obtained on HOPG under ultrahigh vacuum conditions (solid|gas interface) and on HOPG in trichlorobenzene (solid|liquid interface) indicates that the intermolecular interactions are not severely affected by the solvent.

  6. Distinct structural features of TFAM drive mitochondrial DNA packaging versus transcriptional activation.

    Science.gov (United States)

    Ngo, Huu B; Lovely, Geoffrey A; Phillips, Rob; Chan, David C

    2014-01-01

    TFAM (transcription factor A, mitochondrial) is a DNA-binding protein that activates transcription at the two major promoters of mitochondrial DNA (mtDNA)--the light strand promoter (LSP) and the heavy strand promoter 1 (HSP1). Equally important, it coats and packages the mitochondrial genome. TFAM has been shown to impose a U-turn on LSP DNA; however, whether this distortion is relevant at other sites is unknown. Here we present crystal structures of TFAM bound to HSP1 and to nonspecific DNA. In both, TFAM similarly distorts the DNA into a U-turn. Yet, TFAM binds to HSP1 in the opposite orientation from LSP explaining why transcription from LSP requires DNA bending, whereas transcription at HSP1 does not. Moreover, the crystal structures reveal dimerization of DNA-bound TFAM. This dimerization is dispensable for DNA bending and transcriptional activation but is important in DNA compaction. We propose that TFAM dimerization enhances mitochondrial DNA compaction by promoting looping of the DNA.

  7. Investigation of support vector machine for the detection of architectural distortion in mammographic images

    International Nuclear Information System (INIS)

    Guo, Q; Shao, J; Ruiz, V

    2005-01-01

    This paper investigates detection of architectural distortion in mammographic images using support vector machine. Hausdorff dimension is used to characterise the texture feature of mammographic images. Support vector machine, a learning machine based on statistical learning theory, is trained through supervised learning to detect architectural distortion. Compared to the Radial Basis Function neural networks, SVM produced more accurate classification results in distinguishing architectural distortion abnormality from normal breast parenchyma

  8. Investigation of support vector machine for the detection of architectural distortion in mammographic images

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Q [Department of Cybernetics, University of Reading, Reading RG6 6AY (United Kingdom); Shao, J [Department of Electronics, University of Kent at Canterbury, Kent CT2 7NT (United Kingdom); Ruiz, V [Department of Cybernetics, University of Reading, Reading RG6 6AY (United Kingdom)

    2005-01-01

    This paper investigates detection of architectural distortion in mammographic images using support vector machine. Hausdorff dimension is used to characterise the texture feature of mammographic images. Support vector machine, a learning machine based on statistical learning theory, is trained through supervised learning to detect architectural distortion. Compared to the Radial Basis Function neural networks, SVM produced more accurate classification results in distinguishing architectural distortion abnormality from normal breast parenchyma.

  9. Semiquantitative theory for high-field low-temperature properties of a distorted diamond spin chain

    Directory of Open Access Journals (Sweden)

    O. Derzhko

    2012-12-01

    Full Text Available We consider the antiferromagnetic Heisenberg model on a distorted diamond chain and use the localized-magnon picture adapted to a distorted geometry to discuss some of its high-field low-temperature properties. More specifically, in our study we assume that the partition function for a slightly distorted geometry has the same form as for ideal geometry, though with slightly dispersive one-magnon energies. We also discuss the relevance of such a description to azurite.

  10. The effect of redshift-space distortions on projected 2-pt clustering measurements

    OpenAIRE

    Nock, Kelly; Percival, Will J.; Ross, Ashley J.

    2010-01-01

    Although redshift-space distortions only affect inferred distances and not angles, they still distort the projected angular clustering of galaxy samples selected using redshift dependent quantities. From an Eulerian view-point, this effect is caused by the apparent movement of galaxies into or out of the sample. From a Lagrangian view-point, we find that projecting the redshift-space overdensity field over a finite radial distance does not remove all the anisotropic distortions. We investigat...

  11. Sealed substrate carrier for electroplating

    Science.gov (United States)

    Ganti, Kalyana Bhargava [Fremont, CA

    2012-07-17

    One embodiment relates to a substrate carrier for use in electroplating a plurality of substrates. The substrate carrier includes a non-conductive carrier body on which the substrates are held, and conductive lines are embedded within the carrier body. A conductive bus bar is embedded into a top side of the carrier body and is conductively coupled to the conductive lines. A thermoplastic overmold covers a portion of the bus bar, and there is a plastic-to-plastic bond between the thermoplastic overmold and the non-conductive carrier body. Other embodiments, aspects and features are also disclosed.

  12. Comparative analysis of the end-joining activity of several DNA ligases.

    Directory of Open Access Journals (Sweden)

    Robert J Bauer

    Full Text Available DNA ligases catalyze the repair of phosphate backbone breaks in DNA, acting with highest activity on breaks in one strand of duplex DNA. Some DNA ligases have also been observed to ligate two DNA fragments with short complementary overhangs or blunt-ended termini. In this study, several wild-type DNA ligases (phage T3, T4, and T7 DNA ligases, Paramecium bursaria chlorella virus 1 (PBCV1 DNA ligase, human DNA ligase 3, and Escherichia coli DNA ligase were tested for their ability to ligate DNA fragments with several difficult to ligate end structures (blunt-ended termini, 3'- and 5'- single base overhangs, and 5'-two base overhangs. This analysis revealed that T4 DNA ligase, the most common enzyme utilized for in vitro ligation, had its greatest activity on blunt- and 2-base overhangs, and poorest on 5'-single base overhangs. Other ligases had different substrate specificity: T3 DNA ligase ligated only blunt ends well; PBCV1 DNA ligase joined 3'-single base overhangs and 2-base overhangs effectively with little blunt or 5'- single base overhang activity; and human ligase 3 had highest activity on blunt ends and 5'-single base overhangs. There is no correlation of activity among ligases on blunt DNA ends with their activity on single base overhangs. In addition, DNA binding domains (Sso7d, hLig3 zinc finger, and T4 DNA ligase N-terminal domain were fused to PBCV1 DNA ligase to explore whether modified binding to DNA would lead to greater activity on these difficult to ligate substrates. These engineered ligases showed both an increased binding affinity for DNA and increased activity, but did not alter the relative substrate preferences of PBCV1 DNA ligase, indicating active site structure plays a role in determining substrate preference.

  13. The proofreading 3'→5' exonuclease activity of DNA polymerases: a kinetic barrier to translesion DNA synthesis

    International Nuclear Information System (INIS)

    Khare, Vineeta; Eckert, Kristin A.

    2002-01-01

    The 3'→5' exonuclease activity intrinsic to several DNA polymerases plays a primary role in genetic stability; it acts as a first line of defense in correcting DNA polymerase errors. A mismatched basepair at the primer terminus is the preferred substrate for the exonuclease activity over a correct basepair. The efficiency of the exonuclease as a proofreading activity for mispairs containing a DNA lesion varies, however, being dependent upon both the DNA polymerase/exonuclease and the type of DNA lesion. The exonuclease activities intrinsic to the T4 polymerase (family B) and DNA polymerase γ (family A) proofread DNA mispairs opposite endogenous DNA lesions, including alkylation, oxidation, and abasic adducts. However, the exonuclease of the Klenow polymerase cannot discriminate between correct and incorrect bases opposite alkylation and oxidative lesions. DNA damage alters the dynamics of the intramolecular partitioning of DNA substrates between the 3'→5' exonuclease and polymerase activities. Enzymatic idling at lesions occurs when an exonuclease activity efficiently removes the same base that is preferentially incorporated by the DNA polymerase activity. Thus, the exonuclease activity can also act as a kinetic barrier to translesion synthesis (TLS) by preventing the stable incorporation of bases opposite DNA lesions. Understanding the downstream consequences of exonuclease activity at DNA lesions is necessary for elucidating the mechanisms of translesion synthesis and damage-induced cytotoxicity

  14. Effect of pion external distortion on low energy pion double-charge-exchange

    International Nuclear Information System (INIS)

    Khankhasaev, M.Kh.; Kurmanov, Zh.B.; Johnson, M.B.

