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Sample records for ef hand motifs

  1. Interleukin-11 binds specific EF-hand proteins via their conserved structural motifs.

    Science.gov (United States)

    Kazakov, Alexei S; Sokolov, Andrei S; Vologzhannikova, Alisa A; Permyakova, Maria E; Khorn, Polina A; Ismailov, Ramis G; Denessiouk, Konstantin A; Denesyuk, Alexander I; Rastrygina, Victoria A; Baksheeva, Viktoriia E; Zernii, Evgeni Yu; Zinchenko, Dmitry V; Glazatov, Vladimir V; Uversky, Vladimir N; Mirzabekov, Tajib A; Permyakov, Eugene A; Permyakov, Sergei E

    2017-01-01

    Interleukin-11 (IL-11) is a hematopoietic cytokine engaged in numerous biological processes and validated as a target for treatment of various cancers. IL-11 contains intrinsically disordered regions that might recognize multiple targets. Recently we found that aside from IL-11RA and gp130 receptors, IL-11 interacts with calcium sensor protein S100P. Strict calcium dependence of this interaction suggests a possibility of IL-11 interaction with other calcium sensor proteins. Here we probed specificity of IL-11 to calcium-binding proteins of various types: calcium sensors of the EF-hand family (calmodulin, S100B and neuronal calcium sensors: recoverin, NCS-1, GCAP-1, GCAP-2), calcium buffers of the EF-hand family (S100G, oncomodulin), and a non-EF-hand calcium buffer (α-lactalbumin). A specific subset of the calcium sensor proteins (calmodulin, S100B, NCS-1, GCAP-1/2) exhibits metal-dependent binding of IL-11 with dissociation constants of 1-19 μM. These proteins share several amino acid residues belonging to conservative structural motifs of the EF-hand proteins, 'black' and 'gray' clusters. Replacements of the respective S100P residues by alanine drastically decrease its affinity to IL-11, suggesting their involvement into the association process. Secondary structure and accessibility of the hinge region of the EF-hand proteins studied are predicted to control specificity and selectivity of their binding to IL-11. The IL-11 interaction with the EF-hand proteins is expected to occur under numerous pathological conditions, accompanied by disintegration of plasma membrane and efflux of cellular components into the extracellular milieu.

  2. Engineering recombinant EF-hand peptides for selective uranium uptake

    Energy Technology Data Exchange (ETDEWEB)

    Berthomieu, C.; Pardoux, R.; Beccia, M.R.; Lemaire, D.; Sauge-Merle, S. [CEA, DSV, IBEB, UMR7265 CNRS CEA Aix-Marseille Univ. (France); Guilbaud, P. [CEA, DRCPC, SMCS, LILA (France); Delangle, P. [CEA, INAC, Service de Chimie Inorganique et Biologique (France)

    2014-07-01

    In spite of an increasing number of publications in recent years, information regarding the mechanism of uranium interaction with proteins at the molecular level is limited and few quantitative studies have investigated the binding properties of uranyl with proteins or peptides. It is thus of great interest to better characterize these interactions, and to analyze structural factors governing uranyl binding and thermodynamic stabilization in proteins. Research in this direction will benefit our understanding of the molecular factors governing uranyl toxicity and speciation in cells and will also aid in developing new molecules for selectively binding uranium that could be used for uranium bioremediation purposes. Uranyl coordination properties have similarities with those of calcium, i.e electrostatic interactions preferentially with hard donor oxygen ligands and pentagonal bipyramidal structures. The EF-hand structural motif is the most prevalent Ca2{sup +-}binding site in proteins and is very appealing to analyse uranyl binding properties and develop affine and specific uranyl binding sites for biotechnology approaches. We selected the recombinant N-terminal domain of calmodulin from A. thaliana as a structured template that contains two EF-hand motifs (site I and site II) to analyze its uranyl binding properties and to engineer peptide variants with increased uranyl affinity and specificity. We showed that both site I and site II bind uranyl, with a dissociation constant in the nano-molar range for site I (K{sub d} ≅ 25 nM at pH 6). Using in vitro phosphorylation of a threonine located in the uranyl binding loop, we measured how adding a phosphoryl group affects the calcium and uranium binding affinities. The phosphorylated peptide exhibited a very large affinity for uranyl at pH 7, with a dissociation constant in the sub-nano-molar range K{sub d} = 0.25 ±0.06 nM, and FTIR analysis demonstrated that the phosphoryl group plays a determining role in uranyl

  3. Functional role of EF-hands 3 and 4 in membrane-binding of KChIP1

    Indian Academy of Sciences (India)

    The aim of the present study is to explore whether membrane targeting of K+ channel-interacting protein 1 (KChIP1) is associated with its EF-hand motifs and varies with specific phospholipids. Truncated KChIP1, in which the EF-hands 3 and 4 were deleted, retained the -helix structure, indicating that the N-terminal half of ...

  4. Remodeling of the AB site of rat parvalbumin and oncomodulin into a canonical EF-hand

    DEFF Research Database (Denmark)

    Cox, J A; Durussel, I; Scott, D J

    1999-01-01

    -residue canonical loop. To create an optical conformational probe we also expressed the homologs with a F102W replacement. Unexpectedly, in none of the proteins did the mutation reactivate the AB site. The AB-remodeled parvalbumins bind two Ca2+ ions with strong positive cooperativity (nH = 2......Parvalbumin (PV) and the homologous protein oncomodulin (OM) contain three EF-hand motifs, but the first site (AB) cannot bind Ca2+. Here we aimed to recreate the putative ancestral proteins [D19-28E]PV and [D19-28E]OM by replacing the 10-residue-long nonfunctional loop in the AB site by a 12...... conformations. The AB-remodeled oncomodulins also bind two Ca2+ with [Ca2+]0.5 = 43 microM and nH = 1.45. Mg2+ does not affect Ca2+ binding. Again the Ca2+ forms display two-thirds of the alpha-helical content in the wild-type, while their core is still strongly hydrophobic as monitored by Trp and Tyr...

  5. Electrostatics effects on Ca(2+) binding and conformational changes in EF-hand domains: Functional implications for EF-hand proteins.

    Science.gov (United States)

    Ababou, Abdessamad; Zaleska, Mariola

    2015-12-01

    Mutations of Gln41 and Lys75 with nonpolar residues in the N-terminal domain of calmodulin (N-Cam) revealed the importance of solvation energetics in conformational change of Ca(2+) sensor EF-hand domains. While in general these domains have polar residues at these corresponding positions yet the extent of their conformational response to Ca(2+) binding and their Ca(2+) binding affinity can be different from N-Cam. Consequently, here we address the charge state of the polar residues at these positions. The results show that the charge state of these polar residues can affect substantially the conformational change and the Ca(2+) binding affinity of our N-Cam variants. Since all the variants kept their conformational activity in the presence of Ca(2+) suggests that the differences observed among them mainly originate from the difference in their molecular dynamics. Hence we propose that the molecular dynamics of Ca(2+) sensor EF-hand domains is a key factor in the multifunctional aspect of EF-hand proteins. Copyright © 2015 Elsevier Inc. All rights reserved.

  6. Evolution of EF-hand calcium-modulated proteins. IV. Exon shuffling did not determine the domain compositions of EF-hand proteins

    Science.gov (United States)

    Kretsinger, R. H.; Nakayama, S.

    1993-01-01

    In the previous three reports in this series we demonstrated that the EF-hand family of proteins evolved by a complex pattern of gene duplication, transposition, and splicing. The dendrograms based on exon sequences are nearly identical to those based on protein sequences for troponin C, the essential light chain myosin, the regulatory light chain, and calpain. This validates both the computational methods and the dendrograms for these subfamilies. The proposal of congruence for calmodulin, troponin C, essential light chain, and regulatory light chain was confirmed. There are, however, significant differences in the calmodulin dendrograms computed from DNA and from protein sequences. In this study we find that introns are distributed throughout the EF-hand domain and the interdomain regions. Further, dendrograms based on intron type and distribution bear little resemblance to those based on protein or on DNA sequences. We conclude that introns are inserted, and probably deleted, with relatively high frequency. Further, in the EF-hand family exons do not correspond to structural domains and exon shuffling played little if any role in the evolution of this widely distributed homolog family. Calmodulin has had a turbulent evolution. Its dendrograms based on protein sequence, exon sequence, 3'-tail sequence, intron sequences, and intron positions all show significant differences.

  7. Modulating uranium binding affinity in engineered calmodulin EF-hand peptides: effect of phosphorylation.

    Directory of Open Access Journals (Sweden)

    Romain Pardoux

    Full Text Available To improve our understanding of uranium toxicity, the determinants of uranyl affinity in proteins must be better characterized. In this work, we analyzed the contribution of a phosphoryl group on uranium binding affinity in a protein binding site, using the site 1 EF-hand motif of calmodulin. The recombinant domain 1 of calmodulin from A. thaliana was engineered to impair metal binding at site 2 and was used as a structured template. Threonine at position 9 of the loop was phosphorylated in vitro, using the recombinant catalytic subunit of protein kinase CK2. Hence, the T(9TKE(12 sequence was substituted by the CK2 recognition sequence TAAE. A tyrosine was introduced at position 7, so that uranyl and calcium binding affinities could be determined by following tyrosine fluorescence. Phosphorylation was characterized by ESI-MS spectrometry, and the phosphorylated peptide was purified to homogeneity using ion-exchange chromatography. The binding constants for uranyl were determined by competition experiments with iminodiacetate. At pH 6, phosphorylation increased the affinity for uranyl by a factor of ∼5, from K(d = 25±6 nM to K(d = 5±1 nM. The phosphorylated peptide exhibited a much larger affinity at pH 7, with a dissociation constant in the subnanomolar range (K(d = 0.25±0.06 nM. FTIR analyses showed that the phosphothreonine side chain is partly protonated at pH 6, while it is fully deprotonated at pH 7. Moreover, formation of the uranyl-peptide complex at pH 7 resulted in significant frequency shifts of the ν(as(P-O and ν(s(P-O IR modes of phosphothreonine, supporting its direct interaction with uranyl. Accordingly, a bathochromic shift in ν(as(UO(2(2+ vibration (from 923 cm(-1 to 908 cm(-1 was observed upon uranyl coordination to the phosphorylated peptide. Together, our data demonstrate that the phosphoryl group plays a determining role in uranyl binding affinity to proteins at physiological pH.

  8. Modulating uranium binding affinity in engineered Calmodulin EF-hand peptides: effect of phosphorylation

    International Nuclear Information System (INIS)

    Pardoux, Romain; Sauge-Merle, Sandrine; Lemaire, David; Guilloreau, Luc; Berthomieu, Catherine; Delangle, Pascale; Adriano, Jean-Marc

    2012-01-01

    To improve our understanding of uranium toxicity, the determinants of uranyl affinity in proteins must be better characterized. In this work, we analyzed the contribution of a phosphoryl group on uranium binding affinity in a protein binding site, using the site 1 EF-hand motif of calmodulin. The recombinant domain 1 of calmodulin from A. thaliana was engineered to impair metal binding at site 2 and was used as a structured template. Threonine at position 9 of the loop was phosphorylated in vitro, using the recombinant catalytic subunit of protein kinase CK2. Hence, the T 9 TKE 12 sequence was substituted by the CK2 recognition sequence TAAE. A tyrosine was introduced at position 7, so that uranyl and calcium binding affinities could be determined by following tyrosine fluorescence. Phosphorylation was characterized by ESI-MS spectrometry, and the phosphorylated peptide was purified to homogeneity using ion-exchange chromatography. The binding constants for uranyl were determined by competition experiments with iminodiacetate. At pH 6, phosphorylation increased the affinity for uranyl by a factor of ∼5, from K d =25±6 nM to K d =5±1 nM. The phosphorylated peptide exhibited a much larger affinity at pH 7, with a dissociation constant in the sub-nanomolar range (K d = 0.25±0.06 nM). FTIR analyses showed that the phospho-threonine side chain is partly protonated at pH 6, while it is fully deprotonated at pH 7. Moreover, formation of the uranyl-peptide complex at pH 7 resulted in significant frequency shifts of the ν as (P-O) and ν s (P-O) IR modes of phospho-threonine, supporting its direct interaction with uranyl. Accordingly, a bathochromic shift in ν as (UO 2 ) 2+ vibration (from 923 cm -1 to 908 cm -1 ) was observed upon uranyl coordination to the phosphorylated peptide. Together, our data demonstrate that the phosphoryl group plays a determining role in uranyl binding affinity to proteins at physiological pH. (authors)

  9. 15N NMR relaxation studies of calcium-loaded parvalbumin show tight dynamics compared to those of other EF-hand proteins

    DEFF Research Database (Denmark)

    Baldellon, C; Alattia, J R; Strub, M P

    1998-01-01

    Dynamics of the rat alpha-parvalbumin calcium-loaded form have been determined by measurement of 15N nuclear relaxation using proton-detected heteronuclear NMR spectroscopy. The relaxation data were analyzed using spectral density functions and the Lipari-Szabo formalism. The major dynamic features...... for the rat alpha-parvalbumin calcium-loaded form are (1) the extreme rigidity of the helix-loop-helix EF-hand motifs and the linker segment connecting them, (2) the N and C termini of the protein being restricted in their mobility, (3) a conformational exchange occurring at the kink of helix D, and (4...... properties which are conserved in the EF-hand domains from different members of this superfamily: (1) a tendency toward higher mobility of NH vectors at relative position 2 in the Ca2+-binding loop, (2) a restricted mobility for the other residues in the binding loop, and (3) an overall rigidity...

  10. Single-molecule folding mechanism of an EF-hand neuronal calcium sensor

    DEFF Research Database (Denmark)

    Heiðarsson, Pétur Orri; Otazo, Mariela R.; Bellucci, Luca

    2013-01-01

    EF-hand calcium sensors respond structurally to changes in intracellular Ca2+ concentration, triggering diverse cellular responses and resulting in broad interactomes. Despite impressive advances in decoding their structure-function relationships, the folding mechanism of neuronal calcium sensors...... of the N domain, showing striking interdomain dependence. Molecular dynamics results reveal the atomistic details of the unfolding process and rationalize the different domain stabilities during mechanical unfolding. Through constant-force experiments and hidden Markov model analysis, the free energy...

  11. Designing sequence to control protein function in an EF-hand protein.

    Science.gov (United States)

    Bunick, Christopher G; Nelson, Melanie R; Mangahas, Sheryll; Hunter, Michael J; Sheehan, Jonathan H; Mizoue, Laura S; Bunick, Gerard J; Chazin, Walter J

    2004-05-19

    The extent of conformational change that calcium binding induces in EF-hand proteins is a key biochemical property specifying Ca(2+) sensor versus signal modulator function. To understand how differences in amino acid sequence lead to differences in the response to Ca(2+) binding, comparative analyses of sequence and structures, combined with model building, were used to develop hypotheses about which amino acid residues control Ca(2+)-induced conformational changes. These results were used to generate a first design of calbindomodulin (CBM-1), a calbindin D(9k) re-engineered with 15 mutations to respond to Ca(2+) binding with a conformational change similar to that of calmodulin. The gene for CBM-1 was synthesized, and the protein was expressed and purified. Remarkably, this protein did not exhibit any non-native-like molten globule properties despite the large number of mutations and the nonconservative nature of some of them. Ca(2+)-induced changes in CD intensity and in the binding of the hydrophobic probe, ANS, implied that CBM-1 does undergo Ca(2+) sensorlike conformational changes. The X-ray crystal structure of Ca(2+)-CBM-1 determined at 1.44 A resolution reveals the anticipated increase in hydrophobic surface area relative to the wild-type protein. A nascent calmodulin-like hydrophobic docking surface was also found, though it is occluded by the inter-EF-hand loop. The results from this first calbindomodulin design are discussed in terms of progress toward understanding the relationships between amino acid sequence, protein structure, and protein function for EF-hand CaBPs, as well as the additional mutations for the next CBM design.

  12. A Medicago truncatula EF-hand family gene, MtCaMP1, is involved in drought and salt stress tolerance.

    Directory of Open Access Journals (Sweden)

    Tian-Zuo Wang

    Full Text Available BACKGROUND: Calcium-binding proteins that contain EF-hand motifs have been reported to play important roles in transduction of signals associated with biotic and abiotic stresses. To functionally characterize genes of EF-hand family in response to abiotic stress, an MtCaMP1 gene belonging to EF-hand family from legume model plant Medicago truncatula was isolated and its function in response to drought and salt stress was investigated by expressing MtCaMP1 in Arabidopsis. METHODOLOGY/PRINCIPAL FINDINGS: Transgenic Arabidopsis seedlings expressing MtCaMP1 exhibited higher survival rate than wild-type seedlings under drought and salt stress, suggesting that expression of MtCaMP1 confers tolerance of Arabidopsis to drought and salt stress. The transgenic plants accumulated greater amounts of Pro due to up-regulation of P5CS1 and down-regulation of ProDH than wild-type plants under drought stress. There was a less accumulation of Na(+ in the transgenic plants than in WT plants due to reduced up-regulation of AtHKT1 and enhanced regulation of AtNHX1 in the transgenic plants compared to WT plants under salt stress. There was a reduced accumulation of H2O2 and malondialdehyde in the transgenic plants than in WT plants under both drought and salt stress. CONCLUSIONS/SIGNIFICANCE: The expression of MtCaMP1 in Arabidopsis enhanced tolerance of the transgenic plants to drought and salt stress by effective osmo-regulation due to greater accumulation of Pro and by minimizing toxic Na(+ accumulation, respectively. The enhanced accumulation of Pro and reduced accumulation of Na(+ under drought and salt stress would protect plants from water default and Na(+ toxicity, and alleviate the associated oxidative stress. These findings demonstrate that MtCaMP1 encodes a stress-responsive EF-hand protein that plays a regulatory role in response of plants to drought and salt stress.

  13. Characterization of the 1st and 2nd EF-hands of NADPH oxidase 5 by fluorescence, isothermal titration calorimetry, and circular dichroism

    Directory of Open Access Journals (Sweden)

    Wei Chin-Chuan

    2012-04-01

    Full Text Available Abstract Background Superoxide generated by non-phagocytic NADPH oxidases (NOXs is of growing importance for physiology and pathobiology. The calcium binding domain (CaBD of NOX5 contains four EF-hands, each binding one calcium ion. To better understand the metal binding properties of the 1st and 2nd EF-hands, we characterized the N-terminal half of CaBD (NCaBD and its calcium-binding knockout mutants. Results The isothermal titration calorimetry measurement for NCaBD reveals that the calcium binding of two EF-hands are loosely associated with each other and can be treated as independent binding events. However, the Ca2+ binding studies on NCaBD(E31Q and NCaBD(E63Q showed their binding constants to be 6.5 × 105 and 5.0 × 102 M-1 with ΔHs of -14 and -4 kJ/mol, respectively, suggesting that intrinsic calcium binding for the 1st non-canonical EF-hand is largely enhanced by the binding of Ca2+ to the 2nd canonical EF-hand. The fluorescence quenching and CD spectra support a conformational change upon Ca2+ binding, which changes Trp residues toward a more non-polar and exposed environment and also increases its α-helix secondary structure content. All measurements exclude Mg2+-binding in NCaBD. Conclusions We demonstrated that the 1st non-canonical EF-hand of NOX5 has very weak Ca2+ binding affinity compared with the 2nd canonical EF-hand. Both EF-hands interact with each other in a cooperative manner to enhance their Ca2+ binding affinity. Our characterization reveals that the two EF-hands in the N-terminal NOX5 are Ca2+ specific. Graphical abstract

  14. EF-hands at atomic resolution: The structure of human psoriasin (S100A7) solved by MAD phasing

    DEFF Research Database (Denmark)

    Brodersen, Ditlev Egeskov; Etzerodt, Michael; Madsen, Peder Søndergaard

    1998-01-01

    psoriasin reveals that this protein, in contrast to other S100 proteins with known structure, is not likely to strongly bind more than one calcium ion per monomer. The present study contradicts the idea that calcium binding induces large changes in conformation, as suggested by previously determined......The S100 family consists of small acidic proteins, belonging to the EF-hand class of calcium-binding proteins. They are primarily regulatory proteins, involved in cell growth, cell structure regulation and signal transduction. Psoriasin (S100A7) is an 11.7 kDa protein that is highly upregulated...... in the epidermis of patients suffering from the chronic skin disease psoriasis. Although its exact function is not known, psoriasin is believed to participate in the biochemical response which follows transient changes in the cellular Ca2+ concentration. RESULTS: The three-dimensional structure of holmium...

  15. The ability of AIF-1 to activate human vascular smooth muscle cells is lost by mutations in the EF-hand calcium-binding region

    International Nuclear Information System (INIS)

    Autieri, Michael V.; Chen Xing

    2005-01-01

    Allograft Inflammatory Factor-1 (AIF-1) is a cytoplasmic calcium-binding protein expressed in vascular smooth muscle cells (VSMC) in response to injury or cytokine stimulation. AIF-1 contains a partially conserved EF-hand calcium-binding domain, and participates in VSMC activation by activation of Rac1 and induction of Granulocyte-Colony Stimulating Factor (G-CSF) expression; however, the mechanism whereby AIF-1 mediates these effects is presently uncharacterized. To determine if calcium binding plays a functional role in AIF-1 activity, a single site-specific mutation was made in the EF-hand calcium-binding domain to abrogate binding of calcium (AIF-1ΔA), which was confirmed by calcium overlay. Functionally, similar to wild-type AIF-1, AIF-1ΔA was able to polymerize F-actin in vitro. However, in contrast to wild-type AIF-1, over-expression of AIF-1ΔA was unable to increase migration or proliferation of primary human VSMC. Further, it was unable to activate Rac1, or induce G-CSF expression to the degree as wild-type AIF-1. Taken together, modification of the wild-type EF-hand domain and native calcium-binding activity results in a loss of AIF-1 function. We conclude that appropriate calcium-binding potential is critical in AIF-1-mediated effects on VSMC pathophysiology, and that AIF-1 activity is mediated by Rac1 activation and G-CSF expression

  16. A salivary EF-hand calcium-binding protein of the brown planthopper Nilaparvata lugens functions as an effector for defense responses in rice

    OpenAIRE

    Ye, Wenfeng; Yu, Haixin; Jian, Yukun; Zeng, Jiamei; Ji, Rui; Chen, Hongdan; Lou, Yonggen

    2017-01-01

    The brown planthopper (BPH), Nilaparvata lugens (St?l) (Hemiptera: Delphacidae), a major pest of rice in Asia, is able to successfully puncture sieve tubes in rice with its piercing stylet and then to ingest phloem sap. How BPH manages to continuously feed on rice remains unclear. Here, we cloned the gene NlSEF1, which is highly expressed in the salivary glands of BPH. The NlSEF1 protein has EF-hand Ca2+-binding activity and can be secreted into rice plants when BPH feed. Infestation of rice ...

  17. The CREC family, a novel family of multiple EF-hand, low-affinity Ca(2+)-binding proteins localised to the secretory pathway of mammalian cells

    DEFF Research Database (Denmark)

    Honoré, B; Vorum, H

    2000-01-01

    The CREC family consists of a number of recently discovered multiple (up to seven) EF-hand proteins that localise to the secretory pathway of mammalian cells. At present, the family includes reticulocalbin, ERC-55/TCBP-49/E6BP, Cab45, calumenin and crocalbin/CBP-50. Similar proteins are found......(2+)-regulated activities. Recent evidence has been obtained that some CREC family members are involved in pathological activities such as malignant cell transformation, mediation of the toxic effects of snake venom toxins and putative participation in amyloid formation. Udgivelsesdato: 2000-Jan-21...

  18. A salivary EF-hand calcium-binding protein of the brown planthopper Nilaparvata lugens functions as an effector for defense responses in rice

    Science.gov (United States)

    Ye, Wenfeng; Yu, Haixin; Jian, Yukun; Zeng, Jiamei; Ji, Rui; Chen, Hongdan; Lou, Yonggen

    2017-01-01

    The brown planthopper (BPH), Nilaparvata lugens (Stål) (Hemiptera: Delphacidae), a major pest of rice in Asia, is able to successfully puncture sieve tubes in rice with its piercing stylet and then to ingest phloem sap. How BPH manages to continuously feed on rice remains unclear. Here, we cloned the gene NlSEF1, which is highly expressed in the salivary glands of BPH. The NlSEF1 protein has EF-hand Ca2+-binding activity and can be secreted into rice plants when BPH feed. Infestation of rice by BPH nymphs whose NlSEF1 was knocked down elicited higher levels of Ca2+ and H2O2 but not jasmonic acid, jasmonoyl-isoleucine (JA-Ile) and SA in rice than did infestation by control nymphs; Consistently, wounding plus the recombination protein NlSEF1 suppressed the production of H2O2 in rice. Bioassays revealed that NlSEF1-knockdown BPH nymphs had a higher mortality rate and lower feeding capacity on rice than control nymphs. These results indicate that the salivary protein in BPH, NlSEF1, functions as an effector and plays important roles in interactions between BPH and rice by mediating the plant’s defense responses. PMID:28098179

  19. LETM1, a novel gene encoding a putative EF-hand Ca(2+)-binding protein, flanks the Wolf-Hirschhorn syndrome (WHS) critical region and is deleted in most WHS patients.

    Science.gov (United States)

    Endele, S; Fuhry, M; Pak, S J; Zabel, B U; Winterpacht, A

    1999-09-01

    Deletions within human chromosome 4p16.3 cause Wolf-Hirschhorn syndrome (WHS), which is characterized by severe mental and developmental defects. It is thought that haploinsufficiency of more than one gene contributes to the complex phenotype. We have cloned and characterized a novel gene (LETM1) that is deleted in nearly all WHS patients. LETM1 encodes a putative member of the EF-hand family of Ca(2+)-binding proteins. The protein contains two EF-hands, a transmembrane domain, a leucine zipper, and several coiled-coil domains. On the basis of its possible Ca(2+)-binding property and involvement in Ca(2+) signaling and/or homeostasis, we propose that haploinsufficiency of LETM1 may contribute to the neuromuscular features of WHS patients. Copyright 1999 Academic Press.

  20. Role of the EF-hand-like Motif in the 14-3-3 Protein- mediated Activation of Yeast Neutral Trehalase Nth1

    Czech Academy of Sciences Publication Activity Database

    Kopecká, Miroslava; Košek, Dalibor; Kukačka, Zdeněk; Řežábková, Lenka; Man, Petr; Novák, Petr; Obšil, T.; Obšilová, Veronika

    2014-01-01

    Roč. 289, č. 20 (2014), s. 13948-13961 ISSN 0021-9258 R&D Projects: GA ČR(CZ) GAP207/11/0455 Grant - others:Univerzita Karlova(CZ) 644313; Univerzita Karlova(CZ) 800413 Institutional support: RVO:67985823 ; RVO:61388971 Keywords : calcium * enzyme mechanisms * mass spectrometry (MS) * protein cross-linking * protein structure * 14-3-3 * Bmh * H/D exchange * neutral trehalase * SAXS Subject RIV: CE - Biochemistry Impact factor: 4.573, year: 2014

  1. The structure of Plasmodium vivax phosphatidylethanolamine-binding protein suggests a functional motif containing a left-handed helix

    International Nuclear Information System (INIS)

    Arakaki, Tracy; Neely, Helen; Boni, Erica; Mueller, Natasha; Buckner, Frederick S.; Van Voorhis, Wesley C.; Lauricella, Angela; DeTitta, George; Luft, Joseph; Hol, Wim G. J.; Merritt, Ethan A.

    2007-01-01

    The crystal structure of a phosphatidylethanolamine-binding protein from P. vivax, a homolog of Raf-kinase inhibitor protein (RKIP), has been solved to a resolution of 1.3 Å. The inferred interaction surface near the anion-binding site is found to include a distinctive left-handed α-helix. The structure of a putative Raf kinase inhibitor protein (RKIP) homolog from the eukaryotic parasite Plasmodium vivax has been studied to a resolution of 1.3 Å using multiple-wavelength anomalous diffraction at the Se K edge. This protozoan protein is topologically similar to previously studied members of the phosphatidylethanolamine-binding protein (PEBP) sequence family, but exhibits a distinctive left-handed α-helical region at one side of the canonical phospholipid-binding site. Re-examination of previously determined PEBP structures suggests that the P. vivax protein and yeast carboxypeptidase Y inhibitor may represent a structurally distinct subfamily of the diverse PEBP-sequence family

  2. Education for Sustainability (EfS): Practice and Practice Architectures

    Science.gov (United States)

    Kemmis, Stephen; Mutton, Rebecca

    2012-01-01

    This paper reports some findings from an investigation of educational practice in ten (formal and informal) education for sustainability (EfS) initiatives, to characterise exemplary practice in school and community education for sustainability, considered crucial to Australia's future. The study focused on rural/regional Australia, specifically…

  3. Engineering of blood vessel patterns by angio-morphogens [angiotropins]: non-mitogenic copper-ribonucleoprotein cytokins [CuRNP ribokines] with their metalloregulated constituents of RAGE-binding S100-EF-hand proteins and extracellular RNA bioaptamers in vascular remodeling of tissue and angiogenesis in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Wissler, J.H. [ARCONS Applied Research, Bad Nauheim (Germany)

    2001-12-01

    Tissue vascularization is requisite to successful cell-based therapies, biomaterial design and implant integration. Thus, known problems in ossointegration of avascular implants in connection with the generation of bone tissue reflect arrays of general problems of socio-economic relevance existing in reparative medicine still waiting for to be solved. For this purpose, morphogenesis and remodeling of endothelial angio-architectures in tissue and in vitro by isolated non-mitogenic angio-morphogens [angiotropins] are considered in terms of their structure, function and action mechanisms. Extracellular angiotropins are secreted by activated leukocytes/monocytes/macrophages. They are a family of cytokines with morphogen bioactivity selectively directed to endothelial cells. Their structure was deciphered as metalloregulated copper-ribonucleoproteins [CuRNP ribokines]. They are built up of angiotropin-related S100-EF-hand protein [ARP] and highly modified and edited 5'end-phosphorylated RNA [ARNA], complexed together by copper ions. Oxidant-sensitive ARNA and their precursors represent novel types in a RNA world: They are the first isolated and sequenced forms of extracellular RNA [eRNA], may act as cytokine and bioaptamer, contain isoguanosine [crotonoside] as modified nucleoside and show up copper as RNA-structuring transition metal ion. By metalloregulated bioaptamer functions, ARNA impart novel biofunctions to RAGE-binding S100-EF-hand proteins. Angiotropin morphogens were shown suitable for neointiation and remodeling of blood vessel patterns in different, adult, embryonal and artificial tissues. These neovascular patterns manifest regulated hemodynamics for preventing tissue necrosis, supporting tissue functions and promoting wound healing. As evaluated in skin and muscle vascularization, the neovascular patterns are integrated into homeostatic control mechanisms of tissue. Thus, the morphogens show up beneficial perspectives and are suggested useful tools

  4. CompariMotif: quick and easy comparisons of sequence motifs.

    Science.gov (United States)

    Edwards, Richard J; Davey, Norman E; Shields, Denis C

    2008-05-15

    CompariMotif is a novel tool for making motif-motif comparisons, identifying and describing similarities between regular expression motifs. CompariMotif can identify a number of different relationships between motifs, including exact matches, variants of degenerate motifs and complex overlapping motifs. Motif relationships are scored using shared information content, allowing the best matches to be easily identified in large comparisons. Many input and search options are available, enabling a list of motifs to be compared to itself (to identify recurring motifs) or to datasets of known motifs. CompariMotif can be run online at http://bioware.ucd.ie/ and is freely available for academic use as a set of open source Python modules under a GNU General Public License from http://bioinformatics.ucd.ie/shields/software/comparimotif/

  5. Cloning and Characterization of EF-Tu and EF-Ts from Pseudomonas aeruginosa

    Directory of Open Access Journals (Sweden)

    Stephanie O. Palmer

    2013-01-01

    Full Text Available We have cloned genes encoding elongation factors EF-Tu and EF-Ts from Pseudomonas aeruginosa and expressed and purified the proteins to greater than 95% homogeneity. Sequence analysis indicated that P. aeruginosa EF-Tu and EF-Ts are 84% and 55% identical to E. coli counterparts, respectively. P. aeruginosa EF-Tu was active when assayed in GDP exchange assays. Kinetic parameters for the interaction of EF-Tu with GDP in the absence of EF-Ts were observed to be = 33 μM, = 0.003 s−1, and the specificity constant was  s−1 μM−1. In the presence of EF-Ts, these values were shifted to = 2 μM, = 0.005 s−1, and the specificity constant was  s−1 μM−1. The equilibrium dissociation constants governing the binding of EF-Tu to GDP ( were 30–75 nM and to GTP ( were 125–200 nM. EF-Ts stimulated the exchange of GDP by EF-Tu 10-fold. P. aeruginosa EF-Tu was active in forming a ternary complex with GTP and aminoacylated tRNA and was functional in poly(U-dependent binding of Phe-tRNAPhe at the A-site of P. aeruginosa ribosomes. P. aeruginosa EF-Tu was active in poly(U-programmed polyphenylalanine protein synthesis system composed of all P. aeruginosa components.

  6. Extracellular and circulating redox- and metalloregulated eRNA and eRNP: copper ion-structured RNA cytokines (angiotropin ribokines) and bioaptamer targets imparting RNA chaperone and novel biofunctions to S100-EF-hand and disease-associated proteins.

    Science.gov (United States)

    Wissler, Josef H

    2004-06-01

    Bioassays for cellular differentiation and tissue morphogenesis were used to design methods for isolation of bioactive redox- and metalloregulated nucleic acids and copper ion complexes with proteins from extracellular, circulating, wound, and supernatant fluids of cultured cells. In extracellular biospheres, diversities of nucleic acids were found to be secreted by cells upon activation. They may reflect nucleic acid biolibraries with molecular imprints of cellular history. After removal of protein components, eRNA prototypes exuded by activated cells were sequenced. They are small, endogenous, highly modified and edited, redox- and metalloregulated 5'-end phosphorylated extracellular eRNA (approximately 2-200 bases) with cellular, enzymic, and bioaptamer functions. Fenton-type OH* radical redox reactions may form modified nucleotides in RNA as wobbles eRNA per se, or as copper ion-complex with protein (e.g., S100A12-EF-hand protein, angiotropin-related protein, calgranulin-C, hippocampal neurite differentiation factor) are shown to be bioactive in vivo and in vitro as cytokines (ribokines) and as nonmitogenic angiomorphogens for endothelial cell differentiation in the formation of organoid supracellular capillary structures. As bioaptamers, copper ion-structured eRNA imparts novel biofunctions to proteins that they do not have on their own. The origin of extracellular RNA and intermediate precursors (up to 500 bases) was traced to intracellular parent nucleic acids. Intermediate precursors with and without partial homology were found. This suggests that bioaptamers are not directly retranslatable gene products. Metalloregulated eRNA bioaptamer function was investigated by domains (e.g. 5'...CUG...3' hairpin loop) for folding, bioactivity, and binding of protein with copper, calcium, and alkali metal ion affinity. Vice versa, metalloregulated nucleic acid-binding domains (K3H, R3H) in proteins were identified. Interaction of protein and eRNA docking potentials

  7. Brownfields/IGD: EF_ACRES

    Data.gov (United States)

    U.S. Environmental Protection Agency — EF_ACRES is a subset of facilities from FRS_INTEREST and FRS_FACILITY_SITE which are updated on a monthly basis as part of the Locational Reference Tables (LRT)...

  8. Hazardous Waste/IGD: EF_RCRA

    Data.gov (United States)

    U.S. Environmental Protection Agency — EF_RCRA is a subset of facilities from FRS_INTEREST and FRS_FACILITY_SITE which are updated on a monthly basis as part of the Locational Reference Tables (LRT)...

  9. Air Emissions/IGD: EF_AFS

    Data.gov (United States)

    U.S. Environmental Protection Agency — EF_AFS is a subset of facilities from FRS_INTEREST and FRS_FACILITY_SITE which are updated on a monthly basis as part of the Locational Reference Tables (LRT)...

  10. Water Dischargers/IGD: EF_NPDES

    Data.gov (United States)

    U.S. Environmental Protection Agency — EF_NPDES is a subset of facilities from FRS_INTEREST and FRS_FACILITY_SITE which are updated on a monthly basis as part of the Locational Reference Tables (LRT)...

  11. Superfund/IGD: EF_NPL

    Data.gov (United States)

    U.S. Environmental Protection Agency — EF_NPL is a subset of facilities from FRS_INTEREST and FRS_FACILITY_SITE which are updated on a monthly basis as part of the Locational Reference Tables (LRT)...

  12. Toxic Releases/IGD: EF_TRI

    Data.gov (United States)

    U.S. Environmental Protection Agency — EF_TRI is a subset of facilities from FRS_INTEREST and FRS_FACILITY_SITE which are updated on a monthly basis as part of the Locational Reference Tables (LRT)...

  13. Heart Failure with Recovered EF and Heart Failure with Mid-Range EF: Current Recommendations and Controversies.

    Science.gov (United States)

    Unkovic, Peter; Basuray, Anupam

    2018-04-03

    This review explores key features and potential management controversies in two emerging populations in heart failure: heart failure with recovered ejection fraction (HF-recovered EF) and heart failure with mid-range ejection fraction (HFmrEF). While HF-recovered EF patients have better outcomes than heart failure with reduced ejection fraction (HFrEF), they continue to have symptoms, persistent biomarker elevations, and abnormal outcomes suggesting a continued disease process. HFmrEF patients appear to have features of HFrEF and heart failure with preserved ejection fraction (HFpEF), but have a high prevalence of ischemic heart disease and may represent a transitory phase between the HFrEF and HFpEF. Management strategies have insufficient data to warrant standardization at this time. HF-recovered EF and HFmrEF represent new populations with unmet needs and expose the pitfalls of an EF basis for heart failure classification.

  14. MHC motif viewer

    DEFF Research Database (Denmark)

    Rapin, Nicolas Philippe Jean-Pierre; Hoof, Ilka; Lund, Ole

    2008-01-01

    . Algorithms that predict which peptides MHC molecules bind have recently been developed and cover many different alleles, but the utility of these algorithms is hampered by the lack of tools for browsing and comparing the specificity of these molecules. We have, therefore, developed a web server, MHC motif....... A special viewing feature, MHC fight, allows for display of the specificity of two different MHC molecules side by side. We show how the web server can be used to discover and display surprising similarities as well as differences between MHC molecules within and between different species. The MHC motif...

  15. [Personal motif in art].

    Science.gov (United States)

    Gerevich, József

    2015-01-01

    One of the basic questions of the art psychology is whether a personal motif is to be found behind works of art and if so, how openly or indirectly it appears in the work itself. Analysis of examples and documents from the fine arts and literature allow us to conclude that the personal motif that can be identified by the viewer through symbols, at times easily at others with more difficulty, gives an emotional plus to the artistic product. The personal motif may be found in traumatic experiences, in communication to the model or with other emotionally important persons (mourning, disappointment, revenge, hatred, rivalry, revolt etc.), in self-searching, or self-analysis. The emotions are expressed in artistic activity either directly or indirectly. The intention nourished by the artist's identity (Kunstwollen) may stand in the way of spontaneous self-expression, channelling it into hidden paths. Under the influence of certain circumstances, the artist may arouse in the viewer, consciously or unconsciously, an illusionary, misleading image of himself. An examination of the personal motif is one of the important research areas of art therapy.

  16. Isoforms of elongation factor eEF1A may be differently regulated at post-transcriptional level in breast cancer progression

    Directory of Open Access Journals (Sweden)

    Vislovukh A. A.

    2013-01-01

    Full Text Available Eukaryotic translation elongation factor 1A exists as two 98 % homologous isoforms: eEF1A1 (A1 and eEF1A2 (A2 which are tissue and development specific. Despite high homology in an open reading frame (ORF region, mRNAs coding for eEF1A1 and eEF1A2 are different in their untranslated regions (UTR, suggesting a possibility of their dissimilar post-transcriptional regulation. Aim. To analyze the existence of cis-acting motifs in the UTRs of EEF1A1/A2 mRNAs, to confirm the possibility of post-transcriptional control of eEF1A1 and eEF1A2 expression. Methods. An ensemble of bioinformatic methods was applied to predict regulatory motifs in the UTRs of EEF1A1/A2 mRNAs. Dual-luciferase reporter assay was employed to detect post-transcriptional regulation of eEF1A1/A2 expression. Results. Numerous regulatory motifs in the UTR of EEF1A1/A2 mRNAs were found bioinformatically. The experimental evidence was obtained for the existence of negative regulation of EEF1A1 and positive regulation of EEF1A2 mRNA in the model of breast cancer development. Conclusions. EEF1A1 and EEF1A2 mRNAs contain distinct motifs in the UTRs and are differently regulated in cancer suggesting the possibility of their control by different cellular signals.

  17. delta-EF1 is a negative regulator of Ihh in the developing growth plate.

    Science.gov (United States)

    Bellon, Ellen; Luyten, Frank P; Tylzanowski, Przemko

    2009-11-30

    Indian hedgehog (Ihh) regulates proliferation and differentiation of chondrocytes in the growth plate. Although the biology of Ihh is currently well documented, its transcriptional regulation is poorly understood. delta-EF1 is a two-handed zinc finger/homeodomain transcriptional repressor. Targeted inactivation of mouse delta-EF1 leads to skeletal abnormalities including disorganized growth plates, shortening of long bones, and joint fusions, which are reminiscent of defects associated with deregulation of Ihh signaling. Here, we show that the absence of delta-EF1 results in delayed hypertrophic differentiation of chondrocytes and increased cell proliferation in the growth plate. Further, we demonstrate that delta-EF1 binds to the putative regulatory elements in intron 1 of Ihh in vitro and in vivo, resulting in down-regulation of Ihh expression. Finally, we show that delta-EF1 haploinsufficiency leads to a postnatal increase in trabecular bone mass associated with enhanced Ihh expression. In summary, we have identified delta-EF1 as an in vivo negative regulator of Ihh expression in the growth plate.

  18. Motif enrichment tool.

    Science.gov (United States)

    Blatti, Charles; Sinha, Saurabh

    2014-07-01

    The Motif Enrichment Tool (MET) provides an online interface that enables users to find major transcriptional regulators of their gene sets of interest. MET searches the appropriate regulatory region around each gene and identifies which transcription factor DNA-binding specificities (motifs) are statistically overrepresented. Motif enrichment analysis is currently available for many metazoan species including human, mouse, fruit fly, planaria and flowering plants. MET also leverages high-throughput experimental data such as ChIP-seq and DNase-seq from ENCODE and ModENCODE to identify the regulatory targets of a transcription factor with greater precision. The results from MET are produced in real time and are linked to a genome browser for easy follow-up analysis. Use of the web tool is free and open to all, and there is no login requirement. ADDRESS: http://veda.cs.uiuc.edu/MET/. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. HFpEF and HFrEF Display Different Phenotypes as Assessed by IGF-1 and IGFBP-1.

    Science.gov (United States)

    Faxén, Ulrika Ljung; Hage, Camilla; Benson, Lina; Zabarovskaja, Stanislava; Andreasson, Anna; Donal, Erwan; Daubert, Jean-Claude; Linde, Cecilia; Brismar, Kerstin; Lund, Lars H

    2017-04-01

    Anabolic drive is impaired in heart failure with reduced ejection fraction (HFrEF) but insufficiently studied in heart failure with preserved ejection fraction (HFpEF). Insulin-like growth factor 1 (IGF-1) mediates growth hormone effects and IGF binding protein 1 (IGFBP-1) regulates IGF-1 activity. We tested the hypothesis that HFpEF and HFrEF are similar with regard to IGF-1 and IGFBP-1. In patients with HFpEF (n = 79), HFrEF (n = 85), and controls (n = 136), we analyzed serum IGF-1 and IGFBP-1 concentrations, correlations, and associations with outcome. Age-standardized scores of IGF-1 were higher in HFpEF, median arbitrary units (interquartile range); 1.21 (0.57-1.96) vs HFrEF, 0.09 (-1.40-1.62), and controls, 0.22 (-0.47-0.96), P overall IGF-1 was associated with outcomes in HFrEF, hazard ratio per natural logarithmic increase in IGF-1 SD score 0.51 (95% confidence interval 0.32-0.82, P = .005), but not significantly in HFpEF. IGFBP-1 was not associated with outcomes in either HFpEF nor HFrEF. HFpEF and HFrEF phenotypes were similar with regard to increased IGFBP-1 concentrations but differed regarding IGF-1 levels and prognostic role. HFrEF and HFpEF may display different impairment in anabolic drive. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. The Potential of Devices for HFpEF

    Directory of Open Access Journals (Sweden)

    Andrew J Stewart Coats

    2017-01-01

    Full Text Available The 2016 ESC/HFA HF guidelines list the very many drug and device therapies that are proven to be beneficial in terms of life prolongation and hospitalisation prevention for HFrEF. The list of recommended therapies or devices for HFpEF and HFmrEF is limited to diuretics and the management of comorbidities and so far there is no clinical evidence for an electrical or mechanical device for HFpEF. The Cardiac Contractility Modulation (CCM device that may have a role in selected HFrEF and HFmrEF patients has been reviewed in another paper in this issue but here we survey the results so far of a novel device for patients with HFpEF. Despite lagging many years behind HFrEF, HFpEF patients are now being targeted with novel devices with the potential to improve symptoms, improve quality of life, reduce hospitalization and delay progression of the syndrome. The front-runner is a novel inter-atrial left atrial pressure decompression device the Corvia IASD, which currently enrolling patients in a randomized trial. This device is a CE-marked investigational, non- surgical transcatheter implant designed to provide continuous and dynamic decompression of the left atrium, in an effort to reduce symptoms, HF hospitalizations, and improve quality of life as well as potentially slowing the progression of HFpEF.

  1. MotifMark: Finding regulatory motifs in DNA sequences.

    Science.gov (United States)

    Hassanzadeh, Hamid Reza; Kolhe, Pushkar; Isbell, Charles L; Wang, May D

    2017-07-01

    The interaction between proteins and DNA is a key driving force in a significant number of biological processes such as transcriptional regulation, repair, recombination, splicing, and DNA modification. The identification of DNA-binding sites and the specificity of target proteins in binding to these regions are two important steps in understanding the mechanisms of these biological activities. A number of high-throughput technologies have recently emerged that try to quantify the affinity between proteins and DNA motifs. Despite their success, these technologies have their own limitations and fall short in precise characterization of motifs, and as a result, require further downstream analysis to extract useful and interpretable information from a haystack of noisy and inaccurate data. Here we propose MotifMark, a new algorithm based on graph theory and machine learning, that can find binding sites on candidate probes and rank their specificity in regard to the underlying transcription factor. We developed a pipeline to analyze experimental data derived from compact universal protein binding microarrays and benchmarked it against two of the most accurate motif search methods. Our results indicate that MotifMark can be a viable alternative technique for prediction of motif from protein binding microarrays and possibly other related high-throughput techniques.

  2. Identification of a Novel EF-Loop in the N-terminus of TRPM2 Channel Involved in Calcium Sensitivity

    Directory of Open Access Journals (Sweden)

    Yuhuan Luo

    2018-06-01

    Full Text Available As an oxidative stress sensor, transient receptor potential melastatin 2 (TRPM2 channel is involved in many physiological and pathological processes including warmth sensing, ischemia injury, inflammatory diseases and diabetes. Intracellular calcium is critical for TRPM2 channel activation and the IQ-like motif in the N-terminus has been shown to be important by mediating calmodulin binding. Sequence analysis predicted two potential EF-loops in the N-terminus of TRPM2. Site-directed mutagenesis combining with functional assay showed that substitution with alanine of several residues, most of which are conserved in the typical EF-loop, including D267, D278, D288, and E298 dramatically reduced TRPM2 channel currents. By further changing the charges or side chain length of these conserved residues, our results indicate that the negative charge of D267 and the side chain length of D278 are critical for calcium-induced TRPM2 channel activation. G272I mutation also dramatically reduced the channel currents, suggesting that this site is critical for calcium-induced TRPM2 channel activation. Furthermore, D267A mutant dramatically reduced the currents induced by calcium alone compared with that by ADPR, indicating that D267 residue in D267–D278 motif is the most important site for calcium sensitivity of TRPM2. In addition, inside-out recordings showed that mutations at D267, G272, D278, and E298 had no effect on single-channel conductance. Taken together, our data indicate that D267–D278 motif in the N-terminus as a novel EF-loop is critical for calcium-induced TRPM2 channel activation.

  3. Stiff Hands

    Science.gov (United States)

    ... All Topics A-Z Videos Infographics Symptom Picker Anatomy Bones Joints Muscles Nerves Vessels Tendons About Hand Surgery What is a Hand Surgeon? What is a Hand Therapist? Media Find a Hand Surgeon Home Anatomy Stiff Hands Email to a friend * required fields ...

  4. Hand Infections

    Science.gov (United States)

    ... All Topics A-Z Videos Infographics Symptom Picker Anatomy Bones Joints Muscles Nerves Vessels Tendons About Hand Surgery What is a Hand Surgeon? What is a Hand Therapist? Media Find a Hand Surgeon Home Anatomy Hand Infections Email to a friend * required fields ...

  5. Pneumonia cases following an EF-5 tornado.

    Science.gov (United States)

    Forshee-Hakala, Beth A

    2015-07-01

    Infections following a natural disaster such as an EF-5 tornado can be atypical and difficult to treat. Studies have looked at illness following several natural disasters, but few have studied respiratory illness following a tornado. A review of patients with pneumonia admitted during the period from May 22, 2009, through May 21, 2012, was completed. The Tornado Zone Group included adult patients who lived or worked in the tornado zone during the year following the tornado. Data were isolated by number of pneumonia cases within and outside the tornado zone per month per year. An analysis of variance comparing the number of pneumonia cases from the tornado zone per month per year was significant at F2,38 = 12.93 and P Tornado Zone Group (P Tornado Zone patients to be younger than controls (t390 = 5.14; P Tornado Zone Group included uncommon pathogens not isolated during the 2 years prior. The number of pneumonia cases may increase following tornadoes. Although current guidelines recommend narrow-spectrum antibiotics for community-acquired pneumonia, results of this study suggest the possible need for broader antimicrobial coverage after tornadoes. Copyright © 2015 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

  6. Joint resistance measurements of pancake and terminal joints for JT-60SA EF coils

    Energy Technology Data Exchange (ETDEWEB)

    Obana, Tetsuhiro, E-mail: obana.tetsuhiro@LHD.nifs.ac.jp [National Institute for Fusion Science, 322-6 Oroshi, Toki, Gifu 509-5292 (Japan); Takahata, Kazuya; Hamaguchi, Shinji; Mito, Toshiyuki; Imagawa, Shinsaku [National Institute for Fusion Science, 322-6 Oroshi, Toki, Gifu 509-5292 (Japan); Kizu, Kaname; Murakami, Haruyuki; Yoshida, Kiyoshi [Japan Atomic Energy Agency, 801-1 Mukoyama, Naka, Ibaraki 311-0193 (Japan)

    2013-11-15

    Highlights: • To evaluate the joint fabrication technology for the JT-60SA EF coils, joint resistance measurements were conducted with a joint sample. • The joint sample was composed of pancake and terminal joints. • The measurements demonstrated that both joints fulfilled the design requirement. • Considering the measurements, the characteristics of both joints were investigated using an analytical model that represents the joints. -- Abstract: To evaluate the joint fabrication technology for the JT-60SA EF coils, joint resistance measurements were conducted using a sample consisting of pancake and terminal joints. Both joints are shake-hands lap joints composed of cable-in-conduit conductors and a pure copper saddle-shaped spacer. The measurements demonstrated that both joints fulfilled the design requirement. Considering these measurements, the characteristics of both joints were investigated using analytical models that represent the joints. The analyses indicated that the characteristics of the conductors used in the joints affect the characteristics of the joints.

  7. Embedding EfS in Teacher Education through a Multi-Level Systems Approach: Lessons from Queensland

    Science.gov (United States)

    Evans, Neus; Ferreira, Jo-Anne; Davis, Julie; Stevenson, Robert B.

    2016-01-01

    This article reports on the fourth stage of an evolving study to develop a systems model for embedding education for sustainability (EfS) into preservice teacher education. The fourth stage trialled the extension of the model to a comprehensive state-wide systems approach involving representatives from all eight Queensland teacher education…

  8. Hand Fractures

    Science.gov (United States)

    ... All Topics A-Z Videos Infographics Symptom Picker Anatomy Bones Joints Muscles Nerves Vessels Tendons About Hand Surgery What is ... Hand Therapist? Media Find a Hand Surgeon Home Anatomy ... DESCRIPTION The bones of the hand serve as a framework. This framework supports the muscles that make the wrist and fingers move. When ...

  9. Motif signatures of transcribed enhancers

    KAUST Repository

    Kleftogiannis, Dimitrios

    2017-09-14

    In mammalian cells, transcribed enhancers (TrEn) play important roles in the initiation of gene expression and maintenance of gene expression levels in spatiotemporal manner. One of the most challenging questions in biology today is how the genomic characteristics of enhancers relate to enhancer activities. This is particularly critical, as several recent studies have linked enhancer sequence motifs to specific functional roles. To date, only a limited number of enhancer sequence characteristics have been investigated, leaving space for exploring the enhancers genomic code in a more systematic way. To address this problem, we developed a novel computational method, TELS, aimed at identifying predictive cell type/tissue specific motif signatures. We used TELS to compile a comprehensive catalog of motif signatures for all known TrEn identified by the FANTOM5 consortium across 112 human primary cells and tissues. Our results confirm that distinct cell type/tissue specific motif signatures characterize TrEn. These signatures allow discriminating successfully a) TrEn from random controls, proxy of non-enhancer activity, and b) cell type/tissue specific TrEn from enhancers expressed and transcribed in different cell types/tissues. TELS codes and datasets are publicly available at http://www.cbrc.kaust.edu.sa/TELS.

  10. Prevalence of Prediabetes and Undiagnosed Diabetes in Patients with HFpEF and HFrEF and Associated Clinical Outcomes

    DEFF Research Database (Denmark)

    Kristensen, Søren L; Jhund, Pardeep S; Lee, Matthew M Y

    2017-01-01

    PURPOSE: The prevalence and consequences of prediabetic dysglycemia and undiagnosed diabetes is unknown in patients with heart failure (HF) and preserved ejection fraction (HFpEF) and has not been compared to heart failure and reduced ejection fraction (HFrEF). METHODS: We examined the prevalence...... and outcomes associated with normoglycemia, prediabetic dysglycemia and diabetes (diagnosed and undiagnosed) among individuals with a baseline glycated hemoglobin (hemoglobin A1c, HbA1c) measurement stratified by HFrEF or HFpEF in the Candesartan in Heart failure Assessment of Reduction in Mortality...... and was available in 1072/3023 (35%) of patients with HFpEF and 1578/4576 (34%) patients with HFrEF. 18 and 16% had normoglycemia (HbA1c prediabetes (HbA1c 6.0-6.4), respectively. Finally among patients with HFpEF 22% had undiagnosed diabetes (HbA1c > 6.4), and 40% had known diabetes (any Hb...

  11. Hand Therapy

    Science.gov (United States)

    ... from conditions such as carpal tunnel syndrome and tennis elbow , as well as from chronic problems such as ... Tools Advice from a Certified Hand Therapist on Tennis Elbow Advice from a Certified Hand Therapist: Living with( ...

  12. Hand Anatomy

    Science.gov (United States)

    ... All Topics A-Z Videos Infographics Symptom Picker Anatomy Bones Joints Muscles Nerves Vessels Tendons About Hand Surgery What is ... Hand Therapist? Media Find a Hand Surgeon Home Anatomy Bones Joints Muscles Nerves Vessels Tendons Anatomy The upper extremity is ...

  13. Myostatin inhibits eEF2K-eEF2 by regulating AMPK to suppress protein synthesis.

    Science.gov (United States)

    Deng, Zhao; Luo, Pei; Lai, Wen; Song, Tongxing; Peng, Jian; Wei, Hong-Kui

    2017-12-09

    Growth of skeletal muscle is dependent on the protein synthesis, and the rate of protein synthesis is mainly regulated in the stage of translation initiation and elongation. Myostatin, a member of the transforming growth factor-β (TGF-β) superfamily, is a negative regulator of protein synthesis. C2C12 myotubes was incubated with 0, 0.01, 0.1, 1, 2, 3 μg/mL myostatin recombinant protein, and then we detected the rates of protein synthesis by the method of SUnSET. We found that high concentrations of myostatin (2 and 3 μg/mL) inhibited protein synthesis by blocking mTOR and eEF2K-eEF2 pathway, while low concentration of myostatin (0.01, 0.1 and 1 μg/mL) regulated eEF2K-eEF2 pathway activity to block protein synthesis without affected mTOR pathway, and myostatin inhibited eEF2K-eEF2 pathway through regulating AMPK pathway to suppress protein synthesis. It provided a new mechanism for myostatin regulating protein synthesis and treating muscle atrophy. Copyright © 2017. Published by Elsevier Inc.

  14. [Hand osteoarthritis].

    Science.gov (United States)

    Šenolt, Ladislav

    Hand osteoarthritis (OA) is a common chronic disorder causing pain and limitation of mobility of affected joints. The prevalence of hand OA increases with age and more often affects females. Clinical signs obviously do not correlate with radiographic findings - symptomatic hand OA affects approximately 26 % of adult subjects, but radiographic changes can be found in up to two thirds of females and half of males older than 55 years.Disease course differ among individual patients. Hand OA is a heterogeneous disease. Nodal hand OA is the most common subtype affecting interphalangeal joints, thumb base OA affects first carpometacarpal joint. Erosive OA represents a specific subtype of hand OA, which is associated with joint inflammation, more pain, functional limitation and erosive findings on radiographs.Treatment of OA is limited. Analgesics and nonsteroidal anti-inflammatory drugs are the only agents reducing symptoms. New insights into the pathogenesis of disease should contribute to the development of novel effective treatment of hand OA.

  15. TH-EF-BRC-02: FMEA

    International Nuclear Information System (INIS)

    Huq, M.

    2016-01-01

    This Hands-on Workshop will be focused on providing participants with experience with the principal tools of TG 100 and hence start to build both competence and confidence in the use of risk-based quality management techniques. The three principal tools forming the basis of TG 100’s risk analysis: Process mapping, Failure-Modes and Effects Analysis and fault-tree analysis will be introduced with a 5 minute refresher presentation and each presentation will be followed by a 30 minute small group exercise. An exercise on developing QM from the risk analysis follows. During the exercise periods, participants will apply the principles in 2 different clinical scenarios. At the conclusion of each exercise there will be ample time for participants to discuss with each other and the faculty their experience and any challenges encountered. Learning Objectives: To review the principles of Process Mapping, Failure Modes and Effects Analysis and Fault Tree Analysis. To gain familiarity with these three techniques in a small group setting. To share and discuss experiences with the three techniques with faculty and participants. Director, TreatSafely, LLC. Director, Center for the Assessment of Radiological Sciences. Occasional Consultant to the IAEA and Varian.

  16. TH-EF-BRC-02: FMEA

    Energy Technology Data Exchange (ETDEWEB)

    Huq, M. [University of Pittsburgh Cancer Institute (United States)

    2016-06-15

    This Hands-on Workshop will be focused on providing participants with experience with the principal tools of TG 100 and hence start to build both competence and confidence in the use of risk-based quality management techniques. The three principal tools forming the basis of TG 100’s risk analysis: Process mapping, Failure-Modes and Effects Analysis and fault-tree analysis will be introduced with a 5 minute refresher presentation and each presentation will be followed by a 30 minute small group exercise. An exercise on developing QM from the risk analysis follows. During the exercise periods, participants will apply the principles in 2 different clinical scenarios. At the conclusion of each exercise there will be ample time for participants to discuss with each other and the faculty their experience and any challenges encountered. Learning Objectives: To review the principles of Process Mapping, Failure Modes and Effects Analysis and Fault Tree Analysis. To gain familiarity with these three techniques in a small group setting. To share and discuss experiences with the three techniques with faculty and participants. Director, TreatSafely, LLC. Director, Center for the Assessment of Radiological Sciences. Occasional Consultant to the IAEA and Varian.

  17. TH-EF-BRC-01: Process Mapping

    Energy Technology Data Exchange (ETDEWEB)

    Dunscombe, P. [University of Calgary (Canada)

    2016-06-15

    This Hands-on Workshop will be focused on providing participants with experience with the principal tools of TG 100 and hence start to build both competence and confidence in the use of risk-based quality management techniques. The three principal tools forming the basis of TG 100’s risk analysis: Process mapping, Failure-Modes and Effects Analysis and fault-tree analysis will be introduced with a 5 minute refresher presentation and each presentation will be followed by a 30 minute small group exercise. An exercise on developing QM from the risk analysis follows. During the exercise periods, participants will apply the principles in 2 different clinical scenarios. At the conclusion of each exercise there will be ample time for participants to discuss with each other and the faculty their experience and any challenges encountered. Learning Objectives: To review the principles of Process Mapping, Failure Modes and Effects Analysis and Fault Tree Analysis. To gain familiarity with these three techniques in a small group setting. To share and discuss experiences with the three techniques with faculty and participants. Director, TreatSafely, LLC. Director, Center for the Assessment of Radiological Sciences. Occasional Consultant to the IAEA and Varian.

  18. TH-EF-BRC-01: Process Mapping

    International Nuclear Information System (INIS)

    Dunscombe, P.

    2016-01-01

    This Hands-on Workshop will be focused on providing participants with experience with the principal tools of TG 100 and hence start to build both competence and confidence in the use of risk-based quality management techniques. The three principal tools forming the basis of TG 100’s risk analysis: Process mapping, Failure-Modes and Effects Analysis and fault-tree analysis will be introduced with a 5 minute refresher presentation and each presentation will be followed by a 30 minute small group exercise. An exercise on developing QM from the risk analysis follows. During the exercise periods, participants will apply the principles in 2 different clinical scenarios. At the conclusion of each exercise there will be ample time for participants to discuss with each other and the faculty their experience and any challenges encountered. Learning Objectives: To review the principles of Process Mapping, Failure Modes and Effects Analysis and Fault Tree Analysis. To gain familiarity with these three techniques in a small group setting. To share and discuss experiences with the three techniques with faculty and participants. Director, TreatSafely, LLC. Director, Center for the Assessment of Radiological Sciences. Occasional Consultant to the IAEA and Varian.

  19. Kopi dan Kakao dalam Kreasi Motif Batik Khas Jember

    Directory of Open Access Journals (Sweden)

    Irfa'ina Rohana Salma

    2015-06-01

    Full Text Available ABSTRAK Batik Jember selama ini identik dengan motif daun tembakau. Visualisasi daun tembakau dalam motif Batik Jember cukup lemah, yaitu kurang berkarakter karena motif yang muncul adalah seperti gambar daun pada umumnya. Oleh karena itu perlu diciptakan desain motif batik khas Jember yang sumber inspirasinya digali dari kekayaan alam lainnya dari Jember yang mempunyai bentuk spesifik dan karakteristik sehingga identitas motif bisa didapatkan dengan lebih kuat. Hasil alam khas Jember tersebut adalah kopi dan kakao. Tujuan penciptaan seni ini adalah untuk menghasilkan motif batik  baru yang mempunyai ciri khas Jember. Metode yang digunakan yaitu pengumpulan data, pengamatan mendalam terhadap objek penciptaan, pengkajian sumber inspirasi, pembuatan desain motif, dan perwujudan menjadi batik. Dari penciptaan seni ini berhasil dikreasikan 6 (enam motif batik yaitu: (1 Motif Uwoh Kopi; (2 Motif Godong Kopi;  (3 Motif Ceplok Kakao; (4 Motif Kakao Raja; (5 Motif Kakao Biru; dan (6 Motif Wiji Mukti. Berdasarkan hasil penilaian “Selera Estetika” diketahui bahwa motif yang paling banyak disukai adalah Motif Uwoh Kopi dan Motif Kakao Raja. Kata kunci: Motif Woh Kopi, Motif Godong Kopi, Motif Ceplok Kakao, Motif Kakao Raja, Motif Kakao Biru, Motif Wiji Mukti ABSTRACTBatik Jember is synonymous with tobacco leaf motif. Tobacco leaf shape is quite weak in the visual appearance characterized as that motif emerges like a picture of leaves in general. Therefore, it is necessary to create a distinctive design motif extracted from other natural resources of Jember that have specific shapes and characteristics that can be obtained as the stronger motif identity. The typical natural resources from Jember are coffee and cocoa. The purpose of the creation of this art is to produce the unique, creative and innovative batik and have specific characteristics of Jember. The method used are data collection, observation of the object, reviewing inspiration sources

  20. Statistical tests to compare motif count exceptionalities

    Directory of Open Access Journals (Sweden)

    Vandewalle Vincent

    2007-03-01

    Full Text Available Abstract Background Finding over- or under-represented motifs in biological sequences is now a common task in genomics. Thanks to p-value calculation for motif counts, exceptional motifs are identified and represent candidate functional motifs. The present work addresses the related question of comparing the exceptionality of one motif in two different sequences. Just comparing the motif count p-values in each sequence is indeed not sufficient to decide if this motif is significantly more exceptional in one sequence compared to the other one. A statistical test is required. Results We develop and analyze two statistical tests, an exact binomial one and an asymptotic likelihood ratio test, to decide whether the exceptionality of a given motif is equivalent or significantly different in two sequences of interest. For that purpose, motif occurrences are modeled by Poisson processes, with a special care for overlapping motifs. Both tests can take the sequence compositions into account. As an illustration, we compare the octamer exceptionalities in the Escherichia coli K-12 backbone versus variable strain-specific loops. Conclusion The exact binomial test is particularly adapted for small counts. For large counts, we advise to use the likelihood ratio test which is asymptotic but strongly correlated with the exact binomial test and very simple to use.

  1. 75 FR 27986 - Electronic Filing System-Web (EFS-Web) Contingency Option

    Science.gov (United States)

    2010-05-19

    ...] Electronic Filing System--Web (EFS-Web) Contingency Option AGENCY: United States Patent and Trademark Office... contingency option when the primary portal to EFS-Web has an unscheduled outage. Previously, the entire EFS-Web system is not available to the users during such an outage. The contingency option in EFS-Web will...

  2. POTENTIAL MARKETING PLAN FOR EF, REGARDING LANGUAGE COURSES IN CHINA

    OpenAIRE

    Saarni, Helena

    2017-01-01

    This bachelor’s thesis was conducted as a potential marketing plan for EF. The aim and purpose of the project was to create a marketing plan for a company called EF regarding their Chinese language courses in China, where they offer these courses to young adults already. These courses however are not marketed in Finland as much as the other language courses. The theoretical part was gathered by collecting information and theories from various sources including books and e-books about mark...

  3. Contribution of effluent organic matter (EfOM) to ultrafiltration (UF) membrane fouling: Isolation, characterization, and fouling effect of EfOM fractions

    KAUST Repository

    Zheng, Xing; Khan, Muhammad; Croue, Jean-Philippe

    2014-01-01

    EfOM has been regarded as a major organic foulant resulting in UF membrane fouling in wastewater reclamation. To investigate fouling potential of different EfOM fractions, the present study isolated EfOM into hydrophobic neutrals (HPO-N), colloids

  4. BayesMotif: de novo protein sorting motif discovery from impure datasets.

    Science.gov (United States)

    Hu, Jianjun; Zhang, Fan

    2010-01-18

    Protein sorting is the process that newly synthesized proteins are transported to their target locations within or outside of the cell. This process is precisely regulated by protein sorting signals in different forms. A major category of sorting signals are amino acid sub-sequences usually located at the N-terminals or C-terminals of protein sequences. Genome-wide experimental identification of protein sorting signals is extremely time-consuming and costly. Effective computational algorithms for de novo discovery of protein sorting signals is needed to improve the understanding of protein sorting mechanisms. We formulated the protein sorting motif discovery problem as a classification problem and proposed a Bayesian classifier based algorithm (BayesMotif) for de novo identification of a common type of protein sorting motifs in which a highly conserved anchor is present along with a less conserved motif regions. A false positive removal procedure is developed to iteratively remove sequences that are unlikely to contain true motifs so that the algorithm can identify motifs from impure input sequences. Experiments on both implanted motif datasets and real-world datasets showed that the enhanced BayesMotif algorithm can identify anchored sorting motifs from pure or impure protein sequence dataset. It also shows that the false positive removal procedure can help to identify true motifs even when there is only 20% of the input sequences containing true motif instances. We proposed BayesMotif, a novel Bayesian classification based algorithm for de novo discovery of a special category of anchored protein sorting motifs from impure datasets. Compared to conventional motif discovery algorithms such as MEME, our algorithm can find less-conserved motifs with short highly conserved anchors. Our algorithm also has the advantage of easy incorporation of additional meta-sequence features such as hydrophobicity or charge of the motifs which may help to overcome the limitations of

  5. Fitness for synchronization of network motifs

    DEFF Research Database (Denmark)

    Vega, Y.M.; Vázquez-Prada, M.; Pacheco, A.F.

    2004-01-01

    We study the synchronization of Kuramoto's oscillators in small parts of networks known as motifs. We first report on the system dynamics for the case of a scale-free network and show the existence of a non-trivial critical point. We compute the probability that network motifs synchronize, and fi...... that the fitness for synchronization correlates well with motifs interconnectedness and structural complexity. Possible implications for present debates about network evolution in biological and other systems are discussed....

  6. Robotic Hand

    Science.gov (United States)

    1993-01-01

    The Omni-Hand was developed by Ross-Hime Designs, Inc. for Marshall Space Flight Center (MSFC) under a Small Business Innovation Research (SBIR) contract. The multiple digit hand has an opposable thumb and a flexible wrist. Electric muscles called Minnacs power wrist joints and the interchangeable digits. Two hands have been delivered to NASA for evaluation for potential use on space missions and the unit is commercially available for applications like hazardous materials handling and manufacturing automation. Previous SBIR contracts resulted in the Omni-Wrist and Omni-Wrist II robotic systems, which are commercially available for spray painting, sealing, ultrasonic testing, as well as other uses.

  7. Contrast in atomically resolved EF-SCEM imaging

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Peng [National Laboratory of Solid State Microstructures and Department of Materials Science and Engineering, Nanjing University, Nanjing 210093 (China); D’Alfonso, Adrian J. [School of Physics, University of Melbourne, Parkville, Victoria 3010 (Australia); Hashimoto, Ayako [Surface Physics and Structure Unit, National Institute for Materials Science, 1-2-1 Sengen, Tsukuba 305-0047 (Japan); Global Research Center for Environment and Energy based on Nanomaterials Science, National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, 305-0047 (Japan); Electron Microscopy Station, National Institute for Materials Science, 3-13 Sakura, Tsukuba 305-0003 (Japan); Morgan, Andrew J. [School of Physics, University of Melbourne, Parkville, Victoria 3010 (Australia); Takeguchi, Masaki [Surface Physics and Structure Unit, National Institute for Materials Science, 1-2-1 Sengen, Tsukuba 305-0047 (Japan); Electron Microscopy Station, National Institute for Materials Science, 3-13 Sakura, Tsukuba 305-0003 (Japan); Mitsuishi, Kazutaka [Surface Physics and Structure Unit, National Institute for Materials Science, 1-2-1 Sengen, Tsukuba 305-0047 (Japan); Global Research Center for Environment and Energy based on Nanomaterials Science, National Institute for Materials Science, 1-2-1 Sengen, Tsukuba, 305-0047 (Japan); Electron Microscopy Station, National Institute for Materials Science, 3-13 Sakura, Tsukuba 305-0003 (Japan); Shimojo, Masayuki [Department of Materials Science and Engineering, Shibaura Institute of Technology, 3-7-5, Toyosu, Koto-ku, Tokyo, 135-8548 (Japan); Kirkland, Angus I. [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom); Allen, Leslie J. [School of Physics, University of Melbourne, Parkville, Victoria 3010 (Australia); Nellist, Peter D., E-mail: peter.nellist@materials.ox.ac.uk [Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH (United Kingdom)

    2013-11-15

    Energy-filtered scanning confocal electron microscopy (EF-SCEM) is a technique that uses the reduced depth of field of an aberration-corrected transmission electron microscope to provide three-dimensional (3D) compositional information. Using a silicon sample in the <110> orientation, we show that EF-SCEM image data can be recorded that shows lattice resolution in the plane perpendicular to the incident beam direction. The confocal effect is demonstrated through the reduction of the mean intensity as the confocal plane is displaced from the sample mid-plane, unlike optical sectioning in high-angle annular dark-field scanning transmission electron microscopy (STEM). Simulations of the EF-SCEM data show agreement with the experimental data, and allow the interpretability of the data to be explored. The effects of channelling, absorption and delocalisation complicate the quantitative and qualitative interpretation of the data, highlighting the need for matching to simulations. Finally the effects of the finite detector pin-hole aperture size are explored, and we show that the EF-SCEM contrast in the plane perpendicular to the beam direction starts to resemble that of a STEM spectrum imaging experiment as the aperture size increases. - Highlights: • Atomically resolved energy-filtered scanning confocal electron microscopy (EF-SCEM) is demonstrated. • The confocal effect is demonstrated through the reduction of the mean intensity as the confocal plane is displaced from the sample mid-plane. • Simulations show agreement with the experimental data. • The effects of channelling, absorption and delocalisation complicate the quantitative and qualitative interpretation of the data. • The effects of the finite detector pin-hole aperture size are explored.

  8. Contrast in atomically resolved EF-SCEM imaging

    International Nuclear Information System (INIS)

    Wang, Peng; D’Alfonso, Adrian J.; Hashimoto, Ayako; Morgan, Andrew J.; Takeguchi, Masaki; Mitsuishi, Kazutaka; Shimojo, Masayuki; Kirkland, Angus I.; Allen, Leslie J.; Nellist, Peter D.

    2013-01-01

    Energy-filtered scanning confocal electron microscopy (EF-SCEM) is a technique that uses the reduced depth of field of an aberration-corrected transmission electron microscope to provide three-dimensional (3D) compositional information. Using a silicon sample in the orientation, we show that EF-SCEM image data can be recorded that shows lattice resolution in the plane perpendicular to the incident beam direction. The confocal effect is demonstrated through the reduction of the mean intensity as the confocal plane is displaced from the sample mid-plane, unlike optical sectioning in high-angle annular dark-field scanning transmission electron microscopy (STEM). Simulations of the EF-SCEM data show agreement with the experimental data, and allow the interpretability of the data to be explored. The effects of channelling, absorption and delocalisation complicate the quantitative and qualitative interpretation of the data, highlighting the need for matching to simulations. Finally the effects of the finite detector pin-hole aperture size are explored, and we show that the EF-SCEM contrast in the plane perpendicular to the beam direction starts to resemble that of a STEM spectrum imaging experiment as the aperture size increases. - Highlights: • Atomically resolved energy-filtered scanning confocal electron microscopy (EF-SCEM) is demonstrated. • The confocal effect is demonstrated through the reduction of the mean intensity as the confocal plane is displaced from the sample mid-plane. • Simulations show agreement with the experimental data. • The effects of channelling, absorption and delocalisation complicate the quantitative and qualitative interpretation of the data. • The effects of the finite detector pin-hole aperture size are explored

  9. A survey of motif finding Web tools for detecting binding site motifs in ChIP-Seq data.

    Science.gov (United States)

    Tran, Ngoc Tam L; Huang, Chun-Hsi

    2014-02-20

    ChIP-Seq (chromatin immunoprecipitation sequencing) has provided the advantage for finding motifs as ChIP-Seq experiments narrow down the motif finding to binding site locations. Recent motif finding tools facilitate the motif detection by providing user-friendly Web interface. In this work, we reviewed nine motif finding Web tools that are capable for detecting binding site motifs in ChIP-Seq data. We showed each motif finding Web tool has its own advantages for detecting motifs that other tools may not discover. We recommended the users to use multiple motif finding Web tools that implement different algorithms for obtaining significant motifs, overlapping resemble motifs, and non-overlapping motifs. Finally, we provided our suggestions for future development of motif finding Web tool that better assists researchers for finding motifs in ChIP-Seq data.

  10. MSDmotif: exploring protein sites and motifs

    Directory of Open Access Journals (Sweden)

    Henrick Kim

    2008-07-01

    Full Text Available Abstract Background Protein structures have conserved features – motifs, which have a sufficient influence on the protein function. These motifs can be found in sequence as well as in 3D space. Understanding of these fragments is essential for 3D structure prediction, modelling and drug-design. The Protein Data Bank (PDB is the source of this information however present search tools have limited 3D options to integrate protein sequence with its 3D structure. Results We describe here a web application for querying the PDB for ligands, binding sites, small 3D structural and sequence motifs and the underlying database. Novel algorithms for chemical fragments, 3D motifs, ϕ/ψ sequences, super-secondary structure motifs and for small 3D structural motif associations searches are incorporated. The interface provides functionality for visualization, search criteria creation, sequence and 3D multiple alignment options. MSDmotif is an integrated system where a results page is also a search form. A set of motif statistics is available for analysis. This set includes molecule and motif binding statistics, distribution of motif sequences, occurrence of an amino-acid within a motif, correlation of amino-acids side-chain charges within a motif and Ramachandran plots for each residue. The binding statistics are presented in association with properties that include a ligand fragment library. Access is also provided through the distributed Annotation System (DAS protocol. An additional entry point facilitates XML requests with XML responses. Conclusion MSDmotif is unique by combining chemical, sequence and 3D data in a single search engine with a range of search and visualisation options. It provides multiple views of data found in the PDB archive for exploring protein structures.

  11. Temporal motifs in time-dependent networks

    International Nuclear Information System (INIS)

    Kovanen, Lauri; Karsai, Márton; Kaski, Kimmo; Kertész, János; Saramäki, Jari

    2011-01-01

    Temporal networks are commonly used to represent systems where connections between elements are active only for restricted periods of time, such as telecommunication, neural signal processing, biochemical reaction and human social interaction networks. We introduce the framework of temporal motifs to study the mesoscale topological–temporal structure of temporal networks in which the events of nodes do not overlap in time. Temporal motifs are classes of similar event sequences, where the similarity refers not only to topology but also to the temporal order of the events. We provide a mapping from event sequences to coloured directed graphs that enables an efficient algorithm for identifying temporal motifs. We discuss some aspects of temporal motifs, including causality and null models, and present basic statistics of temporal motifs in a large mobile call network

  12. Motif discovery in ranked lists of sequences

    DEFF Research Database (Denmark)

    Nielsen, Morten Muhlig; Tataru, Paula; Madsen, Tobias

    2016-01-01

    Motif analysis has long been an important method to characterize biological functionality and the current growth of sequencing-based genomics experiments further extends its potential. These diverse experiments often generate sequence lists ranked by some functional property. There is therefore...... advantage of the regular expression feature, including enrichments for combinations of different microRNA seed sites. The method is implemented and made publicly available as an R package and supports high parallelization on multi-core machinery....... a growing need for motif analysis methods that can exploit this coupled data structure and be tailored for specific biological questions. Here, we present an exploratory motif analysis tool, Regmex (REGular expression Motif EXplorer), which offers several methods to evaluate the correlation of motifs...

  13. MotifNet: a web-server for network motif analysis.

    Science.gov (United States)

    Smoly, Ilan Y; Lerman, Eugene; Ziv-Ukelson, Michal; Yeger-Lotem, Esti

    2017-06-15

    Network motifs are small topological patterns that recur in a network significantly more often than expected by chance. Their identification emerged as a powerful approach for uncovering the design principles underlying complex networks. However, available tools for network motif analysis typically require download and execution of computationally intensive software on a local computer. We present MotifNet, the first open-access web-server for network motif analysis. MotifNet allows researchers to analyze integrated networks, where nodes and edges may be labeled, and to search for motifs of up to eight nodes. The output motifs are presented graphically and the user can interactively filter them by their significance, number of instances, node and edge labels, and node identities, and view their instances. MotifNet also allows the user to distinguish between motifs that are centered on specific nodes and motifs that recur in distinct parts of the network. MotifNet is freely available at http://netbio.bgu.ac.il/motifnet . The website was implemented using ReactJs and supports all major browsers. The server interface was implemented in Python with data stored on a MySQL database. estiyl@bgu.ac.il or michaluz@cs.bgu.ac.il. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  14. Hand eczema

    DEFF Research Database (Denmark)

    Ibler, K.S.; Jemec, G.B.E.; Flyvholm, M.-A.

    2012-01-01

    Background. Healthcare workers are at increased risk of developing hand eczema. Objectives. To investigate the prevalence and severity of self-reported hand eczema, and to relate the findings to demographic data, occupation, medical speciality, wards, shifts, and working hours. Patients/materials......Background. Healthcare workers are at increased risk of developing hand eczema. Objectives. To investigate the prevalence and severity of self-reported hand eczema, and to relate the findings to demographic data, occupation, medical speciality, wards, shifts, and working hours. Patients...... dermatitis, younger age, male sex (male doctors), and working hours. Eighty nine per cent of subjects reported mild/moderate lesions. Atopic dermatitis was the only factor significantly related to severity. Sick leave was reported by 8% of subjects, and notification to the authorities by 12%. Conclusions...... or severity, but cultural differences between professions with respect to coping with the eczema were significant. Atopic dermatitis was related to increased prevalence and severity, and preventive efforts should be made for healthcare workers with atopic dermatitis....

  15. Hand Osteoblastoma

    Directory of Open Access Journals (Sweden)

    M. Farzan

    2006-06-01

    Full Text Available Background and Aim: Osteoblastoma is one of the rarest primary bone tumors. Although, small bones of the hands and feet are the third most common location for this tumor, the hand involvement is very rare and few case observations were published in the English-language literature. Materials and Methods: In this study, we report five cases of benign osteoblastoma of the hand, 3 in metacarpals and two in phalanxes. The clinical feature is not specific. The severe nocturnal, salicylate-responsive pain is not present in patients with osteoblastoma. The pain is dull, persistent and less localized. The clinical course is usually long and there is often symptoms for months before medical attention are sought. Swelling is a more persistent finding in osteoblastoma of the hand that we found in all of our patients. The radiologic findings are indistinctive, so preoperative diagnosis based on X-ray appearance is difficult. In all of our 5 cases, we fail to consider osteoblastoma as primary diagnosis. Pathologically, osteoblastoma consisting of a well-vascularized connective tissue stroma in which there is active production of osteoid and primitive woven bone. Treatment depends on the stage and localization of the tumor. Curettage and bone grafting is sufficient in stage 1 or stage 2, but in stage 3 wide resection is necessary for prevention of recurrence. Osteosarcoma is the most important differential diagnosis that may lead to inappropriate operation.

  16. After the storm: personal experiences following an EF4 tornado.

    Science.gov (United States)

    May, Olivia W; Bigham, Amy B

    2012-08-01

    In April of 2011, an EF4 tornado ripped through the city of Tuscaloosa, AL, leaving in its wake thousands of destroyed homes and businesses. In the hours and days that followed, the health care community of this city, as well as the entire state of Alabama and the southeastern United States, came together to provide care to hundreds of victims, recovery workers, and volunteers. Copyright © 2012 Elsevier Inc. All rights reserved.

  17. Skeletal muscle eEF2 and 4EBP1 phosphorylation during endurance exercise is dependent on intensity and muscle fiber type

    DEFF Research Database (Denmark)

    Rose, Adam John; Bisiani, Bruno; Vistisen, Bodil

    2009-01-01

    that the increase in skeletal muscle eEF2 Thr(56) phosphorylation was restricted to type I myofibers. Taken together, these data suggest that the depression of skeletal muscle protein synthesis with endurance-type exercise may be regulated at both initiation (i.e. 4EBP1) and elongation (i.e. eEF2) steps, with eEF2......Protein synthesis in skeletal muscle is known to decrease during exercise and it has been suggested that this may depend on the magnitude of the relative metabolic stress within the contracting muscle. To examine the mechanisms behind this, the effect of exercise intensity on skeletal muscle......) increased during exercise but was not influenced by exercise intensity, and was lower than rest 30min after exercise. On the other hand, 4EBP1 phosphorylation at Thr(37/46) decreased during exercise and this decrease was greater at higher exercise intensities, and was similar to rest 30min after exercise...

  18. Automated classification of RNA 3D motifs and the RNA 3D Motif Atlas

    Science.gov (United States)

    Petrov, Anton I.; Zirbel, Craig L.; Leontis, Neocles B.

    2013-01-01

    The analysis of atomic-resolution RNA three-dimensional (3D) structures reveals that many internal and hairpin loops are modular, recurrent, and structured by conserved non-Watson–Crick base pairs. Structurally similar loops define RNA 3D motifs that are conserved in homologous RNA molecules, but can also occur at nonhomologous sites in diverse RNAs, and which often vary in sequence. To further our understanding of RNA motif structure and sequence variability and to provide a useful resource for structure modeling and prediction, we present a new method for automated classification of internal and hairpin loop RNA 3D motifs and a new online database called the RNA 3D Motif Atlas. To classify the motif instances, a representative set of internal and hairpin loops is automatically extracted from a nonredundant list of RNA-containing PDB files. Their structures are compared geometrically, all-against-all, using the FR3D program suite. The loops are clustered into motif groups, taking into account geometric similarity and structural annotations and making allowance for a variable number of bulged bases. The automated procedure that we have implemented identifies all hairpin and internal loop motifs previously described in the literature. All motif instances and motif groups are assigned unique and stable identifiers and are made available in the RNA 3D Motif Atlas (http://rna.bgsu.edu/motifs), which is automatically updated every four weeks. The RNA 3D Motif Atlas provides an interactive user interface for exploring motif diversity and tools for programmatic data access. PMID:23970545

  19. Hunting Motifs in Situla Art

    Directory of Open Access Journals (Sweden)

    Andrej Preložnik

    2013-07-01

    Full Text Available Situla art developed as an echo of the toreutic style which had spread from the Near East through the Phoenicians, Greeks and Etruscans as far as the Veneti, Raeti, Histri, and their eastern neighbours in the region of Dolenjska (Lower Carniola. An Early Iron Age phenomenon (c. 600—300 BC, it rep- resents the major and most arresting form of the contemporary visual arts in an area stretching from the foot of the Apennines in the south to the Drava and Sava rivers in the east. Indeed, individual pieces have found their way across the Alpine passes and all the way north to the Danube. In the world and art of the situlae, a prominent role is accorded to ani- mals. They are displayed in numerous representations of human activities on artefacts crafted in the classic situla style – that is, between the late 6th  and early 5th centuries BC – as passive participants (e.g. in pageants or in harness or as an active element of the situla narrative. The most typical example of the latter is the hunting scene. Today we know at least four objects decorat- ed exclusively with hunting themes, and a number of situlae and other larger vessels where hunting scenes are embedded in composite narratives. All this suggests a popularity unparallelled by any other genre. Clearly recognisable are various hunting techniques and weapons, each associated with a particu- lar type of game (Fig. 1. The chase of a stag with javelin, horse and hound is depicted on the long- familiar and repeatedly published fibula of Zagorje (Fig. 2. It displays a hound mauling the stag’s back and a hunter on horseback pursuing a hind, her neck already pierced by the javelin. To judge by the (so far unnoticed shaft end un- der the stag’s muzzle, the hunter would have been brandishing a second jave- lin as well, like the warrior of the Vače fibula or the rider of the Nesactium situla, presumably himself a hunter. Many parallels to his motif are known from Greece, Etruria, and

  20. Parallel motif extraction from very long sequences

    KAUST Repository

    Sahli, Majed; Mansour, Essam; Kalnis, Panos

    2013-01-01

    Motifs are frequent patterns used to identify biological functionality in genomic sequences, periodicity in time series, or user trends in web logs. In contrast to a lot of existing work that focuses on collections of many short sequences, modern

  1. Deciphering functional glycosaminoglycan motifs in development.

    Science.gov (United States)

    Townley, Robert A; Bülow, Hannes E

    2018-03-23

    Glycosaminoglycans (GAGs) such as heparan sulfate, chondroitin/dermatan sulfate, and keratan sulfate are linear glycans, which when attached to protein backbones form proteoglycans. GAGs are essential components of the extracellular space in metazoans. Extensive modifications of the glycans such as sulfation, deacetylation and epimerization create structural GAG motifs. These motifs regulate protein-protein interactions and are thereby repsonsible for many of the essential functions of GAGs. This review focusses on recent genetic approaches to characterize GAG motifs and their function in defined signaling pathways during development. We discuss a coding approach for GAGs that would enable computational analyses of GAG sequences such as alignments and the computation of position weight matrices to describe GAG motifs. Copyright © 2018 Elsevier Ltd. All rights reserved.

  2. Bayesian centroid estimation for motif discovery.

    Science.gov (United States)

    Carvalho, Luis

    2013-01-01

    Biological sequences may contain patterns that signal important biomolecular functions; a classical example is regulation of gene expression by transcription factors that bind to specific patterns in genomic promoter regions. In motif discovery we are given a set of sequences that share a common motif and aim to identify not only the motif composition, but also the binding sites in each sequence of the set. We propose a new centroid estimator that arises from a refined and meaningful loss function for binding site inference. We discuss the main advantages of centroid estimation for motif discovery, including computational convenience, and how its principled derivation offers further insights about the posterior distribution of binding site configurations. We also illustrate, using simulated and real datasets, that the centroid estimator can differ from the traditional maximum a posteriori or maximum likelihood estimators.

  3. Bayesian centroid estimation for motif discovery.

    Directory of Open Access Journals (Sweden)

    Luis Carvalho

    Full Text Available Biological sequences may contain patterns that signal important biomolecular functions; a classical example is regulation of gene expression by transcription factors that bind to specific patterns in genomic promoter regions. In motif discovery we are given a set of sequences that share a common motif and aim to identify not only the motif composition, but also the binding sites in each sequence of the set. We propose a new centroid estimator that arises from a refined and meaningful loss function for binding site inference. We discuss the main advantages of centroid estimation for motif discovery, including computational convenience, and how its principled derivation offers further insights about the posterior distribution of binding site configurations. We also illustrate, using simulated and real datasets, that the centroid estimator can differ from the traditional maximum a posteriori or maximum likelihood estimators.

  4. Roles of Protein Synthesis Elongation Factor EF-Tu in Heat Tolerance in Plants

    Directory of Open Access Journals (Sweden)

    Jianming Fu

    2012-01-01

    Full Text Available EF-Tu proteins of plastids, mitochondria, and the cytosolic counterpart EF-1α in plants, as well as EF-Tu proteins of bacteria, are highly conserved and multifunctional. The functions of EF-Tu include transporting the aminoacyl-tRNA complex to the A site of the ribosome during protein biosynthesis; chaperone activity in protecting other proteins from aggregation caused by environmental stresses, facilitating renaturation of proteins when conditions return to normal; displaying a protein disulfide isomerase activity; participating in the degradation of N-terminally blocked proteins by the proteasome; eliciting innate immunity and triggering resistance to pathogenic bacteria in plants; participating in transcription when an E. coli host is infected with phages. EF-Tu genes are upregulated by abiotic stresses in plants, and EF-Tu plays important role in stress responses. Expression of a plant EF-Tu gene confers heat tolerance in E. coli, maize knock-out EF-Tu null mutants are heat susceptible, and over-expression of an EF-Tu gene improves heat tolerance in crop plants. This review paper summarizes the current knowledge of EF-Tu proteins in stress responses in plants and progress on application of EF-Tu for developing crop varieties tolerant to abiotic stresses, such as high temperatures.

  5. Sordarin derivatives induce a novel conformation of the yeast ribosome translocation factor eEF2

    DEFF Research Database (Denmark)

    Søe, Rikke; Mosley, R.T.; Justice, M.

    2007-01-01

    EF2 that form the ligand binding pocket are oriented in a different manner relative to the rest of eEF2 compared to our previous structure of eEF2 in complex with the parent natural product sordarin. Yeast eEF2 is also shown to bind adenylic nucleotides, which can be displaced by sordarin, suggesting...... that ADP or ATP also bind to the three C-terminal domains of eEF2. Fusidic acid is a universal inhibitor of translation that targets EF-G or eEF2, and is widely used as an antibiotic against gram positive bacteria. Based on mutations conferring resistance to fusidic acid, cryo-EM reconstructions, and X...

  6. Space-related pharma-motifs for fast search of protein binding motifs and polypharmacological targets.

    Science.gov (United States)

    Chiu, Yi-Yuan; Lin, Chun-Yu; Lin, Chih-Ta; Hsu, Kai-Cheng; Chang, Li-Zen; Yang, Jinn-Moon

    2012-01-01

    To discover a compound inhibiting multiple proteins (i.e. polypharmacological targets) is a new paradigm for the complex diseases (e.g. cancers and diabetes). In general, the polypharmacological proteins often share similar local binding environments and motifs. As the exponential growth of the number of protein structures, to find the similar structural binding motifs (pharma-motifs) is an emergency task for drug discovery (e.g. side effects and new uses for old drugs) and protein functions. We have developed a Space-Related Pharmamotifs (called SRPmotif) method to recognize the binding motifs by searching against protein structure database. SRPmotif is able to recognize conserved binding environments containing spatially discontinuous pharma-motifs which are often short conserved peptides with specific physico-chemical properties for protein functions. Among 356 pharma-motifs, 56.5% interacting residues are highly conserved. Experimental results indicate that 81.1% and 92.7% polypharmacological targets of each protein-ligand complex are annotated with same biological process (BP) and molecular function (MF) terms, respectively, based on Gene Ontology (GO). Our experimental results show that the identified pharma-motifs often consist of key residues in functional (active) sites and play the key roles for protein functions. The SRPmotif is available at http://gemdock.life.nctu.edu.tw/SRP/. SRPmotif is able to identify similar pharma-interfaces and pharma-motifs sharing similar binding environments for polypharmacological targets by rapidly searching against the protein structure database. Pharma-motifs describe the conservations of binding environments for drug discovery and protein functions. Additionally, these pharma-motifs provide the clues for discovering new sequence-based motifs to predict protein functions from protein sequence databases. We believe that SRPmotif is useful for elucidating protein functions and drug discovery.

  7. [The EFS metrology: From the production to the reason].

    Science.gov (United States)

    Reifenberg, J-M; Riout, E; Leroy, A; Begue, S

    2014-06-01

    In order to answer statutory requirements and to anticipate the future needs and standards, the EFS is committed, since a few years, in a process of harmonization of its metrology function. In particular, the institution has opted for the skills development by internalizing the metrological traceability of the main critical quantities (temperature, volumetric) measurements. The development of metrology so resulted in a significant increase in calibration and testing activities. Methods are homogenized and improved through accreditations. The investment strategies are based on more and more demanding specifications. The performance of the equipments is better known and mastered. Technical expertise and maturity of the national metrology function today are assets to review in more informed ways the appropriateness of the applied periodicities. Analysis of numerous information and data in the calibration and testing reports could be pooled and operated on behalf of the unique establishment. The objective of this article is to illustrate these reflections with a few examples from of a feedback of the EFS Pyrénées Méditerranée. The analysis of some methods of qualification, the exploitation of the historical metrology in order to quantify the risk of non-compliance, and to adapt the control strategy, analysis of the criticality of an instrument in a measurement process, risk analyses are tools that deserve to be more widely exploited for that discipline wins in efficiency at the national level. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

  8. Fabrication and tests of EF conductors for JT-60SA

    Energy Technology Data Exchange (ETDEWEB)

    Kizu, Kaname, E-mail: kizu.kaname@jaea.go.jp [Japan Atomic Energy Agency, Naka, Ibaraki 311-0193 (Japan); Kashiwa, Yoshitoshi; Murakami, Haruyuki [Japan Atomic Energy Agency, Naka, Ibaraki 311-0193 (Japan); Obana, Tetsuhiro; Takahata, Kazuya [National Institute for Fusion Science, Toki, Gifu 509-5292 (Japan); Tsuchiya, Katsuhiko; Yoshida, Kiyoshi [Japan Atomic Energy Agency, Naka, Ibaraki 311-0193 (Japan); Hamaguchi, Shinji [National Institute for Fusion Science, Toki, Gifu 509-5292 (Japan); Matsui, Kunihiro [Japan Atomic Energy Agency, Naka, Ibaraki 311-0193 (Japan); Nakamura, Kazuya; Takao, Tomoaki [Sophia University, Tokyo 102-8554 (Japan); Yanagi, Nagato; Imagawa, Shinsaku; Mito, Toshiyuki [National Institute for Fusion Science, Toki, Gifu 509-5292 (Japan)

    2011-10-15

    The conductors for plasma equilibrium field (EF) coils of JT-60SA are NbTi cable-in-conduit (CIC) conductor with stainless steel 316L jacket. The production of superconductors for actual EF coils started from February 2010. Nine superconductors with 444 m in length were produced up to July 2010. More than 300 welding of jackets were performed. Six nonconformities were found by inspections as go gauge, visual inspection and X-ray test. In order to shorten the manufacturing time schedule, helium leak test was conducted at once after connecting the long length jacket not just after the welding. The maximum force to pull the cable into jacket was about 7.6 kN on average. The mass flow rates of 9 conductors showed almost same values indicating that there are no blockages in the conductors. The measured current sharing temperature agreed with the expectation values from strand performance indicating that no degradation was caused by production process. The coupling time constants of conductors ranged from 80 to 90 ms which are much smaller than the design value of 200 ms.

  9. The MHC motif viewer: a visualization tool for MHC binding motifs

    DEFF Research Database (Denmark)

    Rapin, Nicolas; Hoof, Ilka; Lund, Ole

    2010-01-01

    is hampered by the lack of tools for browsing and comparing specificity of these molecules. We have developed a Web server, MHC Motif Viewer, which allows the display of the binding motif for MHC class I proteins for human, chimpanzee, rhesus monkey, mouse, and swine, as well as HLA-DR protein sequences...

  10. Clinical efficacy of gamma knife and surgery treatment of mesial temporal lobe epilepsy and their effects on EF-Tumt and EF-Tsmt expression.

    Science.gov (United States)

    Wang, X-Q; Zhang, X-D; Han, Y-M; Shi, X-F; Lan, Z-B; Men, X-X; Pan, Y-W

    2017-04-01

    To study the clinical efficacy of gamma knife and surgery treatment of mesial temporal lobe epilepsy (MTLE) and their effects on EF-Tumt and EF-Tsmt expression. The data of 78 cases of MTLE patients treated in our hospital from April 2011 to March 2013 were retrospectively analyzed. The patients were divided into two groups according to the treatment methods: the surgery group (including 41 cases) and the gamma knife group (including 37 cases). The clinical efficacy, the occurrence and recurrence of complications were evaluated, respectively; meanwhile, the expression of the EF-Tumt protein and EF-Tsmt protein in brain tissue were analyzed. The difference between the efficacy rate of the two groups showed no statistical significance (χ2=0.960, p>0.05). The complication rate of the gamma knife group was significantly lower than that of the control group (χ2=6.430, pknife group was significantly lower than that of the patients in the surgery group (p>0.05). Within the two groups, the positive expression granum of EF-Tsmt protein and EF-Tumt protein of the two groups after treatment were significantly lower than that before treatment (pknife group was obviously more than that of the patients in the surgery group (p0.05). Before and after treatment within the group, the positive cell of EF-Tsmt protein and EF-Tumt protein of the two groups of patients after treatment were significantly lower than that before treatment (p0.05). Both surgery and gamma knife could treat MTLE effectively, and the efficacy may be related to the ability to reduce the expression of EF-Tsmt protein and EF-Tumt protein in brain tissue.

  11. Analisis Unsur Matematika pada Motif Sulam Usus

    Directory of Open Access Journals (Sweden)

    Fredi Ganda Putra

    2017-12-01

    Full Text Available Based on interviews with researchers sources said that the beginning of the intestine embroidery is an art of genuine crafts. Called the intestine embroidery because this technique is a technique of combining a strand of cloth resembling the intestine formed according to the pattern by means of embroidered using a thread. Intestinal embroidery techniques were originally used to create a cover of the women's customary wardrobe of Lampung or often referred to as bebe. But not many people in Lampung, especially people who live in Lampung are still many who do not know and recognize the intestine embroidery because most only know tapis only characteristic of Lampung, besides that there are other cultural results that is embroidered intestine. There are still many who do not know that the intestine motif there is a knowledge of mathematics. The researcher's problem formulation is whether there are mathematical elements contained in the intestine embroidery motif based on the concept of geometry. The purpose of this study is to determine whether there are elements of mathematics contained in the intestine motif based on the concept of geometry. Subjects in this study consisted of 4 people obtained by purposive sampling technique. From the results of data analysis conducted by using descriptive analysis and discussion as follows: (1 Intestinal embroidery motif contains the meaning of mathematics and culture or often called Etnomatematika. On the meaning of culture there is a link between the embroidery intestine with a culture that has been there before as the existence of cultural linkage between Hindu belief Buddhism and there are similarities of motifs and decorative patterns contained in the motif embroidery intestine with ornamental variety in Indonesia. (2 The relationship between the intestine with mathematical motifs there are elements of mathematics such as geometry elements in the form of geometry of dimension one and dimension two, and the

  12. The eEF1A proteins: at the crossroads of oncogenesis, apoptosis and viral infections.

    Directory of Open Access Journals (Sweden)

    Georges eHerbein

    2015-04-01

    Full Text Available Eukaryotic translation elongation factors 1 alpha, eEF1A1 and eEF1A2, are not only translation factors, but also pleiotropic proteins that are highly expressed in human tumors, including breast cancer, ovarian cancer and lung cancer. eEF1A1 modulates cytoskeleton, exhibits chaperone-like activity and also controls cell proliferation and cell death. By contrast eEF1A2 protein favors oncogenesis as shown by the fact that overexpression of eEF1A2 leads to cellular transformation and gives rise to tumors in nude mice. The eEF1A2 protein stimulates the phospholipid signaling and activates the Akt-dependent cell migration and actin remodeling that ultimately favors tumorigenesis. By contrast, inactivation of eEF1A proteins leads to immunodeficiency, neural and muscular defects, and favors apoptosis. Finally, eEF1A proteins interact with several viral proteins resulting in enhanced viral replication, decreased apoptosis and increased cellular transformation. This review summarizes the recent findings on eEF1A proteins indicating that eEF1A proteins play a critical role in numerous human diseases through enhancement of oncogenesis, blockade of apoptosis and increased viral pathogenesis.

  13. Armadillo motifs involved in vesicular transport.

    Directory of Open Access Journals (Sweden)

    Harald Striegl

    Full Text Available Armadillo (ARM repeat proteins function in various cellular processes including vesicular transport and membrane tethering. They contain an imperfect repeating sequence motif that forms a conserved three-dimensional structure. Recently, structural and functional insight into tethering mediated by the ARM-repeat protein p115 has been provided. Here we describe the p115 ARM-motifs for reasons of clarity and nomenclature and show that both sequence and structure are highly conserved among ARM-repeat proteins. We argue that there is no need to invoke repeat types other than ARM repeats for a proper description of the structure of the p115 globular head region. Additionally, we propose to define a new subfamily of ARM-like proteins and show lack of evidence that the ARM motifs found in p115 are present in other long coiled-coil tethering factors of the golgin family.

  14. Direct AUC optimization of regulatory motifs.

    Science.gov (United States)

    Zhu, Lin; Zhang, Hong-Bo; Huang, De-Shuang

    2017-07-15

    The discovery of transcription factor binding site (TFBS) motifs is essential for untangling the complex mechanism of genetic variation under different developmental and environmental conditions. Among the huge amount of computational approaches for de novo identification of TFBS motifs, discriminative motif learning (DML) methods have been proven to be promising for harnessing the discovery power of accumulated huge amount of high-throughput binding data. However, they have to sacrifice accuracy for speed and could fail to fully utilize the information of the input sequences. We propose a novel algorithm called CDAUC for optimizing DML-learned motifs based on the area under the receiver-operating characteristic curve (AUC) criterion, which has been widely used in the literature to evaluate the significance of extracted motifs. We show that when the considered AUC loss function is optimized in a coordinate-wise manner, the cost function of each resultant sub-problem is a piece-wise constant function, whose optimal value can be found exactly and efficiently. Further, a key step of each iteration of CDAUC can be efficiently solved as a computational geometry problem. Experimental results on real world high-throughput datasets illustrate that CDAUC outperforms competing methods for refining DML motifs, while being one order of magnitude faster. Meanwhile, preliminary results also show that CDAUC may also be useful for improving the interpretability of convolutional kernels generated by the emerging deep learning approaches for predicting TF sequences specificities. CDAUC is available at: https://drive.google.com/drive/folders/0BxOW5MtIZbJjNFpCeHlBVWJHeW8 . dshuang@tongji.edu.cn. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

  15. Discovery of optical flickering from the symbiotic star EF Aquilae

    Science.gov (United States)

    Zamanov, R. K.; Boeva, S.; Nikolov, Y. M.; Petrov, B.; Bachev, R.; Latev, G. Y.; Popov, V. A.; Stoyanov, K. A.; Bode, M. F.; Martí, J.; Tomov, T.; Antonova, A.

    2017-07-01

    We report optical CCD photometry of the recently identified symbiotic star EF Aql. Our observations in Johnson V and B bands clearly show the presence of stochastic light variations with an amplitude of about 0.2 mag on a time scale of minutes. The observations point toward a white dwarf (WD) as the hot component in the system. It is the 11-th object among more than 200 symbiotic stars known with detected optical flickering. Estimates of the mass accretion rate onto the WD and the mass loss rate in the wind of the Mira secondary star lead to the conclusion that less than 1 per cent of the wind is captured by the WD. Eight further candidates for the detection of flickering in similar systems are suggested.

  16. A comparison of HFrEF vs HFpEF's clinical workload and cost in the first year following hospitalization and enrollment in a disease management program.

    Science.gov (United States)

    Murphy, T M; Waterhouse, D F; James, S; Casey, C; Fitzgerald, E; O'Connell, E; Watson, C; Gallagher, J; Ledwidge, M; McDonald, K

    2017-04-01

    Admission with heart failure (HF) is a milestone in the progression of the disease, often resulting in higher intensity medical care and ensuing readmissions. Whilst there is evidence supporting enrolling patients in a heart failure disease management program (HF-DMP), not all reported HF-DMPs have systematically enrolled patients with HF with preserved ejection fraction (HFpEF) and there is a scarcity of literature differentiating costs based on HF-phenotype. 1292 consenting, consecutive patients admitted with a primary diagnosis of HF were enrolled in a hospital based HF-DMP and categorized as HFpEF (EF≥45%) or HFrEF (EFHospitalizations, primary care, medications, and DMP workload with associated costs were evaluated assessing DMP clinic-visits, telephonic contact, medication changes over 1year using a mixture of casemix and micro-costing techniques. The total average annual cost per patient was marginally higher in patients with HFrEF €13,011 (12,011, 14,078) than HFpEF, €12,206 (11,009, 13,518). However, emergency non-cardiovascular admission rates and average cost per patient were higher in the HFpEF vs HFrEF group (0.46 vs 0.31 per patient/12months) & €655 (318, 1073) vs €584 (396, 812). In the first 3months of the outpatient HF-DMP the HFrEF population cost more on average €791 (764, 819) vs €693 (660, 728). There are greater short-term (3-month) costs of HFrEF versus HFpEF as part of a HF-DMP following an admission. However, long-term (3-12month) costs of HFpEF are greater because of higher non-cardiovascular rehospitalisations. As HFpEF becomes the dominant form of HF, more work is required in HF-DMPs to address prevention of non-cardiovascular rehospitalisations and to integrate hospital based HF-DMPs into primary healthcare structures. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

  17. Highly scalable Ab initio genomic motif identification

    KAUST Repository

    Marchand, Benoit; Bajic, Vladimir B.; Kaushik, Dinesh

    2011-01-01

    We present results of scaling an ab initio motif family identification system, Dragon Motif Finder (DMF), to 65,536 processor cores of IBM Blue Gene/P. DMF seeks groups of mutually similar polynucleotide patterns within a set of genomic sequences and builds various motif families from them. Such information is of relevance to many problems in life sciences. Prior attempts to scale such ab initio motif-finding algorithms achieved limited success. We solve the scalability issues using a combination of mixed-mode MPI-OpenMP parallel programming, master-slave work assignment, multi-level workload distribution, multi-level MPI collectives, and serial optimizations. While the scalability of our algorithm was excellent (94% parallel efficiency on 65,536 cores relative to 256 cores on a modest-size problem), the final speedup with respect to the original serial code exceeded 250,000 when serial optimizations are included. This enabled us to carry out many large-scale ab initio motiffinding simulations in a few hours while the original serial code would have needed decades of execution time. Copyright 2011 ACM.

  18. Parallel motif extraction from very long sequences

    KAUST Repository

    Sahli, Majed

    2013-01-01

    Motifs are frequent patterns used to identify biological functionality in genomic sequences, periodicity in time series, or user trends in web logs. In contrast to a lot of existing work that focuses on collections of many short sequences, modern applications require mining of motifs in one very long sequence (i.e., in the order of several gigabytes). For this case, there exist statistical approaches that are fast but inaccurate; or combinatorial methods that are sound and complete. Unfortunately, existing combinatorial methods are serial and very slow. Consequently, they are limited to very short sequences (i.e., a few megabytes), small alphabets (typically 4 symbols for DNA sequences), and restricted types of motifs. This paper presents ACME, a combinatorial method for extracting motifs from a single very long sequence. ACME arranges the search space in contiguous blocks that take advantage of the cache hierarchy in modern architectures, and achieves almost an order of magnitude performance gain in serial execution. It also decomposes the search space in a smart way that allows scalability to thousands of processors with more than 90% speedup. ACME is the only method that: (i) scales to gigabyte-long sequences; (ii) handles large alphabets; (iii) supports interesting types of motifs with minimal additional cost; and (iv) is optimized for a variety of architectures such as multi-core systems, clusters in the cloud, and supercomputers. ACME reduces the extraction time for an exact-length query from 4 hours to 7 minutes on a typical workstation; handles 3 orders of magnitude longer sequences; and scales up to 16, 384 cores on a supercomputer. Copyright is held by the owner/author(s).

  19. DNA motif elucidation using belief propagation

    KAUST Repository

    Wong, Ka-Chun; Chan, Tak-Ming; Peng, Chengbin; Li, Yue; Zhang, Zhaolei

    2013-01-01

    Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k = 8 ?10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors' websites: e.g. http://www.cs.toronto.edu/?wkc/kmerHMM. 2013 The Author(s).

  20. DNA motif elucidation using belief propagation.

    Science.gov (United States)

    Wong, Ka-Chun; Chan, Tak-Ming; Peng, Chengbin; Li, Yue; Zhang, Zhaolei

    2013-09-01

    Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k=8∼10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors' websites: e.g. http://www.cs.toronto.edu/∼wkc/kmerHMM.

  1. DNA motif elucidation using belief propagation

    KAUST Repository

    Wong, Ka-Chun

    2013-06-29

    Protein-binding microarray (PBM) is a high-throughout platform that can measure the DNA-binding preference of a protein in a comprehensive and unbiased manner. A typical PBM experiment can measure binding signal intensities of a protein to all the possible DNA k-mers (k = 8 ?10); such comprehensive binding affinity data usually need to be reduced and represented as motif models before they can be further analyzed and applied. Since proteins can often bind to DNA in multiple modes, one of the major challenges is to decompose the comprehensive affinity data into multimodal motif representations. Here, we describe a new algorithm that uses Hidden Markov Models (HMMs) and can derive precise and multimodal motifs using belief propagations. We describe an HMM-based approach using belief propagations (kmerHMM), which accepts and preprocesses PBM probe raw data into median-binding intensities of individual k-mers. The k-mers are ranked and aligned for training an HMM as the underlying motif representation. Multiple motifs are then extracted from the HMM using belief propagations. Comparisons of kmerHMM with other leading methods on several data sets demonstrated its effectiveness and uniqueness. Especially, it achieved the best performance on more than half of the data sets. In addition, the multiple binding modes derived by kmerHMM are biologically meaningful and will be useful in interpreting other genome-wide data such as those generated from ChIP-seq. The executables and source codes are available at the authors\\' websites: e.g. http://www.cs.toronto.edu/?wkc/kmerHMM. 2013 The Author(s).

  2. CombiMotif: A new algorithm for network motifs discovery in protein-protein interaction networks

    Science.gov (United States)

    Luo, Jiawei; Li, Guanghui; Song, Dan; Liang, Cheng

    2014-12-01

    Discovering motifs in protein-protein interaction networks is becoming a current major challenge in computational biology, since the distribution of the number of network motifs can reveal significant systemic differences among species. However, this task can be computationally expensive because of the involvement of graph isomorphic detection. In this paper, we present a new algorithm (CombiMotif) that incorporates combinatorial techniques to count non-induced occurrences of subgraph topologies in the form of trees. The efficiency of our algorithm is demonstrated by comparing the obtained results with the current state-of-the art subgraph counting algorithms. We also show major differences between unicellular and multicellular organisms. The datasets and source code of CombiMotif are freely available upon request.

  3. Clean Hands Count

    Medline Plus

    Full Text Available ... has been rented. This feature is not available right now. Please try again later. Published on May ... 34 How The Clean Hands - Safe Hands System Works - Duration: 3:38. Clean Hands-Safe Hands 5, ...

  4. Pathophysiological understanding of HFpEF: microRNAs as part of the puzzle.

    Science.gov (United States)

    Rech, Monika; Barandiarán Aizpurua, Arantxa; van Empel, Vanessa; van Bilsen, Marc; Schroen, Blanche

    2018-05-01

    Half of all heart failure patients have preserved ejection fraction (HFpEF). Comorbidities associated with and contributing to HFpEF include obesity, diabetes and hypertension. Still, the underlying pathophysiological mechanisms of HFpEF are unknown. A preliminary consensus proposes that the multi-morbidity triggers a state of systemic, chronic low-grade inflammation, and microvascular dysfunction, causing reduced nitric oxide bioavailability to adjacent cardiomyocytes. As a result, the cardiomyocyte remodels its contractile elements and fails to relax properly, causing diastolic dysfunction, and eventually HFpEF. HFpEF is a complex syndrome for which currently no efficient therapies exist. This is notably due to the current one-size-fits-all therapy approach that ignores individual patient differences. MicroRNAs have been studied in relation to pathophysiological mechanisms and comorbidities underlying and contributing to HFpEF. As regulators of gene expression, microRNAs may contribute to the pathophysiology of HFpEF. In addition, secreted circulating microRNAs are potential biomarkers and as such, they could help stratify the HFpEF population and open new ways for individualized therapies. In this review, we provide an overview of the ever-expanding world of non-coding RNAs and their contribution to the molecular mechanisms underlying HFpEF. We propose prospects for microRNAs in stratifying the HFpEF population. MicroRNAs add a new level of complexity to the regulatory network controlling cardiac function and hence the understanding of gene regulation becomes a fundamental piece in solving the HFpEF puzzle.

  5. 75 FR 41894 - Wapakoneta Machine Company, Currently Known as EF Industrial Technologies, Inc., Wapakoneta, OH...

    Science.gov (United States)

    2010-07-19

    ... of early 2010, Wapakoneta Machine Company is currently known as EF Industrial Technologies, Inc. Some... Wapakoneta Machine Company, currently known as EF Industrial Technologies, Inc., Wapakoneta, Ohio became... DEPARTMENT OF LABOR Employment and Training Administration [TA-W-73,211] Wapakoneta Machine...

  6. Mapping the human translation elongation factor eEF1H complex using the yeast two-hybrid system

    DEFF Research Database (Denmark)

    Mansilla, Francisco; Friis, Irene; Jadidi, Mandana

    2002-01-01

    In eukaryotes, the eukaryotic translation elongation factor eEF1A responsible for transporting amino-acylated tRNA to the ribosome forms a higher-order complex, eEF1H, with its guanine-nucleotide-exchange factor eEF1B. In metazoans, eEF1B consists of three subunits: eEF1B alpha, eEF1B eta and eEF1B...... of in vitro experiments have been proposed for the macromolecular organization of the eEF1H complex. However, these models differ in various aspects. This might be due to the difficulties of handling, particularly the eEF1B beta and eEF1B gamma subunits in vitro. Here, the human eEF1H complex is for the first...... gamma:eEF1B beta, where the last was observed using a three-hybrid approach. Surprisingly, eEF1A2 showed no or only little affinity for the guanine-nucleotide-exchange factors. Truncated versions of the subunits of eEF1B were used to orientate these subunits within the resulting model. The model unit...

  7. Annotating RNA motifs in sequences and alignments.

    Science.gov (United States)

    Gardner, Paul P; Eldai, Hisham

    2015-01-01

    RNA performs a diverse array of important functions across all cellular life. These functions include important roles in translation, building translational machinery and maturing messenger RNA. More recent discoveries include the miRNAs and bacterial sRNAs that regulate gene expression, the thermosensors, riboswitches and other cis-regulatory elements that help prokaryotes sense their environment and eukaryotic piRNAs that suppress transposition. However, there can be a long period between the initial discovery of a RNA and determining its function. We present a bioinformatic approach to characterize RNA motifs, which are critical components of many RNA structure-function relationships. These motifs can, in some instances, provide researchers with functional hypotheses for uncharacterized RNAs. Moreover, we introduce a new profile-based database of RNA motifs--RMfam--and illustrate some applications for investigating the evolution and functional characterization of RNA. All the data and scripts associated with this work are available from: https://github.com/ppgardne/RMfam. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. Dynamic motifs in socio-economic networks

    Science.gov (United States)

    Zhang, Xin; Shao, Shuai; Stanley, H. Eugene; Havlin, Shlomo

    2014-12-01

    Socio-economic networks are of central importance in economic life. We develop a method of identifying and studying motifs in socio-economic networks by focusing on “dynamic motifs,” i.e., evolutionary connection patterns that, because of “node acquaintances” in the network, occur much more frequently than random patterns. We examine two evolving bi-partite networks: i) the world-wide commercial ship chartering market and ii) the ship build-to-order market. We find similar dynamic motifs in both bipartite networks, even though they describe different economic activities. We also find that “influence” and “persistence” are strong factors in the interaction behavior of organizations. When two companies are doing business with the same customer, it is highly probable that another customer who currently only has business relationship with one of these two companies, will become customer of the second in the future. This is the effect of influence. Persistence means that companies with close business ties to customers tend to maintain their relationships over a long period of time.

  9. Complex distribution of EFL and EF-1α proteins in the green algal lineage

    Directory of Open Access Journals (Sweden)

    Keeling Patrick J

    2007-05-01

    Full Text Available Abstract Background EFL (or elongation factor-like is a member of the translation superfamily of GTPase proteins. It is restricted to eukaryotes, where it is found in a punctate distribution that is almost mutually exclusive with elongation factor-1 alpha (EF-1α. EF-1α is a core translation factor previously thought to be essential in eukaryotes, so its relationship to EFL has prompted the suggestion that EFL has spread by horizontal or lateral gene transfer (HGT or LGT and replaced EF-1α multiple times. Among green algae, trebouxiophyceans and chlorophyceans have EFL, but the ulvophycean Acetabularia and the sister group to green algae, land plants, have EF-1α. This distribution singles out green algae as a particularly promising group to understand the origin of EFL and the effects of its presence on EF-1α. Results We have sampled all major lineages of green algae for both EFL and EF-1α. EFL is unexpectedly broad in its distribution, being found in all green algal lineages (chlorophyceans, trebouxiophyceans, ulvophyceans, prasinophyceans, and mesostigmatophyceans, except charophyceans and the genus Acetabularia. The presence of EFL in the genus Mesostigma and EF-1α in Acetabularia are of particular interest, since the opposite is true of all their closest relatives. The phylogeny of EFL is poorly resolved, but the Acetabularia EF-1α is clearly related to homologues from land plants and charophyceans, demonstrating that EF-1α was present in the common ancestor of the green lineage. Conclusion The distribution of EFL and EF-1α in the green lineage is not consistent with the phylogeny of the organisms, indicating a complex history of both genes. Overall, we suggest that after the introduction of EFL (in the ancestor of green algae or earlier, both genes co-existed in green algal genomes for some time before one or the other was lost on multiple occasions.

  10. Large-scale discovery of promoter motifs in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Thomas A Down

    2007-01-01

    Full Text Available A key step in understanding gene regulation is to identify the repertoire of transcription factor binding motifs (TFBMs that form the building blocks of promoters and other regulatory elements. Identifying these experimentally is very laborious, and the number of TFBMs discovered remains relatively small, especially when compared with the hundreds of transcription factor genes predicted in metazoan genomes. We have used a recently developed statistical motif discovery approach, NestedMICA, to detect candidate TFBMs from a large set of Drosophila melanogaster promoter regions. Of the 120 motifs inferred in our initial analysis, 25 were statistically significant matches to previously reported motifs, while 87 appeared to be novel. Analysis of sequence conservation and motif positioning suggested that the great majority of these discovered motifs are predictive of functional elements in the genome. Many motifs showed associations with specific patterns of gene expression in the D. melanogaster embryo, and we were able to obtain confident annotation of expression patterns for 25 of our motifs, including eight of the novel motifs. The motifs are available through Tiffin, a new database of DNA sequence motifs. We have discovered many new motifs that are overrepresented in D. melanogaster promoter regions, and offer several independent lines of evidence that these are novel TFBMs. Our motif dictionary provides a solid foundation for further investigation of regulatory elements in Drosophila, and demonstrates techniques that should be applicable in other species. We suggest that further improvements in computational motif discovery should narrow the gap between the set of known motifs and the total number of transcription factors in metazoan genomes.

  11. In vivo and in vitro suppression of hepatocellular carcinoma by EF24, a curcumin analog.

    Directory of Open Access Journals (Sweden)

    Haitao Liu

    Full Text Available The synthetic compound 3,5-bis(2-flurobenzylidenepiperidin-4-one (EF24 is a potent analog of curcumin that exhibits enhanced biological activity and bioavailability without increasing toxicity. EF24 exerts antitumor activity by arresting the cell cycle and inducing apoptosis, suppressing many types of cancer cells in vitro. The antiproliferative and antiangiogenic properties of EF24 provide theoretical support for its development and application to liver cancers. We investigated the in vitro and in vivo activities of EF24 on liver cancer to better understand its therapeutic effects and mechanisms. EF24 induced significant apoptosis and G2/M-phase cell cycle arrest in mouse liver cancer cell lines, Hepa1-6 and H22. The expression levels of G2/M cell cycle regulating factors, cyclin B1 and Cdc2, were significantly decreased, pp53, p53, and p21 were significantly increased in EF24-treated cells. In addition, EF24 treatment significantly reduced Bcl-2 concomitant with an increase in Bax, enhanced the release of cytochrome c from the mitochondria into the cytosol, resulting in an upregulation of cleaved-caspase-3, which promoted poly (ADP-ribose polymerase cleavage. EF24-treated cells also displayed decreases in phosphorylated Akt, phosphorylated extracellular signal-regulated kinase and vascular endothelial growth factor. Our in vitro protein expression data were confirmed in vivo using a subcutaneous hepatocellular carcinoma (HCC tumor model. This mouse HCC model confirmed that total body weight was unchanged following EF24 treatment, although tumor weight was significantly decreased. Using an orthotopic HCC model, EF24 significantly reduced the liver/body weight ratio and relative tumor areas compared to the control group. In situ detection of apoptotic cells and quantification of Ki-67, a biomarker of cell proliferation, all indicated significant tumor suppression with EF24 treatment. These results suggest that EF24 exhibits anti-tumor activity

  12. Hand Surgery: Anesthesia

    Science.gov (United States)

    ... All Topics A-Z Videos Infographics Symptom Picker Anatomy Bones Joints Muscles Nerves Vessels Tendons About Hand Surgery What is a Hand Surgeon? What is a Hand Therapist? Media Find a Hand Surgeon Home Anatomy Hand Surgery Anesthesia Email to a friend * required ...

  13. CONTEMPORARY USAGE OF TRADITIONAL TURKISH MOTIFS IN PRODUCT DESIGNS

    Directory of Open Access Journals (Sweden)

    Tulay Gumuser

    2012-12-01

    Full Text Available The aim of this study is to identify the traditional Turkish motifs and its relations among present industrial designs. Traditional Turkish motifs played a very important role in 16th century onwards. The arts of the Ottoman Empire were used because of their symbolic meanings and unique styles. When we examine these motifs we encounter; Tiger Stripe, Three Spot (Çintemani, Rumi, Hatayi, Penç, Cloud, Crescent, Star, Crown, Hyacinth, Tulip and Carnation motifs. Nowadays, Turkish designers have begun to use these traditional Turkish motifs in their designs so as to create differences and awareness in the world design. The examples of these industrial designs, using the Turkish motifs, have survived and have Ottoman heritage and historical value. In this study, the Turkish motifs will be examined along with their focus on contemporary Turkish industrial designs used today.