    1993-01-01

    The effects of the external pion distortion for iso-elastic charge exchange scattering (within the framework of the isospin invariant optical model) is considered. An approximated method of taking into account the distortion based on the separable expansion of the optical potential in momentum space is developed. The result of external distortions for sequential scattering 14 C(π + , π - ) 14 O at 50 MeV is presented. It is shown that this distortion gives a small enhancement to forward and reduced the differential cross sections at large angels. 22 refs., 5 figs., 1 tab

  15. Tomosynthesis-detected Architectural Distortion: Management Algorithm with Radiologic-Pathologic Correlation.

    Science.gov (United States)

    Durand, Melissa A; Wang, Steven; Hooley, Regina J; Raghu, Madhavi; Philpotts, Liane E

    2016-01-01

    As use of digital breast tomosynthesis becomes increasingly widespread, new management challenges are inevitable because tomosynthesis may reveal suspicious lesions not visible at conventional two-dimensional (2D) full-field digital mammography. Architectural distortion is a mammographic finding associated with a high positive predictive value for malignancy. It is detected more frequently at tomosynthesis than at 2D digital mammography and may even be occult at conventional 2D imaging. Few studies have focused on tomosynthesis-detected architectural distortions to date, and optimal management of these distortions has yet to be well defined. Since implementing tomosynthesis at our institution in 2011, we have learned some practical ways to assess architectural distortion. Because distortions may be subtle, tomosynthesis localization tools plus improved visualization of adjacent landmarks are crucial elements in guiding mammographic identification of elusive distortions. These same tools can guide more focused ultrasonography (US) of the breast, which facilitates detection and permits US-guided tissue sampling. Some distortions may be sonographically occult, in which case magnetic resonance imaging may be a reasonable option, both to increase diagnostic confidence and to provide a means for image-guided biopsy. As an alternative, tomosynthesis-guided biopsy, conventional stereotactic biopsy (when possible), or tomosynthesis-guided needle localization may be used to achieve tissue diagnosis. Practical uses for tomosynthesis in evaluation of architectural distortion are highlighted, potential complications are identified, and a working algorithm for management of tomosynthesis-detected architectural distortion is proposed. (©)RSNA, 2016.

  16. Performance and Adaptive Surge-Preventing Acceleration Prediction of a Turboshaft Engine under Inlet Flow Distortion

    Directory of Open Access Journals (Sweden)

    Cao Dalu

    2017-01-01

    Full Text Available The intention of this paper is to research the inlet flow distortion influence on overall performance of turboshaft engine and put forward a method called Distortion Factor Item (DFI to improve the fuel supply plan for surge-preventing acceleration when turboshaft engine suddenly encounters inlet flow distortion. Based on the parallel compressor theory, steady-state and transition-state numerical simulation model of turboshaft engine with sub-compressor model were established for researching the influence of inlet flow distortion on turboshaft engine. This paper made a detailed analysis on the compressor operation from the aspects of performance and stability, and then analyzed the overall performance and dynamic response of the whole engine under inlet flow distortion. Improved fuel supply plan with DFI method was applied to control the acceleration process adaptively when encountering different inlet flow distortion. Several simulation examples about extreme natural environments were calculated to testify DFI method’s environmental applicability. The result shows that the inlet flow distortion reduces the air inflow and decreases the surge margin of compressor, and increase the engine exhaust loss. Encountering inlet flow distortion has many adverse influences such as sudden rotor acceleration, turbine inlet temperature rise and power output reduction. By using improved fuel supply plan with DFI, turboshaft engine above-idle acceleration can avoid surge effectively under inlet flow distortion with environmental applicability.

  17. The role of visual similarity and memory in body model distortions.

    Science.gov (United States)

    Saulton, Aurelie; Longo, Matthew R; Wong, Hong Yu; Bülthoff, Heinrich H; de la Rosa, Stephan

    2016-02-01

    Several studies have shown that the perception of one's own hand size is distorted in proprioceptive localization tasks. It has been suggested that those distortions mirror somatosensory anisotropies. Recent research suggests that non-corporeal items also show some spatial distortions. In order to investigate the psychological processes underlying the localization task, we investigated the influences of visual similarity and memory on distortions observed on corporeal and non-corporeal items. In experiment 1, participants indicated the location of landmarks on: their own hand, a rubber hand (rated as most similar to the real hand), and a rake (rated as least similar to the real hand). Results show no significant differences between rake and rubber hand distortions but both items were significantly less distorted than the hand. Experiments 2 and 3 explored the role of memory in spatial distance judgments of the hand, the rake and the rubber hand. Spatial representations of items measured in experiments 2 and 3 were also distorted but showed the tendency to be smaller than in localization tasks. While memory and visual similarity seem to contribute to explain qualitative similarities in distortions between the hand and non-corporeal items, those factors cannot explain the larger magnitude observed in hand distortions. Copyright © 2015. Published by Elsevier B.V.

  18. Ubiquitous log odds: a common representation of probability and frequency distortion in perception, action and cognition

    Directory of Open Access Journals (Sweden)

    Hang eZhang

    2012-01-01

    Full Text Available In decision from experience, the source of probability information affects how probability is distorted in the decision task. Understanding how and why probability is distorted is a key issue in understanding the peculiar character of experience-based decision. We consider how probability information is used not just in decision making but also in a wide variety of cognitive, perceptual and motor tasks. Very similar patterns of distortion of probability/frequency information have been found in visual frequency estimation, frequency estimation based on memory, signal detection theory, and in the use of probability information in decision-making under risk and uncertainty. We show that distortion of probability in all cases is well captured as linear transformations of the log odds of frequency and/or probability, a model with a slope parameter and an intercept parameter. We then consider how task and experience influence these two parameters and the resulting distortion of probability. We review how the probability distortions change in systematic ways with task and report three experiments on frequency distortion where the distortions change systematically in the same task. We found that the slope of frequency distortions decreases with the sample size, which is echoed by findings in decision from experience. We review previous models of the representation of uncertainty and find that none can account for the empirical findings.

  19. Simulation of 125I-induced DNA strand breaks in a CAP-DNA complex

    International Nuclear Information System (INIS)

    Li, W.; Friedland, W.; Jacob, P.

    2000-01-01

    DNA strand breakage induced by decay of 125 I incorporated into the pyrimidine of a small piece of DNA with a specific base pair sequence has been investigated theoretically and experimentally (Lobachevsky and Martin 2000a, 2000b; Nikjoo et al., 1996; Pomplun and Terrissol, 1994; Charlton and Humm, 1988). Recently an attempt was made to analyse the DNA kinks in a CAP-DNA complex with 125 I induced DNA strand breakage (Karamychev et al., 1999). This method could be used as a so called radioprobing for such DNa distortions like other chemical and biological assays, provided that it has been tested and confirmed in a corresponding theoretical simulation. In the measurement, the distribution of the first breaks on the DNA strands starting from their labeled end can be determined. Based on such first breakage distributions, the simulation calculation could then be used to derive information on the structure of a given DNA-protein complex. The biophysical model PARTRAC has been applied successfully in simulating DNA damage induced by irradiation (Friedland et al., 1998; 1999). In the present study PARTRAC is adapted to a DNA-protein complex in which a specific sequence of 30 base pairs of DNA is connected with the catabolite gene activator protein (CAP). This report presents the first step of the analysis in which the CAP-DNA model used in NIH is overlaid with electron track structures in liquid water and the strand breaks due to direct ionization and due to radical attack are simulated. The second step will be to take into account the neutralization of the heavily charged tellurium and the protective effect of the CAP protein against radical attack. (orig.)

  20. Repair of DNA damage in Deinococcus radiodurans

    International Nuclear Information System (INIS)

    Evans, D.M.

    1984-01-01

    The repair of DNA lesions in Deinococcus radiodurans was examined with particular reference to DNA excision repair of ultraviolet light (UV) induced pyrimidine dimers. The characteristics of excision repair via UV endonucleases α and β in vivo varied with respect to (a) the substrate range of the enzymes, (b) the rate of repair of DNA damage (c) the requirement for a protein synthesised in response to DNA damage to attenuate exonuclease action at repairing regions. UV endonuclease α is postulated to incise DNA in a different manner from UV endonuclease β thus defining the method of subsequent repair. Several DNA damage specific endonuclease activities independent of α and β are described. Mutations of the uvsA, uvsF and uvsG genes resulted in an increase in single-strand breaks in response to DNA damage producing uncontrolled DNA degradation. Evidence is presented that these genes have a role in limiting the access of UV endonuclease β to DNA lesions. uvsF and uvsG are also shown to be linked to the mtoA gene. Mutation of uvsH and reo-1 produces further distinct phenotypes which are discussed. An overall model of excision repair of DNA damage in Deinococcus radiodurans is presented. (author)

  1. Distinct kinetics of human DNA ligases I, IIIalpha, IIIbeta, and IV reveal direct DNA sensing ability and differential physiological functions in DNA repair

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Xi; Ballin, Jeff D.; Della-Maria, Julie; Tsai, Miaw-Sheue; White, Elizabeth J.; Tomkinson, Alan E.; Wilson, Gerald M.

    2009-05-11

    The three human LIG genes encode polypeptides that catalyze phosphodiester bond formation during DNA replication, recombination and repair. While numerous studies have identified protein partners of the human DNA ligases (hLigs), there has been little characterization of the catalytic properties of these enzymes. In this study, we developed and optimized a fluorescence-based DNA ligation assay to characterize the activities of purified hLigs. Although hLigI joins DNA nicks, it has no detectable activity on linear duplex DNA substrates with short, cohesive single-strand ends. By contrast, hLigIII{beta} and the hLigIII{alpha}/XRCC1 and hLigIV/XRCC4 complexes are active on both nicked and linear duplex DNA substrates. Surprisingly, hLigIV/XRCC4, which is a key component of the major non-homologous end joining (NHEJ) pathway, is significantly less active than hLigIII on a linear duplex DNA substrate. Notably, hLigIV/XRCC4 molecules only catalyze a single ligation event in the absence or presence of ATP. The failure to catalyze subsequent ligation events reflects a defect in the enzyme-adenylation step of the next ligation reaction and suggests that, unless there is an in vivo mechanism to reactivate DNA ligase IV/XRCC4 following phosphodiester bond formation, the cellular NHEJ capacity will be determined by the number of adenylated DNA ligaseIV/XRCC4 molecules.

  2. Distortion in fingerprints: a statistical investigation using shape measurement tools.

    Science.gov (United States)

    Sheets, H David; Torres, Anne; Langenburg, Glenn; Bush, Peter J; Bush, Mary A

    2014-07-01

    Friction ridge impression appearance can be affected due to the type of surface touched and pressure exerted during deposition. Understanding the magnitude of alterations, regions affected, and systematic/detectable changes occurring would provide useful information. Geometric morphometric techniques were used to statistically characterize these changes. One hundred and fourteen prints were obtained from a single volunteer and impressed with heavy, normal, and light pressure on computer paper, soft gloss paper, 10-print card stock, and retabs. Six hundred prints from 10 volunteers were rolled with heavy, normal, and light pressure on soft gloss paper and 10-print card stock. Results indicate that while different substrates/pressure levels produced small systematic changes in fingerprints, the changes were small in magnitude: roughly the width of one ridge. There were no detectable changes in the degree of random variability of prints associated with either pressure or substrate. In conclusion, the prints transferred reliably regardless of pressure or substrate. © 2014 American Academy of Forensic Sciences.

  3. Substrate Discrimination by ClpB and Hsp104

    Directory of Open Access Journals (Sweden)

    Danielle M. Johnston

    2017-05-01

    Full Text Available ClpB of E. coli and yeast Hsp104 are homologous molecular chaperones and members of the AAA+ (ATPases Associated with various cellular Activities superfamily of ATPases. They are required for thermotolerance and function in disaggregation and reactivation of aggregated proteins that form during severe stress conditions. ClpB and Hsp104 collaborate with the DnaK or Hsp70 chaperone system, respectively, to dissolve protein aggregates both in vivo and in vitro. In yeast, the propagation of prions depends upon Hsp104. Since protein aggregation and amyloid formation are associated with many diseases, including neurodegenerative diseases and cancer, understanding how disaggregases function is important. In this study, we have explored the innate substrate preferences of ClpB and Hsp104 in the absence of the DnaK and Hsp70 chaperone system. The results suggest that substrate specificity is determined by nucleotide binding domain-1.

  4. DNA Vaccines

    Indian Academy of Sciences (India)

    diseases. Keywords. DNA vaccine, immune response, antibodies, infectious diseases. GENERAL .... tein vaccines require expensive virus/protein purification tech- niques as ... sphere continue to remain major health hazards in developing nations. ... significance since it can be produced at a very low cost and can be stored ...

  5. DNA Investigations.

    Science.gov (United States)

    Mayo, Ellen S.; Bertino, Anthony J.

    1991-01-01

    Presents a simulation activity that allow students to work through the exercise of DNA profiling and to grapple with some analytical and ethical questions involving a couple arranging with a surrogate mother to have a baby. Can be used to teach the principles of restriction enzyme digestion, gel electrophoresis, and probe hybridization. (MDH)

  6. Portion distortion: typical portion sizes selected by young adults.

    Science.gov (United States)

    Schwartz, Jaime; Byrd-Bredbenner, Carol

    2006-09-01

    The incidence of obesity has increased in parallel with increasing portion sizes of individually packaged and ready-to-eat prepared foods as well as foods served at restaurants. Portion distortion (perceiving large portion sizes as appropriate amounts to eat at a single eating occasion) may contribute to increasing energy intakes and expanding waistlines. The purpose of this study was to determine typical portion sizes that young adults select, how typical portion sizes compare with reference portion sizes (based in this study on the Nutrition Labeling and Education Act's quantities of food customarily eaten per eating occasion), and whether the size of typical portions has changed over time. Young adults (n=177, 75% female, age range 16 to 26 years) at a major northeastern university. Participants served themselves typical portion sizes of eight foods at breakfast (n=63) or six foods at lunch or dinner (n=62, n=52, respectively). Typical portion-size selections were unobtrusively weighed. A unit score was calculated by awarding 1 point for each food with a typical portion size that was within 25% larger or smaller than the reference portion; larger or smaller portions were given 0 points. Thus, each participant's unit score could range from 0 to 8 at breakfast or 0 to 6 at lunch and dinner. Analysis of variance or t tests were used to determine whether typical and reference portion sizes differed, and whether typical portion sizes changed over time. Mean unit scores (+/-standard deviation) were 3.63+/-1.27 and 1.89+/-1.14, for breakfast and lunch/dinner, respectively, indicating little agreement between typical and reference portion sizes. Typical portions sizes in this study tended to be significantly different from those selected by young adults in a similar study conducted 2 decades ago. Portion distortion seems to affect the portion sizes selected by young adults for some foods. This phenomenon has the potential to hinder weight loss, weight maintenance, and

  7. Lattice distortion and strain relaxation in epitaxial thin films of multiferroic TbMnO3 probed by X-ray diffractometry and micro-Raman spectroscopy

    Science.gov (United States)

    Hu, Y.; Stender, D.; Medarde, M.; Lippert, T.; Wokaun, A.; Schneider, C. W.