  14. Aplikasi Ornamen Khas Maluku untuk Pengembangan Desain Motif Batik

    Directory of Open Access Journals (Sweden)

    Masiswo Masiswo

    2016-04-01

    Full Text Available ABSTRAKMaluku memiliki banyak ragam hias budaya warisan nilai leluhur berupa ornamen etnis yang merupakan kesenian dan keterampilan kerajinan. Hasil warisan tersebut sampai saat ini masih lestari hidup serta dapat dinikmati sebagai konsumsi rohani yang memuaskan manusia. Berkaitan dengan keberlangsungan nilai-nilai tradisi etnis yang berwujud pada ornamen-ornamen daerah Maluku, maka dikembangkan untuk kebutuhan manusia berupa motif batik pada kain. Pengembangan ornamen ini lebih menekankan pada representasi akan bentuk-bentuk ornamen yang diterapkan pada kerajinan batik berupa motif khas Maluku. Pengembangan alternatif desain motif batik dibuat tiga variasi yang bersumber dari ornamen khas Maluku dibuat prototipe produknya dan diuji ketahanan luntur warnanya. Hasil uji ketahanan luntur warna terhadap gosokan basah dari tiga prototipe produk berpredikat baik sekali terdapat pada “Motif Siwa” dan predikat baik pada motif “Siwa Talang” dan motif “Matahari Siwa Talang”.Kata kunci: desain, Maluku, motif batik, ornamenABSTRACTMaluku has much decorative ancestral cultural heritage value in the form of ornament ethnic arts and crafts skills. The result of the legacy is still sustainable living can be enjoyed as well as satisfying spiritual human consumption.Related to the sustainability of traditional values in the form of ethnic ornaments Maluku, it was developed for human needs in the form of batik cloth . The development of these ornaments will be more emphasis on the representation forms of ornamentation that is applied to a batik motif Maluku. Development of alternative design motif made three variations. The development of three alternative design motifs derived from the Maluku ornaments made and tested a prototype product color fastness. The test results of color fastness to wet rubbing of the three prototypes are excellent products predicated on the "Motif Siwa" and a good rating on the motif "Siwa Talang" and motif "Matahari Siwa

  15. Identity and functions of CxxC-derived motifs.

    Science.gov (United States)

    Fomenko, Dmitri E; Gladyshev, Vadim N

    2003-09-30

    Two cysteines separated by two other residues (the CxxC motif) are employed by many redox proteins for formation, isomerization, and reduction of disulfide bonds and for other redox functions. The place of the C-terminal cysteine in this motif may be occupied by serine (the CxxS motif), modifying the functional repertoire of redox proteins. Here we found that the CxxC motif may also give rise to a motif, in which the C-terminal cysteine is replaced with threonine (the CxxT motif). Moreover, in contrast to a view that the N-terminal cysteine in the CxxC motif always serves as a nucleophilic attacking group, this residue could also be replaced with threonine (the TxxC motif), serine (the SxxC motif), or other residues. In each of these CxxC-derived motifs, the presence of a downstream alpha-helix was strongly favored. A search for conserved CxxC-derived motif/helix patterns in four complete genomes representing bacteria, archaea, and eukaryotes identified known redox proteins and suggested possible redox functions for several additional proteins. Catalytic sites in peroxiredoxins were major representatives of the TxxC motif, whereas those in glutathione peroxidases represented the CxxT motif. Structural assessments indicated that threonines in these enzymes could stabilize catalytic thiolates, suggesting revisions to previously proposed catalytic triads. Each of the CxxC-derived motifs was also observed in natural selenium-containing proteins, in which selenocysteine was present in place of a catalytic cysteine.

  16. Functional role of EF-hands 3 and 4 in membrane-binding of KChIP1

    Indian Academy of Sciences (India)

    Prakash

    type KChIP1, truncated KChIP1 exhibited lower lipid-binding capability. Compared with wild-type KChIP1, increasing membrane permeability by the use of digitonin caused a marked .... with sonication, the supernatant (soluble protein fractions).

  17. Regulation of eukaryotic elongation factor 1 alpha (eEF1A) by dynamic lysine methylation

    DEFF Research Database (Denmark)

    Jakobsson, Magnus E; Małecki, Jędrzej; Falnes, Pål Ø

    2018-01-01

    Lysine methylation is a frequent post-translational protein modification, which has been intensively studied in the case of histone proteins. Lysine methylations are also found on many non-histone proteins, and one prominent example is eukaryotic elongation factor 1 alpha (eEF1A). Besides its...... essential role in the protein synthesis machinery, a number of non-canonical functions have also been described for eEF1A, such as regulation of the actin cytoskeleton and the promotion of viral replication. The functional significance of the extensive lysine methylations on eEF1A, as well as the identity...

  18. Dual-Polarimetric Radar-Based Tornado Debris Paths Associated with EF-4 and EF-5 Tornadoes over Northern Alabama During the Historic Outbreak of 27 April 2011

    Science.gov (United States)

    Carey, Lawrence D.; Schultz, Chrstopher J.; Schultz, Elise V.; Petersen, Walter A.; Gatlin, Patrick N.; Knupp, Kevin R.; Molthan, Andrew L.; Jedlovec, Gary J.; Darden, Christopher B.

    2012-01-01

    An historic tornado and severe weather outbreak devastated much of the southeastern United States between 25 and 28 April 2011. On 27 April 2011, northern Alabama was particularly hard hit by a large number of tornadoes, including several that reached EF-4 and EF-5 on the Enhanced Fujita damage scale. In northern Alabama alone, there were approximately 100 fatalities and hundreds of more people who were injured or lost their homes during the havoc caused by these violent tornadic storms. Two long-track and violent (EF-4 and EF-5) tornadoes occurred within range of the University of Alabama in Huntsville (UAHuntsville) Advanced Radar for Meteorological and Operational Research (ARMOR, C-band dual-polarimetric). A unique capability of dual-polarimetric radar is the near-real time identification of lofted debris associated with ongoing tornadoes on the ground. The focus of this paper is to analyze the dual-polarimetric radar-inferred tornado debris signatures and identify the associated debris paths of the long-track EF-4 and EF-5 tornadoes near ARMOR. The relative locations of the debris and damage paths for each tornado will be ascertained by careful comparison of the ARMOR analysis with NASA MODIS (Moderate Resolution Imaging Spectroradiometer) and ASTER (Advanced Spaceborne Thermal Emission and Reflection Radiometer) satellite imagery of the tornado damage scenes and the National Weather Service tornado damage surveys. With the ongoing upgrade of the WSR-88D (Weather Surveillance Radar 1988 Doppler) operational network to dual-polarimetry and a similar process having already taken place or ongoing for many private sector radars, dual-polarimetric radar signatures of tornado debris promise the potential to assist in the situational awareness of government and private sector forecasters and emergency managers during tornadic events. As such, a companion abstract (Schultz et al.) also submitted to this conference explores The use of dual-polarimetric tornadic debris

  19. UKIRAN KERAWANG ACEH GAYO SEBAGAI INSPIRASI PENCIPTAAN MOTIF BATIK KHAS GAYO

    Directory of Open Access Journals (Sweden)

    Irfa ina Rohana Salma

    2016-12-01

    Full Text Available ABSTRAK Industri batik mulai berkembang di Gayo, tetapi belum memiliki motif batik khas daerah. Oleh karena itu perlu diciptakan motif batik khas Gayo, dengan mengambil inspirasi dari ukiran yang terdapat pada rumah tradisional yang biasa disebut ukiran kerawang Gayo. Tujuan penciptaan seni ini adalah untuk menciptakan motif batik yang memiliki ciri khas Gayo. Metode yang digunakan yaitu eksplorasi ide, perancangan, dan perwujudan menjadi motif batik. Dalam kegiatan ini telah diciptakan enam motif batik khas Gayo yaitu: (1 Motif Ceplok Gayo; (2 Motif Gayo Tegak; (3 Motif Gayo Lurus; (4 Motif Parang Gayo; (5 Motif Gayo Lembut; dan (6 Motif Geometris Gayo. Hasil uji kesukaan terhadap motif kepada lima puluh responden menunjukkan bahwa Motif Ceplok Gayo paling banyak dipilih oleh responden yaitu sebesar 19%, sedangkan Motif Parang Gayo 18%, Motif Gayo Lembut 17%, Motif Geometris Gayo 17%, Motif Gayo Lurus 15% dan Motif Gayo Tegak 14%. Rata-rata motif yang dihasilkan mendapatkan apresiasi yang baik dari responden, sehingga semua motif layak diproduksi sebagai batik khas Gayo.Kata kunci: batik Gayo, Motif Ceplok Gayo, Motif Parang Gayo.ABSTRACTBatik industry began to develop in Gayo, but have not had a typical batik motif itself. Therefore, it is necessary to create batik motifs of Gayo, by taking inspiration from the carvings found in traditional houses commonly called kerawang Gayo. The purpose of this art is to create motifs those have a Gayo characteristic. The method used are the idea exploration, design, and motifs embodiment. In this activity has created six Gayo batik motifs, namely: (1 Motif Ceplok Gayo; (2 Motif Gayo Tegak; (3 Motif GayoLurus; (4 Motif Parang Gayo; (5 Motif Gayo Lembut; dan (6 Motif Geometris Gayo. The test results fondness of the motives to fifty respondents indicated that the Motif Ceplok Gayo most preferred by respondents ie 19%, while Motif Parang Gayo 18%, Motif Gayo Lembut 17%, Motif Geometris Gayo 17%, Motif Gayo

  20. RMOD: a tool for regulatory motif detection in signaling network.

    Directory of Open Access Journals (Sweden)

    Jinki Kim

    Full Text Available Regulatory motifs are patterns of activation and inhibition that appear repeatedly in various signaling networks and that show specific regulatory properties. However, the network structures of regulatory motifs are highly diverse and complex, rendering their identification difficult. Here, we present a RMOD, a web-based system for the identification of regulatory motifs and their properties in signaling networks. RMOD finds various network structures of regulatory motifs by compressing the signaling network and detecting the compressed forms of regulatory motifs. To apply it into a large-scale signaling network, it adopts a new subgraph search algorithm using a novel data structure called path-tree, which is a tree structure composed of isomorphic graphs of query regulatory motifs. This algorithm was evaluated using various sizes of signaling networks generated from the integration of various human signaling pathways and it showed that the speed and scalability of this algorithm outperforms those of other algorithms. RMOD includes interactive analysis and auxiliary tools that make it possible to manipulate the whole processes from building signaling network and query regulatory motifs to analyzing regulatory motifs with graphical illustration and summarized descriptions. As a result, RMOD provides an integrated view of the regulatory motifs and mechanism underlying their regulatory motif activities within the signaling network. RMOD is freely accessible online at the following URL: http://pks.kaist.ac.kr/rmod.

  1. The mazEF toxin-antitoxin system as an attractive target in clinical isolates of Enterococcus faecium and Enterococcus faecalis.

    Science.gov (United States)

    Soheili, Sara; Ghafourian, Sobhan; Sekawi, Zamberi; Neela, Vasantha Kumari; Sadeghifard, Nourkhoda; Taherikalani, Morovat; Khosravi, Afra; Ramli, Ramliza; Hamat, Rukman Awang

    2015-01-01

    The toxin-antitoxin (TA) system is a regulatory system where two sets of genes encode the toxin and its corresponding antitoxin. In this study, the prevalence of TA systems in independently isolated clinical isolates of Enterococcus faecium and Enterococcus faecalis was determined, the dominant TA system was identified, different virulence genes in E. faecium and E. faecalis were surveyed, the level of expression of the virulence and TA genes in normal and stress conditions was determined, and finally their associations with the TA genes were defined. Remarkably, the analysis demonstrated higBA and mazEF in all clinical isolates, and their locations were on chromosomes and plasmids, respectively. On the other hand, a quantitative analysis of TA and virulence genes revealed that the expression level in both genes is different under normal and stress conditions. The results obtained by anti-mazF peptide nucleic acids demonstrated that the expression level of virulence genes had decreased. These findings demonstrate an association between TA systems and virulence factors. The mazEF on the plasmids and the higBA TA genes on the chromosomes of all E. faecium and E. faecalis strains were dominant. Additionally, there was a decrease in the expression of virulence genes in the presence of anti-mazF peptide nucleic acids. Therefore, it is suggested that mazEF TA systems are potent and sensitive targets in all E. faecium and E. faecalis strains.

  2. The mazEF toxin–antitoxin system as an attractive target in clinical isolates of Enterococcus faecium and Enterococcus faecalis

    Science.gov (United States)

    Soheili, Sara; Ghafourian, Sobhan; Sekawi, Zamberi; Neela, Vasantha Kumari; Sadeghifard, Nourkhoda; Taherikalani, Morovat; Khosravi, Afra; Ramli, Ramliza; Hamat, Rukman Awang

    2015-01-01

    The toxin–antitoxin (TA) system is a regulatory system where two sets of genes encode the toxin and its corresponding antitoxin. In this study, the prevalence of TA systems in independently isolated clinical isolates of Enterococcus faecium and Enterococcus faecalis was determined, the dominant TA system was identified, different virulence genes in E. faecium and E. faecalis were surveyed, the level of expression of the virulence and TA genes in normal and stress conditions was determined, and finally their associations with the TA genes were defined. Remarkably, the analysis demonstrated higBA and mazEF in all clinical isolates, and their locations were on chromosomes and plasmids, respectively. On the other hand, a quantitative analysis of TA and virulence genes revealed that the expression level in both genes is different under normal and stress conditions. The results obtained by anti-mazF peptide nucleic acids demonstrated that the expression level of virulence genes had decreased. These findings demonstrate an association between TA systems and virulence factors. The mazEF on the plasmids and the higBA TA genes on the chromosomes of all E. faecium and E. faecalis strains were dominant. Additionally, there was a decrease in the expression of virulence genes in the presence of anti-mazF peptide nucleic acids. Therefore, it is suggested that mazEF TA systems are potent and sensitive targets in all E. faecium and E. faecalis strains. PMID:26005332

  3. Structural motifs of pre-nucleation clusters.

    Science.gov (United States)

    Zhang, Y; Türkmen, I R; Wassermann, B; Erko, A; Rühl, E

    2013-10-07

    Structural motifs of pre-nucleation clusters prepared in single, optically levitated supersaturated aqueous aerosol microparticles containing CaBr2 as a model system are reported. Cluster formation is identified by means of X-ray absorption in the Br K-edge regime. The salt concentration beyond the saturation point is varied by controlling the humidity in the ambient atmosphere surrounding the 15-30 μm microdroplets. This leads to the formation of metastable supersaturated liquid particles. Distinct spectral shifts in near-edge spectra as a function of salt concentration are observed, in which the energy position of the Br K-edge is red-shifted by up to 7.1 ± 0.4 eV if the dilute solution is compared to the solid. The K-edge positions of supersaturated solutions are found between these limits. The changes in electronic structure are rationalized in terms of the formation of pre-nucleation clusters. This assumption is verified by spectral simulations using first-principle density functional theory and molecular dynamics calculations, in which structural motifs are considered, explaining the experimental results. These consist of solvated CaBr2 moieties, rather than building blocks forming calcium bromide hexahydrates, the crystal system that is formed by drying aqueous CaBr2 solutions.

  4. POWRS: position-sensitive motif discovery.

    Directory of Open Access Journals (Sweden)

    Ian W Davis

    Full Text Available Transcription factors and the short, often degenerate DNA sequences they recognize are central regulators of gene expression, but their regulatory code is challenging to dissect experimentally. Thus, computational approaches have long been used to identify putative regulatory elements from the patterns in promoter sequences. Here we present a new algorithm "POWRS" (POsition-sensitive WoRd Set for identifying regulatory sequence motifs, specifically developed to address two common shortcomings of existing algorithms. First, POWRS uses the position-specific enrichment of regulatory elements near transcription start sites to significantly increase sensitivity, while providing new information about the preferred localization of those elements. Second, POWRS forgoes position weight matrices for a discrete motif representation that appears more resistant to over-generalization. We apply this algorithm to discover sequences related to constitutive, high-level gene expression in the model plant Arabidopsis thaliana, and then experimentally validate the importance of those elements by systematically mutating two endogenous promoters and measuring the effect on gene expression levels. This provides a foundation for future efforts to rationally engineer gene expression in plants, a problem of great importance in developing biotech crop varieties.BSD-licensed Python code at http://grassrootsbio.com/papers/powrs/.

  5. Promoter Motifs in NCLDVs: An Evolutionary Perspective

    Science.gov (United States)

    Oliveira, Graziele Pereira; Andrade, Ana Cláudia dos Santos Pereira; Rodrigues, Rodrigo Araújo Lima; Arantes, Thalita Souza; Boratto, Paulo Victor Miranda; Silva, Ludmila Karen dos Santos; Dornas, Fábio Pio; Trindade, Giliane de Souza; Drumond, Betânia Paiva; La Scola, Bernard; Kroon, Erna Geessien; Abrahão, Jônatas Santos

    2017-01-01

    For many years, gene expression in the three cellular domains has been studied in an attempt to discover sequences associated with the regulation of the transcription process. Some specific transcriptional features were described in viruses, although few studies have been devoted to understanding the evolutionary aspects related to the spread of promoter motifs through related viral families. The discovery of giant viruses and the proposition of the new viral order Megavirales that comprise a monophyletic group, named nucleo-cytoplasmic large DNA viruses (NCLDV), raised new questions in the field. Some putative promoter sequences have already been described for some NCLDV members, bringing new insights into the evolutionary history of these complex microorganisms. In this review, we summarize the main aspects of the transcription regulation process in the three domains of life, followed by a systematic description of what is currently known about promoter regions in several NCLDVs. We also discuss how the analysis of the promoter sequences could bring new ideas about the giant viruses’ evolution. Finally, considering a possible common ancestor for the NCLDV group, we discussed possible promoters’ evolutionary scenarios and propose the term “MEGA-box” to designate an ancestor promoter motif (‘TATATAAAATTGA’) that could be evolved gradually by nucleotides’ gain and loss and point mutations. PMID:28117683

  6. Promoter Motifs in NCLDVs: An Evolutionary Perspective

    Directory of Open Access Journals (Sweden)

    Graziele Pereira Oliveira

    2017-01-01

    Full Text Available For many years, gene expression in the three cellular domains has been studied in an attempt to discover sequences associated with the regulation of the transcription process. Some specific transcriptional features were described in viruses, although few studies have been devoted to understanding the evolutionary aspects related to the spread of promoter motifs through related viral families. The discovery of giant viruses and the proposition of the new viral order Megavirales that comprise a monophyletic group, named nucleo-cytoplasmic large DNA viruses (NCLDV, raised new questions in the field. Some putative promoter sequences have already been described for some NCLDV members, bringing new insights into the evolutionary history of these complex microorganisms. In this review, we summarize the main aspects of the transcription regulation process in the three domains of life, followed by a systematic description of what is currently known about promoter regions in several NCLDVs. We also discuss how the analysis of the promoter sequences could bring new ideas about the giant viruses’ evolution. Finally, considering a possible common ancestor for the NCLDV group, we discussed possible promoters’ evolutionary scenarios and propose the term “MEGA-box” to designate an ancestor promoter motif (‘TATATAAAATTGA’ that could be evolved gradually by nucleotides’ gain and loss and point mutations.

  7. Bacterial elongation factors EF-Tu, their mutants, chimeric forms, and domains: isolation and purification

    Czech Academy of Sciences Publication Activity Database

    Jonák, Jiří

    2007-01-01

    Roč. 849, 1-2 (2007), s. 141-153 ISSN 1570-0232 R&D Projects: GA AV ČR IAA5052206; GA AV ČR KJB500520503; GA MŠk 2B06065 Institutional research plan: CEZ:AV0Z50520514 Keywords : bacterial elongation factors EF-Tu, , G-domain * recombinant EF-Tus * preparation Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.935, year: 2007

  8. Osteoarthritis of the Hand

    Science.gov (United States)

    ... All Topics A-Z Videos Infographics Symptom Picker Anatomy Bones Joints Muscles Nerves Vessels Tendons About Hand Surgery What is a Hand Surgeon? What is a Hand Therapist? Media Find a Hand Surgeon Home Anatomy Osteoarthritis Email to a friend * required fields From * ...

  9. Hands in Systemic Disease

    Science.gov (United States)

    ... All Topics A-Z Videos Infographics Symptom Picker Anatomy Bones Joints Muscles Nerves Vessels Tendons About Hand Surgery What is ... Hand Therapist? Media Find a Hand Surgeon Home Anatomy ... hands, being composed of many types of tissue, including blood vessels, nerves, skin and skin-related tissues, bones, and muscles/tendons/ligaments, may show changes that reflect a ...

  10. Parole, Sintagmatik, dan Paradigmatik Motif Batik Mega Mendung

    Directory of Open Access Journals (Sweden)

    Rudi - Nababan

    2012-04-01

    Full Text Available ABSTRACT   Discussing traditional batik is related a lot to the organization system of fine arts element ac- companying it, either the pattern of the motif or the technique of the making. In this case, the motif of Mega Mendung Cirebon certainly has patterns and rules which are traditionally different from the other motifs in other areas. Through  semiotics analysis especially with Saussure and Pierce concept, it can be traced that batik with Cirebon motif, in this case Mega Mendung motif, has parole and langue system, as unique fine arts language in batik, and structure of visual syntagmatic and paradigmatic. In the context of batik motif as fine arts language, it is surely related to sign system as symbol and icon.       Keywords: visual semiotic, Cirebon’s batik.

  11. Denmark: HAND in HAND Policy Questionnaire

    DEFF Research Database (Denmark)

    Laursen, Hilmar Dyrborg; Nielsen, Birgitte Lund

    2018-01-01

    Som del af det internationale EU finansierede projekt Hand in Hand, der fokuserer på de såkaldte SEI-kompetencer (Social, Emotional, Intercultural), er dansk policy i relation til elevernes sociale, emotionelle og interkulturelle læring kortlagt i denne rapport. Der refereres bl.a. til "elevernes...

  12. Heat-Killed Enterococcus faecalis EF-2001 Ameliorates Atopic Dermatitis in a Murine Model

    Science.gov (United States)

    Choi, Eun-Ju; Iwasa, Masahiro; Han, Kwon-Il; Kim, Wan-Jae; Tang, Yujiao; Hwang, Young Joung; Chae, Jeong Ryong; Han, Weon Cheol; Shin, Yu-Su; Kim, Eun-Kyung

    2016-01-01

    Recent reports have shown the immunomodulatory effect of heat-killed lactic acid bacteria. Atopic dermatitis (AD) is an allergic skin disease, caused by immune dysregulation among other factors. The aim of this study was to assess the effect of heat-killed Enterococcus faecalis EF-2001 (EF-2001) on AD. We established an in vivo AD model by repeated local exposure of Dermatophagoides farinae extract (DFE; house dust mite extract) and 2,4-dinitrochlorobenzene (DNCB) to the ears of mice. After oral administration of EF-2001 for four weeks, the epidermal and dermal ear thickness, mast cell infiltration, and serum immunoglobulin levels were measured. In addition, the gene expression levels of pathogenic cytokines in the ears, lymph nodes, and splenocytes were assayed. EF-2001 attenuated AD symptoms based on the ear thickness, histopathological analysis, and serum immunoglobulin levels. Moreover, EF-2001 decreased the DFE/DNCB-induced expression of various pathogenic cytokines in the ears, lymph nodes, and splenocytes. These results suggest that EF-2001 has therapeutic potential in the treatment of AD owing to its immunomodulatory effects. PMID:26959058

  13. Heat-Killed Enterococcus faecalis EF-2001 Ameliorates Atopic Dermatitis in a Murine Model

    Directory of Open Access Journals (Sweden)

    Eun-Ju Choi

    2016-03-01

    Full Text Available Recent reports have shown the immunomodulatory effect of heat-killed lactic acid bacteria. Atopic dermatitis (AD is an allergic skin disease, caused by immune dysregulation among other factors. The aim of this study was to assess the effect of heat-killed Enterococcus faecalis EF-2001 (EF-2001 on AD. We established an in vivo AD model by repeated local exposure of Dermatophagoides farinae extract (DFE; house dust mite extract and 2,4-dinitrochlorobenzene (DNCB to the ears of mice. After oral administration of EF-2001 for four weeks, the epidermal and dermal ear thickness, mast cell infiltration, and serum immunoglobulin levels were measured. In addition, the gene expression levels of pathogenic cytokines in the ears, lymph nodes, and splenocytes were assayed. EF-2001 attenuated AD symptoms based on the ear thickness, histopathological analysis, and serum immunoglobulin levels. Moreover, EF-2001 decreased the DFE/DNCB-induced expression of various pathogenic cytokines in the ears, lymph nodes, and splenocytes. These results suggest that EF-2001 has therapeutic potential in the treatment of AD owing to its immunomodulatory effects.

  14. Labeled EF-Tus for rapid kinetic studies of pretranslocation complex formation

    DEFF Research Database (Denmark)

    Liu, Wei; Kavaliauskas, Darius; Schrader, Jared

    2014-01-01

    The universally conserved translation elongation factor EF-Tu delivers aminoacyl(aa)-tRNA in the form of an aa-tRNA·EF-Tu·GTP ternary complex (TC) to the ribosome where it binds to the cognate mRNA codon within the ribosomal A-site, leading to formation of a pretranslocation (PRE) complex. Here we...... describe preparation of QSY9 and Cy5 derivatives of the variant E348C-EF-Tu that are functional in translation elongation. Together with fluorophore derivatives of aa-tRNA and of ribosomal protein L11, located within the GTPase associated center (GAC), these labeled EF-Tus allow development of two new FRET...... assays that permit the dynamics of distance changes between EF-Tu and both L11 (Tu-L11 assay) and aa-tRNA (Tu-tRNA assay) to be determined during the decoding process. We use these assays to examine: (i) the relative rates of EF-Tu movement away from the GAC and from aa-tRNA during decoding, (ii...

  15. Contribution of effluent organic matter (EfOM) to ultrafiltration (UF) membrane fouling: Isolation, characterization, and fouling effect of EfOM fractions

    KAUST Repository

    Zheng, Xing

    2014-11-01

    EfOM has been regarded as a major organic foulant resulting in UF membrane fouling in wastewater reclamation. To investigate fouling potential of different EfOM fractions, the present study isolated EfOM into hydrophobic neutrals (HPO-N), colloids, hydrophobic acids (HPO-A), transphilic neutrals and acids (TPI), and hydrophilics (HPI), and tested their fouling effect in both salt solution and pure water during ultrafiltration (UF). Major functional groups and chemical structure of the isolates were identified using Fourier transform infrared spectroscopy (FT-IR) and solid-state carbon nuclear magnetic resonance (13C NMR) analysis. The influence of the isolation process on the properties of EfOM fractions was minor because the raw and reconstituted secondary effluents were found similar with respect to UV absorbance, molecular size distribution, and fluorescence character. In membrane filtration tests, unified membrane fouling index (UMFI) and hydraulic resistance were used to quantify irreversible fouling potential of different water samples. Results show that under similar DOC level in feed water, colloids present much more irreversible fouling than other fractions. The fouling effect of the isolates is related to their size, chemical properties, and solution chemistry. Further investigations have identified that the interaction between colloids and other fractions also influences the performance of colloids in fouling phenomena. © 2014 Elsevier Ltd.

  16. Motif-role-fingerprints: the building-blocks of motifs, clustering-coefficients and transitivities in directed networks.

    Directory of Open Access Journals (Sweden)

    Mark D McDonnell

    Full Text Available Complex networks are frequently characterized by metrics for which particular subgraphs are counted. One statistic from this category, which we refer to as motif-role fingerprints, differs from global subgraph counts in that the number of subgraphs in which each node participates is counted. As with global subgraph counts, it can be important to distinguish between motif-role fingerprints that are 'structural' (induced subgraphs and 'functional' (partial subgraphs. Here we show mathematically that a vector of all functional motif-role fingerprints can readily be obtained from an arbitrary directed adjacency matrix, and then converted to structural motif-role fingerprints by multiplying that vector by a specific invertible conversion matrix. This result demonstrates that a unique structural motif-role fingerprint exists for any given functional motif-role fingerprint. We demonstrate a similar result for the cases of functional and structural motif-fingerprints without node roles, and global subgraph counts that form the basis of standard motif analysis. We also explicitly highlight that motif-role fingerprints are elemental to several popular metrics for quantifying the subgraph structure of directed complex networks, including motif distributions, directed clustering coefficient, and transitivity. The relationships between each of these metrics and motif-role fingerprints also suggest new subtypes of directed clustering coefficients and transitivities. Our results have potential utility in analyzing directed synaptic networks constructed from neuronal connectome data, such as in terms of centrality. Other potential applications include anomaly detection in networks, identification of similar networks and identification of similar nodes within networks. Matlab code for calculating all stated metrics following calculation of functional motif-role fingerprints is provided as S1 Matlab File.

  17. Executive function (EF) in dyslexia: examining an EF profile associated with dyslexia and comorbid dyslexia-ADHD and exploring the near and far transfer effects of EF training in dyslexia alone.

    OpenAIRE

    Doyle, Caoilainn

    2017-01-01

    Although there are several competing theories to explain dyslexia, no clear causal pathway has been established. Current theories also fail to address associated socio-emotional difficulties and high co-occurrence of dyslexia with ADHD. Executive function (EF), an umbrella term for a triad of high-level cognitive processes associated with pre-frontal brain regions – response inhibition (RI), working memory updating and switching, is a candidate factor for explaining the overlap between dyslex...

  18. Rekayasa Pengembangan Desain Motif Batik Khas Melayu

    Directory of Open Access Journals (Sweden)

    Eustasia Sri Murwati

    2016-04-01

    Full Text Available ABSTRAKPengembangan desain batik melalui rancang bangun perekayasaan desain menurut ragam hias Melayu meliputi pengembangan motif dan proses, termasuk pemilihan komposisi warna. Proses yang sering dilakukan yaitu proses celup, penghilangan lilin dan celup warna tumpangan atau proses colet, celup, penghilangan lilin atau celup kemudian penghilangan lilin yang disebut Batik Kelengan. Setiap pulau di Indonesia mempunyai ciri khas budaya dan kesenian yang dikenal dengan corak/ragam hias khas daerah, juga ornamen yang diminati oleh masyarakat dari daerah tersebut atau dari daerah lain. Kondisi demikian mendorong pertumbuhan industri kerajinan yang memanfaatkan unsur–unsur seni. Adapun motif yang diperoleh adalah: Ayam Berlaga, Bungo Matahari, Kuntum Bersanding, Lancang Kuning, Encong Kerinci, Durian Pecah, Bungo Bintang, Bungo Pauh Kecil, Riang-riang, Bungo Nagaro. Pengembangan desain tersebut dipilih 3 produk terbaik yang dinilai oleh 5 penilai yang ahli di bidang desain batik, yaitu motif Durian Pecah, Ayam Berlaga, dan Bungo Matahari. Rancang bangun diversifikasi desain dengan memanfaatkan unsur–unsur seni dan ketrampilan etnis Melayu yaitu pemilihan ragam hias dan motif batik Melayu untuk diterapkan ke bahan sandang dengan komposisi warna yang menarik, sehingga produk memenuhi selera konsumen. Memperbaiki keberagaman batik dengan meningkatkan desain produk antara lain menuangkan ragam hias Melayu ke dalam proses batik yang menggunakan berbagai macam warna sehingga komposisi warna memadai. Diperoleh hasil produk batik dengan ragam hias Melayu yang berkualitas dan komposisi warna yang sesuai dengan karakter ragam hias Melayu. Rancang bangun desain produk untuk mendapatkan formulasi desain serta kelayakan prosesnya dengan penekanan pada teknologi akrab lingkungan dilaksanakan dengan alternatif pendekatan yaitu penciptaan desain bentuk baru.Kata kunci: desain, batik, rancang bangun, ragam hias, MelayuABSTRACTDevelopment of batik design through

  19. Transnationalism as a motif in family stories.

    Science.gov (United States)

    Stone, Elizabeth; Gomez, Erica; Hotzoglou, Despina; Lipnitsky, Jane Y

    2005-12-01

    Family stories have long been recognized as a vehicle for assessing components of a family's emotional and social life, including the degree to which an immigrant family has been willing to assimilate. Transnationalism, defined as living in one or more cultures and maintaining connections to both, is now increasingly common. A qualitative study of family stories in the family of those who appear completely "American" suggests that an affiliation with one's home country is nevertheless detectable in the stories via motifs such as (1) positively connotated home remedies, (2) continuing denigration of home country "enemies," (3) extensive knowledge of the home country history and politics, (4) praise of endogamy and negative assessment of exogamy, (5) superiority of home country to America, and (6) beauty of home country. Furthermore, an awareness of which model--assimilationist or transnational--governs a family's experience may help clarify a clinician's understanding of a family's strengths, vulnerabilities, and mode of framing their cultural experiences.

  20. Motif decomposition of the phosphotyrosine proteome reveals a new N-terminal binding motif for SHIP2

    DEFF Research Database (Denmark)

    Miller, Martin Lee; Hanke, S.; Hinsby, A. M.

    2008-01-01

    set of 481 unique phosphotyrosine (Tyr(P)) peptides by sequence similarity to known ligands of the Src homology 2 (SH2) and the phosphotyrosine binding (PTB) domains. From 20 clusters we extracted 16 known and four new interaction motifs. Using quantitative mass spectrometry we pulled down Tyr......(P)-specific binding partners for peptides corresponding to the extracted motifs. We confirmed numerous previously known interaction motifs and found 15 new interactions mediated by phosphosites not previously known to bind SH2 or PTB. Remarkably, a novel hydrophobic N-terminal motif ((L/V/I)(L/V/I)pY) was identified...

  1. The limits of de novo DNA motif discovery.

    Directory of Open Access Journals (Sweden)

    David Simcha

    Full Text Available A major challenge in molecular biology is reverse-engineering the cis-regulatory logic that plays a major role in the control of gene expression. This program includes searching through DNA sequences to identify "motifs" that serve as the binding sites for transcription factors or, more generally, are predictive of gene expression across cellular conditions. Several approaches have been proposed for de novo motif discovery-searching sequences without prior knowledge of binding sites or nucleotide patterns. However, unbiased validation is not straightforward. We consider two approaches to unbiased validation of discovered motifs: testing the statistical significance of a motif using a DNA "background" sequence model to represent the null hypothesis and measuring performance in predicting membership in gene clusters. We demonstrate that the background models typically used are "too null," resulting in overly optimistic assessments of significance, and argue that performance in predicting TF binding or expression patterns from DNA motifs should be assessed by held-out data, as in predictive learning. Applying this criterion to common motif discovery methods resulted in universally poor performance, although there is a marked improvement when motifs are statistically significant against real background sequences. Moreover, on synthetic data where "ground truth" is known, discriminative performance of all algorithms is far below the theoretical upper bound, with pronounced "over-fitting" in training. A key conclusion from this work is that the failure of de novo discovery approaches to accurately identify motifs is basically due to statistical intractability resulting from the fixed size of co-regulated gene clusters, and thus such failures do not necessarily provide evidence that unfound motifs are not active biologically. Consequently, the use of prior knowledge to enhance motif discovery is not just advantageous but necessary. An implementation of

  2. DNA motif alignment by evolving a population of Markov chains.

    Science.gov (United States)

    Bi, Chengpeng

    2009-01-30

    Deciphering cis-regulatory elements or de novo motif-finding in genomes still remains elusive although much algorithmic effort has been expended. The Markov chain Monte Carlo (MCMC) method such as Gibbs motif samplers has been widely employed to solve the de novo motif-finding problem through sequence local alignment. Nonetheless, the MCMC-based motif samplers still suffer from local maxima like EM. Therefore, as a prerequisite for finding good local alignments, these motif algorithms are often independently run a multitude of times, but without information exchange between different chains. Hence it would be worth a new algorithm design enabling such information exchange. This paper presents a novel motif-finding algorithm by evolving a population of Markov chains with information exchange (PMC), each of which is initialized as a random alignment and run by the Metropolis-Hastings sampler (MHS). It is progressively updated through a series of local alignments stochastically sampled. Explicitly, the PMC motif algorithm performs stochastic sampling as specified by a population-based proposal distribution rather than individual ones, and adaptively evolves the population as a whole towards a global maximum. The alignment information exchange is accomplished by taking advantage of the pooled motif site distributions. A distinct method for running multiple independent Markov chains (IMC) without information exchange, or dubbed as the IMC motif algorithm, is also devised to compare with its PMC counterpart. Experimental studies demonstrate that the performance could be improved if pooled information were used to run a population of motif samplers. The new PMC algorithm was able to improve the convergence and outperformed other popular algorithms tested using simulated and biological motif sequences.

  3. Robotic hand project

    OpenAIRE

    Karaçizmeli, Cengiz; Çakır, Gökçe; Tükel, Dilek

    2014-01-01

    In this work, the mechatronic based robotic hand is controlled by the position data taken from the glove which has flex sensors mounted to capture finger bending of the human hand. The angular movement of human hand’s fingers are perceived and processed by a microcontroller, and the robotic hand is controlled by actuating servo motors. It has seen that robotic hand can simulate the movement of the human hand that put on the glove, during tests have done. This robotic hand can be used not only...

  4. TH-EF-BRC-04: Quality Management Program

    International Nuclear Information System (INIS)

    Yorke, E.

    2016-01-01

    This Hands-on Workshop will be focused on providing participants with experience with the principal tools of TG 100 and hence start to build both competence and confidence in the use of risk-based quality management techniques. The three principal tools forming the basis of TG 100’s risk analysis: Process mapping, Failure-Modes and Effects Analysis and fault-tree analysis will be introduced with a 5 minute refresher presentation and each presentation will be followed by a 30 minute small group exercise. An exercise on developing QM from the risk analysis follows. During the exercise periods, participants will apply the principles in 2 different clinical scenarios. At the conclusion of each exercise there will be ample time for participants to discuss with each other and the faculty their experience and any challenges encountered. Learning Objectives: To review the principles of Process Mapping, Failure Modes and Effects Analysis and Fault Tree Analysis. To gain familiarity with these three techniques in a small group setting. To share and discuss experiences with the three techniques with faculty and participants. Director, TreatSafely, LLC. Director, Center for the Assessment of Radiological Sciences. Occasional Consultant to the IAEA and Varian.

  5. TH-EF-BRC-03: Fault Tree Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Thomadsen, B. [University of Wisconsin (United States)

    2016-06-15

    This Hands-on Workshop will be focused on providing participants with experience with the principal tools of TG 100 and hence start to build both competence and confidence in the use of risk-based quality management techniques. The three principal tools forming the basis of TG 100’s risk analysis: Process mapping, Failure-Modes and Effects Analysis and fault-tree analysis will be introduced with a 5 minute refresher presentation and each presentation will be followed by a 30 minute small group exercise. An exercise on developing QM from the risk analysis follows. During the exercise periods, participants will apply the principles in 2 different clinical scenarios. At the conclusion of each exercise there will be ample time for participants to discuss with each other and the faculty their experience and any challenges encountered. Learning Objectives: To review the principles of Process Mapping, Failure Modes and Effects Analysis and Fault Tree Analysis. To gain familiarity with these three techniques in a small group setting. To share and discuss experiences with the three techniques with faculty and participants. Director, TreatSafely, LLC. Director, Center for the Assessment of Radiological Sciences. Occasional Consultant to the IAEA and Varian.

  6. TH-EF-BRC-04: Quality Management Program

    Energy Technology Data Exchange (ETDEWEB)

    Yorke, E. [Memorial Sloan-Kettering Cancer Center (United States)

    2016-06-15

    This Hands-on Workshop will be focused on providing participants with experience with the principal tools of TG 100 and hence start to build both competence and confidence in the use of risk-based quality management techniques. The three principal tools forming the basis of TG 100’s risk analysis: Process mapping, Failure-Modes and Effects Analysis and fault-tree analysis will be introduced with a 5 minute refresher presentation and each presentation will be followed by a 30 minute small group exercise. An exercise on developing QM from the risk analysis follows. During the exercise periods, participants will apply the principles in 2 different clinical scenarios. At the conclusion of each exercise there will be ample time for participants to discuss with each other and the faculty their experience and any challenges encountered. Learning Objectives: To review the principles of Process Mapping, Failure Modes and Effects Analysis and Fault Tree Analysis. To gain familiarity with these three techniques in a small group setting. To share and discuss experiences with the three techniques with faculty and participants. Director, TreatSafely, LLC. Director, Center for the Assessment of Radiological Sciences. Occasional Consultant to the IAEA and Varian.

  7. TH-EF-BRC-00: TG-100 Workshop

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2016-06-15

    This Hands-on Workshop will be focused on providing participants with experience with the principal tools of TG 100 and hence start to build both competence and confidence in the use of risk-based quality management techniques. The three principal tools forming the basis of TG 100’s risk analysis: Process mapping, Failure-Modes and Effects Analysis and fault-tree analysis will be introduced with a 5 minute refresher presentation and each presentation will be followed by a 30 minute small group exercise. An exercise on developing QM from the risk analysis follows. During the exercise periods, participants will apply the principles in 2 different clinical scenarios. At the conclusion of each exercise there will be ample time for participants to discuss with each other and the faculty their experience and any challenges encountered. Learning Objectives: To review the principles of Process Mapping, Failure Modes and Effects Analysis and Fault Tree Analysis. To gain familiarity with these three techniques in a small group setting. To share and discuss experiences with the three techniques with faculty and participants. Director, TreatSafely, LLC. Director, Center for the Assessment of Radiological Sciences. Occasional Consultant to the IAEA and Varian.

  8. TH-EF-BRC-00: TG-100 Workshop

    International Nuclear Information System (INIS)

    2016-01-01

    This Hands-on Workshop will be focused on providing participants with experience with the principal tools of TG 100 and hence start to build both competence and confidence in the use of risk-based quality management techniques. The three principal tools forming the basis of TG 100’s risk analysis: Process mapping, Failure-Modes and Effects Analysis and fault-tree analysis will be introduced with a 5 minute refresher presentation and each presentation will be followed by a 30 minute small group exercise. An exercise on developing QM from the risk analysis follows. During the exercise periods, participants will apply the principles in 2 different clinical scenarios. At the conclusion of each exercise there will be ample time for participants to discuss with each other and the faculty their experience and any challenges encountered. Learning Objectives: To review the principles of Process Mapping, Failure Modes and Effects Analysis and Fault Tree Analysis. To gain familiarity with these three techniques in a small group setting. To share and discuss experiences with the three techniques with faculty and participants. Director, TreatSafely, LLC. Director, Center for the Assessment of Radiological Sciences. Occasional Consultant to the IAEA and Varian.

  9. TH-EF-BRC-03: Fault Tree Analysis

    International Nuclear Information System (INIS)

    Thomadsen, B.

    2016-01-01

    This Hands-on Workshop will be focused on providing participants with experience with the principal tools of TG 100 and hence start to build both competence and confidence in the use of risk-based quality management techniques. The three principal tools forming the basis of TG 100’s risk analysis: Process mapping, Failure-Modes and Effects Analysis and fault-tree analysis will be introduced with a 5 minute refresher presentation and each presentation will be followed by a 30 minute small group exercise. An exercise on developing QM from the risk analysis follows. During the exercise periods, participants will apply the principles in 2 different clinical scenarios. At the conclusion of each exercise there will be ample time for participants to discuss with each other and the faculty their experience and any challenges encountered. Learning Objectives: To review the principles of Process Mapping, Failure Modes and Effects Analysis and Fault Tree Analysis. To gain familiarity with these three techniques in a small group setting. To share and discuss experiences with the three techniques with faculty and participants. Director, TreatSafely, LLC. Director, Center for the Assessment of Radiological Sciences. Occasional Consultant to the IAEA and Varian.

  10. Assessing local structure motifs using order parameters for motif recognition, interstitial identification, and diffusion path characterization

    Science.gov (United States)

    Zimmermann, Nils E. R.; Horton, Matthew K.; Jain, Anubhav; Haranczyk, Maciej

    2017-11-01

    Structure-property relationships form the basis of many design rules in materials science, including synthesizability and long-term stability of catalysts, control of electrical and optoelectronic behavior in semiconductors as well as the capacity of and transport properties in cathode materials for rechargeable batteries. The immediate atomic environments (i.e., the first coordination shells) of a few atomic sites are often a key factor in achieving a desired property. Some of the most frequently encountered coordination patterns are tetrahedra, octahedra, body and face-centered cubic as well as hexagonal closed packed-like environments. Here, we showcase the usefulness of local order parameters to identify these basic structural motifs in inorganic solid materials by developing classification criteria. We introduce a systematic testing framework, the Einstein crystal test rig, that probes the response of order parameters to distortions in perfect motifs to validate our approach. Subsequently, we highlight three important application cases. First, we map basic crystal structure information of a large materials database in an intuitive manner by screening the Materials Project (MP) database (61,422 compounds) for element-specific motif distributions. Second, we use the structure-motif recognition capabilities to automatically find interstitials in metals, semiconductor, and insulator materials. Our Interstitialcy Finding Tool (InFiT) facilitates high-throughput screenings of defect properties. Third, the order parameters are reliable and compact quantitative structure descriptors for characterizing diffusion hops of intercalants as our example of magnesium in MnO2-spinel indicates. Finally, the tools developed in our work are readily and freely available as software implementations in the pymatgen library, and we expect them to be further applied to machine-learning approaches for emerging applications in materials science.

  11. Assessing Local Structure Motifs Using Order Parameters for Motif Recognition, Interstitial Identification, and Diffusion Path Characterization

    Directory of Open Access Journals (Sweden)

    Nils E. R. Zimmermann

    2017-11-01

    Full Text Available Structure–property relationships form the basis of many design rules in materials science, including synthesizability and long-term stability of catalysts, control of electrical and optoelectronic behavior in semiconductors, as well as the capacity of and transport properties in cathode materials for rechargeable batteries. The immediate atomic environments (i.e., the first coordination shells of a few atomic sites are often a key factor in achieving a desired property. Some of the most frequently encountered coordination patterns are tetrahedra, octahedra, body and face-centered cubic as well as hexagonal close packed-like environments. Here, we showcase the usefulness of local order parameters to identify these basic structural motifs in inorganic solid materials by developing classification criteria. We introduce a systematic testing framework, the Einstein crystal test rig, that probes the response of order parameters to distortions in perfect motifs to validate our approach. Subsequently, we highlight three important application cases. First, we map basic crystal structure information of a large materials database in an intuitive manner by screening the Materials Project (MP database (61,422 compounds for element-specific motif distributions. Second, we use the structure-motif recognition capabilities to automatically find interstitials in metals, semiconductor, and insulator materials. Our Interstitialcy Finding Tool (InFiT facilitates high-throughput screenings of defect properties. Third, the order parameters are reliable and compact quantitative structure descriptors for characterizing diffusion hops of intercalants as our example of magnesium in MnO2-spinel indicates. Finally, the tools developed in our work are readily and freely available as software implementations in the pymatgen library, and we expect them to be further applied to machine-learning approaches for emerging applications in materials science.

  12. Clean Hands Count

    Medline Plus

    Full Text Available ... to promote or encourage adherence to CDC hand hygiene recommendations. It is a component of the Clean ... aims to address myths and misperceptions about hand hygiene and empower patients to play a role in ...

  13. Clean Hands Count

    Medline Plus

    Full Text Available ... intended to promote or encourage adherence to CDC hand hygiene recommendations. It is a component of the Clean ... also aims to address myths and misperceptions about hand hygiene and empower patients to play a role in ...

  14. Clean Hands Count

    Science.gov (United States)

    ... intended to promote or encourage adherence to CDC hand hygiene recommendations. It is a component of the Clean ... also aims to address myths and misperceptions about hand hygiene and empower patients to play a role in ...

  15. Wash Your Hands

    Science.gov (United States)

    ... hand sanitizers might not remove harmful chemicals like pesticides and heavy metals from hands. Be cautious when ... Health Promotion Materials Fact Sheets Podcasts Posters Stickers Videos Web Features Training & Education Our Partners Publications, Data & ...

  16. Probing structural changes of self assembled i-motif DNA

    KAUST Repository

    Lee, Iljoon; Patil, Sachin; Fhayli, Karim; Alsaiari, Shahad K.; Khashab, Niveen M.

    2015-01-01

    We report an i-motif structural probing system based on Thioflavin T (ThT) as a fluorescent sensor. This probe can discriminate the structural changes of RET and Rb i-motif sequences according to pH change. This journal is

  17. The identification of functional motifs in temporal gene expression analysis

    Directory of Open Access Journals (Sweden)

    Michael G. Surette

    2005-01-01

    Full Text Available The identification of transcription factor binding sites is essential to the understanding of the regulation of gene expression and the reconstruction of genetic regulatory networks. The in silico identification of cis-regulatory motifs is challenging due to sequence variability and lack of sufficient data to generate consensus motifs that are of quantitative or even qualitative predictive value. To determine functional motifs in gene expression, we propose a strategy to adopt false discovery rate (FDR and estimate motif effects to evaluate combinatorial analysis of motif candidates and temporal gene expression data. The method decreases the number of predicted motifs, which can then be confirmed by genetic analysis. To assess the method we used simulated motif/expression data to evaluate parameters. We applied this approach to experimental data for a group of iron responsive genes in Salmonella typhimurium 14028S. The method identified known and potentially new ferric-uptake regulator (Fur binding sites. In addition, we identified uncharacterized functional motif candidates that correlated with specific patterns of expression. A SAS code for the simulation and analysis gene expression data is available from the first author upon request.

  18. RNA recognition motif (RRM)-containing proteins in Bombyx mori

    African Journals Online (AJOL)

    STORAGESEVER

    2009-03-20

    Mar 20, 2009 ... Recognition Motif (RRM), sometimes referred to as. RNP1, is one of the first identified domains for RNA interaction. RRM is very common ..... Apart from the RRM motif, eIF3-S9 has a Trp-Asp. (WD) repeat domain, Poly (A) ...

  19. BlockLogo: Visualization of peptide and sequence motif conservation

    DEFF Research Database (Denmark)

    Olsen, Lars Rønn; Kudahl, Ulrich Johan; Simon, Christian

    2013-01-01

    BlockLogo is a web-server application for the visualization of protein and nucleotide fragments, continuous protein sequence motifs, and discontinuous sequence motifs using calculation of block entropy from multiple sequence alignments. The user input consists of a multiple sequence alignment, se...

  20. Fingerprint motifs of phytases | Fan | African Journal of Biotechnology

    African Journals Online (AJOL)

    Among the total of potential 173 phytases gained in 11 plant genomes through MAST, PAPhys are the major phytases, and HAPhys are the minor, and other phytase groups are not found in planta. Keywords: Phytase, fingerprint motif, multiple EM for motif elicitation (MEME), MAST African Journal of Biotechnology Vol.

  1. Hand hygiene strategies

    OpenAIRE

    Yazaji, Eskandar Alex

    2011-01-01

    Hand hygiene is one of the major players in preventing healthcare associated infections. However, healthcare workers compliance with hand hygiene continues to be a challenge. This article will address strategies to help improving hand hygiene compliance. Keywords: hand hygiene; healthcare associated infections; multidisciplinary program; system change; accountability; education; feedback(Published: 18 July 2011)Citation: Journal of Community Hospital Internal Medicine Perspectives 2011, 1: 72...

  2. Identification of sequence motifs significantly associated with antisense activity

    Directory of Open Access Journals (Sweden)

    Peek Andrew S

    2007-06-01

    Full Text Available Abstract Background Predicting the suppression activity of antisense oligonucleotide sequences is the main goal of the rational design of nucleic acids. To create an effective predictive model, it is important to know what properties of an oligonucleotide sequence associate significantly with antisense activity. Also, for the model to be efficient we must know what properties do not associate significantly and can be omitted from the model. This paper will discuss the results of a randomization procedure to find motifs that associate significantly with either high or low antisense suppression activity, analysis of their properties, as well as the results of support vector machine modelling using these significant motifs as features. Results We discovered 155 motifs that associate significantly with high antisense suppression activity and 202 motifs that associate significantly with low suppression activity. The motifs range in length from 2 to 5 bases, contain several motifs that have been previously discovered as associating highly with antisense activity, and have thermodynamic properties consistent with previous work associating thermodynamic properties of sequences with their antisense activity. Statistical analysis revealed no correlation between a motif's position within an antisense sequence and that sequences antisense activity. Also, many significant motifs existed as subwords of other significant motifs. Support vector regression experiments indicated that the feature set of significant motifs increased correlation compared to all possible motifs as well as several subsets of the significant motifs. Conclusion The thermodynamic properties of the significantly associated motifs support existing data correlating the thermodynamic properties of the antisense oligonucleotide with antisense efficiency, reinforcing our hypothesis that antisense suppression is strongly associated with probe/target thermodynamics, as there are no enzymatic

  3. About Hand Surgery

    Science.gov (United States)

    ... Find a hand surgeon near you. © 2009 American Society for Surgery of the Hand. Definition developed by ASSH Council. Other Links CME Mission Statement and Disclaimer Policies and Technical Requirements Exhibits and Partners ASSH 822 W. Washington Blvd. ... 2018 by American Society for Surgery of the Hand × Search Tips Tip ...

  4. Guideline Implementation: Hand Hygiene.

    Science.gov (United States)

    Goldberg, Judith L

    2017-02-01

    Performing proper hand hygiene and surgical hand antisepsis is essential to reducing the rates of health care-associated infections, including surgical site infections. The updated AORN "Guideline for hand hygiene" provides guidance on hand hygiene and surgical hand antisepsis, the wearing of fingernail polish and artificial nails, proper skin care to prevent dermatitis, the wearing of jewelry, hand hygiene product selection, and quality assurance and performance improvement considerations. This article focuses on key points of the guideline to help perioperative personnel make informed decisions about hand hygiene and surgical hand antisepsis. The key points address the necessity of keeping fingernails and skin healthy, not wearing jewelry on the hands or wrists in the perioperative area, properly performing hand hygiene and surgical hand antisepsis, and involving patients and visitors in hand hygiene initiatives. Perioperative RNs should review the complete guideline for additional information and for guidance when writing and updating policies and procedures. Copyright © 2017 AORN, Inc. Published by Elsevier Inc. All rights reserved.

  5. Robotic hand and fingers

    Science.gov (United States)

    Salisbury, Curt Michael; Dullea, Kevin J.

    2017-06-06

    Technologies pertaining to a robotic hand are described herein. The robotic hand includes one or more fingers releasably attached to a robotic hand frame. The fingers can abduct and adduct as well as flex and tense. The fingers are releasably attached to the frame by magnets that allow for the fingers to detach from the frame when excess force is applied to the fingers.

  6. eEF-2 Phosphorylation Down-Regulates P-Glycoprotein Over-Expression in Rat Brain Microvessel Endothelial Cells.

    Directory of Open Access Journals (Sweden)

    Xing Hua Tang

    Full Text Available We investigated whether glutamate, NMDA receptors, and eukaryote elongation factor-2 kinase (eEF-2K/eEF-2 regulate P-glycoprotein expression, and the effects of the eEF-2K inhibitor NH125 on the expression of P-glycoprotein in rat brain microvessel endothelial cells (RBMECs.Cortex was obtained from newborn Wistar rat brains. After surface vessels and meninges were removed, the pellet containing microvessels was resuspended and incubated at 37°C in culture medium. Cell viability was assessed by the MTT assay. RBMECs were identified by immunohistochemistry with anti-vWF. P-glycoprotein, phospho-eEF-2, and eEF-2 expression were determined by western blot analysis. Mdr1a gene expression was analyzed by RT-PCR.Mdr1a mRNA, P-glycoprotein and phospho-eEF-2 expression increased in L-glutamate stimulated RBMECs. P-glycoprotein and phospho-eEF-2 expression were down-regulated after NH125 treatment in L-glutamate stimulated RBMECs.eEF-2K/eEF-2 should have played an important role in the regulation of P-glycoprotein expression in RBMECs. eEF-2K inhibitor NH125 could serve as an efficacious anti-multidrug resistant agent.

  7. Automatic annotation of protein motif function with Gene Ontology terms

    Directory of Open Access Journals (Sweden)

    Gopalakrishnan Vanathi

    2004-09-01

    Full Text Available Abstract Background Conserved protein sequence motifs are short stretches of amino acid sequence patterns that potentially encode the function of proteins. Several sequence pattern searching algorithms and programs exist foridentifying candidate protein motifs at the whole genome level. However, amuch needed and importanttask is to determine the functions of the newly identified protein motifs. The Gene Ontology (GO project is an endeavor to annotate the function of genes or protein sequences with terms from a dynamic, controlled vocabulary and these annotations serve well as a knowledge base. Results This paperpresents methods to mine the GO knowledge base and use the association between the GO terms assigned to a sequence and the motifs matched by the same sequence as evidence for predicting the functions of novel protein motifs automatically. The task of assigning GO terms to protein motifsis viewed as both a binary classification and information retrieval problem, where PROSITE motifs are used as samples for mode training and functional prediction. The mutual information of a motif and aGO term association isfound to be a very useful feature. We take advantageof the known motifs to train a logistic regression classifier, which allows us to combine mutual information with other frequency-based features and obtain a probability of correctassociation. The trained logistic regression model has intuitively meaningful and logically plausible parameter values, and performs very well empirically according to our evaluation criteria. Conclusions In this research, different methods for automatic annotation of protein motifs have been investigated. Empirical result demonstrated that the methods have a great potential for detecting and augmenting information about thefunctions of newly discovered candidate protein motifs.

  8. Effects of Exergame Play on EF in Children and Adolescents at a Summer Camp for Low Income Youth.

    Science.gov (United States)

    Flynn, Rachel M; Richert, Rebekah A; Staiano, Amanda E; Wartella, Ellen; Calvert, Sandra L

    2014-01-01

    Past research has suggested exergame play improves adolescents' executive function (EF) skills. EF change in 70 African American and Hispanic/Latino 10- to 16-year-olds participating in an inner-city summer camp was assessed following five 30-minute exergame play sessions. Children's EF scores improved from pre- to posttest, and factors related to this change were examined. The number of exergame sessions the participants attended predicted posttest scores. In addition, level of achievement during game play was related to EF scores. Finally, the children's level of enjoyment was not related to EF; however, frustration and boredom during game play were negatively related to EF. The findings are discussed in terms of their implications for the relationship between exergame play and cognitive benefits for adolescent players.

  9. Motif statistics and spike correlations in neuronal networks

    International Nuclear Information System (INIS)

    Hu, Yu; Shea-Brown, Eric; Trousdale, James; Josić, Krešimir

    2013-01-01

    Motifs are patterns of subgraphs of complex networks. We studied the impact of such patterns of connectivity on the level of correlated, or synchronized, spiking activity among pairs of cells in a recurrent network of integrate and fire neurons. For a range of network architectures, we find that the pairwise correlation coefficients, averaged across the network, can be closely approximated using only three statistics of network connectivity. These are the overall network connection probability and the frequencies of two second order motifs: diverging motifs, in which one cell provides input to two others, and chain motifs, in which two cells are connected via a third intermediary cell. Specifically, the prevalence of diverging and chain motifs tends to increase correlation. Our method is based on linear response theory, which enables us to express spiking statistics using linear algebra, and a resumming technique, which extrapolates from second order motifs to predict the overall effect of coupling on network correlation. Our motif-based results seek to isolate the effect of network architecture perturbatively from a known network state. (paper)

  10. Computational analyses of synergism in small molecular network motifs.

    Directory of Open Access Journals (Sweden)

    Yili Zhang

    2014-03-01

    Full Text Available Cellular functions and responses to stimuli are controlled by complex regulatory networks that comprise a large diversity of molecular components and their interactions. However, achieving an intuitive understanding of the dynamical properties and responses to stimuli of these networks is hampered by their large scale and complexity. To address this issue, analyses of regulatory networks often focus on reduced models that depict distinct, reoccurring connectivity patterns referred to as motifs. Previous modeling studies have begun to characterize the dynamics of small motifs, and to describe ways in which variations in parameters affect their responses to stimuli. The present study investigates how variations in pairs of parameters affect responses in a series of ten common network motifs, identifying concurrent variations that act synergistically (or antagonistically to alter the responses of the motifs to stimuli. Synergism (or antagonism was quantified using degrees of nonlinear blending and additive synergism. Simulations identified concurrent variations that maximized synergism, and examined the ways in which it was affected by stimulus protocols and the architecture of a motif. Only a subset of architectures exhibited synergism following paired changes in parameters. The approach was then applied to a model describing interlocked feedback loops governing the synthesis of the CREB1 and CREB2 transcription factors. The effects of motifs on synergism for this biologically realistic model were consistent with those for the abstract models of single motifs. These results have implications for the rational design of combination drug therapies with the potential for synergistic interactions.

  11. Triadic motifs in the dependence networks of virtual societies

    Science.gov (United States)

    Xie, Wen-Jie; Li, Ming-Xia; Jiang, Zhi-Qiang; Zhou, Wei-Xing

    2014-06-01

    In friendship networks, individuals have different numbers of friends, and the closeness or intimacy between an individual and her friends is heterogeneous. Using a statistical filtering method to identify relationships about who depends on whom, we construct dependence networks (which are directed) from weighted friendship networks of avatars in more than two hundred virtual societies of a massively multiplayer online role-playing game (MMORPG). We investigate the evolution of triadic motifs in dependence networks. Several metrics show that the virtual societies evolved through a transient stage in the first two to three weeks and reached a relatively stable stage. We find that the unidirectional loop motif (M9) is underrepresented and does not appear, open motifs are also underrepresented, while other close motifs are overrepresented. We also find that, for most motifs, the overall level difference of the three avatars in the same motif is significantly lower than average, whereas the sum of ranks is only slightly larger than average. Our findings show that avatars' social status plays an important role in the formation of triadic motifs.

  12. RNA motif search with data-driven element ordering.

    Science.gov (United States)

    Rampášek, Ladislav; Jimenez, Randi M; Lupták, Andrej; Vinař, Tomáš; Brejová, Broňa

    2016-05-18

    In this paper, we study the problem of RNA motif search in long genomic sequences. This approach uses a combination of sequence and structure constraints to uncover new distant homologs of known functional RNAs. The problem is NP-hard and is traditionally solved by backtracking algorithms. We have designed a new algorithm for RNA motif search and implemented a new motif search tool RNArobo. The tool enhances the RNAbob descriptor language, allowing insertions in helices, which enables better characterization of ribozymes and aptamers. A typical RNA motif consists of multiple elements and the running time of the algorithm is highly dependent on their ordering. By approaching the element ordering problem in a principled way, we demonstrate more than 100-fold speedup of the search for complex motifs compared to previously published tools. We have developed a new method for RNA motif search that allows for a significant speedup of the search of complex motifs that include pseudoknots. Such speed improvements are crucial at a time when the rate of DNA sequencing outpaces growth in computing. RNArobo is available at http://compbio.fmph.uniba.sk/rnarobo .

  13. Triadic motifs in the dependence networks of virtual societies.

    Science.gov (United States)

    Xie, Wen-Jie; Li, Ming-Xia; Jiang, Zhi-Qiang; Zhou, Wei-Xing

    2014-06-10

    In friendship networks, individuals have different numbers of friends, and the closeness or intimacy between an individual and her friends is heterogeneous. Using a statistical filtering method to identify relationships about who depends on whom, we construct dependence networks (which are directed) from weighted friendship networks of avatars in more than two hundred virtual societies of a massively multiplayer online role-playing game (MMORPG). We investigate the evolution of triadic motifs in dependence networks. Several metrics show that the virtual societies evolved through a transient stage in the first two to three weeks and reached a relatively stable stage. We find that the unidirectional loop motif (M9) is underrepresented and does not appear, open motifs are also underrepresented, while other close motifs are overrepresented. We also find that, for most motifs, the overall level difference of the three avatars in the same motif is significantly lower than average, whereas the sum of ranks is only slightly larger than average. Our findings show that avatars' social status plays an important role in the formation of triadic motifs.