    2013-08-01

    A detailed structural XRD analysis of (1 1 0)-oriented TbMnO3 thin films grown on (1 1 0)-YAlO3 substrates shows the co-existence of a strained and relaxed "sublayer" within the films due to strain relaxation during epitaxial growth by pulsed laser deposition. The substrate-film lattice mismatch yields a compressive strain anisotropy along the two in-plane directions, i.e. [1 -1 0] and [0 0 1] and a monoclinic distortion. A further manifestation of the growth-induced strain is the hardening of Raman active modes as a result of changed atomic motions along the [1 -1 0] and [0 0 1] directions.

  8. Lattice distortion and strain relaxation in epitaxial thin films of multiferroic TbMnO{sub 3} probed by X-ray diffractometry and micro-Raman spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Hu, Y.; Stender, D. [Paul Scherrer Institute, General Energy Research Department, 5232 Villigen-PSI (Switzerland); Medarde, M. [Paul Scherrer Institute, Laboratory for Developments and Methods, 5232 Villigen-PSI (Switzerland); Lippert, T., E-mail: thomas.lippert@psi.ch [Paul Scherrer Institute, General Energy Research Department, 5232 Villigen-PSI (Switzerland); Wokaun, A.; Schneider, C.W. [Paul Scherrer Institute, General Energy Research Department, 5232 Villigen-PSI (Switzerland)

    2013-08-01

    A detailed structural XRD analysis of (1 1 0)-oriented TbMnO{sub 3} thin films grown on (1 1 0)-YAlO{sub 3} substrates shows the co-existence of a strained and relaxed “sublayer” within the films due to strain relaxation during epitaxial growth by pulsed laser deposition. The substrate-film lattice mismatch yields a compressive strain anisotropy along the two in-plane directions, i.e. [1 −1 0] and [0 0 1] and a monoclinic distortion. A further manifestation of the growth-induced strain is the hardening of Raman active modes as a result of changed atomic motions along the [1 −1 0] and [0 0 1] directions.

  9. Processing of free radical damaged DNA bases

    International Nuclear Information System (INIS)

    Wallace, S.

    2003-01-01

    Free radicals produced during the radiolysis of water gives rise to a plethora of DNA damages including single strand breaks, sites of base loss and a wide variety of purine and pyrimidine base lesions. All these damages are processed in cells by base excision repair. The oxidative DNA glycosylases which catalyze the first step in the removal of a base damage during base excision repair evolved primarily to protect the cells from the deleterious mutagenic effects of single free radical-induced DNA lesions arising during oxidative metabolism. This is evidenced by the high spontaneous mutation rate in bacterial mutants lacking the oxidative DNA glycosylases. However, when a low LET photon transverses the DNA molecule, a burst of free radicals is produced during the radiolysis of water that leads to the formation of clustered damages in the DNA molecule, that are recognized by the oxidative DNA glycosylases. When substrates containing two closely opposed sugar damages or base and sugar damages are incubated with the oxidative DNA glycosylases in vitro, one strand is readily incised by the lyase activity of the DNA glycosylase. Whether or not the second strand is incised depends on the distance between the strand break resulting from the incised first strand and the remaining DNA lesion on the other strand. If the lesions are more than two or three base pairs apart, the second strand is readily cleaved by the DNA glycosylase, giving rise to a double strand break. Even if the entire base excision repair system is reconstituted in vitro, whether or not a double strand break ensues depends solely upon the ability of the DNA glycosylase to cleave the second strand. These data predicted that cells deficient in the oxidative DNA glycosylases would be radioresistant while those that overproduce an oxidative DNA glycosylase would be radiosensitive. This prediction was indeed borne in Escherichia coli that is, mutants lacking the oxidative DNA glycosylases are radioresistant

  10. Damage and repair of ancient DNA

    DEFF Research Database (Denmark)

    Mitchell, David; Willerslev, Eske; Hansen, Anders

    2005-01-01

    degradation, these studies are limited to species that lived within the past 10(4)-10(5) years (Late Pleistocene), although DNA sequences from 10(6) years have been reported. Ancient DNA (aDNA) has been used to study phylogenetic relationships of protists, fungi, algae, plants, and higher eukaryotes...... such as extinct horses, cave bears, the marsupial wolf, the moa, and Neanderthal. In the past few years, this technology has been extended to the study of infectious disease in ancient Egyptian and South American mummies, the dietary habits of ancient animals, and agricultural practices and population dynamics......, and extensive degradation. In the course of this review, we will discuss the current aDNA literature describing the importance of aDNA studies as they relate to important biological questions and the difficulties associated with extracting useful information from highly degraded and damaged substrates derived...

  11. Wireless infrared indoor communications: how to combat the multipath distortion

    Science.gov (United States)

    Jivkova, Svetla T.; Kavehrad, Mohsen

    2001-02-01

    12 Currently, higher and higher transmission speeds are being pursuit for wireless LANs. The present investigation deals with one of the most prospective candidates for high-speed in-house wireless communications, namely, Multi-Spot Diffusing Configuration (MSDC). Since it uses optical medium for data transmission, it possesses inherent potential for achieving very high capacity level. Channel characteristics in MSDC are simulated and the causes for channel distortion are analyzed. Then, conditions for creation of a virtually ideal channel are derived. It is shown that the 3 dB-channel bandwidth can be extended up to frequencies beyond 2 GHz. The large bandwidth comes at the cost of poor power efficiency. In order to compensate for this, a novel receiver optical front-end design is proposed and its performance is analyzed. Taking advantage of unique properties of holographic optical elements, conventional optical front-end consisting of a concentrator and a filter, is replaced by a single holographic curved mirror. Utilization of such a holographic optical element improves the signal-to-shot noise ratio by up to 18.5 dB.

  12. Distortion-Free Watermarking Approach for Relational Database Integrity Checking

    Directory of Open Access Journals (Sweden)

    Lancine Camara

    2014-01-01

    Full Text Available Nowadays, internet is becoming a suitable way of accessing the databases. Such data are exposed to various types of attack with the aim to confuse the ownership proofing or the content protection. In this paper, we propose a new approach based on fragile zero watermarking for the authentication of numeric relational data. Contrary to some previous databases watermarking techniques which cause some distortions in the original database and may not preserve the data usability constraints, our approach simply seeks to generate the watermark from the original database. First, the adopted method partitions the database relation into independent square matrix groups. Then, group-based watermarks are securely generated and registered in a trusted third party. The integrity verification is performed by computing the determinant and the diagonal’s minor for each group. As a result, tampering can be localized up to attribute group level. Theoretical and experimental results demonstrate that the proposed technique is resilient against tuples insertion, tuples deletion, and attributes values modification attacks. Furthermore, comparison with recent related effort shows that our scheme performs better in detecting multifaceted attacks.

  13. Distorted Character Recognition Via An Associative Neural Network

    Science.gov (United States)

    Messner, Richard A.; Szu, Harold H.

    1987-03-01

    The purpose of this paper is two-fold. First, it is intended to provide some preliminary results of a character recognition scheme which has foundations in on-going neural network architecture modeling, and secondly, to apply some of the neural network results in a real application area where thirty years of effort has had little effect on providing the machine an ability to recognize distorted objects within the same object class. It is the author's belief that the time is ripe to start applying in ernest the results of over twenty years of effort in neural modeling to some of the more difficult problems which seem so hard to solve by conventional means. The character recognition scheme proposed utilizes a preprocessing stage which performs a 2-dimensional Walsh transform of an input cartesian image field, then sequency filters this spectrum into three feature bands. Various features are then extracted and organized into three sets of feature vectors. These vector patterns that are stored and recalled associatively. Two possible associative neural memory models are proposed for further investigation. The first being an outer-product linear matrix associative memory with a threshold function controlling the strength of the output pattern (similar to Kohonen's crosscorrelation approach [1]). The second approach is based upon a modified version of Grossberg's neural architecture [2] which provides better self-organizing properties due to its adaptive nature. Preliminary results of the sequency filtering and feature extraction preprocessing stage and discussion about the use of the proposed neural architectures is included.

  14. Magnetoelastic couplings in the distorted diamond-chain compound azurite

    Science.gov (United States)

    Cong, Pham Thanh; Wolf, Bernd; Manna, Rudra Sekhar; Tutsch, Ulrich; de Souza, Mariano; Brühl, Andreas; Lang, Michael

    2014-05-01

    We present results of ultrasonic measurements on a single crystal of the distorted diamond-chain compound azurite Cu3(CO3)2(OH)2. Pronounced elastic anomalies are observed in the temperature dependence of the longitudinal elastic mode c22 which can be assigned to the relevant magnetic interactions in the system and their couplings to the lattice degrees of freedom. From a semiquantitative analysis of the magnetic contribution to c22 the magnetoelastic coupling G =∂J2/∂ɛb can be estimated, where J2 is the intradimer coupling constant and ɛb the strain along the intrachain b axis. We find an exceptionally large coupling constant of |G |˜ 3650 K highlighting an extraordinarily strong sensitivity of J2 against changes of the b-axis lattice parameter. These results are complemented by measurements of the hydrostatic pressure dependence of J2 by means of thermal expansion and magnetic susceptibility measurements performed both at ambient and finite hydrostatic pressure. We propose that a structural peculiarity of this compound, in which Cu2O6 dimer units are incorporated in an unusually stretched manner, is responsible for the anomalously large magnetoelastic coupling.

  15. Constraints in distortion-invariant target recognition system simulation

    Science.gov (United States)

    Iftekharuddin, Khan M.; Razzaque, Md A.

    2000-11-01

    Automatic target recognition (ATR) is a mature but active research area. In an earlier paper, we proposed a novel ATR approach for recognition of targets varying in fine details, rotation, and translation using a Learning Vector Quantization (LVQ) Neural Network (NN). The proposed approach performed segmentation of multiple objects and the identification of the objects using LVQNN. In this current paper, we extend the previous approach for recognition of targets varying in rotation, translation, scale, and combination of all three distortions. We obtain the analytical results of the system level design to show that the approach performs well with some constraints. The first constraint determines the size of the input images and input filters. The second constraint shows the limits on amount of rotation, translation, and scale of input objects. We present the simulation verification of the constraints using DARPA's Moving and Stationary Target Recognition (MSTAR) images with different depression and pose angles. The simulation results using MSTAR images verify the analytical constraints of the system level design.

  16. Distortion, Messianism, and Apocalyptic Time in The Satanic Verses

    Directory of Open Access Journals (Sweden)

    Clara Eisinger

    2013-05-01

    Full Text Available Salman Rushdie’s novel The Satanic Verses presents its readers with a striking perspective on apocalypse. Taking place in the context of a modernist, migrant worldview, this apocalypse works to unsettle its participating characters by teaching them how to create a world in which they might someday belong. Though often defined as destructive, the apocalypse as I define it involves a reaching for or gesture towards the impossible, which the Verses achieves through massive temporal distortion. Linear time finds itself subverted; characters’ narratives speed up or slow down, forcing them to question their various adventures in 1980s London. Rushdie’s protagonist Saladin Chamcha re-grasps and reinvents his world; his other protagonist, Gibreel Farishta, does not. For one man, apocalypse becomes a means of empowerment; for another, it develops into a black hole. Unlike real black holes, however, Rushdie’s apocalypse does not kill all who venture into it, but instead stretches its hardiest entrants both emotionally and intellectually before dropping them into a new universe. Apocalypse and the post-apocalyptic are not therefore to be feared but to be reached for: worthy achievements for those individuals who can survive the risk, the compression, and the disorientation to emerge in a ‘post’ that is not a wasteland but a realm of ceaseless energetic creation—a realm which allows migrants to construct for themselves better lives in the 21st century world.

  17. Impacts of satellite galaxies on the redshift-space distortions

    Energy Technology Data Exchange (ETDEWEB)

    Hikage, Chiaki [Kobayashi-Maskawa Institute, Nagoya University, Nagoya 464-8602 (Japan); Yamamoto, Kazuhiro, E-mail: hikage@kmi.nagoya-u.ac.jp, E-mail: kazuhiro@hiroshima-u.ac.jp [Department of Physical Sciences, Hiroshima University, Higashi-hiroshima, Kagamiyama 1-3-1, 739-8526 (Japan)

    2013-08-01

    We study the impacts of the satellite galaxies on the redshift-space distortions. In our multipole power spectrum analysis of the luminous red galaxies (LRGs) samples of the Sloan digital sky survey (SDSS), we have clearly detected the non-zero signature of the hexadecapole and tetrahexadecapole spectrum, which almost disappears in the power spectrum with the sample of the brightest LRGs only. We thus demonstrate that the satellite LRGs in multiple systems make a significant contribution to the multipole power spectrum though its fraction is small. The behavior can be understood by a simple halo model, in which the one-halo term, describing the Finger of God (FoG) effect from the satellite galaxies, makes the dominant contribution to the higher multipole spectra. We demonstrate that the small-scale information of higher multipole spectrum is useful for calibrating the satellite FoG effect and improves the measurement of the cosmic growth rate dramatically. We further demonstrate that the fiber collision in the galaxy survey influences the one-halo term and the higher multipole spectra, because the number of satellite galaxies in the halo occupation distribution (HOD) is changed. We also discuss about the impact of satellite galaxies on future high-redshift surveys targeting the H-alpha emitters.

  18. Rate-distortion optimization for compressive video sampling

    Science.gov (United States)

    Liu, Ying; Vijayanagar, Krishna R.; Kim, Joohee

    2014-05-01

    The recently introduced compressed sensing (CS) framework enables low complexity video acquisition via sub- Nyquist rate sampling. In practice, the resulting CS samples are quantized and indexed by finitely many bits (bit-depth) for transmission. In applications where the bit-budget for video transmission is constrained, rate- distortion optimization (RDO) is essential for quality video reconstruction. In this work, we develop a double-level RDO scheme for compressive video sampling, where frame-level RDO is performed by adaptively allocating the fixed bit-budget per frame to each video block based on block-sparsity, and block-level RDO is performed by modelling the block reconstruction peak-signal-to-noise ratio (PSNR) as a quadratic function of quantization bit-depth. The optimal bit-depth and the number of CS samples are then obtained by setting the first derivative of the function to zero. In the experimental studies the model parameters are initialized with a small set of training data, which are then updated with local information in the model testing stage. Simulation results presented herein show that the proposed double-level RDO significantly enhances the reconstruction quality for a bit-budget constrained CS video transmission system.