  14. A speedup technique for (l, d-motif finding algorithms

    Directory of Open Access Journals (Sweden)

    Dinh Hieu

    2011-03-01

    Full Text Available Abstract Background The discovery of patterns in DNA, RNA, and protein sequences has led to the solution of many vital biological problems. For instance, the identification of patterns in nucleic acid sequences has resulted in the determination of open reading frames, identification of promoter elements of genes, identification of intron/exon splicing sites, identification of SH RNAs, location of RNA degradation signals, identification of alternative splicing sites, etc. In protein sequences, patterns have proven to be extremely helpful in domain identification, location of protease cleavage sites, identification of signal peptides, protein interactions, determination of protein degradation elements, identification of protein trafficking elements, etc. Motifs are important patterns that are helpful in finding transcriptional regulatory elements, transcription factor binding sites, functional genomics, drug design, etc. As a result, numerous papers have been written to solve the motif search problem. Results Three versions of the motif search problem have been proposed in the literature: Simple Motif Search (SMS, (l, d-motif search (or Planted Motif Search (PMS, and Edit-distance-based Motif Search (EMS. In this paper we focus on PMS. Two kinds of algorithms can be found in the literature for solving the PMS problem: exact and approximate. An exact algorithm identifies the motifs always and an approximate algorithm may fail to identify some or all of the motifs. The exact version of PMS problem has been shown to be NP-hard. Exact algorithms proposed in the literature for PMS take time that is exponential in some of the underlying parameters. In this paper we propose a generic technique that can be used to speedup PMS algorithms. Conclusions We present a speedup technique that can be used on any PMS algorithm. We have tested our speedup technique on a number of algorithms. These experimental results show that our speedup technique is indeed very

  15. The Effect of dcEFs on migration behavior of A549 cells and Integrin beta1 expression

    Directory of Open Access Journals (Sweden)

    Yunjie WANG

    2008-04-01

    Full Text Available Background and objective The effect of direct-current electric fields (dcEFs on cells attracted extensive attention. Moreover the metastasis and its potential are considered to be related to dcEFs. The aim is to study the effect of dcEFs on migration behavior of A549 cells, Integrin ?1 and its signal pathways. Methods According to exposure to 5 V/cm dcEFs or not and the time of exposure, the A549 cells were divided into 4 groups. Images were taken per 5 min within 2 h to recode the migration of the cells. The data of results were analyzed statistically. Results Most of A549cells exposed to the dcEFs aligned and elongated perpendicularly to the electric field lines and migrated to the cathode continually during 2 h. On the contrary, cells unexposed to dcEFs showed slightly random movements. Immunofluorescence showed that Integrin ?1 on plasma membrane polarized to the cathode of the dcEFs. Western blot showed that Integrin beta1 downstream signal pathways p-FAK and p-ERK were overexpressed in the dcEFs. Conclusion A549 cells have a galvanotatic feature of cathodal directed migration while exposed to the dcEFs. The polarization of Integrin beta1 and the promotion of its downstream signal pathways may play an important roles in the galvanotaxis of A549 cells.

  16. Influence of activated carbon preloading by EfOM fractions from treated wastewater on adsorption of pharmaceutically active compounds.

    Science.gov (United States)

    Hu, Jingyi; Shang, Ran; Heijman, Bas; Rietveld, Luuk

    2016-05-01

    In this study, the preloading effects of different fractions of wastewater effluent organic matter (EfOM) on the adsorption of trace-level pharmaceutically active compounds (PhACs) onto granular activated carbon (GAC) were investigated. A nanofiltration (NF) membrane was employed to separate the EfOM by size, and two GACs with distinct pore structures were chosen for comparison. The results showed that preloading with EfOM substantially decreased PhAC uptake of the GACs; however, comparable PhAC adsorption capacities were achieved on GACs preloaded by feed EfOM and the NF-permeating EfOM. This indicates that: (1) the NF-rejected, larger EfOM molecules with an expectation to block the PhAC adsorption pores exerted little impact on the adsorbability of PhACs; (2) the smaller EfOM molecules present in the NF permeate contributed mainly to the decrease in PhAC uptake, mostly due to site competition. Of the two examined GACs, the wide pore-size-distributed GAC was found to be more susceptible to EfOM preloading than the microporous GAC. Furthermore, among the fourteen investigated PhACs, the negatively charged hydrophilic PhACs were generally subjected to a greater EfOM preloading impact. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. The Avocado Hand

    LENUS (Irish Health Repository)

    Rahmani, G

    2017-11-01

    Accidental self-inflicted knife injuries to digits are a common cause of tendon and nerve injury requiring hand surgery. There has been an apparent increase in avocado related hand injuries. Classically, the patients hold the avocado in their non-dominant hand while using a knife to cut\\/peel the fruit with their dominant hand. The mechanism of injury is usually a stabbing injury to the non-dominant hand as the knife slips past the stone, through the soft avocado fruit. Despite their apparent increased incidence, we could not find any cases in the literature which describe the “avocado hand”. We present a case of a 32-year-old woman who sustained a significant hand injury while preparing an avocado. She required exploration and repair of a digital nerve under regional anaesthesia and has since made a full recovery.

  18. Hand eczema classification

    DEFF Research Database (Denmark)

    Diepgen, T L; Andersen, Klaus Ejner; Brandao, F M

    2008-01-01

    of the disease is rarely evidence based, and a classification system for different subdiagnoses of hand eczema is not agreed upon. Randomized controlled trials investigating the treatment of hand eczema are called for. For this, as well as for clinical purposes, a generally accepted classification system...... A classification system for hand eczema is proposed. Conclusions It is suggested that this classification be used in clinical work and in clinical trials....

  19. Coordination of hand shape.

    Science.gov (United States)

    Pesyna, Colin; Pundi, Krishna; Flanders, Martha

    2011-03-09

    The neural control of hand movement involves coordination of the sensory, motor, and memory systems. Recent studies have documented the motor coordinates for hand shape, but less is known about the corresponding patterns of somatosensory activity. To initiate this line of investigation, the present study characterized the sense of hand shape by evaluating the influence of differences in the amount of grasping or twisting force, and differences in forearm orientation. Human subjects were asked to use the left hand to report the perceived shape of the right hand. In the first experiment, six commonly grasped items were arranged on the table in front of the subject: bottle, doorknob, egg, notebook, carton, and pan. With eyes closed, subjects used the right hand to lightly touch, forcefully support, or imagine holding each object, while 15 joint angles were measured in each hand with a pair of wired gloves. The forces introduced by supporting or twisting did not influence the perceptual report of hand shape, but for most objects, the report was distorted in a consistent manner by differences in forearm orientation. Subjects appeared to adjust the intrinsic joint angles of the left hand, as well as the left wrist posture, so as to maintain the imagined object in its proper spatial orientation. In a second experiment, this result was largely replicated with unfamiliar objects. Thus, somatosensory and motor information appear to be coordinated in an object-based, spatial-coordinate system, sensitive to orientation relative to gravitational forces, but invariant to grasp forcefulness.

  20. Targeting functional motifs of a protein family

    Science.gov (United States)

    Bhadola, Pradeep; Deo, Nivedita

    2016-10-01

    The structural organization of a protein family is investigated by devising a method based on the random matrix theory (RMT), which uses the physiochemical properties of the amino acid with multiple sequence alignment. A graphical method to represent protein sequences using physiochemical properties is devised that gives a fast, easy, and informative way of comparing the evolutionary distances between protein sequences. A correlation matrix associated with each property is calculated, where the noise reduction and information filtering is done using RMT involving an ensemble of Wishart matrices. The analysis of the eigenvalue statistics of the correlation matrix for the β -lactamase family shows the universal features as observed in the Gaussian orthogonal ensemble (GOE). The property-based approach captures the short- as well as the long-range correlation (approximately following GOE) between the eigenvalues, whereas the previous approach (treating amino acids as characters) gives the usual short-range correlations, while the long-range correlations are the same as that of an uncorrelated series. The distribution of the eigenvector components for the eigenvalues outside the bulk (RMT bound) deviates significantly from RMT observations and contains important information about the system. The information content of each eigenvector of the correlation matrix is quantified by introducing an entropic estimate, which shows that for the β -lactamase family the smallest eigenvectors (low eigenmodes) are highly localized as well as informative. These small eigenvectors when processed gives clusters involving positions that have well-defined biological and structural importance matching with experiments. The approach is crucial for the recognition of structural motifs as shown in β -lactamase (and other families) and selectively identifies the important positions for targets to deactivate (activate) the enzymatic actions.

  1. ROMANIAN FOLKLORE MOTIFS IN FASHION DESIGN

    Directory of Open Access Journals (Sweden)

    MOCENCO Alexandra

    2014-05-01

    Full Text Available The traditional Romanian costume such as the entire popular art (architecture, woodcarvins, pottery etc. was born and lasted in our country since ancient times. Closely related to human existence, the traditional costume reflected over the years as reflected nowadays, the mentality and artistic conception of the people. Today the traditional Romanian costume became an inspiration source to the wholesale fashion production industry designers, both Romanian and international. Although the contemporary designers are working in accordance with a vision, using a wide area of styles, methods and current technology, they usually return to traditional techniques and ethnic folklore motifs, which converts and resize them, integrating them in their contemporary space. Adrian Oianu is a very appreciated Romanian designer who launched two collections inspired by his native’s country traditional costumes: “Suflecata pan’ la brau” (“Turned up ‘til the belt” and “Bucurie” (“Joy”. Dorin Negrau had as inspiration for his “Lost” collection the traditional costume from the Bihor region. Yves Saint Laurent had a collection inspired by the Romanian traditional flax blouses called “La blouse roumaine”. The paper presents the traditional Romanian values throw fashion collections. The research activity will create innovative concepts to support the garment industry in order to develop their own brand and to bring the design activities in Romania at an international level. The research was conducted during the initial stage of a project, financed through national founds, consisting in a documentary study on ethnographic characteristics of the popular costume from different regions of the country.

  2. Membrane Fouling Potential of Secondary Effluent Organic Matter (EfOM) from Conventional Activated Sludge Process

    KAUST Repository

    Wei, Chunhai; Amy, Gary L.

    2012-01-01

    Secondary effluent organic matter (EfOM) from a conventional activated sludge process was filtered through constant-pressure dead-end filtration tests with a sequential ultrafiltration (UF, molecular weight cut-off (MWCO) of 10k Dalton) and nanofiltration (NF, MWCO of 200 Dalton) array to investigate its membrane fouling potential. Advanced analytical methods including liquid chromatography with online carbon detection (LC-OCD) and fluorescent excitation-emission matrix (F-EEM) were employed for EfOM characterization. EfOM consisted of humic substances and building blocks, low molecular weight (LMW) neutrals, biopolymers (mainly proteins) and hydrophobic organics according to the sequence of their organic carbon fractions. The UF rejected only biopolymers and the NF rejected most humics and building blocks and a significant part of LMW neutrals. Simultaneous occurrence of cake layer and standard blocking during the filtration process of both UF and NF was identified according to constant-pressure filtration equations, which was possibly caused by the heterogeneous nature of EfOM with a wide MW distribution (several ten to several million Dalton). Thus the corresponding two fouling indices (kc for cake layer and ks for standard blocking) from UF and NF could characterize the fouling potential of macromolecular biopolymers and low to intermediate MW organics (including humics, building blocks, LMW neutrals), respectively. Compared with macromolecular biopolymers, low to intermediate MW organics exhibited a much higher fouling potential due to their lower molecular weight and higher concentration.

  3. The Fic protein Doc uses an inverted substrate to phosphorylate and inactivate EF-Tu.

    Science.gov (United States)

    Castro-Roa, Daniel; Garcia-Pino, Abel; De Gieter, Steven; van Nuland, Nico A J; Loris, Remy; Zenkin, Nikolay

    2013-12-01

    Fic proteins are ubiquitous in all of the domains of life and have critical roles in multiple cellular processes through AMPylation of (transfer of AMP to) target proteins. Doc from the doc-phd toxin-antitoxin module is a member of the Fic family and inhibits bacterial translation by an unknown mechanism. Here we show that, in contrast to having AMPylating activity, Doc is a new type of kinase that inhibits bacterial translation by phosphorylating the conserved threonine (Thr382) of the translation elongation factor EF-Tu, rendering EF-Tu unable to bind aminoacylated tRNAs. We provide evidence that EF-Tu phosphorylation diverged from AMPylation by antiparallel binding of the NTP relative to the catalytic residues of the conserved Fic catalytic core of Doc. The results bring insights into the mechanism and role of phosphorylation of EF-Tu in bacterial physiology as well as represent an example of the catalytic plasticity of enzymes and a mechanism for the evolution of new enzymatic activities.

  4. Review article: The mountain motif in the plot of Matthew

    Directory of Open Access Journals (Sweden)

    Gert J. Volschenk

    2010-09-01

    Full Text Available This article reviewed T.L. Donaldson’s book, Jesus on the mountain: A study in Matthean theology, published in 1985 by JSOT Press, Sheffield, and focused on the mountain motif in the structure and plot of the Gospel of Matthew, in addition to the work of Donaldson on the mountain motif as a literary motif and as theological symbol. The mountain is a primary theological setting for Jesus’ ministry and thus is an important setting, serving as one of the literary devices by which Matthew structured and progressed his narrative. The Zion theological and eschatological significance and Second Temple Judaism serve as the historical and theological background for the mountain motif. The last mountain setting (Mt 28:16–20 is the culmination of the three theological themes in the plot of Matthew, namely Christology, ecclesiology and salvation history.

  5. Methods and statistics for combining motif match scores.

    Science.gov (United States)

    Bailey, T L; Gribskov, M

    1998-01-01

    Position-specific scoring matrices are useful for representing and searching for protein sequence motifs. A sequence family can often be described by a group of one or more motifs, and an effective search must combine the scores for matching a sequence to each of the motifs in the group. We describe three methods for combining match scores and estimating the statistical significance of the combined scores and evaluate the search quality (classification accuracy) and the accuracy of the estimate of statistical significance of each. The three methods are: 1) sum of scores, 2) sum of reduced variates, 3) product of score p-values. We show that method 3) is superior to the other two methods in both regards, and that combining motif scores indeed gives better search accuracy. The MAST sequence homology search algorithm utilizing the product of p-values scoring method is available for interactive use and downloading at URL http:/(/)www.sdsc.edu/MEME.

  6. DNA regulatory motif selection based on support vector machine ...

    African Journals Online (AJOL)

    ... machine (SVM) and its application in microarray experiment of Kashin-Beck disease. ... speed and amount of the corresponding mRNA in gene replication process. ... and revealed that some motifs may be related to the immune reactions.

  7. Murine elongation factor 1 alpha (EF-1 alpha) is posttranslationally modified by novel amide-linked ethanolamine-phosphoglycerol moieties. Addition of ethanolamine-phosphoglycerol to specific glutamic acid residues on EF-1 alpha

    International Nuclear Information System (INIS)

    Whiteheart, S.W.; Shenbagamurthi, P.; Chen, L.; Cotter, R.J.; Hart, G.W.

    1989-01-01

    Elongation Factor 1 alpha (EF-1 alpha), an important eukaryotic translation factor, transports charged aminoacyl-tRNA from the cytosol to the ribosomes during poly-peptide synthesis. Metabolic radiolabeling with [ 3 H] ethanolamine shows that, in all cells examined, EF-1 alpha is the major radiolabeled protein. Radiolabeled EF-1 alpha has an apparent Mr = 53,000 and a basic isoelectric point. It is cytosolic and does not contain N-linked oligosaccharides. Trypsin digestion of murine EF-1 alpha generated two major [ 3 H]ethanolamine-labeled peptides. Three peptides were sequenced and were identical to two distinct regions of the human EF-1 alpha protein. Blank sequencing cycles coinciding with glutamic acid in the human cDNA-derived sequence were also found to release [ 3 H]ethanolamine, and compositional analysis of these peptides confirmed the presence of glutamic acid. Dansylation analysis demonstrates that the amine group of the ethanolamine is blocked. These results indicate that EF-1 alpha is posttranslationally modified by the covalent attachment of ethanolamine via an amide bond to at least two specific glutamic acid residues (Glu-301 and Glu-374). The hydroxyl group of the attached ethanolamine was shown by mass spectrometry and compositional analysis, to be further modified by the addition of a phosphoglycerol unit. This novel posttranslational modification may represent an important alteration of EF-1 alpha, comparable to the regulatory effects of posttranslational methylation of EF-1 alpha lysine residues

  8. Clean Hands Count

    Medline Plus

    Full Text Available ... 585 views 3:10 Wash 'Em - Hand Hygiene Music Video - Duration: 5:46. Jefferson Health 413,097 ... 089,212 views 4:50 Hand hygiene FULL music video - Duration: 2:33. AlfredHealthTV 26,032 views ...

  9. Mind the hand

    DEFF Research Database (Denmark)

    Davidsen, Jacob; Christiansen, Ellen Tove

    2014-01-01

    Apart from touching the screen, what is the role of the hands for children collaborating around touchscreens? Based on embodied and multimodal interaction analysis of 8- and 9-year old pairs collaborating around touchscreens, we conclude that children use their hands to constrain and control acce...

  10. Clean Hands Count

    Medline Plus

    Full Text Available ... 024 views 2:58 Wash 'Em - Hand Hygiene Music Video - Duration: 5:46. Jefferson Health 412,404 ... 2,805 views 3:13 Hand hygiene FULL music video - Duration: 2:33. AlfredHealthTV 25,574 views ...

  11. HAND INJURIES IN VOLLEYBALL

    NARCIS (Netherlands)

    BHAIRO, NH; NIJSTEN, MWN; VANDALEN, KC; TENDUIS, HJ

    We studied the long-term sequelae of hand injuries as a result of playing volleyball. In a retrospective study, 226 patients with injuries of the hand who were seen over a 5-year period at our Trauma Department, were investigated. Females accounted for 66 % of all injuries. The mean age was 26

  12. Clean Hands Count

    Medline Plus

    Full Text Available ... 585 views 3:10 Wash 'Em - Hand Hygiene Music Video - Duration: 5:46. Jefferson Health 412,760 ... 536,963 views 1:46 Hand hygiene FULL music video - Duration: 2:33. AlfredHealthTV 25,574 views ...

  13. Clean Hands Count

    Medline Plus

    Full Text Available ... today; no cure tomorrow - Duration: 3:10. World Health Organization 74,478 views 3:10 Wash 'Em - Hand Hygiene Music Video - Duration: 5:46. Jefferson Health 411,292 views 5:46 Hand Washing Technique - ...

  14. Clean Hands Count

    Medline Plus

    Full Text Available ... 029 views 3:10 Wash 'Em - Hand Hygiene Music Video - Duration: 5:46. Jefferson Health 412,404 ... 081,511 views 4:50 Hand hygiene FULL music video - Duration: 2:33. AlfredHealthTV 25,194 views ...

  15. Clean Hands Count

    Medline Plus

    Full Text Available ... today; no cure tomorrow - Duration: 3:10. World Health Organization 75,362 views 3:10 Wash 'Em - Hand Hygiene Music Video - Duration: 5:46. Jefferson Health 412,404 views 5:46 Hand Washing Technique - ...

  16. Clean Hands Count

    Medline Plus

    Full Text Available ... 585 views 3:10 Wash 'Em - Hand Hygiene Music Video - Duration: 5:46. Jefferson Health 413,097 ... 086,746 views 4:50 Hand hygiene FULL music video - Duration: 2:33. AlfredHealthTV 25,802 views ...

  17. Clean Hands Count

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    Full Text Available ... 453 views 3:10 Wash 'Em - Hand Hygiene Music Video - Duration: 5:46. Jefferson Health 413,702 ... 28,656 views 3:40 Hand hygiene FULL music video - Duration: 2:33. AlfredHealthTV 26,480 views ...

  18. Clean Hands Count

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    Full Text Available ... 362 views 3:10 Wash 'Em - Hand Hygiene Music Video - Duration: 5:46. Jefferson Health 412,404 ... 219,427 views 1:27 Hand hygiene FULL music video - Duration: 2:33. AlfredHealthTV 25,194 views ...

  19. Clean Hands Count

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    Full Text Available ... 03. R Mayer 371,490 views 4:03 The psychological trick behind getting people to say yes - Duration: 8:06. PBS NewsHour 606,671 views 8:06 Should You Really Wash Your Hands? - Duration: 4:51. Gross Science 57,828 views 4:51 Healthcare Worker Hand ...

  20. Clean Hands Count

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    Full Text Available ... 585 views 3:10 Wash 'Em - Hand Hygiene Music Video - Duration: 5:46. Jefferson Health 413,097 ... 28,656 views 3:40 Hand hygiene FULL music video - Duration: 2:33. AlfredHealthTV 26,032 views ...

  1. Clean Hands Count

    Medline Plus

    Full Text Available ... 5 Moments of Hand Hygiene - Duration: 1:53. Salem Health 13,972 views 1:53 Hand Hygiene ... Mode: Off History Help Loading... Loading... Loading... About Press Copyright Creators Advertise Developers +YouTube Terms Privacy Policy & ...

  2. Role of four conserved aspartic acid residues of EF-loops in the metal ion binding and in the self-assembly of ciliate Euplotes octocarinatus centrin.

    Science.gov (United States)

    Liu, Wen; Duan, Lian; Sun, Tijian; Yang, Binsheng

    2016-12-01

    Ciliate Euplotes octocarinatus centrin (EoCen) is an EF-hand calcium-binding protein closely related to the prototypical calcium sensor protein calmodulin. Four mutants (D37K, D73K, D110K and D146K) were created firstly to elucidate the importance of the first aspartic acid residues (Asp37, Asp73, Asp110 and Asp146) in the beginning of the four EF-loops of EoCen. Aromatic-sensitized Tb 3+ fluorescence indicates that the aspartic acid residues are very important for the metal-binding of EoCen, except for Asp73 (in EF-loop II). Resonance light scattering (RLS) measurements for different metal ions (Ca 2+ and Tb 3+ ) binding proteins suggest that the order of four conserved aspartic acid residues for contributing to the self-assembly of EoCen is Asp37 > Asp146 > Asp110 > Asp73. Cross-linking experiment also exhibits that Asp37 and Asp146 play critical role in the self-assembly of EoCen. Asp37, in site I, which is located in the N-terminal domain, plays the most important role in the metal ion-dependent self-assembly of EoCen, and there is cooperativity between N-terminal and C-terminal domain (especially the site IV). In addition, the dependence of Tb 3+ induced self-assembly of EoCen and the mutants on various factors, including ionic strength and pH, were characterized using RLS. Finally, 2-p-toluidinylnaphthalene-6-sulfonate (TNS) binding, ionic strength and pH control experiments indicate that in the process of EoCen self-assembly, molecular interactions are mediated by both electrostatic and hydrophobic forces, and the hydrophobic interaction has the important status.

  3. "Puffy hand syndrome".

    Science.gov (United States)

    Chouk, Mickaël; Vidon, Claire; Deveza, Elise; Verhoeven, Frank; Pelletier, Fabien; Prati, Clément; Wendling, Daniel

    2017-01-01

    Intravenous drug addiction is responsible for many complications, especially cutaneous and infectious. There is a syndrome, rarely observed in rheumatology, resulting in "puffy hands": the puffy hand syndrome. We report two cases of this condition from our rheumatologic consultation. Our two patients had intravenous drug addiction. They presented with an edema of the hands, bilateral, painless, no pitting, occurring in one of our patient during heroin intoxication, and in the other 2 years after stopping injections. In our two patients, additional investigations (biological, radiological, ultrasound) were unremarkable, which helped us, in the context, to put the diagnosis of puffy hand syndrome. The pathophysiology, still unclear, is based in part on a lymphatic toxicity of drugs and their excipients. There is no etiological treatment but elastic compression by night has improved edema of the hands in one of our patients. Copyright © 2016 Société française de rhumatologie. Published by Elsevier SAS. All rights reserved.

  4. BEAM web server: a tool for structural RNA motif discovery.

    Science.gov (United States)

    Pietrosanto, Marco; Adinolfi, Marta; Casula, Riccardo; Ausiello, Gabriele; Ferrè, Fabrizio; Helmer-Citterich, Manuela

    2018-03-15

    RNA structural motif finding is a relevant problem that becomes computationally hard when working on high-throughput data (e.g. eCLIP, PAR-CLIP), often represented by thousands of RNA molecules. Currently, the BEAM server is the only web tool capable to handle tens of thousands of RNA in input with a motif discovery procedure that is only limited by the current secondary structure prediction accuracies. The recently developed method BEAM (BEAr Motifs finder) can analyze tens of thousands of RNA molecules and identify RNA secondary structure motifs associated to a measure of their statistical significance. BEAM is extremely fast thanks to the BEAR encoding that transforms each RNA secondary structure in a string of characters. BEAM also exploits the evolutionary knowledge contained in a substitution matrix of secondary structure elements, extracted from the RFAM database of families of homologous RNAs. The BEAM web server has been designed to streamline data pre-processing by automatically handling folding and encoding of RNA sequences, giving users a choice for the preferred folding program. The server provides an intuitive and informative results page with the list of secondary structure motifs identified, the logo of each motif, its significance, graphic representation and information about its position in the RNA molecules sharing it. The web server is freely available at http://beam.uniroma2.it/ and it is implemented in NodeJS and Python with all major browsers supported. marco.pietrosanto@uniroma2.it. Supplementary data are available at Bioinformatics online.

  5. Characterizing Motif Dynamics of Electric Brain Activity Using Symbolic Analysis

    Directory of Open Access Journals (Sweden)

    Massimiliano Zanin

    2014-10-01

    Full Text Available Motifs are small recurring circuits of interactions which constitute the backbone of networked systems. Characterizing motif dynamics is therefore key to understanding the functioning of such systems. Here we propose a method to define and quantify the temporal variability and time scales of electroencephalogram (EEG motifs of resting brain activity. Given a triplet of EEG sensors, links between them are calculated by means of linear correlation; each pattern of links (i.e., each motif is then associated to a symbol, and its appearance frequency is analyzed by means of Shannon entropy. Our results show that each motif becomes observable with different coupling thresholds and evolves at its own time scale, with fronto-temporal sensors emerging at high thresholds and changing at fast time scales, and parietal ones at low thresholds and changing at slower rates. Finally, while motif dynamics differed across individuals, for each subject, it showed robustness across experimental conditions, indicating that it could represent an individual dynamical signature.

  6. Efficient motif finding algorithms for large-alphabet inputs

    Directory of Open Access Journals (Sweden)

    Pavlovic Vladimir

    2010-10-01

    Full Text Available Abstract Background We consider the problem of identifying motifs, recurring or conserved patterns, in the biological sequence data sets. To solve this task, we present a new deterministic algorithm for finding patterns that are embedded as exact or inexact instances in all or most of the input strings. Results The proposed algorithm (1 improves search efficiency compared to existing algorithms, and (2 scales well with the size of alphabet. On a synthetic planted DNA motif finding problem our algorithm is over 10× more efficient than MITRA, PMSPrune, and RISOTTO for long motifs. Improvements are orders of magnitude higher in the same setting with large alphabets. On benchmark TF-binding site problems (FNP, CRP, LexA we observed reduction in running time of over 12×, with high detection accuracy. The algorithm was also successful in rapidly identifying protein motifs in Lipocalin, Zinc metallopeptidase, and supersecondary structure motifs for Cadherin and Immunoglobin families. Conclusions Our algorithm reduces computational complexity of the current motif finding algorithms and demonstrate strong running time improvements over existing exact algorithms, especially in important and difficult cases of large-alphabet sequences.

  7. Discovering Motifs in Biological Sequences Using the Micron Automata Processor.

    Science.gov (United States)

    Roy, Indranil; Aluru, Srinivas

    2016-01-01

    Finding approximately conserved sequences, called motifs, across multiple DNA or protein sequences is an important problem in computational biology. In this paper, we consider the (l, d) motif search problem of identifying one or more motifs of length l present in at least q of the n given sequences, with each occurrence differing from the motif in at most d substitutions. The problem is known to be NP-complete, and the largest solved instance reported to date is (26,11). We propose a novel algorithm for the (l,d) motif search problem using streaming execution over a large set of non-deterministic finite automata (NFA). This solution is designed to take advantage of the micron automata processor, a new technology close to deployment that can simultaneously execute multiple NFA in parallel. We demonstrate the capability for solving much larger instances of the (l, d) motif search problem using the resources available within a single automata processor board, by estimating run-times for problem instances (39,18) and (40,17). The paper serves as a useful guide to solving problems using this new accelerator technology.

  8. An experimental test of a fundamental food web motif.

    Science.gov (United States)

    Rip, Jason M K; McCann, Kevin S; Lynn, Denis H; Fawcett, Sonia

    2010-06-07

    Large-scale changes to the world's ecosystem are resulting in the deterioration of biostructure-the complex web of species interactions that make up ecological communities. A difficult, yet crucial task is to identify food web structures, or food web motifs, that are the building blocks of this baroque network of interactions. Once identified, these food web motifs can then be examined through experiments and theory to provide mechanistic explanations for how structure governs ecosystem stability. Here, we synthesize recent ecological research to show that generalist consumers coupling resources with different interaction strengths, is one such motif. This motif amazingly occurs across an enormous range of spatial scales, and so acts to distribute coupled weak and strong interactions throughout food webs. We then perform an experiment that illustrates the importance of this motif to ecological stability. We find that weak interactions coupled to strong interactions by generalist consumers dampen strong interaction strengths and increase community stability. This study takes a critical step by isolating a common food web motif and through clear, experimental manipulation, identifies the fundamental stabilizing consequences of this structure for ecological communities.

  9. PISMA: A Visual Representation of Motif Distribution in DNA Sequences

    Directory of Open Access Journals (Sweden)

    Rogelio Alcántara-Silva

    2017-03-01

    Full Text Available Background: Because the graphical presentation and analysis of motif distribution can provide insights for experimental hypothesis, PISMA aims at identifying motifs on DNA sequences, counting and showing them graphically. The motif length ranges from 2 to 10 bases, and the DNA sequences range up to 10 kb. The motif distribution is shown as a bar-code–like, as a gene-map–like, and as a transcript scheme. Results: We obtained graphical schemes of the CpG site distribution from 91 human papillomavirus genomes. Also, we present 2 analyses: one of DNA motifs associated with either methylation-resistant or methylation-sensitive CpG islands and another analysis of motifs associated with exosome RNA secretion. Availability and Implementation: PISMA is developed in Java; it is executable in any type of hardware and in diverse operating systems. PISMA is freely available to noncommercial users. The English version and the User Manual are provided in Supplementary Files 1 and 2, and a Spanish version is available at www.biomedicas.unam.mx/wp-content/software/pisma.zip and www.biomedicas.unam.mx/wp-content/pdf/manual/pisma.pdf .

  10. Bacterial translation elongation factor EF-Tu interacts and colocalizes with actin-like MreB protein.

    Science.gov (United States)

    Defeu Soufo, Hervé Joël; Reimold, Christian; Linne, Uwe; Knust, Tobias; Gescher, Johannes; Graumann, Peter L

    2010-02-16

    We show that translation initiation factor EF-Tu plays a second important role in cell shape maintenance in the bacterium Bacillus subtilis. EF-Tu localizes in a helical pattern underneath the cell membrane and colocalizes with MreB, an actin-like cytoskeletal element setting up rod cell shape. The localization of MreB and of EF-Tu is interdependent, but in contrast to the dynamic MreB filaments, EF-Tu structures are more static and may serve as tracks for MreB filaments. In agreement with this idea, EF-Tu and MreB interact in vivo and in vitro. Lowering of the EF-Tu levels had a minor effect on translation but a strong effect on cell shape and on the localization of MreB, and blocking of the function of EF-Tu in translation did not interfere with the localization of MreB, showing that, directly or indirectly, EF-Tu affects the cytoskeletal MreB structure and thus serves two important functions in a bacterium.

  11. Structure of eEF3 and the mechanism of transfer RNA release from the E-site

    DEFF Research Database (Denmark)

    Andersen, Christian Brix Folsted; Becker, T.; Blau, M.

    2006-01-01

    Elongation factor eEF3 is an ATPase, which, in addition to the two canonical factors eEF1A and eEF2, serves an essential function in the translation cycle of fungi. eEF3 is required for the binding of the aatRNA-eEF1A-GTP ternary complex to the ribosomal A-site and has been suggested to facilitate...... the clearance of deacyl-tRNA from the E-site. Here, we present the crystal structure of eEF3 showing that it consists of an N-terminal HEAT repeat domain, followed by a four-helix bundle and two ABC-type ATPase domains with a chromo-domain inserted in ABC2. Moreover, we present the cryo-EM structure of the ATP......-bound form of eEF3 in complex with the post-translocational state 80S ribosome from yeast. eEF3 uses an entirely new factor binding site near the ribosomal E-site, with the chromodomain stabilizing the ribosomal L1 stalk in an open conformation, thus, allowing tRNA release....

  12. Up-regulation of eEF1A2 promotes proliferation and inhibits apoptosis in prostate cancer

    International Nuclear Information System (INIS)

    Sun, Yue; Du, Chengli; Wang, Bo; Zhang, Yanling; Liu, Xiaoyan; Ren, Guoping

    2014-01-01

    Highlights: • The expression of eEF1A2 is up-regulated in prostate cancer tissues. • Suppression of eEF1A2 inhibits the proliferation and promotes apoptosis. • Inhibition of eEF1A2 enhances the expression of apoptotic relevant proteins. • The expressions of eEF1A2 and cleavage-caspase3 are inversely correlated. - Abstract: Background: eEF1A2 is a protein translation factor involved in protein synthesis, which possesses important function roles in cancer development. This study aims at investigating the expression pattern of eEF1A2 in prostate cancer and its potential role in prostate cancer development. Methods: We examined the expression level of eEF1A2 in 30 pairs of prostate cancer tissues by using RT-PCR and immunohistochemical staining (IHC). Then we applied siRNA specifically targeting eEF1A2 to down-regulate its expression in DU-145 and PC-3 cells. Flow cytometer was used to explore apoptosis and Western-blot was used to detect the pathway proteins of apoptosis. Results: Our results showed that the expression level of eEF1A2 in prostate cancer tissues was significantly higher compared to their corresponding normal tissues. Reduction of eEF1A2 expression in DU-145 and PC-3 cells led to a dramatic inhibition of proliferation accompanied with enhanced apoptosis rate. Western blot revealed that apoptosis pathway proteins (caspase3, BAD, BAX, PUMA) were significantly up-regulated after suppression of eEF1A2. More importantly, the levels of eEF1A2 and caspase3 were inversely correlated in prostate cancer tissues. Conclusion: Our data suggests that eEF1A2 plays an important role in prostate cancer development, especially in inhibiting apoptosis. So eEF1A2 might serve as a potential therapeutic target in prostate cancer

  13. Function and structure in phage Qbeta RNA replicase. Association of EF-Tu-Ts with the other enzyme subunits

    DEFF Research Database (Denmark)

    Blumenthal, T; Young, R A; Brown, S

    1976-01-01

    alters its quaternary structure: the EF-Tu-Ts cannot be covalently attached to the other enzyme subunits with bifunctional cross-linking reagents in the presence of RNA. This conformational change is not influenced by ionic strength. The addition of Qbeta RNA to the enzyme, does not result in the release...... for one another increases with increasing ionic strength. The enzyme is capable of initiation of RNA synthesis with synthetic templates only when in the low ionic strength conformation. Elongation of initiated polynucleotide chains is not affectedby ionic strength. Addition of Qbeta RNA to the enzyme also...... of EF-Tu-Ts from the other enzyme subunits: whereas free EF-Tu-Ts binds GDP independently of salt concentration, this binding by Qbeta replicase is sensitive to high ionic strength and remains so in the presence of Qbeta RNA. Furthermore, RNA does not allow the release of EF-Ts from EF-Tu by GTP...

  14. (In)Visible Hand(s)

    OpenAIRE

    Predrag Zima

    2007-01-01

    In this paper, the author discusses the regulatory role of the state and legal norms, in market economy, especially in so-called transition countries. Legal policy, and other questions of the state and free market economy are here closely connected, because the state must ensure with legal norms that economic processes are not interrupted: only the state can establish the legal basis for a market economy. The free market’s invisible hand is acting in questions such as: what is to be produced,...

  15. Prevention of hand eczema

    DEFF Research Database (Denmark)

    Fisker, Maja H; Ebbehøj, Niels E; Vejlstrup, Søren Grove

    2018-01-01

    Objective Occupational hand eczema has adverse health and socioeconomic impacts for the afflicted individuals and society. Prevention and treatment strategies are needed. This study aimed to assess the effectiveness of an educational intervention on sickness absence, quality of life and severity...... of hand eczema. Methods PREVEX (PreVention of EXema) is an individually randomized, parallel-group superiority trial investigating the pros and cons of one-time, 2-hour, group-based education in skin-protective behavior versus treatment as usual among patients with newly notified occupational hand eczema...

  16. Verification of the MOTIF code version 3.0

    International Nuclear Information System (INIS)

    Chan, T.; Guvanasen, V.; Nakka, B.W.; Reid, J.A.K.; Scheier, N.W.; Stanchell, F.W.

    1996-12-01

    As part of the Canadian Nuclear Fuel Waste Management Program (CNFWMP), AECL has developed a three-dimensional finite-element code, MOTIF (Model Of Transport In Fractured/ porous media), for detailed modelling of groundwater flow, heat transport and solute transport in a fractured rock mass. The code solves the transient and steady-state equations of groundwater flow, solute (including one-species radionuclide) transport, and heat transport in variably saturated fractured/porous media. The initial development was completed in 1985 (Guvanasen 1985) and version 3.0 was completed in 1986. This version is documented in detail in Guvanasen and Chan (in preparation). This report describes a series of fourteen verification cases which has been used to test the numerical solution techniques and coding of MOTIF, as well as demonstrate some of the MOTIF analysis capabilities. For each case the MOTIF solution has been compared with a corresponding analytical or independently developed alternate numerical solution. Several of the verification cases were included in Level 1 of the International Hydrologic Code Intercomparison Project (HYDROCOIN). The MOTIF results for these cases were also described in the HYDROCOIN Secretariat's compilation and comparison of results submitted by the various project teams (Swedish Nuclear Power Inspectorate 1988). It is evident from the graphical comparisons presented that the MOTIF solutions for the fourteen verification cases are generally in excellent agreement with known analytical or numerical solutions obtained from independent sources. This series of verification studies has established the ability of the MOTIF finite-element code to accurately model the groundwater flow and solute and heat transport phenomena for which it is intended. (author). 20 refs., 14 tabs., 32 figs

  17. Mechanisms of zero-lag synchronization in cortical motifs.

    Directory of Open Access Journals (Sweden)

    Leonardo L Gollo

    2014-04-01

    Full Text Available Zero-lag synchronization between distant cortical areas has been observed in a diversity of experimental data sets and between many different regions of the brain. Several computational mechanisms have been proposed to account for such isochronous synchronization in the presence of long conduction delays: Of these, the phenomenon of "dynamical relaying"--a mechanism that relies on a specific network motif--has proven to be the most robust with respect to parameter mismatch and system noise. Surprisingly, despite a contrary belief in the community, the common driving motif is an unreliable means of establishing zero-lag synchrony. Although dynamical relaying has been validated in empirical and computational studies, the deeper dynamical mechanisms and comparison to dynamics on other motifs is lacking. By systematically comparing synchronization on a variety of small motifs, we establish that the presence of a single reciprocally connected pair--a "resonance pair"--plays a crucial role in disambiguating those motifs that foster zero-lag synchrony in the presence of conduction delays (such as dynamical relaying from those that do not (such as the common driving triad. Remarkably, minor structural changes to the common driving motif that incorporate a reciprocal pair recover robust zero-lag synchrony. The findings are observed in computational models of spiking neurons, populations of spiking neurons and neural mass models, and arise whether the oscillatory systems are periodic, chaotic, noise-free or driven by stochastic inputs. The influence of the resonance pair is also robust to parameter mismatch and asymmetrical time delays amongst the elements of the motif. We call this manner of facilitating zero-lag synchrony resonance-induced synchronization, outline the conditions for its occurrence, and propose that it may be a general mechanism to promote zero-lag synchrony in the brain.

  18. Phyloproteomic Analysis of 11780 Six-Residue-Long Motifs Occurrences

    Directory of Open Access Journals (Sweden)

    O. V. Galzitskaya

    2015-01-01

    Full Text Available How is it possible to find good traits for phylogenetic reconstructions? Here, we present a new phyloproteomic criterion that is an occurrence of simple motifs which can be imprints of evolution history. We studied the occurrences of 11780 six-residue-long motifs consisting of two randomly located amino acids in 97 eukaryotic and 25 bacterial proteomes. For all eukaryotic proteomes, with the exception of the Amoebozoa, Stramenopiles, and Diplomonadida kingdoms, the number of proteins containing the motifs from the first group (one of the two amino acids occurs once at the terminal position made about 20%; in the case of motifs from the second (one of two amino acids occurs one time within the pattern and third (the two amino acids occur randomly groups, 30% and 50%, respectively. For bacterial proteomes, this relationship was 10%, 27%, and 63%, respectively. The matrices of correlation coefficients between numbers of proteins where a motif from the set of 11780 motifs appears at least once in 9 kingdoms and 5 phyla of bacteria were calculated. Among the correlation coefficients for eukaryotic proteomes, the correlation between the animal and fungi kingdoms (0.62 is higher than between fungi and plants (0.54. Our study provides support that animals and fungi are sibling kingdoms. Comparison of the frequencies of six-residue-long motifs in different proteomes allows obtaining phylogenetic relationships based on similarities between these frequencies: the Diplomonadida kingdoms are more close to Bacteria than to Eukaryota; Stramenopiles and Amoebozoa are more close to each other than to other kingdoms of Eukaryota.

  19. Clean Hands Count

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    Full Text Available ... myths and misperceptions about hand hygiene and empower patients to play a role in their care by ... Copyright Creators Advertise Developers +YouTube Terms Privacy Policy & Safety Send feedback Test new features Loading... Working... Sign ...

  20. Clean Hands Count

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  1. Clean Hands Count

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  2. Tropical Diabetic Hand Syndrome

    African Journals Online (AJOL)

    2015 Annals of Medical and Health Sciences Research | Published by Wolters Kluwer - Medknow. 473. Introduction ... diabetes.[2,3] Tropical diabetic hand syndrome is a terminology .... the importance of seeking medical attention immediately.

  3. Clean Hands Count

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    Full Text Available ... now. Please try again later. Published on May 5, 2017 This video for healthcare providers is intended ... 36 Wash 'Em - Hand Hygiene Music Video - Duration: 5:46. Jefferson Health 413,702 views 5:46 ...

  4. Clean Hands Count

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    Full Text Available ... reminding healthcare providers to clean their hands. See: https://www.cdc.gov/handhygiene/campa... . Comments on this ... are allowed in accordance with our comment policy: http://www.cdc.gov/SocialMedia/Tools/... This video can ...

  5. Clean Hands Count

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    Full Text Available ... empower patients to play a role in their care by asking or reminding healthcare providers to clean ... It's in your hands - prevent sepsis in health care' A 5 May 2018 advocacy message from WHO - ...

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    Full Text Available ... why Close Clean Hands Count Centers for Disease Control and Prevention (CDC) Loading... Unsubscribe from Centers for Disease Control and Prevention (CDC)? Cancel Unsubscribe Working... Subscribe Subscribed ...

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    Full Text Available ... has been rented. This feature is not available right now. Please try again later. Published on May ... Wash your Hands - it just makes sense. - Duration: 1:36. Seema Marwaha 404,414 views 1:36 ...

  8. Clean Hands Count

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    Full Text Available ... Washing Video from CDC called "Put Your Hands Together" - Duration: 3:40. Patrick Boshell 27,834 views ... Policy & Safety Send feedback Test new features Loading... Working... Sign in to add this to Watch Later ...

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    Full Text Available ... Published on May 5, 2017 This video for healthcare providers is intended to promote or encourage adherence ... role in their care by asking or reminding healthcare providers to clean their hands. See: https://www. ...

  10. A Comparative Study on the Origin and Variety of Motifs in Shahsavan Salt Bags and Caucasian Textiles

    Directory of Open Access Journals (Sweden)

    Siamak Egharloo

    2017-12-01

    Full Text Available Shahsavan tribes of Iran and the Caucasus region have had considerable and often inevitable intercourse and associations during the history due to their common borders and special geographical locations. The result of this has been manifested in different forms of intermingled factors and elements, specifically the textiles of tribes and ethnic groups. The interactions of the mentioned realm, i.e. textile industry, have best been appeared in patterns, motifs, colors and compositions and weaving of the hand-woven textiles among which Shahsavan "salt bags" (NAMAKDᾹN are a case in point. According to the facts and the importance of this subject, we can propose some questions as follows: What influences have the field of weaving had in these two regions as a result of their interactions and historical background? What are the motifs and their classifications in these two regions and which ones share common patterns? And which ones abound? Having been done in analytical and comparative method, the present research has examined the field of weaving in Shahsavan tribe with emphasis on its salt bags together with other Caucasian textiles (salt bags, etc.. The objectives of the research have been the study of the influences and interactions between the two regions and the recognition of patterns and motifs on their textiles. Finally, we can infer that the certain location of Iran and its common borders with the Caucasus besides tribal distribution of groups in northern and southern areas could be considered the reasons for cultural influences in the mentioned regions. The dominant motifs to be noticed here are dragons (S shape, diamonds and stars, crab-like and cross motifs as well as negative and positive spaces.

  11. Liposome-encapsulated EF24-HPβCD inclusion complex: a preformulation study and biodistribution in a rat model

    International Nuclear Information System (INIS)

    Agashe, H.; Lagisetty, P.; Sahoo, K.; Bourne, D.; Grady, B.; Awasthi, V.

    2011-01-01

    3,5-Bis(2-fluorobenzylidene)-4-piperidone (EF24) is an anti-proliferative diphenyldifluoroketone analog of curcumin with more potent activity. The authors describe a liposome preparation of EF24 using a “drug-in-CD-in liposome” approach. An aqueous solution of EF24 and hydroxypropyl-β-cyclodextrin (HPβCD) inclusion complex (IC) was used to prepare EF24 liposomes. The liposome size was reduced by a combination of multiple freeze–thaw cycles. Co-encapsulation of glutathione inside the liposomes conferred them with the capability of labeling with imageable radionuclide Tc-99m. Phase solubility analysis of EF24-HPβCD mixture provided k 1:1 value of 9.9 M −1 . The enhanced aqueous solubility of EF24 (from 1.64 to 13.8 mg/mL) due to the presence of HPβCD helped in the liposome preparation. About 19% of the EF24 IC was encapsulated inside the liposomes (320.5 ± 2.6 nm) by dehydration–rehydration technique. With extrusion technique, the size of 177 ± 6.5 nm was obtained without any effect on encapsulation efficiency. The EF24-liposomes were evaluated for anti-proliferative activity in lung adenocarcinoma H441 and prostate cancer PC-3 cells. The EF24-liposomes demonstrated anti-proliferative activity superior to that of plain EF24 at 10 μM dose. When injected in rats, the Tc-99m-labeled EF24-liposomes cleared from blood with an α-t 1/2 of 21.4 min and β-t 1/2 of 397 min. Tissue radioactivity counting upon necropsy showed that the majority of clearance was due to the uptake in liver and spleen. The results suggest that using “drug-in-CD-in liposome” approach is a feasible strategy to formulate an effective parenteral preparation of EF24. In vitro studies show that the liposomal EF24 remains anti-proliferative, while presenting an opportunity to image its biodistribution.

  12. Liposome-encapsulated EF24-HPβCD inclusion complex: a preformulation study and biodistribution in a rat model

    Science.gov (United States)

    Agashe, H.; Lagisetty, P.; Sahoo, K.; Bourne, D.; Grady, B.; Awasthi, V.

    2011-06-01

    3,5-Bis(2-fluorobenzylidene)-4-piperidone (EF24) is an anti-proliferative diphenyldifluoroketone analog of curcumin with more potent activity. The authors describe a liposome preparation of EF24 using a "drug-in-CD-in liposome" approach. An aqueous solution of EF24 and hydroxypropyl-β-cyclodextrin (HPβCD) inclusion complex (IC) was used to prepare EF24 liposomes. The liposome size was reduced by a combination of multiple freeze-thaw cycles. Co-encapsulation of glutathione inside the liposomes conferred them with the capability of labeling with imageable radionuclide Tc-99m. Phase solubility analysis of EF24-HPβCD mixture provided k 1:1 value of 9.9 M-1. The enhanced aqueous solubility of EF24 (from 1.64 to 13.8 mg/mL) due to the presence of HPβCD helped in the liposome preparation. About 19% of the EF24 IC was encapsulated inside the liposomes (320.5 ± 2.6 nm) by dehydration-rehydration technique. With extrusion technique, the size of 177 ± 6.5 nm was obtained without any effect on encapsulation efficiency. The EF24-liposomes were evaluated for anti-proliferative activity in lung adenocarcinoma H441 and prostate cancer PC-3 cells. The EF24-liposomes demonstrated anti-proliferative activity superior to that of plain EF24 at 10 μM dose. When injected in rats, the Tc-99m-labeled EF24-liposomes cleared from blood with an α- t 1/2 of 21.4 min and β- t 1/2 of 397 min. Tissue radioactivity counting upon necropsy showed that the majority of clearance was due to the uptake in liver and spleen. The results suggest that using "drug-in-CD-in liposome" approach is a feasible strategy to formulate an effective parenteral preparation of EF24. In vitro studies show that the liposomal EF24 remains anti-proliferative, while presenting an opportunity to image its biodistribution.

  13. Liposome-encapsulated EF24-HP{beta}CD inclusion complex: a preformulation study and biodistribution in a rat model

    Energy Technology Data Exchange (ETDEWEB)

    Agashe, H; Lagisetty, P; Sahoo, K; Bourne, D [University of Oklahoma Health Sciences Center, Department of Pharmaceutical Sciences (United States); Grady, B [School of Chemical, Biological and Materials Engineering (United States); Awasthi, V [University of Oklahoma Health Sciences Center, Department of Pharmaceutical Sciences (United States)

    2011-06-15

    3,5-Bis(2-fluorobenzylidene)-4-piperidone (EF24) is an anti-proliferative diphenyldifluoroketone analog of curcumin with more potent activity. The authors describe a liposome preparation of EF24 using a 'drug-in-CD-in liposome' approach. An aqueous solution of EF24 and hydroxypropyl-{beta}-cyclodextrin (HP{beta}CD) inclusion complex (IC) was used to prepare EF24 liposomes. The liposome size was reduced by a combination of multiple freeze-thaw cycles. Co-encapsulation of glutathione inside the liposomes conferred them with the capability of labeling with imageable radionuclide Tc-99m. Phase solubility analysis of EF24-HP{beta}CD mixture provided k{sub 1:1} value of 9.9 M{sup -1}. The enhanced aqueous solubility of EF24 (from 1.64 to 13.8 mg/mL) due to the presence of HP{beta}CD helped in the liposome preparation. About 19% of the EF24 IC was encapsulated inside the liposomes (320.5 {+-} 2.6 nm) by dehydration-rehydration technique. With extrusion technique, the size of 177 {+-} 6.5 nm was obtained without any effect on encapsulation efficiency. The EF24-liposomes were evaluated for anti-proliferative activity in lung adenocarcinoma H441 and prostate cancer PC-3 cells. The EF24-liposomes demonstrated anti-proliferative activity superior to that of plain EF24 at 10 {mu}M dose. When injected in rats, the Tc-99m-labeled EF24-liposomes cleared from blood with an {alpha}-t{sub 1/2} of 21.4 min and {beta}-t{sub 1/2} of 397 min. Tissue radioactivity counting upon necropsy showed that the majority of clearance was due to the uptake in liver and spleen. The results suggest that using 'drug-in-CD-in liposome' approach is a feasible strategy to formulate an effective parenteral preparation of EF24. In vitro studies show that the liposomal EF24 remains anti-proliferative, while presenting an opportunity to image its biodistribution.

  14. Liposome-encapsulated EF24-HP{beta}CD inclusion complex: a preformulation study and biodistribution in a rat model

    Energy Technology Data Exchange (ETDEWEB)

    Agashe, H.; Lagisetty, P.; Sahoo, K.; Bourne, D. [University of Oklahoma Health Sciences Center, Department of Pharmaceutical Sciences (United States); Grady, B. [School of Chemical, Biological and Materials Engineering (United States); Awasthi, V., E-mail: vawasthi@ouhsc.edu [University of Oklahoma Health Sciences Center, Department of Pharmaceutical Sciences (United States)

    2011-06-15

    3,5-Bis(2-fluorobenzylidene)-4-piperidone (EF24) is an anti-proliferative diphenyldifluoroketone analog of curcumin with more potent activity. The authors describe a liposome preparation of EF24 using a 'drug-in-CD-in liposome' approach. An aqueous solution of EF24 and hydroxypropyl-{beta}-cyclodextrin (HP{beta}CD) inclusion complex (IC) was used to prepare EF24 liposomes. The liposome size was reduced by a combination of multiple freeze-thaw cycles. Co-encapsulation of glutathione inside the liposomes conferred them with the capability of labeling with imageable radionuclide Tc-99m. Phase solubility analysis of EF24-HP{beta}CD mixture provided k{sub 1:1} value of 9.9 M{sup -1}. The enhanced aqueous solubility of EF24 (from 1.64 to 13.8 mg/mL) due to the presence of HP{beta}CD helped in the liposome preparation. About 19% of the EF24 IC was encapsulated inside the liposomes (320.5 {+-} 2.6 nm) by dehydration-rehydration technique. With extrusion technique, the size of 177 {+-} 6.5 nm was obtained without any effect on encapsulation efficiency. The EF24-liposomes were evaluated for anti-proliferative activity in lung adenocarcinoma H441 and prostate cancer PC-3 cells. The EF24-liposomes demonstrated anti-proliferative activity superior to that of plain EF24 at 10 {mu}M dose. When injected in rats, the Tc-99m-labeled EF24-liposomes cleared from blood with an {alpha}-t{sub 1/2} of 21.4 min and {beta}-t{sub 1/2} of 397 min. Tissue radioactivity counting upon necropsy showed that the majority of clearance was due to the uptake in liver and spleen. The results suggest that using 'drug-in-CD-in liposome' approach is a feasible strategy to formulate an effective parenteral preparation of EF24. In vitro studies show that the liposomal EF24 remains anti-proliferative, while presenting an opportunity to image its biodistribution.

  15. Safety aspects of the emergency filtration system (EFS) for NRU reactor

    International Nuclear Information System (INIS)

    Hickey, D.L.; Lounsbury, R.I.

    1990-01-01

    A description of the NRU emergency filter system (EFS) is presented, including operation, testing and hazards. Operation of the NRU EFS reduces the dose to the thyroid for members of the public and site personnel by a factor of 100. The calculated thyroid doses for off-site and on-site locations for the current system configuration are 91 and 160 mSv, respectively. An unavailability analysis was performed on the control system which recognized subtle problems in the current system. Modifications to the system result in a system unavailability of 2.0 E-3. The thyroid risk analysis revealed that these improvements in system availability result in risk reduction by approximately a factor of three. Improvements beyond the availability analysis recommendations do not result in substantial risk benefit for members of the public or on-site personnel

  16. Velocity ratio predicts outcomes in patients with low gradient severe aortic stenosis and preserved EF

    DEFF Research Database (Denmark)

    Jander, Nikolaus; Hochholzer, Willibald; Kaufmann, Beat A

    2014-01-01

    OBJECTIVE: To evaluate the usefulness of velocity ratio (VR) in patients with low gradient severe aortic stenosis (LGSAS) and preserved EF. BACKGROUND: LGSAS despite preserved EF represents a clinically challenging entity. Reliance on mean pressure gradient (MPG) may underestimate stenosis severity...... for severe stenosis. We hypothesised that VR may have conceptual advantages over MPG and AVA, predict clinical outcomes and thereby be useful in the management of patients with LGSAS. METHODS: Patients from the prospective Simvastatin and Ezetimibe in Aortic Stenosis (SEAS) study with an AVA...≤40 mm Hg and EF≥55% and asymptomatic at baseline were stratified according to VR with a cut-off value of 0.25. Outcomes were evaluated according to aortic valve-related events and cardiovascular death. RESULTS: Of 435 patients with LGSAS, 197 (45%) had VRVR≥0...

  17. Binding properties of SUMO-interacting motifs (SIMs) in yeast.

    Science.gov (United States)

    Jardin, Christophe; Horn, Anselm H C; Sticht, Heinrich

    2015-03-01

    Small ubiquitin-like modifier (SUMO) conjugation and interaction play an essential role in many cellular processes. A large number of yeast proteins is known to interact non-covalently with SUMO via short SUMO-interacting motifs (SIMs), but the structural details of this interaction are yet poorly characterized. In the present work, sequence analysis of a large dataset of 148 yeast SIMs revealed the existence of a hydrophobic core binding motif and a preference for acidic residues either within or adjacent to the core motif. Thus the sequence properties of yeast SIMs are highly similar to those described for human. Molecular dynamics simulations were performed to investigate the binding preferences for four representative SIM peptides differing in the number and distribution of acidic residues. Furthermore, the relative stability of two previously observed alternative binding orientations (parallel, antiparallel) was assessed. For all SIMs investigated, the antiparallel binding mode remained stable in the simulations and the SIMs were tightly bound via their hydrophobic core residues supplemented by polar interactions of the acidic residues. In contrary, the stability of the parallel binding mode is more dependent on the sequence features of the SIM motif like the number and position of acidic residues or the presence of additional adjacent interaction motifs. This information should be helpful to enhance the prediction of SIMs and their binding properties in different organisms to facilitate the reconstruction of the SUMO interactome.

  18. RegRNA: an integrated web server for identifying regulatory RNA motifs and elements

    OpenAIRE

    Huang, Hsi-Yuan; Chien, Chia-Hung; Jen, Kuan-Hua; Huang, Hsien-Da

    2006-01-01

    Numerous regulatory structural motifs have been identified as playing essential roles in transcriptional and post-transcriptional regulation of gene expression. RegRNA is an integrated web server for identifying the homologs of regulatory RNA motifs and elements against an input mRNA sequence. Both sequence homologs and structural homologs of regulatory RNA motifs can be recognized. The regulatory RNA motifs supported in RegRNA are categorized into several classes: (i) motifs in mRNA 5′-untra...

  19. CARRYING OF FRENCH VISAS FOR HOLDERS OF CATEGORY 'EF' FRENCH ATTESTATIONS DE FONCTIONS

    CERN Multimedia

    Service des Relations avec les Pays Hôtes

    1999-01-01

    The French Ministry of Foreign Affairs has informed the Organisation that members of the personnel resident in Switzerland and holding Category 'EF' French Attestations de functions are not obliged to be in possession of French visas. When temporarily travelling through France on OFFICIAL CERN BUSINESS, provided they are carrying the valid Attestation and a valid national passport with them.Relations with the Host States Servicehttp://www.cern.ch/relations/Tel. 72848

  20. Energy-filtered Photoelectron Emission Microscopy (EF-PEEM) for imaging nanoelectronic materials

    International Nuclear Information System (INIS)

    Renault, Olivier; Chabli, Amal

    2007-01-01

    Photoelectron-Emission Microscopy (PEEM) is the most promising approach to photoemission-based (XPS, UPS) imaging techniques with high lateral resolution, typically below 100 nm. It has now reached its maturity with a new generation of instruments with energy-filtering capabilities. Therefore UPS and XPS imaging with energy-filtered PEEM (EF-PEEM) can be applied to technologically-relevant samples. UPS images with contrast in local work function, obtained with laboratory UV sources, are obtained in ultra-high vacuum environment with lateral resolutions better than 50 nm and sensitivies of 20 meV. XPS images with elemental and bonding state contrast can show up lateral resolution better than 200 nm with synchrotron excitation. In this paper, we present the principles and capabilities of EF-PEEM and nanospectroscopy. Then, we focus on an example of application to non-destructive work-function imaging of polycrystalline copper for advanced interconnects, where it is shown that EF-PEEM is an alternative to Kelvin probes

  1. The mazEF toxin-antitoxin system as a novel antibacterial target in Acinetobacter baumannii

    Directory of Open Access Journals (Sweden)

    Sobhan Ghafourian

    2014-07-01

    Full Text Available Although analysis of toxin-antitoxin (TA systems can be instructive, to date, there is no information on the prevalence and identity of TA systems based on a large panel of Acinetobacter baumannii clinical isolates. The aim of the current study was to screen for functional TA systems among clinical isolates of A. baumannii and to identify the systems’ locations. For this purpose, we screened 85 A. baumannii isolates collected from different clinical sources for the presence of the mazEF, relBE and higBA TA genes. The results revealed that the genes coding for the mazEF TA system were commonly present in all clinical isolates of A. baumannii. Reverse transcriptase-polymerase chain reaction analysis showed that transcripts were produced in the clinical isolates. Our findings showed that TA genes are prevalent, harboured by chromosomes and transcribed within A. baumannii. Hence, activation of the toxin proteins in the mazEF TA system should be investigated further as an effective antibacterial strategy against this bacterium.

  2. The mazEF toxin-antitoxin system as a novel antibacterial target in Acinetobacter baumannii.

    Science.gov (United States)

    Ghafourian, Sobhan; Good, Liam; Sekawi, Zamberi; Hamat, Rukman Awang; Soheili, Sara; Sadeghifard, Nourkhoda; Neela, Vasanthakumari

    2014-07-01

    Although analysis of toxin-antitoxin (TA) systems can be instructive, to date, there is no information on the prevalence and identity of TA systems based on a large panel of Acinetobacter baumannii clinical isolates. The aim of the current study was to screen for functional TA systems among clinical isolates of A. baumannii and to identify the systems' locations. For this purpose, we screened 85 A. baumannii isolates collected from different clinical sources for the presence of the mazEF, relBE and higBA TA genes. The results revealed that the genes coding for the mazEF TA system were commonly present in all clinical isolates of A. baumannii. Reverse transcriptase-polymerase chain reaction analysis showed that transcripts were produced in the clinical isolates. Our findings showed that TA genes are prevalent, harboured by chromosomes and transcribed within A. baumannii. Hence, activation of the toxin proteins in the mazEF TA system should be investigated further as an effective antibacterial strategy against this bacterium.

  3. TRIO-EF a general thermal hydraulics computer code applied to the Avlis process

    International Nuclear Information System (INIS)

    Magnaud, J.P.; Claveau, M.; Coulon, N.; Yala, P.; Guilbaud, D.; Mejane, A.