  19. Galaxy bispectrum, primordial non-Gaussianity and redshift space distortions

    Energy Technology Data Exchange (ETDEWEB)

    Tellarini, Matteo; Ross, Ashley J.; Wands, David [Institute of Cosmology and Gravitation, University of Portsmouth, Dennis Sciama Building, Portsmouth, PO1 3FX (United Kingdom); Tasinato, Gianmassimo, E-mail: matteo.tellarini@port.ac.uk, E-mail: ross.1333@osu.edu, E-mail: g.tasinato@swansea.ac.uk, E-mail: david.wands@port.ac.uk [Department of Physics, Swansea University, Singleton Park, Swansea, SA2 8PP (United Kingdom)

    2016-06-01

    Measurements of the non-Gaussianity of the primordial density field have the power to considerably improve our understanding of the physics of inflation. Indeed, if we can increase the precision of current measurements by an order of magnitude, a null-detection would rule out many classes of scenarios for generating primordial fluctuations. Large-scale galaxy redshift surveys represent experiments that hold the promise to realise this goal. Thus, we model the galaxy bispectrum and forecast the accuracy with which it will probe the parameter f {sub NL}, which represents the degree of primordial local-type non Gaussianity. Specifically, we address the problem of modelling redshift space distortions (RSD) in the tree-level galaxy bispectrum including f {sub NL}. We find novel contributions associated with RSD, with the characteristic large scale amplification induced by local-type non-Gaussianity. These RSD effects must be properly accounted for in order to obtain un-biased measurements of f {sub NL} from the galaxy bispectrum. We propose an analytic template for the monopole which can be used to fit against data on large scales, extending models used in the recent measurements. Finally, we perform idealised forecasts on σ {sub f} {sub N{sub L}}—the accuracy of the determination of local non-linear parameter f {sub NL}—from measurements of the galaxy bispectrum. Our findings suggest that current surveys can in principle provide f {sub NL} constraints competitive with Planck , and future surveys could improve them further.

  20. Galaxy bispectrum, primordial non-Gaussianity and redshift space distortions

    International Nuclear Information System (INIS)

    Tellarini, Matteo; Ross, Ashley J.; Wands, David; Tasinato, Gianmassimo

    2016-01-01

    Measurements of the non-Gaussianity of the primordial density field have the power to considerably improve our understanding of the physics of inflation. Indeed, if we can increase the precision of current measurements by an order of magnitude, a null-detection would rule out many classes of scenarios for generating primordial fluctuations. Large-scale galaxy redshift surveys represent experiments that hold the promise to realise this goal. Thus, we model the galaxy bispectrum and forecast the accuracy with which it will probe the parameter f NL , which represents the degree of primordial local-type non Gaussianity. Specifically, we address the problem of modelling redshift space distortions (RSD) in the tree-level galaxy bispectrum including f NL . We find novel contributions associated with RSD, with the characteristic large scale amplification induced by local-type non-Gaussianity. These RSD effects must be properly accounted for in order to obtain un-biased measurements of f NL from the galaxy bispectrum. We propose an analytic template for the monopole which can be used to fit against data on large scales, extending models used in the recent measurements. Finally, we perform idealised forecasts on σ f NL —the accuracy of the determination of local non-linear parameter f NL —from measurements of the galaxy bispectrum. Our findings suggest that current surveys can in principle provide f NL constraints competitive with Planck , and future surveys could improve them further.

  1. An inventory of bispectrum estimators for redshift space distortions

    Science.gov (United States)

    Regan, Donough

    2017-12-01

    In order to best improve constraints on cosmological parameters and on models of modified gravity using current and future galaxy surveys it is necessary maximally exploit the available data. As redshift-space distortions mean statistical translation invariance is broken for galaxy observations, this will require measurement of the monopole, quadrupole and hexadecapole of not just the galaxy power spectrum, but also the galaxy bispectrum. A recent (2015) paper by Scoccimarro demonstrated how the standard bispectrum estimator may be expressed in terms of Fast Fourier Transforms (FFTs) to afford an extremely efficient algorithm, allowing the bispectrum multipoles on all scales and triangle shapes to be measured in comparable time to those of the power spectrum. In this paper we present a suite of alternative proxies to measure the three-point correlation multipoles. In particular, we describe a modal (or plane wave) decomposition to capture the information in each multipole in a series of basis coefficients, and also describe three compressed estimators formed using the skew-spectrum, the line correlation function and the integrated bispectrum, respectively. As well as each of the estimators offering a different measurement channel, and thereby a robustness check, it is expected that some (especially the modal estimator) will offer a vast data compression, and so a much reduced covariance matrix. This compression may be vital to reduce the computational load involved in extracting the available three-point information.

  2. A new structural framework for integrating replication protein A into DNA processing machinery

    Energy Technology Data Exchange (ETDEWEB)

    Brosey, Chris; Yan, Chunli; Tsutakawa, Susan; Heller, William; Rambo, Robert; Tainer, John; Ivanov, Ivaylo; Chazin, Walter

    2013-01-17

    By coupling the protection and organization of single-stranded DNA (ssDNA) with recruitment and alignment of DNA processing factors, replication protein A (RPA) lies at the heart of dynamic multi-protein DNA processing machinery. Nevertheless, how RPA coordinates biochemical functions of its eight domains remains unknown. We examined the structural biochemistry of RPA's DNA-binding activity, combining small-angle X-ray and neutron scattering with all-atom molecular dynamics simulations to investigate the architecture of RPA's DNA-binding core. The scattering data reveal compaction promoted by DNA binding; DNA-free RPA exists in an ensemble of states with inter-domain mobility and becomes progressively more condensed and less dynamic on binding ssDNA. Our results contrast with previous models proposing RPA initially binds ssDNA in a condensed state and becomes more extended as it fully engages the substrate. Moreover, the consensus view that RPA engages ssDNA in initial, intermediate and final stages conflicts with our data revealing that RPA undergoes two (not three) transitions as it binds ssDNA with no evidence for a discrete intermediate state. These results form a framework for understanding how RPA integrates the ssDNA substrate into DNA processing machinery, provides substrate access to its binding partners and promotes the progression and selection of DNA processing pathways.

  3. Cognitive distortions as a component and treatment focus of pathological gambling: a review.

    Science.gov (United States)

    Fortune, Erica E; Goodie, Adam S

    2012-06-01

    The literature on the role of cognitive distortions in the understanding and treatment of pathological gambling (PG) is reviewed, with sections focusing on (a) conceptual underpinnings of cognitive distortions, (b) cognitive distortions related to PG, (c) PG therapies that target cognitive distortions, (d) methodological factors and outcome variations, and (e) conclusions and prescriptive recommendations. The conceptual background for distortions related to PG lies in the program of heuristics and biases (Kahneman & Tversky, 1974) as well as other errors identified in basic psychology. The literature has focused on distortions arising from the representativeness heuristic (gambler's fallacy, overconfidence, and trends in number picking), the availability heuristic (illusory correlation, other individuals' wins, and inherent memory bias), and other sources (the illusion of control and double switching). Some therapies have incorporated cognitive restructuring within broader cognitive-behavioral therapies, with success. Other therapies have focused more narrowly on correcting distorted beliefs, more often with limited success. It is concluded that the literature establishes the role of cognitive distortions in PG and suggests therapies with particularly good promise, but is in need of further enrichment.

  4. Distorted Pattern Recognition and Analysis with the Help of IEf Graph Representation

    Directory of Open Access Journals (Sweden)

    Adam Sedziwy

    2002-01-01

    Full Text Available An algorithm for distorted pattern recognition is presented. lt's generalization of M Flasinski results (Pattern Recognition, 27, 1-16, 1992. A new formalism allows to make both qualitative and quantitive distortion analysis. It also enlarges parser flexibility by extending the set of patterns which may be recognized.

  5. Detailed dynamic model for semiconductor optical amplifiers and their crosstalk and intermodulation distortion

    DEFF Research Database (Denmark)

    Durhuus, Terji; Mikkelsen, Benny; Stubkjær, Kristian

    1992-01-01

    . The model is used to assess intermodulation distortion and crosstalk. Cascaded amplifiers are considered, and the crosstalk and intermodulation distortion due to cascaded amplifiers are found to accumulate by adding together in amplitude; this may limit the number or cascaded amplifiers in multichannel...

  6. Rate-distortion functions of non-stationary Markoff chains and their block-independent approximations

    OpenAIRE

    Agarwal, Mukul

    2018-01-01

    It is proved that the limit of the normalized rate-distortion functions of block independent approximations of an irreducible, aperiodic Markoff chain is independent of the initial distribution of the Markoff chain and thus, is also equal to the rate-distortion function of the Markoff chain.

  7. Shape distortion and dimensional precision in tungsten heavy alloy liquid phase sintering

    International Nuclear Information System (INIS)

    Wuwen Yi; German, R.M.; Lu, P.K.

    2001-01-01

    Microstructure effects on densification and shape distortion in liquid phase sintering of tungsten heavy alloy were investigated. Microstructure parameters such as the solid volume fraction, dihedral angle, initial porosity, and pore size were varied to measure densification and distortion behavior during LPS using W-Ni-Cu alloys. Green compacts were formed using ethylene-bis-stearamide as a pore-forming agent with the amount of polymer controlling the initial porosity. Different initial pore sizes were generated by varying the polymer particle size. Dihedral angle was varied by changing the Ni:Cu ratio in the alloys. Finally, the solid volume fraction was adjusted via the tungsten content. Distortion was quantified using profiles determined with a coordinate measuring machine to calculate a distortion parameter. Sintering results showed that solid volume fraction and dihedral angle are the dominant factors on densification and distortion during liquid phase sintering. Distortion decreases with increasing solid volume fraction and dihedral angle, while initial porosity and pore size have no observable effect on distortion at nearly full densification. Various strategies emerge to improve distortion control in liquid phase sintering. (author)

  8. Distortion Correction in Fetal EPI Using Non-Rigid Registration With a Laplacian Constraint.

    Science.gov (United States)

    Kuklisova-Murgasova, Maria; Lockwood Estrin, Georgia; Nunes, Rita G; Malik, Shaihan J; Rutherford, Mary A; Rueckert, Daniel; Hajnal, Joseph V

    2018-01-01

    Geometric distortion induced by the main B0 field disrupts the consistency of fetal echo planar imaging (EPI) data, on which diffusion and functional magnetic resonance imaging is based. In this paper, we present a novel data-driven method for simultaneous motion and distortion correction of fetal EPI. A motion-corrected and reconstructed T2 weighted single shot fast spin echo (ssFSE) volume is used as a model of undistorted fetal brain anatomy. Our algorithm interleaves two registration steps: estimation of fetal motion parameters by aligning EPI slices to the model; and deformable registration of EPI slices to slices simulated from the undistorted model to estimate the distortion field. The deformable registration is regularized by a physically inspired Laplacian constraint, to model distortion induced by a source-free background B0 field. Our experiments show that distortion correction significantly improves consistency of reconstructed EPI volumes with ssFSE volumes. In addition, the estimated distortion fields are consistent with fields calculated from acquired field maps, and the Laplacian constraint is essential for estimation of plausible distortion fields. The EPI volumes reconstructed from different scans of the same subject were more consistent when the proposed method was used in comparison with EPI volumes reconstructed from data distortion corrected using a separately acquired B0 field map.

  9. Models of brachial to finger pulse wave distortion and pressure decrement

    NARCIS (Netherlands)

    Gizdulich, P.; Prentza, A.; Wesseling, K.H.

    1997-01-01

    Objective: To model the pulse wave distortion and pressure decrement occurring between brachial and finger arteries. Distortion reversion and decrement correction were also our aims. Methods: Brachial artery pressure was recorded intra-arterially and finger pressure was recorded non-invasively by

  10. Numerical and semi-analytical modelling of the process induced distortions in pultrusion

    DEFF Research Database (Denmark)

    Baran, Ismet; Carlone, P.; Hattel, Jesper Henri

    2013-01-01

    , the transient distortions are inferred adopting a semi-analytical procedure, i.e. post processing numerical results by means of analytical methods. The predictions of the process induced distortion development using the aforementioned methods are found to be qualitatively close to each other...

  11. Analyzing Reaction Rates with the Distortion/Interaction-Activation Strain Model

    NARCIS (Netherlands)

    Bickelhaupt, F. Matthias; Houk, Kendall N.

    2017-01-01

    The activation strain or distortion/interaction model is a tool to analyze activation barriers that determine reaction rates. For bimolecular reactions, the activation energies are the sum of the energies to distort the reactants into geometries they have in transition states plus the interaction

  12. Robust Bayes Forecasting For Grouped Binary Data With Known Distortion Interval

    OpenAIRE

    Pashkevich, M.

    2004-01-01

    The paper is devoted the problem of robust forecasting for the beta-mixed hierarchical models of grouped binary data in the case of stochastic additive distortions of binary observations. In the case of known lower and upper bounds of the distortion intervals, a new robust minimax Bayes predictor is developed. The performance of the proposed forecasting technique is validated by computer simulationtadata.

  13. Analytical Expressions for Harmonic Distortion at Low Frequencies due to Device Mismatch in CMOS Current Mirrors

    DEFF Research Database (Denmark)

    Bruun, Erik

    1999-01-01

    One of the origins of harmonic distortion in current mirrors is the inevitable mismatch between the mirror transistors. In this brief we examine both single current mirrors and complementary class AB current mirrors and develop analytical expressions for the mismatch induced harmonic distortion. ...