    1993-01-01

    TRIO(EF is a general purpose Fluid Mechanics 3D Finite Element Code. The system capabilities cover areas such as steady state or transient, laminar or turbulent, isothermal or temperature dependent fluid flows; it is applicable to the study of coupled thermo-fluid problems involving heat conduction and possibly radiative heat transfer. It has been used to study the thermal behaviour of the AVLIS process separation module. In this process, a linear electron beam impinges the free surface of a uranium ingot, generating a two dimensional curtain emission of vapour from a water-cooled crucible. The energy transferred to the metal causes its partial melting, forming a pool where strong convective motion increases heat transfer towards the crucible. In the upper part of the Separation Module, the internal structures are devoted to two main functions: vapor containment and reflux, irradiation and physical separation. They are subjected to very high temperature levels and heat transfer occurs mainly by radiation. Moreover, special attention has to be paid to electron backscattering. These two major points have been simulated numerically with TRIO-EF and the paper presents and comments the results of such a computation, for each of them. After a brief overview of the computer code, two examples of the TRIO-EF capabilities are given: a crucible thermal hydraulics model, a thermal analysis of the internal structures

  4. Hands of early primates.

    Science.gov (United States)

    Boyer, Doug M; Yapuncich, Gabriel S; Chester, Stephen G B; Bloch, Jonathan I; Godinot, Marc

    2013-12-01

    Questions surrounding the origin and early evolution of primates continue to be the subject of debate. Though anatomy of the skull and inferred dietary shifts are often the focus, detailed studies of postcrania and inferred locomotor capabilities can also provide crucial data that advance understanding of transitions in early primate evolution. In particular, the hand skeleton includes characteristics thought to reflect foraging, locomotion, and posture. Here we review what is known about the early evolution of primate hands from a comparative perspective that incorporates data from the fossil record. Additionally, we provide new comparative data and documentation of skeletal morphology for Paleogene plesiadapiforms, notharctines, cercamoniines, adapines, and omomyiforms. Finally, we discuss implications of these data for understanding locomotor transitions during the origin and early evolutionary history of primates. Known plesiadapiform species cannot be differentiated from extant primates based on either intrinsic hand proportions or hand-to-body size proportions. Nonetheless, the presence of claws and a different metacarpophalangeal [corrected] joint form in plesiadapiforms indicate different grasping mechanics. Notharctines and cercamoniines have intrinsic hand proportions with extremely elongated proximal phalanges and digit rays relative to metacarpals, resembling tarsiers and galagos. But their hand-to-body size proportions are typical of many extant primates (unlike those of tarsiers, and possibly Teilhardina, which have extremely large hands). Non-adapine adapiforms and omomyids exhibit additional carpal features suggesting more limited dorsiflexion, greater ulnar deviation, and a more habitually divergent pollex than observed plesiadapiforms. Together, features differentiating adapiforms and omomyiforms from plesiadapiforms indicate increased reliance on vertical prehensile-clinging and grasp-leaping, possibly in combination with predatory behaviors in

  5. Hand eczema: An update

    Directory of Open Access Journals (Sweden)

    Chembolli Lakshmi

    2012-01-01

    Full Text Available Eczema, the commonest disorders afflicting the hands, is also the commonest occupational skin disease (OSD. In the dermatology outpatient departments, only the severe cases are diagnosed since patients rarely report with early hand dermatitis. Mild forms are picked up only during occupational screening. Hand eczema (HE can evolve into a chronic condition with persistent disease even after avoiding contact with the incriminated allergen / irritant. The important risk factors for hand eczema are atopy (especially the presence of dermatitis, wet work, and contact allergy. The higher prevalence in women as compared to men in most studies is related to environmental factors and is mainly applicable to younger women in their twenties. Preventive measures play a very important role in therapy as they enable the affected individuals to retain their employment and livelihood. This article reviews established preventive and therapeutic options and newer drugs like alitretinoin in hand eczema with a mention on the etiology and morphology. Identifying the etiological factors is of paramount importance as avoiding or minimizing these factors play an important role in treatment.

  6. How pathogens use linear motifs to perturb host cell networks

    KAUST Repository

    Via, Allegra; Uyar, Bora; Brun, Christine; Zanzoni, Andreas

    2015-01-01

    Molecular mimicry is one of the powerful stratagems that pathogens employ to colonise their hosts and take advantage of host cell functions to guarantee their replication and dissemination. In particular, several viruses have evolved the ability to interact with host cell components through protein short linear motifs (SLiMs) that mimic host SLiMs, thus facilitating their internalisation and the manipulation of a wide range of cellular networks. Here we present convincing evidence from the literature that motif mimicry also represents an effective, widespread hijacking strategy in prokaryotic and eukaryotic parasites. Further insights into host motif mimicry would be of great help in the elucidation of the molecular mechanisms behind host cell invasion and the development of anti-infective therapeutic strategies.

  7. Discovery of candidate KEN-box motifs using cell cycle keyword enrichment combined with native disorder prediction and motif conservation.

    Science.gov (United States)

    Michael, Sushama; Travé, Gilles; Ramu, Chenna; Chica, Claudia; Gibson, Toby J

    2008-02-15

    KEN-box-mediated target selection is one of the mechanisms used in the proteasomal destruction of mitotic cell cycle proteins via the APC/C complex. While annotating the Eukaryotic Linear Motif resource (ELM, http://elm.eu.org/), we found that KEN motifs were significantly enriched in human protein entries with cell cycle keywords in the UniProt/Swiss-Prot database-implying that KEN-boxes might be more common than reported. Matches to short linear motifs in protein database searches are not, per se, significant. KEN-box enrichment with cell cycle Gene Ontology terms suggests that collectively these motifs are functional but does not prove that any given instance is so. Candidates were surveyed for native disorder prediction using GlobPlot and IUPred and for motif conservation in homologues. Among >25 strong new candidates, the most notable are human HIPK2, CHFR, CDC27, Dab2, Upf2, kinesin Eg5, DNA Topoisomerase 1 and yeast Cdc5 and Swi5. A similar number of weaker candidates were present. These proteins have yet to be tested for APC/C targeted destruction, providing potential new avenues of research.

  8. Selection against spurious promoter motifs correlates withtranslational efficiency across bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Froula, Jeffrey L.; Francino, M. Pilar

    2007-05-01

    Because binding of RNAP to misplaced sites could compromise the efficiency of transcription, natural selection for the optimization of gene expression should regulate the distribution of DNA motifs capable of RNAP-binding across the genome. Here we analyze the distribution of the -10 promoter motifs that bind the {sigma}{sup 70} subunit of RNAP in 42 bacterial genomes. We show that selection on these motifs operates across the genome, maintaining an over-representation of -10 motifs in regulatory sequences while eliminating them from the nonfunctional and, in most cases, from the protein coding regions. In some genomes, however, -10 sites are over-represented in the coding sequences; these sites could induce pauses effecting regulatory roles throughout the length of a transcriptional unit. For nonfunctional sequences, the extent of motif under-representation varies across genomes in a manner that broadly correlates with the number of tRNA genes, a good indicator of translational speed and growth rate. This suggests that minimizing the time invested in gene transcription is an important selective pressure against spurious binding. However, selection against spurious binding is detectable in the reduced genomes of host-restricted bacteria that grow at slow rates, indicating that components of efficiency other than speed may also be important. Minimizing the number of RNAP molecules per cell required for transcription, and the corresponding energetic expense, may be most relevant in slow growers. These results indicate that genome-level properties affecting the efficiency of transcription and translation can respond in an integrated manner to optimize gene expression. The detection of selection against promoter motifs in nonfunctional regions also implies that no sequence may evolve free of selective constraints, at least in the relatively small and unstructured genomes of bacteria.

  9. Genome Analysis of Conserved Dehydrin Motifs in Vascular Plants

    Directory of Open Access Journals (Sweden)

    Ahmad A. Malik

    2017-05-01

    Full Text Available Dehydrins, a large family of abiotic stress proteins, are defined by the presence of a mostly conserved motif known as the K-segment, and may also contain two other conserved motifs known as the Y-segment and S-segment. Using the dehydrin literature, we developed a sequence motif definition of the K-segment, which we used to create a large dataset of dehydrin sequences by searching the Pfam00257 dehydrin dataset and the Phytozome 10 sequences of vascular plants. A comprehensive analysis of these sequences reveals that lysine residues are highly conserved in the K-segment, while the amino acid type is often conserved at other positions. Despite the Y-segment name, the central tyrosine is somewhat conserved, but can be substituted with two other small aromatic amino acids (phenylalanine or histidine. The S-segment contains a series of serine residues, but in some proteins is also preceded by a conserved LHR sequence. In many dehydrins containing all three of these motifs the S-segment is linked to the K-segment by a GXGGRRKK motif (where X can be any amino acid, suggesting a functional linkage between these two motifs. An analysis of the sequences shows that the dehydrin architecture and several biochemical properties (isoelectric point, molecular mass, and hydrophobicity score are dependent on each other, and that some dehydrin architectures are overexpressed during certain abiotic stress, suggesting that they may be optimized for a specific abiotic stress while others are involved in all forms of dehydration stress (drought, cold, and salinity.

  10. Hand Hygiene: When and How

    Science.gov (United States)

    Hand Hygiene When and How August 2009 How to handrub? How to handwash? RUB HANDS FOR HAND HYGIENE! WASH HANDS WHEN VISIBLY SOILED Duration of the ... its use. When? YOUR 5 MOMENTS FOR HAND HYGIENE 1 BEFORETOUCHINGA PATIENT 2 B P ECFLOER R ...

  11. BayesMD: flexible biological modeling for motif discovery

    DEFF Research Database (Denmark)

    Tang, Man-Hung Eric; Krogh, Anders; Winther, Ole

    2008-01-01

    We present BayesMD, a Bayesian Motif Discovery model with several new features. Three different types of biological a priori knowledge are built into the framework in a modular fashion. A mixture of Dirichlets is used as prior over nucleotide probabilities in binding sites. It is trained on trans......We present BayesMD, a Bayesian Motif Discovery model with several new features. Three different types of biological a priori knowledge are built into the framework in a modular fashion. A mixture of Dirichlets is used as prior over nucleotide probabilities in binding sites. It is trained...

  12. Sport as the Pragmatic Determiner, Motif and Theme of Pindaric Odes

    Directory of Open Access Journals (Sweden)

    Brane Senegačnik

    2015-07-01

    Full Text Available The vast majority of Pindar’s integrally preserved poetry is linked to sport: his epinicia, collected in four volumes, are dedicated to victors in various sporting disciplines at the four pan-Hellenic games. This is more than an external pragmatic circumstance: an obligatory constituent of the epinicium is the victor’s genealogy, often accompanied by a detailed account of the victor’s feat and career as well as the sporting achievements of his ancestors. Sporting success is a peak of human life, worth any exertion or cost, but even so it cannot lead to transcendence: it is a single moment blending into the shadow of transience. The sporting victory motif thus expands into the theme of human identity, which is in Pindar’s religious world crucially determined by man’s closeness or semblance to the gods on the one hand and the insurmountable difference on the other.

  13. Predictors and Prognostic Value of Worsening Renal Function During Admission in HFpEF Versus HFrEF: Data From the KorAHF (Korean Acute Heart Failure) Registry.

    Science.gov (United States)

    Kang, Jeehoon; Park, Jin Joo; Cho, Young-Jin; Oh, Il-Young; Park, Hyun-Ah; Lee, Sang Eun; Kim, Min-Seok; Cho, Hyun-Jai; Lee, Hae-Young; Choi, Jin Oh; Hwang, Kyung-Kuk; Kim, Kye Hun; Yoo, Byung-Su; Kang, Seok-Min; Baek, Sang Hong; Jeon, Eun-Seok; Kim, Jae-Joong; Cho, Myeong-Chan; Chae, Shung Chull; Oh, Byung-Hee; Choi, Dong-Ju

    2018-03-13

    Worsening renal function (WRF) is associated with adverse outcomes in patients with heart failure. We investigated the predictors and prognostic value of WRF during admission, in patients with preserved ejection fraction (HFpEF) versus those with reduced ejection fraction (HFrEF). A total of 5625 patients were enrolled in the KorAHF (Korean Acute Heart Failure) registry. WRF was defined as an absolute increase in creatinine of ≥0.3 mg/dL. Transient WRF was defined as recovery of creatinine at discharge, whereas persistent WRF was indicated by a nonrecovered creatinine level. HFpEF and HFrEF were defined as a left ventricle ejection fraction ≥50% and ≤40%, respectively. Among the total population, WRF occurred in 3101 patients (55.1%). By heart failure subgroup, WRF occurred more frequently in HFrEF (57.0% versus 51.3%; P failure subgroups. Among various predictors of WRF, chronic renal failure was the strongest predictor. WRF was an independent predictor of adverse in-hospital outcomes (HFrEF: odds ratio; 2.75; 95% confidence interval, 1.50-5.02; P =0.001; HFpEF: odds ratio, 9.48; 95% confidence interval, 1.19-75.89; P =0.034) and 1-year mortality (HFrEF: hazard ratio, 1.41; 95% confidence interval, 1.12-1.78; P =0.004 versus HFpEF: hazard ratio, 1.72; 95% confidence interval, 1.23-2.42; P =0.002). Transient WRF was a risk factor for 1-year mortality, whereas persistent WRF had no additive risk compared to transient WRF. In patients with acute heart failure patients, WRF is an independent predictor of adverse in-hospital and follow-up outcomes in both HFrEF and HFpEF, though with a different effect size. URL: https://www.clinicaltrials.gov. Unique identifier: NCT01389843. © 2018 The Authors. Published on behalf of the American Heart Association, Inc., by Wiley.

  14. Positional bias of general and tissue-specific regulatory motifs in mouse gene promoters

    Directory of Open Access Journals (Sweden)

    Farré Domènec

    2007-12-01

    Full Text Available Abstract Background The arrangement of regulatory motifs in gene promoters, or promoter architecture, is the result of mutation and selection processes that have operated over many millions of years. In mammals, tissue-specific transcriptional regulation is related to the presence of specific protein-interacting DNA motifs in gene promoters. However, little is known about the relative location and spacing of these motifs. To fill this gap, we have performed a systematic search for motifs that show significant bias at specific promoter locations in a large collection of housekeeping and tissue-specific genes. Results We observe that promoters driving housekeeping gene expression are enriched in particular motifs with strong positional bias, such as YY1, which are of little relevance in promoters driving tissue-specific expression. We also identify a large number of motifs that show positional bias in genes expressed in a highly tissue-specific manner. They include well-known tissue-specific motifs, such as HNF1 and HNF4 motifs in liver, kidney and small intestine, or RFX motifs in testis, as well as many potentially novel regulatory motifs. Based on this analysis, we provide predictions for 559 tissue-specific motifs in mouse gene promoters. Conclusion The study shows that motif positional bias is an important feature of mammalian proximal promoters and that it affects both general and tissue-specific motifs. Motif positional constraints define very distinct promoter architectures depending on breadth of expression and type of tissue.

  15. Clean Hands Count

    Medline Plus

    Full Text Available ... CDC) 97,825 views 5:12 CDC Flu Education Video - Duration: 10:26. Nicole Shelton 213 views ... Infection Control Video - Duration: 20:55. Paramedical Services Education Page 4,735 views 20:55 Hand Washing ...

  16. Hand Eczema: Treatment options

    DEFF Research Database (Denmark)

    Lund, Tamara Theresia; Agner, Tove

    2017-01-01

    Hand eczema is a common disease, it affects young people, is often work-related, and the burden of the disease is significant for the individual as well as for society. Factors to be considered when choosing a treatment strategy are, among others, whether the eczema is acute or chronic, the sever...

  17. Clean Hands Count

    Medline Plus

    Full Text Available ... Queue __count__/__total__ It’s YouTube. Uninterrupted. Loading... Want music and videos with zero ads? Get YouTube Red. ... 824 views 1:36 Wash 'Em - Hand Hygiene Music Video - Duration: 5:46. Jefferson Health 409,492 ...

  18. Clean Hands Count

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    Full Text Available ... Queue __count__/__total__ It’s YouTube. Uninterrupted. Loading... Want music and videos with zero ads? Get YouTube Red. ... 786 views 1:36 Wash 'Em - Hand Hygiene Music Video - Duration: 5:46. Jefferson Health 413,702 ...

  19. Clean Hands Count

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    Full Text Available ... Queue __count__/__total__ It’s YouTube. Uninterrupted. Loading... Want music and videos with zero ads? Get YouTube Red. ... 414 views 3:10 Wash 'Em - Hand Hygiene Music Video - Duration: 5:46. Thomas Jefferson University & Jefferson ...

  20. Clean Hands Count

    Medline Plus

    Full Text Available ... Queue __count__/__total__ It’s YouTube. Uninterrupted. Loading... Want music and videos with zero ads? Get YouTube Red. ... 869 views 1:36 Wash 'Em - Hand Hygiene Music Video - Duration: 5:46. Jefferson Health 410,052 ...

  1. Wash Your Hands

    Centers for Disease Control (CDC) Podcasts

    2010-03-08

    This video shows kids how to properly wash their hands, one of the most important steps we can take to avoid getting sick and spreading germs to others.  Created: 3/8/2010 by Centers for Disease Control and Prevention (CDC).   Date Released: 3/8/2010.

  2. Clean Hands Count

    Medline Plus

    Full Text Available ... no cure tomorrow - Duration: 3:10. World Health Organization 75,585 views 3:10 Wash 'Em - Hand ... soap and water - Duration: 1:27. World Health Organization 224,180 views 1:27 The five moments ...

  3. Clean Hands Count

    Medline Plus

    Full Text Available ... Queue __count__/__total__ It’s YouTube. Uninterrupted. Loading... Want music and videos with zero ads? Get YouTube Red. ... 460 views 3:10 Wash 'Em - Hand Hygiene Music Video - Duration: 5:46. Thomas Jefferson University & Jefferson ...

  4. Clean Hands Count

    Medline Plus

    Full Text Available ... action today; no cure tomorrow - Duration: 3:10. World Health Organization 75,362 views 3:10 Wash ' ... handwash? With soap and water - Duration: 1:27. World Health Organization 219,427 views 1:27 Hand ...

  5. Clean Hands Count

    Medline Plus

    Full Text Available ... action today; no cure tomorrow - Duration: 3:10. World Health Organization 74,478 views 3:10 Wash your Hands - ... handwash? With soap and water - Duration: 1:27. World Health Organization 215,487 views 1:27 Infection Control Video - ...

  6. Clean Hands Count

    Medline Plus

    Full Text Available ... Queue __count__/__total__ It’s YouTube. Uninterrupted. Loading... Want music and videos with zero ads? Get YouTube Red. ... 741 views 3:10 Wash 'Em - Hand Hygiene Music Video - Duration: 5:46. Jefferson Health 410,052 ...

  7. Matching hand radiographs

    NARCIS (Netherlands)

    Kauffman, J.A.; Slump, Cornelis H.; Bernelot Moens, H.J.

    2005-01-01

    Biometric verification and identification methods of medical images can be used to find possible inconsistencies in patient records. Such methods may also be useful for forensic research. In this work we present a method for identifying patients by their hand radiographs. We use active appearance

  8. Clean Hands Count

    Medline Plus

    Full Text Available ... today; no cure tomorrow - Duration: 3:10. World Health Organization 72,885 views 3:10 Wash 'Em - Hand Hygiene Music Video - Duration: 5:46. Jefferson Health 410,052 views 5:46 'It's in your ...

  9. Clean Hands Count

    Medline Plus

    Full Text Available ... Queue __count__/__total__ It’s YouTube. Uninterrupted. Loading... Want music and videos with zero ads? Get YouTube Red. ... 029 views 3:10 Wash 'Em - Hand Hygiene Music Video - Duration: 5:46. Jefferson Health 411,974 ...

  10. Clean Hands Count

    Medline Plus

    Full Text Available ... no cure tomorrow - Duration: 3:10. World Health Organization 78,256 views 3:10 Wash 'Em - Hand ... message from WHO - Duration: 10:07. World Health Organization 9,045 views 10:07 A very serious ...

  11. Hands-On Calculus

    Science.gov (United States)

    Sutherland, Melissa

    2006-01-01

    In this paper we discuss manipulatives and hands-on investigations for Calculus involving volume, arc length, and surface area to motivate and develop formulae which can then be verified using techniques of integration. Pre-service teachers in calculus courses using these activities experience a classroom in which active learning is encouraged and…

  12. Clean Hands Count

    Medline Plus

    Full Text Available ... action today; no cure tomorrow - Duration: 3:10. World Health Organization 78,256 views 3:10 Wash ... handwash? With soap and water - Duration: 1:27. World Health Organization 230,361 views 1:27 Hand ...

  13. Hands-on Humidity.

    Science.gov (United States)

    Pankiewicz, Philip R.

    1992-01-01

    Presents five hands-on activities that allow students to detect, measure, reduce, and eliminate moisture. Students make a humidity detector and a hygrometer, examine the effects of moisture on different substances, calculate the percent of water in a given food, and examine the absorption potential of different desiccants. (MDH)

  14. Clean Hands Count

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  17. Clean Hands Count

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    Full Text Available ... today; no cure tomorrow - Duration: 3:10. World Health Organization 69,414 views 3:10 Hand Washing ... Video - Duration: 5:46. Thomas Jefferson University & Jefferson Health 408,436 views 5:46 83 videos Play ...

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  1. Clean Hands Count

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    Full Text Available ... action today; no cure tomorrow - Duration: 3:10. World Health Organization 72,319 views 3:10 Wash 'Em - Hand ... handwash? With soap and water - Duration: 1:27. World Health Organization 205,878 views 1:27 Germ Smart - Wash ...

  2. Hands On Earth Science.

    Science.gov (United States)

    Weisgarber, Sherry L.; Van Doren, Lisa; Hackathorn, Merrianne; Hannibal, Joseph T.; Hansgen, Richard

    This publication is a collection of 13 hands-on activities that focus on earth science-related activities and involve students in learning about growing crystals, tectonics, fossils, rock and minerals, modeling Ohio geology, geologic time, determining true north, and constructing scale-models of the Earth-moon system. Each activity contains…

  3. Clean Hands Count

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    Full Text Available ... Queue __count__/__total__ It’s YouTube. Uninterrupted. Loading... Want music and videos with zero ads? Get YouTube Red. ... 384 views 1:19 Wash 'Em - Hand Hygiene Music Video - Duration: 5:46. Thomas Jefferson University & Jefferson ...

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    Full Text Available ... Queue __count__/__total__ It’s YouTube. Uninterrupted. Loading... Want music and videos with zero ads? Get YouTube Red. ... 285 views 1:36 Wash 'Em - Hand Hygiene Music Video - Duration: 5:46. Jefferson Health 410,052 ...

  5. Clean Hands Count

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    Full Text Available ... Gorin 243,451 views 2:57 Hand Hygiene Dance - Duration: 3:15. mohd hafiz 34,146 views ... Language: English Location: United States Restricted Mode: Off History Help Loading... Loading... Loading... About Press Copyright Creators ...

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    Full Text Available ... YouTube. Uninterrupted. Loading... Want music and videos with zero ads? Get YouTube Red. Working... Not now Try ... Wash your Hands - it just makes sense. - Duration: 1:36. Seema Marwaha 400,493 views 1:36 ...

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    Full Text Available ... Em - Hand Hygiene Music Video - Duration: 5:46. Thomas Jefferson University & Jefferson Health 408,436 views 5: ... Prevention (CDC) 97,277 views 5:12 Loading more suggestions... Show more Language: English Location: United States ...

  9. Hands-On Hydrology

    Science.gov (United States)

    Mathews, Catherine E.; Monroe, Louise Nelson

    2004-01-01

    A professional school and university collaboration enables elementary students and their teachers to explore hydrology concepts and realize the beneficial functions of wetlands. Hands-on experiences involve young students in determining water quality at field sites after laying the groundwork with activities related to the hydrologic cycle,…

  10. Clean Hands Count

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    Full Text Available ... News 581,131 views 18:49 Just Good Music 24/7 ● Classic Live Radio classics. 1,406 ... 611,013 views 1:46 Hand hygiene FULL music video - Duration: 2:33. AlfredHealthTV 26,798 views ...

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    Full Text Available ... 52 Hand Sanitizers and Soaps Put to the Test - Duration: 2:26. ABC News 42,006 views ... Developers +YouTube Terms Privacy Policy & Safety Send feedback Test new features Loading... Working... Sign in to add ...

  13. Is the mazEF toxin-antitoxin system responsible for vancomycin resistance in clinical isolates of Enterococcus faecalis?

    Science.gov (United States)

    Sadeghifard, Nourkhoda; Soheili, Sara; Sekawi, Zamberi; Ghafourian, Sobhan

    2014-01-01

    The current study was conducted to investigate the relationship between vancomycin-resistant Enterococcus faecalis (VRE) and the presence of mazEF toxin-antitoxin (TA) system, which may be useful as target for novel antimicrobial therapy concepts. The susceptibility of E. faecalis was determined by MIC, and the presence of the mazEF TA system was evaluated by PCR. Among 200 E. faecalis isolates 39.5% showed resistance to vancomycin (VRE), while 60.5% were susceptible strains (VSE). The mazEF TA system was positive in all VRE isolates (100%), but less prevalent (38/121, 31.4%) among the 121 VSE strains. In conclusion, our study demonstrated a positive relationship between the presence of vancomycin resistance and mazEF TA system. This observation may introduce therapeutic options against a novel antimicrobial target in enterococci.

  14. Belisa-Dido’s Suicide: Variations on a Vergilian Motif in Lope de Vega’s Non-Dramatic Works

    Directory of Open Access Journals (Sweden)

    Antonio Sánchez Jiménez

    2018-05-01

    Full Text Available This article examines the theme of the abandoned beloved in four texts by Lope de Vega in which the motif combines subtexts of different origin: on the one hand, a conspicuous biographical key, filtered by literature (Belisa’s and Filis’ attempted suicide; on the other, erudite sources (Dido’s suicide. Analyzing these four texts, dating from Lope’s youth and de senectute periods, we also suggest how Lope could have come up with the idea of combining these strains inspiring himself in an anonymous romance (La desesperada Dido that appears to be the source of the famous De pechos sobre una torre.

  15. SSTRAP: A computational model for genomic motif discovery ...

    African Journals Online (AJOL)

    Computational methods can potentially provide high-quality prediction of biological molecules such as DNA binding sites and Transcription factors and therefore reduce the time needed for experimental verification and challenges associated with experimental methods. These biological molecules or motifs have significant ...

  16. Identification of a Baeyer-Villiger monooxygenase sequence motif

    NARCIS (Netherlands)

    Fraaije, MW; Kamerbeek, NM; van Berkel, WJH; Janssen, DB; Kamerbeek, Nanne M.; Berkel, Willem J.H. van

    2002-01-01

    Baeyer-Villiger monooxygenases (BVMOs) form a distinct class of flavoproteins that catalyze the insertion of an oxygen atom in a C-C bond using dioxygen and NAD(P)H. Using newly characterized BVMO sequences, we have uncovered a BVMO-identifying sequence motif: FXGXXXRXXXW(P/D). Studies with

  17. Linear motif atlas for phosphorylation-dependent signaling

    DEFF Research Database (Denmark)

    Miller, Martin Lee; Jensen, LJ; Diella, F

    2008-01-01

    bind to them remains a challenge. NetPhorest is an atlas of consensus sequence motifs that covers 179 kinases and 104 phosphorylation-dependent binding domains [Src homology 2 (SH2), phosphotyrosine binding (PTB), BRCA1 C-terminal (BRCT), WW, and 14-3-3]. The atlas reveals new aspects of signaling...

  18. [Cover motifs of the Tidsskrift. A 14-year cavalcade].

    Science.gov (United States)

    Nylenna, M

    1998-12-10

    In 1985 the Journal of the Norwegian Medical Association changed its cover policy, moving the table of contents inside the Journal and introducing cover illustrations. This article provides an analysis of all cover illustrations published over this 14-year period, 420 covers in all. There is a great variation in cover motifs and designs and a development towards more general motifs. The initial emphasis on historical and medical aspects is now less pronounced, while the use of works of art and nature motifs has increased, and the cover now more often has a direct bearing on the specific contents of the issue. Professor of medical history Oivind Larsen has photographed two thirds of the covers and contributed 95% of the inside essay-style reflections on the cover motif. Over the years, he has expanded the role of the historian of medicine disseminating knowledge to include that of the raconteur with a personal tone of voice. The Journal's covers are now one of its most characteristic features, emblematic of the Journal's ambition of standing for quality and timelessness vis-à-vis the news media, and of its aim of bridging the gap between medicine and the humanities.

  19. Perspektif Psikologi Humanistik Abraham Maslow dalam Meninjau Motif Pelaku Pembunuhan

    OpenAIRE

    Nurwatie, Azrina; Fauzia, Rahmi; Akbar, Sukma Noor

    2014-01-01

    Fokus penelitian ini diarahkan pada motif pelaku pembunuhan dengan meninjaunya melalui perspektif psikologi humanistik Abraham Maslow. Subyek dalam penelitian ini berjumlah dua orang narapidana yang berada di Lapas Kelas IIA Anak Martapura dengan kasus pembunuhan. Metode penelitian yang digunakan dalam penelitian ini adalah metode penelitian kualitatif. Teknik pengumpulan data melalui wawancara, observasi, dokumentasi,dan pemeriksaan psikologis (tes grafis). Berdasarkan hasil analisis data da...

  20. Motifs in triadic random graphs based on Steiner triple systems

    Science.gov (United States)

    Winkler, Marco; Reichardt, Jörg

    2013-08-01

    Conventionally, pairwise relationships between nodes are considered to be the fundamental building blocks of complex networks. However, over the last decade, the overabundance of certain subnetwork patterns, i.e., the so-called motifs, has attracted much attention. It has been hypothesized that these motifs, instead of links, serve as the building blocks of network structures. Although the relation between a network's topology and the general properties of the system, such as its function, its robustness against perturbations, or its efficiency in spreading information, is the central theme of network science, there is still a lack of sound generative models needed for testing the functional role of subgraph motifs. Our work aims to overcome this limitation. We employ the framework of exponential random graph models (ERGMs) to define models based on triadic substructures. The fact that only a small portion of triads can actually be set independently poses a challenge for the formulation of such models. To overcome this obstacle, we use Steiner triple systems (STSs). These are partitions of sets of nodes into pair-disjoint triads, which thus can be specified independently. Combining the concepts of ERGMs and STSs, we suggest generative models capable of generating ensembles of networks with nontrivial triadic Z-score profiles. Further, we discover inevitable correlations between the abundance of triad patterns, which occur solely for statistical reasons and need to be taken into account when discussing the functional implications of motif statistics. Moreover, we calculate the degree distributions of our triadic random graphs analytically.

  1. Genetic analysis of beta1 integrin "activation motifs" in mice

    DEFF Research Database (Denmark)

    Czuchra, Aleksandra; Meyer, Hannelore; Legate, Kyle R

    2006-01-01

    -null phenotype in vivo. Surprisingly, neither the substitution of the tyrosines with phenylalanine nor the aspartic acid with alanine resulted in an obvious defect. These data suggest that the NPXY motifs of the beta1 integrin tail are essential for beta1 integrin function, whereas tyrosine phosphorylation...

  2. Insights into the motif preference of APOBEC3 enzymes.

    Directory of Open Access Journals (Sweden)

    Diako Ebrahimi

    Full Text Available We used a multivariate data analysis approach to identify motifs associated with HIV hypermutation by different APOBEC3 enzymes. The analysis showed that APOBEC3G targets G mainly within GG, TG, TGG, GGG, TGGG and also GGGT. The G nucleotides flanked by a C at the 3' end (in +1 and +2 positions were indicated as disfavoured targets by APOBEC3G. The G nucleotides within GGGG were found to be targeted at a frequency much less than what is expected. We found that the infrequent G-to-A mutation within GGGG is not limited to the inaccessibility, to APOBEC3, of poly Gs in the central and 3'polypurine tracts (PPTs which remain double stranded during the HIV reverse transcription. GGGG motifs outside the PPTs were also disfavoured. The motifs GGAG and GAGG were also found to be disfavoured targets for APOBEC3. The motif-dependent mutation of G within the HIV genome by members of the APOBEC3 family other than APOBEC3G was limited to GA→AA changes. The results did not show evidence of other types of context dependent G-to-A changes in the HIV genome.

  3. Translation elongation factor EF-Tu modulates filament formation of actin-like MreB protein in vitro.

    Science.gov (United States)

    Defeu Soufo, Hervé Joël; Reimold, Christian; Breddermann, Hannes; Mannherz, Hans G; Graumann, Peter L

    2015-04-24

    EF-Tu has been shown to interact with actin-like protein MreB and to affect its localization in Escherichia coli and in Bacillus subtilis cells. We have purified YFP-MreB in an active form, which forms filaments on glass slides in vitro and was active in dynamic light-scattering assays, polymerizing in milliseconds after addition of magnesium. Purified EF-Tu enhanced the amount of MreB filaments, as seen by sedimentation assays, the speed of filament formation and the length of MreB filaments in vitro. EF-Tu had the strongest impact on MreB filaments in a 1:1 ratio, and EF-Tu co-sedimented with MreB filaments, revealing a stoichiometric interaction between both proteins. This was supported by cross-linking assays where 1:1 species were well detectable. When expressed in E. coli cells, B. subtilis MreB formed filaments and induced the formation of co-localizing B. subtilis EF-Tu structures, indicating that MreB can direct the positioning of EF-Tu structures in a heterologous cell system. Fluorescence recovery after photobleaching analysis showed that MreB filaments have a higher turnover in B. subtilis cells than in E. coli cells, indicating different filament kinetics in homologous or heterologous cell systems. The data show that MreB can direct the localization of EF-Tu in vivo, which in turn positively affects the formation and dynamics of MreB filaments. Thus, EF-Tu is a modulator of the activity of a bacterial actin-like protein. Copyright © 2015. Published by Elsevier Ltd.

  4. Development of the finite element method in the thermal field. TRIO-EF software for thermal and radiation analysis

    International Nuclear Information System (INIS)

    Casalotti, N.; Magnaud, J.P.

    1989-01-01

    The possibilities of the TRIO-EF software in the thermal field are presented. The TRIO-EF is a computer program based on the finite element method and used for three-dimensional incompressible flow analysis. It enables the calculation of three-dimensional heat transfer and the fluid/structure analysis. The geometrically complex radiative reactor systems are taken into account in the form factor calculation. The implemented algorithms are described [fr

  5. Kidney-Sparing Methods for Extended-Field Intensity-Modulated Radiotherapy (EF-IMRT) in Cervical Carcinoma Treatment.

    Science.gov (United States)

    Kunogi, Hiroaki; Yamaguchi, Nanae; Terao, Yasuhisa; Sasai, Keisuke

    2016-01-01

    Coplanar extended-field intensity-modulated radiation therapy (EF-IMRT) targeting the whole-pelvic and para-aortic lymph nodes in patients with advanced cervical cancer results in impaired creatinine clearance. An improvement in renal function cannot be expected unless low-dose (approximately 10 Gy) kidney exposure is reduced. The dosimetric method should be considered during EF-IMRT planning to further reduce low-dose exposure to the kidneys. To assess the usefulness of non-coplanar EF-IMRT with kidney-avoiding beams to spare the kidneys during cervical carcinoma treatment in dosimetric analysis between non-coplanar and coplanar EF-IMRT, we compared the doses of the target organ and organs at risk, including the kidney, in 10 consecutive patients. To estimate the influence of EFRT on renal dysfunction, creatinine clearance values after treatment were also examined in 18 consecutive patients. Of these 18 patients, 10 patients who were included in the dosimetric analysis underwent extended field radiation therapy (EFRT) with concurrent chemotherapy, and eight patients underwent whole-pelvis radiation therapy with concurrent chemotherapy to treat cervical carcinoma between April 2012 and March 2015 at our institution. In the dosimetric analysis, non-coplanar EF-IMRT was effective at reducing low-dose (approximately 10 Gy) exposure to the kidneys, thus maintaining target coverage and sparing other organs at risk, such as the small bowel, rectum, and bladder, compared with coplanar EF-IMRT. Renal function in all 10 patients who underwent EFRT, including coplanar EF-IMRT (with kidney irradiation), was low after treatment, and differed significantly from that of the eight patients who underwent WPRT (no kidney irradiation) 6 months after the first day of treatment (P = 0.005). In conclusion, non-coplanar EF-IMRT should be considered in patients with advanced cervical cancer, particularly in patients with a long life expectancy or with pre-existing renal dysfunction.

  6. A neutron scattering study of the ternary complex EF-Tu.GTP-valyl-tRNAVal1A

    DEFF Research Database (Denmark)

    Österberg, R.; Elias, P.; Kjems, Jørgen

    1986-01-01

    The complex formation between elongation factor Tu (EF-Tu), GTP, and valyl-tRNAVal1A has been investigated in a hepes buffer of "pH" 7.4 and 0.2 M ionic strength using the small-angle neutron scattering method at concentrations of D2O where EF-Tu (42% D2O) and tRNA (71% D2O) are successively...

  7. Everyday Prospective Memory and Executive Function Deficits Associated with Exposure to Second-Hand Smoke

    Directory of Open Access Journals (Sweden)

    Thomas M. Heffernan

    2013-01-01

    Full Text Available This study explored whether exposure to second-hand smoke (SHS has a detrimental impact upon everyday memory in two groups of non-smokers; one which reported regular exposure to SHS and one that reported never having been exposed to SHS. Thirty-four non-smokers who reported having been regularly exposed to SHS (SHS group and 34 non-smokers who reported never having been exposed to SHS (non-SHS group were compared on self-reports of prospective memory (PM: remembering future intentions and/or activities and executive function (EF: those processes involved in attention, multitasking and decision-making. The Prospective and Retrospective Memory Questionnaire (PRMQ assessed everyday PM lapses; the Executive Function Questionnaire (EFQ assessed self-reported problems in EF; a drug-use questionnaire and a mood questionnaire were also administered. Two univariate ANCOVAs were applied to the PM and EF data, controlling for between-group differences in age, weekly alcohol use, anxiety and depression scores, and self-reported retrospective memory scores. The SHS group reported significantly more lapses on the PRMQ and more deficits on the EFQ than the non-SHS group. These findings provide new insights into PM and EF deficits associated with prolonged exposure to SHS in a group of non-smokers. Possible explanations and suggestions for future research are also considered.

  8. Simultaneous Binding of Multiple EF-Tu Copies to Translating Ribosomes in Live Escherichia coli.

    Science.gov (United States)

    Mustafi, Mainak; Weisshaar, James C

    2018-01-16

    In bacteria, elongation factor Tu is a translational cofactor that forms ternary complexes with aminoacyl-tRNA (aa-tRNA) and GTP. Binding of a ternary complex to one of four flexible L7/L12 units on the ribosome tethers a charged tRNA in close proximity to the ribosomal A site. Two sequential tests for a match between the aa-tRNA anticodon and the current mRNA codon then follow. Because one elongation cycle can occur in as little as 50 ms and the vast majority of aa-tRNA copies are not cognate with the current mRNA codon, this testing must occur rapidly. We present a single-molecule localization and tracking study of fluorescently labeled EF-Tu in live Escherichia coli Imaging at 2 ms/frame distinguishes 60% slowly diffusing EF-Tu copies (assigned as transiently bound to translating ribosome) from 40% rapidly diffusing copies (assigned as a mixture of free ternary complexes and free EF-Tu). Combining these percentages with copy number estimates, we infer that the four L7/L12 sites are essentially saturated with ternary complexes in vivo. The results corroborate an earlier inference that all four sites can simultaneously tether ternary complexes near the A site, creating a high local concentration that may greatly enhance the rate of testing of aa-tRNAs. Our data and a combinatorial argument both suggest that the initial recognition test for a codon-anticodon match occurs in less than 1 to 2 ms per aa-tRNA copy. The results refute a recent study (A. Plochowietz, I. Farrell, Z. Smilansky, B. S. Cooperman, and A. N. Kapanidis, Nucleic Acids Res 45:926-937, 2016, https://doi.org/10.1093/nar/gkw787) of tRNA diffusion in E. coli that inferred that aa-tRNAs arrive at the ribosomal A site as bare monomers, not as ternary complexes. IMPORTANCE Ribosomes catalyze translation of the mRNA codon sequence into the corresponding sequence of amino acids within the nascent polypeptide chain. Polypeptide elongation can be as fast as 50 ms per added amino acid. Each amino acid

  9. Maltravieso. A hands sanctuary in Extremadura

    Directory of Open Access Journals (Sweden)

    Ripoll López, Sergio

    1999-12-01

    Full Text Available The project of investigation carried out in the cave of Maltravieso has not only yielded a notable increase in the inventory of artistic depictions -hands, zoomorphs and ideomorphs- that are known in the cave, but has also produced some new information with regard to the chronological framework of the production of the various depictions, their phases'of execution, the techniques used in creating the figures, and the typology of the motifs. Another important contribution of our work has been the observation that mutilations of these hands do not exist. The supposed amputations, which have been commented on widely in the traditional literature, are nothing of the kind-they are simply an obscuring of the little finger, with the same pigment as was used to make the hand stencil.

    El proyecto de investigación llevado a cabo en la cueva de Maltravieso, no sólo ha supuesto un notable incremento en el inventario de representaciones artísticas -manos, zoomorfos e ideomorfos- conocidos en la cueva de Maltravieso, sino que aporta importantes novedades, respecto al momento cronológico de realización de las distintas manifestaciones, fases de ejecución, técnica empleada en la elaboración de las figuras y tipología de los motivos. Otra novedad importante derivada de nuestra investigación, ha sido la constatación de la inexistencia de mutilaciones en las manos. Estas amputaciones, tan largamente comentadas por la bibliografía tradicional, no son tales, sino simples ocultaciones intencionales del dedo meñique con el mismo pigmento empleado para plasmar la mano en negativo.

  10. Decoding the biosynthesis and function of diphthamide, an enigmatic modification of translation elongation factor 2 (EF2

    Directory of Open Access Journals (Sweden)

    Raffael Schaffrath

    2014-05-01

    Full Text Available Diphthamide is a highly conserved modification of archaeal and eukaryal translation elongation factor 2 (EF2 and yet why cells need EF2 to contain diphthamide is unclear. In yeast, the first steps of diphthamide synthesis and the genes (DPH1-DPH5 required to form the intermediate diphthine are well-documented. However, the last step, amidadation of diphthine to diphthamide, had largely been ill-defined. Remarkably, through mining genome-wide synthetic gene array (SGA and chemical genomics databases, recent studies by Uthman et al. [PLoS Genetics (2013 9, e1003334] and Su et al. [Proc. Natl. Acad. Sci. USA (2012 109, 19983-19987] have identified two more diphthamide players, DPH6 and DPH7. Consistent with roles in the amidation step, dph6 and dph7 deletion strains fail to complete diphthamide synthesis and accumulate diphthine-modified EF2. In contrast to Dph6, the catalytically relevant amidase, Dph7 appears to be regulatory. As shown by Uthman et al., it promotes dissociation of diphthine synthase (Dph5 from EF2, allowing diphthine amidation by Dph6 to occur and thereby coupling diphthine synthesis to the terminal step in the pathway. Remarkably, the study by Uthman et al. suggests that Dph5 has a novel role as an EF2 inhibitor that affects cell growth when diphthamide synthesis is blocked or incomplete and, importantly, shows that diphthamide promotes the accuracy of EF2 performance during translation.

  11. The Influence of the Toxin/Antitoxin mazEF on Growth and Survival of Listeria monocytogenes under Stress.

    Science.gov (United States)

    Curtis, Thomas D; Takeuchi, Ippei; Gram, Lone; Knudsen, Gitte M

    2017-01-13

    A major factor in the resilience of Listeria monocytogenes is the alternative sigma factor B (σ B ). Type II Toxin/Antitoxin (TA) systems are also known to have a role in the bacterial stress response upon activation via the ClpP or Lon proteases. Directly upstream of the σ B operon in L. monocytogenes is the TA system mazEF , which can cleave mRNA at UACMU sites. In this study, we showed that the mazEF TA locus does not affect the level of persister formation during treatment with antibiotics in lethal doses, but exerts different effects according to the sub-inhibitory stress added. Growth of a Δ mazEF mutant was enhanced relative to the wildtype in the presence of sub-inhibitory norfloxacin and at 42 °C, but was decreased when challenged with ampicillin and gentamicin. In contrast to studies in Staphylococcus aureus , we found that the mazEF locus did not affect transcription of genes within the σ B operon, but MazEF effected the expression of the σ B -dependent genes opuCA and lmo0880 , with a 0.22 and 0.05 fold change, respectively, compared to the wildtype under sub-inhibitory norfloxacin conditions. How exactly this system operates remains an open question, however, our data indicates it is not analogous to the system of S. aureus , suggesting a novel mode of action for MazEF in L. monocytogenes.

  12. Sequence alignment reveals possible MAPK docking motifs on HIV proteins.

    Directory of Open Access Journals (Sweden)

    Perry Evans

    Full Text Available Over the course of HIV infection, virus replication is facilitated by the phosphorylation of HIV proteins by human ERK1 and ERK2 mitogen-activated protein kinases (MAPKs. MAPKs are known to phosphorylate their substrates by first binding with them at a docking site. Docking site interactions could be viable drug targets because the sequences guiding them are more specific than phosphorylation consensus sites. In this study we use multiple bioinformatics tools to discover candidate MAPK docking site motifs on HIV proteins known to be phosphorylated by MAPKs, and we discuss the possibility of targeting docking sites with drugs. Using sequence alignments of HIV proteins of different subtypes, we show that MAPK docking patterns previously described for human proteins appear on the HIV matrix, Tat, and Vif proteins in a strain dependent manner, but are absent from HIV Rev and appear on all HIV Nef strains. We revise the regular expressions of previously annotated MAPK docking patterns in order to provide a subtype independent motif that annotates all HIV proteins. One revision is based on a documented human variant of one of the substrate docking motifs, and the other reduces the number of required basic amino acids in the standard docking motifs from two to one. The proposed patterns are shown to be consistent with in silico docking between ERK1 and the HIV matrix protein. The motif usage on HIV proteins is sufficiently different from human proteins in amino acid sequence similarity to allow for HIV specific targeting using small-molecule drugs.

  13. Proof of U(VI) sorption on Acidovorax facilis by TRLFS and EF-TEM/EELS

    Energy Technology Data Exchange (ETDEWEB)

    Krawczyk-Baersch, Evelyn; Gerber, Ulrike [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Div. Biogeochemistry; Steudtner, Robin [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Div. Surface Processes

    2016-07-01

    In EF-TEM/EELS studies it was shown that U(VI) is sorbed mainly on the outer membrane of Acidovorax facilis. The results are supported by TRLFS measurements, which were performed on the pellet of the cells. In comparison to reference spectra of some cell membrane components, the measured emission spectra of the A. facilis pellet show the best agreement with those of the Uranyl-lipopolysaccharide-complex. Hence, it can be concluded that phosphoryl groups may be the main binding sites for uranyl, located in the lipopolysaccharide unit in the outer membrane.

  14. Estimating Daily Evapotranspiration Based on A Model of Evapotranspiration Fraction (EF) for Mixed Pixels

    Science.gov (United States)

    Xin, X.; Li, F.; Peng, Z.; Qinhuo, L.

    2017-12-01

    Land surface heterogeneities significantly affect the reliability and accuracy of remotely sensed evapotranspiration (ET), and it gets worse for lower resolution data. At the same time, temporal scale extrapolation of the instantaneous latent heat flux (LE) at satellite overpass time to daily ET are crucial for applications of such remote sensing product. The purpose of this paper is to propose a simple but efficient model for estimating daytime evapotranspiration considering heterogeneity of mixed pixels. In order to do so, an equation to calculate evapotranspiration fraction (EF) of mixed pixels was derived based on two key assumptions. Assumption 1: the available energy (AE) of each sub-pixel equals approximately to that of any other sub-pixels in the same mixed pixel within acceptable margin of bias, and as same as the AE of the mixed pixel. It's only for a simpification of the equation, and its uncertainties and resulted errors in estimated ET are very small. Assumption 2: EF of each sub-pixel equals to the EF of the nearest pure pixel(s) of same land cover type. This equation is supposed to be capable of correcting the spatial scale error of the mixed pixels EF and can be used to calculated daily ET with daily AE data.The model was applied to an artificial oasis in the midstream of Heihe River. HJ-1B satellite data were used to estimate the lumped fluxes at the scale of 300 m after resampling the 30-m resolution datasets to 300 m resolution, which was used to carry on the key step of the model. The results before and after correction were compare to each other and validated using site data of eddy-correlation systems. Results indicated that the new model is capable of improving accuracy of daily ET estimation relative to the lumped method. Validations at 12 sites of eddy-correlation systems for 9 days of HJ-1B overpass showed that the R² increased to 0.82 from 0.62; the RMSE decreased to 1.60 MJ/m² from 2.47MJ/m²; the MBE decreased from 1.92 MJ/m² to 1

  15. Compact Dexterous Robotic Hand

    Science.gov (United States)

    Lovchik, Christopher Scott (Inventor); Diftler, Myron A. (Inventor)

    2001-01-01

    A compact robotic hand includes a palm housing, a wrist section, and a forearm section. The palm housing supports a plurality of fingers and one or more movable palm members that cooperate with the fingers to grasp and/or release an object. Each flexible finger comprises a plurality of hingedly connected segments, including a proximal segment pivotally connected to the palm housing. The proximal finger segment includes at least one groove defining first and second cam surfaces for engagement with a cable. A plurality of lead screw assemblies each carried by the palm housing are supplied with power from a flexible shaft rotated by an actuator and output linear motion to a cable move a finger. The cable is secured within a respective groove and enables each finger to move between an opened and closed position. A decoupling assembly pivotally connected to a proximal finger segment enables a cable connected thereto to control movement of an intermediate and distal finger segment independent of movement of the proximal finger segment. The dexterous robotic hand closely resembles the function of a human hand yet is light weight and capable of grasping both heavy and light objects with a high degree of precision.

  16. Mammalian translation elongation factor eEF1A2: X-ray structure and new features of GDP/GTP exchange mechanism in higher eukaryotes.

    Science.gov (United States)

    Crepin, Thibaut; Shalak, Vyacheslav F; Yaremchuk, Anna D; Vlasenko, Dmytro O; McCarthy, Andrew; Negrutskii, Boris S; Tukalo, Michail A; El'skaya, Anna V

    2014-11-10

    Eukaryotic elongation factor eEF1A transits between the GTP- and GDP-bound conformations during the ribosomal polypeptide chain elongation. eEF1A*GTP establishes a complex with the aminoacyl-tRNA in the A site of the 80S ribosome. Correct codon-anticodon recognition triggers GTP hydrolysis, with subsequent dissociation of eEF1A*GDP from the ribosome. The structures of both the 'GTP'- and 'GDP'-bound conformations of eEF1A are unknown. Thus, the eEF1A-related ribosomal mechanisms were anticipated only by analogy with the bacterial homolog EF-Tu. Here, we report the first crystal structure of the mammalian eEF1A2*GDP complex which indicates major differences in the organization of the nucleotide-binding domain and intramolecular movements of eEF1A compared to EF-Tu. Our results explain the nucleotide exchange mechanism in the mammalian eEF1A and suggest that the first step of eEF1A*GDP dissociation from the 80S ribosome is the rotation of the nucleotide-binding domain observed after GTP hydrolysis. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  17. Arthritis of the hand - Rheumatoid

    Science.gov (United States)

    ... All Topics A-Z Videos Infographics Symptom Picker Anatomy Bones Joints Muscles Nerves Vessels Tendons About Hand Surgery What is a Hand Surgeon? What is a Hand Therapist? Media Find a Hand Surgeon Home Anatomy Rheumatoid Arthritis Email to a friend * required fields ...

  18. Convergent evolution and mimicry of protein linear motifs in host-pathogen interactions.

    Science.gov (United States)

    Chemes, Lucía Beatriz; de Prat-Gay, Gonzalo; Sánchez, Ignacio Enrique

    2015-06-01

    Pathogen linear motif mimics are highly evolvable elements that facilitate rewiring of host protein interaction networks. Host linear motifs and pathogen mimics differ in sequence, leading to thermodynamic and structural differences in the resulting protein-protein interactions. Moreover, the functional output of a mimic depends on the motif and domain repertoire of the pathogen protein. Regulatory evolution mediated by linear motifs can be understood by measuring evolutionary rates, quantifying positive and negative selection and performing phylogenetic reconstructions of linear motif natural history. Convergent evolution of linear motif mimics is widespread among unrelated proteins from viral, prokaryotic and eukaryotic pathogens and can also take place within individual protein phylogenies. Statistics, biochemistry and laboratory models of infection link pathogen linear motifs to phenotypic traits such as tropism, virulence and oncogenicity. In vitro evolution experiments and analysis of natural sequences suggest that changes in linear motif composition underlie pathogen adaptation to a changing environment. Copyright © 2015 Elsevier Ltd. All rights reserved.

  19. Proteome-level assessment of origin, prevalence and function of Leucine-Aspartic Acid (LD) motifs

    KAUST Repository

    Alam, Tanvir; Alazmi, Meshari; Naser, Rayan Mohammad Mahmoud; Huser, Franceline; Momin, Afaque Ahmad Imtiyaz; Walkiewicz, Katarzyna Wiktoria; Canlas, Christian; Huser, Raphaë l; Ali, Amal J.; Merzaban, Jasmeen; Bajic, Vladimir B.; Gao, Xin; Arold, Stefan T.

    2018-01-01

    and migration, and revealed a new type of inverse LD motif consensus. Our evolutionary analysis suggested that LD motif signalling originated in the common unicellular ancestor of opisthokonts and amoebozoa by co-opting nuclear export sequences. Inter

  20. Arabidopsis EF-Tu receptor enhances bacterial disease resistance in transgenic wheat.

    Science.gov (United States)

    Schoonbeek, Henk-Jan; Wang, Hsi-Hua; Stefanato, Francesca L; Craze, Melanie; Bowden, Sarah; Wallington, Emma; Zipfel, Cyril; Ridout, Christopher J

    2015-04-01

    Perception of pathogen (or microbe)-associated molecular patterns (PAMPs/MAMPs) by pattern recognition receptors (PRRs) is a key component of plant innate immunity. The Arabidopsis PRR EF-Tu receptor (EFR) recognizes the bacterial PAMP elongation factor Tu (EF-Tu) and its derived peptide elf18. Previous work revealed that transgenic expression of AtEFR in Solanaceae confers elf18 responsiveness and broad-spectrum bacterial disease resistance. In this study, we developed a set of bioassays to study the activation of PAMP-triggered immunity (PTI) in wheat. We generated transgenic wheat (Triticum aestivum) plants expressing AtEFR driven by the constitutive rice actin promoter and tested their response to elf18. We show that transgenic expression of AtEFR in wheat confers recognition of elf18, as measured by the induction of immune marker genes and callose deposition. When challenged with the cereal bacterial pathogen Pseudomonas syringae pv. oryzae, transgenic EFR wheat lines had reduced lesion size and bacterial multiplication. These results demonstrate that AtEFR can be transferred successfully from dicot to monocot species, further revealing that immune signalling pathways are conserved across these distant phyla. As novel PRRs are identified, their transfer between plant families represents a useful strategy for enhancing resistance to pathogens in crops. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  1. The mazEF toxin–antitoxin system as an attractive target in clinical isolates of Enterococcus faecium and Enterococcus faecalis

    Directory of Open Access Journals (Sweden)

    Soheili S

    2015-05-01

    Full Text Available Sara Soheili,1 Sobhan Ghafourian,2 Zamberi Sekawi,1 Vasantha Kumari Neela,1 Nourkhoda Sadeghifard,2 Morovat Taherikalani,2 Afra Khosravi,2 Ramliza Ramli,3 Rukman Awang Hamat11Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health sciences, Universiti Putra Malaysia, Serdang, Malaysia; 2Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran; 3Department of Medical Microbiology and Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaakob Latif, Bandar Tun Razak, Kuala Lumpur, Malaysia Abstract: The toxin–antitoxin (TA system is a regulatory system where two sets of genes encode the toxin and its corresponding antitoxin. In this study, the prevalence of TA systems in independently isolated clinical isolates of Enterococcus faecium and Enterococcus faecalis was determined, the dominant TA system was identified, different virulence genes in E. faecium and E. faecalis were surveyed, the level of expression of the virulence and TA genes in normal and stress conditions was determined, and finally their associations with the TA genes were defined. Remarkably, the analysis demonstrated higBA and mazEF in all clinical isolates, and their locations were on chromosomes and plasmids, respectively. On the other hand, a quantitative analysis of TA and virulence genes revealed that the expression level in both genes is different under normal and stress conditions. The results obtained by anti-mazF peptide nucleic acids demonstrated that the expression level of virulence genes had decreased. These findings demonstrate an association between TA systems and virulence factors. The mazEF on the plasmids and the higBA TA genes on the chromosomes of all E. faecium and E. faecalis strains were dominant. Additionally, there was a decrease in the expression of virulence genes in the presence of anti-mazF peptide nucleic acids. Therefore, it is suggested that mazEF TA systems

  2. Performance Comparison Between FEDERICA Hand and LARM Hand

    OpenAIRE

    Carbone, Giuseppe; Rossi, Cesare; Savino, Sergio

    2015-01-01

    This paper describes two robotic hands that have been\\ud developed at University Federico II of Naples and at the\\ud University of Cassino. FEDERICA Hand and LARM Hand\\ud are described in terms of design and operational features.\\ud In particular, careful attention is paid to the differences\\ud between the above-mentioned hands in terms of transmission\\ud systems. FEDERICA Hand uses tendons and pulleys\\ud to drive phalanxes, while LARM Hand uses cross four-bar\\ud linkages. Results of experime...

  3. Second-hand signals

    DEFF Research Database (Denmark)

    Bergenholtz, Carsten

    2014-01-01

    Studies of signaling theory have traditionally focused on the dyadic link between the sender and receiver of the signal. Within a science‐based perspective this framing has led scholars to investigate how patents and publications of firms function as signals. I explore another important type...... used by various agents in their search for and assessment of products and firms. I conclude by arguing how this second‐hand nature of signals goes beyond a simple dyadic focus on senders and receivers of signals, and thus elucidates the more complex interrelations of the various types of agents...

  4. Hand grip strength

    DEFF Research Database (Denmark)

    Frederiksen, Henrik; Gaist, David; Petersen, Hans Christian

    2002-01-01

    in life is a major problem in terms of prevalence, morbidity, functional limitations, and quality of life. It is therefore of interest to find a phenotype reflecting physical functioning which has a relatively high heritability and which can be measured in large samples. Hand grip strength is known......-55%). A powerful design to detect genes associated with a phenotype is obtained using the extreme discordant and concordant sib pairs, of whom 28 and 77 dizygotic twin pairs, respectively, were found in this study. Hence grip strength is a suitable phenotype for identifying genetic variants of importance to mid...

  5. The hand and wrist

    International Nuclear Information System (INIS)

    Wood, M.B.; Berquist, T.H.

    1985-01-01

    Trauma is the most common etiologic factor leading to disability in the hand and wrist. Judicious radiographic evaluation is required for accurate assessment in practically all but the most minor of such injuries. Frequently serial radiographic evaluation is essential for directing the course of treatment and for following the healing process. A meaningful radiographic evaluation requires a comprehensive knowledge of the normal radiographic anatomy, an overview of the spectrum of pathology, and an awareness of the usual mechanisms of injury, appropriate treatment options, and relevant array of complications

  6. Finding a Leucine in a Haystack: Searching the Proteome for ambigous Leucine-Aspartic Acid motifs

    KAUST Repository

    Arold, Stefan T.

    2016-01-01

    LDMF predicted 13 new LD motifs in humans. Using biophysical assays, we experimentally confirmed in vitro interactions for four novel LD motif proteins. Thus, LDMF allows proteome-wide discovery of LD motifs, despite a highly ambiguous sequence pattern. Functional implications will be discussed.

  7. DMINDA: an integrated web server for DNA motif identification and analyses.

    Science.gov (United States)

    Ma, Qin; Zhang, Hanyuan; Mao, Xizeng; Zhou, Chuan; Liu, Bingqiang; Chen, Xin; Xu, Ying

    2014-07-01

    DMINDA (DNA motif identification and analyses) is an integrated web server for DNA motif identification and analyses, which is accessible at http://csbl.bmb.uga.edu/DMINDA/. This web site is freely available to all users and there is no login requirement. This server provides a suite of cis-regulatory motif analysis functions on DNA sequences, which are important to elucidation of the mechanisms of transcriptional regulation: (i) de novo motif finding for a given set of promoter sequences along with statistical scores for the predicted motifs derived based on information extracted from a control set, (ii) scanning motif instances of a query motif in provided genomic sequences, (iii) motif comparison and clustering of identified motifs, and (iv) co-occurrence analyses of query motifs in given promoter sequences. The server is powered by a backend computer cluster with over 150 computing nodes, and is particularly useful for motif prediction and analyses in prokaryotic genomes. We believe that DMINDA, as a new and comprehensive web server for cis-regulatory motif finding and analyses, will benefit the genomic research community in general and prokaryotic genome researchers in particular. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  8. Distinct configurations of protein complexes and biochemical pathways revealed by epistatic interaction network motifs

    LENUS (Irish Health Repository)

    Casey, Fergal

    2011-08-22

    Abstract Background Gene and protein interactions are commonly represented as networks, with the genes or proteins comprising the nodes and the relationship between them as edges. Motifs, or small local configurations of edges and nodes that arise repeatedly, can be used to simplify the interpretation of networks. Results We examined triplet motifs in a network of quantitative epistatic genetic relationships, and found a non-random distribution of particular motif classes. Individual motif classes were found to be associated with different functional properties, suggestive of an underlying biological significance. These associations were apparent not only for motif classes, but for individual positions within the motifs. As expected, NNN (all negative) motifs were strongly associated with previously reported genetic (i.e. synthetic lethal) interactions, while PPP (all positive) motifs were associated with protein complexes. The two other motif classes (NNP: a positive interaction spanned by two negative interactions, and NPP: a negative spanned by two positives) showed very distinct functional associations, with physical interactions dominating for the former but alternative enrichments, typical of biochemical pathways, dominating for the latter. Conclusion We present a model showing how NNP motifs can be used to recognize supportive relationships between protein complexes, while NPP motifs often identify opposing or regulatory behaviour between a gene and an associated pathway. The ability to use motifs to point toward underlying biological organizational themes is likely to be increasingly important as more extensive epistasis mapping projects in higher organisms begin.

  9. Gene regulatory and signaling networks exhibit distinct topological distributions of motifs

    Science.gov (United States)

    Ferreira, Gustavo Rodrigues; Nakaya, Helder Imoto; Costa, Luciano da Fontoura

    2018-04-01

    The biological processes of cellular decision making and differentiation involve a plethora of signaling pathways and gene regulatory circuits. These networks in turn exhibit a multitude of motifs playing crucial parts in regulating network activity. Here we compare the topological placement of motifs in gene regulatory and signaling networks and observe that it suggests different evolutionary strategies in motif distribution for distinct cellular subnetworks.

  10. Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs.

    Science.gov (United States)

    Regad, Leslie; Martin, Juliette; Camproux, Anne-Claude

    2011-06-20

    One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet), which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i) ubiquitous motifs, shared by several superfamilies and (ii) superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P) and SAH/SAM. Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.

  11. Back to basics: hand hygiene and surgical hand antisepsis.

    Science.gov (United States)

    Spruce, Lisa

    2013-11-01

    Health care-associated infections (HAIs) are a significant issue in the United States and throughout the world, but following proper hand hygiene practices is the most effective and least expensive way to prevent HAIs. Hand hygiene is inexpensive and protects patients and health care personnel alike. The four general types of hand hygiene that should be performed in the perioperative environment are washing hands that are visibly soiled, hand hygiene using alcohol-based products, surgical hand scrubs, and surgical hand scrubs using an alcohol-based surgical hand rub product. Barriers to proper hand hygiene may include not thinking about it, forgetting, skin irritation, a lack of role models, or a lack of a safety culture. One strategy for improving hand hygiene practices is monitoring hand hygiene as part of a quality improvement project, but the most important aspect for perioperative team members is to set an example for other team members by following proper hand hygiene practices and reminding each other to perform hand hygiene. Copyright © 2013 AORN, Inc. Published by Elsevier Inc. All rights reserved.

  12. WildSpan: mining structured motifs from protein sequences

    Directory of Open Access Journals (Sweden)

    Chen Chien-Yu

    2011-03-01

    Full Text Available Abstract Background Automatic extraction of motifs from biological sequences is an important research problem in study of molecular biology. For proteins, it is desired to discover sequence motifs containing a large number of wildcard symbols, as the residues associated with functional sites are usually largely separated in sequences. Discovering such patterns is time-consuming because abundant combinations exist when long gaps (a gap consists of one or more successive wildcards are considered. Mining algorithms often employ constraints to narrow down the search space in order to increase efficiency. However, improper constraint models might degrade the sensitivity and specificity of the motifs discovered by computational methods. We previously proposed a new constraint model to handle large wildcard regions for discovering functional motifs of proteins. The patterns that satisfy the proposed constraint model are called W-patterns. A W-pattern is a structured motif that groups motif symbols into pattern blocks interleaved with large irregular gaps. Considering large gaps reflects the fact that functional residues are not always from a single region of protein sequences, and restricting motif symbols into clusters corresponds to the observation that short motifs are frequently present within protein families. To efficiently discover W-patterns for large-scale sequence annotation and function prediction, this paper first formally introduces the problem to solve and proposes an algorithm named WildSpan (sequential pattern mining across large wildcard regions that incorporates several pruning strategies to largely reduce the mining cost. Results WildSpan is shown to efficiently find W-patterns containing conserved residues that are far separated in sequences. We conducted experiments with two mining strategies, protein-based and family-based mining, to evaluate the usefulness of W-patterns and performance of WildSpan. The protein-based mining mode

  13. Core signalling motif displaying multistability through multi-state enzymes

    DEFF Research Database (Denmark)

    Feng, Song; Saez Cornellana, Meritxell; Wiuf, Carsten Henrik

    2016-01-01

    Bistability, and more generally multistability, is a key system dynamics feature enabling decision-making and memory in cells. Deciphering the molecular determinants of multistability is thus crucial for a better understanding of cellular pathways and their (re)engineering in synthetic biology....... Here, we show that a key motif found predominantly in eukaryotic signalling systems, namely a futile signalling cycle, can display bistability when featuring a two-state kinase. We provide necessary and sufficient mathematical conditions on the kinetic parameters of this motif that guarantee...... the existence of multiple steady states. These conditions foster the intuition that bistability arises as a consequence of competition between the two states of the kinase. Extending from this result, we find that increasing the number of kinase states linearly translates into an increase in the number...

  14. Factoring local sequence composition in motif significance analysis.

    Science.gov (United States)

    Ng, Patrick; Keich, Uri

    2008-01-01

    We recently introduced a biologically realistic and reliable significance analysis of the output of a popular class of motif finders. In this paper we further improve our significance analysis by incorporating local base composition information. Relying on realistic biological data simulation, as well as on FDR analysis applied to real data, we show that our method is significantly better than the increasingly popular practice of using the normal approximation to estimate the significance of a finder's output. Finally we turn to leveraging our reliable significance analysis to improve the actual motif finding task. Specifically, endowing a variant of the Gibbs Sampler with our improved significance analysis we demonstrate that de novo finders can perform better than has been perceived. Significantly, our new variant outperforms all the finders reviewed in a recently published comprehensive analysis of the Harbison genome-wide binding location data. Interestingly, many of these finders incorporate additional information such as nucleosome positioning and the significance of binding data.

  15. Neoanalysis, Orality, and Intertextuality: An Examination of Homeric Motif Transference

    Directory of Open Access Journals (Sweden)

    Jonathan Burgess

    2006-03-01

    Full Text Available In Homeric studies scholars have speculated on the influence of (non-surviving preHomeric material on the Iliad. This article expands this line of argument from an oralist perspective, with reference to modern intertextual theory. It concludes that preHomeric and nonHomeric motifs from oral traditions were transferred into the epic poem, creating an intertextually allusive poetics that would have been recognizable to an early Greek audience informed of mythological traditions.

  16. Motif Subscriber Menonton Channel YouTube Raditya Dika

    OpenAIRE

    Mellyaningsih, Adinda

    2016-01-01

    Penelitian ini dilakukan untuk mengetahui motif para subscriber dalam menonton channelYouTube Raditya Dika. Raditya Dika merupakan YouTuber Indonesia dengan jumlah subscriber terbanyak dan merupakan orang pertama di Indonesia yang mendapatkan penghargaan Certifies Award oleh YouTube. Peneliti menggunakan teori Uses and Gratification dengan empat indikator, yaitu hiburan dan relaksasi, hubungan antar pribadi, mencari informasi, dan persahabatan. Metode dalam penelitian ini adalah online survei...

  17. Perception Enhancement using Visual Attributes in Sequence Motif Visualization

    OpenAIRE

    Oon, Yin; Lee, Nung; Kok, Wei

    2016-01-01

    Sequence logo is a well-accepted scientific method to visualize the conservation characteristics of biological sequence motifs. Previous studies found that using sequence logo graphical representation for scientific evidence reports or arguments could seriously cause biases and misinterpretation by users. This study investigates on the visual attributes performance of a sequence logo in helping users to perceive and interpret the information based on preattentive theories and Gestalt principl...

  18. Exon silencing by UAGG motifs in response to neuronal excitation.

    Directory of Open Access Journals (Sweden)

    Ping An

    2007-02-01

    Full Text Available Alternative pre-mRNA splicing plays fundamental roles in neurons by generating functional diversity in proteins associated with the communication and connectivity of the synapse. The CI cassette of the NMDA R1 receptor is one of a variety of exons that show an increase in exon skipping in response to cell excitation, but the molecular nature of this splicing responsiveness is not yet understood. Here we investigate the molecular basis for the induced changes in splicing of the CI cassette exon in primary rat cortical cultures in response to KCl-induced depolarization using an expression assay with a tight neuron-specific readout. In this system, exon silencing in response to neuronal excitation was mediated by multiple UAGG-type silencing motifs, and transfer of the motifs to a constitutive exon conferred a similar responsiveness by gain of function. Biochemical analysis of protein binding to UAGG motifs in extracts prepared from treated and mock-treated cortical cultures showed an increase in nuclear hnRNP A1-RNA binding activity in parallel with excitation. Evidence for the role of the NMDA receptor and calcium signaling in the induced splicing response was shown by the use of specific antagonists, as well as cell-permeable inhibitors of signaling pathways. Finally, a wider role for exon-skipping responsiveness is shown to involve additional exons with UAGG-related silencing motifs, and transcripts involved in synaptic functions. These results suggest that, at the post-transcriptional level, excitable exons such as the CI cassette may be involved in strategies by which neurons mount adaptive responses to hyperstimulation.

  19. Multiple TPR motifs characterize the Fanconi anemia FANCG protein.

    Science.gov (United States)

    Blom, Eric; van de Vrugt, Henri J; de Vries, Yne; de Winter, Johan P; Arwert, Fré; Joenje, Hans

    2004-01-05

    The genome protection pathway that is defective in patients with Fanconi anemia (FA) is controlled by at least eight genes, including BRCA2. A key step in the pathway involves the monoubiquitylation of FANCD2, which critically depends on a multi-subunit nuclear 'core complex' of at least six FANC proteins (FANCA, -C, -E, -F, -G, and -L). Except for FANCL, which has WD40 repeats and a RING finger domain, no significant domain structure has so far been recognized in any of the core complex proteins. By using a homology search strategy comparing the human FANCG protein sequence with its ortholog sequences in Oryzias latipes (Japanese rice fish) and Danio rerio (zebrafish) we identified at least seven tetratricopeptide repeat motifs (TPRs) covering a major part of this protein. TPRs are degenerate 34-amino acid repeat motifs which function as scaffolds mediating protein-protein interactions, often found in multiprotein complexes. In four out of five TPR motifs tested (TPR1, -2, -5, and -6), targeted missense mutagenesis disrupting the motifs at the critical position 8 of each TPR caused complete or partial loss of FANCG function. Loss of function was evident from failure of the mutant proteins to complement the cellular FA phenotype in FA-G lymphoblasts, which was correlated with loss of binding to FANCA. Although the TPR4 mutant fully complemented the cells, it showed a reduced interaction with FANCA, suggesting that this TPR may also be of functional importance. The recognition of FANCG as a typical TPR protein predicts this protein to play a key role in the assembly and/or stabilization of the nuclear FA protein core complex.

  20. Efficient sequential and parallel algorithms for planted motif search.

    Science.gov (United States)

    Nicolae, Marius; Rajasekaran, Sanguthevar

    2014-01-31

    Motif searching is an important step in the detection of rare events occurring in a set of DNA or protein sequences. One formulation of the problem is known as (l,d)-motif search or Planted Motif Search (PMS). In PMS we are given two integers l and d and n biological sequences. We want to find all sequences of length l that appear in each of the input sequences with at most d mismatches. The PMS problem is NP-complete. PMS algorithms are typically evaluated on certain instances considered challenging. Despite ample research in the area, a considerable performance gap exists because many state of the art algorithms have large runtimes even for moderately challenging instances. This paper presents a fast exact parallel PMS algorithm called PMS8. PMS8 is the first algorithm to solve the challenging (l,d) instances (25,10) and (26,11). PMS8 is also efficient on instances with larger l and d such as (50,21). We include a comparison of PMS8 with several state of the art algorithms on multiple problem instances. This paper also presents necessary and sufficient conditions for 3 l-mers to have a common d-neighbor. The program is freely available at http://engr.uconn.edu/~man09004/PMS8/. We present PMS8, an efficient exact algorithm for Planted Motif Search. PMS8 introduces novel ideas for generating common neighborhoods. We have also implemented a parallel version for this algorithm. PMS8 can solve instances not solved by any previous algorithms.

  1. Aplikasi Ornamen Khas Maluku untuk Pengembangan Desain Motif Batik

    OpenAIRE

    Masiswo Masiswo; Vivin Atika

    2016-01-01

    ABSTRAKMaluku memiliki banyak ragam hias budaya warisan nilai leluhur berupa ornamen etnis yang merupakan kesenian dan keterampilan kerajinan. Hasil warisan tersebut sampai saat ini masih lestari hidup serta dapat dinikmati sebagai konsumsi rohani yang memuaskan manusia. Berkaitan dengan keberlangsungan nilai-nilai tradisi etnis yang berwujud pada ornamen-ornamen daerah Maluku, maka dikembangkan untuk kebutuhan manusia berupa motif batik pada kain. Pengembangan ornamen ini lebih menekankan pa...

  2. ROMANIAN TRADITIONAL MOTIF ELEMENT OF MODERNITY IN CLOTHING

    Directory of Open Access Journals (Sweden)

    ŞUTEU Marius Darius

    2017-05-01

    Full Text Available In this paper are presented the phases for improving from an aesthetic point of view a clothing item, the T-shirt for women using software design patterns, computerised graphics and textile different modern technologies including: industrial embroidery, digital printing, sublimation. In the first phase a documentation was prepared in the University of Oradea and traditional motif was selected from a collection comprising a number of Romanian traditional motifs from different parts of the country and were reintepreted and stylized whilst preserving the symbolism and color range specified to the area. For the styling phase was used CorelDraw vector graphics program that allows changing the shape, size and color of the drawings without affecting the identity of the pattern. The embroidery was done using BERNINA Embroidery Software Designer Plus Software. This software allows you to export the model to any domestic or industrial embroidery machine regardless of brand. Finally we observed the resistance of the printed and embroided model to various: elasticity, resistance to abrasion and a sensory analysis on the preservation of color. After testing we noticed the imprint resistance applied to the fabric, resulting in a quality that makes possible to keep the Romanian traditional motif from generation to generation.

  3. Insertion of tetracysteine motifs into dopamine transporter extracellular domains.

    Directory of Open Access Journals (Sweden)

    Deanna M Navaroli

    Full Text Available The neuronal dopamine transporter (DAT is a major determinant of extracellular dopamine (DA levels and is the primary target for a variety of addictive and therapeutic psychoactive drugs. DAT is acutely regulated by protein kinase C (PKC activation and amphetamine exposure, both of which modulate DAT surface expression by endocytic trafficking. In order to use live imaging approaches to study DAT endocytosis, methods are needed to exclusively label the DAT surface pool. The use of membrane impermeant, sulfonated biarsenic dyes holds potential as one such approach, and requires introduction of an extracellular tetracysteine motif (tetraCys; CCPGCC to facilitate dye binding. In the current study, we took advantage of intrinsic proline-glycine (Pro-Gly dipeptides encoded in predicted DAT extracellular domains to introduce tetraCys motifs into DAT extracellular loops 2, 3, and 4. [(3H]DA uptake studies, surface biotinylation and fluorescence microscopy in PC12 cells indicate that tetraCys insertion into the DAT second extracellular loop results in a functional transporter that maintains PKC-mediated downregulation. Introduction of tetraCys into extracellular loops 3 and 4 yielded DATs with severely compromised function that failed to mature and traffic to the cell surface. This is the first demonstration of successful introduction of a tetracysteine motif into a DAT extracellular domain, and may hold promise for use of biarsenic dyes in live DAT imaging studies.

  4. Codon based co-occurrence network motifs in human mitochondria

    Directory of Open Access Journals (Sweden)

    Pramod Shinde

    2017-10-01

    Full Text Available The nucleotide polymorphism in human mitochondrial genome (mtDNA tolled by codon position bias plays an indispensable role in human population dispersion and expansion. Herein, we constructed genome-wide nucleotide co-occurrence networks using a massive data consisting of five different geographical regions and around 3000 samples for each region. We developed a powerful network model to describe complex mitochondrial evolutionary patterns between codon and non-codon positions. It was interesting to report a different evolution of Asian genomes than those of the rest which is divulged by network motifs. We found evidence that mtDNA undergoes substantial amounts of adaptive evolution, a finding which was supported by a number of previous studies. The dominance of higher order motifs indicated the importance of long-range nucleotide co-occurrence in genomic diversity. Most notably, codon motifs apparently underpinned the preferences among codon positions for co-evolution which is probably highly biased during the origin of the genetic code. Our analyses manifested that codon position co-evolution is very well conserved across human sub-populations and independently maintained within human sub-populations implying the selective role of evolutionary processes on codon position co-evolution. Ergo, this study provided a framework to investigate cooperative genomic interactions which are critical in underlying complex mitochondrial evolution.

  5. Organofluorine chemistry: synthesis and conformation of vicinal fluoromethylene motifs.

    Science.gov (United States)

    O'Hagan, David

    2012-04-20

    The C-F bond is the most polar bond in organic chemistry, and thus the bond has a relatively large dipole moment with a significant -ve charge density on the fluorine atom and correspondingly a +ve charge density on carbon. The electrostatic nature of the bond renders it the strongest one in organic chemistry. However, the fluorine atom itself is nonpolarizable, and thus, despite the charge localization on fluorine, it is a poor hydrogen-bonding acceptor. These properties of the C-F bond make it attractive in the design of nonviscous but polar organic compounds, with a polarity limited to influencing the intramolecular nature of the molecule and less so intermolecular interactions with the immediate environment. In this Perspective, the synthesis of aliphatic chains carrying multivicinal fluoromethylene motifs is described. It emerges that the dipoles of adjacent C-F bonds orientate relative to each other, and thus, individual diastereoisomers display different backbone carbon chain conformations. These conformational preferences recognize the influence of the well-known gauche effect associated with 1,2-difluoroethane but extend to considering 1,3-fluorine-fluorine dipolar repulsions. The synthesis of carbon chains carrying two, three, four, five, and six vicinal fluoromethylene motifs is described, with an emphasis on our own research contributions. These motifs obey almost predictable conformational behavior, and they emerge as candidates for inclusion in the design of performance organic molecules. © 2012 American Chemical Society

  6. iFORM: Incorporating Find Occurrence of Regulatory Motifs.

    Science.gov (United States)

    Ren, Chao; Chen, Hebing; Yang, Bite; Liu, Feng; Ouyang, Zhangyi; Bo, Xiaochen; Shu, Wenjie

    2016-01-01

    Accurately identifying the binding sites of transcription factors (TFs) is crucial to understanding the mechanisms of transcriptional regulation and human disease. We present incorporating Find Occurrence of Regulatory Motifs (iFORM), an easy-to-use and efficient tool for scanning DNA sequences with TF motifs described as position weight matrices (PWMs). Both performance assessment with a receiver operating characteristic (ROC) curve and a correlation-based approach demonstrated that iFORM achieves higher accuracy and sensitivity by integrating five classical motif discovery programs using Fisher's combined probability test. We have used iFORM to provide accurate results on a variety of data in the ENCODE Project and the NIH Roadmap Epigenomics Project, and the tool has demonstrated its utility in further elucidating individual roles of functional elements. Both the source and binary codes for iFORM can be freely accessed at https://github.com/wenjiegroup/iFORM. The identified TF binding sites across human cell and tissue types using iFORM have been deposited in the Gene Expression Omnibus under the accession ID GSE53962.

  7. THE MOTIF OF THE PRODIGAL SON IN IVAN TURGENEV'S NOVELS

    Directory of Open Access Journals (Sweden)

    Valentina Ivanovna Gabdullina

    2013-11-01

    Full Text Available The author questions the perception of Ivan Turgenev as a “non- Christian writer” and studies the problem of the prodigal son motif functioning in a series of his novels. In his novels, Turgenev pictured different phases of the archetypal story, originating from the Gospel parable of the prodigal son. In the novel Rudin he depicted the phase of spiritual wanderings of the hero who had lost touch with his native land — Russia. In his next novels (Home of the Gentry, Fathers and Sons and Smoke, after leading his hero in circles and sending him back to his paternal home, Turgenev reconstructs the model of human behavior, represented in the parable, thereby recognizing the immutability of the idea formalized in the Gospel. The motif of the return to Russian land gets its completion in Turgenev's last novel Virgin Soil, in which the author paradoxically connects the Westernist idea with the Gospel imperative. Solomin, the son of a deacon, sent by his wise father out to Europe “to get education”, studies in England, masters the European knowledge and returns back “to his native land” to establish his own business in inland Russia. Thus, a series of Turgenev's novels, in which he portrayed different phases of social life, are interlinked with the motif of the prodigal son, who is represented by novels' main characters.

  8. The city as a motif in Slovene youth literature

    Directory of Open Access Journals (Sweden)

    Milena Mileva Blažić

    2003-01-01

    Full Text Available The article presents the city as motif of Slovenian youth literature in four different periods, beginning in the first period of original Slovenian youth literature in the second half of the 19th century, second period in the first half of the 20th century, third period in the second half of the 20th century and after 1950, when significant books were produced in the field of short modern stories, emphasising on picture books and realistic narrative prose, and the fourth period after 1990. A discernable shift can be observed in the thirties of the 20th century, during the times of socialist realism. The most significant change occurred after 1960, when massive migration from rural to urban environments caused by industrialisation began. The motif of urban environment especially marked modern realistic narrative, coined problematic narrative after 1990, with its focus on issues of growing up in such environments. The city as motif or theme doesn’t appear only in realistic narrative, but since the early 20th century also in fantastic narrative, thus it dichotomically presents the image of real world in Slovenian youth realistic narrative.

  9. TOPDOM: database of conservatively located domains and motifs in proteins.

    Science.gov (United States)

    Varga, Julia; Dobson, László; Tusnády, Gábor E

    2016-09-01

    The TOPDOM database-originally created as a collection of domains and motifs located consistently on the same side of the membranes in α-helical transmembrane proteins-has been updated and extended by taking into consideration consistently localized domains and motifs in globular proteins, too. By taking advantage of the recently developed CCTOP algorithm to determine the type of a protein and predict topology in case of transmembrane proteins, and by applying a thorough search for domains and motifs as well as utilizing the most up-to-date version of all source databases, we managed to reach a 6-fold increase in the size of the whole database and a 2-fold increase in the number of transmembrane proteins. TOPDOM database is available at http://topdom.enzim.hu The webpage utilizes the common Apache, PHP5 and MySQL software to provide the user interface for accessing and searching the database. The database itself is generated on a high performance computer. tusnady.gabor@ttk.mta.hu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  10. Translation elongation factor eEF1A2 is a potential oncoprotein that is overexpressed in two-thirds of breast tumours

    Directory of Open Access Journals (Sweden)

    Miller William R

    2005-09-01

    Full Text Available Abstract Background The tissue-specific translation elongation factor eEF1A2 was recently shown to be a potential oncogene that is overexpressed in ovarian cancer. Although there is no direct evidence for an involvement of eEF1A2 in breast cancer, the genomic region to which EEF1A2 maps, 20q13, is frequently amplified in breast tumours. We therefore sought to establish whether eEF1A2 expression might be upregulated in breast cancer. Methods eEF1A2 is highly similar (98% to the near-ubiquitously expressed eEF1A1 (formerly known as EF1-α making analysis with commercial antibodies difficult. We have developed specific anti-eEF1A2 antibodies and used them in immunohistochemical analyses of tumour samples. We report the novel finding that although eEF1A2 is barely detectable in normal breast it is moderately to strongly expressed in two-thirds of breast tumours. This overexpression is strongly associated with estrogen receptor positivity. Conclusion eEF1A2 should be considered as a putative oncogene in breast cancer that may be a useful diagnostic marker and therapeutic target for a high proportion of breast tumours. The oncogenicity of eEF1A2 may be related to its role in protein synthesis or to its potential non-canonical functions in cytoskeletal remodelling or apoptosis.

  11. Translation elongation factor eEF1A2 is a potential oncoprotein that is overexpressed in two-thirds of breast tumours

    International Nuclear Information System (INIS)

    Tomlinson, Victoria AL; Newbery, Helen J; Wray, Naomi R; Jackson, Juliette; Larionov, Alexey; Miller, William R; Dixon, J Michael; Abbott, Catherine M

    2005-01-01

    The tissue-specific translation elongation factor eEF1A2 was recently shown to be a potential oncogene that is overexpressed in ovarian cancer. Although there is no direct evidence for an involvement of eEF1A2 in breast cancer, the genomic region to which EEF1A2 maps, 20q13, is frequently amplified in breast tumours. We therefore sought to establish whether eEF1A2 expression might be upregulated in breast cancer. eEF1A2 is highly similar (98%) to the near-ubiquitously expressed eEF1A1 (formerly known as EF1-α) making analysis with commercial antibodies difficult. We have developed specific anti-eEF1A2 antibodies and used them in immunohistochemical analyses of tumour samples. We report the novel finding that although eEF1A2 is barely detectable in normal breast it is moderately to strongly expressed in two-thirds of breast tumours. This overexpression is strongly associated with estrogen receptor positivity. eEF1A2 should be considered as a putative oncogene in breast cancer that may be a useful diagnostic marker and therapeutic target for a high proportion of breast tumours. The oncogenicity of eEF1A2 may be related to its role in protein synthesis or to its potential non-canonical functions in cytoskeletal remodelling or apoptosis

  12. Fluctuations between multiple EF-G-induced chimeric tRNA states during translocation on the ribosome

    Science.gov (United States)

    Adio, Sarah; Senyushkina, Tamara; Peske, Frank; Fischer, Niels; Wintermeyer, Wolfgang; Rodnina, Marina V.

    2015-06-01

    The coupled translocation of transfer RNA and messenger RNA through the ribosome entails large-scale structural rearrangements, including step-wise movements of the tRNAs. Recent structural work has visualized intermediates of translocation induced by elongation factor G (EF-G) with tRNAs trapped in chimeric states with respect to 30S and 50S ribosomal subunits. The functional role of the chimeric states is not known. Here we follow the formation of translocation intermediates by single-molecule fluorescence resonance energy transfer. Using EF-G mutants, a non-hydrolysable GTP analogue, and fusidic acid, we interfere with either translocation or EF-G release from the ribosome and identify several rapidly interconverting chimeric tRNA states on the reaction pathway. EF-G engagement prevents backward transitions early in translocation and increases the fraction of ribosomes that rapidly fluctuate between hybrid, chimeric and posttranslocation states. Thus, the engagement of EF-G alters the energetics of translocation towards a flat energy landscape, thereby promoting forward tRNA movement.

  13. The SOS response is permitted in Escherichia coli strains deficient in the expression of the mazEF pathway.

    Science.gov (United States)

    Kalderon, Ziva; Kumar, Sathish; Engelberg-Kulka, Hanna

    2014-01-01

    The Escherichia coli (E. coli) SOS response is the largest, most complex, and best characterized bacterial network induced by DNA damage. It is controlled by a complex network involving the RecA and LexA proteins. We have previously shown that the SOS response to DNA damage is inhibited by various elements involved in the expression of the E. coli toxin-antitoxin mazEF pathway. Since the mazEF module is present on the chromosomes of most E. coli strains, here we asked: Why is the SOS response found in so many E. coli strains? Is the mazEF module present but inactive in those strains? We examined three E. coli strains used for studies of the SOS response, strains AB1932, BW25113, and MG1655. We found that each of these strains is either missing or inhibiting one of several elements involved in the expression of the mazEF-mediated death pathway. Thus, the SOS response only takes place in E. coli cells in which one or more elements of the E. coli toxin-antitoxin module mazEF or its downstream pathway is not functioning.

  14. A comparison of EF-18 agar and modified brilliant green agar with lutensit for isolation of Salmonella from poultry samples

    DEFF Research Database (Denmark)

    Petersen, Line Hedegård

    1997-01-01

    -Vassiliadis broth, and 3) Plating onto EF-18 agar and BGA/L simultaneously. From a total of 1101 samples, Salmonella was isolated from 158, 157 of which were faecal samples. Thirtyone of these isolates were recovered on one medium only, 18 could not be found on BGA/L and 13 could not be found on EF-18 agar....... The relative specificity and sensitivity of each plating agar was determined by enumeration of false-positive and false-negative reactions. EF-18 agar compared favourably with BGA/L, displaying a sensitivity of 0.92 as opposed to 0.89 for BGA/L, calculated for the ''fecal samples'' group only. The calculated...... specificities for each group of samples were likewise considerably higher for EF-18 agar (0.75-0.91) than for BGA/L (0.35-0.55). Though EF-18 agar is slightly more expensive than BGA/L, the routine use of the former may result in a considerable reduction in overall laboratory costs due to its superior...

  15. Hand Matters: Left-Hand Gestures Enhance Metaphor Explanation

    Science.gov (United States)

    Argyriou, Paraskevi; Mohr, Christine; Kita, Sotaro

    2017-01-01

    Research suggests that speech-accompanying gestures influence cognitive processes, but it is not clear whether the gestural benefit is specific to the gesturing hand. Two experiments tested the "(right/left) hand-specificity" hypothesis for self-oriented functions of gestures: gestures with a particular hand enhance cognitive processes…

  16. Flow motifs reveal limitations of the static framework to represent human interactions

    Science.gov (United States)

    Rocha, Luis E. C.; Blondel, Vincent D.

    2013-04-01

    Networks are commonly used to define underlying interaction structures where infections, information, or other quantities may spread. Although the standard approach has been to aggregate all links into a static structure, some studies have shown that the time order in which the links are established may alter the dynamics of spreading. In this paper, we study the impact of the time ordering in the limits of flow on various empirical temporal networks. By using a random walk dynamics, we estimate the flow on links and convert the original undirected network (temporal and static) into a directed flow network. We then introduce the concept of flow motifs and quantify the divergence in the representativity of motifs when using the temporal and static frameworks. We find that the regularity of contacts and persistence of vertices (common in email communication and face-to-face interactions) result on little differences in the limits of flow for both frameworks. On the other hand, in the case of communication within a dating site and of a sexual network, the flow between vertices changes significantly in the temporal framework such that the static approximation poorly represents the structure of contacts. We have also observed that cliques with 3 and 4 vertices containing only low-flow links are more represented than the same cliques with all high-flow links. The representativity of these low-flow cliques is higher in the temporal framework. Our results suggest that the flow between vertices connected in cliques depend on the topological context in which they are placed and in the time sequence in which the links are established. The structure of the clique alone does not completely characterize the potential of flow between the vertices.

  17. Classification of hand eczema

    DEFF Research Database (Denmark)

    Agner, T; Aalto-Korte, K; Andersen, K E

    2015-01-01

    BACKGROUND: Classification of hand eczema (HE) is mandatory in epidemiological and clinical studies, and also important in clinical work. OBJECTIVES: The aim was to test a recently proposed classification system of HE in clinical practice in a prospective multicentre study. METHODS: Patients were...... recruited from nine different tertiary referral centres. All patients underwent examination by specialists in dermatology and were checked using relevant allergy testing. Patients were classified into one of the six diagnostic subgroups of HE: allergic contact dermatitis, irritant contact dermatitis, atopic...... system investigated in the present study was useful, being able to give an appropriate main diagnosis for 89% of HE patients, and for another 7% when using two main diagnoses. The fact that more than half of the patients had one or more additional diagnoses illustrates that HE is a multifactorial disease....

  18. Wide Awake Hand Surgery.

    Science.gov (United States)

    Lied, Line; Borchgrevink, Grethe E; Finsen, Vilhjalmur

    2017-09-01

    "Wide awake hand surgery", where surgery is performed in local anaesthesia with adrenaline, without sedation or a tourniquet, has become widespread in some countries. It has a number of potential advantages and we wished to evaluate it among our patients. All 122 patients treated by this method during one year were evaluated by the surgeons and the patients on a numerical scale from 0 (best/least) to 10 (worst/most). Theatre time was compared to that recorded for a year when regional or general anaesthesia had been used. The patients' mean score for the general care they had received was 0.1 (SD 0.6), for pain during lidocaine injection 2.4 (SD 2.2), for pain during surgery 0.9 (SD 1.5), and for other discomfort during surgery 0.5 (SD 1.4). Eight reported that they would want general anaesthesia if they were to be operated again. The surgeons' mean evaluation of bleeding during surgery was 1.6 (SD 1.8), oedema during surgery 0.4 (SD 1.1), general disadvantages with the method 1.0 (SD 1.6) and general advantages 6.5 (SD 4.3). The estimation of advantages was 9.9 (DS 0.5) for tendon suture. 28 patients needed intra-operative additional anaesthesia. The proportion was lower among trained hand surgeons and fell significantly during the study period. Non-surgical theatre time was 46 (SD 15) minutes during the study period and 55 (SD 22) minutes during the regional/general period (p theatre.

  19. Rheumatoid arthritis and hand surgery

    DEFF Research Database (Denmark)

    Peretz, Anne Sofie Rosenborg; Madsen, Ole Rintek; Brogren, Elisabeth

    2017-01-01

    Rheumatoid arthritis results in characteristic deformities of the hand. Medical treatment has undergone a remarkable development. However, not all patients achieve remission or tolerate the treatment. Patients who suffer from deformities and persistent synovitis may be candidates for hand surgery...

  20. High performance message passing for the ATLAS DAQ/EF-1 project

    CERN Document Server

    Mornacchi, Giuseppe

    1999-01-01

    Summary form only. A message passing library has been developed in the context of the ATLAS DAQ/EF-1 project. It is used for time critical applications within the front-end part of the DAQ system, mainly to exchange data control messages between I/O processors. Key objectives of the design were low message overheads, efficient use of the data transfer buses, provision of broadcast functionality and a hardware and operating system independent implementation of the application interface. The design and implementation of the message passing library are presented. As required by the project, the implementation is based on commercial components, namely VMEbus, PCI, the Lynx-OS real-time operating system and an additional inter- processor link, PVIC. The latter offers broadcast functionality identified as being important to the overall performance of the message passing. In addition, performance benchmarks for all implementing buses are presented for both simple test programs and the full DAQ applications. (0 refs)...

  1. Orbital period variations of two W UMa-type binaries: UY UMa and EF Boo

    Science.gov (United States)

    Yu, Yun-Xia; Zhang, Xu-Dong; Hu, Ke; Xiang, Fu-Yuan

    2017-08-01

    The orbital period variations of two W UMa-type contact binaries, UY UMa and EF Boo, are analyzed by using all available times of light minimum. It is detected that the general trends of their (O - C) curves show an upward parabolic variation, which reveals their continuous period increases at the rates of dP / dt = 2.545 ×10-7 days yr-1 and dP / dt = 2.623 ×10-7 days yr-1 , respectively. Meanwhile, UY UMa also shows a cyclic period variation with a small amplitude of A = 0.0026 days superposed on the long-term increase. Due to their contact configurations, the secular period increases are interpreted as a result of mass transfer from the less massive component to the more massive one. The cyclic period variation of UY UMa may be interpreted in terms of either the magnetic activity or the light time effect.

  2. Ef: Software for Nonrelativistic Beam Simulation by Particle-in-Cell Algorithm

    Directory of Open Access Journals (Sweden)

    Boytsov A. Yu.

    2018-01-01

    Full Text Available Understanding of particle dynamics is crucial in construction of electron guns, ion sources and other types of nonrelativistic beam devices. Apart from external guiding and focusing systems, a prominent role in evolution of such low-energy beams is played by particle-particle interaction. Numerical simulations taking into account these effects are typically accomplished by a well-known particle-in-cell method. In practice, for convenient work a simulation program should not only implement this method, but also support parallelization, provide integration with CAD systems and allow access to details of the simulation algorithm. To address the formulated requirements, development of a new open source code - Ef - has been started. It's current features and main functionality are presented. Comparison with several analytical models demonstrates good agreement between the numerical results and the theory. Further development plans are discussed.

  3. Ef: Software for Nonrelativistic Beam Simulation by Particle-in-Cell Algorithm

    Science.gov (United States)

    Boytsov, A. Yu.; Bulychev, A. A.

    2018-04-01

    Understanding of particle dynamics is crucial in construction of electron guns, ion sources and other types of nonrelativistic beam devices. Apart from external guiding and focusing systems, a prominent role in evolution of such low-energy beams is played by particle-particle interaction. Numerical simulations taking into account these effects are typically accomplished by a well-known particle-in-cell method. In practice, for convenient work a simulation program should not only implement this method, but also support parallelization, provide integration with CAD systems and allow access to details of the simulation algorithm. To address the formulated requirements, development of a new open source code - Ef - has been started. It's current features and main functionality are presented. Comparison with several analytical models demonstrates good agreement between the numerical results and the theory. Further development plans are discussed.

  4. Gestão do processo de design de arquitetura efêmera em museus

    OpenAIRE

    Veiga, Ana Cecilia Nascimento Rocha; Andery, Paulo Roberto Pereira

    2014-01-01

    A gestão de empreendimentos de museus e espaços museográficos têm crescido em complexidade, particularmente na sua fase de concepção. Contribui para isso o reduzido ciclo de vida dos empreendimentos, a arquitetura efêmera, que supõe pouco tempo para projetação, execução e montagem. Soma-se a mudança de significado que os espaços museográficos tiveram em anos recentes, com a interação entre acervo, ambiente construído e público, gerando um briefing mais dinâmico e complexo. Nesse contexto, o p...

  5. The Influence of the Toxin/Antitoxin mazEF on Growth and Survival of Listeria monocytogenes under Stress

    DEFF Research Database (Denmark)

    Curtis, Thomas; Takeuchi, Ippei; Gram, Lone

    2017-01-01

    A major factor in the resilience of Listeria monocytogenes is the alternative sigma factor B (σB). Type II Toxin/Antitoxin (TA) systems are also known to have a role in the bacterial stress response upon activation via the ClpP or Lon proteases. Directly upstream of the σB operon in L....... monocytogenes is the TA system mazEF, which can cleave mRNA at UACMU sites. In this study, we showed that the mazEF TA locus does not affect the level of persister formation during treatment with antibiotics in lethal doses, but exerts different effects according to the sub-inhibitory stress added. Growth...... it is not analogous to the system of S. aureus, suggesting a novel mode of action for MazEF in L. monocytogenes....

  6. Leucine-based receptor sorting motifs are dependent on the spacing relative to the plasma membrane

    DEFF Research Database (Denmark)

    Geisler, C; Dietrich, J; Nielsen, B L

    1998-01-01

    Many integral membrane proteins contain leucine-based motifs within their cytoplasmic domains that mediate internalization and intracellular sorting. Two types of leucine-based motifs have been identified. One type is dependent on phosphorylation, whereas the other type, which includes an acidic...... amino acid, is constitutively active. In this study, we have investigated how the spacing relative to the plasma membrane affects the function of both types of leucine-based motifs. For phosphorylation-dependent leucine-based motifs, a minimal spacing of 7 residues between the plasma membrane...... and the phospho-acceptor was required for phosphorylation and thereby activation of the motifs. For constitutively active leucine-based motifs, a minimal spacing of 6 residues between the plasma membrane and the acidic residue was required for optimal activity of the motifs. In addition, we found that the acidic...

  7. Organization of feed-forward loop motifs reveals architectural principles in natural and engineered networks.

    Science.gov (United States)

    Gorochowski, Thomas E; Grierson, Claire S; di Bernardo, Mario

    2018-03-01

    Network motifs are significantly overrepresented subgraphs that have been proposed as building blocks for natural and engineered networks. Detailed functional analysis has been performed for many types of motif in isolation, but less is known about how motifs work together to perform complex tasks. To address this issue, we measure the aggregation of network motifs via methods that extract precisely how these structures are connected. Applying this approach to a broad spectrum of networked systems and focusing on the widespread feed-forward loop motif, we uncover striking differences in motif organization. The types of connection are often highly constrained, differ between domains, and clearly capture architectural principles. We show how this information can be used to effectively predict functionally important nodes in the metabolic network of Escherichia coli . Our findings have implications for understanding how networked systems are constructed from motif parts and elucidate constraints that guide their evolution.

  8. Management of Atopic Hand Dermatitis

    DEFF Research Database (Denmark)

    Halling-Overgaard, Anne-Sofie; Zachariae, Claus; Thyssen, Jacob P

    2017-01-01

    This article provides an overview of clinical aspects of hand eczema in patients with atopic dermatitis. Hand eczema can be a part of atopic dermatitis itself or a comorbidity, for example, as irritant or allergic contact dermatitis. When managing hand eczema, it is important to first categorize...

  9. Hand Washing: Do's and Dont's

    Science.gov (United States)

    ... hands frequently can help limit the transfer of bacteria, viruses and other microbes. Always wash your hands before: Preparing food or eating Treating wounds or caring for a sick person Inserting or removing contact lenses Always wash your hands after: Preparing food Using ...

  10. Hand aperture patterns in prehension.

    Science.gov (United States)

    Bongers, Raoul M; Zaal, Frank T J M; Jeannerod, Marc

    2012-06-01

    Although variations in the standard prehensile pattern can be found in the literature, these alternative patterns have never been studied systematically. This was the goal of the current paper. Ten participants picked up objects with a pincer grip. Objects (3, 5, or 7cm in diameter) were placed at 30, 60, 90, or 120cm from the hands' starting location. Usually the hand was opened gradually to a maximum immediately followed by hand closing, called the standard hand opening pattern. In the alternative opening patterns the hand opening was bumpy, or the hand aperture stayed at a plateau before closing started. Two participants in particular delayed the start of grasping with respect to start of reaching, with the delay time increasing with object distance. For larger object distances and smaller object sizes, the bumpy and plateau hand opening patterns were used more often. We tentatively concluded that the alternative hand opening patterns extended the hand opening phase, to arrive at the appropriate hand aperture at the appropriate time to close the hand for grasping the object. Variations in hand opening patterns deserve attention because this might lead to new insights into the coordination of reaching and grasping. Copyright © 2011 Elsevier B.V. All rights reserved.

  11. Repeatability of tumour hypoxia imaging using [{sup 18}F]EF5 PET/CT in head and neck cancer

    Energy Technology Data Exchange (ETDEWEB)

    Silvoniemi, Antti [University of Turku, Turku PET Centre (Finland); Turku University Hospital, Department of Otorhinolaryngology - Head and Neck Surgery (Finland); Suilamo, Sami [Turku University Hospital, Department of Oncology and Radiotherapy (Finland); Turku University Hospital, Department of Medical Physics (Finland); Laitinen, Timo; Forsback, Sarita; Solin, Olof [University of Turku, Turku PET Centre (Finland); Loeyttyniemi, Eliisa [University of Turku, Department of Biostatistics, Turku (Finland); Vaittinen, Samuli [Turku University Hospital, Department of Pathology (Finland); Saunavaara, Virva [University of Turku, Turku PET Centre (Finland); Turku University Hospital, Department of Medical Physics (Finland); Groenroos, Tove J.; Minn, Heikki [University of Turku, Turku PET Centre (Finland); Turku University Hospital, Department of Oncology and Radiotherapy (Finland)

    2018-02-15

    Hypoxia contributes to radiotherapy resistance and more aggressive behaviour of several types of cancer. This study was designed to evaluate the repeatability of intratumour uptake of the hypoxia tracer [{sup 18}F]EF5 in paired PET/CT scans. Ten patients with newly diagnosed head and neck cancer (HNC) received three static PET/CT scans before chemoradiotherapy: two with [{sup 18}F]EF5 a median of 7 days apart and one with [{sup 18}F]FDG. Metabolically active primary tumour volumes were defined in [{sup 18}F]FDG images and transferred to co-registered [{sup 18}F]EF5 images for repeatability analysis. A tumour-to-muscle uptake ratio (TMR) of 1.5 at 3 h from injection of [{sup 18}F]EF5 was used as a threshold representing hypoxic tissue. In 10 paired [{sup 18}F]EF5 PET/CT image sets, SUVmean, SUVmax, and TMR showed a good correlation with the intraclass correlation coefficients of 0.81, 0.85, and 0.87, respectively. The relative coefficients of repeatability for these parameters were 15%, 17%, and 10%, respectively. Fractional hypoxic volumes of the tumours in the repeated scans had a high correlation using the Spearman rank correlation test (r = 0.94). In a voxel-by-voxel TMR analysis between the repeated scans, the mean of Pearson correlation coefficients of individual patients was 0.65. The mean (± SD) difference of TMR in the pooled data set was 0.03 ± 0.20. Pretreatment [{sup 18}F]EF5 PET/CT within one week shows high repeatability and is feasible for the guiding of hypoxia-targeted treatment interventions in HNC. (orig.)

  12. Predictive potential of macrophage migration inhibitory factor (MIF) in patients with heart failure with preserved ejection fraction (HFpEF).

    Science.gov (United States)

    Luedike, Peter; Alatzides, Georgios; Papathanasiou, Maria; Heisler, Martin; Pohl, Julia; Lehmann, Nils; Rassaf, Tienush

    2018-05-04

    Prognostication in heart failure with preserved ejection fraction (HFpEF) is challenging and novel biomarkers are urgently needed. Macrophage migration inhibitory factor (MIF) is a pro-inflammatory cytokine that plays a crucial role in cardiovascular and various inflammatory diseases. Whether MIF is involved in HFpEF is unknown. Sixty-two patients with HFpEF were enrolled and followed up for 180 days. MIF plasma levels as well as natriuretic peptide (NP) levels were assessed. High MIF levels significantly predicted the combined end-point of all-cause death or hospitalization at 180 days in the univariate analysis (HR 2.41, 95% CI 1.12-5.19, p = 0.025) and after adjustment for relevant covariates in a Cox proportional hazard regression model (HR 2.35, 95% CI 1.05-5.27, p = 0.0374). Furthermore, MIF levels above the median were associated with higher pulmonary artery systolic pressure (PASP) as assessed by echocardiography (PASP 31 mmHg vs 48 mmHg in the low- and high-MIF group, respectively, p = 0.017). NPs significantly correlated with MIF in HFpEF patients (BNP p = 0.011; r = 0.32; NT-proBNP p = 0.027; r = 0.28). MIF was associated with clinical outcomes and might be involved in the pathophysiology of pulmonary hypertension in patients with HFpEF. These first data on MIF in HFpEF should stimulate further research to elucidate the role of this cytokine in heart failure. Trial registration NCT03232671.

  13. Evolutionarily conserved bias of amino-acid usage refines the definition of PDZ-binding motif

    Directory of Open Access Journals (Sweden)

    Launey Thomas

    2011-06-01

    Full Text Available Abstract Background The interactions between PDZ (PSD-95, Dlg, ZO-1 domains and PDZ-binding motifs play central roles in signal transductions within cells. Proteins with PDZ domains bind to PDZ-binding motifs almost exclusively when the motifs are located at the carboxyl (C- terminal ends of their binding partners. However, it remains little explored whether PDZ-binding motifs show any preferential location at the C-terminal ends of proteins, at genome-level. Results Here, we examined the distribution of the type-I (x-x-S/T-x-I/L/V or type-II (x-x-V-x-I/V PDZ-binding motifs in proteins encoded in the genomes of five different species (human, mouse, zebrafish, fruit fly and nematode. We first established that these PDZ-binding motifs are indeed preferentially present at their C-terminal ends. Moreover, we found specific amino acid (AA bias for the 'x' positions in the motifs at the C-terminal ends. In general, hydrophilic AAs were favored. Our genomics-based findings confirm and largely extend the results of previous interaction-based studies, allowing us to propose refined consensus sequences for all of the examined PDZ-binding motifs. An ontological analysis revealed that the refined motifs are functionally relevant since a large fraction of the proteins bearing the motif appear to be involved in signal transduction. Furthermore, co-precipitation experiments confirmed two new protein interactions predicted by our genomics-based approach. Finally, we show that influenza virus pathogenicity can be correlated with PDZ-binding motif, with high-virulence viral proteins bearing a refined PDZ-binding motif. Conclusions Our refined definition of PDZ-binding motifs should provide important clues for identifying functional PDZ-binding motifs and proteins involved in signal transduction.

  14. Hb taradale [beta82(EF6)Lys-->Arg]: a novel mutation at a 2,3-diphosphoglycerate binding site.

    Science.gov (United States)

    Brennan, Stephen O; Sheen, Campbell; Chan, Tim; George, Peter M

    2005-01-01

    Hb Taradale [beta82(EF6)Lys-->Arg] was initially detected as a split Hb A0 peak on Hb A1c, monitoring. Red cell parameters, hemoglobin (Hb) electrophoresis and stability tests were normal. Mass spectrometry (ms) clearly identified a variant beta chain with a mass increase of 28 Da and peptide mapping located the mutation site to peptide betaT-9. DNA sequencing confirmed the presence of a novel beta82(EF6)Lys-->Arg mutation. This conservative substitution at a 2,3-diphosphoglycerate (2,3-DPG) binding site did not, however, appear to affect the P50 for oxygen binding.

  15. The CREC family, a novel family of multiple EF-hand, low-affinity Ca(2+)-binding proteins localised to the secretory pathway of mammalian cells

    DEFF Research Database (Denmark)

    Honoré, B; Vorum, H

    2000-01-01

    (2+)-regulated activities. Recent evidence has been obtained that some CREC family members are involved in pathological activities such as malignant cell transformation, mediation of the toxic effects of snake venom toxins and putative participation in amyloid formation. Udgivelsesdato: 2000-Jan-21...

  16. Unimanual SNARC Effect: Hand Matters.

    Science.gov (United States)

    Riello, Marianna; Rusconi, Elena

    2011-01-01

    A structural representation of the hand embedding information about the identity and relative position of fingers is necessary to counting routines. It may also support associations between numbers and allocentric spatial codes that predictably interact with other known numerical spatial representations, such as the mental number line (MNL). In this study, 48 Western participants whose typical counting routine proceeded from thumb-to-little on both hands performed magnitude and parity binary judgments. Response keys were pressed either with the right index and middle fingers or with the left index and middle fingers in separate blocks. 24 participants responded with either hands in prone posture (i.e., palm down) and 24 participants responded with either hands in supine (i.e., palm up) posture. When hands were in prone posture, the counting direction of the left hand conflicted with the direction of the left-right MNL, whereas the counting direction of the right hand was consistent with it. When hands were in supine posture, the opposite was true. If systematic associations existed between relative number magnitude and an allocentric spatial representation of the finger series within each hand, as predicted on the basis of counting habits, interactions would be expected between hand posture and a unimanual version of the spatial-numerical association of response codes (SNARC) effect. Data revealed that with hands in prone posture a unimanual SNARC effect was present for the right hand, and with hands in supine posture a unimanual SNARC effect was present for the left hand. We propose that a posture-invariant body structural representation of the finger series provides a relevant frame of reference, a within-hand directional vector, that is associated to simple number processing. Such frame of reference can significantly interact with stimulus-response correspondence effects, like the SNARC, that have been typically attributed to the mapping of numbers on a left

  17. Unimanual SNARC Effect: Hand Matters

    Directory of Open Access Journals (Sweden)

    Marianna eRiello

    2011-12-01

    Full Text Available A structural representation of the hand embedding information about the identity and relative position of fingers is necessary to counting routines. It may also support associations between numbers and allocentric spatial codes that predictably interact with other known numerical spatial representations, such as the mental number line. In this study, 48 Western participants whose typical counting routine proceeded from thumb-to-little on both hands performed magnitude and parity binary judgments. Response keys were pressed either with the right index and middle fingers or with the left index and middle fingers in separate blocks. 24 participants responded with either hands in prone posture (i.e. palm down and 24 participants responded with either hands in supine (i.e. palm up posture. When hands were in prone posture, the counting direction of the left hand conflicted with the direction of the left-right mental number line, whereas the counting direction of the right hand was consistent with it. When hands were in supine posture, the opposite was true. If systematic associations existed between relative number magnitude and an allocentric spatial representation of the finger series within each hand, as predicted on the basis of counting habits, interactions would be expected between hand posture and a unimanual version of the Spatial-Numerical Association of Response Codes (SNARC effect. Data revealed that with hands in prone posture a unimanual SNARC effect was present for the right hand, and with hands in supine posture a unimanual SNARC effect was present for the left hand. We propose that a posture-invariant body structural representation of the finger series provides a relevant frame of reference, a within-hand directional vector, that is associated to simple number processing. Such frame of reference can significantly interact with stimulus-response correspondence effects that have been attributed to the mapping of numbers on a mental

  18. Duplication of Drosophila melanogaster mitochondrial EF-Tu: pre-adaptation to T-arm truncation and exclusion of bulky aminoacyl residues.

    Science.gov (United States)

    Sato, Aya; Suematsu, Takuma; Aihara, Koh-Ki; Kita, Kiyoshi; Suzuki, Tsutomu; Watanabe, Kimitsuna; Ohtsuki, Takashi; Watanabe, Yoh-Ichi

    2017-03-07

    Translation elongation factor Tu (EF-Tu) delivers aminoacyl-tRNA (aa-tRNA) to ribosomes in protein synthesis. EF-Tu generally recognizes aminoacyl moieties and acceptor- and T-stems of aa-tRNAs. However, nematode mitochondrial (mt) tRNAs frequently lack all or part of the T-arm that is recognized by canonical EF-Tu. We previously reported that two distinct EF-Tu species, EF-Tu1 and EF-Tu2, respectively, recognize mt tRNAs lacking T-arms and D-arms in the mitochondria of the chromadorean nematode Caenorhabditis elegans C. elegans EF-Tu2 specifically recognizes the seryl moiety of serylated D-armless tRNAs. Mitochondria of the enoplean nematode Trichinella possess three structural types of tRNAs: T-armless tRNAs, D-armless tRNAs, and cloverleaf tRNAs with a short T-arm. Trichinella mt EF-Tu1 binds to all three types and EF-Tu2 binds only to D-armless Ser-tRNAs, showing an evolutionary intermediate state from canonical EF-Tu to chromadorean nematode (e.g. C. elegans ) EF-Tu species. We report here that two EF-Tu species also participate in Drosophila melanogaster mitochondria. Both D. melanogaster EF-Tu1 and EF-Tu2 bound to cloverleaf and D-armless tRNAs. D. melanogaster EF-Tu1 has the ability to recognize T-armless tRNAs that do not evidently exist in D. melanogaster mitochondria, but do exist in related arthropod species. In addition, D. melanogaster EF-Tu2 preferentially bound to aa-tRNAs carrying small amino acids, but not to aa-tRNAs carrying bulky amino acids. These results suggest that the Drosophila mt translation system could be another intermediate state between the canonical and nematode mitochondria-type translation systems. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

  19. Robotically enhanced rubber hand illusion.

    Science.gov (United States)

    Arata, Jumpei; Hattori, Masashi; Ichikawa, Shohei; Sakaguchi, Masamichi

    2014-01-01

    The rubber hand illusion is a well-known multisensory illusion. In brief, watching a rubber hand being stroked by a paintbrush while one's own unseen hand is synchronously stroked causes the rubber hand to be attributed to one's own body and to "feel like it's my hand." The rubber hand illusion is thought to be triggered by the synchronized tactile stimulation of both the subject's hand and the fake hand. To extend the conventional rubber hand illusion, we introduce robotic technology in the form of a master-slave telemanipulator. The developed one degree-of-freedom master-slave system consists of an exoskeleton master equipped with an optical encoder that is worn on the subject's index finger and a motor-actuated index finger on the rubber hand, which allows the subject to perform unilateral telemanipulation. The moving rubber hand illusion has been studied by several researchers in the past with mechanically connected rigs between the subject's body and the fake limb. The robotic instruments let us investigate the moving rubber hand illusion with less constraints, thus behaving closer to the classic rubber hand illusion. In addition, the temporal delay between the body and the fake limb can be precisely manipulated. The experimental results revealed that the robotic instruments significantly enhance the rubber hand illusion. The time delay is significantly correlated with the effect of the multisensory illusion, and the effect significantly decreased at time delays over 100 ms. These findings can potentially contribute to the investigations of neural mechanisms in the field of neuroscience and of master-slave systems in the field of robotics.

  20. Fat suppression at 2D MR imaging of the hands: Dixon method versus CHESS technique and STIR sequence.

    Science.gov (United States)

    Kirchgesner, Thomas; Perlepe, Vasiliki; Michoux, Nicolas; Larbi, Ahmed; Vande Berg, Bruno

    2017-04-01

    To compare the effectiveness of fat suppression and the signal-to-noise ratio (SNR) of the Dixon method with those of the CHESS (Chemical Shift-Selective) technique and STIR (Short Tau Inversion Recovery) sequence in hands of normal subjects at 2D MR imaging. 14 healthy volunteers (mean age of 29.4 years) consented to have both hands prospectively imaged with SE T1 Dixon, T1 CHESS, T2 Dixon, T2 CHESS and STIR sequences in a 1.5T MR scanner. Three radiologists scored the effectiveness of fat suppression in bone marrow (EFS BM ) and soft tissues (EFS ST ) in 20 joints per subject. One radiologist measured the SNR in 10 bones per subject. Statistical analysis used two-way ANOVA with random effects, paired t-test and observed agreement to assess differences in effectiveness of fat suppression, differences in SNR and inter-observer agreement. EFS BM was statistically significantly higher for T1 Dixon than for T1 CHESS and for T2 Dixon than for T2 CHESS (pCHESS and for T2 Dixon than for STIR (pCHESS (pCHESS technique at 2D T1-weighted MR imaging of the hands. At T2-weighted MR imaging, fat suppression is more effective with the Dixon method while SNR is higher with the CHESS technique. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Sequence-based classification using discriminatory motif feature selection.

    Directory of Open Access Journals (Sweden)

    Hao Xiong

    Full Text Available Most existing methods for sequence-based classification use exhaustive feature generation, employing, for example, all k-mer patterns. The motivation behind such (enumerative approaches is to minimize the potential for overlooking important features. However, there are shortcomings to this strategy. First, practical constraints limit the scope of exhaustive feature generation to patterns of length ≤ k, such that potentially important, longer (> k predictors are not considered. Second, features so generated exhibit strong dependencies, which can complicate understanding of derived classification rules. Third, and most importantly, numerous irrelevant features are created. These concerns can compromise prediction and interpretation. While remedies have been proposed, they tend to be problem-specific and not broadly applicable. Here, we develop a generally applicable methodology, and an attendant software pipeline, that is predicated on discriminatory motif finding. In addition to the traditional training and validation partitions, our framework entails a third level of data partitioning, a discovery partition. A discriminatory motif finder is used on sequences and associated class labels in the discovery partition to yield a (small set of features. These features are then used as inputs to a classifier in the training partition. Finally, performance assessment occurs on the validation partition. Important attributes of our approach are its modularity (any discriminatory motif finder and any classifier can be deployed and its universality (all data, including sequences that are unaligned and/or of unequal length, can be accommodated. We illustrate our approach on two nucleosome occupancy datasets and a protein solubility dataset, previously analyzed using enumerative feature generation. Our method achieves excellent performance results, with and without optimization of classifier tuning parameters. A Python pipeline implementing the approach is

  2. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    Energy Technology Data Exchange (ETDEWEB)

    Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

    2007-02-21

    Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by

  3. Divergent protein motifs direct elongation factor P-mediated translational regulation in Salmonella enterica and Escherichia coli

    DEFF Research Database (Denmark)

    Hersch, Steven J; Wang, Mengchi; Zou, S Betty

    2013-01-01

    number of proteins are affected by the loss of EF-P, and it has recently been determined that EF-P plays a critical role in rescuing ribosomes stalled at PPP and PPG peptide sequences. Here we present an unbiased in vivo investigation of the specific targets of EF-P by employing stable isotope labeling...

  4. Indonesian Traditional Toys and the Development of Batik Motifs

    Directory of Open Access Journals (Sweden)

    Bagus Indrayana

    2016-06-01

    Full Text Available There is a wide array of traditional toys in Indonesia. In the past, traditional toys played an important role for skill and creativity development of children. Today, the position of traditional toys in the society is displaced by toys from large-scale manufacturers. Given the critical role of traditional toys for children’s motoric and social development, there is a need to develop media that can be used to promote these traditional products and strengthen their position in the public. We propose to use Batik as a way to effectively disseminate and promote traditional toys to the general public. Apart from this, using traditional toys to create new Batik motifs can have an economic value for the producers of Batik, promote Indonesian products and enrich the Indonesian Batik. This study aims to explore the variety of traditional toys, mainly from Klaten and Magelang, in the Central Java province of Indonesia, and use them as the basis for the development of Batik motif creation. This study used Trilogi Keseimbangan (or Harmony Trilogy aesthetic theory analytical approach that explains the creation of craft consists of the following phases: exploration, design, and materialization. The creation method in this study adopts Tiga Tahap Enam Langkah (Three Phases, Six Steps method offered in the theory. The finding in the field found that the traditional toys material used in Klaten and Magelang, mostly made from waste wood, plywood, and zinc. The manufacturing process is done manually by two or three craftsmen using a simple technology. The traditional toys are designed by the artisans mostly, although there may be designs from the clients. In addition, we also found that the traditional toys have never been used as a Batik motif. The traditional toys Batik motif presented in this work is researcher’s design. For the purposes of this study, we first research the variety of traditional toys available in the market today in Indonesia. We look

  5. Dimensionality of social networks using motifs and eigenvalues.

    Directory of Open Access Journals (Sweden)

    Anthony Bonato

    Full Text Available We consider the dimensionality of social networks, and develop experiments aimed at predicting that dimension. We find that a social network model with nodes and links sampled from an m-dimensional metric space with power-law distributed influence regions best fits samples from real-world networks when m scales logarithmically with the number of nodes of the network. This supports a logarithmic dimension hypothesis, and we provide evidence with two different social networks, Facebook and LinkedIn. Further, we employ two different methods for confirming the hypothesis: the first uses the distribution of motif counts, and the second exploits the eigenvalue distribution.

  6. Hand-related physical function in rheumatic hand conditions

    DEFF Research Database (Denmark)

    Klokker, Louise; Terwee, Caroline; Wæhrens, Eva Elisabet Ejlersen

    2016-01-01

    INTRODUCTION: There is no consensus about what constitutes the most appropriate patient-reported outcome measurement (PROM) instrument for measuring physical function in patients with rheumatic hand conditions. Existing instruments lack psychometric testing and vary in feasibility...... and their psychometric qualities. We aim to develop a PROM instrument to assess hand-related physical function in rheumatic hand conditions. METHODS AND ANALYSIS: We will perform a systematic search to identify existing PROMs to rheumatic hand conditions, and select items relevant for hand-related physical function...... as well as those items from the Patient Reported Outcomes Measurement Information System (PROMIS) Physical Function (PF) item bank that are relevant to patients with rheumatic hand conditions. Selection will be based on consensus among reviewers. Content validity of selected items will be established...

  7. Hand-related physical function in rheumatic hand conditions

    DEFF Research Database (Denmark)

    Klokker, Louise; Terwee, Caroline B; Wæhrens, Eva Ejlersen

    2016-01-01

    as well as those items from the Patient Reported Outcomes Measurement Information System (PROMIS) Physical Function (PF) item bank that are relevant to patients with rheumatic hand conditions. Selection will be based on consensus among reviewers. Content validity of selected items will be established......INTRODUCTION: There is no consensus about what constitutes the most appropriate patient-reported outcome measurement (PROM) instrument for measuring physical function in patients with rheumatic hand conditions. Existing instruments lack psychometric testing and vary in feasibility...... and their psychometric qualities. We aim to develop a PROM instrument to assess hand-related physical function in rheumatic hand conditions. METHODS AND ANALYSIS: We will perform a systematic search to identify existing PROMs to rheumatic hand conditions, and select items relevant for hand-related physical function...

  8. RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections.

    Science.gov (United States)

    Castro-Mondragon, Jaime Abraham; Jaeger, Sébastien; Thieffry, Denis; Thomas-Chollier, Morgane; van Helden, Jacques

    2017-07-27

    Transcription factor (TF) databases contain multitudes of binding motifs (TFBMs) from various sources, from which non-redundant collections are derived by manual curation. The advent of high-throughput methods stimulated the production of novel collections with increasing numbers of motifs. Meta-databases, built by merging these collections, contain redundant versions, because available tools are not suited to automatically identify and explore biologically relevant clusters among thousands of motifs. Motif discovery from genome-scale data sets (e.g. ChIP-seq) also produces redundant motifs, hampering the interpretation of results. We present matrix-clustering, a versatile tool that clusters similar TFBMs into multiple trees, and automatically creates non-redundant TFBM collections. A feature unique to matrix-clustering is its dynamic visualisation of aligned TFBMs, and its capability to simultaneously treat multiple collections from various sources. We demonstrate that matrix-clustering considerably simplifies the interpretation of combined results from multiple motif discovery tools, and highlights biologically relevant variations of similar motifs. We also ran a large-scale application to cluster ∼11 000 motifs from 24 entire databases, showing that matrix-clustering correctly groups motifs belonging to the same TF families, and drastically reduced motif redundancy. matrix-clustering is integrated within the RSAT suite (http://rsat.eu/), accessible through a user-friendly web interface or command-line for its integration in pipelines. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  9. CMD: A Database to Store the Bonding States of Cysteine Motifs with Secondary Structures

    Directory of Open Access Journals (Sweden)

    Hamed Bostan

    2012-01-01

    Full Text Available Computational approaches to the disulphide bonding state and its connectivity pattern prediction are based on various descriptors. One descriptor is the amino acid sequence motifs flanking the cysteine residue motifs. Despite the existence of disulphide bonding information in many databases and applications, there is no complete reference and motif query available at the moment. Cysteine motif database (CMD is the first online resource that stores all cysteine residues, their flanking motifs with their secondary structure, and propensity values assignment derived from the laboratory data. We extracted more than 3 million cysteine motifs from PDB and UniProt data, annotated with secondary structure assignment, propensity value assignment, and frequency of occurrence and coefficiency of their bonding status. Removal of redundancies generated 15875 unique flanking motifs that are always bonded and 41577 unique patterns that are always nonbonded. Queries are based on the protein ID, FASTA sequence, sequence motif, and secondary structure individually or in batch format using the provided APIs that allow remote users to query our database via third party software and/or high throughput screening/querying. The CMD offers extensive information about the bonded, free cysteine residues, and their motifs that allows in-depth characterization of the sequence motif composition.