  14. Studies of field distortions in a time projection chamber for the International Linear Collider

    International Nuclear Information System (INIS)

    Zenker, Klaus

    2014-12-01

    The International Linear Collider (ILC) will allow to do precision measurements of Standard Model parameter and to search for new physics. The ILD detector concept, which is developed for the ILC, uses a Time Projection Chamber (TPC) as central tracking device. The momentum resolution goal for the ILD TPC is δ(1/p t ) ≅ 10 -4 (GeV/c) -1 at a magnetic field of B=3.5 T. Field distortions of the magnetic or electric field inside the sensitive volume of the TPC distort the momentum measurements. Therefore, one needs to keep them under control and correct them with high precision. In this thesis the main sources of field distortions in the TPC are identified and their effects are determined. Furthermore, possibilities to reduce the identified field distortions are presented. One known source of distortions of the electric field are ions, produced by the gas amplification in the TPC anode, that drift into the sensitive volume of the TPC. In the first part of this work the creation of these ions in Gas Electron Multiplier (GEM), which are used for the gas amplification, is studied. It will be shown that the resulting field distortions are not acceptable at the ILD TPC. By tuning the parameters of the gas amplification at the anode the field distortion can be reduced, which is shown in measurements and simulations. In addition measurements using a modified GEM show that it is possible to further reduce the field distortions with such a GEM. In the second part of this work field distortions arising at boundaries between individual readout modules are investigated using simulation studies. It will be shown in simulations, which are verified by measurement results, that these field distortions significantly influence the readout module performance. Based on the simulation results the GEM based readout module developed at DESY is optimised and the field distortions are reduced. These performance improvements could also be verified in measurements. Finally, a laser

  15. Structure of human DNA polymerase iota and the mechanism of DNA synthesis.

    Science.gov (United States)

    Makarova, A V; Kulbachinskiy, A V

    2012-06-01

    Cellular DNA polymerases belong to several families and carry out different functions. Highly accurate replicative DNA polymerases play the major role in cell genome replication. A number of new specialized DNA polymerases were discovered at the turn of XX-XXI centuries and have been intensively studied during the last decade. Due to the special structure of the active site, these enzymes efficiently perform synthesis on damaged DNA but are characterized by low fidelity. Human DNA polymerase iota (Pol ι) belongs to the Y-family of specialized DNA polymerases and is one of the most error-prone enzymes involved in DNA synthesis. In contrast to other DNA polymerases, Pol ι is able to use noncanonical Hoogsteen interactions for nucleotide base pairing. This allows it to incorporate nucleotides opposite various lesions in the DNA template that impair Watson-Crick interactions. Based on the data of X-ray structural analysis of Pol ι in complexes with various DNA templates and dNTP substrates, we consider the structural peculiarities of the Pol ι active site and discuss possible mechanisms that ensure the unique behavior of the enzyme on damaged and undamaged DNA.

  16. Visualization of Hyperconjugation and Subsequent Structural Distortions through 3D Printing of Crystal Structures.

    Science.gov (United States)

    Mithila, Farha J; Oyola-Reynoso, Stephanie; Thuo, Martin M; Atkinson, Manza Bj

    2016-01-01

    Structural distortions due to hyperconjugation in organic molecules, like norbornenes, are well captured through X-ray crystallographic data, but are sometimes difficult to visualize especially for those applying chemical knowledge and are not chemists. Crystal structure from the Cambridge database were downloaded and converted to .stl format. The structures were then printed at the desired scale using a 3D printer. Replicas of the crystal structures were accurately reproduced in scale and any resulting distortions were clearly visible from the macroscale models. Through space interactions or effect of through space hyperconjugation was illustrated through loss of symmetry or distortions thereof. The norbornene structures exhibits distortion that cannot be observed through conventional ball and stick modelling kits. We show that 3D printed models derived from crystallographic data capture even subtle distortions in molecules. We translate such crystallographic data into scaled-up models through 3D printing.

  17. Carrier Distortion in Hysteretic Self-Oscillating Class-D Audio Power

    DEFF Research Database (Denmark)

    Høyerby, Mikkel Christian Kofod; Andersen, Michael A. E.

    2009-01-01

    An important distortion mechanism in hysteretic self-oscillating (SO) class-D (switch mode) power amplifiers-–carrier distortion-–is analyzed and an optimization method is proposed. This mechanism is an issue in any power amplifier application where a high degree of proportionality between input...... and output is required, such as in audio power amplifiers or xDSL drivers. From an average-mode point of view, carrier distortion is shown to be caused by nonlinear variation of the hysteretic comparator input average voltage with the output average voltage. This easily causes total harmonic distortion...... figures in excess of 0.1–0.2%, inadequate for high-quality audio applications. Carrier distortion is shown to be minimized when the feedback system is designed to provide a triangular carrier (sliding) signal at the input of a hysteretic comparator. The proposed optimization method is experimentally...

  18. Evidence of two-channel distortion effects in positronium formation reactions

    International Nuclear Information System (INIS)

    Macri, P A; Miraglia, J E; Hanssen, J; Fojon, O A; Rivarola, R D

    2004-01-01

    The formation of ground-state positronium in collisions of positrons on hydrogen-like atoms is considered. In previous theoretical works, two-centre distorted wavefunctions were employed to approximate either the initial or the final channel. Here we report results obtained by means of the eikonal final state continuum distorted wave approximation for which asymptotically correct distorted wavefunctions are used for both the initial and final states of the scattering system. Comparison of the present theoretical total cross sections with experimental data reveals that distortion effects become important in both channels as the impact energy decreases. This work also shows that distorted-wave theories may be extended from their usual domain of high impact energies to lower ones. (letter to the editor)

  19. Bending Distortion Analysis of a Steel Shaft Manufacturing Chain from Cold Drawing to Grinding

    Science.gov (United States)

    Dias, Vinicius Waechter; da Silva Rocha, Alexandre; Zottis, Juliana; Dong, Juan; Epp, Jérémy; Zoch, Hans Werner

    2017-04-01

    Shafts are usually manufactured from bars that are cold drawn, cut machined, induction hardened, straightened, and finally ground. The main distortion is characterized by bending that appears after induction hardening and is corrected by straightening and/or grinding. In this work, the consequence of the variation of manufacturing parameters on the distortion was analyzed for a complete manufacturing route for production of induction hardened shafts made of Grade 1045 steel. A DoE plan was implemented varying the drawing angle, cutting method, induction hardening layer depth, and grinding penetration depth. The distortion was determined by calculating curvature vectors from dimensional analysis by 3D coordinate measurements. Optical microscopy, microhardness testing, residual stress analysis, and FEM process simulation were used to evaluate and understand effects of the main carriers of distortion potential. The drawing process was identified as the most significant influence on the final distortion of the shafts.

  20. Evidence of two-channel distortion effects in positronium formation reactions

    Energy Technology Data Exchange (ETDEWEB)

    Macri, P A [Instituto de AstronomIa y FIsica del Espacio, Consejo Nacional de Investigaciones CientIficas y Tecnicas-Universidad de Buenos Aires, Casilla de Correo 67, Suc. 28, 1428 Buenos Aires (Argentina); Miraglia, J E [Instituto de AstronomIa y FIsica del Espacio, Consejo Nacional de Investigaciones CientIficas y Tecnicas-Universidad de Buenos Aires, Casilla de Correo 67, Suc. 28, 1428 Buenos Aires (Argentina); Hanssen, J [Laboratoire de Physique Moleculaire et des Collisions, Institute de Physique Rue Arago, Tecnopole 2000, Metz (France); Fojon, O A [Instituto de FIsica de Rosario, Consejo Nacional de Investigaciones CientIficas y Tecnicas-Universidad Nacional de Rosario, Av. Pellegrini 250, 2000 Rosario (Argentina); Rivarola, R D [Instituto de FIsica de Rosario, Consejo Nacional de Investigaciones CientIficas y Tecnicas-Universidad Nacional de Rosario, Av. Pellegrini 250, 2000 Rosario (Argentina)

    2004-03-28

    The formation of ground-state positronium in collisions of positrons on hydrogen-like atoms is considered. In previous theoretical works, two-centre distorted wavefunctions were employed to approximate either the initial or the final channel. Here we report results obtained by means of the eikonal final state continuum distorted wave approximation for which asymptotically correct distorted wavefunctions are used for both the initial and final states of the scattering system. Comparison of the present theoretical total cross sections with experimental data reveals that distortion effects become important in both channels as the impact energy decreases. This work also shows that distorted-wave theories may be extended from their usual domain of high impact energies to lower ones. (letter to the editor)