  10. Finding a Leucine in a Haystack: Searching the Proteome for ambigous Leucine-Aspartic Acid motifs

    KAUST Repository

    Arold, Stefan T.

    2016-01-25

    Leucine-aspartic acid (LD) motifs are short helical protein-protein interaction motifs involved in cell motility, survival and communication. LD motif interactions are also implicated in cancer metastasis and are targeted by several viruses. LD motifs are notoriously difficult to detect because sequence pattern searches lead to an excessively high number of false positives. Hence, despite 20 years of research, only six LD motif–containing proteins are known in humans, three of which are close homologues of the paxillin family. To enable the proteome-wide discovery of LD motifs, we developed LD Motif Finder (LDMF), a web tool based on machine learning that combines sequence information with structural predictions to detect LD motifs with high accuracy. LDMF predicted 13 new LD motifs in humans. Using biophysical assays, we experimentally confirmed in vitro interactions for four novel LD motif proteins. Thus, LDMF allows proteome-wide discovery of LD motifs, despite a highly ambiguous sequence pattern. Functional implications will be discussed.

  11. Transduction motif analysis of gastric cancer based on a human signaling network

    Energy Technology Data Exchange (ETDEWEB)

    Liu, G.; Li, D.Z.; Jiang, C.S.; Wang, W. [Fuzhou General Hospital of Nanjing Command, Department of Gastroenterology, Fuzhou, China, Department of Gastroenterology, Fuzhou General Hospital of Nanjing Command, Fuzhou (China)

    2014-04-04

    To investigate signal regulation models of gastric cancer, databases and literature were used to construct the signaling network in humans. Topological characteristics of the network were analyzed by CytoScape. After marking gastric cancer-related genes extracted from the CancerResource, GeneRIF, and COSMIC databases, the FANMOD software was used for the mining of gastric cancer-related motifs in a network with three vertices. The significant motif difference method was adopted to identify significantly different motifs in the normal and cancer states. Finally, we conducted a series of analyses of the significantly different motifs, including gene ontology, function annotation of genes, and model classification. A human signaling network was constructed, with 1643 nodes and 5089 regulating interactions. The network was configured to have the characteristics of other biological networks. There were 57,942 motifs marked with gastric cancer-related genes out of a total of 69,492 motifs, and 264 motifs were selected as significantly different motifs by calculating the significant motif difference (SMD) scores. Genes in significantly different motifs were mainly enriched in functions associated with cancer genesis, such as regulation of cell death, amino acid phosphorylation of proteins, and intracellular signaling cascades. The top five significantly different motifs were mainly cascade and positive feedback types. Almost all genes in the five motifs were cancer related, including EPOR, MAPK14, BCL2L1, KRT18, PTPN6, CASP3, TGFBR2, AR, and CASP7. The development of cancer might be curbed by inhibiting signal transductions upstream and downstream of the selected motifs.

  12. HENRY'S "HAND OF GOD"

    Directory of Open Access Journals (Sweden)

    Željko Kaluđerović

    2014-04-01

    Full Text Available In this paper the author discusses the views and statements of the French football player Thierry Henry he gave after his illegal play during the playoff match between France and the Republic of Ireland to claim one of the final spots in the World Cup 2010 in South Africa. First, by controlling the ball with his hand before passing it on for the goal Henry has shown disregard for the constitutive rules of football. Then, by stating that he is "not a referee" he demonstrated that for some players rules are not inherent to football and that they can be relativized, given that for them winning is the goal of the highest ontological status. Furthermore, he has rejected the rules of sportsmanship, thus expressing his opinion that the opponents are just obstacles which have to be removed in order to achieve your goals. Henry's action has disrupted major moral values, such as justice, honesty, responsibility and beneficence. The rules of fair play have totally been ignored both in Henry's action and in the Football Association of France's unwillingness to comment on whether a replay should take place. They have ignored one of the basic principles stated in the "Declaration of the International Fair Play Committee", according to which, fair play is much more than playing to the rules of the game; it's about the attitude of the sportsperson. It's about respecting your opponent and preserving his or her physical and psychological integrity. Finally, the author believes that the rules, moral values and fair play in football are required for this game to become actually possible to play

  13. HENRY'S "HAND OF GOD"

    Directory of Open Access Journals (Sweden)

    Željko Kaluđerović

    2014-04-01

    Full Text Available In this paper the author discusses the views and statements of the French football player Thierry Henry he gave after his illegal play during the playoff match between France and the Republic of Ireland to claim one of the final spots in the World Cup 2010 in South Africa. First, by controlling the ball with his hand before passing it on for the goal Henry has shown disregard for the constitutive rules of football. Then, by stating that he is "not a referee" he demonstrated that for some players rules are not inherent to football and that they can be relativized, given that for them winning is the goal of the highest ontological status. Furthermore, he has rejected the rules of sportsmanship, thus expressing his opinion that the opponents are just obstacles which have to be removed in order to achieve your goals. Henry's action has disrupted major moral values, such as justice, honesty, responsibility and beneficence. The rules of fair play have totally been ignored both in Henry's action and in the Football Association of France's unwillingness to comment on whether a replay should take place. They have ignored one of the basic principles stated in the "Declaration of the International Fair Play Committee", according to which, fair play is much more than playing to the rules of the game; it's about the attitude of the sportsperson. It's about respecting your opponent and preserving his or her physical and psychological integrity. Finally, the author believes that the rules, moral values and fair play in football are required for this game to become actually possible to play.

  14. Effect of Enterococcus faecium EF 55 on morphometry and proliferative activity of intestinal mucosa in broilers infected with Salmonella Enteritidis

    Directory of Open Access Journals (Sweden)

    Ševčíková Zuzana

    2016-09-01

    Full Text Available Introduction: The present study aimed to investigate the effect of Enterococcus faecium EF55 on chickens, as well as its influence on proliferative activity of epithelial intestinal cells after infection with Salmonella enterica serovar Enteritidis phage type 4 (SE PT4. Moreover, the length and area of duodenal and jejunal villi of the birds were examined.

  15. Efímero Festín, el video danza antártico

    OpenAIRE

    Pombo, Ernesto; Costa Chimene

    2013-01-01

    Efímero Festín es un video danza pensado específicamente para ser realizado en la Antártida argentina. Pretende a través del arte y de una forma poética, colaborar con la concientización del cuidado del medio ambiente.

  16. Romanian traditional motif - element of modernity in clothing

    Science.gov (United States)

    Doble, L.; Stan, O.; Suteu, M. D.; Albu, A.; Bohm, G.; Tsatsarou-Michalaki, A.; Gialinou, E.

    2017-10-01

    In this paper are presented the phases for improving from an aesthetic point of view a clothing item, the jacket respectively, with a straight cut for women using software design patterns, computerised graphics and textile different modern technologies including: industrial embroidery, digital printing, sublimation. In the first phase a documentation was prepared in the Ethnographic Museum of Transylvania from Cluj Napoca where more traditional motifs were selected specific to Transylvania etnographic region and were reintepreted and stylized whilst preserving the symbolism and color range specified to the area. For the styling phase was used CorelDraw vector graphics program that allows changing the shape, size and color of the drawings without affecting the identity of the pattern. In the patterns design phase Gemini CAD software was used and for the modeling and model development Optitex software was used. The part for garnishing the model was performed using Embrodery machine software reproducing the stylized motif identically. In order to obtain a significantly improved aesthetic look and an added artistic value the pattern chosen for the jacket was done using a combination of modern textile technologies. This has allowed the realization of a particular texture on the surface of the designed product, demonstrating that traditional patterns can be reintepreted in modern clothing

  17. THE MOTIF OF THE SECOND COMING IN RUSSIAN FANTASTIC FICTION

    Directory of Open Access Journals (Sweden)

    Tatyana I. Khoruzhenko

    2017-06-01

    Full Text Available The motif of the Second Coming of Christ takes a special place in Russian fantastic fiction at the turn of the millennium. In the recent decades allusions to the Gospel topic appears in increasing frequency in the genre of fantasy. The aim of the given article was to analyze the peculiarities of the depiction of the subject of Advent in Russian fantastic fiction. As the basis for the research the novels of Y. Voznesenskaya, N. Perumov, V. Khlumov, S. Lukyanenko and T. Ustimenko are of particular interest. The Advent motif appears in the story line of each of the novels in question. Though, the attitude of the authors to the image of the Savior and his second coming to the world fluctuates: from a respectful expectation (Y. Voznesenskaya, T. Ustimenko, S. Lukyanenko to the depiction of the Savior as a monster (N. Perumov. The possibility of an ambivalent interpretation of the Savior is the eloquent evidence of desacralization of this image. The profaning of the sacred is one of the tendencies of the modern popular culture. The genre of fantastic fiction, as a product of mass culture, has caught this trend quite precisely.

  18. Regulation of amyloid precursor protein processing by its KFERQ motif.

    Science.gov (United States)

    Park, Ji-Seon; Kim, Dong-Hou; Yoon, Seung-Yong

    2016-06-01

    Understanding of trafficking, processing, and degradation mechanisms of amyloid precursor protein (APP) is important because APP can be processed to produce β-amyloid (Aβ), a key pathogenic molecule in Alzheimer's disease (AD). Here, we found that APP contains KFERQ motif at its C-terminus, a consensus sequence for chaperone-mediated autophagy (CMA) or microautophagy which are another types of autophagy for degradation of pathogenic molecules in neurodegenerative diseases. Deletion of KFERQ in APP increased C-terminal fragments (CTFs) and secreted N-terminal fragments of APP and kept it away from lysosomes. KFERQ deletion did not abolish the interaction of APP or its cleaved products with heat shock cognate protein 70 (Hsc70), a protein necessary for CMA or microautophagy. These findings suggest that KFERQ motif is important for normal processing and degradation of APP to preclude the accumulation of APP-CTFs although it may not be important for CMA or microautophagy. [BMB Reports 2016; 49(6): 337-342].

  19. Network motif frequency vectors reveal evolving metabolic network organisation.

    Science.gov (United States)

    Pearcy, Nicole; Crofts, Jonathan J; Chuzhanova, Nadia

    2015-01-01

    At the systems level many organisms of interest may be described by their patterns of interaction, and as such, are perhaps best characterised via network or graph models. Metabolic networks, in particular, are fundamental to the proper functioning of many important biological processes, and thus, have been widely studied over the past decade or so. Such investigations have revealed a number of shared topological features, such as a short characteristic path-length, large clustering coefficient and hierarchical modular structure. However, the extent to which evolutionary and functional properties of metabolism manifest via this underlying network architecture remains unclear. In this paper, we employ a novel graph embedding technique, based upon low-order network motifs, to compare metabolic network structure for 383 bacterial species categorised according to a number of biological features. In particular, we introduce a new global significance score which enables us to quantify important evolutionary relationships that exist between organisms and their physical environments. Using this new approach, we demonstrate a number of significant correlations between environmental factors, such as growth conditions and habitat variability, and network motif structure, providing evidence that organism adaptability leads to increased complexities in the resultant metabolic networks.

  20. Neurite outgrowth mediated by translation elongation factor eEF1A1: a target for antiplatelet agent cilostazol.

    Directory of Open Access Journals (Sweden)

    Kenji Hashimoto

    Full Text Available Cilostazol, a type-3 phosphodiesterase (PDE3 inhibitor, has become widely used as an antiplatelet drug worldwide. A recent second Cilostazol Stroke Prevention Study demonstrated that cilostazol is superior to aspirin for prevention of stroke after an ischemic stroke. However, its precise mechanisms of action remain to be determined. Here, we report that cilostazol, but not the PDE3 inhibitors cilostamide and milrinone, significantly potentiated nerve growth factor (NGF-induced neurite outgrowth in PC12 cells. Furthermore, specific inhibitors for the endoplasmic reticulum protein inositol 1,4,5-triphosphate (IP(3 receptors and several common signaling pathways (PLC-γ, PI3K, Akt, p38 MAPK, and c-Jun N-terminal kinase (JNK, and the Ras/Raf/ERK/MAPK significantly blocked the potentiation of NGF-induced neurite outgrowth by cilostazol. Using a proteomics analysis, we identified that levels of eukaryotic translation elongation factor eEF1A1 protein were significantly increased by treatment with cilostazol, but not cilostamide, in PC12 cells. Moreover, the potentiating effects of cilostazol on NGF-induced neurite outgrowth were significantly antagonized by treatment with eEF1A1 RNAi, but not the negative control of eEF1A1. These findings suggest that eEF1A1 and several common cellular signaling pathways might play a role in the mechanism of cilostazol-induced neurite outgrowth. Therefore, agents that can increase the eEF1A1 protein may have therapeutic relevance in diverse conditions with altered neurite outgrowth.

  1. Anion induced conformational preference of Cα NN motif residues in functional proteins.

    Science.gov (United States)

    Patra, Piya; Ghosh, Mahua; Banerjee, Raja; Chakrabarti, Jaydeb

    2017-12-01

    Among different ligand binding motifs, anion binding C α NN motif consisting of peptide backbone atoms of three consecutive residues are observed to be important for recognition of free anions, like sulphate or biphosphate and participate in different key functions. Here we study the interaction of sulphate and biphosphate with C α NN motif present in different proteins. Instead of total protein, a peptide fragment has been studied keeping C α NN motif flanked in between other residues. We use classical force field based molecular dynamics simulations to understand the stability of this motif. Our data indicate fluctuations in conformational preferences of the motif residues in absence of the anion. The anion gives stability to one of these conformations. However, the anion induced conformational preferences are highly sequence dependent and specific to the type of anion. In particular, the polar residues are more favourable compared to the other residues for recognising the anion. © 2017 Wiley Periodicals, Inc.

  2. Multi-fingered robotic hand

    Science.gov (United States)

    Ruoff, Carl F. (Inventor); Salisbury, Kenneth, Jr. (Inventor)

    1990-01-01

    A robotic hand is presented having a plurality of fingers, each having a plurality of joints pivotally connected one to the other. Actuators are connected at one end to an actuating and control mechanism mounted remotely from the hand and at the other end to the joints of the fingers for manipulating the fingers and passing externally of the robot manipulating arm in between the hand and the actuating and control mechanism. The fingers include pulleys to route the actuators within the fingers. Cable tension sensing structure mounted on a portion of the hand are disclosed, as is covering of the tip of each finger with a resilient and pliable friction enhancing surface.

  3. Application of BET_EF at Mount Etna: a retrospective analysis (years 2001-2005

    Directory of Open Access Journals (Sweden)

    Jacopo Selva

    2011-12-01

    Full Text Available Advances in volcano monitoring and forecasting need a multidisciplinary collaborative framework. In light of this, a Bayesian Event Tree (BET approach was performed by the application of the BET for Eruption Forecasting (BET_EF code to analyze the space-time distribution of the volcanic activity of Mount Etna from 2001-2005. First, a reliable monitoring dataset was set up after some sessions to elicit geophysical, volcanological and geochemical ‘precursor’ parameters. A constant unrest probability of 100%, with a magma involvement usually greater than 95%, was computed throughout the time period analyzed. Eruption probabilities higher than 90% were estimated a few days before the onsets of the 2001 and 2002-2003 flank eruptions. Values slightly higher than 75% were observed during the lava fountaining period in June-July 2001. However, the probabilities flattened to around 30% for the 2004-2005 flank eruption. With suitable data, a good depiction of the actual location of the eruptive scenario for the 2001 and 2002-2003 events was provided. Conversely, the size of the eruptions was not indicated.

  4. A safe potential juice clarifying pectinase from Trichoderma viride EF-8 utilizing Egyptian onion skins

    Directory of Open Access Journals (Sweden)

    Abdel-Mohsen S. Ismail

    2016-06-01

    Full Text Available The production of a notable, safe and highly active pectinase by the local fungal strain Trichoderma viride EF-8 utilizing the abundant pigmented Egyptian onion (Allium cepa L. skins (6.5%, w/v was achieved in 4 days submerged fermentation (SMF cultures, at temperature and pH of 30 °C and 4.0, respectively. The indigenously produced pectinase was partially purified by 50% batch ethanol precipitation and its general properties were studied following the standard procedures. The lyophilized enzyme preparation was free of any ochra or aflatoxins. The optimum conditions for the partially purified enzyme form were 2 mg/mL and 1% (w/v enzyme protein and substrate (citrus pectin concentrations, reaction pH and temperature of 7.0 and 40 °C, respectively. The results presented the low cost onion skins waste as the major substrate for the fungal pectinase production and its subsequent use in perfect fruit (apple, lemon and orange juices clarification with remarkable stability during and after this process, which certainly enhance fruit juices processing in the tropics.

  5. The human hand as an inspiration for robot hand development

    CERN Document Server

    Santos, Veronica

    2014-01-01

    “The Human Hand as an Inspiration for Robot Hand Development” presents an edited collection of authoritative contributions in the area of robot hands. The results described in the volume are expected to lead to more robust, dependable, and inexpensive distributed systems such as those endowed with complex and advanced sensing, actuation, computation, and communication capabilities. The twenty-four chapters discuss the field of robotic grasping and manipulation viewed in light of the human hand’s capabilities and push the state-of-the-art in robot hand design and control. Topics discussed include human hand biomechanics, neural control, sensory feedback and perception, and robotic grasp and manipulation. This book will be useful for researchers from diverse areas such as robotics, biomechanics, neuroscience, and anthropologists.

  6. I-Ad-binding peptides derived from unrelated protein antigens share a common structural motif

    DEFF Research Database (Denmark)

    Sette, A; Buus, S; Colon, S

    1988-01-01

    on the I-Ad binding of the immunogenic peptide OVA 323-339. The results obtained demonstrated the very permissive nature of Ag-Ia interaction. We also showed that unrelated peptides that are good I-Ad binders share a common structural motif and speculated that recognition of such motifs could represent...... that I-Ad molecules recognize a large library of Ag by virtue of common structural motifs present in peptides derived from phylogenetically unrelated proteins....

  7. Lucky Motifs in Chinese Folk Art: Interpreting Paper-cut from Chinese Shaanxi

    OpenAIRE

    Xuxiao WANG

    2013-01-01

    Paper-cut is not simply a form of traditional Chinese folk art. Lucky motifs developed in paper-cut certainly acquired profound cultural connotations. As paper-cut is a time-honoured skill across the nation, interpreting those motifs requires cultural receptiveness and anthropological sensitivity. The author of this article analyzes examples of paper-cut from Northern Shaanxi, China, to identify the cohesive motifs and explore the auspiciousness of the specific concepts of Fu, Lu, Shou, Xi. T...

  8. Low-dimensional morphospace of topological motifs in human fMRI brain networks

    Directory of Open Access Journals (Sweden)

    Sarah E. Morgan

    2018-06-01

    Full Text Available We present a low-dimensional morphospace of fMRI brain networks, where axes are defined in a data-driven manner based on the network motifs. The morphospace allows us to identify the key variations in healthy fMRI networks in terms of their underlying motifs, and we observe that two principal components (PCs can account for 97% of the motif variability. The first PC of the motif distribution is correlated with efficiency and inversely correlated with transitivity. Hence this axis approximately conforms to the well-known economical small-world trade-off between integration and segregation in brain networks. Finally, we show that the economical clustering generative model proposed by Vértes et al. (2012 can approximately reproduce the motif morphospace of the real fMRI brain networks, in contrast to other generative models. Overall, the motif morphospace provides a powerful way to visualize the relationships between network properties and to investigate generative or constraining factors in the formation of complex human brain functional networks. Motifs have been described as the building blocks of complex networks. Meanwhile, a morphospace allows networks to be placed in a common space and can reveal the relationships between different network properties and elucidate the driving forces behind network topology. We combine the concepts of motifs and morphospaces to create the first motif morphospace of fMRI brain networks. Crucially, the morphospace axes are defined by the motifs, in a data-driven manner. We observe strong correlations between the networks’ positions in morphospace and their global topological properties, suggesting that motif morphospaces are a powerful way to capture the topology of networks in a low-dimensional space and to compare generative models of brain networks. Motif morphospaces could also be used to study other complex networks’ topologies.

  9. An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes.

    Science.gov (United States)

    Liu, Bingqiang; Zhang, Hanyuan; Zhou, Chuan; Li, Guojun; Fennell, Anne; Wang, Guanghui; Kang, Yu; Liu, Qi; Ma, Qin

    2016-08-09

    Phylogenetic footprinting is an important computational technique for identifying cis-regulatory motifs in orthologous regulatory regions from multiple genomes, as motifs tend to evolve slower than their surrounding non-functional sequences. Its application, however, has several difficulties for optimizing the selection of orthologous data and reducing the false positives in motif prediction. Here we present an integrative phylogenetic footprinting framework for accurate motif predictions in prokaryotic genomes (MP(3)). The framework includes a new orthologous data preparation procedure, an additional promoter scoring and pruning method and an integration of six existing motif finding algorithms as basic motif search engines. Specifically, we collected orthologous genes from available prokaryotic genomes and built the orthologous regulatory regions based on sequence similarity of promoter regions. This procedure made full use of the large-scale genomic data and taxonomy information and filtered out the promoters with limited contribution to produce a high quality orthologous promoter set. The promoter scoring and pruning is implemented through motif voting by a set of complementary predicting tools that mine as many motif candidates as possible and simultaneously eliminate the effect of random noise. We have applied the framework to Escherichia coli k12 genome and evaluated the prediction performance through comparison with seven existing programs. This evaluation was systematically carried out at the nucleotide and binding site level, and the results showed that MP(3) consistently outperformed other popular motif finding tools. We have integrated MP(3) into our motif identification and analysis server DMINDA, allowing users to efficiently identify and analyze motifs in 2,072 completely sequenced prokaryotic genomes. The performance evaluation indicated that MP(3) is effective for predicting regulatory motifs in prokaryotic genomes. Its application may enhance

  10. Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs

    Directory of Open Access Journals (Sweden)

    Martin Juliette

    2011-06-01

    Full Text Available Abstract Background One of the strategies for protein function annotation is to search particular structural motifs that are known to be shared by proteins with a given function. Results Here, we present a systematic extraction of structural motifs of seven residues from protein loops and we explore their correspondence with functional sites. Our approach is based on the structural alphabet HMM-SA (Hidden Markov Model - Structural Alphabet, which allows simplification of protein structures into uni-dimensional sequences, and advanced pattern statistics adapted to short sequences. Structural motifs of interest are selected by looking for structural motifs significantly over-represented in SCOP superfamilies in protein loops. We discovered two types of structural motifs significantly over-represented in SCOP superfamilies: (i ubiquitous motifs, shared by several superfamilies and (ii superfamily-specific motifs, over-represented in few superfamilies. A comparison of ubiquitous words with known small structural motifs shows that they contain well-described motifs as turn, niche or nest motifs. A comparison between superfamily-specific motifs and biological annotations of Swiss-Prot reveals that some of them actually correspond to functional sites involved in the binding sites of small ligands, such as ATP/GTP, NAD(P and SAH/SAM. Conclusions Our findings show that statistical over-representation in SCOP superfamilies is linked to functional features. The detection of over-represented motifs within structures simplified by HMM-SA is therefore a promising approach for prediction of functional sites and annotation of uncharacterized proteins.

  11. Self-Portrait of an Artist with a Book in her Hand

    Directory of Open Access Journals (Sweden)

    Alenka Spacal

    2010-12-01

    Full Text Available This article considers the book as an important emancipatory motif, expressing the tendency of women self-portrait painters to present themselves as educated and accomplished, and to establish their own subjectivity. In traditional self-portraits, since the Renaissance some female artists have presented themselves as autonomous active individuals depicted painting, reading, or playing a musical instrument. In the past, the motif of the reader has symbolized female erudition, education, and sophistication. In a time when women could only rarely attend school, the use of this motif represented an important and liberating gesture. In a period when artists preferred to portray women as nude seducers rather than as learned ladies, it was all the more important that some female artists endeavored to stress the role of women as readers. Although images of women authors with a book in their hands represented a symbol of learning and wisdom, this same motif could also be used to replace a female author’s signature. This is examined here with reference to the works of the Renaissance painter Sofonisba Anguissola.

  12. Vurdering af effekten af en vindmøllepark ved Overgaard på forekomsten af fugle i EF-fuglebeskyttelsesområde nr. 15

    DEFF Research Database (Denmark)

    Clausen, P.; Larsen, J. K.

    forekomsten af en række arter der enten yngler eller raster inden for EF-fuglebeskyttelsesområdet, og er omfattet af EF-fuglebeskyttelsesdirektivets bilag I. Det drejer sig om arterne skarv Phalacrocorax carbo sinensis, blå kærhøg Circus cyaneus, hjejle Pluvialis apricaria, brushane Philomachus pugnax, klyde...

  13. Hybrid DNA i-motif: Aminoethylprolyl-PNA (pC5) enhance the stability of DNA (dC5) i-motif structure.

    Science.gov (United States)

    Gade, Chandrasekhar Reddy; Sharma, Nagendra K

    2017-12-15

    This report describes the synthesis of C-rich sequence, cytosine pentamer, of aep-PNA and its biophysical studies for the formation of hybrid DNA:aep-PNAi-motif structure with DNA cytosine pentamer (dC 5 ) under acidic pH conditions. Herein, the CD/UV/NMR/ESI-Mass studies strongly support the formation of stable hybrid DNA i-motif structure with aep-PNA even near acidic conditions. Hence aep-PNA C-rich sequence cytosine could be considered as potential DNA i-motif stabilizing agents in vivo conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Enrichment of Circular Code Motifs in the Genes of the Yeast Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Christian J. Michel

    2017-12-01

    Full Text Available A set X of 20 trinucleotides has been found to have the highest average occurrence in the reading frame, compared to the two shifted frames, of genes of bacteria, archaea, eukaryotes, plasmids and viruses. This set X has an interesting mathematical property, since X is a maximal C 3 self-complementary trinucleotide circular code. Furthermore, any motif obtained from this circular code X has the capacity to retrieve, maintain and synchronize the original (reading frame. Since 1996, the theory of circular codes in genes has mainly been developed by analysing the properties of the 20 trinucleotides of X , using combinatorics and statistical approaches. For the first time, we test this theory by analysing the X motifs, i.e., motifs from the circular code X , in the complete genome of the yeast Saccharomyces cerevisiae. Several properties of X motifs are identified by basic statistics (at the frequency level, and evaluated by comparison to R motifs, i.e., random motifs generated from 30 different random codes R . We first show that the frequency of X motifs is significantly greater than that of R motifs in the genome of S. cerevisiae. We then verify that no significant difference is observed between the frequencies of X and R motifs in the non-coding regions of S. cerevisiae, but that the occurrence number of X motifs is significantly higher than R motifs in the genes (protein-coding regions. This property is true for all cardinalities of X motifs (from 4 to 20 and for all 16 chromosomes. We further investigate the distribution of X motifs in the three frames of S. cerevisiae genes and show that they occur more frequently in the reading frame, regardless of their cardinality or their length. Finally, the ratio of X genes, i.e., genes with at least one X motif, to non- X genes, in the set of verified genes is significantly different to that observed in the set of putative or dubious genes with no experimental evidence. These results, taken together

  15. Enrichment of Circular Code Motifs in the Genes of the Yeast Saccharomyces cerevisiae.

    Science.gov (United States)

    Michel, Christian J; Ngoune, Viviane Nguefack; Poch, Olivier; Ripp, Raymond; Thompson, Julie D

    2017-12-03

    A set X of 20 trinucleotides has been found to have the highest average occurrence in the reading frame, compared to the two shifted frames, of genes of bacteria, archaea, eukaryotes, plasmids and viruses. This set X has an interesting mathematical property, since X is a maximal C3 self-complementary trinucleotide circular code. Furthermore, any motif obtained from this circular code X has the capacity to retrieve, maintain and synchronize the original (reading) frame. Since 1996, the theory of circular codes in genes has mainly been developed by analysing the properties of the 20 trinucleotides of X, using combinatorics and statistical approaches. For the first time, we test this theory by analysing the X motifs, i.e., motifs from the circular code X, in the complete genome of the yeast Saccharomyces cerevisiae . Several properties of X motifs are identified by basic statistics (at the frequency level), and evaluated by comparison to R motifs, i.e., random motifs generated from 30 different random codes R. We first show that the frequency of X motifs is significantly greater than that of R motifs in the genome of S. cerevisiae . We then verify that no significant difference is observed between the frequencies of X and R motifs in the non-coding regions of S. cerevisiae , but that the occurrence number of X motifs is significantly higher than R motifs in the genes (protein-coding regions). This property is true for all cardinalities of X motifs (from 4 to 20) and for all 16 chromosomes. We further investigate the distribution of X motifs in the three frames of S. cerevisiae genes and show that they occur more frequently in the reading frame, regardless of their cardinality or their length. Finally, the ratio of X genes, i.e., genes with at least one X motif, to non-X genes, in the set of verified genes is significantly different to that observed in the set of putative or dubious genes with no experimental evidence. These results, taken together, represent the first

  16. Purification and functional motifs of the recombinant ATPase of orf virus.

    Science.gov (United States)

    Lin, Fong-Yuan; Chan, Kun-Wei; Wang, Chi-Young; Wong, Min-Liang; Hsu, Wei-Li

    2011-10-01

    Our previous study showed that the recombinant ATPase encoded by the A32L gene of orf virus displayed ATP hydrolysis activity as predicted from its amino acids sequence. This viral ATPase contains four known functional motifs (motifs I-IV) and a novel AYDG motif; they are essential for ATP hydrolysis reaction by binding ATP and magnesium ions. The motifs I and II correspond with the Walker A and B motifs of the typical ATPase, respectively. To examine the biochemical roles of these five conserved motifs, recombinant ATPases of five deletion mutants derived from the Taiping strain were expressed and purified. Their ATPase functions were assayed and compared with those of two wild type strains, Taiping and Nantou isolated in Taiwan. Our results showed that deletions at motifs I-III or IV exhibited lower activity than that of the wild type. Interestingly, deletion of AYDG motif decreased the ATPase activity more significantly than those of motifs I-IV deletions. Divalent ions such as magnesium and calcium were essential for ATPase activity. Moreover, our recombinant proteins of orf virus also demonstrated GTPase activity, though weaker than the original ATPase activity. Copyright © 2011 Elsevier Inc. All rights reserved.

  17. Systematic comparison of the response properties of protein and RNA mediated gene regulatory motifs.

    Science.gov (United States)

    Iyengar, Bharat Ravi; Pillai, Beena; Venkatesh, K V; Gadgil, Chetan J

    2017-05-30

    We present a framework enabling the dissection of the effects of motif structure (feedback or feedforward), the nature of the controller (RNA or protein), and the regulation mode (transcriptional, post-transcriptional or translational) on the response to a step change in the input. We have used a common model framework for gene expression where both motif structures have an activating input and repressing regulator, with the same set of parameters, to enable a comparison of the responses. We studied the global sensitivity of the system properties, such as steady-state gain, overshoot, peak time, and peak duration, to parameters. We find that, in all motifs, overshoot correlated negatively whereas peak duration varied concavely with peak time. Differences in the other system properties were found to be mainly dependent on the nature of the controller rather than the motif structure. Protein mediated motifs showed a higher degree of adaptation i.e. a tendency to return to baseline levels; in particular, feedforward motifs exhibited perfect adaptation. RNA mediated motifs had a mild regulatory effect; they also exhibited a lower peaking tendency and mean overshoot. Protein mediated feedforward motifs showed higher overshoot and lower peak time compared to the corresponding feedback motifs.

  18. Giant lipomas of the hand

    Directory of Open Access Journals (Sweden)

    Gokce Yildiran

    2015-04-01

    Conclusion: Giant lipomas of the hand are very rare and may cause compressions and other complications. Thus, they require a careful preoperative evaluation in order to make a proper differential diagnosis. [Hand Microsurg 2015; 4(1.000: 8-11

  19. Canadian hand dermatitis management guidelines

    DEFF Research Database (Denmark)

    Lynde, Charles; Guenther, Lyn; Diepgen, Thomas L

    2010-01-01

    Hand dermatitis (HD) is one of the most common skin conditions; however, it is not a homogeneous disease entity. The severity of HD may range from very mild cases to severe chronic forms, which may result in prolonged disability and, occasionally, refractory HD. Chronic hand dermatitis (CHD...

  20. Hand, Foot, and Mouth Disease

    Centers for Disease Control (CDC) Podcasts

    Hand, foot, and mouth disease is a contagious illness that mainly affects children under five. In this podcast, Dr. Eileen Schneider talks about the symptoms of hand, foot, and mouth disease, how it spreads, and ways to help protect yourself and your children from getting infected with the virus.

  1. Effect of hand sanitizer location on hand hygiene compliance.

    Science.gov (United States)

    Cure, Laila; Van Enk, Richard

    2015-09-01

    Hand hygiene is the most important intervention to prevent infection in hospitals. Health care workers should clean their hands at least before and after contact with patients. Hand sanitizer dispensers are important to support hand hygiene because they can be made available throughout hospital units. The aim of this study was to determine whether the usability of sanitizer dispensers correlates with compliance of staff in using the sanitizer in a hospital. This study took place in a Midwest, 404-bed, private, nonprofit community hospital with 15 inpatient care units in addition to several ambulatory units. The usability and standardization of sanitizers in 12 participating inpatient units were evaluated. The hospital measured compliance of staff with hand hygiene as part of their quality improvement program. Data from 2010-2012 were analyzed to measure the relationship between compliance and usability using mixed-effects logistic regression models. The total usability score (P = .0046), visibility (P = .003), and accessibility of the sanitizer on entrance to the patient room (P = .00055) were statistically associated with higher observed compliance rates. Standardization alone showed no significant impact on observed compliance (P = .37). Hand hygiene compliance can be influenced by visibility and accessibility of dispensers. The sanitizer location should be part of multifaceted interventions to improve hand hygiene. Copyright © 2015 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

  2. Degloving injuries of the hand

    Directory of Open Access Journals (Sweden)

    R Krishnamoorthy

    2011-01-01

    Full Text Available Avulsion of skin from the hand or fingers is an injury that has a dramatic presentation. The entire musculo-skeletal unit of the finger is intact, and the patient can often move the parts of his naked hand quite normally. The challenge for the reconstructive surgeon lies in resurfacing the hand or finger with a good quality pliable sensate skin cover while preserving the movements and function of the hand. Traditionally, skin grafting has been the standard method of reconstruction in such injuries. However, skin grafting does have many disadvantages, too. This article deals with the features of such injuries, management protocols and other reconstructive options available in the armamentarium of the hand surgeon.

  3. 3D Printed Robotic Hand

    Science.gov (United States)

    Pizarro, Yaritzmar Rosario; Schuler, Jason M.; Lippitt, Thomas C.

    2013-01-01

    Dexterous robotic hands are changing the way robots and humans interact and use common tools. Unfortunately, the complexity of the joints and actuations drive up the manufacturing cost. Some cutting edge and commercially available rapid prototyping machines now have the ability to print multiple materials and even combine these materials in the same job. A 3D model of a robotic hand was designed using Creo Parametric 2.0. Combining "hard" and "soft" materials, the model was printed on the Object Connex350 3D printer with the purpose of resembling as much as possible the human appearance and mobility of a real hand while needing no assembly. After printing the prototype, strings where installed as actuators to test mobility. Based on printing materials, the manufacturing cost of the hand was $167, significantly lower than other robotic hands without the actuators since they have more complex assembly processes.

  4. The hand of Homo naledi

    Science.gov (United States)

    Kivell, Tracy L.; Deane, Andrew S.; Tocheri, Matthew W.; Orr, Caley M.; Schmid, Peter; Hawks, John; Berger, Lee R.; Churchill, Steven E.

    2015-01-01

    A nearly complete right hand of an adult hominin was recovered from the Rising Star cave system, South Africa. Based on associated hominin material, the bones of this hand are attributed to Homo naledi. This hand reveals a long, robust thumb and derived wrist morphology that is shared with Neandertals and modern humans, and considered adaptive for intensified manual manipulation. However, the finger bones are longer and more curved than in most australopiths, indicating frequent use of the hand during life for strong grasping during locomotor climbing and suspension. These markedly curved digits in combination with an otherwise human-like wrist and palm indicate a significant degree of climbing, despite the derived nature of many aspects of the hand and other regions of the postcranial skeleton in H. naledi. PMID:26441219

  5. The eukaryotic translation elongation factor eEF1A2 induces neoplastic properties and mediates tumorigenic effects of ZNF217 in precursor cells of human ovarian carcinomas

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Yu; Wong, Nicholas; Guan, Yinghui; Salamanca, Clara M.; Cheng, Jung Chien; Lee, Jonathan M.; Gray, Joe W.; Auersperg, Nelly

    2008-04-25

    Ovarian epithelial carcinomas (OEC) frequently exhibit amplifications at the 20q13 locus which is the site of several oncogenes, including the eukaryotic elongation factor EEF1A2 and the transcription factor ZNF217. We reported previously that overexpressed ZNF217 induces neoplastic characteristics in precursor cells of OEC. Unexpectedly, ZNF217, which is a transcriptional repressor, enhanced expression of eEF1A2. In this study, array comparative genomic hybridization, single nucleotide polymorphism and Affymetrix analysis of ZNF217-overexpressing cell lines confirmed consistently increased expression of eEF1A2 but not of other oncogenes, and revealed early changes in EEF1A2 gene copy numbers and increased expression at crisis during immortalization. We defined the influence of eEF1A2 overexpression on immortalized ovarian surface epithelial cells, and investigated interrelationships between effects of ZNF217 and eEF1A2 on cellular phenotypes. Lentivirally induced eEF1A2 overexpression caused delayed crisis, apoptosis resistance and increases in serum-independence, saturation densities, and anchorage independence. siRNA to eEF1A2 reversed apoptosis resistance and reduced anchorage independence in eEF1A2-overexpressing lines. Remarkably, siRNA to eEF1A2 was equally efficient in inhibiting both anchorage independence and resistance to apoptosis conferred by ZNF217 overexpression. Our data define neoplastic properties that are caused by eEF1A2 in nontumorigenic ovarian cancer precursor cells, and suggest that eEF1A2 plays a role in mediating ZNF217-induced neoplastic progression.

  6. A Ca2+-calmodulin-eEF2K-eEF2 signalling cascade, but not AMPK, contributes to the suppression of skeletal muscle protein synthesis during contractions

    DEFF Research Database (Denmark)

    Rose, Adam John; Alsted, Thomas Junker; Jensen, Thomas Elbenhardt

    2009-01-01

    Skeletal muscle protein synthesis rate decreases during contractions but the underlying regulatory mechanisms are poorly understood. It was hypothesised that there would be a coordinated regulation of eukaryotic elongation factor 2 (eEF2) and eukaryotic initiation factor 4E-binding protein 1 (4EBP1......) phosphorylation by signalling cascades downstream of rises in intracellular [Ca(2+)] and decreased energy charge via AMP activated protein kinase (AMPK) in contracting skeletal muscle. When fast-twitch skeletal muscles were contracted ex vivo using different protocols, the suppression of protein synthesis...... correlated more closely with changes in eEF2 rather than 4EBP1 phosphorylation. Using a combination of Ca(2+) release agents and ATPase inhibitors it was shown that the 60-70% suppression of fast-twitch skeletal muscle protein synthesis during contraction was equally distributed between Ca(2+) and energy...

  7. Sulfur-induced structural motifs on copper and gold surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Walen, Holly [Iowa State Univ., Ames, IA (United States)

    2016-01-01

    The interaction of sulfur with copper and gold surfaces plays a fundamental role in important phenomena that include coarsening of surface nanostructures, and self-assembly of alkanethiols. Here, we identify and analyze unique sulfur-induced structural motifs observed on the low-index surfaces of these two metals. We seek out these structures in an effort to better understand the fundamental interactions between these metals and sulfur that lends to the stability and favorability of metal-sulfur complexes vs. chemisorbed atomic sulfur. The experimental observations presented here—made under identical conditions—together with extensive DFT analyses, allow comparisons and insights into factors that favor the existence of metal-sulfur complexes, vs. chemisorbed atomic sulfur, on metal terraces. We believe this data will be instrumental in better understanding the complex phenomena occurring between the surfaces of coinage metals and sulfur.

  8. Sequential dynamics in the motif of excitatory coupled elements

    Science.gov (United States)

    Korotkov, Alexander G.; Kazakov, Alexey O.; Osipov, Grigory V.

    2015-11-01

    In this article a new model of motif (small ensemble) of neuron-like elements is proposed. It is built with the use of the generalized Lotka-Volterra model with excitatory couplings. The main motivation for this work comes from the problems of neuroscience where excitatory couplings are proved to be the predominant type of interaction between neurons of the brain. In this paper it is shown that there are two modes depending on the type of coupling between the elements: the mode with a stable heteroclinic cycle and the mode with a stable limit cycle. Our second goal is to examine the chaotic dynamics of the generalized three-dimensional Lotka-Volterra model.

  9. Study on online community user motif using web usage mining

    Science.gov (United States)

    Alphy, Meera; Sharma, Ajay

    2016-04-01

    The Web usage mining is the application of data mining, which is used to extract useful information from the online community. The World Wide Web contains at least 4.73 billion pages according to Indexed Web and it contains at least 228.52 million pages according Dutch Indexed web on 6th august 2015, Thursday. It’s difficult to get needed data from these billions of web pages in World Wide Web. Here is the importance of web usage mining. Personalizing the search engine helps the web user to identify the most used data in an easy way. It reduces the time consumption; automatic site search and automatic restore the useful sites. This study represents the old techniques to latest techniques used in pattern discovery and analysis in web usage mining from 1996 to 2015. Analyzing user motif helps in the improvement of business, e-commerce, personalisation and improvement of websites.

  10. μXRF analysis of decoration motifs on Majolica pottery

    International Nuclear Information System (INIS)

    Padilla Lavarez, Roman; Van Espen, Pierr M.; Janssens, K; Schalm, O.

    2001-01-01

    μXRF analysis of decoration motifs on Majolica pottery in fragments corresponding to several Majolica types was carried out using an spectrometer comprising a low power Mo X-ray tube and a elliptic-shape concentration lens with a 60 um spot. Both surface scanning and spot measurements were carried a out, allowing the qualitative identification of the inorganic pigments used for the surface painting decoration and the quantitative analysis of the main glaze composition. The absence of interference signal arising from the excitation on the underlying paste when analysing thin-lead glazing was evaluated, allowing ensuring the suitable of the analytical procedures. A distinction was found between different types of majolica by the composition of the lead tin glaze enamel and by the presence of other elements in the blue, black and orange decoration

  11. Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells

    KAUST Repository

    Wong, Ka-Chun; Li, Yue; Peng, Chengbin

    2015-01-01

    Motivation: The protein-DNA interactions between transcription factors (TFs) and transcription factor binding sites (TFBSs, also known as DNA motifs) are critical activities in gene transcription. The identification of the DNA motifs is a vital task for downstream analysis. Unfortunately, the long-range coupling information between different DNA motifs is still lacking. To fill the void, as the first-of-its-kind study, we have identified the coupling DNA motif pairs on long-range chromatin interactions in human. Results: The coupling DNA motif pairs exhibit substantially higher DNase accessibility than the background sequences. Half of the DNA motifs involved are matched to the existing motif databases, although nearly all of them are enriched with at least one gene ontology term. Their motif instances are also found statistically enriched on the promoter and enhancer regions. Especially, we introduce a novel measurement called motif pairing multiplicity which is defined as the number of motifs that are paired with a given motif on chromatin interactions. Interestingly, we observe that motif pairing multiplicity is linked to several characteristics such as regulatory region type, motif sequence degeneracy, DNase accessibility and pairing genomic distance. Taken into account together, we believe the coupling DNA motif pairs identified in this study can shed lights on the gene transcription mechanism under long-range chromatin interactions. © The Author 2015. Published by Oxford University Press.

  12. Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells

    KAUST Repository

    Wong, Ka-Chun

    2015-09-27

    Motivation: The protein-DNA interactions between transcription factors (TFs) and transcription factor binding sites (TFBSs, also known as DNA motifs) are critical activities in gene transcription. The identification of the DNA motifs is a vital task for downstream analysis. Unfortunately, the long-range coupling information between different DNA motifs is still lacking. To fill the void, as the first-of-its-kind study, we have identified the coupling DNA motif pairs on long-range chromatin interactions in human. Results: The coupling DNA motif pairs exhibit substantially higher DNase accessibility than the background sequences. Half of the DNA motifs involved are matched to the existing motif databases, although nearly all of them are enriched with at least one gene ontology term. Their motif instances are also found statistically enriched on the promoter and enhancer regions. Especially, we introduce a novel measurement called motif pairing multiplicity which is defined as the number of motifs that are paired with a given motif on chromatin interactions. Interestingly, we observe that motif pairing multiplicity is linked to several characteristics such as regulatory region type, motif sequence degeneracy, DNase accessibility and pairing genomic distance. Taken into account together, we believe the coupling DNA motif pairs identified in this study can shed lights on the gene transcription mechanism under long-range chromatin interactions. © The Author 2015. Published by Oxford University Press.

  13. Structural fragment clustering reveals novel structural and functional motifs in α-helical transmembrane proteins

    Directory of Open Access Journals (Sweden)

    Vassilev Boris

    2010-04-01

    Full Text Available Abstract Background A large proportion of an organism's genome encodes for membrane proteins. Membrane proteins are important for many cellular processes, and several diseases can be linked to mutations in them. With the tremendous growth of sequence data, there is an increasing need to reliably identify membrane proteins from sequence, to functionally annotate them, and to correctly predict their topology. Results We introduce a technique called structural fragment clustering, which learns sequential motifs from 3D structural fragments. From over 500,000 fragments, we obtain 213 statistically significant, non-redundant, and novel motifs that are highly specific to α-helical transmembrane proteins. From these 213 motifs, 58 of them were assigned to function and checked in the scientific literature for a biological assessment. Seventy percent of the motifs are found in co-factor, ligand, and ion binding sites, 30% at protein interaction interfaces, and 12% bind specific lipids such as glycerol or cardiolipins. The vast majority of motifs (94% appear across evolutionarily unrelated families, highlighting the modularity of functional design in membrane proteins. We describe three novel motifs in detail: (1 a dimer interface motif found in voltage-gated chloride channels, (2 a proton transfer motif found in heme-copper oxidases, and (3 a convergently evolved interface helix motif found in an aspartate symporter, a serine protease, and cytochrome b. Conclusions Our findings suggest that functional modules exist in membrane proteins, and that they occur in completely different evolutionary contexts and cover different binding sites. Structural fragment clustering allows us to link sequence motifs to function through clusters of structural fragments. The sequence motifs can be applied to identify and characterize membrane proteins in novel genomes.

  14. Hand in Hand - SEI Programmes for School Staff

    DEFF Research Database (Denmark)

    Nielsen, Birgitte Lund; Réol, Lise Andersen; Laursen, Hilmar Dyrborg

    2017-01-01

    This catalogue of research in the field of SEI programmes for the school staff’s and teachers’ SEI competencies is based on a review performed by the main researchers Birgitte Lund Nielsen, Lise Andersen Réol and Hilmar Dyrborg Laursen, VIA University College, Denmark, but discussed by the entire...... team of Hand in Hand partner countries and researchers. The aim was to identify the central aspects and elements concerning successful implementation, and school staff’s development of professional competencies in the specific field of supporting students’ social, emotional and intercultural (SEI......) competencies. Abstract: Framed by the EU-project Hand in Hand focusing on Social, Emotional and Intercultural (SEI) competencies among students and school staff, the paper discusses implementation and professional competencies based on a research review. The following five topics were identified: 1...

  15. The Marble-Hand Illusion.

    Science.gov (United States)

    Senna, Irene; Maravita, Angelo; Bolognini, Nadia; Parise, Cesare V

    2014-01-01

    Our body is made of flesh and bones. We know it, and in our daily lives all the senses constantly provide converging information about this simple, factual truth. But is this always the case? Here we report a surprising bodily illusion demonstrating that humans rapidly update their assumptions about the material qualities of their body, based on their recent multisensory perceptual experience. To induce a misperception of the material properties of the hand, we repeatedly gently hit participants' hand with a small hammer, while progressively replacing the natural sound of the hammer against the skin with the sound of a hammer hitting a piece of marble. After five minutes, the hand started feeling stiffer, heavier, harder, less sensitive, unnatural, and showed enhanced Galvanic skin response (GSR) to threatening stimuli. Notably, such a change in skin conductivity positively correlated with changes in perceived hand stiffness. Conversely, when hammer hits and impact sounds were temporally uncorrelated, participants did not spontaneously report any changes in the perceived properties of the hand, nor did they show any modulation in GSR. In two further experiments, we ruled out that mere audio-tactile synchrony is the causal factor triggering the illusion, further demonstrating the key role of material information conveyed by impact sounds in modulating the perceived material properties of the hand. This novel bodily illusion, the 'Marble-Hand Illusion', demonstrates that the perceived material of our body, surely the most stable attribute of our bodily self, can be quickly updated through multisensory integration.

  16. A Model for the Sounding Rocket Measurement on an Ionospheric E-F Valley at the Hainan Low Latitude Station

    International Nuclear Information System (INIS)

    Wang Zheng; Shi Jiankui; Guan Yibing; Liu Chao; Zhu Guangwu; Torkar Klaus; Fredrich Martin

    2014-01-01

    To understand the physics of an ionospheric E-F valley, a new overlapping three-Chapman-layer model is developed to interpret the sounding rocket measurement in the morning (sunrise) on May 7, 2011 at the Hainan low latitude ionospheric observation station (19.5°N, 109.1°E). From our model, the valley width, depth and height are 43.0 km, 62.9% and 121.0 km, respectively. From the sounding rocket observation, the valley width, depth and height are 42.2 km, 47.0% and 123.5 km, respectively. The model results are well consistent with the sounding rocket observation. The observed E-F valley at Hainan station is very wide and deep, and rapid development of the photochemical process in the ionosphere should be the underlying reason. (astrophysics and space plasma)

  17. In vivo colocalization of 2-nitroimidazole EF5 fluorescence intensity and electron paramagnetic resonance oximetry in mouse tumors

    International Nuclear Information System (INIS)

    Mahy, Pierre; Bast, Marc de; Gallez, Bernard; Gueulette, John; Koch, Cameron J.; Scalliet, Pierre; Gregoire, Vincent

    2003-01-01

    Background and purpose: The primary objective of this study was to establish in vivo the relationship between 2-2-nitro-1H-imidazol-1yl-N-(2,2,3,3,3-pentafluoropropyl)-acetamide (EF5) adduct formation and intratumoral oxygen concentrations measured by electron paramagnetic resonance (EPR) in a tumor model mimicking a clinical situation. The secondary objective was an attempt to calibrate in situ the immunofluorescence (IF) signal with EPR oximetry. Materials and methods: IM syngeneic fibrosarcoma (NFSA) bearing C3H mice were used. Three days after injection of a paramagnetic charcoal into the tumor, the mice were anesthetized, injected with the hypoxic marker EF5, and monitored every 20 min for 3 h with a low-frequency EPR spectrometer. Animals were allowed to breath either under 21 or 100% O 2 . Tumors were then harvested, frozen, cut into sections including the charcoal and processed for EF5 adducts detection using monoclonal antibodies. Slices were viewed with a fluorescence microscope and 190x140 μm areas surrounding the charcoal were digitized and analyzed with the NIH-Image and Adobe Photoshop TM software. The fluorescence intensity (FI) was measured in the whole pictures and in strips of 10 μm around the charcoal. Results: EF5 binding increased with decreasing pO 2 , most substantially at pO 2 below 5 mm Hg. Baseline (ambient air) pO 2 reached 3.2±2.1 mm Hg in NFSA tumors. It increased to 9.8±3.2 mm Hg under 100% O 2 . A statistically significant correlation was observed on an individual tumor basis between the FI in the first 10 μm strip around the charcoal and the pO 2 determined by EPR oximetry (Wilcoxon signed rank test: P 2 in an in vivo environment under biologically-relevant pO 2 values of less than 10 mm Hg

  18. Thermostability of Multidomain Proteins: Elongation Factors EF-Tu from Escherichia coli and Bacillus stearothermophilus and Their Chimeric Forms

    Czech Academy of Sciences Publication Activity Database

    Šanderová, Hana; Hůlková, Marta; Maloň, Petr; Kepková, M.; Jonák, Jiří

    2004-01-01

    Roč. 13, č. 1 (2004), s. 89-99 ISSN 0961-8368 R&D Projects: GA AV ČR IPP1050128; GA ČR GA204/98/0863; GA ČR GA303/02/0689 Institutional research plan: CEZ:AV0Z4055905; CEZ:AV0Z5052915 Keywords : elongation factor EF-Tu, thermostability, chimeric protein Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 4.116, year: 2004

  19. Wayward Warriors: The Viking Motif in Swedish and English Children's Literature

    Science.gov (United States)

    Sundmark, Björn

    2014-01-01

    In this article the Viking motif in children's literature is explored--from its roots in (adult) nationalist and antiquarian discourse, over pedagogical and historical texts for children, to the eventual diversification (or dissolution) of the motif into different genres and forms. The focus is on Swedish Viking narratives, but points of…

  20. Physical-chemical property based sequence motifs and methods regarding same

    Science.gov (United States)

    Braun, Werner [Friendswood, TX; Mathura, Venkatarajan S [Sarasota, FL; Schein, Catherine H [Friendswood, TX

    2008-09-09

    A data analysis system, program, and/or method, e.g., a data mining/data exploration method, using physical-chemical property motifs. For example, a sequence database may be searched for identifying segments thereof having physical-chemical properties similar to the physical-chemical property motifs.

  1. Gene Isolation Using Degenerate Primers Targeting Protein Motif: A Laboratory Exercise

    Science.gov (United States)

    Yeo, Brandon Pei Hui; Foong, Lian Chee; Tam, Sheh May; Lee, Vivian; Hwang, Siaw San

    2018-01-01

    Structures and functions of protein motifs are widely included in many biology-based course syllabi. However, little emphasis is placed to link this knowledge to applications in biotechnology to enhance the learning experience. Here, the conserved motifs of nucleotide binding site-leucine rich repeats (NBS-LRR) proteins, successfully used for the…

  2. MOMFER: A Search Engine of Thompson's Motif-Index of Folk Literature

    NARCIS (Netherlands)

    Karsdorp, F.B.; van der Meulen, Marten; Meder, Theo; van den Bosch, Antal

    2015-01-01

    More than fifty years after the first edition of Thompson's seminal Motif-Indexof Folk Literature, we present an online search engine tailored to fully disclose the index digitally. This search engine, called MOMFER, greatly enhances the searchability of the Motif-Index and provides exciting new

  3. Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network

    Directory of Open Access Journals (Sweden)

    Barabási Albert-László

    2004-01-01

    Full Text Available Abstract Background Transcriptional regulation of cellular functions is carried out through a complex network of interactions among transcription factors and the promoter regions of genes and operons regulated by them.To better understand the system-level function of such networks simplification of their architecture was previously achieved by identifying the motifs present in the network, which are small, overrepresented, topologically distinct regulatory interaction patterns (subgraphs. However, the interaction of such motifs with each other, and their form of integration into the full network has not been previously examined. Results By studying the transcriptional regulatory network of the bacterium, Escherichia coli, we demonstrate that the two previously identified motif types in the network (i.e., feed-forward loops and bi-fan motifs do not exist in isolation, but rather aggregate into homologous motif clusters that largely overlap with known biological functions. Moreover, these clusters further coalesce into a supercluster, thus establishing distinct topological hierarchies that show global statistical properties similar to the whole network. Targeted removal of motif links disintegrates the network into small, isolated clusters, while random disruptions of equal number of links do not cause such an effect. Conclusion Individual motifs aggregate into homologous motif clusters and a supercluster forming the backbone of the E. coli transcriptional regulatory network and play a central role in defining its global topological organization.

  4. High affinity recognition of a Phytophthora protein by Arabidopsis via an RGD motif

    NARCIS (Netherlands)

    Senchou, V.; Weide, R.L.; Carrasco, A.; Bouyssou, H.; Pont-Lezica, R.; Govers, F.; Canut, H.

    2004-01-01

    The RGD tripeptide sequence, a cell adhesion motif present in several extracellular matrix proteins of mammalians, is involved in numerous plant processes. In plant-pathogen interactions, the RGD motif is believed to reduce plant defence responses by disrupting adhesions between the cell wall and

  5. Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium

    Directory of Open Access Journals (Sweden)

    Lynch Michael

    2010-05-01

    Full Text Available Abstract Background In protozoa, the identification of preserved motifs by comparative genomics is often impeded by difficulties to generate reliable alignments for non-coding sequences. Moreover, the evolutionary dynamics of regulatory elements in 3' untranslated regions (both in protozoa and metazoa remains a virtually unexplored issue. Results By screening Paramecium tetraurelia's 3' untranslated regions for 8-mers that were previously found to be preserved in mammalian 3' UTRs, we detect and characterize a motif that is distinctly conserved in the ribosomal genes of this ciliate. The motif appears to be conserved across Paramecium aurelia species but is absent from the ribosomal genes of four additional non-Paramecium species surveyed, including another ciliate, Tetrahymena thermophila. Motif-free ribosomal genes retain fewer paralogs in the genome and appear to be lost more rapidly relative to motif-containing genes. Features associated with the discovered preserved motif are consistent with this 8-mer playing a role in post-transcriptional regulation. Conclusions Our observations 1 shed light on the evolution of a putative regulatory motif across large phylogenetic distances; 2 are expected to facilitate the understanding of the modulation of ribosomal genes expression in Paramecium; and 3 reveal a largely unexplored--and presumably not restricted to Paramecium--association between the presence/absence of a DNA motif and the evolutionary fate of its host genes.

  6. Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium.

    Science.gov (United States)

    Catania, Francesco; Lynch, Michael

    2010-05-04

    In protozoa, the identification of preserved motifs by comparative genomics is often impeded by difficulties to generate reliable alignments for non-coding sequences. Moreover, the evolutionary dynamics of regulatory elements in 3' untranslated regions (both in protozoa and metazoa) remains a virtually unexplored issue. By screening Paramecium tetraurelia's 3' untranslated regions for 8-mers that were previously found to be preserved in mammalian 3' UTRs, we detect and characterize a motif that is distinctly conserved in the ribosomal genes of this ciliate. The motif appears to be conserved across Paramecium aurelia species but is absent from the ribosomal genes of four additional non-Paramecium species surveyed, including another ciliate, Tetrahymena thermophila. Motif-free ribosomal genes retain fewer paralogs in the genome and appear to be lost more rapidly relative to motif-containing genes. Features associated with the discovered preserved motif are consistent with this 8-mer playing a role in post-transcriptional regulation. Our observations 1) shed light on the evolution of a putative regulatory motif across large phylogenetic distances; 2) are expected to facilitate the understanding of the modulation of ribosomal genes expression in Paramecium; and 3) reveal a largely unexplored--and presumably not restricted to Paramecium--association between the presence/absence of a DNA motif and the evolutionary fate of its host genes.

  7. Mechanism for activation of the growth factor-activated AGC kinases by turn motif phosphorylation

    DEFF Research Database (Denmark)

    Hauge, Camilla; Antal, Torben L; Hirschberg, Daniel

    2007-01-01

    investigated the role of the third, so-called turn motif phosphate, also located in the tail, in the AGC kinases PKB, S6K, RSK, MSK, PRK and PKC. We report cooperative action of the HM phosphate and the turn motif phosphate, because it binds a phosphoSer/Thr-binding site above the glycine-rich loop within...

  8. Proteome-level assessment of origin, prevalence and function of Leucine-Aspartic Acid (LD) motifs

    KAUST Repository

    Alam, Tanvir

    2018-03-11

    Short Linear Motifs (SLiMs) contribute to almost every cellular function by connecting appropriate protein partners. Accurate prediction of SLiMs is difficult due to their shortness and sequence degeneracy. Leucine-aspartic acid (LD) motifs are SLiMs that link paxillin family proteins to factors controlling (cancer) cell adhesion, motility and survival. The existence and importance of LD motifs beyond the paxillin family is poorly understood. To enable a proteome-wide assessment of these motifs, we developed an active-learning based framework that iteratively integrates computational predictions with experimental validation. Our analysis of the human proteome identified a dozen proteins that contain LD motifs, all being involved in cell adhesion and migration, and revealed a new type of inverse LD motif consensus. Our evolutionary analysis suggested that LD motif signalling originated in the common unicellular ancestor of opisthokonts and amoebozoa by co-opting nuclear export sequences. Inter-species comparison revealed a conserved LD signalling core, and reveals the emergence of species-specific adaptive connections, while maintaining a strong functional focus of the LD motif interactome. Collectively, our data elucidate the mechanisms underlying the origin and adaptation of an ancestral SLiM.

  9. A proposed vestigial translation initiation motif in VP1 of hepatitis A virus.

    Science.gov (United States)

    Kang, Jeong-Ah; Funkhouser, Ann W

    2002-07-01

    The internal ribosome entry site (IRES) of picornaviruses has a 3' polypyrimidine tract (PPT) 16-24 bases upstream of an AUG triplet (PPT/AUG motif). This motif is critical in determining the efficiency of cap-independent translation. HAV has a conserved PPT/AUG motif consisting of a nine base sequence (AGGUUUUUC) 23 bases upstream of the preferred AUG start codon. This HAV-specific PPT/AUG motif is repeated and conserved in VP1 of HAV, but not of other picornaviruses. We proposed that the PPT/AUG motif in the open reading frame initiated translation and/or had an impact on the life cycle of the virus. In vitro translation of mutant bicistronic mRNAs and growth in cell culture of mutant viruses provided no evidence that the VP1 PPT/AUG motif had any impact on either translation or growth. HAV differs from other picornaviruses in its inefficient growth in cell culture. Since the HAV-specific PPT/AUG motif is found in only 1 in 300,000 reported viral sequences outside the hepatovirus genus, this motif may be a vestigial translation initiation element and may have played a role in determining the unusual phenotype of HAV.

  10. Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated

    Directory of Open Access Journals (Sweden)

    Down Thomas A

    2010-09-01

    Full Text Available Abstract Background DNA methylation can regulate gene expression by modulating the interaction between DNA and proteins or protein complexes. Conserved consensus motifs exist across the human genome ("predicted transcription factor binding sites": "predicted TFBS" but the large majority of these are proven by chromatin immunoprecipitation and high throughput sequencing (ChIP-seq not to be biological transcription factor binding sites ("empirical TFBS". We hypothesize that DNA methylation at conserved consensus motifs prevents promiscuous or disorderly transcription factor binding. Results Using genome-wide methylation maps of the human heart and sperm, we found that all conserved consensus motifs as well as the subset of those that reside outside CpG islands have an aggregate profile of hyper-methylation. In contrast, empirical TFBS with conserved consensus motifs have a profile of hypo-methylation. 40% of empirical TFBS with conserved consensus motifs resided in CpG islands whereas only 7% of all conserved consensus motifs were in CpG islands. Finally we further identified a minority subset of TF whose profiles are either hypo-methylated or neutral at their respective conserved consensus motifs implicating that these TF may be responsible for establishing or maintaining an un-methylated DNA state, or whose binding is not regulated by DNA methylation. Conclusions Our analysis supports the hypothesis that at least for a subset of TF, empirical binding to conserved consensus motifs genome-wide may be controlled by DNA methylation.

  11. Composite Structural Motifs of Binding Sites for Delineating Biological Functions of Proteins

    Science.gov (United States)

    Kinjo, Akira R.; Nakamura, Haruki

    2012-01-01

    Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the relation between protein interactions and biological functions, we conducted exhaustive all-against-all atomic structure comparisons of all known binding sites for ligands including small molecules, proteins and nucleic acids, and identified recurring elementary motifs. By integrating the elementary motifs associated with each subunit, we defined composite motifs that represent context-dependent combinations of elementary motifs. It is demonstrated that function similarity can be better inferred from composite motif similarity compared to the similarity of protein sequences or of individual binding sites. By integrating the composite motifs associated with each protein function, we define meta-composite motifs each of which is regarded as a time-independent diagrammatic representation of a biological process. It is shown that meta-composite motifs provide richer annotations of biological processes than sequence clusters. The present results serve as a basis for bridging atomic structures to higher-order biological phenomena by classification and integration of binding site structures. PMID:22347478

  12. Identification of novel mazEF/pemIK family toxin-antitoxin loci and their distribution in the Staphylococcus genus.

    Science.gov (United States)

    Bukowski, Michal; Hyz, Karolina; Janczak, Monika; Hydzik, Marcin; Dubin, Grzegorz; Wladyka, Benedykt

    2017-10-18

    The versatile roles of toxin-antitoxin (TA) systems in bacterial physiology and pathogenesis have been investigated for more than three decades. Diverse TA loci in Bacteria and Archaea have been identified in genome-wide studies. The advent of massive parallel sequencing has substantially expanded the number of known bacterial genomic sequences over the last 5 years. In staphylococci, this has translated into an impressive increase from a few tens to a several thousands of available genomes, which has allowed us for the re-evalution of prior conclusions. In this study, we analysed the distribution of mazEF/pemIK family TA system operons in available staphylococcal genomes and their prevalence in mobile genetic elements. 10 novel m azEF/pemIK homologues were identified, each with a corresponding toxin that plays a potentially different and undetermined physiological role. A detailed characterisation of these TA systems would be exceptionally useful. Of particular interest are those associated with an SCCmec mobile genetic element (responsible for multidrug resistance transmission) or representing the joint horizontal transfer of TA systems and determinants of vancomycin resistance from enterococci. The involvement of TA systems in maintaining mobile genetic elements and the associations between novel mazEF/pemIK loci and those which carry drug resistance genes highlight their potential medical importance.

  13. Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae

    Science.gov (United States)

    Fauteux, François; Strömvik, Martina V

    2009-01-01

    Background Accurate computational identification of cis-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate DNA sequences bound by several interacting factors. Enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. This provides a basis for the computational identification of cis-regulatory motifs. Results We have used a discriminative seeding DNA motif discovery algorithm for an in-depth analysis of 54 seed storage protein (SSP) gene promoters from three plant families, namely Brassicaceae (mustards), Fabaceae (legumes) and Poaceae (grasses) using backgrounds based on complete sets of promoters from a representative species in each family, namely Arabidopsis (Arabidopsis thaliana (L.) Heynh.), soybean (Glycine max (L.) Merr.) and rice (Oryza sativa L.) respectively. We have identified three conserved motifs (two RY-like and one ACGT-like) in Brassicaceae and Fabaceae SSP gene promoters that are similar to experimentally characterized seed-specific cis-regulatory elements. Fabaceae SSP gene promoter sequences are also enriched in a novel, seed-specific E2Fb-like motif. Conserved motifs identified in Poaceae SSP gene promoters include a GCN4-like motif, two prolamin-box-like motifs and an Skn-1-like motif. Evidence of the presence of a variant of the TATA-box is found in the SSP gene promoters from the three plant families. Motifs discovered in SSP gene promoters were used to score whole-genome sets of promoters from Arabidopsis, soybean and rice. The highest-scoring promoters are associated with genes coding for different subunits or precursors of seed storage proteins. Conclusion Seed storage protein gene promoter motifs are conserved in diverse species, and different plant families are characterized by a distinct combination of conserved motifs

  14. Seed storage protein gene promoters contain conserved DNA motifs in Brassicaceae, Fabaceae and Poaceae

    Directory of Open Access Journals (Sweden)

    Fauteux François

    2009-10-01

    Full Text Available Abstract Background Accurate computational identification of cis-regulatory motifs is difficult, particularly in eukaryotic promoters, which typically contain multiple short and degenerate DNA sequences bound by several interacting factors. Enrichment in combinations of rare motifs in the promoter sequence of functionally or evolutionarily related genes among several species is an indicator of conserved transcriptional regulatory mechanisms. This provides a basis for the computational identification of cis-regulatory motifs. Results We have used a discriminative seeding DNA motif discovery algorithm for an in-depth analysis of 54 seed storage protein (SSP gene promoters from three plant families, namely Brassicaceae (mustards, Fabaceae (legumes and Poaceae (grasses using backgrounds based on complete sets of promoters from a representative species in each family, namely Arabidopsis (Arabidopsis thaliana (L. Heynh., soybean (Glycine max (L. Merr. and rice (Oryza sativa L. respectively. We have identified three conserved motifs (two RY-like and one ACGT-like in Brassicaceae and Fabaceae SSP gene promoters that are similar to experimentally characterized seed-specific cis-regulatory elements. Fabaceae SSP gene promoter sequences are also enriched in a novel, seed-specific E2Fb-like motif. Conserved motifs identified in Poaceae SSP gene promoters include a GCN4-like motif, two prolamin-box-like motifs and an Skn-1-like motif. Evidence of the presence of a variant of the TATA-box is found in the SSP gene promoters from the three plant families. Motifs discovered in SSP gene promoters were used to score whole-genome sets of promoters from Arabidopsis, soybean and rice. The highest-scoring promoters are associated with genes coding for different subunits or precursors of seed storage proteins. Conclusion Seed storage protein gene promoter motifs are conserved in diverse species, and different plant families are characterized by a distinct combination

  15. Hand-assisted laparoscopic splenectomy

    NARCIS (Netherlands)

    Bemelman, W. A.; de Wit, L. T.; Busch, O. R.; Gouma, D. J.

    2000-01-01

    Laparoscopic splenectomy is performed routinely in patients with small and moderately enlarged spleens at specialized centers. Large spleens are difficult to handle laparoscopically and hand-assisted laparoscopic splenectomy might facilitate the procedure through enhanced vascular control, easier

  16. Animal Bites of the Hand

    Science.gov (United States)

    ... Therapist? Media Find a Hand Surgeon Home Anatomy Animal Bites Email to a friend * required fields From * ... key to prevent problems from a bite. CAUSES Animal Bites Millions of animal bites occur in the ...

  17. Hand and foot contamination monitor

    International Nuclear Information System (INIS)

    Jakati, R.K.; Kaptral, R.S.; Ananthkrishnan, T.S.; Pansare, M.G.

    1989-01-01

    In order to make quick measurements of beta and gamma contaminations on hands and feet of personnel working in radioactive environments, hand and foot contamination monitors are widely used. This paper describes such a monitor system designed with Intel 8085 based microcomputer. The monitoring and warning system is designed to perform measurement of activity spread over surface of hands and soles of shoes or feet. Even though the system has many features to aid testing and maintainance operation, it is easy to use for unskilled persons. In order to check the contamination, the person stands on platform and inserts both his hands into detector assemblies thereby actuating the sensing switches. After a preset interval, annunciation of clean or contaminated status is declared by the system. (author)

  18. Thermal Stability of Modified i-Motif Oligonucleotides with Naphthalimide Intercalating Nucleic Acids

    DEFF Research Database (Denmark)

    El-Sayed, Ahmed Ali; Pedersen, Erik B.; Khaireldin, Nahid Y.

    2016-01-01

    In continuation of our investigation of characteristics and thermodynamic properties of the i-motif 5′-d[(CCCTAA)3CCCT)] upon insertion of intercalating nucleotides into the cytosine-rich oligonucleotide, this article evaluates the stabilities of i-motif oligonucleotides upon insertion of naphtha......In continuation of our investigation of characteristics and thermodynamic properties of the i-motif 5′-d[(CCCTAA)3CCCT)] upon insertion of intercalating nucleotides into the cytosine-rich oligonucleotide, this article evaluates the stabilities of i-motif oligonucleotides upon insertion...... of naphthalimide (1H-benzo[de]isoquinoline-1,3(2H)-dione) as the intercalating nucleic acid. The stabilities of i-motif structures with inserted naphthalimide intercalating nucleotides were studied using UV melting temperatures (Tm) and circular dichroism spectra at different pH values and conditions (crowding...

  19. I-motif DNA structures are formed in the nuclei of human cells

    Science.gov (United States)

    Zeraati, Mahdi; Langley, David B.; Schofield, Peter; Moye, Aaron L.; Rouet, Romain; Hughes, William E.; Bryan, Tracy M.; Dinger, Marcel E.; Christ, Daniel

    2018-06-01

    Human genome function is underpinned by the primary storage of genetic information in canonical B-form DNA, with a second layer of DNA structure providing regulatory control. I-motif structures are thought to form in cytosine-rich regions of the genome and to have regulatory functions; however, in vivo evidence for the existence of such structures has so far remained elusive. Here we report the generation and characterization of an antibody fragment (iMab) that recognizes i-motif structures with high selectivity and affinity, enabling the detection of i-motifs in the nuclei of human cells. We demonstrate that the in vivo formation of such structures is cell-cycle and pH dependent. Furthermore, we provide evidence that i-motif structures are formed in regulatory regions of the human genome, including promoters and telomeric regions. Our results support the notion that i-motif structures provide key regulatory roles in the genome.

  20. The Plastic Surgery Hand Curriculum.

    Science.gov (United States)

    Silvestre, Jason; Levin, L Scott; Serletti, Joseph M; Chang, Benjamin

    2015-12-01

    Designing an effective hand rotation for plastic surgery residents is difficult. The authors address this limitation by elucidating the critical components of the hand curriculum during plastic surgery residency. Hand questions on the Plastic Surgery In-Service Training Exam for six consecutive years (2008 to 2013) were characterized by presence of imaging, vignette setting, question taxonomy, answer domain, anatomy, and topic. Answer references were quantified by source and year of publication. Two hundred sixty-six questions were related to hand surgery (22.7 percent of all questions; 44.3 per year) and 61 were accompanied by an image (22.9 percent). Vignettes tended to be clinic- (50.0 percent) and emergency room-based (35.3 percent) (p < 0.001). Questions required decision-making (60.5 percent) over interpretation (25.9 percent) and recall skills (13.5 percent) (p < 0.001). Answers focused on interventions (57.5 percent) over anatomy/pathology (25.2 percent) and diagnoses (17.3 percent) (p < 0.001). Nearly half of the questions focused on the digits. The highest yield topics were trauma (35.3 percent), reconstruction (24.4 percent), and aesthetic and functional problems (14.2 percent). The Journal of Hand Surgery (American volume) (20.5 percent) and Plastic and Reconstructive Surgery (18.0 percent) were the most-cited journals, and the median publication lag was 7 years. Green's Operative Hand Surgery was the most-referenced textbook (41.8 percent). These results will enable trainees to study hand surgery topics with greater efficiency. Faculty can use these results to ensure that tested topics are covered during residency training. Thus, a benchmark is established to improve didactic, clinical, and operative experiences in hand surgery.

  1. Hand, Foot, and Mouth Disease

    Centers for Disease Control (CDC) Podcasts

    2013-08-08

    Hand, foot, and mouth disease is a contagious illness that mainly affects children under five. In this podcast, Dr. Eileen Schneider talks about the symptoms of hand, foot, and mouth disease, how it spreads, and ways to help protect yourself and your children from getting infected with the virus.  Created: 8/8/2013 by National Center for Immunization and Respiratory Diseases (NCIRD).   Date Released: 8/8/2013.

  2. Hand Grasping Synergies As Biometrics.

    Science.gov (United States)

    Patel, Vrajeshri; Thukral, Poojita; Burns, Martin K; Florescu, Ionut; Chandramouli, Rajarathnam; Vinjamuri, Ramana

    2017-01-01

    Recently, the need for more secure identity verification systems has driven researchers to explore other sources of biometrics. This includes iris patterns, palm print, hand geometry, facial recognition, and movement patterns (hand motion, gait, and eye movements). Identity verification systems may benefit from the complexity of human movement that integrates multiple levels of control (neural, muscular, and kinematic). Using principal component analysis, we extracted spatiotemporal hand synergies (movement synergies) from an object grasping dataset to explore their use as a potential biometric. These movement synergies are in the form of joint angular velocity profiles of 10 joints. We explored the effect of joint type, digit, number of objects, and grasp type. In its best configuration, movement synergies achieved an equal error rate of 8.19%. While movement synergies can be integrated into an identity verification system with motion capture ability, we also explored a camera-ready version of hand synergies-postural synergies. In this proof of concept system, postural synergies performed well, but only when specific postures were chosen. Based on these results, hand synergies show promise as a potential biometric that can be combined with other hand-based biometrics for improved security.

  3. Hand Grasping Synergies As Biometrics

    Directory of Open Access Journals (Sweden)

    Ramana Vinjamuri

    2017-05-01

    Full Text Available Recently, the need for more secure identity verification systems has driven researchers to explore other sources of biometrics. This includes iris patterns, palm print, hand geometry, facial recognition, and movement patterns (hand motion, gait, and eye movements. Identity verification systems may benefit from the complexity of human movement that integrates multiple levels of control (neural, muscular, and kinematic. Using principal component analysis, we extracted spatiotemporal hand synergies (movement synergies from an object grasping dataset to explore their use as a potential biometric. These movement synergies are in the form of joint angular velocity profiles of 10 joints. We explored the effect of joint type, digit, number of objects, and grasp type. In its best configuration, movement synergies achieved an equal error rate of 8.19%. While movement synergies can be integrated into an identity verification system with motion capture ability, we also explored a camera-ready version of hand synergies—postural synergies. In this proof of concept system, postural synergies performed well, but only when specific postures were chosen. Based on these results, hand synergies show promise as a potential biometric that can be combined with other hand-based biometrics for improved security.

  4. Elucidating the Role of Injury-Induced Electric Fields (EFs in Regulating the Astrocytic Response to Injury in the Mammalian Central Nervous System.

    Directory of Open Access Journals (Sweden)

    Matthew L Baer

    Full Text Available Injury to the vertebrate central nervous system (CNS induces astrocytes to change their morphology, to increase their rate of proliferation, and to display directional migration to the injury site, all to facilitate repair. These astrocytic responses to injury occur in a clear temporal sequence and, by their intensity and duration, can have both beneficial and detrimental effects on the repair of damaged CNS tissue. Studies on highly regenerative tissues in non-mammalian vertebrates have demonstrated that the intensity of direct-current extracellular electric fields (EFs at the injury site, which are 50-100 fold greater than in uninjured tissue, represent a potent signal to drive tissue repair. In contrast, a 10-fold EF increase has been measured in many injured mammalian tissues where limited regeneration occurs. As the astrocytic response to CNS injury is crucial to the reparative outcome, we exposed purified rat cortical astrocytes to EF intensities associated with intact and injured mammalian tissues, as well as to those EF intensities measured in regenerating non-mammalian vertebrate tissues, to determine whether EFs may contribute to the astrocytic injury response. Astrocytes exposed to EF intensities associated with uninjured tissue showed little change in their cellular behavior. However, astrocytes exposed to EF intensities associated with injured tissue showed a dramatic increase in migration and proliferation. At EF intensities associated with regenerating non-mammalian vertebrate tissues, these cellular responses were even more robust and included morphological changes consistent with a regenerative phenotype. These findings suggest that endogenous EFs may be a crucial signal for regulating the astrocytic response to injury and that their manipulation may be a novel target for facilitating CNS repair.

  5. Elucidating the Role of Injury-Induced Electric Fields (EFs) in Regulating the Astrocytic Response to Injury in the Mammalian Central Nervous System.

    Science.gov (United States)

    Baer, Matthew L; Henderson, Scott C; Colello, Raymond J

    2015-01-01

    Injury to the vertebrate central nervous system (CNS) induces astrocytes to change their morphology, to increase their rate of proliferation, and to display directional migration to the injury site, all to facilitate repair. These astrocytic responses to injury occur in a clear temporal sequence and, by their intensity and duration, can have both beneficial and detrimental effects on the repair of damaged CNS tissue. Studies on highly regenerative tissues in non-mammalian vertebrates have demonstrated that the intensity of direct-current extracellular electric fields (EFs) at the injury site, which are 50-100 fold greater than in uninjured tissue, represent a potent signal to drive tissue repair. In contrast, a 10-fold EF increase has been measured in many injured mammalian tissues where limited regeneration occurs. As the astrocytic response to CNS injury is crucial to the reparative outcome, we exposed purified rat cortical astrocytes to EF intensities associated with intact and injured mammalian tissues, as well as to those EF intensities measured in regenerating non-mammalian vertebrate tissues, to determine whether EFs may contribute to the astrocytic injury response. Astrocytes exposed to EF intensities associated with uninjured tissue showed little change in their cellular behavior. However, astrocytes exposed to EF intensities associated with injured tissue showed a dramatic increase in migration and proliferation. At EF intensities associated with regenerating non-mammalian vertebrate tissues, these cellular responses were even more robust and included morphological changes consistent with a regenerative phenotype. These findings suggest that endogenous EFs may be a crucial signal for regulating the astrocytic response to injury and that their manipulation may be a novel target for facilitating CNS repair.

  6. Evidence of MexT-independent overexpression of MexEF-OprN multidrug efflux pump of Pseudomonas aeruginosa in presence of metabolic stress.

    Directory of Open Access Journals (Sweden)

    Ayush Kumar

    Full Text Available The Pseudomonas aeruginosa MexEF-OprN efflux pump confers resistance to clinically significant antibiotics. Regulation of mexEF-oprN operon expression is multifaceted with the MexT activator being one of the most prominent regulatory proteins.We have exploited the impaired metabolic fitness of a P. aeruginosa mutant strain lacking several efflux pump of the resistance nodulation cell division superfamily and the TolC homolog OpmH, and isolated derivatives (large colony variants that regained fitness by incubation on nutrient-rich medium in the absence of antibiotics. Although the mexEF-oprN operon is uninducible in this mutant due to a 8-bp mexT insertion present in some P. aeruginosa PAO1 strains, the large colony variants expressed high levels of MexEF-OprN. Unlike large colony variants obtained after plating on antibiotic containing medium which expressed mexEF-oprN in a MexT-dependent fashion as evidenced by clean excision of the 8-bp insertion from mexT, mexEF-oprN expression was MexT-independent in the large colony variants obtained by plating on LB alone since the mexT gene remained inactivated. A search for possible regulators of mexEF-oprN expression using transposon mutagenesis and genomic library expression approaches yielded several candidates but proved inconclusive.Our results show that antibiotic and metabolic stress lead to up-regulation of MexEF-OprN expression via different mechanisms and that MexEF-OprN does not only extrude antimicrobials but rather serves other important metabolic functions.

  7. MOCCS: Clarifying DNA-binding motif ambiguity using ChIP-Seq data.

    Science.gov (United States)

    Ozaki, Haruka; Iwasaki, Wataru

    2016-08-01

    As a key mechanism of gene regulation, transcription factors (TFs) bind to DNA by recognizing specific short sequence patterns that are called DNA-binding motifs. A single TF can accept ambiguity within its DNA-binding motifs, which comprise both canonical (typical) and non-canonical motifs. Clarification of such DNA-binding motif ambiguity is crucial for revealing gene regulatory networks and evaluating mutations in cis-regulatory elements. Although chromatin immunoprecipitation sequencing (ChIP-seq) now provides abundant data on the genomic sequences to which a given TF binds, existing motif discovery methods are unable to directly answer whether a given TF can bind to a specific DNA-binding motif. Here, we report a method for clarifying the DNA-binding motif ambiguity, MOCCS. Given ChIP-Seq data of any TF, MOCCS comprehensively analyzes and describes every k-mer to which that TF binds. Analysis of simulated datasets revealed that MOCCS is applicable to various ChIP-Seq datasets, requiring only a few minutes per dataset. Application to the ENCODE ChIP-Seq datasets proved that MOCCS directly evaluates whether a given TF binds to each DNA-binding motif, even if known position weight matrix models do not provide sufficient information on DNA-binding motif ambiguity. Furthermore, users are not required to provide numerous parameters or background genomic sequence models that are typically unavailable. MOCCS is implemented in Perl and R and is freely available via https://github.com/yuifu/moccs. By complementing existing motif-discovery software, MOCCS will contribute to the basic understanding of how the genome controls diverse cellular processes via DNA-protein interactions. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Blood donors--Serious adverse reactions (SAR) 2010-2014 EFS Châteauroux, France.

    Science.gov (United States)

    Riga, A; Sapey, T; Bacanu, M; Py, J-Y; Dehaut, F

    2015-06-01

    In 2013, the national French incidence of serious adverse reactions (SAR) was 155.7 per 100,000 donations and 82% of SAR were grade 2 (French classification of SAR related to blood donors) The purpose of our study was to describe the profile of blood donator candidate which had a SAR in our center. The study contains all the SAR superior to grade 1 occurred on the site EFS Châteauroux (site and mobile blood collection) from January 2010 to October 31, 2014. We analyzed 37 parameters from the e-fit files (e-site French blood vigilance) and In-log software. We identified 82 SAR for 72,553 blood donations (incidence: 113.02 SAR per 100,000 donations). Forty-one men and 41 women, middle age 39 years (18-66). Average height: 1.68 m (1.49-1.85); average weight: 68 kg (50-98); body mass index (kg/m(2)): 24,13(18.6-31.9). All donors were Caucasian and 30% unemployed. We found 74 vasovagal syncope (VVS), 5 hematomas, 2 arterial injuries and an adverse reaction to citrate. In 90%, the SAR was immediate and of grade 2 in 85% of cases. Thirty-seven percent of SAR were first donation in connection with whole blood in 87% of cases. Regarding the seniority of donors, the number of average donations (whole blood, plasma, platelets) was 16.5. An SAR determined the stop of blood donation in 65% of cases with nearly 80% stoppage if it was a first donation. Seventy-three percent of SAR as a VVS took place during blood collection or within 5 minutes following the end of the donation. Sixty-one percent were men. Forty-four percent of cases were a first donation and 83% occurred in mobile blood collection. Average age was 36 years. The result was a permanent stop of all type of donations in 76% of cases. Twenty-seven percent of SAR as a VVS took place beyond 5 minutes after the end of the donation. Seventy-five percent were women. Thirty percent of cases were a first donation and 95% of SAR occurred in mobile blood collection. Average age was 42 years. The result was a permanent stop of

  9. The fsr Quorum-Sensing System and Cognate Gelatinase Orchestrate the Expression and Processing of Proprotein EF_1097 into the Mature Antimicrobial Peptide Enterocin O16

    OpenAIRE

    Dundar, Halil; Brede, Dag A.; La Rosa, Sabina Leanti; El-Gendy, Ahmed Osama; Diep, Dzung B.; Nes, Ingolf F.

    2015-01-01

    A novel antimicrobial peptide designated enterocin O16 was purified from Enterococcus faecalis. Mass spectrometry showed a monoisotopic mass of 7,231 Da, and N-terminal Edman degradation identified a 29-amino-acid sequence corresponding to residues 90 to 119 of the EF_1097 protein. Bioinformatic analysis showed that enterocin O16 is composed of the 68 most C-terminal residues of the EF_1097 protein. Introduction of an in-frame isogenic deletion in the ef1097 gene abolished the production of e...

  10. A Repeating Sulfated Galactan Motif Resuscitates Dormant Micrococcus luteus Bacteria.

    Science.gov (United States)

    Böttcher, Thomas; Szamosvári, Dávid; Clardy, Jon

    2018-07-01

    Only a small fraction of bacteria can autonomously initiate growth on agar plates. Nongrowing bacteria typically enter a metabolically inactive dormant state and require specific chemical trigger factors or signals to exit this state and to resume growth. Micrococcus luteus has become a model organism for this important yet poorly understood phenomenon. Only a few resuscitation signals have been described to date, and all of them are produced endogenously by bacterial species. We report the discovery of a novel type of resuscitation signal that allows M. luteus to grow on agar but not agarose plates. Fractionation of the agar polysaccharide complex and sulfation of agarose allowed us to identify the signal as highly sulfated saccharides found in agar or carrageenans. Purification of hydrolyzed κ-carrageenan ultimately led to the identification of the signal as a small fragment of a large linear polysaccharide, i.e., an oligosaccharide of five or more sugars with a repeating disaccharide motif containing d-galactose-4-sulfate (G4S) 1,4-linked to 3,6-anhydro-α-d-galactose (DA), G4S-(DA-G4S) n ≥2 IMPORTANCE Most environmental bacteria cannot initiate growth on agar plates, but they can flourish on the same plates once growth is initiated. While there are a number of names for and manifestations of this phenomenon, the underlying cause appears to be the requirement for a molecular signal indicating safe growing conditions. Micrococcus luteus has become a model organism for studying this growth initiation process, often called resuscitation, because of its apparent connection with the persistent or dormant form of Mycobacterium tuberculosis , an important human pathogen. In this report, we identify a highly sulfated saccharide from agar or carrageenans that robustly resuscitates dormant M. luteus on agarose plates. We identified and characterized the signal as a small repeating disaccharide motif. Our results indicate that signals inherent in or absent from the

  11. One motif to bind them: A small-XXX-small motif affects transmembrane domain 1 oligomerization, function, localization, and cross-talk between two yeast GPCRs.

    Science.gov (United States)

    Lock, Antonia; Forfar, Rachel; Weston, Cathryn; Bowsher, Leo; Upton, Graham J G; Reynolds, Christopher A; Ladds, Graham; Dixon, Ann M

    2014-12-01

    G protein-coupled receptors (GPCRs) are the largest family of cell-surface receptors in mammals and facilitate a range of physiological responses triggered by a variety of ligands. GPCRs were thought to function as monomers, however it is now accepted that GPCR homo- and hetero-oligomers also exist and influence receptor properties. The Schizosaccharomyces pombe GPCR Mam2 is a pheromone-sensing receptor involved in mating and has previously been shown to form oligomers in vivo. The first transmembrane domain (TMD) of Mam2 contains a small-XXX-small motif, overrepresented in membrane proteins and well-known for promoting helix-helix interactions. An ortholog of Mam2 in Saccharomyces cerevisiae, Ste2, contains an analogous small-XXX-small motif which has been shown to contribute to receptor homo-oligomerization, localization and function. Here we have used experimental and computational techniques to characterize the role of the small-XXX-small motif in function and assembly of Mam2 for the first time. We find that disruption of the motif via mutagenesis leads to reduction of Mam2 TMD1 homo-oligomerization and pheromone-responsive cellular signaling of the full-length protein. It also impairs correct targeting to the plasma membrane. Mutation of the analogous motif in Ste2 yielded similar results, suggesting a conserved mechanism for assembly. Using co-expression of the two fungal receptors in conjunction with computational models, we demonstrate a functional change in G protein specificity and propose that this is brought about through hetero-dimeric interactions of Mam2 with Ste2 via the complementary small-XXX-small motifs. This highlights the potential of these motifs to affect a range of properties that can be investigated in other GPCRs. Copyright © 2014. Published by Elsevier B.V.

  12. Nudging to improve hand hygiene.

    Science.gov (United States)

    Caris, M G; Labuschagne, H A; Dekker, M; Kramer, M H H; van Agtmael, M A; Vandenbroucke-Grauls, C M J E

    2018-04-01

    Hand hygiene is paramount to prevent healthcare-associated infections, but improving compliance is challenging. When healthcare workers seldom encounter healthcare-associated infections, they will consider the odds of causing infections through poor hand hygiene negligible. Cognitive biases such as these may induce non-compliance. Nudging, 'a friendly push to encourage desired behaviour', could provide an easily implemented, inexpensive measure to address cognitive biases and thus support hand hygiene interventions. To investigate whether behavioural nudges, displayed as posters, can increase the use of alcohol-based hand rub. We developed nudges based on a systematic review of previously described cognitive biases, and tested these through a cross-sectional survey among the target audience. We then conducted a controlled before-after trial on two hospital wards, to assess the effect of these nudges on the use of alcohol-based hand rub, measured with electronic dispensers. Poisson regression analyses adjusted for workload showed that nudges displayed next to dispensers increased their overall use on one ward [poster 1: relative risk: 1.6 (95% confidence interval: 1.2-2.2); poster 2: 1.7 (1.2-2.5)] and during doctor's rounds on both wards [poster 1: ward A: 1.7 (1.1-2.6); ward B: 2.2 (1.3-3.8)]. Use of dispensers without adjacent nudges did not increase. Nudges based on cognitive biases that play a role in hand hygiene, and displayed as posters, could provide an easy, inexpensive measure to increase use of alcohol-based hand rub. When applying nudges to change behaviour, it is important to identify the right nudge for the right audience. Copyright © 2017 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

  13. Perkembangan Motif Sineas Film Indie dalam Menghadapi Industri Film Mainstream

    Directory of Open Access Journals (Sweden)

    Yoppy Ardiyono

    2016-03-01

    Full Text Available The research aims to review to review determine the effect and its impact raised by motive - a motive the ada in the hearts period travel time history of film short against cinematographer-filmmaker as principal especially filmmakers left path (indie. The used platform theory research hearts singer adopts from theory commodification media vincent mosco. Singer helped shift theory understanding the motive filmmakers working hearts differences fundamental basis of political pressure economic happens under with demands regime. The method used is descriptive qualitative research methods. Data collection techniques through observation of the environment of an independent film live and in-depth interviews with speakers including mr. Yang prayer orangutan direct contact 'with realm of research. Coupled with study to review the literature references adding insight research. And that was concluded change appears motif among indie film cinematographer it is true the situation is closely linked to the mainstream industry, konstilasi politics, and the orientation of capitalism. Necessary their one thing is clear and systematic regulation from the government to the future movement of currents sidestream (indie more with good operates professionally arranged, the air so that the contribution of indie cinema film land for progress can feels good to yourself indie filmmakers as well as those of its main industries.

  14. Crammed signaling motifs in the T-cell receptor.

    Science.gov (United States)

    Borroto, Aldo; Abia, David; Alarcón, Balbino

    2014-09-01

    Although the T cell antigen receptor (TCR) is long known to contain multiple signaling subunits (CD3γ, CD3δ, CD3ɛ and CD3ζ), their role in signal transduction is still not well understood. The presence of at least one immunoreceptor tyrosine-based activation motif (ITAM) in each CD3 subunit has led to the idea that the multiplication of such elements essentially serves to amplify signals. However, the evolutionary conservation of non-ITAM sequences suggests that each CD3 subunit is likely to have specific non-redundant roles at some stage of development or in mature T cell function. The CD3ɛ subunit is paradigmatic because in a relatively short cytoplasmic sequence (∼55 amino acids) it contains several docking sites for proteins involved in intracellular trafficking and signaling, proteins whose relevance in T cell activation is slowly starting to be revealed. In this review we will summarize our current knowledge on the signaling effectors that bind directly to the TCR and we will propose a hierarchy in their response to TCR triggering. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. DNA mutation motifs in the genes associated with inherited diseases.

    Directory of Open Access Journals (Sweden)

    Michal Růžička

    Full Text Available Mutations in human genes can be responsible for inherited genetic disorders and cancer. Mutations can arise due to environmental factors or spontaneously. It has been shown that certain DNA sequences are more prone to mutate. These sites are termed hotspots and exhibit a higher mutation frequency than expected by chance. In contrast, DNA sequences with lower mutation frequencies than expected by chance are termed coldspots. Mutation hotspots are usually derived from a mutation spectrum, which reflects particular population where an effect of a common ancestor plays a role. To detect coldspots/hotspots unaffected by population bias, we analysed the presence of germline mutations obtained from HGMD database in the 5-nucleotide segments repeatedly occurring in genes associated with common inherited disorders, in particular, the PAH, LDLR, CFTR, F8, and F9 genes. Statistically significant sequences (mutational motifs rarely associated with mutations (coldspots and frequently associated with mutations (hotspots exhibited characteristic sequence patterns, e.g. coldspots contained purine tract while hotspots showed alternating purine-pyrimidine bases, often with the presence of CpG dinucleotide. Using molecular dynamics simulations and free energy calculations, we analysed the global bending properties of two selected coldspots and two hotspots with a G/T mismatch. We observed that the coldspots were inherently more flexible than the hotspots. We assume that this property might be critical for effective mismatch repair as DNA with a mutation recognized by MutSα protein is noticeably bent.

  16. ARCHETYPES AND MYTHOLOGICAL MOTIFS: JOHN UPDIKE’S LEGACY REVISITED

    Directory of Open Access Journals (Sweden)

    Loreta Ulvydienė

    2018-04-01

    Full Text Available John Updike is widely considered to be one of the greatest, one of the most popular and sometimes most controversial writers concerned with the American small town and middle-class materialism. A lot of literary critics and researchers observe that Updike’s finest work came from his exploration of ordinary America and from his use of elegant prose, rich with metaphor, to portray the public and private feelings of Americans, their daily rounds of life. In addition, discussing Updike’s individual works a lot of literary critics and researchers have observed the writer’s attempts to re-write myth in “the mythical age”1 of the twentieth century. Naturally enough, as the return to myth is assumed to be a certain feature of the Modernist movement, half a century later since Updike’s famous novel Centaur was penned, it is indispensable to re-examine the writer’s fictional intentions in the usage of myth. More importantly, it is needful to determine whether we can see the mythic elements and realistic details as a continuum or as the contrasted opposites in his so called “historical chronicles”. Updike’s novels and stories are filled with mythological motifs and character archetypes. Thus, the study aims at revisiting John Updike’s creation considering mythological elements and archetypal images of his heroes alongside with heroic masculinity, war, terrorism and American perfectionism.

  17. Dystroglycan versatility in cell adhesion: a tale of multiple motifs

    Directory of Open Access Journals (Sweden)

    Winder Steve J

    2010-02-01

    Full Text Available Abstract Dystroglycan is a ubiquitously expressed heterodimeric adhesion receptor. The extracellular α-subunit makes connections with a number of laminin G domain ligands including laminins, agrin and perlecan in the extracellular matrix and the transmembrane β-subunit makes connections to the actin filament network via cytoskeletal linkers including dystrophin, utrophin, ezrin and plectin, depending on context. Originally discovered as part of the dystrophin glycoprotein complex of skeletal muscle, dystroglycan is an important adhesion molecule and signalling scaffold in a multitude of cell types and tissues and is involved in several diseases. Dystroglycan has emerged as a multifunctional adhesion platform with many interacting partners associating with its short unstructured cytoplasmic domain. Two particular hotspots are the cytoplasmic juxtamembrane region and at the very carboxy terminus of dystroglycan. Regions which between them have several overlapping functions: in the juxtamembrane region; a nuclear localisation signal, ezrin/radixin/moesin protein, rapsyn and ERK MAP Kinase binding function, and at the C terminus a regulatory tyrosine governing WW, SH2 and SH3 domain interactions. We will discuss the binding partners for these motifs and how their interactions and regulation can modulate the involvement of dystroglycan in a range of different adhesion structures and functions depending on context. Thus dystroglycan presents as a multifunctional scaffold involved in adhesion and adhesion-mediated signalling with its functions under exquisite spatio-temporal regulation.

  18. Hand infections: a retrospective analysis

    Directory of Open Access Journals (Sweden)

    Tolga Türker

    2014-09-01

    Full Text Available Purpose. Hand infections are common, usually resulting from an untreated injury. In this retrospective study, we report on hand infection cases needing surgical drainage in order to assess patient demographics, causation of infection, clinical course, and clinical management.Methods. Medical records of patients presenting with hand infections, excluding post-surgical infections, treated with incision and debridement over a one-year period were reviewed. Patient demographics; past medical history; infection site(s and causation; intervals between onset of infection, hospital admission, surgical intervention and days of hospitalization; gram stains and cultures; choice of antibiotics; complications; and outcomes were reviewed.Results. Most infections were caused by laceration and the most common site of infection was the palm or dorsum of the hand. Mean length of hospitalization was 6 days. Methicillin-resistant Staphylococcus aureus, beta-hemolytic Streptococcus and methicillin-susceptible Staphylococcus aureus were the most commonly cultured microorganisms. Cephalosporins, clindamycin, amoxicillin/clavulanate, penicillin, vancomycin, and trimethoprim/sulfamethoxazole were major antibiotic choices. Amputations and contracture were the primary complications.Conclusions. Surgery along with medical management were key to treatment and most soft tissue infections resolved without further complications. With prompt and appropriate care, most hand infection patients can achieve full resolution of their infection.

  19. Myelopathy hand in cervical radiculopathy

    International Nuclear Information System (INIS)

    Hosono, Noboru; Mukai, Yoshihiro; Takenaka, Shota; Fuji, Takeshi; Sakaura, Hironobu; Miwa, Toshitada; Makino, Takahiro

    2010-01-01

    The so-called 'myelopathy hand', or characteristic finger paralysis, often recognized in cervical compression myelopathy, has been considered a unique manifestation of cervical myelopathy. We used our original grip and release test, a 15-second test in which finger motion is captured with a digital camera, to investigate whether cervical radiculopathy has the same characteristics as myelopathy hand. Thirty patients with pure radiculopathy, id est (i.e.), who had radiating arm pain and evidence of corresponding nerve root impingement on X-ray images or MRI scans, but did not have spinal cord compression, served as the subjects. In contrast to other radiculopathies, C7 radiculopathy was manifested by a significant reduction in the number of finger motion cycles on the affected side in comparison with the unaffected side, the same as in myelopathy hand. Uncoordinated finger motion was significantly more frequent on the affected side in C6 radiculopathy than on the unaffected side. These findings contradict the conventional notion that myelopathy hand is a unique manifestation of cervical myelopathy, but some radiculopathies manifested the same kinds of finger paralysis observed in myelopathy hand. (author)

  20. Argo_CUDA: Exhaustive GPU based approach for motif discovery in large DNA datasets.

    Science.gov (United States)

    Vishnevsky, Oleg V; Bocharnikov, Andrey V; Kolchanov, Nikolay A

    2018-02-01

    The development of chromatin immunoprecipitation sequencing (ChIP-seq) technology has revolutionized the genetic analysis of the basic mechanisms underlying transcription regulation and led to accumulation of information about a huge amount of DNA sequences. There are a lot of web services which are currently available for de novo motif discovery in datasets containing information about DNA/protein binding. An enormous motif diversity makes their finding challenging. In order to avoid the difficulties, researchers use different stochastic approaches. Unfortunately, the efficiency of the motif discovery programs dramatically declines with the query set size increase. This leads to the fact that only a fraction of top "peak" ChIP-Seq segments can be analyzed or the area of analysis should be narrowed. Thus, the motif discovery in massive datasets remains a challenging issue. Argo_Compute Unified Device Architecture (CUDA) web service is designed to process the massive DNA data. It is a program for the detection of degenerate oligonucleotide motifs of fixed length written in 15-letter IUPAC code. Argo_CUDA is a full-exhaustive approach based on the high-performance GPU technologies. Compared with the existing motif discovery web services, Argo_CUDA shows good prediction quality on simulated sets. The analysis of ChIP-Seq sequences revealed the motifs which correspond to known transcription factor binding sites.

  1. A Novel Protein Interaction between Nucleotide Binding Domain of Hsp70 and p53 Motif

    Directory of Open Access Journals (Sweden)

    Asita Elengoe

    2015-01-01

    Full Text Available Currently, protein interaction of Homo sapiens nucleotide binding domain (NBD of heat shock 70 kDa protein (PDB: 1HJO with p53 motif remains to be elucidated. The NBD-p53 motif complex enhances the p53 stabilization, thereby increasing the tumor suppression activity in cancer treatment. Therefore, we identified the interaction between NBD and p53 using STRING version 9.1 program. Then, we modeled the three-dimensional structure of p53 motif through homology modeling and determined the binding affinity and stability of NBD-p53 motif complex structure via molecular docking and dynamics (MD simulation. Human DNA binding domain of p53 motif (SCMGGMNR retrieved from UniProt (UniProtKB: P04637 was docked with the NBD protein, using the Autodock version 4.2 program. The binding energy and intermolecular energy for the NBD-p53 motif complex were −0.44 Kcal/mol and −9.90 Kcal/mol, respectively. Moreover, RMSD, RMSF, hydrogen bonds, salt bridge, and secondary structure analyses revealed that the NBD protein had a strong bond with p53 motif and the protein-ligand complex was stable. Thus, the current data would be highly encouraging for designing Hsp70 structure based drug in cancer therapy.

  2. Conserved binding of GCAC motifs by MEC-8, couch potato, and the RBPMS protein family

    Science.gov (United States)

    Soufari, Heddy

    2017-01-01

    Precise regulation of mRNA processing, translation, localization, and stability relies on specific interactions with RNA-binding proteins whose biological function and target preference are dictated by their preferred RNA motifs. The RBPMS family of RNA-binding proteins is defined by a conserved RNA recognition motif (RRM) domain found in metazoan RBPMS/Hermes and RBPMS2, Drosophila couch potato, and MEC-8 from Caenorhabditis elegans. In order to determine the parameters of RNA sequence recognition by the RBPMS family, we have first used the N-terminal domain from MEC-8 in binding assays and have demonstrated a preference for two GCAC motifs optimally separated by >6 nucleotides (nt). We have also determined the crystal structure of the dimeric N-terminal RRM domain from MEC-8 in the unbound form, and in complex with an oligonucleotide harboring two copies of the optimal GCAC motif. The atomic details reveal the molecular network that provides specificity to all four bases in the motif, including multiple hydrogen bonds to the initial guanine. Further studies with human RBPMS, as well as Drosophila couch potato, confirm a general preference for this double GCAC motif by other members of the protein family and the presence of this motif in known targets. PMID:28003515

  3. Distance-dependent duplex DNA destabilization proximal to G-quadruplex/i-motif sequences

    Science.gov (United States)

    König, Sebastian L. B.; Huppert, Julian L.; Sigel, Roland K. O.; Evans, Amanda C.

    2013-01-01

    G-quadruplexes and i-motifs are complementary examples of non-canonical nucleic acid substructure conformations. G-quadruplex thermodynamic stability has been extensively studied for a variety of base sequences, but the degree of duplex destabilization that adjacent quadruplex structure formation can cause has yet to be fully addressed. Stable in vivo formation of these alternative nucleic acid structures is likely to be highly dependent on whether sufficient spacing exists between neighbouring duplex- and quadruplex-/i-motif-forming regions to accommodate quadruplexes or i-motifs without disrupting duplex stability. Prediction of putative G-quadruplex-forming regions is likely to be assisted by further understanding of what distance (number of base pairs) is required for duplexes to remain stable as quadruplexes or i-motifs form. Using oligonucleotide constructs derived from precedented G-quadruplexes and i-motif-forming bcl-2 P1 promoter region, initial biophysical stability studies indicate that the formation of G-quadruplex and i-motif conformations do destabilize proximal duplex regions. The undermining effect that quadruplex formation can have on duplex stability is mitigated with increased distance from the duplex region: a spacing of five base pairs or more is sufficient to maintain duplex stability proximal to predicted quadruplex/i-motif-forming regions. PMID:23771141

  4. MODA: an efficient algorithm for network motif discovery in biological networks.

    Science.gov (United States)

    Omidi, Saeed; Schreiber, Falk; Masoudi-Nejad, Ali

    2009-10-01

    In recent years, interest has been growing in the study of complex networks. Since Erdös and Rényi (1960) proposed their random graph model about 50 years ago, many researchers have investigated and shaped this field. Many indicators have been proposed to assess the global features of networks. Recently, an active research area has developed in studying local features named motifs as the building blocks of networks. Unfortunately, network motif discovery is a computationally hard problem and finding rather large motifs (larger than 8 nodes) by means of current algorithms is impractical as it demands too much computational effort. In this paper, we present a new algorithm (MODA) that incorporates techniques such as a pattern growth approach for extracting larger motifs efficiently. We have tested our algorithm and found it able to identify larger motifs with more than 8 nodes more efficiently than most of the current state-of-the-art motif discovery algorithms. While most of the algorithms rely on induced subgraphs as motifs of the networks, MODA is able to extract both induced and non-induced subgraphs simultaneously. The MODA source code is freely available at: http://LBB.ut.ac.ir/Download/LBBsoft/MODA/

  5. Cross-cultural adaptation and validity of the "Edmonton Frail Scale - EFS" in a Brazilian elderly sample Adaptación cultural y validez de la Edmonton Frail Scale - EFS en una muestra de ancianos brasileños Adaptação cultural e validade da Edmonton Frail Scale - EFS em uma amostra de idosos brasileiros

    Directory of Open Access Journals (Sweden)

    Suzele Cristina Coelho Fabrício-Wehbe

    2009-12-01

    Full Text Available This study aimed to assess the cross-cultural adaptation of the Edmonton Frail Scale (EFS and its validity in a Brazilian elderly sample. Translation and back-translation were performed, as well as discussion with professionals and elderly for conceptual equivalence, semantic validation and pre-test of the scale. The scale was applied to 137 elderly aged 65 years or older who lived in the community. In the know-groups validation of the frailty diagnosis between gender, age and cognitive deficit, elder elderly, female and with a cognitive deficit scored higher on the frailty diagnosis. A negative convergent correlation was found between the EFS and the Functional Independence Measure (FIM (-0.53, pEl objetivo de este estudio fue evaluar la adaptación cultural de la Edmonton Frail Scale (EFS y su validez en una muestra de ancianos brasileños. Fueron realizadas las etapas de traducción y retrotraducción, discusión con profesionales y ancianos para equivalencia conceptual, validación semántica y prueba piloto de la escala. El instrumento fue aplicado en 137 ancianos, con 65 años o más de edad, que vivían en la comunidad. En la validación de grupos conocidos, del diagnóstico de fragilidad entre sexo, edad y déficit cognitivo, los ancianos con edad más avanzada, sexo femenino y con déficit cognitivo tuvieron mayor puntuación en el diagnóstico de fragilidad. Hubo una correlación convergente negativa de la EFS con la Medida de Independencia Funcional (MIF (-0,53, pO objetivo deste estudo foi avaliar a adaptação cultural da Edmonton Frail Scale (EFS e sua validade em uma amostra de idosos brasileiros. Foram realizadas as etapas de tradução e retrotradução, discussão com profissionais e idosos para equivalência conceitual, validação semântica e pré-teste da escala. O instrumento foi aplicado em 137 idosos, com 65 anos ou mais de idade, que viviam na comunidade. Na validação de grupos conhecidos, do diagnóstico de

  6. Hand-Based Biometric Analysis

    Science.gov (United States)

    Bebis, George (Inventor); Amayeh, Gholamreza (Inventor)

    2015-01-01

    Hand-based biometric analysis systems and techniques are described which provide robust hand-based identification and verification. An image of a hand is obtained, which is then segmented into a palm region and separate finger regions. Acquisition of the image is performed without requiring particular orientation or placement restrictions. Segmentation is performed without the use of reference points on the images. Each segment is analyzed by calculating a set of Zernike moment descriptors for the segment. The feature parameters thus obtained are then fused and compared to stored sets of descriptors in enrollment templates to arrive at an identity decision. By using Zernike moments, and through additional manipulation, the biometric analysis is invariant to rotation, scale, or translation or an in put image. Additionally, the analysis utilizes re-use of commonly-seen terms in Zernike calculations to achieve additional efficiencies over traditional Zernike moment calculation.

  7. Natural control capabilities of robotic hands by hand amputated subjects.

    Science.gov (United States)

    Atzori, Manfredo; Gijsberts, Arjan; Caputo, Barbara; Muller, Henning

    2014-01-01

    People with transradial hand amputations who own a myoelectric prosthesis currently have some control capabilities via sEMG. However, the control systems are still limited and not natural. The Ninapro project is aiming at helping the scientific community to overcome these limits through the creation of publicly available electromyography data sources to develop and test machine learning algorithms. In this paper we describe the movement classification results gained from three subjects with an homogeneous level of amputation, and we compare them with the results of 40 intact subjects. The number of considered subjects can seem small at first sight, but it is not considering the literature of the field (which has to face the difficulty of recruiting trans-radial hand amputated subjects). The classification is performed with four different classifiers and the obtained balanced classification rates are up to 58.6% on 50 movements, which is an excellent result compared to the current literature. Successively, for each subject we find a subset of up to 9 highly independent movements, (defined as movements that can be distinguished with more than 90% accuracy), which is a deeply innovative step in literature. The natural control of a robotic hand in so many movements could lead to an immediate progress in robotic hand prosthetics and it could deeply change the quality of life of amputated subjects.

  8. Urunana Audiences at Home and Away: Together 'Hand in Hand'?

    NARCIS (Netherlands)

    H.M. Hintjens (Helen); F. Bayisenge

    2011-01-01

    textabstractUrunana (‘Hand in Hand’) is Rwanda’s first radio soap opera. The production emerged during the late 1990s from a three-way transnational production partnership between: The Great Lakes section of the BBC World Service; the Well Woman Media Project of the London-based NGO, Health

  9. eEF1A Mediates the Nuclear Export of SNAG-Containing Proteins via the Exportin5-Aminoacyl-tRNA Complex

    Directory of Open Access Journals (Sweden)

    José Manuel Mingot

    2013-11-01

    Full Text Available Exportin5 mediates the nuclear export of double-stranded RNAs, including pre-microRNAs, adenoviral RNAs, and tRNAs. When tRNAs are aminoacylated, the Exportin5-aminoacyl (aa-tRNA complex recruits and coexports the translation elongation factor eEF1A. Here, we show that eEF1A binds to Snail transcription factors when bound to their main target, the E-cadherin promoter, facilitating their export to the cytoplasm in association with the aa-tRNA-Exportin5 complex. Snail binds to eEF1A through the SNAG domain, a protein nuclear export signal present in several transcription factor families, and this binding is regulated by phosphorylation. Thus, we describe a nuclear role for eEF1A and provide a mechanism for protein nuclear export that attenuates the activity of SNAG-containing transcription factors.

  10. Comparative analysis of evolutionarily conserved motifs of epidermal growth factor receptor 2 (HER2) predicts novel potential therapeutic epitopes

    DEFF Research Database (Denmark)

    Deng, Xiaohong; Zheng, Xuxu; Yang, Huanming

    2014-01-01

    druggable epitopes/targets. We employed the PROSITE Scan to detect structurally conserved motifs and PRINTS to search for linearly conserved motifs of ECD HER2. We found that the epitopes recognized by trastuzumab and pertuzumab are located in the predicted conserved motifs of ECD HER2, supporting our...

  11. Identification of a putative nuclear export signal motif in human NANOG homeobox domain

    International Nuclear Information System (INIS)

    Park, Sung-Won; Do, Hyun-Jin; Huh, Sun-Hyung; Sung, Boreum; Uhm, Sang-Jun; Song, Hyuk; Kim, Nam-Hyung; Kim, Jae-Hwan

    2012-01-01

    Highlights: ► We found the putative nuclear export signal motif within human NANOG homeodomain. ► Leucine-rich residues are important for human NANOG homeodomain nuclear export. ► CRM1-specific inhibitor LMB blocked the potent human NANOG NES-mediated nuclear export. -- Abstract: NANOG is a homeobox-containing transcription factor that plays an important role in pluripotent stem cells and tumorigenic cells. To understand how nuclear localization of human NANOG is regulated, the NANOG sequence was examined and a leucine-rich nuclear export signal (NES) motif ( 125 MQELSNILNL 134 ) was found in the homeodomain (HD). To functionally validate the putative NES motif, deletion and site-directed mutants were fused to an EGFP expression vector and transfected into COS-7 cells, and the localization of the proteins was examined. While hNANOG HD exclusively localized to the nucleus, a mutant with both NLSs deleted and only the putative NES motif contained (hNANOG HD-ΔNLSs) was predominantly cytoplasmic, as observed by nucleo/cytoplasmic fractionation and Western blot analysis as well as confocal microscopy. Furthermore, site-directed mutagenesis of the putative NES motif in a partial hNANOG HD only containing either one of the two NLS motifs led to localization in the nucleus, suggesting that the NES motif may play a functional role in nuclear export. Furthermore, CRM1-specific nuclear export inhibitor LMB blocked the hNANOG potent NES-mediated export, suggesting that the leucine-rich motif may function in CRM1-mediated nuclear export of hNANOG. Collectively, a NES motif is present in the hNANOG HD and may be functionally involved in CRM1-mediated nuclear export pathway.

  12. Diagnostic imaging of the hand

    Energy Technology Data Exchange (ETDEWEB)

    Schmitt, Rainer [Hospital for Cardiovascular Diseases, Bad Neustadt an der Saale (Germany). Dept. of Radiology; Lanz, Ulrich [Perlach Hospital, Munich (Germany). Dept. of Hand Surgery

    2008-07-01

    With its complex anatomy and specialized biomechanics, the human hand has always presented physicians with a unique challenge when it comes to diagnosing and treating the diseases that afflict it. And while recent decades have seen a rapid increase in the number of therapeutic options, many diseases and injuries of the hand are still commonly misinterpreted. In diagnostic imaging of the hand, an interdisciplinary team, comprisingspecialists in radiology, surgery, and rheumatology, presents a comprehensive,reliable guide to this topographically intricate area. Highlights include: - More than 1000 high-quality illustrations - All state-of-the-art imaging modalities-including multidetector CT, with 2D displays and 3D reconstructions, and contrast-enhanced MRI with multi-channel, phased-array coils - An overview of all currently used methods of examination - A detailed presentation of the anatomic and functional foundations necessary for diagnosis - Full coverage of all disorders of the hand - Systematic treatment of each disease's definition, pathogenesis, and clinical symptoms, according to a graduated diagnostic plan - Easy-to-use format, featuring crisp images and line drawings seamlessly integrated with concise text, summary tables, and handy checklists - A heavily cross-referenced appendix of differential diagnosis tables - Emphasis on interdisciplinary consultation throughout designed to help both radiologists and clinicians develop the most efficient and effective strategies for evaluating and treating patients, Diagnostic imaging of the hand will leave specialists of all levels with a fresh appreciation for - and a richer understanding of - the expanding array of cutting-edge alternatives for diagnosing and treating disorders of the hand. (orig.)

  13. Diagnostic imaging of the hand

    International Nuclear Information System (INIS)

    Schmitt, Rainer; Lanz, Ulrich

    2008-01-01

    With its complex anatomy and specialized biomechanics, the human hand has always presented physicians with a unique challenge when it comes to diagnosing and treating the diseases that afflict it. And while recent decades have seen a rapid increase in the number of therapeutic options, many diseases and injuries of the hand are still commonly misinterpreted. In diagnostic imaging of the hand, an interdisciplinary team, comprisingspecialists in radiology, surgery, and rheumatology, presents a comprehensive,reliable guide to this topographically intricate area. Highlights include: - More than 1000 high-quality illustrations - All state-of-the-art imaging modalities-including multidetector CT, with 2D displays and 3D reconstructions, and contrast-enhanced MRI with multi-channel, phased-array coils - An overview of all currently used methods of examination - A detailed presentation of the anatomic and functional foundations necessary for diagnosis - Full coverage of all disorders of the hand - Systematic treatment of each disease's definition, pathogenesis, and clinical symptoms, according to a graduated diagnostic plan - Easy-to-use format, featuring crisp images and line drawings seamlessly integrated with concise text, summary tables, and handy checklists - A heavily cross-referenced appendix of differential diagnosis tables - Emphasis on interdisciplinary consultation throughout designed to help both radiologists and clinicians develop the most efficient and effective strategies for evaluating and treating patients, Diagnostic imaging of the hand will leave specialists of all levels with a fresh appreciation for - and a richer understanding of - the expanding array of cutting-edge alternatives for diagnosing and treating disorders of the hand. (orig.)

  14. The fsr Quorum-Sensing System and Cognate Gelatinase Orchestrate the Expression and Processing of Proprotein EF_1097 into the Mature Antimicrobial Peptide Enterocin O16.

    Science.gov (United States)

    Dundar, Halil; Brede, Dag A; La Rosa, Sabina Leanti; El-Gendy, Ahmed Osama; Diep, Dzung B; Nes, Ingolf F

    2015-07-01

    A novel antimicrobial peptide designated enterocin O16 was purified from Enterococcus faecalis. Mass spectrometry showed a monoisotopic mass of 7,231 Da, and N-terminal Edman degradation identified a 29-amino-acid sequence corresponding to residues 90 to 119 of the EF_1097 protein. Bioinformatic analysis showed that enterocin O16 is composed of the 68 most C-terminal residues of the EF_1097 protein. Introduction of an in-frame isogenic deletion in the ef1097 gene abolished the production of enterocin O16. Enterocin O16 has a narrow inhibitory spectrum, as it inhibits mostly lactobacilli. Apparently, E. faecalis is intrinsically resistant to the antimicrobial peptide, as no immunity connected to the production of enterocin O16 could be identified. ef1097 has previously been identified as one of three loci regulated by the fsr quorum-sensing system. The introduction of a nonsense mutation into fsrB consistently impaired enterocin O16 production, but externally added gelatinase biosynthesis-activating pheromone restored the antimicrobial activity. Functional genetic analysis showed that the EF_1097 proprotein is processed extracellularly into enterocin O16 by the metalloprotease GelE. Thus, it is evident that the fsr quorum-sensing system constitutes the regulatory unit that controls the expression of the EF_1097 precursor protein and the protease GelE and that the latter is required for the formation of enterocin O16. On the basis of these results, this study identified antibacterial antagonism as a novel aspect related to the function of fsr and provides a rationale for why ef1097 is part of the fsr regulon. The fsr quorum-sensing system modulates important physiological functions in E. faecalis via the activity of GelE. The present study presents a new facet of fsr signaling. The system controls the expression of three primary target operons (fsrABCD, gelE-sprE, and ef1097-ef1097b). We demonstrate that the concerted expression of these operons constitutes the

  15. EthoHand: A dexterous robotic hand with ball-joint thumb enables complex in-hand object manipulation

    OpenAIRE

    Konnaris, C; Gavriel, C; Thomik, AAC; Aldo Faisal, A

    2016-01-01

    Our dexterous hand is a fundmanetal human feature that distinguishes us from other animals by enabling us to go beyond grasping to support sophisticated in-hand object manipulation. Our aim was the design of a dexterous anthropomorphic robotic hand that matches the human hand's 24 degrees of freedom, under-actuated by seven motors. With the ability to replicate human hand movements in a naturalistic manner including in-hand object manipulation. Therefore, we focused on the development of a no...

  16. Intrinsic contractures of the hand.

    Science.gov (United States)

    Paksima, Nader; Besh, Basil R

    2012-02-01

    Contractures of the intrinsic muscles of the fingers disrupt the delicate and complex balance of intrinsic and extrinsic muscles, which allows the hand to be so versatile and functional. The loss of muscle function primarily affects the interphalangeal joints but also may affect etacarpophalangeal joints. The resulting clinical picture is often termed, intrinsic contracture or intrinsic-plus hand. Disruption of the balance between intrinsic and extrinsic muscles has many causes and may be secondary to changes within the intrinsic musculature or the tendon unit. This article reviews diagnosis, etiology, and treatment algorithms in the management of intrinsic contractures of the fingers. Copyright © 2012 Elsevier Inc. All rights reserved.

  17. Lionfish envenomation of the hand.

    Science.gov (United States)

    Patel, M R; Wells, S

    1993-05-01

    Lionfish (Pterois volitans) envenomation of the hand causes excruciating pain and occurs in three grades: (1) erythematous reaction, (2) blister formation, and (3) dermal necrosis. The initial treatment in all cases is to soak the hand in nonscalding water (45 degrees C) until the pain subsides by denaturing the thermolabile venom proteins. The blisters should be immediately excised to prevent dermal necrosis, inasmuch as the blister fluid contains residual active venom. To prevent a hypersensitivity reaction, any further contact with the fish should be avoided.

  18. Hand-it-on”

    DEFF Research Database (Denmark)

    Dieckmann, Gerhard Peter; Graae Zeltner, Louise; Helsø, Anne-Mette

    2016-01-01

    Non-technical skills (NTS) are an integral part of the abilities healthcare professionals need to optimally care for patients. Integrating NTS into the already complex tasks of healthcare can be a challenge for clinicians. Integrating NTS into simulation-based training increases the demands...... and where they can apply them in their work. It complements existing approaches to teaching NTS by limiting the complexity of the game and by removing medical content, allowing learners to concentrate on NTS. Hand-it-on is relevant for groups and teams working across the range of different healthcare...... and the replication of Hand-it-on by many simulation teams support its value....

  19. Discovering Hands - México

    OpenAIRE

    Salamanca Cárdenas, Daniela; Castelblanco Domínguez, Junio Andrés; Aguilar Ardila, Laura Andrea

    2016-01-01

    El modelo de Discovering Hands ha sido reconocido internacionalmente como un proyecto innovador que se ha expandido por diferentes países del mundo, como Austria, y se ha empezado a estudiar la propuesta en países como República Checa, India y Colombia. (Discovering Hands, 2016). Esto se debe a que no solo mejora el tratamiento de cáncer de mama, sino que también reduce los costos totales de tratamiento de la enfermedad y aumenta la fuerza laborar de los países donde esté presente. Al represe...

  20. Salt-bridge Swapping in the EXXERFXYY Motif of Proton Coupled Oligopeptide Transporters

    DEFF Research Database (Denmark)

    Aduri, Nanda G; Prabhala, Bala K; Ernst, Heidi A

    2015-01-01

    to as E1XXE2R), located on Helix I, in interactions with the proton. In this study we investigated the intracellular substrate accumulation by motif variants with all possible combinations of glutamate residues changed to glutamine and arginine changed to a tyrosine; the latter being a natural variant......-motif salt bridge, i.e. R-E2 to R-E1, which is consistent with previous structural studies. Molecular dynamics simulations of the motif variants E1XXE2R and E1XXQ2R support this mechanism. The simulations showed that upon changing conformation, arginine pushes Helix V, through interactions with the highly...